Citrus Sinensis ID: 013472

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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--
Protein Sequence
MGMGFRLNLKWVSPVQSHFFTTSSCRLSSTSVRGREGSFNSARLSFLSTISEDSASYFQDPVKAYTCSFVNTQTVENDYSETEEIRQKSTSCIGQDASSRSDFRLLMENLDVLESTFADSDALRLEREILQQLGKLGALKLFNSHLSRIVKTSNVLDLSDVHTEEQKMNDSRDYHMGKILVPSKRKGKRKLKTARVSEESIETSLLSLPSEALQEGLKQPTIFSAERALNSRGRRLTIARNEAEMSKGVQVVANLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQHLAFGWYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNAKYLV
Secondary Structure (PSIPRED)
cccccEEccccccccccccccccccccccccccccccccccccccHHHHHccccccccccccccccccccccHHHHHHHHHHHHHHHHHccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccccccccccHHHccccccccccccccccccHHHHHHHHHHHHHHHHHHHccccccHHHHHHccccccccHHHHHHHHHccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccHHHHHHHccccHHHHHHHHHHHHHHHHHHHHccccEEEHHHHHcccccccHHHHHHHcHHHHHHHHHcccccccccccHHHHHHHHHHHHHHHHHccccccccHHHHHHHHHHHHHHHHHHHHccccccHHHHHHHHcccHHHHHHHHHcccccccccccccccccccccc
Secondary Structure Prediction (SSPRO)
ccccEEEccccccccccccccccccccccccccccEccccccEEccccccccccccccccccccEEccccccccEEcccccccccccccccEcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcHHHHHHHHHccccccccccccccccccccccccccccccccEEEccccHHHHHHHHHHccHHccccccccccHHHHHHHccccccHHHHHHHHHHccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccHHHHHHHccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccHHHHHHHHccccHHHHHHcccccccccHHHHHHHHHHHHHHHHHHHHccccEccHHHHHHHHHHHHHHHHHHHHccccccHHHHHHHccccHHHHHHHHHHcccccEEccccccccccEEcc
Coil and Loop (DISEMBL)
mgmgfrlnlkwvspvqshffttsscrlsstsvrgregsfnsARLSFLSTISedsasyfqdpvkayTCSFVntqtvendyseTEEIRQKstscigqdassrsDFRLLMENLDVlestfadsDALRLEREILQQLGKLGALKLFNSHLSRIvktsnvldlsdvhteeqkmndsrdyhmgkilvpskrkgkrklktaRVSEESIETSLlslpsealqeglkqptiFSAERALNSRGRRLTIARNEAEMSKGVQVVANLERIKTTLEkesgkaasLNCWAQAAGVSERVLKQHLAFGWYCREELIKSTRPLVLFLARNyrglgipfsdllqagnvgvlqgaerfdhtrgykfsTYVQYWIRKSISKMVARHArgikipcklNREISKIQKARKALtnshgkypedieiaKYTGLSLAEIRSASECLRIVGSIDQKIgdclnakylv
Flexible Loop (DISEMBL)
MGMGFRLNLKWVSPVQSHFfttsscrlsstsvrgregsfNSARLSFLSTISEDSASYFQDPVKAYTCSFVNTQTVENDYSETEEirqkstscigqdassRSDFRLLMENLDVLESTFADSDALRLEREILQQLGKLGALKLFNSHLSRivktsnvldlsdvhteeqkmndsrdyhmgkilvpskrkgkrklktarvseesietsllslpsealqeglkqptifsaeralnsRGRRLtiarneaemskgvqvvaNLERIKTTLekesgkaasLNCWAQAAGVSERVLKQHLAFGWYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQgaerfdhtrgykfsTYVQYWIRKSISKMVARHARgikipcklnreiSKIQKARKaltnshgkypediEIAKYTGLSLAEIRSASECLRIVGsidqkigdclnakylv
Low Complexity Region (SEG)
MGMGFRLNLKWVSPVQSHFFTTSSCRLSSTSVRGREGSFNSARLSFLSTISEDSASYFQDPVKAYTCSFVNTQTVENDYSETEEIRQKSTSCIGQDASSRSDFRLLMENLDVLESTFADSDALRLEREIlqqlgklgalklFNSHLSRIVKTSNVLDLSDVHTEEQKMNDSRDYHMGKILVPSKRKGKRKLKTARVseesietsllslpseALQEGLKQPTIFSAERALNSRGRRLTIARNEAEMSKGVQVVANLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQHLAFGWYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNAKYLV
Disordered region (IsUnstruct)
****FRLNLKWVSPVQSHFFTTSSCR*****************LSFLSTISEDSASYFQDPVKAYTCSFVNTQTV***************************FRLLMENLDVLESTFADSDALRLEREILQQLGKLGALKLFNSHLSRIVKTSNVLDL******************************************************************************************VQVVANLERIKTTL*****KAASLNCWAQAAGVSERVLKQHLAFGWYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNAKY**
Disordered Region (DISOPRED)
**MGFRLNLKWVSPVQ*********************************************VKAYTCSFVNTQTVE*********************SSRSDFRLLMENLDVLESTFAD*DALRLEREILQQLGKLGALKLFNS*********************************************************************************ERALNSRGRRLTIARNEAEMSKGVQVVANLERIKTT**********LNCWAQAAGVSERVLKQHLAFGWYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIPCKLNREISKIQKARK*********PEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDC**AKYLV
Disordered Region (DISEMBL)
MGMGFRLNLKWVSPVQSHFFTTSS**************FNSARLSFLSTISEDSASYFQDPVKAYTCSFVNTQTVE********************ASSRSDFRLLMENLDVLESTFADSDALRLEREILQQLGKLGALKLFNSHLSRIVKTSNVLDLSDVHTEEQKMNDSRDYHMGKILVPSK*******************SLLSLPSEALQEGLKQPTIFSAERALNSRGRRLTIARNEAEMSKGVQVVANLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQHLAFGWYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNAKYLV
Disordered Region (DISPRO)
*GMGFRLNLKWVSPVQS*****************REGSFNSARLSFLSTISEDSASYFQDPVKAYTCSFVNTQTVENDYSETEEIRQKSTSCIGQDASSRSDFRLLMENLDVLESTFADSDALRLEREILQQLGKLGALKLFNSHLS***********************************************************************QPTIFSAERALNSRGRRLTIARNEAEMSKGVQVVANLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQHLAFGWYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNA*YLV
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (MEMSAT)
oooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MGMGFRLNLKWVSPVQSHFFTTSSCRLSSTSVRGREGSFNSARLSFLSTISEDSASYFQDPVKAYTCSFVNTQTVENDYSETEEIRQKSTSCIGQDASSRSDFRLLMENLDVLESTFADSDALRLEREILQQLGKLGALKLFNSHLSRIVKTSNVLDLSDVHTEEQKMNDSRDYHMGKILVPSKRKGKRKLKTARVSEESIETSLLSLPSEALQEGLKQPTIFSAERALNSRGRRLTIARNEAEMSKGVQVVANLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQHLAFGWYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNAKYLV
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	442	2.2.26 [Sep-21-2011]
O24621	571	RNA polymerase sigma fact	yes	no	0.898	0.695	0.496	4e-97
O22056	572	RNA polymerase sigma fact	no	no	0.463	0.358	0.385	8e-40
P26683	390	RNA polymerase sigma fact	yes	no	0.450	0.510	0.311	6e-29
Q9LD95	547	RNA polymerase sigma fact	no	no	0.450	0.363	0.331	1e-27
Q31QG5	320	RNA polymerase sigma fact	yes	no	0.438	0.606	0.328	1e-26
P38023	399	RNA polymerase sigma fact	no	no	0.463	0.513	0.325	2e-26
P52322	416	RNA polymerase sigma fact	no	no	0.409	0.435	0.325	2e-24
Q31ME3	320	RNA polymerase sigma fact	no	no	0.468	0.646	0.307	3e-24
P0A602	528	RNA polymerase sigma fact	yes	no	0.319	0.267	0.367	4e-24
P0A603	528	RNA polymerase sigma fact	yes	no	0.319	0.267	0.367	4e-24

>sp|O24621|SIGC_ARATH RNA polymerase sigma factor sigC OS=Arabidopsis thaliana GN=SIGC PE=2 SV=1

 Score =  355 bits (911), Expect = 4e-97,   Method: Compositional matrix adjust.
 Identities = 208/419 (49%), Positives = 282/419 (67%), Gaps = 22/419 (5%)

Query: 32  VRGREGSFNSARLSFLSTISEDSASYFQDPVKAYTCSFVNTQTVEND-YSETEEIRQKST 90
           VR    S  + R SFLS++ E+S  Y  D +KA  C+ V+  T +N+ Y E ++ ++   
Sbjct: 73  VRIPMTSVVATRWSFLSSVKEESRIYQNDSLKACGCASVSPYTAQNNVYVELKDPKEN-- 130

Query: 91  SCIGQDASSRS-------DFRLLMENLDVLESTFADSDALRLEREILQQLGKLGALKLFN 143
             IG  ++ RS        + LL +NL  LE TF   D++R+ER+I+ Q+GKLGA +LF 
Sbjct: 131 --IGVGSAERSYSSRSMLQYNLLAKNLLALEETFVALDSVRMERDIMLQMGKLGAAELFK 188

Query: 144 SHLSRIVKTSNVLDLSDVHTEEQKMNDSRDYHMGKILVPSKRKGKRKLKTARVSEESIET 203
           + LSR   +S    LSD  TE      ++     ++ V S+RK K+K + + V+ E+ + 
Sbjct: 189 TCLSRYRGSSITSCLSDT-TELVDTTPNQ-----QVFVSSRRKVKKKARRSSVTAENGDQ 242

Query: 204 SLLSLPSEALQEGLKQPTIFSAERALNSRGRRLTIARNEAEMSKGVQVVANLERIKTTLE 263
           S L +        +  P +    R    R +R  I+RNE EMS GV++VA++ERI+T LE
Sbjct: 243 SSLPIGLRTTWNNIDVPRV---RRPPKYRKKRERISRNETEMSTGVKIVADMERIRTQLE 299

Query: 264 KESGKAASLNCWAQAAGVSERVLKQHLAFGWYCREELIKSTRPLVLFLARNYRGLGIPFS 323
           +ESGK ASL+CWA AAG++E++L ++L +GWYCR+EL+KSTR LVLFLARNYRGLGI   
Sbjct: 300 EESGKVASLSCWAAAAGMNEKLLMRNLHYGWYCRDELVKSTRSLVLFLARNYRGLGIAHE 359

Query: 324 DLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIPCKLNREISK 383
           DL+QAG VGVLQGAERFDHTRGYKFSTYVQYWIRKS+S MV+RHARG+ IP  + R I+ 
Sbjct: 360 DLIQAGYVGVLQGAERFDHTRGYKFSTYVQYWIRKSMSTMVSRHARGVHIPSSIIRTINH 419

Query: 384 IQKARKALTNSHG-KYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNAKYL 441
           IQKARK L  SHG KY  D EIAK TG S+ +IR+A++CL++VGSID+K+GDC   K+L
Sbjct: 420 IQKARKTLKTSHGIKYAADEEIAKLTGHSVKKIRAANQCLKVVGSIDKKVGDCFTTKFL 478

Sigma factors are initiation factors that promote the attachment of plastid-encoded RNA polymerase (PEP) to specific initiation sites and are then released.
Arabidopsis thaliana (taxid: 3702)

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

 Score =  164 bits (416), Expect = 8e-40,   Method: Compositional matrix adjust.
 Identities = 79/205 (38%), Positives = 133/205 (64%)

Query: 235 RLTIARNEAEMSKGVQVVANLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQHLAFGW 294
           +L   R E E+S G+Q +  LER++T L + SG+  +   WA AAGV ++ L+Q +  G 
Sbjct: 271 KLLTVREEHELSAGIQDLLKLERLQTELTERSGRQPTFAQWASAAGVDQKSLRQRIHHGT 330

Query: 295 YCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQY 354
            C++++IKS   LV+ +A+NY+G G+   DL+Q G  G+++GAE+FD T+G+KFSTY  +
Sbjct: 331 LCKDKMIKSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDATKGFKFSTYAHW 390

Query: 355 WIRKSISKMVARHARGIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAE 414
           WI++++ K ++  +R I++P  +     ++++ARK L +  GK+P++ EIA+ TGLS+  
Sbjct: 391 WIKQAVRKSLSDQSRMIRLPFHMVEATYRVKEARKQLYSETGKHPKNEEIAEATGLSMKR 450

Query: 415 IRSASECLRIVGSIDQKIGDCLNAK 439
           + +     +   S+DQKIG   N K
Sbjct: 451 LMAVLLSPKPPRSLDQKIGMNQNLK 475

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 =  129 bits (323), Expect = 6e-29,   Method: Compositional matrix adjust.
 Identities = 62/199 (31%), Positives = 119/199 (59%)

Query: 235 RLTIARNEAEMSKGVQVVANLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQHLAFGW 294
           RL  A  E E+++ +  +  LER++  L ++  +    + WA+A  +     +  L  G 
Sbjct: 93  RLLRADEEIELARKIADLLELERVRERLSEKLERDPRDSEWAEAVQLPLPAFRYRLHIGR 152

Query: 295 YCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQY 354
             ++++++S   LV+ +A+ Y   G+ F DL+Q G++G+++ AE+FDH +GYKFSTY  +
Sbjct: 153 RAKDKMVQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYATW 212

Query: 355 WIRKSISKMVARHARGIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAE 414
           WIR++I++ +A  +R I++P  L   IS+I+K  K L+   G+ P + EIA    +++ +
Sbjct: 213 WIRQAITRAIADQSRTIRLPVHLYETISRIKKTTKLLSQEMGRKPTEEEIATRMEMTIEK 272

Query: 415 IRSASECLRIVGSIDQKIG 433
           +R  ++  ++  S++  IG
Sbjct: 273 LRFIAKSAQLPISLETPIG 291

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

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

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

 Score =  124 bits (311), Expect = 1e-27,   Method: Compositional matrix adjust.
 Identities = 66/199 (33%), Positives = 114/199 (57%)

Query: 234 RRLTIARNEAEMSKGVQVVANLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQHLAFG 293
           ++L  A+ EAE+   +Q +  LE++KT LE ++G   ++  WA+A G+S  VLK  +  G
Sbjct: 245 KQLLTAKEEAELISHIQHLLKLEKVKTKLESQNGCEPTIGEWAEAMGISSPVLKSDIHRG 304

Query: 294 WYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQ 353
              RE+LI +   LV+ +A+ Y+  G+ F DLLQ G++G+++  E+F    G +F+TY  
Sbjct: 305 RSSREKLITANLRLVVHIAKQYQNRGLNFQDLLQEGSMGLMKSVEKFKPQSGCRFATYAY 364

Query: 354 YWIRKSISKMVARHARGIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLA 413
           +WIR+SI K + +++R I++P  +   + K+ +ARK         P   E+A + G+S  
Sbjct: 365 WWIRQSIRKSIFQNSRTIRLPENVYMLLGKVSEARKTCVQEGNYRPSKEELAGHVGVSTE 424

Query: 414 EIRSASECLRIVGSIDQKI 432
           ++       R   S+ Q I
Sbjct: 425 KLDKLLYNTRTPLSMQQPI 443

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

 Score =  121 bits (303), Expect = 1e-26,   Method: Compositional matrix adjust.
 Identities = 64/195 (32%), Positives = 112/195 (57%), Gaps = 1/195 (0%)

Query: 241 NEAEMSKGVQVVANLERIKTTLEKESGKAASLNC-WAQAAGVSERVLKQHLAFGWYCREE 299
            E  + K VQ    L+ ++ TL+ E G     +  WA AAG+S   L+Q    G   + +
Sbjct: 29  EEVVLGKRVQQWMKLQELRQTLQSEEGDRDPSDLEWAAAAGLSIEELRQQQHLGEQAKRK 88

Query: 300 LIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKS 359
           +I++   LV+ +A+ Y    +   DL+Q G +G+ +G E+FD T+GY+FSTY  +WIR++
Sbjct: 89  MIEANLRLVVSVAKKYLKRNMDLLDLIQEGTIGMQRGVEKFDPTKGYRFSTYAYWWIRQA 148

Query: 360 ISKMVARHARGIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSAS 419
           I++ +A  AR I++P  +  +++KI+K ++ L+   G+     E+A    L+ A++R   
Sbjct: 149 ITRAIAEKARTIRLPIHITEKLNKIKKMQRQLSQQLGRTATLPELAAALDLTPAQVRDYL 208

Query: 420 ECLRIVGSIDQKIGD 434
           E  R   S+D ++GD
Sbjct: 209 EKARHPLSLDLRVGD 223

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

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

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

 Score =  120 bits (302), Expect = 2e-26,   Method: Compositional matrix adjust.
 Identities = 67/206 (32%), Positives = 121/206 (58%), Gaps = 1/206 (0%)

Query: 229 LNSRGR-RLTIARNEAEMSKGVQVVANLERIKTTLEKESGKAASLNCWAQAAGVSERVLK 287
           L   GR RL  A  E E+++ +  +  LERI+  L ++  +  S   WA A        +
Sbjct: 95  LQEIGRIRLLRADEEIELARQIADLLALERIRDELLEQLDRLPSDAEWAAAVDSPLDEFR 154

Query: 288 QHLAFGWYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYK 347
           + L  G   ++++++S   LV+ +A+ Y   G+ F DL+Q G++G+++ AE+FDH +GYK
Sbjct: 155 RRLFRGRRAKDKMVQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKFDHEKGYK 214

Query: 348 FSTYVQYWIRKSISKMVARHARGIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKY 407
           FSTY  +WIR++I++ +A  +R I++P  L   IS+I+K  K L+   G+ P + EIA  
Sbjct: 215 FSTYATWWIRQAITRAIADQSRTIRLPVHLYETISRIKKTTKLLSQEMGRKPTEEEIATR 274

Query: 408 TGLSLAEIRSASECLRIVGSIDQKIG 433
             +++ ++R  ++  ++  S++  IG
Sbjct: 275 MEMTIEKLRFIAKSAQLPISLETPIG 300

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 =  114 bits (285), Expect = 2e-24,   Method: Compositional matrix adjust.
 Identities = 59/181 (32%), Positives = 103/181 (56%)

Query: 253 ANLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQHLAFGWYCREELIKSTRPLVLFLA 312
             L  IK  L K    A  L  W   +       K+ L  G   +E++++S   LV+ +A
Sbjct: 137 PKLSDIKAYLGKTELTAPLLEEWLAKSKEYLSAFKRRLYHGRRAKEKMVQSNLRLVVSIA 196

Query: 313 RNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIK 372
           + Y   G+ F DL+Q G++G+++ AE+FDH +GYKFSTY  +WIR++I++ +A  +R I+
Sbjct: 197 KKYMNRGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYATWWIRQAITRAIADQSRTIR 256

Query: 373 IPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKI 432
           +P  L   IS+I+K  K L+    + P + EIA    +++ ++R  ++  ++  S++  I
Sbjct: 257 LPVHLYETISRIKKTTKILSQEMRRKPTEEEIATKMEMTIEKLRFIAKSAQLPISLETPI 316

Query: 433 G 433
           G
Sbjct: 317 G 317

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

Microcystis aeruginosa (taxid: 1126)

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

 Score =  113 bits (283), Expect = 3e-24,   Method: Compositional matrix adjust.
 Identities = 64/208 (30%), Positives = 115/208 (55%), Gaps = 1/208 (0%)

Query: 229 LNSRGR-RLTIARNEAEMSKGVQVVANLERIKTTLEKESGKAASLNCWAQAAGVSERVLK 287
           L   GR RL  A  E    + VQ +  L   +T L    G   S   WA A  ++   L 
Sbjct: 17  LQEIGRVRLLTAEEELCFGRQVQRLMMLLDAQTELRDRLGHEPSKEEWAAAVDLNLEDLD 76

Query: 288 QHLAFGWYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYK 347
           + +  G   + ++I++   LV+ +A+ Y+   + F DL+Q G +G+ +G E+FD ++GYK
Sbjct: 77  RQIEQGQRAKRKMIEANLRLVVSIAKKYQKRHMEFLDLIQEGTLGLERGVEKFDPSKGYK 136

Query: 348 FSTYVQYWIRKSISKMVARHARGIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKY 407
           FSTY  +WIR++I++ +A+ +R I++P  +  +++K++K ++ L+   G+     E+A+ 
Sbjct: 137 FSTYAYWWIRQAITRAIAQQSRTIRLPIHITEKLNKLKKTQRELSQQLGRSATASELAEV 196

Query: 408 TGLSLAEIRSASECLRIVGSIDQKIGDC 435
             L L ++R   +  R   S+D K+GD 
Sbjct: 197 LELPLEQVREYIQMNRQPVSLDVKVGDS 224

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

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

>sp|P0A602|RPOD_MYCTU RNA polymerase sigma factor RpoD OS=Mycobacterium tuberculosis GN=rpoD PE=1 SV=1

 Score =  113 bits (282), Expect = 4e-24,   Method: Compositional matrix adjust.
 Identities = 54/147 (36%), Positives = 90/147 (61%), Gaps = 6/147 (4%)

Query: 294 WYCRE------ELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYK 347
           W CR+       L+++   LV+ LA+ Y G G+ F DL+Q GN+G+++  E+FD+T+GYK
Sbjct: 283 WICRDGDRAKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLGLIRAVEKFDYTKGYK 342

Query: 348 FSTYVQYWIRKSISKMVARHARGIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKY 407
           FSTY  +WIR++I++ +A  AR I+IP  +   I+K+ + ++ L    G+ P   E+AK 
Sbjct: 343 FSTYATWWIRQAITRAMADQARTIRIPVHMVEVINKLGRIQRELLQDLGREPTPEELAKE 402

Query: 408 TGLSLAEIRSASECLRIVGSIDQKIGD 434
             ++  ++    +  R   S+DQ IGD
Sbjct: 403 MDITPEKVLEIQQYAREPISLDQTIGD 429

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.

Mycobacterium tuberculosis (taxid: 1773)

>sp|P0A603|RPOD_MYCBO RNA polymerase sigma factor RpoD OS=Mycobacterium bovis (strain ATCC BAA-935 / AF2122/97) GN=rpoD PE=3 SV=1

 Score =  113 bits (282), Expect = 4e-24,   Method: Compositional matrix adjust.
 Identities = 54/147 (36%), Positives = 90/147 (61%), Gaps = 6/147 (4%)

Query: 294 WYCRE------ELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYK 347
           W CR+       L+++   LV+ LA+ Y G G+ F DL+Q GN+G+++  E+FD+T+GYK
Sbjct: 283 WICRDGDRAKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLGLIRAVEKFDYTKGYK 342

Query: 348 FSTYVQYWIRKSISKMVARHARGIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKY 407
           FSTY  +WIR++I++ +A  AR I+IP  +   I+K+ + ++ L    G+ P   E+AK 
Sbjct: 343 FSTYATWWIRQAITRAMADQARTIRIPVHMVEVINKLGRIQRELLQDLGREPTPEELAKE 402

Query: 408 TGLSLAEIRSASECLRIVGSIDQKIGD 434
             ++  ++    +  R   S+DQ IGD
Sbjct: 403 MDITPEKVLEIQQYAREPISLDQTIGD 429

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.

Mycobacterium bovis (taxid: 1765)

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	442
225429414	561	PREDICTED: RNA polymerase sigma factor r	0.997	0.786	0.551	1e-141
147865632	611	hypothetical protein VITISV_036980 [Viti	0.927	0.671	0.549	1e-130
224088962	559	predicted protein [Populus trichocarpa]	0.988	0.781	0.525	1e-126
255550882	560	RNA polymerase sigma factor rpoD, putati	0.995	0.785	0.549	1e-125
39840783	548	sigma factor [Spinacia oleracea]	0.988	0.797	0.497	1e-116
449461399	559	PREDICTED: RNA polymerase sigma factor s	0.984	0.778	0.467	1e-106
356565804	551	PREDICTED: RNA polymerase sigma factor r	0.968	0.776	0.490	1e-105
7363220	567	sigma factor 3 [Sinapis alba]	0.875	0.682	0.493	1e-101
312281919	562	unnamed protein product [Thellungiella h	0.837	0.658	0.51	7e-97
297820128	568	predicted protein [Arabidopsis lyrata su	0.943	0.734	0.483	4e-96

>gi|225429414|ref|XP_002275831.1| PREDICTED: RNA polymerase sigma factor rpoD [Vitis vinifera] gi|296081598|emb|CBI20603.3| unnamed protein product [Vitis vinifera]

 Score =  509 bits (1310), Expect = e-141,   Method: Compositional matrix adjust.
 Identities = 258/468 (55%), Positives = 327/468 (69%), Gaps = 27/468 (5%)

Query: 1   MGMGFRLNLKWVSPVQSHFFTTSSCRLSSTSVRGREGSFNSARLSFLSTISEDSASYFQD 60
           MGMGFRLNLKW  P+     T S  RL ++SV+G+E SF+S R SF S  SED  S ++D
Sbjct: 1   MGMGFRLNLKWDFPISCPTLTNSPSRLCTSSVQGKEASFDSTRFSFPSVTSEDCESLYKD 60

Query: 61  PVKAYTCSFVNTQTVENDYSETEEIRQKSTSC---------------IGQD--------- 96
           P K + CS    QT ENDYS  E ++ K   C               IG+D         
Sbjct: 61  PFKPFACSSGALQTFENDYSAMEAMKMKIGKCSHGDLFKIVNASQAPIGEDISASVAGLQ 120

Query: 97  ASSRSDFRLLMENLDVLESTFADSDALRLEREILQQLGKLGALKLFNSHLSRIVKTSNVL 156
           AS  S F LL+ENLD+LE  FADS+ +RLER+I+ QLG+LGALKLF   LSR +KTS   
Sbjct: 121 ASKASQFSLLLENLDILEEMFADSNMVRLERDIMVQLGRLGALKLFQICLSRTLKTSTSF 180

Query: 157 DLSDVHTE---EQKMNDSRDYHMGKILVPSKRKGKRKLKTARVSEESIETSLLSLPSEAL 213
           DL    TE   E + N + D H+ K++V S +K +RK K  R  E++       LPS+ +
Sbjct: 181 DLFSAPTEHIRECQTNGTVDDHLDKVVVRSGKKEERKSKRERALEKADNIYAFPLPSKTI 240

Query: 214 QEGLKQPTIFSAERALNSRGRRLTIARNEAEMSKGVQVVANLERIKTTLEKESGKAASLN 273
           ++G  +P++ + +R LNSR +RL  A+NEAEMSKGV++VANLERI+ TLE+E G  ASL+
Sbjct: 241 RKGPGRPSVSTVKRTLNSRRKRLMNAKNEAEMSKGVKLVANLERIRATLEEEIGHVASLS 300

Query: 274 CWAQAAGVSERVLKQHLAFGWYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGV 333
            WA+AAGV ++VL+Q L FGWYCR+EL++ST  LVL++ARNYRG+G+ F D+LQAGN+GV
Sbjct: 301 NWAEAAGVDKKVLQQQLQFGWYCRDELLRSTHSLVLYIARNYRGMGVAFEDILQAGNLGV 360

Query: 334 LQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIPCKLNREISKIQKARKALTN 393
           LQGAERFDHT+GY+FSTYVQYWIRKS+S +VARHARG+KIP  LNR I +IQKARKAL  
Sbjct: 361 LQGAERFDHTKGYRFSTYVQYWIRKSMSTLVARHARGVKIPFTLNRAIGQIQKARKALYK 420

Query: 394 SHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNAKYL 441
           SHG+YP+D EIAK+TGLSLA+IRSA  CLR+VGS DQ   DC  A  L
Sbjct: 421 SHGRYPDDNEIAKFTGLSLAKIRSAGNCLRVVGSTDQSFQDCWGATIL 468

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147865632|emb|CAN83254.1| hypothetical protein VITISV_036980 [Vitis vinifera]

 Score =  473 bits (1216), Expect = e-130,   Method: Compositional matrix adjust.
 Identities = 240/437 (54%), Positives = 307/437 (70%), Gaps = 27/437 (6%)

Query: 32  VRGREGSFNSARLSFLSTISEDSASYFQDPVKAYTCSFVNTQTVENDYSETEEIRQKSTS 91
           ++G+E SF+S R SF S  SED  S ++DP K + CS    QT ENDYS  E ++ K   
Sbjct: 82  IQGKEASFDSTRFSFPSVTSEDCESLYKDPFKPFACSSGALQTFENDYSAMEAMKMKIGK 141

Query: 92  C---------------IGQD---------ASSRSDFRLLMENLDVLESTFADSDALRLER 127
           C               IG+D         AS  S F LL+ENLD+LE  FADS+ +RLER
Sbjct: 142 CSHGDLFKIVNASQAPIGEDISASVAGLQASKASQFSLLLENLDILEEMFADSNMVRLER 201

Query: 128 EILQQLGKLGALKLFNSHLSRIVKTSNVLDLSDVHTE---EQKMNDSRDYHMGKILVPSK 184
           +I+ QLG+LGALKLF   LSR +KTS   DL    TE   E + N + D H+ K++V S 
Sbjct: 202 DIMVQLGRLGALKLFQICLSRTLKTSTSFDLFSAPTEHIRECQTNGTVDDHLDKVVVRSG 261

Query: 185 RKGKRKLKTARVSEESIETSLLSLPSEALQEGLKQPTIFSAERALNSRGRRLTIARNEAE 244
           +K +RK K  R  E++       LPS+ +++G  +P++ + +R LNSR +RL  A+NEAE
Sbjct: 262 KKEERKSKRERALEKADNIYAFPLPSKTIRKGPGRPSVSTVKRTLNSRRKRLMNAKNEAE 321

Query: 245 MSKGVQVVANLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQHLAFGWYCREELIKST 304
           MSKGV++VANLERI+ TLE+E G  ASL+ WA+AAGV ++VL+Q L FGWYCR+EL++ST
Sbjct: 322 MSKGVKLVANLERIRATLEEEIGHVASLSNWAEAAGVDKKVLQQQLQFGWYCRDELLRST 381

Query: 305 RPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMV 364
             LVL++ARNYRG+G+ F D+LQAGN+GVLQGAERFDHT+GY+FSTYVQYWIRKS+S +V
Sbjct: 382 HSLVLYIARNYRGMGVAFEDILQAGNLGVLQGAERFDHTKGYRFSTYVQYWIRKSMSTLV 441

Query: 365 ARHARGIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRI 424
           ARHARG+KIP  LNR I +IQKARKAL  SHG+YP+D EIAK+TGLSLA+IRSA  CLR+
Sbjct: 442 ARHARGVKIPFTLNRAIGQIQKARKALYKSHGRYPDDNEIAKFTGLSLAKIRSAGNCLRV 501

Query: 425 VGSIDQKIGDCLNAKYL 441
           VGS DQ   DC  A  L
Sbjct: 502 VGSTDQSFQDCWGATIL 518

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224088962|ref|XP_002308586.1| predicted protein [Populus trichocarpa] gi|222854562|gb|EEE92109.1| predicted protein [Populus trichocarpa]

 Score =  458 bits (1179), Expect = e-126,   Method: Compositional matrix adjust.
 Identities = 246/468 (52%), Positives = 325/468 (69%), Gaps = 31/468 (6%)

Query: 1   MGMGFRLNLKWVSPVQSHFFTTSSCRLSSTSVRGREGSFNSARLSFLSTISEDSASYFQD 60
           MG+GFRL  KW SP+QSH  T S+   SS S RG E S N ARLSFLS +SE+     + 
Sbjct: 1   MGVGFRLTPKWGSPMQSHSATNSTSMFSSFSARGMEASVNQARLSFLSVVSEEGDILNKH 60

Query: 61  PVKAYTCSFVNTQTVENDYSETEEIRQKS--------TSCIGQD--------ASSRSDFR 104
             K++ CS    Q VEND  + E ++            + +G D        ++S +  R
Sbjct: 61  SFKSFACSSA-AQNVENDCLQMERLKMNVDKTSHVSINNMMGNDKVSVEEEISTSHTRLR 119

Query: 105 --------LLMENLDVLESTFADSDALRLEREILQQLGKLGALKLFNSHLSRIVKTSNVL 156
                    L++NLD LE   AD DAL+LER+IL QLG+LGAL+ FN+ LSR ++TSNVL
Sbjct: 120 ERMTSRISFLLDNLDTLEKLVADLDALKLERDILLQLGRLGALEFFNACLSRTLQTSNVL 179

Query: 157 DLSDVHTE---EQKMNDSRDYHMGKILVPSKRKGKRKLKTARV-SEESIETSLLSLPSEA 212
           DLS V TE   E K +       GK +V + +K +RK +  R  S+   +T+ LSLPS+ 
Sbjct: 180 DLSAVPTENTGESKTDGMLGDLTGKTVVRTGKKEERKFRRERAASDNGKKTTSLSLPSKT 239

Query: 213 LQEGLKQPTIFSAERALNSRGRRLTIARNEAEMSKGVQVVANLERIKTTLEKESGKAASL 272
           +Q  L +PT    +R  +S  RR  IARNEA+M++GV+V ++LERI+TTLE+E+G+  SL
Sbjct: 240 VQNNLPKPTF--VKRTSSSSSRRSLIARNEAKMTRGVKVASDLERIRTTLEEETGQVVSL 297

Query: 273 NCWAQAAGVSERVLKQHLAFGWYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVG 332
           +CWA+A G+ ++VL+Q L FGWYCR+ELIK+T  LVL++ARNYRG+GI   DL+QAGN+G
Sbjct: 298 SCWAEATGLDKKVLQQQLQFGWYCRDELIKNTHSLVLYIARNYRGMGIAMEDLIQAGNLG 357

Query: 333 VLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIPCKLNREISKIQKARKALT 392
           +LQGAERFD TRGY+FSTYVQYWIRKS+ K+V RHARGI+IP  L+R I+KIQKARKAL+
Sbjct: 358 LLQGAERFDPTRGYRFSTYVQYWIRKSMLKIVERHARGIQIPYALSRSINKIQKARKALS 417

Query: 393 NSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNAKY 440
           NSHG+YP+D E+AK+TGLSLA+I SA +CLR+V S+DQKIG+   AKY
Sbjct: 418 NSHGRYPDDWEVAKFTGLSLAKIESAQKCLRVVASLDQKIGEGHYAKY 465

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255550882|ref|XP_002516489.1| RNA polymerase sigma factor rpoD, putative [Ricinus communis] gi|223544309|gb|EEF45830.1| RNA polymerase sigma factor rpoD, putative [Ricinus communis]

 Score =  453 bits (1165), Expect = e-125,   Method: Compositional matrix adjust.
 Identities = 257/468 (54%), Positives = 337/468 (72%), Gaps = 28/468 (5%)

Query: 1   MGMGFRLNLKWVSPVQSHFFTTSSCRLSSTS-VRGREGSFNSARLSFLSTISEDSASYFQ 59
           MG GFRLNLK   P  S    +      S+S VRGRE +   +RLSFLS ISE+     +
Sbjct: 1   MGFGFRLNLKLDFPFHSPNSPSRLSSSPSSSFVRGREATSYQSRLSFLSVISEEGDIAHR 60

Query: 60  DPVKAYTCSFVNTQTVENDYSETE--------------------EIRQKSTSCIGQDASS 99
           DP+K Y  S+   QTVEN++S+ E                    E+  K    +   ++ 
Sbjct: 61  DPLKTYAYSYA-VQTVENEHSQGEGFKVNFGKRSHFGLNIIGDAEVSLKEDIFVSPSSTK 119

Query: 100 R--SDFRLLMENLDVLESTFADSDALRLEREILQQLGKLGALKLFNSHLSRIVKTSNVLD 157
              S F LL+ENL++LE +FADSDA +LE +IL QLGKLGALKLFN+ L+R ++T+NVL+
Sbjct: 120 ERTSRFSLLLENLNILEQSFADSDASKLEEDILLQLGKLGALKLFNTCLTRTLETTNVLE 179

Query: 158 LSDVHTE---EQKMNDSRDYHMGKILVPSKRKGKRKLKTARVS-EESIETSLLSLPSEAL 213
           +SDVHTE   E  +N +   +  K++V + +K +RK +  R S  +  ++  L LPS  +
Sbjct: 180 VSDVHTEIIGECNINGTSINNQIKVVVHTAKKEERKSRRERASARKGHKSPSLPLPSRPI 239

Query: 214 QEGLKQPTIFSAERALNSRGRRLTIARNEAEMSKGVQVVANLERIKTTLEKESGKAASLN 273
           Q G ++PT+ S ++A  S+ RRL IARNEAEM++G++V+A+LE+I+TTLE+E+ +  SL+
Sbjct: 240 QSGSEKPTVSSGKKASKSKSRRLIIARNEAEMARGIKVLADLEKIRTTLEEETERVVSLS 299

Query: 274 CWAQAAGVSERVLKQHLAFGWYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGV 333
           CWA+AAG+  +VL+Q L+FGWYCR+ELIKSTR LVL+ ARNYRG GI   DLLQAGN+GV
Sbjct: 300 CWAEAAGLDVKVLQQQLSFGWYCRDELIKSTRSLVLYFARNYRGTGIALEDLLQAGNLGV 359

Query: 334 LQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIPCKLNREISKIQKARKALTN 393
           L+GAERFDHTRGY+FSTYVQYWIRKS+SK+V+R ARGI+IPC L+R I +IQKARKALT 
Sbjct: 360 LEGAERFDHTRGYRFSTYVQYWIRKSMSKIVSRLARGIQIPCTLSRAIYQIQKARKALTT 419

Query: 394 SHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNAKYL 441
           S+GKYP+D EIAKYTGLSLA+I SAS CLR+VGSIDQKIG+ LNAKYL
Sbjct: 420 SNGKYPDDDEIAKYTGLSLAKIESASRCLRVVGSIDQKIGESLNAKYL 467

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|39840783|emb|CAD20832.1| sigma factor [Spinacia oleracea]

 Score =  423 bits (1088), Expect = e-116,   Method: Compositional matrix adjust.
 Identities = 229/460 (49%), Positives = 313/460 (68%), Gaps = 23/460 (5%)

Query: 1   MGMGFRLNL-KWVSPVQSHFFTTSSCRLSSTSVRGREGSFNSARLSFLSTISEDSASYFQ 59
           MG G +LN+ + V P     FTT+S    STS RG+E  F SARLS L+   ++S +  +
Sbjct: 1   MGFGCKLNMMRCVLPSLRSPFTTNSSPPCSTSFRGKELDFGSARLSLLTIGFDESETLRK 60

Query: 60  DPVKAYTCSFVNTQTVENDYSETEE-IRQKSTSCIGQDASSRSD---------------- 102
           D ++ +  S     TVENDYS  E  I ++S   +  D    SD                
Sbjct: 61  DTLRPHAGSSSVPLTVENDYSNLETTISKRSCKDLISDTEVLSDRDVSVYVRSVQSCSAS 120

Query: 103 -FRLLMENLDVLESTFADSDALRLEREILQQLGKLGALKLFNSHLSRIVKTSNVLDLSDV 161
            F  LM N+++LE+  +DS+ L+LE++IL QLG+LGAL+LF++ LSRI+  S   DL  +
Sbjct: 121 HFHTLMANINLLENKVSDSELLKLEKDILVQLGRLGALQLFHACLSRIIDMS---DLPGL 177

Query: 162 HTEEQKMNDSRDYHMGKILVPSKRKGKRKLKTARVSEESIETSLLSLPSEALQEGLKQPT 221
            TE+ K N  +D  + K LV SKRK +RKL+  R  + S  +   +  SE+  E      
Sbjct: 178 ITEDGKANVRKDNELKKKLVFSKRKEERKLRQERRLQAST-SKRCACKSESSIESSIHHV 236

Query: 222 IFSAERALNSRGRRLTIARNEAEMSKGVQVVANLERIKTTLEKESGKAASLNCWAQAAGV 281
           + +A +   +RGRR  IA+NEAEMS+G++VVA LE++K TLEKE+GKA SLNCWA+AAG+
Sbjct: 237 VSTAAKKTKARGRRAIIAKNEAEMSRGIKVVAQLEKVKLTLEKETGKAVSLNCWAEAAGI 296

Query: 282 SERVLKQHLAFGWYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFD 341
            E+VL+  L FGWYCR+EL+KS R LVL+L+R YRGLG+   DL+QAGN+G+LQGAERFD
Sbjct: 297 DEKVLQHDLHFGWYCRDELLKSGRSLVLYLSRYYRGLGVAHEDLMQAGNIGILQGAERFD 356

Query: 342 HTRGYKFSTYVQYWIRKSISKMVARHARGIKIPCKLNREISKIQKARKALTNSHGKYPED 401
           HTRGY+FSTYVQYWIRK++S++V+RH RGIK+P  L+  I+++QKARK L  S GK+P+D
Sbjct: 357 HTRGYQFSTYVQYWIRKAMSQLVSRHGRGIKVPTTLSTTINRVQKARKILKRSQGKHPDD 416

Query: 402 IEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNAKYL 441
           +E++K TGLSL +I+SA  CLRIVGS+DQK+G  +N KYL
Sbjct: 417 VEVSKSTGLSLDKIKSADNCLRIVGSLDQKVGHFINMKYL 456

Source: Spinacia oleracea

Species: Spinacia oleracea

Genus: Spinacia

Family: Amaranthaceae

Order: Caryophyllales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449461399|ref|XP_004148429.1| PREDICTED: RNA polymerase sigma factor sigC-like [Cucumis sativus] gi|449507267|ref|XP_004162982.1| PREDICTED: RNA polymerase sigma factor sigC-like [Cucumis sativus]

 Score =  391 bits (1004), Expect = e-106,   Method: Compositional matrix adjust.
 Identities = 221/473 (46%), Positives = 304/473 (64%), Gaps = 38/473 (8%)

Query: 1   MGMGFRLNLKWVSPVQSHFFTTSSCRLSSTSVRGREGSFNSARLSFLSTISEDSASYFQD 60
           MG  FR NL+W   +Q+H    S  +LS  + +GRE +FNS RLSF S+I E+  S  ++
Sbjct: 1   MGTSFRPNLRWGFQIQTHSLKNSPSKLSPHASKGREAAFNSGRLSFFSSICEEGESIPRE 60

Query: 61  PVKAYTCSFVNTQTVENDYSETEEIRQKS------------------------TSCIGQD 96
            +K YTC     QT  ND    EEI   S                        +SC    
Sbjct: 61  TLKTYTCLSEAPQTSANDLLNLEEIEMNSGAKSLGPMHYGIKSTRPSKVEDNFSSCTSLP 120

Query: 97  ASSRSDFRLLMENLDVLESTFADSDALRLEREILQQLGKLGALKLFNSHLSRIVKTSNVL 156
               S F +LMENLDVLE TF +S  L LER+I+ QL KLGAL+ FN+ LSR +KTS+  
Sbjct: 121 TGKASPFGILMENLDVLEETFTESGMLSLERDIVLQLTKLGALEFFNTCLSRTLKTSSFH 180

Query: 157 DLSDV-------HTEEQKMNDSRDYHMGKILVPSKRKGKRKLKT-ARVSEESIETSLLSL 208
           D S +       H   QK ND  D      +  +K+ G+R +K  A  + + I + LL+ 
Sbjct: 181 DSSGLPIEGGEDHNVNQKTNDQND---NVTVYSAKKAGRRSVKKRAMDNADKIASRLLT- 236

Query: 209 PSEALQEGLKQPTIFSAERALNSRGRRLTIARNEAEMSKGVQVVANLERIKTTLEKESGK 268
            + A++E + + T+FS +++ NS  RRL +A NEAEMS GV+VVANLERI+ TLEKESG+
Sbjct: 237 -TRAVKEKIHRSTVFSRKKSSNSSKRRLIVAINEAEMSTGVKVVANLERIRETLEKESGR 295

Query: 269 AASLNCWAQAAGVSERVLKQHLAFGWYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQA 328
            AS++CWA+AA V  + L++ L FG +CR+EL++ST  LV+FLA+ YR  G+P  DL+QA
Sbjct: 296 IASMSCWAEAASVDIKDLQKQLQFGSFCRDELLRSTNSLVVFLAKKYRCSGLPMEDLVQA 355

Query: 329 GNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIPCKLNREISKIQKAR 388
           G +GVLQG ERFD  RG++ STY+QYWIRKS+S++VAR++RGI+IP  L + I++IQKAR
Sbjct: 356 GALGVLQGVERFDPKRGFRISTYIQYWIRKSMSRVVARNSRGIQIPRSLTKAINQIQKAR 415

Query: 389 KALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNAKYL 441
           K L +S  +Y +D +IA+ TGL LA++R AS CL++VGS DQK+GD +N KY+
Sbjct: 416 KVLNHSGRRYSDD-DIARATGLPLAKVRVASNCLKVVGSNDQKMGDGVNMKYM 467

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356565804|ref|XP_003551127.1| PREDICTED: RNA polymerase sigma factor rpoD-like [Glycine max]

 Score =  389 bits (999), Expect = e-105,   Method: Compositional matrix adjust.
 Identities = 230/469 (49%), Positives = 312/469 (66%), Gaps = 41/469 (8%)

Query: 1   MGMGFRLN--LKWVSPVQS-HFFTTSSCRLSSTSVRGREGSFNSARLSFLSTISEDSASY 57
           +G GF LN  L++   + + H FT S   LS +S   RE  FN  RLSF ST  E+  + 
Sbjct: 3   LGFGFGLNPRLRYCLLLHTPHSFTNSPLCLSPSSAGVRETCFNFTRLSFPSTFYEEGEAL 62

Query: 58  FQDPVKAYTCSFVNTQTVENDYSETEEIR----QKSTSCIGQ----------DASSRSD- 102
            +D  + +  S    +T+END    EE +    ++S S + +          + S+ S  
Sbjct: 63  QKDFGRVFAFSSSALETLENDSLGREETQVNKGKRSLSSVHKMIDNTQMPFGEVSTVSKK 122

Query: 103 --------FRLLMENLDVLESTFADSDALRLEREILQQLGKLGALKLFNSHLSRIVKTSN 154
                   FRLLMENL VLE TF DS+ALRLE+ I+ QLGKLGAL+LFN  LSR + TS 
Sbjct: 123 FESFRAQHFRLLMENLCVLEETFVDSEALRLEKAIILQLGKLGALELFNVCLSRSLGTSL 182

Query: 155 VLDLSDVHTEEQKMNDSRDYHMGKILVPSKRKGKRKLKTARVSEESIETSL--LSLPSEA 212
           V + +D      K++D +D    K++V S +K + K +  R   E + T++   SL  +A
Sbjct: 183 VSNYAD------KVDDYKD----KVVVQSSKKKENKTRRKR---EFVSTAVSSQSLTLKA 229

Query: 213 LQEGLKQPTIFSAERALNSRGRRLTIARNEAEMSKGVQVVANLERIKTTLEKESGKAASL 272
            QE L   +    +RA N++ +R+ +A+ EAEMSKGV+V+A LE+I+T +E+++ + ASL
Sbjct: 230 NQEDLLGFSASLVKRAPNTKNKRILVAKREAEMSKGVKVLAELEKIRTAIEEDTKRVASL 289

Query: 273 NCWAQAAGVSERVLKQHLAFGWYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVG 332
           + WA+A+GV E+VL++ L  G+YC++ELI+STR LVL+LAR YRG+GI   DLLQAG VG
Sbjct: 290 STWAEASGVDEKVLQKLLHRGYYCQDELIRSTRSLVLYLARKYRGMGIALDDLLQAGYVG 349

Query: 333 VLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIPCKLNREISKIQKARKALT 392
           VLQGAERFD TRGYKFSTYVQYWIRKSI ++VAR+ARGI IP  LNR I++IQKARKA+ 
Sbjct: 350 VLQGAERFDSTRGYKFSTYVQYWIRKSILRVVARYARGIVIPWSLNRAINQIQKARKAMK 409

Query: 393 NSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNAKYL 441
           ++H K P+D EIAK TGLSL +I+SAS CLRIV SIDQK+GD L  +Y+
Sbjct: 410 STHKKCPDDYEIAKMTGLSLDKIKSASNCLRIVASIDQKVGDYLGVEYM 458

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|7363220|emb|CAB83107.1| sigma factor 3 [Sinapis alba]

 Score =  374 bits (961), Expect = e-101,   Method: Compositional matrix adjust.
 Identities = 204/413 (49%), Positives = 280/413 (67%), Gaps = 26/413 (6%)

Query: 41  SARLSFLSTISEDSASYFQD-PVKAYTCSFVNTQTVENDYSETEEIRQKSTSCIGQDASS 99
           ++R SFLS+I E S S+ +D P+KA  C+   + T EN Y E ++ ++    C+  D  S
Sbjct: 76  ASRWSFLSSIKEGSRSHRRDHPLKACGCA---SATAENVYVELKDPKENIGMCLVGDQMS 132

Query: 100 RSD----------FRLLMENLDVLESTFADSDALRLEREILQQLGKLGALKLFNSHLSRI 149
            ++          + LL +NL  LE TF   D+LR+ER+I+ Q+ KLGA +LFN+ LSR 
Sbjct: 133 SAEKAHLSRSMLQYNLLGKNLLALEQTFVALDSLRMERDIMLQMRKLGAAELFNTCLSRS 192

Query: 150 VKTSNVLDLSDVHTEEQKMNDSRDYHMGKILVPSKRKGKRKLKTARVSEESIETSLLSLP 209
             +S    L D  T E   + +++    K  V S RK ++K +T    + S   S     
Sbjct: 193 RVSSATSCLPDTGTPELVDDTTQEQ---KTFVHSTRKLRKKARTGNGDQGSSTIS----- 244

Query: 210 SEALQEGLKQPTIFSAERALNSRGRRLTIARNEAEMSKGVQVVANLERIKTTLEKESGKA 269
           S    EG+  P +    +    R +R  I+RNEAEMS+GV++VA++ERI+T LE+E+GK 
Sbjct: 245 SRTTWEGIDVPRV---RKPSKYRKKRERISRNEAEMSQGVKIVADMERIRTKLEEETGKV 301

Query: 270 ASLNCWAQAAGVSERVLKQHLAFGWYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAG 329
           AS++CWA+AAG+++++L  +L FGWYCR+EL+KSTR LVLFLARNYRGLGI   DL+QAG
Sbjct: 302 ASMSCWAEAAGMNQKLLMHNLHFGWYCRDELVKSTRSLVLFLARNYRGLGIAHEDLIQAG 361

Query: 330 NVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIPCKLNREISKIQKARK 389
            VGVLQGAERFDHTRGYKFSTYV+YWIRKS+S MV+RHARG+ IP  + R +S+IQKARK
Sbjct: 362 YVGVLQGAERFDHTRGYKFSTYVRYWIRKSMSTMVSRHARGVHIPASIIRTMSQIQKARK 421

Query: 390 ALTNSHG-KYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNAKYL 441
            L  S G KYP D EI+K TG SL +IR+A++CL++VGSID+K+GDC   ++L
Sbjct: 422 TLKTSQGIKYPADEEISKLTGYSLKKIRAANQCLKVVGSIDKKVGDCFTTRFL 474

Source: Sinapis alba

Species: Sinapis alba

Genus: Sinapis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|312281919|dbj|BAJ33825.1| unnamed protein product [Thellungiella halophila]

 Score =  360 bits (924), Expect = 7e-97,   Method: Compositional matrix adjust.
 Identities = 204/400 (51%), Positives = 271/400 (67%), Gaps = 30/400 (7%)

Query: 57  YFQDPVKAYTCSFVNTQTVENDYSETEEIRQKSTSCIGQDAS------SRS--DFRLLME 108
           Y + P+KA  C+     T EN Y E ++ + KS   + Q +S      SRS   + LL +
Sbjct: 85  YQKYPLKACGCASATPCTAENVYVELKDPK-KSIGVVEQMSSAEKANLSRSMLQYNLLGK 143

Query: 109 NLDVLESTFADSDALRLEREILQQLGKLGALKLFNSHLSRIVKTSNVLDLSD------VH 162
           NL  LE TF   D+LR+ER+I+ Q+GKLGA +LF + LSR   +S    LSD      V 
Sbjct: 144 NLLALEETFVSLDSLRMERDIMLQMGKLGATELFKTCLSRSRGSSVTSCLSDTGTELVVA 203

Query: 163 TEEQKMNDSRDYHMGKILVPSKRKGKRKLKTARVSEESIETSLLSLPSEALQEGLKQPTI 222
           TEEQ+             VPS+RK K+K + + +S    +   L + S      +  P +
Sbjct: 204 TEEQQ-----------TFVPSRRKLKKKARRSSLSTGKGDQGSLLIGSRTTWNDIDAPRL 252

Query: 223 FSAERALNSRGRRLTIARNEAEMSKGVQVVANLERIKTTLEKESGKAASLNCWAQAAGVS 282
               ++   R +R  I+RNEAEMS G ++VA++ERI+T LE+ESGK AS++CWA+AAG++
Sbjct: 253 ---RKSSKYRKKRERISRNEAEMSAGAKIVADMERIRTKLEEESGKVASMSCWAEAAGMN 309

Query: 283 ERVLKQHLAFGWYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDH 342
           E +L ++L +GWYCR+EL+KSTR LVLFL+RNYRGLGI   DL+QAGNVGVLQGAERFDH
Sbjct: 310 EILLMRNLHYGWYCRDELLKSTRSLVLFLSRNYRGLGIAHEDLIQAGNVGVLQGAERFDH 369

Query: 343 TRGYKFSTYVQYWIRKSISKMVARHARGIKIPCKLNREISKIQKARKALTNSHG-KYPED 401
           TRGYKFSTYVQYWIRKS+S MV+RHARG+ IP  + R +S+IQKARK L  SHG KYP D
Sbjct: 370 TRGYKFSTYVQYWIRKSMSMMVSRHARGVYIPSSVIRTMSQIQKARKTLKTSHGIKYPAD 429

Query: 402 IEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNAKYL 441
            EI+K TG SL +IR+A++CL++VGSID+K+GDC   K+L
Sbjct: 430 EEISKETGYSLKKIRAANQCLKVVGSIDKKVGDCFTTKFL 469

Source: Thellungiella halophila

Species: Eutrema halophilum

Genus: Eutrema

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297820128|ref|XP_002877947.1| predicted protein [Arabidopsis lyrata subsp. lyrata] gi|297323785|gb|EFH54206.1| predicted protein [Arabidopsis lyrata subsp. lyrata]

 Score =  358 bits (918), Expect = 4e-96,   Method: Compositional matrix adjust.
 Identities = 210/434 (48%), Positives = 291/434 (67%), Gaps = 17/434 (3%)

Query: 14  PVQSHFFTTSSCRLSSTS--VRGREGSFNSARLSFLSTISEDSASYFQDPVKAYTCSFVN 71
           P+  H+ +   C  +S    VR    SF + R SFLS++ E+S  Y +DP+KA  C+   
Sbjct: 53  PLIKHWLSLLRCDQTSFPIFVRIPVSSFVATRWSFLSSVKEESRIYQKDPLKA--CASSA 110

Query: 72  TQTVENDYSETEEIRQK-STSCIGQDASSRS--DFRLLMENLDVLESTFADSDALRLERE 128
             T EN + E ++ ++        +  SSRS   + LL +NL  LE TF   D+ R+ER+
Sbjct: 111 PYTAENVFLELKDPKENIGVGSAEKSCSSRSMLQYNLLAKNLLALEETFVALDSARMERD 170

Query: 129 ILQQLGKLGALKLFNSHLSRIVKTSNVLDLSDVHTEEQKMNDSRDYHMGKILVPSKRKGK 188
           I+ Q+GKLGA  LF + LSR   +S    LSD  TE      ++     ++ V S+RK K
Sbjct: 171 IMLQMGKLGAADLFKTCLSRSRGSSVASCLSDT-TELVGTTPNQ-----QVFVSSRRKLK 224

Query: 189 RKLKTARVSEESIETSLLSLPSEALQEGLKQPTIFSAERALNSRGRRLTIARNEAEMSKG 248
           +K + + V+ E+ +   L +        +  P +    R    R +R  I++NEAEMS G
Sbjct: 225 KKARRSTVTAENGDQGSLPMGLRTTWNNIDVPRV---RRPPKYRKKRERISKNEAEMSTG 281

Query: 249 VQVVANLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQHLAFGWYCREELIKSTRPLV 308
           V++VA++ERI+T LE+ESGK ASL+CWA+AAG++E++L ++L +GWYCR+EL+KSTR LV
Sbjct: 282 VKIVADMERIRTQLEEESGKVASLSCWAEAAGMNEKLLMRNLHYGWYCRDELLKSTRSLV 341

Query: 309 LFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHA 368
           LFLARNYRGLGI   DL+QAG VGVLQGAERFDHTRGYKFSTYVQYWIRKS+S MV+RHA
Sbjct: 342 LFLARNYRGLGIAHEDLIQAGYVGVLQGAERFDHTRGYKFSTYVQYWIRKSMSMMVSRHA 401

Query: 369 RGIKIPCKLNREISKIQKARKALTNSHG-KYPEDIEIAKYTGLSLAEIRSASECLRIVGS 427
           RG+ IP  + R I++IQKARK L  SHG KYP D +I+K T LS+ +IR+A++CL++VGS
Sbjct: 402 RGVHIPSSIIRTINQIQKARKTLKTSHGIKYPADEDISKLTSLSVKKIRAANQCLKVVGS 461

Query: 428 IDQKIGDCLNAKYL 441
           I++K+GDC + K+L
Sbjct: 462 IEKKVGDCFSTKFL 475

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	442
TAIR|locus:2084420	571	SIGC "AT3G53920" [Arabidopsis	0.886	0.686	0.482	3.6e-89
TAIR|locus:2025650	572	SIG2 "AT1G08540" [Arabidopsis	0.479	0.370	0.384	7e-38
TAIR|locus:2057996	547	SIGF "AT2G36990" [Arabidopsis	0.409	0.330	0.349	2.4e-27
UNIPROTKB|Q84LK8	572	SIG6 "Sig6" [Oryza sativa Japo	0.398	0.307	0.305	1.3e-21
TAIR|locus:2173249	419	SIG4 "AT5G13730" [Arabidopsis	0.395	0.417	0.342	2.3e-21
UNIPROTKB|Q59563	323	mysB "RNA polymerase sigma fac	0.319	0.436	0.340	2.5e-21
UNIPROTKB|P0A602	528	rpoD "RNA polymerase sigma fac	0.319	0.267	0.367	1.3e-20
TIGR_CMR|GSU_3089	577	GSU_3089 "RNA polymerase sigma	0.436	0.334	0.315	2e-20
TIGR_CMR|CHY_0455	370	CHY_0455 "RNA polymerase sigma	0.312	0.372	0.362	2.2e-19
TIGR_CMR|APH_0576	627	APH_0576 "RNA polymerase sigma	0.312	0.220	0.326	3.6e-19

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

 Score = 890 (318.4 bits), Expect = 3.6e-89, P = 3.6e-89
 Identities = 196/406 (48%), Positives = 262/406 (64%)

Query:    41 SARLSFLSTISEDSASYFQDPVKAYTCSFVNTQTVEND-YSETEEIRQK-STSCIGQDAS 98
             + R SFLS++ E+S  Y  D +KA  C+ V+  T +N+ Y E ++ ++        +  S
Sbjct:    82 ATRWSFLSSVKEESRIYQNDSLKACGCASVSPYTAQNNVYVELKDPKENIGVGSAERSYS 141

Query:    99 SRS--DFRLLMENLDVLESTFADSDALRLEREIXXXXXXXXXXXXFNSHLSRIVKTSNVL 156
             SRS   + LL +NL  LE TF   D++R+ER+I            F + LSR   +S   
Sbjct:   142 SRSMLQYNLLAKNLLALEETFVALDSVRMERDIMLQMGKLGAAELFKTCLSRYRGSSITS 201

Query:   157 DLSDVHTEEQKMNDSRDYHMGKILVPSKRKGKRKLKTARVXXXXXXXXXXXXXXXALQEG 216
              LSD  TE   + D+      ++ V S+RK K+K + + V                    
Sbjct:   202 CLSDT-TE---LVDTTPNQ--QVFVSSRRKVKKKARRSSVTAENGDQSSLPIGLRTTWNN 255

Query:   217 LKQPTIFSAERALNSRGRRLTIARNEAEMSKGVQVVANLERIKTTLEKESGKAASLNCWA 276
             +  P +    R    R +R  I+RNE EMS GV++VA++ERI+T LE+ESGK ASL+CWA
Sbjct:   256 IDVPRV---RRPPKYRKKRERISRNETEMSTGVKIVADMERIRTQLEEESGKVASLSCWA 312

Query:   277 QAAGVSERVLKQHLAFGWYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQG 336
              AAG++E++L ++L +GWYCR+EL+KSTR LVLFLARNYRGLGI   DL+QAG VGVLQG
Sbjct:   313 AAAGMNEKLLMRNLHYGWYCRDELVKSTRSLVLFLARNYRGLGIAHEDLIQAGYVGVLQG 372

Query:   337 AERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIPCKLNREISKIQKARKALTNSHG 396
             AERFDHTRGYKFSTYVQYWIRKS+S MV+RHARG+ IP  + R I+ IQKARK L  SHG
Sbjct:   373 AERFDHTRGYKFSTYVQYWIRKSMSTMVSRHARGVHIPSSIIRTINHIQKARKTLKTSHG 432

Query:   397 -KYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNAKYL 441
              KY  D EIAK TG S+ +IR+A++CL++VGSID+K+GDC   K+L
Sbjct:   433 IKYAADEEIAKLTGHSVKKIRAANQCLKVVGSIDKKVGDCFTTKFL 478

GO:0003677 "DNA binding" evidence=ISS

GO:0003700 "sequence-specific DNA binding transcription factor activity" evidence=ISS

GO:0003899 "DNA-directed RNA polymerase activity" evidence=ISS;IMP

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

GO:0009507 "chloroplast" evidence=ISM;IDA

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

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

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

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

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

GO:0016987 "sigma factor activity" evidence=ISS

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

 Score = 406 (148.0 bits), Expect = 7.0e-38, P = 7.0e-38
 Identities = 82/213 (38%), Positives = 137/213 (64%)

Query:   227 RALNSRGRRLTIARNEAEMSKGVQVVANLERIKTTLEKESGKAASLNCWAQAAGVSERVL 286
             R   S  + LT+ R E E+S G+Q +  LER++T L + SG+  +   WA AAGV ++ L
Sbjct:   264 RMTTSSSKLLTV-REEHELSAGIQDLLKLERLQTELTERSGRQPTFAQWASAAGVDQKSL 322

Query:   287 KQHLAFGWYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGY 346
             +Q +  G  C++++IKS   LV+ +A+NY+G G+   DL+Q G  G+++GAE+FD T+G+
Sbjct:   323 RQRIHHGTLCKDKMIKSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDATKGF 382

Query:   347 KFSTYVQYWIRKSISKMVARHARGIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAK 406
             KFSTY  +WI++++ K ++  +R I++P  +     ++++ARK L +  GK+P++ EIA+
Sbjct:   383 KFSTYAHWWIKQAVRKSLSDQSRMIRLPFHMVEATYRVKEARKQLYSETGKHPKNEEIAE 442

Query:   407 YTGLSLAEIRSASECLRIVGSIDQKIGDCLNAK 439
              TGLS+  + +     +   S+DQKIG   N K
Sbjct:   443 ATGLSMKRLMAVLLSPKPPRSLDQKIGMNQNLK 475

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 = 312 (114.9 bits), Expect = 2.4e-27, P = 2.4e-27
 Identities = 64/183 (34%), Positives = 111/183 (60%)

Query:   234 RRLTIARNEAEMSKGVQVVANLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQHLAFG 293
             ++L  A+ EAE+   +Q +  LE++KT LE ++G   ++  WA+A G+S  VLK  +  G
Sbjct:   245 KQLLTAKEEAELISHIQHLLKLEKVKTKLESQNGCEPTIGEWAEAMGISSPVLKSDIHRG 304

Query:   294 WYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQ 353
                RE+LI +   LV+ +A+ Y+  G+ F DLLQ G++G+++  E+F    G +F+TY  
Sbjct:   305 RSSREKLITANLRLVVHIAKQYQNRGLNFQDLLQEGSMGLMKSVEKFKPQSGCRFATYAY 364

Query:   354 YWIRKSISKMVARHARGIKIPCKLNREISKIQKARKALTNSHGKY-PEDIEIAKYTGLSL 412
             +WIR+SI K + +++R I++P  +   + K+ +ARK      G Y P   E+A + G+S 
Sbjct:   365 WWIRQSIRKSIFQNSRTIRLPENVYMLLGKVSEARKTCVQE-GNYRPSKEELAGHVGVST 423

Query:   413 AEI 415
              ++
Sbjct:   424 EKL 426

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 = 275 (101.9 bits), Expect = 1.3e-21, P = 1.3e-21
 Identities = 54/177 (30%), Positives = 103/177 (58%)

Query:   239 ARNEAEMSKGVQVVANLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQHLAFGWYCRE 298
             A+ E  +   +Q++  +E     LE + G+  +L  WA+A G+S + L+  +  G  CRE
Sbjct:   276 AKEERHLFSKIQILMKIEEAHRKLEVQCGREPTLAEWAEAVGMSSKELQSSIRTGRRCRE 335

Query:   299 ELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRK 358
             ++ +S   LV+ +AR Y G G+   DL+Q G  G+++  E+F+ ++G +F TY  +WIR+
Sbjct:   336 KMARSNFRLVIHVARKYEGYGLDIQDLVQDGCSGLMKTFEKFNPSKGCRFPTYAYWWIRQ 395

Query:   359 SISKMVARHARGIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEI 415
             SI K + +++R I++P  +   + K+ KAR       G+ P +  +A+  G+++ ++
Sbjct:   396 SIKKSIFKNSRLIRLPESVYALLRKVGKARMECI-MEGEQPTNANVARRAGITIEKL 451

GO:0009536 "plastid" evidence=RCA

TAIR|locus:2173249 SIG4 "AT5G13730" [Arabidopsis thaliana (taxid:3702)]

 Score = 265 (98.3 bits), Expect = 2.3e-21, Sum P(2) = 2.3e-21
 Identities = 61/178 (34%), Positives = 102/178 (57%)

Query:   253 ANLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQHLAFGWYCREELIKSTRPLVLFLA 312
             A LE + T++E+    +  L   A   G  +R   + L      RE++ +  R LV+ +A
Sbjct:   139 AKLENLGTSVEENEMVSVLL---ASGRGKKKRSANEILCRRKEAREKITRCYRRLVVSIA 195

Query:   313 RNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIK 372
               Y+G G+   DL+Q G++G+L+GAERFD  RGYK STYV +WI+++I + +A  +R +K
Sbjct:   196 TGYQGKGLNLQDLIQEGSIGLLRGAERFDPDRGYKLSTYVYWWIKQAILRAIAHKSRLVK 255

Query:   373 IPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQ 430
             +P  +    +K+ +A   LT    + P   EIA++  L+++ +R A E  R   S+D+
Sbjct:   256 LPGSMWELTAKVAEASNVLTRKLRRQPSCEEIAEHLNLNVSAVRLAVERSRSPVSLDR 313

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

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

GO:0016987 "sigma factor activity" evidence=ISS

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

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

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

GO:0000023 "maltose metabolic process" evidence=RCA

GO:0006098 "pentose-phosphate shunt" evidence=RCA

GO:0016556 "mRNA modification" evidence=RCA

GO:0019252 "starch biosynthetic process" evidence=RCA

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

 Score = 253 (94.1 bits), Expect = 2.5e-21, P = 2.5e-21
 Identities = 48/141 (34%), Positives = 88/141 (62%)

Query:   293 GWYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYV 352
             G   R  L+++   LV+ LA+ Y G G+P  DL+Q GN+G+++  E+FD+T+G+KFSTY 
Sbjct:    83 GEAARRHLLEANLRLVVSLAKRYTGRGMPLLDLIQEGNLGLIRAMEKFDYTKGFKFSTYA 142

Query:   353 QYWIRKSISKMVARHARGIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSL 412
              +WIR++I++ +A  +R I++P  L  +++K+ + ++ +    G+   D E+A  +G+ +
Sbjct:   143 TWWIRQAITRGMADQSRTIRLPVHLVEQVNKLARIKREMHQHLGREATDEELAAESGIPI 202

Query:   413 AEIRSASECLRIVGSIDQKIG 433
              +I    E  R   S+D  +G
Sbjct:   203 DKINDLLEHSRDPVSLDMPVG 223

GO:0001666 "response to hypoxia" evidence=IEP

GO:0005829 "cytosol" evidence=IDA

GO:0005886 "plasma membrane" evidence=IDA

GO:0009408 "response to heat" evidence=IEP

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

GO:0016987 "sigma factor activity" evidence=IGI

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

GO:0040007 "growth" evidence=IMP

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

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

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

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

 Score = 266 (98.7 bits), Expect = 1.3e-20, P = 1.3e-20
 Identities = 54/147 (36%), Positives = 90/147 (61%)

Query:   294 WYCRE------ELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYK 347
             W CR+       L+++   LV+ LA+ Y G G+ F DL+Q GN+G+++  E+FD+T+GYK
Sbjct:   283 WICRDGDRAKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLGLIRAVEKFDYTKGYK 342

Query:   348 FSTYVQYWIRKSISKMVARHARGIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKY 407
             FSTY  +WIR++I++ +A  AR I+IP  +   I+K+ + ++ L    G+ P   E+AK 
Sbjct:   343 FSTYATWWIRQAITRAMADQARTIRIPVHMVEVINKLGRIQRELLQDLGREPTPEELAKE 402

Query:   408 TGLSLAEIRSASECLRIVGSIDQKIGD 434
               ++  ++    +  R   S+DQ IGD
Sbjct:   403 MDITPEKVLEIQQYAREPISLDQTIGD 429

GO:0003677 "DNA binding" evidence=IDA

GO:0005515 "protein binding" evidence=IPI

GO:0005618 "cell wall" evidence=IDA

GO:0005886 "plasma membrane" evidence=IDA

GO:0009405 "pathogenesis" evidence=IMP

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

GO:0016987 "sigma factor activity" evidence=IDA

GO:0040007 "growth" evidence=IMP

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

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

 Score = 264 (98.0 bits), Expect = 2.0e-20, Sum P(2) = 2.0e-20
 Identities = 64/203 (31%), Positives = 115/203 (56%)

Query:   233 GRRLTIARNEAEMSKGVQVVANLERIKTTLEKESG-KAASLNCWAQAAGVSERVLKQHLA 291
             G+ + ++  +A+  K  + V + E+    +E+ESG KA  L+   +A    E   K  LA
Sbjct:   285 GKGIKLSLEDAQ--KHEKKVRSAEKKLKKVEEESGFKARELSDALRAIDRGEA--KSKLA 340

Query:   292 FGWYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTY 351
                  + EL+++   LV+ +A+ Y   G+ F DL+Q GN+G+++  ++F++ RGYKFSTY
Sbjct:   341 -----KSELVEANLRLVVSIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYQRGYKFSTY 395

Query:   352 VQYWIRKSISKMVARHARGIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLS 411
               +WIR++I++ +A  AR I+IP  +   I+K+ +  + L    G+ P   EIA+   L 
Sbjct:   396 ATWWIRQAITRAIADQARTIRIPVHMIETINKLIRTSRQLVQEIGREPSPEEIAERMNLP 455

Query:   412 LAEIRSASECLRIVGSIDQKIGD 434
             L ++R   +  +   S++  IG+
Sbjct:   456 LDKVRKVLKIAKEPISLETPIGE 478

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

GO:0016987 "sigma factor activity" evidence=ISS

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

 Score = 249 (92.7 bits), Expect = 2.2e-19, P = 2.2e-19
 Identities = 50/138 (36%), Positives = 86/138 (62%)

Query:   297 REELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWI 356
             + +L ++   LV+ +A+ Y G G+ F DL+Q GN+G+L+  E+FD+ +GYKFSTY  +WI
Sbjct:   134 KRKLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNLGLLKAVEKFDYRKGYKFSTYATWWI 193

Query:   357 RKSISKMVARHARGIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIR 416
             R++I++ +A  AR I+IP  +   I+K+ +  + L    G+ P   EIAK  G+S  ++R
Sbjct:   194 RQAITRAIADQARTIRIPVHMVETINKLIRVSRNLLQELGREPTPEEIAKEMGISEDKVR 253

Query:   417 SASECLRIVGSIDQKIGD 434
                +  +   S++  IG+
Sbjct:   254 EIMKIAQEPVSLETPIGE 271

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

GO:0016987 "sigma factor activity" evidence=ISS

TIGR_CMR|APH_0576 APH_0576 "RNA polymerase sigma factor RpoD" [Anaplasma phagocytophilum HZ (taxid:212042)]

 Score = 254 (94.5 bits), Expect = 3.6e-19, Sum P(3) = 3.6e-19
 Identities = 45/138 (32%), Positives = 88/138 (63%)

Query:   297 REELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWI 356
             ++E+IK+   LV+ +A+ Y   G+ F DL+Q GN+G+++  ++FD+ RGYKFSTY  +W+
Sbjct:   391 KQEMIKANLRLVVSIAKKYSNRGLQFLDLVQEGNIGLMKAVDKFDYKRGYKFSTYATWWV 450

Query:   357 RKSISKMVARHARGIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIR 416
             R++I++ +A  AR I+IP  +   ++KI +  + + +  G+ P   E++    +++ +IR
Sbjct:   451 RQAITRAIADQARTIRIPVHMIETVNKINRTLRQMLHEIGREPTLEELSARLNINVEKIR 510

Query:   417 SASECLRIVGSIDQKIGD 434
                + ++   S++  IGD
Sbjct:   511 KVMKIVKDPVSLESPIGD 528

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

GO:0016987 "sigma factor activity" evidence=ISS

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Fail to connect to STRING server

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	442
TIGR02997	298	TIGR02997, Sig70-cyanoRpoD, RNA polymerase sigma f	2e-37
PRK05949	327	PRK05949, PRK05949, RNA polymerase sigma factor; V	2e-33
PRK07405	317	PRK07405, PRK07405, RNA polymerase sigma factor Si	5e-32
PRK07406	373	PRK07406, PRK07406, RNA polymerase sigma factor Rp	1e-31
TIGR02393	238	TIGR02393, RpoD_Cterm, RNA polymerase sigma factor	2e-31
COG0568	342	COG0568, RpoD, DNA-directed RNA polymerase, sigma	9e-31
TIGR02394	285	TIGR02394, rpoS_proteo, RNA polymerase sigma facto	6e-25
PRK07598	415	PRK07598, PRK07598, RNA polymerase sigma factor Si	3e-23
PRK07921	324	PRK07921, PRK07921, RNA polymerase sigma factor Si	8e-23
PRK09210	367	PRK09210, PRK09210, RNA polymerase sigma factor Rp	2e-20
PRK05901	509	PRK05901, PRK05901, RNA polymerase sigma factor; P	2e-19
TIGR02980	227	TIGR02980, SigBFG, RNA polymerase sigma-70 factor,	4e-19
PRK05658	619	PRK05658, PRK05658, RNA polymerase sigma factor Rp	1e-16
PRK05657	325	PRK05657, PRK05657, RNA polymerase sigma factor Rp	4e-16
pfam04542	71	pfam04542, Sigma70_r2, Sigma-70 region 2	1e-13
COG1191	247	COG1191, FliA, DNA-directed RNA polymerase special	5e-13
TIGR02392	270	TIGR02392, rpoH_proteo, alternative sigma factor R	5e-13
PRK07500	289	PRK07500, rpoH2, RNA polymerase factor sigma-32; R	1e-12
TIGR02479	224	TIGR02479, FliA_WhiG, RNA polymerase sigma factor,	5e-12
PRK07408	256	PRK07408, PRK07408, RNA polymerase sigma factor Si	7e-12
PRK06596	284	PRK06596, PRK06596, RNA polymerase factor sigma-32	2e-10
TIGR02885	231	TIGR02885, spore_sigF, RNA polymerase sigma-F fact	2e-09
TIGR02941	255	TIGR02941, Sigma_B, RNA polymerase sigma-B factor	2e-09
PRK06288	268	PRK06288, PRK06288, RNA polymerase sigma factor Wh	2e-09
PRK05572	252	PRK05572, PRK05572, sporulation sigma factor SigF;	7e-09
PRK06986	236	PRK06986, fliA, flagellar biosynthesis sigma facto	4e-08
PRK08583	257	PRK08583, PRK08583, RNA polymerase sigma factor Si	4e-07
TIGR02850	254	TIGR02850, spore_sigG, RNA polymerase sigma-G fact	1e-06
PRK07122	264	PRK07122, PRK07122, RNA polymerase sigma factor Si	2e-06
TIGR02937	158	TIGR02937, sigma70-ECF, RNA polymerase sigma facto	4e-06
PRK08215	258	PRK08215, PRK08215, sporulation sigma factor SigG;	8e-06
pfam04539	78	pfam04539, Sigma70_r3, Sigma-70 region 3	9e-04
PRK05911	257	PRK05911, PRK05911, RNA polymerase sigma factor si	0.001
PRK07670	251	PRK07670, PRK07670, RNA polymerase sigma factor Si	0.002

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

 Score =  138 bits (349), Expect = 2e-37
 Identities = 74/207 (35%), Positives = 124/207 (59%), Gaps = 1/207 (0%)

Query: 229 LNSRGR-RLTIARNEAEMSKGVQVVANLERIKTTLEKESGKAASLNCWAQAAGVSERVLK 287
           L   GR  L     E E+++ VQ +  LE ++  LE++ G+  S   WA AAG+SE  L+
Sbjct: 7   LQEIGRVPLLTPEEEIELARQVQQMMVLEELREELEEQLGREPSKEEWAAAAGLSEAELR 66

Query: 288 QHLAFGWYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYK 347
           Q L  G   +E++IK+   LV+ +A+ Y+  G+   DL+Q G++G+ +  E+FD TRGYK
Sbjct: 67  QRLRQGQRAKEKMIKANLRLVVSVAKKYQNRGLELLDLIQEGSLGLERAVEKFDPTRGYK 126

Query: 348 FSTYVQYWIRKSISKMVARHARGIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKY 407
           FSTY  +WIR+ I++ +A  +R I++P  +  +++KI+K ++ L+   G+ P + EIA+ 
Sbjct: 127 FSTYAYWWIRQGITRAIANQSRTIRLPIHITEKLNKIKKVQRELSQKLGRTPSEAEIAEA 186

Query: 408 TGLSLAEIRSASECLRIVGSIDQKIGD 434
             L   ++R   +  R   S+D  +GD
Sbjct: 187 LELEPEQVRELLQRARQPVSLDAPVGD 213

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

 Score =  128 bits (322), Expect = 2e-33
 Identities = 70/188 (37%), Positives = 115/188 (61%)

Query: 247 KGVQVVANLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQHLAFGWYCREELIKSTRP 306
           K VQ + +L   K  L K+ G+  SL  WA+A  +SE  LKQ L  G   ++++I++   
Sbjct: 43  KQVQQMMSLLEAKEALAKKLGREPSLPEWAEAVNLSETELKQTLKQGKRAKQKMIEANLR 102

Query: 307 LVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVAR 366
           LV+ +A+ Y+   + F DL+Q G +G+ +G E+FD TRGYKFSTY  +WIR++I++ +A+
Sbjct: 103 LVVAIAKKYQKRNMEFLDLIQEGTLGLERGVEKFDPTRGYKFSTYAYWWIRQAITRAIAQ 162

Query: 367 HARGIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVG 426
            AR I++P  +  +++KI+K ++ L+   G+     EIAK   L  ++IR      R   
Sbjct: 163 QARTIRLPIHITEKLNKIKKTQRELSQKLGRSATPAEIAKELELEPSQIREYLSMARQPI 222

Query: 427 SIDQKIGD 434
           S+D ++GD
Sbjct: 223 SLDVRVGD 230

Length = 327

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

 Score =  123 bits (311), Expect = 5e-32
 Identities = 62/193 (32%), Positives = 115/193 (59%)

Query: 242 EAEMSKGVQVVANLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQHLAFGWYCREELI 301
           E    K VQ +  L+ I+  L +E G+  +   WA+AA +SE  L+  +A G   + +++
Sbjct: 28  EILYGKQVQRLVALQEIREELAEELGREPTDAEWAKAAKLSEEELRSAIAEGEAAKRKMV 87

Query: 302 KSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSIS 361
           ++   LV+ +A+ Y    +   DL+Q G +G+ +G E+FD T+GY+FSTY  +WIR++I+
Sbjct: 88  EANLRLVVSVAKKYLKRNVDLLDLIQEGTIGMQRGVEKFDPTKGYRFSTYAYWWIRQAIT 147

Query: 362 KMVARHARGIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASEC 421
           + +A  +R I++P  +  +++KI+KA++ L+   G+     E+A+   L+  ++R   E 
Sbjct: 148 RAIAEKSRTIRLPIHITEKLNKIKKAQRQLSQQLGRAATIGELAEELELTPKQVREYLER 207

Query: 422 LRIVGSIDQKIGD 434
            R   S+D ++GD
Sbjct: 208 ARQPLSLDLRVGD 220

Length = 317

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

 Score =  124 bits (312), Expect = 1e-31
 Identities = 61/174 (35%), Positives = 104/174 (59%), Gaps = 1/174 (0%)

Query: 233 GR-RLTIARNEAEMSKGVQVVANLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQHLA 291
           GR RL     E E+++ +  +  LE ++   E E G+  S   WA+   +     ++ L 
Sbjct: 73  GRIRLLRPDEEIELARKIADLLELEELREQFESELGREPSDKEWAELVDMPLPKFRRRLM 132

Query: 292 FGWYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTY 351
            G   +E++++S   LV+ +A+ Y   G+ F DL+Q G++G+++ AE+FDH +GYKFSTY
Sbjct: 133 LGRRAKEKMVQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTY 192

Query: 352 VQYWIRKSISKMVARHARGIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIA 405
             +WIR++I++ +A  +R I++P  L   IS+I+K  K L+   G+ P + EIA
Sbjct: 193 ATWWIRQAITRAIADQSRTIRLPVHLYETISRIKKTTKVLSQEFGRKPTEEEIA 246

Length = 373

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

 Score =  120 bits (302), Expect = 2e-31
 Identities = 50/138 (36%), Positives = 89/138 (64%)

Query: 297 REELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWI 356
           +++L++S   LV+ +A+ Y   G+ F DL+Q GN+G+++  E+FD+ +GYKFSTY  +WI
Sbjct: 2   KKQLVESNLRLVVSIAKKYTNRGLSFLDLIQEGNIGLMKAVEKFDYRKGYKFSTYATWWI 61

Query: 357 RKSISKMVARHARGIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIR 416
           R++I++ +A  AR I+IP  +   I+K+ KA + LT   G+ P D E+A+  G+   ++R
Sbjct: 62  RQAITRAIADQARTIRIPVHMVETINKLIKAERQLTQELGREPTDEELAERMGMPAEKVR 121

Query: 417 SASECLRIVGSIDQKIGD 434
              +  +   S++  IG+
Sbjct: 122 EIKKIAQEPISLETPIGE 139

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

 Score =  120 bits (304), Expect = 9e-31
 Identities = 51/139 (36%), Positives = 88/139 (63%)

Query: 296 CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYW 355
            +++L++S   LV+ +A+ Y G G+PF DL+Q GN+G+++  E+FD  +G+KFSTY  +W
Sbjct: 103 AKKKLVESNLRLVVSIAKKYTGRGLPFLDLIQEGNIGLMKAVEKFDPEKGFKFSTYATWW 162

Query: 356 IRKSISKMVARHARGIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEI 415
           IR++I++ +A  AR I+IP      I+K+++ ++ L    G+ P   EIA+  G+S  ++
Sbjct: 163 IRQAITRAIADQARTIRIPVHQVELINKLRRVKRELLQELGREPTPEEIAEELGVSPDKV 222

Query: 416 RSASECLRIVGSIDQKIGD 434
           R   +      S+D  IGD
Sbjct: 223 REMLKRASEPISLDTPIGD 241

Length = 342

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

 Score =  103 bits (258), Expect = 6e-25
 Identities = 42/138 (30%), Positives = 79/138 (57%)

Query: 297 REELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWI 356
           R+ +I+S   LV+ +A++Y   G+P  DL++ GN+G++   E+FD  RG++FSTY  +WI
Sbjct: 48  RKVMIESNLRLVVSIAKHYVNRGLPLLDLIEEGNLGLMHAVEKFDPERGFRFSTYATWWI 107

Query: 357 RKSISKMVARHARGIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIR 416
           R++I + +   AR I++P  + +E++   +A + L    G+ P   EIA+     + ++ 
Sbjct: 108 RQTIERAIMNQARTIRLPVHVIKELNVYLRAARQLEKKLGREPSVEEIAELLDKPVEDVS 167

Query: 417 SASECLRIVGSIDQKIGD 434
                   + S+D  + D
Sbjct: 168 RVLALNERITSLDAPLDD 185

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|236067 PRK07598, PRK07598, RNA polymerase sigma factor SigC; Validated

 Score =  100 bits (251), Expect = 3e-23
 Identities = 60/205 (29%), Positives = 106/205 (51%), Gaps = 23/205 (11%)

Query: 235 RLTIARNEAEMSKGVQV-VANLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQHLAFG 293
           +L +  N A+    V      L  ++  L  E G   SL  WA+ A +S   LK  LA G
Sbjct: 92  KLIVLANAAKEGDEVIKPYLRLIEVRERLTSELGHRPSLERWAKTADISLADLKPTLAEG 151

Query: 294 ---WY-------------------CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNV 331
              W                     +E +IK+   LV+ +A+ Y+  G+   DL+Q G +
Sbjct: 152 KRRWAEIAKLTVEELEQIQKQGLRAKEHMIKANLRLVVSVAKKYQNRGLELLDLVQEGTL 211

Query: 332 GVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIPCKLNREISKIQKARKAL 391
           G+ +  E+FD T+GY+FSTY  +WIR+ I++ +A  +R I++P  +  +++KI+KA++ +
Sbjct: 212 GLERAVEKFDPTKGYRFSTYAYWWIRQGITRAIATQSRTIRLPVHITEKLNKIKKAQRKI 271

Query: 392 TNSHGKYPEDIEIAKYTGLSLAEIR 416
           +   G+ P   +IA+   ++  ++R
Sbjct: 272 SQEKGRTPTIEDIAQELEMTPTQVR 296

Length = 415

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

 Score = 98.3 bits (245), Expect = 8e-23
 Identities = 48/137 (35%), Positives = 87/137 (63%)

Query: 297 REELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWI 356
           R  L+++   LV+ LA+ Y G G+P  DL+Q GN+G+++  E+FD+T+G+KFSTY  +WI
Sbjct: 88  RRHLLEANLRLVVSLAKRYTGRGMPLLDLIQEGNLGLIRAMEKFDYTKGFKFSTYATWWI 147

Query: 357 RKSISKMVARHARGIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIR 416
           R++I++ +A  +R I++P  L  +++K+ + ++ L    G+   D E+A+ +G+   +I 
Sbjct: 148 RQAITRGMADQSRTIRLPVHLVEQVNKLARIKRELHQQLGREATDEELAEESGIPEEKIA 207

Query: 417 SASECLRIVGSIDQKIG 433
              E  R   S+D  +G
Sbjct: 208 DLLEHSRDPVSLDMPVG 224

Length = 324

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

 Score = 92.0 bits (229), Expect = 2e-20
 Identities = 44/118 (37%), Positives = 76/118 (64%), Gaps = 3/118 (2%)

Query: 307 LVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVAR 366
           LV+ +A+ Y G G+ F DL+Q GN+G+++  E+FD+ +G+KFSTY  +WIR++I++ +A 
Sbjct: 141 LVVSIAKRYVGRGMLFLDLIQEGNMGLMKAVEKFDYRKGFKFSTYATWWIRQAITRAIAD 200

Query: 367 HARGIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRI 424
            AR I+IP  +   I+K+ + ++ L    G+ P   EIA+   +   ++R   E L+I
Sbjct: 201 QARTIRIPVHMVETINKLIRVQRQLLQELGREPTPEEIAEEMDMPPEKVR---EILKI 255

Length = 367

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

 Score = 90.4 bits (225), Expect = 2e-19
 Identities = 46/124 (37%), Positives = 76/124 (61%)

Query: 283 ERVLKQHLAFGWYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDH 342
            R L+     G   +  L+++   LV+ LA+ Y   G+ F DL+Q GN+G+++  E+FD+
Sbjct: 259 RRDLQWIGRDGKRAKNHLLEANLRLVVSLAKRYTNRGLSFLDLIQEGNLGLIKAVEKFDY 318

Query: 343 TRGYKFSTYVQYWIRKSISKMVARHARGIKIPCKLNREISKIQKARKALTNSHGKYPEDI 402
           T+GYKFSTY  +WIR++I++ +A  AR I+IP  +   I+K+ +  + L    G+ P   
Sbjct: 319 TKGYKFSTYATWWIRQAITRAMADQARTIRIPVHMVETINKLGRIERELLQELGREPTPE 378

Query: 403 EIAK 406
           E+AK
Sbjct: 379 ELAK 382

Length = 509

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

 Score = 85.7 bits (213), Expect = 4e-19
 Identities = 48/140 (34%), Positives = 72/140 (51%), Gaps = 2/140 (1%)

Query: 297 REELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWI 356
           RE+L++   PLV  +AR +R  G P  DL+Q G +G+++  +RFD + G KFST+    I
Sbjct: 5   REKLVELNLPLVRSIARRFRNRGEPHEDLVQVGTIGLVKAIDRFDPSYGVKFSTFAVPTI 64

Query: 357 RKSISKMVARHARGIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIR 416
              I +        +++P +L     KI KA + LT   G+ P   EIA+  G+S  E+ 
Sbjct: 65  MGEIKRFFRDDTWAVRVPRRLKELGVKINKATEELTQRLGRSPTIAEIAERLGVSEEEVV 124

Query: 417 SASECLR--IVGSIDQKIGD 434
            A E        S+D  I D
Sbjct: 125 EALEAGNAYQALSLDASIED 144

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

 Score = 81.8 bits (203), Expect = 1e-16
 Identities = 46/127 (36%), Positives = 76/127 (59%), Gaps = 18/127 (14%)

Query: 299 ELIKSTRPLVLFLARNY--RGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWI 356
           E++++   LV+ +A+ Y  RGL   F DL+Q GN+G+++  ++F++ RGYKFSTY  +WI
Sbjct: 384 EMVEANLRLVISIAKKYTNRGL--QFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWI 441

Query: 357 RKSISKMVARHARGIKIPC-------KLNREISKIQKARKALTNSHGKYPEDIEIAKYTG 409
           R++I++ +A  AR I+IP        KLNR        R+ L    G+ P   E+A+  G
Sbjct: 442 RQAITRSIADQARTIRIPVHMIETINKLNRIS------RQML-QEIGREPTPEELAERLG 494

Query: 410 LSLAEIR 416
           +   ++R
Sbjct: 495 MPEDKVR 501

Length = 619

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

 Score = 78.8 bits (195), Expect = 4e-16
 Identities = 36/120 (30%), Positives = 70/120 (58%)

Query: 297 REELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWI 356
           R+ +I+S   LV+ +A+ Y   G+   DL++ GN+G+++  E+FD  RG++FSTY  +WI
Sbjct: 88  RQRMIESNLRLVVKIAKRYLNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWI 147

Query: 357 RKSISKMVARHARGIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIR 416
           R++I + +    R I++P  + +E++   +A + L +     P   EIA+     + ++ 
Sbjct: 148 RQTIERAIMNQTRTIRLPVHVVKELNVYLRAARELEHKLDHEPSAEEIAELLDKPVDDVS 207

Length = 325

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

 Score = 65.3 bits (160), Expect = 1e-13
 Identities = 29/70 (41%), Positives = 40/70 (57%)

Query: 300 LIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKS 359
           L++   PLV  LAR Y G G    DL+Q G +G+L+  ERFD  RG  FST++   IR +
Sbjct: 1   LVERYLPLVYSLARRYLGDGADAEDLVQEGFLGLLRAVERFDPERGVSFSTWLYTIIRNA 60

Query: 360 ISKMVARHAR 369
           I   + +  R
Sbjct: 61  IIDALRKQRR 70

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

 Score = 68.5 bits (168), Expect = 5e-13
 Identities = 43/137 (31%), Positives = 67/137 (48%), Gaps = 4/137 (2%)

Query: 299 ELIKSTRPLVLFLARNYRGLGIP-FSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIR 357
            LI+   PLV  +AR +   G   + DL+Q G +G+++  ER+D ++G KFSTY    IR
Sbjct: 27  RLIERYLPLVKSIARKFENRGPSEYDDLIQIGMIGLIKAIERYDPSKGTKFSTYAVRRIR 86

Query: 358 KSISKMVARHARGIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRS 417
             I     R    +K+P  L     +I++A   L    G+ P D EIA+  G+   E   
Sbjct: 87  GEI-LDYLRKNDSVKVPRSLRELGRRIEEAIDELEQELGREPTDEEIAEELGIDKEEYIE 145

Query: 418 ASECLRIVG--SIDQKI 432
           A   +      S+D+ +
Sbjct: 146 ALLAINGSQLLSLDEDV 162

Length = 247

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

 Score = 68.5 bits (168), Expect = 5e-13
 Identities = 41/126 (32%), Positives = 70/126 (55%), Gaps = 13/126 (10%)

Query: 299 ELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRK 358
           +L+ S    V+ +AR YRG G+P +DL+Q GN+G+++  +RFD  RG +  ++  +WI+ 
Sbjct: 39  KLVLSHLRFVVKIARGYRGYGLPQADLIQEGNIGLMKAVKRFDPERGVRLVSFAVHWIKA 98

Query: 359 SISKMVARHARGIKIPCKLNREISKIQKA-----RKALTNSHGKY-PEDIE-IAKYTGLS 411
            I + + R+ R +K+        +K Q+      RK      G   PE++E IA+  G+S
Sbjct: 99  EIHEYILRNWRLVKVA------TTKAQRKLFFNLRKMKKRLQGWLNPEEVEAIAEELGVS 152

Query: 412 LAEIRS 417
             E+R 
Sbjct: 153 EREVRE 158

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

 Score = 67.8 bits (166), Expect = 1e-12
 Identities = 27/60 (45%), Positives = 39/60 (65%)

Query: 307 LVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVAR 366
           LV+ +A  +R  G+P +DL+Q G VG+L+ A RF+  R  +FSTY  +WIR SI   + R
Sbjct: 52  LVISMAGKFRRFGLPMNDLIQEGYVGLLEAAARFEPDREVRFSTYATWWIRASIQDYILR 111

Length = 289

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

 Score = 65.0 bits (159), Expect = 5e-12
 Identities = 46/140 (32%), Positives = 71/140 (50%), Gaps = 12/140 (8%)

Query: 300 LIKSTRPLVLFLARNYRGLGIP----FSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYW 355
           LI+   PLV  +A      G+P      DL+QAG  G+L   ER+D +RG KF TY    
Sbjct: 1   LIRRYLPLVKRIAGRLSV-GLPSSVELDDLIQAGMFGLLDAIERYDPSRGAKFETYAVQR 59

Query: 356 IRKSISKMVARHARGIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEI 415
           IR ++   + R      +P  L ++  K+++A + L    G+ P + EIA+  G+ L E 
Sbjct: 60  IRGAMLDELRRLDW---VPRSLRQKARKLERAIRELEARLGREPTEEEIAEELGMDLKEY 116

Query: 416 RSASE---CLRIVGSIDQKI 432
           R A      L +V S+D+ +
Sbjct: 117 RQALNEINALSLV-SLDELL 135

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|180965 PRK07408, PRK07408, RNA polymerase sigma factor SigF; Reviewed

 Score = 64.9 bits (159), Expect = 7e-12
 Identities = 35/117 (29%), Positives = 62/117 (52%), Gaps = 4/117 (3%)

Query: 321 PFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIPCKLNRE 380
           P+ DL+Q G++G+++  ERFD ++G+ FS++   +IR  I   +   +  ++IP +    
Sbjct: 52  PYEDLVQVGSLGLIRAIERFDPSKGHAFSSFAIPYIRGEIQHYLRDKSPTVRIPRRWQEL 111

Query: 381 ISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAE---IRSASECLRIVGSIDQKIGD 434
             + +K R+ L    G+ P D EIA+   +SL E   I+ A    R   S+D  +  
Sbjct: 112 QRQAKKVRQELRQELGRQPTDQEIAQALDISLEEWQEIKLAL-QNRTPLSLDAPVNQ 167

Length = 256

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

 Score = 61.3 bits (150), Expect = 2e-10
 Identities = 26/75 (34%), Positives = 48/75 (64%)

Query: 299 ELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRK 358
           +L+ S    V+ +AR YRG G+P +DL+Q GN+G+++  +RFD   G +  ++  +WI+ 
Sbjct: 52  QLVLSHLRFVVHIARGYRGYGLPQADLIQEGNIGLMKAVKRFDPEVGVRLVSFAVHWIKA 111

Query: 359 SISKMVARHARGIKI 373
            I + + R+ R +K+
Sbjct: 112 EIHEYILRNWRIVKV 126

Length = 284

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

 Score = 57.4 bits (139), Expect = 2e-09
 Identities = 39/136 (28%), Positives = 65/136 (47%), Gaps = 1/136 (0%)

Query: 297 REELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWI 356
           R++LI+    LV  + + +   G    DL Q G +G+++  ++FD +   KFSTY    I
Sbjct: 13  RDKLIECNLRLVWSIVKRFLNRGYEPEDLFQIGCIGLVKAIDKFDLSYDVKFSTYAVPMI 72

Query: 357 RKSISKMVARHARGIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIR 416
              I + + R    IK+   L     KI+  ++ L+   G+ P   E+A+  G+S  EI 
Sbjct: 73  MGEIKRFL-RDDGIIKVSRSLKELARKIRYMKEELSKELGREPTINELAEALGVSPEEIV 131

Query: 417 SASECLRIVGSIDQKI 432
            A E  R   S+   +
Sbjct: 132 MALESARSPQSLYDTV 147

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

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

 Score = 57.6 bits (139), Expect = 2e-09
 Identities = 36/124 (29%), Positives = 60/124 (48%)

Query: 297 REELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWI 356
           +E+L+   + LV  +A  Y   G    DL+Q G +G+L    R+D++ G  F  +    I
Sbjct: 31  QEKLVDHYQNLVYSIAYKYSKGGPMHEDLVQVGMLGLLGAIRRYDYSIGNAFEPFAIPTI 90

Query: 357 RKSISKMVARHARGIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIR 416
              I + +      + +P ++     KI+KA   LT+   + P+ IEIA + GLS  E+ 
Sbjct: 91  IGEIKRYLRDKTWSVHVPRRIKELGPKIKKAIDELTDHLQRSPKIIEIADHLGLSEEEVL 150

Query: 417 SASE 420
              E
Sbjct: 151 EIME 154

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

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

 Score = 57.8 bits (140), Expect = 2e-09
 Identities = 44/126 (34%), Positives = 62/126 (49%), Gaps = 10/126 (7%)

Query: 297 REELIKSTRPLVLFLARNYRGLGIP----FSDLLQAGNVGVLQGAERFDHTRGYKFSTYV 352
           RE LI    PLV ++A     +G+P    F DL+  G  G++   E+FD  R  KF TY 
Sbjct: 33  REYLILKYSPLVKYVA-GRIAVGMPQNVEFDDLVSYGVFGLIDAIEKFDPEREIKFKTYA 91

Query: 353 QYWIRKSISKMVARHARGI-KIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLS 411
              IR +I   +    R I  IP  + ++  +I++A   L    G+ P D EIA   G+S
Sbjct: 92  VTRIRGAIFDEL----RSIDWIPRSVRQKARQIERAIAMLEARLGRTPSDEEIADELGIS 147

Query: 412 LAEIRS 417
           L E  S
Sbjct: 148 LEEYNS 153

Length = 268

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

 Score = 56.1 bits (136), Expect = 7e-09
 Identities = 43/144 (29%), Positives = 66/144 (45%), Gaps = 17/144 (11%)

Query: 297 REELIKSTRPLVL-----FLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTY 351
           R+ L++    LV      FL R Y        DL Q G +G+L+  ++FD +   KFSTY
Sbjct: 34  RDTLVEKNLRLVWSVVQRFLNRGYE-----PDDLFQIGCIGLLKAVDKFDLSYDVKFSTY 88

Query: 352 VQYWIRKSISKMVARHARG---IKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYT 408
               I   I     R  R    +K+   L    +KI+K +  L+   G+ P   E+A+Y 
Sbjct: 89  AVPMIIGEIQ----RFLRDDGTVKVSRSLKETANKIRKDKDELSKELGREPTIEELAEYL 144

Query: 409 GLSLAEIRSASECLRIVGSIDQKI 432
           G++  E+  A E  R   SI + +
Sbjct: 145 GVTPEEVVLAQEASRSPQSIHETV 168

Length = 252

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

 Score = 53.3 bits (129), Expect = 4e-08
 Identities = 41/131 (31%), Positives = 64/131 (48%), Gaps = 18/131 (13%)

Query: 297 REELIKSTRPLVLFLARNYRG-LG--IPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQ 353
           ++EL++   PLV  +A   +  L   +   DL+QAG +G+L+ A R+D  +G  F TY  
Sbjct: 10  QDELVEQYAPLVKRIALRLKARLPASVDLDDLIQAGMIGLLEAARRYDGEQGASFETYAG 69

Query: 354 YWIRKSI------SKMVARHARGIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKY 407
             IR ++         V R  R      +  RE+++   A + L    G+ P D E+A+ 
Sbjct: 70  QRIRGAMLDELRSLDWVPRSVR------RNAREVAQ---AIRQLEQELGREPTDTEVAEK 120

Query: 408 TGLSLAEIRSA 418
            GLSL E R  
Sbjct: 121 LGLSLEEYREM 131

Length = 236

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

 Score = 50.8 bits (122), Expect = 4e-07
 Identities = 37/123 (30%), Positives = 56/123 (45%)

Query: 298 EELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIR 357
           E+L+K  + LV  LA  Y        DL+Q G VG+L    R+D + G  F  +    I 
Sbjct: 32  EKLVKHYKNLVESLAYKYSKGQSHHEDLVQVGMVGLLGAIRRYDPSFGRSFEAFAVPTII 91

Query: 358 KSISKMVARHARGIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRS 417
             I + +      + +P ++     KI+KA   LT    + P+  EIA   G+S  E+  
Sbjct: 92  GEIKRYLRDKTWSVHVPRRIKELGPKIKKAVDELTTELQRSPKISEIADRLGVSEEEVLE 151

Query: 418 ASE 420
           A E
Sbjct: 152 AME 154

Length = 257

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

 Score = 49.1 bits (117), Expect = 1e-06
 Identities = 37/120 (30%), Positives = 59/120 (49%), Gaps = 3/120 (2%)

Query: 297 REELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWI 356
           RE+LI     LVL + + +   G    DL Q G +G+++  + FD ++  KFSTY    I
Sbjct: 36  REKLINGNLRLVLSVIQRFNNRGEYVDDLFQVGCIGLMKSIDNFDLSQNVKFSTYAVPMI 95

Query: 357 RKSISKMVARHARGIKIPCKLNREIS-KIQKARKALTNSHGKYPEDIEIAKYTGLSLAEI 415
              I + + R    I++   L R+I+ K  + R  L + + K P   EIAK   +   E+
Sbjct: 96  IGEIRRYL-RDNNPIRVSRSL-RDIAYKALQVRDKLISENSKEPTVSEIAKELKVPQEEV 153

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|168831 PRK07122, PRK07122, RNA polymerase sigma factor SigF; Reviewed

 Score = 49.0 bits (117), Expect = 2e-06
 Identities = 41/148 (27%), Positives = 64/148 (43%), Gaps = 18/148 (12%)

Query: 297 REELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWI 356
           R+ ++    PL   +AR + G G P  DL+Q   VG++    RFD   G  F ++     
Sbjct: 42  RDRIVTRCLPLADHIARRFDGRGEPRDDLVQVARVGLVNAVNRFDVETGSDFVSFAV--- 98

Query: 357 RKSISKMVARHAR----GIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSL 412
             +I   V RH R     +K+P +L     ++ +A   L+   G+ P   E+A   G+  
Sbjct: 99  -PTIMGEVRRHFRDNSWSVKVPRRLKELHLRLGRATAELSQRLGRAPTASELAAELGMDR 157

Query: 413 AEIRSASECLRIVG------SIDQKIGD 434
            E+    E L + G      SID   G 
Sbjct: 158 EEV---VEGL-VAGSAYNTLSIDSGGGS 181

Length = 264

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

 Score = 46.6 bits (111), Expect = 4e-06
 Identities = 22/77 (28%), Positives = 32/77 (41%), Gaps = 2/77 (2%)

Query: 297 REELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWI 356
            EEL +   PLV   AR Y G      DL+Q   + +L+  +RFD      F  ++    
Sbjct: 3   FEELYERYLPLVYRYARRYLGDDADAEDLVQEAFLKLLEALDRFDP--EGSFKAWLFRIA 60

Query: 357 RKSISKMVARHARGIKI 373
           R  I   + R  R  + 
Sbjct: 61  RNLILDYLRRKRRLRRE 77

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|181296 PRK08215, PRK08215, sporulation sigma factor SigG; Reviewed

 Score = 46.9 bits (112), Expect = 8e-06
 Identities = 39/124 (31%), Positives = 60/124 (48%), Gaps = 9/124 (7%)

Query: 296 CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYW 355
            RE+LI     LVL + + +   G    DL Q G +G+++  + FD ++  KFSTY    
Sbjct: 38  AREKLINGNLRLVLSVIQRFNNRGENVDDLFQVGCIGLMKAIDNFDLSQNVKFSTYAVPM 97

Query: 356 IRKSISKMVARHAR---GIKIPCKLNREIS-KIQKARKALTNSHGKYPEDIEIAKYTGLS 411
           I   I     R+ R    I++   L R+I+ K  + R+ L N + K P   EIAK   + 
Sbjct: 98  IIGEIR----RYLRDNNPIRVSRSL-RDIAYKALQVREKLINENSKEPTVEEIAKELEVP 152

Query: 412 LAEI 415
             E+
Sbjct: 153 REEV 156

Length = 258

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

 Score = 37.6 bits (88), Expect = 9e-04
 Identities = 17/56 (30%), Positives = 31/56 (55%)

Query: 379 REISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGD 434
             ++KI++A++ L    G+ P   EIA+  G+S  ++R   E  R   S+D  +G+
Sbjct: 1   ELLNKIKRAQRELEQELGREPTPEEIAEELGISEEKVREVLEAAREPVSLDLPVGE 56

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

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

 Score = 40.4 bits (94), Expect = 0.001
 Identities = 34/122 (27%), Positives = 62/122 (50%), Gaps = 6/122 (4%)

Query: 297 REELIKSTRPLVLFLA-RNYRGL--GIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQ 353
           R+ LI+   PLV  +A R   G+   +   DL  +G  G+++  ERFD  +  +F  Y  
Sbjct: 25  RDVLIEFYLPLVKNVAHRLISGMPSHVKTEDLYASGVEGLVRAVERFDPEKSRRFEGYAL 84

Query: 354 YWIRKSISKMVARHARGIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLA 413
           + I+ +I   + +      +P  ++++ +K+  A  +L  S GK P D E+ +Y  +S  
Sbjct: 85  FLIKAAIIDDLRKQDW---VPRSVHQKANKLADAMDSLRQSLGKEPTDGELCEYLNISQQ 141

Query: 414 EI 415
           E+
Sbjct: 142 EL 143

Length = 257

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

 Score = 39.3 bits (92), Expect = 0.002
 Identities = 38/146 (26%), Positives = 66/146 (45%), Gaps = 16/146 (10%)

Query: 298 EELIKSTRPLVLF-LARNYRGL--GIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQY 354
           +ELI+   PLV + + R   GL   +   DL   G +G+    E+FD +R  KF TY  +
Sbjct: 25  DELIRRYMPLVHYHVQRISVGLPKSVSKDDLKSLGMLGLYDALEKFDPSRDLKFDTYASF 84

Query: 355 WIRKSISKMVARHARGIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAE 414
            IR +I   + +      +P  +  +  K++ A + L   + +     E+A   G++  E
Sbjct: 85  RIRGAIIDGLRKEDW---LPRSMREKTKKVEAAIEKLEQRYMRNVTPKEVAAELGMTEEE 141

Query: 415 IRSA------SECLRIVGSIDQKIGD 434
           + +       +  L    SID+K  D
Sbjct: 142 VEATMNEGFFANLL----SIDEKTHD 163

Length = 251

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	442
PRK07598	415	RNA polymerase sigma factor SigC; Validated	100.0
PRK05949	327	RNA polymerase sigma factor; Validated	100.0
TIGR02997	298	Sig70-cyanoRpoD RNA polymerase sigma factor, cyano	100.0
PRK07406	373	RNA polymerase sigma factor RpoD; Validated	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
PRK07122	264	RNA polymerase sigma factor SigF; Reviewed	99.97
TIGR02393	238	RpoD_Cterm RNA polymerase sigma factor RpoD, C-ter	99.97
PRK07500	289	rpoH2 RNA polymerase factor sigma-32; Reviewed	99.97
PRK07408	256	RNA polymerase sigma factor SigF; Reviewed	99.96
TIGR02850	254	spore_sigG RNA polymerase sigma-G factor. Members	99.96
PRK06596	284	RNA polymerase factor sigma-32; Reviewed	99.96
TIGR02392	270	rpoH_proteo alternative sigma factor RpoH. A sigma	99.95
PRK05657	325	RNA polymerase sigma factor RpoS; Validated	99.95
PRK08215	258	sporulation sigma factor SigG; Reviewed	99.95
TIGR02885	231	spore_sigF RNA polymerase sigma-F factor. Members	99.94
COG1191	247	FliA DNA-directed RNA polymerase specialized sigma	99.94
PRK05911	257	RNA polymerase sigma factor sigma-28; Reviewed	99.94
TIGR02980	227	SigBFG RNA polymerase sigma-70 factor, sigma-B/F/G	99.93
TIGR02941	255	Sigma_B RNA polymerase sigma-B factor. This sigma	99.92
PRK06288	268	RNA polymerase sigma factor WhiG; Reviewed	99.92
TIGR02394	285	rpoS_proteo RNA polymerase sigma factor RpoS. A si	99.92
PRK07670	251	RNA polymerase sigma factor SigD; Validated	99.92
PRK12427	231	flagellar biosynthesis sigma factor; Provisional	99.91
PRK05572	252	sporulation sigma factor SigF; Validated	99.91
PRK08583	257	RNA polymerase sigma factor SigB; Validated	99.9
TIGR02479	224	FliA_WhiG RNA polymerase sigma factor, FliA/WhiG f	99.89
PRK06986	236	fliA flagellar biosynthesis sigma factor; Validate	99.87
PRK05803	233	sporulation sigma factor SigK; Reviewed	99.79
TIGR02895	218	spore_sigI RNA polymerase sigma-I factor. Members	99.77
TIGR02846	227	spore_sigmaK RNA polymerase sigma-K factor. The sp	99.77
PRK08301	234	sporulation sigma factor SigE; Reviewed	99.75
PRK05602	186	RNA polymerase sigma factor; Reviewed	99.75
TIGR02859	198	spore_sigH RNA polymerase sigma-H factor. Members	99.74
TIGR02835	234	spore_sigmaE RNA polymerase sigma-E factor. Member	99.74
PRK08295	208	RNA polymerase factor sigma-70; Validated	99.74
PRK12513	194	RNA polymerase sigma factor; Provisional	99.72
PRK09646	194	RNA polymerase sigma factor SigK; Reviewed	99.72
PRK06811	189	RNA polymerase factor sigma-70; Validated	99.72
PRK09648	189	RNA polymerase sigma factor SigD; Reviewed	99.7
PRK13919	186	putative RNA polymerase sigma E protein; Provision	99.7
TIGR02954	169	Sig70_famx3 RNA polymerase sigma-70 factor, TIGR02	99.7
PRK09640	188	RNA polymerase sigma factor SigX; Reviewed	99.7
PRK12514	179	RNA polymerase sigma factor; Provisional	99.7
PRK12537	182	RNA polymerase sigma factor; Provisional	99.69
PRK12524	196	RNA polymerase sigma factor; Provisional	99.69
PRK09638	176	RNA polymerase sigma factor SigY; Reviewed	99.69
TIGR02948	187	SigW_bacill RNA polymerase sigma-W factor. This si	99.69
PRK06759	154	RNA polymerase factor sigma-70; Validated	99.69
PRK09643	192	RNA polymerase sigma factor SigM; Reviewed	99.68
TIGR02952	170	Sig70_famx2 RNA polymerase sigma-70 factor, TIGR02	99.68
PRK09641	187	RNA polymerase sigma factor SigW; Provisional	99.68
PRK12534	187	RNA polymerase sigma factor; Provisional	99.67
PRK12531	194	RNA polymerase sigma factor; Provisional	99.67
PRK12538	233	RNA polymerase sigma factor; Provisional	99.67
TIGR02939	190	RpoE_Sigma70 RNA polymerase sigma factor RpoE. A s	99.67
PRK12519	194	RNA polymerase sigma factor; Provisional	99.66
PRK12526	206	RNA polymerase sigma factor; Provisional	99.66
PRK12536	181	RNA polymerase sigma factor; Provisional	99.66
PRK11922	231	RNA polymerase sigma factor; Provisional	99.65
PRK12539	184	RNA polymerase sigma factor; Provisional	99.65
PRK11923	193	algU RNA polymerase sigma factor AlgU; Provisional	99.65
PRK12542	185	RNA polymerase sigma factor; Provisional	99.65
PRK09652	182	RNA polymerase sigma factor RpoE; Provisional	99.64
PRK12515	189	RNA polymerase sigma factor; Provisional	99.64
TIGR02999	183	Sig-70_X6 RNA polymerase sigma factor, TIGR02999 f	99.63
TIGR03001	244	Sig-70_gmx1 RNA polymerase sigma-70 factor, Myxoco	99.63
PRK09649	185	RNA polymerase sigma factor SigC; Reviewed	99.63
COG1595	182	RpoE DNA-directed RNA polymerase specialized sigma	99.62
PRK12512	184	RNA polymerase sigma factor; Provisional	99.61
TIGR02989	159	Sig-70_gvs1 RNA polymerase sigma-70 factor, Rhodop	99.61
PRK12520	191	RNA polymerase sigma factor; Provisional	99.59
PRK11924	179	RNA polymerase sigma factor; Provisional	99.59
PRK12522	173	RNA polymerase sigma factor; Provisional	99.59
PRK12543	179	RNA polymerase sigma factor; Provisional	99.58
TIGR02947	193	SigH_actino RNA polymerase sigma-70 factor, TIGR02	99.58
PRK09415	179	RNA polymerase factor sigma C; Reviewed	99.57
PRK09645	173	RNA polymerase sigma factor SigL; Provisional	99.57
PRK12518	175	RNA polymerase sigma factor; Provisional	99.57
PRK12516	187	RNA polymerase sigma factor; Provisional	99.56
TIGR02937	158	sigma70-ECF RNA polymerase sigma factor, sigma-70	99.56
PRK08241	339	RNA polymerase factor sigma-70; Validated	99.55
PRK12547	164	RNA polymerase sigma factor; Provisional	99.55
TIGR02983	162	SigE-fam_strep RNA polymerase sigma-70 factor, sig	99.55
PRK12529	178	RNA polymerase sigma factor; Provisional	99.55
PRK12541	161	RNA polymerase sigma factor; Provisional	99.54
TIGR02984	189	Sig-70_plancto1 RNA polymerase sigma-70 factor, Pl	99.54
PRK12535	196	RNA polymerase sigma factor; Provisional	99.54
TIGR02985	161	Sig70_bacteroi1 RNA polymerase sigma-70 factor, Ba	99.53
PRK12523	172	RNA polymerase sigma factor; Reviewed	99.53
PRK09644	165	RNA polymerase sigma factor SigM; Provisional	99.52
PRK12533	216	RNA polymerase sigma factor; Provisional	99.52
TIGR02960	324	SigX5 RNA polymerase sigma-70 factor, TIGR02960 fa	99.51
PRK09642	160	RNA polymerase sigma factor SigW; Reviewed	99.51
PRK12528	161	RNA polymerase sigma factor; Provisional	99.5
PRK12540	182	RNA polymerase sigma factor; Provisional	99.48
PRK08311	237	putative RNA polymerase sigma factor SigI; Reviewe	99.48
PRK09639	166	RNA polymerase sigma factor SigX; Provisional	99.48
PRK12545	201	RNA polymerase sigma factor; Provisional	99.47
PRK12532	195	RNA polymerase sigma factor; Provisional	99.47
PRK12530	189	RNA polymerase sigma factor; Provisional	99.47
PRK09647	203	RNA polymerase sigma factor SigE; Reviewed	99.47
PRK09637	181	RNA polymerase sigma factor SigZ; Provisional	99.46
PRK12517	188	RNA polymerase sigma factor; Provisional	99.46
TIGR02950	154	SigM_subfam RNA polymerase sigma factor, SigM fami	99.45
PRK12544	206	RNA polymerase sigma factor; Provisional	99.45
TIGR02943	188	Sig70_famx1 RNA polymerase sigma-70 factor, TIGR02	99.44
TIGR02959	170	SigZ RNA polymerase sigma factor, SigZ family. Thi	99.43
PRK12546	188	RNA polymerase sigma factor; Provisional	99.43
PF04542	71	Sigma70_r2: Sigma-70 region 2 ; InterPro: IPR00762	99.41
PRK12511	182	RNA polymerase sigma factor; Provisional	99.41
PRK09651	172	RNA polymerase sigma factor FecI; Provisional	99.4
PRK06704	228	RNA polymerase factor sigma-70; Validated	99.36
PRK07037	163	extracytoplasmic-function sigma-70 factor; Validat	99.36
PRK12527	159	RNA polymerase sigma factor; Reviewed	99.35
PRK12525	168	RNA polymerase sigma factor; Provisional	99.35
PRK09636	293	RNA polymerase sigma factor SigJ; Provisional	99.26
PRK09635	290	sigI RNA polymerase sigma factor SigI; Provisional	99.2
PRK09191	261	two-component response regulator; Provisional	99.2
TIGR02957	281	SigX4 RNA polymerase sigma-70 factor, TIGR02957 fa	99.2
TIGR03209	142	P21_Cbot clostridium toxin-associated regulator Bo	99.18
PRK09047	161	RNA polymerase factor sigma-70; Validated	99.1
PF04539	78	Sigma70_r3: Sigma-70 region 3; InterPro: IPR007624	98.83
PF07638	185	Sigma70_ECF: ECF sigma factor	98.82
PF00140	37	Sigma70_r1_2: Sigma-70 factor, region 1.2; InterPr	97.09
TIGR02393	238	RpoD_Cterm RNA polymerase sigma factor RpoD, C-ter	96.42
PRK07670	251	RNA polymerase sigma factor SigD; Validated	96.17
PRK07408	256	RNA polymerase sigma factor SigF; Reviewed	96.03
PRK09210	367	RNA polymerase sigma factor RpoD; Validated	95.95
PRK06288	268	RNA polymerase sigma factor WhiG; Reviewed	95.76
PF12645	65	HTH_16: Helix-turn-helix domain; InterPro: IPR0247	95.61
PRK05901	509	RNA polymerase sigma factor; Provisional	95.38
PRK05949	327	RNA polymerase sigma factor; Validated	95.38
PRK07122	264	RNA polymerase sigma factor SigF; Reviewed	95.37
COG1191	247	FliA DNA-directed RNA polymerase specialized sigma	95.35
PRK05911	257	RNA polymerase sigma factor sigma-28; Reviewed	95.31
PRK07921	324	RNA polymerase sigma factor SigB; Reviewed	95.02
TIGR02479	224	FliA_WhiG RNA polymerase sigma factor, FliA/WhiG f	94.9
PRK07598	415	RNA polymerase sigma factor SigC; Validated	94.83
TIGR02850	254	spore_sigG RNA polymerase sigma-G factor. Members	94.66
TIGR02997	298	Sig70-cyanoRpoD RNA polymerase sigma factor, cyano	94.61
TIGR02885	231	spore_sigF RNA polymerase sigma-F factor. Members	94.38
PRK07500	289	rpoH2 RNA polymerase factor sigma-32; Reviewed	94.33
PF04539	78	Sigma70_r3: Sigma-70 region 3; InterPro: IPR007624	94.1
PRK07405	317	RNA polymerase sigma factor SigD; Validated	93.92
PRK06986	236	fliA flagellar biosynthesis sigma factor; Validate	93.78
PRK07406	373	RNA polymerase sigma factor RpoD; Validated	93.66
PF08281	54	Sigma70_r4_2: Sigma-70, region 4; InterPro: IPR013	93.64
TIGR02941	255	Sigma_B RNA polymerase sigma-B factor. This sigma	93.45
TIGR02394	285	rpoS_proteo RNA polymerase sigma factor RpoS. A si	93.0
PRK08215	258	sporulation sigma factor SigG; Reviewed	92.95
PRK08583	257	RNA polymerase sigma factor SigB; Validated	92.57
PRK05658	619	RNA polymerase sigma factor RpoD; Validated	92.41
TIGR02980	227	SigBFG RNA polymerase sigma-70 factor, sigma-B/F/G	92.21
PHA02547	179	55 RNA polymerase sigma factor; Provisional	92.08
PF01726	65	LexA_DNA_bind: LexA DNA binding domain; InterPro:	92.01
PRK12427	231	flagellar biosynthesis sigma factor; Provisional	91.73
PRK05572	252	sporulation sigma factor SigF; Validated	91.72
PF04545	50	Sigma70_r4: Sigma-70, region 4; InterPro: IPR00763	90.87
PRK05657	325	RNA polymerase sigma factor RpoS; Validated	89.73
PRK06596	284	RNA polymerase factor sigma-32; Reviewed	85.3
COG0568	342	RpoD DNA-directed RNA polymerase, sigma subunit (s	85.22
TIGR03879	73	near_KaiC_dom probable regulatory domain. This mod	81.77
COG4941	415	Predicted RNA polymerase sigma factor containing a	80.22

>PRK07598 RNA polymerase sigma factor SigC; Validated

Probab=100.00  E-value=3.8e-47  Score=393.22  Aligned_cols=221  Identities=29%  Similarity=0.491  Sum_probs=207.6

Q ss_pred             ChhHHHHHHhcccCC-CCCChHHHHHHHHHhHHHHH--------------------HHHHHHHHHHHhCCCCChHHHHH-
Q 013472          220 PTIFSAERALNSRGR-RLTIARNEAEMSKGVQVVAN--------------------LERIKTTLEKESGKAASLNCWAQ-  277 (442)
Q Consensus       220 ~~~~~~~~~~~~~~~-~lLt~eeE~eL~~~iq~~~~--------------------le~~~~~L~~~~gr~pt~~ewA~-  277 (442)
                      ++.|.++-|+..+++ ||||++||++|+++||.++.                    |++++..|++++|++||..+||. 
T Consensus        57 ~~~d~v~~yl~~igr~~lL~~~eEv~l~~~vq~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~l~~~~g~~pt~~ewa~~  136 (415)
T PRK07598         57 RSTDLVRLYLQEIGRVRLLGRDEEVSEAQKVQRYMKLIVLANAAKEGDEVIKPYLRLIEVRERLTSELGHRPSLERWAKT  136 (415)
T ss_pred             CCCChHHHHHHhcccccCCCHHHHHHHHHHHHHHHHHhhhhhhhhcccchhhhHHHHHHHHHHHHHHhCCCCCHHHHHHH
Confidence            345667778888887 99999999999999999999                    89999999999999999999994 


Q ss_pred             ---------------------HcCCCHHHHHHHHHhchHHHHHHHHHhHHHHHHHHHHhhCCCCCHHhHHHHHHHHHHHh
Q 013472          278 ---------------------AAGVSERVLKQHLAFGWYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQG  336 (442)
Q Consensus       278 ---------------------a~g~deeeL~~~l~~G~~Are~LI~~nlrLV~sIAkrY~g~g~d~EDLIQEG~IGLirA  336 (442)
                                           ++||++++|+..++.|..|+++||.+|+++|+++|++|.++|++++||||||++|||+|
T Consensus       137 ~~~~~~~l~~~l~~~~~~~~~~~~l~~~eL~~~l~~G~~A~e~LI~~nlrLVvsiAkky~~~g~~~eDLiQEG~iGL~ra  216 (415)
T PRK07598        137 ADISLADLKPTLAEGKRRWAEIAKLTVEELEQIQKQGLRAKEHMIKANLRLVVSVAKKYQNRGLELLDLVQEGTLGLERA  216 (415)
T ss_pred             hCCcHHHHHHhhhhhhhhhhhhccCCHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHccCCCCHHHHHHHHHHHHHHH
Confidence                                 45566777778888998899999999999999999999999999999999999999999


Q ss_pred             HHhcCCCCCCChHHHHHHHHHHHHHHHHHhhcCceecccccHHHHHHHHHHHHHHHHHcCCCCcHHHHHHHhCCCHHHHH
Q 013472          337 AERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIR  416 (442)
Q Consensus       337 ieKFDp~kG~rFSTYa~~wIRnaI~r~LRkqsr~irlP~~v~e~i~kI~ka~~~L~~elgr~PS~eEIAe~LGIS~etVk  416 (442)
                      +++|||.+|++|+||+|||||++|.++++++++++++|.|+.+.+++++++...|.+++|+.||.+|||+.|||++++|+
T Consensus       217 vekFDp~rG~rFSTYa~wwIRqaI~r~i~~~srtIrlP~~i~e~l~~lrk~~r~L~~~lgR~pt~~EiA~~l~is~~~vr  296 (415)
T PRK07598        217 VEKFDPTKGYRFSTYAYWWIRQGITRAIATQSRTIRLPVHITEKLNKIKKAQRKISQEKGRTPTIEDIAQELEMTPTQVR  296 (415)
T ss_pred             HHHcCcccCCCHHHHHHHHHHHHHHHHHHHcCCceehhHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHhcccCCCCccccCCCCCccc
Q 013472          417 SASECLRIVGSIDQKIGDCLNAKY  440 (442)
Q Consensus       417 ~~l~~ar~~~SLD~~v~~~~d~~~  440 (442)
                      .++..++.++|||.++|+++++++
T Consensus       297 ~~l~~~~~~~SLd~~vg~~~d~~l  320 (415)
T PRK07598        297 EVLLRVPRSVSLETKVGKDKDTEL  320 (415)
T ss_pred             HHHHHccCCcccccccCCCccccH
Confidence            999999999999999998887653

>PRK05949 RNA polymerase sigma factor; Validated

Probab=100.00  E-value=2e-43  Score=356.76  Aligned_cols=217  Identities=35%  Similarity=0.549  Sum_probs=208.4

Q ss_pred             hHHHHHHhcccCC-CCCChHHHHHHHHHhHHHHHHHHHHHHHHHHhCCCCChHHHHHHcCCCHHHHHHHHHhchHHHHHH
Q 013472          222 IFSAERALNSRGR-RLTIARNEAEMSKGVQVVANLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQHLAFGWYCREEL  300 (442)
Q Consensus       222 ~~~~~~~~~~~~~-~lLt~eeE~eL~~~iq~~~~le~~~~~L~~~~gr~pt~~ewA~a~g~deeeL~~~l~~G~~Are~L  300 (442)
                      .+.+..|++.+++ ||||++||++|++.|+.++.+++.+..|+..+|+.|+..+||.++++++.+|+..++.|+.|++.|
T Consensus        17 ~d~~~~yl~~i~~~~lLt~eeE~~l~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~eL~~~~~~g~~A~~~L   96 (327)
T PRK05949         17 ADMVRTYLHEIGRVPLLTHEQEIVYGKQVQQMMSLLEAKEALAKKLGREPSLPEWAEAVNLSETELKQTLKQGKRAKQKM   96 (327)
T ss_pred             CCHHHHHHHHcCCccCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhccCCchHHHHHhccCCHHHHHHHHHccHHHHHHH
Confidence            3455677888886 999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHhHHHHHHHHHHhhCCCCCHHhHHHHHHHHHHHhHHhcCCCCCCChHHHHHHHHHHHHHHHHHhhcCceecccccHHH
Q 013472          301 IKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIPCKLNRE  380 (442)
Q Consensus       301 I~~nlrLV~sIAkrY~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIRnaI~r~LRkqsr~irlP~~v~e~  380 (442)
                      |..|+++|+++|++|.+++.+++||+||||+|||+++++|||++|++|+|||+||||++|.++|.++++++|+|.++.+.
T Consensus        97 i~~~~~~V~~iA~~y~~~~~~~eDLvQEg~igL~~a~~kfd~~~G~rFsTYa~wwIrq~I~r~i~~~~r~iRlP~~~~~~  176 (327)
T PRK05949         97 IEANLRLVVAIAKKYQKRNMEFLDLIQEGTLGLERGVEKFDPTRGYKFSTYAYWWIRQAITRAIAQQARTIRLPIHITEK  176 (327)
T ss_pred             HHHHHHHHHHHHHHHccCCCCHHHHHHHHHHHHHHHHHhcCCcCCCChhhhhHHHHHHHHHHHHHHcCCceeCCHHHHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHcCCCCcHHHHHHHhCCCHHHHHHHHHhcccCCCCccccCCCCCc
Q 013472          381 ISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNA  438 (442)
Q Consensus       381 i~kI~ka~~~L~~elgr~PS~eEIAe~LGIS~etVk~~l~~ar~~~SLD~~v~~~~d~  438 (442)
                      +++++++...+..++|+.||.+|||+.+||++++|..++..++.++|||.|++++++.
T Consensus       177 ~~~l~k~~~~l~~~lgr~pt~~eiA~~l~i~~~~v~~~~~~~~~~~SLd~~~~~~~~~  234 (327)
T PRK05949        177 LNKIKKTQRELSQKLGRSATPAEIAKELELEPSQIREYLSMARQPISLDVRVGDNQDT  234 (327)
T ss_pred             HHHHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHHhccccccCCCcCCCCCc
Confidence            9999999999999999999999999999999999999999999999999999877654

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

Probab=100.00  E-value=2.8e-43  Score=350.51  Aligned_cols=212  Identities=35%  Similarity=0.602  Sum_probs=204.1

Q ss_pred             HHHhcccCC-CCCChHHHHHHHHHhHHHHHHHHHHHHHHHHhCCCCChHHHHHHcCCCHHHHHHHHHhchHHHHHHHHHh
Q 013472          226 ERALNSRGR-RLTIARNEAEMSKGVQVVANLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQHLAFGWYCREELIKST  304 (442)
Q Consensus       226 ~~~~~~~~~-~lLt~eeE~eL~~~iq~~~~le~~~~~L~~~~gr~pt~~ewA~a~g~deeeL~~~l~~G~~Are~LI~~n  304 (442)
                      ..|++.+++ ||||++||++|++.++.++.+++.+.+|+++.|++|+..+||+++|+++.+|+.+++.|..|+++||.+|
T Consensus         4 ~~yl~~~~~~~lLt~eeE~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~g~~A~~~Lv~~~   83 (298)
T TIGR02997         4 RLYLQEIGRVPLLTPEEEIELARQVQQMMVLEELREELEEQLGREPSKEEWAAAAGLSEAELRQRLRQGQRAKEKMIKAN   83 (298)
T ss_pred             HHHHHHccccCCCCHHHHHHHHHHHHHHhHHHHHHHHHHHhhcCCCcHHHHHHhccCCHHHHHHHHhccHHHHHHHHHHh
Confidence            456777775 9999999999999999999999999999999999999999999999999999999999988999999999


Q ss_pred             HHHHHHHHHHhhCCCCCHHhHHHHHHHHHHHhHHhcCCCCCCChHHHHHHHHHHHHHHHHHhhcCceecccccHHHHHHH
Q 013472          305 RPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIPCKLNREISKI  384 (442)
Q Consensus       305 lrLV~sIAkrY~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIRnaI~r~LRkqsr~irlP~~v~e~i~kI  384 (442)
                      +++|+++|++|.++|.+++||+||||+|||+|+++|||.+|++|+||++||||++|.+++.++++++++|.++...++++
T Consensus        84 lrlV~~iA~~y~~~~~~~eDLiQEg~igL~~a~~kfd~~~g~rFsTya~~wIr~~I~r~i~~~~r~vr~p~~~~~~~~~~  163 (298)
T TIGR02997        84 LRLVVSVAKKYQNRGLELLDLIQEGSLGLERAVEKFDPTRGYKFSTYAYWWIRQGITRAIANQSRTIRLPIHITEKLNKI  163 (298)
T ss_pred             HHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHhCccCCCChHHHHHHHHHHHHHHHHHhcCCCeeCcHHHHHHHHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHcCCCCcHHHHHHHhCCCHHHHHHHHHhcccCCCCccccCCCCC
Q 013472          385 QKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLN  437 (442)
Q Consensus       385 ~ka~~~L~~elgr~PS~eEIAe~LGIS~etVk~~l~~ar~~~SLD~~v~~~~d  437 (442)
                      +++...+...+|+.||.+|||+.+|+++++|..++..+..++|||.+++++++
T Consensus       164 rk~~~~l~~~~~~~pt~~eia~~l~~~~~~v~~~~~~~~~~~SLd~~~~~~~~  216 (298)
T TIGR02997       164 KKVQRELSQKLGRTPSEAEIAEALELEPEQVRELLQRARQPVSLDAPVGDEED  216 (298)
T ss_pred             HHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHHcccCcccCCCcCCCCc
Confidence            99999999999999999999999999999999999999999999999876554

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).

>PRK07406 RNA polymerase sigma factor RpoD; Validated

Probab=100.00  E-value=2.4e-43  Score=361.64  Aligned_cols=216  Identities=31%  Similarity=0.590  Sum_probs=208.2

Q ss_pred             HHHHHHhcccCC-CCCChHHHHHHHHHhHHHHHHHHHHHHHHHHhCCCCChHHHHHHcCCCHHHHHHHHHhchHHHHHHH
Q 013472          223 FSAERALNSRGR-RLTIARNEAEMSKGVQVVANLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQHLAFGWYCREELI  301 (442)
Q Consensus       223 ~~~~~~~~~~~~-~lLt~eeE~eL~~~iq~~~~le~~~~~L~~~~gr~pt~~ewA~a~g~deeeL~~~l~~G~~Are~LI  301 (442)
                      +.+..|++.+++ ||||++||++|+++|+.++.+++.+.+|++..|++|+..+||.++|+++.+|..++..|..|+++||
T Consensus        63 d~l~~Yl~~i~~~~lLt~eEE~~La~~i~~~~~~~~~~~~l~~~~g~~~~~~~~~~~~~~~~~~l~~~~~~g~~A~~~Li  142 (373)
T PRK07406         63 DSIRVYLQEIGRIRLLRPDEEIELARKIADLLELEELREQFESELGREPSDKEWAELVDMPLPKFRRRLMLGRRAKEKMV  142 (373)
T ss_pred             CHHHHHHHHhcccCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhcccccchhhHhhhccccHHHHHHHHhcCHHHHHHHH
Confidence            446778888886 9999999999999999999999999999999999999999999999999999999999988999999


Q ss_pred             HHhHHHHHHHHHHhhCCCCCHHhHHHHHHHHHHHhHHhcCCCCCCChHHHHHHHHHHHHHHHHHhhcCceecccccHHHH
Q 013472          302 KSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIPCKLNREI  381 (442)
Q Consensus       302 ~~nlrLV~sIAkrY~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIRnaI~r~LRkqsr~irlP~~v~e~i  381 (442)
                      .+|+++|+++|++|.+++.+++||+|||+||||+|+++||+.+|++|+|||+||||++|.++|+++++++++|.++.+.+
T Consensus       143 ~~~l~lV~~iA~ry~~~~~~~eDLiQEG~igL~~Ai~kFd~~kg~~FsTYA~wWIRqaI~~~I~~~~r~IRlP~~~~~~~  222 (373)
T PRK07406        143 QSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYATWWIRQAITRAIADQSRTIRLPVHLYETI  222 (373)
T ss_pred             HHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHhcCCccCCCHHHHHHHHHHHHHHHHHHhcCCceeCCHHHHHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHcCCCCcHHHHHHHhCCCHHHHHHHHHhcccCCCCccccCCCCCc
Q 013472          382 SKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNA  438 (442)
Q Consensus       382 ~kI~ka~~~L~~elgr~PS~eEIAe~LGIS~etVk~~l~~ar~~~SLD~~v~~~~d~  438 (442)
                      ++|+++...|.+.+|+.||.+|||+.||+++++|..++..+..++|||.|++++++.
T Consensus       223 ~~i~~a~~~l~~~lgr~Pt~~EIA~~lg~~~e~v~~~~~~~~~~~SLd~~i~~~~~~  279 (373)
T PRK07406        223 SRIKKTTKVLSQEFGRKPTEEEIAESMEMTIEKLRFIAKSAQLPISLETPIGKEEDS  279 (373)
T ss_pred             HHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCcc
Confidence            999999999999999999999999999999999999999889999999999876654

>PRK07405 RNA polymerase sigma factor SigD; Validated

Probab=100.00  E-value=3.2e-42  Score=346.48  Aligned_cols=216  Identities=31%  Similarity=0.509  Sum_probs=207.4

Q ss_pred             HHHHHHhcccCC-CCCChHHHHHHHHHhHHHHHHHHHHHHHHHHhCCCCChHHHHHHcCCCHHHHHHHHHhchHHHHHHH
Q 013472          223 FSAERALNSRGR-RLTIARNEAEMSKGVQVVANLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQHLAFGWYCREELI  301 (442)
Q Consensus       223 ~~~~~~~~~~~~-~lLt~eeE~eL~~~iq~~~~le~~~~~L~~~~gr~pt~~ewA~a~g~deeeL~~~l~~G~~Are~LI  301 (442)
                      +.+..|++.+++ ||||++||++|+++|+.++.+++++..|++++|+.|+..+||.++++++.+|+..++.|+.|+++||
T Consensus         8 ~~~~~yl~~i~~~~lLt~eeE~~La~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~L~~~~~~g~~A~~~L~   87 (317)
T PRK07405          8 DLVRTYLREIGRVPLLTHEEEILYGKQVQRLVALQEIREELAEELGREPTDAEWAKAAKLSEEELRSAIAEGEAAKRKMV   87 (317)
T ss_pred             cHHHHHHHHccccCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhcccccchHHHhhhccCCHHHHHHHHhccHHHHHHHH
Confidence            345677888886 9999999999999999999999999999999999999999999999999999999999988999999


Q ss_pred             HHhHHHHHHHHHHhhCCCCCHHhHHHHHHHHHHHhHHhcCCCCCCChHHHHHHHHHHHHHHHHHhhcCceecccccHHHH
Q 013472          302 KSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIPCKLNREI  381 (442)
Q Consensus       302 ~~nlrLV~sIAkrY~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIRnaI~r~LRkqsr~irlP~~v~e~i  381 (442)
                      ..|+++|+++|++|.+++.+++||+||||+|||+++++|||.+|++|+||++||||++|.++|.++++++++|.++.+.+
T Consensus        88 ~~~~~~V~~~a~~~~~~~~~~eDLvQEg~i~L~~a~~~fd~~~g~rf~tYa~~wIR~~I~~~i~~~~~~ir~p~~~~~~~  167 (317)
T PRK07405         88 EANLRLVVSVAKKYLKRNVDLLDLIQEGTIGMQRGVEKFDPTKGYRFSTYAYWWIRQAITRAIAEKSRTIRLPIHITEKL  167 (317)
T ss_pred             HHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHhCcCCCCChHHHHHHHHHHHHHHHHHhcCCCccCChHHHHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHcCCCCcHHHHHHHhCCCHHHHHHHHHhcccCCCCccccCCCCCc
Q 013472          382 SKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNA  438 (442)
Q Consensus       382 ~kI~ka~~~L~~elgr~PS~eEIAe~LGIS~etVk~~l~~ar~~~SLD~~v~~~~d~  438 (442)
                      ++++++...+...+|+.||.+|||+.+|+++++|..++...+.++|||.|++++++.
T Consensus       168 ~~l~~~~~~l~~~~gr~pt~~eiA~~~~~~~~~v~~~~~~~~~~~SLd~~~~~~~~~  224 (317)
T PRK07405        168 NKIKKAQRQLSQQLGRAATIGELAEELELTPKQVREYLERARQPLSLDLRVGDNQDT  224 (317)
T ss_pred             HHHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHHcCCCeeecCCCCCCCCc
Confidence            999999999999999999999999999999999999999888999999999876654

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

Probab=100.00  E-value=8.3e-40  Score=330.14  Aligned_cols=220  Identities=30%  Similarity=0.503  Sum_probs=200.9

Q ss_pred             hhHHHHHHhcccCC-CCCChHHHHHHHHHhHHHHHHHHHHHHHHH-HhCCCCChH---------------HHHHHcCCCH
Q 013472          221 TIFSAERALNSRGR-RLTIARNEAEMSKGVQVVANLERIKTTLEK-ESGKAASLN---------------CWAQAAGVSE  283 (442)
Q Consensus       221 ~~~~~~~~~~~~~~-~lLt~eeE~eL~~~iq~~~~le~~~~~L~~-~~gr~pt~~---------------ewA~a~g~de  283 (442)
                      ..+.+..|+...+. ++++.++|.++.++++....+......|.. .++..|+..               +|+.....++
T Consensus         7 ~~d~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~E   86 (342)
T COG0568           7 SADAVRAYLDEIGRIPLLVREAEVELAKQLEDEQLLVELGEDLTDLKLGREPSERARRPAGRLSFYIRAIEAAPLLTPEE   86 (342)
T ss_pred             chhHHHHHHHHhcchhhhhHHHHHHHHHHHhHhhhhhHHHHHHHhcccccccchhhhhhhhhHHHHHHHHhhhcccChHH
Confidence            35667788888886 999999999999999988877777777766 667888886               6665555554


Q ss_pred             -HHHHHHHHhch--H-HHHHHHHHhHHHHHHHHHHhhCCCCCHHhHHHHHHHHHHHhHHhcCCCCCCChHHHHHHHHHHH
Q 013472          284 -RVLKQHLAFGW--Y-CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKS  359 (442)
Q Consensus       284 -eeL~~~l~~G~--~-Are~LI~~nlrLV~sIAkrY~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIRna  359 (442)
                       ..|..++..|.  . |+.+||.+|+++|++||++|.|+|+++.||||||+|||++|++||||++|++|||||+||||++
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             67888999995  3 9999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHhhcCceecccccHHHHHHHHHHHHHHHHHcCCCCcHHHHHHHhCCCHHHHHHHHHhcccCCCCccccCCCCCcc
Q 013472          360 ISKMVARHARGIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNAK  439 (442)
Q Consensus       360 I~r~LRkqsr~irlP~~v~e~i~kI~ka~~~L~~elgr~PS~eEIAe~LGIS~etVk~~l~~ar~~~SLD~~v~~~~d~~  439 (442)
                      |.++|.++.++|++|.|+.+.++++.++.++|.+++|++|+++|||+.||+++++|+.++..++.|+|||.|+|+++|+.
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            99999999999999999999999999999999999999999999999999999999999999999999999999988764


Q ss_pred             c
Q 013472          440 Y  440 (442)
Q Consensus       440 ~  440 (442)
                      +
T Consensus       247 l  247 (342)
T COG0568         247 L  247 (342)
T ss_pred             H
Confidence            3

>PRK05901 RNA polymerase sigma factor; Provisional

Probab=100.00  E-value=2.7e-39  Score=342.10  Aligned_cols=205  Identities=30%  Similarity=0.476  Sum_probs=184.1

Q ss_pred             hHHHHHHhcccCC-CCCChHHHHHHHHHhHHHHHHHHHHHHHHHHhCCCCChHHHHHHcCCCHHHHHHHHHhchHHHHHH
Q 013472          222 IFSAERALNSRGR-RLTIARNEAEMSKGVQVVANLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQHLAFGWYCREEL  300 (442)
Q Consensus       222 ~~~~~~~~~~~~~-~lLt~eeE~eL~~~iq~~~~le~~~~~L~~~~gr~pt~~ewA~a~g~deeeL~~~l~~G~~Are~L  300 (442)
                      .+.++.|++.+++ ||||++||++|+++|+.+..++....          ....|+.+   ...+|...+..|..|+++|
T Consensus       210 ~d~l~~YL~~i~~~~lLt~eEE~~La~~i~~g~~~~~~~~----------~~~~~~~~---~~~~l~~~~~~g~~Ar~~L  276 (509)
T PRK05901        210 ADPVKAYLKQIGKVKLLNAEEEVELAKRIEAGLYAEELLA----------EGEKLDPE---LRRDLQWIGRDGKRAKNHL  276 (509)
T ss_pred             ccHHHHHHHHhccCCCCCHHHHHHHHHHHHhCCchhhhhh----------hcccchhh---hhhhhhhhccchHHHHHHH
Confidence            3556778888886 99999999999999998865554221          11234322   4567888899999999999


Q ss_pred             HHHhHHHHHHHHHHhhCCCCCHHhHHHHHHHHHHHhHHhcCCCCCCChHHHHHHHHHHHHHHHHHhhcCceecccccHHH
Q 013472          301 IKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIPCKLNRE  380 (442)
Q Consensus       301 I~~nlrLV~sIAkrY~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIRnaI~r~LRkqsr~irlP~~v~e~  380 (442)
                      |.+|++||++||++|.++|++++||||||+|||++|+++|||.+|++|+|||+||||++|.++|+++.+.+++|.++.+.
T Consensus       277 I~sNLrLVvsIAkrY~~~Gl~~eDLIQEGnIGLikAvekFDp~rG~rFSTYA~wWIRqaI~raI~d~~r~IRvP~~~~e~  356 (509)
T PRK05901        277 LEANLRLVVSLAKRYTNRGLSFLDLIQEGNLGLIKAVEKFDYTKGYKFSTYATWWIRQAITRAMADQARTIRIPVHMVET  356 (509)
T ss_pred             HHHhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHhCcccCCCchhhhHHHHHHHHHHHHHHcCCceecCHHHHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHcCCCCcHHHHHHHhCCCHHHHHHHHHhcccCCCCccccCCCCCcc
Q 013472          381 ISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNAK  439 (442)
Q Consensus       381 i~kI~ka~~~L~~elgr~PS~eEIAe~LGIS~etVk~~l~~ar~~~SLD~~v~~~~d~~  439 (442)
                      +++|.++...|.+.+|+.||.+|||+.|||++++|..++...+.++|||.+++++++..
T Consensus       357 i~kl~~~~~~L~~~lgr~PT~eELAe~Lgis~e~V~~~~~~~~~~~SLD~~i~~d~~~~  415 (509)
T PRK05901        357 INKLGRIERELLQELGREPTPEELAKEMGFTPEKVREIQKYNREPISLDKTIGKEGDSQ  415 (509)
T ss_pred             HHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccccccccCCccc
Confidence            99999999999999999999999999999999999999998899999999998776654

>PRK07921 RNA polymerase sigma factor SigB; Reviewed

Probab=100.00  E-value=4.5e-38  Score=317.57  Aligned_cols=203  Identities=31%  Similarity=0.492  Sum_probs=182.0

Q ss_pred             HHHHHHhcccCC-CCCChHHHHHHHHHhHHHHHHHHHHHHHHHHhCCCCChHHHHHHcCCCHHHHHHHHHhchHHHHHHH
Q 013472          223 FSAERALNSRGR-RLTIARNEAEMSKGVQVVANLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQHLAFGWYCREELI  301 (442)
Q Consensus       223 ~~~~~~~~~~~~-~lLt~eeE~eL~~~iq~~~~le~~~~~L~~~~gr~pt~~ewA~a~g~deeeL~~~l~~G~~Are~LI  301 (442)
                      +.+..|++.+++ ||||++||++|+++|+.+..++..           |+..+|+...  ...+|...++.|..|+++||
T Consensus        26 ~~~~~Yl~~i~~~~lLt~eeE~~La~~~~~g~~~~~~-----------~~~~~~~~~~--~~~~l~~~~~~~~~A~~~Lv   92 (324)
T PRK07921         26 DLVRVYLNGIGKTALLTAADEVELAKRIEAGLYAEHL-----------LETRKRLSEA--RKRDLAAVVRDGEAARRHLL   92 (324)
T ss_pred             ChHHHHHHHhcccCCCCHHHHHHHHHHHHhhhhhhhh-----------hccccccchh--HHHHHHHHHhcCHHHHHHHH
Confidence            345677887876 999999999999999988776654           1122232111  35678999999999999999


Q ss_pred             HHhHHHHHHHHHHhhCCCCCHHhHHHHHHHHHHHhHHhcCCCCCCChHHHHHHHHHHHHHHHHHhhcCceecccccHHHH
Q 013472          302 KSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIPCKLNREI  381 (442)
Q Consensus       302 ~~nlrLV~sIAkrY~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIRnaI~r~LRkqsr~irlP~~v~e~i  381 (442)
                      ..|+++|+++|++|.+++.+++||+|||+||||+|+++|||++|++|+|||+||||++|.++|+++.+.+++|.++.+.+
T Consensus        93 ~~~~~lV~~iA~r~~~~~~~~eDLvQEg~igL~~a~~~fdp~~G~rFsTYA~~wIr~aI~~~i~~~~r~vrlP~~~~~~~  172 (324)
T PRK07921         93 EANLRLVVSLAKRYTGRGMPLLDLIQEGNLGLIRAMEKFDYTKGFKFSTYATWWIRQAITRGMADQSRTIRLPVHLVEQV  172 (324)
T ss_pred             HHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHcCCccCCCHHHHHHHHHHHHHHHHHHHcCCCccCCHHHHHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHcCCCCcHHHHHHHhCCCHHHHHHHHHhcccCCCCccccCCCCCc
Q 013472          382 SKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNA  438 (442)
Q Consensus       382 ~kI~ka~~~L~~elgr~PS~eEIAe~LGIS~etVk~~l~~ar~~~SLD~~v~~~~d~  438 (442)
                      ++++++...|.+.+|+.||.+|||+.||+++++|..++..+..++|||.|++++++.
T Consensus       173 ~~l~~~~~~l~~~lgr~pt~~EiA~~lgi~~~~v~~~~~~~~~~~SLd~~~~~~~~~  229 (324)
T PRK07921        173 NKLARIKRELHQQLGREATDEELAEESGIPEEKIADLLEHSRDPVSLDMPVGSDEEA  229 (324)
T ss_pred             HHHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHHcCCCceecCCCCCCCCc
Confidence            999999999999999999999999999999999999998888999999999876654

>PRK09210 RNA polymerase sigma factor RpoD; Validated

Probab=100.00  E-value=1.9e-33  Score=288.10  Aligned_cols=177  Identities=30%  Similarity=0.514  Sum_probs=164.9

Q ss_pred             hHHHHHHhcccCC-CCCChHHHHHHHHHhHHHHHHHHHHHHHHHHhCCCCChHHHHHHcCCCHHHHHHHHHhchHHHHHH
Q 013472          222 IFSAERALNSRGR-RLTIARNEAEMSKGVQVVANLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQHLAFGWYCREEL  300 (442)
Q Consensus       222 ~~~~~~~~~~~~~-~lLt~eeE~eL~~~iq~~~~le~~~~~L~~~~gr~pt~~ewA~a~g~deeeL~~~l~~G~~Are~L  300 (442)
                      .++++.|++.+++ |+||++||.+|++.++.+                                        +..|++.|
T Consensus        95 ~d~~~~yl~~i~~~~~l~~~ee~~L~~~~~~G----------------------------------------d~~A~~~L  134 (367)
T PRK09210         95 NDPVRMYLKEIGRVPLLTAEEEIELAKRIEEG----------------------------------------DEEAKQRL  134 (367)
T ss_pred             CcHHHHHHHHhhccCCCCHHHHHHHHHHHHhh----------------------------------------HHHHHHHH
Confidence            4567888988886 999999999998866532                                        02389999


Q ss_pred             HHHhHHHHHHHHHHhhCCCCCHHhHHHHHHHHHHHhHHhcCCCCCCChHHHHHHHHHHHHHHHHHhhcCceecccccHHH
Q 013472          301 IKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIPCKLNRE  380 (442)
Q Consensus       301 I~~nlrLV~sIAkrY~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIRnaI~r~LRkqsr~irlP~~v~e~  380 (442)
                      |..|+++|+++|++|.+++.+++||+|||+||||+|+++|||.+|++|+|||+||||++|.++|+++.+.+++|.++.+.
T Consensus       135 i~~~~~lV~~iA~~~~~~~~~~eDLiQEg~igL~~a~~~fd~~~g~~FsTyA~~wIr~aI~~~i~~~~r~irip~~~~~~  214 (367)
T PRK09210        135 AEANLRLVVSIAKRYVGRGMLFLDLIQEGNMGLMKAVEKFDYRKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET  214 (367)
T ss_pred             HHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHhcCCCCCCchHHHHHHHHHHHHHHHHHHcCCceeccHHHHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHcCCCCcHHHHHHHhCCCHHHHHHHHHhcccCCCCccccCCCCCc
Q 013472          381 ISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNA  438 (442)
Q Consensus       381 i~kI~ka~~~L~~elgr~PS~eEIAe~LGIS~etVk~~l~~ar~~~SLD~~v~~~~d~  438 (442)
                      ++++.++.+.|..++|+.||.+|||+.|||++++|+.++..++.++|||.|++++++.
T Consensus       215 ~~~~~~~~~~l~~~lgr~pt~~EiA~~l~~~~~~v~~~~~~~~~~~SLd~~~~~~~~~  272 (367)
T PRK09210        215 INKLIRVQRQLLQELGREPTPEEIAEEMDMPPEKVREILKIAQEPVSLETPIGEEDDS  272 (367)
T ss_pred             HHHHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHHhcCCCCcCCCCCCCCcc
Confidence            9999999999999999999999999999999999999999988999999999876554

>PRK05658 RNA polymerase sigma factor RpoD; Validated

Probab=100.00  E-value=3.1e-32  Score=295.65  Aligned_cols=164  Identities=28%  Similarity=0.592  Sum_probs=152.0

Q ss_pred             HHHcCCCH---HHHHHHHHhch----HHHHHHHHHhHHHHHHHHHHhhCCCCCHHhHHHHHHHHHHHhHHhcCCCCCCCh
Q 013472          276 AQAAGVSE---RVLKQHLAFGW----YCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKF  348 (442)
Q Consensus       276 A~a~g~de---eeL~~~l~~G~----~Are~LI~~nlrLV~sIAkrY~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rF  348 (442)
                      ....+++.   ..+.++++.|+    .|+++||.+|++||++||++|.++|++++||||||+|||++|+++|||.+|++|
T Consensus       354 e~~~~Ls~eElk~l~~~i~~g~~~~~~a~~~Li~~nlrlV~~iA~ky~~~gl~~~DLiQeG~iGL~~Av~kfd~~~G~~F  433 (619)
T PRK05658        354 EEETGLTIEELKEINRQISKGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF  433 (619)
T ss_pred             HHHhCCCHHHHHHHHHHHhccchhhhHHHHHHHHHHHHHHHHHHHHHhhCCCCHHHHHHHHHHHHHHHHHhcCccCCCch
Confidence            33445554   44567778884    489999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHHHhhcCceecccccHHHHHHHHHHHHHHHHHcCCCCcHHHHHHHhCCCHHHHHHHHHhcccCCCC
Q 013472          349 STYVQYWIRKSISKMVARHARGIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSI  428 (442)
Q Consensus       349 STYa~~wIRnaI~r~LRkqsr~irlP~~v~e~i~kI~ka~~~L~~elgr~PS~eEIAe~LGIS~etVk~~l~~ar~~~SL  428 (442)
                      +|||+||||++|.++|+++.+++++|.|+.+.++++.++...+.+++|+.||.+|||+.||+|+++|+.++..+..++||
T Consensus       434 stYA~~wIr~aI~~~i~~~~r~irip~~~~~~~~k~~~~~~~~~~~~gr~pt~~eiA~~l~~~~~~v~~~~~~~~~~~Sl  513 (619)
T PRK05658        434 STYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEIGREPTPEELAERLGMPEDKVRKVLKIAKEPISL  513 (619)
T ss_pred             HHHhHHHHHHHHHHHHHHcCCceecCHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCCcC
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ccccCCCCCcc
Q 013472          429 DQKIGDCLNAK  439 (442)
Q Consensus       429 D~~v~~~~d~~  439 (442)
                      |.|++++++..
T Consensus       514 d~~i~~~~~~~  524 (619)
T PRK05658        514 ETPIGDDEDSH  524 (619)
T ss_pred             CCCCCCCCCCc
Confidence            99998777653

>PRK07122 RNA polymerase sigma factor SigF; Reviewed

Probab=99.97  E-value=8.9e-31  Score=257.20  Aligned_cols=142  Identities=24%  Similarity=0.363  Sum_probs=135.0

Q ss_pred             HHHHHHHHHhHHHHHHHHHHhhCCCCCHHhHHHHHHHHHHHhHHhcCCCCCCChHHHHHHHHHHHHHHHHHhhcCceecc
Q 013472          295 YCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIP  374 (442)
Q Consensus       295 ~Are~LI~~nlrLV~sIAkrY~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIRnaI~r~LRkqsr~irlP  374 (442)
                      .++++||..|++||+++|++|.++|++++||||||+|||++|+++|||++|++|+|||+|||+++|.++++++.+.+++|
T Consensus        40 ~~r~~Lv~~~l~LV~~iA~~y~~~g~~~~DLiQeG~iGLi~AierFDp~~G~~FsTYA~~~Irg~I~~~lr~~~~~ir~P  119 (264)
T PRK07122         40 RQRDRIVTRCLPLADHIARRFDGRGEPRDDLVQVARVGLVNAVNRFDVETGSDFVSFAVPTIMGEVRRHFRDNSWSVKVP  119 (264)
T ss_pred             HHHHHHHHHhHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHHHHHHcCCCCCCChHHHHHHHHHHHHHHHHHHcCCccccC
Confidence            38999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cccHHHHHHHHHHHHHHHHHcCCCCcHHHHHHHhCCCHHHHHHHHHh--cccCCCCccccCCCC
Q 013472          375 CKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASEC--LRIVGSIDQKIGDCL  436 (442)
Q Consensus       375 ~~v~e~i~kI~ka~~~L~~elgr~PS~eEIAe~LGIS~etVk~~l~~--ar~~~SLD~~v~~~~  436 (442)
                      .++.+..++++++...|.+++|+.||.+|||+.||+++++|..++..  ...++|||.++++++
T Consensus       120 r~~~~~~~~i~~~~~~l~~~lg~~pt~~eiA~~lg~~~~~v~~~~~~~~~~~~~SLd~~~~~~~  183 (264)
T PRK07122        120 RRLKELHLRLGRATAELSQRLGRAPTASELAAELGMDREEVVEGLVAGSAYNTLSIDSGGGSGD  183 (264)
T ss_pred             HHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHHhhcCCCCcccccccCCC
Confidence            99999999999999999999999999999999999999999998764  347899999987543

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

Probab=99.97  E-value=5.2e-30  Score=247.04  Aligned_cols=143  Identities=35%  Similarity=0.673  Sum_probs=137.4

Q ss_pred             HHHHHHHHhHHHHHHHHHHhhCCCCCHHhHHHHHHHHHHHhHHhcCCCCCCChHHHHHHHHHHHHHHHHHhhcCceeccc
Q 013472          296 CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIPC  375 (442)
Q Consensus       296 Are~LI~~nlrLV~sIAkrY~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIRnaI~r~LRkqsr~irlP~  375 (442)
                      |+++||..|+++|+++|++|.+++.+++||+|||+|||++|+++|||.+|++|+|||+||||++|.++++++.+.+++|.
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             ccHHHHHHHHHHHHHHHHHcCCCCcHHHHHHHhCCCHHHHHHHHHhcccCCCCccccCCCCCc
Q 013472          376 KLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNA  438 (442)
Q Consensus       376 ~v~e~i~kI~ka~~~L~~elgr~PS~eEIAe~LGIS~etVk~~l~~ar~~~SLD~~v~~~~d~  438 (442)
                      ++.+.++++.++...|..++|+.||.+|||+.||+++++|..++.....++|||.+++++++.
T Consensus        81 ~~~~~~~~~~~~~~~l~~~~g~~pt~~eia~~l~~~~~~v~~~~~~~~~~~SLd~~~~~~~~~  143 (238)
T TIGR02393        81 HMVETINKLIKAERQLTQELGREPTDEELAERMGMPAEKVREIKKIAQEPISLETPIGEEEDS  143 (238)
T ss_pred             HHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHHhccCCCcCCCCCCCCcc
Confidence            999999999999999999999999999999999999999999988888899999999766553

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=99.97  E-value=4.2e-29  Score=248.43  Aligned_cols=176  Identities=23%  Similarity=0.322  Sum_probs=149.2

Q ss_pred             hHHHHHHhcccCC-CCCChHHHHHHHHHhHHHHHHHHHHHHHHHHhCCCCChHHHHHHcCCCHHHHHHHHHhch-HHHHH
Q 013472          222 IFSAERALNSRGR-RLTIARNEAEMSKGVQVVANLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQHLAFGW-YCREE  299 (442)
Q Consensus       222 ~~~~~~~~~~~~~-~lLt~eeE~eL~~~iq~~~~le~~~~~L~~~~gr~pt~~ewA~a~g~deeeL~~~l~~G~-~Are~  299 (442)
                      ++.+..|++.+++ |+||+++|.+|++.++                                        ..|+ .|+++
T Consensus         5 ~~~~~~y~~~~~~~~~l~~~~e~~L~~~~~----------------------------------------~~gd~~A~~~   44 (289)
T PRK07500          5 ASADRSMIRSAMKAPYLEREEEHALAYRWK----------------------------------------DHRDEDALHR   44 (289)
T ss_pred             hhHHHHHHHHHhcCCCCCHHHHHHHHHHHH----------------------------------------HCCCHHHHHH
Confidence            4556678888876 9999999998888542                                        1233 49999


Q ss_pred             HHHHhHHHHHHHHHHhhCCCCCHHhHHHHHHHHHHHhHHhcCCCCCCChHHHHHHHHHHHHHHHHHhhcCceecccccHH
Q 013472          300 LIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIPCKLNR  379 (442)
Q Consensus       300 LI~~nlrLV~sIAkrY~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIRnaI~r~LRkqsr~irlP~~v~e  379 (442)
                      ||..|+++|+++|++|.+++.+++||+||||+|||+++++|||.+|.+|+|||+|||+++|.++|+++.+.+|+|.+..+
T Consensus        45 Lv~~~~~lV~~~a~~~~~~~~~~eDLvQeg~i~L~~a~~~fd~~~~~~f~tya~~~Ir~~I~~~lr~~~~~iR~p~~~~~  124 (289)
T PRK07500         45 IISAHMRLVISMAGKFRRFGLPMNDLIQEGYVGLLEAAARFEPDREVRFSTYATWWIRASIQDYILRNWSIVRGGTSSAQ  124 (289)
T ss_pred             HHHHhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHcCCCCCCChHHHHHHHHHHHHHHHHHHCCCceecCccHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999988655


Q ss_pred             --HHHHHHHHHHHHHH---HcCCCCcHHHHHHHhCCCHHHHHHHHH-hcccCCCCccccCCCCC
Q 013472          380 --EISKIQKARKALTN---SHGKYPEDIEIAKYTGLSLAEIRSASE-CLRIVGSIDQKIGDCLN  437 (442)
Q Consensus       380 --~i~kI~ka~~~L~~---elgr~PS~eEIAe~LGIS~etVk~~l~-~ar~~~SLD~~v~~~~d  437 (442)
                        ...+++++...+..   .+|+.||.+|||+.||+++++|..+.. ....++|||.+++++++
T Consensus       125 ~~~~~~~~~~~~~~~~~~~~l~~~pt~~eiA~~l~~~~~~v~~~~~~~~~~~~SLd~~~~~~~~  188 (289)
T PRK07500        125 KALFFNLRRLRARLAQADEELTKQEIHREIATALGVSLSDVEMMDARLSGPDASLNAPQSEEDE  188 (289)
T ss_pred             HHHHHHHHHHHHHHHhhhcccCCCCCHHHHHHHhCcCHHHHHHHHHHhcCCCccccCCCCCCCC
Confidence              33455555555544   679999999999999999999987753 34578999999976554

>PRK07408 RNA polymerase sigma factor SigF; Reviewed

Probab=99.96  E-value=5.9e-29  Score=242.90  Aligned_cols=147  Identities=26%  Similarity=0.388  Sum_probs=135.8

Q ss_pred             HhchH-HHHHHHHHhHHHHHHHHHHhhCC-CCCHHhHHHHHHHHHHHhHHhcCCCCCCChHHHHHHHHHHHHHHHHHhhc
Q 013472          291 AFGWY-CREELIKSTRPLVLFLARNYRGL-GIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHA  368 (442)
Q Consensus       291 ~~G~~-Are~LI~~nlrLV~sIAkrY~g~-g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIRnaI~r~LRkqs  368 (442)
                      ..|+. |+++||..|+++|+++|++|.+. +.+++||+|||+||||+|+++|||++|++|+|||+|||+|+|.++++++.
T Consensus        20 ~~gd~~a~~~Lv~~~~~lV~~ia~~~~~~~~~~~eDL~Qeg~igL~~a~~~fd~~~g~~F~tya~~~Ir~~i~~~lr~~~   99 (256)
T PRK07408         20 QNPSIALRNQLVELNLGLVRKEAHRWSNQCSEPYEDLVQVGSLGLIRAIERFDPSKGHAFSSFAIPYIRGEIQHYLRDKS   99 (256)
T ss_pred             HCCCHHHHHHHHHHhHHHHHHHHHHHhccCCCCHHHHHHHHHHHHHHHHHhcCCCCCCCcHHHHHHHHHHHHHHHHHHcC
Confidence            46654 99999999999999999999876 67799999999999999999999999999999999999999999999999


Q ss_pred             CceecccccHHHHHHHHHHHHHHHHHcCCCCcHHHHHHHhCCCHHHHHHHHH--hcccCCCCccccCCCCC
Q 013472          369 RGIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASE--CLRIVGSIDQKIGDCLN  437 (442)
Q Consensus       369 r~irlP~~v~e~i~kI~ka~~~L~~elgr~PS~eEIAe~LGIS~etVk~~l~--~ar~~~SLD~~v~~~~d  437 (442)
                      +.+++|.++.+.++++.++...|.+++|+.||.+|||+.||+++++|..++.  ....++|||.+++++++
T Consensus       100 ~~vr~pr~~~~~~~~~~~~~~~l~~~lgr~pt~~elA~~lgi~~~~v~~~~~~~~~~~~~SLd~~~~~~~~  170 (256)
T PRK07408        100 PTVRIPRRWQELQRQAKKVRQELRQELGRQPTDQEIAQALDISLEEWQEIKLALQNRTPLSLDAPVNQDED  170 (256)
T ss_pred             CeeeeCHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHhhccCCccccccCCCCCC
Confidence            9999999999999999999999999999999999999999999999999864  34568999999865433

>TIGR02850 spore_sigG RNA polymerase sigma-G factor

Probab=99.96  E-value=8e-28  Score=234.13  Aligned_cols=141  Identities=26%  Similarity=0.318  Sum_probs=133.8

Q ss_pred             HHHHHHHHHhHHHHHHHHHHhhCCCCCHHhHHHHHHHHHHHhHHhcCCCCCCChHHHHHHHHHHHHHHHHHhhcCceecc
Q 013472          295 YCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIP  374 (442)
Q Consensus       295 ~Are~LI~~nlrLV~sIAkrY~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIRnaI~r~LRkqsr~irlP  374 (442)
                      .|+++||..|.++|+++|++|.+++.+++||+||||+|||+++++||+.+|.+|+||+++||+|.|.++++++ ..+++|
T Consensus        34 ~a~~~L~~~~~~~v~~~a~~~~~~~~~aeDlvQe~~i~l~~a~~~fd~~~~~~f~tyl~~~irn~~~~~lr~~-~~ir~p  112 (254)
T TIGR02850        34 TAREKLINGNLRLVLSVIQRFNNRGEYVDDLFQVGCIGLMKSIDNFDLSQNVKFSTYAVPMIIGEIRRYLRDN-NPIRVS  112 (254)
T ss_pred             HHHHHHHHHhHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCChHHHHHHHHHHHHHHHHHhC-CCccCc
Confidence            3899999999999999999999999999999999999999999999999999999999999999999999987 478999


Q ss_pred             cccHHHHHHHHHHHHHHHHHcCCCCcHHHHHHHhCCCHHHHHHHHHhcccCCCCccccCCCC
Q 013472          375 CKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCL  436 (442)
Q Consensus       375 ~~v~e~i~kI~ka~~~L~~elgr~PS~eEIAe~LGIS~etVk~~l~~ar~~~SLD~~v~~~~  436 (442)
                      .++.+...++.++...+..++|+.||.+|||+.||+++++|..++.....++|||.++.+++
T Consensus       113 ~~~~~~~~~~~~~~~~l~~~l~~~pt~~elA~~l~~~~e~v~~~~~~~~~~~Sld~~~~~~~  174 (254)
T TIGR02850       113 RSLRDIAYKALQVRDKLISENSKEPTVSEIAKELKVPQEEVVFALDAIQDPVSLFEPIYNDG  174 (254)
T ss_pred             hHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHCcCHHHHHHHHHhcCCCCcccCCCCCCC
Confidence            99999999999999999999999999999999999999999999998888999999986443

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.

>PRK06596 RNA polymerase factor sigma-32; Reviewed

Probab=99.96  E-value=9.8e-28  Score=237.98  Aligned_cols=171  Identities=26%  Similarity=0.412  Sum_probs=141.3

Q ss_pred             HHHHHHhcccCC-CCCChHHHHHHHHHhHHHHHHHHHHHHHHHHhCCCCChHHHHHHcCCCHHHHHHHHHhch-HHHHHH
Q 013472          223 FSAERALNSRGR-RLTIARNEAEMSKGVQVVANLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQHLAFGW-YCREEL  300 (442)
Q Consensus       223 ~~~~~~~~~~~~-~lLt~eeE~eL~~~iq~~~~le~~~~~L~~~~gr~pt~~ewA~a~g~deeeL~~~l~~G~-~Are~L  300 (442)
                      +++..|++..++ |+|++++|.+|+...+                                        ..|+ .|++.|
T Consensus        14 ~~~~~y~~~~~~~~~l~~~~e~~l~~~~~----------------------------------------~~Gd~~a~~~L   53 (284)
T PRK06596         14 GNLDAYIQAVNKIPMLTAEEEYMLAKRLR----------------------------------------EHGDLEAAKQL   53 (284)
T ss_pred             cHHHHHHHHHhccCCCCHHHHHHHHHHHH----------------------------------------HcCCHHHHHHH
Confidence            455667776664 8999999988877421                                        1243 399999


Q ss_pred             HHHhHHHHHHHHHHhhCCCCCHHhHHHHHHHHHHHhHHhcCCCCCCChHHHHHHHHHHHHHHHHHhhcCceecccccHH-
Q 013472          301 IKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIPCKLNR-  379 (442)
Q Consensus       301 I~~nlrLV~sIAkrY~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIRnaI~r~LRkqsr~irlP~~v~e-  379 (442)
                      |..|+++|+++|++|.+.+.+++||+|||++||++|+++|||.+|++|+|||+|||+++|.++++++.+.+++|.+... 
T Consensus        54 v~~~~~lV~~ia~~~~~~~~~~eDLvQeg~igL~~a~~~fd~~~~~~FstYA~~~Ir~~i~~~l~~~~~~vr~p~~~~~~  133 (284)
T PRK06596         54 VLSHLRFVVHIARGYRGYGLPQADLIQEGNIGLMKAVKRFDPEVGVRLVSFAVHWIKAEIHEYILRNWRIVKVATTKAQR  133 (284)
T ss_pred             HHHhHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHHHhCcccCCCHHHHHHHHHHHHHHHHHHHcCCeeeccchHHHH
Confidence            9999999999999999999999999999999999999999999999999999999999999999998778899987542 


Q ss_pred             -HHHHHHHHHHHHHHHcCCCCcHHHHHHHhCCCHHHHHHHHHhc-ccCCCCccccCCC
Q 013472          380 -EISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECL-RIVGSIDQKIGDC  435 (442)
Q Consensus       380 -~i~kI~ka~~~L~~elgr~PS~eEIAe~LGIS~etVk~~l~~a-r~~~SLD~~v~~~  435 (442)
                       ...++.+...++.  .++.||.+|||+.|||++++|..++... ..++|||.+++++
T Consensus       134 ~~~~~~~~~~~~l~--~~~~~t~~eiA~~l~~~~~~v~~~~~~~~~~~~SLd~~~~~~  189 (284)
T PRK06596        134 KLFFNLRKAKKRLG--WLNPEEVEMVAEELGVSEEEVREMESRLSGQDASLDAPIDDD  189 (284)
T ss_pred             HHHHHHHHHHHHhc--cCCCCCHHHHHHHhCcCHHHHHHHHHHhcCCCcCcCCCCCCC
Confidence             2334444444442  3489999999999999999999987543 3789999998755

>TIGR02392 rpoH_proteo alternative sigma factor RpoH

Probab=99.95  E-value=3.9e-27  Score=231.56  Aligned_cols=141  Identities=30%  Similarity=0.480  Sum_probs=119.7

Q ss_pred             HHHHHHHHHhHHHHHHHHHHhhCCCCCHHhHHHHHHHHHHHhHHhcCCCCCCChHHHHHHHHHHHHHHHHHhhcCceecc
Q 013472          295 YCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIP  374 (442)
Q Consensus       295 ~Are~LI~~nlrLV~sIAkrY~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIRnaI~r~LRkqsr~irlP  374 (442)
                      .|++.||..|+++|+++|++|.+++.+++||+|||++||++|+++|||++|++|+|||+|||+++|.++++++.+.+++|
T Consensus        35 ~a~~~Lv~~~~~lV~~~a~~~~~~~~~~eDLvQeg~igl~~a~~~fd~~~~~~FsTYA~~~Ir~~i~~~l~~~~~~ir~p  114 (270)
T TIGR02392        35 DAAKKLVLSHLRFVVKIARGYRGYGLPQADLIQEGNIGLMKAVKRFDPERGVRLVSFAVHWIKAEIHEYILRNWRLVKVA  114 (270)
T ss_pred             HHHHHHHHHhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHhCcccCCChHHhhHHHHHHHHHHHHHHcCCceecC
Confidence            49999999999999999999999999999999999999999999999999999999999999999999999887788999


Q ss_pred             cccH--HHHHHHHHHHHHHHHHcCCCC-cHHHHHHHhCCCHHHHHHHHHhcc-cCCCCccccCCCCC
Q 013472          375 CKLN--REISKIQKARKALTNSHGKYP-EDIEIAKYTGLSLAEIRSASECLR-IVGSIDQKIGDCLN  437 (442)
Q Consensus       375 ~~v~--e~i~kI~ka~~~L~~elgr~P-S~eEIAe~LGIS~etVk~~l~~ar-~~~SLD~~v~~~~d  437 (442)
                      .+..  +...++.++...+.  ..+.| +.+|||+.||+++++|..++.... .++|||.+++++++
T Consensus       115 ~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~eiA~~l~~~~~~v~~~~~~~~~~~~Sld~~~~~~~~  179 (270)
T TIGR02392       115 TTKAQRKLFFNLRKMKKRLQ--GWLNPEEVEAIAEELGVSEREVREMESRLSGQDMSLNASIDDDED  179 (270)
T ss_pred             chHHHHHHHHHHHHHHHHHh--cCCCCCCHHHHHHHhCCCHHHHHHHHHHccCCCccCCCCCCCCCC
Confidence            7643  33445555544442  12455 699999999999999999865443 47999999976543

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.

>PRK05657 RNA polymerase sigma factor RpoS; Validated

Probab=99.95  E-value=5.5e-27  Score=237.00  Aligned_cols=176  Identities=26%  Similarity=0.493  Sum_probs=159.9

Q ss_pred             hhHHHHHHhcccCC-CCCChHHHHHHHHHhHHHHHHHHHHHHHHHHhCCCCChHHHHHHcCCCHHHHHHHHHhchH-HHH
Q 013472          221 TIFSAERALNSRGR-RLTIARNEAEMSKGVQVVANLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQHLAFGWY-CRE  298 (442)
Q Consensus       221 ~~~~~~~~~~~~~~-~lLt~eeE~eL~~~iq~~~~le~~~~~L~~~~gr~pt~~ewA~a~g~deeeL~~~l~~G~~-Are  298 (442)
                      ..+.+..|++.++. |+||+++|.+|...+                                         +.|+. |++
T Consensus        51 ~~~~~~~y~~~~~~~~~l~~~ee~~li~~~-----------------------------------------~~Gd~~A~~   89 (325)
T PRK05657         51 VLDATQLYLNEIGYSPLLTAEEEVYFARRA-----------------------------------------LRGDFAARQ   89 (325)
T ss_pred             cccHHHHHHHHHhcCCCCCHHHHHHHHHHH-----------------------------------------HcCCHHHHH
Confidence            45667889988886 999999998777643                                         23433 999


Q ss_pred             HHHHHhHHHHHHHHHHhhCCCCCHHhHHHHHHHHHHHhHHhcCCCCCCChHHHHHHHHHHHHHHHHHhhcCceecccccH
Q 013472          299 ELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIPCKLN  378 (442)
Q Consensus       299 ~LI~~nlrLV~sIAkrY~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIRnaI~r~LRkqsr~irlP~~v~  378 (442)
                      .||..|.++|+++|++|.+++.+++||+||||||+|+++++||+.+|++|+||++||||++|.++++++.+.+++|.++.
T Consensus        90 ~Li~~y~~~V~~~a~~~~~~~~~aeDLvQE~fi~l~~ai~~fd~~rg~~Fstyatw~iR~ai~~~i~~~~r~ir~p~~~~  169 (325)
T PRK05657         90 RMIESNLRLVVKIAKRYLNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPVHVV  169 (325)
T ss_pred             HHHHHhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHhCCccCCCHHHHHHHHHHHHHHHHHHHcCCccccCHHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             HHHHHHHHHHHHHHHHcCCCCcHHHHHHHhCCCHHHHHHHHHhcccCCCCccccCCCCC
Q 013472          379 REISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLN  437 (442)
Q Consensus       379 e~i~kI~ka~~~L~~elgr~PS~eEIAe~LGIS~etVk~~l~~ar~~~SLD~~v~~~~d  437 (442)
                      ..++.+.++...|...+|+.|+.+|||+.||+++++|..++.....+.|||.+++++..
T Consensus       170 ~~l~~~~R~~~~l~~~l~r~~t~~eiA~~l~~~~~~v~~~l~~~~~~~sld~~~~~~~~  228 (325)
T PRK05657        170 KELNVYLRAARELEHKLDHEPSAEEIAELLDKPVDDVSRMLALNERITSLDTPLGGDPE  228 (325)
T ss_pred             HHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHhccCCcccCCCCCCCCC
Confidence            88888889999999999999999999999999999999999877788999999876554

>PRK08215 sporulation sigma factor SigG; Reviewed

Probab=99.95  E-value=1.6e-26  Score=225.36  Aligned_cols=142  Identities=27%  Similarity=0.322  Sum_probs=134.1

Q ss_pred             HHHHHHHHHhHHHHHHHHHHhhCCCCCHHhHHHHHHHHHHHhHHhcCCCCCCChHHHHHHHHHHHHHHHHHhhcCceecc
Q 013472          295 YCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIP  374 (442)
Q Consensus       295 ~Are~LI~~nlrLV~sIAkrY~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIRnaI~r~LRkqsr~irlP  374 (442)
                      .|+++||..|.++|+.+|++|.+++.+++||+|||++|||+++++||+.+|.+|+||+++||+|+|.++++++ +.+++|
T Consensus        37 ~a~~~l~~~~~~~v~~~a~~~~~~~~~aeDlvQe~~i~l~~a~~~fd~~~~~~f~t~l~~~ir~~i~~~lr~~-~~vrip  115 (258)
T PRK08215         37 EAREKLINGNLRLVLSVIQRFNNRGENVDDLFQVGCIGLMKAIDNFDLSQNVKFSTYAVPMIIGEIRRYLRDN-NPIRVS  115 (258)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCCcHHHHHHHHHHHHHHHHHhC-CceEec
Confidence            3899999999999999999999999999999999999999999999999999999999999999999999988 488999


Q ss_pred             cccHHHHHHHHHHHHHHHHHcCCCCcHHHHHHHhCCCHHHHHHHHHhcccCCCCccccCCCCC
Q 013472          375 CKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLN  437 (442)
Q Consensus       375 ~~v~e~i~kI~ka~~~L~~elgr~PS~eEIAe~LGIS~etVk~~l~~ar~~~SLD~~v~~~~d  437 (442)
                      .++.....++.++...+..++|+.|+.+|||+.|||++++|...+.....+.|||.++.++++
T Consensus       116 ~~~~~~~~~~~~~~~~l~~~~~r~p~~~eia~~l~v~~~~v~~~~~~~~~~~sl~~~~~~~~~  178 (258)
T PRK08215        116 RSLRDIAYKALQVREKLINENSKEPTVEEIAKELEVPREEVVFALDAIQDPVSLFEPIYHDGG  178 (258)
T ss_pred             HHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHCcCHHHHHHHHHhcCCCccccCCCCCCCC
Confidence            999999999999999999999999999999999999999999998888888999999865443

>TIGR02885 spore_sigF RNA polymerase sigma-F factor

Probab=99.94  E-value=4.5e-26  Score=217.91  Aligned_cols=149  Identities=26%  Similarity=0.328  Sum_probs=139.1

Q ss_pred             HHHHhchH-HHHHHHHHhHHHHHHHHHHhhCCCCCHHhHHHHHHHHHHHhHHhcCCCCCCChHHHHHHHHHHHHHHHHHh
Q 013472          288 QHLAFGWY-CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVAR  366 (442)
Q Consensus       288 ~~l~~G~~-Are~LI~~nlrLV~sIAkrY~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIRnaI~r~LRk  366 (442)
                      .+++.|+. |+++||..|.++|+++|++|.+++.+++||+|||++|||+++++||+.+|.+|+||+++||+|.|.+++|+
T Consensus         3 ~~~~~gd~~a~~~l~~~y~~~v~~~a~~~~~~~~~aeDl~Qe~~i~l~~a~~~f~~~~~~~f~tyl~~~i~~~i~~~lr~   82 (231)
T TIGR02885         3 KLAQNGDKEARDKLIECNLRLVWSIVKRFLNRGYEPEDLFQIGCIGLVKAIDKFDLSYDVKFSTYAVPMIMGEIKRFLRD   82 (231)
T ss_pred             HHHHcCCHHHHHHHHHHhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHhcCCCCCCCcHHHHHHHHHHHHHHHHHh
Confidence            44566755 99999999999999999999999999999999999999999999999989999999999999999999999


Q ss_pred             hcCceecccccHHHHHHHHHHHHHHHHHcCCCCcHHHHHHHhCCCHHHHHHHHHhcccCCCCccccCCCCC
Q 013472          367 HARGIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLN  437 (442)
Q Consensus       367 qsr~irlP~~v~e~i~kI~ka~~~L~~elgr~PS~eEIAe~LGIS~etVk~~l~~ar~~~SLD~~v~~~~d  437 (442)
                      +. .+++|.++.+...++.++...|..++|+.||.+|||+.||+++++|..++..+..+.|||.+++++++
T Consensus        83 ~~-~i~~p~~~~~~~~~~~~~~~~l~~~~~r~pt~~ela~~l~~~~~~v~~~~~~~~~~~sl~~~~~~~~~  152 (231)
T TIGR02885        83 DG-IIKVSRSLKELARKIRYMKEELSKELGREPTINELAEALGVSPEEIVMALESARSPQSLYDTVHQDDG  152 (231)
T ss_pred             CC-CeECCHHHHHHHHHHHHHHHHHHHHHCcCCCHHHHHHHHCcCHHHHHHHHHHccCCcCcccCCCCCCC
Confidence            85 78999999999999999999999999999999999999999999999999888889999999876543

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.

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

Probab=99.94  E-value=5.3e-26  Score=221.89  Aligned_cols=152  Identities=30%  Similarity=0.425  Sum_probs=140.2

Q ss_pred             HHHHHHHHhchH-HHHHHHHHhHHHHHHHHHHhhCCCC-CHHhHHHHHHHHHHHhHHhcCCCCCCChHHHHHHHHHHHHH
Q 013472          284 RVLKQHLAFGWY-CREELIKSTRPLVLFLARNYRGLGI-PFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSIS  361 (442)
Q Consensus       284 eeL~~~l~~G~~-Are~LI~~nlrLV~sIAkrY~g~g~-d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIRnaI~  361 (442)
                      +.+....+.|+. ++ .||+.|+|||.++|++|.+++. +.|||+|.|+|||++|+++|||++|.+|+|||...|+++|+
T Consensus        12 ~~~~~~~~~g~~~~~-~Li~~ylpLV~~ia~k~~~r~~~~~dDLiqiG~iGLi~Aieryd~~kg~kF~tyA~~~I~Gei~   90 (247)
T COG1191          12 EKLLEYYAEGDEEAR-RLIERYLPLVKSIARKFENRGPSEYDDLIQIGMIGLIKAIERYDPSKGTKFSTYAVRRIRGEIL   90 (247)
T ss_pred             HHHHHHHHhcCHHHH-HHHHHHHHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHHHHHcCcccCcchHHHHHHHHHHHHH
Confidence            456677777866 88 9999999999999999998877 99999999999999999999999999999999999999999


Q ss_pred             HHHHhhcCceecccccHHHHHHHHHHHHHHHHHcCCCCcHHHHHHHhCCCHHHHHHHHHhcc--cCCCCccccCCCCC
Q 013472          362 KMVARHARGIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLR--IVGSIDQKIGDCLN  437 (442)
Q Consensus       362 r~LRkqsr~irlP~~v~e~i~kI~ka~~~L~~elgr~PS~eEIAe~LGIS~etVk~~l~~ar--~~~SLD~~v~~~~d  437 (442)
                      +++|++. .+++|+.+++..+++..+...|..++|++||++|||+.|||+.+.|..++....  ..+|+|..+..++|
T Consensus        91 d~LR~~~-~v~vpR~~~~~~~~i~~~~~~l~~el~r~pt~~EIA~~L~i~~ee~~~~~~~~~~~~~~sld~~~~~~~d  167 (247)
T COG1191          91 DYLRKND-SVKVPRSLRELGRRIEEAIDELEQELGREPTDEEIAEELGIDKEEYIEALLAINGSQLLSLDEDVLKDDD  167 (247)
T ss_pred             HHHHhCC-CccCcHHHHHHHHHHHHHHHHHHHHhCCCCcHHHHHHHhCCCHHHHHHHHHHhccccccchhhhhccccc
Confidence            9999997 899999999999999999999999999999999999999999999999987664  77899887764444

>PRK05911 RNA polymerase sigma factor sigma-28; Reviewed

Probab=99.94  E-value=1e-25  Score=220.41  Aligned_cols=140  Identities=24%  Similarity=0.363  Sum_probs=127.7

Q ss_pred             hch-HHHHHHHHHhHHHHHHHHHHhhC---CCCCHHhHHHHHHHHHHHhHHhcCCCCCCChHHHHHHHHHHHHHHHHHhh
Q 013472          292 FGW-YCREELIKSTRPLVLFLARNYRG---LGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARH  367 (442)
Q Consensus       292 ~G~-~Are~LI~~nlrLV~sIAkrY~g---~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIRnaI~r~LRkq  367 (442)
                      .|+ .|+++||..|+++|+.+|++|.+   .+++++||+|||+||||+|+++|||++|++|+||++|||+++|.+++|++
T Consensus        19 ~~~~~ar~~Li~~~~~lV~~ia~~~~~~~~~~~~~eDL~QeG~igL~~ai~~fd~~~g~~F~tya~~~Ir~~i~~~lr~~   98 (257)
T PRK05911         19 TQEIEYRDVLIEFYLPLVKNVAHRLISGMPSHVKTEDLYASGVEGLVRAVERFDPEKSRRFEGYALFLIKAAIIDDLRKQ   98 (257)
T ss_pred             cCCHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHHHHHhcCCccCCCHHHHHHHHHHHHHHHHHHhc
Confidence            454 49999999999999999999862   35689999999999999999999999999999999999999999999987


Q ss_pred             cCceecccccHHHHHHHHHHHHHHHHHcCCCCcHHHHHHHhCCCHHHHHHHHHhcc--cCCCCccccCC
Q 013472          368 ARGIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLR--IVGSIDQKIGD  434 (442)
Q Consensus       368 sr~irlP~~v~e~i~kI~ka~~~L~~elgr~PS~eEIAe~LGIS~etVk~~l~~ar--~~~SLD~~v~~  434 (442)
                      .   ++|.++.+.++++.++...|.+.+|+.||.+|||+.|||++++|..++..++  .++|||.++.+
T Consensus        99 ~---~~pr~~~~~~~~l~~~~~~l~~~~gr~pt~~eiA~~l~i~~~~v~~~~~~~~~~~~~Sld~~~~~  164 (257)
T PRK05911         99 D---WVPRSVHQKANKLADAMDSLRQSLGKEPTDGELCEYLNISQQELSGWFSSARPALILSLNEEFPC  164 (257)
T ss_pred             C---CCCHHHHHHHHHHHHHHHHHHHHHCcCCCHHHHHHHhCcCHHHHHHHHHHhhccceeeccccCCC
Confidence            4   5899999999999999999999999999999999999999999999987665  46899988643

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

Probab=99.93  E-value=7.8e-25  Score=208.60  Aligned_cols=140  Identities=34%  Similarity=0.487  Sum_probs=133.7

Q ss_pred             HHHHHHHHHhHHHHHHHHHHhhCCCCCHHhHHHHHHHHHHHhHHhcCCCCCCChHHHHHHHHHHHHHHHHHhhcCceecc
Q 013472          295 YCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIP  374 (442)
Q Consensus       295 ~Are~LI~~nlrLV~sIAkrY~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIRnaI~r~LRkqsr~irlP  374 (442)
                      .|+++||..|.++|+++|++|.+++.+++||+|||++||++|+++||+.+|.+|+||+++||+|.|.++++++.+.+++|
T Consensus         3 ~a~~~lv~~y~~~v~~~a~~~~~~~~~~eDl~Qe~~i~l~~a~~~f~~~~~~~F~ty~~~~i~~~~~~~~r~~~~~~ri~   82 (227)
T TIGR02980         3 EAREKLVELNLPLVRSIARRFRNRGEPHEDLVQVGTIGLVKAIDRFDPSYGVKFSTFAVPTIMGEIKRFFRDDTWAVRVP   82 (227)
T ss_pred             HHHHHHHHHhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHhcCcccCCCcHHHHHHHHHHHHHHHHHHcCCceecC
Confidence            48999999999999999999999999999999999999999999999999999999999999999999999998899999


Q ss_pred             cccHHHHHHHHHHHHHHHHHcCCCCcHHHHHHHhCCCHHHHHHHHHhccc--CCCCccccCC
Q 013472          375 CKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRI--VGSIDQKIGD  434 (442)
Q Consensus       375 ~~v~e~i~kI~ka~~~L~~elgr~PS~eEIAe~LGIS~etVk~~l~~ar~--~~SLD~~v~~  434 (442)
                      .++.+...+++++...+...+|+.|+.+|+|+.||+++++|..++.....  +.|||.++++
T Consensus        83 ~~~~~~~~~~~~~~~~l~~~~~~~p~~~ela~~l~~~~~~v~~~~~~~~~~~~~sld~~~~~  144 (227)
T TIGR02980        83 RRLKELGLKINKATEELTQRLGRSPTIAEIAEELGVSEEEVVEALEAGNSYSALSLDAPIED  144 (227)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHhCCCHHHHHHHHHhhccCCCeeccccCCC
Confidence            99999999999999999999999999999999999999999998876664  8999999873

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

>TIGR02941 Sigma_B RNA polymerase sigma-B factor

Probab=99.92  E-value=2.8e-24  Score=208.84  Aligned_cols=155  Identities=25%  Similarity=0.271  Sum_probs=142.0

Q ss_pred             HHHHHHHHHh-chH-HHHHHHHHhHHHHHHHHHHhhCCCCCHHhHHHHHHHHHHHhHHhcCCCCCCChHHHHHHHHHHHH
Q 013472          283 ERVLKQHLAF-GWY-CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSI  360 (442)
Q Consensus       283 eeeL~~~l~~-G~~-Are~LI~~nlrLV~sIAkrY~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIRnaI  360 (442)
                      +.+|+.+++. |+. |+++|+..|.++|+.+|++|.+++.+++||+||||+|||+++++||++.|.+|.||+++||+|.|
T Consensus        15 ~~~li~~~~~~gd~~a~~~l~~~y~~~v~~~a~~~~~~~~~aeDlvQe~~i~l~~a~~~~~~~~~~~f~tyl~~~i~n~~   94 (255)
T TIGR02941        15 VIQWIAEFQQNQNGEAQEKLVDHYQNLVYSIAYKYSKGGPMHEDLVQVGMLGLLGAIRRYDYSIGNAFEPFAIPTIIGEI   94 (255)
T ss_pred             HHHHHHHHHHCCCHHHHHHHHHHhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHcCCcCCCCcHhHHHHHHHHHH
Confidence            4567777777 554 99999999999999999999999999999999999999999999999989999999999999999


Q ss_pred             HHHHHhhcCceecccccHHHHHHHHHHHHHHHHHcCCCCcHHHHHHHhCCCHHHHHHHHHhc--ccCCCCccccCCCCC
Q 013472          361 SKMVARHARGIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECL--RIVGSIDQKIGDCLN  437 (442)
Q Consensus       361 ~r~LRkqsr~irlP~~v~e~i~kI~ka~~~L~~elgr~PS~eEIAe~LGIS~etVk~~l~~a--r~~~SLD~~v~~~~d  437 (442)
                      .++++++...+++|.++.+..+++..+...+...+|+.|+.+|||+.+|++.+.+..++...  ..+.|||.+++++.+
T Consensus        95 ~~~lr~~~~~iri~~~~~~~~~~~~~~~~~l~~~~~r~p~~~eia~~l~i~~~~~~~~~~~~~~~~~~sl~~~~~~~~~  173 (255)
T TIGR02941        95 KRYLRDKTWSVHVPRRIKELGPKIKKAIDELTDHLQRSPKIIEIADHLGLSEEEVLEIMEMGQSYRALSVDDVIEADSD  173 (255)
T ss_pred             HHHHHHcCCCcCCCHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHHHhccCCccccccccCCCC
Confidence            99999998889999999999999999999999999999999999999999999999887654  367899998865443

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

>PRK06288 RNA polymerase sigma factor WhiG; Reviewed

Probab=99.92  E-value=6.9e-24  Score=208.05  Aligned_cols=136  Identities=32%  Similarity=0.408  Sum_probs=124.6

Q ss_pred             HHHHHHHHHhHHHHHHHHHHhh-C--CCCCHHhHHHHHHHHHHHhHHhcCCCCCCChHHHHHHHHHHHHHHHHHhhcCce
Q 013472          295 YCREELIKSTRPLVLFLARNYR-G--LGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGI  371 (442)
Q Consensus       295 ~Are~LI~~nlrLV~sIAkrY~-g--~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIRnaI~r~LRkqsr~i  371 (442)
                      .|++.++..|.++|+.+|++|. +  .+.+++||+||||+|||+++++||+.+|++|+||++|||+|.|.+++|+.   +
T Consensus        31 ~a~~~l~~~y~~lv~~~a~~~~~~~~~~~~~eDl~Qeg~l~L~~a~~~fd~~~~~~f~ty~~~~ir~~i~d~~R~~---~  107 (268)
T PRK06288         31 KIREYLILKYSPLVKYVAGRIAVGMPQNVEFDDLVSYGVFGLIDAIEKFDPEREIKFKTYAVTRIRGAIFDELRSI---D  107 (268)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHHHHHHcCcccCCCHHHHHHHHHHHHHHHHHHhc---C
Confidence            3899999999999999999986 3  46789999999999999999999999889999999999999999999965   5


Q ss_pred             ecccccHHHHHHHHHHHHHHHHHcCCCCcHHHHHHHhCCCHHHHHHHHHhc--ccCCCCccccC
Q 013472          372 KIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECL--RIVGSIDQKIG  433 (442)
Q Consensus       372 rlP~~v~e~i~kI~ka~~~L~~elgr~PS~eEIAe~LGIS~etVk~~l~~a--r~~~SLD~~v~  433 (442)
                      ++|.++.....++.++...|...+++.||.+|||+.+|++++.|..++...  ..++|||.++.
T Consensus       108 ~~p~~~~~~~~~i~~~~~~l~~~~~~~pt~~eia~~lg~~~~~v~~~~~~~~~~~~~sld~~~~  171 (268)
T PRK06288        108 WIPRSVRQKARQIERAIAMLEARLGRTPSDEEIADELGISLEEYNSLLSKLSGTSVVSLNDLWF  171 (268)
T ss_pred             ccCHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHcCCCHHHHHHHHHHHhcccccchhhhhc
Confidence            689999999999999999999999999999999999999999999998654  36789998864

>TIGR02394 rpoS_proteo RNA polymerase sigma factor RpoS

Probab=99.92  E-value=1.3e-23  Score=208.01  Aligned_cols=174  Identities=28%  Similarity=0.500  Sum_probs=155.7

Q ss_pred             hHHHHHHhcccCC-CCCChHHHHHHHHHhHHHHHHHHHHHHHHHHhCCCCChHHHHHHcCCCHHHHHHHHHhchH-HHHH
Q 013472          222 IFSAERALNSRGR-RLTIARNEAEMSKGVQVVANLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQHLAFGWY-CREE  299 (442)
Q Consensus       222 ~~~~~~~~~~~~~-~lLt~eeE~eL~~~iq~~~~le~~~~~L~~~~gr~pt~~ewA~a~g~deeeL~~~l~~G~~-Are~  299 (442)
                      .++++.|+..+.. |.|+.++|.+|...+                                         +.|+. |++.
T Consensus        12 ~~~~~~~~~~~~~~~~~~~~~~~~li~~~-----------------------------------------~~gd~~a~~~   50 (285)
T TIGR02394        12 ADVTQLYLREIGFKPLLTAEEEIAYARRA-----------------------------------------LAGDFEARKV   50 (285)
T ss_pred             chHHHHHHHHHhccCCCCHHHHHHHHHHH-----------------------------------------HcCCHHHHHH
Confidence            4677778877775 788888877666533                                         34433 9999


Q ss_pred             HHHHhHHHHHHHHHHhhCCCCCHHhHHHHHHHHHHHhHHhcCCCCCCChHHHHHHHHHHHHHHHHHhhcCceecccccHH
Q 013472          300 LIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIPCKLNR  379 (442)
Q Consensus       300 LI~~nlrLV~sIAkrY~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIRnaI~r~LRkqsr~irlP~~v~e  379 (442)
                      ||..|.++|+++|++|.+++.+++||+|||+||||+|+++||+.+|++|+||+.|||+.++.++++++.+.+++|.++.+
T Consensus        51 L~~~y~~~v~~~a~~~~~~~~~aeDLvQe~~i~l~~a~~~fd~~~g~~f~tya~w~i~~ain~~i~~~~~~~~~p~~~~~  130 (285)
T TIGR02394        51 MIESNLRLVVSIAKHYVNRGLPLLDLIEEGNLGLMHAVEKFDPERGFRFSTYATWWIRQTIERAIMNQARTIRLPVHVIK  130 (285)
T ss_pred             HHHHhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHhCCCCCCCcHhhhHHHHHHHHHHHHHHcCCceeCcHHHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHcCCCCcHHHHHHHhCCCHHHHHHHHHhcccCCCCccccCCCC
Q 013472          380 EISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCL  436 (442)
Q Consensus       380 ~i~kI~ka~~~L~~elgr~PS~eEIAe~LGIS~etVk~~l~~ar~~~SLD~~v~~~~  436 (442)
                      ..+.+.+..+.+...+|+.|+.+|+|+.+|+++..|..++..+...+|||.++.++.
T Consensus       131 ~~~~~~r~~~~l~~~~~r~~~~~e~a~~l~~~~~~~~~~~~~~~~~~sld~~~~~~~  187 (285)
T TIGR02394       131 ELNVYLRAARQLEKKLGREPSVEEIAELLDKPVEDVSRVLALNERITSLDAPLDDDS  187 (285)
T ss_pred             HHHHHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHhhcCCCcCCCCCCCCC
Confidence            999888888888888899999999999999999999999988888899998876544

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).

>PRK07670 RNA polymerase sigma factor SigD; Validated

Probab=99.92  E-value=8.2e-24  Score=205.50  Aligned_cols=153  Identities=24%  Similarity=0.309  Sum_probs=136.8

Q ss_pred             CHHHHHHHHHh-chH-HHHHHHHHhHHHHHHHHHHhhC---CCCCHHhHHHHHHHHHHHhHHhcCCCCCCChHHHHHHHH
Q 013472          282 SERVLKQHLAF-GWY-CREELIKSTRPLVLFLARNYRG---LGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWI  356 (442)
Q Consensus       282 deeeL~~~l~~-G~~-Are~LI~~nlrLV~sIAkrY~g---~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wI  356 (442)
                      ++.+|+++.+. |+. |++.||..|.++|+.+|++|.+   ++.+++||+||||+|||+++++||+.+|.+|+||+++||
T Consensus         7 ~e~~l~~~~~~~~d~~a~~~L~~~y~~~v~~~~~~~~~~~~~~~~~eDl~Qe~~i~l~~~~~~f~~~~~~~f~tyl~~~i   86 (251)
T PRK07670          7 EEQKLWDRWKEERDPDAADELIRRYMPLVHYHVQRISVGLPKSVSKDDLKSLGMLGLYDALEKFDPSRDLKFDTYASFRI   86 (251)
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHHHHHHHHHcCcccCCCHHHHHHHHH
Confidence            45667777444 555 9999999999999999999976   689999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHhhcCceecccccHHHHHHHHHHHHHHHHHcCCCCcHHHHHHHhCCCHHHHHHHHH--hcccCCCCccccCC
Q 013472          357 RKSISKMVARHARGIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASE--CLRIVGSIDQKIGD  434 (442)
Q Consensus       357 RnaI~r~LRkqsr~irlP~~v~e~i~kI~ka~~~L~~elgr~PS~eEIAe~LGIS~etVk~~l~--~ar~~~SLD~~v~~  434 (442)
                      +|.|++++|++.   ++|..+.+.+.+++++...+.+.+|+.|+.+|||+.||+++++|..++.  ....++|||.++.+
T Consensus        87 rn~~~d~lR~~~---~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~eia~~l~~~~~~v~~~~~~~~~~~~~sld~~~~~  163 (251)
T PRK07670         87 RGAIIDGLRKED---WLPRSMREKTKKVEAAIEKLEQRYMRNVTPKEVAAELGMTEEEVEATMNEGFFANLLSIDEKTHD  163 (251)
T ss_pred             HHHHHHHHHhcC---CCCHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHhCcCHHHHHHHHHHHhccCccccCccccC
Confidence            999999999874   6899999999999999999999999999999999999999999999976  34578999999865


Q ss_pred             CCC
Q 013472          435 CLN  437 (442)
Q Consensus       435 ~~d  437 (442)
                      +++
T Consensus       164 ~~~  166 (251)
T PRK07670        164 QDD  166 (251)
T ss_pred             CCC
Confidence            544

>PRK12427 flagellar biosynthesis sigma factor; Provisional

Probab=99.91  E-value=2.3e-23  Score=201.03  Aligned_cols=139  Identities=20%  Similarity=0.213  Sum_probs=124.2

Q ss_pred             HHHHHHHHhHHHHHHHHHHhhC---CCCCHHhHHHHHHHHHHHhHHhcCCCCCCChHHHHHHHHHHHHHHHHHhhcCcee
Q 013472          296 CREELIKSTRPLVLFLARNYRG---LGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIK  372 (442)
Q Consensus       296 Are~LI~~nlrLV~sIAkrY~g---~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIRnaI~r~LRkqsr~ir  372 (442)
                      ....|+..|+++|+++|++|..   .+.+++||+|||+||||+|+++||+.+| +|+||++|||+|+|.+++++.   .+
T Consensus        16 ~~~~lv~~y~~lV~~la~~~~~~~~~~~~~eDLvQeg~igL~~a~~~fd~~~~-~F~tYa~~~Ir~~il~~lr~~---~~   91 (231)
T PRK12427         16 EEGKYLNAYLPLVKKVVRQLAFQADSVIDREDMEQIALMGLLEALRRYGHPDE-QFAAYAVHRIRGAILDELREL---DW   91 (231)
T ss_pred             hHHHHHHHHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHHHHHHHHhcCCCCC-ChHHHHHHHHHHHHHHHHHhc---CC
Confidence            3558899999999999999875   4689999999999999999999998666 899999999999999999975   35


Q ss_pred             cccccHHHHHHHHHHHHHHHHHcCCCCcHHHHHHHhCCCHHHHHHHHHh--cccCCCCccccCCCCCc
Q 013472          373 IPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASEC--LRIVGSIDQKIGDCLNA  438 (442)
Q Consensus       373 lP~~v~e~i~kI~ka~~~L~~elgr~PS~eEIAe~LGIS~etVk~~l~~--ar~~~SLD~~v~~~~d~  438 (442)
                      .|..+....++++++...|.+++|+.||.+|||+.||+++++|..++..  +..++|||.+++++++.
T Consensus        92 ~~r~vr~~~~~i~~~~~~l~~~~g~~pt~~eiA~~lg~~~~~v~~~~~~~~~~~~~SLd~~~~~~~~~  159 (231)
T PRK12427         92 RPRRLRQKTHKTNDAIREIAKRLGHEPNFEEISAELNLTAEEYQEYLLLENAGTLESLDELLALEAHN  159 (231)
T ss_pred             CCHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHhCCCHHHHHHHHHHhccCCceeccCcccCCCcc
Confidence            7888899999999999999999999999999999999999999998764  45789999998766543

>PRK05572 sporulation sigma factor SigF; Validated

Probab=99.91  E-value=4.3e-23  Score=200.56  Aligned_cols=152  Identities=26%  Similarity=0.385  Sum_probs=140.6

Q ss_pred             HHHHHHHHhchH-HHHHHHHHhHHHHHHHHHHhhCCCCCHHhHHHHHHHHHHHhHHhcCCCCCCChHHHHHHHHHHHHHH
Q 013472          284 RVLKQHLAFGWY-CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISK  362 (442)
Q Consensus       284 eeL~~~l~~G~~-Are~LI~~nlrLV~sIAkrY~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIRnaI~r  362 (442)
                      .+|+..+..|+. |+++||..|.++|+.+|++|.+++.+++||+||||+++|+++++||+.+|.+|.||+++||++.|.+
T Consensus        20 ~~li~~~~~gd~~a~~~L~~~y~~~v~~~a~~~~~~~~~aeDl~Qe~~l~l~~~~~~f~~~~~~~f~twl~~~i~~~i~~   99 (252)
T PRK05572         20 KELIKKSQDGDQEARDTLVEKNLRLVWSVVQRFLNRGYEPDDLFQIGCIGLLKAVDKFDLSYDVKFSTYAVPMIIGEIQR   99 (252)
T ss_pred             HHHHHHHHcCCHHHHHHHHHHhHHHHHHHHHHHccCCCCHHHHHHHHHHHHHHHHHHcCCCCCCChHHHHHHHHHHHHHH
Confidence            446666777765 9999999999999999999999999999999999999999999999988889999999999999999


Q ss_pred             HHHhhcCceecccccHHHHHHHHHHHHHHHHHcCCCCcHHHHHHHhCCCHHHHHHHHHhcccCCCCccccCCCC
Q 013472          363 MVARHARGIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCL  436 (442)
Q Consensus       363 ~LRkqsr~irlP~~v~e~i~kI~ka~~~L~~elgr~PS~eEIAe~LGIS~etVk~~l~~ar~~~SLD~~v~~~~  436 (442)
                      ++++. ..+++|..+.+...++.++...+..++|+.|+..|||+.+|++++.|..++.....+.||+.++.+++
T Consensus       100 ~lr~~-~~~r~~~~~~~~~~~~~~~~~~l~~~~~r~p~~~eia~~l~~~~~~v~~~~~~~~~~~sl~~~~~~~~  172 (252)
T PRK05572        100 FLRDD-GTVKVSRSLKETANKIRKDKDELSKELGREPTIEELAEYLGVTPEEVVLAQEASRSPQSIHETVHEND  172 (252)
T ss_pred             HHHhC-CCCCCCHHHHHHHHHHHHHHHHHHHHHCcCCCHHHHHHHhCcCHHHHHHHHHhcCCCcCcccCcccCC
Confidence            99987 47899999999999999999999999999999999999999999999999888888999999886544

>PRK08583 RNA polymerase sigma factor SigB; Validated

Probab=99.90  E-value=1.7e-22  Score=196.52  Aligned_cols=155  Identities=26%  Similarity=0.272  Sum_probs=140.7

Q ss_pred             HHHHHHHHHh-chH-HHHHHHHHhHHHHHHHHHHhhCCCCCHHhHHHHHHHHHHHhHHhcCCCCCCChHHHHHHHHHHHH
Q 013472          283 ERVLKQHLAF-GWY-CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSI  360 (442)
Q Consensus       283 eeeL~~~l~~-G~~-Are~LI~~nlrLV~sIAkrY~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIRnaI  360 (442)
                      +.+|+..++. |+. |+++||..|.++|+++|++|.+++.+++||+||||++||+++++||+..|.+|+||+++||+|.|
T Consensus        15 ~~~li~~~~~~gd~~a~~~l~~~~~~~v~~~a~~~~~~~~~aeDlvQe~~l~l~~~~~~f~~~~~~~f~tyl~~~i~n~~   94 (257)
T PRK08583         15 VNKWIAEYQENQDEEAQEKLVKHYKNLVESLAYKYSKGQSHHEDLVQVGMVGLLGAIRRYDPSFGRSFEAFAVPTIIGEI   94 (257)
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHcCccCCCChHHHHHHHHHHHH
Confidence            4567777764 655 99999999999999999999999999999999999999999999999988899999999999999


Q ss_pred             HHHHHhhcCceecccccHHHHHHHHHHHHHHHHHcCCCCcHHHHHHHhCCCHHHHHHHHHhcc--cCCCCccccCCCCC
Q 013472          361 SKMVARHARGIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLR--IVGSIDQKIGDCLN  437 (442)
Q Consensus       361 ~r~LRkqsr~irlP~~v~e~i~kI~ka~~~L~~elgr~PS~eEIAe~LGIS~etVk~~l~~ar--~~~SLD~~v~~~~d  437 (442)
                      .++++++...+++|.++.+..+++..+...+...+++.|+.+|+|+.+|++.+.|..++....  .++|+|.+++++.+
T Consensus        95 ~~~lr~~~~~~~i~r~~~~~~~~~~~~~~~~~~~~~r~~~~~e~a~~~~~~~~~~~~~~~~~~~~~~~sld~~~~~~~~  173 (257)
T PRK08583         95 KRYLRDKTWSVHVPRRIKELGPKIKKAVDELTTELQRSPKISEIADRLGVSEEEVLEAMEMGKSYQALSVDHSIEADSD  173 (257)
T ss_pred             HHHHHhcCCCcCCCHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHHhccCCceecCccccCCCC
Confidence            999999989999999999999999999999999999999999999999999999988876543  67899998865443

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

Probab=99.89  E-value=2.2e-22  Score=191.89  Aligned_cols=132  Identities=32%  Similarity=0.475  Sum_probs=121.6

Q ss_pred             HHHHhHHHHHHHHHHhhC---CCCCHHhHHHHHHHHHHHhHHhcCCCCCCChHHHHHHHHHHHHHHHHHhhcCceecccc
Q 013472          300 LIKSTRPLVLFLARNYRG---LGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIPCK  376 (442)
Q Consensus       300 LI~~nlrLV~sIAkrY~g---~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIRnaI~r~LRkqsr~irlP~~  376 (442)
                      |+..|.++|+.+|++|.+   ++.+++||+|||++|||+++++|||.+|++|+||+++||+|.+++++|+..   ++|..
T Consensus         1 L~~~~~~lv~~~a~~~~~~~~~~~~~eDl~Qe~~~~l~~a~~~fd~~~~~~f~t~~~~~i~~~~~~~lr~~~---~~p~~   77 (224)
T TIGR02479         1 LIRRYLPLVKRIAGRLSVGLPSSVELDDLIQAGMFGLLDAIERYDPSRGAKFETYAVQRIRGAMLDELRRLD---WVPRS   77 (224)
T ss_pred             CHHHHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHHHHHHHHhcCCccCCCHHHHHHHHHHHHHHHHHHHcC---ccCHH
Confidence            588999999999999986   789999999999999999999999999999999999999999999999763   68999


Q ss_pred             cHHHHHHHHHHHHHHHHHcCCCCcHHHHHHHhCCCHHHHHHHHHhcc--cCCCCccccCC
Q 013472          377 LNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLR--IVGSIDQKIGD  434 (442)
Q Consensus       377 v~e~i~kI~ka~~~L~~elgr~PS~eEIAe~LGIS~etVk~~l~~ar--~~~SLD~~v~~  434 (442)
                      +...++++.++..+|...+|+.|+.+|||+.||++++.|..++..+.  .++|+|.++.+
T Consensus        78 ~~~~~~~l~~~~~~l~~~~~~~~~~~ela~~l~~~~~~v~~~~~~~~~~~~~sl~~~~~~  137 (224)
T TIGR02479        78 LRQKARKLERAIRELEARLGREPTEEEIAEELGMDLKEYRQALNEINALSLVSLDELLES  137 (224)
T ss_pred             HHHHHHHHHHHHHHHHHHHCcCCCHHHHHHHhCCCHHHHHHHHHHHhcCCccccCCcccC
Confidence            99999999999999999999999999999999999999999986443  57889887654

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

>PRK06986 fliA flagellar biosynthesis sigma factor; Validated

Probab=99.87  E-value=1.6e-21  Score=187.60  Aligned_cols=142  Identities=30%  Similarity=0.416  Sum_probs=127.1

Q ss_pred             hchHHHHHHHHHhHHHHHHHHHHhh---CCCCCHHhHHHHHHHHHHHhHHhcCCCCCCChHHHHHHHHHHHHHHHHHhhc
Q 013472          292 FGWYCREELIKSTRPLVLFLARNYR---GLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHA  368 (442)
Q Consensus       292 ~G~~Are~LI~~nlrLV~sIAkrY~---g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIRnaI~r~LRkqs  368 (442)
                      .|.-++++|+..|.++|+.+|++|.   +++.+++||+||||+|||+++++||+..|.+|+||+++||+|.|.+++|++.
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            4666999999999999999999997   6789999999999999999999999998899999999999999999999875


Q ss_pred             CceecccccHHHHHHHHHHHHHHHHHcCCCCcHHHHHHHhCCCHHHHHHHHHhc--ccCCCCccccCCCC
Q 013472          369 RGIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECL--RIVGSIDQKIGDCL  436 (442)
Q Consensus       369 r~irlP~~v~e~i~kI~ka~~~L~~elgr~PS~eEIAe~LGIS~etVk~~l~~a--r~~~SLD~~v~~~~  436 (442)
                         ++|..+.....++.++...+.+.+++.||.+|||+.||+++++|..++...  ..++|+|.++++++
T Consensus        85 ---~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ela~~l~i~~~~v~~~~~~~~~~~~~sl~~~~~~~~  151 (236)
T PRK06986         85 ---WVPRSVRRNAREVAQAIRQLEQELGREPTDTEVAEKLGLSLEEYREMLLDTNISQLFSIDELRGEHG  151 (236)
T ss_pred             ---CCCHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHcCCCHHHHHHHHHHHhccCCccccccccCCC
Confidence               368777777788899999999999999999999999999999999987743  35678998865543

>PRK05803 sporulation sigma factor SigK; Reviewed

Probab=99.79  E-value=7e-18  Score=162.17  Aligned_cols=170  Identities=22%  Similarity=0.252  Sum_probs=127.7

Q ss_pred             HHHHhHHHHHHHHHHHHHHHHhCCCCChHHHHHHcCCCHHHHHHHHHhchH-HHHHHHHHhHHHHHHHHHHhhCCCCCHH
Q 013472          245 MSKGVQVVANLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQHLAFGWY-CREELIKSTRPLVLFLARNYRGLGIPFS  323 (442)
Q Consensus       245 L~~~iq~~~~le~~~~~L~~~~gr~pt~~ewA~a~g~deeeL~~~l~~G~~-Are~LI~~nlrLV~sIAkrY~g~g~d~E  323 (442)
                      |.--++..++|.+....+    ++.|.+..      .++..|+..+..|+. |++.|+..|.++|+++|.+|.+++.+++
T Consensus         8 ~~~~~~~~~~~~~~~~~~----~~~~~~~~------~~e~~l~~~~~~gd~~a~~~l~~~y~~~l~~~a~~~~~~~~dae   77 (233)
T PRK05803          8 LLYIVKEILFLVSYVKNN----SFPQPLSE------EEERKYLELMKEGDEEARNILIERNLRLVAHIVKKFENTGEDVD   77 (233)
T ss_pred             HHHHHHHHHHHHHHHHHh----cccCCCCH------HHHHHHHHHHHcCCHHHHHHHHHHhHHHHHHHHHHHhcCCCCHH
Confidence            344456667776666554    44443322      124567888888866 9999999999999999999999999999


Q ss_pred             hHHHHHHHHHHHhHHhcCCCCCCChHHHHHHHHHHHHHHHHHhhcCce---ec-------------------cc---ccH
Q 013472          324 DLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGI---KI-------------------PC---KLN  378 (442)
Q Consensus       324 DLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIRnaI~r~LRkqsr~i---rl-------------------P~---~v~  378 (442)
                      |++|||+|++|+++++||+++|.+|.||+++|++|.+++++|+..+..   .+                   +.   ...
T Consensus        78 DlvQE~fi~l~~~~~~f~~~~~~~f~~wl~~i~rn~~id~~Rk~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  157 (233)
T PRK05803         78 DLISIGTIGLIKAIESFDAGKGTKLATYAARCIENEILMHLRNLKKTKKEVSLQDPIGVDKEGNEISLIDILGSEEDDVI  157 (233)
T ss_pred             HHHHHHHHHHHHHHHhcCcccCCChHHHHHHHHHHHHHHHHHHHhccccCCCccccccCCCCcCcccHHHHccCCCCCHH
Confidence            999999999999999999988889999999999999999999764321   00                   00   000


Q ss_pred             ------HHHHHHHHHHHHHHHHc------------CCCCcHHHHHHHhCCCHHHHHHHHHhccc
Q 013472          379 ------REISKIQKARKALTNSH------------GKYPEDIEIAKYTGLSLAEIRSASECLRI  424 (442)
Q Consensus       379 ------e~i~kI~ka~~~L~~el------------gr~PS~eEIAe~LGIS~etVk~~l~~ar~  424 (442)
                            +....+.++...|+...            ..+.|++|||+.+|+|.++|+..+++++.
T Consensus       158 ~~~~~~~~~~~l~~~l~~Lp~~~R~i~~l~y~~~~~e~~S~~EIA~~lgis~~tV~~~~~rA~~  221 (233)
T PRK05803        158 EQVELKMEVEKLYKKIDILDEREKEVIEMRYGLGNGKEKTQREIAKALGISRSYVSRIEKRALK  221 (233)
T ss_pred             HHHHHHHHHHHHHHHHHhCCHHHHHHHHHHhCCCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence                  12223555555554432            24579999999999999999999877653

>TIGR02895 spore_sigI RNA polymerase sigma-I factor

Probab=99.77  E-value=4.8e-18  Score=163.52  Aligned_cols=129  Identities=18%  Similarity=0.301  Sum_probs=114.0

Q ss_pred             HHHhchHHHHHHHHHhHHHHHHHHHHhhCCC--CCHHhHHHHHHHHHHHhHHhcCCCCCCChHHHHHHHHHHHHHHHHHh
Q 013472          289 HLAFGWYCREELIKSTRPLVLFLARNYRGLG--IPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVAR  366 (442)
Q Consensus       289 ~l~~G~~Are~LI~~nlrLV~sIAkrY~g~g--~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIRnaI~r~LRk  366 (442)
                      .++.|+..+++||..|.|+|.++|.+|.++.  .+.+|++|+|+||||+|+++||+++|.+|.|||.++|++.|++++|+
T Consensus         3 ~~~~gd~~~e~LI~~Y~plI~~~a~~~~~~~~~~e~dDlvQ~glial~eAi~~yd~~kg~~F~sya~~~Ir~~i~dylRk   82 (218)
T TIGR02895         3 PIQPGNEEREELIRQYKPFIAKIVSSVCGRYIDTKSDDELSIGLIAFNEAIESYDSNKGKSFLSFAKLIIKRRLIDYIRK   82 (218)
T ss_pred             hhhcCChHHHHHHHHhHHHHHHHHHHHHccCCCCChhHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHh
Confidence            5678887899999999999999999998775  58999999999999999999999999999999999999999999998


Q ss_pred             hc---CceecccccHHHHHHHHHHHHHHHHHcCCCCcHHHHHHH------hCCCHHHHHH
Q 013472          367 HA---RGIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKY------TGLSLAEIRS  417 (442)
Q Consensus       367 qs---r~irlP~~v~e~i~kI~ka~~~L~~elgr~PS~eEIAe~------LGIS~etVk~  417 (442)
                      ..   ..+++|....+....+..+..++..+.++.|+.+||+..      .||+.+.+-+
T Consensus        83 ~~k~~~~v~~~~~~~e~~~~~~~~~~~~~~~~~~~~~~eEI~~~~~~L~~~gi~~~dLv~  142 (218)
T TIGR02895        83 NQKYQNLLYLDEDYDENPLEFNKSMEEYRNEIENENRRLEILEYKKLLKQFGIEFVELVK  142 (218)
T ss_pred             cccccCeeeCCchHHHHHHHHHHHHHHHHHHHccccHHHHHHHHHHHHHHcCCcHHHHhh
Confidence            87   456888766666778888888999999999999999954      4888877643

Members of this sigma factor protein family are strictly limited to endospore-forming species in the Firmicutes lineage of bacteria, but are not universally present among such species. Sigma-I was shown to be induced by heat shock (PubMed:11157964) in Bacillus subtilis and is suggested by its phylogenetic profile to be connected to the program of sporulation (PubMed:16311624).

>TIGR02846 spore_sigmaK RNA polymerase sigma-K factor

Probab=99.77  E-value=2.8e-17  Score=157.57  Aligned_cols=143  Identities=24%  Similarity=0.354  Sum_probs=115.7

Q ss_pred             CHHHHHHHHHhchH-HHHHHHHHhHHHHHHHHHHhhCCCCCHHhHHHHHHHHHHHhHHhcCCCCCCChHHHHHHHHHHHH
Q 013472          282 SERVLKQHLAFGWY-CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSI  360 (442)
Q Consensus       282 deeeL~~~l~~G~~-Are~LI~~nlrLV~sIAkrY~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIRnaI  360 (442)
                      .+..|+..++.|+. |++.|+..|.+.|+++|.+|.++..+++|++||+|+++|+++++|+++.+.+|.||+++|++|.|
T Consensus        34 ~~~~li~~~~~gd~~af~~l~~~y~~~v~~~~~~~~~~~~dAEDlvQevfi~l~~~~~~~~~~~~~~f~twl~~i~rN~~  113 (227)
T TIGR02846        34 EEKKYLDRLKEGDEEARNVLIERNLRLVAHIVKKFSNTGEDVDDLISIGTIGLIKAIDSFDPDKGTRLATYAARCIENEI  113 (227)
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHhHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHHhCCcccCCChHHHHHHHHHHHH
Confidence            35778888999976 99999999999999999999999999999999999999999999999888889999999999999


Q ss_pred             HHHHHhhcCcee-c---------------------cc---c------cHHHHHHHHHHHHHHHHHc--------C----C
Q 013472          361 SKMVARHARGIK-I---------------------PC---K------LNREISKIQKARKALTNSH--------G----K  397 (442)
Q Consensus       361 ~r~LRkqsr~ir-l---------------------P~---~------v~e~i~kI~ka~~~L~~el--------g----r  397 (442)
                      ++++|+..+... .                     +.   .      ..+....|.+++..|+...        -    .
T Consensus       114 ~d~~Rk~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~L~~~~r~il~l~y~~~~~e  193 (227)
T TIGR02846       114 LMHLRALKKTKGEVSLQDPIGVDKEGNEISLIDILGSDGDSVIEQVELNLEIKKLYKKLSVLDGREREVIEMRYGLGDGR  193 (227)
T ss_pred             HHHHHHHhccccceeccccccCCcccCcccHHHHhcCCCCChHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHcCCCCC
Confidence            999998754211 0                     00   0      0012233555566555443        1    5


Q ss_pred             CCcHHHHHHHhCCCHHHHHHHHHhccc
Q 013472          398 YPEDIEIAKYTGLSLAEIRSASECLRI  424 (442)
Q Consensus       398 ~PS~eEIAe~LGIS~etVk~~l~~ar~  424 (442)
                      +.|.+|||++||+|+++|+..+++++.
T Consensus       194 ~~S~~EIAe~lgis~~tV~~~~~rAl~  220 (227)
T TIGR02846       194 RKTQREIAKILGISRSYVSRIEKRALM  220 (227)
T ss_pred             CcCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            679999999999999999999887764

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=99.75  E-value=1.6e-17  Score=159.27  Aligned_cols=143  Identities=24%  Similarity=0.387  Sum_probs=116.8

Q ss_pred             CHHHHHHHHHhchH-HHHHHHHHhHHHHHHHHHHhhCCCCCHHhHHHHHHHHHHHhHHhcCCCCCCChHHHHHHHHHHHH
Q 013472          282 SERVLKQHLAFGWY-CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSI  360 (442)
Q Consensus       282 deeeL~~~l~~G~~-Are~LI~~nlrLV~sIAkrY~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIRnaI  360 (442)
                      .+..|+..++.|+. |++.++..|.++|+.+|++|.+++.+++|++||+|+++|+++++|++..+++|.||++++++|.|
T Consensus        38 ~~~~L~~~~~~gd~~af~~l~~~y~~~l~~~a~~~~~~~~~AeDlvQevfl~l~~~~~~f~~~~~~~f~twl~~iarn~~  117 (234)
T PRK08301         38 EEEYLLNKLPKGDEAVRSLLIERNLRLVVYIARKFENTGINIEDLISIGTIGLIKAVNTFNPEKKIKLATYASRCIENEI  117 (234)
T ss_pred             HHHHHHHHHHccCHHHHHHHHHHhHHHHHHHHHHhhcCCCCHHHHHHHHHHHHHHHHHhcCcccCCCHHHHHHHHHHHHH
Confidence            46778888999976 99999999999999999999999999999999999999999999999877889999999999999


Q ss_pred             HHHHHhhcCcee---c--c-----------------c--cc----H---HHHHHHHHHHHHHHHHc------------CC
Q 013472          361 SKMVARHARGIK---I--P-----------------C--KL----N---REISKIQKARKALTNSH------------GK  397 (442)
Q Consensus       361 ~r~LRkqsr~ir---l--P-----------------~--~v----~---e~i~kI~ka~~~L~~el------------gr  397 (442)
                      ++++|++.+...   +  +                 .  ..    .   .....+.+++.+|+.+.            ..
T Consensus       118 ~d~lRk~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~al~~Lp~~~R~v~~L~y~l~~~e  197 (234)
T PRK08301        118 LMYLRRNNKVKAEVSFDEPLNIDWDGNELLLSDVLGTDNDIIYKDIEDEVDRKLLKKALKKLSDREKQIMELRFGLNGGE  197 (234)
T ss_pred             HHHHHHHhccccccccccccccccCCCcccHHHhccCcccchHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHhccCCCC
Confidence            999997654211   0  0                 0  00    0   01224666776665543            25


Q ss_pred             CCcHHHHHHHhCCCHHHHHHHHHhccc
Q 013472          398 YPEDIEIAKYTGLSLAEIRSASECLRI  424 (442)
Q Consensus       398 ~PS~eEIAe~LGIS~etVk~~l~~ar~  424 (442)
                      +.|++|||+.||||+++|+..+++++.
T Consensus       198 g~s~~EIA~~lgis~~tVk~~~~rA~~  224 (234)
T PRK08301        198 EKTQKEVADMLGISQSYISRLEKRIIK  224 (234)
T ss_pred             CCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            789999999999999999999887763

>PRK05602 RNA polymerase sigma factor; Reviewed

Probab=99.75  E-value=1.1e-17  Score=154.19  Aligned_cols=144  Identities=17%  Similarity=0.129  Sum_probs=117.9

Q ss_pred             CCCHHHHHHHHHhchH-HHHHHHHHhHHHHHHHHHHhhCCCCCHHhHHHHHHHHHHHhHHhcCCCCCCChHHHHHHHHHH
Q 013472          280 GVSERVLKQHLAFGWY-CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRK  358 (442)
Q Consensus       280 g~deeeL~~~l~~G~~-Are~LI~~nlrLV~sIAkrY~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIRn  358 (442)
                      .++++.|+..++.|+. |++.|+..|.++|+.+|++|.+++.+++|++||+|+++|+++.+|++. +.+|.||++.+++|
T Consensus         4 ~~~~~~l~~~~~~~d~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeDlvQe~fi~l~~~~~~~~~~-~~~f~~wl~~ia~n   82 (186)
T PRK05602          4 ADPDEELLARVAAGDPAAFRVLVARKLPRLLALATRMLGDPAEAEDVAQETFLRIWKQAPSWRPG-EARFDTWLHRVVLN   82 (186)
T ss_pred             cccHHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHhhhcCCC-CCcHHHHHHHHHHH
Confidence            3567889999999976 999999999999999999999999999999999999999999999975 35799999999999


Q ss_pred             HHHHHHHhhcCcee--ccc---------c---cHHHHHHHHHHHHHHHHHc--------CCCCcHHHHHHHhCCCHHHHH
Q 013472          359 SISKMVARHARGIK--IPC---------K---LNREISKIQKARKALTNSH--------GKYPEDIEIAKYTGLSLAEIR  416 (442)
Q Consensus       359 aI~r~LRkqsr~ir--lP~---------~---v~e~i~kI~ka~~~L~~el--------gr~PS~eEIAe~LGIS~etVk  416 (442)
                      .+.+++|+++....  ++.         .   ..+....+.++...|+.+.        -.+.+++|||+.||+|..+|+
T Consensus        83 ~~~d~~R~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~i~~l~~~~g~s~~EIA~~lgis~~tV~  162 (186)
T PRK05602         83 LCYDRLRRRREVPVEDAPDVPDPAPGPDAGLEARQRARRVEQALAALPERQREAIVLQYYQGLSNIEAAAVMDISVDALE  162 (186)
T ss_pred             HHHHHHHhcCCCCcccccccCCCCCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHhhHHHhcCCCHHHHHHHhCcCHHHHH
Confidence            99999997754211  110         0   0122334666666665443        267799999999999999999


Q ss_pred             HHHHhccc
Q 013472          417 SASECLRI  424 (442)
Q Consensus       417 ~~l~~ar~  424 (442)
                      ..+++++.
T Consensus       163 ~~l~Rar~  170 (186)
T PRK05602        163 SLLARGRR  170 (186)
T ss_pred             HHHHHHHH
Confidence            99998875

>TIGR02859 spore_sigH RNA polymerase sigma-H factor

Probab=99.74  E-value=3.8e-17  Score=151.24  Aligned_cols=144  Identities=18%  Similarity=0.200  Sum_probs=114.1

Q ss_pred             CCHHHHHHHHHhchH-HHHHHHHHhHHHHHHHHHHhhCCCCCHHhHHHHHHHHHHHhHHhcCCCCCCChHHHHHHHHHHH
Q 013472          281 VSERVLKQHLAFGWY-CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKS  359 (442)
Q Consensus       281 ~deeeL~~~l~~G~~-Are~LI~~nlrLV~sIAkrY~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIRna  359 (442)
                      |++.+|+..++.|+. |++.|+..|.+.|+.+|+++.++..+++|++||+|+++|+++.+|++..+..|.||++.+|++.
T Consensus         4 ~~~~~l~~~~~~~d~~a~~~l~~~~~~~l~~~a~~~~~~~~~aeDlvQe~fl~~~~~~~~~~~~~~~~f~~wl~~~~~~~   83 (198)
T TIGR02859         4 LEDEEIVELARQGNTHALEYLINKYKNFVRAKARSYFLIGADKEDIIQEGMIGLYKAIRDFRPDKLSSFKAFAELCVTRQ   83 (198)
T ss_pred             cchHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHccccCcHHHHHHHHHHHHHHHHHHhCcccCCChHHHHHHHHHHH
Confidence            567889999999976 9999999999999999999999999999999999999999999999977778999999999999


Q ss_pred             HHHHHHhhcCceec----------------------------cccc-------HHHHHHHHHHHHHHHHHc--------C
Q 013472          360 ISKMVARHARGIKI----------------------------PCKL-------NREISKIQKARKALTNSH--------G  396 (442)
Q Consensus       360 I~r~LRkqsr~irl----------------------------P~~v-------~e~i~kI~ka~~~L~~el--------g  396 (442)
                      +.+++++..+..+.                            +...       .+....+.++...|+...        -
T Consensus        84 ~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~e~~~~l~~~l~~Ll~~~~~~i~~~~~  163 (198)
T TIGR02859        84 IITAIKTATRQKHIPLNSYVSLNKPIYDEESDRTLLDVISGAKVTDPEELIISQEEYGDIESKMNELLSDLEWKVLQSYL  163 (198)
T ss_pred             HHHHHHHHHHhcccchhhhcCcccccccccccchHHHHhhccccCCHHHHHHHHHHHHHHHHHHHHhcCHHHHHHHHHHH
Confidence            98888743111000                            0000       111233555555542221        2


Q ss_pred             CCCcHHHHHHHhCCCHHHHHHHHHhccc
Q 013472          397 KYPEDIEIAKYTGLSLAEIRSASECLRI  424 (442)
Q Consensus       397 r~PS~eEIAe~LGIS~etVk~~l~~ar~  424 (442)
                      .+.|++|||+.||+|+++|+.++++++.
T Consensus       164 ~~~s~~eIA~~l~~s~~tV~~~l~r~r~  191 (198)
T TIGR02859       164 DGKSYQEIACDLNRHVKSIDNALQRVKR  191 (198)
T ss_pred             cCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            6779999999999999999999998874

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.

>TIGR02835 spore_sigmaE RNA polymerase sigma-E factor

Probab=99.74  E-value=4.4e-17  Score=156.88  Aligned_cols=143  Identities=24%  Similarity=0.385  Sum_probs=116.3

Q ss_pred             CHHHHHHHHHhchH-HHHHHHHHhHHHHHHHHHHhhCCCCCHHhHHHHHHHHHHHhHHhcCCCCCCChHHHHHHHHHHHH
Q 013472          282 SERVLKQHLAFGWY-CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSI  360 (442)
Q Consensus       282 deeeL~~~l~~G~~-Are~LI~~nlrLV~sIAkrY~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIRnaI  360 (442)
                      .++.|+..+..|+. |++.++..|.+.|+.+|++|.+++.+++|++||+|+++|+++++|++..+++|.||++++++|.+
T Consensus        38 ~~~~l~~~~~~~d~~a~~~l~~~y~~~l~~~~~~~~~~~~~AEDlvQE~fl~l~~~~~~f~~~~~~~f~~wl~~iarN~~  117 (234)
T TIGR02835        38 EEEALLQKLTQGDESAKSTLIERNLRLVVYIARKFENTGIGIEDLVSIGTIGLIKAVNTFNPSKKIKLATYASRCIENEI  117 (234)
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHhHHHHHHHHHHhccCCCCHHHHHHHHHHHHHHHHHHhCcccCCCHHHHHHHHHHHHH
Confidence            35678888888866 99999999999999999999999999999999999999999999998877789999999999999


Q ss_pred             HHHHHhhcCce-ecc----------------------c-----cc---HHHHHHHHHHHHHHHHHc------------CC
Q 013472          361 SKMVARHARGI-KIP----------------------C-----KL---NREISKIQKARKALTNSH------------GK  397 (442)
Q Consensus       361 ~r~LRkqsr~i-rlP----------------------~-----~v---~e~i~kI~ka~~~L~~el------------gr  397 (442)
                      ++++|++.+.. ..+                      .     ..   ......+.+++..|+...            ..
T Consensus       118 ~d~~Rk~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~ai~~Lp~~~R~ii~L~~~l~~~e  197 (234)
T TIGR02835       118 LMYLRRNNKTRSEVSFDEPLNVDWDGNELLLSDVLGTDSDIVYKYLEEEVDRELLRKALAKLNDREKKIMELRFGLVGGT  197 (234)
T ss_pred             HHHHHHhccccCcccccccccCCCCCCcchHHHhcCCCCCcHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHccCCCC
Confidence            99999865421 100                      0     00   011234667777665543            14


Q ss_pred             CCcHHHHHHHhCCCHHHHHHHHHhccc
Q 013472          398 YPEDIEIAKYTGLSLAEIRSASECLRI  424 (442)
Q Consensus       398 ~PS~eEIAe~LGIS~etVk~~l~~ar~  424 (442)
                      +.|++|||+.||+|+++|+..+++++.
T Consensus       198 g~s~~EIA~~Lgis~~tV~~~l~ra~~  224 (234)
T TIGR02835       198 EKTQKEVADMLGISQSYISRLEKRILK  224 (234)
T ss_pred             CCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            689999999999999999999887763

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=99.74  E-value=5.5e-17  Score=151.48  Aligned_cols=145  Identities=21%  Similarity=0.254  Sum_probs=113.1

Q ss_pred             CCCHHHHHHHHHhchH-HHHHHHHHhHHHHHHHHHHhhCCCCCHHhHHHHHHHHHHHhHHhcCCCCCCChHHHHHHHHHH
Q 013472          280 GVSERVLKQHLAFGWY-CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRK  358 (442)
Q Consensus       280 g~deeeL~~~l~~G~~-Are~LI~~nlrLV~sIAkrY~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIRn  358 (442)
                      .++++.|+..++.|+. |++.|+..|.++|+.+|.+|.++..+++|++||+++++|+++++||+.++.+|.||++.+++|
T Consensus         8 ~~~~~~l~~~~~~~d~~a~~~l~~~y~~~v~~~~~~~~~~~~~aeDlvQe~~l~l~~~~~~~~~~~~~~f~twl~~i~~n   87 (208)
T PRK08295          8 ELEDEELVELARSGDKEALEYLIEKYKNFVRAKARSYFLIGADREDIVQEGMIGLYKAIRDYDKDKLSSFKSFAELCITR   87 (208)
T ss_pred             CCChHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHhCcccCCCHHHHHHHHHHH
Confidence            4567788888988976 999999999999999999999999999999999999999999999998777999999999999


Q ss_pred             HHHHHHHhhcCceeccc-----------------------------ccH------HHHHHH-HHHHHHHHHH-------c
Q 013472          359 SISKMVARHARGIKIPC-----------------------------KLN------REISKI-QKARKALTNS-------H  395 (442)
Q Consensus       359 aI~r~LRkqsr~irlP~-----------------------------~v~------e~i~kI-~ka~~~L~~e-------l  395 (442)
                      .+.+++++..+..+.+.                             ...      +....+ ..+...|+..       +
T Consensus        88 ~~~d~~r~~~r~~~~~~~~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~L~~~~r~vl~l~  167 (208)
T PRK08295         88 QIITAIKTANRQKHIPLNSYVSLDKPIYDEESDRTLLDVISEAKVTDPEELIISKEELEDIEEKIEELLSELEKEVLELY  167 (208)
T ss_pred             HHHHHHHHhhhhccccccceeecCCcccCCccchhHHHHhcCcccCCHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHH
Confidence            99999986433211110                             000      011111 1222222222       2


Q ss_pred             CCCCcHHHHHHHhCCCHHHHHHHHHhccc
Q 013472          396 GKYPEDIEIAKYTGLSLAEIRSASECLRI  424 (442)
Q Consensus       396 gr~PS~eEIAe~LGIS~etVk~~l~~ar~  424 (442)
                      -.+.|++|||+.||+|+++|+.++++++.
T Consensus       168 ~e~~s~~EIA~~lgis~~tV~~~l~rar~  196 (208)
T PRK08295        168 LDGKSYQEIAEELNRHVKSIDNALQRVKR  196 (208)
T ss_pred             HccCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            36789999999999999999999988874

>PRK12513 RNA polymerase sigma factor; Provisional

Probab=99.72  E-value=9.4e-17  Score=149.07  Aligned_cols=142  Identities=18%  Similarity=0.143  Sum_probs=116.7

Q ss_pred             CCHHHHHHHHHhchH-HHHHHHHHhHHHHHHHHHHhhCCCCCHHhHHHHHHHHHHHhHHhcCCCCCCChHHHHHHHHHHH
Q 013472          281 VSERVLKQHLAFGWY-CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKS  359 (442)
Q Consensus       281 ~deeeL~~~l~~G~~-Are~LI~~nlrLV~sIAkrY~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIRna  359 (442)
                      ++++.|+..+..|+. |++.|+..|.+.|+++|.++.++..+++|++||+|+++|+++++|++.  ..|.+|++++++|.
T Consensus        11 ~~~~~l~~~~~~gd~~a~~~l~~~y~~~l~~~~~~~~~~~~daeDlvQe~fi~l~~~~~~~~~~--~~f~~wl~~i~~n~   88 (194)
T PRK12513         11 ASDEALMLRYRAGDAAAFEALYARHRTGLYRFLLRLARDRALAEDIFQETWLRVIRARAQYQPR--ARFRTWLYQIARNL   88 (194)
T ss_pred             CCHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHhcCCC--CchHHHHHHHHHHH
Confidence            457889999999976 999999999999999999999999999999999999999999999974  36999999999999


Q ss_pred             HHHHHHhhcCceeccc------------c--------cHHHHHHHHHHHHHHHHHcC--------CCCcHHHHHHHhCCC
Q 013472          360 ISKMVARHARGIKIPC------------K--------LNREISKIQKARKALTNSHG--------KYPEDIEIAKYTGLS  411 (442)
Q Consensus       360 I~r~LRkqsr~irlP~------------~--------v~e~i~kI~ka~~~L~~elg--------r~PS~eEIAe~LGIS  411 (442)
                      +++++|++.+....+.            .        ..+....+..+...|+....        .+.|++|||+.||||
T Consensus        89 ~~~~~R~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~i~~l~~~~g~s~~EIA~~lgis  168 (194)
T PRK12513         89 LIDHWRRHGARQAPSLDADEQLHALADDGAAPEQQLSLFRDRRRLQAALETLPDEQREVFLLREHGDLELEEIAELTGVP  168 (194)
T ss_pred             HHHHHHHhccccccccccchhhhhcCCCCCCHHHHHHHHHHHHHHHHHHHhCCHhHhhheeeehccCCCHHHHHHHHCCC
Confidence            9999998765332210            0        01122346666666665542        567999999999999


Q ss_pred             HHHHHHHHHhccc
Q 013472          412 LAEIRSASECLRI  424 (442)
Q Consensus       412 ~etVk~~l~~ar~  424 (442)
                      +++|+..+++++.
T Consensus       169 ~~tV~~~l~ra~~  181 (194)
T PRK12513        169 EETVKSRLRYALQ  181 (194)
T ss_pred             HHHHHHHHHHHHH
Confidence            9999999888774

>PRK09646 RNA polymerase sigma factor SigK; Reviewed

Probab=99.72  E-value=8.3e-17  Score=150.03  Aligned_cols=142  Identities=18%  Similarity=0.098  Sum_probs=115.4

Q ss_pred             CHHHHHHHHHhchH-HHHHHHHHhHHHHHHHHHHhhCCCCCHHhHHHHHHHHHHHhHHhcCCCCCCChHHHHHHHHHHHH
Q 013472          282 SERVLKQHLAFGWY-CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSI  360 (442)
Q Consensus       282 deeeL~~~l~~G~~-Are~LI~~nlrLV~sIAkrY~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIRnaI  360 (442)
                      ++..|+..+..|+. |+++|+..|.++|+.+|.+|.++..+++|++||+|+++|+++++||+.+| .|.+|++.+++|.+
T Consensus        16 ~~~~li~~~~~g~~~a~~~l~~~y~~~l~~~~~~~~~~~~dAeDivQe~fi~l~~~~~~~~~~~~-~~~~wl~~ia~n~~   94 (194)
T PRK09646         16 DLDALLRRVARGDQDAFAELYDRTSSRVYGLVRRVLRDPGYSEETTQEVYLEVWRTASRFDPARG-SALAWLLTLAHRRA   94 (194)
T ss_pred             cHHHHHHHHHccCHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhhhhcCcccc-cHHHHHHHHHHHHH
Confidence            45778888898976 99999999999999999999999999999999999999999999998655 79999999999999


Q ss_pred             HHHHHhhcCceec---------cc---cc------HHHHHHHHHHHHHHHHHc--------CCCCcHHHHHHHhCCCHHH
Q 013472          361 SKMVARHARGIKI---------PC---KL------NREISKIQKARKALTNSH--------GKYPEDIEIAKYTGLSLAE  414 (442)
Q Consensus       361 ~r~LRkqsr~irl---------P~---~v------~e~i~kI~ka~~~L~~el--------gr~PS~eEIAe~LGIS~et  414 (442)
                      +++++++.+..+.         +.   ..      .+....+..++..|+...        ..+.|++|||+.||+|+.+
T Consensus        95 ~d~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~vl~l~~~~~~s~~EIA~~Lgis~~t  174 (194)
T PRK09646         95 VDRVRSEQAASQREVRYGARNVDPAFDQVAEEVEARLERERVRDCLDALTDTQRESVTLAYYGGLTYREVAERLAVPLGT  174 (194)
T ss_pred             HHHHHhhccccccccccccccccccccchHHHHHHHhHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHhCCChHh
Confidence            9999986532111         00   00      112234556666555443        2678999999999999999


Q ss_pred             HHHHHHhccc
Q 013472          415 IRSASECLRI  424 (442)
Q Consensus       415 Vk~~l~~ar~  424 (442)
                      |+..+++++.
T Consensus       175 Vk~~l~ra~~  184 (194)
T PRK09646        175 VKTRMRDGLI  184 (194)
T ss_pred             HHHHHHHHHH
Confidence            9999988874

>PRK06811 RNA polymerase factor sigma-70; Validated

Probab=99.72  E-value=1.1e-16  Score=148.65  Aligned_cols=143  Identities=16%  Similarity=0.127  Sum_probs=115.5

Q ss_pred             CCCHHHHHHHHHhchH-HHHHHHHHhHHHHHHHHHHhhCCC---CCHHhHHHHHHHHHHHhHHhcCCCCCCChHHHHHHH
Q 013472          280 GVSERVLKQHLAFGWY-CREELIKSTRPLVLFLARNYRGLG---IPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYW  355 (442)
Q Consensus       280 g~deeeL~~~l~~G~~-Are~LI~~nlrLV~sIAkrY~g~g---~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~w  355 (442)
                      .++++.|+..+..|+. |+++|+..|.+.|+.++.++.+++   .+++|++||+++++|+++++|++..+ .|.||++.+
T Consensus         2 ~~~~~~li~~~~~gd~~a~~~l~~~y~~~l~~~~~~~~~~~~~~~daeDi~Qe~~i~l~~~~~~~~~~~~-~~~~wl~~i   80 (189)
T PRK06811          2 KINEDNFIKELKKKNEKALEFIVDTYGNLVKKIVHKVLGTVNYSQLIEECVNDIFLSIWNNIDKFDEEKG-SFKKWIAAI   80 (189)
T ss_pred             CCcHHHHHHHHHccCHHHHHHHHHHHHHHHHHHHHHHHcccCchhHHHHHHHHHHHHHHHhHHHhccccc-cHHHHHHHH
Confidence            4678889999999976 999999999999999999998853   57999999999999999999997544 799999999


Q ss_pred             HHHHHHHHHHhhcCceecc---c-------c------cHHHHHHHHHHHHHHHHHc--------CCCCcHHHHHHHhCCC
Q 013472          356 IRKSISKMVARHARGIKIP---C-------K------LNREISKIQKARKALTNSH--------GKYPEDIEIAKYTGLS  411 (442)
Q Consensus       356 IRnaI~r~LRkqsr~irlP---~-------~------v~e~i~kI~ka~~~L~~el--------gr~PS~eEIAe~LGIS  411 (442)
                      ++|.+++++|++.+.....   .       .      ..+....+.++...|+.+.        -.+.|++|||+.||+|
T Consensus        81 arn~~~d~~rk~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~l~~~l~~L~~~~r~i~~l~~~~g~s~~EIAe~lgis  160 (189)
T PRK06811         81 SKYKAIDYKRKLTKNNEIDSIDEFILISEESIENEIILKENKEEILKLINDLEKLDREIFIRRYLLGEKIEEIAKKLGLT  160 (189)
T ss_pred             HHHHHHHHHHHhccccccccchhhhhcccCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHccCCHHHHHHHHCCC
Confidence            9999999999876432211   0       0      0112233556666665543        2678999999999999


Q ss_pred             HHHHHHHHHhcc
Q 013472          412 LAEIRSASECLR  423 (442)
Q Consensus       412 ~etVk~~l~~ar  423 (442)
                      ..+|+..+++++
T Consensus       161 ~~~V~~~l~Ra~  172 (189)
T PRK06811        161 RSAIDNRLSRGR  172 (189)
T ss_pred             HHHHHHHHHHHH
Confidence            999999998886

>PRK09648 RNA polymerase sigma factor SigD; Reviewed

Probab=99.70  E-value=2.9e-16  Score=145.25  Aligned_cols=141  Identities=18%  Similarity=0.187  Sum_probs=112.6

Q ss_pred             HHHHHHHHHhchH-HHHHHHHHhHHHHHHHHHHhhCC----CCCHHhHHHHHHHHHHHhHHhcCCCCCCChHHHHHHHHH
Q 013472          283 ERVLKQHLAFGWY-CREELIKSTRPLVLFLARNYRGL----GIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIR  357 (442)
Q Consensus       283 eeeL~~~l~~G~~-Are~LI~~nlrLV~sIAkrY~g~----g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIR  357 (442)
                      ...|+..+..|+. |+++|+..|.+.|+.+|.++.++    ..+++|++||+|+++|+++.+|++. +..|.||++.+++
T Consensus        11 ~~~l~~~~~~gd~~a~~~l~~~~~~~l~~~~~~~~~~~~~~~~~aeDlvQe~fi~l~~~~~~~~~~-~~~~~~wl~~i~~   89 (189)
T PRK09648         11 LDALVAEAVAGDRRALREVLEIIRPLVVRYCRARLGGVERPGLSADDVAQEVCLAVITALPRYRDQ-GRPFLAFVYGIAA   89 (189)
T ss_pred             HHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHhcccccCCCCHHHHHHHHHHHHHHHHHHHhcc-CCcHHHHHHHHHH
Confidence            3567888899966 99999999999999999998765    4689999999999999999999864 4579999999999


Q ss_pred             HHHHHHHHhhcCceec-----cc------cc------HHHHHHHHHHHHHHHHHc--------CCCCcHHHHHHHhCCCH
Q 013472          358 KSISKMVARHARGIKI-----PC------KL------NREISKIQKARKALTNSH--------GKYPEDIEIAKYTGLSL  412 (442)
Q Consensus       358 naI~r~LRkqsr~irl-----P~------~v------~e~i~kI~ka~~~L~~el--------gr~PS~eEIAe~LGIS~  412 (442)
                      |.++++++++.+....     +.      ..      .+....+.+++..|+...        ..+.|++|||+.||+|+
T Consensus        90 n~~~d~~r~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~l~~~l~~L~~~~r~i~~l~~~~g~s~~EIA~~lgis~  169 (189)
T PRK09648         90 HKVADAHRAAGRDKAVPTEEVPERPSDDAGPEERALRSESSNRMRELLDTLPEKQREILILRVVVGLSAEETAEAVGSTP  169 (189)
T ss_pred             HHHHHHHHHhCCCccccccccccccccCCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHHCCCH
Confidence            9999999987653221     10      00      112234566666665543        26789999999999999


Q ss_pred             HHHHHHHHhccc
Q 013472          413 AEIRSASECLRI  424 (442)
Q Consensus       413 etVk~~l~~ar~  424 (442)
                      .+|+..+++++.
T Consensus       170 ~tV~~~l~Ra~~  181 (189)
T PRK09648        170 GAVRVAQHRALA  181 (189)
T ss_pred             HHHHHHHHHHHH
Confidence            999999988764

>PRK13919 putative RNA polymerase sigma E protein; Provisional

Probab=99.70  E-value=2.1e-16  Score=145.30  Aligned_cols=143  Identities=21%  Similarity=0.195  Sum_probs=115.4

Q ss_pred             CCHHHHHHHHHhchH-HHHHHHHHhHHHHHHHHHHhhCCCCCHHhHHHHHHHHHHHhHHhcCCCCCCChHHHHHHHHHHH
Q 013472          281 VSERVLKQHLAFGWY-CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKS  359 (442)
Q Consensus       281 ~deeeL~~~l~~G~~-Are~LI~~nlrLV~sIAkrY~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIRna  359 (442)
                      +++.+|+..++.|+. |++.++..|.+.|+.+|++|.+++.+++|++||+|+++|+++++|++.. ..|.+|++++++|.
T Consensus         8 ~~~~~l~~~~~~~d~~a~~~l~~~y~~~l~~~~~~~~~~~~~aeDlvQe~~i~l~~~~~~~~~~~-~~~~~wl~~ia~n~   86 (186)
T PRK13919          8 LSDEALLALVARGEEEALRALFRRYAGAFLALARRMGLDGAAAEDVVQEVFIRVWKKAKEFDPRR-GSARAWLLALAHHA   86 (186)
T ss_pred             cCHHHHHHHHHcCcHHHHHHHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHhhhccCccc-cchHHHHHHHHHHH
Confidence            467888888988976 9999999999999999999999999999999999999999999998754 36999999999999


Q ss_pred             HHHHHHhhcCcee-c------c------cc--c---HHHHHHHHHHHHHHHHHcC--------CCCcHHHHHHHhCCCHH
Q 013472          360 ISKMVARHARGIK-I------P------CK--L---NREISKIQKARKALTNSHG--------KYPEDIEIAKYTGLSLA  413 (442)
Q Consensus       360 I~r~LRkqsr~ir-l------P------~~--v---~e~i~kI~ka~~~L~~elg--------r~PS~eEIAe~LGIS~e  413 (442)
                      +++++|++.+... +      +      ..  .   ......+.++...|+....        .+.+++|||+.||||+.
T Consensus        87 ~~d~~rk~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~vl~l~~~~~~s~~eIA~~lgis~~  166 (186)
T PRK13919         87 AVDHVRRRAARPQPLEPDEREPEAFDLPGPGLDEEGHLDRTRLGRALKALSPEERRVIEVLYYQGYTHREAAQLLGLPLG  166 (186)
T ss_pred             HHHHHHhhhcccccccccccccccccCCCccccHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHHCcCHH
Confidence            9999997653211 1      0      00  0   0112336666666655432        67799999999999999


Q ss_pred             HHHHHHHhccc
Q 013472          414 EIRSASECLRI  424 (442)
Q Consensus       414 tVk~~l~~ar~  424 (442)
                      +|+..+++++.
T Consensus       167 ~V~~~l~ra~~  177 (186)
T PRK13919        167 TLKTRARRALS  177 (186)
T ss_pred             HHHHHHHHHHH
Confidence            99999988874

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

Probab=99.70  E-value=2.5e-16  Score=143.00  Aligned_cols=142  Identities=14%  Similarity=0.080  Sum_probs=115.7

Q ss_pred             CCHHHHHHHHHhchH-HHHHHHHHhHHHHHHHHHHhhCCCCCHHhHHHHHHHHHHHhHHhcCCCCCCChHHHHHHHHHHH
Q 013472          281 VSERVLKQHLAFGWY-CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKS  359 (442)
Q Consensus       281 ~deeeL~~~l~~G~~-Are~LI~~nlrLV~sIAkrY~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIRna  359 (442)
                      |+++.|+..+..|+. |++.++..|.+.|+.+|.++.++..+++|++||+++.+|+++++|++..  +|.||++.+++|.
T Consensus         1 ~~~~~l~~~~~~gd~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeD~~Qe~~l~~~~~~~~~~~~~--~~~~wl~~i~~n~   78 (169)
T TIGR02954         1 MNDEELVKKAKRGNKPAFESLIKKHKEKLYKTAFIYVKNEHDALDVIQETVYKAYLSIDKLKHPK--YFNTWLTRILINE   78 (169)
T ss_pred             CCHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHhccCcc--ccHHHHHHHHHHH
Confidence            457788888999966 9999999999999999999999999999999999999999999999753  6999999999999


Q ss_pred             HHHHHHhhcCceecccc----------cHHHHHHHHHHHHHHHHHc--------CCCCcHHHHHHHhCCCHHHHHHHHHh
Q 013472          360 ISKMVARHARGIKIPCK----------LNREISKIQKARKALTNSH--------GKYPEDIEIAKYTGLSLAEIRSASEC  421 (442)
Q Consensus       360 I~r~LRkqsr~irlP~~----------v~e~i~kI~ka~~~L~~el--------gr~PS~eEIAe~LGIS~etVk~~l~~  421 (442)
                      +++++|+..+...++..          ..+....+..+...|+...        -.+.|++|||+.||+|+++|+..+.+
T Consensus        79 ~~d~~R~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~i~~l~~~~g~s~~eiA~~lgis~~tv~~~l~R  158 (169)
T TIGR02954        79 CIDLLKKKKKVIPFDPNTSIEKGECETHADSRLDLYKAIDTLNDKYQTAIILRYYHDLTIKEIAEVMNKPEGTVKTYLHR  158 (169)
T ss_pred             HHHHHHhcCCcCccccccccccchhhhchHHHHHHHHHHHhCCHHHhHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHH
Confidence            99999987654322111          0111224555555555443        26789999999999999999999988


Q ss_pred             ccc
Q 013472          422 LRI  424 (442)
Q Consensus       422 ar~  424 (442)
                      ++.
T Consensus       159 a~~  161 (169)
T TIGR02954       159 ALK  161 (169)
T ss_pred             HHH
Confidence            874

This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family. This family is found in certain Bacillus and Clostridium species.

>PRK09640 RNA polymerase sigma factor SigX; Reviewed

Probab=99.70  E-value=3e-16  Score=145.44  Aligned_cols=144  Identities=15%  Similarity=0.109  Sum_probs=117.2

Q ss_pred             cCCCHHHHHHHHHh---chH-HHHHHHHHhHHHHHHHHHHhhCCCCCHHhHHHHHHHHHHHhHHhcCCCCCCChHHHHHH
Q 013472          279 AGVSERVLKQHLAF---GWY-CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQY  354 (442)
Q Consensus       279 ~g~deeeL~~~l~~---G~~-Are~LI~~nlrLV~sIAkrY~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~  354 (442)
                      ..++++.|+..++.   |+. |++.|+..|.+.|+.+|.+|.++..+++|++||+|+++|+++++|++.  .+|.||+++
T Consensus         6 ~~~~~~~li~~~~~~~~gd~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeDlvQe~f~~l~~~~~~~~~~--~~~~~wl~~   83 (188)
T PRK09640          6 RELNDEELVARVHVELFHVTRAYEELMRRYQRTLFNVCARYLGNDRDADDVCQEVMLKVLYGLKNFEGK--SKFKTWLYS   83 (188)
T ss_pred             CCCCHHHHHHHHhcccCCCHHHHHHHHHHHHHHHHHHHHHHhCCHhhHHHHHHHHHHHHHHHHHHhcCC--CcchHHHHH
Confidence            35677888888885   455 999999999999999999999999999999999999999999999963  479999999


Q ss_pred             HHHHHHHHHHHhhcCceecc---------c---c---cHHHHHHHHHHHHHHHHHcC--------CCCcHHHHHHHhCCC
Q 013472          355 WIRKSISKMVARHARGIKIP---------C---K---LNREISKIQKARKALTNSHG--------KYPEDIEIAKYTGLS  411 (442)
Q Consensus       355 wIRnaI~r~LRkqsr~irlP---------~---~---v~e~i~kI~ka~~~L~~elg--------r~PS~eEIAe~LGIS  411 (442)
                      +++|.+++++|+..+.....         .   .   ..+....+.++...|+....        .+.|++|||+.||||
T Consensus        84 ia~n~~~d~~R~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~v~~l~~~~g~s~~EIA~~lgis  163 (188)
T PRK09640         84 ITYNECITQYRKERRKRRLMDALSLDPLEEASEEKAPKPEERGGLDRWLVHVNPIDREILVLRFVAELEFQEIADIMHMG  163 (188)
T ss_pred             HHHHHHHHHHHHhcccccCcchhhhcccccccccccccHHHHHHHHHHHHhcChhheeeeeeHHhcCCCHHHHHHHHCCC
Confidence            99999999999764322111         0   0   11233457777777766542        567999999999999


Q ss_pred             HHHHHHHHHhccc
Q 013472          412 LAEIRSASECLRI  424 (442)
Q Consensus       412 ~etVk~~l~~ar~  424 (442)
                      +++|+..+.+++.
T Consensus       164 ~~tV~~~l~Ra~~  176 (188)
T PRK09640        164 LSATKMRYKRALD  176 (188)
T ss_pred             HHHHHHHHHHHHH
Confidence            9999999988874

>PRK12514 RNA polymerase sigma factor; Provisional

Probab=99.70  E-value=2.1e-16  Score=144.70  Aligned_cols=142  Identities=14%  Similarity=0.054  Sum_probs=114.4

Q ss_pred             CHHHHHHHHHhchH-HHHHHHHHhHHHHHHHHHHhhCCCCCHHhHHHHHHHHHHHhHHhcCCCCCCChHHHHHHHHHHHH
Q 013472          282 SERVLKQHLAFGWY-CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSI  360 (442)
Q Consensus       282 deeeL~~~l~~G~~-Are~LI~~nlrLV~sIAkrY~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIRnaI  360 (442)
                      +...|+..+..|+. |++.|+..|.+.|+.+|.++.++..+++|++||+|+++|+++++|++.. ..|.||++.+++|.+
T Consensus         5 ~~~~li~~~~~g~~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeD~~Qe~fl~~~~~~~~~~~~~-~~~~~wl~~ia~n~~   83 (179)
T PRK12514          5 DIEKLIVRVSLGDRDAFSSLYDATSAKLFGICLRVLKDRSEAEEALQDVYVKIWTKADRFAVSG-LSPMTWLITIARNHA   83 (179)
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHHcCHHHHHHHHHHHHHHHHHhHHhcCccc-ccHHHHHHHHHHHHH
Confidence            45678888888866 9999999999999999999999999999999999999999999999654 369999999999999


Q ss_pred             HHHHHhhcCce-ec------cc------cc---HHHHHHHHHHHHHHHHHcC--------CCCcHHHHHHHhCCCHHHHH
Q 013472          361 SKMVARHARGI-KI------PC------KL---NREISKIQKARKALTNSHG--------KYPEDIEIAKYTGLSLAEIR  416 (442)
Q Consensus       361 ~r~LRkqsr~i-rl------P~------~v---~e~i~kI~ka~~~L~~elg--------r~PS~eEIAe~LGIS~etVk  416 (442)
                      ++++|++.+.. .+      +.      ..   .+....+..+...|+....        .+.|++|||+.||||+.+|+
T Consensus        84 ~d~~R~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~l~~~l~~L~~~~r~i~~l~~~~g~s~~eIA~~lgis~~tV~  163 (179)
T PRK12514         84 IDRLRARKAVAVDIDEAHDLADPSPGPEAEVIAGDEGQRIDACLEELEKDRAAAVRRAYLEGLSYKELAERHDVPLNTMR  163 (179)
T ss_pred             HHHHHhcCCcccccccchhccccCCCHHHHHHhHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHHCCChHHHH
Confidence            99999865421 00      00      00   1122345566666654432        67899999999999999999


Q ss_pred             HHHHhccc
Q 013472          417 SASECLRI  424 (442)
Q Consensus       417 ~~l~~ar~  424 (442)
                      ..+++++.
T Consensus       164 ~~l~Rar~  171 (179)
T PRK12514        164 TWLRRSLL  171 (179)
T ss_pred             HHHHHHHH
Confidence            99998874

>PRK12537 RNA polymerase sigma factor; Provisional

Probab=99.69  E-value=2.9e-16  Score=144.81  Aligned_cols=143  Identities=16%  Similarity=0.103  Sum_probs=116.3

Q ss_pred             CCHHHHHHHHHhchH-HHHHHHHHhHHHHHHHHHHhhCCCCCHHhHHHHHHHHHHHhHHhcCCCCCCChHHHHHHHHHHH
Q 013472          281 VSERVLKQHLAFGWY-CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKS  359 (442)
Q Consensus       281 ~deeeL~~~l~~G~~-Are~LI~~nlrLV~sIAkrY~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIRna  359 (442)
                      ++..+|+..+..|+. |++.|+..|.+.|+.++.++.++..+++|++||+|+.+|+.+++|++.. ..|.+|++.+++|.
T Consensus         8 ~~~~~l~~~~~~~d~~a~~~l~~~~~~~l~~~~~~~~~~~~~AeDivQe~fl~l~~~~~~~~~~~-~~~~~wL~~iarn~   86 (182)
T PRK12537          8 FDYEACLLACARGDRRALQALYQQESARLLGVARRIVRDRALAEDIVHDAFIKIWTGAASFDPAR-GSARGWIYSVTRHL   86 (182)
T ss_pred             hhHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHhCCHhHHHHHHHHHHHHHHhccccCCccc-ccHHHHHHHHHHHH
Confidence            355678999999966 9999999999999999999999999999999999999999999998643 37999999999999


Q ss_pred             HHHHHHhhcCceeccc----------c------cHHHHHHHHHHHHHHHHHc--------CCCCcHHHHHHHhCCCHHHH
Q 013472          360 ISKMVARHARGIKIPC----------K------LNREISKIQKARKALTNSH--------GKYPEDIEIAKYTGLSLAEI  415 (442)
Q Consensus       360 I~r~LRkqsr~irlP~----------~------v~e~i~kI~ka~~~L~~el--------gr~PS~eEIAe~LGIS~etV  415 (442)
                      ++++++++.+......          .      ..+....+.++...|+...        -.+.+++|||+.||||+++|
T Consensus        87 ~~d~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~i~~l~~~~~~s~~eIA~~lgis~~tV  166 (182)
T PRK12537         87 ALNVLRDTRREVVLDDDAEETAQTLHEIIDDFDLWANSGKIHRCLEQLEPARRNCILHAYVDGCSHAEIAQRLGAPLGTV  166 (182)
T ss_pred             HHHHHHhccccCccccchhhhcccccchHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHHCCChhhH
Confidence            9999998864322110          0      0112334666666655543        26789999999999999999


Q ss_pred             HHHHHhccc
Q 013472          416 RSASECLRI  424 (442)
Q Consensus       416 k~~l~~ar~  424 (442)
                      +..+++++.
T Consensus       167 ~~~l~ra~~  175 (182)
T PRK12537        167 KAWIKRSLK  175 (182)
T ss_pred             HHHHHHHHH
Confidence            999998874

>PRK12524 RNA polymerase sigma factor; Provisional

Probab=99.69  E-value=3.7e-16  Score=145.83  Aligned_cols=144  Identities=17%  Similarity=0.137  Sum_probs=116.8

Q ss_pred             CCCHHHHHHHHHhchH-HHHHHHHHhHHHHHHHHHHhhCCCCCHHhHHHHHHHHHHHhHHhcCCCCCCChHHHHHHHHHH
Q 013472          280 GVSERVLKQHLAFGWY-CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRK  358 (442)
Q Consensus       280 g~deeeL~~~l~~G~~-Are~LI~~nlrLV~sIAkrY~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIRn  358 (442)
                      .+++..|+.++..|+. |++.|+..|.+.|+.+|.++.++..+++|++||+++++|+.+.+|++.. ..|.||++.+++|
T Consensus        10 ~~~~~~li~~~~~gd~~a~~~l~~~y~~~l~~~~~~~~~~~~~AeDlvQe~~l~l~~~~~~~~~~~-~~~~~wl~~ia~n   88 (196)
T PRK12524         10 DVSDEALLVLYANGDPAAARALTLRLAPRALAVATRVLGDRAEAEDVTQEAMLRLWRIAPDWRQGE-ARVSTWLYRVVCN   88 (196)
T ss_pred             CcCHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhhhcccccc-chHHHHHHHHHHH
Confidence            4567889999999966 9999999999999999999999999999999999999999999998533 4799999999999


Q ss_pred             HHHHHHHhhcCce-ec---c------c---c---cHHHHHHHHHHHHHHHHHc--------CCCCcHHHHHHHhCCCHHH
Q 013472          359 SISKMVARHARGI-KI---P------C---K---LNREISKIQKARKALTNSH--------GKYPEDIEIAKYTGLSLAE  414 (442)
Q Consensus       359 aI~r~LRkqsr~i-rl---P------~---~---v~e~i~kI~ka~~~L~~el--------gr~PS~eEIAe~LGIS~et  414 (442)
                      .+++++|++.+.. .+   +      .   .   ..+....+.++...|+...        -.+.+++|||+.||+|+.+
T Consensus        89 ~~~d~~Rk~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~i~~L~~~~g~s~~eIA~~lgis~~t  168 (196)
T PRK12524         89 LCTDRLRRRRRASVDLDDAPEPADAAPGAEEALIEGDRMRALDAALAALPERQRQAVVLRHIEGLSNPEIAEVMEIGVEA  168 (196)
T ss_pred             HHHHHHHhhcCCCCCccccccccccCCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHHCcCHHH
Confidence            9999999764421 11   0      0   0   0112234666666665543        3678999999999999999


Q ss_pred             HHHHHHhccc
Q 013472          415 IRSASECLRI  424 (442)
Q Consensus       415 Vk~~l~~ar~  424 (442)
                      |+..+++++.
T Consensus       169 V~~~l~Ra~~  178 (196)
T PRK12524        169 VESLTARGKR  178 (196)
T ss_pred             HHHHHHHHHH
Confidence            9999998874

>PRK09638 RNA polymerase sigma factor SigY; Reviewed

Probab=99.69  E-value=4.7e-16  Score=141.62  Aligned_cols=143  Identities=16%  Similarity=0.048  Sum_probs=116.6

Q ss_pred             CCCHHHHHHHHHhchH-HHHHHHHHhHHHHHHHHHHhhCCCCCHHhHHHHHHHHHHHhHHhcCCCCCCChHHHHHHHHHH
Q 013472          280 GVSERVLKQHLAFGWY-CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRK  358 (442)
Q Consensus       280 g~deeeL~~~l~~G~~-Are~LI~~nlrLV~sIAkrY~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIRn  358 (442)
                      .|++..++..+..|+. |++.|+..|.+.|+.+|++|.++..+++|++||+|+++|++++.|++.  .+|.+|++.+++|
T Consensus         2 ~~~~~~l~~~~~~~d~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeD~vQe~~l~l~~~~~~~~~~--~~~~~wl~~i~~n   79 (176)
T PRK09638          2 QMDEKELIQKAKKGDDAALTTLFQQHYSFLYKYLLKLTLDPDLAEDLVQETMLKAIENLSSFQGR--SKFSTWLISIASR   79 (176)
T ss_pred             CccHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHcCCHhHHHHHHHHHHHHHHHHHHhcCCc--ccHHHHHHHHHHH
Confidence            4567888899999976 999999999999999999999999999999999999999999999874  4799999999999


Q ss_pred             HHHHHHHhhcCceeccc-------c-c-------HHHHHHHHHHHHHHHHHcC--------CCCcHHHHHHHhCCCHHHH
Q 013472          359 SISKMVARHARGIKIPC-------K-L-------NREISKIQKARKALTNSHG--------KYPEDIEIAKYTGLSLAEI  415 (442)
Q Consensus       359 aI~r~LRkqsr~irlP~-------~-v-------~e~i~kI~ka~~~L~~elg--------r~PS~eEIAe~LGIS~etV  415 (442)
                      .+++++++.++......       . .       ......+.++...|+....        .+.+++|||+.||+|+.+|
T Consensus        80 ~~~d~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~v~~l~~~~g~s~~eIA~~l~is~~~V  159 (176)
T PRK09638         80 LYKDHLRKQKREKLRLQRAKEETLRKEKWEAAIKGAEWSEMLDALSKLDPEFRAPVILKHYYGYTYEEIAKMLNIPEGTV  159 (176)
T ss_pred             HHHHHHHHhccccchhhhcccccCCccchHHHHHhhhHHHHHHHHHcCCHHHhheeeehhhcCCCHHHHHHHHCCChhHH
Confidence            99999998754322110       0 0       1123345556666655442        5679999999999999999


Q ss_pred             HHHHHhccc
Q 013472          416 RSASECLRI  424 (442)
Q Consensus       416 k~~l~~ar~  424 (442)
                      +..+.+++.
T Consensus       160 ~~~l~ra~~  168 (176)
T PRK09638        160 KSRVHHGIK  168 (176)
T ss_pred             HHHHHHHHH
Confidence            999988874

>TIGR02948 SigW_bacill RNA polymerase sigma-W factor

Probab=99.69  E-value=4.4e-16  Score=142.70  Aligned_cols=140  Identities=14%  Similarity=0.069  Sum_probs=112.3

Q ss_pred             HHHHHHHHHhchH-HHHHHHHHhHHHHHHHHHHhhCCCCCHHhHHHHHHHHHHHhHHhcCCCCCCChHHHHHHHHHHHHH
Q 013472          283 ERVLKQHLAFGWY-CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSIS  361 (442)
Q Consensus       283 eeeL~~~l~~G~~-Are~LI~~nlrLV~sIAkrY~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIRnaI~  361 (442)
                      ++.|+..++.|+. |+++|+..|.+.|+.+|.+|.+++.+++|++||+|+++|+++.+|++..  .|.||++.+++|.+.
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            4567888999976 9999999999999999999999999999999999999999999999865  599999999999999


Q ss_pred             HHHHhhcCceeccc-------------------cc------HHHHHHHHHHHHHHHHHc--------CCCCcHHHHHHHh
Q 013472          362 KMVARHARGIKIPC-------------------KL------NREISKIQKARKALTNSH--------GKYPEDIEIAKYT  408 (442)
Q Consensus       362 r~LRkqsr~irlP~-------------------~v------~e~i~kI~ka~~~L~~el--------gr~PS~eEIAe~L  408 (442)
                      +++|+..+......                   ..      .+....+.++...|+...        -.+.|++|||+.|
T Consensus        83 ~~~rk~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~l~~~l~~L~~~~r~v~~l~~~~g~s~~eIA~~l  162 (187)
T TIGR02948        83 DRLRKRKPDFYLDDEVQGTDGLTMESQLAADEAPPEDQVISLELRDTIQQEIQALPPKYRMVIVLKYMEDLSLKEISEIL  162 (187)
T ss_pred             HHHHhhcccccccccccCccccccccccccCcCCHHHHHHHHHHHHHHHHHHHhCCHHHhHHhhhHHhcCCCHHHHHHHH
Confidence            99998654211000                   00      011223555555554433        2567999999999


Q ss_pred             CCCHHHHHHHHHhccc
Q 013472          409 GLSLAEIRSASECLRI  424 (442)
Q Consensus       409 GIS~etVk~~l~~ar~  424 (442)
                      |+|+.+|+..+++++.
T Consensus       163 gis~~~v~~~l~Rar~  178 (187)
T TIGR02948       163 DLPVGTVKTRIHRGRE  178 (187)
T ss_pred             CCCHHHHHHHHHHHHH
Confidence            9999999999998874

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

>PRK06759 RNA polymerase factor sigma-70; Validated

Probab=99.69  E-value=3.9e-16  Score=139.00  Aligned_cols=128  Identities=16%  Similarity=0.146  Sum_probs=103.4

Q ss_pred             HHHHHHHHHhHHHHHHHHHHhhCCCCCHHhHHHHHHHHHHHhHHhcCCCCCCChHHHHHHHHHHHHHHHHHhhcCc----
Q 013472          295 YCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARG----  370 (442)
Q Consensus       295 ~Are~LI~~nlrLV~sIAkrY~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIRnaI~r~LRkqsr~----  370 (442)
                      .|+++|+..|.++|+.+++++ +...++||++|||++++|+++++|++..| .|.+|++.+++|.+++++|++.+.    
T Consensus         4 ~af~~l~~~y~~~l~~~~~~~-~~~~~aeDi~Qe~~l~l~~~~~~~~~~~~-~f~~wl~~i~~n~~ld~~rk~~~~~~~~   81 (154)
T PRK06759          4 ATFTEAVVLYEGLIVNQIKKL-GIYQDYEEYYQCGLIGLWHAYERYDEKKG-SFPAYAVVTVRGYILERLKKEFAVQEKC   81 (154)
T ss_pred             ccHHHHHHHHHHHHHHHHHHh-CCcccHHHHHHHHHHHHHHHHHHhCccCC-chHHHHHHHHHHHHHHHHHHHHhhcccc
Confidence            489999999999999999986 56789999999999999999999998666 799999999999999999987431    


Q ss_pred             --eecccc---cHHHHHHHHHHHHHHHHHc--------CCCCcHHHHHHHhCCCHHHHHHHHHhccc
Q 013472          371 --IKIPCK---LNREISKIQKARKALTNSH--------GKYPEDIEIAKYTGLSLAEIRSASECLRI  424 (442)
Q Consensus       371 --irlP~~---v~e~i~kI~ka~~~L~~el--------gr~PS~eEIAe~LGIS~etVk~~l~~ar~  424 (442)
                        ...|..   ..+....+..+...|+...        ..+.|++|||+.||+|+++|+..+.+++.
T Consensus        82 ~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~ii~l~~~~~~s~~EIA~~l~is~~tV~~~~~ra~~  148 (154)
T PRK06759         82 VCVGEYEDHFHFEDVEMKVKDFMSVLDEKEKYIIFERFFVGKTMGEIALETEMTYYQVRWIYRQALE  148 (154)
T ss_pred             cccCCCcccccHHHHHHHHHHHHHhCCHHHHHHHHHHHhcCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence              111222   1223345666666665443        37789999999999999999999988764

>PRK09643 RNA polymerase sigma factor SigM; Reviewed

Probab=99.68  E-value=5.6e-16  Score=144.55  Aligned_cols=142  Identities=16%  Similarity=0.117  Sum_probs=117.4

Q ss_pred             CCHHHHHHHHHhchH-HHHHHHHHhHHHHHHHHHHhhCCCCCHHhHHHHHHHHHHHhHHhcCCCCCCChHHHHHHHHHHH
Q 013472          281 VSERVLKQHLAFGWY-CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKS  359 (442)
Q Consensus       281 ~deeeL~~~l~~G~~-Are~LI~~nlrLV~sIAkrY~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIRna  359 (442)
                      +++..++..+..|+. +++.++..|.+.|++++.++.++..++||++||+|+.+|+++++|++..  .|.+|++.+++|.
T Consensus        12 ~~~~~l~~~~~~gd~~~~~~l~~~y~~~l~~~~~~~~~~~~~AeDlvQEvfl~l~~~~~~~~~~~--~f~~wL~~i~rn~   89 (192)
T PRK09643         12 RSDAELLAAHVAGDRYAFGELFRRHHRRLWAVARRTSGTREDAADALQDAMLSAHRAAGSFRGDA--AVSSWLHRIVVNA   89 (192)
T ss_pred             cCHHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHHcCCHhhHHHHHHHHHHHHHHHHHhcCCCC--ccHHHHHHHHHHH
Confidence            467888999999976 9999999999999999999999999999999999999999999999753  6999999999999


Q ss_pred             HHHHHHhhcCceecc-----------cc---cHHHHHHHHHHHHHHHHHcC--------CCCcHHHHHHHhCCCHHHHHH
Q 013472          360 ISKMVARHARGIKIP-----------CK---LNREISKIQKARKALTNSHG--------KYPEDIEIAKYTGLSLAEIRS  417 (442)
Q Consensus       360 I~r~LRkqsr~irlP-----------~~---v~e~i~kI~ka~~~L~~elg--------r~PS~eEIAe~LGIS~etVk~  417 (442)
                      +++++|+.++....+           ..   ..+....+..+...|+....        .+.+++|||+.||+|+.+|+.
T Consensus        90 ~~d~~Rk~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~l~~~l~~Lp~~~r~i~~l~~~~g~s~~EIA~~lg~s~~tV~~  169 (192)
T PRK09643         90 CLDRLRRAKARPTVPLDDVYPVAQLERDPTARVETALAVQRALMRLPVEQRAALVAVDMQGYSVADAARMLGVAEGTVKS  169 (192)
T ss_pred             HHHHHHccccCCCCCccccccccCCcccHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHH
Confidence            999999765432211           01   11233456677777665442        678999999999999999999


Q ss_pred             HHHhccc
Q 013472          418 ASECLRI  424 (442)
Q Consensus       418 ~l~~ar~  424 (442)
                      .+.+++.
T Consensus       170 rl~rar~  176 (192)
T PRK09643        170 RCARGRA  176 (192)
T ss_pred             HHHHHHH
Confidence            9988874

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

Probab=99.68  E-value=5.4e-16  Score=139.78  Aligned_cols=137  Identities=15%  Similarity=0.067  Sum_probs=109.7

Q ss_pred             HHHHHhchH-HHHHHHHHhHHHHHHHHHHhhCCCCCHHhHHHHHHHHHHHhHHhcCCCCCCChHHHHHHHHHHHHHHHHH
Q 013472          287 KQHLAFGWY-CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVA  365 (442)
Q Consensus       287 ~~~l~~G~~-Are~LI~~nlrLV~sIAkrY~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIRnaI~r~LR  365 (442)
                      +..+.+|+. |++.|+..|.+.++.++.++.++..+++|++||+|+++|+++++|+...+ .|.+|++.+++|.+++++|
T Consensus         2 i~~~~~~d~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeD~vQe~~l~l~~~~~~~~~~~~-~~~~wl~~i~~n~~~d~~R   80 (170)
T TIGR02952         2 LERAQDREEDAFARIYETYSDRVYRYIYYRVGCKYTAEDLTSEVFERVLRKIDSFKEQKN-SFEAWLFTIARNVVNDYFR   80 (170)
T ss_pred             hHHHHccCHHHHHHHHHHHHHHHHHHHHHHHCChhhHHHHHHHHHHHHHHhHHhcccccc-cHHHHHHHHHHHHHHHHHH
Confidence            456777866 99999999999999999999999999999999999999999999997544 7999999999999999999


Q ss_pred             hhcCceeccc-----------cc------HHHHHHHHHHHHHHHHHc--------CCCCcHHHHHHHhCCCHHHHHHHHH
Q 013472          366 RHARGIKIPC-----------KL------NREISKIQKARKALTNSH--------GKYPEDIEIAKYTGLSLAEIRSASE  420 (442)
Q Consensus       366 kqsr~irlP~-----------~v------~e~i~kI~ka~~~L~~el--------gr~PS~eEIAe~LGIS~etVk~~l~  420 (442)
                      ++.+....+.           ..      .+....+.++...|+...        -.+.+++|||+.||||+.+|+..++
T Consensus        81 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~vl~l~~~~g~s~~eIA~~l~is~~tv~~~l~  160 (170)
T TIGR02952        81 GSKRHPLFSLDVFKELLSNEPNPEEAILKEEANEKLLKALKILTPKQQHVIALRFGQNLPIAEVARILGKTEGAVKILQF  160 (170)
T ss_pred             hcCCCCCCcHHHHhhcCCCCCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHhcCCCHHHHHHHHCCCHHHHHHHHH
Confidence            8754322110           00      112234555555555433        3678999999999999999999998


Q ss_pred             hccc
Q 013472          421 CLRI  424 (442)
Q Consensus       421 ~ar~  424 (442)
                      +++.
T Consensus       161 ra~~  164 (170)
T TIGR02952       161 RAIK  164 (170)
T ss_pred             HHHH
Confidence            8764

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.

>PRK09641 RNA polymerase sigma factor SigW; Provisional

Probab=99.68  E-value=5.1e-16  Score=142.23  Aligned_cols=142  Identities=15%  Similarity=0.086  Sum_probs=114.3

Q ss_pred             CCHHHHHHHHHhchH-HHHHHHHHhHHHHHHHHHHhhCCCCCHHhHHHHHHHHHHHhHHhcCCCCCCChHHHHHHHHHHH
Q 013472          281 VSERVLKQHLAFGWY-CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKS  359 (442)
Q Consensus       281 ~deeeL~~~l~~G~~-Are~LI~~nlrLV~sIAkrY~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIRna  359 (442)
                      ...+.|+..++.|+. |++.++..|.++|+.+|+++.++..+++|++||++++||+++++|++..  +|.+|++.+++|.
T Consensus         3 ~~~~~li~~~~~~d~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeDivQe~~l~l~~~~~~~~~~~--~~~~wl~~iarn~   80 (187)
T PRK09641          3 LLIKRLIKQVKKGDQNAFAELVDLYKDKIYQLCYRMLGNRHEAEDAAQEAFIRAYVNIDSYDINR--KFSTWLYRIATNL   80 (187)
T ss_pred             hHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHhhCCCc--chhHHHHHHHHHH
Confidence            345678888999976 9999999999999999999999999999999999999999999999753  6999999999999


Q ss_pred             HHHHHHhhcCceec----------------ccc---c------HHHHHHHHHHHHHHHHHc--------CCCCcHHHHHH
Q 013472          360 ISKMVARHARGIKI----------------PCK---L------NREISKIQKARKALTNSH--------GKYPEDIEIAK  406 (442)
Q Consensus       360 I~r~LRkqsr~irl----------------P~~---v------~e~i~kI~ka~~~L~~el--------gr~PS~eEIAe  406 (442)
                      +++++|++++...+                +..   .      .+....+.++...|+...        -.+.+++|||+
T Consensus        81 ~~d~~R~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~il~l~~~~~~s~~eIA~  160 (187)
T PRK09641         81 TIDRLRKRKPDYYLDAEVAGTEGLTMYSQLAADDALPEEQVVSLELQETIQEAILQLPEKYRTVIVLKYIEDLSLKEISE  160 (187)
T ss_pred             HHHHHHhcCccccccccccCCcchhhhcccccCcCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHhhhHHhhCCCHHHHHH
Confidence            99999987543211                000   0      111223555555554433        26779999999


Q ss_pred             HhCCCHHHHHHHHHhccc
Q 013472          407 YTGLSLAEIRSASECLRI  424 (442)
Q Consensus       407 ~LGIS~etVk~~l~~ar~  424 (442)
                      .||||+++|+..+++++.
T Consensus       161 ~lgis~~~v~~~l~Rar~  178 (187)
T PRK09641        161 ILDLPVGTVKTRIHRGRE  178 (187)
T ss_pred             HHCCCHHHHHHHHHHHHH
Confidence            999999999999988874

>PRK12534 RNA polymerase sigma factor; Provisional

Probab=99.67  E-value=5.5e-16  Score=142.93  Aligned_cols=142  Identities=15%  Similarity=0.034  Sum_probs=114.3

Q ss_pred             CHHHHHHHHHhchH-HHHHHHHHhHHHHHHHHHHhhCCCCCHHhHHHHHHHHHHHhHHhcCCCCCCChHHHHHHHHHHHH
Q 013472          282 SERVLKQHLAFGWY-CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSI  360 (442)
Q Consensus       282 deeeL~~~l~~G~~-Are~LI~~nlrLV~sIAkrY~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIRnaI  360 (442)
                      +...++..+..|+. +++.|+..|.+.|+.+|+++.++..++||++||+|+++|+++++|++.++ .|.||++.+++|.+
T Consensus        11 ~~~~l~~~~~~~~~~~~~~l~~~y~~~l~~~~~~~~~~~~~aeDlvQe~fl~~~~~~~~~~~~~~-~~~~wl~~I~~n~~   89 (187)
T PRK12534         11 ETGRLLTATAGGDRHAFEALYRQTSPKLFGVCLRMIPQRAEAEEVLQDVFTLIWHKAGQFDPSRA-RGLTWLAMIARNKA   89 (187)
T ss_pred             hHHHHHHHHHcCCHHHHHHHHHHhhHHHHHHHHHHhcCHHHHHHHHHHHHHHHHhccccCCcccc-cHHHHHHHHHHHHH
Confidence            34567777778865 99999999999999999999999999999999999999999999998654 68999999999999


Q ss_pred             HHHHHhhcCce-e-----ccc---------c---cHHHHHHHHHHHHHHHHHc--------CCCCcHHHHHHHhCCCHHH
Q 013472          361 SKMVARHARGI-K-----IPC---------K---LNREISKIQKARKALTNSH--------GKYPEDIEIAKYTGLSLAE  414 (442)
Q Consensus       361 ~r~LRkqsr~i-r-----lP~---------~---v~e~i~kI~ka~~~L~~el--------gr~PS~eEIAe~LGIS~et  414 (442)
                      ++++|++.+.. .     .+.         .   ..+....+..++..|+...        -.+.+++|||+.||||+++
T Consensus        90 ~d~~R~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~l~~~l~~L~~~~r~i~~l~~~~g~s~~eIA~~lgis~~~  169 (187)
T PRK12534         90 IDHLRANAPQRRNVALDDAGELRAADASPLERTERASTRRRIDHCLAELEPPRSELIRTAFFEGITYEELAARTDTPIGT  169 (187)
T ss_pred             HHHHHhcccccccccccchhhhccccCChhhHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHhCCChhH
Confidence            99999865321 0     110         0   1122345666666665543        2678999999999999999


Q ss_pred             HHHHHHhccc
Q 013472          415 IRSASECLRI  424 (442)
Q Consensus       415 Vk~~l~~ar~  424 (442)
                      |+..+++++.
T Consensus       170 v~~~l~Rar~  179 (187)
T PRK12534        170 VKSWIRRGLA  179 (187)
T ss_pred             HHHHHHHHHH
Confidence            9999998874

>PRK12531 RNA polymerase sigma factor; Provisional

Probab=99.67  E-value=6e-16  Score=144.25  Aligned_cols=141  Identities=14%  Similarity=0.058  Sum_probs=112.9

Q ss_pred             HHHHHHHHHhchH-HHHHHHHHhHHHHHHHHHHhhCCCCCHHhHHHHHHHHHHHhHHhcCCCCCCChHHHHHHHHHHHHH
Q 013472          283 ERVLKQHLAFGWY-CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSIS  361 (442)
Q Consensus       283 eeeL~~~l~~G~~-Are~LI~~nlrLV~sIAkrY~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIRnaI~  361 (442)
                      ..+|+..+..|+. |++.|+..|.+.|+.+|.++.++..+++|++||+|+.+|+...+|++..+ .|.||++.+++|.++
T Consensus        14 ~~~li~~~~~~d~~af~~l~~~y~~~l~~~~~~~~~~~~~AeDlvQev~l~l~~~~~~~~~~~~-~~~~wL~~iarn~~l   92 (194)
T PRK12531         14 WLECMEKVKSRDKQAFALVFSYYAPKLKQFAMKHVGNEQVAMEMVQETMSTVWQKAHLFDGQKS-ALSTWIYTIIRNLCF   92 (194)
T ss_pred             HHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhHHhcCcccc-hHHHHHHHHHHHHHH
Confidence            3457888888976 99999999999999999999999999999999999999999999997544 699999999999999


Q ss_pred             HHHHhhcCcee-c------cc---------c-cH---HHHHHHHHHHHHHHHHcC--------CCCcHHHHHHHhCCCHH
Q 013472          362 KMVARHARGIK-I------PC---------K-LN---REISKIQKARKALTNSHG--------KYPEDIEIAKYTGLSLA  413 (442)
Q Consensus       362 r~LRkqsr~ir-l------P~---------~-v~---e~i~kI~ka~~~L~~elg--------r~PS~eEIAe~LGIS~e  413 (442)
                      +++|++++... .      +.         . ..   .....+.++...|+.+..        .+.+++|||+.||||++
T Consensus        93 d~~Rk~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~l~~~l~~Lp~~~r~v~~l~~~eg~s~~EIA~~lgis~~  172 (194)
T PRK12531         93 DLLRKQKGKDLHIHADDIWPSDYYPPDLVDHYSPEQDMLKEQVMKFLDRLPKAQRDVLQAVYLEELPHQQVAEMFDIPLG  172 (194)
T ss_pred             HHHHHhcccccccchhhcccccccccccccccCHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHhCcCHH
Confidence            99998653211 0      00         0 00   112345556666555432        57799999999999999


Q ss_pred             HHHHHHHhccc
Q 013472          414 EIRSASECLRI  424 (442)
Q Consensus       414 tVk~~l~~ar~  424 (442)
                      +|+..+++++.
T Consensus       173 tVk~rl~ra~~  183 (194)
T PRK12531        173 TVKSRLRLAVE  183 (194)
T ss_pred             HHHHHHHHHHH
Confidence            99999988874

>PRK12538 RNA polymerase sigma factor; Provisional

Probab=99.67  E-value=8.8e-16  Score=148.55  Aligned_cols=143  Identities=18%  Similarity=0.133  Sum_probs=115.7

Q ss_pred             CCHHHHHHHHHhchH-HHHHHHHHhHHHHHHHHHHhhCCCCCHHhHHHHHHHHHHHhHHhcCCCCCCChHHHHHHHHHHH
Q 013472          281 VSERVLKQHLAFGWY-CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKS  359 (442)
Q Consensus       281 ~deeeL~~~l~~G~~-Are~LI~~nlrLV~sIAkrY~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIRna  359 (442)
                      .++.+|+..++.|+. |++.|+..|.+.|+.+++++.++..++||++||+|+++|+.+++|++..+ .|.+|++.+++|.
T Consensus        48 ~~d~~Li~~~~~gd~~af~~L~~~y~~~l~~~~~~~~~d~~dAEDivQEvfl~l~~~~~~~~~~~~-~f~~WL~~IarN~  126 (233)
T PRK12538         48 DEDEELLDRLATDDEAAFRLLVERHIDRAYAIALRIVGNRADAEDVVQDTMLKVWTHRGRWQHGRA-KFSTWLYRVVSNR  126 (233)
T ss_pred             ccHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHcccccc-cHHHHHHHHHHHH
Confidence            456788888999976 99999999999999999999999999999999999999999999986544 7999999999999


Q ss_pred             HHHHHHhhcCce--ec-------ccc-----cHHHHHHHHHHHHHHHHHcC--------CCCcHHHHHHHhCCCHHHHHH
Q 013472          360 ISKMVARHARGI--KI-------PCK-----LNREISKIQKARKALTNSHG--------KYPEDIEIAKYTGLSLAEIRS  417 (442)
Q Consensus       360 I~r~LRkqsr~i--rl-------P~~-----v~e~i~kI~ka~~~L~~elg--------r~PS~eEIAe~LGIS~etVk~  417 (442)
                      +++++|++.+..  ..       |..     ..+....+..+...|+....        .+.|++|||+.||+|+++|+.
T Consensus       127 ~id~~Rk~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~l~~~L~~Lp~~~R~v~~L~~~eg~s~~EIA~~Lgis~~tVk~  206 (233)
T PRK12538        127 CIDLRRKPRTENVDAVPEVADGKPDAVSVIERNELSDLLEAAMQRLPEQQRIAVILSYHENMSNGEIAEVMDTTVAAVES  206 (233)
T ss_pred             HHHHHHhhcccccccccccccCCCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHhhhHHhcCCCHHHHHHHHCcCHHHHHH
Confidence            999999764321  11       110     01122346666666655432        677999999999999999999


Q ss_pred             HHHhccc
Q 013472          418 ASECLRI  424 (442)
Q Consensus       418 ~l~~ar~  424 (442)
                      .+++++.
T Consensus       207 ~l~RAr~  213 (233)
T PRK12538        207 LLKRGRQ  213 (233)
T ss_pred             HHHHHHH
Confidence            9988874

>TIGR02939 RpoE_Sigma70 RNA polymerase sigma factor RpoE

Probab=99.67  E-value=1.6e-15  Score=139.38  Aligned_cols=142  Identities=15%  Similarity=0.087  Sum_probs=114.0

Q ss_pred             CCHHHHHHHHHhchH-HHHHHHHHhHHHHHHHHHHhhCCCCCHHhHHHHHHHHHHHhHHhcCCCCCCChHHHHHHHHHHH
Q 013472          281 VSERVLKQHLAFGWY-CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKS  359 (442)
Q Consensus       281 ~deeeL~~~l~~G~~-Are~LI~~nlrLV~sIAkrY~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIRna  359 (442)
                      .++..|+..+..|+. |++.|+..|.+.|+.+|+++.++..+++|++||+|+++|+++.+|++.  .+|.+|++.+++|.
T Consensus         5 ~~d~~l~~~~~~gd~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeDlvQe~fi~l~~~~~~~~~~--~~~~~wl~~iarn~   82 (190)
T TIGR02939         5 ELDLELVERVQRGEKQAFDLLVRKYQHKVVALVGRYVRDSSEVEDVAQEAFVKAYRALSSFRGD--SAFYTWLYRIAVNT   82 (190)
T ss_pred             ccHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHhCCHhhHHHHHHHHHHHHHHhHHhcCCC--CccHhHHHHHHHHH
Confidence            356778889999976 999999999999999999999999999999999999999999999975  36999999999999


Q ss_pred             HHHHHHhhcCceecc----------------------cc---cHHHHHHHHHHHHHHHHHcC--------CCCcHHHHHH
Q 013472          360 ISKMVARHARGIKIP----------------------CK---LNREISKIQKARKALTNSHG--------KYPEDIEIAK  406 (442)
Q Consensus       360 I~r~LRkqsr~irlP----------------------~~---v~e~i~kI~ka~~~L~~elg--------r~PS~eEIAe  406 (442)
                      ++++++++.+.....                      ..   ..+....+..+...|+....        .+.+++|||+
T Consensus        83 ~~~~~r~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~l~~~l~~L~~~~r~v~~l~~~~~~s~~EIA~  162 (190)
T TIGR02939        83 AKNHLVAQGRRPPTSDVEIEDAEHFEGADRLREIDTPERLLLSRELEQTVMRAVEALPEDLRTAITLRELEGLSYEDIAR  162 (190)
T ss_pred             HHHHHHHhccCCCcccccccchhhhcccccccccCChHHHHHHHHHHHHHHHHHHcCCHHHhhhhhhhhhcCCCHHHHHH
Confidence            999998654422110                      00   00112235556666655432        5679999999


Q ss_pred             HhCCCHHHHHHHHHhccc
Q 013472          407 YTGLSLAEIRSASECLRI  424 (442)
Q Consensus       407 ~LGIS~etVk~~l~~ar~  424 (442)
                      .||||+.+|+..+++++.
T Consensus       163 ~lgis~~tv~~~l~rar~  180 (190)
T TIGR02939       163 IMDCPVGTVRSRIFRARE  180 (190)
T ss_pred             HHCcCHHHHHHHHHHHHH
Confidence            999999999999998875

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

>PRK12519 RNA polymerase sigma factor; Provisional

Probab=99.66  E-value=1.2e-15  Score=141.36  Aligned_cols=141  Identities=21%  Similarity=0.193  Sum_probs=112.8

Q ss_pred             CHHHHHHHHHhchH-HHHHHHHHhHHHHHHHHHHhhCCCCCHHhHHHHHHHHHHHhHHhcCCCCCCChHHHHHHHHHHHH
Q 013472          282 SERVLKQHLAFGWY-CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSI  360 (442)
Q Consensus       282 deeeL~~~l~~G~~-Are~LI~~nlrLV~sIAkrY~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIRnaI  360 (442)
                      ++.+|+..+..|+. |++.|+..|.+.|+.+++++.++..+++|++||+|+++|+. ..|++..+ .|.||++.+++|.+
T Consensus        15 ~~~~l~~~~~~gd~~a~~~L~~~y~~~l~~~~~~~~~~~~~aeDlvQe~fl~l~~~-~~~~~~~~-~f~~wl~~iarn~~   92 (194)
T PRK12519         15 SDAELFSALKAGQSAALGVLYDRHAGLVYGLALKILGNSQEAEDLTQEIFLSLWRK-SSYDPKRG-SLSSYLLTLTRSRA   92 (194)
T ss_pred             cHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHh-cCCCcccc-cHHHHHHHHHHHHH
Confidence            56788888999976 99999999999999999999999999999999999999976 67887554 79999999999999


Q ss_pred             HHHHHhhcCceecc------------c-c------cHHHHHHHHHHHHHHHHHcC--------CCCcHHHHHHHhCCCHH
Q 013472          361 SKMVARHARGIKIP------------C-K------LNREISKIQKARKALTNSHG--------KYPEDIEIAKYTGLSLA  413 (442)
Q Consensus       361 ~r~LRkqsr~irlP------------~-~------v~e~i~kI~ka~~~L~~elg--------r~PS~eEIAe~LGIS~e  413 (442)
                      ++++|++.+.....            . .      ..+....+..+...|+.+..        .+.++.|||+.||+|+.
T Consensus        93 ~d~~Rk~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~~~v~~l~~~~g~s~~EIA~~lgis~~  172 (194)
T PRK12519         93 IDRLRSRRSRQRLLERWQQELLGEASEDTPLEQASLAERSQRVQTALAQLPESQRQVLELAYYEGLSQSEIAKRLGIPLG  172 (194)
T ss_pred             HHHHHhcccccchhhhhhhhhcccccCCCHHHHHHHHHHHHHHHHHHHhCCHHHhhhhhhhhhcCCCHHHHHHHhCCCHH
Confidence            99999865421110            0 0      01122345666666655442        57799999999999999


Q ss_pred             HHHHHHHhccc
Q 013472          414 EIRSASECLRI  424 (442)
Q Consensus       414 tVk~~l~~ar~  424 (442)
                      +|+..+++++.
T Consensus       173 tV~~~l~Ra~~  183 (194)
T PRK12519        173 TVKARARQGLL  183 (194)
T ss_pred             HHHHHHHHHHH
Confidence            99999888764

>PRK12526 RNA polymerase sigma factor; Provisional

Probab=99.66  E-value=9.3e-16  Score=144.75  Aligned_cols=140  Identities=14%  Similarity=0.073  Sum_probs=111.0

Q ss_pred             HHHHHHHHhchH-HHHHHHHHhHHHHHHHHHHhhCCCCCHHhHHHHHHHHHHHhHHhcCCCCCCChHHHHHHHHHHHHHH
Q 013472          284 RVLKQHLAFGWY-CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISK  362 (442)
Q Consensus       284 eeL~~~l~~G~~-Are~LI~~nlrLV~sIAkrY~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIRnaI~r  362 (442)
                      ..|...+..|+. |+++|+..|.+.|+.++.++.++..+++|++||+|+.+|+++.+|++.++ .|.||++.+++|.+++
T Consensus        26 ~~l~~~~~~~d~~a~~~l~~~y~~~l~~~~~~~~~~~~~AeDivQe~fl~l~~~~~~~~~~~~-~~~~wl~~I~rn~~~d  104 (206)
T PRK12526         26 QWLILVAISRDKQAFTHLFQFFAPKIKRFGIKQLGNEAQANELVQETMSNVWRKAHLYNGDKG-AATTWVYTVMRNAAFD  104 (206)
T ss_pred             HHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHhCCHhhHHHHHHHHHHHHHHhHHhcCCccc-chhHHHHHHHHHHHHH
Confidence            345666777866 99999999999999999999999999999999999999999999997655 5999999999999999


Q ss_pred             HHHhhcCceec-------cc-------c-c-HH-----HHHHHHHHHHHHHHHc--------CCCCcHHHHHHHhCCCHH
Q 013472          363 MVARHARGIKI-------PC-------K-L-NR-----EISKIQKARKALTNSH--------GKYPEDIEIAKYTGLSLA  413 (442)
Q Consensus       363 ~LRkqsr~irl-------P~-------~-v-~e-----~i~kI~ka~~~L~~el--------gr~PS~eEIAe~LGIS~e  413 (442)
                      ++|++.+....       |.       . . .+     ....+.+++..|+.+.        ..+.|++|||+.||+|+.
T Consensus       105 ~~Rk~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~vl~l~~~~g~s~~EIA~~lgis~~  184 (206)
T PRK12526        105 MLRKIKAKKEQNLGDDIWPIEQALAESQSESEEFSDHLMDKQILSYIEKLPEAQQTVVKGVYFQELSQEQLAQQLNVPLG  184 (206)
T ss_pred             HHHHhccccccccccccchhhhhcccccCchHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHHCCCHH
Confidence            99986532110       10       0 0 00     1123555555555443        367899999999999999


Q ss_pred             HHHHHHHhccc
Q 013472          414 EIRSASECLRI  424 (442)
Q Consensus       414 tVk~~l~~ar~  424 (442)
                      +|+..+++++.
T Consensus       185 tV~~~l~Ra~~  195 (206)
T PRK12526        185 TVKSRLRLALA  195 (206)
T ss_pred             HHHHHHHHHHH
Confidence            99999998875

>PRK12536 RNA polymerase sigma factor; Provisional

Probab=99.66  E-value=2.1e-15  Score=138.93  Aligned_cols=140  Identities=15%  Similarity=0.075  Sum_probs=111.9

Q ss_pred             HHHHHHHHHhchH-HHHHHHHHhHHHHHHHHHHhhC-CCCCHHhHHHHHHHHHHHhHHhcCCCCCCChHHHHHHHHHHHH
Q 013472          283 ERVLKQHLAFGWY-CREELIKSTRPLVLFLARNYRG-LGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSI  360 (442)
Q Consensus       283 eeeL~~~l~~G~~-Are~LI~~nlrLV~sIAkrY~g-~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIRnaI  360 (442)
                      ...++..+..|+. |++.++..|.+.|+.++.++.+ ...+++|++||+|+++|+.++.|++.  ..|.+|++.+++|.+
T Consensus         8 ~~~~~~~~~~~d~~a~~~l~~~~~~~l~~~~~~~~~~~~~~aeDlvQevfl~l~~~~~~~~~~--~~~~~wl~~iarN~~   85 (181)
T PRK12536          8 LRALLLRGLAGDAAAYRQFLSELAAHLRGFLRRRLPQLPDEVEDLVQEILLAVHNARHTYRAD--QPLTAWVHAIARYKL   85 (181)
T ss_pred             HHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHcCCChhhHHHHHHHHHHHHHHhHHhcCCC--CchHHHHHHHHHHHH
Confidence            4567788888876 9999999999999999998764 57899999999999999999999974  369999999999999


Q ss_pred             HHHHHhhcCceecc--------------cccHHHHHHHHHHHHHHHHHcC--------CCCcHHHHHHHhCCCHHHHHHH
Q 013472          361 SKMVARHARGIKIP--------------CKLNREISKIQKARKALTNSHG--------KYPEDIEIAKYTGLSLAEIRSA  418 (442)
Q Consensus       361 ~r~LRkqsr~irlP--------------~~v~e~i~kI~ka~~~L~~elg--------r~PS~eEIAe~LGIS~etVk~~  418 (442)
                      ++++|++.+.....              ....+....+.+++..|+....        .+.|++|||+.||||+++|+..
T Consensus        86 ~d~~Rk~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~v~~l~~~~g~s~~EIA~~l~is~~tV~~~  165 (181)
T PRK12536         86 MDFLRSRARREALHDPLDDESELFATSDDEAAEARRDLGKLLEQLPDRQRLPIVHVKLEGLSVAETAQLTGLSESAVKVG  165 (181)
T ss_pred             HHHHHHHhccccccCCccchhhhcCCCCcchHHHHHHHHHHHHHCCHHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHH
Confidence            99999864422110              0112233346666666655332        6779999999999999999999


Q ss_pred             HHhccc
Q 013472          419 SECLRI  424 (442)
Q Consensus       419 l~~ar~  424 (442)
                      +++++.
T Consensus       166 l~rar~  171 (181)
T PRK12536        166 IHRGLK  171 (181)
T ss_pred             HHHHHH
Confidence            998874

>PRK11922 RNA polymerase sigma factor; Provisional

Probab=99.65  E-value=2.4e-15  Score=144.40  Aligned_cols=141  Identities=16%  Similarity=0.136  Sum_probs=115.8

Q ss_pred             CCHHHHHHHHHhchH-HHHHHHHHhHHHHHHHHHHhhCCCCCHHhHHHHHHHHHHHhHHhcCCCCCCChHHHHHHHHHHH
Q 013472          281 VSERVLKQHLAFGWY-CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKS  359 (442)
Q Consensus       281 ~deeeL~~~l~~G~~-Are~LI~~nlrLV~sIAkrY~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIRna  359 (442)
                      ++++.|+..+..|+. |++.|+..|.+.|+.+|.++.+.+.+++|++||+|+++|+++++|++.  ..|.||++.+++|.
T Consensus        15 ~~~~~l~~~~~~gd~~a~~~l~~~y~~~l~~~a~~~~~~~~~AEDlvQE~fi~l~~~~~~~~~~--~~~~~wL~~iarn~   92 (231)
T PRK11922         15 ASDRELVARVLAGDEAAFEALMRRHNRRLYRTARAILRNDAEAEDVVQEAYLRAFRALGTFRGD--ASLSTWLSRIVLNE   92 (231)
T ss_pred             ccHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHhCChhhHHHHHHHHHHHHHHHHHhcCCC--chhHHHHHHHHHHH
Confidence            456778888888866 999999999999999999999999999999999999999999999985  37999999999999


Q ss_pred             HHHHHHhhcCceeccc------------------c--------cHHHHHHHHHHHHHHHHHcC--------CCCcHHHHH
Q 013472          360 ISKMVARHARGIKIPC------------------K--------LNREISKIQKARKALTNSHG--------KYPEDIEIA  405 (442)
Q Consensus       360 I~r~LRkqsr~irlP~------------------~--------v~e~i~kI~ka~~~L~~elg--------r~PS~eEIA  405 (442)
                      +++++|+..+...++.                  .        ..+....+.+++..|+....        .+.|++|||
T Consensus        93 ~~d~~Rk~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~e~~~~l~~~l~~L~~~~r~i~~l~~~~g~s~~EIA  172 (231)
T PRK11922         93 ALGRLRRRRRLVNLAEMVMASTIAGGERTPLADPAEDPERAAARREIRALLERAIDALPDAFRAVFVLRVVEELSVEETA  172 (231)
T ss_pred             HHHHHHhhcccccchhcccccccccccccccCcccCChHHHHHHHHHHHHHHHHHHhCCHHHhhhheeehhcCCCHHHHH
Confidence            9999998765322210                  0        01122346666666665542        567999999


Q ss_pred             HHhCCCHHHHHHHHHhcc
Q 013472          406 KYTGLSLAEIRSASECLR  423 (442)
Q Consensus       406 e~LGIS~etVk~~l~~ar  423 (442)
                      +.||+|+++|+..+++++
T Consensus       173 e~lgis~~tVk~~l~Rar  190 (231)
T PRK11922        173 QALGLPEETVKTRLHRAR  190 (231)
T ss_pred             HHHCcCHHHHHHHHHHHH
Confidence            999999999999988876

>PRK12539 RNA polymerase sigma factor; Provisional

Probab=99.65  E-value=2.5e-15  Score=138.81  Aligned_cols=141  Identities=11%  Similarity=0.059  Sum_probs=113.5

Q ss_pred             CHHHHHHHHHhchH-HHHHHHHHhHHHHHHHHH----HhhCCCCCHHhHHHHHHHHHHHhHHhcCCCCCCChHHHHHHHH
Q 013472          282 SERVLKQHLAFGWY-CREELIKSTRPLVLFLAR----NYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWI  356 (442)
Q Consensus       282 deeeL~~~l~~G~~-Are~LI~~nlrLV~sIAk----rY~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wI  356 (442)
                      +...|+..++.|+. |++.|+..|.+.|+.+|+    ++.++..+++|++||+++.+|++++.|++..  .|.+|++.++
T Consensus         7 ~~~~l~~~~~~gd~~af~~l~~~~~~~l~~~~~~~~~~~~~~~~~AeDlvQe~~l~l~~~~~~~~~~~--~f~~wl~~i~   84 (184)
T PRK12539          7 ELKALMLASLDGDAAAHRALLERLSGHLRAYYKGKLARIGRGAEEAEDLVQEALMAIHTRRHTYDPEQ--PLTPWVYAIA   84 (184)
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHHHhccCCcchHHHHHHHHHHHHHHHHhhcCCCC--ChHHHHHHHH
Confidence            35678888888976 999999999999999987    5557889999999999999999999999753  6999999999


Q ss_pred             HHHHHHHHHhhcCc-eecc---------c---ccHHHHHHHHHHHHHHHHHcC--------CCCcHHHHHHHhCCCHHHH
Q 013472          357 RKSISKMVARHARG-IKIP---------C---KLNREISKIQKARKALTNSHG--------KYPEDIEIAKYTGLSLAEI  415 (442)
Q Consensus       357 RnaI~r~LRkqsr~-irlP---------~---~v~e~i~kI~ka~~~L~~elg--------r~PS~eEIAe~LGIS~etV  415 (442)
                      +|.+++++|+..+. ...+         .   ...+....+..+...|++...        .+.+++|||+.||+|+++|
T Consensus        85 ~n~~~d~~R~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~l~~~l~~L~~~~r~v~~l~~~~g~s~~eIA~~lgis~~tV  164 (184)
T PRK12539         85 RYKLIDHLRRTRASLADVPIDDADELVAHDDHAAVESTLDLGRLLARLPEKMRLAIQAVKLEGLSVAEAATRSGMSESAV  164 (184)
T ss_pred             HHHHHHHHHHHhccccccChhhhccccCCcHHhhHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCcHHHHHHHHCcCHHHH
Confidence            99999999986542 1111         0   012334456777776665542        6789999999999999999


Q ss_pred             HHHHHhccc
Q 013472          416 RSASECLRI  424 (442)
Q Consensus       416 k~~l~~ar~  424 (442)
                      +..+++++.
T Consensus       165 ~~~l~ra~~  173 (184)
T PRK12539        165 KVSVHRGLK  173 (184)
T ss_pred             HHHHHHHHH
Confidence            999988874

>PRK11923 algU RNA polymerase sigma factor AlgU; Provisional

Probab=99.65  E-value=2.9e-15  Score=138.78  Aligned_cols=141  Identities=12%  Similarity=0.073  Sum_probs=112.5

Q ss_pred             CHHHHHHHHHhchH-HHHHHHHHhHHHHHHHHHHhhCCCCCHHhHHHHHHHHHHHhHHhcCCCCCCChHHHHHHHHHHHH
Q 013472          282 SERVLKQHLAFGWY-CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSI  360 (442)
Q Consensus       282 deeeL~~~l~~G~~-Are~LI~~nlrLV~sIAkrY~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIRnaI  360 (442)
                      +++.|+..++.|+. |++.|+..|.+.|+.+++++.++..+++|++||+|+++|+++.+|++..  .|.+|++.+++|.+
T Consensus         6 ~~~~ll~~~~~gd~~a~~~l~~~y~~~l~~~~~~~~~~~~daeDlvQe~~i~l~~~~~~~~~~~--~~~~wl~~ia~n~~   83 (193)
T PRK11923          6 EDQQLVERVQRGDKRAFDLLVLKYQHKILGLIVRFVHDTAEAQDVAQEAFIKAYRALGNFRGDS--AFYTWLYRIAINTA   83 (193)
T ss_pred             cHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHhCCHhhHHHHHHHHHHHHHHhHhCcCCCC--ccHhHHHHHHHHHH
Confidence            45678888899976 9999999999999999999999999999999999999999999999864  59999999999999


Q ss_pred             HHHHHhhcCcee---ccc-------------c---------cHHHHHHHHHHHHHHHHHcC--------CCCcHHHHHHH
Q 013472          361 SKMVARHARGIK---IPC-------------K---------LNREISKIQKARKALTNSHG--------KYPEDIEIAKY  407 (442)
Q Consensus       361 ~r~LRkqsr~ir---lP~-------------~---------v~e~i~kI~ka~~~L~~elg--------r~PS~eEIAe~  407 (442)
                      +++++++.+...   .+.             .         ..+....+..+...|+.+..        .+.+++|||+.
T Consensus        84 ~d~~rk~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~l~~~l~~L~~~~r~v~~l~~~~g~s~~eIA~~  163 (193)
T PRK11923         84 KNHLVSRGRRPPDSDVSSEDAEFYDGDHALKDIESPERALLRDEIEGTVHRTIQQLPEDLRTALTLREFDGLSYEDIASV  163 (193)
T ss_pred             HHHHHHhcCCCccccccccchhhhcccccccCcCCHHHHHHHHHHHHHHHHHHHhCCHHHhHHHhhHHhcCCCHHHHHHH
Confidence            999987644211   000             0         00112235555555554432        56799999999


Q ss_pred             hCCCHHHHHHHHHhccc
Q 013472          408 TGLSLAEIRSASECLRI  424 (442)
Q Consensus       408 LGIS~etVk~~l~~ar~  424 (442)
                      ||+|+.+|+..+.+++.
T Consensus       164 lgis~~tv~~~l~Rar~  180 (193)
T PRK11923        164 MQCPVGTVRSRIFRARE  180 (193)
T ss_pred             HCCCHHHHHHHHHHHHH
Confidence            99999999999988874

>PRK12542 RNA polymerase sigma factor; Provisional

Probab=99.65  E-value=4.1e-16  Score=143.96  Aligned_cols=134  Identities=16%  Similarity=0.108  Sum_probs=107.4

Q ss_pred             HhchH-HHHHHHHHhHHHHHHHHHHhhCCCCCHHhHHHHHHHHHHHhHHhcCCCCCCChHHHHHHHHHHHHHHHHHhhcC
Q 013472          291 AFGWY-CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHAR  369 (442)
Q Consensus       291 ~~G~~-Are~LI~~nlrLV~sIAkrY~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIRnaI~r~LRkqsr  369 (442)
                      ..|+. |++.|+..|.+.|+.+|.+++++..+++|++||+|+.+|+++++|+...+..|.||++.+++|.+++++|++.+
T Consensus         4 ~~gd~~a~~~l~~~y~~~l~~~~~~~~~~~~~AeDlvQe~fl~~~~~~~~~~~~~~~~~~~wL~~Iarn~~~d~~Rk~~~   83 (185)
T PRK12542          4 TNNDYEKMEELYELYEQKVYYVAYSILNNIQQAEDAVQETFITLYKNLEKLHSLNTQELKRYILRVAKNKAIDSYRKNKR   83 (185)
T ss_pred             cccCHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHhcccccHHHHHHHHHHHHHHHHHHHHHHhhh
Confidence            35654 99999999999999999999999999999999999999999999986544579999999999999999998754


Q ss_pred             ceecc------------ccc------HHHHHHHHHHHHHHHHHc--------CCCCcHHHHHHHhCCCHHHHHHHHHhcc
Q 013472          370 GIKIP------------CKL------NREISKIQKARKALTNSH--------GKYPEDIEIAKYTGLSLAEIRSASECLR  423 (442)
Q Consensus       370 ~irlP------------~~v------~e~i~kI~ka~~~L~~el--------gr~PS~eEIAe~LGIS~etVk~~l~~ar  423 (442)
                      .....            ...      .+....+.+++..|+...        -.+.|++|||+.||+|+++|+..+.+++
T Consensus        84 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~i~~l~~~~g~s~~EIA~~lgis~~tVk~~l~Rar  163 (185)
T PRK12542         84 HETFLEEYERESIEAVDENIEEWEKRKMSEVQIDTLLKELNESNRQVFKYKVFYNLTYQEISSVMGITEANVRKQFERAR  163 (185)
T ss_pred             hhhhhhhccccchhhhhccHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence            32110            000      011234666666665543        2678999999999999999999999887


Q ss_pred             c
Q 013472          424 I  424 (442)
Q Consensus       424 ~  424 (442)
                      .
T Consensus       164 ~  164 (185)
T PRK12542        164 K  164 (185)
T ss_pred             H
Confidence            5

>PRK09652 RNA polymerase sigma factor RpoE; Provisional

Probab=99.64  E-value=1.6e-15  Score=137.19  Aligned_cols=134  Identities=17%  Similarity=0.118  Sum_probs=106.3

Q ss_pred             HHHhchH-HHHHHHHHhHHHHHHHHHHhhCCCCCHHhHHHHHHHHHHHhHHhcCCCCCCChHHHHHHHHHHHHHHHHHhh
Q 013472          289 HLAFGWY-CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARH  367 (442)
Q Consensus       289 ~l~~G~~-Are~LI~~nlrLV~sIAkrY~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIRnaI~r~LRkq  367 (442)
                      +++.|+. |+++|+..|.++|+.++++|.+++.+++|++||++++||+++++|+  .+.+|.||++.++++.+.+++++.
T Consensus         3 ~~~~gd~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeDl~Qe~~l~l~~~~~~~~--~~~~~~~~l~~~~~~~~~~~~r~~   80 (182)
T PRK09652          3 RVQRGDRAAFALLVRRYQPRVKRLLSRLTRDPADAEDLVQETFIKAYRALHSFR--GGAAFYTWLYRIARNTAINYLRKQ   80 (182)
T ss_pred             hhhcCCHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHhcC--CCcchHHHHHHHHHHHHHHHHHcc
Confidence            4677866 9999999999999999999999999999999999999999999999  345899999999999999999976


Q ss_pred             cCceecc-------c---------c---c------HHHHHHHHHHHHHHHHHc--------CCCCcHHHHHHHhCCCHHH
Q 013472          368 ARGIKIP-------C---------K---L------NREISKIQKARKALTNSH--------GKYPEDIEIAKYTGLSLAE  414 (442)
Q Consensus       368 sr~irlP-------~---------~---v------~e~i~kI~ka~~~L~~el--------gr~PS~eEIAe~LGIS~et  414 (442)
                      .+....+       .         .   .      .+....+..+...|+...        ..+.+++|||+.||||+.+
T Consensus        81 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~vl~l~~~~~~s~~eIA~~lgis~~t  160 (182)
T PRK09652         81 GRRPPASDVDAEEAEDFDLADALRDISTPENELLSAELEQRVRAAIESLPEELRTAITLREIEGLSYEEIAEIMGCPIGT  160 (182)
T ss_pred             cCCCCccccccccccccccccccccccChHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHHCCCHHH
Confidence            5432211       0         0   0      012334455555444332        2677999999999999999


Q ss_pred             HHHHHHhccc
Q 013472          415 IRSASECLRI  424 (442)
Q Consensus       415 Vk~~l~~ar~  424 (442)
                      |+..+++++.
T Consensus       161 V~~~l~ra~~  170 (182)
T PRK09652        161 VRSRIFRARE  170 (182)
T ss_pred             HHHHHHHHHH
Confidence            9999887764

>PRK12515 RNA polymerase sigma factor; Provisional

Probab=99.64  E-value=3.9e-15  Score=137.88  Aligned_cols=143  Identities=13%  Similarity=0.073  Sum_probs=115.4

Q ss_pred             CCCHHHHHHHHHhchH-HHHHHHHHhHHHHHHHHHHhhCCCCCHHhHHHHHHHHHHHhHHhcCCCCCCChHHHHHHHHHH
Q 013472          280 GVSERVLKQHLAFGWY-CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRK  358 (442)
Q Consensus       280 g~deeeL~~~l~~G~~-Are~LI~~nlrLV~sIAkrY~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIRn  358 (442)
                      .+++.+|+..+..|+. |++.|+..|.+.|+.++.++.++..+++|++||+|+.+|++.++|++.  ..|.||++.+++|
T Consensus         6 ~~~~~~l~~~~~~gd~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeDivQe~f~~l~~~~~~~~~~--~~~~~wl~~i~~n   83 (189)
T PRK12515          6 ATTDEMLLARIAQGDRTAMQTLYGRHHVRVYRFGLRLVRDEQTAEDLVSEVFLDVWRQAGQFEGR--SQVSTWLLSIARF   83 (189)
T ss_pred             ccCHHHHHHHHHccCHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHhcCCC--CChHHHHHHHHHH
Confidence            3577889999999976 999999999999999999999999999999999999999999999974  3799999999999


Q ss_pred             HHHHHHHhhcCceec-------ccc---c------HHHHHHHHHHHHHHHHHc--------CCCCcHHHHHHHhCCCHHH
Q 013472          359 SISKMVARHARGIKI-------PCK---L------NREISKIQKARKALTNSH--------GKYPEDIEIAKYTGLSLAE  414 (442)
Q Consensus       359 aI~r~LRkqsr~irl-------P~~---v------~e~i~kI~ka~~~L~~el--------gr~PS~eEIAe~LGIS~et  414 (442)
                      .++++++++.+....       +..   .      .+....+.++...|+.+.        -.+.+++|||+.||+|+.+
T Consensus        84 ~~~d~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~vl~l~~~~~~s~~eIA~~lgis~~t  163 (189)
T PRK12515         84 KALSALRRRKHEEIDDEAAAAIEDGADTPEVALQKSDTSAALRACLAKLSPAHREIIDLVYYHEKSVEEVGEIVGIPEST  163 (189)
T ss_pred             HHHHHHHccCCCCCccccccccCCCCCCHHHHHHhHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHHCcCHHH
Confidence            999999976432111       000   0      011223555555555443        2678999999999999999


Q ss_pred             HHHHHHhccc
Q 013472          415 IRSASECLRI  424 (442)
Q Consensus       415 Vk~~l~~ar~  424 (442)
                      |+..+.+++.
T Consensus       164 V~~~l~Rar~  173 (189)
T PRK12515        164 VKTRMFYARK  173 (189)
T ss_pred             HHHHHHHHHH
Confidence            9999998874

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

Probab=99.63  E-value=3.4e-15  Score=136.76  Aligned_cols=140  Identities=16%  Similarity=0.145  Sum_probs=109.0

Q ss_pred             HHHHHHHHHhchH-HHHHHHHHhHHHHHHHHHHhhCCCC-----CHHhHHHHHHHHHHH-hHHhcCCCCCCChHHHHHHH
Q 013472          283 ERVLKQHLAFGWY-CREELIKSTRPLVLFLARNYRGLGI-----PFSDLLQAGNVGVLQ-GAERFDHTRGYKFSTYVQYW  355 (442)
Q Consensus       283 eeeL~~~l~~G~~-Are~LI~~nlrLV~sIAkrY~g~g~-----d~EDLIQEG~IGLir-AieKFDp~kG~rFSTYa~~w  355 (442)
                      ...|+..+..|+. |++.|+..|.+.|+.+|++|.++..     +++|++||+|+.+|+ ...+|++.  ..|.||++.+
T Consensus         4 ~~~li~~~~~gd~~a~~~l~~~~~~~l~~~~~~~~~~~~~~~~~~AeDlvQevfl~~~~~~~~~~~~~--~~~~~wl~~i   81 (183)
T TIGR02999         4 VTELLQQWQNGDAAARDQLFPQLYQELRRIARRQLRRERSGQTLQTTALVHEAYLRLSDQDEQKWDDR--AHFFAAAAKA   81 (183)
T ss_pred             HHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHhhcccccccchHHHHHHHHHHHHhhcccCCCCch--HHHHHHHHHH
Confidence            4567888888976 9999999999999999999999877     899999999999998 78889764  3699999999


Q ss_pred             HHHHHHHHHHhhcCcee------c------cc---ccHHHHHHHHHHHHH---HHHHc--------CCCCcHHHHHHHhC
Q 013472          356 IRKSISKMVARHARGIK------I------PC---KLNREISKIQKARKA---LTNSH--------GKYPEDIEIAKYTG  409 (442)
Q Consensus       356 IRnaI~r~LRkqsr~ir------l------P~---~v~e~i~kI~ka~~~---L~~el--------gr~PS~eEIAe~LG  409 (442)
                      ++|.+++++|++.+..+      .      |.   ...+....+..+...   |+...        -.+.|++|||+.||
T Consensus        82 ~~n~~~d~~R~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~l~~Lp~~~r~v~~l~~~~g~s~~EIA~~lg  161 (183)
T TIGR02999        82 MRRILVDHARRRRAQKRGGGAVRVPLDEVLPDAEADLDEELLDLDDALDKLAQVDPRQAEVVELRFFAGLTVEEIAELLG  161 (183)
T ss_pred             HHHHHHHHHHHHHHHhccCCccccccccccCCCCccHHHHHHHHHHHHHHhhcCCHHHHHHHHHHHHcCCCHHHHHHHhC
Confidence            99999999997543211      0      11   011222223333333   44443        26789999999999


Q ss_pred             CCHHHHHHHHHhccc
Q 013472          410 LSLAEIRSASECLRI  424 (442)
Q Consensus       410 IS~etVk~~l~~ar~  424 (442)
                      ||+++|+..+++++.
T Consensus       162 is~~tVk~~l~Rar~  176 (183)
T TIGR02999       162 VSVRTVERDWRFARA  176 (183)
T ss_pred             CCHHHHHHHHHHHHH
Confidence            999999999998874

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.

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

Probab=99.63  E-value=4.2e-15  Score=145.00  Aligned_cols=145  Identities=12%  Similarity=-0.019  Sum_probs=116.9

Q ss_pred             HcCCCHHHHHHHHHhchH-HHHHHHHHhHHHHHHHHHHhhCCCCCHHhHHHHHHHHHHH-------hHHhcCCCCCCChH
Q 013472          278 AAGVSERVLKQHLAFGWY-CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQ-------GAERFDHTRGYKFS  349 (442)
Q Consensus       278 a~g~deeeL~~~l~~G~~-Are~LI~~nlrLV~sIAkrY~g~g~d~EDLIQEG~IGLir-------AieKFDp~kG~rFS  349 (442)
                      .++.++..|+..++.|+. |++.|+..|.+.|+.++.++.++..++||++||+|+.+|.       .+.+|++.  ..|.
T Consensus        21 ~~~~~d~~Li~~~~~gd~~Af~~L~~~y~~~l~~~~~~~~~~~~dAEDivQEvFlkl~~~~~~~~~~~~~~~~~--~~~~   98 (244)
T TIGR03001        21 QLHAADLYLACACAQGEPAALAALERHVLSKVPARLAGLRPPTAFVDEVLQRLRQRLLVPRAERPPRIAEYSGR--GPLL   98 (244)
T ss_pred             cccccHHHHHHHHHcCcHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhccchhhhhhccCCC--CchH
Confidence            345678889999999976 9999999999999999999999999999999999999994       78889864  3699


Q ss_pred             HHHHHHHHHHHHHHHHhhcCceeccc---------c--c-H----------HHHHHHHHHHHHHHHHcC--------CCC
Q 013472          350 TYVQYWIRKSISKMVARHARGIKIPC---------K--L-N----------REISKIQKARKALTNSHG--------KYP  399 (442)
Q Consensus       350 TYa~~wIRnaI~r~LRkqsr~irlP~---------~--v-~----------e~i~kI~ka~~~L~~elg--------r~P  399 (442)
                      ||++.+++|.++++++++.+...+..         .  . .          +....|.+++.+|+....        .+.
T Consensus        99 tWL~~Ia~N~~id~lRk~~r~~~~~~~~~~~~~~~~~~~~e~~~~~~e~~~e~~~~l~~aL~~Lp~~~R~v~~L~~~eg~  178 (244)
T TIGR03001        99 SWVRIVATRIALELQAQERRHSPVEEPTELAALPAPGSDPELDLLRERYRQDFRQALREALAALSERERHLLRLHFVDGL  178 (244)
T ss_pred             hHHHHHHHHHHHHHHHHhcccCccccccccccccCCCCCHHHHHHHHhhHHHHHHHHHHHHHhCCHHHHHHHHHHHHcCC
Confidence            99999999999999997654322110         0  0 0          122346677777766542        678


Q ss_pred             cHHHHHHHhCCCHHHHHHHHHhccc
Q 013472          400 EDIEIAKYTGLSLAEIRSASECLRI  424 (442)
Q Consensus       400 S~eEIAe~LGIS~etVk~~l~~ar~  424 (442)
                      |++|||+.||||+++|+..+++++.
T Consensus       179 S~~EIA~~Lgis~~TVk~rl~RAr~  203 (244)
T TIGR03001       179 SMDRIGAMYQVHRSTVSRWVAQARE  203 (244)
T ss_pred             CHHHHHHHHCcCHHHHHHHHHHHHH
Confidence            9999999999999999999887763

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.

>PRK09649 RNA polymerase sigma factor SigC; Reviewed

Probab=99.63  E-value=4.2e-15  Score=137.92  Aligned_cols=140  Identities=18%  Similarity=0.102  Sum_probs=113.2

Q ss_pred             HHHHHHHHHhchH-HHHHHHHHhHHHHHHHHHHhhCCCCCHHhHHHHHHHHHHHhHHhcCCCCCCChHHHHHHHHHHHHH
Q 013472          283 ERVLKQHLAFGWY-CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSIS  361 (442)
Q Consensus       283 eeeL~~~l~~G~~-Are~LI~~nlrLV~sIAkrY~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIRnaI~  361 (442)
                      ...|+.++..|+. |++.|+..|.+.|+.++. +.++..+++|++||.|+.+|+..++|++.  ..|.+|++.+++|.++
T Consensus        11 ~~~l~~~~~~gd~~af~~l~~~~~~~l~~~~~-~~~~~~~AeDivQe~flkl~~~~~~~~~~--~~~~~Wl~~Iarn~~~   87 (185)
T PRK09649         11 VTALALSAAKGNGRALEAFIKATQQDVWRFVA-YLSDVGSADDLTQETFLRAIGAIPRFSAR--SSARTWLLAIARHVVA   87 (185)
T ss_pred             HHHHHHHHHccCHHHHHHHHHHHHHHHHHHHH-HhCCHHHHHHHHHHHHHHHHHhccccCcc--chHHHHHHHHHHHHHH
Confidence            3567888888976 999999999999999995 67888999999999999999999999964  3699999999999999


Q ss_pred             HHHHhhcCceec-----ccc---------cHHHHHHHHHHHHHHHHHcC--------CCCcHHHHHHHhCCCHHHHHHHH
Q 013472          362 KMVARHARGIKI-----PCK---------LNREISKIQKARKALTNSHG--------KYPEDIEIAKYTGLSLAEIRSAS  419 (442)
Q Consensus       362 r~LRkqsr~irl-----P~~---------v~e~i~kI~ka~~~L~~elg--------r~PS~eEIAe~LGIS~etVk~~l  419 (442)
                      +++|++.+....     +..         ..+....+.+++..|+....        .+.|++|||+.||+|+++|+..+
T Consensus        88 d~~Rk~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~l~~~l~~Lp~~~r~v~~L~~~~g~s~~EIA~~lgis~~tVk~~l  167 (185)
T PRK09649         88 DHIRHVRSRPRTTRGARPEHLIDGDRHARGFEDLVEVTTMIADLTTDQREALLLTQLLGLSYADAAAVCGCPVGTIRSRV  167 (185)
T ss_pred             HHHHHhccccccccccchhhccChhhhhhhHHHHHHHHHHHHhCCHHHhHHhhhHHHcCCCHHHHHHHHCCCHHHHHHHH
Confidence            999975432211     110         01223456677777766543        67799999999999999999999


Q ss_pred             HhcccC
Q 013472          420 ECLRIV  425 (442)
Q Consensus       420 ~~ar~~  425 (442)
                      ++++..
T Consensus       168 ~Rar~~  173 (185)
T PRK09649        168 ARARDA  173 (185)
T ss_pred             HHHHHH
Confidence            998863

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

Probab=99.62  E-value=1.1e-14  Score=134.37  Aligned_cols=134  Identities=20%  Similarity=0.199  Sum_probs=110.9

Q ss_pred             HHHhc-hHHHHHHHHHhHHHHHHHHHHhhCCCCCHHhHHHHHHHHHHHhHHhcCCCCCCChHHHHHHHHHHHHHHHHHhh
Q 013472          289 HLAFG-WYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARH  367 (442)
Q Consensus       289 ~l~~G-~~Are~LI~~nlrLV~sIAkrY~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIRnaI~r~LRkq  367 (442)
                      ....| ..+++.++..|.+.++.+|++++++..++|||+||+|+.+|+++..| .. +..|.||++.+++|.++|++|+.
T Consensus         8 ~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~dAeDlvQE~~lr~~~~~~~~-~~-~~~~~~wl~~Ia~n~~iD~~R~~   85 (182)
T COG1595           8 EALRGDRAAFEELLERLRPRLRRLARRLLGDRADAEDLVQETFLRAWRAIDSF-RG-RSSFKAWLYRIARNLAIDRLRKR   85 (182)
T ss_pred             HHHhcchHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHhhc-CC-CCchHHHHHHHHHHHHHHHHHHh
Confidence            33344 45999999999999999999999998899999999999999999999 33 34799999999999999999987


Q ss_pred             cCceec-c-------------ccc-----HHHHHHHHHHHHHHHHHcC--------CCCcHHHHHHHhCCCHHHHHHHHH
Q 013472          368 ARGIKI-P-------------CKL-----NREISKIQKARKALTNSHG--------KYPEDIEIAKYTGLSLAEIRSASE  420 (442)
Q Consensus       368 sr~irl-P-------------~~v-----~e~i~kI~ka~~~L~~elg--------r~PS~eEIAe~LGIS~etVk~~l~  420 (442)
                      ++.... +             ...     .+....+.++...|+....        .+.|++|||+.||||+++|+..++
T Consensus        86 ~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~al~~Lp~~~R~~~~l~~~~gls~~EIA~~l~i~~~tVks~l~  165 (182)
T COG1595          86 KRRRARVEEADLLPEEADPAPDLAELLLAEEELERLRRALARLPPRQREAFLLRYLEGLSYEEIAEILGISVGTVKSRLH  165 (182)
T ss_pred             cccccccccccccccccCcccccchHHHHHHHHHHHHHHHHhCCHHHhHHhhhHhhcCCCHHHHHHHHCCCHHHHHHHHH
Confidence            653321 0             101     2344568888888877764        678999999999999999999999


Q ss_pred             hccc
Q 013472          421 CLRI  424 (442)
Q Consensus       421 ~ar~  424 (442)
                      +++.
T Consensus       166 ra~~  169 (182)
T COG1595         166 RARK  169 (182)
T ss_pred             HHHH
Confidence            8874

>PRK12512 RNA polymerase sigma factor; Provisional

Probab=99.61  E-value=1.4e-14  Score=133.28  Aligned_cols=139  Identities=15%  Similarity=0.094  Sum_probs=110.6

Q ss_pred             HHHHHHHHhchH-HHHHHHHHhHHHHHHHHHHhhC----CCCCHHhHHHHHHHHHHHhHHhcCCCCCCChHHHHHHHHHH
Q 013472          284 RVLKQHLAFGWY-CREELIKSTRPLVLFLARNYRG----LGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRK  358 (442)
Q Consensus       284 eeL~~~l~~G~~-Are~LI~~nlrLV~sIAkrY~g----~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIRn  358 (442)
                      ..|+..+..|+. |+++|+..|.+.|+.+|+++++    ...+++|++||+++.+|...++|+..  ..|.+|++.+++|
T Consensus        10 ~~l~~~~~~gd~~a~~~l~~~y~~~l~~~~~~~l~~~~~~~~~aeDlvQe~fl~l~~~~~~~~~~--~~~~~wl~~i~rn   87 (184)
T PRK12512         10 TDLMRSANAGDAAAYRRLLKAVTPVLRAAARRGLARAGQPADQAEDIVQEILLAVHLKRHTWDPG--APFAPWLFAIARN   87 (184)
T ss_pred             HHHHHHHHccCHHHHHHHHHHHHHHHHHHHHHHHHhccCCcccHHHHHHHHHHHHHHhHHhcCcc--ccHHHHHHHHHHH
Confidence            346777777866 9999999999999999999876    34799999999999999999999873  4699999999999


Q ss_pred             HHHHHHHhhcCceecc---------cc---cHHHHHHHHHHHHHHHHHcC--------CCCcHHHHHHHhCCCHHHHHHH
Q 013472          359 SISKMVARHARGIKIP---------CK---LNREISKIQKARKALTNSHG--------KYPEDIEIAKYTGLSLAEIRSA  418 (442)
Q Consensus       359 aI~r~LRkqsr~irlP---------~~---v~e~i~kI~ka~~~L~~elg--------r~PS~eEIAe~LGIS~etVk~~  418 (442)
                      .+.++++++.+....+         ..   .......+.++...|+....        .+.|++|||+.||+|+.+|+..
T Consensus        88 ~~~d~~Rr~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~v~~l~~~~g~s~~eIA~~l~is~~tV~~~  167 (184)
T PRK12512         88 KLIDALRRRGRRVFVDIDDFAETLPAEPATETLPAGDVGRHLETLPPRQRDVVQSISVEGASIKETAAKLSMSEGAVRVA  167 (184)
T ss_pred             HHHHHHHhhcccccCCchhccccccccchhhHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHH
Confidence            9999999875432221         11   11223456666666655442        6779999999999999999999


Q ss_pred             HHhccc
Q 013472          419 SECLRI  424 (442)
Q Consensus       419 l~~ar~  424 (442)
                      +++++.
T Consensus       168 l~ra~~  173 (184)
T PRK12512        168 LHRGLA  173 (184)
T ss_pred             HHHHHH
Confidence            988875

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

Probab=99.61  E-value=8.4e-15  Score=130.88  Aligned_cols=127  Identities=14%  Similarity=0.136  Sum_probs=103.3

Q ss_pred             HHHHHHHHhHHHHHHHHHHhhCCCCCHHhHHHHHHHHHHHhHHhcCCCCCCChHHHHHHHHHHHHHHHHHhhcCceeccc
Q 013472          296 CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIPC  375 (442)
Q Consensus       296 Are~LI~~nlrLV~sIAkrY~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIRnaI~r~LRkqsr~irlP~  375 (442)
                      |++.++..|.+.|+.+|+++.++..++||++||+++.+|+++++|++..  .|.+|++.+++|.++++++++.+......
T Consensus         2 ~~~~~~~~~~~~l~~~~~~~~~~~~~aEDivQe~~l~l~~~~~~~~~~~--~~~~wl~~i~~n~~~d~~r~~~~~~~~~~   79 (159)
T TIGR02989         2 AFAALLQRHQRSLRAFVRSLVPDRDDADDVLQETFVTAWRKFDEFDPGT--DFGAWARGIARNKVLNHRRKLGRDRLVFD   79 (159)
T ss_pred             HHHHHHHHhHHHHHHHHHHHcCChhhHHHHHHHHHHHHHHHHHhCCCCC--chHHHHHHHHHHHHHHHHHHhcccccccC
Confidence            7899999999999999999999999999999999999999999999754  59999999999999999998755322100


Q ss_pred             c-----------------cHHHHHHHHHHHHHHHHHc--------CCCCcHHHHHHHhCCCHHHHHHHHHhccc
Q 013472          376 K-----------------LNREISKIQKARKALTNSH--------GKYPEDIEIAKYTGLSLAEIRSASECLRI  424 (442)
Q Consensus       376 ~-----------------v~e~i~kI~ka~~~L~~el--------gr~PS~eEIAe~LGIS~etVk~~l~~ar~  424 (442)
                      .                 ..+....+.+++..|+...        -.+.+++|||+.||||+.+|+..+++++.
T Consensus        80 ~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~L~~~~r~v~~l~~~~g~~~~eIA~~l~is~~tv~~~l~Rar~  153 (159)
T TIGR02989        80 DELLEALAAEAEATEADRSEDELQALEGCLEKLPERQRELLQLRYQRGVSLTALAEQLGRTVNAVYKALSRLRV  153 (159)
T ss_pred             HHHHHHHHhhcccchHhhHHHHHHHHHHHHHHCCHHHHHHHHHHHhcCCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence            0                 0111233555565555443        26789999999999999999999998875

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).

>PRK12520 RNA polymerase sigma factor; Provisional

Probab=99.59  E-value=1e-14  Score=135.31  Aligned_cols=127  Identities=17%  Similarity=0.160  Sum_probs=103.8

Q ss_pred             HHHHHHHHhHHHHHHHHHHhhCCCCCHHhHHHHHHHHHHHhHHhcCCCCCCChHHHHHHHHHHHHHHHHHhhcCceeccc
Q 013472          296 CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIPC  375 (442)
Q Consensus       296 Are~LI~~nlrLV~sIAkrY~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIRnaI~r~LRkqsr~irlP~  375 (442)
                      +|+.|+..|.+.|+.+|.+++++..+++|++||.|+.+|+.+++|++..  +|.||++.+++|.+++++|++++....+.
T Consensus         3 ~~~~l~~~~~~~l~~~a~~~~~~~~~AeDivQevfl~~~~~~~~~~~~~--~~~~WL~~ia~n~~~d~~Rk~~r~~~~~~   80 (191)
T PRK12520          3 IAPAQLEALRPHLLRFARLQLRDPALAEDAVSETLLAVLEHPERFAGQS--SLKTYLVGILKHKIIDAIRSGRREVRLSL   80 (191)
T ss_pred             chHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhhhhhcccc--cHHHHHHHHHHHHHHHHHHhhcCcCcccc
Confidence            6899999999999999999999999999999999999999999998643  69999999999999999998754322111


Q ss_pred             ------------------------------cc------HHHHHHHHHHHHHHHHHcC--------CCCcHHHHHHHhCCC
Q 013472          376 ------------------------------KL------NREISKIQKARKALTNSHG--------KYPEDIEIAKYTGLS  411 (442)
Q Consensus       376 ------------------------------~v------~e~i~kI~ka~~~L~~elg--------r~PS~eEIAe~LGIS  411 (442)
                                                    ..      .+....+..++..|+....        .+.|++|||+.||+|
T Consensus        81 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~Lp~~~r~v~~l~~~~g~s~~EIA~~lgis  160 (191)
T PRK12520         81 DDADEQSDDDLFDALFAADGHYREPPSDWGDPDAALSRREFFEVLQACVDRLPPRTGRVFMMREWLELETEEICQELQIT  160 (191)
T ss_pred             cccccchhhhhhhhhcccccccccCccccCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHHCCC
Confidence                                          00      0112346666666665543        567999999999999


Q ss_pred             HHHHHHHHHhccc
Q 013472          412 LAEIRSASECLRI  424 (442)
Q Consensus       412 ~etVk~~l~~ar~  424 (442)
                      +++|+..+++++.
T Consensus       161 ~~tV~~~l~Rar~  173 (191)
T PRK12520        161 ATNAWVLLYRARM  173 (191)
T ss_pred             HHHHHHHHHHHHH
Confidence            9999999998874

>PRK11924 RNA polymerase sigma factor; Provisional

Probab=99.59  E-value=2.6e-14  Score=128.87  Aligned_cols=137  Identities=20%  Similarity=0.165  Sum_probs=108.8

Q ss_pred             HHHHHHhchH-HHHHHHHHhHHHHHHHHHHhhCCCCCHHhHHHHHHHHHHHhHHhcCCCCCCChHHHHHHHHHHHHHHHH
Q 013472          286 LKQHLAFGWY-CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMV  364 (442)
Q Consensus       286 L~~~l~~G~~-Are~LI~~nlrLV~sIAkrY~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIRnaI~r~L  364 (442)
                      |...+..|+. |++.++..|.+.|+.+|+++.++..+++|++||++++||.+.++|+  .+..|.+|++.++++.+++++
T Consensus         3 ~~~~~~~~~~~a~~~l~~~y~~~l~~~~~~~~~~~~~aeDl~qe~~~~l~~~~~~~~--~~~~~~~~l~~i~~~~~~d~~   80 (179)
T PRK11924          3 LMPVDATGDKEAFSELFRPHAPDLLRYARRQLGDRALAEDAVQEAFLRAWRKADLFN--GKGSARTWLLTIARNVCYDLL   80 (179)
T ss_pred             HHHHHHccCHHHHHHHHHHHHHHHHHHHHHHhCCHhhHHHHHHHHHHHHHHHHhhcC--CcchHHHHHHHHHHHHHHHHH
Confidence            5566778865 9999999999999999999999999999999999999999999998  345899999999999999999


Q ss_pred             HhhcCceeccc-----c--------------cHHHHHHHHHHHHHHHHHc--------CCCCcHHHHHHHhCCCHHHHHH
Q 013472          365 ARHARGIKIPC-----K--------------LNREISKIQKARKALTNSH--------GKYPEDIEIAKYTGLSLAEIRS  417 (442)
Q Consensus       365 Rkqsr~irlP~-----~--------------v~e~i~kI~ka~~~L~~el--------gr~PS~eEIAe~LGIS~etVk~  417 (442)
                      ++..+......     .              ..+....+..+...|+...        ..+.+.+|||+.||||+.+|+.
T Consensus        81 r~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~e~~~~l~~~l~~L~~~~r~i~~l~~~~~~~~~eIA~~lgis~~tv~~  160 (179)
T PRK11924         81 RRRRREKAVLSDDALEPEFAETAETPEAALLAKDDLARIDRCLDALPVKQREVFLLRYVEGLSYREIAEILGVPVGTVKS  160 (179)
T ss_pred             HhcccccccCcccccccccCCccCCHHHHHhhHHHHHHHHHHHHhCCHHHHHHhhHHHHcCCCHHHHHHHHCCCHHHHHH
Confidence            97654322110     0              0112233455555444432        3577999999999999999999


Q ss_pred             HHHhccc
Q 013472          418 ASECLRI  424 (442)
Q Consensus       418 ~l~~ar~  424 (442)
                      .+++++.
T Consensus       161 ~~~ra~~  167 (179)
T PRK11924        161 RLRRARQ  167 (179)
T ss_pred             HHHHHHH
Confidence            9888764

>PRK12522 RNA polymerase sigma factor; Provisional

Probab=99.59  E-value=1.7e-14  Score=131.65  Aligned_cols=127  Identities=10%  Similarity=0.109  Sum_probs=103.5

Q ss_pred             HHHHHHHHhHHHHHHHHHHhhCCCCCHHhHHHHHHHHHHHhHHhcCCCCCCChHHHHHHHHHHHHHHHHHhhcCceec--
Q 013472          296 CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKI--  373 (442)
Q Consensus       296 Are~LI~~nlrLV~sIAkrY~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIRnaI~r~LRkqsr~irl--  373 (442)
                      .+++|+..|.++|+.+|++|.++..+++|++||+++.+|++.++|++..  +|.+|++.+++|.+++++|++++....  
T Consensus         4 ~~~~l~~~y~~~i~~~~~~~~~~~~daeDvvQe~~i~l~~~~~~~~~~~--~~~~wl~~i~~n~~~d~~Rk~~~~~~~~~   81 (173)
T PRK12522          4 KVEELIDIYKQQIYSLCYKLAKTKEDAEDIFQETWIKVFSSRHQLSYVE--NYKKWITTICVRTFYDFYRKKKRWKDRIL   81 (173)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHcCCcc--chHHHHHHHHHHHHHHHHHHhcccccccc
Confidence            6899999999999999999999999999999999999999999999753  799999999999999999986543110  


Q ss_pred             -------------cc--cc------HHHHHHHHHHHHHHHHHc--------CCCCcHHHHHHHhCCCHHHHHHHHHhccc
Q 013472          374 -------------PC--KL------NREISKIQKARKALTNSH--------GKYPEDIEIAKYTGLSLAEIRSASECLRI  424 (442)
Q Consensus       374 -------------P~--~v------~e~i~kI~ka~~~L~~el--------gr~PS~eEIAe~LGIS~etVk~~l~~ar~  424 (442)
                                   +.  ..      .+....+.++...|+...        -.+.+++|||+.||||+++|+..+.+++.
T Consensus        82 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~i~~l~~~~~~s~~EIA~~lgis~~tV~~~l~Ra~~  161 (173)
T PRK12522         82 DLFHKEDGGEIEFADDVNISEEFIQKVEAEMIREVIQLLNEKYKTVLVLYYYEQYSYKEMSEILNIPIGTVKYRLNYAKK  161 (173)
T ss_pred             cccchhhhhhhccccCCCChHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence                         00  00      112234666666665543        26779999999999999999999988874

>PRK12543 RNA polymerase sigma factor; Provisional

Probab=99.58  E-value=1.6e-14  Score=132.92  Aligned_cols=131  Identities=12%  Similarity=0.084  Sum_probs=105.0

Q ss_pred             hchH-HHHHHHHHhHHHHHHHHHHhhCCCCCHHhHHHHHHHHHHHhHHhcCCCCCCChHHHHHHHHHHHHHHHHHhhcCc
Q 013472          292 FGWY-CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARG  370 (442)
Q Consensus       292 ~G~~-Are~LI~~nlrLV~sIAkrY~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIRnaI~r~LRkqsr~  370 (442)
                      .|+. |++.|+..|.+.|+.++++|.++..+++|++||+|+.+|+++.+|++..  .|.+|++.+++|.+.+++++..+.
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            4544 9999999999999999999999999999999999999999999999864  699999999999999999865421


Q ss_pred             ee---------------ccccc--HHHHHHHHHHHHHHHHHcC--------CCCcHHHHHHHhCCCHHHHHHHHHhccc
Q 013472          371 IK---------------IPCKL--NREISKIQKARKALTNSHG--------KYPEDIEIAKYTGLSLAEIRSASECLRI  424 (442)
Q Consensus       371 ir---------------lP~~v--~e~i~kI~ka~~~L~~elg--------r~PS~eEIAe~LGIS~etVk~~l~~ar~  424 (442)
                      .+               .|.++  .+....+.++...|+....        .+.|++|||+.||||+++|+..+++++.
T Consensus        81 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~Lp~~~r~i~~l~~~e~~s~~EIA~~lgis~~tV~~~l~ra~~  159 (179)
T PRK12543         81 FRIFEKAEEQRKPVSIDFSEDVLSKESNQELIELIHKLPYKLRQVIILRYLHDYSQEEIAQLLQIPIGTVKSRIHAALK  159 (179)
T ss_pred             cccccccccccccccccChHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHccCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            11               01110  1223456666666655442        6779999999999999999999888764

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

Probab=99.58  E-value=1.7e-14  Score=134.01  Aligned_cols=128  Identities=13%  Similarity=0.012  Sum_probs=105.0

Q ss_pred             HHHHHHHHHhHHHHHHHHHHhhCCCCCHHhHHHHHHHHHHHhHHhcCCCCCCChHHHHHHHHHHHHHHHHHhhcCceecc
Q 013472          295 YCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIP  374 (442)
Q Consensus       295 ~Are~LI~~nlrLV~sIAkrY~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIRnaI~r~LRkqsr~irlP  374 (442)
                      .+|++|+..|.+.|+.+|++++++..+++|++||+|+.+|+++.+|++.  ..|.+|++.+++|.+++++|++.+.....
T Consensus        11 ~~f~~l~~~~~~~l~~~~~~~~~~~~~AEDlvQevfl~~~~~~~~~~~~--~~~~~wL~~iarN~~~d~~Rk~~~~~~~~   88 (193)
T TIGR02947        11 QRFERDALEYLDQLYGAALRMTRNPADAEDLVQEAYAKAFSSFHQFKPG--TNLKAWLYRILTNTYINSYRKAQRRPQQS   88 (193)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhhcccCCC--CcchHHHHHHHHHHHHHHHHHhcCCcccc
Confidence            4899999999999999999999999999999999999999999999864  36999999999999999999765432110


Q ss_pred             --------------cc------cH-------HHHHHHHHHHHHHHHHcC--------CCCcHHHHHHHhCCCHHHHHHHH
Q 013472          375 --------------CK------LN-------REISKIQKARKALTNSHG--------KYPEDIEIAKYTGLSLAEIRSAS  419 (442)
Q Consensus       375 --------------~~------v~-------e~i~kI~ka~~~L~~elg--------r~PS~eEIAe~LGIS~etVk~~l  419 (442)
                                    .+      ..       .....+..++..|+....        .+.|++|||+.||||+++|+..+
T Consensus        89 ~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~l~~~l~~Lp~~~r~i~~L~~~~g~s~~EIA~~lgis~~tVk~~l  168 (193)
T TIGR02947        89 DDDDIEDWQLAKAASHTSNGLRSAELEALDGLPDQDIKDALQGLPEEFRQAVYLADVEGFAYKEIAEIMGTPIGTVMSRL  168 (193)
T ss_pred             cchhhhhhhhccccccccccccchhHHHHhhhhHHHHHHHHHhCCHHHhhheeehhhcCCCHHHHHHHHCCCHHHHHHHH
Confidence                          00      00       112456677777766553        56799999999999999999999


Q ss_pred             Hhccc
Q 013472          420 ECLRI  424 (442)
Q Consensus       420 ~~ar~  424 (442)
                      ++++.
T Consensus       169 ~Rar~  173 (193)
T TIGR02947       169 HRGRK  173 (193)
T ss_pred             HHHHH
Confidence            98874

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.

>PRK09415 RNA polymerase factor sigma C; Reviewed

Probab=99.57  E-value=3.4e-14  Score=130.85  Aligned_cols=129  Identities=16%  Similarity=0.058  Sum_probs=103.9

Q ss_pred             hHHHHHHHHHhHHHHHHHHHHhhCCCCCHHhHHHHHHHHHHHhHHhcCCCCCCChHHHHHHHHHHHHHHHHHhhcCceec
Q 013472          294 WYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKI  373 (442)
Q Consensus       294 ~~Are~LI~~nlrLV~sIAkrY~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIRnaI~r~LRkqsr~irl  373 (442)
                      ..|+++|+..|.+.|+.+|.++.++..+++|++||+|+.+|+++.+|++.  ..|.+|++.+++|.+++++|+..+....
T Consensus        15 ~~a~~~l~~~~~~~l~~~~~~~~~~~~~AeDlvQd~fl~l~~~~~~~~~~--~~~~awl~~ia~n~~~d~~Rk~~~~~~~   92 (179)
T PRK09415         15 EDLIDEIMNEYGQEVLQLVYSYVKNKEVAEDLTQEIFVKCYKSLHTYKGK--SSLKTWLYRIAINHCKDYLKSWHNKKVI   92 (179)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHhcCCC--cccHHHHHHHHHHHHHHHHHhhcccccc
Confidence            34999999999999999999999999999999999999999999999874  3699999999999999999975321111


Q ss_pred             c---------c---c------cHHHHHHHHHHHHHHHHHcC--------CCCcHHHHHHHhCCCHHHHHHHHHhccc
Q 013472          374 P---------C---K------LNREISKIQKARKALTNSHG--------KYPEDIEIAKYTGLSLAEIRSASECLRI  424 (442)
Q Consensus       374 P---------~---~------v~e~i~kI~ka~~~L~~elg--------r~PS~eEIAe~LGIS~etVk~~l~~ar~  424 (442)
                      +         .   .      ..+....+.++...|+....        .+.|++|||+.||||+++|+..+++++.
T Consensus        93 ~~~~~~~~~~~~~~~~e~~~~~~e~~~~l~~~l~~L~~~~r~v~~l~~~~g~s~~EIA~~l~is~~tv~~~l~Ra~~  169 (179)
T PRK09415         93 VTEDIFTYMESQKESVEEEVIQNAEDERLASAVMSLPIKYREVIYLFYYEELSIKEIAEVTGVNENTVKTRLKKAKE  169 (179)
T ss_pred             ccccccccccccccCcHHHHHHHHHHHHHHHHHHhCCHHHhhHhHhHHhcCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            0         0   0      11223446666666655442        5679999999999999999999998875

>PRK09645 RNA polymerase sigma factor SigL; Provisional

Probab=99.57  E-value=3e-14  Score=129.63  Aligned_cols=130  Identities=13%  Similarity=0.022  Sum_probs=104.1

Q ss_pred             hHHHHHHHHHhHHHHHHHHHHhhCCCCCHHhHHHHHHHHHHHhHHhcCCCCCCChHHHHHHHHHHHHHHHHHhhcCcee-
Q 013472          294 WYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIK-  372 (442)
Q Consensus       294 ~~Are~LI~~nlrLV~sIAkrY~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIRnaI~r~LRkqsr~ir-  372 (442)
                      ..|++.|+..|.+.|+.+|.++.++..++||++||.|+.+|+..++|++.. ..|.+|++.+++|.+++++|++++... 
T Consensus         8 ~~~~~~l~~~~~~~l~~~~~~~~~~~~~AeD~vQevfl~~~~~~~~~~~~~-~~~~~wL~~iarn~~~d~~Rk~~~~~~~   86 (173)
T PRK09645          8 AALMRALYDEHAAPLWRYALRLTGDRARAEDVVQETLLRAWQHPEVLADTG-RSARAWLFTVARNLVIDERRSARARPVE   86 (173)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhHHhcCccc-ccHHHHHHHHHHHHHHHHHHhhcccccc
Confidence            349999999999999999999999999999999999999999999997532 479999999999999999997643211 


Q ss_pred             -------cccc-----c--HHHHHHHHHHHHHHHHHc--------CCCCcHHHHHHHhCCCHHHHHHHHHhccc
Q 013472          373 -------IPCK-----L--NREISKIQKARKALTNSH--------GKYPEDIEIAKYTGLSLAEIRSASECLRI  424 (442)
Q Consensus       373 -------lP~~-----v--~e~i~kI~ka~~~L~~el--------gr~PS~eEIAe~LGIS~etVk~~l~~ar~  424 (442)
                             .|..     .  ......+..++..|+...        -.+.|++|||+.||+|+++|+..+++++.
T Consensus        87 ~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~vl~L~~~~g~s~~EIA~~lgis~~tV~~~l~ra~~  160 (173)
T PRK09645         87 GGDDVLGVPEQSAPDEVDRALDRLLVADALAQLSPEHRAVLVRSYYRGWSTAQIAADLGIPEGTVKSRLHYALR  160 (173)
T ss_pred             cccccccCCCCCCchHHHHHhHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence                   1100     1  111224666666665554        26789999999999999999999988875

>PRK12518 RNA polymerase sigma factor; Provisional

Probab=99.57  E-value=3.6e-14  Score=129.14  Aligned_cols=135  Identities=16%  Similarity=0.093  Sum_probs=105.0

Q ss_pred             HHHHHhchH-HHHHHHHHhHHHHHHHHHHhhCCCCCHHhHHHHHHHHHHHhHHhcCCCCCCChHHHHHHHHHHHHHHHHH
Q 013472          287 KQHLAFGWY-CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVA  365 (442)
Q Consensus       287 ~~~l~~G~~-Are~LI~~nlrLV~sIAkrY~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIRnaI~r~LR  365 (442)
                      +..++.|+. |++.++..|.+.|+.+++++.+ ..+++|++||+|+.+|+.++.|++.  ..|.+|++.+++|.+++++|
T Consensus         2 ~~~~~~gd~~a~~~l~~~~~~~l~~~~~~~~~-~~~aeDivQe~~l~l~~~~~~~~~~--~~~~~wl~~ia~n~~~d~~R   78 (175)
T PRK12518          2 ILRCQRGDRQSFRQLYRRYQQKVRSTLYQLCG-RELLDDLVQEVFLRVWKGLPKLRNP--AYFSTWLYRITWNVATDARR   78 (175)
T ss_pred             hhHHHcCCHHHHHHHHHHHHHHHHHHHHHHcC-HhHHHHHHHHHHHHHHHhHHhhCCc--ccHHHHHHHHHHHHHHHHHH
Confidence            455677866 9999999999999999999875 4789999999999999999999974  46999999999999999999


Q ss_pred             hhcCce----ecc--------cc---c--HHHHHHHHHHHHHHHHHcC--------CCCcHHHHHHHhCCCHHHHHHHHH
Q 013472          366 RHARGI----KIP--------CK---L--NREISKIQKARKALTNSHG--------KYPEDIEIAKYTGLSLAEIRSASE  420 (442)
Q Consensus       366 kqsr~i----rlP--------~~---v--~e~i~kI~ka~~~L~~elg--------r~PS~eEIAe~LGIS~etVk~~l~  420 (442)
                      +..+..    ..+        ..   .  .+....+..+...|+....        .+.|++|||+.||+|+++|+..++
T Consensus        79 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~vl~l~~~~g~s~~eIA~~lg~s~~tv~~~l~  158 (175)
T PRK12518         79 QFAQRPSRIQDDSLNDQPSRPSDTPDLMQLHYQDLVQQGLQTLSLEHRAVLVLHDLEDLPQKEIAEILNIPVGTVKSRLF  158 (175)
T ss_pred             HhhccccchhcccccccccCCCCcHHHHHHHHHHHHHHHHHhCCHHHeeeeeehHhcCCCHHHHHHHHCCCHHHHHHHHH
Confidence            764321    110        00   0  0111235555555555432        566999999999999999999999


Q ss_pred             hccc
Q 013472          421 CLRI  424 (442)
Q Consensus       421 ~ar~  424 (442)
                      +++.
T Consensus       159 Rar~  162 (175)
T PRK12518        159 YARR  162 (175)
T ss_pred             HHHH
Confidence            8875

>PRK12516 RNA polymerase sigma factor; Provisional

Probab=99.56  E-value=3.9e-14  Score=132.13  Aligned_cols=129  Identities=13%  Similarity=0.099  Sum_probs=105.5

Q ss_pred             hHHHHHHHHHhHHHHHHHHHHhhCCCCCHHhHHHHHHHHHHHhHHhcCCCCCCChHHHHHHHHHHHHHHHHHhhcCceec
Q 013472          294 WYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKI  373 (442)
Q Consensus       294 ~~Are~LI~~nlrLV~sIAkrY~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIRnaI~r~LRkqsr~irl  373 (442)
                      ..++++|+..|.+.|+.+|++++++..++||++||.|+.+|+..++|+...  .|.+|++.+++|.+++++|++++....
T Consensus         9 ~~~f~~l~~~~~~~L~~~a~~~~~~~~~AEDivQevfl~~~~~~~~~~~~~--~~~awL~~Ia~n~~~d~~R~~~~~~~~   86 (187)
T PRK12516          9 TPPFKRELLAALPSLRAFAVSLIGRHDRADDLVQDTIMKAWAKQDHFEVGT--NMKAWLFTILRNEFYSQMRKRGREVQD   86 (187)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHcCCHhHHHHHHHHHHHHHHHhhhccCCcc--cHHHHHHHHHHHHHHHHHHhhcCCccc
Confidence            349999999999999999999999999999999999999999999998643  699999999999999999987653211


Q ss_pred             cc---------c----cHHHHHHHHHHHHHHHHHcC--------CCCcHHHHHHHhCCCHHHHHHHHHhccc
Q 013472          374 PC---------K----LNREISKIQKARKALTNSHG--------KYPEDIEIAKYTGLSLAEIRSASECLRI  424 (442)
Q Consensus       374 P~---------~----v~e~i~kI~ka~~~L~~elg--------r~PS~eEIAe~LGIS~etVk~~l~~ar~  424 (442)
                      ..         .    .......+..++..|+....        .+.+++|||+.||||+++|+..+.+++.
T Consensus        87 ~~~~~~~~~~~~~~~~~~~~~~~l~~~L~~Lp~~~r~i~~L~~~~g~s~~EIA~~Lgis~~tVk~~l~Rar~  158 (187)
T PRK12516         87 TDGMFTEQLAVHPSQYGTLDLQDFRAALDQLPDDQREAIILVGASGFAYEEAAEICGCAVGTIKSRVNRARQ  158 (187)
T ss_pred             cccccccccCCCcchhhHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            00         0    11123456677777766542        6789999999999999999999988874

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

Probab=99.56  E-value=3.8e-14  Score=122.37  Aligned_cols=127  Identities=24%  Similarity=0.288  Sum_probs=101.1

Q ss_pred             HHHHHHHHhHHHHHHHHHHhhCCCCCHHhHHHHHHHHHHHhHHhcCCCCCCChHHHHHHHHHHHHHHHHHhhcC------
Q 013472          296 CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHAR------  369 (442)
Q Consensus       296 Are~LI~~nlrLV~sIAkrY~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIRnaI~r~LRkqsr------  369 (442)
                      |++.++..|.++|+++++++.+++.+.+|++|||+++++++++.|++.  .+|.+|+++++++.+.++++++.+      
T Consensus         2 a~~~l~~~~~~~v~~~~~~~~~~~~~~~D~~qe~~~~l~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~rk~~~~~~~~~   79 (158)
T TIGR02937         2 AFEELYERYLPLLYRYARRYLGDDADAEDLVQEAFLKLLEALDRFDPE--GSFKAWLFRIARNLILDYLRRKRRLRRELD   79 (158)
T ss_pred             HHHHHHHHHHHHHHHHHHHHhCCHhHHHHHHHHHHHHHHHhHHhcCCc--chHHHHHHHHHHHHHHHHHHHhccCCcchh
Confidence            789999999999999999999999999999999999999999999997  589999999999999999998764      


Q ss_pred             c-eec------ccc---cHHHHHHHHHHHHHHHHHc--------CCCCcHHHHHHHhCCCHHHHHHHHHhccc
Q 013472          370 G-IKI------PCK---LNREISKIQKARKALTNSH--------GKYPEDIEIAKYTGLSLAEIRSASECLRI  424 (442)
Q Consensus       370 ~-irl------P~~---v~e~i~kI~ka~~~L~~el--------gr~PS~eEIAe~LGIS~etVk~~l~~ar~  424 (442)
                      . ...      |..   .......+.++...|+...        ..+.+..|||+.+|+|+.+|+..+..++.
T Consensus        80 ~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~~~ii~~~~~~g~s~~eIA~~l~~s~~~v~~~~~~~~~  152 (158)
T TIGR02937        80 LLEELLDSDPSPEEELEQEEEREALREALEKLPEREREVLVLRYLEGLSYKEIAEILGISVGTVKRRLKRARK  152 (158)
T ss_pred             hhhhcccccCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHhhHHhcCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            0 000      000   1122233445544443322        36779999999999999999999887653

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.

>PRK08241 RNA polymerase factor sigma-70; Validated

Probab=99.55  E-value=5.8e-14  Score=141.51  Aligned_cols=139  Identities=18%  Similarity=0.104  Sum_probs=112.4

Q ss_pred             HHHHHHHHhchH-HHHHHHHHhHHHHHHHHHHhhCCCCCHHhHHHHHHHHHHHhHHhcCCCCCCChHHHHHHHHHHHHHH
Q 013472          284 RVLKQHLAFGWY-CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISK  362 (442)
Q Consensus       284 eeL~~~l~~G~~-Are~LI~~nlrLV~sIAkrY~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIRnaI~r  362 (442)
                      .+|+..++.|+. |+++|+..|.+.|+.+|++++++..+++|++||.|+.+|+.+++|++.  ..|.+|++.+++|.+++
T Consensus         7 ~~l~~~~~~gd~~af~~l~~~y~~~l~~~~~~~~~~~~dAEDivQevfl~~~~~~~~~~~~--~~~~~wL~~Ia~n~~~d   84 (339)
T PRK08241          7 AALLARAAAGDRDAFAALVEPHRRELLAHCYRMLGSVHDAEDAVQETLLRAWRGYDRFEGR--SSLRTWLYRIATNVCLD   84 (339)
T ss_pred             HHHHHHhhcCCHHHHHHHHHHHHHHHHHHHHHHhCChhhHHHHHHHHHHHHHhhhhccccc--cchHHHHHHHHHHHHHH
Confidence            578889999976 999999999999999999999999999999999999999999999853  36999999999999999


Q ss_pred             HHHhhcCcee---c-----------------------cc-----------cc---HHH-HHHHHHHHHHHHHHcC-----
Q 013472          363 MVARHARGIK---I-----------------------PC-----------KL---NRE-ISKIQKARKALTNSHG-----  396 (442)
Q Consensus       363 ~LRkqsr~ir---l-----------------------P~-----------~v---~e~-i~kI~ka~~~L~~elg-----  396 (442)
                      ++|++++...   .                       +.           ..   .+. ...+..++..|+....     
T Consensus        85 ~~Rk~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~e~~~~~l~~~l~~Lp~~~R~v~~L  164 (339)
T PRK08241         85 ALEGRARRPLPTDLGAPAADPVDELVERPEVPWLEPYPDALLDPAAADPAARVVARESVRLAFVAALQHLPPRQRAVLIL  164 (339)
T ss_pred             HHHhhccccCccccCCCcCcccccccccccccccCCCCcccccccCCChHHHHHHHHHHHHHHHHHHHhCCHHHhhhhhh
Confidence            9997653210   0                       00           00   011 1235566666665543     


Q ss_pred             ---CCCcHHHHHHHhCCCHHHHHHHHHhccc
Q 013472          397 ---KYPEDIEIAKYTGLSLAEIRSASECLRI  424 (442)
Q Consensus       397 ---r~PS~eEIAe~LGIS~etVk~~l~~ar~  424 (442)
                         .+.|++|||+.||+|+++|+..+++++.
T Consensus       165 ~~~~g~s~~EIA~~lgis~~tVk~~l~RAr~  195 (339)
T PRK08241        165 RDVLGWSAAEVAELLDTSVAAVNSALQRARA  195 (339)
T ss_pred             HHhhCCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence               5679999999999999999999988874

>PRK12547 RNA polymerase sigma factor; Provisional

Probab=99.55  E-value=6.3e-14  Score=127.20  Aligned_cols=128  Identities=13%  Similarity=0.107  Sum_probs=104.1

Q ss_pred             HHHHHHHHHhHHHHHHHHHHhhCCCCCHHhHHHHHHHHHHHhHHhcCCCCCCChHHHHHHHHHHHHHHHHHhhcCceecc
Q 013472          295 YCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIP  374 (442)
Q Consensus       295 ~Are~LI~~nlrLV~sIAkrY~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIRnaI~r~LRkqsr~irlP  374 (442)
                      ..|.+++..|.+.|+.+|+++.++..++||++||+|+.+|+..++|+...  .|.+|++.+++|.+++++|++++.....
T Consensus         6 ~~f~~~~~~~~~~l~~~a~~~~~~~~~AeDivQe~fl~l~~~~~~~~~~~--~~~~wl~~i~~n~~~d~~R~~~~~~~~~   83 (164)
T PRK12547          6 KNFKQELLLALPALRAFAVSLSSKHDKAEDLVQDTLMKAWAKQDSFEMGT--NLKAWLFTILRNEFYSQMRKRGREVQDS   83 (164)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHcCCHhhHHHHHHHHHHHHHHhhhhcCCcc--cHHHHHHHHHHHHHHHHHHhhccccccc
Confidence            47899999999999999999999999999999999999999999998643  5999999999999999999765432110


Q ss_pred             ---------cc----cHHHHHHHHHHHHHHHHHcC--------CCCcHHHHHHHhCCCHHHHHHHHHhccc
Q 013472          375 ---------CK----LNREISKIQKARKALTNSHG--------KYPEDIEIAKYTGLSLAEIRSASECLRI  424 (442)
Q Consensus       375 ---------~~----v~e~i~kI~ka~~~L~~elg--------r~PS~eEIAe~LGIS~etVk~~l~~ar~  424 (442)
                               ..    .......+..++..|+....        .+.|++|||+.||||+++|+..+++++.
T Consensus        84 ~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~v~~l~~~~g~s~~eIA~~lgis~~tV~~~l~Rar~  154 (164)
T PRK12547         84 DGVFTARVAVHPAQYGSLDLQDFKKALNLLSADQREAIILIGASGFSYEDAAAICGCAVGTIKSRVSRARN  154 (164)
T ss_pred             cccccccCCCCchhhhHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence                     00    01122346666666655432        6789999999999999999999998875

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

Probab=99.55  E-value=5.3e-14  Score=126.48  Aligned_cols=131  Identities=15%  Similarity=0.030  Sum_probs=104.5

Q ss_pred             hch-HHHHHHHHHhHHHHHHHHHHhhCCCCCHHhHHHHHHHHHHHhHHhcCCCCCCChHHHHHHHHHHHHHHHHHhhcCc
Q 013472          292 FGW-YCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARG  370 (442)
Q Consensus       292 ~G~-~Are~LI~~nlrLV~sIAkrY~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIRnaI~r~LRkqsr~  370 (442)
                      .|+ .+++.++..|.+.|+.+|.+++++..+++|++||+|+.+|++.++|+.  ...|.+|++.+++|.++++++++.+.
T Consensus         2 ~~~~~~~~~l~~~~~~~l~~~~~~~~~~~~~aeDivQe~f~~~~~~~~~~~~--~~~~~~wl~~i~~n~~~d~~rk~~~~   79 (162)
T TIGR02983         2 SATEEEFTAFVAARYPRLLRTAYLLTGDPHEAEDLVQEALVRTYVRWDRIRD--PDAPDAYVRRVLVNLARSRWRRRRLL   79 (162)
T ss_pred             CCcHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHhhcCC--cccHHHHHHHHHHHHHHHHHHhhccc
Confidence            354 499999999999999999999999999999999999999999999964  34799999999999999999977541


Q ss_pred             eec----cc----c---cHHHHHHHHHHHHHHHHHcC--------CCCcHHHHHHHhCCCHHHHHHHHHhccc
Q 013472          371 IKI----PC----K---LNREISKIQKARKALTNSHG--------KYPEDIEIAKYTGLSLAEIRSASECLRI  424 (442)
Q Consensus       371 irl----P~----~---v~e~i~kI~ka~~~L~~elg--------r~PS~eEIAe~LGIS~etVk~~l~~ar~  424 (442)
                      ...    |.    .   .......+..+...|+....        .+.+++|||+.||+|+++|+..+.+++.
T Consensus        80 ~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~i~~l~~~~g~s~~eIA~~lgis~~tV~~~l~ra~~  152 (162)
T TIGR02983        80 ELPTRELPDAAAPDPAPDVALRAALARALRRLPARQRAVVVLRYYEDLSEAQVAEALGISVGTVKSRLSRALA  152 (162)
T ss_pred             cccccccCcccCCccchhHHHHHHHHHHHHhCCHHHHHHhhhHHHhcCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence            110    10    0   11233445566665555432        5679999999999999999999988874

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.

>PRK12529 RNA polymerase sigma factor; Provisional

Probab=99.55  E-value=3.8e-14  Score=130.57  Aligned_cols=134  Identities=9%  Similarity=-0.013  Sum_probs=104.9

Q ss_pred             HhchH-HHHHHHHHhHHHHHHHHHHhhC--CCCCHHhHHHHHHHHHHHhHHhcCCCCCCChHHHHHHHHHHHHHHHHHhh
Q 013472          291 AFGWY-CREELIKSTRPLVLFLARNYRG--LGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARH  367 (442)
Q Consensus       291 ~~G~~-Are~LI~~nlrLV~sIAkrY~g--~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIRnaI~r~LRkq  367 (442)
                      ..|+. ||+.|+..|.+.|+.++.++.+  +..+++|++||.|+.+|+..++|+......|.||++.+++|.+++++|++
T Consensus         8 ~~~d~~af~~ly~~~~~~l~~~~~~~~~~~~~~~AeDivQevFl~~~~~~~~~~~~~~~~~~~wL~~ia~n~~~d~~Rk~   87 (178)
T PRK12529          8 LSADRDKVATLYRENHAWLRNWLAYRLRSWGRGVADDLAHDIFLRILASRDGGQREAIRQPRAYLARIANCVLVSWRRRQ   87 (178)
T ss_pred             CCCCHHHHHHHHHHHHHHHHHHHHHHhCCCChHHHHHHHHHHHHHHHhcccccccccccCHHHHHHHHHHHHHHHHHHHH
Confidence            34544 9999999999999998766665  46889999999999999999999754345799999999999999999976


Q ss_pred             cCce-------ecc-------cc---cHHHHHHHHHHHHHHHHHcC--------CCCcHHHHHHHhCCCHHHHHHHHHhc
Q 013472          368 ARGI-------KIP-------CK---LNREISKIQKARKALTNSHG--------KYPEDIEIAKYTGLSLAEIRSASECL  422 (442)
Q Consensus       368 sr~i-------rlP-------~~---v~e~i~kI~ka~~~L~~elg--------r~PS~eEIAe~LGIS~etVk~~l~~a  422 (442)
                      .+..       ..+       ..   ..+....|.+++.+|+.+..        .+.|++|||+.||+|+++|+..++++
T Consensus        88 ~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~l~~~l~~Lp~~~R~v~~L~~~~g~s~~EIA~~lgis~~tVk~~l~rA  167 (178)
T PRK12529         88 SLELAWLEALATLPEPLHPSPEQQSVILETLHEIDALLDTLRPRVKQAFLMATLDGMKQKDIAQALDIALPTVKKYIHQA  167 (178)
T ss_pred             HHHhhhhhHhhhccCcCCCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence            4311       011       10   11234457777777777653        57899999999999999999998877


Q ss_pred             cc
Q 013472          423 RI  424 (442)
Q Consensus       423 r~  424 (442)
                      ..
T Consensus       168 l~  169 (178)
T PRK12529        168 YV  169 (178)
T ss_pred             HH
Confidence            63

>PRK12541 RNA polymerase sigma factor; Provisional

Probab=99.54  E-value=7.9e-14  Score=125.65  Aligned_cols=127  Identities=17%  Similarity=0.101  Sum_probs=101.5

Q ss_pred             HHHHHHHHHhHHHHHHHHHHhhCCCCCHHhHHHHHHHHHHHhHHhcCCCCCCChHHHHHHHHHHHHHHHHHhhcCceec-
Q 013472          295 YCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKI-  373 (442)
Q Consensus       295 ~Are~LI~~nlrLV~sIAkrY~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIRnaI~r~LRkqsr~irl-  373 (442)
                      .|+++++..|.+.|+.+|.+++++..+++|++||+|+.+|+..++|++.   .|.||++.+++|.+++++|++.+.... 
T Consensus         5 ~a~~~l~~~~~~~l~~~~~~~~~~~~~AeDv~Qe~f~~~~~~~~~~~~~---~~~~wl~~i~~n~~~d~~R~~~~~~~~~   81 (161)
T PRK12541          5 QSLEEIYSEHMQDLFRYLLSLTGDSHFAEDLMQETFYRMLVHIDYYKGE---EIRPWLFTIAYNAFIDWYRKEKKYKTTT   81 (161)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHhHHHccCC---ChHHHHHHHHHHHHHHHHHhcccccccc
Confidence            3899999999999999999999999999999999999999999999863   599999999999999999986542111 


Q ss_pred             ---------ccc-----cHHHHHHHHHHHHHHHHHc--------CCCCcHHHHHHHhCCCHHHHHHHHHhccc
Q 013472          374 ---------PCK-----LNREISKIQKARKALTNSH--------GKYPEDIEIAKYTGLSLAEIRSASECLRI  424 (442)
Q Consensus       374 ---------P~~-----v~e~i~kI~ka~~~L~~el--------gr~PS~eEIAe~LGIS~etVk~~l~~ar~  424 (442)
                               |..     ..+....+..+...|+...        -.+.+++|||+.||+|+++|+..+++++.
T Consensus        82 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~L~~~~r~v~~l~~~~~~s~~eIA~~lgis~~tv~~~l~Rar~  154 (161)
T PRK12541         82 IEEFHLPNVPSTEHEYFIKHEIASWLDSLSSLPLERRNVLLLRDYYGFSYKEIAEMTGLSLAKVKIELHRGRK  154 (161)
T ss_pred             hhhhhccCCCCcHHHHHHHhHHHHHHHHHHHCCHHHHHHhhhHHhcCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence                     000     0112223344555555433        26779999999999999999999998874

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

Probab=99.54  E-value=7.5e-14  Score=127.89  Aligned_cols=133  Identities=17%  Similarity=0.098  Sum_probs=102.1

Q ss_pred             hchH-HHHHHHHHhHHHHHHHHHHhh----CCCCCHHhHHHHHHHHHHHhHHhcCCCCCCChHHHHHHHHHHHHHHHHHh
Q 013472          292 FGWY-CREELIKSTRPLVLFLARNYR----GLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVAR  366 (442)
Q Consensus       292 ~G~~-Are~LI~~nlrLV~sIAkrY~----g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIRnaI~r~LRk  366 (442)
                      .|+. |++.|+..|.+.|+.+|++|.    ++..+++|++||+++.+|+++.+|+...+.+|.+|++.+++|.+++++++
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            4554 999999999999999999875    35689999999999999999999987655689999999999999999986


Q ss_pred             hc----Cce--ecc-------------------------cc---cHHHHHHHHHHHHHHHHHc--------CCCCcHHHH
Q 013472          367 HA----RGI--KIP-------------------------CK---LNREISKIQKARKALTNSH--------GKYPEDIEI  404 (442)
Q Consensus       367 qs----r~i--rlP-------------------------~~---v~e~i~kI~ka~~~L~~el--------gr~PS~eEI  404 (442)
                      +.    +..  ..+                         ..   ..+....+.++...|+...        ..+.+.+||
T Consensus        83 ~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~l~~~l~~L~~~~r~vi~l~~~~g~s~~eI  162 (189)
T TIGR02984        83 HLGAQKRDIRREQSLDAGGRLDESSVRLAAQLAADGPSPSQVAARREAAVRLAQALAKLPEDYREVILLRHLEGLSFAEV  162 (189)
T ss_pred             HHHHHhhhcccccCCCcccccCCcchhHHHHccCCCCCHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHhcCCCHHHH
Confidence            51    110  000                         00   0112234555555554432        367899999


Q ss_pred             HHHhCCCHHHHHHHHHhccc
Q 013472          405 AKYTGLSLAEIRSASECLRI  424 (442)
Q Consensus       405 Ae~LGIS~etVk~~l~~ar~  424 (442)
                      |+.||||+++|+..+++++.
T Consensus       163 A~~lgis~~~v~~~l~Ra~~  182 (189)
T TIGR02984       163 AERMDRSEGAVSMLWVRGLA  182 (189)
T ss_pred             HHHHCcCHHHHHHHHHHHHH
Confidence            99999999999999988764

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).

>PRK12535 RNA polymerase sigma factor; Provisional

Probab=99.54  E-value=1.1e-13  Score=130.11  Aligned_cols=138  Identities=19%  Similarity=0.058  Sum_probs=109.9

Q ss_pred             HHHHHHHHhchH-HHHHHHHHhHHHHHHHHHHhhCCCCCHHhHHHHHHHHHHHhHHhcCCCCCCChHHHHHHHHHHHHHH
Q 013472          284 RVLKQHLAFGWY-CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISK  362 (442)
Q Consensus       284 eeL~~~l~~G~~-Are~LI~~nlrLV~sIAkrY~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIRnaI~r  362 (442)
                      .+|+..+..|+. |++.++..|.+.++.++. +.++..+++|++||.|+.+|+..++|++.  ..|.+|++.+++|.+++
T Consensus        13 ~~l~~~~~~~d~~a~~~l~~~y~~~l~~~~~-~~~~~~~AEDivQevflkl~~~~~~~~~~--~~~~~WL~~Iarn~~id   89 (196)
T PRK12535         13 TDLALAAGRGDRAALTEFIRETQDDVWRLLA-HLGGHDIADDLTQETYLRVMSALPRFAAR--SSARTWLLSLARRVWVD   89 (196)
T ss_pred             HHHHHHHHcCCHHHHHHHHHHHHHHHHHHHH-HhCCHHHHHHHHHHHHHHHHHHhhhcCCc--ccHHHHHHHHHHHHHHH
Confidence            567778888876 999999999999999975 67888999999999999999999999864  36999999999999999


Q ss_pred             HHHhhcCceec--------------ccc--cHHHHHHHHHHHHHHHHHcC--------CCCcHHHHHHHhCCCHHHHHHH
Q 013472          363 MVARHARGIKI--------------PCK--LNREISKIQKARKALTNSHG--------KYPEDIEIAKYTGLSLAEIRSA  418 (442)
Q Consensus       363 ~LRkqsr~irl--------------P~~--v~e~i~kI~ka~~~L~~elg--------r~PS~eEIAe~LGIS~etVk~~  418 (442)
                      ++|++.+....              |..  ..+....+.+++..|+....        .+.|++|||+.||+|+++|+..
T Consensus        90 ~~Rk~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~Lp~~~r~v~~l~~~~g~s~~EIAe~lgis~~tV~~~  169 (196)
T PRK12535         90 NIRHDMARPRKSATEYEDAAATTASNETTGSWSEWIDVRTLIDALPPERREALILTQVLGYTYEEAAKIADVRVGTIRSR  169 (196)
T ss_pred             HHHhhccCCCcccccccccccccCCcchhHHHHHHHHHHHHHHcCCHHHHHHhhhHHHhCCCHHHHHHHhCCCHHHHHHH
Confidence            99976432110              000  11222346666666665442        5679999999999999999999


Q ss_pred             HHhccc
Q 013472          419 SECLRI  424 (442)
Q Consensus       419 l~~ar~  424 (442)
                      +++++.
T Consensus       170 l~Rar~  175 (196)
T PRK12535        170 VARARA  175 (196)
T ss_pred             HHHHHH
Confidence            988774

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

Probab=99.53  E-value=5.8e-14  Score=124.30  Aligned_cols=127  Identities=17%  Similarity=0.082  Sum_probs=99.9

Q ss_pred             HHHHHHHHhHHHHHHHHHHhhCCCCCHHhHHHHHHHHHHHhHHhcCCCCCCChHHHHHHHHHHHHHHHHHhhcCceec--
Q 013472          296 CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKI--  373 (442)
Q Consensus       296 Are~LI~~nlrLV~sIAkrY~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIRnaI~r~LRkqsr~irl--  373 (442)
                      |+++|+..|.+.|+.+++++.++..+++|++||+++++|+++.+|++.  .+|.+|++.++++.+.+++++..+....  
T Consensus         2 a~~~l~~~~~~~l~~~~~~~~~~~~~aeD~~Qe~~~~~~~~~~~~~~~--~~~~~wl~~i~r~~~~d~~r~~~~~~~~~~   79 (161)
T TIGR02985         2 AFEQLYRRYYPKLCAFAYRYVKDEEEAEDIVQDVFVKLWENRETLEEV--ESFKAYLFTIVKNRSLNYLRHKQVEEKYQE   79 (161)
T ss_pred             hHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhHHhcccc--ccHHHHHHHHHHHHHHHHHHHHHhHhHHHH
Confidence            789999999999999999999999999999999999999999999874  3799999999999999999977532111  


Q ss_pred             ------cc--------c---cHHHHHHHHHHHHHHHHHc--------CCCCcHHHHHHHhCCCHHHHHHHHHhccc
Q 013472          374 ------PC--------K---LNREISKIQKARKALTNSH--------GKYPEDIEIAKYTGLSLAEIRSASECLRI  424 (442)
Q Consensus       374 ------P~--------~---v~e~i~kI~ka~~~L~~el--------gr~PS~eEIAe~LGIS~etVk~~l~~ar~  424 (442)
                            +.        .   ..+....+..+...|+...        ..+.|..|||+.+|+|+.+|+..+++++.
T Consensus        80 ~~~~~~~~~~~~~~~~~~~~~~e~~~~l~~~l~~L~~~~r~il~l~~~~~~~~~eIA~~lgis~~tv~~~~~ra~~  155 (161)
T TIGR02985        80 EILEIEVDELSENDPEEELEAKELQLIIYKAIEKLPEQCRKIFILSRFEGKSYKEIAEELGISVKTVEYHISKALK  155 (161)
T ss_pred             HHHhhcccccCCCCcHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence                  00        0   0112223444444433322        35779999999999999999999988764

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.

>PRK12523 RNA polymerase sigma factor; Reviewed

Probab=99.53  E-value=4.3e-14  Score=129.02  Aligned_cols=131  Identities=15%  Similarity=0.070  Sum_probs=102.4

Q ss_pred             HhchH-HHHHHHHHhHHHHHHHHHHhhCCCCCHHhHHHHHHHHHHHhHHhcCCCCCCChHHHHHHHHHHHHHHHHHhhcC
Q 013472          291 AFGWY-CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHAR  369 (442)
Q Consensus       291 ~~G~~-Are~LI~~nlrLV~sIAkrY~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIRnaI~r~LRkqsr  369 (442)
                      +.|+. |+..|+..|.+.|+.+|.++.++..+++|++||+|+.+|+. ..|+..  ..|.+|++.+++|.+++++|++.+
T Consensus         5 ~~~~~~a~~~l~~~~~~~l~~~~~~~~~~~~~AeDlvQevflk~~~~-~~~~~~--~~~~~wL~~Iarn~~~d~~Rk~~~   81 (172)
T PRK12523          5 QSPHSELVGALYRDHRGWLLAWLRRNVACRQRAEDLSQDTFVRLLGR-PELPTP--REPRAFLAAVAKGLMFDHFRRAAL   81 (172)
T ss_pred             CCCCcHHHHHHHHHHHHHHHHHHHHHcCCHhhHHHHHHHHHHHHHcc-cccCcc--hhHHHHHHHHHHHHHHHHHHHHHH
Confidence            45654 99999999999999999999999999999999999999986 446543  369999999999999999998643


Q ss_pred             cee-------cc-------cc---cHHHHHHHHHHHHHHHHHc--------CCCCcHHHHHHHhCCCHHHHHHHHHhccc
Q 013472          370 GIK-------IP-------CK---LNREISKIQKARKALTNSH--------GKYPEDIEIAKYTGLSLAEIRSASECLRI  424 (442)
Q Consensus       370 ~ir-------lP-------~~---v~e~i~kI~ka~~~L~~el--------gr~PS~eEIAe~LGIS~etVk~~l~~ar~  424 (442)
                      ...       .+       ..   ..+....+..++..|+.+.        -.+.+++|||+.||||+++|+..+.+++.
T Consensus        82 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~Lp~~~r~v~~L~~~~g~s~~EIA~~lgis~~tV~~~l~ra~~  161 (172)
T PRK12523         82 EQAYLAELALVPEAEQPSPEEQHLILEDLKAIDRLLGKLSSKARAAFLYNRLDGMGHAEIAERLGVSVSRVRQYLAQGLR  161 (172)
T ss_pred             HHHHHHHHhhcccccCCChHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            110       00       00   0122234666666665543        26789999999999999999999988764

>PRK09644 RNA polymerase sigma factor SigM; Provisional

Probab=99.52  E-value=1.1e-13  Score=125.38  Aligned_cols=125  Identities=16%  Similarity=0.008  Sum_probs=100.4

Q ss_pred             HHHHHHHhHHHHHHHHHHhhCCCCCHHhHHHHHHHHHHHhHHhcCCCCCCChHHHHHHHHHHHHHHHHHhhcCceecc--
Q 013472          297 REELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIP--  374 (442)
Q Consensus       297 re~LI~~nlrLV~sIAkrY~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIRnaI~r~LRkqsr~irlP--  374 (442)
                      ++.|+..|.+.|+.+|++|.++..+++|++||+|+.+|++++.|++.   .|.+|++.+++|.+++++|+.++.....  
T Consensus         3 ~~~l~~~y~~~l~~~~~~~~~~~~~AeDlvQe~fl~~~~~~~~~~~~---~~~~wL~~i~~n~~~d~~R~~~~~~~~~~~   79 (165)
T PRK09644          3 IEEIYKMYINDVYRYLFSLTKSHHAAEDLLQETFYRAYIYLEDYDNQ---KVKPWLFKVAYHTFIDFVRKEKKVSFVGTD   79 (165)
T ss_pred             HHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhHHhcccc---chHHHHHHHHHHHHHHHHHhhhhccccchh
Confidence            67899999999999999999999999999999999999999999863   5999999999999999999876432111  


Q ss_pred             ----------ccc---HHHHHHHHHHHHHHHHHc--------CCCCcHHHHHHHhCCCHHHHHHHHHhccc
Q 013472          375 ----------CKL---NREISKIQKARKALTNSH--------GKYPEDIEIAKYTGLSLAEIRSASECLRI  424 (442)
Q Consensus       375 ----------~~v---~e~i~kI~ka~~~L~~el--------gr~PS~eEIAe~LGIS~etVk~~l~~ar~  424 (442)
                                ...   .+....+..+...|+...        -.+.+++|||+.||+|+++|+..+++++.
T Consensus        80 ~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~v~~l~~~~g~s~~eIA~~lgis~~tv~~~l~Rar~  150 (165)
T PRK09644         80 EIEAIQAESTEEYVVAKNSYEKLIQIIHTLPVIEAQAILLCDVHELTYEEAASVLDLKLNTYKSHLFRGRK  150 (165)
T ss_pred             HHhhhcccChHHHHHHHHHHHHHHHHHHhCCHHHHHHHHhHHHhcCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence                      000   112234555555554443        25679999999999999999999998874

>PRK12533 RNA polymerase sigma factor; Provisional

Probab=99.52  E-value=1.8e-13  Score=131.08  Aligned_cols=130  Identities=15%  Similarity=0.056  Sum_probs=104.9

Q ss_pred             hchHHHHHHHHHhHHHHHHHHHHhhCCCCCHHhHHHHHHHHHHHhHHhcCCCCCCChHHHHHHHHHHHHHHHHHhhcCce
Q 013472          292 FGWYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGI  371 (442)
Q Consensus       292 ~G~~Are~LI~~nlrLV~sIAkrY~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIRnaI~r~LRkqsr~i  371 (442)
                      ....+++.|+..|.+.|+.+++++.++..++||++||+|+.+|+.+++|++.   .|.+|++++++|.++++++++++..
T Consensus        15 ~~~~~f~~l~~~~~~~l~~~~~~~~~d~~dAEDlvQEvflkl~~~~~~~~~~---~~~aWL~~IarN~~~d~~Rk~~~~~   91 (216)
T PRK12533         15 ARGERFRQLVLPHLDAAYNLARWLCGNASDADDVVQEACMRALRFFDSFRGD---NARPWLLAIVRHTWYSEWRRRANAH   91 (216)
T ss_pred             hhHHHHHHHHHHHHHHHHHHHHHHhCCHhhHHHHHHHHHHHHHHhHHhcCcc---chHhHHHHHHHHHHHHHHHhhcccc
Confidence            3355999999999999999999999999999999999999999999999852   4999999999999999999765321


Q ss_pred             ec------cc------------c------cHHHHHHHHHHHHHHHHHcC--------CCCcHHHHHHHhCCCHHHHHHHH
Q 013472          372 KI------PC------------K------LNREISKIQKARKALTNSHG--------KYPEDIEIAKYTGLSLAEIRSAS  419 (442)
Q Consensus       372 rl------P~------------~------v~e~i~kI~ka~~~L~~elg--------r~PS~eEIAe~LGIS~etVk~~l  419 (442)
                      ..      +.            .      ..+....+.+++..|+....        .+.|++|||+.||||+++|+..+
T Consensus        92 ~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~e~~~~l~~al~~Lp~~~R~v~~L~y~eg~s~~EIAe~LgiS~~tVk~~L  171 (216)
T PRK12533         92 EVAAPDTLDDADSLDDWQPAGEDPLALLLRAEDVRLVNAALAKLPVEYREVLVLRELEDMSYREIAAIADVPVGTVMSRL  171 (216)
T ss_pred             cccccccccccccccccccCCCCHHHHHHHHHHHHHHHHHHHcCCHHHHhHhhhHHhcCCCHHHHHHHHCCCHHHHHHHH
Confidence            10      00            0      01233456666666665442        67899999999999999999999


Q ss_pred             Hhccc
Q 013472          420 ECLRI  424 (442)
Q Consensus       420 ~~ar~  424 (442)
                      ++++.
T Consensus       172 ~RAr~  176 (216)
T PRK12533        172 ARARR  176 (216)
T ss_pred             HHHHH
Confidence            88874

>TIGR02960 SigX5 RNA polymerase sigma-70 factor, TIGR02960 family

Probab=99.51  E-value=1.3e-13  Score=137.56  Aligned_cols=130  Identities=17%  Similarity=0.075  Sum_probs=103.6

Q ss_pred             chH-HHHHHHHHhHHHHHHHHHHhhCCCCCHHhHHHHHHHHHHHhHHhcCCCCCCChHHHHHHHHHHHHHHHHHhhcCce
Q 013472          293 GWY-CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGI  371 (442)
Q Consensus       293 G~~-Are~LI~~nlrLV~sIAkrY~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIRnaI~r~LRkqsr~i  371 (442)
                      |+. |+++|+..|.+.|+.+|++++++..++||++||.|+.+|+.+++|+..  ..|.||++.+++|.+++++|++++..
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            444 999999999999999999999999999999999999999999999864  36999999999999999999764321


Q ss_pred             e--------------------------ccc-----------c---c---HHH-HHHHHHHHHHHHHHcC--------CCC
Q 013472          372 K--------------------------IPC-----------K---L---NRE-ISKIQKARKALTNSHG--------KYP  399 (442)
Q Consensus       372 r--------------------------lP~-----------~---v---~e~-i~kI~ka~~~L~~elg--------r~P  399 (442)
                      .                          ++.           .   .   .+. ...+..++.+|+....        .+.
T Consensus        80 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~l~~~l~~Lp~~~R~v~~L~~~~g~  159 (324)
T TIGR02960        80 RPVGLGAPSADGTAAASEAAEVTWLEPLPDLTLDLDDPAAADPSVAAGSRESVRLAFVAAIQYLPPRQRAVLLLRDVLGW  159 (324)
T ss_pred             CccccCCCCCcccccccccccccccCCCCccccccccCCCCCHHHHHHHHHHHHHHHHHHHHhCCHHHhhHhhhHHHhCC
Confidence            1                          000           0   0   011 1235556666655442        567


Q ss_pred             cHHHHHHHhCCCHHHHHHHHHhccc
Q 013472          400 EDIEIAKYTGLSLAEIRSASECLRI  424 (442)
Q Consensus       400 S~eEIAe~LGIS~etVk~~l~~ar~  424 (442)
                      +++|||+.||+|+++|+..+++++.
T Consensus       160 s~~EIA~~lgis~~tV~~~l~Rar~  184 (324)
T TIGR02960       160 RAAETAELLGTSTASVNSALQRARA  184 (324)
T ss_pred             CHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            9999999999999999999988874

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.

>PRK09642 RNA polymerase sigma factor SigW; Reviewed

Probab=99.51  E-value=9.3e-14  Score=124.87  Aligned_cols=121  Identities=11%  Similarity=0.060  Sum_probs=96.5

Q ss_pred             HHHhHHHHHHHHHHhhCCCCCHHhHHHHHHHHHHHhHHhcCCCCCCChHHHHHHHHHHHHHHHHHhhcCcee-cc-----
Q 013472          301 IKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIK-IP-----  374 (442)
Q Consensus       301 I~~nlrLV~sIAkrY~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIRnaI~r~LRkqsr~ir-lP-----  374 (442)
                      ++.|.+.|+.+|++++++..+++|++||+|+.+|+++++|++.   .|.||++.+++|.+++++|++.+... ..     
T Consensus         1 ~~~y~~~l~~~~~~~~~~~~~AeDlvQe~fl~~~~~~~~~~~~---~~~~wl~~ia~n~~~d~~Rk~~~~~~~~~~~~~~   77 (160)
T PRK09642          1 MQTYRHYIFQVIFSILRHEEDAKDVTQEVFVKIHASLPNYQFR---GLKTWMARIATNHAIDYKRKKARENEELSLCKET   77 (160)
T ss_pred             CchHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHhcccccccc---hhHHHHHHHHHHHHHHHHHHhcccccccccchhh
Confidence            3578999999999999999999999999999999999999863   49999999999999999998654211 00     


Q ss_pred             -----c--cc------HHHHHHHHHHHHHHHHHc--------CCCCcHHHHHHHhCCCHHHHHHHHHhccc
Q 013472          375 -----C--KL------NREISKIQKARKALTNSH--------GKYPEDIEIAKYTGLSLAEIRSASECLRI  424 (442)
Q Consensus       375 -----~--~v------~e~i~kI~ka~~~L~~el--------gr~PS~eEIAe~LGIS~etVk~~l~~ar~  424 (442)
                           .  ..      .+....+..++..|+...        -.+.|++|||+.||+|+++|+..+++++.
T Consensus        78 ~~~~~~~~~~~~~~~~~e~~~~l~~~l~~Lp~~~r~v~~l~~~~g~s~~EIA~~lgis~~tV~~~l~Rar~  148 (160)
T PRK09642         78 EENIKSSHNIEDLLLTKEQKLLIAQKLRELPENYRDVVLAHYLEEKSYQEIALQEKIEVKTVEMKLYRARK  148 (160)
T ss_pred             hhhccCCCChHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHhCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence                 0  00      112234666666666553        26789999999999999999999998875

>PRK12528 RNA polymerase sigma factor; Provisional

Probab=99.50  E-value=1.9e-13  Score=123.22  Aligned_cols=127  Identities=17%  Similarity=0.096  Sum_probs=101.3

Q ss_pred             HHHHHHHHHhHHHHHHHHHHhhCCCCCHHhHHHHHHHHHHHhHHhcCCCCCCChHHHHHHHHHHHHHHHHHhhcCce---
Q 013472          295 YCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGI---  371 (442)
Q Consensus       295 ~Are~LI~~nlrLV~sIAkrY~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIRnaI~r~LRkqsr~i---  371 (442)
                      .|+++|+..|.+.|+.+|.++.++..++||++||+|+.+|+..+.|++   ..|.+|++++++|.+++++|++.+..   
T Consensus         4 ~a~~~l~~~~~~~l~~~~~~~~~~~~~AeDivQe~flk~~~~~~~~~~---~~~~~wl~~i~~n~~~d~~R~~~~~~~~~   80 (161)
T PRK12528          4 ATVEGLYSAHHHWLTGWLRRRLGCPQSAADLAQDTFVKVLVARETAQI---IEPRAFLTTIAKRVLCNHYRRQDLERAYL   80 (161)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHcCCcccHHHHHHHHHHHHHhccccccc---cCHHHHHHHHHHHHHHHHHHHHHHHHhhH
Confidence            489999999999999999999999999999999999999999988864   26999999999999999999764211   


Q ss_pred             ----eccc----c------cHHHHHHHHHHHHHHHHHc--------CCCCcHHHHHHHhCCCHHHHHHHHHhccc
Q 013472          372 ----KIPC----K------LNREISKIQKARKALTNSH--------GKYPEDIEIAKYTGLSLAEIRSASECLRI  424 (442)
Q Consensus       372 ----rlP~----~------v~e~i~kI~ka~~~L~~el--------gr~PS~eEIAe~LGIS~etVk~~l~~ar~  424 (442)
                          ..|.    .      ..+....+.+++.+|+...        -.+.+++|||+.||+|+++|+..+++++.
T Consensus        81 ~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~v~~L~~~~g~s~~EIA~~l~is~~tV~~~l~ra~~  155 (161)
T PRK12528         81 EALAQLPERVAPSEEERAIILETLVELDQLLDGLPPLVKRAFLLAQVDGLGYGEIATELGISLATVKRYLNKAAM  155 (161)
T ss_pred             HHhhccccccCCCHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence                0110    0      0122234556666665543        26789999999999999999999988753

>PRK12540 RNA polymerase sigma factor; Provisional

Probab=99.48  E-value=4.3e-13  Score=124.59  Aligned_cols=127  Identities=16%  Similarity=0.156  Sum_probs=103.3

Q ss_pred             HHHHHHHHhHHHHHHHHHHhhCCCCCHHhHHHHHHHHHHHhHHhcCCCCCCChHHHHHHHHHHHHHHHHHhhcCceec--
Q 013472          296 CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKI--  373 (442)
Q Consensus       296 Are~LI~~nlrLV~sIAkrY~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIRnaI~r~LRkqsr~irl--  373 (442)
                      ++..++..|.+.|+.+|.+++++..+++|++||+|+.+|+..++|++..  .|.+|++.+++|.++++++++.+....  
T Consensus         6 ~~~~~~~~~~~~l~~~~~~~~~~~~~AEDivQevflkl~~~~~~~~~~~--~~~~WL~~Ia~n~~~d~~Rk~~~~~~~~~   83 (182)
T PRK12540          6 SLRDDILAAVPSLRAFAISLSGNGDRADDLVQETLLRALANIDSFQPGS--NLPAWLFTILRNLFRSDYRKRRREVEDAD   83 (182)
T ss_pred             HHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhHHhcCCCc--hHHHHHHHHHHHHHHHHHHhccccccccc
Confidence            6789999999999999999999999999999999999999999998753  699999999999999999986543211  


Q ss_pred             --------ccc---cHHHHHHHHHHHHHHHHHc--------CCCCcHHHHHHHhCCCHHHHHHHHHhccc
Q 013472          374 --------PCK---LNREISKIQKARKALTNSH--------GKYPEDIEIAKYTGLSLAEIRSASECLRI  424 (442)
Q Consensus       374 --------P~~---v~e~i~kI~ka~~~L~~el--------gr~PS~eEIAe~LGIS~etVk~~l~~ar~  424 (442)
                              +..   .......+..++.+|+...        -.+.|++|||+.||||+.+|+..+++++.
T Consensus        84 ~~~~~~~~~~~~~~~~~~~~~l~~~l~~Lp~~~R~v~~L~~~~g~s~~EIA~~Lgis~~tV~~~l~RAr~  153 (182)
T PRK12540         84 GSYAKTLKSQPGQNAHLEFEEFRAALDKLPQDQREALILVGASGFSYEDAAAICGCAVGTIKSRVNRARS  153 (182)
T ss_pred             ccccccccCCCchHHHHHHHHHHHHHHhCCHHHHHHhhHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence                    000   0112234666677665554        26789999999999999999999988874

>PRK08311 putative RNA polymerase sigma factor SigI; Reviewed

Probab=99.48  E-value=6.1e-13  Score=129.71  Aligned_cols=91  Identities=19%  Similarity=0.293  Sum_probs=82.1

Q ss_pred             CHHHHHHHHHhchH-HHHHHHHHhHHHHHHHHHHhhCCCC--CHHhHHHHHHHHHHHhHHhcCCCCCCChHHHHHHHHHH
Q 013472          282 SERVLKQHLAFGWY-CREELIKSTRPLVLFLARNYRGLGI--PFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRK  358 (442)
Q Consensus       282 deeeL~~~l~~G~~-Are~LI~~nlrLV~sIAkrY~g~g~--d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIRn  358 (442)
                      +.++|+..++.|+. |++.|+..|.++|+++|.+++++..  +++|++|||++++|+++++|++.+|.+|.+|++++|+|
T Consensus         4 ~~~~Li~~~~~gD~~AfeeLi~~Y~p~I~~~a~~~~~~~~~~eaeDlvQe~fi~l~eai~~y~~~kg~sF~awl~~Iirn   83 (237)
T PRK08311          4 SLEDILEKIKNGDEELREELIEEYKPFIAKVVSSVCGRYIDWENDDELSIGLIAFNEAIDSYDEEKGKSFLSFAELVIKR   83 (237)
T ss_pred             cHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHhcccCCCCchHHHHHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHH
Confidence            45678888899966 9999999999999999999998875  59999999999999999999999888899999999999


Q ss_pred             HHHHHHHhhcCcee
Q 013472          359 SISKMVARHARGIK  372 (442)
Q Consensus       359 aI~r~LRkqsr~ir  372 (442)
                      .+++++|++.+...
T Consensus        84 ~~iDylRk~~~~~~   97 (237)
T PRK08311         84 RLIDYFRKESKHNL   97 (237)
T ss_pred             HHHHHHHHhhcccc
Confidence            99999998766433

>PRK09639 RNA polymerase sigma factor SigX; Provisional

Probab=99.48  E-value=4.1e-13  Score=121.00  Aligned_cols=126  Identities=15%  Similarity=0.035  Sum_probs=99.5

Q ss_pred             HHHHHHHHHhHHHHHHHHHHhhCCCCCHHhHHHHHHHHHHHhHHhcCCCCCCChHHHHHHHHHHHHHHHHHhhcCceecc
Q 013472          295 YCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIP  374 (442)
Q Consensus       295 ~Are~LI~~nlrLV~sIAkrY~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIRnaI~r~LRkqsr~irlP  374 (442)
                      .|++.++..|.+.|+.+|.++.++..+++|++||+|+.+|++  .|+.  +..|.||++.+++|.+++++|+..+.....
T Consensus         3 ~~f~~l~~~y~~~l~~~~~~~~~~~~~aeDlvQe~fi~~~~~--~~~~--~~~~~~wl~~i~rn~~~d~~rk~~~~~~~~   78 (166)
T PRK09639          3 ETFEDLFEQYYPDVVQQIFYIVKDRTQAEDLAQEVFLRLYRS--DFKG--IENEKGWLIKSARNVAYNYLRSEKRRRARI   78 (166)
T ss_pred             hHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHH--hccc--ccchHHHHHHHHHHHHHHHHHHhccccccc
Confidence            489999999999999999999999999999999999999999  6764  347999999999999999999875432111


Q ss_pred             ---------------cc---cHHHHHHHHHHHHHHHHHcC-------CCCcHHHHHHHhCCCHHHHHHHHHhccc
Q 013472          375 ---------------CK---LNREISKIQKARKALTNSHG-------KYPEDIEIAKYTGLSLAEIRSASECLRI  424 (442)
Q Consensus       375 ---------------~~---v~e~i~kI~ka~~~L~~elg-------r~PS~eEIAe~LGIS~etVk~~l~~ar~  424 (442)
                                     ..   ..+....+.++...|+....       .+.+++|||+.||+|+.+|+..+.+++.
T Consensus        79 ~~~~~~~~~~~~~~~e~~~~~~~~~~~l~~~l~~L~~~~r~il~l~~~g~s~~eIA~~lgis~~tV~~~i~ra~~  153 (166)
T PRK09639         79 LGEFQWQEVDNEPSPEEIWIRKEEITKVQEVLAKMTERDRTVLLLRFSGYSYKEIAEALGIKESSVGTTLARAKK  153 (166)
T ss_pred             cchhhhhhccCCCChHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence                           00   01222345555555543321       6789999999999999999999988764

>PRK12545 RNA polymerase sigma factor; Provisional

Probab=99.47  E-value=3.4e-13  Score=126.85  Aligned_cols=124  Identities=15%  Similarity=0.046  Sum_probs=98.7

Q ss_pred             HHHHHhHHHHHHHHHHhhCCCCCHHhHHHHHHHHHHHhHHhcCCCCCCChHHHHHHHHHHHHHHHHHhhcCceecc---c
Q 013472          299 ELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIP---C  375 (442)
Q Consensus       299 ~LI~~nlrLV~sIAkrY~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIRnaI~r~LRkqsr~irlP---~  375 (442)
                      .++..|.+.|+.+|++++++..+++|++||+|+.+|+.+++|++..  .|.||++.+++|.+++++|++.+...++   .
T Consensus        12 ~~~~~~~~~l~~~~~~~~~d~~~AEDivQe~fl~~~~~~~~~~~~~--~~~~WL~~IarN~~~d~~Rk~~r~~~~~~~~~   89 (201)
T PRK12545         12 AYLAQLRHDLLRFARLQLRDADAAEDAVQEALAAAWSQAGRFAGQS--AHKTWVFGILRNKLIDTLRARQRTVNLSALDA   89 (201)
T ss_pred             HHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhhhhccccc--hHHHHHHHHHHHHHHHHHHhhccccccccccc
Confidence            4488999999999999999999999999999999999999999753  6999999999999999999876432211   0


Q ss_pred             -----------------------------ccH------HHHHHHHHHHHHHHHHc--------CCCCcHHHHHHHhCCCH
Q 013472          376 -----------------------------KLN------REISKIQKARKALTNSH--------GKYPEDIEIAKYTGLSL  412 (442)
Q Consensus       376 -----------------------------~v~------e~i~kI~ka~~~L~~el--------gr~PS~eEIAe~LGIS~  412 (442)
                                                   ...      +....+.+++..|+...        ..+.+++|||+.||+|+
T Consensus        90 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~L~~Lp~~~r~v~~L~~~eg~s~~EIA~~lgis~  169 (201)
T PRK12545         90 ELDGEALLDRELFKDNGHWAAHAKPRPWPKPETILQQQQFWTLFETCLDHLPEQIGRVFMMREFLDFEIDDICTELTLTA  169 (201)
T ss_pred             ccchhhhhhhhhhcccccccccccCcCCCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHHCcCH
Confidence                                         000      11123555666665543        36789999999999999


Q ss_pred             HHHHHHHHhccc
Q 013472          413 AEIRSASECLRI  424 (442)
Q Consensus       413 etVk~~l~~ar~  424 (442)
                      ++|+..+.+++.
T Consensus       170 ~tVk~~l~RAr~  181 (201)
T PRK12545        170 NHCSVLLYRART  181 (201)
T ss_pred             HHHHHHHHHHHH
Confidence            999999888874

>PRK12532 RNA polymerase sigma factor; Provisional

Probab=99.47  E-value=4.2e-13  Score=124.92  Aligned_cols=125  Identities=16%  Similarity=0.102  Sum_probs=98.7

Q ss_pred             HHHHHHhHHHHHHHHHHhhCCCCC-HHhHHHHHHHHHHHhHHhcCCCCCCChHHHHHHHHHHHHHHHHHhhcCceecc--
Q 013472          298 EELIKSTRPLVLFLARNYRGLGIP-FSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIP--  374 (442)
Q Consensus       298 e~LI~~nlrLV~sIAkrY~g~g~d-~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIRnaI~r~LRkqsr~irlP--  374 (442)
                      +..+..|.+.|+.+|++++++..+ ++|++||+|+.+|++.++|++.  .+|.||++.+++|.+++++|++++.....  
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            456788999999999999999888 9999999999999999999864  37999999999999999999875422110  


Q ss_pred             ----------------------c----c---------cHHHHHHHHHHHHHHHHHc--------CCCCcHHHHHHHhCCC
Q 013472          375 ----------------------C----K---------LNREISKIQKARKALTNSH--------GKYPEDIEIAKYTGLS  411 (442)
Q Consensus       375 ----------------------~----~---------v~e~i~kI~ka~~~L~~el--------gr~PS~eEIAe~LGIS  411 (442)
                                            .    .         ..+....+.++...|+...        -.+.|++|||+.||+|
T Consensus        86 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~e~~~~l~~~l~~L~~~~r~i~~L~~~~g~s~~EIA~~lgis  165 (195)
T PRK12532         86 LDDELLDEAFESHFSQNGHWTPEGQPQHWNTPEKSLNNNEFQKILQSCLYNLPENTARVFTLKEILGFSSDEIQQMCGIS  165 (195)
T ss_pred             ccccccchhhhhhhccccccccccCccccCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHhhhHHHhCCCHHHHHHHHCCC
Confidence                                  0    0         0112233566666665543        2577999999999999


Q ss_pred             HHHHHHHHHhccc
Q 013472          412 LAEIRSASECLRI  424 (442)
Q Consensus       412 ~etVk~~l~~ar~  424 (442)
                      +++|+..+++++.
T Consensus       166 ~~tVk~~l~Rar~  178 (195)
T PRK12532        166 TSNYHTIMHRARE  178 (195)
T ss_pred             HHHHHHHHHHHHH
Confidence            9999999988874

>PRK12530 RNA polymerase sigma factor; Provisional

Probab=99.47  E-value=4.5e-13  Score=124.77  Aligned_cols=125  Identities=13%  Similarity=0.079  Sum_probs=99.2

Q ss_pred             HHHHHHhHHHHHHHHHHhhCCCCCHHhHHHHHHHHHHHhHHhcCCCCCCChHHHHHHHHHHHHHHHHHhhcCceecc---
Q 013472          298 EELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIP---  374 (442)
Q Consensus       298 e~LI~~nlrLV~sIAkrY~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIRnaI~r~LRkqsr~irlP---  374 (442)
                      +..|..|.+.|+.+|.+++++..+++|++||+|+.+|+..++|++..  +|.||++++++|.+++++|++++.....   
T Consensus        10 ~~~~~~~~~~l~~~~~~~~~d~~~AeDivQe~flk~~~~~~~~~~~~--~~~~wL~~Ia~n~~~d~~Rk~~~~~~~~~~~   87 (189)
T PRK12530         10 SLEIEEIRLQMLKFATLQLKDADLAEDVVQEALVSAYKNADSFKGQS--ALKTWIFAILKNKIIDLIRYRKRFVNESELI   87 (189)
T ss_pred             HHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHhchhccCCc--cHHHHHHHHHHHHHHHHHHhhccCCCccccc
Confidence            35578889999999999999999999999999999999999998753  6999999999999999999875432110   


Q ss_pred             ----------------------cc--c-------HHHHHHHHHHHHHHHHHcC--------CCCcHHHHHHHhCCCHHHH
Q 013472          375 ----------------------CK--L-------NREISKIQKARKALTNSHG--------KYPEDIEIAKYTGLSLAEI  415 (442)
Q Consensus       375 ----------------------~~--v-------~e~i~kI~ka~~~L~~elg--------r~PS~eEIAe~LGIS~etV  415 (442)
                                            ..  .       .+....+..++.+|+....        .+.|++|||+.||+|+++|
T Consensus        88 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~Lp~~~R~v~~L~~~~g~s~~EIA~~lgis~~tV  167 (189)
T PRK12530         88 EEDSPNSFFDEKGHWKPEYYEPSEWQEVENTVYKEEFWLIFEACLNHLPAQQARVFMMREYLELSSEQICQECDISTSNL  167 (189)
T ss_pred             ccccchhhhcccccccccccCCccccCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHhHHHHcCCCHHHHHHHHCCCHHHH
Confidence                                  00  0       0111235666666665542        5789999999999999999


Q ss_pred             HHHHHhccc
Q 013472          416 RSASECLRI  424 (442)
Q Consensus       416 k~~l~~ar~  424 (442)
                      +..+++++.
T Consensus       168 k~~l~RAr~  176 (189)
T PRK12530        168 HVLLYRARL  176 (189)
T ss_pred             HHHHHHHHH
Confidence            999998874

>PRK09647 RNA polymerase sigma factor SigE; Reviewed

Probab=99.47  E-value=6e-13  Score=126.04  Aligned_cols=127  Identities=24%  Similarity=0.212  Sum_probs=102.3

Q ss_pred             HHHHHHHHHhHHHHHHHHHHhhCCCCCHHhHHHHHHHHHHHhHHhcCCCCCCChHHHHHHHHHHHHHHHHHhhcCc--ee
Q 013472          295 YCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARG--IK  372 (442)
Q Consensus       295 ~Are~LI~~nlrLV~sIAkrY~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIRnaI~r~LRkqsr~--ir  372 (442)
                      .++++|+..|.+.|+.++.++.++..+++|++||+|+.+|++..+|++  + +|.+|++.+++|.+++++|+..+.  ..
T Consensus        28 ~a~~~l~~~~~~~L~~~~~~~~~~~~~AEDivQEvflkl~~~~~~~~~--~-~~~~wL~~iarn~~~d~~Rk~~~~~~~~  104 (203)
T PRK09647         28 PSWEELVRQHADRVYRLAYRLSGNQHDAEDLTQETFIRVFRSLQNYQP--G-TFEGWLHRITTNLFLDMVRRRARIRMEA  104 (203)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHhCCHhHHHHHHHHHHHHHHHhHHhcCC--c-ccHHHHHHHHHHHHHHHHHhcccCcccc
Confidence            399999999999999999999999999999999999999999999985  3 699999999999999999987531  10


Q ss_pred             cc-------cc---------cHHHHHHHHHHHHHHHHHc--------CCCCcHHHHHHHhCCCHHHHHHHHHhccc
Q 013472          373 IP-------CK---------LNREISKIQKARKALTNSH--------GKYPEDIEIAKYTGLSLAEIRSASECLRI  424 (442)
Q Consensus       373 lP-------~~---------v~e~i~kI~ka~~~L~~el--------gr~PS~eEIAe~LGIS~etVk~~l~~ar~  424 (442)
                      ++       ..         ..+....+..++..|+...        ..+.+++|||+.||||+++|+..+.+++.
T Consensus       105 ~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~L~~L~~~~r~v~~L~~~~g~s~~EIA~~Lgis~~tV~~~l~RArk  180 (203)
T PRK09647        105 LPEDYDRVPGDEPNPEQIYHDARLDPDLQAALDSLPPEFRAAVVLCDIEGLSYEEIAATLGVKLGTVRSRIHRGRQ  180 (203)
T ss_pred             ccccccccCCCCCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            10       00         0112334555555555443        26789999999999999999999988874

>PRK09637 RNA polymerase sigma factor SigZ; Provisional

Probab=99.46  E-value=7.4e-13  Score=122.78  Aligned_cols=125  Identities=15%  Similarity=0.107  Sum_probs=99.7

Q ss_pred             HHHHHHHhHHHHHHHHHHhhCCCCCHHhHHHHHHHHHHHhHHhcCCCCCCChHHHHHHHHHHHHHHHHHhhcCceecccc
Q 013472          297 REELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIPCK  376 (442)
Q Consensus       297 re~LI~~nlrLV~sIAkrY~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIRnaI~r~LRkqsr~irlP~~  376 (442)
                      ++.|+..|.+.|+.+|.++.++..+++|++||.++.+|+.+..|++.  .+|.+|++.+++|.+++++|++++...++..
T Consensus         3 ~~~l~~~y~~~l~~~~~~~~~~~~~aeDi~QEvflkl~~~~~~~~~~--~~~~~wL~~i~~n~~~d~~Rk~~~~~~~~~~   80 (181)
T PRK09637          3 LESIWSEYKAQLKAFLHSRVSNEADVDDLLQEVLIKTHSNLHSLKDG--SSIKSWLYQIANNTIIDFYRKKNRSEELPDD   80 (181)
T ss_pred             HHHHHHHHHHHHHHHHHHHhCChhhHHHHHHHHHHHHHHhHHHhccc--cchHHHHHHHHHHHHHHHHHhccccCCcchh
Confidence            67899999999999999999999999999999999999999999853  4799999999999999999987543322110


Q ss_pred             ------------cHHHHHHHHHHHHHHHHHc--------CCCCcHHHHHHHhCCCHHHHHHHHHhcc
Q 013472          377 ------------LNREISKIQKARKALTNSH--------GKYPEDIEIAKYTGLSLAEIRSASECLR  423 (442)
Q Consensus       377 ------------v~e~i~kI~ka~~~L~~el--------gr~PS~eEIAe~LGIS~etVk~~l~~ar  423 (442)
                                  ..+....+..+...|+...        -.+.+.+|||+.||+|+++|+..+.+++
T Consensus        81 ~~~~~~~~~~~~~~e~~~~l~~~l~~L~~~~r~i~~l~~~~g~~~~EIA~~lgis~~tV~~~l~Rar  147 (181)
T PRK09637         81 LLFEDEEREENAKKELAPCLRPFIDALPEKYAEALRLTELEGLSQKEIAEKLGLSLSGAKSRVQRGR  147 (181)
T ss_pred             hhccCCChhHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHhcCCCHHHHHHHhCCCHHHHHHHHHHHH
Confidence                        0112223444444444332        2677999999999999999999988776

>PRK12517 RNA polymerase sigma factor; Provisional

Probab=99.46  E-value=9.7e-13  Score=122.69  Aligned_cols=130  Identities=13%  Similarity=0.012  Sum_probs=104.0

Q ss_pred             chHHHHHHHHHhHHHHHHHHHHhhCCCCCHHhHHHHHHHHHHHhHHhcCCCCCCChHHHHHHHHHHHHHHHHHhhcCce-
Q 013472          293 GWYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGI-  371 (442)
Q Consensus       293 G~~Are~LI~~nlrLV~sIAkrY~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIRnaI~r~LRkqsr~i-  371 (442)
                      ...+++.++..|.+.|+.+|.++.++..+++|++||+|+.+|+.++.|++.  ..|.+|++.+++|.+.+..+++.+.. 
T Consensus        21 ~~~~f~~l~~~y~~~l~~~~~~~~~~~~~AeDlvQdvflkl~~~~~~~~~~--~~~~~wL~~Iarn~~~~~~r~~~~~~~   98 (188)
T PRK12517         21 KQRRYEALVKALHADIYRYAYWLCKDKHIAEDLVQETFLRAWRSLDSLKDE--KAAKAWLITILRRENARRFERKQFDLV   98 (188)
T ss_pred             cHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhHHhhcCc--cchHHHHHHHHHHHHHHHHHHhccCcc
Confidence            455999999999999999999999999999999999999999999999864  36999999999999988877643211 


Q ss_pred             e-----ccc---c---cHHHHHHHHHHHHHHHHHcC--------CCCcHHHHHHHhCCCHHHHHHHHHhccc
Q 013472          372 K-----IPC---K---LNREISKIQKARKALTNSHG--------KYPEDIEIAKYTGLSLAEIRSASECLRI  424 (442)
Q Consensus       372 r-----lP~---~---v~e~i~kI~ka~~~L~~elg--------r~PS~eEIAe~LGIS~etVk~~l~~ar~  424 (442)
                      .     .+.   .   .......+..++..|+....        .+.+++|||+.||||+.+|+..+++++.
T Consensus        99 ~~~~~~~~~~~~~~~e~~~~~~~l~~~l~~Lp~~~r~v~~l~~~~g~s~~EIA~~lgis~~tV~~~l~Rar~  170 (188)
T PRK12517         99 DIEDDSIEDDASHSSEEEMEQEWLRRQIAKLDPEYREPLLLQVIGGFSGEEIAEILDLNKNTVMTRLFRARN  170 (188)
T ss_pred             CcccccccCccccChhHHHHHHHHHHHHHhCCHHHHHHHHHHHHhCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            0     010   0   01112346677777766543        6779999999999999999999988874

>TIGR02950 SigM_subfam RNA polymerase sigma factor, SigM family

Probab=99.45  E-value=4.6e-13  Score=119.05  Aligned_cols=120  Identities=18%  Similarity=0.052  Sum_probs=96.6

Q ss_pred             HHhHHHHHHHHHHhhCCCCCHHhHHHHHHHHHHHhHHhcCCCCCCChHHHHHHHHHHHHHHHHHhhcCceec-----c--
Q 013472          302 KSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKI-----P--  374 (442)
Q Consensus       302 ~~nlrLV~sIAkrY~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIRnaI~r~LRkqsr~irl-----P--  374 (442)
                      ..|.+.|+.+|.++.++..+++|++||+++.+|+.+++|++   .+|.||++.++++.++++++++.+....     +  
T Consensus         2 ~~~~~~l~~~~~~~~~~~~~aeD~~Qe~~~~l~~~~~~~~~---~~f~~wl~~i~~~~~~d~~r~~~~~~~~~~~~~~~~   78 (154)
T TIGR02950         2 REYMHDVFRYLYRLTKDKHLAEDLLQETFLKAYIHLHSFKD---SSIKPWLFRIARNAFIDWYRKDKKIQTIDDDAIGDL   78 (154)
T ss_pred             chHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhHHHhcC---CchHHHHHHHHHHHHHHHHHHhhhhccccHhhhhhc
Confidence            57899999999999999999999999999999999999997   3799999999999999999976532211     0  


Q ss_pred             --------ccc---HHHHHHHHHHHHHHHHHcC--------CCCcHHHHHHHhCCCHHHHHHHHHhccc
Q 013472          375 --------CKL---NREISKIQKARKALTNSHG--------KYPEDIEIAKYTGLSLAEIRSASECLRI  424 (442)
Q Consensus       375 --------~~v---~e~i~kI~ka~~~L~~elg--------r~PS~eEIAe~LGIS~etVk~~l~~ar~  424 (442)
                              ...   .+....+.++...|+....        .+.+++|||+.||+|+.+|+..+++++.
T Consensus        79 ~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~i~~l~~~~g~s~~eIA~~lgis~~tv~~~l~Ra~~  147 (154)
T TIGR02950        79 EQHPVESPEHHLLIKIEQEEITHHLSRLPENYRTVLILREFKEFSYKEIAELLNLSLAKVKSNLFRARK  147 (154)
T ss_pred             cccccCChhHHHHHHHHHHHHHHHHHhCCHhheeeeeehhhccCcHHHHHHHHCCCHHHHHHHHHHHHH
Confidence                    000   1122446677777765442        5679999999999999999999998864

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.

>PRK12544 RNA polymerase sigma factor; Provisional

Probab=99.45  E-value=8.5e-13  Score=125.25  Aligned_cols=126  Identities=16%  Similarity=0.136  Sum_probs=99.9

Q ss_pred             HHHHHHHhHHHHHHHHHHhhCCCCCHHhHHHHHHHHHHHhHHhcCCCCCCChHHHHHHHHHHHHHHHHHhhcCceeccc-
Q 013472          297 REELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIPC-  375 (442)
Q Consensus       297 re~LI~~nlrLV~sIAkrY~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIRnaI~r~LRkqsr~irlP~-  375 (442)
                      -..++..|.+.|+.+|+++.++..+++|++||+|+.+|+.+.+|+..  .+|.+|++++++|.+++++|++++....+. 
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            35788999999999999999999999999999999999999999864  369999999999999999997654321110 


Q ss_pred             ------------------------------c---c---HHHHHHHHHHHHHHHHHc--------CCCCcHHHHHHHhCCC
Q 013472          376 ------------------------------K---L---NREISKIQKARKALTNSH--------GKYPEDIEIAKYTGLS  411 (442)
Q Consensus       376 ------------------------------~---v---~e~i~kI~ka~~~L~~el--------gr~PS~eEIAe~LGIS  411 (442)
                                                    .   .   .+....+..++..|+.+.        -.+.+++|||+.||+|
T Consensus        98 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~e~~~~l~~~L~~L~~~~r~v~~L~~~~g~s~~EIAe~lgis  177 (206)
T PRK12544         98 LRDEEEEEDFEELFDESGHWQKDERPQAWGNPEESLEQEQFWRIFEACLDGLPAKYARVFMMREFIELETNEICHAVDLS  177 (206)
T ss_pred             ccccchhhHHHHhhcccccccccccccccCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHHCcC
Confidence                                          0   0   011123455555555443        2677999999999999


Q ss_pred             HHHHHHHHHhccc
Q 013472          412 LAEIRSASECLRI  424 (442)
Q Consensus       412 ~etVk~~l~~ar~  424 (442)
                      +++|+..+++++.
T Consensus       178 ~~tV~~~l~RAr~  190 (206)
T PRK12544        178 VSNLNVLLYRARL  190 (206)
T ss_pred             HHHHHHHHHHHHH
Confidence            9999999998875

>TIGR02943 Sig70_famx1 RNA polymerase sigma-70 factor, TIGR02943 family

Probab=99.44  E-value=8.5e-13  Score=122.96  Aligned_cols=124  Identities=15%  Similarity=0.059  Sum_probs=98.9

Q ss_pred             HHHHHhHHHHHHHHHHhhCCCCCHHhHHHHHHHHHHHhHHhcCCCCCCChHHHHHHHHHHHHHHHHHhhcCceeccc---
Q 013472          299 ELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIPC---  375 (442)
Q Consensus       299 ~LI~~nlrLV~sIAkrY~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIRnaI~r~LRkqsr~irlP~---  375 (442)
                      +.+..|.+.|+.+|++++++..+++|++||+|+.+|+..++|++.  .+|.+|++.+++|.+++++|++.+....+.   
T Consensus         6 ~~~~~~~~~l~~~~~~~~~~~~dAeDivQevfl~l~~~~~~~~~~--~~~~~wL~~iarn~~~d~~R~~~r~~~~~~~~~   83 (188)
T TIGR02943         6 QELEQLRRDLLRFARLQLRDRDLAEDAVQETLLAALSHRDSFAGR--SALKTWLFAILKNKIIDALRAKGREVKVSDLDD   83 (188)
T ss_pred             HHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhhhhhccc--cHHHHHHHHHHHHHHHHHHHhhcccCCcccccc
Confidence            678889999999999999999999999999999999999999964  479999999999999999998754322110   


Q ss_pred             c--------------------------c-------HHHHHHHHHHHHHHHHHc--------CCCCcHHHHHHHhCCCHHH
Q 013472          376 K--------------------------L-------NREISKIQKARKALTNSH--------GKYPEDIEIAKYTGLSLAE  414 (442)
Q Consensus       376 ~--------------------------v-------~e~i~kI~ka~~~L~~el--------gr~PS~eEIAe~LGIS~et  414 (442)
                      .                          .       .+....+.+++..|+...        -.+.+++|||+.||+|+++
T Consensus        84 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~e~~~~l~~~l~~L~~~~r~v~~l~~~~g~s~~EIA~~lgis~~t  163 (188)
T TIGR02943        84 ELDDEAFNALFTQNGHWAQHGQPQHWNTPEKQLENKEFWEVFEACLYHLPEQTARVFMMREVLGFESDEICQELEISTSN  163 (188)
T ss_pred             ccccchhhhhhccccchhccccccccCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHhCCCHHHHHHHhCCCHHH
Confidence            0                          0       011233555655555433        2678999999999999999


Q ss_pred             HHHHHHhccc
Q 013472          415 IRSASECLRI  424 (442)
Q Consensus       415 Vk~~l~~ar~  424 (442)
                      |+..+.+++.
T Consensus       164 vk~rl~Rar~  173 (188)
T TIGR02943       164 CHVLLYRARL  173 (188)
T ss_pred             HHHHHHHHHH
Confidence            9999988874

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.

>TIGR02959 SigZ RNA polymerase sigma factor, SigZ family

Probab=99.43  E-value=1.1e-12  Score=120.14  Aligned_cols=121  Identities=19%  Similarity=0.168  Sum_probs=96.0

Q ss_pred             HHhHHHHHHHHHHhhCCCCCHHhHHHHHHHHHHHhHHhcCCCCCCChHHHHHHHHHHHHHHHHHhhcCceeccccc----
Q 013472          302 KSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIPCKL----  377 (442)
Q Consensus       302 ~~nlrLV~sIAkrY~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIRnaI~r~LRkqsr~irlP~~v----  377 (442)
                      ..|.+.|+.+++++.++..+++|++||+|+.+|+++++|+..  .+|.+|++.+++|.+++++|+..+...++...    
T Consensus         2 ~~~~~~l~~~~~~~~~~~~~AeDlvQe~fl~l~~~~~~~~~~--~~f~~wl~~iarn~~~d~~Rk~~~~~~~~~~~~~~~   79 (170)
T TIGR02959         2 DEFRSELKAFIKSRVSDASDVEDLLQEVFIKIHRNLPSLKDG--QKIQSWLYQIARNTIIDFYRSKSRSVELPESLLAAD   79 (170)
T ss_pred             chHHHHHHHHHHHHcCCHhhHHHHHHHHHHHHHHHHHhcCCc--ccHHHHHHHHHHHHHHHHHHhccCccccchhhcccC
Confidence            468899999999999999999999999999999999999963  47999999999999999999876543332111    


Q ss_pred             --------HHHHHHHHHHHHHHHHHc--------CCCCcHHHHHHHhCCCHHHHHHHHHhccc
Q 013472          378 --------NREISKIQKARKALTNSH--------GKYPEDIEIAKYTGLSLAEIRSASECLRI  424 (442)
Q Consensus       378 --------~e~i~kI~ka~~~L~~el--------gr~PS~eEIAe~LGIS~etVk~~l~~ar~  424 (442)
                              .+....+.+++..|+...        -.+.+++|||+.||||+.+|+..+++++.
T Consensus        80 ~~~~~~~~~e~~~~l~~~l~~L~~~~r~v~~l~~~~g~s~~eIA~~lgis~~tV~~~l~Rar~  142 (170)
T TIGR02959        80 SAREETFVKELSQCIPPMIKELPDEYREAIRLTELEGLSQQEIAEKLGLSLSGAKSRVQRGRK  142 (170)
T ss_pred             CccHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence                    112223455555554432        26789999999999999999999888763

This family of RNA polymerase sigma factors is a member of the Sigma-70 subfamily (TIGR02937). One of these is designated as SigZ in B. subtilis (Swiss_Prot: SIGZ_BACSU). Interestingly, this group has a very sporatic distribution, B. subtilis, for instance, being the only sequenced strain of Bacilli with a member. Dechloromonas aromatica RCB appears to have two of these sigma factors. A member appears on a plasmid found in Photobacterium profundum SS9 and Vibrio fischeri ES114 (where a second one is chromosomally encoded).

>PRK12546 RNA polymerase sigma factor; Provisional

Probab=99.43  E-value=1.8e-12  Score=121.20  Aligned_cols=126  Identities=17%  Similarity=0.198  Sum_probs=100.1

Q ss_pred             HHHHHHHHhHHHHHHHHHHhhCCCCCHHhHHHHHHHHHHHhHHhcCCCCCCChHHHHHHHHHHHHHHHHHhhcCceecc-
Q 013472          296 CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIP-  374 (442)
Q Consensus       296 Are~LI~~nlrLV~sIAkrY~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIRnaI~r~LRkqsr~irlP-  374 (442)
                      +++.|+. |.+.|+.+|+++.++..+++|++||.|+.+|+.+..|+..  ..|.+|++.+++|.+++++|++.+..... 
T Consensus         9 ~~~~l~~-~~~~l~~~a~~~l~~~~~AEDivQevfl~l~~~~~~~~~~--~~~~awL~~ia~n~~~d~~Rk~~r~~~~~~   85 (188)
T PRK12546          9 PRDELVE-HLPALRAFAISLTRNVAVADDLVQDTIVKAWTNFDKFQEG--TNLRAWLFTILRNTFYSDRRKHKREVPDPE   85 (188)
T ss_pred             HHHHHHH-HHHHHHHHHHHHcCChhhHHHHHHHHHHHHHHHHhccCCC--cchHHHHHHHHHHHHHHHHHHhcccccCcc
Confidence            5666655 7799999999999999999999999999999999999864  36999999999999999999875422110 


Q ss_pred             -----------cc-cHHHHHHHHHHHHHHHHHcC--------CCCcHHHHHHHhCCCHHHHHHHHHhccc
Q 013472          375 -----------CK-LNREISKIQKARKALTNSHG--------KYPEDIEIAKYTGLSLAEIRSASECLRI  424 (442)
Q Consensus       375 -----------~~-v~e~i~kI~ka~~~L~~elg--------r~PS~eEIAe~LGIS~etVk~~l~~ar~  424 (442)
                                 .. .......+..++..|+....        .+.+.+|||+.||||+.+|+..+++++.
T Consensus        86 ~~~~~~~~~~~~~~~~~~~~~l~~~L~~Lp~~~r~v~~L~~~~g~s~~EIA~~LgiS~~tVk~~l~Rar~  155 (188)
T PRK12546         86 GVHAASLAVKPAHDGRLAMSDFRAAFAQLPDEQREALILVGASGFSYEEAAEMCGVAVGTVKSRANRARA  155 (188)
T ss_pred             cccccccccCCcchhHHHHHHHHHHHHhCCHHHhHHhhhHHhcCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence                       00 01112346667776665543        6779999999999999999999988874

>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=99.41  E-value=7.5e-13  Score=102.85  Aligned_cols=70  Identities=24%  Similarity=0.375  Sum_probs=67.0

Q ss_pred             HHHHhHHHHHHHHHHhhCCCCCHHhHHHHHHHHHHHhHHhcCCCCCCChHHHHHHHHHHHHHHHHHhhcC
Q 013472          300 LIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHAR  369 (442)
Q Consensus       300 LI~~nlrLV~sIAkrY~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIRnaI~r~LRkqsr  369 (442)
                      |++.|.++|+.+|.+|.+++.+++|++||++++||+++++||+..+..|.+|++.++++.++++++++++
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            6899999999999999999999999999999999999999999998899999999999999999998754

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 ....

>PRK12511 RNA polymerase sigma factor; Provisional

Probab=99.41  E-value=2.3e-12  Score=119.87  Aligned_cols=126  Identities=13%  Similarity=0.083  Sum_probs=100.0

Q ss_pred             HHHHHHHhHHHHHHHHHHhhCCCCCHHhHHHHHHHHHHHhHHhcCCCCCCChHHHHHHHHHHHHHHHHHhhcCceecc--
Q 013472          297 REELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIP--  374 (442)
Q Consensus       297 re~LI~~nlrLV~sIAkrY~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIRnaI~r~LRkqsr~irlP--  374 (442)
                      .+..+..+.+.|+.+|.++.++..+++|++||.|+.+|+....|+..  .+|.||++.+++|.+++++|++++.....  
T Consensus         6 ~~~~~~~~~~~l~~~~~~~~~~~~dAEDivQe~flkl~~~~~~~~~~--~~~~~WL~~Iarn~~id~~Rk~~~~~~~~~~   83 (182)
T PRK12511          6 KRFDVLDQLVPLRRYARSLTRDSAEAEDLVHDALVRALERRASFRSG--GNLRTWLMSILHNAFIDELRRRRVEARRADE   83 (182)
T ss_pred             hhhhHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhHHhcCCc--cchHHHHHHHHHHHHHHHHHhhccccccccc
Confidence            45568889999999999999999999999999999999999999864  36999999999999999999865421110  


Q ss_pred             ----------cc--cHHHHHHHHHHHHHHHHHcC--------CCCcHHHHHHHhCCCHHHHHHHHHhccc
Q 013472          375 ----------CK--LNREISKIQKARKALTNSHG--------KYPEDIEIAKYTGLSLAEIRSASECLRI  424 (442)
Q Consensus       375 ----------~~--v~e~i~kI~ka~~~L~~elg--------r~PS~eEIAe~LGIS~etVk~~l~~ar~  424 (442)
                                ..  .......+.+++..|+....        .+.|++|||+.||||+++|+..+++++.
T Consensus        84 ~~~~~~~~~~~~~~~~~~~~~l~~~l~~Lp~~~R~v~~L~~~eg~s~~EIA~~lgis~~tV~~~l~Rar~  153 (182)
T PRK12511         84 LAVLADASLPAAQEHAVRLAQIRDAFFDLPEEQRAALHLVAIEGLSYQEAAAVLGIPIGTLMSRIGRARA  153 (182)
T ss_pred             hhhccccCCCcchHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHhCcCHHHHHHHHHHHHH
Confidence                      00  11122345666666655542        6789999999999999999999888763

>PRK09651 RNA polymerase sigma factor FecI; Provisional

Probab=99.40  E-value=2.6e-12  Score=117.68  Aligned_cols=127  Identities=13%  Similarity=0.076  Sum_probs=99.8

Q ss_pred             HHHHHHHHHhHHHHHHHHHHhhCCCCCHHhHHHHHHHHHHHhHHhcCCCCCCChHHHHHHHHHHHHHHHHHhhcCce---
Q 013472          295 YCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGI---  371 (442)
Q Consensus       295 ~Are~LI~~nlrLV~sIAkrY~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIRnaI~r~LRkqsr~i---  371 (442)
                      .|++.++..|.+.|+.++.++.++..++||++||.|+.+|+. ..|++-.  .|.+|++.+++|.+++++|++.+..   
T Consensus        10 ~af~~l~~~~~~~l~~~~~~~~~~~~~AEDlvQe~flkl~~~-~~~~~~~--~~~~wL~~iarn~~~d~~R~~~~~~~~~   86 (172)
T PRK09651         10 LTFESLYGTHHGWLKSWLTRKLQSAFDADDIAQDTFLRVMVS-ETLSTIR--DPRSFLCTIAKRVMVDLFRRNALEKAYL   86 (172)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHcCCHhHHHHHHHHHHHHHHhh-ccccccc--CHHHHHHHHHHHHHHHHHHHHHHHhhhh
Confidence            489999999999999999999999999999999999999998 3565432  5999999999999999999754211   


Q ss_pred             ----eccc----c---c---HHHHHHHHHHHHHHHHHc--------CCCCcHHHHHHHhCCCHHHHHHHHHhccc
Q 013472          372 ----KIPC----K---L---NREISKIQKARKALTNSH--------GKYPEDIEIAKYTGLSLAEIRSASECLRI  424 (442)
Q Consensus       372 ----rlP~----~---v---~e~i~kI~ka~~~L~~el--------gr~PS~eEIAe~LGIS~etVk~~l~~ar~  424 (442)
                          .++.    .   .   .+....+..++..|+.+.        ..+.+++|||+.||+|+++|+..+++++.
T Consensus        87 ~~~~~~~~~~~~~~~~~~~~~e~~~~l~~~l~~L~~~~r~i~~l~~~~g~s~~EIA~~lgis~~tV~~~l~Ra~~  161 (172)
T PRK09651         87 EMLALMPEGGAPSPEERESQLETLQLLDSMLDGLNGKTREAFLLSQLDGLTYSEIAHKLGVSVSSVKKYVAKATE  161 (172)
T ss_pred             hHHhhccccCCCChHHHHHHHHHHHHHHHHHHhCCHHHhHHhhhhhccCCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence                1110    0   0   122334566666666544        26779999999999999999999988763

>PRK06704 RNA polymerase factor sigma-70; Validated

Probab=99.36  E-value=5.9e-12  Score=122.13  Aligned_cols=132  Identities=15%  Similarity=-0.041  Sum_probs=100.1

Q ss_pred             HHHHHhchH-HHHHHHHHhHHHHHHHHHHhhCCCCCHHhHHHHHHHHHHHhHHhcCCCCCCChHHHHHHHHHHHHHHHHH
Q 013472          287 KQHLAFGWY-CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVA  365 (442)
Q Consensus       287 ~~~l~~G~~-Are~LI~~nlrLV~sIAkrY~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIRnaI~r~LR  365 (442)
                      .++...|+. +++.+++.| +.|+.+|.++.++..++|||+||.|+.+|+.   |+..  ..|.+|++.+++|.+++++|
T Consensus         9 ~~~~~~~~~~~~~~l~~~y-~~L~r~~~~~~~d~~dAEDlvQE~flk~~~~---~~~~--~~~~~WL~~IarN~~id~~R   82 (228)
T PRK06704          9 LKNHIDMNHSNINFLIEQY-GELKRYCTFLTKNKWDGEDLAQETVCKVLQK---YSNK--DICMTLVYKIARNRWLDQIK   82 (228)
T ss_pred             HhcccCCCHHHHHHHHHHH-HHHHHHHHHHhCCHHHHHHHHHHHHHHHHHH---cCcc--ccHHHHHHHHHHHHHHHHHh
Confidence            344445544 888888777 7899999999999999999999999999986   6543  25999999999999999999


Q ss_pred             hhcCceecccc---------cHHHHHHHHHHHHHHHHHcC--------CCCcHHHHHHHhCCCHHHHHHHHHhccc
Q 013472          366 RHARGIKIPCK---------LNREISKIQKARKALTNSHG--------KYPEDIEIAKYTGLSLAEIRSASECLRI  424 (442)
Q Consensus       366 kqsr~irlP~~---------v~e~i~kI~ka~~~L~~elg--------r~PS~eEIAe~LGIS~etVk~~l~~ar~  424 (442)
                      ++++...+...         ..+....+..+...|+....        .+.|++|||+.||+|+++|+..+++++.
T Consensus        83 k~k~~~~~~~~~~~~~~~~~~~~~~~~l~~~L~~Lp~~~R~v~lL~~~eg~S~~EIAe~LgiS~~tVksrL~Rark  158 (228)
T PRK06704         83 SKSVHEKIRDQITFEEPHEKIADLHEMVGKVLSSLNVQQSAILLLKDVFQYSIADIAKVCSVSEGAVKASLFRSRN  158 (228)
T ss_pred             ccccccccccccccCChHHHHHHHHHHHHHHHHhCCHHHhhHhhhHHhhCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence            87543221110         11222345666666665432        5679999999999999999999998874

>PRK07037 extracytoplasmic-function sigma-70 factor; Validated

Probab=99.36  E-value=7e-12  Score=112.85  Aligned_cols=123  Identities=15%  Similarity=0.142  Sum_probs=95.1

Q ss_pred             HHHHHhHHHHHHHHHHhhCCCCCHHhHHHHHHHHHHHhHHhcCCCCCCChHHHHHHHHHHHHHHHHHhhcCcee------
Q 013472          299 ELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIK------  372 (442)
Q Consensus       299 ~LI~~nlrLV~sIAkrY~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIRnaI~r~LRkqsr~ir------  372 (442)
                      .++..|.+.|+.+|.++.++..+++|++||+++++|+....|++.   .|.+|++.+++|.+++++|++++...      
T Consensus         2 ~~~~~~~~~l~~~~~~~~~~~~~aeDivQe~~l~l~~~~~~~~~~---~~~~wl~~iarn~~~d~~R~~~~~~~~~~~~~   78 (163)
T PRK07037          2 DVFVDNRSMLVKIAARIVGCRSRAEDVVQDAFVKLVEAPNQDAVK---QPVAYLFRIVRNLAIDHYRRQALENKYHGDEE   78 (163)
T ss_pred             hHHHHHHHHHHHHHHHHcCCHhHHHHHHHHHHHHHHhccccCCcc---cHHHHHHHHHHHHHHHHHHhhccccccccccc
Confidence            467888999999999999999999999999999999998888753   48999999999999999997653211      


Q ss_pred             ----ccc---c------cHHHHHHHHHHHHHHHHHc--------CCCCcHHHHHHHhCCCHHHHHHHHHhccc
Q 013472          373 ----IPC---K------LNREISKIQKARKALTNSH--------GKYPEDIEIAKYTGLSLAEIRSASECLRI  424 (442)
Q Consensus       373 ----lP~---~------v~e~i~kI~ka~~~L~~el--------gr~PS~eEIAe~LGIS~etVk~~l~~ar~  424 (442)
                          .+.   .      ..+....+.++...|+.+.        -.+.|++|||+.||+|+.+|+..+.+++.
T Consensus        79 ~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~v~~l~~~~~~s~~EIA~~lgis~~tV~~~l~ra~~  151 (163)
T PRK07037         79 DGLDVPSPEASPEAALINRDTLRHVADALSELPARTRYAFEMYRLHGETQKDIARELGVSPTLVNFMIRDALV  151 (163)
T ss_pred             cccccCCCCCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence                110   0      0112233455555554433        26779999999999999999999887764

>PRK12527 RNA polymerase sigma factor; Reviewed

Probab=99.35  E-value=6.4e-12  Score=112.99  Aligned_cols=121  Identities=12%  Similarity=0.030  Sum_probs=94.9

Q ss_pred             HHHhHHHHHHHHHHhhCCCCCHHhHHHHHHHHHHHhHHhcCCCCCCChHHHHHHHHHHHHHHHHHhhcCceec-------
Q 013472          301 IKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKI-------  373 (442)
Q Consensus       301 I~~nlrLV~sIAkrY~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIRnaI~r~LRkqsr~irl-------  373 (442)
                      +..|.+.++.++.+++++..+++|++||+|+.+|+..+.|++  + +|.||++.+++|.+++++|++......       
T Consensus         1 ~~~~~~~l~~~~~~~~~~~~~aeDi~Qevf~~l~~~~~~~~~--~-~~~~wL~~ia~n~~~d~~R~~~~~~~~~~~~~~~   77 (159)
T PRK12527          1 MENYYRELVRFLSARLGNRQAAEDVAHDAYLRVLERSSSAQI--E-HPRAFLYRTALNLVVDRHRRHRVRQAEPLEVLDE   77 (159)
T ss_pred             ChhHHHHHHHHHHHHcCCHhhHHHHHHHHHHHHHhccccccc--c-chHHHHHHHHHHHHHHHHHHHhcccccchhhhhc
Confidence            357889999999999999999999999999999999999875  2 799999999999999999975321110       


Q ss_pred             ------c--ccc---HHHHHHHHHHHHHHHHHc--------CCCCcHHHHHHHhCCCHHHHHHHHHhccc
Q 013472          374 ------P--CKL---NREISKIQKARKALTNSH--------GKYPEDIEIAKYTGLSLAEIRSASECLRI  424 (442)
Q Consensus       374 ------P--~~v---~e~i~kI~ka~~~L~~el--------gr~PS~eEIAe~LGIS~etVk~~l~~ar~  424 (442)
                            |  ...   .+....+..+...|+.+.        ..+.|++|||+.||+|+++|+..+.+++.
T Consensus        78 ~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~v~~l~~~~~~s~~eIA~~lgis~~tv~~~l~ra~~  147 (159)
T PRK12527         78 EERLHSPSPQTRLDLGQRLALLQRALAELPPACRDSFLLRKLEGLSHQQIAEHLGISRSLVEKHIVNAMK  147 (159)
T ss_pred             cccccCCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence                  0  000   112234666666665553        26779999999999999999999988874

>PRK12525 RNA polymerase sigma factor; Provisional

Probab=99.35  E-value=1.1e-11  Score=112.95  Aligned_cols=128  Identities=12%  Similarity=0.009  Sum_probs=98.8

Q ss_pred             hHHHHHHHHHhHHHHHHHHHHhhCCCCCHHhHHHHHHHHHHHhHHhcCCCCCCChHHHHHHHHHHHHHHHHHhhcCce--
Q 013472          294 WYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGI--  371 (442)
Q Consensus       294 ~~Are~LI~~nlrLV~sIAkrY~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIRnaI~r~LRkqsr~i--  371 (442)
                      +.++.+++..|.+.++.+|.++.++..+++|++||.|+.+|+..+.++.   ..|.+|++++++|.+++++|+.....  
T Consensus         8 ~~~~~~~~~~~~~~l~~~~~~~~~~~~~aeDlvQevf~~l~~~~~~~~~---~~~~~wl~~Iarn~~~d~~Rr~~~~~~~   84 (168)
T PRK12525          8 NTLIGQMFQQDYDWLCKKLSRQLGCPHSAEDIASETFLQVLALPDPASI---REPRALLTTIARRLMYEGWRRQDLERAY   84 (168)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHcCCcCcHHHHHHHHHHHHHhCCCcccc---cCHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3489999999999999999999999999999999999999986665542   36999999999999999998753210  


Q ss_pred             -----eccc----c------cHHHHHHHHHHHHHHHHHcC--------CCCcHHHHHHHhCCCHHHHHHHHHhccc
Q 013472          372 -----KIPC----K------LNREISKIQKARKALTNSHG--------KYPEDIEIAKYTGLSLAEIRSASECLRI  424 (442)
Q Consensus       372 -----rlP~----~------v~e~i~kI~ka~~~L~~elg--------r~PS~eEIAe~LGIS~etVk~~l~~ar~  424 (442)
                           ..|.    .      ..+....+.+++..|+....        .+.|++|||+.||+|+++|+..+.+++.
T Consensus        85 ~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~v~~L~~~eg~s~~EIA~~l~is~~tV~~~l~ra~~  160 (168)
T PRK12525         85 LQSLAEAPEAVQPSPEEQWMVIETLLAIDRLLDGLSGKARAAFLMSQLEGLTYVEIGERLGVSLSRIHQYMVEAFK  160 (168)
T ss_pred             HHHHhcccccccCChHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence                 0110    0      11123345566666655432        6779999999999999999999887763

>PRK09636 RNA polymerase sigma factor SigJ; Provisional

Probab=99.26  E-value=4.8e-11  Score=118.61  Aligned_cols=125  Identities=16%  Similarity=0.060  Sum_probs=96.4

Q ss_pred             HHHHHHHHhHHHHHHHHHHhhCCCCCHHhHHHHHHHHHHHhHHhcCCCCCCChHHHHHHHHHHHHHHHHHhhcCc--e--
Q 013472          296 CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARG--I--  371 (442)
Q Consensus       296 Are~LI~~nlrLV~sIAkrY~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIRnaI~r~LRkqsr~--i--  371 (442)
                      ...+++..|.+.++.+|++++++..++||++||.|+. |.....|+.   ..|.||++++++|.|++++|++++.  .  
T Consensus         5 ~~~~l~~~~~~~l~~~a~~~~~~~~dAEDlvQe~fl~-~~~~~~~~~---~~~~~WL~~Ia~n~~~d~lR~~~~~~~~~~   80 (293)
T PRK09636          5 DAAAEFEPLRPHLLSVAYRMLGSVADAEDIVQEAWLR-WNNADRAQI---RDPRAWLTRVVTRLCLDRLRSARHRRETYV   80 (293)
T ss_pred             HHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHH-HHhcccccc---cCHHHHHHHHHHHHHHHHHHhhhccccccc
Confidence            4668999999999999999999999999999999999 556677762   4799999999999999999975421  1  


Q ss_pred             --eccccc-------------HHH-HHHHHHHHHHHHHHcC--------CCCcHHHHHHHhCCCHHHHHHHHHhccc
Q 013472          372 --KIPCKL-------------NRE-ISKIQKARKALTNSHG--------KYPEDIEIAKYTGLSLAEIRSASECLRI  424 (442)
Q Consensus       372 --rlP~~v-------------~e~-i~kI~ka~~~L~~elg--------r~PS~eEIAe~LGIS~etVk~~l~~ar~  424 (442)
                        .+|...             .+. ...+..+...|+....        .+.+++|||+.||+|+.+|+..+++++.
T Consensus        81 ~~~~~e~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~R~v~~L~~~~g~s~~EIA~~lg~s~~tVk~~l~RAr~  157 (293)
T PRK09636         81 GPWLPEPVVEELDDPLEAVVAAEDLSLALMLALERLSPLERAAFLLHDVFGVPFDEIASTLGRSPAACRQLASRARK  157 (293)
T ss_pred             CCcCCcCCCCCCCChHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHhCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence              111110             111 1234555565555432        5779999999999999999999998874

>PRK09635 sigI RNA polymerase sigma factor SigI; Provisional

Probab=99.20  E-value=1.1e-10  Score=116.85  Aligned_cols=126  Identities=10%  Similarity=-0.103  Sum_probs=96.4

Q ss_pred             HHHHHHHHHhHHHHHHHHHHhhCCCCCHHhHHHHHHHHHHHhHHhcCCCCCCChHHHHHHHHHHHHHHHHHhhcCc--e-
Q 013472          295 YCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARG--I-  371 (442)
Q Consensus       295 ~Are~LI~~nlrLV~sIAkrY~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIRnaI~r~LRkqsr~--i-  371 (442)
                      ..+..++..|.+.++.+|+++.++..++||++||.|+.+|++...+.    ..|.+|++.+++|.|++++|+..+.  . 
T Consensus         5 ~~~~~l~~~~~~~L~~~a~r~lgs~~dAEDvvQE~flr~~~~~~~~~----~~~~aWL~~Ia~n~~id~lRk~~~rr~~~   80 (290)
T PRK09635          5 DPVSAAWRAHRAYLVDLAFRMVGDIGVAEDMVQEAFSRLLRAPVGDI----DDERGWLIVVTSRLCLDHIKSASTRRERP   80 (290)
T ss_pred             cHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHhcCcccc----ccHHHHHHHHHHHHHHHHHhhhhccCcCc
Confidence            36889999999999999999999999999999999999999875431    3699999999999999999974321  0 


Q ss_pred             -----ecccc-------c------H-HHHHHHHHHHHHHHHHc--------CCCCcHHHHHHHhCCCHHHHHHHHHhccc
Q 013472          372 -----KIPCK-------L------N-REISKIQKARKALTNSH--------GKYPEDIEIAKYTGLSLAEIRSASECLRI  424 (442)
Q Consensus       372 -----rlP~~-------v------~-e~i~kI~ka~~~L~~el--------gr~PS~eEIAe~LGIS~etVk~~l~~ar~  424 (442)
                           +.|..       -      . +....+..+...|+...        -.+.+++|||+.||+|+.+|+..+++++.
T Consensus        81 ~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~al~~~L~~L~p~~R~vf~L~~~~g~s~~EIA~~Lgis~~tVr~~l~RAr~  160 (290)
T PRK09635         81 QDIAAWHDGDASVSSVDPADRVTLDDEVRLALLIMLERLGPAERVVFVLHEIFGLPYQQIATTIGSQASTCRQLAHRARR  160 (290)
T ss_pred             ccccccCccccCCCCCCcHHHHHHHHHHHHHHHHHHHhCCHHHHHHhhHHHHhCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence                 11100       0      0 01123445555554433        25679999999999999999999998875

>PRK09191 two-component response regulator; Provisional

Probab=99.20  E-value=7.4e-11  Score=112.59  Aligned_cols=121  Identities=16%  Similarity=0.037  Sum_probs=95.8

Q ss_pred             HHHHHHHHhHHHHHHHHHHhhCCCCCHHhHHHHHHHHHHHhHHhcCCCCCCChHHHHHHHHHHHHHHHHHhhcCceeccc
Q 013472          296 CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIPC  375 (442)
Q Consensus       296 Are~LI~~nlrLV~sIAkrY~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIRnaI~r~LRkqsr~irlP~  375 (442)
                      |+.+++..|.+.|+.+|.++.++..+++|++||+|+.+|+...+|++.  ..|.||+++++++...+.....    ..+.
T Consensus         2 ~~~~l~~~~~~~l~~~~~~~~~~~~~aeDi~qd~~~~~~~~~~~~~~~--~~~~~wl~~~~~~~~~~~~~~~----~~~~   75 (261)
T PRK09191          2 SLSQRIAPHLPYLRRYARALTGSQSSGDAYVAATLEALLADPSIFPEA--SSPRVGLYRLFHRLWSSAGAND----PEPG   75 (261)
T ss_pred             chHHHHHHHhHHHHHHHHHhcCChhhHHHHHHHHHHHHHHhHHhcCCC--cchhhHHHHHHHHHhccccccC----CCCC
Confidence            578999999999999999999999999999999999999999999874  3699999999988764432211    0111


Q ss_pred             ccHHHHHHHHHHHHHHHHHcC--------CCCcHHHHHHHhCCCHHHHHHHHHhccc
Q 013472          376 KLNREISKIQKARKALTNSHG--------KYPEDIEIAKYTGLSLAEIRSASECLRI  424 (442)
Q Consensus       376 ~v~e~i~kI~ka~~~L~~elg--------r~PS~eEIAe~LGIS~etVk~~l~~ar~  424 (442)
                        ......+.+++.+|+....        .+.|++|||+.||+|+++|+..+.+++.
T Consensus        76 --~~~~~~l~~~l~~L~~~~r~v~~l~~~~~~s~~eIA~~l~~s~~tV~~~l~ra~~  130 (261)
T PRK09191         76 --SPFEARAERRLAGLTPLPRQAFLLTALEGFSVEEAAEILGVDPAEAEALLDDARA  130 (261)
T ss_pred             --CCchHHHHHHHHhCCHHHhHHHHHHHHhcCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence              1111256667777665543        5779999999999999999999888774

>TIGR02957 SigX4 RNA polymerase sigma-70 factor, TIGR02957 family

Probab=99.20  E-value=1.5e-10  Score=114.78  Aligned_cols=122  Identities=17%  Similarity=0.070  Sum_probs=91.3

Q ss_pred             HHHHHhHHHHHHHHHHhhCCCCCHHhHHHHHHHHHHHhHHhcCCCCCCChHHHHHHHHHHHHHHHHHhhcCc------ee
Q 013472          299 ELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARG------IK  372 (442)
Q Consensus       299 ~LI~~nlrLV~sIAkrY~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIRnaI~r~LRkqsr~------ir  372 (442)
                      +++..|.+.++.+|++++++..++||++||+|+.+++.  .|+..  ..|.+|++++++|.+++++|++++.      .+
T Consensus         1 ~l~~~~~~~l~~~a~r~lg~~~dAEDvvQE~flk~~~~--~~~~~--~~~~awL~~Ia~n~~ld~lR~~~~~~~~~~~~~   76 (281)
T TIGR02957         1 EEFEALRPLLFSLAYRMLGSVADAEDIVQETFLRWQEA--DRAQI--ENPKAYLTKVVTRRCIDVLRSARARREVYVGPW   76 (281)
T ss_pred             ChHHHHHHHHHHHHHHHhCCHhHHHHHHHHHHHHHHhC--Ccccc--cCHHHHHHHHHHHHHHHHHHHhhhcccccCCCC
Confidence            47899999999999999999999999999999998775  55532  3699999999999999999976421      12


Q ss_pred             ccccc----------HH---HH-HHHHHHHHHHHHHc--------CCCCcHHHHHHHhCCCHHHHHHHHHhccc
Q 013472          373 IPCKL----------NR---EI-SKIQKARKALTNSH--------GKYPEDIEIAKYTGLSLAEIRSASECLRI  424 (442)
Q Consensus       373 lP~~v----------~e---~i-~kI~ka~~~L~~el--------gr~PS~eEIAe~LGIS~etVk~~l~~ar~  424 (442)
                      +|...          ..   .+ ..+..+...|+...        -.+.+++|||+.||+|+.+|+..+++++.
T Consensus        77 ~~e~~~~~~~~~~~~~~~~e~~~~~l~~~l~~L~~~~R~v~~L~~~~g~s~~EIA~~lg~s~~tVr~~l~RAr~  150 (281)
T TIGR02957        77 LPEPLLTTSADPAESVELAESLSMAYLLLLERLSPLERAVFVLREVFDYPYEEIASIVGKSEANCRQLVSRARR  150 (281)
T ss_pred             CCcccCCCCCChHHHHHHHHHHHHHHHHHHhhCCHHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            22110          01   11 12333444444332        25779999999999999999999998874

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.

>TIGR03209 P21_Cbot clostridium toxin-associated regulator BotR

Probab=99.18  E-value=9.7e-11  Score=103.59  Aligned_cols=113  Identities=16%  Similarity=0.152  Sum_probs=84.9

Q ss_pred             HHHHHHHhHHHHHHHHHHhhCCCCCHHhHHHHHHHHHHHhHHh-----cCCCCCCChHHHHHHHHHHHHHHHHHhhcCce
Q 013472          297 REELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAER-----FDHTRGYKFSTYVQYWIRKSISKMVARHARGI  371 (442)
Q Consensus       297 re~LI~~nlrLV~sIAkrY~g~g~d~EDLIQEG~IGLirAieK-----FDp~kG~rFSTYa~~wIRnaI~r~LRkqsr~i  371 (442)
                      ++.++..|.+.++.+|++|...    +| +||.++.+|....+     |++.  ..|.||++.+++|.+++++|++.+..
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            4689999999999999999662    34 49999999999865     5543  46999999999999999999765421


Q ss_pred             ecc-------------cc--cHHHHHHHHHHHHHHHHHcC--------CCCcHHHHHHHhCCCHHHHH
Q 013472          372 KIP-------------CK--LNREISKIQKARKALTNSHG--------KYPEDIEIAKYTGLSLAEIR  416 (442)
Q Consensus       372 rlP-------------~~--v~e~i~kI~ka~~~L~~elg--------r~PS~eEIAe~LGIS~etVk  416 (442)
                      ...             ..  ..+....+.+++..|+....        .+.|++|||+.||||+++|+
T Consensus        74 ~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~Lp~~~r~v~~l~~~~~~s~~EIA~~l~is~~tV~  141 (142)
T TIGR03209        74 KIIYNSEITDIKLSLINVYSSNDLEFEFNDLISILPNKQKKIIYMKFFEDMKEIDIAKKLHISRQSVY  141 (142)
T ss_pred             hhhhhhhhhccccchhHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHHCcCHHhhc
Confidence            110             00  01123346677777766543        67899999999999999996

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.

>PRK09047 RNA polymerase factor sigma-70; Validated

Probab=99.10  E-value=4e-10  Score=100.86  Aligned_cols=105  Identities=11%  Similarity=0.042  Sum_probs=78.4

Q ss_pred             CCCCCHHhHHHHHHHHHHHhHHhcCCCCCCChHHHHHHHHHHHHHHHHHhhcCceecc----------------------
Q 013472          317 GLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIP----------------------  374 (442)
Q Consensus       317 g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIRnaI~r~LRkqsr~irlP----------------------  374 (442)
                      ++..+++|++||+|+.+|+..+. ++  +..|.+|++.+++|.+++++|++.+.....                      
T Consensus         2 ~~~~~AeDivQe~fl~~~~~~~~-~~--~~~~~~wl~~ia~n~~~d~~Rk~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   78 (161)
T PRK09047          2 RDDDAALDIVQDAMIKLAEKYGD-RP--AAEWPPLFQRILQNRIHDWFRRQKVRNTWVSLFSSFSDDDDDDDFDPLETLD   78 (161)
T ss_pred             CCHHHHHHHHHHHHHHHHHHHhh-cc--cCchHHHHHHHHHHHHHHHHHhhcccccccccccccccccccccccHHHHhc
Confidence            45568999999999999999886 33  347999999999999999999865321110                      


Q ss_pred             ------ccc------HHHHHHHHHHHHHHHHHcC--------CCCcHHHHHHHhCCCHHHHHHHHHhccc
Q 013472          375 ------CKL------NREISKIQKARKALTNSHG--------KYPEDIEIAKYTGLSLAEIRSASECLRI  424 (442)
Q Consensus       375 ------~~v------~e~i~kI~ka~~~L~~elg--------r~PS~eEIAe~LGIS~etVk~~l~~ar~  424 (442)
                            ...      .+....+.+++..|+....        .+.|++|||+.||||+++|+..+++++.
T Consensus        79 ~~~~~~~~~~~~~~~~~~~~~l~~~l~~Lp~~~r~v~~l~~~~g~s~~EIA~~lgis~~tV~~~l~ra~~  148 (161)
T PRK09047         79 SADEGAESPADKLERAQVLQLIEEAIQKLPARQREAFLLRYWEDMDVAETAAAMGCSEGSVKTHCSRATH  148 (161)
T ss_pred             cccccCCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHhcCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence                  000      1123346666666655542        6779999999999999999999988874

>PF04539 Sigma70_r3: Sigma-70 region 3; InterPro: IPR007624 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription

Probab=98.83  E-value=7.8e-09  Score=83.24  Aligned_cols=62  Identities=32%  Similarity=0.480  Sum_probs=54.8

Q ss_pred             HHHHHHHHHHHHHHHHcCCCCcHHHHHHHhCCCHHHHHHHHHhcccCCCCccccCCCCCccc
Q 013472          379 REISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNAKY  440 (442)
Q Consensus       379 e~i~kI~ka~~~L~~elgr~PS~eEIAe~LGIS~etVk~~l~~ar~~~SLD~~v~~~~d~~~  440 (442)
                      +.+++|.++..+|.+++||.||.+|||+.|||++++|+.++.+++.++|||.+++.+++.++
T Consensus         1 E~l~~i~~a~~~L~~~lgr~Pt~eEiA~~lgis~~~v~~~l~~~~~~~Sl~~~~~~~~~~~l   62 (78)
T PF04539_consen    1 EKLRKIERARRELEQELGREPTDEEIAEELGISVEEVRELLQASRRPVSLDLPVGDEDDSTL   62 (78)
T ss_dssp             HHHHHHHHHHHHHHHHHSS--BHHHHHHHHTS-HHHHHHHHHHHSCCEESSHCCSSSSSEEG
T ss_pred             ChHHHHHHHHHHHHHHhCCCCCHHHHHHHHcccHHHHHHHHHhCCCCeEEeeeecCCCCCch
Confidence            46789999999999999999999999999999999999999999999999999998877654

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 ....

>PF07638 Sigma70_ECF: ECF sigma factor

Probab=98.82  E-value=9.6e-08  Score=89.23  Aligned_cols=141  Identities=16%  Similarity=0.125  Sum_probs=100.3

Q ss_pred             HHHHHHHHHhchH-HHHHHHHHhHHHHHHHHHHhhCC---CCCHHh--HHHHHHHHHHHhHHhcCCCCCCChHHHHHHHH
Q 013472          283 ERVLKQHLAFGWY-CREELIKSTRPLVLFLARNYRGL---GIPFSD--LLQAGNVGVLQGAERFDHTRGYKFSTYVQYWI  356 (442)
Q Consensus       283 eeeL~~~l~~G~~-Are~LI~~nlrLV~sIAkrY~g~---g~d~ED--LIQEG~IGLirAieKFDp~kG~rFSTYa~~wI  356 (442)
                      -.+|+.+++.|+. |.++|+..|.+-++.+|+++...   +.+.+|  |++|.|+.+++.-...+.+.-..|-.|+..++
T Consensus         4 it~ll~~~~~GD~~A~~~L~~~~y~~L~~~a~~~l~~~~~~~~~~~~~lv~ea~lrl~~~~~~~~~~~~~~f~~~~~~~~   83 (185)
T PF07638_consen    4 ITELLDRWRQGDEAALDQLFERYYPELRRLARRRLRRERRGHDLQDTALVHEAFLRLARRGRFVQFSDRRHFWALLARIM   83 (185)
T ss_pred             HHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHhccccCCchhHHHHHHHHHHHHhccccccCCCCHHHHHHHHHHHH
Confidence            3578899999987 99999999999999999987643   345555  57788888877333223332246999999999


Q ss_pred             HHHHHHHHHhhcCcee------cc---------cccHHHHHHHHHHHHHHHH-----------HcCCCCcHHHHHHHhCC
Q 013472          357 RKSISKMVARHARGIK------IP---------CKLNREISKIQKARKALTN-----------SHGKYPEDIEIAKYTGL  410 (442)
Q Consensus       357 RnaI~r~LRkqsr~ir------lP---------~~v~e~i~kI~ka~~~L~~-----------elgr~PS~eEIAe~LGI  410 (442)
                      ++.+++++|++....+      .+         ....+..-.+.++...|..           ..-.+.|.+|||+.|||
T Consensus        84 rr~lid~~R~~~a~KRg~~~~~~~l~~~~~~~~~~~~~~~~~l~e~l~~L~~l~~~~~~~v~l~~~~Gls~~EIA~~lgi  163 (185)
T PF07638_consen   84 RRKLIDHARRRQAQKRGGDQVRVELDERADSGDEPSPEELLELEEALERLLALDPRQRRVVELRFFEGLSVEEIAERLGI  163 (185)
T ss_pred             HHHHHHHHHHHHHHhcCCCCcccchhhhhccccCCCHHHHHHHHHHHHHHHccCHHHHHHHHHHHHCCCCHHHHHHHHCc
Confidence            9999999997654322      11         1122233344444444432           11256799999999999


Q ss_pred             CHHHHHHHHHhcc
Q 013472          411 SLAEIRSASECLR  423 (442)
Q Consensus       411 S~etVk~~l~~ar  423 (442)
                      |+.+|+..+..++
T Consensus       164 S~~tV~r~l~~aR  176 (185)
T PF07638_consen  164 SERTVRRRLRRAR  176 (185)
T ss_pred             CHHHHHHHHHHHH
Confidence            9999999998876

>PF00140 Sigma70_r1_2: Sigma-70 factor, region 1

Probab=97.09  E-value=0.00028  Score=50.03  Aligned_cols=34  Identities=24%  Similarity=0.220  Sum_probs=27.3

Q ss_pred             HHHHHHhcccCC-CCCChHHHHHHHHHhHHHHHHH
Q 013472          223 FSAERALNSRGR-RLTIARNEAEMSKGVQVVANLE  256 (442)
Q Consensus       223 ~~~~~~~~~~~~-~lLt~eeE~eL~~~iq~~~~le  256 (442)
                      +.++.|++.+++ ||||++||++|+++|+.+...+
T Consensus         2 D~l~~Yl~ei~~~~LLt~eeE~~LA~~i~~g~~~a   36 (37)
T PF00140_consen    2 DSLRLYLKEIGRYPLLTAEEEIELARRIRKGDEAA   36 (37)
T ss_dssp             HHHHHHHHHHHHS-EETTHHHHHHHHHHHHHHHHH
T ss_pred             cHHHHHHHHHcCCCCCCHHHHHHHHHHHHHhHHhc
Confidence            456778887875 9999999999999999886643

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 ....

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

Probab=96.42  E-value=0.072  Score=51.61  Aligned_cols=35  Identities=17%  Similarity=0.311  Sum_probs=29.0

Q ss_pred             HHHHHHHHHHHHhCCCCChHHHHHHcCCCHHHHHH
Q 013472          254 NLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQ  288 (442)
Q Consensus       254 ~le~~~~~L~~~~gr~pt~~ewA~a~g~deeeL~~  288 (442)
                      .+.+....+...+|++||.++.|+.+|++.+.+..
T Consensus        88 ~~~~~~~~l~~~~g~~pt~~eia~~l~~~~~~v~~  122 (238)
T TIGR02393        88 KLIKAERQLTQELGREPTDEELAERMGMPAEKVRE  122 (238)
T ss_pred             HHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHH
Confidence            34556677888899999999999999999887654

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

>PRK07670 RNA polymerase sigma factor SigD; Validated

Probab=96.17  E-value=0.076  Score=51.86  Aligned_cols=36  Identities=17%  Similarity=0.178  Sum_probs=28.9

Q ss_pred             HHHHHHHHHHHHhCCCCChHHHHHHcCCCHHHHHHH
Q 013472          254 NLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQH  289 (442)
Q Consensus       254 ~le~~~~~L~~~~gr~pt~~ewA~a~g~deeeL~~~  289 (442)
                      .+.+....+...+|+.|+..++|+..|++.+++...
T Consensus       110 ~~~~~~~~~~~~~~~~~~~~eia~~l~~~~~~v~~~  145 (251)
T PRK07670        110 KVEAAIEKLEQRYMRNVTPKEVAAELGMTEEEVEAT  145 (251)
T ss_pred             HHHHHHHHHHHHHCCCCCHHHHHHHhCcCHHHHHHH
Confidence            344556667778899999999999999998887653

>PRK07408 RNA polymerase sigma factor SigF; Reviewed

Probab=96.03  E-value=0.027  Score=55.39  Aligned_cols=35  Identities=20%  Similarity=0.280  Sum_probs=29.7

Q ss_pred             HHHHHHHHHHHHhCCCCChHHHHHHcCCCHHHHHH
Q 013472          254 NLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQ  288 (442)
Q Consensus       254 ~le~~~~~L~~~~gr~pt~~ewA~a~g~deeeL~~  288 (442)
                      ++.+.+.+|...+|++|+.++.|+.+|++.+++..
T Consensus       114 ~~~~~~~~l~~~lgr~pt~~elA~~lgi~~~~v~~  148 (256)
T PRK07408        114 QAKKVRQELRQELGRQPTDQEIAQALDISLEEWQE  148 (256)
T ss_pred             HHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHH
Confidence            45567778888999999999999999999887654

>PRK09210 RNA polymerase sigma factor RpoD; Validated

Probab=95.95  E-value=0.12  Score=53.76  Aligned_cols=128  Identities=13%  Similarity=0.157  Sum_probs=72.2

Q ss_pred             HHHHHHHHHHHHhCCCCChHHHHHHcCCCHHHHHHHHHhchHHHHHHHHHhHHHHHHHHHHhhCCCCCHHhHHHHH-HHH
Q 013472          254 NLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQHLAFGWYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAG-NVG  332 (442)
Q Consensus       254 ~le~~~~~L~~~~gr~pt~~ewA~a~g~deeeL~~~l~~G~~Are~LI~~nlrLV~sIAkrY~g~g~d~EDLIQEG-~IG  332 (442)
                      ++.+...+|...+|+.||.++.|+.+|++.+.+...+...                   .    ...++++.+.++ -..
T Consensus       217 ~~~~~~~~l~~~lgr~pt~~EiA~~l~~~~~~v~~~~~~~-------------------~----~~~SLd~~~~~~~~~~  273 (367)
T PRK09210        217 KLIRVQRQLLQELGREPTPEEIAEEMDMPPEKVREILKIA-------------------Q----EPVSLETPIGEEDDSH  273 (367)
T ss_pred             HHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHHh-------------------c----CCCCcCCCCCCCCcch
Confidence            3455677788889999999999999999998865532211                   1    111111111110 011


Q ss_pred             HHHhHHhcCCCCCCChHHHHHHHHHHHHHHHHHhhcCceecccccHHHHHHHHHHHHHHHHHc----CCCCcHHHHHHHh
Q 013472          333 VLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIPCKLNREISKIQKARKALTNSH----GKYPEDIEIAKYT  408 (442)
Q Consensus       333 LirAieKFDp~kG~rFSTYa~~wIRnaI~r~LRkqsr~irlP~~v~e~i~kI~ka~~~L~~el----gr~PS~eEIAe~L  408 (442)
                      +...+.  |..............++..+.++|.      .+|..-    ..|      |...+    |.+.|.+|||+.|
T Consensus       274 l~d~i~--d~~~~~p~~~~~~~~~~~~l~~~l~------~L~~rE----r~V------l~lrygl~~~~~~tl~EIa~~l  335 (367)
T PRK09210        274 LGDFIE--DQDATSPADHAAYELLKEQLEDVLD------TLTDRE----ENV------LRLRFGLDDGRTRTLEEVGKVF  335 (367)
T ss_pred             hhhhcc--CCCCCCHHHHHHHHHHHHHHHHHHH------hCCHHH----HHH------HHHHhccCCCCCccHHHHHHHH
Confidence            111111  1111223444555566666666653      234321    111      11122    3678999999999


Q ss_pred             CCCHHHHHHHHHhc
Q 013472          409 GLSLAEIRSASECL  422 (442)
Q Consensus       409 GIS~etVk~~l~~a  422 (442)
                      |+|.++|+.+...|
T Consensus       336 gvs~erVrQi~~~A  349 (367)
T PRK09210        336 GVTRERIRQIEAKA  349 (367)
T ss_pred             CCCHHHHHHHHHHH
Confidence            99999999885544

>PRK06288 RNA polymerase sigma factor WhiG; Reviewed

Probab=95.76  E-value=0.27  Score=48.60  Aligned_cols=35  Identities=26%  Similarity=0.284  Sum_probs=29.2

Q ss_pred             HHHHHHHHHHHHhCCCCChHHHHHHcCCCHHHHHH
Q 013472          254 NLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQ  288 (442)
Q Consensus       254 ~le~~~~~L~~~~gr~pt~~ewA~a~g~deeeL~~  288 (442)
                      .+.+.+..|+..+|++||.++.|...|++.+.+..
T Consensus       119 ~i~~~~~~l~~~~~~~pt~~eia~~lg~~~~~v~~  153 (268)
T PRK06288        119 QIERAIAMLEARLGRTPSDEEIADELGISLEEYNS  153 (268)
T ss_pred             HHHHHHHHHHHHHCCCCCHHHHHHHcCCCHHHHHH
Confidence            45566777888899999999999999999877654

>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=95.61  E-value=0.046  Score=43.52  Aligned_cols=57  Identities=21%  Similarity=0.243  Sum_probs=47.9

Q ss_pred             HHHHHHHhchH-HHHHHHHHhHHHHHHHHHHhh----C--CCCCHHhHHHHHHHHHHHhHHhcC
Q 013472          285 VLKQHLAFGWY-CREELIKSTRPLVLFLARNYR----G--LGIPFSDLLQAGNVGVLQGAERFD  341 (442)
Q Consensus       285 eL~~~l~~G~~-Are~LI~~nlrLV~sIAkrY~----g--~g~d~EDLIQEG~IGLirAieKFD  341 (442)
                      +++.++.+|+. |.++++..|.++|.+++.|-.    +  .+.-=+|+-|+--..|++++-+|+
T Consensus         2 ~vI~~A~~GD~~A~~~IL~~y~~yI~kls~r~~~d~~g~~~~~vDedl~q~l~~kLi~~I~~F~   65 (65)
T PF12645_consen    2 EVIKAAKQGDPEAMEEILKHYEPYISKLSTRTLYDEYGNVYGYVDEDLKQRLEIKLIEAILKFE   65 (65)
T ss_pred             HHHHHHHcCCHHHHHHHHHHHHHHHHHHHHhhcccccCCcCceeCHHHHHHHHHHHHHHHHccC
Confidence            35677888977 999999999999999998732    2  245569999999999999999996

Some proteins with this domain are annotated as conjugative transposon proteins.

>PRK05901 RNA polymerase sigma factor; Provisional

Probab=95.38  E-value=0.46  Score=51.84  Aligned_cols=132  Identities=16%  Similarity=0.199  Sum_probs=70.2

Q ss_pred             HHHHHHHHHHHHhCCCCChHHHHHHcCCCHHHHHHHHHhchHHHHHHHHHhHHHHHHHHHHhhCCCCCHHhHHHH-HHHH
Q 013472          254 NLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQHLAFGWYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQA-GNVG  332 (442)
Q Consensus       254 ~le~~~~~L~~~~gr~pt~~ewA~a~g~deeeL~~~l~~G~~Are~LI~~nlrLV~sIAkrY~g~g~d~EDLIQE-G~IG  332 (442)
                      ++.+...+|...+|+.||.++.|+.+|++.+.+....+                       +....+.+++.+.+ +-..
T Consensus       359 kl~~~~~~L~~~lgr~PT~eELAe~Lgis~e~V~~~~~-----------------------~~~~~~SLD~~i~~d~~~~  415 (509)
T PRK05901        359 KLGRIERELLQELGREPTPEELAKEMGFTPEKVREIQK-----------------------YNREPISLDKTIGKEGDSQ  415 (509)
T ss_pred             HHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHH-----------------------hcCCCcccccccccCCccc
Confidence            45566778888899999999999999999887655221                       11122233332221 1111


Q ss_pred             HHHhHHhcCCCCCCChHHHHHHHHHHHHHHHHHhhcCceecccccHHHHHHHHHHHHHHHHHcCCCCcHHHHHHHhCCCH
Q 013472          333 VLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSL  412 (442)
Q Consensus       333 LirAieKFDp~kG~rFSTYa~~wIRnaI~r~LRkqsr~irlP~~v~e~i~kI~ka~~~L~~elgr~PS~eEIAe~LGIS~  412 (442)
                      +...+.  |+..............+..+..++.      .+|..    -..|-....-|  ..+...|.+|||+.||||.
T Consensus       416 l~d~l~--D~~~~~p~~~~~~~~l~~~L~~aL~------~L~eR----Er~VI~lRyGL--~~~e~~TL~EIa~~lGVSr  481 (509)
T PRK05901        416 FGDFIE--DSEAVSPVDAVSFTLLQDQLQEVLE------TLSER----EAGVIRMRFGL--TDGQPKTLDEIGQVYGVTR  481 (509)
T ss_pred             HHHhcc--CCCCCCHHHHHHHHHHHHHHHHHHh------hCCHH----HHHHHHHHhhc--cCCCCCCHHHHHHHHCCCH
Confidence            111111  1111112333334444444444443      12321    11111111111  0136789999999999999


Q ss_pred             HHHHHHHHhc
Q 013472          413 AEIRSASECL  422 (442)
Q Consensus       413 etVk~~l~~a  422 (442)
                      ++|+++...+
T Consensus       482 ERVRQIe~kA  491 (509)
T PRK05901        482 ERIRQIESKT  491 (509)
T ss_pred             HHHHHHHHHH
Confidence            9999885544

>PRK05949 RNA polymerase sigma factor; Validated

Probab=95.38  E-value=0.31  Score=50.04  Aligned_cols=35  Identities=11%  Similarity=0.275  Sum_probs=28.2

Q ss_pred             HHHHHHHHHHHHhCCCCChHHHHHHcCCCHHHHHH
Q 013472          254 NLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQ  288 (442)
Q Consensus       254 ~le~~~~~L~~~~gr~pt~~ewA~a~g~deeeL~~  288 (442)
                      .+.+...++...+|++|+.++.|+.+|++.+.+..
T Consensus       179 ~l~k~~~~l~~~lgr~pt~~eiA~~l~i~~~~v~~  213 (327)
T PRK05949        179 KIKKTQRELSQKLGRSATPAEIAKELELEPSQIRE  213 (327)
T ss_pred             HHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHH
Confidence            34455667777889999999999999999877654

>PRK07122 RNA polymerase sigma factor SigF; Reviewed

Probab=95.37  E-value=0.27  Score=48.80  Aligned_cols=34  Identities=21%  Similarity=0.311  Sum_probs=28.5

Q ss_pred             HHHHHHHHHHHhCCCCChHHHHHHcCCCHHHHHH
Q 013472          255 LERIKTTLEKESGKAASLNCWAQAAGVSERVLKQ  288 (442)
Q Consensus       255 le~~~~~L~~~~gr~pt~~ewA~a~g~deeeL~~  288 (442)
                      +.+....|...+|+.||.++.|+.+|++.+++..
T Consensus       129 i~~~~~~l~~~lg~~pt~~eiA~~lg~~~~~v~~  162 (264)
T PRK07122        129 LGRATAELSQRLGRAPTASELAAELGMDREEVVE  162 (264)
T ss_pred             HHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHH
Confidence            4456667778889999999999999999988765

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

Probab=95.35  E-value=0.35  Score=48.13  Aligned_cols=126  Identities=15%  Similarity=0.079  Sum_probs=73.3

Q ss_pred             HHHHHHHHHHHHhCCCCChHHHHHHcCCCHHHHHHHHHhchHHHHHHHHHhHHHHHHHHHHhhCCCCCHHhHHHHHHHHH
Q 013472          254 NLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQHLAFGWYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGV  333 (442)
Q Consensus       254 ~le~~~~~L~~~~gr~pt~~ewA~a~g~deeeL~~~l~~G~~Are~LI~~nlrLV~sIAkrY~g~g~d~EDLIQEG~IGL  333 (442)
                      .++++..+|+.++|++||.++.|+..|++.+++...+..+.          -....++--.....+..  +         
T Consensus       111 ~i~~~~~~l~~el~r~pt~~EIA~~L~i~~ee~~~~~~~~~----------~~~~~sld~~~~~~~d~--~---------  169 (247)
T COG1191         111 RIEEAIDELEQELGREPTDEEIAEELGIDKEEYIEALLAIN----------GSQLLSLDEDVLKDDDD--D---------  169 (247)
T ss_pred             HHHHHHHHHHHHhCCCCcHHHHHHHhCCCHHHHHHHHHHhc----------cccccchhhhhcccccc--c---------
Confidence            45567888999999999999999999999988776443332          11111111111111100  0         


Q ss_pred             HHhHHhcCCCCCCChHHHHHHHHHHHHHHHHHhhcCceecccccHHHHHHHHHHHHHHHHHcCCCCcHHHHHHHhCCCHH
Q 013472          334 LQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLA  413 (442)
Q Consensus       334 irAieKFDp~kG~rFSTYa~~wIRnaI~r~LRkqsr~irlP~~v~e~i~kI~ka~~~L~~elgr~PS~eEIAe~LGIS~e  413 (442)
                         +   +...+..+..+-.+...+.+...+.      .+|..        .+.+-.  -.+..+.|..|||+.||||+.
T Consensus       170 ---~---~~~~~~~~~~~~~~~~~~~l~~ai~------~L~ER--------Ek~Vl~--l~y~eelt~kEI~~~LgISes  227 (247)
T COG1191         170 ---V---DDQIENPDDGVEKEELLEILKEAIE------PLPER--------EKLVLV--LRYKEELTQKEIAEVLGISES  227 (247)
T ss_pred             ---h---hhccccchhHHHHHHHHHHHHHHHH------ccCHH--------HHHHHH--HHHHhccCHHHHHHHhCccHH
Confidence               0   1112234555556666666666664      12321        111111  123456799999999999999


Q ss_pred             HHHHHHHhc
Q 013472          414 EIRSASECL  422 (442)
Q Consensus       414 tVk~~l~~a  422 (442)
                      +|-.+...+
T Consensus       228 ~VSql~kka  236 (247)
T COG1191         228 RVSRLHKKA  236 (247)
T ss_pred             HHHHHHHHH
Confidence            998775443

>PRK05911 RNA polymerase sigma factor sigma-28; Reviewed

Probab=95.31  E-value=0.28  Score=48.37  Aligned_cols=34  Identities=18%  Similarity=0.200  Sum_probs=27.3

Q ss_pred             HHHHHHHHHHHhCCCCChHHHHHHcCCCHHHHHH
Q 013472          255 LERIKTTLEKESGKAASLNCWAQAAGVSERVLKQ  288 (442)
Q Consensus       255 le~~~~~L~~~~gr~pt~~ewA~a~g~deeeL~~  288 (442)
                      +.+....|...+|++|+.++.|+.+|++.+++..
T Consensus       112 l~~~~~~l~~~~gr~pt~~eiA~~l~i~~~~v~~  145 (257)
T PRK05911        112 LADAMDSLRQSLGKEPTDGELCEYLNISQQELSG  145 (257)
T ss_pred             HHHHHHHHHHHHCcCCCHHHHHHHhCcCHHHHHH
Confidence            3445556777889999999999999999887644

>PRK07921 RNA polymerase sigma factor SigB; Reviewed

Probab=95.02  E-value=0.45  Score=48.91  Aligned_cols=35  Identities=29%  Similarity=0.470  Sum_probs=29.6

Q ss_pred             HHHHHHHHHHHHhCCCCChHHHHHHcCCCHHHHHH
Q 013472          254 NLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQ  288 (442)
Q Consensus       254 ~le~~~~~L~~~~gr~pt~~ewA~a~g~deeeL~~  288 (442)
                      ++.++...|...+|++||.++.|+.+|++.+.+..
T Consensus       174 ~l~~~~~~l~~~lgr~pt~~EiA~~lgi~~~~v~~  208 (324)
T PRK07921        174 KLARIKRELHQQLGREATDEELAEESGIPEEKIAD  208 (324)
T ss_pred             HHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHH
Confidence            45567778888899999999999999999887654

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

Probab=94.90  E-value=0.58  Score=44.74  Aligned_cols=35  Identities=26%  Similarity=0.333  Sum_probs=28.6

Q ss_pred             HHHHHHHHHHHHhCCCCChHHHHHHcCCCHHHHHH
Q 013472          254 NLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQ  288 (442)
Q Consensus       254 ~le~~~~~L~~~~gr~pt~~ewA~a~g~deeeL~~  288 (442)
                      .+.+...+|...+|+.|+.++.|+.+|++.+.+..
T Consensus        84 ~l~~~~~~l~~~~~~~~~~~ela~~l~~~~~~v~~  118 (224)
T TIGR02479        84 KLERAIRELEARLGREPTEEEIAEELGMDLKEYRQ  118 (224)
T ss_pred             HHHHHHHHHHHHHCcCCCHHHHHHHhCCCHHHHHH
Confidence            45566677888889999999999999999877654

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.

>PRK07598 RNA polymerase sigma factor SigC; Validated

Probab=94.83  E-value=0.46  Score=50.61  Aligned_cols=36  Identities=11%  Similarity=0.325  Sum_probs=30.5

Q ss_pred             HHHHHHHHHHHHhCCCCChHHHHHHcCCCHHHHHHH
Q 013472          254 NLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQH  289 (442)
Q Consensus       254 ~le~~~~~L~~~~gr~pt~~ewA~a~g~deeeL~~~  289 (442)
                      .+.+.+..|...+|+.|+.++.|+.+|++.+.+...
T Consensus       263 ~lrk~~r~L~~~lgR~pt~~EiA~~l~is~~~vr~~  298 (415)
T PRK07598        263 KIKKAQRKISQEKGRTPTIEDIAQELEMTPTQVREV  298 (415)
T ss_pred             HHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHH
Confidence            466677788888999999999999999999887653

>TIGR02850 spore_sigG RNA polymerase sigma-G factor

Probab=94.66  E-value=0.33  Score=47.60  Aligned_cols=35  Identities=14%  Similarity=0.144  Sum_probs=28.9

Q ss_pred             HHHHHHHHHHHhCCCCChHHHHHHcCCCHHHHHHH
Q 013472          255 LERIKTTLEKESGKAASLNCWAQAAGVSERVLKQH  289 (442)
Q Consensus       255 le~~~~~L~~~~gr~pt~~ewA~a~g~deeeL~~~  289 (442)
                      +.+...++..++|++||.++.|+.+|++.+++...
T Consensus       122 ~~~~~~~l~~~l~~~pt~~elA~~l~~~~e~v~~~  156 (254)
T TIGR02850       122 ALQVRDKLISENSKEPTVSEIAKELKVPQEEVVFA  156 (254)
T ss_pred             HHHHHHHHHHHhCCCCCHHHHHHHHCcCHHHHHHH
Confidence            44556677788899999999999999999887654

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.

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

Probab=94.61  E-value=0.7  Score=46.50  Aligned_cols=35  Identities=14%  Similarity=0.308  Sum_probs=28.4

Q ss_pred             HHHHHHHHHHHHhCCCCChHHHHHHcCCCHHHHHH
Q 013472          254 NLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQ  288 (442)
Q Consensus       254 ~le~~~~~L~~~~gr~pt~~ewA~a~g~deeeL~~  288 (442)
                      .+.+.+..+...+|+.|+.++.|+.+|++.+.+..
T Consensus       162 ~~rk~~~~l~~~~~~~pt~~eia~~l~~~~~~v~~  196 (298)
T TIGR02997       162 KIKKVQRELSQKLGRTPSEAEIAEALELEPEQVRE  196 (298)
T ss_pred             HHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHH
Confidence            34455667777889999999999999999887654

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).

>TIGR02885 spore_sigF RNA polymerase sigma-F factor

Probab=94.38  E-value=0.34  Score=46.42  Aligned_cols=34  Identities=32%  Similarity=0.446  Sum_probs=27.2

Q ss_pred             HHHHHHHHHHHhCCCCChHHHHHHcCCCHHHHHH
Q 013472          255 LERIKTTLEKESGKAASLNCWAQAAGVSERVLKQ  288 (442)
Q Consensus       255 le~~~~~L~~~~gr~pt~~ewA~a~g~deeeL~~  288 (442)
                      +.+....+...+|+.||.++.|+.+|++.+++..
T Consensus        99 ~~~~~~~l~~~~~r~pt~~ela~~l~~~~~~v~~  132 (231)
T TIGR02885        99 IRYMKEELSKELGREPTINELAEALGVSPEEIVM  132 (231)
T ss_pred             HHHHHHHHHHHHCcCCCHHHHHHHHCcCHHHHHH
Confidence            3345567777889999999999999999887654

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.

>PRK07500 rpoH2 RNA polymerase factor sigma-32; Reviewed

Probab=94.33  E-value=0.47  Score=47.72  Aligned_cols=28  Identities=11%  Similarity=-0.003  Sum_probs=24.8

Q ss_pred             CCCcHHHHHHHhCCCHHHHHHHHHhccc
Q 013472          397 KYPEDIEIAKYTGLSLAEIRSASECLRI  424 (442)
Q Consensus       397 r~PS~eEIAe~LGIS~etVk~~l~~ar~  424 (442)
                      .+.|.+|||+.||||.++|+.+.+.+..
T Consensus       244 ~~~t~~EIa~~lgvs~~~V~q~~~~Al~  271 (289)
T PRK07500        244 DGATLEALGEELGISKERVRQIEARALE  271 (289)
T ss_pred             CCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            5779999999999999999999877653

>PF04539 Sigma70_r3: Sigma-70 region 3; InterPro: IPR007624 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription

Probab=94.10  E-value=0.12  Score=41.27  Aligned_cols=38  Identities=26%  Similarity=0.408  Sum_probs=30.1

Q ss_pred             HHHHHHHHHHHHHhCCCCChHHHHHHcCCCHHHHHHHH
Q 013472          253 ANLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQHL  290 (442)
Q Consensus       253 ~~le~~~~~L~~~~gr~pt~~ewA~a~g~deeeL~~~l  290 (442)
                      .++.+++.+|+..+||.||.++.|+.+|++.+++...+
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            45778899999999999999999999999998876543

Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 3 forms a discrete compact three helical domain within the sigma-factor. Region is not normally involved in the recognition of promoter DNA, but in some specific bacterial promoters containing an extended -10 promoter element, residues within region 3 play an important role. Region 3 primarily is involved in binding the core RNA polymerase in the holoenzyme [].; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 1L0O_C 1KU2_B 1RP3_C 1SC5_A 1TTY_A 2BE5_F 2A6E_F 2CW0_F 2A69_P 2A6H_P ....

>PRK07405 RNA polymerase sigma factor SigD; Validated

Probab=93.92  E-value=0.75  Score=46.97  Aligned_cols=35  Identities=14%  Similarity=0.389  Sum_probs=28.8

Q ss_pred             HHHHHHHHHHHHhCCCCChHHHHHHcCCCHHHHHH
Q 013472          254 NLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQ  288 (442)
Q Consensus       254 ~le~~~~~L~~~~gr~pt~~ewA~a~g~deeeL~~  288 (442)
                      .+.+....+...+|+.||.++.|+.+|++.+.+..
T Consensus       169 ~l~~~~~~l~~~~gr~pt~~eiA~~~~~~~~~v~~  203 (317)
T PRK07405        169 KIKKAQRQLSQQLGRAATIGELAEELELTPKQVRE  203 (317)
T ss_pred             HHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHH
Confidence            45566777788889999999999999999877654

>PRK06986 fliA flagellar biosynthesis sigma factor; Validated

Probab=93.78  E-value=1.3  Score=42.82  Aligned_cols=29  Identities=14%  Similarity=-0.011  Sum_probs=25.4

Q ss_pred             CCCCcHHHHHHHhCCCHHHHHHHHHhccc
Q 013472          396 GKYPEDIEIAKYTGLSLAEIRSASECLRI  424 (442)
Q Consensus       396 gr~PS~eEIAe~LGIS~etVk~~l~~ar~  424 (442)
                      ..+.|++|||+.||||+++|+..+++++.
T Consensus       198 ~~g~s~~EIA~~lgis~~tV~~~~~ra~~  226 (236)
T PRK06986        198 QEELNLKEIGAVLGVSESRVSQIHSQAIK  226 (236)
T ss_pred             ccCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            45779999999999999999999887763

>PRK07406 RNA polymerase sigma factor RpoD; Validated

Probab=93.66  E-value=1.2  Score=46.88  Aligned_cols=35  Identities=14%  Similarity=0.230  Sum_probs=28.9

Q ss_pred             HHHHHHHHHHHHhCCCCChHHHHHHcCCCHHHHHH
Q 013472          254 NLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQ  288 (442)
Q Consensus       254 ~le~~~~~L~~~~gr~pt~~ewA~a~g~deeeL~~  288 (442)
                      ++.+....|...+|+.||.++.|+.+|++.+.+..
T Consensus       224 ~i~~a~~~l~~~lgr~Pt~~EIA~~lg~~~e~v~~  258 (373)
T PRK07406        224 RIKKTTKVLSQEFGRKPTEEEIAESMEMTIEKLRF  258 (373)
T ss_pred             HHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHH
Confidence            45566777888889999999999999999887643

>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=93.64  E-value=0.064  Score=39.98  Aligned_cols=30  Identities=20%  Similarity=0.067  Sum_probs=22.8

Q ss_pred             cCCCCcHHHHHHHhCCCHHHHHHHHHhccc
Q 013472          395 HGKYPEDIEIAKYTGLSLAEIRSASECLRI  424 (442)
Q Consensus       395 lgr~PS~eEIAe~LGIS~etVk~~l~~ar~  424 (442)
                      +..+.|++|||+.+|+|+.+|+..+++++.
T Consensus        23 ~~~g~s~~eIa~~l~~s~~~v~~~l~ra~~   52 (54)
T PF08281_consen   23 YFQGMSYAEIAEILGISESTVKRRLRRARK   52 (54)
T ss_dssp             HTS---HHHHHHHCTS-HHHHHHHHHHHHH
T ss_pred             HHHCcCHHHHHHHHCcCHHHHHHHHHHHHh
Confidence            457789999999999999999999988753

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.

>TIGR02941 Sigma_B RNA polymerase sigma-B factor

Probab=93.45  E-value=0.49  Score=46.21  Aligned_cols=34  Identities=15%  Similarity=0.200  Sum_probs=26.9

Q ss_pred             HHHHHHHHHHHhCCCCChHHHHHHcCCCHHHHHH
Q 013472          255 LERIKTTLEKESGKAASLNCWAQAAGVSERVLKQ  288 (442)
Q Consensus       255 le~~~~~L~~~~gr~pt~~ewA~a~g~deeeL~~  288 (442)
                      +.+....+...+|+.|+.++.|...|++.+++..
T Consensus       118 ~~~~~~~l~~~~~r~p~~~eia~~l~i~~~~~~~  151 (255)
T TIGR02941       118 IKKAIDELTDHLQRSPKIIEIADHLGLSEEEVLE  151 (255)
T ss_pred             HHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHH
Confidence            4445666777789999999999999999877654

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

>TIGR02394 rpoS_proteo RNA polymerase sigma factor RpoS

Probab=93.00  E-value=1.5  Score=43.82  Aligned_cols=29  Identities=17%  Similarity=0.013  Sum_probs=25.7

Q ss_pred             CCCCcHHHHHHHhCCCHHHHHHHHHhccc
Q 013472          396 GKYPEDIEIAKYTGLSLAEIRSASECLRI  424 (442)
Q Consensus       396 gr~PS~eEIAe~LGIS~etVk~~l~~ar~  424 (442)
                      ..+.|+.|||+.||+|+++|+.++++++.
T Consensus       240 ~e~~s~~EIA~~Lgis~~tVk~~l~rAlk  268 (285)
T TIGR02394       240 YEPATLEEVAAEVGLTRERVRQIQVEALK  268 (285)
T ss_pred             CCCccHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            35679999999999999999999888763

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).

>PRK08215 sporulation sigma factor SigG; Reviewed

Probab=92.95  E-value=1.1  Score=43.89  Aligned_cols=34  Identities=15%  Similarity=0.152  Sum_probs=27.9

Q ss_pred             HHHHHHHHHHHhCCCCChHHHHHHcCCCHHHHHH
Q 013472          255 LERIKTTLEKESGKAASLNCWAQAAGVSERVLKQ  288 (442)
Q Consensus       255 le~~~~~L~~~~gr~pt~~ewA~a~g~deeeL~~  288 (442)
                      +.+...++...+|+.|+..+.|..+|++.+++..
T Consensus       125 ~~~~~~~l~~~~~r~p~~~eia~~l~v~~~~v~~  158 (258)
T PRK08215        125 ALQVREKLINENSKEPTVEEIAKELEVPREEVVF  158 (258)
T ss_pred             HHHHHHHHHHHhCCCCCHHHHHHHHCcCHHHHHH
Confidence            3445667777889999999999999999988654

>PRK08583 RNA polymerase sigma factor SigB; Validated

Probab=92.57  E-value=5.2  Score=39.08  Aligned_cols=28  Identities=11%  Similarity=-0.005  Sum_probs=25.1

Q ss_pred             CCCCcHHHHHHHhCCCHHHHHHHHHhcc
Q 013472          396 GKYPEDIEIAKYTGLSLAEIRSASECLR  423 (442)
Q Consensus       396 gr~PS~eEIAe~LGIS~etVk~~l~~ar  423 (442)
                      ..+.|.+|||+.||||+++|+..+++++
T Consensus       219 ~~g~s~~eIA~~l~is~~tV~~~~~ra~  246 (257)
T PRK08583        219 IENLSQKETGERLGISQMHVSRLQRQAI  246 (257)
T ss_pred             hCCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence            4778999999999999999999988765

>PRK05658 RNA polymerase sigma factor RpoD; Validated

Probab=92.41  E-value=1.5  Score=48.70  Aligned_cols=35  Identities=23%  Similarity=0.402  Sum_probs=29.2

Q ss_pred             HHHHHHHHHHHHhCCCCChHHHHHHcCCCHHHHHH
Q 013472          254 NLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQ  288 (442)
Q Consensus       254 ~le~~~~~L~~~~gr~pt~~ewA~a~g~deeeL~~  288 (442)
                      ++.+....+...+|++||.++.|+.+|++.+.+..
T Consensus       468 k~~~~~~~~~~~~gr~pt~~eiA~~l~~~~~~v~~  502 (619)
T PRK05658        468 KLNRISRQMLQEIGREPTPEELAERLGMPEDKVRK  502 (619)
T ss_pred             HHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHH
Confidence            45566777888899999999999999999887654

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

Probab=92.21  E-value=0.62  Score=44.48  Aligned_cols=29  Identities=17%  Similarity=0.020  Sum_probs=25.2

Q ss_pred             CCCCcHHHHHHHhCCCHHHHHHHHHhccc
Q 013472          396 GKYPEDIEIAKYTGLSLAEIRSASECLRI  424 (442)
Q Consensus       396 gr~PS~eEIAe~LGIS~etVk~~l~~ar~  424 (442)
                      ..+.|++|||+.+|+|..+|...++++..
T Consensus       192 ~~~~s~~eIA~~lgis~~~v~~~~~ra~~  220 (227)
T TIGR02980       192 FEDKTQSEIAERLGISQMHVSRLLRRALK  220 (227)
T ss_pred             hcCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence            35779999999999999999999887653

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.

>PHA02547 55 RNA polymerase sigma factor; Provisional

Probab=92.08  E-value=0.47  Score=44.73  Aligned_cols=65  Identities=15%  Similarity=0.179  Sum_probs=53.1

Q ss_pred             hHHHHHHHHHHhhCCCCC---HHhHHHHHHHHHHHhHHhcCCCCCCChHHHHHHHHHHHHHHHHHhhc
Q 013472          304 TRPLVLFLARNYRGLGIP---FSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHA  368 (442)
Q Consensus       304 nlrLV~sIAkrY~g~g~d---~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIRnaI~r~LRkqs  368 (442)
                      -+..+-.++++|.-++..   -+|.|.+|.-.+++.+..||+++...+-+|++.++-++..+.|.+.+
T Consensus        46 imkIa~glS~r~nF~~Yt~~wKedMI~DgIe~~i~ylhNFD~~k~~Np~aYiT~~~~~AF~~RI~kEk  113 (179)
T PHA02547         46 IMKIAEGLSRRPNFSGYTQTWKEDMIADGIEACIKGLHNFDETKYKNPHAYITQACFNAFVQRIKKEK  113 (179)
T ss_pred             HHHHHhccccCCccccchHHHHHHHHHHHHHHHHHHhhcCCcccccChHHHHHHHHHHHHHHHHHHHH
Confidence            345555566666444444   68999999999999999999999999999999999999999887654

>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=92.01  E-value=0.51  Score=37.49  Aligned_cols=44  Identities=18%  Similarity=0.240  Sum_probs=34.0

Q ss_pred             HHHHHHHHHHHHHHHHcCCCCcHHHHHHHhCCC-HHHHHHHHHhc
Q 013472          379 REISKIQKARKALTNSHGKYPEDIEIAKYTGLS-LAEIRSASECL  422 (442)
Q Consensus       379 e~i~kI~ka~~~L~~elgr~PS~eEIAe~LGIS-~etVk~~l~~a  422 (442)
                      +...+|-.++.+...+.|..||..|||+.+|++ ..+|...+...
T Consensus         6 ~rQ~~vL~~I~~~~~~~G~~Pt~rEIa~~~g~~S~~tv~~~L~~L   50 (65)
T PF01726_consen    6 ERQKEVLEFIREYIEENGYPPTVREIAEALGLKSTSTVQRHLKAL   50 (65)
T ss_dssp             HHHHHHHHHHHHHHHHHSS---HHHHHHHHTSSSHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCChHHHHHHHHHH
Confidence            344567778888888899999999999999997 99999887654

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.

>PRK12427 flagellar biosynthesis sigma factor; Provisional

Probab=91.73  E-value=1.7  Score=42.31  Aligned_cols=34  Identities=6%  Similarity=0.120  Sum_probs=28.4

Q ss_pred             HHHHHHHHHHHhCCCCChHHHHHHcCCCHHHHHH
Q 013472          255 LERIKTTLEKESGKAASLNCWAQAAGVSERVLKQ  288 (442)
Q Consensus       255 le~~~~~L~~~~gr~pt~~ewA~a~g~deeeL~~  288 (442)
                      +.+....+...+|+.|+.++.|+.+|++.+++..
T Consensus       103 i~~~~~~l~~~~g~~pt~~eiA~~lg~~~~~v~~  136 (231)
T PRK12427        103 TNDAIREIAKRLGHEPNFEEISAELNLTAEEYQE  136 (231)
T ss_pred             HHHHHHHHHHHHCCCCCHHHHHHHhCCCHHHHHH
Confidence            4456677778889999999999999999887654

>PRK05572 sporulation sigma factor SigF; Validated

Probab=91.72  E-value=2.1  Score=41.84  Aligned_cols=34  Identities=24%  Similarity=0.357  Sum_probs=26.8

Q ss_pred             HHHHHHHHHHHHhCCCCChHHHHHHcCCCHHHHH
Q 013472          254 NLERIKTTLEKESGKAASLNCWAQAAGVSERVLK  287 (442)
Q Consensus       254 ~le~~~~~L~~~~gr~pt~~ewA~a~g~deeeL~  287 (442)
                      ++.+....+..++|+.|+..+.|+..|++.+.+.
T Consensus       119 ~~~~~~~~l~~~~~r~p~~~eia~~l~~~~~~v~  152 (252)
T PRK05572        119 KIRKDKDELSKELGREPTIEELAEYLGVTPEEVV  152 (252)
T ss_pred             HHHHHHHHHHHHHCcCCCHHHHHHHhCcCHHHHH
Confidence            3455566777778999999999999999887654

>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=90.87  E-value=0.65  Score=34.18  Aligned_cols=30  Identities=20%  Similarity=-0.005  Sum_probs=25.0

Q ss_pred             HcCCCCcHHHHHHHhCCCHHHHHHHHHhcc
Q 013472          394 SHGKYPEDIEIAKYTGLSLAEIRSASECLR  423 (442)
Q Consensus       394 elgr~PS~eEIAe~LGIS~etVk~~l~~ar  423 (442)
                      .+..+.|.+|||+.||+|.++|+.+...+.
T Consensus        16 ~y~~~~t~~eIa~~lg~s~~~V~~~~~~al   45 (50)
T PF04545_consen   16 RYFEGLTLEEIAERLGISRSTVRRILKRAL   45 (50)
T ss_dssp             HHTST-SHHHHHHHHTSCHHHHHHHHHHHH
T ss_pred             HhcCCCCHHHHHHHHCCcHHHHHHHHHHHH
Confidence            347788999999999999999999887653

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 ....

>PRK05657 RNA polymerase sigma factor RpoS; Validated

Probab=89.73  E-value=5.1  Score=41.14  Aligned_cols=29  Identities=14%  Similarity=0.038  Sum_probs=25.7

Q ss_pred             CCCCcHHHHHHHhCCCHHHHHHHHHhccc
Q 013472          396 GKYPEDIEIAKYTGLSLAEIRSASECLRI  424 (442)
Q Consensus       396 gr~PS~eEIAe~LGIS~etVk~~l~~ar~  424 (442)
                      ..+.|.+|||+.||+|+++|+.++++++.
T Consensus       280 ~e~~s~~EIA~~Lgis~~tV~~~~~rAl~  308 (325)
T PRK05657        280 YEAATLEDVAREIGLTRERVRQIQVEALR  308 (325)
T ss_pred             CCCcCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence            35789999999999999999999887764

>PRK06596 RNA polymerase factor sigma-32; Reviewed

Probab=85.30  E-value=10  Score=38.10  Aligned_cols=27  Identities=19%  Similarity=0.129  Sum_probs=23.7

Q ss_pred             CCCcHHHHHHHhCCCHHHHHHHHHhcc
Q 013472          397 KYPEDIEIAKYTGLSLAEIRSASECLR  423 (442)
Q Consensus       397 r~PS~eEIAe~LGIS~etVk~~l~~ar  423 (442)
                      .+.|.+|||+.||||.++|+.+.+.+.
T Consensus       247 ~~~Tl~EIA~~lgvS~~rVrqi~~~Al  273 (284)
T PRK06596        247 DKSTLQELAAEYGVSAERVRQIEKNAM  273 (284)
T ss_pred             CCcCHHHHHHHHCCCHHHHHHHHHHHH
Confidence            578999999999999999999876553

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

Probab=85.22  E-value=23  Score=37.07  Aligned_cols=36  Identities=28%  Similarity=0.417  Sum_probs=29.4

Q ss_pred             HHHHHHHHHHHHHHhCCCCChHHHHHHcCCCHHHHH
Q 013472          252 VANLERIKTTLEKESGKAASLNCWAQAAGVSERVLK  287 (442)
Q Consensus       252 ~~~le~~~~~L~~~~gr~pt~~ewA~a~g~deeeL~  287 (442)
                      .-++.+++.+|...+|++|+.++.|+.+|++..+..
T Consensus       188 ~nkl~r~~r~l~q~~~r~p~~eeia~~l~~~~~~V~  223 (342)
T COG0568         188 INKLRRVKRELLQELGREPTPEEIAEELGVSPDKVR  223 (342)
T ss_pred             HHHHHHHHHHHHHHhcCCCCHHHHHHHhCCCHHHHH
Confidence            345667788888889999999999999999987543

>TIGR03879 near_KaiC_dom probable regulatory domain

Probab=81.77  E-value=1.7  Score=35.57  Aligned_cols=25  Identities=20%  Similarity=0.106  Sum_probs=22.6

Q ss_pred             CCCcHHHHHHHhCCCHHHHHHHHHh
Q 013472          397 KYPEDIEIAKYTGLSLAEIRSASEC  421 (442)
Q Consensus       397 r~PS~eEIAe~LGIS~etVk~~l~~  421 (442)
                      .+.|+.|||+.||+|+.+|+..+..
T Consensus        31 eGlS~kEIAe~LGIS~~TVk~~l~~   55 (73)
T TIGR03879        31 AGKTASEIAEELGRTEQTVRNHLKG   55 (73)
T ss_pred             cCCCHHHHHHHHCcCHHHHHHHHhc
Confidence            5779999999999999999998863

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.

>COG4941 Predicted RNA polymerase sigma factor containing a TPR repeat domain [Transcription]

Probab=80.22  E-value=11  Score=39.45  Aligned_cols=123  Identities=20%  Similarity=0.056  Sum_probs=78.6

Q ss_pred             HHHHHhHHHHHHHHHHhhCCCCCHHhHHHHHHHHHHHhHHhcCCCCCCChHHHHHHHHHHHHHHHHHhhcCceecccccH
Q 013472          299 ELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIPCKLN  378 (442)
Q Consensus       299 ~LI~~nlrLV~sIAkrY~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIRnaI~r~LRkqsr~irlP~~v~  378 (442)
                      ..+..-.+.++.---+|+++-..+||.+||.|+...+.--+=-+-+  .-..|++-..|+.-+|.+|++.+....|.+..
T Consensus         9 ~~~r~~~~r~~a~L~r~~rd~dlAEEa~~dA~~~Ale~WPr~G~P~--~PaAWL~~v~R~~aiD~~Rr~~~~~~~~~el~   86 (415)
T COG4941           9 AAARIERPRAMAALARYLRDLDLAEEALQDAFAAALERWPRAGPPR--NPAAWLIAVGRNRAIDRVRRRARRDAAPPELL   86 (415)
T ss_pred             HHHHHhhhHHHHHHHHHhcccchHHHHHHHHHHHHHHhCcccCCCC--ChHHHHHHHHhhhHHHHHHHHHHhccCChhhc
Confidence            3344445555555556777778899999999876544433333333  47899999999999999999877655544322


Q ss_pred             HHH--HHHHHH----------------------------HHHHHHHcCCCCcHHHHHHHhCCCHHHHHHHHHhcc
Q 013472          379 REI--SKIQKA----------------------------RKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLR  423 (442)
Q Consensus       379 e~i--~kI~ka----------------------------~~~L~~elgr~PS~eEIAe~LGIS~etVk~~l~~ar  423 (442)
                      ...  ..+..+                            .-.|.-..--+.|.+|||...=+++.++.+.+-+++
T Consensus        87 ~~~e~~e~~~a~~~~d~~i~Dd~LRLiFvccHPal~~~~riALtLR~v~GLs~~eIArAFLv~e~am~QRivRAK  161 (415)
T COG4941          87 LSDEDEEMEEAEALDDEHIRDDRLRLIFVCCHPALPPEQRIALTLRLVGGLSTAEIARAFLVPEAAMAQRIVRAK  161 (415)
T ss_pred             ccccchhhhccccccccccchhhHHhhhhhcCCCCChhhHHHHHHHHHcCCcHHHHHHHHcCCcHHHHHHHHHHH
Confidence            111  111111                            011111112456889999999999999988877766

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	442
3iyd_F	613	Three-Dimensional Em Structure Of An Intact Activat		2e-21
4igc_X	613	X-ray Crystal Structure Of Escherichia Coli Sigma70		2e-21
1l9z_H	438	Thermus Aquaticus Rna Polymerase HoloenzymeFORK-Jun		1e-20
1l9u_H	332	Thermus Aquaticus Rna Polymerase Holoenzyme At 4 A		1e-20
3dxj_F	423	Crystal Structure Of Thermus Thermophilus Rna Polym		1e-20
1iw7_F	423	Crystal Structure Of The Rna Polymerase Holoenzyme		1e-20
4g7h_F	443	Crystal Structure Of Thermus Thermophilus Transcrip		2e-20
1ku2_A	241	Crystal Structure Of Thermus Aquaticus Rna Polymera		1e-19
3ugo_A	245	Crystal Structure Of Rna-Polymerase Sigma Subunit D		1e-19
1sig_A	339	Crystal Structure Of A Sigma70 Subunit Fragment Fro		1e-14
3les_A	179	2f5 Epitope Scaffold Es2 Length = 179		3e-14
1l0o_C	243	Crystal Structure Of The Bacillus Stearothermophilu		4e-11

>pdb|3IYD|F Chain F, Three-Dimensional Em Structure Of An Intact Activator-Dependent Transcription Initiation Complex Length = 613

Iteration: 1
 Score =  100 bits (248), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 44/139 (31%), Positives = 85/139 (61%)
Query: 296 CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYW 355
            ++E++++   LV+ +A+ Y   G+ F DL+Q GN+G+++  ++F++ RGYKFSTY  +W
Sbjct: 375 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 434
Query: 356 IRKSISKMVARHARGIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEI 415
           IR++I++ +A  AR I+IP  +   I+K+ +  + +    G+ P   E+A+   +   +I
Sbjct: 435 IRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELAERMLMPEDKI 494
Query: 416 RSASECLRIVGSIDQKIGD 434
           R   +  +   S++  IGD
Sbjct: 495 RKVLKIAKEPISMETPIGD 513

>pdb|4IGC|X Chain X, X-ray Crystal Structure Of Escherichia Coli Sigma70 Holoenzyme Length = 613

Iteration: 1
 Score =  100 bits (248), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 44/139 (31%), Positives = 85/139 (61%)
Query: 296 CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYW 355
            ++E++++   LV+ +A+ Y   G+ F DL+Q GN+G+++  ++F++ RGYKFSTY  +W
Sbjct: 375 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 434
Query: 356 IRKSISKMVARHARGIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEI 415
           IR++I++ +A  AR I+IP  +   I+K+ +  + +    G+ P   E+A+   +   +I
Sbjct: 435 IRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELAERMLMPEDKI 494
Query: 416 RSASECLRIVGSIDQKIGD 434
           R   +  +   S++  IGD
Sbjct: 495 RKVLKIAKEPISMETPIGD 513

>pdb|1L9Z|H Chain H, Thermus Aquaticus Rna Polymerase HoloenzymeFORK-Junction Promoter Dna Complex At 6.5 A Resolution Length = 438

Iteration: 1
 Score = 97.8 bits (242), Expect = 1e-20,   Method: Compositional matrix adjust.
 Identities = 61/186 (32%), Positives = 102/186 (54%), Gaps = 17/186 (9%)
Query: 261 TLEKESGKAASLNCWAQAAGVSERVLKQHLAF---GWYCREELIKSTRPLVLFLARNYRG 317
           T+E+  GK  SL           + LK++L     G   R+ LI++   LV+ +A+ Y G
Sbjct: 170 TVEEVDGKLKSLP----------KELKRYLHIAREGEAARQHLIEANLRLVVSIAKKYTG 219
Query: 318 LGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIPCKL 377
            G+ F DL+Q GN G+++  E+F++ R +KFSTY  +WIR++I++ +A  AR I+IP  +
Sbjct: 220 RGLSFLDLIQEGNQGLIRAVEKFEYKRRFKFSTYATWWIRQAINRAIADQARTIRIPVHM 279
Query: 378 NREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVG---SIDQKIGD 434
              I+K+ +  + L    G+ P   EIA+  G    + +   E L+I     S++  IGD
Sbjct: 280 VETINKLSRTARQLQQELGREPSYEEIAEAMGPGW-DAKRVEETLKIAQEPVSLETPIGD 338
Query: 435 CLNAKY 440
             ++ Y
Sbjct: 339 EKDSFY 344

>pdb|1L9U|H Chain H, Thermus Aquaticus Rna Polymerase Holoenzyme At 4 A Resolution Length = 332

Iteration: 1
 Score = 97.8 bits (242), Expect = 1e-20,   Method: Compositional matrix adjust.
 Identities = 55/161 (34%), Positives = 93/161 (57%), Gaps = 7/161 (4%)
Query: 286 LKQHLAF---GWYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDH 342
           LK++L     G   R+ LI++   LV+ +A+ Y G G+ F DL+Q GN G+++  E+F++
Sbjct: 79  LKRYLHIAREGEAARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQEGNQGLIRAVEKFEY 138
Query: 343 TRGYKFSTYVQYWIRKSISKMVARHARGIKIPCKLNREISKIQKARKALTNSHGKYPEDI 402
            R +KFSTY  +WIR++I++ +A  AR I+IP  +   I+K+ +  + L    G+ P   
Sbjct: 139 KRRFKFSTYATWWIRQAINRAIADQARTIRIPVHMVETINKLSRTARQLQQELGREPSYE 198
Query: 403 EIAKYTGLSLAEIRSASECLRIVG---SIDQKIGDCLNAKY 440
           EIA+  G    + +   E L+I     S++  IGD  ++ Y
Sbjct: 199 EIAEAMGPGW-DAKRVEETLKIAQEPVSLETPIGDEKDSFY 238

>pdb|3DXJ|F Chain F, Crystal Structure Of Thermus Thermophilus Rna Polymerase Holoenzyme In Complex With The Antibiotic Myxopyronin Length = 423

Iteration: 1
 Score = 97.4 bits (241), Expect = 1e-20,   Method: Compositional matrix adjust.
 Identities = 54/156 (34%), Positives = 91/156 (58%), Gaps = 5/156 (3%)
Query: 289 HLAF-GWYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYK 347
           H+A  G   R+ LI++   LV+ +A+ Y G G+ F DL+Q GN G+++  E+F++ R +K
Sbjct: 175 HIAREGEAARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQEGNQGLIRAVEKFEYKRRFK 234
Query: 348 FSTYVQYWIRKSISKMVARHARGIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKY 407
           FSTY  +WIR++I++ +A  AR I+IP  +   I+K+ +  + L    G+ P   EIA+ 
Sbjct: 235 FSTYATWWIRQAINRAIADQARTIRIPVHMVETINKLSRTARQLQQELGREPTYEEIAEA 294
Query: 408 TGLSLAEIRSASECLRIVG---SIDQKIGDCLNAKY 440
            G    + +   E L+I     S++  IGD  ++ Y
Sbjct: 295 MGPGW-DAKRVEETLKIAQEPVSLETPIGDEKDSFY 329

>pdb|1IW7|F Chain F, Crystal Structure Of The Rna Polymerase Holoenzyme From Thermus Thermophilus At 2.6a Resolution Length = 423

Iteration: 1
 Score = 97.4 bits (241), Expect = 1e-20,   Method: Compositional matrix adjust.
 Identities = 54/156 (34%), Positives = 91/156 (58%), Gaps = 5/156 (3%)
Query: 289 HLAF-GWYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYK 347
           H+A  G   R+ LI++   LV+ +A+ Y G G+ F DL+Q GN G+++  E+F++ R +K
Sbjct: 175 HIAREGEAARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQEGNQGLIRAVEKFEYKRRFK 234
Query: 348 FSTYVQYWIRKSISKMVARHARGIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKY 407
           FSTY  +WIR++I++ +A  AR I+IP  +   I+K+ +  + L    G+ P   EIA+ 
Sbjct: 235 FSTYATWWIRQAINRAIADQARTIRIPVHMVETINKLSRTARQLQQELGREPTYEEIAEA 294
Query: 408 TGLSLAEIRSASECLRIVG---SIDQKIGDCLNAKY 440
            G    + +   E L+I     S++  IGD  ++ Y
Sbjct: 295 MGPGW-DAKRVEETLKIAQEPVSLETPIGDEKDSFY 329

>pdb|4G7H|F Chain F, Crystal Structure Of Thermus Thermophilus Transcription Initiation Complex Length = 443

Iteration: 1
 Score = 97.1 bits (240), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 52/151 (34%), Positives = 88/151 (58%), Gaps = 4/151 (2%)
Query: 293 GWYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYV 352
           G   R+ LI++   LV+ +A+ Y G G+ F DL+Q GN G+++  E+F++ R +KFSTY 
Sbjct: 200 GEAARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQEGNQGLIRAVEKFEYKRRFKFSTYA 259
Query: 353 QYWIRKSISKMVARHARGIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSL 412
            +WIR++I++ +A  AR I+IP  +   I+K+ +  + L    G+ P   EIA+  G   
Sbjct: 260 TWWIRQAINRAIADQARTIRIPVHMVETINKLSRTARQLQQELGREPTYEEIAEAMGPGW 319
Query: 413 AEIRSASECLRIVG---SIDQKIGDCLNAKY 440
            + +   E L+I     S++  IGD  ++ Y
Sbjct: 320 -DAKRVEETLKIAQEPVSLETPIGDEKDSFY 349

>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 = 94.4 bits (233), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 53/152 (34%), Positives = 87/152 (57%), Gaps = 13/152 (8%)
Query: 261 TLEKESGKAASLNCWAQAAGVSERVLKQHLAF---GWYCREELIKSTRPLVLFLARNYRG 317
           T+E+  GK  SL           + LK++L     G   R+ LI++   LV+ +A+ Y G
Sbjct: 79  TVEEVDGKLKSLP----------KELKRYLHIAREGEAARQHLIEANLRLVVSIAKKYTG 128
Query: 318 LGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIPCKL 377
            G+ F DL+Q GN G+++  E+F++ R +KFSTY  +WIR++I++ +A  AR I+IP  +
Sbjct: 129 RGLSFLDLIQEGNQGLIRAVEKFEYKRRFKFSTYATWWIRQAINRAIADQARTIRIPVHM 188
Query: 378 NREISKIQKARKALTNSHGKYPEDIEIAKYTG 409
              I+K+ +  + L    G+ P   EIA+  G
Sbjct: 189 VETINKLSRTARQLQQELGREPSYEEIAEAMG 220

>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 = 94.4 bits (233), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 53/152 (34%), Positives = 87/152 (57%), Gaps = 13/152 (8%)
Query: 261 TLEKESGKAASLNCWAQAAGVSERVLKQHLAF---GWYCREELIKSTRPLVLFLARNYRG 317
           T+E+  GK  SL           + LK++L     G   R+ LI++   LV+ +A+ Y G
Sbjct: 83  TVEEVDGKLKSLP----------KELKRYLHIAREGEAARQHLIEANLRLVVSIAKKYTG 132
Query: 318 LGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIPCKL 377
            G+ F DL+Q GN G+++  E+F++ R +KFSTY  +WIR++I++ +A  AR I+IP  +
Sbjct: 133 RGLSFLDLIQEGNQGLIRAVEKFEYKRRFKFSTYATWWIRQAINRAIADQARTIRIPVHM 192
Query: 378 NREISKIQKARKALTNSHGKYPEDIEIAKYTG 409
              I+K+ +  + L    G+ P   EIA+  G
Sbjct: 193 VETINKLSRTARQLQQELGREPSYEEIAEAMG 224

>pdb|1SIG|A Chain A, Crystal Structure Of A Sigma70 Subunit Fragment From Escherichia Coli Rna Polymerase Length = 339

Iteration: 1
 Score = 77.8 bits (190), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 29/74 (39%), Positives = 54/74 (72%)
Query: 296 CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYW 355
            ++E++++   LV+ +A+ Y   G+ F DL+Q GN+G+++  ++F++ RGYKFSTY  +W
Sbjct: 266 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 325
Query: 356 IRKSISKMVARHAR 369
           IR++I++ +A  AR
Sbjct: 326 IRQAITRSIADQAR 339

>pdb|3LES|A Chain A, 2f5 Epitope Scaffold Es2 Length = 179

Iteration: 1
 Score = 76.3 bits (186), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 41/112 (36%), Positives = 67/112 (59%), Gaps = 13/112 (11%)
Query: 261 TLEKESGKAASLNCWAQAAGVSERVLKQHLAF---GWYCREELIKSTRPLVLFLARNYRG 317
           T+E+  GK  SL           + LK++L     G   R+ LI++   LV+ +A+ Y G
Sbjct: 78  TVEEVDGKLKSLP----------KELKRYLHIAREGEAARQHLIEANLRLVVSIAKKYTG 127
Query: 318 LGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHAR 369
            G+ F DL+Q GN G+++  E+F++ RG+ FSTY  +WIR++I++ +A  AR
Sbjct: 128 RGLSFLDLIQEGNQGLIRAVEKFEYKRGFAFSTYATWWIRQAINRAIADQAR 179

>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 = 65.9 bits (159), Expect = 4e-11,   Method: Compositional matrix adjust.
 Identities = 41/137 (29%), Positives = 71/137 (51%), Gaps = 1/137 (0%)
Query: 296 CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYW 355
            R+E+I+    LV  + + +   G    DL Q G +G+L+  ++FD +   KFSTY    
Sbjct: 29  ARDEIIEKNMRLVWSVVQRFLNRGYEADDLFQIGCIGLLKSVDKFDLSYDVKFSTYAVPM 88
Query: 356 IRKSISKMVARHARGIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEI 415
           I   I + + R    +K+   L    +KI+KA+  L+ + G+ P   EIA + G+S  ++
Sbjct: 89  IIGEIQRFL-RDDGTVKVSRSLKEMGNKIRKAKDELSKTRGRAPTVTEIADHLGISPEDV 147
Query: 416 RSASECLRIVGSIDQKI 432
             A E +R+  SI + +
Sbjct: 148 VLAQEAVRLPTSIHETV 164

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	442
1l0o_C	243	Sigma factor; bergerat fold, helix-turn-helix, pro	3e-27
1rp3_A	239	RNA polymerase sigma factor sigma-28 (FLIA); trans	1e-25
3iyd_F	613	RNA polymerase sigma factor RPOD; transcription, i	2e-25
3ugo_A	245	RNA polymerase sigma factor; protein-DNA complex,	2e-23
2a6h_F	423	RNA polymerase sigma factor RPOD; RNA polymerase h	7e-23
1l9z_H	438	Sigma factor SIGA; helix-turn-helix, coiled-coil,	2e-22
1sig_A	339	Sigma70, RNA polymerase primary sigma factor; RNA	2e-15
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	2e-05
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	8e-05

>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 =  108 bits (272), Expect = 3e-27
 Identities = 42/141 (29%), Positives = 71/141 (50%), Gaps = 7/141 (4%)

Query: 297 REELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWI 356
           R+E+I+    LV  + + +   G    DL Q G +G+L+  ++FD +   KFSTY    I
Sbjct: 30  RDEIIEKNMRLVWSVVQRFLNRGYEADDLFQIGCIGLLKSVDKFDLSYDVKFSTYAVPMI 89

Query: 357 RKSISKMVARHAR---GIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLA 413
              I     R  R    +K+   L    +KI+KA+  L+ + G+ P   EIA + G+S  
Sbjct: 90  IGEIQ----RFLRDDGTVKVSRSLKEMGNKIRKAKDELSKTRGRAPTVTEIADHLGISPE 145

Query: 414 EIRSASECLRIVGSIDQKIGD 434
           ++  A E +R+  SI + + +
Sbjct: 146 DVVLAQEAVRLPTSIHETVYE 166

>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 =  103 bits (259), Expect = 1e-25
 Identities = 33/144 (22%), Positives = 64/144 (44%), Gaps = 10/144 (6%)

Query: 297 REELIKSTRPLVLFLARNYR---GLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQ 353
           REELI    PLV  +A N +      +   DL+  G +G+++  +        +   Y++
Sbjct: 14  REELILKYLPLVKAIATNIKKHLPEDVDIRDLISYGVIGLIKAVDNLSTENPKRAEAYIK 73

Query: 354 YWIRKSISKMVARHARGIKIPCKLNREIS-KIQKARKALTNSHGKYPEDIEIAKYTGLSL 412
             I+ +I      + R +    +  RE   +I++  + L    G+ P D E+AK  G+S 
Sbjct: 74  LRIKGAI----YDYLRSLDFGSRQVREKERRIKEVVEKLKEKLGREPTDEEVAKELGIST 129

Query: 413 AEIRSASECLRI--VGSIDQKIGD 434
            E+    + +    + S+++   D
Sbjct: 130 EELFKTLDKINFSYILSLEEVFRD 153

>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 =  108 bits (270), Expect = 2e-25
 Identities = 44/138 (31%), Positives = 85/138 (61%)

Query: 297 REELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWI 356
           ++E++++   LV+ +A+ Y   G+ F DL+Q GN+G+++  ++F++ RGYKFSTY  +WI
Sbjct: 376 KKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWI 435

Query: 357 RKSISKMVARHARGIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIR 416
           R++I++ +A  AR I+IP  +   I+K+ +  + +    G+ P   E+A+   +   +IR
Sbjct: 436 RQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELAERMLMPEDKIR 495

Query: 417 SASECLRIVGSIDQKIGD 434
              +  +   S++  IGD
Sbjct: 496 KVLKIAKEPISMETPIGD 513

>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 = 97.6 bits (243), Expect = 2e-23
 Identities = 43/122 (35%), Positives = 73/122 (59%), Gaps = 2/122 (1%)

Query: 297 REELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWI 356
           R+ LI++   LV+ +A+ Y G G+ F DL+Q GN G+++  E+F++ R +KFSTY  +WI
Sbjct: 112 RQHLIEANLRLVVSIAKKYTGRGLSFLDLIQEGNQGLIRAVEKFEYKRRFKFSTYATWWI 171

Query: 357 RKSISKMVARHARGIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAK--YTGLSLAE 414
           R++I++ +A  AR I+IP  +   I+K+ +  + L    G+ P   EIA+    G     
Sbjct: 172 RQAINRAIADQARTIRIPVHMVETINKLSRTARQLQQELGREPSYEEIAEAMGPGWDAKR 231

Query: 415 IR 416
           + 
Sbjct: 232 VE 233

>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 = 99.2 bits (247), Expect = 7e-23
 Identities = 63/288 (21%), Positives = 125/288 (43%), Gaps = 40/288 (13%)

Query: 157 DLSDVHTEEQKMNDS-RDY--HMGKILVPSKRKGKRKLKTARVSEESIETSLLSLPSEA- 212
           +  D+   +   +D  R Y   +G++ + +  +     +      E+I+        +  
Sbjct: 66  EEEDLPIPKISTSDPVRQYLHEIGQVPLLTLEEEVELARKVEEGMEAIKKLSEITGLDPD 125

Query: 213 -LQEGLKQPTIFSAERALNSRGRRLTIARNEAEMSKGVQVVANLERIKTTLEKESGKAAS 271
            ++E ++   + SA        +     +   E+ + ++ +    +    + +E   A  
Sbjct: 126 LIREVVRAKILGSARVRHIPGLKETLDPKTVEEIDQKLKSLPKEHKRYLHIAREGEAA-- 183

Query: 272 LNCWAQAAGVSERVLKQHLAFGWYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNV 331
                                    R+ LI++   LV+ +A+ Y G G+ F DL+Q GN 
Sbjct: 184 -------------------------RQHLIEANLRLVVSIAKKYTGRGLSFLDLIQEGNQ 218

Query: 332 GVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIPCKLNREISKIQKARKAL 391
           G+++  E+F++ R +KFSTY  +WIR++I++ +A  AR I+IP  +   I+K+ +  + L
Sbjct: 219 GLIRAVEKFEYKRRFKFSTYATWWIRQAINRAIADQARTIRIPVHMVETINKLSRTARQL 278

Query: 392 TNSHGKYPEDIEIAK--YTGLSLAEIRSASECLRIVG---SIDQKIGD 434
               G+ P   EIA+    G     +    E L+I     S++  IGD
Sbjct: 279 QQELGREPTYEEIAEAMGPGWDAKRVE---ETLKIAQEPVSLETPIGD 323

>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 = 98.1 bits (244), Expect = 2e-22
 Identities = 50/143 (34%), Positives = 83/143 (58%), Gaps = 8/143 (5%)

Query: 297 REELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWI 356
           R+ LI++   LV+ +A+ Y G G+ F DL+Q GN G+++  E+F++ R +KFSTY  +WI
Sbjct: 199 RQHLIEANLRLVVSIAKKYTGRGLSFLDLIQEGNQGLIRAVEKFEYKRRFKFSTYATWWI 258

Query: 357 RKSISKMVARHARGIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAK--YTGLSLAE 414
           R++I++ +A  AR I+IP  +   I+K+ +  + L    G+ P   EIA+    G     
Sbjct: 259 RQAINRAIADQARTIRIPVHMVETINKLSRTARQLQQELGREPSYEEIAEAMGPGWDAKR 318

Query: 415 IRSASECLRIVG---SIDQKIGD 434
           +    E L+I     S++  IGD
Sbjct: 319 VE---ETLKIAQEPVSLETPIGD 338

>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 = 76.5 bits (188), Expect = 2e-15
 Identities = 29/71 (40%), Positives = 52/71 (73%)

Query: 299 ELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRK 358
           E++++   LV+ +A+ Y   G+ F DL+Q GN+G+++  ++F++ RGYKFSTY  +WIR+
Sbjct: 269 EMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQ 328

Query: 359 SISKMVARHAR 369
           +I++ +A  AR
Sbjct: 329 AITRSIADQAR 339

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221

 Score = 46.0 bits (108), Expect = 2e-05
 Identities = 61/397 (15%), Positives = 113/397 (28%), Gaps = 115/397 (28%)

Query: 74  TVENDYSETEEIRQKSTSC--IGQDASSRSDF----RLLMENL-DVLESTFADSD---AL 123
            ++N  S    +         I  + +SRSD     +L + ++   L            L
Sbjct: 188 NLKNCNSPETVLEMLQKLLYQIDPNWTSRSDHSSNIKLRIHSIQAELRRLLKSKPYENCL 247

Query: 124 RLEREILQQLGKLGALKLFNSHLSRIVKTS---NVLD-LSDVHTEEQKMNDSRDYHMGKI 179
            L   +L  +    A   FN    +I+ T+    V D LS   T    ++     H    
Sbjct: 248 -L---VLLNVQNAKAWNAFNLS-CKILLTTRFKQVTDFLSAATTTHISLD-----HHSMT 297

Query: 180 LVPSKRKGKRKLKTARVSEESIETSLLSLPSEALQEGLKQPTIFSAERALNSRGRRLTIA 239
           L P +           +  + ++     LP E L      P      R L+     +   
Sbjct: 298 LTPDE--------VKSLLLKYLDCRPQDLPREVLTTN---P------RRLSIIAESI--- 337

Query: 240 RNEAEMSKGVQVVANLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQHLAFGWYCREE 299
           R+        + V N +++ T +E      +SLN       +     ++      +    
Sbjct: 338 RDGLATWDNWKHV-NCDKLTTIIE------SSLNV------LEPAEYRKM-----F---- 375

Query: 300 LIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVL------QGAERFDHT--------RG 345
                  L +F         IP + LL      ++             +         + 
Sbjct: 376 -----DRLSVFPP----SAHIP-TILLS-----LIWFDVIKSDVMVVVNKLHKYSLVEKQ 420

Query: 346 YKFSTY----VQYWIRKSISKMVARHARGIKIPCKLNREISKIQKARKALTNSHGKYPED 401
            K ST     +   ++  +    A H     I       +      +   ++       D
Sbjct: 421 PKESTISIPSIYLELKVKLENEYALHR---SI-------VDHYNIPKTFDSDDLIPPYLD 470

Query: 402 IEIAKYTGLSLAEIRSA--SECLRIV----GSIDQKI 432
                + G  L  I         R+V      ++QKI
Sbjct: 471 QYFYSHIGHHLKNIEHPERMTLFRMVFLDFRFLEQKI 507

>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 = 44.1 bits (103), Expect = 8e-05
 Identities = 46/317 (14%), Positives = 95/317 (29%), Gaps = 65/317 (20%)

Query: 126 EREILQQLGKLGALKLFNSHLSRIVKTSNVLDLSDVHTEEQKMNDSRDYHMGKILVPSKR 185
             E+   L K   L      L R V T+N   LS +    +    + D          K 
Sbjct: 300 PDEVKSLLLK--YLDCRPQDLPREVLTTNPRRLSIIAESIRDGLATWDN--------WKH 349

Query: 186 KGKRKLKTARVSEESIETSLLSLPSEALQEGLKQPTIFSAERALNSRGRRLTIARNEAEM 245
               KL T       IE+SL  L     ++   + ++F     + +      ++    ++
Sbjct: 350 VNCDKLTTI------IESSLNVLEPAEYRKMFDRLSVFPPSAHIPTI----LLSLIWFDV 399

Query: 246 SKGVQVVANLERIKTTLEKESGKAASLNCWAQAAGVS----ERVLKQHLAFGWYCREELI 301
            K          +   L K S     +    + + +S       LK  L   +     ++
Sbjct: 400 IKSDV-----MVVVNKLHKYS----LVEKQPKESTISIPSIYLELKVKLENEYALHRSIV 450

Query: 302 KSTRPLVLFLARNYRGLGIPFSD----------LLQAGNVGVLQGAERFDHTRGYKFSTY 351
                   F   +   L  P+ D          L    +       ER    R      +
Sbjct: 451 DHYNIPKTF---DSDDLIPPYLDQYFYSHIGHHLKNIEH------PERMTLFR----MVF 497

Query: 352 VQY-WIRKSISKMVARHA-RGIKIPCKLNREISKIQKARKALTNSHGKYPEDI-EIAKYT 408
           + + ++ + I     RH          +   + +++  +  + ++  KY   +  I  + 
Sbjct: 498 LDFRFLEQKI-----RHDSTAWNASGSILNTLQQLKFYKPYICDNDPKYERLVNAILDFL 552

Query: 409 GLSLAEIRSASECLRIV 425
              + E    S+   ++
Sbjct: 553 -PKIEENLICSKYTDLL 568

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	442
3ugo_A	245	RNA polymerase sigma factor; protein-DNA complex,	100.0
1l9z_H	438	Sigma factor SIGA; helix-turn-helix, coiled-coil,	100.0
2a6h_F	423	RNA polymerase sigma factor RPOD; RNA polymerase h	100.0
3iyd_F	613	RNA polymerase sigma factor RPOD; transcription, i	99.92
1l0o_C	243	Sigma factor; bergerat fold, helix-turn-helix, pro	99.81
1rp3_A	239	RNA polymerase sigma factor sigma-28 (FLIA); trans	99.77
1or7_A	194	Sigma-24, RNA polymerase sigma-E factor; regulatio	99.73
1sig_A	339	Sigma70, RNA polymerase primary sigma factor; RNA	99.72
2q1z_A	184	RPOE, ECF SIGE; ECF sigma factor, cupin fold, zinc	99.7
3mzy_A	164	RNA polymerase sigma-H factor; PSI, MCSG, structur	99.48
2lfw_A	157	PHYR sigma-like domain; signal transduction, respo	99.44
3n0r_A	286	Response regulator; sigma factor, receiver, two-co	99.41
2o7g_A	112	Probable RNA polymerase sigma-C factor; sigma fact	99.28
1h3l_A	87	RNA polymerase sigma factor; transcription, DNA-bi	99.2
3clo_A	258	Transcriptional regulator; NP_811094.1, bacterial	97.66
1rp3_A	239	RNA polymerase sigma factor sigma-28 (FLIA); trans	92.81
3hug_A	92	RNA polymerase sigma factor; ECF sigma factor, zin	91.75
1l9z_H	438	Sigma factor SIGA; helix-turn-helix, coiled-coil,	91.73
3t72_q	99	RNA polymerase sigma factor RPOD, DNA-directed RN	90.82
1x3u_A	79	Transcriptional regulatory protein FIXJ; helix-tur	90.48
2p7v_B	68	Sigma-70, RNA polymerase sigma factor RPOD; RSD, r	90.28
1ku3_A	73	Sigma factor SIGA; helix-turn-helix, transcription	89.45
1tty_A	87	Sigma-A, RNA polymerase sigma factor RPOD; helix-t	89.29
2o8x_A	70	Probable RNA polymerase sigma-C factor; promoter r	88.7
1je8_A	82	Nitrate/nitrite response regulator protein NARL; p	88.0
1tc3_C	51	Protein (TC3 transposase); DNA binding, helix-turn	87.25
2jt1_A	77	PEFI protein; solution structure, winged helix-tur	86.88
3c57_A	95	Two component transcriptional regulatory protein;	86.3
2jpc_A	61	SSRB; DNA binding protein, structural genomics, PS	86.28
1xsv_A	113	Hypothetical UPF0122 protein SAV1236; helix-turn-h	84.15
2x48_A	55	CAG38821; archeal virus, viral protein; 2.60A {Sul	84.11
1fse_A	74	GERE; helix-turn-helix DNA-binding protein transcr	83.29
2rnj_A	91	Response regulator protein VRAR; HTH LUXR-type dom	81.39
3ulq_B	90	Transcriptional regulatory protein COMA; tetratric	80.89

>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=8.8e-38  Score=302.47  Aligned_cols=209  Identities=25%  Similarity=0.399  Sum_probs=128.3

Q ss_pred             ChhHHHHHHhcccCC-CCCChHHHHHHHHHhHHHHHHH-HHHHHH--HHH-----------------------hCCCCCh
Q 013472          220 PTIFSAERALNSRGR-RLTIARNEAEMSKGVQVVANLE-RIKTTL--EKE-----------------------SGKAASL  272 (442)
Q Consensus       220 ~~~~~~~~~~~~~~~-~lLt~eeE~eL~~~iq~~~~le-~~~~~L--~~~-----------------------~gr~pt~  272 (442)
                      .+.|.++-|++.+++ ||||++||++|+++|+.++.+. .+....  +..                       .+.+|+.
T Consensus         4 ~~~d~~~~yl~~i~~~~llt~~~e~~la~~i~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~~~~~g~~~~~~~~~   83 (245)
T 3ugo_A            4 MTSDPVRQYLHEIGQVPLLTLEEEIDLARKVEEGMEAIKKLSEATGLDQELIREVVRAKILGTARIQKIPGLKEKPDPKT   83 (245)
T ss_dssp             -CCHHHHHHHHHHTTSCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHTTGGGCSCCCCTTCCCCCCHHH
T ss_pred             CCCCcHHHHHHHcccccCCCHHHHHHHHHHHHHHHHHHHHHHhccCCcHHHHHHhhhhhhhccchhcccccccccccchh
Confidence            345778999999997 9999999999999999987633 332210  000                       1468889


Q ss_pred             HHHHHHcCCCH----HHHHHHHHhchHHHHHHHHHhHHHHHHHHHHhhCCCCCHHhHHHHHHHHHHHhHHhcCCCCCCCh
Q 013472          273 NCWAQAAGVSE----RVLKQHLAFGWYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKF  348 (442)
Q Consensus       273 ~ewA~a~g~de----eeL~~~l~~G~~Are~LI~~nlrLV~sIAkrY~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rF  348 (442)
                      .+||.+.+++.    ..|+..++.|..|+++||..|.++|+++|++|.+++.+++||+||||+|||+++++||+.+|++|
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            99999987753    45666677777899999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHHHhhcCceecccccHHHHHHHHHHHHHHHHHcCCCCcHHHHHHHhC--CCHHHHHHHHHhcccCC
Q 013472          349 STYVQYWIRKSISKMVARHARGIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTG--LSLAEIRSASECLRIVG  426 (442)
Q Consensus       349 STYa~~wIRnaI~r~LRkqsr~irlP~~v~e~i~kI~ka~~~L~~elgr~PS~eEIAe~LG--IS~etVk~~l~~ar~~~  426 (442)
                      +||++||||++|.++++++.+.+++|.++.+.+.++.++.+.|...+++.||++|||+.||  ||+++|++++..++.++
T Consensus       164 ~tya~~~ir~~i~~~ir~~~r~~r~p~~l~e~i~~l~~~~~~L~~~~~~~ps~~EIAe~Lg~~is~~tVk~~l~~ar~~l  243 (245)
T 3ugo_A          164 STYATWWIRQAINRAIADQARTIRIPVHMVETINKLSRTARQLQQELGREPSYEEIAEAMGPGWDAKRVEETLKIAQEPV  243 (245)
T ss_dssp             HHHHHHHHHHHHHHHHHHHTC-----------------------------------------------------------
T ss_pred             HHHHHHHHHHHHHHHHHHhcccccccHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHCCCCCHHHHHHHHHHHhhcc
Confidence            9999999999999999999999999999999999999999999999999999999999999  99999999999999988


Q ss_pred             CC
Q 013472          427 SI  428 (442)
Q Consensus       427 SL  428 (442)
                      ||
T Consensus       244 sl  245 (245)
T 3ugo_A          244 SL  245 (245)
T ss_dssp             --
T ss_pred             CC
Confidence            86

>1l9z_H Sigma factor SIGA; helix-turn-helix, coiled-coil, transcription/DNA complex; 6.50A {Thermus aquaticus} SCOP: i.8.1.1

Probab=100.00  E-value=3.6e-36  Score=312.95  Aligned_cols=215  Identities=26%  Similarity=0.404  Sum_probs=190.4

Q ss_pred             HHHHHHhcccCC-CCCChHHHHHHHHHhHHHHHHHHHHHH------------------HHHHhCCCCChHHHHH------
Q 013472          223 FSAERALNSRGR-RLTIARNEAEMSKGVQVVANLERIKTT------------------LEKESGKAASLNCWAQ------  277 (442)
Q Consensus       223 ~~~~~~~~~~~~-~lLt~eeE~eL~~~iq~~~~le~~~~~------------------L~~~~gr~pt~~ewA~------  277 (442)
                      +.++.|++.+++ ||||++||++|+++|+.+..++.....                  .....++.|+..+|+.      
T Consensus        94 d~~~~Yl~ei~~~pLLt~eEE~~La~~i~~g~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  173 (438)
T 1l9z_H           94 DPVRQYLHEIGQVPLLTLEEEIDLARKVEEGMEAIKKLSEATGLDQELIREVVRAKILGTARIQKIPGLKEKPDPKTVEE  173 (438)
T ss_pred             ChHHHHHHHhccCCCCCHHHHHHHHHHHHHhhhHHHHHHhhhccchhhhhhhhhhhhhhcccccccccccccccchhhhh
Confidence            445678888886 999999999999999998665443221                  1223567888888743      


Q ss_pred             ------HcCCCHHHHHHHHHhchHHHHHHHHHhHHHHHHHHHHhhCCCCCHHhHHHHHHHHHHHhHHhcCCCCCCChHHH
Q 013472          278 ------AAGVSERVLKQHLAFGWYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTY  351 (442)
Q Consensus       278 ------a~g~deeeL~~~l~~G~~Are~LI~~nlrLV~sIAkrY~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTY  351 (442)
                            +.+++..+|+..++.|..|+++||.+|+++|+++|++|.++|.+++|||||||||||+|+++|||.+|++|+||
T Consensus       174 ~~~~~~~~~~~~~eLi~~~~~d~~A~~~Li~~nlrlVv~iA~ry~~~g~~aeDLIQEg~IgL~kAvekFDp~kG~rFsTY  253 (438)
T 1l9z_H          174 VDGKLKSLPKELKRYLHIAREGEAARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQEGNQGLIRAVEKFEYKRRFKFSTY  253 (438)
T ss_pred             hhhhhhcccchHHHHHHHHhcCHHHHHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHhcCcccCCChHHH
Confidence                  23556688888888888899999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHhhcCceecccccHHHHHHHHHHHHHHHHHcCCCCcHHHHHHHhC--CCHHHHHHHHHhcccCCCCc
Q 013472          352 VQYWIRKSISKMVARHARGIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTG--LSLAEIRSASECLRIVGSID  429 (442)
Q Consensus       352 a~~wIRnaI~r~LRkqsr~irlP~~v~e~i~kI~ka~~~L~~elgr~PS~eEIAe~LG--IS~etVk~~l~~ar~~~SLD  429 (442)
                      ++|||+|.|.++|+++.+.+++|.++.+.+++++++.+.+.+.+|+.|+.+|||+.+|  +++++|..++..+..++|||
T Consensus       254 A~~wIR~~I~~~i~~~~R~irlp~~~~~~l~~lrr~~r~l~~~lgr~pt~eeiA~~l~~~v~~e~V~~~~~~~~~~~SLd  333 (438)
T 1l9z_H          254 ATWWIRQAINRAIADQARTIRIPVHMVETINKLSRTARQLQQELGREPSYEEIAEAMGPGWDAKRVEETLKIAQEPVSLE  333 (438)
T ss_pred             HHHHHHHHHHHHHHHhcchhccchHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCCCHHHHHHHHHhcccccccc
Confidence            9999999999999999999999999999999999999999999999999999999999  99999999999888999999


Q ss_pred             cccCCCCC
Q 013472          430 QKIGDCLN  437 (442)
Q Consensus       430 ~~v~~~~d  437 (442)
                      .+++++++
T Consensus       334 ~~~~~d~d  341 (438)
T 1l9z_H          334 TPIGDEKD  341 (438)
T ss_pred             cccccccc
Confidence            99876654

>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=4.1e-36  Score=311.25  Aligned_cols=217  Identities=26%  Similarity=0.416  Sum_probs=189.4

Q ss_pred             hHHHHHHhcccCC-CCCChHHHHHHHHHhHHHHHHHHHHHHH------------------HHHhCCCCChHHHH------
Q 013472          222 IFSAERALNSRGR-RLTIARNEAEMSKGVQVVANLERIKTTL------------------EKESGKAASLNCWA------  276 (442)
Q Consensus       222 ~~~~~~~~~~~~~-~lLt~eeE~eL~~~iq~~~~le~~~~~L------------------~~~~gr~pt~~ewA------  276 (442)
                      .+.++.|++.+++ ||||++||++|+++|+.+..+.......                  ....++.|+..+|+      
T Consensus        78 ~d~~~~Yl~ei~~~plLt~eEE~~La~ri~~g~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  157 (423)
T 2a6h_F           78 SDPVRQYLHEIGQVPLLTLEEEVELARKVEEGMEAIKKLSEITGLDPDLIREVVRAKILGSARVRHIPGLKETLDPKTVE  157 (423)
T ss_dssp             HHHHHHHHHHHHHCCCCTTHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHCCHHHHHTTSCSSSCTTHHHH
T ss_pred             CcHHHHHHHHhcccCCCCHHHHHHHHHHHHhchhHHHHHHHhhccchhhhhhhHhhhhhhhhhcccccchhhhhhhhhhh
Confidence            4567778888875 9999999999999999986544322211                  11234566655432      


Q ss_pred             ---H---HcCCCHHHHHHHHHhchHHHHHHHHHhHHHHHHHHHHhhCCCCCHHhHHHHHHHHHHHhHHhcCCCCCCChHH
Q 013472          277 ---Q---AAGVSERVLKQHLAFGWYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFST  350 (442)
Q Consensus       277 ---~---a~g~deeeL~~~l~~G~~Are~LI~~nlrLV~sIAkrY~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFST  350 (442)
                         .   +.++++.+|+..++.|..|+++||.+|+++|+++|++|.++|.+++|||||||||||+|+++|||.+|++|+|
T Consensus       158 ~~~~~~~~~~~~~~~L~~~~~~d~~A~~~Li~~~lrlV~~iA~~y~~~~~~~eDLiQEg~igL~kav~kFd~~~g~~Fst  237 (423)
T 2a6h_F          158 EIDQKLKSLPKEHKRYLHIAREGEAARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQEGNQGLIRAVEKFEYKRRFKFST  237 (423)
T ss_dssp             HHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHHHTHHHHHHHHTTTCTTTSCHHHHHHHHHHHHHHHHHHCCTTSCCCHHH
T ss_pred             hhhhhhhcccccHHHHHHHHhcCHHHHHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHhcCcccCCCHHH
Confidence               2   3466778899999988889999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHhhcCceecccccHHHHHHHHHHHHHHHHHcCCCCcHHHHHHHhC--CCHHHHHHHHHhcccCCCC
Q 013472          351 YVQYWIRKSISKMVARHARGIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTG--LSLAEIRSASECLRIVGSI  428 (442)
Q Consensus       351 Ya~~wIRnaI~r~LRkqsr~irlP~~v~e~i~kI~ka~~~L~~elgr~PS~eEIAe~LG--IS~etVk~~l~~ar~~~SL  428 (442)
                      |++|||++.|.++|+++.+.+++|.|+.+.+++++++.+.+.+.+|+.|+.+|||+.+|  +++++|..++..+..++||
T Consensus       238 Ya~~wIr~~i~~~i~~~~r~ir~p~~~~~~~~~lrr~~~~l~~~~~r~p~~~eiA~~l~~~~~~~~v~~~~~~~~~~~Sl  317 (423)
T 2a6h_F          238 YATWWIRQAINRAIADQARTIRIPVHMVETINKLSRTARQLQQELGREPTYEEIAEAMGPGWDAKRVEETLKIAQEPVSL  317 (423)
T ss_dssp             HHHHHHHHHHHHHHHHHSSSSCCCHHHHHHHHHHHHHHHHHHHHHSSCCCHHHHHHHHCTTCCHHHHHHHHHHHSCCEES
T ss_pred             HHHHHHHHHHHHHHHHccceeeccHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCCCHHHHHHHHHhccCCccc
Confidence            99999999999999999999999999999999999999999999999999999999999  9999999999999999999


Q ss_pred             ccccCCCCCc
Q 013472          429 DQKIGDCLNA  438 (442)
Q Consensus       429 D~~v~~~~d~  438 (442)
                      |.|++++++.
T Consensus       318 d~~~~~~~~~  327 (423)
T 2a6h_F          318 ETPIGDEKDS  327 (423)
T ss_dssp             SCBCSSSSSC
T ss_pred             ccccCCCCcc
Confidence            9999876543

>3iyd_F RNA polymerase sigma factor RPOD; transcription, initiation, class I, activator, RNA polymeras holoenzyme, sigma70, open complex, CAP, CRP; HET: DNA CMP; 19.80A {Escherichia coli k-12}

Probab=99.92  E-value=3.1e-27  Score=254.66  Aligned_cols=176  Identities=27%  Similarity=0.533  Sum_probs=158.3

Q ss_pred             HHHHHHHHHHHHHhCCCCChHHHHHHcCCCHHHHHHHHHhchH-H---HHHHHHHhHHHHHHHHHHhhCCCCCHHhHHHH
Q 013472          253 ANLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQHLAFGWY-C---REELIKSTRPLVLFLARNYRGLGIPFSDLLQA  328 (442)
Q Consensus       253 ~~le~~~~~L~~~~gr~pt~~ewA~a~g~deeeL~~~l~~G~~-A---re~LI~~nlrLV~sIAkrY~g~g~d~EDLIQE  328 (442)
                      ..+++....++...|-.+          .+..+|+.+++.|+. |   |+.||..|.++|+++|++|++++.+++||+||
T Consensus       338 ~~~q~kL~~ie~~~~~~~----------~~~~~Li~~~~~Gd~~A~~A~~~L~~~y~~~v~~ia~r~~~~~~~aeDlvQE  407 (613)
T 3iyd_F          338 HRALQKLQQIEEETGLTI----------EQVKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQE  407 (613)
T ss_dssp             HHHHHHHHHHHHHHTSCT----------TTHHHHHHTHHHHHHHHHHHHTTTTTTTTHHHHHGGGSSSTTSSCSTTTTHH
T ss_pred             HHHHHHHHHHHHHhCCCh----------HHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHhcCCCCHHHHHHH
Confidence            344444445555555432          235678899999976 6   99999999999999999999999999999999


Q ss_pred             HHHHHHHhHHhcCCCCCCChHHHHHHHHHHHHHHHHHhhcCceecccccHHHHHHHHHHHHHHHHHcCCCCcHHHHHHHh
Q 013472          329 GNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYT  408 (442)
Q Consensus       329 G~IGLirAieKFDp~kG~rFSTYa~~wIRnaI~r~LRkqsr~irlP~~v~e~i~kI~ka~~~L~~elgr~PS~eEIAe~L  408 (442)
                      ||||||+++++||+.+|++|+||++|||+|+|+++++++.+.+++|.++.+.+++++++...+.+++|+.||.+|||+.|
T Consensus       408 ~fi~l~~a~~~fd~~~g~~Fstyl~~~irn~i~~~lr~~~r~~rip~~~~~~~~k~~r~~~~l~~~~gr~pt~eela~~l  487 (613)
T 3iyd_F          408 GNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELAERM  487 (613)
T ss_dssp             HHHHHHHHTTSCCTTSSSCSTTTHHHHHHHHHHHHTTTSCSSSCCCSHHHHTTTTTTTTTTTTTTTTCSCCCTTTTTTTS
T ss_pred             HHHHHHHHHHHcCccccCcHHHHHHHHHHHHHHHHHHhcCcceeCcHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHh
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCHHHHHHHHHhcccCCCCccccCCCCCc
Q 013472          409 GLSLAEIRSASECLRIVGSIDQKIGDCLNA  438 (442)
Q Consensus       409 GIS~etVk~~l~~ar~~~SLD~~v~~~~d~  438 (442)
                      ||++++|+.++..++.++|||.+++++.+.
T Consensus       488 ~~~~~~v~~~~~~~~~~~sld~~~~~~~~~  517 (613)
T 3iyd_F          488 LMPEDKIRKVLKIAKEPISMETPIGDDEDS  517 (613)
T ss_dssp             SCCSSHHHHHHHHSCCCCCSSCCCSSSSSC
T ss_pred             CCCHHHHHHHHHhccCCcccCCCCCCCCCc
Confidence            999999999999999999999999876654

>1l0o_C Sigma factor; bergerat fold, helix-turn-helix, protein binding; HET: ADP; 2.90A {Geobacillus stearothermophilus} SCOP: a.4.13.2

Probab=99.81  E-value=8.2e-21  Score=175.82  Aligned_cols=152  Identities=28%  Similarity=0.413  Sum_probs=52.8

Q ss_pred             CHHHHHHHHHhchH-HHHHHHHHhHHHHHHHHHHhhCCCCCHHhHHHHHHHHHHHhHHhcCCCCCCChHHHHHHHHHHHH
Q 013472          282 SERVLKQHLAFGWY-CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSI  360 (442)
Q Consensus       282 deeeL~~~l~~G~~-Are~LI~~nlrLV~sIAkrY~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIRnaI  360 (442)
                      ++.+|+..++.|+. |++.|+..|.++|+.+|++|.++..+++||+|||++++|+++++||+.+|.+|.||+++|++|.+
T Consensus        14 ~~~~l~~~~~~gd~~a~~~l~~~~~~~v~~~~~~~~~~~~~aeDl~Qe~~l~l~~~~~~~~~~~~~~f~~~l~~i~~~~~   93 (243)
T 1l0o_C           14 EMKELIRRSQEGDQEARDEIIEKNMRLVWSVVQRFLNRGYEADDLFQIGCIGLLKSVDKFDLSYDVKFSTYAVPMIIGEI   93 (243)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHhHHHHHHHHHHHhccCCCHHHHHHHHHHHHHHHHHHcCcccCCCHHHHHHHHHHHHH
Confidence            45678889999976 99999999999999999999999999999999999999999999999988899999999999999


Q ss_pred             HHHHHhhcCceecccccHHHHHHHHHHHHHHHHHcCCCCcHHHHHHHhCCCHHHHHHHHHhcccCCCCccccCC
Q 013472          361 SKMVARHARGIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGD  434 (442)
Q Consensus       361 ~r~LRkqsr~irlP~~v~e~i~kI~ka~~~L~~elgr~PS~eEIAe~LGIS~etVk~~l~~ar~~~SLD~~v~~  434 (442)
                      .++++++. .+++|.++.....+++++...+....++.|+.++|++.+|++.+.+...+.....+.|+|.|+.+
T Consensus        94 ~d~~r~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~  166 (243)
T 1l0o_C           94 QRFLRDDG-TVKVSRSLKEMGNKIRKAKDELSKTRGRAPTVTEIADHLGISPEDVVLAQEAVRLPTSIHETVYE  166 (243)
T ss_dssp             ------CC-CCTTHHHHHHHHHHHHHHHHHHHHHHTSCCBHHHHHHHHTSCHHHHHHHHHHHHC----------
T ss_pred             HHHHHhcC-CccCcHHHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHHCCCHHHHHHHHHHhccccCccccccc
Confidence            99999886 78899999999999999999999999999999999999999999999888777778888887543

>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=99.77  E-value=4.7e-18  Score=157.52  Aligned_cols=135  Identities=21%  Similarity=0.329  Sum_probs=120.4

Q ss_pred             HHHHHHHHHhHHHHHHHHHHhh---CCCCCHHhHHHHHHHHHHHhHHhcCCCCCCChHHHHHHHHHHHHHHHHHhhcCce
Q 013472          295 YCREELIKSTRPLVLFLARNYR---GLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGI  371 (442)
Q Consensus       295 ~Are~LI~~nlrLV~sIAkrY~---g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIRnaI~r~LRkqsr~i  371 (442)
                      .|+++|+..|.++|+.+|++|.   +++.+++||+|||+++||+++++||+.+|.+|.||+++||+|.|+++++++.   
T Consensus        12 ~a~~~l~~~~~~~v~~~a~~~~~~~~~~~~aeDl~Qe~~l~l~~~~~~~~~~~~~~f~~~l~~~~~~~~~d~~r~~~---   88 (239)
T 1rp3_A           12 IEREELILKYLPLVKAIATNIKKHLPEDVDIRDLISYGVIGLIKAVDNLSTENPKRAEAYIKLRIKGAIYDYLRSLD---   88 (239)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHTTSCTTSCHHHHHHHHHHHHHHHHHTCCCCCTHHHHHHHHHHHHHHHHHHHHTSS---
T ss_pred             hHHHHHHHHhHHHHHHHHHHHHHhccCCCCHHHHHHHHHHHHHHHHHHcCcccCCCHHHHHHHHHHHHHHHHHHhcC---
Confidence            4899999999999999999998   6789999999999999999999999998889999999999999999999874   


Q ss_pred             ecccccHHHHHHHHHHHHHHHHHcCCCCcHHHHHHHhCCCHHHHHHHHHhcc--cCCCCcccc
Q 013472          372 KIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLR--IVGSIDQKI  432 (442)
Q Consensus       372 rlP~~v~e~i~kI~ka~~~L~~elgr~PS~eEIAe~LGIS~etVk~~l~~ar--~~~SLD~~v  432 (442)
                      +.|........++.++...+....++.|+.+|||+.+|++++++..++....  .++|+|.++
T Consensus        89 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~sl~~~~  151 (239)
T 1rp3_A           89 FGSRQVREKERRIKEVVEKLKEKLGREPTDEEVAKELGISTEELFKTLDKINFSYILSLEEVF  151 (239)
T ss_dssp             TTCHHHHHHHHHHHHHHHHHHHHHSSCCCHHHHHHHHTSCHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             ccchHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHHhccCCCccccccc
Confidence            4677777888899999999999999999999999999999999988765442  334666543

>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=99.73  E-value=2.1e-17  Score=149.30  Aligned_cols=140  Identities=15%  Similarity=0.100  Sum_probs=114.7

Q ss_pred             CHHHHHHHHHhchH-HHHHHHHHhHHHHHHHHHHhhCCCCCHHhHHHHHHHHHHHhHHhcCCCCCCChHHHHHHHHHHHH
Q 013472          282 SERVLKQHLAFGWY-CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSI  360 (442)
Q Consensus       282 deeeL~~~l~~G~~-Are~LI~~nlrLV~sIAkrY~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIRnaI  360 (442)
                      ++.+|+..++.|+. |++.|+..|.+.|+.+|++|.+ ..+++|++||+|+++|+++++|++..  .|.||++.+++|.+
T Consensus         9 ~~~~l~~~~~~gd~~a~~~l~~~~~~~l~~~~~~~~~-~~~aeDl~Qe~~l~~~~~~~~~~~~~--~~~~~l~~i~~n~~   85 (194)
T 1or7_A            9 TDQVLVERVQKGDQKAFNLLVVRYQHKVASLVSRYVP-SGDVPDVVQEAFIKAYRALDSFRGDS--AFYTWLYRIAVNTA   85 (194)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHHTTTSC-GGGHHHHHHHHHHHHHHHGGGCCSSS--CHHHHHHHHHHHHH
T ss_pred             ChHHHHHHHHccCHHHHHHHHHHHHHHHHHHHHHHcC-HHhHHHHHHHHHHHHHHhHHhcCCcc--chHHHHHHHHHHHH
Confidence            35778999999976 9999999999999999999999 99999999999999999999999864  59999999999999


Q ss_pred             HHHHHhhcCceec----------------------ccc---cHHHHHHHHHHHHHHHHHc--------CCCCcHHHHHHH
Q 013472          361 SKMVARHARGIKI----------------------PCK---LNREISKIQKARKALTNSH--------GKYPEDIEIAKY  407 (442)
Q Consensus       361 ~r~LRkqsr~irl----------------------P~~---v~e~i~kI~ka~~~L~~el--------gr~PS~eEIAe~  407 (442)
                      ++++|++.+....                      |..   ..+....+..+...|+...        ..+.|++|||+.
T Consensus        86 ~d~~R~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~l~~~l~~L~~~~r~vl~l~~~~g~s~~EIA~~  165 (194)
T 1or7_A           86 KNYLVAQGRRPPSSDVDAIEAENFESGGALKEISNPENLMLSEELRQIVFRTIESLPEDLRMAITLRELDGLSYEEIAAI  165 (194)
T ss_dssp             HHHHHHHTTCCTHHHHHHHHHHSCCSSCC--------CEEEHHHHHHHHHHHHHHSCHHHHHHHHHHHTTCCCHHHHHHH
T ss_pred             HHHHHHHhccCccccccccccccccccccccCCCChHHHHHHHHHHHHHHHHHHhCCHHHHHHhHHHHHcCCCHHHHHHH
Confidence            9999987653211                      111   0123344556666554432        478899999999


Q ss_pred             hCCCHHHHHHHHHhccc
Q 013472          408 TGLSLAEIRSASECLRI  424 (442)
Q Consensus       408 LGIS~etVk~~l~~ar~  424 (442)
                      ||||+.+|+..+++++.
T Consensus       166 lgis~~tV~~~l~ra~~  182 (194)
T 1or7_A          166 MDCPVGTVRSRIFRARE  182 (194)
T ss_dssp             TTSCHHHHHHHHHHHHH
T ss_pred             HCCCHHHHHHHHHHHHH
Confidence            99999999999988764

>1sig_A Sigma70, RNA polymerase primary sigma factor; RNA polymerase sigma factor, transcription regulation; 2.60A {Escherichia coli} SCOP: a.177.1.1

Probab=99.72  E-value=1.7e-17  Score=166.24  Aligned_cols=86  Identities=34%  Similarity=0.773  Sum_probs=80.4

Q ss_pred             HHHHHHHHHhch----HHHHHHHHHhHHHHHHHHHHhhCCCCCHHhHHHHHHHHHHHhHHhcCCCCCCChHHHHHHHHHH
Q 013472          283 ERVLKQHLAFGW----YCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRK  358 (442)
Q Consensus       283 eeeL~~~l~~G~----~Are~LI~~nlrLV~sIAkrY~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIRn  358 (442)
                      ...|+.+++.|+    .|++.||..|.++|+++|++|++++.+++||+||||||||+++++|++.+|++|+||++|||+|
T Consensus       249 ~~~l~~~~~~gd~~~~~A~~~L~~~~~~~v~~~a~~~~~~~~~aeDlvQe~~i~l~~a~~~f~~~~g~~f~twl~~iirn  328 (339)
T 1sig_A          249 VKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQ  328 (339)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHTHHHHHHHHTTSTTSSSCHHHHHHHHHHHHHHHHHHCCGGGCCCHHHHHHHHHHH
T ss_pred             HHHHHHHHHhccccchhhhHHHHHHHHHHHHHHHHHHhcCCCCHhHHHHHHHHHHHHHHHHhCCccCCCHHHHHHHHHHH
Confidence            356788888995    5999999999999999999999999999999999999999999999999889999999999999


Q ss_pred             HHHHHHHhhc
Q 013472          359 SISKMVARHA  368 (442)
Q Consensus       359 aI~r~LRkqs  368 (442)
                      .|++++|++.
T Consensus       329 ~~~~~lr~~~  338 (339)
T 1sig_A          329 AITRSIADQA  338 (339)
T ss_dssp             HHHHHHHHC-
T ss_pred             HHHHHHHHhc
Confidence            9999999874

>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=99.48  E-value=1.1e-13  Score=120.68  Aligned_cols=105  Identities=22%  Similarity=0.302  Sum_probs=76.8

Q ss_pred             CCCHHhHHHHHHHHHHHhHHhcCCCCCCChHHHHHHHHHHHHHHHHHhhcCceecc------------------------
Q 013472          319 GIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIP------------------------  374 (442)
Q Consensus       319 g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIRnaI~r~LRkqsr~irlP------------------------  374 (442)
                      |.+++|++|||++++|+++++||+.+ .+|.||++++++|.+++++|++.+..+.+                        
T Consensus         1 g~daeDl~Qe~~~~l~~~~~~~~~~~-~~f~~~l~~i~~n~~~d~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   79 (164)
T 3mzy_A            1 GAEKEDLVQEGILGLLKAIKFYDETK-SSFSSFAFLCIRREMISAIRKANTQKHMVLNEALKTNAILEDSAYFDDEGHNI   79 (164)
T ss_dssp             ----CTTHHHHHHHHHHHHHHCCTTT-SCHHHHHHHHHHHHHHHHHHHHHHCC---------------------------
T ss_pred             CCcHHHHHHHHHHHHHHHHHHhCccC-CChHHHhHHHHHHHHHHHHHHhhcccchhhHHHhhhhhhhccCCCCCcccchh
Confidence            57899999999999999999999987 68999999999999999999875432211                        


Q ss_pred             ----------cc---cHHHHHHHHHHHH-HHHH-------HcCCCCcHHHHHHHhCCCHHHHHHHHHhccc
Q 013472          375 ----------CK---LNREISKIQKARK-ALTN-------SHGKYPEDIEIAKYTGLSLAEIRSASECLRI  424 (442)
Q Consensus       375 ----------~~---v~e~i~kI~ka~~-~L~~-------elgr~PS~eEIAe~LGIS~etVk~~l~~ar~  424 (442)
                                ..   ..+....+..++. .|+.       .+-.+.|++|||+.||||+.+|+..+++++.
T Consensus        80 ~~~~~~~~~~~~~~~~~e~~~~l~~~l~~~L~~~~r~v~~~~~~g~s~~EIA~~lgis~~tV~~~~~ra~~  150 (164)
T 3mzy_A           80 NNYKSSESNPEEAYLLKEEIEEFKKFSENNFSKFEKEVLTYLIRGYSYREIATILSKNLKSIDNTIQRIRK  150 (164)
T ss_dssp             ----------CHHHHHHHHHHHHHHHHHHHSCHHHHHHHHHHTTTCCHHHHHHHHTCCHHHHHHHHHHHHH
T ss_pred             hhhcccCCCHHHHHHHHHHHHHHHHHHHhhCCHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence                      00   1122233444444 3332       3357889999999999999999999888764

>2lfw_A PHYR sigma-like domain; signal transduction, response regulator, sigma factor mimicr sigma factor, general stress response, signaling protein; NMR {Sphingomonas SP}

Probab=99.44  E-value=1.1e-15  Score=136.41  Aligned_cols=125  Identities=7%  Similarity=-0.032  Sum_probs=96.4

Q ss_pred             HHHHHHHhHHHHHHHHHHhhCCCCCHHhHHHHHHHHHHHhHHhcCCCCCCChHHHHHHHHHHHHHHHHHhhcCceecccc
Q 013472          297 REELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIPCK  376 (442)
Q Consensus       297 re~LI~~nlrLV~sIAkrY~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIRnaI~r~LRkqsr~irlP~~  376 (442)
                      |+.|+..|.+.|+.+|++++++..+++|++||+|+++|+++++|++..  .|.+|++.+++|.+++++|+......-| .
T Consensus         3 f~~l~~~~~~~l~~~~~~~~~~~~~AeDlvQe~fl~~~~~~~~~~~~~--~~~~wl~~ia~n~~~d~~R~~~~~~~~~-e   79 (157)
T 2lfw_A            3 LGQQLAPHLPFLRRYGRALTGSQNQGDKYVRATLEAIVAAPDQFPRDV--DPRLGLYRMFQGIWASANADGEAQTSQS-D   79 (157)
T ss_dssp             GGGGTGGGGGGGTTTGGGTTSCHHHHHHHHHHHHHTTTTCGGGCCCSS--CTTHHHHHHHHHHHHHHTTTTSCCCCCC-S
T ss_pred             HHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhHHHcCCCC--cHHHHHHHHHHHHHHHHhhccCcccCCc-c
Confidence            678899999999999999999999999999999999999999999753  6999999999999999998763211111 1


Q ss_pred             cHHHHHHHHHHHHHHHH--------HcCCCCcHHHHHHHhCCCHHHHHHHHHhccc
Q 013472          377 LNREISKIQKARKALTN--------SHGKYPEDIEIAKYTGLSLAEIRSASECLRI  424 (442)
Q Consensus       377 v~e~i~kI~ka~~~L~~--------elgr~PS~eEIAe~LGIS~etVk~~l~~ar~  424 (442)
                      ..+....+..+...|+.        .+-.+.|++|||+.||||+++|+..+.+++.
T Consensus        80 ~~~~~~~l~~~l~~Lp~~~r~vl~L~~~~g~s~~EIA~~lgis~~tV~~~l~rar~  135 (157)
T 2lfw_A           80 AEGTEAVARARLARMTPLSRQALLLTAMEGFSPEDAAYLIEVDTSEVETLVTEALA  135 (157)
T ss_dssp             CSSSSSTTTTTTTTSCTTHHHHHTTTSSSCCCHHHHHHTTTSCHHHHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence            11111122222222222        1246789999999999999999999988873

>3n0r_A Response regulator; sigma factor, receiver, two-component SI transduction, signaling protein; HET: MSE GOL; 1.25A {Caulobacter vibrioides} PDB: 3t0y_A

Probab=99.41  E-value=8.5e-14  Score=136.08  Aligned_cols=127  Identities=9%  Similarity=-0.066  Sum_probs=99.0

Q ss_pred             hchH-HHHHHHHHhHHHHHHHHHHhhCCCCCHHhHHHHHHHHHHHhHHhcCCCCCCChHHHHHHHHHHHHHHHHHhhcCc
Q 013472          292 FGWY-CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARG  370 (442)
Q Consensus       292 ~G~~-Are~LI~~nlrLV~sIAkrY~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIRnaI~r~LRkqsr~  370 (442)
                      .|+. +|++|+..|.+.++.+|++|+++..+++|++||.|+.+|+..++|++.  ..|.||++++++|.+++++|+....
T Consensus        17 ~g~~~~f~~l~~~~~~~l~~~a~~~~~~~~~AeD~vQe~fl~~~~~~~~~~~~--~~~~~wL~~ia~n~~~d~~r~~~~~   94 (286)
T 3n0r_A           17 RGSEMHLLARLAPHLPYIRRYARALTGDQATGDHYVRVALEALAAGELVLDAN--LSPRVALYRVFHAIWLSSGAQLEVG   94 (286)
T ss_dssp             ---CCCHHHHHGGGHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHTTSSCCCSS--SCHHHHHHHHHHHHHSCTTC----C
T ss_pred             CCCcCCHHHHHHHHHHHHHHHHHHHhCCHhhHHHHHHHHHHHHHhCchhcCCC--cChHHHHHHHHHHHHHhhccccccC
Confidence            3444 899999999999999999999999999999999999999999999974  3699999999999999999864321


Q ss_pred             eecccccHHHHHHHHHHHHHHHHHc--------CCCCcHHHHHHHhCCCHHHHHHHHHhcc
Q 013472          371 IKIPCKLNREISKIQKARKALTNSH--------GKYPEDIEIAKYTGLSLAEIRSASECLR  423 (442)
Q Consensus       371 irlP~~v~e~i~kI~ka~~~L~~el--------gr~PS~eEIAe~LGIS~etVk~~l~~ar  423 (442)
                      ....   .+....+.+++.+|+...        -.+.|++|||+.+|+++++|+..+..++
T Consensus        95 ~~~~---~~~~~~l~~al~~Lp~~~R~v~~L~~~eg~s~~EIA~~lgis~~tVks~l~rA~  152 (286)
T 3n0r_A           95 HDQG---LHAGDDAAQRLMRIAPRSRQAFLLTALEGFTPTEAAQILDCDFGEVERLIGDAQ  152 (286)
T ss_dssp             CCCC---CCTTSHHHHHHHHHSCHHHHHHHHHHTTCCCHHHHHHHHTCCHHHHHHHHHHHH
T ss_pred             CCcc---cchHHHHHHHHHhCCHHHeeEEEEEeeCCCCHHHHHHHhCcCHHHHHHHHHHHH
Confidence            1111   111233555555554433        4778999999999999999999887765

>2o7g_A Probable RNA polymerase sigma-C factor; sigma factor, transcription regulation, -10 element recognit domain, transcription; 2.70A {Mycobacterium tuberculosis}

Probab=99.28  E-value=7.5e-12  Score=104.87  Aligned_cols=85  Identities=18%  Similarity=0.086  Sum_probs=73.0

Q ss_pred             HHHHHHHhchH-HHHHHHHHhHHHHHHHHHHhhCCCCCHHhHHHHHHHHHHHhHHhcCCCCCCChHHHHHHHHHHHHHHH
Q 013472          285 VLKQHLAFGWY-CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKM  363 (442)
Q Consensus       285 eL~~~l~~G~~-Are~LI~~nlrLV~sIAkrY~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIRnaI~r~  363 (442)
                      +|+..++.|+. |++.|+..|.+.|+.+|.++ ++..+++|++||+|+.+|+.+.+|++.  ..|.+|++.+++|.++++
T Consensus        13 ~l~~~~~~gd~~a~~~l~~~~~~~l~~~~~~~-~~~~~aeD~vQe~fl~~~~~~~~~~~~--~~~~~wl~~i~~n~~~d~   89 (112)
T 2o7g_A           13 ALALSAAKGNGRALEAFIKATQQDVWRFVAYL-SDVGSADDLTQETFLRAIGAIPRFSAR--SSARTWLLAIARHVVADH   89 (112)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHHHHHHHHHHH-SCHHHHHHHHHHHHHHHHHHGGGCCCS--SCHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHh-CCHHHHHHHHHHHHHHHHHHHHhcCCC--CCHHHHHHHHHHHHHHHH
Confidence            67888889966 99999999999999999999 988999999999999999999999974  369999999999999999


Q ss_pred             HHhhcCcee
Q 013472          364 VARHARGIK  372 (442)
Q Consensus       364 LRkqsr~ir  372 (442)
                      +|++.+...
T Consensus        90 ~R~~~~~~~   98 (112)
T 2o7g_A           90 IRHVRSRPR   98 (112)
T ss_dssp             TC-------
T ss_pred             HHHhhcccc
Confidence            998765433

>1h3l_A RNA polymerase sigma factor; transcription, DNA-binding, transcription regulation; 2.37A {Streptomyces coelicolor A3} SCOP: a.177.1.1

Probab=99.20  E-value=1.5e-11  Score=98.53  Aligned_cols=77  Identities=8%  Similarity=-0.048  Sum_probs=68.4

Q ss_pred             HHhchH-HHHHHHHHhHHHHHHHHHHhhCCCCCHHhHHHHHHHHHHHhHHhcCCCCCCChHHHHHHHHHHHHHHHHHhhc
Q 013472          290 LAFGWY-CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHA  368 (442)
Q Consensus       290 l~~G~~-Are~LI~~nlrLV~sIAkrY~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIRnaI~r~LRkqs  368 (442)
                      +..|+. |++.|+..|.+.|+.+|.++.++..++||++||+|+.+|+.+++|++.  ..|.+|++.+++|.+++++|++.
T Consensus         6 ~~~g~~~af~~l~~~~~~~l~~~~~~~~~~~~~aeD~vQe~fl~~~~~~~~~~~~--~~~~~wl~~i~~n~~~d~~R~~~   83 (87)
T 1h3l_A            6 STAERSARFERDALEFLDQMYSAALRMTRNPADAEDLVQETYAKAYASFHQFREG--TNLKAWLYRILTNTFINSYRKKQ   83 (87)
T ss_dssp             CHHHHHHHHHHHHHHTHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHGGGCCSS--SCHHHHHHHHHHHHHHHTCC---
T ss_pred             cCcccHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHhcCCC--ccHHHHHHHHHHHHHHHHHHHhc
Confidence            345654 999999999999999999999999999999999999999999999975  47999999999999999998764

>3clo_A Transcriptional regulator; NP_811094.1, bacterial regulatory proteins, LUXR family, structural genomics; 2.04A {Bacteroides thetaiotaomicron vpi-5482}

Probab=97.66  E-value=1.1e-08  Score=98.17  Aligned_cols=138  Identities=7%  Similarity=-0.085  Sum_probs=100.0

Q ss_pred             HHHHHHHhchH-HHHHHHHHhHHHHHHHHHHhhCCCCCHHhHH----HHHHHHHHHhHHhcCCCCCCChHHHHHHHHHHH
Q 013472          285 VLKQHLAFGWY-CREELIKSTRPLVLFLARNYRGLGIPFSDLL----QAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKS  359 (442)
Q Consensus       285 eL~~~l~~G~~-Are~LI~~nlrLV~sIAkrY~g~g~d~EDLI----QEG~IGLirAieKFDp~kG~rFSTYa~~wIRna  359 (442)
                      .|..++..++. +.+.+...|.++|+.+............|+.    ||.++.+|+.+..|++..  .|.+|++.+++|.
T Consensus        86 ~ll~~i~p~D~~~~~~~~~~~~~fi~~l~~~~~~~~~~~~dl~~~~~qe~fl~~~~~~~~~~~~~--~~~~WL~~ia~n~  163 (258)
T 3clo_A           86 CIYRRIHPEDLVEKRLMEYKFFQKTFSMSPGERLKYRGRCRLRMMNEKGVYQYIDNLVQIMQNTP--AGNVWLIFCLYSL  163 (258)
T ss_dssp             HHHTTBCHHHHHHHHHHHHHHHHHHTTSCHHHHTTEEEEEEEEEECTTSCEEEEEEEEEEEEECT--TSCEEEEEEEEEE
T ss_pred             HHHHhCChHHHHHHHHHHHHHHHHHHhcCHHhccCCeeeEEeecCCcCHHHHHHHHhHHhcCCCC--chHHHHHHHHHHH
Confidence            46667766655 8999999999999999998877888888996    999999999999998643  6999999999998


Q ss_pred             HHHHHHhhcCceec----------ccccHHHHHHHHHHHHHHHHHcCCCCcHHHHHHHhCCCHHHHHHHHHhccc
Q 013472          360 ISKMVARHARGIKI----------PCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRI  424 (442)
Q Consensus       360 I~r~LRkqsr~irl----------P~~v~e~i~kI~ka~~~L~~elgr~PS~eEIAe~LGIS~etVk~~l~~ar~  424 (442)
                      +.++.++......+          +..+......+..-.+++..-...+.|.+|||+.||||+++|+..+++++.
T Consensus       164 ~~d~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~~erevl~L~~~G~s~~EIA~~L~iS~~TVk~~l~ra~~  238 (258)
T 3clo_A          164 SADQRPEQGIYATITQMERGEVETLSLSEEHRNILSEREKEILRCIRKGLSSKEIAATLYISVNTVNRHRQNILE  238 (258)
T ss_dssp             CSCCCCCSSCCCEEEETTTTEEEECCCHHHHTTSSCHHHHHHHHHHHTTCCHHHHHHHHTCCHHHHHHHHHHHHH
T ss_pred             HcchhhhhHHHHHHHhhcccccccchhhHHHHccCCHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence            88876542111111          111111112222222222221236789999999999999999999988874

>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=92.81  E-value=3.8  Score=36.74  Aligned_cols=35  Identities=17%  Similarity=0.280  Sum_probs=28.3

Q ss_pred             HHHHHHHHHHHHhCCCCChHHHHHHcCCCHHHHHH
Q 013472          254 NLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQ  288 (442)
Q Consensus       254 ~le~~~~~L~~~~gr~pt~~ewA~a~g~deeeL~~  288 (442)
                      .+.+....+....|+.|+.++.|...|++.+.+..
T Consensus       100 ~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~  134 (239)
T 1rp3_A          100 RIKEVVEKLKEKLGREPTDEEVAKELGISTEELFK  134 (239)
T ss_dssp             HHHHHHHHHHHHHSSCCCHHHHHHHHTSCHHHHHH
T ss_pred             HHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHH
Confidence            45566777778889999999999999999877654

>3hug_A RNA polymerase sigma factor; ECF sigma factor, zinc binding anti-sigma factor, oxidative transcription regulation; 2.35A {Mycobacterium tuberculosis}

Probab=91.75  E-value=0.16  Score=40.59  Aligned_cols=30  Identities=13%  Similarity=-0.012  Sum_probs=26.5

Q ss_pred             cCCCCcHHHHHHHhCCCHHHHHHHHHhccc
Q 013472          395 HGKYPEDIEIAKYTGLSLAEIRSASECLRI  424 (442)
Q Consensus       395 lgr~PS~eEIAe~LGIS~etVk~~l~~ar~  424 (442)
                      +..+.|++|||+.||||+.+|+..+++++.
T Consensus        50 ~~~g~s~~eIA~~lgis~~tV~~~l~ra~~   79 (92)
T 3hug_A           50 YYRGWSTAQIATDLGIAEGTVKSRLHYAVR   79 (92)
T ss_dssp             HTSCCCHHHHHHHHTSCHHHHHHHHHHHHH
T ss_pred             HHcCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence            356789999999999999999999888764

>1l9z_H Sigma factor SIGA; helix-turn-helix, coiled-coil, transcription/DNA complex; 6.50A {Thermus aquaticus} SCOP: i.8.1.1

Probab=91.73  E-value=2.3  Score=44.04  Aligned_cols=28  Identities=18%  Similarity=0.159  Sum_probs=25.1

Q ss_pred             CCCcHHHHHHHhCCCHHHHHHHHHhccc
Q 013472          397 KYPEDIEIAKYTGLSLAEIRSASECLRI  424 (442)
Q Consensus       397 r~PS~eEIAe~LGIS~etVk~~l~~ar~  424 (442)
                      .+.|.+|||+.||||.++|+.+++++..
T Consensus       394 e~~TleEIAe~LgIS~erVRqi~~RAlk  421 (438)
T 1l9z_H          394 REHTLEEVGAYFGVTRERIRQIENKALR  421 (438)
T ss_pred             CCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence            6789999999999999999999877753

>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=90.82  E-value=0.27  Score=40.85  Aligned_cols=27  Identities=15%  Similarity=-0.027  Sum_probs=24.3

Q ss_pred             CCCcHHHHHHHhCCCHHHHHHHHHhcc
Q 013472          397 KYPEDIEIAKYTGLSLAEIRSASECLR  423 (442)
Q Consensus       397 r~PS~eEIAe~LGIS~etVk~~l~~ar  423 (442)
                      .+.|.+|||+.||||.++|+..+..+.
T Consensus        38 e~~s~~EIA~~lgiS~~tVr~~~~rAl   64 (99)
T 3t72_q           38 TDYTLEEVGKQFDVTRERIRQIEAKAL   64 (99)
T ss_pred             CCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence            578999999999999999999977664

>1x3u_A Transcriptional regulatory protein FIXJ; helix-turn-helix; NMR {Sinorhizobium meliloti}

Probab=90.48  E-value=0.44  Score=36.34  Aligned_cols=41  Identities=7%  Similarity=-0.013  Sum_probs=30.7

Q ss_pred             HHHHHHHHHHHcCCCCcHHHHHHHhCCCHHHHHHHHHhccc
Q 013472          384 IQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRI  424 (442)
Q Consensus       384 I~ka~~~L~~elgr~PS~eEIAe~LGIS~etVk~~l~~ar~  424 (442)
                      +.....++...+..+.|..|||+.||+++.+|+..+..++.
T Consensus        17 L~~~e~~vl~l~~~g~s~~eIA~~l~is~~tV~~~~~r~~~   57 (79)
T 1x3u_A           17 LSERERQVLSAVVAGLPNKSIAYDLDISPRTVEVHRANVMA   57 (79)
T ss_dssp             HCHHHHHHHHHHTTTCCHHHHHHHTTSCHHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence            33333443333467889999999999999999999887764

>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=90.28  E-value=0.45  Score=35.75  Aligned_cols=28  Identities=14%  Similarity=-0.054  Sum_probs=25.4

Q ss_pred             CCCcHHHHHHHhCCCHHHHHHHHHhccc
Q 013472          397 KYPEDIEIAKYTGLSLAEIRSASECLRI  424 (442)
Q Consensus       397 r~PS~eEIAe~LGIS~etVk~~l~~ar~  424 (442)
                      .+.|.+|||+.||+|+.+|+..+..+..
T Consensus        24 ~g~s~~eIA~~lgis~~tV~~~~~ra~~   51 (68)
T 2p7v_B           24 TDYTLEEVGKQFDVTRERIRQIEAKALR   51 (68)
T ss_dssp             SCCCHHHHHHHHTCCHHHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence            6889999999999999999999887764

>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=89.45  E-value=0.54  Score=35.81  Aligned_cols=27  Identities=19%  Similarity=0.194  Sum_probs=24.4

Q ss_pred             CCCcHHHHHHHhCCCHHHHHHHHHhcc
Q 013472          397 KYPEDIEIAKYTGLSLAEIRSASECLR  423 (442)
Q Consensus       397 r~PS~eEIAe~LGIS~etVk~~l~~ar  423 (442)
                      .+.|.+|||+.||+|..+|+..+..+.
T Consensus        29 ~~~s~~eIA~~l~is~~tV~~~~~ra~   55 (73)
T 1ku3_A           29 REHTLEEVGAYFGVTRERIRQIENKAL   55 (73)
T ss_dssp             SCCCHHHHHHHHTCCHHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence            688999999999999999999877665

>1tty_A Sigma-A, RNA polymerase sigma factor RPOD; helix-turn-helix, transcription; NMR {Thermotoga maritima} SCOP: a.4.13.2

Probab=89.29  E-value=0.52  Score=37.32  Aligned_cols=28  Identities=18%  Similarity=0.082  Sum_probs=25.4

Q ss_pred             CCCcHHHHHHHhCCCHHHHHHHHHhccc
Q 013472          397 KYPEDIEIAKYTGLSLAEIRSASECLRI  424 (442)
Q Consensus       397 r~PS~eEIAe~LGIS~etVk~~l~~ar~  424 (442)
                      .+.|.+|||+.||||+++|+..+.+++.
T Consensus        37 ~~~s~~EIA~~lgis~~tV~~~~~ra~~   64 (87)
T 1tty_A           37 KPKTLEEVGQYFNVTRERIRQIEVKALR   64 (87)
T ss_dssp             SCCCHHHHHHHHTCCHHHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            7889999999999999999999887763

>2o8x_A Probable RNA polymerase sigma-C factor; promoter recognition, transcription regulation, helix-turn-H motif, transcription; 3.00A {Mycobacterium tuberculosis}

Probab=88.70  E-value=0.67  Score=34.29  Aligned_cols=29  Identities=21%  Similarity=0.009  Sum_probs=25.9

Q ss_pred             CCCCcHHHHHHHhCCCHHHHHHHHHhccc
Q 013472          396 GKYPEDIEIAKYTGLSLAEIRSASECLRI  424 (442)
Q Consensus       396 gr~PS~eEIAe~LGIS~etVk~~l~~ar~  424 (442)
                      ..+.|.+|||+.+|+|+.+|+..+++++.
T Consensus        29 ~~g~s~~eIA~~lgis~~tv~~~~~ra~~   57 (70)
T 2o8x_A           29 LLGLSYADAAAVCGCPVGTIRSRVARARD   57 (70)
T ss_dssp             TSCCCHHHHHHHHTSCHHHHHHHHHHHHH
T ss_pred             HcCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence            56789999999999999999999888764

>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=88.00  E-value=0.2  Score=39.45  Aligned_cols=29  Identities=7%  Similarity=0.040  Sum_probs=25.7

Q ss_pred             CCCCcHHHHHHHhCCCHHHHHHHHHhccc
Q 013472          396 GKYPEDIEIAKYTGLSLAEIRSASECLRI  424 (442)
Q Consensus       396 gr~PS~eEIAe~LGIS~etVk~~l~~ar~  424 (442)
                      ..+.|.+|||+.|||+..+|+..+.+++.
T Consensus        34 ~~g~s~~eIA~~l~is~~tV~~~l~r~~~   62 (82)
T 1je8_A           34 AQGLPNKMIARRLDITESTVKVHVKHMLK   62 (82)
T ss_dssp             TTTCCHHHHHHHHTSCHHHHHHHHHHHHH
T ss_pred             HcCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence            46789999999999999999999887764

>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=87.25  E-value=0.9  Score=30.57  Aligned_cols=26  Identities=15%  Similarity=-0.132  Sum_probs=23.0

Q ss_pred             CCcHHHHHHHhCCCHHHHHHHHHhcc
Q 013472          398 YPEDIEIAKYTGLSLAEIRSASECLR  423 (442)
Q Consensus       398 ~PS~eEIAe~LGIS~etVk~~l~~ar  423 (442)
                      +.+..|||+.+||+..+|...+...+
T Consensus        21 g~s~~~IA~~lgis~~Tv~~~~~~~~   46 (51)
T 1tc3_C           21 NVSLHEMSRKISRSRHCIRVYLKDPV   46 (51)
T ss_dssp             TCCHHHHHHHHTCCHHHHHHHHHCST
T ss_pred             CCCHHHHHHHHCcCHHHHHHHHhhHH
Confidence            56999999999999999999887654

>2jt1_A PEFI protein; solution structure, winged helix-turn-helix, transcripti regulatory protein, structural genomics, PSI-2; NMR {Salmonella typhimurium LT2}

Probab=86.88  E-value=1.1  Score=35.68  Aligned_cols=39  Identities=28%  Similarity=0.269  Sum_probs=28.9

Q ss_pred             HHHHHHHHHHHc-CCCCcHHHHHHHhCCCHHHHHHHHHhc
Q 013472          384 IQKARKALTNSH-GKYPEDIEIAKYTGLSLAEIRSASECL  422 (442)
Q Consensus       384 I~ka~~~L~~el-gr~PS~eEIAe~LGIS~etVk~~l~~a  422 (442)
                      |-..+.....+. |..||..|||+.+|+|..+|+..+...
T Consensus         9 IL~~I~~~i~~~~g~~psv~EIa~~lgvS~~TVrr~L~~L   48 (77)
T 2jt1_A            9 IISIVQERQNMDDGAPVKTRDIADAAGLSIYQVRLYLEQL   48 (77)
T ss_dssp             HHHHHHHHHHHHTTSCEEHHHHHHHHTCCHHHHHHHHHHH
T ss_pred             HHHHHHHHHhhccCCCcCHHHHHHHHCCCHHHHHHHHHHH
Confidence            334444433333 788999999999999999999887654

>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=86.30  E-value=0.36  Score=39.07  Aligned_cols=28  Identities=14%  Similarity=0.019  Sum_probs=24.8

Q ss_pred             CCCCcHHHHHHHhCCCHHHHHHHHHhcc
Q 013472          396 GKYPEDIEIAKYTGLSLAEIRSASECLR  423 (442)
Q Consensus       396 gr~PS~eEIAe~LGIS~etVk~~l~~ar  423 (442)
                      ..+.|+.|||+.||||+.+|+..+.+++
T Consensus        40 ~~g~s~~eIA~~l~is~~tV~~~l~r~~   67 (95)
T 3c57_A           40 SEGLTNKQIADRMFLAEKTVKNYVSRLL   67 (95)
T ss_dssp             HTTCCHHHHHHHHTCCHHHHHHHHHHHH
T ss_pred             HcCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence            4567999999999999999999988765

>2jpc_A SSRB; DNA binding protein, structural genomics, PSI-2, protein structure initiative; NMR {Salmonella typhimurium}

Probab=86.28  E-value=0.53  Score=34.18  Aligned_cols=29  Identities=7%  Similarity=0.014  Sum_probs=24.9

Q ss_pred             CCCCcHHHHHHHhCCCHHHHHHHHHhccc
Q 013472          396 GKYPEDIEIAKYTGLSLAEIRSASECLRI  424 (442)
Q Consensus       396 gr~PS~eEIAe~LGIS~etVk~~l~~ar~  424 (442)
                      ..+.|..|||+.||+|+.+|+..+..+..
T Consensus        11 ~~g~s~~eIA~~l~is~~tV~~~~~~~~~   39 (61)
T 2jpc_A           11 DEGYTNHGISEKLHISIKTVETHRMNMMR   39 (61)
T ss_dssp             HTSCCSHHHHHHTCSCHHHHHHHHHHHHH
T ss_pred             HcCCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence            45679999999999999999998877653

>1xsv_A Hypothetical UPF0122 protein SAV1236; helix-turn-helix, putative DNA-binding protein, signal recognition particle, unknown function; 1.70A {Staphylococcus aureus subsp} SCOP: a.4.13.3

Probab=84.15  E-value=1.4  Score=37.00  Aligned_cols=29  Identities=14%  Similarity=-0.164  Sum_probs=25.8

Q ss_pred             CCCCcHHHHHHHhCCCHHHHHHHHHhccc
Q 013472          396 GKYPEDIEIAKYTGLSLAEIRSASECLRI  424 (442)
Q Consensus       396 gr~PS~eEIAe~LGIS~etVk~~l~~ar~  424 (442)
                      ..+.|+.|||+.||+|+.+|+..+++++.
T Consensus        39 ~~g~s~~EIA~~lgiS~~tV~~~l~ra~~   67 (113)
T 1xsv_A           39 LEDYSLSEIADTFNVSRQAVYDNIRRTGD   67 (113)
T ss_dssp             TSCCCHHHHHHHTTCCHHHHHHHHHHHHH
T ss_pred             HcCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence            56789999999999999999999887763

>2x48_A CAG38821; archeal virus, viral protein; 2.60A {Sulfolobus islandicus rod-shaped virusorganism_taxid}

Probab=84.11  E-value=1.3  Score=31.54  Aligned_cols=25  Identities=24%  Similarity=0.101  Sum_probs=21.7

Q ss_pred             CCCcHHHHHHHhCCCHHHHHHHHHh
Q 013472          397 KYPEDIEIAKYTGLSLAEIRSASEC  421 (442)
Q Consensus       397 r~PS~eEIAe~LGIS~etVk~~l~~  421 (442)
                      .+.|..|||+.+|++..+|...+..
T Consensus        30 ~g~s~~eIA~~lgis~~TV~~~l~~   54 (55)
T 2x48_A           30 MGYTVQQIANALGVSERKVRRYLES   54 (55)
T ss_dssp             TTCCHHHHHHHHTSCHHHHHHHHTC
T ss_pred             cCCCHHHHHHHHCcCHHHHHHHHHh
Confidence            3569999999999999999988754

>1fse_A GERE; helix-turn-helix DNA-binding protein transcriptional regulat transcription; 2.05A {Bacillus subtilis} SCOP: a.4.6.2

Probab=83.29  E-value=1.7  Score=32.37  Aligned_cols=28  Identities=18%  Similarity=-0.035  Sum_probs=24.6

Q ss_pred             CCCCcHHHHHHHhCCCHHHHHHHHHhcc
Q 013472          396 GKYPEDIEIAKYTGLSLAEIRSASECLR  423 (442)
Q Consensus       396 gr~PS~eEIAe~LGIS~etVk~~l~~ar  423 (442)
                      ..+.|..|||+.+|+|..+|+..+..++
T Consensus        24 ~~g~s~~eIA~~l~is~~tV~~~~~~~~   51 (74)
T 1fse_A           24 VQDKTTKEIASELFISEKTVRNHISNAM   51 (74)
T ss_dssp             TTTCCHHHHHHHHTSCHHHHHHHHHHHH
T ss_pred             HcCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence            4567999999999999999999988765

>2rnj_A Response regulator protein VRAR; HTH LUXR-type domain, DNA binding domain, activator, antibiotic resistance, cytoplasm, DNA-binding; NMR {Staphylococcus aureus}

Probab=81.39  E-value=0.92  Score=36.06  Aligned_cols=28  Identities=14%  Similarity=0.167  Sum_probs=24.9

Q ss_pred             CCCcHHHHHHHhCCCHHHHHHHHHhccc
Q 013472          397 KYPEDIEIAKYTGLSLAEIRSASECLRI  424 (442)
Q Consensus       397 r~PS~eEIAe~LGIS~etVk~~l~~ar~  424 (442)
                      .+.|..|||+.||||+.+|+..+.+++.
T Consensus        43 ~g~s~~eIA~~l~is~~tV~~~l~r~~~   70 (91)
T 2rnj_A           43 KGYSNQEIASASHITIKTVKTHVSNILS   70 (91)
T ss_dssp             TTCCTTHHHHHHTCCHHHHHHHHHHHHH
T ss_pred             cCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence            4679999999999999999999887764

>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=80.89  E-value=1.8  Score=34.77  Aligned_cols=28  Identities=25%  Similarity=0.040  Sum_probs=24.8

Q ss_pred             CCCcHHHHHHHhCCCHHHHHHHHHhccc
Q 013472          397 KYPEDIEIAKYTGLSLAEIRSASECLRI  424 (442)
Q Consensus       397 r~PS~eEIAe~LGIS~etVk~~l~~ar~  424 (442)
                      .+.|+.|||+.|||++.+|+..+..+..
T Consensus        43 ~G~s~~eIA~~L~iS~~TV~~~~~~i~~   70 (90)
T 3ulq_B           43 KGFTNQEIADALHLSKRSIEYSLTSIFN   70 (90)
T ss_dssp             TTCCHHHHHHHHTCCHHHHHHHHHHHHH
T ss_pred             cCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence            5779999999999999999999877654

---

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	442
d1siga_	334	a.177.1.1 (A:) Sigma70 {Escherichia coli [TaxId: 5	6e-20
d1ku2a2	180	a.177.1.1 (A:93-272) Sigma factor SigA {Thermus aq	4e-16
d1rp3a3	87	a.177.1.1 (A:0-86) Sigma factor sigma-28 (FliA) {A	2e-14
d1l0oc_	57	a.4.13.2 (C:) SigmaF {Bacillus stearothermophilus	2e-06
d1rp3a1	77	a.4.13.1 (A:87-163) Sigma factor sigma-28 (FliA) {	1e-05
d1ku2a1	60	a.4.13.1 (A:273-332) Sigma factor SigA {Thermus aq	6e-04

>d1siga_ a.177.1.1 (A:) Sigma70 {Escherichia coli [TaxId: 562]} Length = 334

class: All alpha proteins
fold: Sigma2 domain of RNA polymerase sigma factors
superfamily: Sigma2 domain of RNA polymerase sigma factors
family: Sigma2 domain of RNA polymerase sigma factors
domain: Sigma70
species: Escherichia coli [TaxId: 562]

 Score = 88.0 bits (217), Expect = 6e-20
 Identities = 27/71 (38%), Positives = 52/71 (73%)

Query: 295 YCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQY 354
             ++E++++   LV+ +A+ Y   G+ F DL+Q GN+G+++  ++F++ RGYKFSTY  +
Sbjct: 262 RAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATW 321

Query: 355 WIRKSISKMVA 365
           WIR++I++ +A
Sbjct: 322 WIRQAITRSIA 332

>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 = 73.7 bits (180), Expect = 4e-16
 Identities = 35/110 (31%), Positives = 60/110 (54%), Gaps = 3/110 (2%)

Query: 263 EKESGKAASLNCWAQAAGVSERVLKQHLAFGWYCRE---ELIKSTRPLVLFLARNYRGLG 319
            KE     ++           + LK++L            LI++   LV+ +A+ Y G G
Sbjct: 70  LKEKPDPKTVEEVDGKLKSLPKELKRYLHIAREGEAARQHLIEANLRLVVSIAKKYTGRG 129

Query: 320 IPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHAR 369
           + F DL+Q GN G+++  E+F++ R +KFSTY  +WIR++I++ +A  AR
Sbjct: 130 LSFLDLIQEGNQGLIRAVEKFEYKRRFKFSTYATWWIRQAINRAIADQAR 179

>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 = 66.1 bits (161), Expect = 2e-14
 Identities = 17/67 (25%), Positives = 31/67 (46%), Gaps = 3/67 (4%)

Query: 297 REELIKSTRPLVLFLARNYRG---LGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQ 353
           REELI    PLV  +A N +      +   DL+  G +G+++  +        +   Y++
Sbjct: 12  REELILKYLPLVKAIATNIKKHLPEDVDIRDLISYGVIGLIKAVDNLSTENPKRAEAYIK 71

Query: 354 YWIRKSI 360
             I+ +I
Sbjct: 72  LRIKGAI 78

>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 = 42.8 bits (101), Expect = 2e-06
 Identities = 17/54 (31%), Positives = 31/54 (57%)

Query: 371 IKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRI 424
           +K+   L    +KI+KA+  L+ + G+ P   EIA + G+S  ++  A E +R+
Sbjct: 4   VKVSRSLKEMGNKIRKAKDELSKTRGRAPTVTEIADHLGISPEDVVLAQEAVRL 57

>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 = 40.9 bits (96), Expect = 1e-05
 Identities = 13/56 (23%), Positives = 27/56 (48%), Gaps = 2/56 (3%)

Query: 381 ISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLR--IVGSIDQKIGD 434
             +I++  + L    G+ P D E+AK  G+S  E+    + +    + S+++   D
Sbjct: 9   ERRIKEVVEKLKEKLGREPTDEEVAKELGISTEELFKTLDKINFSYILSLEEVFRD 64

>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 = 35.8 bits (83), Expect = 6e-04
 Identities = 13/46 (28%), Positives = 21/46 (45%)

Query: 371 IKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIR 416
           I+IP  +   I+K+ +  + L    G+ P   EIA+  G      R
Sbjct: 1   IRIPVHMVETINKLSRTARQLQQELGREPSYEEIAEAMGPGWDAKR 46

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	442
d1ku2a2	180	Sigma factor SigA {Thermus aquaticus [TaxId: 271]}	99.97
d1siga_	334	Sigma70 {Escherichia coli [TaxId: 562]}	99.85
d1rp3a3	87	Sigma factor sigma-28 (FliA) {Aquifex aeolicus [Ta	99.78
d1or7a2	113	SigmaE factor (RpoE) {Escherichia coli [TaxId: 562	99.47
d1ku2a1	60	Sigma factor SigA {Thermus aquaticus [TaxId: 271]}	98.99
d1h3la_	75	Sigma factor SigR {Streptomyces coelicolor a3(2) [	98.98
d1l0oc_	57	SigmaF {Bacillus stearothermophilus [TaxId: 1422]}	98.79
d1rp3a1	77	Sigma factor sigma-28 (FliA) {Aquifex aeolicus [Ta	98.46
d1l0oc_	57	SigmaF {Bacillus stearothermophilus [TaxId: 1422]}	96.2
d1or7a1	68	SigmaE factor (RpoE) {Escherichia coli [TaxId: 562	95.21
d1rp3a1	77	Sigma factor sigma-28 (FliA) {Aquifex aeolicus [Ta	95.04
d1rp3a2	71	Sigma factor sigma-28 (FliA) {Aquifex aeolicus [Ta	94.51
d1jhfa1	71	LexA repressor, N-terminal DNA-binding domain {Esc	92.83
d1ku2a1	60	Sigma factor SigA {Thermus aquaticus [TaxId: 271]}	92.42
d1xsva_	106	Hypothetical protein SAV1236 {Staphylococcus aureu	88.94
d1s7oa_	106	Hypothetical protein SPy1201 {Streptococcus pyogen	88.93
d1l3la1	65	Quorum-sensing transcription factor TraR, C-termin	84.35
d1fsea_	67	Germination protein GerE {Bacillus subtilis [TaxId	82.78
d1yioa1	70	Response regulatory protein StyR, C-terminal domai	81.02

>d1ku2a2 a.177.1.1 (A:93-272) Sigma factor SigA {Thermus aquaticus [TaxId: 271]}

class: All alpha proteins
fold: Sigma2 domain of RNA polymerase sigma factors
superfamily: Sigma2 domain of RNA polymerase sigma factors
family: Sigma2 domain of RNA polymerase sigma factors
domain: Sigma factor SigA
species: Thermus aquaticus [TaxId: 271]

Probab=99.97  E-value=1.1e-31  Score=244.91  Aligned_cols=148  Identities=27%  Similarity=0.436  Sum_probs=118.7

Q ss_pred             HHHHHHhcccCC-CCCChHHHHHHHHHhHHHHHHHHHHHHHH------------------HHhCCCCChHHHHHHcCC--
Q 013472          223 FSAERALNSRGR-RLTIARNEAEMSKGVQVVANLERIKTTLE------------------KESGKAASLNCWAQAAGV--  281 (442)
Q Consensus       223 ~~~~~~~~~~~~-~lLt~eeE~eL~~~iq~~~~le~~~~~L~------------------~~~gr~pt~~ewA~a~g~--  281 (442)
                      |.++-|++.+++ ||||++||++|+++|+.+..+.+...+..                  ...+..|...+|+.....  
T Consensus         2 DpVr~YLreig~v~LLT~EEEieLAr~Ie~g~~~~~~~~e~~~~~~~l~~e~~~~~~~~~~~~~~~~~~~e~~~~~~~~~   81 (180)
T d1ku2a2           2 DPVRQYLHEIGQVPLLTLEEEIDLARKVEEGMEAIKKLSEATGLDQELIREVVRAKILGTARIQKIPGLKEKPDPKTVEE   81 (180)
T ss_dssp             HHHHHHHHHHTTSCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHTTCSSCCCTTSCCSSCTTTHHH
T ss_pred             CcHHHHHHHhcCcCCCCHHHHHHHHHHHHHHHHHHHHHHHhhhccHHHHHHHHHHHhhhHHHHhcchhhHHHhhHHHHHH
Confidence            346777777776 99999999999999999876554432221                  012334444433322111  


Q ss_pred             ----------CHHHHHHHHHhchHHHHHHHHHhHHHHHHHHHHhhCCCCCHHhHHHHHHHHHHHhHHhcCCCCCCChHHH
Q 013472          282 ----------SERVLKQHLAFGWYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTY  351 (442)
Q Consensus       282 ----------deeeL~~~l~~G~~Are~LI~~nlrLV~sIAkrY~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTY  351 (442)
                                ....+......|..|+++||.+|++||++||++|.+.|++++||||||+|||++|+++|||++|++|+||
T Consensus        82 ~~~~~~~~~~el~~l~~~~~~~~~a~~~li~~~~~lv~~~a~~~~~~~~~~~dl~q~g~~gl~~a~~~fd~~~g~~f~ty  161 (180)
T d1ku2a2          82 VDGKLKSLPKELKRYLHIAREGEAARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQEGNQGLIRAVEKFEYKRRFKFSTY  161 (180)
T ss_dssp             HHHHHHSCCHHHHHHHHHHHHHHHHHHHHHHTTHHHHHHHHHTTCSSSSCHHHHHHHHHHHHHHHHHHCCGGGCSCHHHH
T ss_pred             HHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccCCCcCHHHHHHHHHHHHHHHHHHcCCCCCCCHHHH
Confidence                      1245667778889999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHhhcCc
Q 013472          352 VQYWIRKSISKMVARHARG  370 (442)
Q Consensus       352 a~~wIRnaI~r~LRkqsr~  370 (442)
                      |+|||+++|.++|++++|+
T Consensus       162 a~~~i~~~i~~~~~~~~rt  180 (180)
T d1ku2a2         162 ATWWIRQAINRAIADQART  180 (180)
T ss_dssp             HHHHHHHHHHHHHTTSCCC
T ss_pred             HHHHHHHHHHHHHHHhCCC
Confidence            9999999999999998764

>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=99.85  E-value=1.4e-21  Score=191.22  Aligned_cols=83  Identities=34%  Similarity=0.799  Sum_probs=76.9

Q ss_pred             HHHHHHHhc----hHHHHHHHHHhHHHHHHHHHHhhCCCCCHHhHHHHHHHHHHHhHHhcCCCCCCChHHHHHHHHHHHH
Q 013472          285 VLKQHLAFG----WYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSI  360 (442)
Q Consensus       285 eL~~~l~~G----~~Are~LI~~nlrLV~sIAkrY~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIRnaI  360 (442)
                      .+.+.+..|    ..|+++||.+|++||++||++|.++|++++||+|+|++||++|+++|||.+|++|+|||+||||++|
T Consensus       248 ~i~~~i~~ge~~~~~ak~~~~~~~~~lv~~~~~~~~~~~~~~~dl~~~~~~~l~~~~~~~~~~~~~~f~~~~~~~~~~~~  327 (334)
T d1siga_         248 DINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAI  327 (334)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHTHHHHHHHHTTSTTSSSCHHHHHHHHHHHHHHHHHHCCGGGCCCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhhccchHHHHHHhHHHHHHHHHHhccCCCCCHHHHHHhhHHHHHHHHHhcCCCCCCchHhhhHHHHHHHH
Confidence            445566666    4499999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHhh
Q 013472          361 SKMVARH  367 (442)
Q Consensus       361 ~r~LRkq  367 (442)
                      .++|++|
T Consensus       328 ~~~~~~~  334 (334)
T d1siga_         328 TRSIADQ  334 (334)
T ss_dssp             HHHHHHC
T ss_pred             HHHHhCC
Confidence            9999875

>d1rp3a3 a.177.1.1 (A:0-86) Sigma factor sigma-28 (FliA) {Aquifex aeolicus [TaxId: 63363]}

class: All alpha proteins
fold: Sigma2 domain of RNA polymerase sigma factors
superfamily: Sigma2 domain of RNA polymerase sigma factors
family: Sigma2 domain of RNA polymerase sigma factors
domain: Sigma factor sigma-28 (FliA)
species: Aquifex aeolicus [TaxId: 63363]

Probab=99.78  E-value=2.5e-19  Score=146.18  Aligned_cols=72  Identities=24%  Similarity=0.393  Sum_probs=68.6

Q ss_pred             HHHHHHHHhHHHHHHHHHHhhCC---CCCHHhHHHHHHHHHHHhHHhcCCCCCCChHHHHHHHHHHHHHHHHHhh
Q 013472          296 CREELIKSTRPLVLFLARNYRGL---GIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARH  367 (442)
Q Consensus       296 Are~LI~~nlrLV~sIAkrY~g~---g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIRnaI~r~LRkq  367 (442)
                      .+++||..|++||.++|.+|.++   +++.+||+|+|++||++|+++|||++|.+|+|||.+|||++|++++|+.
T Consensus        11 ~re~li~~~~~LV~~ia~~~~~~~~~~~e~eDL~q~G~igL~~A~~~yd~~~g~~F~tYA~~~Irgai~d~lRk~   85 (87)
T d1rp3a3          11 EREELILKYLPLVKAIATNIKKHLPEDVDIRDLISYGVIGLIKAVDNLSTENPKRAEAYIKLRIKGAIYDYLRSL   85 (87)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHTTSCTTSCHHHHHHHHHHHHHHHHHTCCCCCTHHHHHHHHHHHHHHHHHHHHTS
T ss_pred             HHHHHHHHhHHHHHHHHHHHhccCCCCCCHHHHHHHHHHHHHHHHHhhCCCCCCCHHHHHHHHHHHHHHHHHHhC
Confidence            68999999999999999999764   7899999999999999999999999999999999999999999999975

>d1ku2a1 a.4.13.1 (A:273-332) Sigma factor SigA {Thermus aquaticus [TaxId: 271]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Sigma3 and sigma4 domains of RNA polymerase sigma factors
family: Sigma3 domain
domain: Sigma factor SigA
species: Thermus aquaticus [TaxId: 271]

Probab=98.99  E-value=2.9e-10  Score=85.92  Aligned_cols=58  Identities=22%  Similarity=0.345  Sum_probs=55.2

Q ss_pred             eecccccHHHHHHHHHHHHHHHHHcCCCCcHHHHHHHhCC--CHHHHHHHHHhcccCCCC
Q 013472          371 IKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGL--SLAEIRSASECLRIVGSI  428 (442)
Q Consensus       371 irlP~~v~e~i~kI~ka~~~L~~elgr~PS~eEIAe~LGI--S~etVk~~l~~ar~~~SL  428 (442)
                      ||+|.|+.+.++++.++.++|.+++||+||.+|||+.||+  ++++|+.++..++.++||
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            6899999999999999999999999999999999999985  588999999999999997

>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=98.98  E-value=3e-10  Score=88.03  Aligned_cols=69  Identities=9%  Similarity=-0.040  Sum_probs=64.4

Q ss_pred             HHHHHHHHHhHHHHHHHHHHhhCCCCCHHhHHHHHHHHHHHhHHhcCCCCCCChHHHHHHHHHHHHHHHHH
Q 013472          295 YCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVA  365 (442)
Q Consensus       295 ~Are~LI~~nlrLV~sIAkrY~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIRnaI~r~LR  365 (442)
                      .+|++++..|.+.|+.+|.+++++..+++|++||.++.+|+..++|++.  .+|.+|++.+++|.+++++|
T Consensus         7 ~~f~~~~~~y~~~l~~~~~~~~~d~~~aeDivQd~f~~~~~~~~~~~~~--~~~~~wl~~i~~n~~~d~~R   75 (75)
T d1h3la_           7 ARFERDALEFLDQMYSAALRMTRNPADAEDLVQETYAKAYASFHQFREG--TNLKAWLYRILTNTFINSYR   75 (75)
T ss_dssp             HHHHHHHHHTHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHGGGCCSS--SCHHHHHHHHHHHHHHHTCC
T ss_pred             HHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhhhhcCCC--CCHHHHHHHHHHHHHHHHhC
Confidence            3799999999999999999999999999999999999999999999874  46999999999999998764

>d1l0oc_ a.4.13.2 (C:) SigmaF {Bacillus stearothermophilus [TaxId: 1422]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Sigma3 and sigma4 domains of RNA polymerase sigma factors
family: Sigma4 domain
domain: SigmaF
species: Bacillus stearothermophilus [TaxId: 1422]

Probab=98.79  E-value=2.9e-09  Score=79.38  Aligned_cols=55  Identities=31%  Similarity=0.446  Sum_probs=52.1

Q ss_pred             CceecccccHHHHHHHHHHHHHHHHHcCCCCcHHHHHHHhCCCHHHHHHHHHhcc
Q 013472          369 RGIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLR  423 (442)
Q Consensus       369 r~irlP~~v~e~i~kI~ka~~~L~~elgr~PS~eEIAe~LGIS~etVk~~l~~ar  423 (442)
                      .++++|.++.+.+++|.++..+|.+++|+.||.+|||+.||||+++|..++..++
T Consensus         2 g~IrvPr~~~e~~~ki~~~~~~l~q~lgRePT~~EiA~~l~~~~e~V~~~l~a~r   56 (57)
T d1l0oc_           2 GTVKVSRSLKEMGNKIRKAKDELSKTRGRAPTVTEIADHLGISPEDVVLAQEAVR   56 (57)
T ss_dssp             CCCTTHHHHHHHHHHHHHHHHHHHHHHTSCCBHHHHHHHHTSCHHHHHHHHHHHH
T ss_pred             CCEeCcHHHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHHCcCHHHHHHHHHHhc
Confidence            4689999999999999999999999999999999999999999999999987664

>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=98.46  E-value=1.4e-08  Score=79.27  Aligned_cols=59  Identities=22%  Similarity=0.348  Sum_probs=52.4

Q ss_pred             cHHHHHHHHHHHHHHHHHcCCCCcHHHHHHHhCCCHHHHHHHHHhcc--cCCCCccccCCC
Q 013472          377 LNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLR--IVGSIDQKIGDC  435 (442)
Q Consensus       377 v~e~i~kI~ka~~~L~~elgr~PS~eEIAe~LGIS~etVk~~l~~ar--~~~SLD~~v~~~  435 (442)
                      +.+..++|.++...|.+++||.||.+|||+.|||++++|+.++..+.  .++|||.+++++
T Consensus         5 ~r~~~~ki~~a~~~L~~~lGR~Pt~~EiA~~lg~s~~e~~~~l~~~~~~~~~SLD~~~~d~   65 (77)
T d1rp3a1           5 VREKERRIKEVVEKLKEKLGREPTDEEVAKELGISTEELFKTLDKINFSYILSLEEVFRDF   65 (77)
T ss_dssp             HHHHHHHHHHHHHHHHHHHSSCCCHHHHHHHHTSCHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHCcCCCHHHHHHHHCcCHHHHHHHHHHHhcCCceecccCccCC
Confidence            45778899999999999999999999999999999999999987544  779999987644

>d1l0oc_ a.4.13.2 (C:) SigmaF {Bacillus stearothermophilus [TaxId: 1422]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Sigma3 and sigma4 domains of RNA polymerase sigma factors
family: Sigma4 domain
domain: SigmaF
species: Bacillus stearothermophilus [TaxId: 1422]

Probab=96.20  E-value=0.0058  Score=44.31  Aligned_cols=41  Identities=20%  Similarity=0.225  Sum_probs=35.3

Q ss_pred             HHHHHHHHHHHHHhCCCCChHHHHHHcCCCHHHHHHHHHhc
Q 013472          253 ANLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQHLAFG  293 (442)
Q Consensus       253 ~~le~~~~~L~~~~gr~pt~~ewA~a~g~deeeL~~~l~~G  293 (442)
                      .++.++..+|..++||+||.+|.|+++|++.+++...+..+
T Consensus        15 ~ki~~~~~~l~q~lgRePT~~EiA~~l~~~~e~V~~~l~a~   55 (57)
T d1l0oc_          15 NKIRKAKDELSKTRGRAPTVTEIADHLGISPEDVVLAQEAV   55 (57)
T ss_dssp             HHHHHHHHHHHHHHTSCCBHHHHHHHHTSCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCCCCCHHHHHHHHCcCHHHHHHHHHHh
Confidence            34677888999999999999999999999999988766543

>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=95.21  E-value=0.0079  Score=44.37  Aligned_cols=29  Identities=21%  Similarity=-0.040  Sum_probs=26.3

Q ss_pred             CCCCcHHHHHHHhCCCHHHHHHHHHhccc
Q 013472          396 GKYPEDIEIAKYTGLSLAEIRSASECLRI  424 (442)
Q Consensus       396 gr~PS~eEIAe~LGIS~etVk~~l~~ar~  424 (442)
                      -.+.|++|||+.+|+|+++|+..+++++.
T Consensus        32 ~~~~s~~eIA~~lgis~~tv~~~l~ra~~   60 (68)
T d1or7a1          32 LDGLSYEEIAAIMDCPVGTVRSRIFRARE   60 (68)
T ss_dssp             TTCCCHHHHHHHTTSCHHHHHHHHHHHHH
T ss_pred             HhCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence            47789999999999999999999998864

>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=95.04  E-value=0.021  Score=43.10  Aligned_cols=38  Identities=18%  Similarity=0.285  Sum_probs=33.9

Q ss_pred             HHHHHHHHHHHHHhCCCCChHHHHHHcCCCHHHHHHHH
Q 013472          253 ANLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQHL  290 (442)
Q Consensus       253 ~~le~~~~~L~~~~gr~pt~~ewA~a~g~deeeL~~~l  290 (442)
                      .+++++...|..++||+||.+|.|..+||+.+++...+
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            45888999999999999999999999999998887654

>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=94.51  E-value=0.011  Score=43.58  Aligned_cols=30  Identities=13%  Similarity=-0.042  Sum_probs=26.5

Q ss_pred             cCCCCcHHHHHHHhCCCHHHHHHHHHhccc
Q 013472          395 HGKYPEDIEIAKYTGLSLAEIRSASECLRI  424 (442)
Q Consensus       395 lgr~PS~eEIAe~LGIS~etVk~~l~~ar~  424 (442)
                      +..+.|++|||+.||+|+.+|+..+++++.
T Consensus        34 ~~~~~s~~eIA~~lgis~~tv~~~~~ra~~   63 (71)
T d1rp3a2          34 FYEELPAKEVAKILETSVSRVSQLKAKALE   63 (71)
T ss_dssp             HTSCCCHHHHHHHTTSCHHHHHHHHHHHHH
T ss_pred             HhHhCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            356889999999999999999999888763

>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=92.83  E-value=0.11  Score=38.78  Aligned_cols=44  Identities=18%  Similarity=0.192  Sum_probs=37.5

Q ss_pred             HHHHHHHHHHHHHHHHcCCCCcHHHHHHHhCC-CHHHHHHHHHhc
Q 013472          379 REISKIQKARKALTNSHGKYPEDIEIAKYTGL-SLAEIRSASECL  422 (442)
Q Consensus       379 e~i~kI~ka~~~L~~elgr~PS~eEIAe~LGI-S~etVk~~l~~a  422 (442)
                      ....+|-.++.....+.|..||..|||+.+|+ |..+|...+.+.
T Consensus         5 ~rQ~~vL~~I~~~~~~~G~~Ps~rei~~~~g~~S~stv~~~l~~L   49 (71)
T d1jhfa1           5 ARQQEVFDLIRDHISQTGMPPTRAEIAQRLGFRSPNAAEEHLKAL   49 (71)
T ss_dssp             HHHHHHHHHHHHHHHHHSSCCCHHHHHHHTTCSSHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCCHHHHHHHHHHH
Confidence            44567778888888889999999999999999 799999887654

>d1ku2a1 a.4.13.1 (A:273-332) Sigma factor SigA {Thermus aquaticus [TaxId: 271]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Sigma3 and sigma4 domains of RNA polymerase sigma factors
family: Sigma3 domain
domain: Sigma factor SigA
species: Thermus aquaticus [TaxId: 271]

Probab=92.42  E-value=0.16  Score=36.83  Aligned_cols=38  Identities=24%  Similarity=0.388  Sum_probs=29.9

Q ss_pred             HHHHHHHHHHHHHHhCCCCChHHHHHHcCC--CHHHHHHH
Q 013472          252 VANLERIKTTLEKESGKAASLNCWAQAAGV--SERVLKQH  289 (442)
Q Consensus       252 ~~~le~~~~~L~~~~gr~pt~~ewA~a~g~--deeeL~~~  289 (442)
                      +-++.++..+|..++||+||.+|.|+++|+  +.+.+...
T Consensus        11 i~rv~r~~~~l~qe~gRePt~eEiA~~l~~~l~~ekV~~~   50 (60)
T d1ku2a1          11 INKLSRTARQLQQELGREPSYEEIAEAMGPGWDAKRVEET   50 (60)
T ss_dssp             HHHHHHHHHHHHHHHTSCCCHHHHHHHHCSSCCHHHHHHH
T ss_pred             HHHHHHHHHHHHHHhCCCCCHHHHHHHHCCCCCHHHHHHH
Confidence            346677888999999999999999999974  55555443

>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=88.94  E-value=0.25  Score=39.75  Aligned_cols=31  Identities=13%  Similarity=-0.206  Sum_probs=27.4

Q ss_pred             HcCCCCcHHHHHHHhCCCHHHHHHHHHhccc
Q 013472          394 SHGKYPEDIEIAKYTGLSLAEIRSASECLRI  424 (442)
Q Consensus       394 elgr~PS~eEIAe~LGIS~etVk~~l~~ar~  424 (442)
                      .+-.+.|..|||+.||||.++|+..+++++.
T Consensus        30 ~~~e~ls~~EIA~~lgiS~~aV~~~l~Ra~~   60 (106)
T d1xsva_          30 FYLEDYSLSEIADTFNVSRQAVYDNIRRTGD   60 (106)
T ss_dssp             HHTSCCCHHHHHHHTTCCHHHHHHHHHHHHH
T ss_pred             HHHhCCcHHHHHHHHCcCHHHHHHHHHHHHH
Confidence            3457889999999999999999999988874

>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=88.93  E-value=0.19  Score=40.41  Aligned_cols=30  Identities=17%  Similarity=-0.022  Sum_probs=26.6

Q ss_pred             cCCCCcHHHHHHHhCCCHHHHHHHHHhccc
Q 013472          395 HGKYPEDIEIAKYTGLSLAEIRSASECLRI  424 (442)
Q Consensus       395 lgr~PS~eEIAe~LGIS~etVk~~l~~ar~  424 (442)
                      +..+.|..|||+.||||+++|+..+++++.
T Consensus        29 y~~~ls~~EIA~~lgiS~~aV~~~l~RA~~   58 (106)
T d1s7oa_          29 YADDYSLAEIADEFGVSRQAVYDNIKRTEK   58 (106)
T ss_dssp             HHTCCCHHHHHHHHTCCHHHHHHHHHHHHH
T ss_pred             HHcCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence            346789999999999999999999988864

>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=84.35  E-value=0.78  Score=32.99  Aligned_cols=33  Identities=15%  Similarity=-0.014  Sum_probs=27.2

Q ss_pred             HHHHcCCCCcHHHHHHHhCCCHHHHHHHHHhcc
Q 013472          391 LTNSHGKYPEDIEIAKYTGLSLAEIRSASECLR  423 (442)
Q Consensus       391 L~~elgr~PS~eEIAe~LGIS~etVk~~l~~ar  423 (442)
                      +..-...+.|..|||+.||||+.+|+..+....
T Consensus        12 vl~l~~~G~s~~eIA~~l~iS~~TV~~~~~~i~   44 (65)
T d1l3la1          12 YLRWIAVGKTMEEIADVEGVKYNSVRVKLREAM   44 (65)
T ss_dssp             HHHHHTTTCCHHHHHHHHTCCHHHHHHHHHHHH
T ss_pred             HHHHHHhcCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence            334457788999999999999999999877554

>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=82.78  E-value=0.95  Score=32.58  Aligned_cols=32  Identities=16%  Similarity=-0.086  Sum_probs=26.4

Q ss_pred             HHHcCCCCcHHHHHHHhCCCHHHHHHHHHhcc
Q 013472          392 TNSHGKYPEDIEIAKYTGLSLAEIRSASECLR  423 (442)
Q Consensus       392 ~~elgr~PS~eEIAe~LGIS~etVk~~l~~ar  423 (442)
                      ..-...+.|..|||+.||+++.+|+..+....
T Consensus        13 l~l~~~G~s~~eIA~~L~is~~TV~~~~~~i~   44 (67)
T d1fsea_          13 FELLVQDKTTKEIASELFISEKTVRNHISNAM   44 (67)
T ss_dssp             HHHHTTTCCHHHHHHHHTSCHHHHHHHHHHHH
T ss_pred             HHHHHccCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence            33456788999999999999999999877554

>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=81.02  E-value=0.91  Score=33.18  Aligned_cols=37  Identities=8%  Similarity=0.028  Sum_probs=29.0

Q ss_pred             HHHHHHHcCCCCcHHHHHHHhCCCHHHHHHHHHhccc
Q 013472          388 RKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRI  424 (442)
Q Consensus       388 ~~~L~~elgr~PS~eEIAe~LGIS~etVk~~l~~ar~  424 (442)
                      ..++..-+..+.+..|||+.||||+.+|+..+.....
T Consensus        17 E~~vl~~l~~G~s~~eIA~~l~iS~~TV~~~~~~i~~   53 (70)
T d1yioa1          17 EQQVLQLTIRGLMNKQIAGELGIAEVTVKVHRHNIMQ   53 (70)
T ss_dssp             HHHHHHHHTTTCCHHHHHHHHTCCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            3344444567889999999999999999998776553