Citrus Sinensis ID: 009449

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-------280-------290-------300-------310-------320-------330-------340-------350-------360-------370-------380-------390-------400-------410-------420-------430-------440-------450-------460-------470-------480-------490-------500-------510-------520-------530----
Protein Sequence
MGMGFRLNLKWVSPVQSHFFTTSSCRLSSTSVRGREGSFNSARLSFLSTISEDSASYFQDPVKAYTCSFVNTQTVENDYSETEEIRQKSTSCIGQDASSRSDFRLLMENLDVLESTFADSDALRLEREILQQLGKLGALKLFNSHLSRIVKTSNVLDLSDVHTEEQKMNDSRDYHMGKILVPSKRKGKRKLKTARVSEESIETSLLSLPSEALQEGLKQPTIFSAERALNSRGRRLTIARNEAEMSKGVQVVANLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQHLAFGWYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNAKYLEFAPDRSVKSPKEIVMRQHMKKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDSETCRDLSHFLVL
Secondary Structure (PSIPRED)
cccccEEEcccccccccccccccccccccccccccccccccccccccHHccccccccccccccccccccccccccHHcccHHHHHHHHHccccccccccHHHHHHHHHHHHHHHHHHccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccccccccHHHHHcccccccccccccccccHHHHHHHHHHHHHHHHHHHccccccHHHHHHccccccccHHHHHHHHHccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccHHHHHHHccccHHHHHHHHHHHHHHHHHHHHHcccEEEEEHHccccccccHHHHHHHcHHHHHHHHHcccccccccccHHHHHHHHHHHHHHHHHccccccccHHHHHHHHHHHHHHHHHHHHccccccHHHHHHHHcccHHHHHHHHHcccccccccccccccccccccccccccccccHHHHHHHHHHHHHHHHHHHcccHHHHHHHEEEccccccccccHHHHHccccccHHHHHHHHHHHHHHHcccHHHHcccccccc
Secondary Structure Prediction (SSPRO)
ccccEEEccccccccccccccccccccccccccccccccccEEEccccEEcccccHHcccccccccccccccccEEccHHcccccccccccEcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcHHHHHccccccccccccccccccccccHccccccHHHccccccccccHHHHHHHHHcHccHcccccccccccHHHHHHHcccccccHHHHHHHHHcHHHccHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccHHHHHHHHcccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccHHHHHHHHHHcccHHHHHHHHccccccccHHHHHHHHHHHHHHHHHHHHHccccccHHHHHHHHHHHHHHHHHHHHccccccHHHHHHHccccHHHHHHHHHHccccccccccccccccccccccccccccccHHHHHHHHHHHcccccccccccHHHHHHHHHHccccccccccHHHHHHHHcccHHHHHHHHHHHHHHHHHcccHHHHHHHccc
Coil and Loop (DISEMBL)
mgmgfrlnlkwvspvqshffttsscrlsstsvrgregsfnsARLSFLSTISedsasyfqdpvkayTCSFVntqtvendyseTEEIRQKstscigqdassrsDFRLLMENLDVlestfadsDALRLEREILQQLGKLGALKLFNSHLSRIvktsnvldlsdvhteeqkmndsrdyhmgkilvpskrkgkrklktaRVSEESIETSLlslpsealqeglkqptiFSAERALNSRGRRLTIARNEAEMSKGVQVVANLERIKTTLEkesgkaasLNCWAQAAGVSERVLKQHLAFGWYCREELIKSTRPLVLFLARNyrglgipfsdllqagnvgvlqgaerfdhtrgykfsTYVQYWIRKSISKMVARHArgikipcklNREISKIQKARKALtnshgkypedieiaKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNakylefapdrsvkspkeiVMRQHMKKDVFRILESLDSRERQVLVLRYglndhrpksLEEIGKLFHVSKEWIRKLEKKAMTKLrdsetcrdlshflvl
Flexible Loop (DISEMBL)
MGMGFRLNLKWVSPVQSHFfttsscrlsstsvrgregsfNSARLSFLSTISEDSASYFQDPVKAYTCSFVNTQTVENDYSETEEirqkstscigqdassRSDFRLLMENLDVLESTFADSDALRLEREILQQLGKLGALKLFNSHLSRivktsnvldlsdvhteeqkmndsrdyhmgkilvpskrkgkrklktarvseesietsllslpsealqeglkqptifsaeralnsRGRRLtiarneaemskgvqvvaNLERIKTTLekesgkaasLNCWAQAAGVSERVLKQHLAFGWYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQgaerfdhtrgykfsTYVQYWIRKSISKMVARHARgikipcklnreiSKIQKARKaltnshgkypediEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNAKYlefapdrsvkspkeivmrqhMKKDVFRilesldsrerQVLVLryglndhrpksleeigklfhvskEWIRKLEKKAmtklrdsetcrdlshflvl
Low Complexity Region (SEG)
MGMGFRLNLKWVSPVQSHFFTTSSCRLSSTSVRGREGSFNSARLSFLSTISEDSASYFQDPVKAYTCSFVNTQTVENDYSETEEIRQKSTSCIGQDASSRSDFRLLMENLDVLESTFADSDALRLEREIlqqlgklgalklFNSHLSRIVKTSNVLDLSDVHTEEQKMNDSRDYHMGKILVPSKRKGKRKLKTARVseesietsllslpseALQEGLKQPTIFSAERALNSRGRRLTIARNEAEMSKGVQVVANLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQHLAFGWYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNAKYLEFAPDRSVKSPKEIVMRQHMKKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDSETCRDLSHFLVL
Disordered region (IsUnstruct)
****FRLNLKWVSPVQSHFFTTSSCR*****************LSFLSTISEDSASYFQDPVKAYTCSFVNTQTV***************************FRLLMENLDVLESTFADSDALRLEREILQQLGKLGALKLFNSHLSRIVKTSNVLDL******************************************************************************************VQVVANLERIKTTL*****KAASLNCWAQAAGVSERVLKQHLAFGWYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNAKYLEFAPD********IVMRQHMKKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEK*********************
Disordered Region (DISOPRED)
**MGFRLNLKWVSP*****************************LSF**************PVKAYTCSFVNTQTVENDYSETEEIR**************SDFRLLMENLDVLESTFADSDALRLEREILQQLGKLGALKLFNSH*********************************************************************************RALNSRGRRLTIARNEAEMSKGVQVVANLERIKTTLEK**GKAASLNCWAQAAGVSERVLKQHLAFGWYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIPCKLNREISKIQKARK**********EDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNAKYLEFAPDRSVKSPKEIVMRQHMKKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDSETCRDLSHFLVL
Disordered Region (DISEMBL)
MGMGFRLNLKWVSPVQSHFFTTSS**************FNSARLSFLSTISEDSASYFQDPVKAYTCSFVNTQTVE********************ASSRSDFRLLMENLDVLESTFADSDALRLEREILQQLGKLGALKLFNSHLSRIVKTSNVLDLSDVHTEEQKMNDSRDYHMGKILVPSK*******************SLLSLPSEALQEGLKQPTIFSAERALNSRGRRLTIARNEAEMSKGVQVVANLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQHLAFGWYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNAKYLEFAPDRSVKSPKEIVMRQHMKKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDSETCRDLSHFLVL
Disordered Region (DISPRO)
*GMGFRLNLKWVSPVQS************TSVRGREGSFNSARLSFLSTISEDSASYFQDPVKAYTCSFVNTQTVENDYSETEEIRQKSTSCIGQDASSRSDFRLLMENLDVLESTFADSDALRLEREILQQLGKLGALKLFNSHL*************************************************************************PTIFSAERALNSRGRRLTIARNEAEMSKGVQVVANLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQHLAFGWYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNAKYLEFAPDRSVKSPKEIVMRQHMKKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDSETCRDLS**L*L
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
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Transmembrane Helix (MEMSAT)
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TM Helix, Signal Peptide (MEMSAT_SVM)
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
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Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MGMGFRLNLKWVSPVQSHFFTTSSCRLSSTSVRGREGSFNSARLSFLSTISEDSASYFQDPVKAYTCSFVNTQTVENDYSETEEIRQKSTSCIGQDASSRSDFRLLMENLDVLESTFADSDALRLEREILQQLGKLGALKLFNSHLSRIVKTSNVLDLSDVHTEEQKMNDSRDYHMGKILVPSKRKGKRKLKTARVSEESIETSLLSLPSEALQEGLKQPTIFSAERALNSRGRRLTIARNEAEMSKGVQVVANLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQHLAFGWYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNAKYLEFAPDRSVKSPKEIVMRQHMKKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDSETCRDLSHFLVL
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	534	2.2.26 [Sep-21-2011]
O24621	571	RNA polymerase sigma fact	yes	no	0.913	0.854	0.515	1e-133
O22056	572	RNA polymerase sigma fact	no	no	0.571	0.533	0.363	2e-58
P26683	390	RNA polymerase sigma fact	yes	no	0.533	0.730	0.342	1e-47
P77994	399	RNA polymerase sigma fact	yes	no	0.447	0.598	0.389	2e-45
P38023	399	RNA polymerase sigma fact	yes	no	0.544	0.729	0.351	8e-45
Q9LD95	547	RNA polymerase sigma fact	no	no	0.558	0.544	0.318	4e-44
P52322	416	RNA polymerase sigma fact	yes	no	0.496	0.637	0.353	1e-42
P56835	571	RNA polymerase sigma fact	yes	no	0.470	0.439	0.346	3e-41
Q31QG5	320	RNA polymerase sigma fact	no	no	0.526	0.878	0.321	3e-41
P74565	425	RNA polymerase sigma fact	N/A	no	0.462	0.581	0.346	3e-41

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

 Score =  475 bits (1222), Expect = e-133,   Method: Compositional matrix adjust.
 Identities = 263/510 (51%), Positives = 354/510 (69%), Gaps = 22/510 (4%)

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-KYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNAKYLE 442
           IQKARK L  SHG KY  D EIAK TG S+ +IR+A++CL++VGSID+K+GDC   K+LE
Sbjct: 420 IQKARKTLKTSHGIKYAADEEIAKLTGHSVKKIRAANQCLKVVGSIDKKVGDCFTTKFLE 479

Query: 443 FAPDRSVKSPKEIVMRQHMKKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFH 502
           F PD +++SP+E VMRQ  ++D+  +LE L+ RE+QV+VLRYGL D+RPKSLEEIGKL  
Sbjct: 480 FTPDTTMESPEEAVMRQSARRDIHDLLEGLEPREKQVMVLRYGLQDYRPKSLEEIGKLLK 539

Query: 503 VSKEWIRKLEKKAMTKLRDSETCRDLSHFL 532
           VSKEWIRK+E++AM KLRD     DL ++L
Sbjct: 540 VSKEWIRKIERRAMAKLRDQPNAEDLRYYL 569

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 =  227 bits (578), Expect = 2e-58,   Method: Compositional matrix adjust.
 Identities = 111/305 (36%), Positives = 197/305 (64%)

Query: 229 LNSRGRRLTIARNEAEMSKGVQVVANLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQ 288
           + +   +L   R E E+S G+Q +  LER++T L + SG+  +   WA AAGV ++ L+Q
Sbjct: 265 MTTSSSKLLTVREEHELSAGIQDLLKLERLQTELTERSGRQPTFAQWASAAGVDQKSLRQ 324

Query: 289 HLAFGWYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKF 348
            +  G  C++++IKS   LV+ +A+NY+G G+   DL+Q G  G+++GAE+FD T+G+KF
Sbjct: 325 RIHHGTLCKDKMIKSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDATKGFKF 384

Query: 349 STYVQYWIRKSISKMVARHARGIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYT 408
           STY  +WI++++ K ++  +R I++P  +     ++++ARK L +  GK+P++ EIA+ T
Sbjct: 385 STYAHWWIKQAVRKSLSDQSRMIRLPFHMVEATYRVKEARKQLYSETGKHPKNEEIAEAT 444

Query: 409 GLSLAEIRSASECLRIVGSIDQKIGDCLNAKYLEFAPDRSVKSPKEIVMRQHMKKDVFRI 468
           GLS+  + +     +   S+DQKIG   N K  E   D    + ++I++++ M++D+ ++
Sbjct: 445 GLSMKRLMAVLLSPKPPRSLDQKIGMNQNLKPSEVIADPEAVTSEDILIKEFMRQDLDKV 504

Query: 469 LESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDSETCRDL 528
           L+SL +RE+QV+  R+G+ D R K+L+EIG++  VS+E +R++E  A  KL++ +    L
Sbjct: 505 LDSLGTREKQVIRWRFGMEDGRMKTLQEIGEMMGVSRERVRQIESSAFRKLKNKKRNNHL 564

Query: 529 SHFLV 533
             +LV
Sbjct: 565 QQYLV 569

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

Arabidopsis thaliana (taxid: 3702)

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

 Score =  191 bits (486), Expect = 1e-47,   Method: Compositional matrix adjust.
 Identities = 98/286 (34%), Positives = 182/286 (63%), Gaps = 1/286 (0%)

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 IRSASECLRIVGSIDQKIGDCLNAKYLEFAPDRSVKSPKEIVMRQHMKKDVFRILESLDS 474
           +R  ++  ++  S++  IG   +++  +F  +   ++P++ V +  +++D+ ++L+SL  
Sbjct: 273 LRFIAKSAQLPISLETPIGKEEDSRLGDFI-ESDGETPEDQVSKNLLREDLEKVLDSLSP 331

Query: 475 RERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLR 520
           RER VL LRYGL+D R K+LEEIG++F+V++E IR++E KA+ KLR
Sbjct: 332 RERDVLRLRYGLDDGRMKTLEEIGQIFNVTRERIRQIEAKALRKLR 377

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|P77994|RPOD_THEMA RNA polymerase sigma factor RpoD OS=Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099) GN=rpoD PE=1 SV=3

 Score =  183 bits (465), Expect = 2e-45,   Method: Compositional matrix adjust.
 Identities = 93/239 (38%), Positives = 150/239 (62%)

Query: 296 CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYW 355
            +E+LI S   LV+ +A+ Y G G+ F DL+Q GN+G+L+  E+FD  +GYKFSTY  +W
Sbjct: 155 AKEKLITSNLRLVVSIAKRYMGRGLSFQDLIQEGNIGLLKAVEKFDWRKGYKFSTYATWW 214

Query: 356 IRKSISKMVARHARGIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEI 415
           IR++I++ +A  AR I+IP  +   I+K+ + R+     HG+ P   E+AK  G    +I
Sbjct: 215 IRQAITRAIADQARTIRIPVHMVETINKLNRLRREYYQKHGEEPSIEELAKMMGKPPEKI 274

Query: 416 RSASECLRIVGSIDQKIGDCLNAKYLEFAPDRSVKSPKEIVMRQHMKKDVFRILESLDSR 475
           +   E  +   S++  IG+  ++   +F  D S+ SPK+  MR  M++++ ++L++L  R
Sbjct: 275 KEILEAAKETISLESPIGEDEDSSIEDFVADDSIASPKKEAMRMLMREELEKVLKTLSPR 334

Query: 476 ERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDSETCRDLSHFLVL 534
           E  VL +RYGL D +PK+LEE+G+ F+V++E IR++E KA+ KLR     + L   L L
Sbjct: 335 EAMVLRMRYGLLDGKPKTLEEVGQYFNVTRERIRQIEVKALRKLRHPSRSKYLKSLLSL 393

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.

Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099) (taxid: 243274)

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

 Score =  182 bits (461), Expect = 8e-45,   Method: Compositional matrix adjust.
 Identities = 103/293 (35%), Positives = 182/293 (62%), Gaps = 2/293 (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 TGLSLAEIRSASECLRIVGSIDQKIGDCLNAKYLEFAPDRSVKSPKEIVMRQHMKKDVFR 467
             +++ ++R  ++  ++  S++  IG   +++  +F  +   ++P++ V +  +++D+  
Sbjct: 275 MEMTIEKLRFIAKSAQLPISLETPIGKEEDSRLGDFI-EADGETPEDEVAKNLLREDLEG 333

Query: 468 ILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLR 520
           +L +L  RER VL LRYGL+D R K+LEEIG+LF+V++E IR++E KA+ KLR
Sbjct: 334 VLSTLSPRERDVLRLRYGLDDGRMKTLEEIGQLFNVTRERIRQIEAKALRKLR 386

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

 Score =  179 bits (455), Expect = 4e-44,   Method: Compositional matrix adjust.
 Identities = 95/298 (31%), Positives = 172/298 (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 EIRSASECLRIVGSIDQKIGDCLNAKYLEFAPDRSVKSPKEIVMRQHMKKDVFRILESLD 473
           ++       R   S+ Q I    +  + E  PD  +++P   V +Q M+  V  +L  L 
Sbjct: 425 KLDKLLYNTRTPLSMQQPIWSDQDTTFQEITPDSGIETPTMSVGKQLMRNHVRNLLNVLS 484

Query: 474 SRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDSETCRDLSHF 531
            +ER+++ LR+G++  + +SL EIG+++ +SKE +R+LE +A+ +L+ +     L  +
Sbjct: 485 PKERRIIKLRFGIDGGKQRSLSEIGEIYGLSKERVRQLESRALYRLKQNMNSHGLHAY 542

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

 Score =  174 bits (442), Expect = 1e-42,   Method: Compositional matrix adjust.
 Identities = 94/266 (35%), Positives = 165/266 (62%), Gaps = 1/266 (0%)

Query: 255 LERIKTTLEKESGKAASLNCWAQAAGVSERVLKQHLAFGWYCREELIKSTRPLVLFLARN 314
           L  IK  L K    A  L  W   +       K+ L  G   +E++++S   LV+ +A+ 
Sbjct: 139 LSDIKAYLGKTELTAPLLEEWLAKSKEYLSAFKRRLYHGRRAKEKMVQSNLRLVVSIAKK 198

Query: 315 YRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIP 374
           Y   G+ F DL+Q G++G+++ AE+FDH +GYKFSTY  +WIR++I++ +A  +R I++P
Sbjct: 199 YMNRGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYATWWIRQAITRAIADQSRTIRLP 258

Query: 375 CKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGD 434
             L   IS+I+K  K L+    + P + EIA    +++ ++R  ++  ++  S++  IG 
Sbjct: 259 VHLYETISRIKKTTKILSQEMRRKPTEEEIATKMEMTIEKLRFIAKSAQLPISLETPIGK 318

Query: 435 CLNAKYLEFAPDRSVKSPKEIVMRQHMKKDVFRILESLDSRERQVLVLRYGLNDHRPKSL 494
             +++  +F  +   ++P++ V +  +++D+  +L++L  RER VL LRYGL+D R K+L
Sbjct: 319 EEDSRLGDFI-EADGETPEDEVSKNLLREDLENVLDTLSPRERDVLRLRYGLDDGRMKTL 377

Query: 495 EEIGKLFHVSKEWIRKLEKKAMTKLR 520
           EEIG++F+V++E IR++E KA+ KLR
Sbjct: 378 EEIGQIFNVTRERIRQIEAKALRKLR 403

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|P56835|RPOD_CHLMU RNA polymerase sigma factor RpoD OS=Chlamydia muridarum (strain MoPn / Nigg) GN=rpoD PE=3 SV=1

 Score =  170 bits (430), Expect = 3e-41,   Method: Compositional matrix adjust.
 Identities = 87/251 (34%), Positives = 151/251 (60%)

Query: 284 RVLKQHLAFGWYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHT 343
           R+L++ +      ++E+++S   LV+ +A+ Y   G+ F DL+Q GN+G+++  E+F++ 
Sbjct: 305 RMLQRWMDKSQEAKKEMVESNLRLVISIAKKYTNRGLSFLDLIQEGNMGLMKAVEKFEYR 364

Query: 344 RGYKFSTYVQYWIRKSISKMVARHARGIKIPCKLNREISKIQKARKALTNSHGKYPEDIE 403
           RGYKFSTY  +WIR+++++ +A  AR I+IP  +   I+K+ +  K L    GK P   E
Sbjct: 365 RGYKFSTYATWWIRQAVTRAIADQARTIRIPVHMIETINKVLRGAKKLMMETGKEPTPEE 424

Query: 404 IAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNAKYLEFAPDRSVKSPKEIVMRQHMKK 463
           + +  G +   +R   +  +   S+  ++GD   + + +F  D +V+SP E      +K 
Sbjct: 425 LGEELGFTPDRVREIYKIAQHPISLQAEVGDSGESSFGDFLEDTAVESPAEATGYSMLKD 484

Query: 464 DVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDSE 523
            +  +L++L  RER VL+ R+GL D RPK+LEE+G  F+V++E IR++E KA+ K+R   
Sbjct: 485 KMKEVLKTLTDRERFVLIHRFGLLDGRPKTLEEVGSAFNVTRERIRQIEAKALRKMRHPI 544

Query: 524 TCRDLSHFLVL 534
             + L  FL L
Sbjct: 545 RSKQLRAFLDL 555

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.

Chlamydia muridarum (strain MoPn / Nigg) (taxid: 243161)

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

 Score =  170 bits (430), Expect = 3e-41,   Method: Compositional matrix adjust.
 Identities = 91/283 (32%), Positives = 165/283 (58%), Gaps = 2/283 (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 ECLRIVGSIDQKIGDCLNAKYLEFAPDRSVKSPKEIVMRQHMKKDVFRILESLDSRERQV 479
           E  R   S+D ++GD  + +  +   +    +P+E  ++  M++D+ R+L+ L  ++RQV
Sbjct: 209 EKARHPLSLDLRVGDNQDTELGDLL-ETDCTTPEEFTLQASMRRDIDRLLDQLTEQQRQV 267

Query: 480 LVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDS 522
           + LRYGL D +  +L  IG    +S+E +R+LE++A+  LR +
Sbjct: 268 IALRYGLEDGQVMTLASIGDRLQISRERVRQLEREALHTLRQA 310

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

 Score =  169 bits (429), Expect = 3e-41,   Method: Compositional matrix adjust.
 Identities = 86/248 (34%), Positives = 161/248 (64%), Gaps = 1/248 (0%)

Query: 273 NCWAQAAGVSERVLKQHLAFGWYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVG 332
           N W+Q    +    ++ L      ++++++S   LV+ +A+ Y   G+ F DL+Q G++G
Sbjct: 166 NEWSQQPNKNFAAFRRRLFLDRRAKDKMVQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLG 225

Query: 333 VLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIPCKLNREISKIQKARKALT 392
           +++ AE+FDH +GYKFSTY  +WIR++I++ +A  +R I++P  L   IS+I+K  K L+
Sbjct: 226 LIRAAEKFDHEKGYKFSTYATWWIRQAITRAIADQSRTIRLPVHLYETISRIKKTTKLLS 285

Query: 393 NSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNAKYLEFAPDRSVKSP 452
               + P + EIA+   +++ ++R  ++  ++  S++  IG   +++  +F  +   ++P
Sbjct: 286 QEMRRKPTEEEIAEKMEMTIEKLRFIAKSAQLPISLETPIGKEEDSRLGDFI-EADGETP 344

Query: 453 KEIVMRQHMKKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLE 512
           ++ V +  +++D+  +L++L  RER VL LRYGL+D R K+LEEIG++F+V++E IR++E
Sbjct: 345 EDEVSKNLLREDLENVLDTLSPRERDVLRLRYGLDDGRMKTLEEIGQIFNVTRERIRQIE 404

Query: 513 KKAMTKLR 520
            KA+ KLR
Sbjct: 405 AKALRKLR 412

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

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

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Length	Definition	Q cover	H cover	Identity	E-value
Query	534
225429414	561	PREDICTED: RNA polymerase sigma factor r	0.996	0.948	0.556	1e-175
255550882	560	RNA polymerase sigma factor rpoD, putati	0.994	0.948	0.570	1e-167
147865632	611	hypothetical protein VITISV_036980 [Viti	0.938	0.819	0.554	1e-164
224088962	559	predicted protein [Populus trichocarpa]	0.994	0.949	0.533	1e-161
39840783	548	sigma factor [Spinacia oleracea]	0.990	0.965	0.500	1e-145
449461399	559	PREDICTED: RNA polymerase sigma factor s	0.985	0.940	0.501	1e-145
356565804	551	PREDICTED: RNA polymerase sigma factor r	0.975	0.945	0.498	1e-137
7363220	567	sigma factor 3 [Sinapis alba]	0.895	0.843	0.505	1e-132
2398853	571	plastid RNA polymerase sigma-subunit [Ar	0.913	0.854	0.515	1e-132
297820128	568	predicted protein [Arabidopsis lyrata su	0.951	0.894	0.502	1e-131

>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 =  622 bits (1604), Expect = e-175,   Method: Compositional matrix adjust.
 Identities = 311/559 (55%), Positives = 397/559 (71%), Gaps = 27/559 (4%)

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 SHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNAKYLEFAPDRSVKSPK 453
           SHG+YP+D EIAK+TGLSLA+IRSA  CLR+VGS DQ   DC  A  LEF PD S+KSP+
Sbjct: 421 SHGRYPDDNEIAKFTGLSLAKIRSAGNCLRVVGSTDQSFQDCWGATILEFTPDTSIKSPE 480

Query: 454 EIVMRQHMKKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEK 513
           E  M+Q  +KD+  +L+ LD RERQ+LVLRYG  + + KSLEEIG+ F+VSKEWIRKLEK
Sbjct: 481 EGFMQQCKRKDIHNLLKGLDPRERQILVLRYGFGEQQRKSLEEIGRRFNVSKEWIRKLEK 540

Query: 514 KAMTKLRDSETCRDLSHFL 532
            A+  LRD E C++L H++
Sbjct: 541 TALANLRDEEICQNLRHYV 559

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

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 =  594 bits (1531), Expect = e-167,   Method: Compositional matrix adjust.
 Identities = 319/559 (57%), Positives = 418/559 (74%), Gaps = 28/559 (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 SHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNAKYLEFAPDRSVKSPK 453
           S+GKYP+D EIAKYTGLSLA+I SAS CLR+VGSIDQKIG+ LNAKYLEF PD SV+SP+
Sbjct: 420 SNGKYPDDDEIAKYTGLSLAKIESASRCLRVVGSIDQKIGESLNAKYLEFLPDTSVQSPE 479

Query: 454 EIVMRQHMKKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEK 513
           E+VMRQHM +D+  +L SLDSRERQVL+LR+GLND++PKSLEEIG+ FHVSKEW+R+LEK
Sbjct: 480 EVVMRQHMIQDMHNLLRSLDSRERQVLILRFGLNDYQPKSLEEIGRHFHVSKEWVRRLEK 539

Query: 514 KAMTKLRDSETCRDLSHFL 532
           + MT+LR+ ETCR+L H++
Sbjct: 540 RVMTRLRNEETCRNLRHYI 558

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  586 bits (1510), Expect = e-164,   Method: Compositional matrix adjust.
 Identities = 293/528 (55%), Positives = 377/528 (71%), Gaps = 27/528 (5%)

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 VGSIDQKIGDCLNAKYLEFAPDRSVKSPKEIVMRQHMKKDVFRILESLDSRERQVLVLRY 484
           VGS DQ   DC  A  LEF PD S+KSP+E  M+Q  +KD+  +L+ LD RERQ+LVLRY
Sbjct: 502 VGSTDQSFQDCWGATILEFTPDTSIKSPEEGFMQQCKRKDIHNLLKGLDPRERQILVLRY 561

Query: 485 GLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDSETCRDLSHFL 532
           G  + + KSLEEIG+ F+VSKEWIRKLEK A+  LRD E C++L H++
Sbjct: 562 GFGEQQRKSLEEIGRRFNVSKEWIRKLEKTALANLRDEEICQNLRHYV 609

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 =  575 bits (1482), Expect = e-161,   Method: Compositional matrix adjust.
 Identities = 300/562 (53%), Positives = 397/562 (70%), Gaps = 31/562 (5%)

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--------TSCIGQDASS------------- 99
             K++ CS    Q VEND  + E ++            + +G D  S             
Sbjct: 61  SFKSFACSSA-AQNVENDCLQMERLKMNVDKTSHVSINNMMGNDKVSVEEEISTSHTRLR 119

Query: 100 ---RSDFRLLMENLDVLESTFADSDALRLEREILQQLGKLGALKLFNSHLSRIVKTSNVL 156
               S    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 NSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNAKYLEFAPDRSVKSP 452
           NSHG+YP+D E+AK+TGLSLA+I SA +CLR+V S+DQKIG+   AKY EF PD S+++P
Sbjct: 418 NSHGRYPDDWEVAKFTGLSLAKIESAQKCLRVVASLDQKIGEGHYAKYSEFIPDMSIQNP 477

Query: 453 KEIVMRQHMKKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLE 512
           +E VMRQHM+++++ +L  LDSRE+QV+VLRYG  D++PKSL EIG+LF VSKE +RK+E
Sbjct: 478 EEAVMRQHMREEIYDLLRGLDSREKQVMVLRYGFKDNQPKSLAEIGRLFRVSKERVRKIE 537

Query: 513 KKAMTKLRDSETCRDLSHFLVL 534
           KK M KLRD    R+LS +++L
Sbjct: 538 KKIMIKLRDEGIRRNLSRYMIL 559

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  522 bits (1344), Expect = e-145,   Method: Compositional matrix adjust.
 Identities = 277/553 (50%), Positives = 382/553 (69%), Gaps = 24/553 (4%)

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 IEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNAKYLEFAPDRSVKSPKEIVMRQHM 461
           +E++K TGLSL +I+SA  CLRIVGS+DQK+G  +N KYLE  PD +++ P++ VM+QHM
Sbjct: 417 VEVSKSTGLSLDKIKSADNCLRIVGSLDQKVGHFINMKYLECTPDTALEMPEKTVMKQHM 476

Query: 462 KKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRD 521
           + DV ++L+ LD +ER+VL+ RYGL  H   SL E+GK+F VSKEWIRK+EK+A+TKLR 
Sbjct: 477 RNDVHKLLQELDPKERRVLIHRYGLEGH-CMSLHEVGKVFDVSKEWIRKMEKRALTKLRT 535

Query: 522 SETCRDLSHFLVL 534
            +   +L H+L L
Sbjct: 536 EQNQTNLKHYLNL 548

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 =  521 bits (1343), Expect = e-145,   Method: Compositional matrix adjust.
 Identities = 283/564 (50%), Positives = 380/564 (67%), Gaps = 38/564 (6%)

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 KALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNAKYLEFAPDRS 448
           K L +S  +Y +D +IA+ TGL LA++R AS CL++VGS DQK+GD +N KY+EF  D S
Sbjct: 416 KVLNHSGRRYSDD-DIARATGLPLAKVRVASNCLKVVGSNDQKMGDGVNMKYMEFTADMS 474

Query: 449 VKSPKEIVMRQHMKKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWI 508
           ++SP+E V R+ MKKD+F IL+ L+SRERQVLVLRYGL D  PKSLEEIGKL H+SKEW+
Sbjct: 475 IQSPEETVKRKLMKKDIFNILQRLESRERQVLVLRYGLVDFEPKSLEEIGKLLHISKEWV 534

Query: 509 RKLEKKAMTKLRDSETCRDLSHFL 532
           RK+EKKAMTKL++ ET + LSH+L
Sbjct: 535 RKIEKKAMTKLKNEETVKHLSHYL 558

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 =  495 bits (1274), Expect = e-137,   Method: Compositional matrix adjust.
 Identities = 280/562 (49%), Positives = 386/562 (68%), Gaps = 41/562 (7%)

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 NSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNAKYLEFAPDRSVKSP 452
           ++H K P+D EIAK TGLSL +I+SAS CLRIV SIDQK+GD L  +Y+E  PD +++SP
Sbjct: 410 STHKKCPDDYEIAKMTGLSLDKIKSASNCLRIVASIDQKVGDYLGVEYMELLPDATIESP 469

Query: 453 KEIVMRQHMKKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLE 512
           ++ VM+QHM+KDV  +L+ L+ RER++L LR+GLND++P+SL++IG LF VSKE IRK+E
Sbjct: 470 EDAVMKQHMRKDVHDLLKGLNLRERKILTLRFGLNDNQPRSLQDIGTLFKVSKERIRKIE 529

Query: 513 KKAMTKLRDSETCRDLSHFLVL 534
           KKA+TKL++  T   L ++L L
Sbjct: 530 KKALTKLKNEATISKLHYYLDL 551

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 =  479 bits (1233), Expect = e-132,   Method: Compositional matrix adjust.
 Identities = 255/504 (50%), Positives = 349/504 (69%), Gaps = 26/504 (5%)

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-KYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNAKYLEFAPDRS 448
            L  S G KYP D EI+K TG SL +IR+A++CL++VGSID+K+GDC   ++LEF PD +
Sbjct: 422 TLKTSQGIKYPADEEISKLTGYSLKKIRAANQCLKVVGSIDKKVGDCFTTRFLEFTPDPT 481

Query: 449 VKSPKEIVMRQHMKKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWI 508
           ++SP+E VMRQ  + +V  +LE L+ RE+QV+VLRYGL D+ PKSLEEIGK+  VSKE I
Sbjct: 482 MESPEEAVMRQSARGEVHNLLEGLEPREKQVMVLRYGLQDYSPKSLEEIGKILRVSKEGI 541

Query: 509 RKLEKKAMTKLRDSETCRDLSHFL 532
           RK+E++AM KLRD     +L ++L
Sbjct: 542 RKIERRAMAKLRDQPKADNLRYYL 565

Source: Sinapis alba

Species: Sinapis alba

Genus: Sinapis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|2398853|dbj|BAA22215.1| plastid RNA polymerase sigma-subunit [Arabidopsis thaliana]

 Score =  477 bits (1227), Expect = e-132,   Method: Compositional matrix adjust.
 Identities = 263/510 (51%), Positives = 355/510 (69%), Gaps = 22/510 (4%)

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 LVLFLARNYRG+GI   
Sbjct: 300 EESGKVASLSCWAAAAGMNEKLLMRNLHYGWYCRDELVKSTRSLVLFLARNYRGMGIAHE 359

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

Query: 384 IQKARKALTNSHG-KYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNAKYLE 442
           IQKARK L  SHG KY  D EIAK TG S+ +IR+A++CL++VGSID+K+GDC   K+LE
Sbjct: 420 IQKARKTLKTSHGIKYAADEEIAKLTGHSVKKIRAANQCLKVVGSIDKKVGDCFTTKFLE 479

Query: 443 FAPDRSVKSPKEIVMRQHMKKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFH 502
           F PD +++SP+E VMRQ  ++D+  +LE L+ RE+QV+VLRYGL D+RPKSLEEIGKLF 
Sbjct: 480 FTPDTTMESPEEAVMRQSARRDIHDLLEGLEPREKQVMVLRYGLQDYRPKSLEEIGKLFK 539

Query: 503 VSKEWIRKLEKKAMTKLRDSETCRDLSHFL 532
           VSKEWIRK+E++AM KLRD     DL ++L
Sbjct: 540 VSKEWIRKIERRAMAKLRDQPNAEDLRYYL 569

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

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 =  476 bits (1224), Expect = e-131,   Method: Compositional matrix adjust.
 Identities = 264/525 (50%), Positives = 363/525 (69%), Gaps = 17/525 (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 IDQKIGDCLNAKYLEFAPDRSVKSPKEIVMRQHMKKDVFRILESLDSRERQVLVLRYGLN 487
           I++K+GDC + K+LEF PD +++SP+E VMRQ  ++D+  +LE L+ RE+QV+VLRYGL 
Sbjct: 462 IEKKVGDCFSTKFLEFTPDTTMESPEEAVMRQSARRDIHDLLEGLEPREKQVMVLRYGLQ 521

Query: 488 DHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDSETCRDLSHFL 532
           ++RPKSLEEIGKL  VSKEWIRK+E++AM KLRD     DL ++L
Sbjct: 522 NYRPKSLEEIGKLLRVSKEWIRKIERRAMAKLRDQPNAEDLRYYL 566

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	534
TAIR|locus:2084420	571	SIGC "AT3G53920" [Arabidopsis	0.904	0.845	0.505	7.4e-121
TAIR|locus:2025650	572	SIG2 "AT1G08540" [Arabidopsis	0.573	0.534	0.371	2.3e-55
TAIR|locus:2057996	547	SIGF "AT2G36990" [Arabidopsis	0.539	0.526	0.331	2.2e-43
TIGR_CMR|GSU_3089	577	GSU_3089 "RNA polymerase sigma	0.544	0.504	0.322	9.5e-42
TIGR_CMR|CJE_1081	622	CJE_1081 "RNA polymerase sigma	0.436	0.374	0.346	1.3e-40
TAIR|locus:2173249	419	SIG4 "AT5G13730" [Arabidopsis	0.507	0.646	0.348	1.4e-40
UNIPROTKB|Q59563	323	mysB "RNA polymerase sigma fac	0.432	0.715	0.354	2.9e-39
TIGR_CMR|DET_0551	520	DET_0551 "RNA polymerase sigma	0.436	0.448	0.369	7.8e-39
TIGR_CMR|APH_0576	627	APH_0576 "RNA polymerase sigma	0.440	0.374	0.305	1.2e-38
TIGR_CMR|CHY_0455	370	CHY_0455 "RNA polymerase sigma	0.441	0.637	0.360	2.6e-38

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

 Score = 1189 (423.6 bits), Expect = 7.4e-121, P = 7.4e-121
 Identities = 251/497 (50%), Positives = 334/497 (67%)

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 -KYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNAKYLEFAPDRSVKSPKEI 455
              KY  D EIAK TG S+ +IR+A++CL++VGSID+K+GDC   K+LEF PD +++SP+E 
Sbjct:   433 IKYAADEEIAKLTGHSVKKIRAANQCLKVVGSIDKKVGDCFTTKFLEFTPDTTMESPEEA 492

Query:   456 VMRQHMKKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKA 515
             VMRQ  ++D+  +LE L+ RE+QV+VLRYGL D+RPKSLEEIGKL  VSKEWIRK+E++A
Sbjct:   493 VMRQSARRDIHDLLEGLEPREKQVMVLRYGLQDYRPKSLEEIGKLLKVSKEWIRKIERRA 552

Query:   516 MTKLRDSETCRDLSHFL 532
             M KLRD     DL ++L
Sbjct:   553 MAKLRDQPNAEDLRYYL 569

GO:0003677 "DNA binding" evidence=ISS

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

GO:0003899 "DNA-directed RNA polymerase activity" evidence=ISS;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 = 571 (206.1 bits), Expect = 2.3e-55, P = 2.3e-55
 Identities = 114/307 (37%), Positives = 199/307 (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 YTGLSLAEIRSASECLRIVGSIDQKIGDCLNAKYLEFAPDRSVKSPKEIVMRQHMKKDVF 466
              TGLS+  + +     +   S+DQKIG   N K  E   D    + ++I++++ M++D+ 
Sbjct:   443 ATGLSMKRLMAVLLSPKPPRSLDQKIGMNQNLKPSEVIADPEAVTSEDILIKEFMRQDLD 502

Query:   467 RILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDSETCR 526
             ++L+SL +RE+QV+  R+G+ D R K+L+EIG++  VS+E +R++E  A  KL++ +   
Sbjct:   503 KVLDSLGTREKQVIRWRFGMEDGRMKTLQEIGEMMGVSRERVRQIESSAFRKLKNKKRNN 562

Query:   527 DLSHFLV 533
              L  +LV
Sbjct:   563 HLQQYLV 569

GO:0003677 "DNA binding" evidence=ISS

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

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

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

GO:0009507 "chloroplast" evidence=ISM;IDA

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

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

GO:0009658 "chloroplast organization" evidence=IMP

GO:0006399 "tRNA metabolic process" evidence=IMP

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

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

GO:0009637 "response to blue light" evidence=IGI;RCA

GO:0010114 "response to red light" evidence=IEP;RCA

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

GO:0006364 "rRNA processing" evidence=RCA

GO:0009902 "chloroplast relocation" evidence=RCA

GO:0010027 "thylakoid membrane organization" evidence=RCA

GO:0010218 "response to far red light" evidence=RCA

GO:0016117 "carotenoid biosynthetic process" evidence=RCA

GO:0019288 "isopentenyl diphosphate biosynthetic process, mevalonate-independent pathway" evidence=RCA

GO:0034660 "ncRNA metabolic process" evidence=RCA

GO:0016987 "sigma factor activity" evidence=ISS

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

 Score = 458 (166.3 bits), Expect = 2.2e-43, P = 2.2e-43
 Identities = 96/290 (33%), Positives = 172/290 (59%)

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 AEIRSASECLRIVGSIDQKIGDCLNAKYLEFAPDRSVKSPKEIVMRQHMKKDVFRILESL 472
              ++       R   S+ Q I    +  + E  PD  +++P   V +Q M+  V  +L  L
Sbjct:   424 EKLDKLLYNTRTPLSMQQPIWSDQDTTFQEITPDSGIETPTMSVGKQLMRNHVRNLLNVL 483

Query:   473 DSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDS 522
               +ER+++ LR+G++  + +SL EIG+++ +SKE +R+LE +A+ +L+ +
Sbjct:   484 SPKERRIIKLRFGIDGGKQRSLSEIGEIYGLSKERVRQLESRALYRLKQN 533

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

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

 Score = 419 (152.6 bits), Expect = 9.5e-42, Sum P(2) = 9.5e-42
 Identities = 97/301 (32%), Positives = 174/301 (57%)

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 LAEIRSASECLRIVGSIDQKIGDCLNAKYLEFAPDRSVKSPKEIVMRQHMKKDVFRILES 471
             L ++R   +  +   S++  IG+  ++   +F  D+ V SP E V++ ++ +   R+L +
Sbjct:   456 LDKVRKVLKIAKEPISLETPIGEEEDSHLGDFIEDKGVVSPLEAVIKANLSEQTARVLAT 515

Query:   472 LDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDSETCRDLSHF 531
             L  RE +VL +R+G+ +    +LEE+G+ F V++E IR++E KA+ KLR     + L  F
Sbjct:   516 LTPREEKVLRMRFGIGEKSDHTLEEVGQDFEVTRERIRQIEAKALRKLRHPSRAKKLRSF 575

Query:   532 L 532
             +
Sbjct:   576 V 576

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

GO:0016987 "sigma factor activity" evidence=ISS

TIGR_CMR|CJE_1081 CJE_1081 "RNA polymerase sigma factor RpoD" [Campylobacter jejuni RM1221 (taxid:195099)]

 Score = 414 (150.8 bits), Expect = 1.3e-40, Sum P(2) = 1.3e-40
 Identities = 81/234 (34%), Positives = 148/234 (63%)

Query:   300 LIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKS 359
             + KS   LV+ +A+ Y   G+PF DL+Q GN+G+++  ++F++ RGYKFSTY  +WIR++
Sbjct:   385 MAKSNLRLVVSIAKRYTNRGLPFLDLIQEGNIGLMKAVDKFEYKRGYKFSTYATWWIRQA 444

Query:   360 ISKMVARHARGIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSAS 419
             IS+ +A  AR I+IP  +   I++I K  +      GK P+   IAK  GLS+ +++   
Sbjct:   445 ISRAIADQARTIRIPIHMIETINQINKIIREHLQKDGKEPDVSVIAKEVGLSVDKVKQVI 504

Query:   420 ECLRIVGSIDQKIGDCLNAKYLEFAPDRSVKSPKEIVMRQHMKKDVFRILESLDSRERQV 479
             +  +   S++  IG+  + K+ +F  DR+  SP + +++  +K+ +  +L+ L+ RE+ V
Sbjct:   505 KITKEPISLEAPIGNEDDGKFGDFVEDRNSLSPMDHILKDDLKEQIDEVLDQLNDREKAV 564

Query:   480 LVLRYGL-NDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDSETCRDLSHFL 532
             + +R+GL +D   ++LEEIGK  +V++E +R++E  A+ KL+  +  R L +++
Sbjct:   565 IRMRFGLMDDESDRTLEEIGKELNVTRERVRQIESSAIKKLKHPKVGRKLKNYI 618

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

GO:0016987 "sigma factor activity" evidence=ISS

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

 Score = 411 (149.7 bits), Expect = 1.4e-40, Sum P(2) = 1.4e-40
 Identities = 97/278 (34%), Positives = 159/278 (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 IPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKI 432
             +P  +    +K+ +A   LT    + P   EIA++  L+++ +R A E  R   S+D+  
Sbjct:   256 LPGSMWELTAKVAEASNVLTRKLRRQPSCEEIAEHLNLNVSAVRLAVERSRSPVSLDRVA 315

Query:   433 GDC--LNAKYLEFAPDRSVKSPKEIVMRQHMKKDVFRILESLDSRERQVLVLRYGLNDHR 490
                  +  + +   PD +   P+E+V R+HMK ++ ++L SL +RE +VL L +GLN   
Sbjct:   316 SQNGRMTLQEIVRGPDET--RPEEMVKREHMKHEIEQLLGSLTARESRVLGLYFGLNGET 373

Query:   491 PKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDSETCRDL 528
             P S EEIGK   +S+E +R++   A+ KLR+     DL
Sbjct:   374 PMSFEEIGKSLKLSRERVRQINGIALKKLRNVHNVNDL 411

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 = 419 (152.6 bits), Expect = 2.9e-39, P = 2.9e-39
 Identities = 82/231 (35%), Positives = 145/231 (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 AEIRSASECLRIVGSIDQKIGDCLNAKYLEFAPDRSVKSPKEIVMRQHMKKDVFRILESL 472
              +I    E  R   S+D  +G    A   +F  D    S +  V+ + +  D+  +L +L
Sbjct:   203 DKINDLLEHSRDPVSLDMPVGSEEEAPLGDFIEDAEAMSAENAVIAELLHTDIRSVLATL 262

Query:   473 DSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDSE 523
             D RE QV+ LR+GL+D +P++L++IGKLF +S+E +R++E+  M+KLR  E
Sbjct:   263 DEREHQVIRLRFGLDDGQPRTLDQIGKLFGLSRERVRQIERDVMSKLRHGE 313

GO:0001666 "response to hypoxia" evidence=IEP

GO:0005829 "cytosol" evidence=IDA

GO:0005886 "plasma membrane" evidence=IDA

GO:0009408 "response to heat" evidence=IEP

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

GO:0016987 "sigma factor activity" evidence=IGI

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

GO:0040007 "growth" evidence=IMP

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

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

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

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

 Score = 415 (151.1 bits), Expect = 7.8e-39, P = 7.8e-39
 Identities = 86/233 (36%), Positives = 145/233 (62%)

Query:   300 LIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKS 359
             LI++   LV+ +A+ + G G+P  DL+Q GN+G+++  E+FD  RG+KFSTY  +WIR++
Sbjct:   287 LIQANLRLVVSVAKKHIGRGMPLLDLIQEGNIGLIRAVEKFDFHRGFKFSTYATWWIRQA 346

Query:   360 ISKMVARHARGIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSAS 419
             I++ +A  AR I+IP  +   I+K+    + L+   G+ P   EIA    L   ++R  +
Sbjct:   347 ITRAIADQARTIRIPVHMVETINKLLSISRQLSQKLGREPTPDEIAVEMDLPPEKVREIA 406

Query:   420 ECLRIVGSIDQKIGDCLNAKYLEFAPDRSVKSPKEIVMRQHMKKDVFRILESLDSRERQV 479
             +  ++  S++  IG+  ++   +F  D++  +P +   RQ +K+ +  +L SL  RER+V
Sbjct:   407 KVSQLPVSLESPIGEEEDSHLGDFIEDQNALAPPDAASRQLLKEQIDTVLGSLTPRERRV 466

Query:   480 LVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDSETCRDLSHFL 532
             L LR+GL D R ++LEE+GK F+V++E IR++E KA+ KLR     R L  +L
Sbjct:   467 LQLRFGLEDGRSRTLEEVGKEFNVTRERIRQIEAKALRKLRHPSRSRKLKDYL 519

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 = 379 (138.5 bits), Expect = 1.2e-38, Sum P(3) = 1.2e-38
 Identities = 72/236 (30%), Positives = 144/236 (61%)

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 SASECLRIVGSIDQKIGDCLNAKYLEFAPDRSVKSPKEIVMRQHMKKDVFRILESLDSRE 476
                + ++   S++  IGD  ++ + +   D+    P+   +   +++   ++L +L  +E
Sbjct:   511 KVMKIVKDPVSLESPIGDDDSSTFGDCIEDKRAVKPENAAVLADLREITTKVLSTLTPKE 570

Query:   477 RQVLVLRYGLNDH-RPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDSETCRDLSHF 531
              ++L +R+G+    +  +LEE+G+LF+V++E IR++E KA+ KLR     R L  F
Sbjct:   571 ERILRMRFGIGKSGKDHTLEEVGRLFNVTRERIRQIEAKALRKLRHPSRARKLRGF 626

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 = 410 (149.4 bits), Expect = 2.6e-38, P = 2.6e-38
 Identities = 85/236 (36%), Positives = 147/236 (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 SASECLRIVGSIDQKIGDCLNAKYLEFAPDRSVKSPKEIVMRQHMKKDVFRILESLDSRE 476
                +  +   S++  IG+  ++   +F  D   K+P E      +++ +  +L++L  RE
Sbjct:   254 EIMKIAQEPVSLETPIGEEEDSHLGDFVEDPDAKAPVEEASYTLLREQLDEVLKTLTERE 313

Query:   477 RQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDSETCRDLSHFL 532
             ++VL LR+GL+D R ++LEE+G++F V++E IR++E KA+ KLR     + L  FL
Sbjct:   314 QKVLRLRFGLDDGRARTLEEVGQIFGVTRERIRQIEAKALRKLRHPSRSKKLKDFL 369

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

GO:0016987 "sigma factor activity" evidence=ISS

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
O24621	SIGC_ARATH	No assigned EC number	0.5156	0.9138	0.8546	yes	no

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Fail to connect to STRING server

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	534
TIGR02997	298	TIGR02997, Sig70-cyanoRpoD, RNA polymerase sigma f	1e-63
TIGR02393	238	TIGR02393, RpoD_Cterm, RNA polymerase sigma factor	2e-59
COG0568	342	COG0568, RpoD, DNA-directed RNA polymerase, sigma	1e-57
PRK07406	373	PRK07406, PRK07406, RNA polymerase sigma factor Rp	1e-52
PRK05949	327	PRK05949, PRK05949, RNA polymerase sigma factor; V	9e-51
PRK07405	317	PRK07405, PRK07405, RNA polymerase sigma factor Si	1e-50
PRK07921	324	PRK07921, PRK07921, RNA polymerase sigma factor Si	1e-46
PRK07598	415	PRK07598, PRK07598, RNA polymerase sigma factor Si	3e-44
TIGR02394	285	TIGR02394, rpoS_proteo, RNA polymerase sigma facto	1e-41
PRK09210	367	PRK09210, PRK09210, RNA polymerase sigma factor Rp	1e-41
PRK05901	509	PRK05901, PRK05901, RNA polymerase sigma factor; P	3e-40
PRK05658	619	PRK05658, PRK05658, RNA polymerase sigma factor Rp	7e-30
PRK05657	325	PRK05657, PRK05657, RNA polymerase sigma factor Rp	1e-28
TIGR02980	227	TIGR02980, SigBFG, RNA polymerase sigma-70 factor,	6e-25
TIGR02479	224	TIGR02479, FliA_WhiG, RNA polymerase sigma factor,	7e-25
COG1191	247	COG1191, FliA, DNA-directed RNA polymerase special	2e-23
TIGR02392	270	TIGR02392, rpoH_proteo, alternative sigma factor R	8e-23
PRK06596	284	PRK06596, PRK06596, RNA polymerase factor sigma-32	5e-19
PRK07500	289	PRK07500, rpoH2, RNA polymerase factor sigma-32; R	3e-17
PRK06288	268	PRK06288, PRK06288, RNA polymerase sigma factor Wh	9e-17
PRK06986	236	PRK06986, fliA, flagellar biosynthesis sigma facto	1e-16
TIGR02885	231	TIGR02885, spore_sigF, RNA polymerase sigma-F fact	1e-16
PRK05572	252	PRK05572, PRK05572, sporulation sigma factor SigF;	8e-14
pfam04542	71	pfam04542, Sigma70_r2, Sigma-70 region 2	2e-13
TIGR02941	255	TIGR02941, Sigma_B, RNA polymerase sigma-B factor	1e-12
PRK08583	257	PRK08583, PRK08583, RNA polymerase sigma factor Si	3e-12
pfam04545	50	pfam04545, Sigma70_r4, Sigma-70, region 4	4e-12
PRK07408	256	PRK07408, PRK07408, RNA polymerase sigma factor Si	1e-11
PRK05911	257	PRK05911, PRK05911, RNA polymerase sigma factor si	2e-11
TIGR02846	227	TIGR02846, spore_sigmaK, RNA polymerase sigma-K fa	4e-11
PRK07122	264	PRK07122, PRK07122, RNA polymerase sigma factor Si	1e-10
PRK07670	251	PRK07670, PRK07670, RNA polymerase sigma factor Si	4e-10
TIGR02850	254	TIGR02850, spore_sigG, RNA polymerase sigma-G fact	5e-10
cd06171	55	cd06171, Sigma70_r4, Sigma70, region (SR) 4 refers	9e-10
PRK05803	233	PRK05803, PRK05803, sporulation sigma factor SigK;	3e-09
TIGR02937	158	TIGR02937, sigma70-ECF, RNA polymerase sigma facto	5e-08
PRK08215	258	PRK08215, PRK08215, sporulation sigma factor SigG;	1e-07
TIGR02835	234	TIGR02835, spore_sigmaE, RNA polymerase sigma-E fa	3e-07
pfam04539	78	pfam04539, Sigma70_r3, Sigma-70 region 3	8e-06
TIGR02937	158	TIGR02937, sigma70-ECF, RNA polymerase sigma facto	1e-05
PRK08301	234	PRK08301, PRK08301, sporulation sigma factor SigE;	1e-05

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

 Score =  209 bits (534), Expect = 1e-63
 Identities = 107/293 (36%), Positives = 178/293 (60%), Gaps = 2/293 (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 TGLSLAEIRSASECLRIVGSIDQKIGDCLNAKYLEFAPDRSVKSPKEIVMRQHMKKDVFR 467
             L   ++R   +  R   S+D  +GD  + +  +   D    SP+E V R+ +++D+  
Sbjct: 187 LELEPEQVRELLQRARQPVSLDAPVGDEEDTELGDLLEDDGE-SPEEQVERESLRQDLES 245

Query: 468 ILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLR 520
           +L  L  RERQVL LR+GL+   P +L EIG+  ++S+E +R++E KA+ KLR
Sbjct: 246 LLAELTPRERQVLRLRFGLDGGEPLTLAEIGRRLNLSRERVRQIEAKALRKLR 298

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

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

 Score =  195 bits (499), Expect = 2e-59
 Identities = 87/237 (36%), Positives = 152/237 (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 SASECLRIVGSIDQKIGDCLNAKYLEFAPDRSVKSPKEIVMRQHMKKDVFRILESLDSRE 476
              +  +   S++  IG+  ++   +F  D S++SP +   ++ +++ +  +LE+L  RE
Sbjct: 122 EIKKIAQEPISLETPIGEEEDSFLGDFIEDTSIESPDDYAAKELLREQLDEVLETLTERE 181

Query: 477 RQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDSETCRDLSHFLV 533
            +VL +RYGL D +P +LEE+GK F+V++E IR++E KA+ KLR     + L  FL 
Sbjct: 182 EKVLRMRYGLLDGQPHTLEEVGKEFNVTRERIRQIESKALRKLRHPSRSKKLKSFLD 238

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 =  195 bits (497), Expect = 1e-57
 Identities = 89/239 (37%), Positives = 152/239 (63%), Gaps = 2/239 (0%)

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 RSASECLRIVGSIDQKIGDCLNAKYLEFAPDRSVKSPKEIVMRQHMKKDVFRIL-ESLDS 474
           R   +      S+D  IGD  +++  +F  D    SP++ V R+ +K+D+  +L E+L  
Sbjct: 223 REMLKRASEPISLDTPIGDDEDSELGDFLEDDKSVSPEDAVERESLKEDLNEVLAEALTE 282

Query: 475 RERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDSETCRD-LSHFL 532
           RER+V+ LR+GL+D  PK+LEE+G+ F +S+E +R++E KA+ KLR        L  +L
Sbjct: 283 RERRVIRLRFGLDDGEPKTLEELGEEFGISRERVRQIEAKALRKLRRHPERSALLRSYL 341

Length = 342

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

 Score =  182 bits (464), Expect = 1e-52
 Identities = 101/297 (34%), Positives = 179/297 (60%), Gaps = 18/297 (6%)

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 VQYWIRKSISKMVARHARGIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLS 411
             +WIR++I++ +A  +R I++P  L   IS+I+K  K L+   G+ P + EIA+   ++
Sbjct: 193 ATWWIRQAITRAIADQSRTIRLPVHLYETISRIKKTTKVLSQEFGRKPTEEEIAESMEMT 252

Query: 412 LAEIRSASECLRIVGSI--------DQKIGDCLNAKYLEFAPDRSVKSPKEIVMRQHMKK 463
           + ++R  ++  ++  S+        D ++GD + A           ++P++ V +  +++
Sbjct: 253 IEKLRFIAKSAQLPISLETPIGKEEDSRLGDFIEAD---------GETPEDDVAKNLLRE 303

Query: 464 DVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLR 520
           D+  +L +L  RER VL LRYGL+D R K+LEEIG++F+V++E IR++E KA+ KLR
Sbjct: 304 DLEGVLATLSPRERDVLRLRYGLDDGRMKTLEEIGQIFNVTRERIRQIEAKALRKLR 360

Length = 373

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

 Score =  176 bits (448), Expect = 9e-51
 Identities = 96/274 (35%), Positives = 167/274 (60%), Gaps = 1/274 (0%)

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 SIDQKIGDCLNAKYLEFAPDRSVKSPKEIVMRQHMKKDVFRILESLDSRERQVLVLRYGL 486
           S+D ++GD  + +  E   D    SP + + ++ +++D+  +L  L  ++R+VL LR+GL
Sbjct: 223 SLDVRVGDNQDTELSELLEDEGP-SPDQYITQELLRQDLNNLLAELTPQQREVLTLRFGL 281

Query: 487 NDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLR 520
            D +  SL ++G+  ++S+E +R+LE +A+  LR
Sbjct: 282 EDGKELSLAKVGERLNLSRERVRQLEHQALAHLR 315

Length = 327

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

 Score =  175 bits (446), Expect = 1e-50
 Identities = 88/281 (31%), Positives = 171/281 (60%), Gaps = 1/281 (0%)

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 LRIVGSIDQKIGDCLNAKYLEFAPDRSVKSPKEIVMRQHMKKDVFRILESLDSRERQVLV 481
            R   S+D ++GD  + +  E   D    SP++   +  ++ D+ R++E L  ++++V+ 
Sbjct: 208 ARQPLSLDLRVGDNQDTELGELLEDTGA-SPEDFATQSSLQLDLERLMEDLTPQQKEVIA 266

Query: 482 LRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDS 522
           LR+GL D +P +L +IG+  ++S+E +R++E++A++KLR  
Sbjct: 267 LRFGLEDGQPLTLAKIGERLNISRERVRQIEREALSKLRKR 307

Length = 317

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

 Score =  165 bits (419), Expect = 1e-46
 Identities = 82/227 (36%), Positives = 146/227 (64%)

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 SASECLRIVGSIDQKIGDCLNAKYLEFAPDRSVKSPKEIVMRQHMKKDVFRILESLDSRE 476
              E  R   S+D  +G    A   +F  D    S +  V+   +  D+  +L +LD RE
Sbjct: 208 DLLEHSRDPVSLDMPVGSDEEAPLGDFIEDSEATSAENAVIAGLLHTDIRSVLATLDERE 267

Query: 477 RQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDSE 523
           +QV+ LR+GL+D +P++L++IGKLF +S+E +R++E++ M+KLR+ E
Sbjct: 268 QQVIRLRFGLDDGQPRTLDQIGKLFGLSRERVRQIEREVMSKLRNGE 314

Length = 324

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

 Score =  161 bits (408), Expect = 3e-44
 Identities = 97/317 (30%), Positives = 167/317 (52%), Gaps = 40/317 (12%)

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--------SASECLRIVGSIDQKIGDCLNAKYLEF 443
           +   G+ P   +IA+   ++  ++R        S S   ++    D ++GD L    +  
Sbjct: 272 SQEKGRTPTIEDIAQELEMTPTQVREVLLRVPRSVSLETKVGKDKDTELGDLLETDDI-- 329

Query: 444 APDRSVKSPKEIVMRQHMKKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHV 503
                  SP+E++MR+ +++D+  +L  L SRER V+ +R+GL D    SL EIG+   +
Sbjct: 330 -------SPEEMLMRESLQRDLQHLLADLTSRERDVIRMRFGLADGHTYSLAEIGRALDL 382

Query: 504 SKEWIRKLEKKAMTKLR 520
           S+E +R++E KA+ KLR
Sbjct: 383 SRERVRQIESKALQKLR 399

Length = 415

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

 Score =  151 bits (382), Expect = 1e-41
 Identities = 66/224 (29%), Positives = 126/224 (56%)

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 SASECLRIVGSIDQKIGDCLNAKYLEFAPDRSVKSPKEIVMRQHMKKDVFRILESLDSRE 476
                   + S+D  + D  +   L+   D     P+ +V    +K+ +   L  L+ R+
Sbjct: 168 RVLALNERITSLDAPLDDDSSKSLLDTIADEQSIDPESLVQNDDLKQLIEAWLAELNERQ 227

Query: 477 RQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLR 520
           R+VL  R+GL  + P +LEE+     +++E +R+++ +A+ KLR
Sbjct: 228 REVLARRFGLLGYEPATLEEVAAEVGLTRERVRQIQVEALKKLR 271

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|236413 PRK09210, PRK09210, RNA polymerase sigma factor RpoD; Validated

 Score =  152 bits (387), Expect = 1e-41
 Identities = 83/229 (36%), Positives = 142/229 (62%), Gaps = 6/229 (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 HARGIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVG 426
            AR I+IP  +   I+K+ + ++ L    G+ P   EIA+   +   ++R   E L+I  
Sbjct: 201 QARTIRIPVHMVETINKLIRVQRQLLQELGREPTPEEIAEEMDMPPEKVR---EILKIAQ 257

Query: 427 ---SIDQKIGDCLNAKYLEFAPDRSVKSPKEIVMRQHMKKDVFRILESLDSRERQVLVLR 483
              S++  IG+  ++   +F  D+   SP +    + +K+ +  +L++L  RE  VL LR
Sbjct: 258 EPVSLETPIGEEDDSHLGDFIEDQDATSPADHAAYELLKEQLEDVLDTLTDREENVLRLR 317

Query: 484 YGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDSETCRDLSHFL 532
           +GL+D R ++LEE+GK+F V++E IR++E KA+ KLR     + L  FL
Sbjct: 318 FGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRSKQLKDFL 366

Length = 367

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

 Score =  152 bits (386), Expect = 3e-40
 Identities = 85/243 (34%), Positives = 146/243 (60%), Gaps = 10/243 (4%)

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---YTGLSLAEIRS-ASECLRIVGSIDQKIGDCLNAKYLEFAPDRSVKSPKEIVMR 458
           E+AK   +T   + EI+    E +    S+D+ IG   ++++ +F  D    SP + V  
Sbjct: 379 ELAKEMGFTPEKVREIQKYNREPI----SLDKTIGKEGDSQFGDFIEDSEAVSPVDAVSF 434

Query: 459 QHMKKDVFR-ILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMT 517
             + +D  + +LE+L  RE  V+ +R+GL D +PK+L+EIG+++ V++E IR++E K + 
Sbjct: 435 T-LLQDQLQEVLETLSEREAGVIRMRFGLTDGQPKTLDEIGQVYGVTRERIRQIESKTLR 493

Query: 518 KLR 520
           KLR
Sbjct: 494 KLR 496

Length = 509

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

 Score =  123 bits (311), Expect = 7e-30
 Identities = 80/235 (34%), Positives = 140/235 (59%), Gaps = 26/235 (11%)

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 LSLAEIRS----ASECLRIVGSIDQKIGDCLNAKYLEFAPDRSVKSPKEIVMRQHMKKDV 465
           +   ++R     A E +    S++  IGD  ++   +F  D++ + P +  +++ +++  
Sbjct: 495 MPEDKVRKVLKIAKEPI----SLETPIGDDEDSHLGDFIEDKNAELPIDAAIQESLREAT 550

Query: 466 FRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLR 520
             +L SL  RE +VL +R+G++ +   +LEE+GK F V++E IR++E KA+ KLR
Sbjct: 551 TDVLASLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 605

Length = 619

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

 Score =  115 bits (290), Expect = 1e-28
 Identities = 62/239 (25%), Positives = 128/239 (53%), Gaps = 12/239 (5%)

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

Query: 417 SASECLRIVG------SIDQKIGDCLNAKYLEFAPDRSVKSPKEIVMRQHMKKDVFRILE 470
                 R++       S+D  +G       L+   D     P++      MK+ + + L 
Sbjct: 208 ------RMLALNERITSLDTPLGGDPEKSLLDILADEQENGPEDTTQDDDMKQSIVKWLF 261

Query: 471 SLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDSETCRDLS 529
            L+ ++R+VL  R+GL  +   +LE++ +   +++E +R+++ +A+ +LR+    + LS
Sbjct: 262 ELNDKQREVLARRFGLLGYEAATLEDVAREIGLTRERVRQIQVEALRRLREILQTQGLS 320

Length = 325

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

 Score =  102 bits (257), Expect = 6e-25
 Identities = 68/237 (28%), Positives = 112/237 (47%), Gaps = 29/237 (12%)

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--IVGSIDQKI----------GDCLNAKYLEFAPDRSVKSPKEIVMRQHMKKD 464
            A E        S+D  I           D L  +               +  R  +K  
Sbjct: 125 EALEAGNAYQALSLDASIEDDDGDPIALLDTLGDEDDALE---------TVEDRLALKP- 174

Query: 465 VFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRD 521
              +L +L  RER++L+LR+  +    K+  EI +   +S+  + +L ++A+ KLR+
Sbjct: 175 ---LLAALPERERRILLLRFFED----KTQSEIAERLGISQMHVSRLLRRALKKLRE 224

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

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

 Score =  102 bits (256), Expect = 7e-25
 Identities = 69/231 (29%), Positives = 117/231 (50%), Gaps = 21/231 (9%)

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---CLRIVGSIDQKIGD-CLNAKYLEFAPDRSVKSPKEIVMRQHMKKDVFRILES 471
           R A      L +V S+D+ +         ++   D   + P+E + R+ +++ +   +ES
Sbjct: 117 RQALNEINALSLV-SLDELLESGDDGGSLIDRIEDDKSEDPEEELEREELREALAEAIES 175

Query: 472 LDSRERQVLVLRY--GLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLR 520
           L  RE+ VL L Y   LN      L+EIG++  +++  + ++  +A+ KLR
Sbjct: 176 LSEREQLVLSLYYYEELN------LKEIGEVLGLTESRVSQIHSQALKKLR 220

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

 Score = 99.3 bits (248), Expect = 2e-23
 Identities = 67/227 (29%), Positives = 112/227 (49%), Gaps = 13/227 (5%)

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--SIDQKIGDCLNAKYLEFAPDRSVKSPKEIVMRQHMKKDVFRILESLDSR 475
           A   +      S+D+ +      K  +   D  +++P + V ++ + + +   +E L  R
Sbjct: 146 ALLAINGSQLLSLDEDV-----LKDDDDDVDDQIENPDDGVEKEELLEILKEAIEPLPER 200

Query: 476 ERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDS 522
           E+ VLVLRY        + +EI ++  +S+  + +L KKA+ KLR  
Sbjct: 201 EKLVLVLRYKEE----LTQKEIAEVLGISESRVSRLHKKAIKKLRKE 243

Length = 247

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

 Score = 97.7 bits (244), Expect = 8e-23
 Identities = 70/237 (29%), Positives = 122/237 (51%), Gaps = 25/237 (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 LAEIRSASECLRIVG---SIDQKIGDCLNAKY--LEFAPDRSVKSPKEIVMRQHMKKDVF 466
             E+R      R+ G   S++  I D  +     + +  D+       +   Q  +    
Sbjct: 153 EREVREMES--RLSGQDMSLNASIDDDEDDGGAPIAYLVDKRSDPEDTLEEEQWEELQRQ 210

Query: 467 RI---LESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLR 520
            +   L SLD+R R+++  R+ L+D    +L+E+   + VS E IR++EK AM KL+
Sbjct: 211 ALANALGSLDARSRRIIEARW-LDD-DKLTLQELAAEYGVSAERIRQIEKNAMKKLK 265

A sigma factor is a DNA-binding protein protein that binds to the DNA-directed RNA polymerase core to produce the holoenzyme capable of initiating transcription at specific sites. Different sigma factors act in vegetative growth, heat shock, extracytoplasmic functions (ECF), etc. This model represents the clade of sigma factors called RpoH and further restricted to the Proteobacteria. This protein may be called sigma-32, sigma factor H, heat shock sigma factor, and alternative sigma factor RpoH. Note that in some species the single locus rpoH may be replaced by two or more differentially regulated stress response sigma factors [Cellular processes, Adaptations to atypical conditions, Transcription, Transcription factors]. Length = 270

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

 Score = 87.2 bits (217), Expect = 5e-19
 Identities = 72/241 (29%), Positives = 121/241 (50%), Gaps = 30/241 (12%)

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

Query: 359 SISKMVARHARGIKIPC-----KLNREISKIQKARKALTNSHGKYPEDIE-IAKYTGLSL 412
            I + + R+ R +K+       KL   + K +K    L       PE++E +A+  G+S 
Sbjct: 112 EIHEYILRNWRIVKVATTKAQRKLFFNLRKAKKRLGWLN------PEEVEMVAEELGVSE 165

Query: 413 AEIRSASECLRIVG---SIDQKIGDCLN-----AKYLE---FAPDRSVKSPKEIVMRQHM 461
            E+R      R+ G   S+D  I D          YLE     P   ++       R+ +
Sbjct: 166 EEVREMES--RLSGQDASLDAPIDDDDEESGAPQDYLEDKSSDPADVLEEDNWEDQRRAL 223

Query: 462 KKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRD 521
             D    LE LD R R ++  R+ L+D    +L+E+   + VS E +R++EK AM KL+ 
Sbjct: 224 LADA---LEGLDERSRDIIEARW-LDDD-KSTLQELAAEYGVSAERVRQIEKNAMKKLKA 278

Query: 522 S 522
           +
Sbjct: 279 A 279

Length = 284

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

 Score = 82.0 bits (203), Expect = 3e-17
 Identities = 69/236 (29%), Positives = 120/236 (50%), Gaps = 31/236 (13%)

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

Query: 367 H---ARGIKIPCK------LNREISKIQKARKALTNSHGKYPEDI--EIAKYTGLSLAEI 415
           +    RG     +      L R  +++ +A + LT       ++I  EIA   G+SL+++
Sbjct: 112 NWSIVRGGTSSAQKALFFNLRRLRARLAQADEELTK------QEIHREIATALGVSLSDV 165

Query: 416 RSASECLRIVGS-----IDQKIGDCLNAKYLEFAPDRSVKSPKEIVMRQH----MKKDVF 466
                  R+ G        Q   D   ++ ++F  D S   P E V         ++ + 
Sbjct: 166 EMMDA--RLSGPDASLNAPQSEEDEGRSERMDFLVDDS-PLPDEQVESSIDGERRRRWLT 222

Query: 467 RILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDS 522
           + L++L+ RE +++  R  L +    +LE +G+   +SKE +R++E +A+ KLR +
Sbjct: 223 QALQTLNERELRIIRERR-LRED-GATLEALGEELGISKERVRQIEARALEKLRRA 276

Length = 289

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

 Score = 80.1 bits (198), Expect = 9e-17
 Identities = 73/244 (29%), Positives = 114/244 (46%), Gaps = 39/244 (15%)

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-----------ASECLRIVG--SIDQKIGDCLNAKYLEFAPDRSVKSPKEIVMR 458
           L E  S           +   L   G    +  + D L           +  +P EI  R
Sbjct: 148 LEEYNSLLSKLSGTSVVSLNDLWFGGDEGDEVSLMDTLE--------SPAALNPDEIAER 199

Query: 459 QHMKKDVFRILESLDSRERQVLVLRY--GLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAM 516
           + +K+ +   +++L  RE++VL+L Y   L      +L+EIGK+  V++  I +L  KA+
Sbjct: 200 EEIKRVIVEAIKTLPEREKKVLILYYYEDL------TLKEIGKVLGVTESRISQLHTKAV 253

Query: 517 TKLR 520
            +LR
Sbjct: 254 LQLR 257

Length = 268

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

 Score = 79.1 bits (196), Expect = 1e-16
 Identities = 67/238 (28%), Positives = 117/238 (49%), Gaps = 32/238 (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 TGLSLAEIRS---ASECLRIVGSIDQKIGDCLNAKYLEFAPDRSVKSPKEIVMRQHMKKD 464
            GLSL E R     +   ++  SID+  G+  ++  +    D   + P + +  + +++ 
Sbjct: 121 LGLSLEEYREMLLDTNISQLF-SIDELRGEHGDS--ILVTEDHQDEDPLQQLEDEELREA 177

Query: 465 VFRILESLDSRERQVLVLRY--GLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLR 520
           +   +ESL  RE+ VL L Y   LN      L+EIG +  VS+  + ++  +A+ +LR
Sbjct: 178 LVEAIESLPEREQLVLSLYYQEELN------LKEIGAVLGVSESRVSQIHSQAIKRLR 229

Length = 236

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

 Score = 78.6 bits (194), Expect = 1e-16
 Identities = 59/235 (25%), Positives = 107/235 (45%), Gaps = 28/235 (11%)

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 SASECLRIVGSIDQKIG----------DCLNAKYLEFAPDRSVKSPKEIVMRQHMKKDVF 466
            A E  R   S+   +           D +  K             ++I +++       
Sbjct: 132 MALESARSPQSLYDTVHQDDGDPIYLLDQIADKG-----SEDSDWLEKIALKE------- 179

Query: 467 RILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRD 521
             +  LD RERQ+++LRY     + K+  E+  +  +S+  + +LEKK + K+++
Sbjct: 180 -AISKLDERERQIIMLRY----FKDKTQTEVANMLGISQVQVSRLEKKVLKKMKE 229

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

 Score = 71.2 bits (175), Expect = 8e-14
 Identities = 61/234 (26%), Positives = 108/234 (46%), Gaps = 28/234 (11%)

Query: 297 REELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWI 356
           R+ L++    LV  + + +   G    DL Q G +G+L+  ++FD +   KFSTY    I
Sbjct: 34  RDTLVEKNLRLVWSVVQRFLNRGYEPDDLFQIGCIGLLKAVDKFDLSYDVKFSTYAVPMI 93

Query: 357 RKSISKMVARHARG---IKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLA 413
              I     R  R    +K+   L    +KI+K +  L+   G+ P   E+A+Y G++  
Sbjct: 94  IGEIQ----RFLRDDGTVKVSRSLKETANKIRKDKDELSKELGREPTIEELAEYLGVTPE 149

Query: 414 EIRSASECLRIVGSIDQKI----GDCLNAKYL--EFAPDRSVKSPKEIVMRQHMKKDVFR 467
           E+  A E  R   SI + +    GD +    L  + A         +I +++        
Sbjct: 150 EVVLAQEASRSPQSIHETVHENDGDPI---TLLDQIADQSEEDWFDKIALKE-------- 198

Query: 468 ILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRD 521
            +  LD RER ++ LRY     + K+  E+ K   +S+  + +LEKK + ++++
Sbjct: 199 AIRELDERERLIVYLRY----FKDKTQSEVAKRLGISQVQVSRLEKKILKQMKE 248

Length = 252

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

 Score = 64.9 bits (159), Expect = 2e-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|131987 TIGR02941, Sigma_B, RNA polymerase sigma-B factor

 Score = 67.6 bits (165), Expect = 1e-12
 Identities = 56/231 (24%), Positives = 108/231 (46%), Gaps = 14/231 (6%)

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 SASECLRI--VGSIDQKI---GDCLNAKYLEFAPDRSVKSPKEIVMRQHMKKDVFRILES 471
              E  +     S+D  I    D      L+   +  V+   +   R+ + + +  I   
Sbjct: 151 EIMEMGQSYRALSVDDVIEADSDGSTVARLDSVGE--VEDGYDQTERRMVLEKILPI--- 205

Query: 472 LDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDS 522
           L  RE+ ++   +  N     S +E G+   +S+  + +L+++A++KL+++
Sbjct: 206 LSEREKSIIHCTFEEN----LSQKETGERLGISQMHVSRLQRQAISKLKEA 252

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

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

 Score = 66.3 bits (162), Expect = 3e-12
 Identities = 57/237 (24%), Positives = 102/237 (43%), Gaps = 28/237 (11%)

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 ASECLRI--VGSIDQKIGDCLNAKYLEFAPDRS----------VKSPKEIVMRQHMKKDV 465
           A E  +     S+D  I         E   D S           +   E+  ++ + + +
Sbjct: 152 AMEMGKSYQALSVDHSI---------EADSDGSTVTLLDIVGQQEDGYELTEQRMILEKI 202

Query: 466 FRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDS 522
             +   L  RE+ ++   +  N     S +E G+   +S+  + +L+++A+ KLR++
Sbjct: 203 LPV---LSDREKSIIQCTFIEN----LSQKETGERLGISQMHVSRLQRQAIKKLREA 252

Length = 257

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

 Score = 60.5 bits (148), Expect = 4e-12
 Identities = 26/53 (49%), Positives = 37/53 (69%), Gaps = 4/53 (7%)

Query: 469 LESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRD 521
           L SL  RER+VLVLR+G       +LEEIG+   +S+E +R++EK+A+ KLR 
Sbjct: 2   LASLPPREREVLVLRFG----EGLTLEEIGERLGISRERVRQIEKRALRKLRK 50

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

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

 Score = 64.6 bits (158), Expect = 1e-11
 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|235644 PRK05911, PRK05911, RNA polymerase sigma factor sigma-28; Reviewed

 Score = 64.3 bits (156), Expect = 2e-11
 Identities = 64/249 (25%), Positives = 119/249 (47%), Gaps = 29/249 (11%)

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 EIRS--ASECLRIVGSI--------DQKIGDCLNAKYLEFAPDRSVKSPKEIVMRQHMKK 463
           E+    +S    ++ S+        D + G  L     E   D   ++  ++V ++    
Sbjct: 142 ELSGWFSSARPALILSLNEEFPCQSDDEAGLALE----ERIADERAETGYDVVDKKEFSS 197

Query: 464 DVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDSE 523
            +   + +L+ +ER+V+ L Y    +    L+EIGK+  VS+  + ++  KA+ KLR + 
Sbjct: 198 ILAEAILALEEKERKVMALYY----YEELVLKEIGKILGVSESRVSQIHSKALLKLRAT- 252

Query: 524 TCRDLSHFL 532
               LS FL
Sbjct: 253 ----LSAFL 257

Length = 257

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

 Score = 62.8 bits (153), Expect = 4e-11
 Identities = 57/223 (25%), Positives = 93/223 (41%), Gaps = 50/223 (22%)

Query: 297 REELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWI 356
           R  LI+    LV  + + +   G    DL+  G +G+++  + FD  +G + +TY     
Sbjct: 50  RNVLIERNLRLVAHIVKKFSNTGEDVDDLISIGTIGLIKAIDSFDPDKGTRLATYAA--- 106

Query: 357 RKSISKMVARHARGIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIR 416
            + I   +  H R +K   K   E+S        L +  G   E  EI      SL +I 
Sbjct: 107 -RCIENEILMHLRALK---KTKGEVS--------LQDPIGVDKEGNEI------SLIDIL 148

Query: 417 SASECLRIVGSIDQKIGDCLNAKYLEFAPDRSVKSPKEIVMRQHMKKDVFRILESLDSRE 476
            +                                S  E V      K +++ L  LD RE
Sbjct: 149 GSDG-----------------------------DSVIEQVELNLEIKKLYKKLSVLDGRE 179

Query: 477 RQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKL 519
           R+V+ +RYGL D R K+  EI K+  +S+ ++ ++EK+A+ KL
Sbjct: 180 REVIEMRYGLGDGRRKTQREIAKILGISRSYVSRIEKRALMKL 222

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

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

 Score = 61.7 bits (150), Expect = 1e-10
 Identities = 62/242 (25%), Positives = 105/242 (43%), Gaps = 39/242 (16%)

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------SIDQKIGDCLNAKYLEFAPDRSVKSPKEIV------MRQH 460
            E+    E L + G      SID   G            D   ++  + +      + Q 
Sbjct: 158 EEV---VEGL-VAGSAYNTLSIDSGGGS----------GDDDARAIADTLGDVDAGLDQI 203

Query: 461 MKKDVFR-ILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKL 519
             ++  R +L +L  RER VLVLR+  +  + +  E +G    +S+  + +L  K + +L
Sbjct: 204 ENREALRPLLAALPERERTVLVLRFFESMTQTQIAERVG----ISQMHVSRLLAKTLARL 259

Query: 520 RD 521
           RD
Sbjct: 260 RD 261

Length = 264

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

 Score = 60.1 bits (146), Expect = 4e-10
 Identities = 56/233 (24%), Positives = 111/233 (47%), Gaps = 21/233 (9%)

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------SECLRIVGSIDQKIGDCLNAKYLEFA-PDRSVKSPKEIVMRQHMKKDVFR 467
           + +       +  L    SID+K  D  + + +     D    +P+E ++++ + +++  
Sbjct: 142 VEATMNEGFFANLL----SIDEKTHDQDDGENVSVTIRDDKTPTPEEKLLKEELIEELAE 197

Query: 468 ILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLR 520
            ++ L  +E+ V+ L Y        +L EIG++ ++S   I ++  KA+ KL+
Sbjct: 198 KIKQLSEKEQLVISLFY----KEELTLTEIGQVLNLSTSRISQIHSKALFKLK 246

Length = 251

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

 Score = 59.8 bits (145), Expect = 5e-10
 Identities = 61/230 (26%), Positives = 113/230 (49%), Gaps = 20/230 (8%)

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

Query: 416 RSASECLRIVGSIDQKI-GDCLNAKYL--EFAPDRSVKSP--KEIVMRQHMKKDVFRILE 470
             A + ++   S+ + I  D  +  Y+  + + +++  S   + I +++ MK+       
Sbjct: 154 VFALDAIQDPVSLFEPIYNDGGDPIYVMDQISDEKNKDSQWLEGIALKEAMKR------- 206

Query: 471 SLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLR 520
            L+ RE+ +L +R+     + +  EEIG    +S+  + +LEK A+  +R
Sbjct: 207 -LNEREKMILNMRFFEGKTQMEVAEEIG----ISQAQVSRLEKAALKHMR 251

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

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

 Score = 54.0 bits (131), Expect = 9e-10
 Identities = 19/59 (32%), Positives = 35/59 (59%), Gaps = 4/59 (6%)

Query: 462 KKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLR 520
           ++ +   L+ L  RER+V++LR+G       S EEI ++  +S+  +R+   +A+ KLR
Sbjct: 1   RERLEEALDKLPEREREVILLRFGEG----LSYEEIAEILGISRSTVRQRLHRALKKLR 55

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

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

 Score = 56.9 bits (138), Expect = 3e-09
 Identities = 22/77 (28%), Positives = 46/77 (59%), Gaps = 5/77 (6%)

Query: 454 EIVMRQHMKKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEK 513
           E V  +   + +++ ++ LD RE++V+ +RYGL + + K+  EI K   +S+ ++ ++EK
Sbjct: 158 EQVELKMEVEKLYKKIDILDEREKEVIEMRYGLGNGKEKTQREIAKALGISRSYVSRIEK 217

Query: 514 KAMTKLRDSETCRDLSH 530
           +A+ KL      ++L  
Sbjct: 218 RALKKL-----FKELYR 229

Length = 233

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

 Score = 52.3 bits (126), Expect = 5e-08
 Identities = 26/81 (32%), Positives = 43/81 (53%), Gaps = 4/81 (4%)

Query: 441 LEFAPDRSVKSPKEIVMRQHMKKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKL 500
           L      S  SP+E + ++  ++ +   LE L  RER+VLVLRY        S +EI ++
Sbjct: 80  LLEELLDSDPSPEEELEQEEEREALREALEKLPEREREVLVLRYLEG----LSYKEIAEI 135

Query: 501 FHVSKEWIRKLEKKAMTKLRD 521
             +S   +++  K+A  KLR+
Sbjct: 136 LGISVGTVKRRLKRARKKLRE 156

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 = 53.0 bits (128), Expect = 1e-07
 Identities = 63/237 (26%), Positives = 111/237 (46%), Gaps = 32/237 (13%)

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 LAEIRSA----SECLRIVGSIDQKIGDCLNAKYL--EFAPDRSVKSP--KEIVMRQHMKK 463
             E+  A     + + +   I    GD     Y+  + + +++      +EI +++ MKK
Sbjct: 153 REEVVFALDAIQDPVSLFEPIYHDGGD---PIYVMDQISDEKNKDENWLEEIALKEAMKK 209

Query: 464 DVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLR 520
                   L+ RE+ +L LR+     + K+  E+ +   +S+  + +LEK A+  +R
Sbjct: 210 --------LNDREKLILNLRF----FQGKTQMEVAEEIGISQAQVSRLEKAALKHMR 254

Length = 258

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

 Score = 51.0 bits (122), Expect = 3e-07
 Identities = 45/224 (20%), Positives = 92/224 (41%), Gaps = 50/224 (22%)

Query: 297 REELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWI 356
           +  LI+    LV+++AR +   GI   DL+  G +G+++    F+ ++  K +TY    I
Sbjct: 54  KSTLIERNLRLVVYIARKFENTGIGIEDLVSIGTIGLIKAVNTFNPSKKIKLATYASRCI 113

Query: 357 RKSISKMVARHARGIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIR 416
              I  M  R     +     +  ++      + L +                       
Sbjct: 114 ENEI-LMYLRRNNKTRSEVSFDEPLNVDWDGNELLLSD---------------------- 150

Query: 417 SASECLRIVGSIDQKIGDCLNAKYLEFAPDRSVKSPKEIVMRQHMKKDVFRILESLDSRE 476
                  ++G+    +      KYLE   DR        ++R+ + K        L+ RE
Sbjct: 151 -------VLGTDSDIV-----YKYLEEEVDRE-------LLRKALAK--------LNDRE 183

Query: 477 RQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLR 520
           ++++ LR+GL     K+ +E+  +  +S+ +I +LEK+ + +L+
Sbjct: 184 KKIMELRFGLVGGTEKTQKEVADMLGISQSYISRLEKRILKRLK 227

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

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

 Score = 43.7 bits (104), Expect = 8e-06
 Identities = 21/78 (26%), Positives = 41/78 (52%)

Query: 379 REISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNA 438
             ++KI++A++ L    G+ P   EIA+  G+S  ++R   E  R   S+D  +G+  + 
Sbjct: 1   ELLNKIKRAQRELEQELGREPTPEEIAEELGISEEKVREVLEAAREPVSLDLPVGEEEDG 60

Query: 439 KYLEFAPDRSVKSPKEIV 456
           +  +   D   +SP++ V
Sbjct: 61  ELGDLLEDDDAESPEDAV 78

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

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

 Score = 45.4 bits (108), Expect = 1e-05
 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|236228 PRK08301, PRK08301, sporulation sigma factor SigE; Reviewed

 Score = 46.8 bits (112), Expect = 1e-05
 Identities = 19/59 (32%), Positives = 39/59 (66%)

Query: 462 KKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLR 520
           +K + + L+ L  RE+Q++ LR+GLN    K+ +E+  +  +S+ +I +LEK+ + +L+
Sbjct: 169 RKLLKKALKKLSDREKQIMELRFGLNGGEEKTQKEVADMLGISQSYISRLEKRIIKRLK 227

Length = 234

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	534
PRK07598	415	RNA polymerase sigma factor SigC; Validated	100.0
PRK05949	327	RNA polymerase sigma factor; Validated	100.0
PRK07406	373	RNA polymerase sigma factor RpoD; Validated	100.0
PRK07405	317	RNA polymerase sigma factor SigD; Validated	100.0
TIGR02997	298	Sig70-cyanoRpoD RNA polymerase sigma factor, cyano	100.0
COG0568	342	RpoD DNA-directed RNA polymerase, sigma subunit (s	100.0
PRK05901	509	RNA polymerase sigma factor; Provisional	100.0
PRK07921	324	RNA polymerase sigma factor SigB; Reviewed	100.0
PRK09210	367	RNA polymerase sigma factor RpoD; Validated	100.0
PRK05658	619	RNA polymerase sigma factor RpoD; Validated	100.0
TIGR02393	238	RpoD_Cterm RNA polymerase sigma factor RpoD, C-ter	100.0
PRK07122	264	RNA polymerase sigma factor SigF; Reviewed	100.0
PRK05657	325	RNA polymerase sigma factor RpoS; Validated	100.0
PRK07500	289	rpoH2 RNA polymerase factor sigma-32; Reviewed	100.0
PRK06596	284	RNA polymerase factor sigma-32; Reviewed	100.0
PRK07408	256	RNA polymerase sigma factor SigF; Reviewed	100.0
TIGR02392	270	rpoH_proteo alternative sigma factor RpoH. A sigma	100.0
PRK05911	257	RNA polymerase sigma factor sigma-28; Reviewed	100.0
TIGR02850	254	spore_sigG RNA polymerase sigma-G factor. Members	100.0
TIGR02394	285	rpoS_proteo RNA polymerase sigma factor RpoS. A si	100.0
COG1191	247	FliA DNA-directed RNA polymerase specialized sigma	100.0
PRK08215	258	sporulation sigma factor SigG; Reviewed	100.0
TIGR02885	231	spore_sigF RNA polymerase sigma-F factor. Members	100.0
TIGR02980	227	SigBFG RNA polymerase sigma-70 factor, sigma-B/F/G	100.0
TIGR02941	255	Sigma_B RNA polymerase sigma-B factor. This sigma	100.0
PRK06288	268	RNA polymerase sigma factor WhiG; Reviewed	100.0
PRK07670	251	RNA polymerase sigma factor SigD; Validated	100.0
TIGR02479	224	FliA_WhiG RNA polymerase sigma factor, FliA/WhiG f	100.0
PRK12427	231	flagellar biosynthesis sigma factor; Provisional	100.0
PRK06986	236	fliA flagellar biosynthesis sigma factor; Validate	100.0
PRK08583	257	RNA polymerase sigma factor SigB; Validated	100.0
PRK05572	252	sporulation sigma factor SigF; Validated	100.0
PRK05803	233	sporulation sigma factor SigK; Reviewed	99.95
PRK08301	234	sporulation sigma factor SigE; Reviewed	99.93
TIGR02846	227	spore_sigmaK RNA polymerase sigma-K factor. The sp	99.93
PRK08295	208	RNA polymerase factor sigma-70; Validated	99.92
TIGR02835	234	spore_sigmaE RNA polymerase sigma-E factor. Member	99.92
TIGR02859	198	spore_sigH RNA polymerase sigma-H factor. Members	99.91
PRK05602	186	RNA polymerase sigma factor; Reviewed	99.9
PRK09646	194	RNA polymerase sigma factor SigK; Reviewed	99.9
PRK12513	194	RNA polymerase sigma factor; Provisional	99.9
PRK09648	189	RNA polymerase sigma factor SigD; Reviewed	99.9
TIGR02948	187	SigW_bacill RNA polymerase sigma-W factor. This si	99.9
PRK09641	187	RNA polymerase sigma factor SigW; Provisional	99.9
TIGR02952	170	Sig70_famx2 RNA polymerase sigma-70 factor, TIGR02	99.89
PRK06811	189	RNA polymerase factor sigma-70; Validated	99.88
PRK12514	179	RNA polymerase sigma factor; Provisional	99.88
PRK12519	194	RNA polymerase sigma factor; Provisional	99.88
TIGR02939	190	RpoE_Sigma70 RNA polymerase sigma factor RpoE. A s	99.88
PRK12537	182	RNA polymerase sigma factor; Provisional	99.88
PRK09652	182	RNA polymerase sigma factor RpoE; Provisional	99.88
PRK13919	186	putative RNA polymerase sigma E protein; Provision	99.88
PRK11923	193	algU RNA polymerase sigma factor AlgU; Provisional	99.88
PRK12524	196	RNA polymerase sigma factor; Provisional	99.88
PRK06759	154	RNA polymerase factor sigma-70; Validated	99.88
PRK12534	187	RNA polymerase sigma factor; Provisional	99.87
PRK12538	233	RNA polymerase sigma factor; Provisional	99.87
PRK12526	206	RNA polymerase sigma factor; Provisional	99.87
PRK11922	231	RNA polymerase sigma factor; Provisional	99.87
PRK12515	189	RNA polymerase sigma factor; Provisional	99.87
PRK09640	188	RNA polymerase sigma factor SigX; Reviewed	99.87
PRK11924	179	RNA polymerase sigma factor; Provisional	99.87
TIGR02984	189	Sig-70_plancto1 RNA polymerase sigma-70 factor, Pl	99.86
PRK12542	185	RNA polymerase sigma factor; Provisional	99.86
PRK09643	192	RNA polymerase sigma factor SigM; Reviewed	99.86
TIGR02954	169	Sig70_famx3 RNA polymerase sigma-70 factor, TIGR02	99.86
PRK09638	176	RNA polymerase sigma factor SigY; Reviewed	99.86
PRK12531	194	RNA polymerase sigma factor; Provisional	99.86
PRK12522	173	RNA polymerase sigma factor; Provisional	99.85
TIGR02985	161	Sig70_bacteroi1 RNA polymerase sigma-70 factor, Ba	99.85
PRK12543	179	RNA polymerase sigma factor; Provisional	99.85
PRK12520	191	RNA polymerase sigma factor; Provisional	99.85
TIGR03001	244	Sig-70_gmx1 RNA polymerase sigma-70 factor, Myxoco	99.85
TIGR02937	158	sigma70-ECF RNA polymerase sigma factor, sigma-70	99.85
PRK09415	179	RNA polymerase factor sigma C; Reviewed	99.85
PRK09645	173	RNA polymerase sigma factor SigL; Provisional	99.85
TIGR02989	159	Sig-70_gvs1 RNA polymerase sigma-70 factor, Rhodop	99.84
PRK12539	184	RNA polymerase sigma factor; Provisional	99.84
TIGR02999	183	Sig-70_X6 RNA polymerase sigma factor, TIGR02999 f	99.84
PRK09649	185	RNA polymerase sigma factor SigC; Reviewed	99.84
PRK12512	184	RNA polymerase sigma factor; Provisional	99.84
PRK12533	216	RNA polymerase sigma factor; Provisional	99.84
PRK12536	181	RNA polymerase sigma factor; Provisional	99.83
COG1595	182	RpoE DNA-directed RNA polymerase specialized sigma	99.83
PRK12529	178	RNA polymerase sigma factor; Provisional	99.83
PRK12518	175	RNA polymerase sigma factor; Provisional	99.83
PRK09642	160	RNA polymerase sigma factor SigW; Reviewed	99.83
PRK12523	172	RNA polymerase sigma factor; Reviewed	99.83
TIGR02947	193	SigH_actino RNA polymerase sigma-70 factor, TIGR02	99.82
PRK09644	165	RNA polymerase sigma factor SigM; Provisional	99.82
PRK12528	161	RNA polymerase sigma factor; Provisional	99.82
PRK12516	187	RNA polymerase sigma factor; Provisional	99.82
TIGR02943	188	Sig70_famx1 RNA polymerase sigma-70 factor, TIGR02	99.81
PRK12532	195	RNA polymerase sigma factor; Provisional	99.81
TIGR02983	162	SigE-fam_strep RNA polymerase sigma-70 factor, sig	99.81
PRK12545	201	RNA polymerase sigma factor; Provisional	99.81
PRK12547	164	RNA polymerase sigma factor; Provisional	99.81
PRK09639	166	RNA polymerase sigma factor SigX; Provisional	99.81
PRK12530	189	RNA polymerase sigma factor; Provisional	99.81
PRK12544	206	RNA polymerase sigma factor; Provisional	99.81
PRK09647	203	RNA polymerase sigma factor SigE; Reviewed	99.81
PRK12541	161	RNA polymerase sigma factor; Provisional	99.8
PRK12535	196	RNA polymerase sigma factor; Provisional	99.8
PRK08241	339	RNA polymerase factor sigma-70; Validated	99.8
TIGR02960	324	SigX5 RNA polymerase sigma-70 factor, TIGR02960 fa	99.79
TIGR02950	154	SigM_subfam RNA polymerase sigma factor, SigM fami	99.79
PRK09637	181	RNA polymerase sigma factor SigZ; Provisional	99.79
PRK12540	182	RNA polymerase sigma factor; Provisional	99.79
PRK12527	159	RNA polymerase sigma factor; Reviewed	99.79
TIGR02895	218	spore_sigI RNA polymerase sigma-I factor. Members	99.78
PRK07037	163	extracytoplasmic-function sigma-70 factor; Validat	99.78
PRK09651	172	RNA polymerase sigma factor FecI; Provisional	99.78
TIGR02959	170	SigZ RNA polymerase sigma factor, SigZ family. Thi	99.77
PRK12517	188	RNA polymerase sigma factor; Provisional	99.77
PRK12525	168	RNA polymerase sigma factor; Provisional	99.76
PRK12546	188	RNA polymerase sigma factor; Provisional	99.75
PRK12511	182	RNA polymerase sigma factor; Provisional	99.75
PRK09047	161	RNA polymerase factor sigma-70; Validated	99.73
PRK09636	293	RNA polymerase sigma factor SigJ; Provisional	99.72
TIGR02957	281	SigX4 RNA polymerase sigma-70 factor, TIGR02957 fa	99.68
PRK09635	290	sigI RNA polymerase sigma factor SigI; Provisional	99.68
PRK06704	228	RNA polymerase factor sigma-70; Validated	99.68
TIGR03209	142	P21_Cbot clostridium toxin-associated regulator Bo	99.57
PRK09191	261	two-component response regulator; Provisional	99.56
PRK08311	237	putative RNA polymerase sigma factor SigI; Reviewe	99.45
PF07638	185	Sigma70_ECF: ECF sigma factor	99.44
PF04542	71	Sigma70_r2: Sigma-70 region 2 ; InterPro: IPR00762	99.27
PF04539	78	Sigma70_r3: Sigma-70 region 3; InterPro: IPR007624	99.23
PF04545	50	Sigma70_r4: Sigma-70, region 4; InterPro: IPR00763	99.21
PF08281	54	Sigma70_r4_2: Sigma-70, region 4; InterPro: IPR013	98.95
PRK06930	170	positive control sigma-like factor; Validated	98.74
PRK00118	104	putative DNA-binding protein; Validated	98.43
cd06171	55	Sigma70_r4 Sigma70, region (SR) 4 refers to the mo	98.31
TIGR00721	137	tfx DNA-binding protein, Tfx family. Tfx from Meth	98.18
PRK03975	141	tfx putative transcriptional regulator; Provisiona	98.14
PRK04217	110	hypothetical protein; Provisional	98.11
PF04297	101	UPF0122: Putative helix-turn-helix protein, YlxM /	98.0
TIGR01636	134	phage_rinA phage transcriptional activator, RinA f	97.88
smart00421	58	HTH_LUXR helix_turn_helix, Lux Regulon. lux regulo	97.83
PF00196	58	GerE: Bacterial regulatory proteins, luxR family;	97.73
cd06170	57	LuxR_C_like C-terminal DNA-binding domain of LuxR-	97.63
PF07374	100	DUF1492: Protein of unknown function (DUF1492); In	97.6
TIGR03879	73	near_KaiC_dom probable regulatory domain. This mod	97.6
PF04967	53	HTH_10: HTH DNA binding domain; InterPro: IPR00705	97.48
TIGR01321	94	TrpR trp operon repressor, proteobacterial. This m	97.44
PRK15411	207	rcsA colanic acid capsular biosynthesis activation	97.42
PRK15201	198	fimbriae regulatory protein FimW; Provisional	97.4
PRK10840	216	transcriptional regulator RcsB; Provisional	97.37
PRK13719	217	conjugal transfer transcriptional regulator TraJ;	97.34
PRK11475	207	DNA-binding transcriptional activator BglJ; Provis	97.33
PRK13870	234	transcriptional regulator TraR; Provisional	97.31
TIGR03541	232	reg_near_HchA LuxR family transcriptional regulato	97.29
TIGR03020	247	EpsA transcriptional regulator EpsA. Proteins in t	97.28
PRK10100	216	DNA-binding transcriptional regulator CsgD; Provis	97.26
PRK10188	240	DNA-binding transcriptional activator SdiA; Provis	97.25
COG4566	202	TtrR Response regulator [Signal transduction mecha	97.25
COG2197	211	CitB Response regulator containing a CheY-like rec	97.24
COG2771	65	CsgD DNA-binding HTH domain-containing proteins [T	97.13
PF13936	44	HTH_38: Helix-turn-helix domain; PDB: 2W48_A.	97.11
PF02001	106	DUF134: Protein of unknown function DUF134; InterP	97.1
PRK09483	217	response regulator; Provisional	96.98
COG3413	215	Predicted DNA binding protein [General function pr	96.93
COG4941	415	Predicted RNA polymerase sigma factor containing a	96.86
PRK15369	211	two component system sensor kinase SsrB; Provision	96.77
TIGR01637	132	phage_arpU phage transcriptional regulator, ArpU f	96.64
PRK10651	216	transcriptional regulator NarL; Provisional	96.59
PRK01381	99	Trp operon repressor; Provisional	96.56
COG1356	143	tfx Transcriptional regulator [DNA replication, re	96.51
COG2739	105	Uncharacterized protein conserved in bacteria [Fun	96.5
PRK09390	202	fixJ response regulator FixJ; Provisional	96.47
PF00140	37	Sigma70_r1_2: Sigma-70 factor, region 1.2; InterPr	96.31
PRK15320	251	transcriptional activator SprB; Provisional	96.25
COG1342	99	Predicted DNA-binding proteins [General function p	96.24
PRK10403	215	transcriptional regulator NarP; Provisional	96.03
PRK10360	196	DNA-binding transcriptional activator UhpA; Provis	95.77
PRK09935	210	transcriptional regulator FimZ; Provisional	95.65
PRK13558	665	bacterio-opsin activator; Provisional	95.65
PRK09958	204	DNA-binding transcriptional activator EvgA; Provis	95.64
PRK04841	903	transcriptional regulator MalT; Provisional	95.61
PRK05658	619	RNA polymerase sigma factor RpoD; Validated	95.6
TIGR02531	88	yecD_yerC TrpR-related protein YerC/YecD. This mod	94.9
PF13384	50	HTH_23: Homeodomain-like domain; PDB: 2X48_C.	94.86
PF13613	53	HTH_Tnp_4: Helix-turn-helix of DDE superfamily end	94.57
PRK15418	318	transcriptional regulator LsrR; Provisional	94.47
PF05263	130	DUF722: Protein of unknown function (DUF722); Inte	94.47
PF00325	32	Crp: Bacterial regulatory proteins, crp family; In	94.44
PF13412	48	HTH_24: Winged helix-turn-helix DNA-binding; PDB:	94.35
PF12645	65	HTH_16: Helix-turn-helix domain; InterPro: IPR0247	94.14
PF02796	45	HTH_7: Helix-turn-helix domain of resolvase; Inter	94.02
cd00569	42	HTH_Hin_like Helix-turn-helix domain of Hin and re	93.94
PF06530	125	Phage_antitermQ: Phage antitermination protein Q;	93.49
PRK07598	415	RNA polymerase sigma factor SigC; Validated	93.28
PRK09210	367	RNA polymerase sigma factor RpoD; Validated	92.65
PF09862	113	DUF2089: Protein of unknown function (DUF2089); In	92.52
TIGR02393	238	RpoD_Cterm RNA polymerase sigma factor RpoD, C-ter	92.35
PRK05901	509	RNA polymerase sigma factor; Provisional	92.33
COG2909	894	MalT ATP-dependent transcriptional regulator [Tran	92.02
PF06056	58	Terminase_5: Putative ATPase subunit of terminase	91.82
PF13518	52	HTH_28: Helix-turn-helix domain	91.77
smart00351	125	PAX Paired Box domain.	91.73
PRK10430	239	DNA-binding transcriptional activator DcuR; Provis	91.71
COG2390	321	DeoR Transcriptional regulator, contains sigma fac	91.64
PF01726	65	LexA_DNA_bind: LexA DNA binding domain; InterPro:	91.49
PF04539	78	Sigma70_r3: Sigma-70 region 3; InterPro: IPR007624	91.48
PF04218	53	CENP-B_N: CENP-B N-terminal DNA-binding domain; In	91.32
PF10668	60	Phage_terminase: Phage terminase small subunit; In	91.25
PF13730	55	HTH_36: Helix-turn-helix domain	90.87
PHA00675	78	hypothetical protein	90.86
PF13404	42	HTH_AsnC-type: AsnC-type helix-turn-helix domain;	90.78
PRK07921	324	RNA polymerase sigma factor SigB; Reviewed	90.33
PF02650	85	HTH_WhiA: WhiA C-terminal HTH domain; InterPro: IP	89.82
PHA02591	83	hypothetical protein; Provisional	89.52
PF01022	47	HTH_5: Bacterial regulatory protein, arsR family;	89.24
cd00131	128	PAX Paired Box domain	89.16
TIGR02395	429	rpoN_sigma RNA polymerase sigma-54 factor. A sigma	88.78
TIGR02147	271	Fsuc_second hypothetical protein, TIGR02147. This	88.51
PF08279	55	HTH_11: HTH domain; InterPro: IPR013196 Winged hel	88.5
PF12840	61	HTH_20: Helix-turn-helix domain; PDB: 1ULY_A 2CWE_	88.42
PRK07406	373	RNA polymerase sigma factor RpoD; Validated	88.05
COG1191	247	FliA DNA-directed RNA polymerase specialized sigma	87.66
PF12802	62	MarR_2: MarR family; PDB: 3ECO_B 2QWW_B 3KP6_B 3KP	87.59
COG3355	126	Predicted transcriptional regulator [Transcription	87.55
PF01726	65	LexA_DNA_bind: LexA DNA binding domain; InterPro:	86.57
PRK11083	228	DNA-binding response regulator CreB; Provisional	86.28
PF03444	78	HrcA_DNA-bdg: Winged helix-turn-helix transcriptio	86.0
PHA02547	179	55 RNA polymerase sigma factor; Provisional	85.99
PF01325	60	Fe_dep_repress: Iron dependent repressor, N-termin	85.98
PRK10710	240	DNA-binding transcriptional regulator BaeR; Provis	85.93
PRK10046	225	dpiA two-component response regulator DpiA; Provis	85.89
PRK05932	455	RNA polymerase factor sigma-54; Reviewed	85.75
smart00550	68	Zalpha Z-DNA-binding domain in adenosine deaminase	85.6
PRK05911	257	RNA polymerase sigma factor sigma-28; Reviewed	85.28
PRK07408	256	RNA polymerase sigma factor SigF; Reviewed	85.27
PRK06288	268	RNA polymerase sigma factor WhiG; Reviewed	84.96
PF13542	52	HTH_Tnp_ISL3: Helix-turn-helix domain of transposa	84.92
PRK10336	219	DNA-binding transcriptional regulator QseB; Provis	84.92
smart00342	84	HTH_ARAC helix_turn_helix, arabinose operon contro	84.41
TIGR02997	298	Sig70-cyanoRpoD RNA polymerase sigma factor, cyano	84.12
COG3415	138	Transposase and inactivated derivatives [DNA repli	84.04
TIGR02885	231	spore_sigF RNA polymerase sigma-F factor. Members	84.03
PRK12469	481	RNA polymerase factor sigma-54; Provisional	84.03
PRK07122	264	RNA polymerase sigma factor SigF; Reviewed	83.86
PF12728	51	HTH_17: Helix-turn-helix domain	83.81
PRK05949	327	RNA polymerase sigma factor; Validated	83.7
PF13463	68	HTH_27: Winged helix DNA-binding domain; PDB: 3GFL	83.56
PF00356	46	LacI: Bacterial regulatory proteins, lacI family;	83.4
PF01710	119	HTH_Tnp_IS630: Transposase; InterPro: IPR002622 Tr	83.35
PF01418	77	HTH_6: Helix-turn-helix domain, rpiR family; Inter	83.13
smart00344	108	HTH_ASNC helix_turn_helix ASNC type. AsnC: an auto	82.99
PF11427	50	HTH_Tnp_Tc3_1: Tc3 transposase; PDB: 1U78_A 1TC3_C	82.99
PRK00423	310	tfb transcription initiation factor IIB; Reviewed	82.89
PRK15479	221	transcriptional regulatory protein TctD; Provision	82.84
PRK12423	202	LexA repressor; Provisional	82.77
TIGR02850	254	spore_sigG RNA polymerase sigma-G factor. Members	82.54
PF13744	80	HTH_37: Helix-turn-helix domain; PDB: 2A6C_B 2O38_	82.48
TIGR02154	226	PhoB phosphate regulon transcriptional regulatory	82.29
smart00345	60	HTH_GNTR helix_turn_helix gluconate operon transcr	82.15
PF01371	87	Trp_repressor: Trp repressor protein; InterPro: IP	81.74
cd04762	49	HTH_MerR-trunc Helix-Turn-Helix DNA binding domain	81.63
PRK13413	200	mpi multiple promoter invertase; Provisional	81.44
TIGR01764	49	excise DNA binding domain, excisionase family. An	81.33
TIGR01610	95	phage_O_Nterm phage replication protein O, N-termi	81.32
COG2973	103	TrpR Trp operon repressor [Transcription]	81.29
PRK07670	251	RNA polymerase sigma factor SigD; Validated	80.94
TIGR03787	227	marine_sort_RR proteobacterial dedicated sortase s	80.57
PF01047	59	MarR: MarR family; InterPro: IPR000835 The MarR-ty	80.35
PF13551	112	HTH_29: Winged helix-turn helix	80.2

>PRK07598 RNA polymerase sigma factor SigC; Validated

Probab=100.00  E-value=6.5e-64  Score=530.18  Aligned_cols=312  Identities=29%  Similarity=0.521  Sum_probs=292.0

Q ss_pred             CCchhHHHHHHhhccCCCCCCchHHHHHHhhchHHHH--------------------HHHHHHHHHHHhCCCCchHHHHH
Q 009449          218 KQPTIFSAERALNSRGRRLTIARNEAEMSKGVQVVAN--------------------LERIKTTLEKESGKAASLNCWAQ  277 (534)
Q Consensus       218 ~~~~~~~~~~~~~~~~~~lLt~~eE~~L~~~iq~~~~--------------------le~~~~~l~~~~g~~ps~~ewa~  277 (534)
                      .||.+.|+   ..+.+.||||++||++|+++||.++.                    |++++..|.+++|++||..+||.
T Consensus        59 ~d~v~~yl---~~igr~~lL~~~eEv~l~~~vq~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~l~~~~g~~pt~~ewa~  135 (415)
T PRK07598         59 TDLVRLYL---QEIGRVRLLGRDEEVSEAQKVQRYMKLIVLANAAKEGDEVIKPYLRLIEVRERLTSELGHRPSLERWAK  135 (415)
T ss_pred             CChHHHHH---HhcccccCCCHHHHHHHHHHHHHHHHHhhhhhhhhcccchhhhHHHHHHHHHHHHHHhCCCCCHHHHHH
Confidence            36655555   35555799999999999999999999                    89999999999999999999995


Q ss_pred             HcC----------------------CCHHHHHHHHHhcHHHHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHH
Q 009449          278 AAG----------------------VSERVLKQHLAFGWYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQ  335 (534)
Q Consensus       278 a~g----------------------~d~~~L~~~l~~G~~A~e~LI~~nlrLV~sIArrY~~~g~~~eDLiQEG~lgL~r  335 (534)
                      ++|                      ++.++|++.++.|..|+++||.+|+++|+++|++|.++|++++||+|||++|||+
T Consensus       136 ~~~~~~~~l~~~l~~~~~~~~~~~~l~~~eL~~~l~~G~~A~e~LI~~nlrLVvsiAkky~~~g~~~eDLiQEG~iGL~r  215 (415)
T PRK07598        136 TADISLADLKPTLAEGKRRWAEIAKLTVEELEQIQKQGLRAKEHMIKANLRLVVSVAKKYQNRGLELLDLVQEGTLGLER  215 (415)
T ss_pred             HhCCcHHHHHHhhhhhhhhhhhhccCCHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHccCCCCHHHHHHHHHHHHHH
Confidence            554                      5566666777889899999999999999999999999999999999999999999


Q ss_pred             hhhccCCcCCCchhhHHHHHHHHHHHHHHHHhccccccccchHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHcCCCHHHH
Q 009449          336 GAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEI  415 (534)
Q Consensus       336 A~ekFDp~kG~rFSTYA~~wIR~aI~~~lr~~sr~iRlP~~~~~~i~ki~ka~~~L~~elGr~Pt~eEIA~~lgis~~kv  415 (534)
                      |+++|||++|++|+|||+||||++|.+++++++++||+|.|+.+.+++++++.+.+.+++||.|+.+|||+.+||++++|
T Consensus       216 avekFDp~rG~rFSTYa~wwIRqaI~r~i~~~srtIrlP~~i~e~l~~lrk~~r~L~~~lgR~pt~~EiA~~l~is~~~v  295 (415)
T PRK07598        216 AVEKFDPTKGYRFSTYAYWWIRQGITRAIATQSRTIRLPVHITEKLNKIKKAQRKISQEKGRTPTIEDIAQELEMTPTQV  295 (415)
T ss_pred             HHHHcCcccCCCHHHHHHHHHHHHHHHHHHHcCCceehhHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHhhhhcccccccccchhhhhhhccCCCCCCChHHHHHHHHHHHHHHHHHhhCCHHHHHHHhhHhcCCCCCCCCHH
Q 009449          416 RSASECLRIVGSIDQKIGDCLNAKYLEFAPDRSVKSPKEIVMRQHMKKDVFRILESLDSRERQVLVLRYGLNDHRPKSLE  495 (534)
Q Consensus       416 ~~~l~~~~~~~SLD~~i~~~~~~~l~e~i~d~~~~spee~v~~~el~e~L~~~L~~L~~rEReVL~LryGL~d~e~~Sl~  495 (534)
                      +.++...+.++|||.+++++++..+.+.+.++. .+|++.+....+...|..+|..|||+||+||.|+|||+|++++|++
T Consensus       296 r~~l~~~~~~~SLd~~vg~~~d~~l~d~l~~~~-~~pee~~~~~~l~~~L~~~L~~L~~reR~VI~LRygl~d~~~~Tl~  374 (415)
T PRK07598        296 REVLLRVPRSVSLETKVGKDKDTELGDLLETDD-ISPEEMLMRESLQRDLQHLLADLTSRERDVIRMRFGLADGHTYSLA  374 (415)
T ss_pred             HHHHHHccCCcccccccCCCccccHHHhccCCC-CCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHhcCCCCCCCHH
Confidence            999999999999999999988888888887554 6899999999999999999999999999999999999999999999


Q ss_pred             HHHHHhCCCHHHHHHHHHHHHHHHHhHhhhhcchhhhc
Q 009449          496 EIGKLFHVSKEWIRKLEKKAMTKLRDSETCRDLSHFLV  533 (534)
Q Consensus       496 EIA~~LgISrerVRqi~~RAL~KLR~~l~~~~L~~yl~  533 (534)
                      |||+.||||+++|++++++|++|||++-....|++|+.
T Consensus       375 EIA~~LGvS~erVRqie~rAl~KLR~~~~~~~l~~y~~  412 (415)
T PRK07598        375 EIGRALDLSRERVRQIESKALQKLRQPKRRNRIRDYLE  412 (415)
T ss_pred             HHHHHHCcCHHHHHHHHHHHHHHHhchhHHHHHHHHHH
Confidence            99999999999999999999999999999999999985

>PRK05949 RNA polymerase sigma factor; Validated

Probab=100.00  E-value=4.4e-60  Score=491.04  Aligned_cols=308  Identities=33%  Similarity=0.557  Sum_probs=291.5

Q ss_pred             HHHHHHhhccC-CCCCCchHHHHHHhhchHHHHHHHHHHHHHHHhCCCCchHHHHHHcCCCHHHHHHHHHhcHHHHHHHH
Q 009449          223 FSAERALNSRG-RRLTIARNEAEMSKGVQVVANLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQHLAFGWYCREELI  301 (534)
Q Consensus       223 ~~~~~~~~~~~-~~lLt~~eE~~L~~~iq~~~~le~~~~~l~~~~g~~ps~~ewa~a~g~d~~~L~~~l~~G~~A~e~LI  301 (534)
                      +.+..|++..+ .||||++||++|++.|+.++.+++.+..|.+++|+.|+..+||.++++++.+|+..++.|..|++.||
T Consensus        18 d~~~~yl~~i~~~~lLt~eeE~~l~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~eL~~~~~~g~~A~~~Li   97 (327)
T PRK05949         18 DMVRTYLHEIGRVPLLTHEQEIVYGKQVQQMMSLLEAKEALAKKLGREPSLPEWAEAVNLSETELKQTLKQGKRAKQKMI   97 (327)
T ss_pred             CHHHHHHHHcCCccCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhccCCchHHHHHhccCCHHHHHHHHHccHHHHHHHH
Confidence            33445565555 69999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCchhhHHHHHHHHHHHHHHHHhccccccccchHHHH
Q 009449          302 KSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIPCKLNREI  381 (534)
Q Consensus       302 ~~nlrLV~sIArrY~~~g~~~eDLiQEG~lgL~rA~ekFDp~kG~rFSTYA~~wIR~aI~~~lr~~sr~iRlP~~~~~~i  381 (534)
                      ..|+++|+++|++|.+++.+++||+|||++|||+++++|||++|++|+|||+||||++|.+++.+++++||+|.|+.+.+
T Consensus        98 ~~~~~~V~~iA~~y~~~~~~~eDLvQEg~igL~~a~~kfd~~~G~rFsTYa~wwIrq~I~r~i~~~~r~iRlP~~~~~~~  177 (327)
T PRK05949         98 EANLRLVVAIAKKYQKRNMEFLDLIQEGTLGLERGVEKFDPTRGYKFSTYAYWWIRQAITRAIAQQARTIRLPIHITEKL  177 (327)
T ss_pred             HHHHHHHHHHHHHHccCCCCHHHHHHHHHHHHHHHHHhcCCcCCCChhhhhHHHHHHHHHHHHHHcCCceeCCHHHHHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHHhhhhcccccccccchhhhhhhccCCCCCCChHHHHHHHHH
Q 009449          382 SKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNAKYLEFAPDRSVKSPKEIVMRQHM  461 (534)
Q Consensus       382 ~ki~ka~~~L~~elGr~Pt~eEIA~~lgis~~kv~~~l~~~~~~~SLD~~i~~~~~~~l~e~i~d~~~~spee~v~~~el  461 (534)
                      ++++++.+.+.+++||.||.+|||+.+|+++++|..++.....++|||.+++++++.++.+.+++.. .+|++.+....+
T Consensus       178 ~~l~k~~~~l~~~lgr~pt~~eiA~~l~i~~~~v~~~~~~~~~~~SLd~~~~~~~~~~l~~~l~d~~-~~pe~~~~~~~~  256 (327)
T PRK05949        178 NKIKKTQRELSQKLGRSATPAEIAKELELEPSQIREYLSMARQPISLDVRVGDNQDTELSELLEDEG-PSPDQYITQELL  256 (327)
T ss_pred             HHHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHHhccccccCCCcCCCCCccHHhhcCCCC-CCHHHHHHHHHH
Confidence            9999999999999999999999999999999999999998899999999998887778888888765 689999999999


Q ss_pred             HHHHHHHHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHhhhhcchhhhc
Q 009449          462 KKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDSETCRDLSHFLV  533 (534)
Q Consensus       462 ~e~L~~~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~~l~~~~L~~yl~  533 (534)
                      ...|..+|+.|||+||+||.+||||+|++++|++|||+.||||+++|+|++.+|++|||+.  ...|+.|+.
T Consensus       257 ~~~L~~~L~~L~~rer~Vi~lr~gl~~~e~~Tl~EIa~~lgiS~erVrq~~~rAl~kLr~~--~~~l~~~~~  326 (327)
T PRK05949        257 RQDLNNLLAELTPQQREVLTLRFGLEDGKELSLAKVGERLNLSRERVRQLEHQALAHLRRR--RANVKEYLA  326 (327)
T ss_pred             HHHHHHHHHhCCHHHHHHHHHHhccCCCCCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH--HHHHHHHHh
Confidence            9999999999999999999999999999999999999999999999999999999999994  467788874

>PRK07406 RNA polymerase sigma factor RpoD; Validated

Probab=100.00  E-value=3.6e-60  Score=498.05  Aligned_cols=308  Identities=33%  Similarity=0.618  Sum_probs=294.1

Q ss_pred             HHHHHhhccC-CCCCCchHHHHHHhhchHHHHHHHHHHHHHHHhCCCCchHHHHHHcCCCHHHHHHHHHhcHHHHHHHHH
Q 009449          224 SAERALNSRG-RRLTIARNEAEMSKGVQVVANLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQHLAFGWYCREELIK  302 (534)
Q Consensus       224 ~~~~~~~~~~-~~lLt~~eE~~L~~~iq~~~~le~~~~~l~~~~g~~ps~~ewa~a~g~d~~~L~~~l~~G~~A~e~LI~  302 (534)
                      .+..|++..+ .||||++||++|+++|+.++.+++.+..|+++.|++|+..+||.++|++..+|.+++..|..|++.||.
T Consensus        64 ~l~~Yl~~i~~~~lLt~eEE~~La~~i~~~~~~~~~~~~l~~~~g~~~~~~~~~~~~~~~~~~l~~~~~~g~~A~~~Li~  143 (373)
T PRK07406         64 SIRVYLQEIGRIRLLRPDEEIELARKIADLLELEELREQFESELGREPSDKEWAELVDMPLPKFRRRLMLGRRAKEKMVQ  143 (373)
T ss_pred             HHHHHHHHhcccCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhcccccchhhHhhhccccHHHHHHHHhcCHHHHHHHHH
Confidence            3455666555 699999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCchhhHHHHHHHHHHHHHHHHhccccccccchHHHHH
Q 009449          303 STRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIPCKLNREIS  382 (534)
Q Consensus       303 ~nlrLV~sIArrY~~~g~~~eDLiQEG~lgL~rA~ekFDp~kG~rFSTYA~~wIR~aI~~~lr~~sr~iRlP~~~~~~i~  382 (534)
                      +|+++|+++|++|.++|.+++||+|||++|||+++++|||.+|++|+|||+||||++|.++|++++++||+|.|+.+.++
T Consensus       144 ~~l~lV~~iA~ry~~~~~~~eDLiQEG~igL~~Ai~kFd~~kg~~FsTYA~wWIRqaI~~~I~~~~r~IRlP~~~~~~~~  223 (373)
T PRK07406        144 SNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYATWWIRQAITRAIADQSRTIRLPVHLYETIS  223 (373)
T ss_pred             HHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHhcCCccCCCHHHHHHHHHHHHHHHHHHhcCCceeCCHHHHHHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHHhhhhcccccccccchhhhhhhccCCCCCCChHHHHHHHHHH
Q 009449          383 KIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNAKYLEFAPDRSVKSPKEIVMRQHMK  462 (534)
Q Consensus       383 ki~ka~~~L~~elGr~Pt~eEIA~~lgis~~kv~~~l~~~~~~~SLD~~i~~~~~~~l~e~i~d~~~~spee~v~~~el~  462 (534)
                      +++++...|.+++||.||.+|||+.+|+++++|..++.....++|||.+++++++..+.+++++.. .+|++.+....+.
T Consensus       224 ~i~~a~~~l~~~lgr~Pt~~EIA~~lg~~~e~v~~~~~~~~~~~SLd~~i~~~~~~~l~d~l~d~~-~~pee~~~~~~~~  302 (373)
T PRK07406        224 RIKKTTKVLSQEFGRKPTEEEIAESMEMTIEKLRFIAKSAQLPISLETPIGKEEDSRLGDFIEADG-ETPEDDVAKNLLR  302 (373)
T ss_pred             HHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCcccHHHhcCCCC-CCHHHHHHHHHHH
Confidence            999999999999999999999999999999999999888888999999998877778889888764 5899999999999


Q ss_pred             HHHHHHHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHhhhhcchhhh
Q 009449          463 KDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDSETCRDLSHFL  532 (534)
Q Consensus       463 e~L~~~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~~l~~~~L~~yl  532 (534)
                      ..|..+|..||++||.||.+||||+|++++|++|||+.||||++||||++.+|++|||++.....|..|+
T Consensus       303 ~~L~~aL~~L~~rEr~IL~lrygl~~~~~~Tl~EIA~~lgiS~eRVRQie~rAL~KLR~~~~~~~l~~~~  372 (373)
T PRK07406        303 EDLEGVLATLSPRERDVLRLRYGLDDGRMKTLEEIGQIFNVTRERIRQIEAKALRKLRHPNRNSVLKEYI  372 (373)
T ss_pred             HHHHHHHHcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCcCHHHHHHHHHHHHHHHhchhHHHHHHHHh
Confidence            9999999999999999999999999889999999999999999999999999999999999999999986

>PRK07405 RNA polymerase sigma factor SigD; Validated

Probab=100.00  E-value=6.8e-59  Score=480.50  Aligned_cols=306  Identities=30%  Similarity=0.548  Sum_probs=290.1

Q ss_pred             HHHHhhccC-CCCCCchHHHHHHhhchHHHHHHHHHHHHHHHhCCCCchHHHHHHcCCCHHHHHHHHHhcHHHHHHHHHH
Q 009449          225 AERALNSRG-RRLTIARNEAEMSKGVQVVANLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQHLAFGWYCREELIKS  303 (534)
Q Consensus       225 ~~~~~~~~~-~~lLt~~eE~~L~~~iq~~~~le~~~~~l~~~~g~~ps~~ewa~a~g~d~~~L~~~l~~G~~A~e~LI~~  303 (534)
                      +..|++..+ .||||++||++|+++|+.++.+++++..|++++|+.|+..+||.++++++.+|+..++.|..|++.||..
T Consensus        10 ~~~yl~~i~~~~lLt~eeE~~La~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~L~~~~~~g~~A~~~L~~~   89 (317)
T PRK07405         10 VRTYLREIGRVPLLTHEEEILYGKQVQRLVALQEIREELAEELGREPTDAEWAKAAKLSEEELRSAIAEGEAAKRKMVEA   89 (317)
T ss_pred             HHHHHHHccccCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhcccccchHHHhhhccCCHHHHHHHHhccHHHHHHHHHH
Confidence            445565555 6999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             hHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCchhhHHHHHHHHHHHHHHHHhccccccccchHHHHHH
Q 009449          304 TRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIPCKLNREISK  383 (534)
Q Consensus       304 nlrLV~sIArrY~~~g~~~eDLiQEG~lgL~rA~ekFDp~kG~rFSTYA~~wIR~aI~~~lr~~sr~iRlP~~~~~~i~k  383 (534)
                      |+++|+++|++|.+++.+++||+|||++|||+++++|||++|++|+|||+||||++|.+++.+++++||+|.|+...+++
T Consensus        90 ~~~~V~~~a~~~~~~~~~~eDLvQEg~i~L~~a~~~fd~~~g~rf~tYa~~wIR~~I~~~i~~~~~~ir~p~~~~~~~~~  169 (317)
T PRK07405         90 NLRLVVSVAKKYLKRNVDLLDLIQEGTIGMQRGVEKFDPTKGYRFSTYAYWWIRQAITRAIAEKSRTIRLPIHITEKLNK  169 (317)
T ss_pred             HHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHhCcCCCCChHHHHHHHHHHHHHHHHHhcCCCccCChHHHHHHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHHhhhhcccccccccchhhhhhhccCCCCCCChHHHHHHHHHHH
Q 009449          384 IQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNAKYLEFAPDRSVKSPKEIVMRQHMKK  463 (534)
Q Consensus       384 i~ka~~~L~~elGr~Pt~eEIA~~lgis~~kv~~~l~~~~~~~SLD~~i~~~~~~~l~e~i~d~~~~spee~v~~~el~e  463 (534)
                      ++++.+.+.+.+|+.||.+|||+.+|++++++..+......+.|||.+++++.+..+.+.++++. .+|++.+....+..
T Consensus       170 l~~~~~~l~~~~gr~pt~~eiA~~~~~~~~~v~~~~~~~~~~~SLd~~~~~~~~~~l~~~~~d~~-~~pe~~~~~~~~~~  248 (317)
T PRK07405        170 IKKAQRQLSQQLGRAATIGELAEELELTPKQVREYLERARQPLSLDLRVGDNQDTELGELLEDTG-ASPEDFATQSSLQL  248 (317)
T ss_pred             HHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHHcCCCeeecCCCCCCCCccHHHhhcCCC-CCHHHHHHHHHHHH
Confidence            99999999999999999999999999999999999988888999999998877778888888765 68999999999999


Q ss_pred             HHHHHHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHhhhhcchhhhc
Q 009449          464 DVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDSETCRDLSHFLV  533 (534)
Q Consensus       464 ~L~~~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~~l~~~~L~~yl~  533 (534)
                      .|..+|+.|||+||+||.+||||+|++++|++|||+.||||++||||++.+|++|||+.  ...|..|+.
T Consensus       249 ~l~~al~~L~~rer~Vi~lr~gl~~~~~~Tl~EIa~~lgiS~erVRqi~~rAl~kLr~~--~~~l~~~~~  316 (317)
T PRK07405        249 DLERLMEDLTPQQKEVIALRFGLEDGQPLTLAKIGERLNISRERVRQIEREALSKLRKR--KANIQEYLA  316 (317)
T ss_pred             HHHHHHHcCCHHHHHHHHHHhhcCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH--HHHHHHHHh
Confidence            99999999999999999999999999999999999999999999999999999999985  467777764

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

Probab=100.00  E-value=1.1e-58  Score=475.04  Aligned_cols=293  Identities=36%  Similarity=0.604  Sum_probs=279.3

Q ss_pred             HHhh-ccCCCCCCchHHHHHHhhchHHHHHHHHHHHHHHHhCCCCchHHHHHHcCCCHHHHHHHHHhcHHHHHHHHHHhH
Q 009449          227 RALN-SRGRRLTIARNEAEMSKGVQVVANLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQHLAFGWYCREELIKSTR  305 (534)
Q Consensus       227 ~~~~-~~~~~lLt~~eE~~L~~~iq~~~~le~~~~~l~~~~g~~ps~~ewa~a~g~d~~~L~~~l~~G~~A~e~LI~~nl  305 (534)
                      .|++ ....||||++||++|++.++.+..+++.+..|+++.|++|+..+||+++|++..+|...++.|..|++.||.+|+
T Consensus         5 ~yl~~~~~~~lLt~eeE~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~g~~A~~~Lv~~~l   84 (298)
T TIGR02997         5 LYLQEIGRVPLLTPEEEIELARQVQQMMVLEELREELEEQLGREPSKEEWAAAAGLSEAELRQRLRQGQRAKEKMIKANL   84 (298)
T ss_pred             HHHHHccccCCCCHHHHHHHHHHHHHHhHHHHHHHHHHHhhcCCCcHHHHHHhccCCHHHHHHHHhccHHHHHHHHHHhH
Confidence            3444 445799999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCchhhHHHHHHHHHHHHHHHHhccccccccchHHHHHHHH
Q 009449          306 PLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIPCKLNREISKIQ  385 (534)
Q Consensus       306 rLV~sIArrY~~~g~~~eDLiQEG~lgL~rA~ekFDp~kG~rFSTYA~~wIR~aI~~~lr~~sr~iRlP~~~~~~i~ki~  385 (534)
                      ++|+++|++|.++|.+++||+|||++|||+|+++|||.+|++|+|||+||||++|.+++.+++++||+|.++...+++++
T Consensus        85 rlV~~iA~~y~~~~~~~eDLiQEg~igL~~a~~kfd~~~g~rFsTya~~wIr~~I~r~i~~~~r~vr~p~~~~~~~~~~r  164 (298)
T TIGR02997        85 RLVVSVAKKYQNRGLELLDLIQEGSLGLERAVEKFDPTRGYKFSTYAYWWIRQGITRAIANQSRTIRLPIHITEKLNKIK  164 (298)
T ss_pred             HHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHhCccCCCChHHHHHHHHHHHHHHHHHhcCCCeeCcHHHHHHHHHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHHhhhhcccccccccchhhhhhhccCCCCCCChHHHHHHHHHHHHH
Q 009449          386 KARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNAKYLEFAPDRSVKSPKEIVMRQHMKKDV  465 (534)
Q Consensus       386 ka~~~L~~elGr~Pt~eEIA~~lgis~~kv~~~l~~~~~~~SLD~~i~~~~~~~l~e~i~d~~~~spee~v~~~el~e~L  465 (534)
                      ++.+.+.+.+|+.||.+|||+.+|+++++|..++.....++|||.+++++++..+.+.+++. .++|++.+...++...|
T Consensus       165 k~~~~l~~~~~~~pt~~eia~~l~~~~~~v~~~~~~~~~~~SLd~~~~~~~~~~~~~~~~~~-~~~pe~~~~~~~~~~~L  243 (298)
T TIGR02997       165 KVQRELSQKLGRTPSEAEIAEALELEPEQVRELLQRARQPVSLDAPVGDEEDTELGDLLEDD-GESPEEQVERESLRQDL  243 (298)
T ss_pred             HHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHHcccCcccCCCcCCCCcchHHHhccCC-CCCHHHHHHHHHHHHHH
Confidence            99999999999999999999999999999999999888999999999877666777777774 46899999999999999


Q ss_pred             HHHHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 009449          466 FRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLR  520 (534)
Q Consensus       466 ~~~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR  520 (534)
                      ..+|+.|||+||+||.+||||+|++++|++|||+.||||++||+|++++|++|||
T Consensus       244 ~~~L~~L~~rer~Vi~lr~gl~~~~~~Tl~EIa~~lgiS~erVrq~~~rAl~kLr  298 (298)
T TIGR02997       244 ESLLAELTPRERQVLRLRFGLDGGEPLTLAEIGRRLNLSRERVRQIEAKALRKLR  298 (298)
T ss_pred             HHHHHcCCHHHHHHHHHHhccCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHHcC
Confidence            9999999999999999999999999999999999999999999999999999996

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).

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

Probab=100.00  E-value=2.2e-58  Score=474.61  Aligned_cols=312  Identities=33%  Similarity=0.546  Sum_probs=285.0

Q ss_pred             hHHHHHHhhccC-CCCCCchHHHHHHhhchHHHHHHHHHHHHHH-HhCCCCchH---------------HHHHHcCCCH-
Q 009449          222 IFSAERALNSRG-RRLTIARNEAEMSKGVQVVANLERIKTTLEK-ESGKAASLN---------------CWAQAAGVSE-  283 (534)
Q Consensus       222 ~~~~~~~~~~~~-~~lLt~~eE~~L~~~iq~~~~le~~~~~l~~-~~g~~ps~~---------------ewa~a~g~d~-  283 (534)
                      .+.+..|++..+ .++++.++|+++.++++....+......+.. .++..|+..               +|+.....++ 
T Consensus         8 ~d~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~Ee   87 (342)
T COG0568           8 ADAVRAYLDEIGRIPLLVREAEVELAKQLEDEQLLVELGEDLTDLKLGREPSERARRPAGRLSFYIRAIEAAPLLTPEEE   87 (342)
T ss_pred             hhHHHHHHHHhcchhhhhHHHHHHHHHHHhHhhhhhHHHHHHHhcccccccchhhhhhhhhHHHHHHHHhhhcccChHHH
Confidence            455566666665 4899999999999999988877666777766 567888876               5555444444 


Q ss_pred             HHHHHHHHhcHH---HHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCchhhHHHHHHHHHH
Q 009449          284 RVLKQHLAFGWY---CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSI  360 (534)
Q Consensus       284 ~~L~~~l~~G~~---A~e~LI~~nlrLV~sIArrY~~~g~~~eDLiQEG~lgL~rA~ekFDp~kG~rFSTYA~~wIR~aI  360 (534)
                      ..|..++..|..   |+.+||.+|++||++||++|.++|+++.||||||+|||++|+++|||++||+|||||+||||++|
T Consensus        88 ~~la~~~~~g~~~~~Ak~klv~snLRlVvsIAk~Y~~rGL~~~DLIQEGniGLmkAVekFdp~rG~kFsTYA~wWIrqaI  167 (342)
T COG0568          88 KALARRLKRGERDLDAKKKLVESNLRLVVSIAKKYTGRGLPFLDLIQEGNIGLMKAVEKFDPEKGFKFSTYATWWIRQAI  167 (342)
T ss_pred             HHHHHHHHcCCccHHHHHHHHHHHHHHHHHHHHHhhcCCCcHHHHHhcccHHHHHHHHhcCcccCCcchhHHHHHHHHHH
Confidence            667888888854   99999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHhccccccccchHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHHhhhhcccccccccchhhhh
Q 009449          361 SKMVARHARGIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNAKY  440 (534)
Q Consensus       361 ~~~lr~~sr~iRlP~~~~~~i~ki~ka~~~L~~elGr~Pt~eEIA~~lgis~~kv~~~l~~~~~~~SLD~~i~~~~~~~l  440 (534)
                      .++|.++.|+||+|+|+++.+++++++.+.+.+++|++|+.+|||+.+|+++++|..++.....++|||.|+|++++..+
T Consensus       168 ~raI~~q~rtIRipvh~~e~~nkl~r~~r~l~q~~~r~p~~eeia~~l~~~~~~V~~m~~~~~~~~SLd~~ig~ded~~l  247 (342)
T COG0568         168 TRAIADQARTIRIPVHQVELINKLRRVKRELLQELGREPTPEEIAEELGVSPDKVREMLKRASEPISLDTPIGDDEDSEL  247 (342)
T ss_pred             HHHHHHhcchhhHhHHHHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHhCCCHHHHHHHHHhcccCcccCCcCCCCcccHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             hhccCCCCCCChHHHHHHHHHHHHHHHHHhh-CCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Q 009449          441 LEFAPDRSVKSPKEIVMRQHMKKDVFRILES-LDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKL  519 (534)
Q Consensus       441 ~e~i~d~~~~spee~v~~~el~e~L~~~L~~-L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KL  519 (534)
                      +|+++|....+|++.+....+.+++...|.. |+|+|+.||++|||++|+++.|++|||+.+|||++|||||+.+|++||
T Consensus       248 ~d~leD~~~~~p~~~~~~~~~~~~~~~~L~~~Lt~rE~~Vi~~R~gl~~~~~~TLeevg~~~~isrERvRQIE~kAl~KL  327 (342)
T COG0568         248 GDFLEDDKSVSPEDAVERESLKEDLNEVLAEALTERERRVIRLRFGLDDGEPKTLEELGEEFGISRERVRQIEAKALRKL  327 (342)
T ss_pred             HHHhhcCCcCCHHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhccCCCCcchHHHHHHHhCCcHHHHHHHHHHHHHHH
Confidence            9999999888999999999999999999999 999999999999999999999999999999999999999999999999


Q ss_pred             H-hHhhhhcchhhhc
Q 009449          520 R-DSETCRDLSHFLV  533 (534)
Q Consensus       520 R-~~l~~~~L~~yl~  533 (534)
                      | .+.....+++|++
T Consensus       328 r~~~~~~~~~~~~l~  342 (342)
T COG0568         328 RRHPERSALLRSYLD  342 (342)
T ss_pred             HHhhhhhhHHHHhhC
Confidence            9 5555666788874

>PRK05901 RNA polymerase sigma factor; Provisional

Probab=100.00  E-value=2.2e-57  Score=491.00  Aligned_cols=298  Identities=32%  Similarity=0.521  Sum_probs=271.9

Q ss_pred             HHHHHHhhccC-CCCCCchHHHHHHhhchHHHHHHHHHHHHHHHhCCCCchHHHHHHcCCCHHHHHHHHHhcHHHHHHHH
Q 009449          223 FSAERALNSRG-RRLTIARNEAEMSKGVQVVANLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQHLAFGWYCREELI  301 (534)
Q Consensus       223 ~~~~~~~~~~~-~~lLt~~eE~~L~~~iq~~~~le~~~~~l~~~~g~~ps~~ewa~a~g~d~~~L~~~l~~G~~A~e~LI  301 (534)
                      +.++.|++..+ .||||++||++|+++|+.+..++...   .       ...+|+..   ...+|++.+..|..|+++||
T Consensus       211 d~l~~YL~~i~~~~lLt~eEE~~La~~i~~g~~~~~~~---~-------~~~~~~~~---~~~~l~~~~~~g~~Ar~~LI  277 (509)
T PRK05901        211 DPVKAYLKQIGKVKLLNAEEEVELAKRIEAGLYAEELL---A-------EGEKLDPE---LRRDLQWIGRDGKRAKNHLL  277 (509)
T ss_pred             cHHHHHHHHhccCCCCCHHHHHHHHHHHHhCCchhhhh---h-------hcccchhh---hhhhhhhhccchHHHHHHHH
Confidence            33455666555 59999999999999999875544321   1       11224322   45778888999999999999


Q ss_pred             HHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCchhhHHHHHHHHHHHHHHHHhccccccccchHHHH
Q 009449          302 KSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIPCKLNREI  381 (534)
Q Consensus       302 ~~nlrLV~sIArrY~~~g~~~eDLiQEG~lgL~rA~ekFDp~kG~rFSTYA~~wIR~aI~~~lr~~sr~iRlP~~~~~~i  381 (534)
                      .+|+|||++||++|.++|++++||||||+|||++|+++|||++|++|+|||+||||++|.+++.++.|+||+|.|+++.+
T Consensus       278 ~sNLrLVvsIAkrY~~~Gl~~eDLIQEGnIGLikAvekFDp~rG~rFSTYA~wWIRqaI~raI~d~~r~IRvP~~~~e~i  357 (509)
T PRK05901        278 EANLRLVVSLAKRYTNRGLSFLDLIQEGNLGLIKAVEKFDYTKGYKFSTYATWWIRQAITRAMADQARTIRIPVHMVETI  357 (509)
T ss_pred             HHhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHhCcccCCCchhhhHHHHHHHHHHHHHHcCCceecCHHHHHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHHhhhhcccccccccchhhhhhhccCCCCCCChHHHHHHHHH
Q 009449          382 SKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNAKYLEFAPDRSVKSPKEIVMRQHM  461 (534)
Q Consensus       382 ~ki~ka~~~L~~elGr~Pt~eEIA~~lgis~~kv~~~l~~~~~~~SLD~~i~~~~~~~l~e~i~d~~~~spee~v~~~el  461 (534)
                      +++.++.++|.+.+||.||.+|||+.+|+++++|..++.....++|||.+++++++..+.++++|+...+|++.+....+
T Consensus       358 ~kl~~~~~~L~~~lgr~PT~eELAe~Lgis~e~V~~~~~~~~~~~SLD~~i~~d~~~~l~d~l~D~~~~~p~~~~~~~~l  437 (509)
T PRK05901        358 NKLGRIERELLQELGREPTPEELAKEMGFTPEKVREIQKYNREPISLDKTIGKEGDSQFGDFIEDSEAVSPVDAVSFTLL  437 (509)
T ss_pred             HHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccccccccCCcccHHHhccCCCCCCHHHHHHHHHH
Confidence            99999999999999999999999999999999999999888899999999988877889999999887899999999999


Q ss_pred             HHHHHHHHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHhhhhcchhhhc
Q 009449          462 KKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDSETCRDLSHFLV  533 (534)
Q Consensus       462 ~e~L~~~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~~l~~~~L~~yl~  533 (534)
                      ...|..+|..|+++|+.||.+||||++++++|++|||+.||||++|||||+.+|+.|||+......|++|++
T Consensus       438 ~~~L~~aL~~L~eREr~VI~lRyGL~~~e~~TL~EIa~~lGVSrERVRQIe~kAL~KLR~~~~~~~l~~~l~  509 (509)
T PRK05901        438 QDQLQEVLETLSEREAGVIRMRFGLTDGQPKTLDEIGQVYGVTRERIRQIESKTLRKLRHPSRSQVLRDFLD  509 (509)
T ss_pred             HHHHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhC
Confidence            999999999999999999999999999999999999999999999999999999999999999999999974

>PRK07921 RNA polymerase sigma factor SigB; Reviewed

Probab=100.00  E-value=2.9e-56  Score=461.70  Aligned_cols=295  Identities=33%  Similarity=0.559  Sum_probs=269.3

Q ss_pred             HHHHhhccC-CCCCCchHHHHHHhhchHHHHHHHHHHHHHHHhCCCCchHHHHHHcCCCHHHHHHHHHhcHHHHHHHHHH
Q 009449          225 AERALNSRG-RRLTIARNEAEMSKGVQVVANLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQHLAFGWYCREELIKS  303 (534)
Q Consensus       225 ~~~~~~~~~-~~lLt~~eE~~L~~~iq~~~~le~~~~~l~~~~g~~ps~~ewa~a~g~d~~~L~~~l~~G~~A~e~LI~~  303 (534)
                      +..|++..+ .||||++||++|+++|+.+..++..           |+..+|+...  ...+|...++.|..|++.||..
T Consensus        28 ~~~Yl~~i~~~~lLt~eeE~~La~~~~~g~~~~~~-----------~~~~~~~~~~--~~~~l~~~~~~~~~A~~~Lv~~   94 (324)
T PRK07921         28 VRVYLNGIGKTALLTAADEVELAKRIEAGLYAEHL-----------LETRKRLSEA--RKRDLAAVVRDGEAARRHLLEA   94 (324)
T ss_pred             HHHHHHHhcccCCCCHHHHHHHHHHHHhhhhhhhh-----------hccccccchh--HHHHHHHHHhcCHHHHHHHHHH
Confidence            345555555 6999999999999999988766553           2223332111  3467888999999999999999


Q ss_pred             hHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCchhhHHHHHHHHHHHHHHHHhccccccccchHHHHHH
Q 009449          304 TRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIPCKLNREISK  383 (534)
Q Consensus       304 nlrLV~sIArrY~~~g~~~eDLiQEG~lgL~rA~ekFDp~kG~rFSTYA~~wIR~aI~~~lr~~sr~iRlP~~~~~~i~k  383 (534)
                      |+++|+++|++|.+++.+++||+|||++|||+|+++|||++|++|+|||+||||++|.+++++++++||+|.|+.+.+++
T Consensus        95 ~~~lV~~iA~r~~~~~~~~eDLvQEg~igL~~a~~~fdp~~G~rFsTYA~~wIr~aI~~~i~~~~r~vrlP~~~~~~~~~  174 (324)
T PRK07921         95 NLRLVVSLAKRYTGRGMPLLDLIQEGNLGLIRAMEKFDYTKGFKFSTYATWWIRQAITRGMADQSRTIRLPVHLVEQVNK  174 (324)
T ss_pred             HHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHcCCccCCCHHHHHHHHHHHHHHHHHHHcCCCccCCHHHHHHHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHHhhhhcccccccccchhhhhhhccCCCCCCChHHHHHHHHHHH
Q 009449          384 IQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNAKYLEFAPDRSVKSPKEIVMRQHMKK  463 (534)
Q Consensus       384 i~ka~~~L~~elGr~Pt~eEIA~~lgis~~kv~~~l~~~~~~~SLD~~i~~~~~~~l~e~i~d~~~~spee~v~~~el~e  463 (534)
                      ++++.+.|.+++|+.||.+|||+.+|+++++|..++.....++|||.+++++++.++.++++|+...+|++.+....+..
T Consensus       175 l~~~~~~l~~~lgr~pt~~EiA~~lgi~~~~v~~~~~~~~~~~SLd~~~~~~~~~~l~d~l~d~~~~~pe~~~~~~~~~~  254 (324)
T PRK07921        175 LARIKRELHQQLGREATDEELAEESGIPEEKIADLLEHSRDPVSLDMPVGSDEEAPLGDFIEDSEATSAENAVIAGLLHT  254 (324)
T ss_pred             HHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHHcCCCceecCCCCCCCCchHHHHhcCCCCCCHHHHHHHHHHHH
Confidence            99999999999999999999999999999999999888888999999998877778899999877778999999999999


Q ss_pred             HHHHHHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHhhhhcchhhh
Q 009449          464 DVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDSETCRDLSHFL  532 (534)
Q Consensus       464 ~L~~~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~~l~~~~L~~yl  532 (534)
                      .|..+|..|+++|+.||.+||||+|++++|++|||+.||||+++|||++.+|++|||.......|..|+
T Consensus       255 ~l~~~L~~L~eREr~Vl~~rygl~~~~~~Tl~eIa~~lgvS~eRVrQIe~~Al~KLr~~~~~~~l~~~~  323 (324)
T PRK07921        255 DIRSVLATLDEREQQVIRLRFGLDDGQPRTLDQIGKLFGLSRERVRQIEREVMSKLRNGERADRLRSYA  323 (324)
T ss_pred             HHHHHHHhCCHHHHHHHHHHHhcCCCCCcCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHHHHHHHHhh
Confidence            999999999999999999999999889999999999999999999999999999999999888899886

>PRK09210 RNA polymerase sigma factor RpoD; Validated

Probab=100.00  E-value=4.6e-52  Score=437.50  Aligned_cols=272  Identities=32%  Similarity=0.559  Sum_probs=255.0

Q ss_pred             hHHHHHHhhccC-CCCCCchHHHHHHhhchHHHHHHHHHHHHHHHhCCCCchHHHHHHcCCCHHHHHHHHHhcHHHHHHH
Q 009449          222 IFSAERALNSRG-RRLTIARNEAEMSKGVQVVANLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQHLAFGWYCREEL  300 (534)
Q Consensus       222 ~~~~~~~~~~~~-~~lLt~~eE~~L~~~iq~~~~le~~~~~l~~~~g~~ps~~ewa~a~g~d~~~L~~~l~~G~~A~e~L  300 (534)
                      .++++.|++..+ .|+||++||.+|++.++.+                                        +..|++.|
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            345566676555 5999999999999866532                                        13589999


Q ss_pred             HHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCchhhHHHHHHHHHHHHHHHHhccccccccchHHH
Q 009449          301 IKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIPCKLNRE  380 (534)
Q Consensus       301 I~~nlrLV~sIArrY~~~g~~~eDLiQEG~lgL~rA~ekFDp~kG~rFSTYA~~wIR~aI~~~lr~~sr~iRlP~~~~~~  380 (534)
                      |..|+++|+++|++|.+++.+++||+|||++|||+|+++|||.+|++|+|||+||||++|.++++++.|++|+|.|+++.
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             HHHHHHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHHhhhhcccccccccchhhhhhhccCCCCCCChHHHHHHHH
Q 009449          381 ISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNAKYLEFAPDRSVKSPKEIVMRQH  460 (534)
Q Consensus       381 i~ki~ka~~~L~~elGr~Pt~eEIA~~lgis~~kv~~~l~~~~~~~SLD~~i~~~~~~~l~e~i~d~~~~spee~v~~~e  460 (534)
                      ++++.++.+.|.+++||.||.+|||+.+|+++++|+.++.....++|||.+++++++..+.++++|+...+|++.+....
T Consensus       215 ~~~~~~~~~~l~~~lgr~pt~~EiA~~l~~~~~~v~~~~~~~~~~~SLd~~~~~~~~~~l~d~i~d~~~~~p~~~~~~~~  294 (367)
T PRK09210        215 INKLIRVQRQLLQELGREPTPEEIAEEMDMPPEKVREILKIAQEPVSLETPIGEEDDSHLGDFIEDQDATSPADHAAYEL  294 (367)
T ss_pred             HHHHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHHhcCCCCcCCCCCCCCcchhhhhccCCCCCCHHHHHHHHH
Confidence            99999999999999999999999999999999999999988888999999999887788999999988789999999999


Q ss_pred             HHHHHHHHHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHhhhhcchhhhc
Q 009449          461 MKKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDSETCRDLSHFLV  533 (534)
Q Consensus       461 l~e~L~~~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~~l~~~~L~~yl~  533 (534)
                      ++..|..+|..||++||.||.+||||+|++++|++|||+.||||++||||++.+|++|||++.....|+.|++
T Consensus       295 ~~~~l~~~l~~L~~rEr~Vl~lrygl~~~~~~tl~EIa~~lgvs~erVrQi~~~Al~kLr~~~~~~~l~~~~~  367 (367)
T PRK09210        295 LKEQLEDVLDTLTDREENVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRSKQLKDFLE  367 (367)
T ss_pred             HHHHHHHHHHhCCHHHHHHHHHHhccCCCCCccHHHHHHHHCCCHHHHHHHHHHHHHHHhChHHHhHHHHhhC
Confidence            9999999999999999999999999999999999999999999999999999999999999999999999974

>PRK05658 RNA polymerase sigma factor RpoD; Validated

Probab=100.00  E-value=9.2e-50  Score=445.18  Aligned_cols=259  Identities=30%  Similarity=0.594  Sum_probs=243.6

Q ss_pred             HHHHcCCCHHH---HHHHHHhcH----HHHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCc
Q 009449          275 WAQAAGVSERV---LKQHLAFGW----YCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYK  347 (534)
Q Consensus       275 wa~a~g~d~~~---L~~~l~~G~----~A~e~LI~~nlrLV~sIArrY~~~g~~~eDLiQEG~lgL~rA~ekFDp~kG~r  347 (534)
                      .....+++.++   +.++++.|.    .|+++||.+|+|||++||++|.++|++++||||||++||++|+++|||++|++
T Consensus       353 ie~~~~Ls~eElk~l~~~i~~g~~~~~~a~~~Li~~nlrlV~~iA~ky~~~gl~~~DLiQeG~iGL~~Av~kfd~~~G~~  432 (619)
T PRK05658        353 IEEETGLTIEELKEINRQISKGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYK  432 (619)
T ss_pred             HHHHhCCCHHHHHHHHHHHhccchhhhHHHHHHHHHHHHHHHHHHHHHhhCCCCHHHHHHHHHHHHHHHHHhcCccCCCc
Confidence            34445565544   445566773    58999999999999999999999999999999999999999999999999999


Q ss_pred             hhhHHHHHHHHHHHHHHHHhccccccccchHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHHhhhhcc
Q 009449          348 FSTYVQYWIRKSISKMVARHARGIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGS  427 (534)
Q Consensus       348 FSTYA~~wIR~aI~~~lr~~sr~iRlP~~~~~~i~ki~ka~~~L~~elGr~Pt~eEIA~~lgis~~kv~~~l~~~~~~~S  427 (534)
                      |+|||+||||++|.++++++.++||+|.|+.+.++++.++.+.+.+++||.||.+|||+.+|+++++|..++.....++|
T Consensus       433 FstYA~~wIr~aI~~~i~~~~r~irip~~~~~~~~k~~~~~~~~~~~~gr~pt~~eiA~~l~~~~~~v~~~~~~~~~~~S  512 (619)
T PRK05658        433 FSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEIGREPTPEELAERLGMPEDKVRKVLKIAKEPIS  512 (619)
T ss_pred             hHHHhHHHHHHHHHHHHHHcCCceecCHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCCc
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999998889999


Q ss_pred             cccccccchhhhhhhccCCCCCCChHHHHHHHHHHHHHHHHHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHH
Q 009449          428 IDQKIGDCLNAKYLEFAPDRSVKSPKEIVMRQHMKKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEW  507 (534)
Q Consensus       428 LD~~i~~~~~~~l~e~i~d~~~~spee~v~~~el~e~L~~~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrer  507 (534)
                      ||.|++++++..+.++++|....+|++.+....++..|..+|..||++|+.||++||||+++.++|++|||+.||||+++
T Consensus       513 ld~~i~~~~~~~l~d~i~d~~~~~p~~~~~~~~~~~~l~~~l~~L~~rE~~Vl~~r~g~~~~~~~tl~ei~~~lgvs~eR  592 (619)
T PRK05658        513 LETPIGDDEDSHLGDFIEDKNAELPIDAAIQESLREATTDVLASLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRER  592 (619)
T ss_pred             CCCCCCCCCCCchhhhcCCCCCCChHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHhcCCCCCCCccHHHHHHHhCCCHHH
Confidence            99999988888899999998888999999999999999999999999999999999999988999999999999999999


Q ss_pred             HHHHHHHHHHHHHhHhhhhcchhhhc
Q 009449          508 IRKLEKKAMTKLRDSETCRDLSHFLV  533 (534)
Q Consensus       508 VRqi~~RAL~KLR~~l~~~~L~~yl~  533 (534)
                      |||++.+|++|||++.....|+.|++
T Consensus       593 VrQie~~al~kLr~~~~~~~l~~~~~  618 (619)
T PRK05658        593 IRQIEAKALRKLRHPSRSRKLRSFLD  618 (619)
T ss_pred             HHHHHHHHHHHHhchHHHHHHHHHhc
Confidence            99999999999999999999999986

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

Probab=100.00  E-value=5.6e-48  Score=383.41  Aligned_cols=238  Identities=37%  Similarity=0.685  Sum_probs=228.3

Q ss_pred             HHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCchhhHHHHHHHHHHHHHHHHhcccccccc
Q 009449          296 CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIPC  375 (534)
Q Consensus       296 A~e~LI~~nlrLV~sIArrY~~~g~~~eDLiQEG~lgL~rA~ekFDp~kG~rFSTYA~~wIR~aI~~~lr~~sr~iRlP~  375 (534)
                      |+++||..|+++|+++|++|.+++.+++||+|||++||++|+++|||++|++|+|||+||||++|.++++++.+.+++|.
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             chHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHHhhhhcccccccccchhhhhhhccCCCCCCChHHH
Q 009449          376 KLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNAKYLEFAPDRSVKSPKEI  455 (534)
Q Consensus       376 ~~~~~i~ki~ka~~~L~~elGr~Pt~eEIA~~lgis~~kv~~~l~~~~~~~SLD~~i~~~~~~~l~e~i~d~~~~spee~  455 (534)
                      ++.+.++++.++.+.+.+++|+.||.+|||+.+|++++++..++.....++|||.+++++++.++.+.++|+...+|++.
T Consensus        81 ~~~~~~~~~~~~~~~l~~~~g~~pt~~eia~~l~~~~~~v~~~~~~~~~~~SLd~~~~~~~~~~l~d~l~d~~~~~p~~~  160 (238)
T TIGR02393        81 HMVETINKLIKAERQLTQELGREPTDEELAERMGMPAEKVREIKKIAQEPISLETPIGEEEDSFLGDFIEDTSIESPDDY  160 (238)
T ss_pred             HHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHHhccCCCcCCCCCCCCcccHHHHhcCCCCCChHHH
Confidence            99999999999999999999999999999999999999999998887788999999987766678888998877889999


Q ss_pred             HHHHHHHHHHHHHHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHhhhhcchhhhc
Q 009449          456 VMRQHMKKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDSETCRDLSHFLV  533 (534)
Q Consensus       456 v~~~el~e~L~~~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~~l~~~~L~~yl~  533 (534)
                      +...++...|..+|+.||++|+.||.++|||++++++|++|||+.||||+++|+|++.+|++|||+.+....|+.|++
T Consensus       161 ~~~~~~~~~l~~~l~~L~~~er~vl~l~ygl~~~~~~t~~EIA~~lgis~~~V~q~~~~al~kLr~~~~~~~~~~~~~  238 (238)
T TIGR02393       161 AAKELLREQLDEVLETLTERERKVLRMRYGLLDGRPHTLEEVGKEFNVTRERIRQIESKALRKLRHPSRSKKLKSFLD  238 (238)
T ss_pred             HHHHHHHHHHHHHHHhCCHHHHHHHHHHhCCCCCCCccHHHHHHHHCCCHHHHHHHHHHHHHHHhhhHHHhHHHHhhC
Confidence            999999999999999999999999999999999999999999999999999999999999999999999999999975

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.

>PRK07122 RNA polymerase sigma factor SigF; Reviewed

Probab=100.00  E-value=4.8e-43  Score=353.85  Aligned_cols=220  Identities=23%  Similarity=0.346  Sum_probs=201.0

Q ss_pred             HHHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCchhhHHHHHHHHHHHHHHHHhccccccc
Q 009449          295 YCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIP  374 (534)
Q Consensus       295 ~A~e~LI~~nlrLV~sIArrY~~~g~~~eDLiQEG~lgL~rA~ekFDp~kG~rFSTYA~~wIR~aI~~~lr~~sr~iRlP  374 (534)
                      .++++||.+|++||+++|++|.++|++++||+|||+|||++|+++|||++|++|+|||+||||++|.++++++.++||+|
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            48899999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cchHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHH--hhhhcccccccccchhh--hhhhccCCCCCC
Q 009449          375 CKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASEC--LRIVGSIDQKIGDCLNA--KYLEFAPDRSVK  450 (534)
Q Consensus       375 ~~~~~~i~ki~ka~~~L~~elGr~Pt~eEIA~~lgis~~kv~~~l~~--~~~~~SLD~~i~~~~~~--~l~e~i~d~~~~  450 (534)
                      .++.+.+++++++...+.+++|+.||.+|||+.+|+++++|..++..  ...+.|||.+++++++.  .+.+.+     +
T Consensus       120 r~~~~~~~~i~~~~~~l~~~lg~~pt~~eiA~~lg~~~~~v~~~~~~~~~~~~~SLd~~~~~~~~~~~~~~d~~-----~  194 (264)
T PRK07122        120 RRLKELHLRLGRATAELSQRLGRAPTASELAAELGMDREEVVEGLVAGSAYNTLSIDSGGGSGDDDARAIADTL-----G  194 (264)
T ss_pred             HHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHHhhcCCCCcccccccCCCCCcccchhcc-----C
Confidence            99999999999999999999999999999999999999999998764  34688999998654332  233333     3


Q ss_pred             ChHHHHHHHHHHHHHHHHHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHh
Q 009449          451 SPKEIVMRQHMKKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDSE  523 (534)
Q Consensus       451 spee~v~~~el~e~L~~~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~~l  523 (534)
                      +++..+...+....|..+|+.||++++.||.++|    ++++|++|||+.||||+++|++++++|+++||..+
T Consensus       195 ~~~~~~e~~~~~~~l~~~l~~L~~rer~vl~l~y----~~~~t~~EIA~~lgis~~~V~~~~~ral~kLr~~l  263 (264)
T PRK07122        195 DVDAGLDQIENREALRPLLAALPERERTVLVLRF----FESMTQTQIAERVGISQMHVSRLLAKTLARLRDQL  263 (264)
T ss_pred             CcHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHh----cCCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHc
Confidence            4556667777888899999999999999999999    88999999999999999999999999999999875

>PRK05657 RNA polymerase sigma factor RpoS; Validated

Probab=100.00  E-value=3.3e-42  Score=357.34  Aligned_cols=269  Identities=25%  Similarity=0.477  Sum_probs=246.4

Q ss_pred             hhHHHHHHhhccC-CCCCCchHHHHHHhhchHHHHHHHHHHHHHHHhCCCCchHHHHHHcCCCHHHHHHHHHhcHHHHHH
Q 009449          221 TIFSAERALNSRG-RRLTIARNEAEMSKGVQVVANLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQHLAFGWYCREE  299 (534)
Q Consensus       221 ~~~~~~~~~~~~~-~~lLt~~eE~~L~~~iq~~~~le~~~~~l~~~~g~~ps~~ewa~a~g~d~~~L~~~l~~G~~A~e~  299 (534)
                      ..+.+..|++-.+ .|+||+++|.+|...++.                                        ++..|++.
T Consensus        51 ~~~~~~~y~~~~~~~~~l~~~ee~~li~~~~~----------------------------------------Gd~~A~~~   90 (325)
T PRK05657         51 VLDATQLYLNEIGYSPLLTAEEEVYFARRALR----------------------------------------GDFAARQR   90 (325)
T ss_pred             cccHHHHHHHHHhcCCCCCHHHHHHHHHHHHc----------------------------------------CCHHHHHH
Confidence            3456677786666 599999999888764321                                        12569999


Q ss_pred             HHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCchhhHHHHHHHHHHHHHHHHhccccccccchHH
Q 009449          300 LIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIPCKLNR  379 (534)
Q Consensus       300 LI~~nlrLV~sIArrY~~~g~~~eDLiQEG~lgL~rA~ekFDp~kG~rFSTYA~~wIR~aI~~~lr~~sr~iRlP~~~~~  379 (534)
                      ||..|.++|+++|++|.+++.+++||+|||++|+|+++++||+.+|++|+||++||||++|.+++.++.+++++|.++..
T Consensus        91 Li~~y~~~V~~~a~~~~~~~~~aeDLvQE~fi~l~~ai~~fd~~rg~~Fstyatw~iR~ai~~~i~~~~r~ir~p~~~~~  170 (325)
T PRK05657         91 MIESNLRLVVKIAKRYLNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPVHVVK  170 (325)
T ss_pred             HHHHhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHhCCccCCCHHHHHHHHHHHHHHHHHHHcCCccccCHHHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHHhhhhcccccccccchhhhhhhccCCCCCCChHHHHHHH
Q 009449          380 EISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNAKYLEFAPDRSVKSPKEIVMRQ  459 (534)
Q Consensus       380 ~i~ki~ka~~~L~~elGr~Pt~eEIA~~lgis~~kv~~~l~~~~~~~SLD~~i~~~~~~~l~e~i~d~~~~spee~v~~~  459 (534)
                      .++++.++.+.+.+.+|+.|+.+|||+.+|+++++|..++.....+.|||.++..+...++.+.++++...+|++.+...
T Consensus       171 ~l~~~~R~~~~l~~~l~r~~t~~eiA~~l~~~~~~v~~~l~~~~~~~sld~~~~~~~~~~l~d~l~d~~~~~pe~~~~~~  250 (325)
T PRK05657        171 ELNVYLRAARELEHKLDHEPSAEEIAELLDKPVDDVSRMLALNERITSLDTPLGGDPEKSLLDILADEQENGPEDTTQDD  250 (325)
T ss_pred             HHHHHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHhccCCcccCCCCCCCCCcchhhhccCCCCCCHHHHHHHH
Confidence            99999999999999999999999999999999999999998777888999998877777788888887767899999999


Q ss_pred             HHHHHHHHHHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHhhhhcch
Q 009449          460 HMKKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDSETCRDLS  529 (534)
Q Consensus       460 el~e~L~~~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~~l~~~~L~  529 (534)
                      +....|..+|..||+++|.||.++|||.+++++|++|||+.||||++||++++++|+++||+.+...++.
T Consensus       251 e~~~~L~~aL~~L~~~~R~vl~lrygL~~~e~~s~~EIA~~Lgis~~tV~~~~~rAl~kLr~~l~~~~~~  320 (325)
T PRK05657        251 DMKQSIVKWLFELNDKQREVLARRFGLLGYEAATLEDVAREIGLTRERVRQIQVEALRRLREILQTQGLS  320 (325)
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHhccCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHhCccc
Confidence            9999999999999999999999999999999999999999999999999999999999999999887765

>PRK07500 rpoH2 RNA polymerase factor sigma-32; Reviewed

Probab=100.00  E-value=7.2e-42  Score=349.53  Aligned_cols=260  Identities=24%  Similarity=0.344  Sum_probs=219.2

Q ss_pred             HHHHhhccC-CCCCCchHHHHHHhhchHHHHHHHHHHHHHHHhCCCCchHHHHHHcCCCHHHHHHHHHhcHHHHHHHHHH
Q 009449          225 AERALNSRG-RRLTIARNEAEMSKGVQVVANLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQHLAFGWYCREELIKS  303 (534)
Q Consensus       225 ~~~~~~~~~-~~lLt~~eE~~L~~~iq~~~~le~~~~~l~~~~g~~ps~~ewa~a~g~d~~~L~~~l~~G~~A~e~LI~~  303 (534)
                      +..|++..+ .|+||+++|.+|.++++.                                       .++..|+++||..
T Consensus         8 ~~~y~~~~~~~~~l~~~~e~~L~~~~~~---------------------------------------~gd~~A~~~Lv~~   48 (289)
T PRK07500          8 DRSMIRSAMKAPYLEREEEHALAYRWKD---------------------------------------HRDEDALHRIISA   48 (289)
T ss_pred             HHHHHHHHhcCCCCCHHHHHHHHHHHHH---------------------------------------CCCHHHHHHHHHH
Confidence            344555444 699999999999885421                                       0235699999999


Q ss_pred             hHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCchhhHHHHHHHHHHHHHHHHhccccccccchHH--HH
Q 009449          304 TRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIPCKLNR--EI  381 (534)
Q Consensus       304 nlrLV~sIArrY~~~g~~~eDLiQEG~lgL~rA~ekFDp~kG~rFSTYA~~wIR~aI~~~lr~~sr~iRlP~~~~~--~i  381 (534)
                      |.++|+++|++|.+++.+++||+|||++|||+++++|||.+|.+|+|||+||||++|.++++++.+.+|+|.+...  ..
T Consensus        49 ~~~lV~~~a~~~~~~~~~~eDLvQeg~i~L~~a~~~fd~~~~~~f~tya~~~Ir~~I~~~lr~~~~~iR~p~~~~~~~~~  128 (289)
T PRK07500         49 HMRLVISMAGKFRRFGLPMNDLIQEGYVGLLEAAARFEPDREVRFSTYATWWIRASIQDYILRNWSIVRGGTSSAQKALF  128 (289)
T ss_pred             hHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHcCCCCCCChHHHHHHHHHHHHHHHHHHCCCceecCccHHHHHHH
Confidence            9999999999999999999999999999999999999999999999999999999999999999999999998765  44


Q ss_pred             HHHHHHHHHHHH---hcCCCCCHHHHHHHcCCCHHHHHHHHH-Hhhhhcccccccccchhh--hhhhccCCCCCCChHHH
Q 009449          382 SKIQKARKALTN---SHGKYPEDIEIAKYTGLSLAEIRSASE-CLRIVGSIDQKIGDCLNA--KYLEFAPDRSVKSPKEI  455 (534)
Q Consensus       382 ~ki~ka~~~L~~---elGr~Pt~eEIA~~lgis~~kv~~~l~-~~~~~~SLD~~i~~~~~~--~l~e~i~d~~~~spee~  455 (534)
                      .++++.+..+.+   .+|+.||.+|||+.+|++++++..+.. ....++|||.+++++++.  ++.+.++++. .+|++.
T Consensus       129 ~~~~~~~~~~~~~~~~l~~~pt~~eiA~~l~~~~~~v~~~~~~~~~~~~SLd~~~~~~~~~~~~l~d~i~d~~-~~pe~~  207 (289)
T PRK07500        129 FNLRRLRARLAQADEELTKQEIHREIATALGVSLSDVEMMDARLSGPDASLNAPQSEEDEGRSERMDFLVDDS-PLPDEQ  207 (289)
T ss_pred             HHHHHHHHHHHhhhcccCCCCCHHHHHHHhCcCHHHHHHHHHHhcCCCccccCCCCCCCCCcccHHHhccCCC-CCchHH
Confidence            556666666555   689999999999999999999987753 344689999998765443  5788888765 467766


Q ss_pred             HHH----HHHHHHHHHHHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHhhhh
Q 009449          456 VMR----QHMKKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDSETCR  526 (534)
Q Consensus       456 v~~----~el~e~L~~~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~~l~~~  526 (534)
                      +..    ......|..+|+.||++|++||.++|+.  .+++|++|||+.||||+++|+|++++|++|||..+...
T Consensus       208 ~~~~~~~~~~~~~l~~al~~L~~rer~vl~lr~~~--~~~~t~~EIa~~lgvs~~~V~q~~~~Al~kLr~~l~~~  280 (289)
T PRK07500        208 VESSIDGERRRRWLTQALQTLNERELRIIRERRLR--EDGATLEALGEELGISKERVRQIEARALEKLRRALLSQ  280 (289)
T ss_pred             HHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcC--CCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHhc
Confidence            543    3456779999999999999999999942  37999999999999999999999999999999988644

>PRK06596 RNA polymerase factor sigma-32; Reviewed

Probab=100.00  E-value=5.8e-41  Score=342.03  Aligned_cols=259  Identities=26%  Similarity=0.396  Sum_probs=213.5

Q ss_pred             HHHHHHhhc-cCCCCCCchHHHHHHhhchHHHHHHHHHHHHHHHhCCCCchHHHHHHcCCCHHHHHHHHHhcHHHHHHHH
Q 009449          223 FSAERALNS-RGRRLTIARNEAEMSKGVQVVANLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQHLAFGWYCREELI  301 (534)
Q Consensus       223 ~~~~~~~~~-~~~~lLt~~eE~~L~~~iq~~~~le~~~~~l~~~~g~~ps~~ewa~a~g~d~~~L~~~l~~G~~A~e~LI  301 (534)
                      +++..|.+. .+.|+||+++|.+|+.+.+                                       ..++..|++.||
T Consensus        14 ~~~~~y~~~~~~~~~l~~~~e~~l~~~~~---------------------------------------~~Gd~~a~~~Lv   54 (284)
T PRK06596         14 GNLDAYIQAVNKIPMLTAEEEYMLAKRLR---------------------------------------EHGDLEAAKQLV   54 (284)
T ss_pred             cHHHHHHHHHhccCCCCHHHHHHHHHHHH---------------------------------------HcCCHHHHHHHH
Confidence            344556654 4468899999988877421                                       012256999999


Q ss_pred             HHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCchhhHHHHHHHHHHHHHHHHhccccccccchH--H
Q 009449          302 KSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIPCKLN--R  379 (534)
Q Consensus       302 ~~nlrLV~sIArrY~~~g~~~eDLiQEG~lgL~rA~ekFDp~kG~rFSTYA~~wIR~aI~~~lr~~sr~iRlP~~~~--~  379 (534)
                      ..|+++|+++|++|.+.+.+++||+|||++||++|+++|||++|++|+|||+||||++|.++++++.++|++|.+..  .
T Consensus        55 ~~~~~lV~~ia~~~~~~~~~~eDLvQeg~igL~~a~~~fd~~~~~~FstYA~~~Ir~~i~~~l~~~~~~vr~p~~~~~~~  134 (284)
T PRK06596         55 LSHLRFVVHIARGYRGYGLPQADLIQEGNIGLMKAVKRFDPEVGVRLVSFAVHWIKAEIHEYILRNWRIVKVATTKAQRK  134 (284)
T ss_pred             HHhHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHHHhCcccCCCHHHHHHHHHHHHHHHHHHHcCCeeeccchHHHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999888899998753  2


Q ss_pred             HHHHHHHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHHh-hhhcccccccccch--hhhhhhccCCCCCCChHHHH
Q 009449          380 EISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECL-RIVGSIDQKIGDCL--NAKYLEFAPDRSVKSPKEIV  456 (534)
Q Consensus       380 ~i~ki~ka~~~L~~elGr~Pt~eEIA~~lgis~~kv~~~l~~~-~~~~SLD~~i~~~~--~~~l~e~i~d~~~~spee~v  456 (534)
                      ...++.+....+.  .++.||.+|||+.+|+++++|..++... ..++|||.++++++  +.++.+.++|+. .+|++.+
T Consensus       135 ~~~~~~~~~~~l~--~~~~~t~~eiA~~l~~~~~~v~~~~~~~~~~~~SLd~~~~~~~~~~~~l~~~l~d~~-~~p~~~~  211 (284)
T PRK06596        135 LFFNLRKAKKRLG--WLNPEEVEMVAEELGVSEEEVREMESRLSGQDASLDAPIDDDDEESGAPQDYLEDKS-SDPADVL  211 (284)
T ss_pred             HHHHHHHHHHHhc--cCCCCCHHHHHHHhCcCHHHHHHHHHHhcCCCcCcCCCCCCCCCCcchHHHHcCCCC-CCchHHH
Confidence            3334444444443  3499999999999999999999986533 36889999986552  245778888774 5787776


Q ss_pred             HHH----HHHHHHHHHHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHhhh
Q 009449          457 MRQ----HMKKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDSETC  525 (534)
Q Consensus       457 ~~~----el~e~L~~~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~~l~~  525 (534)
                      +..    ++...|..+|+.||++|+.||.+|||. + +++|++|||+.||||+++|+|++.+|++|||..+..
T Consensus       212 ~~~~~~~~~~~~L~~al~~L~~rEr~VL~lry~~-~-~~~Tl~EIA~~lgvS~~rVrqi~~~Al~kLR~~l~~  282 (284)
T PRK06596        212 EEDNWEDQRRALLADALEGLDERSRDIIEARWLD-D-DKSTLQELAAEYGVSAERVRQIEKNAMKKLKAAIEA  282 (284)
T ss_pred             HHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcC-C-CCcCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHh
Confidence            654    357789999999999999999999953 2 699999999999999999999999999999998754

>PRK07408 RNA polymerase sigma factor SigF; Reviewed

Probab=100.00  E-value=4e-41  Score=338.24  Aligned_cols=229  Identities=23%  Similarity=0.338  Sum_probs=202.8

Q ss_pred             Hhc-HHHHHHHHHHhHHHHHHHHHHhhCC-CCCHHHHHHHHHHHHHHhhhccCCcCCCchhhHHHHHHHHHHHHHHHHhc
Q 009449          291 AFG-WYCREELIKSTRPLVLFLARNYRGL-GIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHA  368 (534)
Q Consensus       291 ~~G-~~A~e~LI~~nlrLV~sIArrY~~~-g~~~eDLiQEG~lgL~rA~ekFDp~kG~rFSTYA~~wIR~aI~~~lr~~s  368 (534)
                      ..| ..|+++||..|+++|+++|++|.+. +.+++||+|||++|||+|+++|||++|++|+|||+||||++|.++++++.
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            355 6799999999999999999999876 66799999999999999999999999999999999999999999999999


Q ss_pred             cccccccchHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHH--hhhhcccccccccchh--hhhhhcc
Q 009449          369 RGIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASEC--LRIVGSIDQKIGDCLN--AKYLEFA  444 (534)
Q Consensus       369 r~iRlP~~~~~~i~ki~ka~~~L~~elGr~Pt~eEIA~~lgis~~kv~~~l~~--~~~~~SLD~~i~~~~~--~~l~e~i  444 (534)
                      ++||+|.++.+.+++++++...|.+++|++||.+|||+.+|++++++..+...  ...+.|||.+++++++  ..+.+.+
T Consensus       100 ~~vr~pr~~~~~~~~~~~~~~~l~~~lgr~pt~~elA~~lgi~~~~v~~~~~~~~~~~~~SLd~~~~~~~~~~~~l~d~~  179 (256)
T PRK07408        100 PTVRIPRRWQELQRQAKKVRQELRQELGRQPTDQEIAQALDISLEEWQEIKLALQNRTPLSLDAPVNQDEDGSTSLGDLL  179 (256)
T ss_pred             CeeeeCHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHhhccCCccccccCCCCCCCcccccccc
Confidence            99999999999999999999999999999999999999999999999998653  3467899999865433  2456666


Q ss_pred             CCCCCCChHHHHHHHHHHHHHHHHHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHhh
Q 009449          445 PDRSVKSPKEIVMRQHMKKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDSET  524 (534)
Q Consensus       445 ~d~~~~spee~v~~~el~e~L~~~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~~l~  524 (534)
                      +++... +..  ...+....|..+|..||+++|.||.++|    ++++|++|||+.||+|.++|++++++|+++||..+.
T Consensus       180 ~d~~~~-~~~--~~~~~~~~l~~~l~~L~~~~r~vl~l~y----~~~~s~~eIA~~lgvs~~~V~~~~~ra~~kLr~~l~  252 (256)
T PRK07408        180 PDPRYR-SFQ--LAQEDRIRLQQALAQLEERTREVLEFVF----LHDLTQKEAAERLGISPVTVSRRVKKGLDQLKKLLQ  252 (256)
T ss_pred             CCcccc-hhh--hhHHHHHHHHHHHHcCCHHHHHHHHHHH----HCCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHhh
Confidence            665432 211  2345567899999999999999999999    789999999999999999999999999999999876


Q ss_pred             hh
Q 009449          525 CR  526 (534)
Q Consensus       525 ~~  526 (534)
                      ..
T Consensus       253 ~~  254 (256)
T PRK07408        253 PE  254 (256)
T ss_pred             cc
Confidence            53

>TIGR02392 rpoH_proteo alternative sigma factor RpoH

Probab=100.00  E-value=5.9e-40  Score=332.09  Aligned_cols=226  Identities=28%  Similarity=0.459  Sum_probs=191.6

Q ss_pred             HHHHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCchhhHHHHHHHHHHHHHHHHhcccccc
Q 009449          294 WYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKI  373 (534)
Q Consensus       294 ~~A~e~LI~~nlrLV~sIArrY~~~g~~~eDLiQEG~lgL~rA~ekFDp~kG~rFSTYA~~wIR~aI~~~lr~~sr~iRl  373 (534)
                      ..|++.||..|+++|+++|++|.+++.+++||+|||++|||+|+++|||++|++|+|||+||||++|.++++++.+++|+
T Consensus        34 ~~a~~~Lv~~~~~lV~~~a~~~~~~~~~~eDLvQeg~igl~~a~~~fd~~~~~~FsTYA~~~Ir~~i~~~l~~~~~~ir~  113 (270)
T TIGR02392        34 LDAAKKLVLSHLRFVVKIARGYRGYGLPQADLIQEGNIGLMKAVKRFDPERGVRLVSFAVHWIKAEIHEYILRNWRLVKV  113 (270)
T ss_pred             HHHHHHHHHHhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHhCcccCCChHHhhHHHHHHHHHHHHHHcCCceec
Confidence            56999999999999999999999999999999999999999999999999999999999999999999999998778999


Q ss_pred             ccchH--HHHHHHHHHHHHHHHhcCCCC-CHHHHHHHcCCCHHHHHHHHHHhh-hhcccccccccchh--hhhhhccCCC
Q 009449          374 PCKLN--REISKIQKARKALTNSHGKYP-EDIEIAKYTGLSLAEIRSASECLR-IVGSIDQKIGDCLN--AKYLEFAPDR  447 (534)
Q Consensus       374 P~~~~--~~i~ki~ka~~~L~~elGr~P-t~eEIA~~lgis~~kv~~~l~~~~-~~~SLD~~i~~~~~--~~l~e~i~d~  447 (534)
                      |.+..  +...++.++...+.  .++.| +.+|||+.+|+++++|..+..... .+.|||.+++++++  ..+.+.++|.
T Consensus       114 p~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~eiA~~l~~~~~~v~~~~~~~~~~~~Sld~~~~~~~~~~~~~~~~l~d~  191 (270)
T TIGR02392       114 ATTKAQRKLFFNLRKMKKRLQ--GWLNPEEVEAIAEELGVSEREVREMESRLSGQDMSLNASIDDDEDDGGAPIAYLVDK  191 (270)
T ss_pred             CchHHHHHHHHHHHHHHHHHh--cCCCCCCHHHHHHHhCCCHHHHHHHHHHccCCCccCCCCCCCCCCccccHHHHhcCC
Confidence            98753  34445555554443  22556 699999999999999999865433 47899999876543  2466777776


Q ss_pred             CCCChHHHHHHH----HHHHHHHHHHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHh
Q 009449          448 SVKSPKEIVMRQ----HMKKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDSE  523 (534)
Q Consensus       448 ~~~spee~v~~~----el~e~L~~~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~~l  523 (534)
                      . .+|++.+...    .+...|..+|..||++||.||.++||.  .+++|++|||+.||||+++|+|++.+|++|||..+
T Consensus       192 ~-~~pe~~~~~~~~~~~~~~~L~~al~~L~~rer~vl~l~y~~--~~~~t~~eIA~~lgvS~~~V~q~~~~Al~kLr~~l  268 (270)
T TIGR02392       192 T-SDPEDTLEEEQWEELQRQALANALGSLDARSRRIIEARWLD--DDKLTLQELAAEYGVSAERIRQIEKNAMKKLKAAL  268 (270)
T ss_pred             C-CChHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHhcC--CCCcCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHh
Confidence            5 4787766643    356789999999999999999999953  35899999999999999999999999999999876


Q ss_pred             h
Q 009449          524 T  524 (534)
Q Consensus       524 ~  524 (534)
                      .
T Consensus       269 ~  269 (270)
T TIGR02392       269 A  269 (270)
T ss_pred             c
Confidence            4

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.

>PRK05911 RNA polymerase sigma factor sigma-28; Reviewed

Probab=100.00  E-value=2e-39  Score=326.24  Aligned_cols=225  Identities=24%  Similarity=0.373  Sum_probs=204.4

Q ss_pred             HHHHHHHHHHhHHHHHHHHHHhhC---CCCCHHHHHHHHHHHHHHhhhccCCcCCCchhhHHHHHHHHHHHHHHHHhccc
Q 009449          294 WYCREELIKSTRPLVLFLARNYRG---LGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARG  370 (534)
Q Consensus       294 ~~A~e~LI~~nlrLV~sIArrY~~---~g~~~eDLiQEG~lgL~rA~ekFDp~kG~rFSTYA~~wIR~aI~~~lr~~sr~  370 (534)
                      ..|+++||..|+++|+++|++|.+   .+.+++||+|||++|||+|+++|||++|++|+|||+||||++|.++++++.  
T Consensus        22 ~~ar~~Li~~~~~lV~~ia~~~~~~~~~~~~~eDL~QeG~igL~~ai~~fd~~~g~~F~tya~~~Ir~~i~~~lr~~~--   99 (257)
T PRK05911         22 IEYRDVLIEFYLPLVKNVAHRLISGMPSHVKTEDLYASGVEGLVRAVERFDPEKSRRFEGYALFLIKAAIIDDLRKQD--   99 (257)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHHHHHhcCCccCCCHHHHHHHHHHHHHHHHHHhcC--
Confidence            679999999999999999999862   356899999999999999999999999999999999999999999999875  


Q ss_pred             cccccchHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHHhh--hhccccccccc--c--hhhhhhhcc
Q 009449          371 IKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLR--IVGSIDQKIGD--C--LNAKYLEFA  444 (534)
Q Consensus       371 iRlP~~~~~~i~ki~ka~~~L~~elGr~Pt~eEIA~~lgis~~kv~~~l~~~~--~~~SLD~~i~~--~--~~~~l~e~i  444 (534)
                       ++|.++.+.++++.++.+.+.+.+|+.|+.+|||+.+|++++++..++....  .++|||.++..  +  .+.++.+.+
T Consensus       100 -~~pr~~~~~~~~l~~~~~~l~~~~gr~pt~~eiA~~l~i~~~~v~~~~~~~~~~~~~Sld~~~~~~~~~~~~~~l~~~l  178 (257)
T PRK05911        100 -WVPRSVHQKANKLADAMDSLRQSLGKEPTDGELCEYLNISQQELSGWFSSARPALILSLNEEFPCQSDDEAGLALEERI  178 (257)
T ss_pred             -CCCHHHHHHHHHHHHHHHHHHHHHCcCCCHHHHHHHhCcCHHHHHHHHHHhhccceeeccccCCCCCCCccccchhhhc
Confidence             4899999999999999999999999999999999999999999999887654  36899987643  1  233567788


Q ss_pred             CCCCCCChHHHHHHHHHHHHHHHHHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHhh
Q 009449          445 PDRSVKSPKEIVMRQHMKKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDSET  524 (534)
Q Consensus       445 ~d~~~~spee~v~~~el~e~L~~~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~~l~  524 (534)
                      +|.....|++.+...++...|..+|+.|||+||+||.++|    ++++|++|||+.||+|+++|++++++|+++||+.+.
T Consensus       179 ~d~~~~~~~~~~~~~~~~~~l~~al~~L~~~er~vi~l~y----~e~~t~~EIA~~lgis~~~V~~~~~ral~kLr~~l~  254 (257)
T PRK05911        179 ADERAETGYDVVDKKEFSSILAEAILALEEKERKVMALYY----YEELVLKEIGKILGVSESRVSQIHSKALLKLRATLS  254 (257)
T ss_pred             cCCCCCCHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHH----hcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHH
Confidence            8877678889898889999999999999999999999999    899999999999999999999999999999999875


Q ss_pred             h
Q 009449          525 C  525 (534)
Q Consensus       525 ~  525 (534)
                      .
T Consensus       255 ~  255 (257)
T PRK05911        255 A  255 (257)
T ss_pred             h
Confidence            3

>TIGR02850 spore_sigG RNA polymerase sigma-G factor

Probab=100.00  E-value=5.2e-39  Score=322.25  Aligned_cols=219  Identities=23%  Similarity=0.300  Sum_probs=197.4

Q ss_pred             HHHHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCchhhHHHHHHHHHHHHHHHHhcccccc
Q 009449          294 WYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKI  373 (534)
Q Consensus       294 ~~A~e~LI~~nlrLV~sIArrY~~~g~~~eDLiQEG~lgL~rA~ekFDp~kG~rFSTYA~~wIR~aI~~~lr~~sr~iRl  373 (534)
                      ..|++.||..|.++|+++|++|.+++.+++||+|||++|||+++++|||.+|.+|+||++|||+|.|.+++++.. .+|+
T Consensus        33 ~~a~~~L~~~~~~~v~~~a~~~~~~~~~aeDlvQe~~i~l~~a~~~fd~~~~~~f~tyl~~~irn~~~~~lr~~~-~ir~  111 (254)
T TIGR02850        33 TTAREKLINGNLRLVLSVIQRFNNRGEYVDDLFQVGCIGLMKSIDNFDLSQNVKFSTYAVPMIIGEIRRYLRDNN-PIRV  111 (254)
T ss_pred             HHHHHHHHHHhHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCChHHHHHHHHHHHHHHHHHhCC-CccC
Confidence            469999999999999999999999999999999999999999999999999999999999999999999999974 8899


Q ss_pred             ccchHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHHhhhhcccccccccchh--hhhhhccCCCCCCC
Q 009449          374 PCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLN--AKYLEFAPDRSVKS  451 (534)
Q Consensus       374 P~~~~~~i~ki~ka~~~L~~elGr~Pt~eEIA~~lgis~~kv~~~l~~~~~~~SLD~~i~~~~~--~~l~e~i~d~~~~s  451 (534)
                      |.++.+.++++.++...+.+++|+.||.+|||+.+|++++++..++.....+.|||.++.++++  ..+.+.+.++..  
T Consensus       112 p~~~~~~~~~~~~~~~~l~~~l~~~pt~~elA~~l~~~~e~v~~~~~~~~~~~Sld~~~~~~~~~~~~~~~~~~d~~~--  189 (254)
T TIGR02850       112 SRSLRDIAYKALQVRDKLISENSKEPTVSEIAKELKVPQEEVVFALDAIQDPVSLFEPIYNDGGDPIYVMDQISDEKN--  189 (254)
T ss_pred             chHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHCcCHHHHHHHHHhcCCCCcccCCCCCCCCCcchhhhhcCCccc--
Confidence            9999999999999999999999999999999999999999999999888888999998854433  245666766532  


Q ss_pred             hHHHHHHHHHHHHHHHHHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhH
Q 009449          452 PKEIVMRQHMKKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDS  522 (534)
Q Consensus       452 pee~v~~~el~e~L~~~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~~  522 (534)
                      +.+   .......+..++..|++++++||.++|    ++++|++|||+.||+|+++|++++.+|++|||+.
T Consensus       190 ~~~---~~~~~~~l~~~l~~L~~rer~vi~~~~----~~~~t~~eIA~~lgis~~~V~~~~~ral~kLr~~  253 (254)
T TIGR02850       190 KDS---QWLEGIALKEAMKRLNEREKMILNMRF----FEGKTQMEVAEEIGISQAQVSRLEKAALKHMRKY  253 (254)
T ss_pred             cHH---HHHhHHHHHHHHHcCCHHHHHHHHHHH----cCCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHhh
Confidence            222   223445789999999999999999999    7899999999999999999999999999999975

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.

>TIGR02394 rpoS_proteo RNA polymerase sigma factor RpoS

Probab=100.00  E-value=5.3e-38  Score=320.02  Aligned_cols=246  Identities=28%  Similarity=0.510  Sum_probs=227.2

Q ss_pred             HHHHHHHHHhc-HHHHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCchhhHHHHHHHHHHH
Q 009449          283 ERVLKQHLAFG-WYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSIS  361 (534)
Q Consensus       283 ~~~L~~~l~~G-~~A~e~LI~~nlrLV~sIArrY~~~g~~~eDLiQEG~lgL~rA~ekFDp~kG~rFSTYA~~wIR~aI~  361 (534)
                      +..|+..++.| ..|++.||..|.++|+++|++|.+++.+++||+|||++|||+++++|||..|++|+||++|||+.++.
T Consensus        33 ~~~li~~~~~gd~~a~~~L~~~y~~~v~~~a~~~~~~~~~aeDLvQe~~i~l~~a~~~fd~~~g~~f~tya~w~i~~ain  112 (285)
T TIGR02394        33 EIAYARRALAGDFEARKVMIESNLRLVVSIAKHYVNRGLPLLDLIEEGNLGLMHAVEKFDPERGFRFSTYATWWIRQTIE  112 (285)
T ss_pred             HHHHHHHHHcCCHHHHHHHHHHhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHhCCCCCCCcHhhhHHHHHHHHH
Confidence            35567777777 77999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHhccccccccchHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHHhhhhcccccccccchhhhhh
Q 009449          362 KMVARHARGIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNAKYL  441 (534)
Q Consensus       362 ~~lr~~sr~iRlP~~~~~~i~ki~ka~~~L~~elGr~Pt~eEIA~~lgis~~kv~~~l~~~~~~~SLD~~i~~~~~~~l~  441 (534)
                      +++.++.+.+++|.++.+.++.+.+..+.+.+.+|+.|+.+++|+.+|++++++..++.......|+|.++.++....+.
T Consensus       113 ~~i~~~~~~~~~p~~~~~~~~~~~r~~~~l~~~~~r~~~~~e~a~~l~~~~~~~~~~~~~~~~~~sld~~~~~~~~~~~~  192 (285)
T TIGR02394       113 RAIMNQARTIRLPVHVIKELNVYLRAARQLEKKLGREPSVEEIAELLDKPVEDVSRVLALNERITSLDAPLDDDSSKSLL  192 (285)
T ss_pred             HHHHHcCCceeCcHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHhhcCCCcCCCCCCCCCCcchh
Confidence            99999999999999999999999999888899999999999999999999999999988877888999888766555666


Q ss_pred             hccCCCCCCChHHHHHHHHHHHHHHHHHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHh
Q 009449          442 EFAPDRSVKSPKEIVMRQHMKKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRD  521 (534)
Q Consensus       442 e~i~d~~~~spee~v~~~el~e~L~~~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~  521 (534)
                      +.+.++...+|++.+...+....|..+|..||+++|.||.|+|||.+++++|++|||+.||||.++|++++++|+++||.
T Consensus       193 ~~~~~~~~~~pe~~~~~~e~~~~L~~al~~Lp~~~R~Vl~l~ygL~~~e~~s~~EIA~~Lgis~~tVk~~l~rAlkkLr~  272 (285)
T TIGR02394       193 DTIADEQSIDPESLVQNDDLKQLIEAWLAELNERQREVLARRFGLLGYEPATLEEVAAEVGLTRERVRQIQVEALKKLRR  272 (285)
T ss_pred             hhhcCCCCCCHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHhCCCCCCCccHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence            67776666789999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             Hhhhhcc
Q 009449          522 SETCRDL  528 (534)
Q Consensus       522 ~l~~~~L  528 (534)
                      .+...++
T Consensus       273 ~l~~~~~  279 (285)
T TIGR02394       273 ILERDGV  279 (285)
T ss_pred             HHHHhhh
Confidence            9876543

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).

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

Probab=100.00  E-value=6.2e-38  Score=312.16  Aligned_cols=229  Identities=30%  Similarity=0.446  Sum_probs=207.9

Q ss_pred             HHHHHHHhc-HHHHHHHHHHhHHHHHHHHHHhhCCCC-CHHHHHHHHHHHHHHhhhccCCcCCCchhhHHHHHHHHHHHH
Q 009449          285 VLKQHLAFG-WYCREELIKSTRPLVLFLARNYRGLGI-PFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISK  362 (534)
Q Consensus       285 ~L~~~l~~G-~~A~e~LI~~nlrLV~sIArrY~~~g~-~~eDLiQEG~lgL~rA~ekFDp~kG~rFSTYA~~wIR~aI~~  362 (534)
                      .+....+.| ..++ .||+.|+|||.++|++|.+++. +.+||+|-|++||++|+++|||++|.+|+|||...|+++|.+
T Consensus        13 ~~~~~~~~g~~~~~-~Li~~ylpLV~~ia~k~~~r~~~~~dDLiqiG~iGLi~Aieryd~~kg~kF~tyA~~~I~Gei~d   91 (247)
T COG1191          13 KLLEYYAEGDEEAR-RLIERYLPLVKSIARKFENRGPSEYDDLIQIGMIGLIKAIERYDPSKGTKFSTYAVRRIRGEILD   91 (247)
T ss_pred             HHHHHHHhcCHHHH-HHHHHHHHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHHHHHcCcccCcchHHHHHHHHHHHHHH
Confidence            344555566 6788 9999999999999999998877 999999999999999999999999999999999999999999


Q ss_pred             HHHHhccccccccchHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHHhh--hhcccccccccchhhhh
Q 009449          363 MVARHARGIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLR--IVGSIDQKIGDCLNAKY  440 (534)
Q Consensus       363 ~lr~~sr~iRlP~~~~~~i~ki~ka~~~L~~elGr~Pt~eEIA~~lgis~~kv~~~l~~~~--~~~SLD~~i~~~~~~~l  440 (534)
                      ++|+.. .+++|..+.+..+++..+...+.+++||+||++|||+.+|++.+++..++....  ...|+|..+..+++.. 
T Consensus        92 ~LR~~~-~v~vpR~~~~~~~~i~~~~~~l~~el~r~pt~~EIA~~L~i~~ee~~~~~~~~~~~~~~sld~~~~~~~d~~-  169 (247)
T COG1191          92 YLRKND-SVKVPRSLRELGRRIEEAIDELEQELGREPTDEEIAEELGIDKEEYIEALLAINGSQLLSLDEDVLKDDDDD-  169 (247)
T ss_pred             HHHhCC-CccCcHHHHHHHHHHHHHHHHHHHHhCCCCcHHHHHHHhCCCHHHHHHHHHHhccccccchhhhhccccccc-
Confidence            999998 999999999999999999999999999999999999999999999999988775  6778887765444433 


Q ss_pred             hhccCCCCCCChHHHHHHHHHHHHHHHHHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 009449          441 LEFAPDRSVKSPKEIVMRQHMKKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLR  520 (534)
Q Consensus       441 ~e~i~d~~~~spee~v~~~el~e~L~~~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR  520 (534)
                          .++...+|.+.+...+..+.|.+++..|+++||.|+.+||    ++++|++|||+.||||..+|+|++.+|++|||
T Consensus       170 ----~~~~~~~~~~~~~~~~~~~~l~~ai~~L~EREk~Vl~l~y----~eelt~kEI~~~LgISes~VSql~kkai~kLr  241 (247)
T COG1191         170 ----VDDQIENPDDGVEKEELLEILKEAIEPLPEREKLVLVLRY----KEELTQKEIAEVLGISESRVSRLHKKAIKKLR  241 (247)
T ss_pred             ----hhhccccchhHHHHHHHHHHHHHHHHccCHHHHHHHHHHH----HhccCHHHHHHHhCccHHHHHHHHHHHHHHHH
Confidence                2333457888888889989999999999999999999999    99999999999999999999999999999999


Q ss_pred             hHhh
Q 009449          521 DSET  524 (534)
Q Consensus       521 ~~l~  524 (534)
                      ..+.
T Consensus       242 ~~l~  245 (247)
T COG1191         242 KELN  245 (247)
T ss_pred             HHhc
Confidence            8875

>PRK08215 sporulation sigma factor SigG; Reviewed

Probab=100.00  E-value=1.2e-37  Score=312.82  Aligned_cols=220  Identities=24%  Similarity=0.305  Sum_probs=197.4

Q ss_pred             HHHHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCchhhHHHHHHHHHHHHHHHHhcccccc
Q 009449          294 WYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKI  373 (534)
Q Consensus       294 ~~A~e~LI~~nlrLV~sIArrY~~~g~~~eDLiQEG~lgL~rA~ekFDp~kG~rFSTYA~~wIR~aI~~~lr~~sr~iRl  373 (534)
                      ..|+++||..|.++|+++|++|.+++.+++||+|||++|+|+++++|||.+|.+|+||+++||+++|.+++++.. .+++
T Consensus        36 ~~a~~~l~~~~~~~v~~~a~~~~~~~~~aeDlvQe~~i~l~~a~~~fd~~~~~~f~t~l~~~ir~~i~~~lr~~~-~vri  114 (258)
T PRK08215         36 KEAREKLINGNLRLVLSVIQRFNNRGENVDDLFQVGCIGLMKAIDNFDLSQNVKFSTYAVPMIIGEIRRYLRDNN-PIRV  114 (258)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCCcHHHHHHHHHHHHHHHHHhCC-ceEe
Confidence            568999999999999999999999999999999999999999999999999999999999999999999999984 8899


Q ss_pred             ccchHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHHhhhhcccccccccchhh--hhhhccCCCCCCC
Q 009449          374 PCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNA--KYLEFAPDRSVKS  451 (534)
Q Consensus       374 P~~~~~~i~ki~ka~~~L~~elGr~Pt~eEIA~~lgis~~kv~~~l~~~~~~~SLD~~i~~~~~~--~l~e~i~d~~~~s  451 (534)
                      |.++.....++.++...+.+++|+.|+.+|||+.+|++++++..++.....+.|||.++.++++.  ++.+.++++.. .
T Consensus       115 p~~~~~~~~~~~~~~~~l~~~~~r~p~~~eia~~l~v~~~~v~~~~~~~~~~~sl~~~~~~~~~~~~~~~~~~~~~~~-~  193 (258)
T PRK08215        115 SRSLRDIAYKALQVREKLINENSKEPTVEEIAKELEVPREEVVFALDAIQDPVSLFEPIYHDGGDPIYVMDQISDEKN-K  193 (258)
T ss_pred             cHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHCcCHHHHHHHHHhcCCCccccCCCCCCCCcchhhhhhccCccc-c
Confidence            99999999999999999999999999999999999999999999988877888999988655432  34566655431 2


Q ss_pred             hHHHHHHHHHHHHHHHHHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHh
Q 009449          452 PKEIVMRQHMKKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDSE  523 (534)
Q Consensus       452 pee~v~~~el~e~L~~~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~~l  523 (534)
                      ++.    ......+..+++.||+++++||.++|    ++++|++|||+.||+|.++|++++++|+++||+.+
T Consensus       194 ~~~----~~~~~~l~~~l~~L~~~er~vi~~~~----~~~~t~~eIA~~lgis~~~V~~~~~~al~kLr~~l  257 (258)
T PRK08215        194 DEN----WLEEIALKEAMKKLNDREKLILNLRF----FQGKTQMEVAEEIGISQAQVSRLEKAALKHMRKYI  257 (258)
T ss_pred             HHH----HHhHHHHHHHHHcCCHHHHHHHHHHH----hcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHh
Confidence            222    23345788999999999999999999    78999999999999999999999999999999875

>TIGR02885 spore_sigF RNA polymerase sigma-F factor

Probab=100.00  E-value=4.1e-37  Score=303.53  Aligned_cols=224  Identities=26%  Similarity=0.366  Sum_probs=200.0

Q ss_pred             HHhc-HHHHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCchhhHHHHHHHHHHHHHHHHhc
Q 009449          290 LAFG-WYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHA  368 (534)
Q Consensus       290 l~~G-~~A~e~LI~~nlrLV~sIArrY~~~g~~~eDLiQEG~lgL~rA~ekFDp~kG~rFSTYA~~wIR~aI~~~lr~~s  368 (534)
                      ++.| ..|++.||..|.++|+++|++|.+++.+++||+|||++|||+++++|||..|.+|+||++|||++.|.++++++.
T Consensus         5 ~~~gd~~a~~~l~~~y~~~v~~~a~~~~~~~~~aeDl~Qe~~i~l~~a~~~f~~~~~~~f~tyl~~~i~~~i~~~lr~~~   84 (231)
T TIGR02885         5 AQNGDKEARDKLIECNLRLVWSIVKRFLNRGYEPEDLFQIGCIGLVKAIDKFDLSYDVKFSTYAVPMIMGEIKRFLRDDG   84 (231)
T ss_pred             HHcCCHHHHHHHHHHhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHhcCCCCCCCcHHHHHHHHHHHHHHHHHhCC
Confidence            3445 679999999999999999999999999999999999999999999999999999999999999999999999985


Q ss_pred             cccccccchHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHHhhhhcccccccccchh--hhhhhccCC
Q 009449          369 RGIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLN--AKYLEFAPD  446 (534)
Q Consensus       369 r~iRlP~~~~~~i~ki~ka~~~L~~elGr~Pt~eEIA~~lgis~~kv~~~l~~~~~~~SLD~~i~~~~~--~~l~e~i~d  446 (534)
                       .+++|.++.....++.++...+..++|+.||.+|||+.+|++++++..++.....+.|||.+++++++  .++.+.+++
T Consensus        85 -~i~~p~~~~~~~~~~~~~~~~l~~~~~r~pt~~ela~~l~~~~~~v~~~~~~~~~~~sl~~~~~~~~~~~~~~~d~~~~  163 (231)
T TIGR02885        85 -IIKVSRSLKELARKIRYMKEELSKELGREPTINELAEALGVSPEEIVMALESARSPQSLYDTVHQDDGDPIYLLDQIAD  163 (231)
T ss_pred             -CeECCHHHHHHHHHHHHHHHHHHHHHCcCCCHHHHHHHHCcCHHHHHHHHHHccCCcCcccCCCCCCCCcchhhhhcCC
Confidence             78999999999999999999999999999999999999999999999998888888999998865533  235566666


Q ss_pred             CCCCChHHHHHHHHHHHHHHHHHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHh
Q 009449          447 RSVKSPKEIVMRQHMKKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDSE  523 (534)
Q Consensus       447 ~~~~spee~v~~~el~e~L~~~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~~l  523 (534)
                      +..  +++..   .....+..+++.||+++++||.++|    ++++|++|||+.||+|+++|++++++|+++||..+
T Consensus       164 ~~~--~~~~~---~~~~~l~~~l~~L~~~e~~i~~~~~----~~~~t~~eIA~~lgis~~~V~~~~~~al~~Lr~~l  231 (231)
T TIGR02885       164 KGS--EDSDW---LEKIALKEAISKLDERERQIIMLRY----FKDKTQTEVANMLGISQVQVSRLEKKVLKKMKEKL  231 (231)
T ss_pred             CCc--cHHhH---HHHHHHHHHHHcCCHHHHHHHHHHH----HcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHhC
Confidence            532  22222   2355788999999999999999999    78999999999999999999999999999999753

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

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

Probab=100.00  E-value=2.1e-36  Score=297.51  Aligned_cols=221  Identities=30%  Similarity=0.429  Sum_probs=199.3

Q ss_pred             HHHHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCchhhHHHHHHHHHHHHHHHHhcccccc
Q 009449          294 WYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKI  373 (534)
Q Consensus       294 ~~A~e~LI~~nlrLV~sIArrY~~~g~~~eDLiQEG~lgL~rA~ekFDp~kG~rFSTYA~~wIR~aI~~~lr~~sr~iRl  373 (534)
                      ..|++.||..|.++|+++|++|.+++.+++||+|||++|+|+|+++||+++|.+|+||++|||++.|.++++++.+.+++
T Consensus         2 ~~a~~~lv~~y~~~v~~~a~~~~~~~~~~eDl~Qe~~i~l~~a~~~f~~~~~~~F~ty~~~~i~~~~~~~~r~~~~~~ri   81 (227)
T TIGR02980         2 KEAREKLVELNLPLVRSIARRFRNRGEPHEDLVQVGTIGLVKAIDRFDPSYGVKFSTFAVPTIMGEIKRFFRDDTWAVRV   81 (227)
T ss_pred             HHHHHHHHHHhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHhcCcccCCCcHHHHHHHHHHHHHHHHHHcCCceec
Confidence            46899999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ccchHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHHhhh--hcccccccccchh--hhhhhccCCCCC
Q 009449          374 PCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRI--VGSIDQKIGDCLN--AKYLEFAPDRSV  449 (534)
Q Consensus       374 P~~~~~~i~ki~ka~~~L~~elGr~Pt~eEIA~~lgis~~kv~~~l~~~~~--~~SLD~~i~~~~~--~~l~e~i~d~~~  449 (534)
                      |.++.+.+++++++...+.+++|+.|+.+|+|+.+|++.+++..++.....  +.|||.++.++++  ..+.+.+     
T Consensus        82 ~~~~~~~~~~~~~~~~~l~~~~~~~p~~~ela~~l~~~~~~v~~~~~~~~~~~~~sld~~~~~~~~~~~~~~d~~-----  156 (227)
T TIGR02980        82 PRRLKELGLKINKATEELTQRLGRSPTIAEIAEELGVSEEEVVEALEAGNSYSALSLDAPIEDDDGDPIALLDTL-----  156 (227)
T ss_pred             CHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHhCCCHHHHHHHHHhhccCCCeeccccCCCCCCCCccccccc-----
Confidence            999999999999999999999999999999999999999999998877665  8899998863222  1222222     


Q ss_pred             CChHHHHHHHHHHHHHHHHHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHh
Q 009449          450 KSPKEIVMRQHMKKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDSE  523 (534)
Q Consensus       450 ~spee~v~~~el~e~L~~~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~~l  523 (534)
                      .+|++.+........|..+|..||+++++||.++|    ++++|++|||+.||+|+++|++++++|+++||+.+
T Consensus       157 ~~~~~~~~~~~~~~~l~~~l~~L~~~~r~vl~l~y----~~~~s~~eIA~~lgis~~~v~~~~~ra~~~Lr~~l  226 (227)
T TIGR02980       157 GDEDDALETVEDRLALKPLLAALPERERRILLLRF----FEDKTQSEIAERLGISQMHVSRLLRRALKKLREQL  226 (227)
T ss_pred             CCcchHHHhHHHHHHHHHHHHcCCHHHHHHHHHHH----hcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHh
Confidence            24455556667778899999999999999999999    78999999999999999999999999999999764

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=100.00  E-value=4e-36  Score=301.01  Aligned_cols=234  Identities=24%  Similarity=0.296  Sum_probs=207.9

Q ss_pred             HHHHHHHHh-c-HHHHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCchhhHHHHHHHHHHH
Q 009449          284 RVLKQHLAF-G-WYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSIS  361 (534)
Q Consensus       284 ~~L~~~l~~-G-~~A~e~LI~~nlrLV~sIArrY~~~g~~~eDLiQEG~lgL~rA~ekFDp~kG~rFSTYA~~wIR~aI~  361 (534)
                      ..|...++. | ..|+++||..|.++|+.+|++|.+++.+++||+|||+++||+++++||++.|.+|+||+++||++.|.
T Consensus        16 ~~li~~~~~~gd~~a~~~l~~~y~~~v~~~a~~~~~~~~~aeDlvQe~~i~l~~a~~~~~~~~~~~f~tyl~~~i~n~~~   95 (255)
T TIGR02941        16 IQWIAEFQQNQNGEAQEKLVDHYQNLVYSIAYKYSKGGPMHEDLVQVGMLGLLGAIRRYDYSIGNAFEPFAIPTIIGEIK   95 (255)
T ss_pred             HHHHHHHHHCCCHHHHHHHHHHhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHcCCcCCCCcHhHHHHHHHHHHH
Confidence            445565655 4 77999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHhccccccccchHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHHhh--hhcccccccccchhhh
Q 009449          362 KMVARHARGIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLR--IVGSIDQKIGDCLNAK  439 (534)
Q Consensus       362 ~~lr~~sr~iRlP~~~~~~i~ki~ka~~~L~~elGr~Pt~eEIA~~lgis~~kv~~~l~~~~--~~~SLD~~i~~~~~~~  439 (534)
                      ++++++.+.+++|.++.+..++++++...+.+.+|+.|+.+|||+.+|++.+++..++....  .+.|||.+++.+++..
T Consensus        96 ~~lr~~~~~iri~~~~~~~~~~~~~~~~~l~~~~~r~p~~~eia~~l~i~~~~~~~~~~~~~~~~~~sl~~~~~~~~~~~  175 (255)
T TIGR02941        96 RYLRDKTWSVHVPRRIKELGPKIKKAIDELTDHLQRSPKIIEIADHLGLSEEEVLEIMEMGQSYRALSVDDVIEADSDGS  175 (255)
T ss_pred             HHHHHcCCCcCCCHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHHHhccCCccccccccCCCCCc
Confidence            99999999999999999999999999999999999999999999999999999998876543  5789999887654433


Q ss_pred             hhhccCCCCCCChHHHHHHHHHHHHHHHHHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Q 009449          440 YLEFAPDRSVKSPKEIVMRQHMKKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKL  519 (534)
Q Consensus       440 l~e~i~d~~~~spee~v~~~el~e~L~~~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KL  519 (534)
                      ....+ + ...+|++.+...+....+..+|+.|||++|.||.++|    ++++|++|||+.||+|.++|++++++|+++|
T Consensus       176 ~~~~~-~-~~~~~~~~~~~~e~~~~l~~~l~~L~~~~r~ii~l~~----~~g~s~~eIA~~lgis~~~V~~~~~ra~~~L  249 (255)
T TIGR02941       176 TVARL-D-SVGEVEDGYDQTERRMVLEKILPILSEREKSIIHCTF----EENLSQKETGERLGISQMHVSRLQRQAISKL  249 (255)
T ss_pred             ccccc-c-ccCCcchHHHHHHHHHHHHHHHHcCCHHHHHHHHHHH----cCCCCHHHHHHHHCcCHHHHHHHHHHHHHHH
Confidence            22221 1 1235677777778888899999999999999999999    8999999999999999999999999999999


Q ss_pred             HhHh
Q 009449          520 RDSE  523 (534)
Q Consensus       520 R~~l  523 (534)
                      |..+
T Consensus       250 r~~~  253 (255)
T TIGR02941       250 KEAA  253 (255)
T ss_pred             HHHh
Confidence            9864

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=100.00  E-value=8.8e-36  Score=301.09  Aligned_cols=226  Identities=30%  Similarity=0.404  Sum_probs=203.6

Q ss_pred             HHHHHHHHHHhHHHHHHHHHHhh-C--CCCCHHHHHHHHHHHHHHhhhccCCcCCCchhhHHHHHHHHHHHHHHHHhccc
Q 009449          294 WYCREELIKSTRPLVLFLARNYR-G--LGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARG  370 (534)
Q Consensus       294 ~~A~e~LI~~nlrLV~sIArrY~-~--~g~~~eDLiQEG~lgL~rA~ekFDp~kG~rFSTYA~~wIR~aI~~~lr~~sr~  370 (534)
                      ..|++.++..|.++|+.+|++|. +  .+.+++||+|||++|||+++++|||.+|++|+||++||||+.|.+++++.   
T Consensus        30 ~~a~~~l~~~y~~lv~~~a~~~~~~~~~~~~~eDl~Qeg~l~L~~a~~~fd~~~~~~f~ty~~~~ir~~i~d~~R~~---  106 (268)
T PRK06288         30 PKIREYLILKYSPLVKYVAGRIAVGMPQNVEFDDLVSYGVFGLIDAIEKFDPEREIKFKTYAVTRIRGAIFDELRSI---  106 (268)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHHHHHHcCcccCCCHHHHHHHHHHHHHHHHHHhc---
Confidence            56899999999999999999986 2  56789999999999999999999999999999999999999999999865   


Q ss_pred             cccccchHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHHh--hhhcccccccccc---hhhhhhhccC
Q 009449          371 IKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECL--RIVGSIDQKIGDC---LNAKYLEFAP  445 (534)
Q Consensus       371 iRlP~~~~~~i~ki~ka~~~L~~elGr~Pt~eEIA~~lgis~~kv~~~l~~~--~~~~SLD~~i~~~---~~~~l~e~i~  445 (534)
                      +++|.++....++++++...|.+++|+.||.+|||+.+|++.+++..+....  ..+.|||.++..+   ....+.+.++
T Consensus       107 ~~~p~~~~~~~~~i~~~~~~l~~~~~~~pt~~eia~~lg~~~~~v~~~~~~~~~~~~~sld~~~~~~~~~~~~~l~~~~~  186 (268)
T PRK06288        107 DWIPRSVRQKARQIERAIAMLEARLGRTPSDEEIADELGISLEEYNSLLSKLSGTSVVSLNDLWFGGDEGDEVSLMDTLE  186 (268)
T ss_pred             CccCHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHcCCCHHHHHHHHHHHhcccccchhhhhccCCCcccchhhhhcc
Confidence            4689999999999999999999999999999999999999999999988655  3568999876422   2234667777


Q ss_pred             CCCCCChHHHHHHHHHHHHHHHHHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHhhh
Q 009449          446 DRSVKSPKEIVMRQHMKKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDSETC  525 (534)
Q Consensus       446 d~~~~spee~v~~~el~e~L~~~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~~l~~  525 (534)
                      ++..++|++.+...+....|..+|+.|||++|+||.++|    ++++|++|||+.||+|.++|++++++|+++||..+..
T Consensus       187 ~~~~~~pe~~~~~~e~~~~l~~~l~~L~~~~r~vl~l~~----~~~~s~~eIA~~lgis~~tV~~~~~ra~~~Lr~~l~~  262 (268)
T PRK06288        187 SPAALNPDEIAEREEIKRVIVEAIKTLPEREKKVLILYY----YEDLTLKEIGKVLGVTESRISQLHTKAVLQLRAKLAE  262 (268)
T ss_pred             CCCCCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHH----HcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHH
Confidence            777778999999999999999999999999999999999    8999999999999999999999999999999998764


Q ss_pred             h
Q 009449          526 R  526 (534)
Q Consensus       526 ~  526 (534)
                      .
T Consensus       263 ~  263 (268)
T PRK06288        263 I  263 (268)
T ss_pred             H
Confidence            3

>PRK07670 RNA polymerase sigma factor SigD; Validated

Probab=100.00  E-value=1.3e-35  Score=296.95  Aligned_cols=235  Identities=23%  Similarity=0.335  Sum_probs=208.2

Q ss_pred             HHHHHHHHH-hc-HHHHHHHHHHhHHHHHHHHHHhhC---CCCCHHHHHHHHHHHHHHhhhccCCcCCCchhhHHHHHHH
Q 009449          283 ERVLKQHLA-FG-WYCREELIKSTRPLVLFLARNYRG---LGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIR  357 (534)
Q Consensus       283 ~~~L~~~l~-~G-~~A~e~LI~~nlrLV~sIArrY~~---~g~~~eDLiQEG~lgL~rA~ekFDp~kG~rFSTYA~~wIR  357 (534)
                      +..|.++++ .| ..|++.||..|.++|+++|++|.+   ++.+++||+|||++|||+++++|||.+|.+|+||+++||+
T Consensus         8 e~~l~~~~~~~~d~~a~~~L~~~y~~~v~~~~~~~~~~~~~~~~~eDl~Qe~~i~l~~~~~~f~~~~~~~f~tyl~~~ir   87 (251)
T PRK07670          8 EQKLWDRWKEERDPDAADELIRRYMPLVHYHVQRISVGLPKSVSKDDLKSLGMLGLYDALEKFDPSRDLKFDTYASFRIR   87 (251)
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHHHHHHHHHcCcccCCCHHHHHHHHHH
Confidence            455666644 34 679999999999999999999975   6889999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHhccccccccchHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHH--hhhhcccccccccc
Q 009449          358 KSISKMVARHARGIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASEC--LRIVGSIDQKIGDC  435 (534)
Q Consensus       358 ~aI~~~lr~~sr~iRlP~~~~~~i~ki~ka~~~L~~elGr~Pt~eEIA~~lgis~~kv~~~l~~--~~~~~SLD~~i~~~  435 (534)
                      |.|.++++++.   ++|.++.+.+++++++.+.+.+.+|+.|+.+|||+.+|+++++|..++..  ...+.|||.++.++
T Consensus        88 n~~~d~lR~~~---~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~eia~~l~~~~~~v~~~~~~~~~~~~~sld~~~~~~  164 (251)
T PRK07670         88 GAIIDGLRKED---WLPRSMREKTKKVEAAIEKLEQRYMRNVTPKEVAAELGMTEEEVEATMNEGFFANLLSIDEKTHDQ  164 (251)
T ss_pred             HHHHHHHHhcC---CCCHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHhCcCHHHHHHHHHHHhccCccccCccccCC
Confidence            99999999865   69999999999999999999999999999999999999999999998763  44678999998654


Q ss_pred             hhh-hhhhccCCCCCCChHHHHHHHHHHHHHHHHHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 009449          436 LNA-KYLEFAPDRSVKSPKEIVMRQHMKKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKK  514 (534)
Q Consensus       436 ~~~-~l~e~i~d~~~~spee~v~~~el~e~L~~~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~R  514 (534)
                      ++. .+.+.+.+....+|++.+...+....|..+|..||+++|+||.++|    ++++|++|||+.||+|.++|++++++
T Consensus       165 ~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~l~~~l~~L~~~~r~vl~l~~----~~~~s~~EIA~~lgis~~tV~~~~~r  240 (251)
T PRK07670        165 DDGENVSVTIRDDKTPTPEEKLLKEELIEELAEKIKQLSEKEQLVISLFY----KEELTLTEIGQVLNLSTSRISQIHSK  240 (251)
T ss_pred             CCcchhhhhhcCcCCCCHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHH----hcCCCHHHHHHHHCcCHHHHHHHHHH
Confidence            433 2333445555568888888888889999999999999999999999    89999999999999999999999999


Q ss_pred             HHHHHHhHhh
Q 009449          515 AMTKLRDSET  524 (534)
Q Consensus       515 AL~KLR~~l~  524 (534)
                      |+++||..+.
T Consensus       241 a~~~Lr~~l~  250 (251)
T PRK07670        241 ALFKLKKLLE  250 (251)
T ss_pred             HHHHHHHHhh
Confidence            9999998764

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

Probab=100.00  E-value=3.3e-35  Score=288.90  Aligned_cols=217  Identities=29%  Similarity=0.453  Sum_probs=196.9

Q ss_pred             HHHHhHHHHHHHHHHhhC---CCCCHHHHHHHHHHHHHHhhhccCCcCCCchhhHHHHHHHHHHHHHHHHhccccccccc
Q 009449          300 LIKSTRPLVLFLARNYRG---LGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIPCK  376 (534)
Q Consensus       300 LI~~nlrLV~sIArrY~~---~g~~~eDLiQEG~lgL~rA~ekFDp~kG~rFSTYA~~wIR~aI~~~lr~~sr~iRlP~~  376 (534)
                      |+..|.++|+++|++|.+   ++.+++||+|||++|||+++++|||++|++|+||+++||++.+.+++++..   ++|.+
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   789999999999999999999999999999999999999999999998764   68999


Q ss_pred             hHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHHhh--hhcccccccccc-hhhhhhhccCCCCCCChH
Q 009449          377 LNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLR--IVGSIDQKIGDC-LNAKYLEFAPDRSVKSPK  453 (534)
Q Consensus       377 ~~~~i~ki~ka~~~L~~elGr~Pt~eEIA~~lgis~~kv~~~l~~~~--~~~SLD~~i~~~-~~~~l~e~i~d~~~~spe  453 (534)
                      +...++++.++..++.+++|+.|+.+|||+.+|+++++|..++....  ...|+|.+..++ +...+.+.++++...+|+
T Consensus        78 ~~~~~~~l~~~~~~l~~~~~~~~~~~ela~~l~~~~~~v~~~~~~~~~~~~~sl~~~~~~~~~~~~~~~~~~~~~~~~~~  157 (224)
T TIGR02479        78 LRQKARKLERAIRELEARLGREPTEEEIAEELGMDLKEYRQALNEINALSLVSLDELLESGDDGGSLIDRIEDDKSEDPE  157 (224)
T ss_pred             HHHHHHHHHHHHHHHHHHHCcCCCHHHHHHHhCCCHHHHHHHHHHHhcCCccccCCcccCCCccchhhhhccccccCCHH
Confidence            99999999999999999999999999999999999999999986544  567888766543 334566667766667899


Q ss_pred             HHHHHHHHHHHHHHHHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHh
Q 009449          454 EIVMRQHMKKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDSE  523 (534)
Q Consensus       454 e~v~~~el~e~L~~~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~~l  523 (534)
                      +.+...+....|..+|+.||+++|+||.++|    ++++|++|||+.||+|.++|++++++|+++||..+
T Consensus       158 ~~~~~~~~~~~l~~~l~~L~~~~r~il~l~y----~~~~s~~eIA~~lgis~~tV~~~~~ra~~~Lr~~l  223 (224)
T TIGR02479       158 EELEREELREALAEAIESLSEREQLVLSLYY----YEELNLKEIGEVLGLTESRVSQIHSQALKKLRAKL  223 (224)
T ss_pred             HHHHHHHHHHHHHHHHHhCCHHHHHHHHHHH----hCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHc
Confidence            9999999999999999999999999999999    89999999999999999999999999999999865

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

>PRK12427 flagellar biosynthesis sigma factor; Provisional

Probab=100.00  E-value=3.8e-34  Score=283.77  Aligned_cols=210  Identities=22%  Similarity=0.284  Sum_probs=182.1

Q ss_pred             HHHHHHHHhHHHHHHHHHHhhC---CCCCHHHHHHHHHHHHHHhhhccCCcCCCchhhHHHHHHHHHHHHHHHHhccccc
Q 009449          296 CREELIKSTRPLVLFLARNYRG---LGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIK  372 (534)
Q Consensus       296 A~e~LI~~nlrLV~sIArrY~~---~g~~~eDLiQEG~lgL~rA~ekFDp~kG~rFSTYA~~wIR~aI~~~lr~~sr~iR  372 (534)
                      ....|+..|+++|.++|++|..   .+.+.+||+|||++|||+|+++|||.+| +|+||++||||++|.+++++..   +
T Consensus        16 ~~~~lv~~y~~lV~~la~~~~~~~~~~~~~eDLvQeg~igL~~a~~~fd~~~~-~F~tYa~~~Ir~~il~~lr~~~---~   91 (231)
T PRK12427         16 EEGKYLNAYLPLVKKVVRQLAFQADSVIDREDMEQIALMGLLEALRRYGHPDE-QFAAYAVHRIRGAILDELRELD---W   91 (231)
T ss_pred             hHHHHHHHHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHHHHHHHHhcCCCCC-ChHHHHHHHHHHHHHHHHHhcC---C
Confidence            3468899999999999999975   4679999999999999999999998666 8999999999999999999764   4


Q ss_pred             cccchHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHH--hhhhcccccccccchhhhhhhccCCCCCC
Q 009449          373 IPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASEC--LRIVGSIDQKIGDCLNAKYLEFAPDRSVK  450 (534)
Q Consensus       373 lP~~~~~~i~ki~ka~~~L~~elGr~Pt~eEIA~~lgis~~kv~~~l~~--~~~~~SLD~~i~~~~~~~l~e~i~d~~~~  450 (534)
                      .|.++....++++++.+.+.+++|+.||.+|||+.+|++++++..++..  ...+.|||.+++++++..   .+++   .
T Consensus        92 ~~r~vr~~~~~i~~~~~~l~~~~g~~pt~~eiA~~lg~~~~~v~~~~~~~~~~~~~SLd~~~~~~~~~~---~~~~---~  165 (231)
T PRK12427         92 RPRRLRQKTHKTNDAIREIAKRLGHEPNFEEISAELNLTAEEYQEYLLLENAGTLESLDELLALEAHND---ILQS---R  165 (231)
T ss_pred             CCHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHhCCCHHHHHHHHHHhccCCceeccCcccCCCccc---ccCC---C
Confidence            7888999999999999999999999999999999999999999998764  346789999987654322   2221   2


Q ss_pred             ChHHHHHHHHHHHHHHHHHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhH
Q 009449          451 SPKEIVMRQHMKKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDS  522 (534)
Q Consensus       451 spee~v~~~el~e~L~~~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~~  522 (534)
                      .+++..   .....|..++..||+++|.||.++|    ++++|++|||+.||||+++|+|++.+|++|||..
T Consensus       166 ~~~~~~---~~~~~l~~~l~~L~~~er~vi~l~~----~~~~t~~EIA~~lgis~~~V~q~~~~~~~kLr~~  230 (231)
T PRK12427        166 DLEENI---IIEDNLKQALSQLDEREQLILHLYY----QHEMSLKEIALVLDLTEARICQLNKKIAQKIKSF  230 (231)
T ss_pred             CHHHHH---HHHHHHHHHHHcCCHHHHHHHHHHH----HcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHhh
Confidence            344333   2455789999999999999999999    8999999999999999999999999999999964

>PRK06986 fliA flagellar biosynthesis sigma factor; Validated

Probab=100.00  E-value=6.1e-34  Score=282.17  Aligned_cols=225  Identities=28%  Similarity=0.423  Sum_probs=199.8

Q ss_pred             hcHHHHHHHHHHhHHHHHHHHHHhh---CCCCCHHHHHHHHHHHHHHhhhccCCcCCCchhhHHHHHHHHHHHHHHHHhc
Q 009449          292 FGWYCREELIKSTRPLVLFLARNYR---GLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHA  368 (534)
Q Consensus       292 ~G~~A~e~LI~~nlrLV~sIArrY~---~~g~~~eDLiQEG~lgL~rA~ekFDp~kG~rFSTYA~~wIR~aI~~~lr~~s  368 (534)
                      .|.-++++|+..|.++|+++|++|.   +++.+++||+|||++|||+++++|||.+|.+|+||+++||+|.|.++++++.
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            4667899999999999999999997   6789999999999999999999999999999999999999999999999875


Q ss_pred             cccccccchHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHHhh--hhcccccccccchhhhhhhccCC
Q 009449          369 RGIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLR--IVGSIDQKIGDCLNAKYLEFAPD  446 (534)
Q Consensus       369 r~iRlP~~~~~~i~ki~ka~~~L~~elGr~Pt~eEIA~~lgis~~kv~~~l~~~~--~~~SLD~~i~~~~~~~l~e~i~d  446 (534)
                      +   +|.++....+++.++...+.+.+|++|+.+|||+.+|++.++|..++....  .+.|+|.+++++++. +.. ..+
T Consensus        85 ~---~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ela~~l~i~~~~v~~~~~~~~~~~~~sl~~~~~~~~~~-~~~-~~~  159 (236)
T PRK06986         85 W---VPRSVRRNAREVAQAIRQLEQELGREPTDTEVAEKLGLSLEEYREMLLDTNISQLFSIDELRGEHGDS-ILV-TED  159 (236)
T ss_pred             C---CCHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHcCCCHHHHHHHHHHHhccCCccccccccCCCcc-ccc-ccC
Confidence            3   688888888889999999999999999999999999999999999887543  466888887655443 222 223


Q ss_pred             CCCCChHHHHHHHHHHHHHHHHHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHhhh
Q 009449          447 RSVKSPKEIVMRQHMKKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDSETC  525 (534)
Q Consensus       447 ~~~~spee~v~~~el~e~L~~~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~~l~~  525 (534)
                      +..++|++.+...+....|..+|+.|||++|+||.++|    .+++|++|||+.||||.++|++++++|+++||+.+..
T Consensus       160 ~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~vl~l~~----~~g~s~~EIA~~lgis~~tV~~~~~ra~~~Lr~~l~~  234 (236)
T PRK06986        160 HQDEDPLQQLEDEELREALVEAIESLPEREQLVLSLYY----QEELNLKEIGAVLGVSESRVSQIHSQAIKRLRARLGE  234 (236)
T ss_pred             CCCCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHhHh----ccCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHhc
Confidence            34467888888888899999999999999999999999    8999999999999999999999999999999998753

>PRK08583 RNA polymerase sigma factor SigB; Validated

Probab=100.00  E-value=9.1e-34  Score=284.32  Aligned_cols=233  Identities=24%  Similarity=0.290  Sum_probs=205.8

Q ss_pred             HHHHHHHH-hc-HHHHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCchhhHHHHHHHHHHH
Q 009449          284 RVLKQHLA-FG-WYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSIS  361 (534)
Q Consensus       284 ~~L~~~l~-~G-~~A~e~LI~~nlrLV~sIArrY~~~g~~~eDLiQEG~lgL~rA~ekFDp~kG~rFSTYA~~wIR~aI~  361 (534)
                      ..|...++ .| ..|++.||..|.++|+++|++|.+++.+++||+||||++||+++++||+..|.+|+||+++||+|.|.
T Consensus        16 ~~li~~~~~~gd~~a~~~l~~~~~~~v~~~a~~~~~~~~~aeDlvQe~~l~l~~~~~~f~~~~~~~f~tyl~~~i~n~~~   95 (257)
T PRK08583         16 NKWIAEYQENQDEEAQEKLVKHYKNLVESLAYKYSKGQSHHEDLVQVGMVGLLGAIRRYDPSFGRSFEAFAVPTIIGEIK   95 (257)
T ss_pred             HHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHcCccCCCChHHHHHHHHHHHHH
Confidence            44555554 34 77999999999999999999999999999999999999999999999999988999999999999999


Q ss_pred             HHHHHhccccccccchHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHHhh--hhcccccccccchhhh
Q 009449          362 KMVARHARGIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLR--IVGSIDQKIGDCLNAK  439 (534)
Q Consensus       362 ~~lr~~sr~iRlP~~~~~~i~ki~ka~~~L~~elGr~Pt~eEIA~~lgis~~kv~~~l~~~~--~~~SLD~~i~~~~~~~  439 (534)
                      ++++++.+.+++|.++.+..+++.++...+...+++.|+.+|+|+.+|++.+.+..+.....  .+.|+|.+++.+++..
T Consensus        96 ~~lr~~~~~~~i~r~~~~~~~~~~~~~~~~~~~~~r~~~~~e~a~~~~~~~~~~~~~~~~~~~~~~~sld~~~~~~~~~~  175 (257)
T PRK08583         96 RYLRDKTWSVHVPRRIKELGPKIKKAVDELTTELQRSPKISEIADRLGVSEEEVLEAMEMGKSYQALSVDHSIEADSDGS  175 (257)
T ss_pred             HHHHhcCCCcCCCHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHHhccCCceecCccccCCCCCc
Confidence            99999999999999999999999999999999999999999999999999999988766542  5678998876543321


Q ss_pred             ---hhhccCCCCCCChHHHHHHHHHHHHHHHHHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHH
Q 009449          440 ---YLEFAPDRSVKSPKEIVMRQHMKKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAM  516 (534)
Q Consensus       440 ---l~e~i~d~~~~spee~v~~~el~e~L~~~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL  516 (534)
                         +.+.+     .+|++.+...+....+..+|..|||++|+||.++|    ++++|++|||+.||||+++|++++++|+
T Consensus       176 ~~~~~~~~-----~~~e~~~~~~~~~~~l~~~l~~L~~~~r~vl~l~~----~~g~s~~eIA~~l~is~~tV~~~~~ra~  246 (257)
T PRK08583        176 TVTLLDIV-----GQQEDGYELTEQRMILEKILPVLSDREKSIIQCTF----IENLSQKETGERLGISQMHVSRLQRQAI  246 (257)
T ss_pred             cchHhhhc-----CCcchhHHHHHHHHHHHHHHHhCCHHHHHHHHHHH----hCCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence               22222     35666677777788899999999999999999999    8999999999999999999999999999


Q ss_pred             HHHHhHhhh
Q 009449          517 TKLRDSETC  525 (534)
Q Consensus       517 ~KLR~~l~~  525 (534)
                      ++||..+..
T Consensus       247 ~kLr~~l~~  255 (257)
T PRK08583        247 KKLREAAFL  255 (257)
T ss_pred             HHHHHHhcc
Confidence            999988753

>PRK05572 sporulation sigma factor SigF; Validated

Probab=100.00  E-value=1.1e-33  Score=283.36  Aligned_cols=228  Identities=26%  Similarity=0.398  Sum_probs=200.3

Q ss_pred             HHHHHHHhc-HHHHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCchhhHHHHHHHHHHHHH
Q 009449          285 VLKQHLAFG-WYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKM  363 (534)
Q Consensus       285 ~L~~~l~~G-~~A~e~LI~~nlrLV~sIArrY~~~g~~~eDLiQEG~lgL~rA~ekFDp~kG~rFSTYA~~wIR~aI~~~  363 (534)
                      .+...+..| ..|++.||..|.++|+++|++|.+++.+++||+|||++++|+++++||+.+|.+|.||+++||++.|.++
T Consensus        21 ~li~~~~~gd~~a~~~L~~~y~~~v~~~a~~~~~~~~~aeDl~Qe~~l~l~~~~~~f~~~~~~~f~twl~~~i~~~i~~~  100 (252)
T PRK05572         21 ELIKKSQDGDQEARDTLVEKNLRLVWSVVQRFLNRGYEPDDLFQIGCIGLLKAVDKFDLSYDVKFSTYAVPMIIGEIQRF  100 (252)
T ss_pred             HHHHHHHcCCHHHHHHHHHHhHHHHHHHHHHHccCCCCHHHHHHHHHHHHHHHHHHcCCCCCCChHHHHHHHHHHHHHHH
Confidence            344555555 6799999999999999999999999999999999999999999999999988899999999999999999


Q ss_pred             HHHhccccccccchHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHHhhhhcccccccccchhh--hhh
Q 009449          364 VARHARGIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNA--KYL  441 (534)
Q Consensus       364 lr~~sr~iRlP~~~~~~i~ki~ka~~~L~~elGr~Pt~eEIA~~lgis~~kv~~~l~~~~~~~SLD~~i~~~~~~--~l~  441 (534)
                      +++.. .+++|.++....++++++...+..++|+.|+.+|||+.+|++++.+..+......+.||+.++.+++..  ++.
T Consensus       101 lr~~~-~~r~~~~~~~~~~~~~~~~~~l~~~~~r~p~~~eia~~l~~~~~~v~~~~~~~~~~~sl~~~~~~~~~~~~~~~  179 (252)
T PRK05572        101 LRDDG-TVKVSRSLKETANKIRKDKDELSKELGREPTIEELAEYLGVTPEEVVLAQEASRSPQSIHETVHENDGDPITLL  179 (252)
T ss_pred             HHhCC-CCCCCHHHHHHHHHHHHHHHHHHHHHCcCCCHHHHHHHhCcCHHHHHHHHHhcCCCcCcccCcccCCCCcchhh
Confidence            99884 789999999999999999999999999999999999999999999999888888889999887654322  233


Q ss_pred             hccCCCCCCChHHHHHHHHHHHHHHHHHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHh
Q 009449          442 EFAPDRSVKSPKEIVMRQHMKKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRD  521 (534)
Q Consensus       442 e~i~d~~~~spee~v~~~el~e~L~~~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~  521 (534)
                      +.++++..   +.    ......|..++..||+++++||.++|    ++++|++|||+.+|+|+++|++++++|+++||.
T Consensus       180 d~~~~~~~---~~----~~~~~~l~~~l~~L~~~~~~v~~l~~----~~~~s~~eIA~~lgis~~~V~~~~~ral~kLr~  248 (252)
T PRK05572        180 DQIADQSE---ED----WFDKIALKEAIRELDERERLIVYLRY----FKDKTQSEVAKRLGISQVQVSRLEKKILKQMKE  248 (252)
T ss_pred             hhcCCCch---hh----HHHHHHHHHHHHcCCHHHHHHHHHHH----hCCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence            44444321   11    23456789999999999999999999    789999999999999999999999999999998


Q ss_pred             Hhh
Q 009449          522 SET  524 (534)
Q Consensus       522 ~l~  524 (534)
                      .+.
T Consensus       249 ~l~  251 (252)
T PRK05572        249 KLD  251 (252)
T ss_pred             Hhc
Confidence            764

>PRK05803 sporulation sigma factor SigK; Reviewed

Probab=99.95  E-value=1.4e-26  Score=229.39  Aligned_cols=185  Identities=24%  Similarity=0.391  Sum_probs=149.7

Q ss_pred             HHHhc-HHHHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCchhhHHHHHHHHHHHHHHHHh
Q 009449          289 HLAFG-WYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARH  367 (534)
Q Consensus       289 ~l~~G-~~A~e~LI~~nlrLV~sIArrY~~~g~~~eDLiQEG~lgL~rA~ekFDp~kG~rFSTYA~~wIR~aI~~~lr~~  367 (534)
                      .+..| ..|++.|+..|.++|+++|.+|.+++.+++|++|||++++|+++++||+++|.+|.||+++|+||.+.+++++.
T Consensus        42 ~~~~gd~~a~~~l~~~y~~~l~~~a~~~~~~~~daeDlvQE~fi~l~~~~~~f~~~~~~~f~~wl~~i~rn~~id~~Rk~  121 (233)
T PRK05803         42 LMKEGDEEARNILIERNLRLVAHIVKKFENTGEDVDDLISIGTIGLIKAIESFDAGKGTKLATYAARCIENEILMHLRNL  121 (233)
T ss_pred             HHHcCCHHHHHHHHHHhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHhcCcccCCChHHHHHHHHHHHHHHHHHHH
Confidence            33344 67999999999999999999999999999999999999999999999998888999999999999999999876


Q ss_pred             ccccccccchHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHHhhhhcccccccccc---hhhhhhhcc
Q 009449          368 ARGIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDC---LNAKYLEFA  444 (534)
Q Consensus       368 sr~iRlP~~~~~~i~ki~ka~~~L~~elGr~Pt~eEIA~~lgis~~kv~~~l~~~~~~~SLD~~i~~~---~~~~l~e~i  444 (534)
                      .+..+                                                    ..+++.+.+.+   ....+.+..
T Consensus       122 ~~~~~----------------------------------------------------~~~~~~~~~~~~~~~~~~~~~~~  149 (233)
T PRK05803        122 KKTKK----------------------------------------------------EVSLQDPIGVDKEGNEISLIDIL  149 (233)
T ss_pred             hcccc----------------------------------------------------CCCccccccCCCCcCcccHHHHc
Confidence            42110                                                    01111111100   111222333


Q ss_pred             CCCCCCChHHHHHHHHHHHHHHHHHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHhh
Q 009449          445 PDRSVKSPKEIVMRQHMKKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDSET  524 (534)
Q Consensus       445 ~d~~~~spee~v~~~el~e~L~~~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~~l~  524 (534)
                      ++. .++|++.+..+...+.|..+|..|||++|+||.++|++.+++++|++|||+.||+|+++|++++++|+++||..+.
T Consensus       150 ~~~-~~~~~~~~~~~~~~~~l~~~l~~Lp~~~R~i~~l~y~~~~~e~~S~~EIA~~lgis~~tV~~~~~rA~~kLr~~l~  228 (233)
T PRK05803        150 GSE-EDDVIEQVELKMEVEKLYKKIDILDEREKEVIEMRYGLGNGKEKTQREIAKALGISRSYVSRIEKRALKKLFKELY  228 (233)
T ss_pred             cCC-CCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHhCCCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHH
Confidence            332 2357777787788889999999999999999999998887799999999999999999999999999999999876


Q ss_pred             hh
Q 009449          525 CR  526 (534)
Q Consensus       525 ~~  526 (534)
                      ..
T Consensus       229 ~~  230 (233)
T PRK05803        229 RA  230 (233)
T ss_pred             Hh
Confidence            43

>PRK08301 sporulation sigma factor SigE; Reviewed

Probab=99.93  E-value=1.8e-24  Score=213.98  Aligned_cols=189  Identities=24%  Similarity=0.385  Sum_probs=148.6

Q ss_pred             HHHHHHHHHhc-HHHHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCchhhHHHHHHHHHHH
Q 009449          283 ERVLKQHLAFG-WYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSIS  361 (534)
Q Consensus       283 ~~~L~~~l~~G-~~A~e~LI~~nlrLV~sIArrY~~~g~~~eDLiQEG~lgL~rA~ekFDp~kG~rFSTYA~~wIR~aI~  361 (534)
                      +..|...++.| ..|++.++..|.++|+.+|++|.+++.+++|++||+|+++|+++++|++..+++|.||++++++|.+.
T Consensus        39 ~~~L~~~~~~gd~~af~~l~~~y~~~l~~~a~~~~~~~~~AeDlvQevfl~l~~~~~~f~~~~~~~f~twl~~iarn~~~  118 (234)
T PRK08301         39 EEYLLNKLPKGDEAVRSLLIERNLRLVVYIARKFENTGINIEDLISIGTIGLIKAVNTFNPEKKIKLATYASRCIENEIL  118 (234)
T ss_pred             HHHHHHHHHccCHHHHHHHHHHhHHHHHHHHHHhhcCCCCHHHHHHHHHHHHHHHHHhcCcccCCCHHHHHHHHHHHHHH
Confidence            56677777777 77999999999999999999999999999999999999999999999998888999999999999999


Q ss_pred             HHHHHhccccccccchHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHHhhhhcccccccccc--hh-h
Q 009449          362 KMVARHARGIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDC--LN-A  438 (534)
Q Consensus       362 ~~lr~~sr~iRlP~~~~~~i~ki~ka~~~L~~elGr~Pt~eEIA~~lgis~~kv~~~l~~~~~~~SLD~~i~~~--~~-~  438 (534)
                      ++++++.+...                                                    ..+++.+...+  .. .
T Consensus       119 d~lRk~~~~~~----------------------------------------------------~~~~~~~~~~~~~~~~~  146 (234)
T PRK08301        119 MYLRRNNKVKA----------------------------------------------------EVSFDEPLNIDWDGNEL  146 (234)
T ss_pred             HHHHHHhcccc----------------------------------------------------ccccccccccccCCCcc
Confidence            99987643100                                                    01112111100  00 0


Q ss_pred             hhhhccCCCCCCChHHHHHHHHHHHHHHHHHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHH
Q 009449          439 KYLEFAPDRSVKSPKEIVMRQHMKKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTK  518 (534)
Q Consensus       439 ~l~e~i~d~~~~spee~v~~~el~e~L~~~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~K  518 (534)
                      ...+..++. ...++..+......+.|..+|+.|||++|+||.|+|||...+++|++|||+.||||.+||++++++|+++
T Consensus       147 ~~~~~~~~~-~~~~~~~~~~~~~~~~l~~al~~Lp~~~R~v~~L~y~l~~~eg~s~~EIA~~lgis~~tVk~~~~rA~~~  225 (234)
T PRK08301        147 LLSDVLGTD-NDIIYKDIEDEVDRKLLKKALKKLSDREKQIMELRFGLNGGEEKTQKEVADMLGISQSYISRLEKRIIKR  225 (234)
T ss_pred             cHHHhccCc-ccchHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHhccCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence            011111111 1233444455556678999999999999999999998776789999999999999999999999999999


Q ss_pred             HHhHhh
Q 009449          519 LRDSET  524 (534)
Q Consensus       519 LR~~l~  524 (534)
                      ||+.+.
T Consensus       226 Lr~~l~  231 (234)
T PRK08301        226 LKKEIN  231 (234)
T ss_pred             HHHHHH
Confidence            998765

>TIGR02846 spore_sigmaK RNA polymerase sigma-K factor

Probab=99.93  E-value=4.5e-24  Score=210.77  Aligned_cols=188  Identities=27%  Similarity=0.412  Sum_probs=149.0

Q ss_pred             HHHHHHHHHhc-HHHHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCchhhHHHHHHHHHHH
Q 009449          283 ERVLKQHLAFG-WYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSIS  361 (534)
Q Consensus       283 ~~~L~~~l~~G-~~A~e~LI~~nlrLV~sIArrY~~~g~~~eDLiQEG~lgL~rA~ekFDp~kG~rFSTYA~~wIR~aI~  361 (534)
                      +..|...++.| ..|++.|+..|.++|+++|.+|.++..+++||+||+|+++|+++++|+++.+.+|.||+++|++|.+.
T Consensus        35 ~~~li~~~~~gd~~af~~l~~~y~~~v~~~~~~~~~~~~dAEDlvQevfi~l~~~~~~~~~~~~~~f~twl~~i~rN~~~  114 (227)
T TIGR02846        35 EKKYLDRLKEGDEEARNVLIERNLRLVAHIVKKFSNTGEDVDDLISIGTIGLIKAIDSFDPDKGTRLATYAARCIENEIL  114 (227)
T ss_pred             HHHHHHHHHcCCHHHHHHHHHHhHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHHhCCcccCCChHHHHHHHHHHHHH
Confidence            45667777777 78999999999999999999999999999999999999999999999998888999999999999999


Q ss_pred             HHHHHhccccccccchHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHHhhhhcccccccccc---hhh
Q 009449          362 KMVARHARGIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDC---LNA  438 (534)
Q Consensus       362 ~~lr~~sr~iRlP~~~~~~i~ki~ka~~~L~~elGr~Pt~eEIA~~lgis~~kv~~~l~~~~~~~SLD~~i~~~---~~~  438 (534)
                      +++++..+..+.                                                    .+++...+.+   ...
T Consensus       115 d~~Rk~~r~~~~----------------------------------------------------~~~~~~~~~~~~~~~~  142 (227)
T TIGR02846       115 MHLRALKKTKGE----------------------------------------------------VSLQDPIGVDKEGNEI  142 (227)
T ss_pred             HHHHHHhccccc----------------------------------------------------eeccccccCCcccCcc
Confidence            999876531100                                                    0111111000   001


Q ss_pred             hhhhccCCCCCCChHHHHHHHHHHHHHHHHHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHH
Q 009449          439 KYLEFAPDRSVKSPKEIVMRQHMKKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTK  518 (534)
Q Consensus       439 ~l~e~i~d~~~~spee~v~~~el~e~L~~~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~K  518 (534)
                      .+.+...+. ..+|++.+...+..+.|.++|+.|||++|+||.++|.+..++++|++|||+.||+|+++|++++++|+++
T Consensus       143 ~~~~~~~~~-~~~~~~~~~~~~~~~~l~~~i~~L~~~~r~il~l~y~~~~~e~~S~~EIAe~lgis~~tV~~~~~rAl~~  221 (227)
T TIGR02846       143 SLIDILGSD-GDSVIEQVELNLEIKKLYKKLSVLDGREREVIEMRYGLGDGRRKTQREIAKILGISRSYVSRIEKRALMK  221 (227)
T ss_pred             cHHHHhcCC-CCChHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHcCCCCCCcCHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence            111222221 2356777777777788999999999999999999995444489999999999999999999999999999


Q ss_pred             HHhHh
Q 009449          519 LRDSE  523 (534)
Q Consensus       519 LR~~l  523 (534)
                      ||+.+
T Consensus       222 Lr~~~  226 (227)
T TIGR02846       222 LYKEL  226 (227)
T ss_pred             HHHHh
Confidence            99864

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.

>PRK08295 RNA polymerase factor sigma-70; Validated

Probab=99.92  E-value=8.7e-24  Score=204.11  Aligned_cols=196  Identities=23%  Similarity=0.321  Sum_probs=154.5

Q ss_pred             CCCHHHHHHHHHhc-HHHHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCchhhHHHHHHHH
Q 009449          280 GVSERVLKQHLAFG-WYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRK  358 (534)
Q Consensus       280 g~d~~~L~~~l~~G-~~A~e~LI~~nlrLV~sIArrY~~~g~~~eDLiQEG~lgL~rA~ekFDp~kG~rFSTYA~~wIR~  358 (534)
                      .++...|...++.| ..|++.|+..|.++|+.+|++|.++..+++|++||+++++|+++++||+.++.+|.||++.++++
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            34566777777777 78999999999999999999999999999999999999999999999998877999999999999


Q ss_pred             HHHHHHHHhccccccccchHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHHhhhhccccccccc-chh
Q 009449          359 SISKMVARHARGIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGD-CLN  437 (534)
Q Consensus       359 aI~~~lr~~sr~iRlP~~~~~~i~ki~ka~~~L~~elGr~Pt~eEIA~~lgis~~kv~~~l~~~~~~~SLD~~i~~-~~~  437 (534)
                      .+.+++++..+..+.+..                                               ...|.+.++.+ +.+
T Consensus        88 ~~~d~~r~~~r~~~~~~~-----------------------------------------------~~~s~~~~~~~~~~~  120 (208)
T PRK08295         88 QIITAIKTANRQKHIPLN-----------------------------------------------SYVSLDKPIYDEESD  120 (208)
T ss_pred             HHHHHHHHhhhhcccccc-----------------------------------------------ceeecCCcccCCccc
Confidence            999999865432221110                                               01233333211 222


Q ss_pred             hhhhhccCCCCCCChHHHHHHHHHHHHHH-HHHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHH
Q 009449          438 AKYLEFAPDRSVKSPKEIVMRQHMKKDVF-RILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAM  516 (534)
Q Consensus       438 ~~l~e~i~d~~~~spee~v~~~el~e~L~-~~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL  516 (534)
                      ..+.+.++++...+|++.+...+....+. .++..||+.+++||.+ |    .+++|++|||+.||+|.++|+..++||+
T Consensus       121 ~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~L~~~~r~vl~l-~----~e~~s~~EIA~~lgis~~tV~~~l~rar  195 (208)
T PRK08295        121 RTLLDVISEAKVTDPEELIISKEELEDIEEKIEELLSELEKEVLEL-Y----LDGKSYQEIAEELNRHVKSIDNALQRVK  195 (208)
T ss_pred             hhHHHHhcCcccCCHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHH-H----HccCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence            23344444444457887776666666664 5679999999999999 7    7999999999999999999999999999


Q ss_pred             HHHHhHhhhhc
Q 009449          517 TKLRDSETCRD  527 (534)
Q Consensus       517 ~KLR~~l~~~~  527 (534)
                      ++||+++....
T Consensus       196 ~~Lr~~l~~~~  206 (208)
T PRK08295        196 RKLEKYLENRE  206 (208)
T ss_pred             HHHHHHHHhhc
Confidence            99999887654

>TIGR02835 spore_sigmaE RNA polymerase sigma-E factor

Probab=99.92  E-value=2.2e-23  Score=206.76  Aligned_cols=190  Identities=23%  Similarity=0.402  Sum_probs=148.3

Q ss_pred             HHHHHHHHHhc-HHHHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCchhhHHHHHHHHHHH
Q 009449          283 ERVLKQHLAFG-WYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSIS  361 (534)
Q Consensus       283 ~~~L~~~l~~G-~~A~e~LI~~nlrLV~sIArrY~~~g~~~eDLiQEG~lgL~rA~ekFDp~kG~rFSTYA~~wIR~aI~  361 (534)
                      +..|...+..| ..|++.++..|.+.|+++|++|.+++.+++|++||+++++|+++++|++..+++|+||++.+++|.+.
T Consensus        39 ~~~l~~~~~~~d~~a~~~l~~~y~~~l~~~~~~~~~~~~~AEDlvQE~fl~l~~~~~~f~~~~~~~f~~wl~~iarN~~~  118 (234)
T TIGR02835        39 EEALLQKLTQGDESAKSTLIERNLRLVVYIARKFENTGIGIEDLVSIGTIGLIKAVNTFNPSKKIKLATYASRCIENEIL  118 (234)
T ss_pred             HHHHHHHHHcCCHHHHHHHHHHhHHHHHHHHHHhccCCCCHHHHHHHHHHHHHHHHHHhCcccCCCHHHHHHHHHHHHHH
Confidence            45566777776 78999999999999999999999999999999999999999999999998888999999999999999


Q ss_pred             HHHHHhccccccccchHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHHhhhhcccccccc---cchhh
Q 009449          362 KMVARHARGIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIG---DCLNA  438 (534)
Q Consensus       362 ~~lr~~sr~iRlP~~~~~~i~ki~ka~~~L~~elGr~Pt~eEIA~~lgis~~kv~~~l~~~~~~~SLD~~i~---~~~~~  438 (534)
                      +++++..+...                                                    ..+++.++.   ++...
T Consensus       119 d~~Rk~~r~~~----------------------------------------------------~~~~~~~~~~~~~~~~~  146 (234)
T TIGR02835       119 MYLRRNNKTRS----------------------------------------------------EVSFDEPLNVDWDGNEL  146 (234)
T ss_pred             HHHHHhccccC----------------------------------------------------cccccccccCCCCCCcc
Confidence            99997653110                                                    001111110   00000


Q ss_pred             hhhhccCCCCCCChHHHHHHHHHHHHHHHHHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHH
Q 009449          439 KYLEFAPDRSVKSPKEIVMRQHMKKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTK  518 (534)
Q Consensus       439 ~l~e~i~d~~~~spee~v~~~el~e~L~~~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~K  518 (534)
                      ...+. .++....+++.+......+.|..+|+.||+++|+|+.|+|.+.+++++|++|||+.||+|.++|++++++|+++
T Consensus       147 ~~~~~-~~~~~~~~~~~~~~~~~~~~l~~ai~~Lp~~~R~ii~L~~~l~~~eg~s~~EIA~~Lgis~~tV~~~l~ra~~~  225 (234)
T TIGR02835       147 LLSDV-LGTDSDIVYKYLEEEVDRELLRKALAKLNDREKKIMELRFGLVGGTEKTQKEVADMLGISQSYISRLEKRILKR  225 (234)
T ss_pred             hHHHh-cCCCCCcHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHccCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence            01111 11122234444555566678999999999999999999996655689999999999999999999999999999


Q ss_pred             HHhHhhh
Q 009449          519 LRDSETC  525 (534)
Q Consensus       519 LR~~l~~  525 (534)
                      ||+.+..
T Consensus       226 LR~~l~~  232 (234)
T TIGR02835       226 LKKEINR  232 (234)
T ss_pred             HHHHhhc
Confidence            9998753

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

>TIGR02859 spore_sigH RNA polymerase sigma-H factor

Probab=99.91  E-value=7.1e-23  Score=196.04  Aligned_cols=191  Identities=21%  Similarity=0.270  Sum_probs=148.4

Q ss_pred             CCHHHHHHHHHhc-HHHHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCchhhHHHHHHHHH
Q 009449          281 VSERVLKQHLAFG-WYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKS  359 (534)
Q Consensus       281 ~d~~~L~~~l~~G-~~A~e~LI~~nlrLV~sIArrY~~~g~~~eDLiQEG~lgL~rA~ekFDp~kG~rFSTYA~~wIR~a  359 (534)
                      |++..|...++.| ..|++.|+..|.+.|+++|+++.++..+++||+||+++.+|+++.+|++..+..|+||++.+|++.
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            5567778888888 779999999999999999999999999999999999999999999999987779999999999999


Q ss_pred             HHHHHHHhccccccccchHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHHhhhhccccccccc-chhh
Q 009449          360 ISKMVARHARGIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGD-CLNA  438 (534)
Q Consensus       360 I~~~lr~~sr~iRlP~~~~~~i~ki~ka~~~L~~elGr~Pt~eEIA~~lgis~~kv~~~l~~~~~~~SLD~~i~~-~~~~  438 (534)
                      +.++++...+..+.+.                                               ....|++.+... +.+.
T Consensus        84 ~~~~~r~~~~~~~~~~-----------------------------------------------~~~~~~~~~~~~~~~~~  116 (198)
T TIGR02859        84 IITAIKTATRQKHIPL-----------------------------------------------NSYVSLNKPIYDEESDR  116 (198)
T ss_pred             HHHHHHHHHHhcccch-----------------------------------------------hhhcCcccccccccccc
Confidence            9988875432111110                                               011233333211 1112


Q ss_pred             hhhhccCCCCCCChHHHHHHHHHHHHHHHHHhhC-CHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 009449          439 KYLEFAPDRSVKSPKEIVMRQHMKKDVFRILESL-DSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMT  517 (534)
Q Consensus       439 ~l~e~i~d~~~~spee~v~~~el~e~L~~~L~~L-~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~  517 (534)
                      ++.+.+++....+|++.+...+..+.|.++|+.| ++.++.|+. +|    .+++|++|||+.||+|.++|++.++||++
T Consensus       117 ~~~~~~~~~~~~~~e~~~~~~e~~~~l~~~l~~Ll~~~~~~i~~-~~----~~~~s~~eIA~~l~~s~~tV~~~l~r~r~  191 (198)
T TIGR02859       117 TLLDVISGAKVTDPEELIISQEEYGDIESKMNELLSDLEWKVLQ-SY----LDGKSYQEIACDLNRHVKSIDNALQRVKR  191 (198)
T ss_pred             hHHHHhhccccCCHHHHHHHHHHHHHHHHHHHHhcCHHHHHHHH-HH----HcCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            2333333333357888888888888899999985 566666664 57    68999999999999999999999999999


Q ss_pred             HHHhHh
Q 009449          518 KLRDSE  523 (534)
Q Consensus       518 KLR~~l  523 (534)
                      +||..+
T Consensus       192 ~L~~~l  197 (198)
T TIGR02859       192 KLEKYL  197 (198)
T ss_pred             HHHHhc
Confidence            999875

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

>PRK05602 RNA polymerase sigma factor; Reviewed

Probab=99.90  E-value=1.1e-22  Score=193.75  Aligned_cols=176  Identities=19%  Similarity=0.202  Sum_probs=147.2

Q ss_pred             CCHHHHHHHHHhc-HHHHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCchhhHHHHHHHHH
Q 009449          281 VSERVLKQHLAFG-WYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKS  359 (534)
Q Consensus       281 ~d~~~L~~~l~~G-~~A~e~LI~~nlrLV~sIArrY~~~g~~~eDLiQEG~lgL~rA~ekFDp~kG~rFSTYA~~wIR~a  359 (534)
                      ++++.|...+..| ..|++.|+..|.++|+.+|++|.+++.+++|++||+|+++|+++.+||+. +..|.+|++..+++.
T Consensus         5 ~~~~~l~~~~~~~d~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeDlvQe~fi~l~~~~~~~~~~-~~~f~~wl~~ia~n~   83 (186)
T PRK05602          5 DPDEELLARVAAGDPAAFRVLVARKLPRLLALATRMLGDPAEAEDVAQETFLRIWKQAPSWRPG-EARFDTWLHRVVLNL   83 (186)
T ss_pred             ccHHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHhhhcCCC-CCcHHHHHHHHHHHH
Confidence            4567788888877 78999999999999999999999999999999999999999999999986 458999999999999


Q ss_pred             HHHHHHHhccccccccchHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHHhhhhcccccccccchhhh
Q 009449          360 ISKMVARHARGIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNAK  439 (534)
Q Consensus       360 I~~~lr~~sr~iRlP~~~~~~i~ki~ka~~~L~~elGr~Pt~eEIA~~lgis~~kv~~~l~~~~~~~SLD~~i~~~~~~~  439 (534)
                      +.++++++...   +..                                                  .++          
T Consensus        84 ~~d~~R~~~~~---~~~--------------------------------------------------~~~----------  100 (186)
T PRK05602         84 CYDRLRRRREV---PVE--------------------------------------------------DAP----------  100 (186)
T ss_pred             HHHHHHhcCCC---Ccc--------------------------------------------------ccc----------
Confidence            99999865311   000                                                  000          


Q ss_pred             hhhccCCCCCCChHHHHHHHHHHHHHHHHHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Q 009449          440 YLEFAPDRSVKSPKEIVMRQHMKKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKL  519 (534)
Q Consensus       440 l~e~i~d~~~~spee~v~~~el~e~L~~~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KL  519 (534)
                        + ..+. ...|++.+...+....+..+|..||+++|+||.|+|    ++++|++|||+.||+|+.+|+++++||+++|
T Consensus       101 --~-~~~~-~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~i~~l~~----~~g~s~~EIA~~lgis~~tV~~~l~Rar~~L  172 (186)
T PRK05602        101 --D-VPDP-APGPDAGLEARQRARRVEQALAALPERQREAIVLQY----YQGLSNIEAAAVMDISVDALESLLARGRRAL  172 (186)
T ss_pred             --c-cCCC-CCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHhhHHH----hcCCCHHHHHHHhCcCHHHHHHHHHHHHHHH
Confidence              0 0111 124566666667777899999999999999999999    8999999999999999999999999999999


Q ss_pred             HhHhhhhcc
Q 009449          520 RDSETCRDL  528 (534)
Q Consensus       520 R~~l~~~~L  528 (534)
                      |+.+...+.
T Consensus       173 r~~l~~~~~  181 (186)
T PRK05602        173 RAQLADLPG  181 (186)
T ss_pred             HHHHHhccc
Confidence            999876554

>PRK09646 RNA polymerase sigma factor SigK; Reviewed

Probab=99.90  E-value=1.8e-22  Score=194.03  Aligned_cols=176  Identities=19%  Similarity=0.161  Sum_probs=143.6

Q ss_pred             CHHHHHHHHHhc-HHHHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCchhhHHHHHHHHHH
Q 009449          282 SERVLKQHLAFG-WYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSI  360 (534)
Q Consensus       282 d~~~L~~~l~~G-~~A~e~LI~~nlrLV~sIArrY~~~g~~~eDLiQEG~lgL~rA~ekFDp~kG~rFSTYA~~wIR~aI  360 (534)
                      +...|...+..| ..|+++|+..|.++|+++|.+|.++..+++|++||+|+++|+++.+||+.+| .|.+|++..++|.+
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            356677777777 7899999999999999999999999999999999999999999999998765 79999999999999


Q ss_pred             HHHHHHhccccccccchHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHHhhhhcccccccccchhhhh
Q 009449          361 SKMVARHARGIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNAKY  440 (534)
Q Consensus       361 ~~~lr~~sr~iRlP~~~~~~i~ki~ka~~~L~~elGr~Pt~eEIA~~lgis~~kv~~~l~~~~~~~SLD~~i~~~~~~~l  440 (534)
                      +++++++.+..+.-.                                                   ..    ...     
T Consensus        95 ~d~~r~~~~~~~~~~---------------------------------------------------~~----~~~-----  114 (194)
T PRK09646         95 VDRVRSEQAASQREV---------------------------------------------------RY----GAR-----  114 (194)
T ss_pred             HHHHHhhcccccccc---------------------------------------------------cc----ccc-----
Confidence            999987642110000                                                   00    000     


Q ss_pred             hhccCCCCCCChHHHHHHHHHHHHHHHHHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 009449          441 LEFAPDRSVKSPKEIVMRQHMKKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLR  520 (534)
Q Consensus       441 ~e~i~d~~~~spee~v~~~el~e~L~~~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR  520 (534)
                       +  .+.....+++.+...+..+.+..+|..||+++|+||.|+|    .+++|++|||+.||+|..+|+++++||+++||
T Consensus       115 -~--~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~vl~l~~----~~~~s~~EIA~~Lgis~~tVk~~l~ra~~~Lr  187 (194)
T PRK09646        115 -N--VDPAFDQVAEEVEARLERERVRDCLDALTDTQRESVTLAY----YGGLTYREVAERLAVPLGTVKTRMRDGLIRLR  187 (194)
T ss_pred             -c--ccccccchHHHHHHHhHHHHHHHHHHhCCHHHHHHHHHHH----HcCCCHHHHHHHhCCChHhHHHHHHHHHHHHH
Confidence             0  0011123445555556667899999999999999999999    89999999999999999999999999999999


Q ss_pred             hHhhh
Q 009449          521 DSETC  525 (534)
Q Consensus       521 ~~l~~  525 (534)
                      ..+..
T Consensus       188 ~~l~~  192 (194)
T PRK09646        188 DCLGV  192 (194)
T ss_pred             HHhcc
Confidence            98764

>PRK12513 RNA polymerase sigma factor; Provisional

Probab=99.90  E-value=2e-22  Score=193.23  Aligned_cols=181  Identities=20%  Similarity=0.211  Sum_probs=149.4

Q ss_pred             CCHHHHHHHHHhc-HHHHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCchhhHHHHHHHHH
Q 009449          281 VSERVLKQHLAFG-WYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKS  359 (534)
Q Consensus       281 ~d~~~L~~~l~~G-~~A~e~LI~~nlrLV~sIArrY~~~g~~~eDLiQEG~lgL~rA~ekFDp~kG~rFSTYA~~wIR~a  359 (534)
                      .++..|...+..| ..|++.|+..|.+.|+++|+++.++..+++|++||+|+++|++..+|++..  .|.+|++.++++.
T Consensus        11 ~~~~~l~~~~~~gd~~a~~~l~~~y~~~l~~~~~~~~~~~~daeDlvQe~fi~l~~~~~~~~~~~--~f~~wl~~i~~n~   88 (194)
T PRK12513         11 ASDEALMLRYRAGDAAAFEALYARHRTGLYRFLLRLARDRALAEDIFQETWLRVIRARAQYQPRA--RFRTWLYQIARNL   88 (194)
T ss_pred             CCHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHhcCCCC--chHHHHHHHHHHH
Confidence            3466777777877 789999999999999999999999999999999999999999999999753  6999999999999


Q ss_pred             HHHHHHHhccccccccchHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHHhhhhcccccccccchhhh
Q 009449          360 ISKMVARHARGIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNAK  439 (534)
Q Consensus       360 I~~~lr~~sr~iRlP~~~~~~i~ki~ka~~~L~~elGr~Pt~eEIA~~lgis~~kv~~~l~~~~~~~SLD~~i~~~~~~~  439 (534)
                      +++++++..+....+..                                                   .+.        .
T Consensus        89 ~~~~~R~~~~~~~~~~~---------------------------------------------------~~~--------~  109 (194)
T PRK12513         89 LIDHWRRHGARQAPSLD---------------------------------------------------ADE--------Q  109 (194)
T ss_pred             HHHHHHHhccccccccc---------------------------------------------------cch--------h
Confidence            99999877542211100                                                   000        0


Q ss_pred             hhhccCCCCCCChHHHHHHHHHHHHHHHHHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Q 009449          440 YLEFAPDRSVKSPKEIVMRQHMKKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKL  519 (534)
Q Consensus       440 l~e~i~d~~~~spee~v~~~el~e~L~~~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KL  519 (534)
                      . ....+ ...+|++.+...+....+..+|+.||+++|+||.|+|    .+++|++|||+.||+|+++|+++++||+++|
T Consensus       110 ~-~~~~~-~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~i~~l~~----~~g~s~~EIA~~lgis~~tV~~~l~ra~~~L  183 (194)
T PRK12513        110 L-HALAD-DGAAPEQQLSLFRDRRRLQAALETLPDEQREVFLLRE----HGDLELEEIAELTGVPEETVKSRLRYALQKL  183 (194)
T ss_pred             h-hhcCC-CCCCHHHHHHHHHHHHHHHHHHHhCCHhHhhheeeeh----ccCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence            0 00111 1236777777777888999999999999999999999    8999999999999999999999999999999


Q ss_pred             HhHhhhhcc
Q 009449          520 RDSETCRDL  528 (534)
Q Consensus       520 R~~l~~~~L  528 (534)
                      |..+...++
T Consensus       184 r~~l~~~~~  192 (194)
T PRK12513        184 RELLAEEVA  192 (194)
T ss_pred             HHHHHHhhc
Confidence            999887654

>PRK09648 RNA polymerase sigma factor SigD; Reviewed

Probab=99.90  E-value=4e-22  Score=190.39  Aligned_cols=172  Identities=21%  Similarity=0.308  Sum_probs=141.9

Q ss_pred             HHHHHHHHhc-HHHHHHHHHHhHHHHHHHHHHhhCC----CCCHHHHHHHHHHHHHHhhhccCCcCCCchhhHHHHHHHH
Q 009449          284 RVLKQHLAFG-WYCREELIKSTRPLVLFLARNYRGL----GIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRK  358 (534)
Q Consensus       284 ~~L~~~l~~G-~~A~e~LI~~nlrLV~sIArrY~~~----g~~~eDLiQEG~lgL~rA~ekFDp~kG~rFSTYA~~wIR~  358 (534)
                      ..|...+..| ..|+++|+..|.+.|+.+|.++.++    ..+++|++||+++++|+++.+|++. +..|.||++..++|
T Consensus        12 ~~l~~~~~~gd~~a~~~l~~~~~~~l~~~~~~~~~~~~~~~~~aeDlvQe~fi~l~~~~~~~~~~-~~~~~~wl~~i~~n   90 (189)
T PRK09648         12 DALVAEAVAGDRRALREVLEIIRPLVVRYCRARLGGVERPGLSADDVAQEVCLAVITALPRYRDQ-GRPFLAFVYGIAAH   90 (189)
T ss_pred             HHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHhcccccCCCCHHHHHHHHHHHHHHHHHHHhcc-CCcHHHHHHHHHHH
Confidence            4567777777 7899999999999999999999765    4689999999999999999999864 45899999999999


Q ss_pred             HHHHHHHHhccccccccchHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHHhhhhcccccccccchhh
Q 009449          359 SISKMVARHARGIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNA  438 (534)
Q Consensus       359 aI~~~lr~~sr~iRlP~~~~~~i~ki~ka~~~L~~elGr~Pt~eEIA~~lgis~~kv~~~l~~~~~~~SLD~~i~~~~~~  438 (534)
                      .+.++++++.+....+.                                                     +.        
T Consensus        91 ~~~d~~r~~~r~~~~~~-----------------------------------------------------~~--------  109 (189)
T PRK09648         91 KVADAHRAAGRDKAVPT-----------------------------------------------------EE--------  109 (189)
T ss_pred             HHHHHHHHhCCCccccc-----------------------------------------------------cc--------
Confidence            99999987653211100                                                     00        


Q ss_pred             hhhhccCCCCCCChHHHHHHHHHHHHHHHHHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHH
Q 009449          439 KYLEFAPDRSVKSPKEIVMRQHMKKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTK  518 (534)
Q Consensus       439 ~l~e~i~d~~~~spee~v~~~el~e~L~~~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~K  518 (534)
                       ..+.. + ...+|++.+...+..+.|..+|..|||++|+||.++|    ++++|++|||+.||+|..+|++.++||+++
T Consensus       110 -~~~~~-~-~~~~~~~~~~~~e~~~~l~~~l~~L~~~~r~i~~l~~----~~g~s~~EIA~~lgis~~tV~~~l~Ra~~~  182 (189)
T PRK09648        110 -VPERP-S-DDAGPEERALRSESSNRMRELLDTLPEKQREILILRV----VVGLSAEETAEAVGSTPGAVRVAQHRALAR  182 (189)
T ss_pred             -ccccc-c-cCCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHH----HcCCCHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence             00000 1 1136777777778888899999999999999999999    899999999999999999999999999999


Q ss_pred             HHhHhh
Q 009449          519 LRDSET  524 (534)
Q Consensus       519 LR~~l~  524 (534)
                      ||+.+.
T Consensus       183 Lr~~l~  188 (189)
T PRK09648        183 LRAEIE  188 (189)
T ss_pred             HHHHhc
Confidence            998764

>TIGR02948 SigW_bacill RNA polymerase sigma-W factor

Probab=99.90  E-value=3.4e-22  Score=189.45  Aligned_cols=179  Identities=15%  Similarity=0.205  Sum_probs=143.2

Q ss_pred             HHHHHHHHhc-HHHHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCchhhHHHHHHHHHHHH
Q 009449          284 RVLKQHLAFG-WYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISK  362 (534)
Q Consensus       284 ~~L~~~l~~G-~~A~e~LI~~nlrLV~sIArrY~~~g~~~eDLiQEG~lgL~rA~ekFDp~kG~rFSTYA~~wIR~aI~~  362 (534)
                      +.|+..+..| ..|+++|+..|.+.|+++|.+|.++..+++|++||+++++|++..+||+..  .|.||++..++|.+.+
T Consensus         6 ~~li~~~~~gd~~a~~~l~~~y~~~v~~~~~~~~~~~~~aeDlvQe~~l~l~~~~~~~~~~~--~~~~wl~~i~~n~~~~   83 (187)
T TIGR02948         6 KKRIKEVRKGDENAFADLVDLYKDKIYQLCYRMLGNVHEAEDVAQEAFIRAYTNIDTYDIQR--KFSTWLYRIATNLTID   83 (187)
T ss_pred             HHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhHHhcCCCC--chHHHHHHHHHHHHHH
Confidence            4456667777 779999999999999999999999999999999999999999999999865  6999999999999999


Q ss_pred             HHHHhccccccccchHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHHhhhhcccccccccchhhhhhh
Q 009449          363 MVARHARGIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNAKYLE  442 (534)
Q Consensus       363 ~lr~~sr~iRlP~~~~~~i~ki~ka~~~L~~elGr~Pt~eEIA~~lgis~~kv~~~l~~~~~~~SLD~~i~~~~~~~l~e  442 (534)
                      ++++..+...                                                       ++......+...+.+
T Consensus        84 ~~rk~~~~~~-------------------------------------------------------~~~~~~~~~~~~~~~  108 (187)
T TIGR02948        84 RLRKRKPDFY-------------------------------------------------------LDDEVQGTDGLTMES  108 (187)
T ss_pred             HHHhhccccc-------------------------------------------------------ccccccCcccccccc
Confidence            9986532100                                                       000000000001111


Q ss_pred             ccCCCCCCChHHHHHHHHHHHHHHHHHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhH
Q 009449          443 FAPDRSVKSPKEIVMRQHMKKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDS  522 (534)
Q Consensus       443 ~i~d~~~~spee~v~~~el~e~L~~~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~~  522 (534)
                      ..++. .++|++.+...+..+.+..+|..|||++|+||.++|    .+++|++|||+.||+|.++|++.++||+++||..
T Consensus       109 ~~~~~-~~~~~~~~~~~e~~~~l~~~l~~L~~~~r~v~~l~~----~~g~s~~eIA~~lgis~~~v~~~l~Rar~~Lr~~  183 (187)
T TIGR02948       109 QLAAD-EAPPEDQVISLELRDTIQQEIQALPPKYRMVIVLKY----MEDLSLKEISEILDLPVGTVKTRIHRGREALRKQ  183 (187)
T ss_pred             ccccC-cCCHHHHHHHHHHHHHHHHHHHhCCHHHhHHhhhHH----hcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence            11111 236777777777778899999999999999999999    8999999999999999999999999999999988


Q ss_pred             hh
Q 009449          523 ET  524 (534)
Q Consensus       523 l~  524 (534)
                      +.
T Consensus       184 l~  185 (187)
T TIGR02948       184 LR  185 (187)
T ss_pred             hh
Confidence            65

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

>PRK09641 RNA polymerase sigma factor SigW; Provisional

Probab=99.90  E-value=4.4e-22  Score=188.71  Aligned_cols=181  Identities=17%  Similarity=0.199  Sum_probs=145.8

Q ss_pred             CHHHHHHHHHhc-HHHHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCchhhHHHHHHHHHH
Q 009449          282 SERVLKQHLAFG-WYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSI  360 (534)
Q Consensus       282 d~~~L~~~l~~G-~~A~e~LI~~nlrLV~sIArrY~~~g~~~eDLiQEG~lgL~rA~ekFDp~kG~rFSTYA~~wIR~aI  360 (534)
                      +.+.|...++.| ..|++.++..|.++|+++|+++.++..+++|++||+++++|++..+|++..  .|.+|++..++|.+
T Consensus         4 ~~~~li~~~~~~d~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeDivQe~~l~l~~~~~~~~~~~--~~~~wl~~iarn~~   81 (187)
T PRK09641          4 LIKRLIKQVKKGDQNAFAELVDLYKDKIYQLCYRMLGNRHEAEDAAQEAFIRAYVNIDSYDINR--KFSTWLYRIATNLT   81 (187)
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHhhCCCc--chhHHHHHHHHHHH
Confidence            345667777777 779999999999999999999999999999999999999999999999853  79999999999999


Q ss_pred             HHHHHHhccccccccchHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHHhhhhcccccccccchhhhh
Q 009449          361 SKMVARHARGIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNAKY  440 (534)
Q Consensus       361 ~~~lr~~sr~iRlP~~~~~~i~ki~ka~~~L~~elGr~Pt~eEIA~~lgis~~kv~~~l~~~~~~~SLD~~i~~~~~~~l  440 (534)
                      .+++++..+..                                                       +++.....++....
T Consensus        82 ~d~~R~~~~~~-------------------------------------------------------~~~~~~~~~~~~~~  106 (187)
T PRK09641         82 IDRLRKRKPDY-------------------------------------------------------YLDAEVAGTEGLTM  106 (187)
T ss_pred             HHHHHhcCccc-------------------------------------------------------cccccccCCcchhh
Confidence            99998754210                                                       01100000111111


Q ss_pred             hhccCCCCCCChHHHHHHHHHHHHHHHHHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 009449          441 LEFAPDRSVKSPKEIVMRQHMKKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLR  520 (534)
Q Consensus       441 ~e~i~d~~~~spee~v~~~el~e~L~~~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR  520 (534)
                      .+.+.+ ...+|++.+...+....+..+|+.||+++++||.++|    ..++|++|||+.||||.++|++.++||+++||
T Consensus       107 ~~~~~~-~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~il~l~~----~~~~s~~eIA~~lgis~~~v~~~l~Rar~~Lr  181 (187)
T PRK09641        107 YSQLAA-DDALPEEQVVSLELQETIQEAILQLPEKYRTVIVLKY----IEDLSLKEISEILDLPVGTVKTRIHRGREALR  181 (187)
T ss_pred             hccccc-CcCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHhhhHH----hhCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence            111122 1235777777778888899999999999999999999    89999999999999999999999999999999


Q ss_pred             hHhh
Q 009449          521 DSET  524 (534)
Q Consensus       521 ~~l~  524 (534)
                      ..+.
T Consensus       182 ~~l~  185 (187)
T PRK09641        182 KQLR  185 (187)
T ss_pred             HHHh
Confidence            8875

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

Probab=99.89  E-value=1e-21  Score=183.17  Aligned_cols=167  Identities=15%  Similarity=0.241  Sum_probs=138.2

Q ss_pred             HHHHhc-HHHHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCchhhHHHHHHHHHHHHHHHH
Q 009449          288 QHLAFG-WYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVAR  366 (534)
Q Consensus       288 ~~l~~G-~~A~e~LI~~nlrLV~sIArrY~~~g~~~eDLiQEG~lgL~rA~ekFDp~kG~rFSTYA~~wIR~aI~~~lr~  366 (534)
                      ..+..| ..|++.|+..|.+.+++++.++.++..+++|++||+++.+|++.++|+...+ .|.+|++.+++|.+.+++++
T Consensus         3 ~~~~~~d~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeD~vQe~~l~l~~~~~~~~~~~~-~~~~wl~~i~~n~~~d~~R~   81 (170)
T TIGR02952         3 ERAQDREEDAFARIYETYSDRVYRYIYYRVGCKYTAEDLTSEVFERVLRKIDSFKEQKN-SFEAWLFTIARNVVNDYFRG   81 (170)
T ss_pred             HHHHccCHHHHHHHHHHHHHHHHHHHHHHHCChhhHHHHHHHHHHHHHHhHHhcccccc-cHHHHHHHHHHHHHHHHHHh
Confidence            344555 7899999999999999999999998899999999999999999999987555 89999999999999999987


Q ss_pred             hccccccccchHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHHhhhhcccccccccchhhhhhhccCC
Q 009449          367 HARGIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNAKYLEFAPD  446 (534)
Q Consensus       367 ~sr~iRlP~~~~~~i~ki~ka~~~L~~elGr~Pt~eEIA~~lgis~~kv~~~l~~~~~~~SLD~~i~~~~~~~l~e~i~d  446 (534)
                      +.+....                                                     +.+.         ..+... 
T Consensus        82 ~~~~~~~-----------------------------------------------------~~~~---------~~~~~~-   98 (170)
T TIGR02952        82 SKRHPLF-----------------------------------------------------SLDV---------FKELLS-   98 (170)
T ss_pred             cCCCCCC-----------------------------------------------------cHHH---------HhhcCC-
Confidence            6431110                                                     0000         000001 


Q ss_pred             CCCCChHHHHHHHHHHHHHHHHHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHh
Q 009449          447 RSVKSPKEIVMRQHMKKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDSE  523 (534)
Q Consensus       447 ~~~~spee~v~~~el~e~L~~~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~~l  523 (534)
                       ...+|++.+...+..+.+..+|..|||++|+||.++|    .+|+|++|||+.||+|.++|++.++||+++||+.+
T Consensus        99 -~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~vl~l~~----~~g~s~~eIA~~l~is~~tv~~~l~ra~~~Lr~~l  170 (170)
T TIGR02952        99 -NEPNPEEAILKEEANEKLLKALKILTPKQQHVIALRF----GQNLPIAEVARILGKTEGAVKILQFRAIKKLARQM  170 (170)
T ss_pred             -CCCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHH----hcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHhC
Confidence             1135777777777788899999999999999999999    89999999999999999999999999999999763

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.

>PRK06811 RNA polymerase factor sigma-70; Validated

Probab=99.88  E-value=1.5e-21  Score=187.00  Aligned_cols=175  Identities=16%  Similarity=0.246  Sum_probs=145.1

Q ss_pred             CCHHHHHHHHHhc-HHHHHHHHHHhHHHHHHHHHHhhCCC---CCHHHHHHHHHHHHHHhhhccCCcCCCchhhHHHHHH
Q 009449          281 VSERVLKQHLAFG-WYCREELIKSTRPLVLFLARNYRGLG---IPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWI  356 (534)
Q Consensus       281 ~d~~~L~~~l~~G-~~A~e~LI~~nlrLV~sIArrY~~~g---~~~eDLiQEG~lgL~rA~ekFDp~kG~rFSTYA~~wI  356 (534)
                      ++++.|+..+..| ..|++.|+..|.+.|+.++.++.++.   .+++|++||+++++|+++++|++..+ .|.||++..+
T Consensus         3 ~~~~~li~~~~~gd~~a~~~l~~~y~~~l~~~~~~~~~~~~~~~daeDi~Qe~~i~l~~~~~~~~~~~~-~~~~wl~~ia   81 (189)
T PRK06811          3 INEDNFIKELKKKNEKALEFIVDTYGNLVKKIVHKVLGTVNYSQLIEECVNDIFLSIWNNIDKFDEEKG-SFKKWIAAIS   81 (189)
T ss_pred             CcHHHHHHHHHccCHHHHHHHHHHHHHHHHHHHHHHHcccCchhHHHHHHHHHHHHHHHhHHHhccccc-cHHHHHHHHH
Confidence            5677888888888 67999999999999999999998853   57999999999999999999997654 8999999999


Q ss_pred             HHHHHHHHHHhccccccccchHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHHhhhhcccccccccch
Q 009449          357 RKSISKMVARHARGIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCL  436 (534)
Q Consensus       357 R~aI~~~lr~~sr~iRlP~~~~~~i~ki~ka~~~L~~elGr~Pt~eEIA~~lgis~~kv~~~l~~~~~~~SLD~~i~~~~  436 (534)
                      +|.+.++++++.+.....                                                    +.+..     
T Consensus        82 rn~~~d~~rk~~~~~~~~----------------------------------------------------~~~~~-----  104 (189)
T PRK06811         82 KYKAIDYKRKLTKNNEID----------------------------------------------------SIDEF-----  104 (189)
T ss_pred             HHHHHHHHHHhccccccc----------------------------------------------------cchhh-----
Confidence            999999998765311000                                                    00000     


Q ss_pred             hhhhhhccCCCCCCChHHHHHHHHHHHHHHHHHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHH
Q 009449          437 NAKYLEFAPDRSVKSPKEIVMRQHMKKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAM  516 (534)
Q Consensus       437 ~~~l~e~i~d~~~~spee~v~~~el~e~L~~~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL  516 (534)
                         .   .  ...++|++.+...+....|..+|..|||++++||.|+|    .+++|++|||+.||+|..+|++.++||+
T Consensus       105 ---~---~--~~~~~~~~~~~~~e~~~~l~~~l~~L~~~~r~i~~l~~----~~g~s~~EIAe~lgis~~~V~~~l~Ra~  172 (189)
T PRK06811        105 ---I---L--ISEESIENEIILKENKEEILKLINDLEKLDREIFIRRY----LLGEKIEEIAKKLGLTRSAIDNRLSRGR  172 (189)
T ss_pred             ---h---h--cccCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHH----HccCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence               0   0  01135677777777888899999999999999999999    8999999999999999999999999999


Q ss_pred             HHHHhHhhh
Q 009449          517 TKLRDSETC  525 (534)
Q Consensus       517 ~KLR~~l~~  525 (534)
                      ++||.....
T Consensus       173 ~~Lr~~~~~  181 (189)
T PRK06811        173 KKLQKNKLN  181 (189)
T ss_pred             HHHHHcccC
Confidence            999986543

>PRK12514 RNA polymerase sigma factor; Provisional

Probab=99.88  E-value=1.5e-21  Score=184.64  Aligned_cols=173  Identities=16%  Similarity=0.150  Sum_probs=141.5

Q ss_pred             CHHHHHHHHHhc-HHHHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCchhhHHHHHHHHHH
Q 009449          282 SERVLKQHLAFG-WYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSI  360 (534)
Q Consensus       282 d~~~L~~~l~~G-~~A~e~LI~~nlrLV~sIArrY~~~g~~~eDLiQEG~lgL~rA~ekFDp~kG~rFSTYA~~wIR~aI  360 (534)
                      +...|...+..| ..|+..|+..|.+.|+.+|.+|.++..+++|++||+|+++|+++++|++.. ..|.||++..++|.+
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            455667777777 779999999999999999999999999999999999999999999998754 369999999999999


Q ss_pred             HHHHHHhccccccccchHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHHhhhhcccccccccchhhhh
Q 009449          361 SKMVARHARGIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNAKY  440 (534)
Q Consensus       361 ~~~lr~~sr~iRlP~~~~~~i~ki~ka~~~L~~elGr~Pt~eEIA~~lgis~~kv~~~l~~~~~~~SLD~~i~~~~~~~l  440 (534)
                      .+++++..+. ..+                                                     ++.         .
T Consensus        84 ~d~~R~~~~~-~~~-----------------------------------------------------~~~---------~  100 (179)
T PRK12514         84 IDRLRARKAV-AVD-----------------------------------------------------IDE---------A  100 (179)
T ss_pred             HHHHHhcCCc-ccc-----------------------------------------------------ccc---------c
Confidence            9999875421 000                                                     000         0


Q ss_pred             hhccCCCCCCChHHHHHHHHHHHHHHHHHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 009449          441 LEFAPDRSVKSPKEIVMRQHMKKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLR  520 (534)
Q Consensus       441 ~e~i~d~~~~spee~v~~~el~e~L~~~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR  520 (534)
                      .+ ..+. ..+|++.+...+....|..+|..||+++++||.++|    ++|+|++|||+.||+|..+|++.++||+++||
T Consensus       101 ~~-~~~~-~~~~e~~~~~~~~~~~l~~~l~~L~~~~r~i~~l~~----~~g~s~~eIA~~lgis~~tV~~~l~Rar~~Lr  174 (179)
T PRK12514        101 HD-LADP-SPGPEAEVIAGDEGQRIDACLEELEKDRAAAVRRAY----LEGLSYKELAERHDVPLNTMRTWLRRSLLKLR  174 (179)
T ss_pred             hh-cccc-CCCHHHHHHhHHHHHHHHHHHHhCCHHHHHHHHHHH----HcCCCHHHHHHHHCCChHHHHHHHHHHHHHHH
Confidence            00 0111 135666666556666799999999999999999999    89999999999999999999999999999999


Q ss_pred             hHhh
Q 009449          521 DSET  524 (534)
Q Consensus       521 ~~l~  524 (534)
                      +++.
T Consensus       175 ~~l~  178 (179)
T PRK12514        175 ECLS  178 (179)
T ss_pred             HHhc
Confidence            9864

>PRK12519 RNA polymerase sigma factor; Provisional

Probab=99.88  E-value=1.6e-21  Score=186.78  Aligned_cols=175  Identities=22%  Similarity=0.207  Sum_probs=141.4

Q ss_pred             CHHHHHHHHHhc-HHHHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCchhhHHHHHHHHHH
Q 009449          282 SERVLKQHLAFG-WYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSI  360 (534)
Q Consensus       282 d~~~L~~~l~~G-~~A~e~LI~~nlrLV~sIArrY~~~g~~~eDLiQEG~lgL~rA~ekFDp~kG~rFSTYA~~wIR~aI  360 (534)
                      +...|...+..| ..|++.|+..|.+.|+++++++.++..+++|++||+|+++|+. ..|++..+ .|.||++.++++.+
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            456677777777 7899999999999999999999999999999999999999976 67887654 79999999999999


Q ss_pred             HHHHHHhccccccccchHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHHhhhhcccccccccchhhhh
Q 009449          361 SKMVARHARGIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNAKY  440 (534)
Q Consensus       361 ~~~lr~~sr~iRlP~~~~~~i~ki~ka~~~L~~elGr~Pt~eEIA~~lgis~~kv~~~l~~~~~~~SLD~~i~~~~~~~l  440 (534)
                      +++++++.+..... +                                                  ..+.        ..
T Consensus        93 ~d~~Rk~~~~~~~~-~--------------------------------------------------~~~~--------~~  113 (194)
T PRK12519         93 IDRLRSRRSRQRLL-E--------------------------------------------------RWQQ--------EL  113 (194)
T ss_pred             HHHHHhcccccchh-h--------------------------------------------------hhhh--------hh
Confidence            99998764311000 0                                                  0000        00


Q ss_pred             hhccCCCCCCChHHHHHHHHHHHHHHHHHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 009449          441 LEFAPDRSVKSPKEIVMRQHMKKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLR  520 (534)
Q Consensus       441 ~e~i~d~~~~spee~v~~~el~e~L~~~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR  520 (534)
                         ..+....+|++.+...+....|..+|..||+++++||.|+|    .+++|++|||+.||+|.++|+++++||+++||
T Consensus       114 ---~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~~~v~~l~~----~~g~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr  186 (194)
T PRK12519        114 ---LGEASEDTPLEQASLAERSQRVQTALAQLPESQRQVLELAY----YEGLSQSEIAKRLGIPLGTVKARARQGLLKLR  186 (194)
T ss_pred             ---cccccCCCHHHHHHHHHHHHHHHHHHHhCCHHHhhhhhhhh----hcCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Confidence               00011134666666667777899999999999999999999    89999999999999999999999999999999


Q ss_pred             hHhh
Q 009449          521 DSET  524 (534)
Q Consensus       521 ~~l~  524 (534)
                      +.+.
T Consensus       187 ~~l~  190 (194)
T PRK12519        187 ELLQ  190 (194)
T ss_pred             HHHH
Confidence            8764

>TIGR02939 RpoE_Sigma70 RNA polymerase sigma factor RpoE

Probab=99.88  E-value=3.3e-21  Score=183.10  Aligned_cols=181  Identities=15%  Similarity=0.182  Sum_probs=144.5

Q ss_pred             CHHHHHHHHHhc-HHHHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCchhhHHHHHHHHHH
Q 009449          282 SERVLKQHLAFG-WYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSI  360 (534)
Q Consensus       282 d~~~L~~~l~~G-~~A~e~LI~~nlrLV~sIArrY~~~g~~~eDLiQEG~lgL~rA~ekFDp~kG~rFSTYA~~wIR~aI  360 (534)
                      ++..|...+..| ..|++.|+..|.+.|+.+|+++.++..+++|++||+++++|+++.+|++.  ..|.+|++..+++.+
T Consensus         6 ~d~~l~~~~~~gd~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeDlvQe~fi~l~~~~~~~~~~--~~~~~wl~~iarn~~   83 (190)
T TIGR02939         6 LDLELVERVQRGEKQAFDLLVRKYQHKVVALVGRYVRDSSEVEDVAQEAFVKAYRALSSFRGD--SAFYTWLYRIAVNTA   83 (190)
T ss_pred             cHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHhCCHhhHHHHHHHHHHHHHHhHHhcCCC--CccHhHHHHHHHHHH
Confidence            456677777777 67999999999999999999999999999999999999999999999975  369999999999999


Q ss_pred             HHHHHHhccccccccchHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHHhhhhcccccccccchhhhh
Q 009449          361 SKMVARHARGIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNAKY  440 (534)
Q Consensus       361 ~~~lr~~sr~iRlP~~~~~~i~ki~ka~~~L~~elGr~Pt~eEIA~~lgis~~kv~~~l~~~~~~~SLD~~i~~~~~~~l  440 (534)
                      .+++++..+......                                                  .+.+..      ..+
T Consensus        84 ~~~~r~~~r~~~~~~--------------------------------------------------~~~~~~------~~~  107 (190)
T TIGR02939        84 KNHLVAQGRRPPTSD--------------------------------------------------VEIEDA------EHF  107 (190)
T ss_pred             HHHHHHhccCCCccc--------------------------------------------------ccccch------hhh
Confidence            999986543211000                                                  000000      000


Q ss_pred             hhccCCCCCCChHHHHHHHHHHHHHHHHHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 009449          441 LEFAPDRSVKSPKEIVMRQHMKKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLR  520 (534)
Q Consensus       441 ~e~i~d~~~~spee~v~~~el~e~L~~~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR  520 (534)
                      .+........+|++.+...+....+..+|..||+++++||.++|    .+++|++|||+.||+|..+|++.++||+++||
T Consensus       108 ~~~~~~~~~~~~e~~~~~~~~~~~l~~~l~~L~~~~r~v~~l~~----~~~~s~~EIA~~lgis~~tv~~~l~rar~~Lr  183 (190)
T TIGR02939       108 EGADRLREIDTPERLLLSRELEQTVMRAVEALPEDLRTAITLRE----LEGLSYEDIARIMDCPVGTVRSRIFRAREAIA  183 (190)
T ss_pred             cccccccccCChHHHHHHHHHHHHHHHHHHcCCHHHhhhhhhhh----hcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHH
Confidence            00000011235777777777888899999999999999999999    89999999999999999999999999999999


Q ss_pred             hHhh
Q 009449          521 DSET  524 (534)
Q Consensus       521 ~~l~  524 (534)
                      +++.
T Consensus       184 ~~l~  187 (190)
T TIGR02939       184 IRLR  187 (190)
T ss_pred             HHhh
Confidence            9875

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

>PRK12537 RNA polymerase sigma factor; Provisional

Probab=99.88  E-value=2.5e-21  Score=184.22  Aligned_cols=173  Identities=17%  Similarity=0.179  Sum_probs=140.4

Q ss_pred             CCHHHHHHHHHhc-HHHHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCchhhHHHHHHHHH
Q 009449          281 VSERVLKQHLAFG-WYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKS  359 (534)
Q Consensus       281 ~d~~~L~~~l~~G-~~A~e~LI~~nlrLV~sIArrY~~~g~~~eDLiQEG~lgL~rA~ekFDp~kG~rFSTYA~~wIR~a  359 (534)
                      ++...|...+..| ..|++.|+..|.+.|+.++.++.++..+++|++||+|+.+|+..++|++..+ .|.+|++..++|.
T Consensus         8 ~~~~~l~~~~~~~d~~a~~~l~~~~~~~l~~~~~~~~~~~~~AeDivQe~fl~l~~~~~~~~~~~~-~~~~wL~~iarn~   86 (182)
T PRK12537          8 FDYEACLLACARGDRRALQALYQQESARLLGVARRIVRDRALAEDIVHDAFIKIWTGAASFDPARG-SARGWIYSVTRHL   86 (182)
T ss_pred             hhHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHhCCHhHHHHHHHHHHHHHHhccccCCcccc-cHHHHHHHHHHHH
Confidence            3456677777777 7899999999999999999999999999999999999999999999986443 7999999999999


Q ss_pred             HHHHHHHhccccccccchHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHHhhhhcccccccccchhhh
Q 009449          360 ISKMVARHARGIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNAK  439 (534)
Q Consensus       360 I~~~lr~~sr~iRlP~~~~~~i~ki~ka~~~L~~elGr~Pt~eEIA~~lgis~~kv~~~l~~~~~~~SLD~~i~~~~~~~  439 (534)
                      +.+++++..+....                                                       +..   .  . 
T Consensus        87 ~~d~~r~~~~~~~~-------------------------------------------------------~~~---~--~-  105 (182)
T PRK12537         87 ALNVLRDTRREVVL-------------------------------------------------------DDD---A--E-  105 (182)
T ss_pred             HHHHHHhccccCcc-------------------------------------------------------ccc---h--h-
Confidence            99999876421100                                                       000   0  0 


Q ss_pred             hhhccCCCCCCChHHHHHHHHHHHHHHHHHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Q 009449          440 YLEFAPDRSVKSPKEIVMRQHMKKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKL  519 (534)
Q Consensus       440 l~e~i~d~~~~spee~v~~~el~e~L~~~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KL  519 (534)
                        +...+  ..++++.....+....|..+|+.|||++|+||.++|    .+++|++|||+.||||.++|++.++||+++|
T Consensus       106 --~~~~~--~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~i~~l~~----~~~~s~~eIA~~lgis~~tV~~~l~ra~~~L  177 (182)
T PRK12537        106 --ETAQT--LHEIIDDFDLWANSGKIHRCLEQLEPARRNCILHAY----VDGCSHAEIAQRLGAPLGTVKAWIKRSLKAL  177 (182)
T ss_pred             --hhccc--ccchHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHH----HcCCCHHHHHHHHCCChhhHHHHHHHHHHHH
Confidence              00000  113334444445566899999999999999999999    8999999999999999999999999999999


Q ss_pred             HhHh
Q 009449          520 RDSE  523 (534)
Q Consensus       520 R~~l  523 (534)
                      |.++
T Consensus       178 r~~l  181 (182)
T PRK12537        178 RECM  181 (182)
T ss_pred             HHHh
Confidence            9875

>PRK09652 RNA polymerase sigma factor RpoE; Provisional

Probab=99.88  E-value=1.8e-21  Score=182.43  Aligned_cols=173  Identities=18%  Similarity=0.190  Sum_probs=139.1

Q ss_pred             HHhc-HHHHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCchhhHHHHHHHHHHHHHHHHhc
Q 009449          290 LAFG-WYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHA  368 (534)
Q Consensus       290 l~~G-~~A~e~LI~~nlrLV~sIArrY~~~g~~~eDLiQEG~lgL~rA~ekFDp~kG~rFSTYA~~wIR~aI~~~lr~~s  368 (534)
                      ++.| ..|+++|+..|.++|+.++++|.+++.+.+|++||+++++|+++.+|+  .+.+|.||++.++++.+.+.+++..
T Consensus         4 ~~~gd~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeDl~Qe~~l~l~~~~~~~~--~~~~~~~~l~~~~~~~~~~~~r~~~   81 (182)
T PRK09652          4 VQRGDRAAFALLVRRYQPRVKRLLSRLTRDPADAEDLVQETFIKAYRALHSFR--GGAAFYTWLYRIARNTAINYLRKQG   81 (182)
T ss_pred             hhcCCHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHhcC--CCcchHHHHHHHHHHHHHHHHHccc
Confidence            4555 679999999999999999999999999999999999999999999999  3458999999999999999998764


Q ss_pred             cccccccchHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHHhhhhcccccccccchhhhhhhccCCCC
Q 009449          369 RGIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNAKYLEFAPDRS  448 (534)
Q Consensus       369 r~iRlP~~~~~~i~ki~ka~~~L~~elGr~Pt~eEIA~~lgis~~kv~~~l~~~~~~~SLD~~i~~~~~~~l~e~i~d~~  448 (534)
                      +....+.                                                  .+.+    +.++....+...+  
T Consensus        82 ~~~~~~~--------------------------------------------------~~~~----~~~~~~~~~~~~~--  105 (182)
T PRK09652         82 RRPPASD--------------------------------------------------VDAE----EAEDFDLADALRD--  105 (182)
T ss_pred             CCCCccc--------------------------------------------------cccc----ccccccccccccc--
Confidence            3211100                                                  0000    0000001111111  


Q ss_pred             CCChHHHHHHHHHHHHHHHHHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHhh
Q 009449          449 VKSPKEIVMRQHMKKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDSET  524 (534)
Q Consensus       449 ~~spee~v~~~el~e~L~~~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~~l~  524 (534)
                      ..+|++.+...+....+..+|..|||++++||.++|    ..++|++|||+.||+|+.+|++.+++|+++||+.+.
T Consensus       106 ~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~vl~l~~----~~~~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~l~  177 (182)
T PRK09652        106 ISTPENELLSAELEQRVRAAIESLPEELRTAITLRE----IEGLSYEEIAEIMGCPIGTVRSRIFRAREALRAKLQ  177 (182)
T ss_pred             ccChHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHH----HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence            135777777777888999999999999999999999    899999999999999999999999999999998765

>PRK13919 putative RNA polymerase sigma E protein; Provisional

Probab=99.88  E-value=2.4e-21  Score=184.13  Aligned_cols=176  Identities=20%  Similarity=0.246  Sum_probs=137.1

Q ss_pred             CCHHHHHHHHHhc-HHHHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCchhhHHHHHHHHH
Q 009449          281 VSERVLKQHLAFG-WYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKS  359 (534)
Q Consensus       281 ~d~~~L~~~l~~G-~~A~e~LI~~nlrLV~sIArrY~~~g~~~eDLiQEG~lgL~rA~ekFDp~kG~rFSTYA~~wIR~a  359 (534)
                      +++..|...+..| ..|++.++..|.+.|+.+|++|.+++.+++|++||+++.+|++.++|++..+ .|.+|++..++|.
T Consensus         8 ~~~~~l~~~~~~~d~~a~~~l~~~y~~~l~~~~~~~~~~~~~aeDlvQe~~i~l~~~~~~~~~~~~-~~~~wl~~ia~n~   86 (186)
T PRK13919          8 LSDEALLALVARGEEEALRALFRRYAGAFLALARRMGLDGAAAEDVVQEVFIRVWKKAKEFDPRRG-SARAWLLALAHHA   86 (186)
T ss_pred             cCHHHHHHHHHcCcHHHHHHHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHhhhccCcccc-chHHHHHHHHHHH
Confidence            3566777777777 7899999999999999999999999999999999999999999999987643 6999999999999


Q ss_pred             HHHHHHHhccccccccchHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHHhhhhcccccccccchhhh
Q 009449          360 ISKMVARHARGIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNAK  439 (534)
Q Consensus       360 I~~~lr~~sr~iRlP~~~~~~i~ki~ka~~~L~~elGr~Pt~eEIA~~lgis~~kv~~~l~~~~~~~SLD~~i~~~~~~~  439 (534)
                      +.+++++..+... +.                                                   +.+.    . +..
T Consensus        87 ~~d~~rk~~~~~~-~~---------------------------------------------------~~~~----~-~~~  109 (186)
T PRK13919         87 AVDHVRRRAARPQ-PL---------------------------------------------------EPDE----R-EPE  109 (186)
T ss_pred             HHHHHHhhhcccc-cc---------------------------------------------------cccc----c-ccc
Confidence            9999987642100 00                                                   0000    0 000


Q ss_pred             hhhccCCCCCCChHHHHHHHHHHHHHHHHHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Q 009449          440 YLEFAPDRSVKSPKEIVMRQHMKKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKL  519 (534)
Q Consensus       440 l~e~i~d~~~~spee~v~~~el~e~L~~~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KL  519 (534)
                      ..+ .++     +..........+.|..++..||+++++||.++|    .+++|++|||+.||+|..+|+..++||+++|
T Consensus       110 ~~~-~~~-----~~~~~~~~~~~~~l~~~l~~L~~~~r~vl~l~~----~~~~s~~eIA~~lgis~~~V~~~l~ra~~~L  179 (186)
T PRK13919        110 AFD-LPG-----PGLDEEGHLDRTRLGRALKALSPEERRVIEVLY----YQGYTHREAAQLLGLPLGTLKTRARRALSRL  179 (186)
T ss_pred             ccc-CCC-----ccccHHHHHHHHHHHHHHHhCCHHHHHHHHHHH----HcCCCHHHHHHHHCcCHHHHHHHHHHHHHHH
Confidence            000 011     111112223345789999999999999999999    8999999999999999999999999999999


Q ss_pred             HhHhh
Q 009449          520 RDSET  524 (534)
Q Consensus       520 R~~l~  524 (534)
                      |..+.
T Consensus       180 r~~l~  184 (186)
T PRK13919        180 KEVLR  184 (186)
T ss_pred             HHHhc
Confidence            98764

>PRK11923 algU RNA polymerase sigma factor AlgU; Provisional

Probab=99.88  E-value=5e-21  Score=183.18  Aligned_cols=179  Identities=16%  Similarity=0.158  Sum_probs=144.2

Q ss_pred             HHHHHHHHHhc-HHHHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCchhhHHHHHHHHHHH
Q 009449          283 ERVLKQHLAFG-WYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSIS  361 (534)
Q Consensus       283 ~~~L~~~l~~G-~~A~e~LI~~nlrLV~sIArrY~~~g~~~eDLiQEG~lgL~rA~ekFDp~kG~rFSTYA~~wIR~aI~  361 (534)
                      .+.|...++.| ..|++.|+..|.+.|+.++++|.++..+++|++||+++++|+++.+|++..  .|.+|++..+++.+.
T Consensus         7 ~~~ll~~~~~gd~~a~~~l~~~y~~~l~~~~~~~~~~~~daeDlvQe~~i~l~~~~~~~~~~~--~~~~wl~~ia~n~~~   84 (193)
T PRK11923          7 DQQLVERVQRGDKRAFDLLVLKYQHKILGLIVRFVHDTAEAQDVAQEAFIKAYRALGNFRGDS--AFYTWLYRIAINTAK   84 (193)
T ss_pred             HHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHhCCHhhHHHHHHHHHHHHHHhHhCcCCCC--ccHhHHHHHHHHHHH
Confidence            45667777777 779999999999999999999999999999999999999999999999874  599999999999999


Q ss_pred             HHHHHhccccccccchHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHHhhhhcccccc-cccchhhhh
Q 009449          362 KMVARHARGIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQK-IGDCLNAKY  440 (534)
Q Consensus       362 ~~lr~~sr~iRlP~~~~~~i~ki~ka~~~L~~elGr~Pt~eEIA~~lgis~~kv~~~l~~~~~~~SLD~~-i~~~~~~~l  440 (534)
                      ++++++.+......                                                  ..++.. ...+ .   
T Consensus        85 d~~rk~~~~~~~~~--------------------------------------------------~~~~~~~~~~~-~---  110 (193)
T PRK11923         85 NHLVSRGRRPPDSD--------------------------------------------------VSSEDAEFYDG-D---  110 (193)
T ss_pred             HHHHHhcCCCcccc--------------------------------------------------ccccchhhhcc-c---
Confidence            99987643211000                                                  000000 0000 0   


Q ss_pred             hhccCCCCCCChHHHHHHHHHHHHHHHHHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 009449          441 LEFAPDRSVKSPKEIVMRQHMKKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLR  520 (534)
Q Consensus       441 ~e~i~d~~~~spee~v~~~el~e~L~~~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR  520 (534)
                       ..+.  ...+|++.+...+..+.+..+|..||+++|+||.++|    .+|+|++|||+.||+|..+|++.+.||+++||
T Consensus       111 -~~~~--~~~~~e~~~~~~~~~~~l~~~l~~L~~~~r~v~~l~~----~~g~s~~eIA~~lgis~~tv~~~l~Rar~~Lr  183 (193)
T PRK11923        111 -HALK--DIESPERALLRDEIEGTVHRTIQQLPEDLRTALTLRE----FDGLSYEDIASVMQCPVGTVRSRIFRAREAID  183 (193)
T ss_pred             -cccc--CcCCHHHHHHHHHHHHHHHHHHHhCCHHHhHHHhhHH----hcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence             0011  1236777777778888999999999999999999999    89999999999999999999999999999999


Q ss_pred             hHhh
Q 009449          521 DSET  524 (534)
Q Consensus       521 ~~l~  524 (534)
                      .++.
T Consensus       184 ~~l~  187 (193)
T PRK11923        184 KALQ  187 (193)
T ss_pred             HHHH
Confidence            9875

>PRK12524 RNA polymerase sigma factor; Provisional

Probab=99.88  E-value=4.2e-21  Score=184.87  Aligned_cols=177  Identities=20%  Similarity=0.202  Sum_probs=146.3

Q ss_pred             CCHHHHHHHHHhc-HHHHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCchhhHHHHHHHHH
Q 009449          281 VSERVLKQHLAFG-WYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKS  359 (534)
Q Consensus       281 ~d~~~L~~~l~~G-~~A~e~LI~~nlrLV~sIArrY~~~g~~~eDLiQEG~lgL~rA~ekFDp~kG~rFSTYA~~wIR~a  359 (534)
                      +++..|+..+..| ..|++.|+..|.+.|+.+|.++.++..+++|++||+++.+|+...+|++.. ..|.||++..+++.
T Consensus        11 ~~~~~li~~~~~gd~~a~~~l~~~y~~~l~~~~~~~~~~~~~AeDlvQe~~l~l~~~~~~~~~~~-~~~~~wl~~ia~n~   89 (196)
T PRK12524         11 VSDEALLVLYANGDPAAARALTLRLAPRALAVATRVLGDRAEAEDVTQEAMLRLWRIAPDWRQGE-ARVSTWLYRVVCNL   89 (196)
T ss_pred             cCHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhhhcccccc-chHHHHHHHHHHHH
Confidence            4567788888877 789999999999999999999999999999999999999999999998533 37999999999999


Q ss_pred             HHHHHHHhccccccccchHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHHhhhhcccccccccchhhh
Q 009449          360 ISKMVARHARGIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNAK  439 (534)
Q Consensus       360 I~~~lr~~sr~iRlP~~~~~~i~ki~ka~~~L~~elGr~Pt~eEIA~~lgis~~kv~~~l~~~~~~~SLD~~i~~~~~~~  439 (534)
                      +.+.++++.+.. .                                                     .++.. .      
T Consensus        90 ~~d~~Rk~~~~~-~-----------------------------------------------------~~~~~-~------  108 (196)
T PRK12524         90 CTDRLRRRRRAS-V-----------------------------------------------------DLDDA-P------  108 (196)
T ss_pred             HHHHHHhhcCCC-C-----------------------------------------------------Ccccc-c------
Confidence            999998753210 0                                                     00000 0      


Q ss_pred             hhhccCCCCCCChHHHHHHHHHHHHHHHHHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Q 009449          440 YLEFAPDRSVKSPKEIVMRQHMKKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKL  519 (534)
Q Consensus       440 l~e~i~d~~~~spee~v~~~el~e~L~~~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KL  519 (534)
                        + ..+. ..+|++.+...+....|..+|+.||+++|+||.|+|    .++++++|||+.||||..+|+++++||+++|
T Consensus       109 --~-~~~~-~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~i~~L~~----~~g~s~~eIA~~lgis~~tV~~~l~Ra~~~L  180 (196)
T PRK12524        109 --E-PADA-APGAEEALIEGDRMRALDAALAALPERQRQAVVLRH----IEGLSNPEIAEVMEIGVEAVESLTARGKRAL  180 (196)
T ss_pred             --c-cccc-CCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHH----HcCCCHHHHHHHHCcCHHHHHHHHHHHHHHH
Confidence              0 0011 124666677777778899999999999999999999    8999999999999999999999999999999


Q ss_pred             HhHhhhhc
Q 009449          520 RDSETCRD  527 (534)
Q Consensus       520 R~~l~~~~  527 (534)
                      |..+...+
T Consensus       181 r~~l~~~~  188 (196)
T PRK12524        181 AALLAGQR  188 (196)
T ss_pred             HHHHHhcc
Confidence            99886533

>PRK06759 RNA polymerase factor sigma-70; Validated

Probab=99.88  E-value=1.5e-21  Score=179.75  Aligned_cols=150  Identities=18%  Similarity=0.269  Sum_probs=124.2

Q ss_pred             HHHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCchhhHHHHHHHHHHHHHHHHhccccccc
Q 009449          295 YCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIP  374 (534)
Q Consensus       295 ~A~e~LI~~nlrLV~sIArrY~~~g~~~eDLiQEG~lgL~rA~ekFDp~kG~rFSTYA~~wIR~aI~~~lr~~sr~iRlP  374 (534)
                      .|++.|++.|.++|+.+++++ ++..+++|++||+++++|+++++|++..| .|.+|++..+++.+.++++++.+..   
T Consensus         4 ~af~~l~~~y~~~l~~~~~~~-~~~~~aeDi~Qe~~l~l~~~~~~~~~~~~-~f~~wl~~i~~n~~ld~~rk~~~~~---   78 (154)
T PRK06759          4 ATFTEAVVLYEGLIVNQIKKL-GIYQDYEEYYQCGLIGLWHAYERYDEKKG-SFPAYAVVTVRGYILERLKKEFAVQ---   78 (154)
T ss_pred             ccHHHHHHHHHHHHHHHHHHh-CCcccHHHHHHHHHHHHHHHHHHhCccCC-chHHHHHHHHHHHHHHHHHHHHhhc---
Confidence            589999999999999999986 56689999999999999999999998766 7999999999999999998763100   


Q ss_pred             cchHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHHhhhhcccccccccchhhhhhhccCCCCCCChHH
Q 009449          375 CKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNAKYLEFAPDRSVKSPKE  454 (534)
Q Consensus       375 ~~~~~~i~ki~ka~~~L~~elGr~Pt~eEIA~~lgis~~kv~~~l~~~~~~~SLD~~i~~~~~~~l~e~i~d~~~~spee  454 (534)
                       .                 .                              . . +                +   ++|++
T Consensus        79 -~-----------------~------------------------------~-~-~----------------~---~~~~~   89 (154)
T PRK06759         79 -E-----------------K------------------------------C-V-C----------------V---GEYED   89 (154)
T ss_pred             -c-----------------c------------------------------c-c-c----------------c---CCCcc
Confidence             0                 0                              0 0 0                0   01122


Q ss_pred             HHHHHHHHHHHHHHHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhH
Q 009449          455 IVMRQHMKKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDS  522 (534)
Q Consensus       455 ~v~~~el~e~L~~~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~~  522 (534)
                      .+...+....|..++..|||++|+||.++|    ++++|++|||+.||+|.++|+++++||+++||+.
T Consensus        90 ~~~~~~~~~~l~~~l~~L~~~~r~ii~l~~----~~~~s~~EIA~~l~is~~tV~~~~~ra~~~Lr~~  153 (154)
T PRK06759         90 HFHFEDVEMKVKDFMSVLDEKEKYIIFERF----FVGKTMGEIALETEMTYYQVRWIYRQALEKMRNS  153 (154)
T ss_pred             cccHHHHHHHHHHHHHhCCHHHHHHHHHHH----hcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHhhc
Confidence            222334456799999999999999999999    8999999999999999999999999999999964

>PRK12534 RNA polymerase sigma factor; Provisional

Probab=99.87  E-value=3.9e-21  Score=183.07  Aligned_cols=174  Identities=16%  Similarity=0.149  Sum_probs=139.7

Q ss_pred             HHHHHHHHHhc-HHHHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCchhhHHHHHHHHHHH
Q 009449          283 ERVLKQHLAFG-WYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSIS  361 (534)
Q Consensus       283 ~~~L~~~l~~G-~~A~e~LI~~nlrLV~sIArrY~~~g~~~eDLiQEG~lgL~rA~ekFDp~kG~rFSTYA~~wIR~aI~  361 (534)
                      ...+...+..| ..+++.++..|.++|+.+|++|.++..+++|++||+|+.+|++.++|++.++ .|.||++..++|.+.
T Consensus        12 ~~~l~~~~~~~~~~~~~~l~~~y~~~l~~~~~~~~~~~~~aeDlvQe~fl~~~~~~~~~~~~~~-~~~~wl~~I~~n~~~   90 (187)
T PRK12534         12 TGRLLTATAGGDRHAFEALYRQTSPKLFGVCLRMIPQRAEAEEVLQDVFTLIWHKAGQFDPSRA-RGLTWLAMIARNKAI   90 (187)
T ss_pred             HHHHHHHHHcCCHHHHHHHHHHhhHHHHHHHHHHhcCHHHHHHHHHHHHHHHHhccccCCcccc-cHHHHHHHHHHHHHH
Confidence            34455555556 7899999999999999999999999999999999999999999999998654 688999999999999


Q ss_pred             HHHHHhccccccccchHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHHhhhhcccccccccchhhhhh
Q 009449          362 KMVARHARGIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNAKYL  441 (534)
Q Consensus       362 ~~lr~~sr~iRlP~~~~~~i~ki~ka~~~L~~elGr~Pt~eEIA~~lgis~~kv~~~l~~~~~~~SLD~~i~~~~~~~l~  441 (534)
                      +++++..+....                                                    .++|..         .
T Consensus        91 d~~R~~~~~~~~----------------------------------------------------~~~~~~---------~  109 (187)
T PRK12534         91 DHLRANAPQRRN----------------------------------------------------VALDDA---------G  109 (187)
T ss_pred             HHHHhccccccc----------------------------------------------------ccccch---------h
Confidence            999876421000                                                    001100         0


Q ss_pred             hccCCCCCCChHHHHHHHHHHHHHHHHHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHh
Q 009449          442 EFAPDRSVKSPKEIVMRQHMKKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRD  521 (534)
Q Consensus       442 e~i~d~~~~spee~v~~~el~e~L~~~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~  521 (534)
                      +. .++ ..+|++.....+....+..+|..||+++++|+.++|    .+++|++|||+.||+|.++|+++++||+++||.
T Consensus       110 ~~-~~~-~~~~~~~~~~~e~~~~l~~~l~~L~~~~r~i~~l~~----~~g~s~~eIA~~lgis~~~v~~~l~Rar~~Lr~  183 (187)
T PRK12534        110 EL-RAA-DASPLERTERASTRRRIDHCLAELEPPRSELIRTAF----FEGITYEELAARTDTPIGTVKSWIRRGLAKLKA  183 (187)
T ss_pred             hh-ccc-cCChhhHHHHHHHHHHHHHHHHhCCHHHHHHHHHHH----HcCCCHHHHHHHhCCChhHHHHHHHHHHHHHHH
Confidence            00 001 123445555566778899999999999999999999    899999999999999999999999999999998


Q ss_pred             Hhh
Q 009449          522 SET  524 (534)
Q Consensus       522 ~l~  524 (534)
                      .+.
T Consensus       184 ~l~  186 (187)
T PRK12534        184 CLE  186 (187)
T ss_pred             HHc
Confidence            764

>PRK12538 RNA polymerase sigma factor; Provisional

Probab=99.87  E-value=5.3e-21  Score=190.10  Aligned_cols=174  Identities=18%  Similarity=0.234  Sum_probs=142.7

Q ss_pred             CHHHHHHHHHhc-HHHHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCchhhHHHHHHHHHH
Q 009449          282 SERVLKQHLAFG-WYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSI  360 (534)
Q Consensus       282 d~~~L~~~l~~G-~~A~e~LI~~nlrLV~sIArrY~~~g~~~eDLiQEG~lgL~rA~ekFDp~kG~rFSTYA~~wIR~aI  360 (534)
                      ++..|...+..| ..|++.|+..|.+.|+++++++.++..+++|++||+|+.+|++.++|++..+ .|.+|++..++|.+
T Consensus        49 ~d~~Li~~~~~gd~~af~~L~~~y~~~l~~~~~~~~~d~~dAEDivQEvfl~l~~~~~~~~~~~~-~f~~WL~~IarN~~  127 (233)
T PRK12538         49 EDEELLDRLATDDEAAFRLLVERHIDRAYAIALRIVGNRADAEDVVQDTMLKVWTHRGRWQHGRA-KFSTWLYRVVSNRC  127 (233)
T ss_pred             cHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHcccccc-cHHHHHHHHHHHHH
Confidence            455666777777 7799999999999999999999999999999999999999999999987544 79999999999999


Q ss_pred             HHHHHHhccccccccchHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHHhhhhcccccccccchhhhh
Q 009449          361 SKMVARHARGIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNAKY  440 (534)
Q Consensus       361 ~~~lr~~sr~iRlP~~~~~~i~ki~ka~~~L~~elGr~Pt~eEIA~~lgis~~kv~~~l~~~~~~~SLD~~i~~~~~~~l  440 (534)
                      +++++++.+. .+  .                                                  .++.          
T Consensus       128 id~~Rk~~~~-~~--~--------------------------------------------------~~~~----------  144 (233)
T PRK12538        128 IDLRRKPRTE-NV--D--------------------------------------------------AVPE----------  144 (233)
T ss_pred             HHHHHhhccc-cc--c--------------------------------------------------cccc----------
Confidence            9998764210 00  0                                                  0000          


Q ss_pred             hhccCCCCCCChHHHHHHHHHHHHHHHHHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 009449          441 LEFAPDRSVKSPKEIVMRQHMKKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLR  520 (534)
Q Consensus       441 ~e~i~d~~~~spee~v~~~el~e~L~~~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR  520 (534)
                        . .+ ...++++.+...+..+.|..+|..||+++|+||.|+|    .+++|++|||+.||+|.++|+++++||+++||
T Consensus       145 --~-~~-~~~~~~~~~~~~e~~~~l~~~L~~Lp~~~R~v~~L~~----~eg~s~~EIA~~Lgis~~tVk~~l~RAr~kLr  216 (233)
T PRK12538        145 --V-AD-GKPDAVSVIERNELSDLLEAAMQRLPEQQRIAVILSY----HENMSNGEIAEVMDTTVAAVESLLKRGRQQLR  216 (233)
T ss_pred             --c-cc-CCCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHhhhHH----hcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHH
Confidence              0 00 1124455566667777899999999999999999999    89999999999999999999999999999999


Q ss_pred             hHhhhhc
Q 009449          521 DSETCRD  527 (534)
Q Consensus       521 ~~l~~~~  527 (534)
                      +.+....
T Consensus       217 ~~l~~~~  223 (233)
T PRK12538        217 DLLRRHE  223 (233)
T ss_pred             HHHHHhh
Confidence            9886544

>PRK12526 RNA polymerase sigma factor; Provisional

Probab=99.87  E-value=8.3e-21  Score=184.63  Aligned_cols=178  Identities=15%  Similarity=0.118  Sum_probs=137.5

Q ss_pred             HHHHHHHHhc-HHHHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCchhhHHHHHHHHHHHH
Q 009449          284 RVLKQHLAFG-WYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISK  362 (534)
Q Consensus       284 ~~L~~~l~~G-~~A~e~LI~~nlrLV~sIArrY~~~g~~~eDLiQEG~lgL~rA~ekFDp~kG~rFSTYA~~wIR~aI~~  362 (534)
                      ..|...+..| ..|+++|+..|.+.|+.++.++.++..+++|++||+|+.+|+++..|++.++ .|.||++.++||.+++
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            3345555555 7899999999999999999999999899999999999999999999998765 6999999999999999


Q ss_pred             HHHHhccccccccchHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHHhhhhcccccccccchhhhhhh
Q 009449          363 MVARHARGIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNAKYLE  442 (534)
Q Consensus       363 ~lr~~sr~iRlP~~~~~~i~ki~ka~~~L~~elGr~Pt~eEIA~~lgis~~kv~~~l~~~~~~~SLD~~i~~~~~~~l~e  442 (534)
                      ++++..+......                         .+++                     .+            ..+
T Consensus       105 ~~Rk~~~~~~~~~-------------------------~~~~---------------------~~------------~~~  126 (206)
T PRK12526        105 MLRKIKAKKEQNL-------------------------GDDI---------------------WP------------IEQ  126 (206)
T ss_pred             HHHHhcccccccc-------------------------cccc---------------------ch------------hhh
Confidence            9987643110000                         0000                     00            000


Q ss_pred             ccCCCCCCChHHHHHHHHHHHHHHHHHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhH
Q 009449          443 FAPDRSVKSPKEIVMRQHMKKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDS  522 (534)
Q Consensus       443 ~i~d~~~~spee~v~~~el~e~L~~~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~~  522 (534)
                      .+.+.. ..+. ..........|..+|..||+++++||.++|    ++++|++|||+.||+|..+|+..++||+++||..
T Consensus       127 ~~~~~~-~~~~-~~~~~~~~~~l~~~l~~L~~~~r~vl~l~~----~~g~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~  200 (206)
T PRK12526        127 ALAESQ-SESE-EFSDHLMDKQILSYIEKLPEAQQTVVKGVY----FQELSQEQLAQQLNVPLGTVKSRLRLALAKLKVQ  200 (206)
T ss_pred             hccccc-CchH-HHHHHHHHHHHHHHHHhCCHHHHHHHHHHH----HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence            011111 1222 232333446799999999999999999999    8999999999999999999999999999999998


Q ss_pred             hhhh
Q 009449          523 ETCR  526 (534)
Q Consensus       523 l~~~  526 (534)
                      +...
T Consensus       201 l~~~  204 (206)
T PRK12526        201 MGEQ  204 (206)
T ss_pred             Hhhc
Confidence            8643

>PRK11922 RNA polymerase sigma factor; Provisional

Probab=99.87  E-value=9.7e-21  Score=187.38  Aligned_cols=184  Identities=18%  Similarity=0.189  Sum_probs=147.8

Q ss_pred             CCHHHHHHHHHhc-HHHHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCchhhHHHHHHHHH
Q 009449          281 VSERVLKQHLAFG-WYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKS  359 (534)
Q Consensus       281 ~d~~~L~~~l~~G-~~A~e~LI~~nlrLV~sIArrY~~~g~~~eDLiQEG~lgL~rA~ekFDp~kG~rFSTYA~~wIR~a  359 (534)
                      +++..|...+..| ..|++.++..|.+.|+++|+++.++..+++|++||+|+++|+++++|++.  ..|.+|++..+++.
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            4456677777777 78999999999999999999999999999999999999999999999986  37999999999999


Q ss_pred             HHHHHHHhccccccccchHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHHhhhhcccccccccchhhh
Q 009449          360 ISKMVARHARGIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNAK  439 (534)
Q Consensus       360 I~~~lr~~sr~iRlP~~~~~~i~ki~ka~~~L~~elGr~Pt~eEIA~~lgis~~kv~~~l~~~~~~~SLD~~i~~~~~~~  439 (534)
                      +.+++++..+....+..                                                  ..+.... + +  
T Consensus        93 ~~d~~Rk~~r~~~~~~~--------------------------------------------------~~~~~~~-~-~--  118 (231)
T PRK11922         93 ALGRLRRRRRLVNLAEM--------------------------------------------------VMASTIA-G-G--  118 (231)
T ss_pred             HHHHHHhhcccccchhc--------------------------------------------------ccccccc-c-c--
Confidence            99999876532211100                                                  0000000 0 0  


Q ss_pred             hhhccCCCCCCChHHHHHHHHHHHHHHHHHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Q 009449          440 YLEFAPDRSVKSPKEIVMRQHMKKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKL  519 (534)
Q Consensus       440 l~e~i~d~~~~spee~v~~~el~e~L~~~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KL  519 (534)
                      ...... ....+|++.+...+..+.|..+|+.||+++++||.++|    .+++|++|||+.||+|.++|++.++||+++|
T Consensus       119 ~~~~~~-~~~~~~e~~~~~~e~~~~l~~~l~~L~~~~r~i~~l~~----~~g~s~~EIAe~lgis~~tVk~~l~Rar~kL  193 (231)
T PRK11922        119 ERTPLA-DPAEDPERAAARREIRALLERAIDALPDAFRAVFVLRV----VEELSVEETAQALGLPEETVKTRLHRARRLL  193 (231)
T ss_pred             cccccC-cccCChHHHHHHHHHHHHHHHHHHhCCHHHhhhheeeh----hcCCCHHHHHHHHCcCHHHHHHHHHHHHHHH
Confidence            000111 12246778888888888999999999999999999999    8999999999999999999999999999999


Q ss_pred             HhHhhh
Q 009449          520 RDSETC  525 (534)
Q Consensus       520 R~~l~~  525 (534)
                      |+.+..
T Consensus       194 r~~l~~  199 (231)
T PRK11922        194 RESLAR  199 (231)
T ss_pred             HHHHHH
Confidence            998864

>PRK12515 RNA polymerase sigma factor; Provisional

Probab=99.87  E-value=1.4e-20  Score=179.80  Aligned_cols=178  Identities=17%  Similarity=0.184  Sum_probs=147.4

Q ss_pred             CCCHHHHHHHHHhc-HHHHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCchhhHHHHHHHH
Q 009449          280 GVSERVLKQHLAFG-WYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRK  358 (534)
Q Consensus       280 g~d~~~L~~~l~~G-~~A~e~LI~~nlrLV~sIArrY~~~g~~~eDLiQEG~lgL~rA~ekFDp~kG~rFSTYA~~wIR~  358 (534)
                      .+++..|...+..| ..|++.|+..|.+.|+.++.++.++..+++|++||+|+.+|++.++|++.  ..|.+|++..+++
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            35677788877777 77999999999999999999999999999999999999999999999974  3799999999999


Q ss_pred             HHHHHHHHhccccccccchHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHHhhhhcccccccccchhh
Q 009449          359 SISKMVARHARGIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNA  438 (534)
Q Consensus       359 aI~~~lr~~sr~iRlP~~~~~~i~ki~ka~~~L~~elGr~Pt~eEIA~~lgis~~kv~~~l~~~~~~~SLD~~i~~~~~~  438 (534)
                      .+.+++++..+. .+.                                                       .    +   
T Consensus        84 ~~~d~~r~~~~~-~~~-------------------------------------------------------~----~---  100 (189)
T PRK12515         84 KALSALRRRKHE-EID-------------------------------------------------------D----E---  100 (189)
T ss_pred             HHHHHHHccCCC-CCc-------------------------------------------------------c----c---
Confidence            999999865310 000                                                       0    0   


Q ss_pred             hhhhccCCCCCCChHHHHHHHHHHHHHHHHHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHH
Q 009449          439 KYLEFAPDRSVKSPKEIVMRQHMKKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTK  518 (534)
Q Consensus       439 ~l~e~i~d~~~~spee~v~~~el~e~L~~~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~K  518 (534)
                       ......+ ..++|++.+...+....+..+|+.||+++|+||.|+|    .+++|++|||+.||+|..+|++.+.||+++
T Consensus       101 -~~~~~~~-~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~vl~l~~----~~~~s~~eIA~~lgis~~tV~~~l~Rar~~  174 (189)
T PRK12515        101 -AAAAIED-GADTPEVALQKSDTSAALRACLAKLSPAHREIIDLVY----YHEKSVEEVGEIVGIPESTVKTRMFYARKK  174 (189)
T ss_pred             -cccccCC-CCCCHHHHHHhHHHHHHHHHHHHhCCHHHHHHHHHHH----HcCCCHHHHHHHHCcCHHHHHHHHHHHHHH
Confidence             0000111 1235666666667778899999999999999999999    899999999999999999999999999999


Q ss_pred             HHhHhhhhcc
Q 009449          519 LRDSETCRDL  528 (534)
Q Consensus       519 LR~~l~~~~L  528 (534)
                      ||..+...++
T Consensus       175 Lr~~l~~~~~  184 (189)
T PRK12515        175 LAELLKAAGV  184 (189)
T ss_pred             HHHHHHHhcc
Confidence            9999877654

>PRK09640 RNA polymerase sigma factor SigX; Reviewed

Probab=99.87  E-value=4.4e-21  Score=183.39  Aligned_cols=173  Identities=20%  Similarity=0.251  Sum_probs=137.2

Q ss_pred             CCCHHHHHHHHHh----cHHHHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCchhhHHHHH
Q 009449          280 GVSERVLKQHLAF----GWYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYW  355 (534)
Q Consensus       280 g~d~~~L~~~l~~----G~~A~e~LI~~nlrLV~sIArrY~~~g~~~eDLiQEG~lgL~rA~ekFDp~kG~rFSTYA~~w  355 (534)
                      .++++.|+..++.    +..|++.|+..|.+.|+++|.+|.++..+++|++||+++.+|+++++|++.  ..|.||++.+
T Consensus         7 ~~~~~~li~~~~~~~~gd~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeDlvQe~f~~l~~~~~~~~~~--~~~~~wl~~i   84 (188)
T PRK09640          7 ELNDEELVARVHVELFHVTRAYEELMRRYQRTLFNVCARYLGNDRDADDVCQEVMLKVLYGLKNFEGK--SKFKTWLYSI   84 (188)
T ss_pred             CCCHHHHHHHHhcccCCCHHHHHHHHHHHHHHHHHHHHHHhCCHhhHHHHHHHHHHHHHHHHHHhcCC--CcchHHHHHH
Confidence            4567777777774    378999999999999999999999999999999999999999999999863  4799999999


Q ss_pred             HHHHHHHHHHHhccccccccchHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHHhhhhcccccccccc
Q 009449          356 IRKSISKMVARHARGIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDC  435 (534)
Q Consensus       356 IR~aI~~~lr~~sr~iRlP~~~~~~i~ki~ka~~~L~~elGr~Pt~eEIA~~lgis~~kv~~~l~~~~~~~SLD~~i~~~  435 (534)
                      ++|.+.+++++..+..... .                         ++                       ..       
T Consensus        85 a~n~~~d~~R~~~~~~~~~-~-------------------------~~-----------------------~~-------  108 (188)
T PRK09640         85 TYNECITQYRKERRKRRLM-D-------------------------AL-----------------------SL-------  108 (188)
T ss_pred             HHHHHHHHHHHhcccccCc-c-------------------------hh-----------------------hh-------
Confidence            9999999998754211000 0                         00                       00       


Q ss_pred             hhhhhhhccCCCCCCChHHHHHHHHHHHHHHHHHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 009449          436 LNAKYLEFAPDRSVKSPKEIVMRQHMKKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKA  515 (534)
Q Consensus       436 ~~~~l~e~i~d~~~~spee~v~~~el~e~L~~~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RA  515 (534)
                            +..+++.    ++.....+....|..+|+.||+++|+||.|+|    .+++|++|||+.||||..+|+..+.||
T Consensus       109 ------~~~~~~~----~~~~~~~~~~~~l~~~l~~L~~~~r~v~~l~~----~~g~s~~EIA~~lgis~~tV~~~l~Ra  174 (188)
T PRK09640        109 ------DPLEEAS----EEKAPKPEERGGLDRWLVHVNPIDREILVLRF----VAELEFQEIADIMHMGLSATKMRYKRA  174 (188)
T ss_pred             ------ccccccc----ccccccHHHHHHHHHHHHhcChhheeeeeeHH----hcCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence                  0000110    01111223445789999999999999999999    899999999999999999999999999


Q ss_pred             HHHHHhHhh
Q 009449          516 MTKLRDSET  524 (534)
Q Consensus       516 L~KLR~~l~  524 (534)
                      +++||..+.
T Consensus       175 ~~~Lr~~l~  183 (188)
T PRK09640        175 LDKLREKFA  183 (188)
T ss_pred             HHHHHHHHH
Confidence            999999764

>PRK11924 RNA polymerase sigma factor; Provisional

Probab=99.87  E-value=1.6e-20  Score=175.47  Aligned_cols=172  Identities=20%  Similarity=0.213  Sum_probs=142.3

Q ss_pred             HHHHHhc-HHHHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCchhhHHHHHHHHHHHHHHH
Q 009449          287 KQHLAFG-WYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVA  365 (534)
Q Consensus       287 ~~~l~~G-~~A~e~LI~~nlrLV~sIArrY~~~g~~~eDLiQEG~lgL~rA~ekFDp~kG~rFSTYA~~wIR~aI~~~lr  365 (534)
                      ...+..| ..|++.+++.|.+.|+++|+++.++..+++|++||+++.+|++.++|+  .+..|.+|++..+++.+.++++
T Consensus         4 ~~~~~~~~~~a~~~l~~~y~~~l~~~~~~~~~~~~~aeDl~qe~~~~l~~~~~~~~--~~~~~~~~l~~i~~~~~~d~~r   81 (179)
T PRK11924          4 MPVDATGDKEAFSELFRPHAPDLLRYARRQLGDRALAEDAVQEAFLRAWRKADLFN--GKGSARTWLLTIARNVCYDLLR   81 (179)
T ss_pred             HHHHHccCHHHHHHHHHHHHHHHHHHHHHHhCCHhhHHHHHHHHHHHHHHHHhhcC--CcchHHHHHHHHHHHHHHHHHH
Confidence            3445555 789999999999999999999999999999999999999999999998  3458999999999999999998


Q ss_pred             HhccccccccchHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHHhhhhcccccccccchhhhhhhccC
Q 009449          366 RHARGIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNAKYLEFAP  445 (534)
Q Consensus       366 ~~sr~iRlP~~~~~~i~ki~ka~~~L~~elGr~Pt~eEIA~~lgis~~kv~~~l~~~~~~~SLD~~i~~~~~~~l~e~i~  445 (534)
                      +..+.....                                                     .+ ...        +...
T Consensus        82 ~~~~~~~~~-----------------------------------------------------~~-~~~--------~~~~   99 (179)
T PRK11924         82 RRRREKAVL-----------------------------------------------------SD-DAL--------EPEF   99 (179)
T ss_pred             hcccccccC-----------------------------------------------------cc-ccc--------cccc
Confidence            764311100                                                     00 000        0000


Q ss_pred             CCCCCChHHHHHHHHHHHHHHHHHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHhhh
Q 009449          446 DRSVKSPKEIVMRQHMKKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDSETC  525 (534)
Q Consensus       446 d~~~~spee~v~~~el~e~L~~~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~~l~~  525 (534)
                      +....+|++.+...+....+..+|..|||++++||.++|    .+++|.+|||+.||+|+.+|++++++|+++||+.+..
T Consensus       100 ~~~~~~~e~~~~~~e~~~~l~~~l~~L~~~~r~i~~l~~----~~~~~~~eIA~~lgis~~tv~~~~~ra~~~lr~~l~~  175 (179)
T PRK11924        100 AETAETPEAALLAKDDLARIDRCLDALPVKQREVFLLRY----VEGLSYREIAEILGVPVGTVKSRLRRARQLLRECLEA  175 (179)
T ss_pred             CCccCCHHHHHhhHHHHHHHHHHHHhCCHHHHHHhhHHH----HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH
Confidence            002357888888889999999999999999999999999    7899999999999999999999999999999998765


Q ss_pred             h
Q 009449          526 R  526 (534)
Q Consensus       526 ~  526 (534)
                      .
T Consensus       176 ~  176 (179)
T PRK11924        176 Q  176 (179)
T ss_pred             H
Confidence            4

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

Probab=99.86  E-value=1.4e-20  Score=178.38  Aligned_cols=177  Identities=18%  Similarity=0.170  Sum_probs=138.5

Q ss_pred             HHHHHHHHHHhHHHHHHHHHHhh----CCCCCHHHHHHHHHHHHHHhhhccCCcCCCchhhHHHHHHHHHHHHHHHHhcc
Q 009449          294 WYCREELIKSTRPLVLFLARNYR----GLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHAR  369 (534)
Q Consensus       294 ~~A~e~LI~~nlrLV~sIArrY~----~~g~~~eDLiQEG~lgL~rA~ekFDp~kG~rFSTYA~~wIR~aI~~~lr~~sr  369 (534)
                      ..|++.|+..|.+.|+.+|++|.    ++..+++|++||+++.+|+++..|++..+..|.+|++..+++.+.+++++..+
T Consensus         6 ~~a~~~l~~~y~~~l~~~~~~~l~~~~~~~~~aeD~vQe~~l~l~~~~~~~~~~~~~~~~~wl~~i~~n~~~d~~r~~~~   85 (189)
T TIGR02984         6 QEALGELLDRYRNYLRLLARVQLDPRLRRRVDPSDLVQETLLEAHRRFDQFRGKTEGEFAGWLRGILSNVLADALRRHLG   85 (189)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHhhhhcCCccCHHHHHHHHHHHHHHHHHhccCcccchHHHHHHHHHHHHHHHHHHHHHH
Confidence            67999999999999999999985    35679999999999999999999998666689999999999999999986520


Q ss_pred             -ccccccchHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHHhhhhcccccccc-cchhhhhhhccCCC
Q 009449          370 -GIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIG-DCLNAKYLEFAPDR  447 (534)
Q Consensus       370 -~iRlP~~~~~~i~ki~ka~~~L~~elGr~Pt~eEIA~~lgis~~kv~~~l~~~~~~~SLD~~i~-~~~~~~l~e~i~d~  447 (534)
                       ..+.+.                                                ...+++.+.. ++....+.+.+.+ 
T Consensus        86 ~~~r~~~------------------------------------------------~~~~~~~~~~~~~~~~~~~~~~~~-  116 (189)
T TIGR02984        86 AQKRDIR------------------------------------------------REQSLDAGGRLDESSVRLAAQLAA-  116 (189)
T ss_pred             HHhhhcc------------------------------------------------cccCCCcccccCCcchhHHHHccC-
Confidence             000000                                                0012222111 1111122233333 


Q ss_pred             CCCChHHHHHHHHHHHHHHHHHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHh
Q 009449          448 SVKSPKEIVMRQHMKKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDSE  523 (534)
Q Consensus       448 ~~~spee~v~~~el~e~L~~~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~~l  523 (534)
                      ..++|++.+...+....|..+|..|||++|+||.++|    ++++|++|||+.||||.++|++.++||+++||+.+
T Consensus       117 ~~~~~~~~~~~~e~~~~l~~~l~~L~~~~r~vi~l~~----~~g~s~~eIA~~lgis~~~v~~~l~Ra~~~Lr~~l  188 (189)
T TIGR02984       117 DGPSPSQVAARREAAVRLAQALAKLPEDYREVILLRH----LEGLSFAEVAERMDRSEGAVSMLWVRGLARLRQIL  188 (189)
T ss_pred             CCCCHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHH----hcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHh
Confidence            2346777777777778899999999999999999999    89999999999999999999999999999999875

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).

>PRK12542 RNA polymerase sigma factor; Provisional

Probab=99.86  E-value=4.4e-21  Score=182.75  Aligned_cols=172  Identities=14%  Similarity=0.148  Sum_probs=137.2

Q ss_pred             HHHHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCchhhHHHHHHHHHHHHHHHHhcccccc
Q 009449          294 WYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKI  373 (534)
Q Consensus       294 ~~A~e~LI~~nlrLV~sIArrY~~~g~~~eDLiQEG~lgL~rA~ekFDp~kG~rFSTYA~~wIR~aI~~~lr~~sr~iRl  373 (534)
                      ..|++.|+..|.+.|+.+|.++.++..+++|++||+|+.+|++..+|++..+..|.||++..++|.+.++++++.+....
T Consensus         8 ~~a~~~l~~~y~~~l~~~~~~~~~~~~~AeDlvQe~fl~~~~~~~~~~~~~~~~~~~wL~~Iarn~~~d~~Rk~~~~~~~   87 (185)
T PRK12542          8 YEKMEELYELYEQKVYYVAYSILNNIQQAEDAVQETFITLYKNLEKLHSLNTQELKRYILRVAKNKAIDSYRKNKRHETF   87 (185)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHhcccccHHHHHHHHHHHHHHHHHHHHHHhhhhhhh
Confidence            67999999999999999999999999999999999999999999999875445899999999999999999876421000


Q ss_pred             ccchHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHHhhhhcccccccccchhhhhhhccCCCCCCChH
Q 009449          374 PCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNAKYLEFAPDRSVKSPK  453 (534)
Q Consensus       374 P~~~~~~i~ki~ka~~~L~~elGr~Pt~eEIA~~lgis~~kv~~~l~~~~~~~SLD~~i~~~~~~~l~e~i~d~~~~spe  453 (534)
                      .                  .                                 ..+.           +.... ..++++
T Consensus        88 ~------------------~---------------------------------~~~~-----------~~~~~-~~~~~~  104 (185)
T PRK12542         88 L------------------E---------------------------------EYER-----------ESIEA-VDENIE  104 (185)
T ss_pred             h------------------h---------------------------------hccc-----------cchhh-hhccHH
Confidence            0                  0                                 0000           00000 011344


Q ss_pred             HHHHHHHHHHHHHHHHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHhhhhcchhhh
Q 009449          454 EIVMRQHMKKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDSETCRDLSHFL  532 (534)
Q Consensus       454 e~v~~~el~e~L~~~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~~l~~~~L~~yl  532 (534)
                      +.....+....|..+|..|||++|+||.|+|    .+++|++|||+.||+|.++|++.++||+++||..+....-..|+
T Consensus       105 ~~~~~~~~~~~l~~~l~~L~~~~r~i~~l~~----~~g~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~l~~~~~~~~~  179 (185)
T PRK12542        105 EWEKRKMSEVQIDTLLKELNESNRQVFKYKV----FYNLTYQEISSVMGITEANVRKQFERARKRVQNMIGGIQHDEFK  179 (185)
T ss_pred             HHHHHHHHHHHHHHHHHhCCHHHHHHHHHHH----HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHcccchHHHH
Confidence            4444444556799999999999999999999    89999999999999999999999999999999998766655553

>PRK09643 RNA polymerase sigma factor SigM; Reviewed

Probab=99.86  E-value=1.9e-20  Score=180.08  Aligned_cols=172  Identities=16%  Similarity=0.173  Sum_probs=141.2

Q ss_pred             CCHHHHHHHHHhc-HHHHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCchhhHHHHHHHHH
Q 009449          281 VSERVLKQHLAFG-WYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKS  359 (534)
Q Consensus       281 ~d~~~L~~~l~~G-~~A~e~LI~~nlrLV~sIArrY~~~g~~~eDLiQEG~lgL~rA~ekFDp~kG~rFSTYA~~wIR~a  359 (534)
                      +++..+...+..| ..+++.+++.|.+.|++++.++.++..+++|++||+|+.+|++.++|++..  .|.+|++..++|.
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            4567777777777 789999999999999999999999999999999999999999999999753  6999999999999


Q ss_pred             HHHHHHHhccccccccchHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHHhhhhcccccccccchhhh
Q 009449          360 ISKMVARHARGIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNAK  439 (534)
Q Consensus       360 I~~~lr~~sr~iRlP~~~~~~i~ki~ka~~~L~~elGr~Pt~eEIA~~lgis~~kv~~~l~~~~~~~SLD~~i~~~~~~~  439 (534)
                      +.+++++..+....                                                     +++.    ..   
T Consensus        90 ~~d~~Rk~~~~~~~-----------------------------------------------------~~~~----~~---  109 (192)
T PRK09643         90 CLDRLRRAKARPTV-----------------------------------------------------PLDD----VY---  109 (192)
T ss_pred             HHHHHHccccCCCC-----------------------------------------------------Cccc----cc---
Confidence            99999876421110                                                     0000    00   


Q ss_pred             hhhccCCCCCCChHHHHHHHHHHHHHHHHHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Q 009449          440 YLEFAPDRSVKSPKEIVMRQHMKKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKL  519 (534)
Q Consensus       440 l~e~i~d~~~~spee~v~~~el~e~L~~~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KL  519 (534)
                        + ..    ..+++.+...+....|..+|+.||+++|+||.|+|    .+++|++|||+.||+|..+|++.++||+++|
T Consensus       110 --~-~~----~~~~~~~~~~e~~~~l~~~l~~Lp~~~r~i~~l~~----~~g~s~~EIA~~lg~s~~tV~~rl~rar~~L  178 (192)
T PRK09643        110 --P-VA----QLERDPTARVETALAVQRALMRLPVEQRAALVAVD----MQGYSVADAARMLGVAEGTVKSRCARGRARL  178 (192)
T ss_pred             --c-cc----CCcccHHHHHHHHHHHHHHHHhCCHHHHHHHHHHH----HcCCCHHHHHHHHCcCHHHHHHHHHHHHHHH
Confidence              0 00    01223344455667899999999999999999999    8999999999999999999999999999999


Q ss_pred             HhHhhh
Q 009449          520 RDSETC  525 (534)
Q Consensus       520 R~~l~~  525 (534)
                      |..+..
T Consensus       179 r~~l~~  184 (192)
T PRK09643        179 AELLGY  184 (192)
T ss_pred             HHHHHH
Confidence            998764

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

Probab=99.86  E-value=2.3e-20  Score=174.96  Aligned_cols=167  Identities=16%  Similarity=0.252  Sum_probs=134.5

Q ss_pred             CCHHHHHHHHHhc-HHHHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCchhhHHHHHHHHH
Q 009449          281 VSERVLKQHLAFG-WYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKS  359 (534)
Q Consensus       281 ~d~~~L~~~l~~G-~~A~e~LI~~nlrLV~sIArrY~~~g~~~eDLiQEG~lgL~rA~ekFDp~kG~rFSTYA~~wIR~a  359 (534)
                      |+++.+...+..| ..|++.++..|.+.|+++|.++.++..+++|++||+++.+|++.++|++..  .|.||++..+++.
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            3556677777777 789999999999999999999999999999999999999999999999753  6999999999999


Q ss_pred             HHHHHHHhccccccccchHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHHhhhhcccccccccchhhh
Q 009449          360 ISKMVARHARGIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNAK  439 (534)
Q Consensus       360 I~~~lr~~sr~iRlP~~~~~~i~ki~ka~~~L~~elGr~Pt~eEIA~~lgis~~kv~~~l~~~~~~~SLD~~i~~~~~~~  439 (534)
                      +++++++..+..  |.                                                     +.....+    
T Consensus        79 ~~d~~R~~~~~~--~~-----------------------------------------------------~~~~~~~----   99 (169)
T TIGR02954        79 CIDLLKKKKKVI--PF-----------------------------------------------------DPNTSIE----   99 (169)
T ss_pred             HHHHHHhcCCcC--cc-----------------------------------------------------ccccccc----
Confidence            999998764211  10                                                     0000000    


Q ss_pred             hhhccCCCCCCChHHHHHHHHHHHHHHHHHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Q 009449          440 YLEFAPDRSVKSPKEIVMRQHMKKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKL  519 (534)
Q Consensus       440 l~e~i~d~~~~spee~v~~~el~e~L~~~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KL  519 (534)
                            +.   .++...   .....+..+|..||+++++||.++|    .+|+|++|||+.||||..+|+..++||+++|
T Consensus       100 ------~~---~~~~~~---~~~~~l~~~l~~L~~~~r~i~~l~~----~~g~s~~eiA~~lgis~~tv~~~l~Ra~~~L  163 (169)
T TIGR02954       100 ------KG---ECETHA---DSRLDLYKAIDTLNDKYQTAIILRY----YHDLTIKEIAEVMNKPEGTVKTYLHRALKKL  163 (169)
T ss_pred             ------cc---hhhhch---HHHHHHHHHHHhCCHHHhHHHHHHH----HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence                  00   000000   1123688899999999999999999    8999999999999999999999999999999


Q ss_pred             HhHhh
Q 009449          520 RDSET  524 (534)
Q Consensus       520 R~~l~  524 (534)
                      |..+.
T Consensus       164 r~~l~  168 (169)
T TIGR02954       164 KKRLE  168 (169)
T ss_pred             HHHhc
Confidence            98764

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.

>PRK09638 RNA polymerase sigma factor SigY; Reviewed

Probab=99.86  E-value=1.7e-20  Score=176.54  Aligned_cols=172  Identities=15%  Similarity=0.145  Sum_probs=136.8

Q ss_pred             CCHHHHHHHHHhc-HHHHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCchhhHHHHHHHHH
Q 009449          281 VSERVLKQHLAFG-WYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKS  359 (534)
Q Consensus       281 ~d~~~L~~~l~~G-~~A~e~LI~~nlrLV~sIArrY~~~g~~~eDLiQEG~lgL~rA~ekFDp~kG~rFSTYA~~wIR~a  359 (534)
                      +++..+...+..| ..|++.|+..|.+.|+.+|++|.++..+++|++||+++++|++++.|++.  .+|.+|++..+++.
T Consensus         3 ~~~~~l~~~~~~~d~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeD~vQe~~l~l~~~~~~~~~~--~~~~~wl~~i~~n~   80 (176)
T PRK09638          3 MDEKELIQKAKKGDDAALTTLFQQHYSFLYKYLLKLTLDPDLAEDLVQETMLKAIENLSSFQGR--SKFSTWLISIASRL   80 (176)
T ss_pred             ccHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHcCCHhHHHHHHHHHHHHHHHHHHhcCCc--ccHHHHHHHHHHHH
Confidence            4566677777777 78999999999999999999999999999999999999999999999874  47999999999999


Q ss_pred             HHHHHHHhccccccccchHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHHhhhhcccccccccchhhh
Q 009449          360 ISKMVARHARGIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNAK  439 (534)
Q Consensus       360 I~~~lr~~sr~iRlP~~~~~~i~ki~ka~~~L~~elGr~Pt~eEIA~~lgis~~kv~~~l~~~~~~~SLD~~i~~~~~~~  439 (534)
                      +.+++++..+......                           .                       ..+.         
T Consensus        81 ~~d~~r~~~~~~~~~~---------------------------~-----------------------~~~~---------  101 (176)
T PRK09638         81 YKDHLRKQKREKLRLQ---------------------------R-----------------------AKEE---------  101 (176)
T ss_pred             HHHHHHHhccccchhh---------------------------h-----------------------cccc---------
Confidence            9999997643110000                           0                       0000         


Q ss_pred             hhhccCCCCCCChHHHHHHHHHHHHHHHHHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Q 009449          440 YLEFAPDRSVKSPKEIVMRQHMKKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKL  519 (534)
Q Consensus       440 l~e~i~d~~~~spee~v~~~el~e~L~~~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KL  519 (534)
                          ..+.  ... +..........|..+|..||+++++||.++|    ..|+|++|||+.||+|..+|++.+.||+.+|
T Consensus       102 ----~~~~--~~~-~~~~~~~~~~~l~~~l~~L~~~~r~v~~l~~----~~g~s~~eIA~~l~is~~~V~~~l~ra~~~l  170 (176)
T PRK09638        102 ----TLRK--EKW-EAAIKGAEWSEMLDALSKLDPEFRAPVILKH----YYGYTYEEIAKMLNIPEGTVKSRVHHGIKQL  170 (176)
T ss_pred             ----cCCc--cch-HHHHHhhhHHHHHHHHHcCCHHHhheeeehh----hcCCCHHHHHHHHCCChhHHHHHHHHHHHHH
Confidence                0000  000 1122233445688999999999999999999    8999999999999999999999999999999


Q ss_pred             HhHhh
Q 009449          520 RDSET  524 (534)
Q Consensus       520 R~~l~  524 (534)
                      |+.+.
T Consensus       171 ~~~l~  175 (176)
T PRK09638        171 RKEWG  175 (176)
T ss_pred             HHHhc
Confidence            98763

>PRK12531 RNA polymerase sigma factor; Provisional

Probab=99.86  E-value=1.8e-20  Score=180.18  Aligned_cols=180  Identities=18%  Similarity=0.145  Sum_probs=138.5

Q ss_pred             HHHHHHHHHhc-HHHHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCchhhHHHHHHHHHHH
Q 009449          283 ERVLKQHLAFG-WYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSIS  361 (534)
Q Consensus       283 ~~~L~~~l~~G-~~A~e~LI~~nlrLV~sIArrY~~~g~~~eDLiQEG~lgL~rA~ekFDp~kG~rFSTYA~~wIR~aI~  361 (534)
                      ...|+..+..| ..|++.|+..|.+.|+.+|.++.++..+++|++||+++.+|+...+|++..+ .|.+|++..++|.++
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            34566677777 7799999999999999999999999899999999999999999999997554 799999999999999


Q ss_pred             HHHHHhccccccccchHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHHhhhhcccccccccchhhhhh
Q 009449          362 KMVARHARGIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNAKYL  441 (534)
Q Consensus       362 ~~lr~~sr~iRlP~~~~~~i~ki~ka~~~L~~elGr~Pt~eEIA~~lgis~~kv~~~l~~~~~~~SLD~~i~~~~~~~l~  441 (534)
                      +++++..+..... .                                                   .+....++   ...
T Consensus        93 d~~Rk~~~~~~~~-~---------------------------------------------------~~~~~~~~---~~~  117 (194)
T PRK12531         93 DLLRKQKGKDLHI-H---------------------------------------------------ADDIWPSD---YYP  117 (194)
T ss_pred             HHHHHhccccccc-c---------------------------------------------------hhhccccc---ccc
Confidence            9999764211000 0                                                   00000000   000


Q ss_pred             hccCCCCCCChHHHHHHHHHHHHHHHHHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHh
Q 009449          442 EFAPDRSVKSPKEIVMRQHMKKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRD  521 (534)
Q Consensus       442 e~i~d~~~~spee~v~~~el~e~L~~~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~  521 (534)
                      ..+.  ....++..    ...+.+..++..||+++++||.|+|    .+++|++|||+.||||.++|+..+++|+++||.
T Consensus       118 ~~~~--~~~~~e~~----~~~~~l~~~l~~Lp~~~r~v~~l~~----~eg~s~~EIA~~lgis~~tVk~rl~ra~~~Lr~  187 (194)
T PRK12531        118 PDLV--DHYSPEQD----MLKEQVMKFLDRLPKAQRDVLQAVY----LEELPHQQVAEMFDIPLGTVKSRLRLAVEKLRH  187 (194)
T ss_pred             cccc--cccCHHHH----HHHHHHHHHHHhCCHHHHHHHHHHH----HcCCCHHHHHHHhCcCHHHHHHHHHHHHHHHHH
Confidence            0000  01123322    2335688899999999999999999    899999999999999999999999999999999


Q ss_pred             Hhhhhcc
Q 009449          522 SETCRDL  528 (534)
Q Consensus       522 ~l~~~~L  528 (534)
                      .+....|
T Consensus       188 ~l~~~~~  194 (194)
T PRK12531        188 SMDAESL  194 (194)
T ss_pred             HhhhccC
Confidence            9876543

>PRK12522 RNA polymerase sigma factor; Provisional

Probab=99.85  E-value=3.2e-20  Score=174.80  Aligned_cols=166  Identities=13%  Similarity=0.160  Sum_probs=132.0

Q ss_pred             HHHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCchhhHHHHHHHHHHHHHHHHhccccccc
Q 009449          295 YCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIP  374 (534)
Q Consensus       295 ~A~e~LI~~nlrLV~sIArrY~~~g~~~eDLiQEG~lgL~rA~ekFDp~kG~rFSTYA~~wIR~aI~~~lr~~sr~iRlP  374 (534)
                      ..+++|+..|.++|+.+|++|.++..+++|++||+++.+|++.++|++..  +|.+|++..++|.+.++++++.+....+
T Consensus         3 ~~~~~l~~~y~~~i~~~~~~~~~~~~daeDvvQe~~i~l~~~~~~~~~~~--~~~~wl~~i~~n~~~d~~Rk~~~~~~~~   80 (173)
T PRK12522          3 EKVEELIDIYKQQIYSLCYKLAKTKEDAEDIFQETWIKVFSSRHQLSYVE--NYKKWITTICVRTFYDFYRKKKRWKDRI   80 (173)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHcCCcc--chHHHHHHHHHHHHHHHHHHhccccccc
Confidence            46899999999999999999999999999999999999999999999854  7999999999999999998775321110


Q ss_pred             cchHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHHhhhhcccccccccchhhhhhhccCCCCCCChHH
Q 009449          375 CKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNAKYLEFAPDRSVKSPKE  454 (534)
Q Consensus       375 ~~~~~~i~ki~ka~~~L~~elGr~Pt~eEIA~~lgis~~kv~~~l~~~~~~~SLD~~i~~~~~~~l~e~i~d~~~~spee  454 (534)
                      ...                                                  .+.    +.....  ..++.. ..++.
T Consensus        81 ~~~--------------------------------------------------~~~----~~~~~~--~~~~~~-~~~~~  103 (173)
T PRK12522         81 LDL--------------------------------------------------FHK----EDGGEI--EFADDV-NISEE  103 (173)
T ss_pred             ccc--------------------------------------------------cch----hhhhhh--ccccCC-CChHH
Confidence            000                                                  000    000000  001111 13333


Q ss_pred             HHHHHHHHHHHHHHHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHhh
Q 009449          455 IVMRQHMKKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDSET  524 (534)
Q Consensus       455 ~v~~~el~e~L~~~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~~l~  524 (534)
                       +...+..+.+..+|..||+++++|+.|+|    .+++|++|||+.||+|.++|+..++||+++||+.+.
T Consensus       104 -~~~~~~~~~l~~~l~~L~~~~r~i~~l~~----~~~~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~l~  168 (173)
T PRK12522        104 -FIQKVEAEMIREVIQLLNEKYKTVLVLYY----YEQYSYKEMSEILNIPIGTVKYRLNYAKKQMREHLE  168 (173)
T ss_pred             -HHHHHHHHHHHHHHHhCCHHHHHHHHHHH----HcCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHH
Confidence             55566778899999999999999999999    899999999999999999999999999999998865

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

Probab=99.85  E-value=2.5e-20  Score=171.12  Aligned_cols=160  Identities=19%  Similarity=0.235  Sum_probs=131.3

Q ss_pred             HHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCchhhHHHHHHHHHHHHHHHHhcccccccc
Q 009449          296 CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIPC  375 (534)
Q Consensus       296 A~e~LI~~nlrLV~sIArrY~~~g~~~eDLiQEG~lgL~rA~ekFDp~kG~rFSTYA~~wIR~aI~~~lr~~sr~iRlP~  375 (534)
                      |+++|+..|.+.|+++++++.++..+++|++||+++++|+++.+|++..  +|.+|++.++|+.+.+++++..+....  
T Consensus         2 a~~~l~~~~~~~l~~~~~~~~~~~~~aeD~~Qe~~~~~~~~~~~~~~~~--~~~~wl~~i~r~~~~d~~r~~~~~~~~--   77 (161)
T TIGR02985         2 AFEQLYRRYYPKLCAFAYRYVKDEEEAEDIVQDVFVKLWENRETLEEVE--SFKAYLFTIVKNRSLNYLRHKQVEEKY--   77 (161)
T ss_pred             hHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhHHhccccc--cHHHHHHHHHHHHHHHHHHHHHhHhHH--
Confidence            7899999999999999999999999999999999999999999998743  799999999999999999876421000  


Q ss_pred             chHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHHhhhhcccccccccchhhhhhhccCCCCCCChHHH
Q 009449          376 KLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNAKYLEFAPDRSVKSPKEI  455 (534)
Q Consensus       376 ~~~~~i~ki~ka~~~L~~elGr~Pt~eEIA~~lgis~~kv~~~l~~~~~~~SLD~~i~~~~~~~l~e~i~d~~~~spee~  455 (534)
                                  .             ..                        +.    +..       ......++|++.
T Consensus        78 ------------~-------------~~------------------------~~----~~~-------~~~~~~~~~~~~   97 (161)
T TIGR02985        78 ------------Q-------------EE------------------------IL----EIE-------VDELSENDPEEE   97 (161)
T ss_pred             ------------H-------------HH------------------------HH----hhc-------ccccCCCCcHHH
Confidence                        0             00                        00    000       000111356666


Q ss_pred             HHHHHHHHHHHHHHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHh
Q 009449          456 VMRQHMKKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDSE  523 (534)
Q Consensus       456 v~~~el~e~L~~~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~~l  523 (534)
                      +...+....|..++..||+++++||.++|    .+++|.+|||+.||+|+++|++++++|+++||+.+
T Consensus        98 ~~~~e~~~~l~~~l~~L~~~~r~il~l~~----~~~~~~~eIA~~lgis~~tv~~~~~ra~~~Lr~~l  161 (161)
T TIGR02985        98 LEAKELQLIIYKAIEKLPEQCRKIFILSR----FEGKSYKEIAEELGISVKTVEYHISKALKELRKEL  161 (161)
T ss_pred             HHHHHHHHHHHHHHHHCCHHHHHHHHHHH----HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhhC
Confidence            77777788899999999999999999999    79999999999999999999999999999999753

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.

>PRK12543 RNA polymerase sigma factor; Provisional

Probab=99.85  E-value=3.1e-20  Score=176.26  Aligned_cols=164  Identities=18%  Similarity=0.244  Sum_probs=134.1

Q ss_pred             HHHHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCchhhHHHHHHHHHHHHHHHHhcccccc
Q 009449          294 WYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKI  373 (534)
Q Consensus       294 ~~A~e~LI~~nlrLV~sIArrY~~~g~~~eDLiQEG~lgL~rA~ekFDp~kG~rFSTYA~~wIR~aI~~~lr~~sr~iRl  373 (534)
                      ..|++.++..|.+.|+.++++|.++..+++|++||+|+.+|+++.+|++..  .|.+|++..+++.+.+++++..+..+.
T Consensus         6 ~~af~~l~~~~~~~l~~~~~~~~~~~~daeDl~Qevfl~l~~~~~~~~~~~--~f~~wl~~iarn~~~~~~r~~~~~~~~   83 (179)
T PRK12543          6 QEAFSEIYDVTIQEVYKTVHFLVEDKQDVDDVVNEIYIQLWESLRKYDSNR--PFRFWLIGLVIKQIHSWRRKRWRRFRI   83 (179)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhHHHcCCCC--ChHHHHHHHHHHHHHHHHHhhcccccc
Confidence            579999999999999999999999999999999999999999999999864  699999999999999988754321000


Q ss_pred             ccchHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHHhhhhcccccccccchhhhhhhccCCCCCCChH
Q 009449          374 PCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNAKYLEFAPDRSVKSPK  453 (534)
Q Consensus       374 P~~~~~~i~ki~ka~~~L~~elGr~Pt~eEIA~~lgis~~kv~~~l~~~~~~~SLD~~i~~~~~~~l~e~i~d~~~~spe  453 (534)
                                                                            ++...  +       .........|+
T Consensus        84 ------------------------------------------------------~~~~~--~-------~~~~~~~~~~~  100 (179)
T PRK12543         84 ------------------------------------------------------FEKAE--E-------QRKPVSIDFSE  100 (179)
T ss_pred             ------------------------------------------------------ccccc--c-------ccccccccChH
Confidence                                                                  00000  0       00000112345


Q ss_pred             HHHHHHHHHHHHHHHHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHhhhhc
Q 009449          454 EIVMRQHMKKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDSETCRD  527 (534)
Q Consensus       454 e~v~~~el~e~L~~~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~~l~~~~  527 (534)
                      . +...+..+.|..+|..|||++|+||.|+|    .+++|++|||+.||||..+|+..++||+++||+.+....
T Consensus       101 ~-~~~~~~~~~l~~~l~~Lp~~~r~i~~l~~----~e~~s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~l~~~~  169 (179)
T PRK12543        101 D-VLSKESNQELIELIHKLPYKLRQVIILRY----LHDYSQEEIAQLLQIPIGTVKSRIHAALKKLRQKEQIEE  169 (179)
T ss_pred             H-HHHHHHHHHHHHHHHhCCHHHHHHHHHHH----HccCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHH
Confidence            5 66667778899999999999999999999    899999999999999999999999999999999887543

>PRK12520 RNA polymerase sigma factor; Provisional

Probab=99.85  E-value=2.6e-20  Score=178.30  Aligned_cols=181  Identities=17%  Similarity=0.187  Sum_probs=138.7

Q ss_pred             HHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCchhhHHHHHHHHHHHHHHHHhcccccccc
Q 009449          296 CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIPC  375 (534)
Q Consensus       296 A~e~LI~~nlrLV~sIArrY~~~g~~~eDLiQEG~lgL~rA~ekFDp~kG~rFSTYA~~wIR~aI~~~lr~~sr~iRlP~  375 (534)
                      +++.|+..|.+.|+.+|.++.++..+++|++||+|+.+|+.+++|++..  +|.||++..++|.++++++++.+....+.
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            7899999999999999999999999999999999999999999998643  69999999999999999998754221111


Q ss_pred             chHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHHhhhhcccccccccchhhhhhhccCCCCCCChHHH
Q 009449          376 KLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNAKYLEFAPDRSVKSPKEI  455 (534)
Q Consensus       376 ~~~~~i~ki~ka~~~L~~elGr~Pt~eEIA~~lgis~~kv~~~l~~~~~~~SLD~~i~~~~~~~l~e~i~d~~~~spee~  455 (534)
                      ..                  ......+++                       ++.....   .......++. ..+|++.
T Consensus        81 ~~------------------~~~~~~~~~-----------------------~~~~~~~---~~~~~~~~~~-~~~~~~~  115 (191)
T PRK12520         81 DD------------------ADEQSDDDL-----------------------FDALFAA---DGHYREPPSD-WGDPDAA  115 (191)
T ss_pred             cc------------------cccchhhhh-----------------------hhhhccc---ccccccCccc-cCCHHHH
Confidence            00                  000000000                       0000000   0000011111 2467777


Q ss_pred             HHHHHHHHHHHHHHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHhhhhc
Q 009449          456 VMRQHMKKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDSETCRD  527 (534)
Q Consensus       456 v~~~el~e~L~~~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~~l~~~~  527 (534)
                      +...+....|..+|..|||++|+||.|+|    .+++|++|||+.||+|.++|++.++||+++||+++....
T Consensus       116 ~~~~~~~~~l~~~l~~Lp~~~r~v~~l~~----~~g~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~~~~  183 (191)
T PRK12520        116 LSRREFFEVLQACVDRLPPRTGRVFMMRE----WLELETEEICQELQITATNAWVLLYRARMRLRECLDLHW  183 (191)
T ss_pred             HHHHHHHHHHHHHHHhCCHHHHHHHHHHH----HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHH
Confidence            77777788899999999999999999999    899999999999999999999999999999999988765

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

Probab=99.85  E-value=6.6e-20  Score=183.60  Aligned_cols=184  Identities=16%  Similarity=0.177  Sum_probs=145.8

Q ss_pred             cCCCHHHHHHHHHhc-HHHHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHH-------hhhccCCcCCCchhh
Q 009449          279 AGVSERVLKQHLAFG-WYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQ-------GAERFDHTRGYKFST  350 (534)
Q Consensus       279 ~g~d~~~L~~~l~~G-~~A~e~LI~~nlrLV~sIArrY~~~g~~~eDLiQEG~lgL~r-------A~ekFDp~kG~rFST  350 (534)
                      .+.++..|...++.| ..|++.|+..|.+.|+.++.++.++..+++|++||+|+.+|.       .+.+|++.  ..|.|
T Consensus        22 ~~~~d~~Li~~~~~gd~~Af~~L~~~y~~~l~~~~~~~~~~~~dAEDivQEvFlkl~~~~~~~~~~~~~~~~~--~~~~t   99 (244)
T TIGR03001        22 LHAADLYLACACAQGEPAALAALERHVLSKVPARLAGLRPPTAFVDEVLQRLRQRLLVPRAERPPRIAEYSGR--GPLLS   99 (244)
T ss_pred             ccccHHHHHHHHHcCcHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhccchhhhhhccCCC--CchHh
Confidence            445677888888888 679999999999999999999999999999999999999994       78889864  37999


Q ss_pred             HHHHHHHHHHHHHHHHhccccccccchHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHHhhhhccccc
Q 009449          351 YVQYWIRKSISKMVARHARGIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQ  430 (534)
Q Consensus       351 YA~~wIR~aI~~~lr~~sr~iRlP~~~~~~i~ki~ka~~~L~~elGr~Pt~eEIA~~lgis~~kv~~~l~~~~~~~SLD~  430 (534)
                      |++.+++|.++++++++.+...+.                                                       .
T Consensus       100 WL~~Ia~N~~id~lRk~~r~~~~~-------------------------------------------------------~  124 (244)
T TIGR03001       100 WVRIVATRIALELQAQERRHSPVE-------------------------------------------------------E  124 (244)
T ss_pred             HHHHHHHHHHHHHHHHhcccCccc-------------------------------------------------------c
Confidence            999999999999998754211000                                                       0


Q ss_pred             ccccchhhhhhhccCCCCCCChHHHHHH----HHHHHHHHHHHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHH
Q 009449          431 KIGDCLNAKYLEFAPDRSVKSPKEIVMR----QHMKKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKE  506 (534)
Q Consensus       431 ~i~~~~~~~l~e~i~d~~~~spee~v~~----~el~e~L~~~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISre  506 (534)
                          +.  ...+ ..+. ..+|++.+..    .+..+.|..+|+.||+++|+||.|+|    .+++|++|||++||||.+
T Consensus       125 ----~~--~~~~-~~~~-~~~~e~~~~~~e~~~e~~~~l~~aL~~Lp~~~R~v~~L~~----~eg~S~~EIA~~Lgis~~  192 (244)
T TIGR03001       125 ----PT--ELAA-LPAP-GSDPELDLLRERYRQDFRQALREALAALSERERHLLRLHF----VDGLSMDRIGAMYQVHRS  192 (244)
T ss_pred             ----cc--cccc-ccCC-CCCHHHHHHHHhhHHHHHHHHHHHHHhCCHHHHHHHHHHH----HcCCCHHHHHHHHCcCHH
Confidence                00  0000 0011 1244544433    23567799999999999999999999    999999999999999999


Q ss_pred             HHHHHHHHHHHHHHhHhhhhcchhh
Q 009449          507 WIRKLEKKAMTKLRDSETCRDLSHF  531 (534)
Q Consensus       507 rVRqi~~RAL~KLR~~l~~~~L~~y  531 (534)
                      +|+..++||+++||+.+.......|
T Consensus       193 TVk~rl~RAr~~Lr~~l~~~~~~~~  217 (244)
T TIGR03001       193 TVSRWVAQARERLLERTRRRLAERL  217 (244)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHhc
Confidence            9999999999999999887665443

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.

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

Probab=99.85  E-value=8e-20  Score=164.16  Aligned_cols=157  Identities=31%  Similarity=0.382  Sum_probs=133.2

Q ss_pred             HHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCchhhHHHHHHHHHHHHHHHHhcccccccc
Q 009449          296 CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIPC  375 (534)
Q Consensus       296 A~e~LI~~nlrLV~sIArrY~~~g~~~eDLiQEG~lgL~rA~ekFDp~kG~rFSTYA~~wIR~aI~~~lr~~sr~iRlP~  375 (534)
                      |++.++..|.++|+++++++.+++.+.+|++|||++++|++++.|++.  ..|.+|+++++++.+.++++++.+   .+.
T Consensus         2 a~~~l~~~~~~~v~~~~~~~~~~~~~~~D~~qe~~~~l~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~rk~~~---~~~   76 (158)
T TIGR02937         2 AFEELYERYLPLLYRYARRYLGDDADAEDLVQEAFLKLLEALDRFDPE--GSFKAWLFRIARNLILDYLRRKRR---LRR   76 (158)
T ss_pred             HHHHHHHHHHHHHHHHHHHHhCCHhHHHHHHHHHHHHHHHhHHhcCCc--chHHHHHHHHHHHHHHHHHHHhcc---CCc
Confidence            789999999999999999999999999999999999999999999998  589999999999999999998764   111


Q ss_pred             chHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHHhhhhcccccccccchhhhhhhccCCCCCCChHHH
Q 009449          376 KLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNAKYLEFAPDRSVKSPKEI  455 (534)
Q Consensus       376 ~~~~~i~ki~ka~~~L~~elGr~Pt~eEIA~~lgis~~kv~~~l~~~~~~~SLD~~i~~~~~~~l~e~i~d~~~~spee~  455 (534)
                      ..                                                   ...          ... ....+.|++.
T Consensus        77 ~~---------------------------------------------------~~~----------~~~-~~~~~~~~~~   94 (158)
T TIGR02937        77 EL---------------------------------------------------DLL----------EEL-LDSDPSPEEE   94 (158)
T ss_pred             ch---------------------------------------------------hhh----------hhc-ccccCCHHHH
Confidence            00                                                   000          000 0112356677


Q ss_pred             HHHHHHHHHHHHHHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHh
Q 009449          456 VMRQHMKKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDSE  523 (534)
Q Consensus       456 v~~~el~e~L~~~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~~l  523 (534)
                      .........|..+++.||+.++.||.++|    ..|+|..|||+.+|+|+.+|+++..+|+++||+.+
T Consensus        95 ~~~~~~~~~l~~~l~~L~~~~~~ii~~~~----~~g~s~~eIA~~l~~s~~~v~~~~~~~~~kl~~~l  158 (158)
T TIGR02937        95 LEQEEEREALREALEKLPEREREVLVLRY----LEGLSYKEIAEILGISVGTVKRRLKRARKKLRELL  158 (158)
T ss_pred             HHHHHHHHHHHHHHHhCCHHHHHHHhhHH----hcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhhC
Confidence            77777888899999999999999999998    78999999999999999999999999999999753

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

>PRK09415 RNA polymerase factor sigma C; Reviewed

Probab=99.85  E-value=5.2e-20  Score=174.84  Aligned_cols=164  Identities=17%  Similarity=0.120  Sum_probs=135.8

Q ss_pred             cHHHHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCchhhHHHHHHHHHHHHHHHHhccccc
Q 009449          293 GWYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIK  372 (534)
Q Consensus       293 G~~A~e~LI~~nlrLV~sIArrY~~~g~~~eDLiQEG~lgL~rA~ekFDp~kG~rFSTYA~~wIR~aI~~~lr~~sr~iR  372 (534)
                      ...|+++++..|.+.|+.+|.++.++..+++|++||+++.+|++..+|++.  ..|.+|++..+++.+.+++++..+...
T Consensus        14 ~~~a~~~l~~~~~~~l~~~~~~~~~~~~~AeDlvQd~fl~l~~~~~~~~~~--~~~~awl~~ia~n~~~d~~Rk~~~~~~   91 (179)
T PRK09415         14 KEDLIDEIMNEYGQEVLQLVYSYVKNKEVAEDLTQEIFVKCYKSLHTYKGK--SSLKTWLYRIAINHCKDYLKSWHNKKV   91 (179)
T ss_pred             cHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHhcCCC--cccHHHHHHHHHHHHHHHHHhhccccc
Confidence            367999999999999999999999999999999999999999999999874  369999999999999999987532110


Q ss_pred             cccchHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHHhhhhcccccccccchhhhhhhccCCCCCCCh
Q 009449          373 IPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNAKYLEFAPDRSVKSP  452 (534)
Q Consensus       373 lP~~~~~~i~ki~ka~~~L~~elGr~Pt~eEIA~~lgis~~kv~~~l~~~~~~~SLD~~i~~~~~~~l~e~i~d~~~~sp  452 (534)
                      .+                                                     .+.        .+... . ...++|
T Consensus        92 ~~-----------------------------------------------------~~~--------~~~~~-~-~~~~~~  108 (179)
T PRK09415         92 IV-----------------------------------------------------TED--------IFTYM-E-SQKESV  108 (179)
T ss_pred             cc-----------------------------------------------------ccc--------ccccc-c-ccccCc
Confidence            00                                                     000        00000 0 111356


Q ss_pred             HHHHHHHHHHHHHHHHHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHhhh
Q 009449          453 KEIVMRQHMKKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDSETC  525 (534)
Q Consensus       453 ee~v~~~el~e~L~~~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~~l~~  525 (534)
                      ++.+...+....+..+|..||+++|+||.|+|    ++|+|++|||+.||||.++|++++.||+++||..+..
T Consensus       109 e~~~~~~e~~~~l~~~l~~L~~~~r~v~~l~~----~~g~s~~EIA~~l~is~~tv~~~l~Ra~~~Lr~~l~~  177 (179)
T PRK09415        109 EEEVIQNAEDERLASAVMSLPIKYREVIYLFY----YEELSIKEIAEVTGVNENTVKTRLKKAKELLKKGLEE  177 (179)
T ss_pred             HHHHHHHHHHHHHHHHHHhCCHHHhhHhHhHH----hcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHhc
Confidence            67777777788899999999999999999999    8999999999999999999999999999999987753

>PRK09645 RNA polymerase sigma factor SigL; Provisional

Probab=99.85  E-value=5.5e-20  Score=172.87  Aligned_cols=163  Identities=18%  Similarity=0.086  Sum_probs=130.9

Q ss_pred             HHHHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCchhhHHHHHHHHHHHHHHHHhcccccc
Q 009449          294 WYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKI  373 (534)
Q Consensus       294 ~~A~e~LI~~nlrLV~sIArrY~~~g~~~eDLiQEG~lgL~rA~ekFDp~kG~rFSTYA~~wIR~aI~~~lr~~sr~iRl  373 (534)
                      ..|++.|+..|.+.|+++|.++.++..+++|++||.|+.+|+..++|++.. ..|.+|++..++|.+.++++++.+....
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            579999999999999999999999989999999999999999999997532 3799999999999999999876421100


Q ss_pred             ccchHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHHhhhhcccccccccchhhhhhhccCCCCCCChH
Q 009449          374 PCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNAKYLEFAPDRSVKSPK  453 (534)
Q Consensus       374 P~~~~~~i~ki~ka~~~L~~elGr~Pt~eEIA~~lgis~~kv~~~l~~~~~~~SLD~~i~~~~~~~l~e~i~d~~~~spe  453 (534)
                                                                           ..+..         .+ .++.   .++
T Consensus        87 -----------------------------------------------------~~~~~---------~~-~~~~---~~~  100 (173)
T PRK09645         87 -----------------------------------------------------GGDDV---------LG-VPEQ---SAP  100 (173)
T ss_pred             -----------------------------------------------------ccccc---------cc-CCCC---CCc
Confidence                                                                 00000         00 0011   122


Q ss_pred             HHHHHHHHHHHHHHHHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHhhhhc
Q 009449          454 EIVMRQHMKKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDSETCRD  527 (534)
Q Consensus       454 e~v~~~el~e~L~~~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~~l~~~~  527 (534)
                      +.+........|..+|+.|||++|+||.|+|    ++++|++|||+.||+|.++|+..++||+++||+.+...+
T Consensus       101 ~~~~~~~~~~~l~~~l~~L~~~~r~vl~L~~----~~g~s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~l~~~~  170 (173)
T PRK09645        101 DEVDRALDRLLVADALAQLSPEHRAVLVRSY----YRGWSTAQIAADLGIPEGTVKSRLHYALRALRLALQERG  170 (173)
T ss_pred             hHHHHHhHHHHHHHHHHhCCHHHHHHHHHHH----HcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHhhccc
Confidence            2333334455789999999999999999999    899999999999999999999999999999999887544

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

Probab=99.84  E-value=4.3e-20  Score=170.67  Aligned_cols=158  Identities=20%  Similarity=0.197  Sum_probs=126.6

Q ss_pred             HHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCchhhHHHHHHHHHHHHHHHHhcccccccc
Q 009449          296 CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIPC  375 (534)
Q Consensus       296 A~e~LI~~nlrLV~sIArrY~~~g~~~eDLiQEG~lgL~rA~ekFDp~kG~rFSTYA~~wIR~aI~~~lr~~sr~iRlP~  375 (534)
                      |++.++..|.+.|+.+|+++.++..++||++||+++.+|++.++||+..  .|.+|++..++|.++++++++.+... +.
T Consensus         2 ~~~~~~~~~~~~l~~~~~~~~~~~~~aEDivQe~~l~l~~~~~~~~~~~--~~~~wl~~i~~n~~~d~~r~~~~~~~-~~   78 (159)
T TIGR02989         2 AFAALLQRHQRSLRAFVRSLVPDRDDADDVLQETFVTAWRKFDEFDPGT--DFGAWARGIARNKVLNHRRKLGRDRL-VF   78 (159)
T ss_pred             HHHHHHHHhHHHHHHHHHHHcCChhhHHHHHHHHHHHHHHHHHhCCCCC--chHHHHHHHHHHHHHHHHHHhccccc-cc
Confidence            7899999999999999999999999999999999999999999999764  69999999999999999998753210 00


Q ss_pred             chHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHHhhhhcccccccccchhhhhhhccCCCCCCChHHH
Q 009449          376 KLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNAKYLEFAPDRSVKSPKEI  455 (534)
Q Consensus       376 ~~~~~i~ki~ka~~~L~~elGr~Pt~eEIA~~lgis~~kv~~~l~~~~~~~SLD~~i~~~~~~~l~e~i~d~~~~spee~  455 (534)
                      .                         ++.                                    .+.+.+.  .+|.+.
T Consensus        79 ~-------------------------~~~------------------------------------~~~~~~~--~~~~~~   95 (159)
T TIGR02989        79 D-------------------------DEL------------------------------------LEALAAE--AEATEA   95 (159)
T ss_pred             C-------------------------HHH------------------------------------HHHHHhh--cccchH
Confidence            0                         000                                    0000000  011122


Q ss_pred             HHHHHHHHHHHHHHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHh
Q 009449          456 VMRQHMKKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDSE  523 (534)
Q Consensus       456 v~~~el~e~L~~~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~~l  523 (534)
                      .........+..+++.||+++++||.++|    .+|+|.+|||+.||||.++|+..++||+++||+++
T Consensus        96 ~~~~~~~~~l~~~i~~L~~~~r~v~~l~~----~~g~~~~eIA~~l~is~~tv~~~l~Rar~~Lr~~~  159 (159)
T TIGR02989        96 DRSEDELQALEGCLEKLPERQRELLQLRY----QRGVSLTALAEQLGRTVNAVYKALSRLRVRLRDCV  159 (159)
T ss_pred             hhHHHHHHHHHHHHHHCCHHHHHHHHHHH----hcCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhcC
Confidence            22334456789999999999999999999    89999999999999999999999999999999753

This group of sigma factors are members of the sigma-70 family (TIGR02937) and are abundantly found in the species Rhodopirellula baltica (11), and Verrucomicrobium spinosum (16) and to a lesser extent in Gemmata obscuriglobus (2).

>PRK12539 RNA polymerase sigma factor; Provisional

Probab=99.84  E-value=1.4e-19  Score=172.43  Aligned_cols=169  Identities=13%  Similarity=0.075  Sum_probs=133.3

Q ss_pred             HHHHHHHHHhc-HHHHHHHHHHhHHHHHHHHH----HhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCchhhHHHHHHH
Q 009449          283 ERVLKQHLAFG-WYCREELIKSTRPLVLFLAR----NYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIR  357 (534)
Q Consensus       283 ~~~L~~~l~~G-~~A~e~LI~~nlrLV~sIAr----rY~~~g~~~eDLiQEG~lgL~rA~ekFDp~kG~rFSTYA~~wIR  357 (534)
                      ...|...+..| ..|++.|+..|.+.|+.+|+    +|.++..+++|++||+++.+|++...|++..  .|.+|++..++
T Consensus         8 ~~~l~~~~~~gd~~af~~l~~~~~~~l~~~~~~~~~~~~~~~~~AeDlvQe~~l~l~~~~~~~~~~~--~f~~wl~~i~~   85 (184)
T PRK12539          8 LKALMLASLDGDAAAHRALLERLSGHLRAYYKGKLARIGRGAEEAEDLVQEALMAIHTRRHTYDPEQ--PLTPWVYAIAR   85 (184)
T ss_pred             HHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHHHhccCCcchHHHHHHHHHHHHHHHHhhcCCCC--ChHHHHHHHHH
Confidence            45666777777 78999999999999999987    4557889999999999999999999999754  69999999999


Q ss_pred             HHHHHHHHHhccccccccchHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHHhhhhcccccccccchh
Q 009449          358 KSISKMVARHARGIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLN  437 (534)
Q Consensus       358 ~aI~~~lr~~sr~iRlP~~~~~~i~ki~ka~~~L~~elGr~Pt~eEIA~~lgis~~kv~~~l~~~~~~~SLD~~i~~~~~  437 (534)
                      |.+.+++++..+.. .+.                                                   +.+.    .  
T Consensus        86 n~~~d~~R~~~~~~-~~~---------------------------------------------------~~~~----~--  107 (184)
T PRK12539         86 YKLIDHLRRTRASL-ADV---------------------------------------------------PIDD----A--  107 (184)
T ss_pred             HHHHHHHHHHhccc-ccc---------------------------------------------------Chhh----h--
Confidence            99999998754210 000                                                   0000    0  


Q ss_pred             hhhhhccCCCCCCChHHHHHHHHHHHHHHHHHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 009449          438 AKYLEFAPDRSVKSPKEIVMRQHMKKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMT  517 (534)
Q Consensus       438 ~~l~e~i~d~~~~spee~v~~~el~e~L~~~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~  517 (534)
                      .   . ..      +.+.....+..+.+..++..||+++|+|+.|+|    .+|+|++|||+.||+|..+|++.++||++
T Consensus       108 ~---~-~~------~~~~~~~~e~~~~l~~~l~~L~~~~r~v~~l~~----~~g~s~~eIA~~lgis~~tV~~~l~ra~~  173 (184)
T PRK12539        108 D---E-LV------AHDDHAAVESTLDLGRLLARLPEKMRLAIQAVK----LEGLSVAEAATRSGMSESAVKVSVHRGLK  173 (184)
T ss_pred             c---c-cc------CCcHHhhHHHHHHHHHHHHhCCHHHHHHHHHHH----HcCCcHHHHHHHHCcCHHHHHHHHHHHHH
Confidence            0   0 00      001111223445789999999999999999999    89999999999999999999999999999


Q ss_pred             HHHhHhhh
Q 009449          518 KLRDSETC  525 (534)
Q Consensus       518 KLR~~l~~  525 (534)
                      +||+.+..
T Consensus       174 ~Lr~~l~~  181 (184)
T PRK12539        174 ALAALIGR  181 (184)
T ss_pred             HHHHHHhh
Confidence            99998754

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

Probab=99.84  E-value=1.5e-19  Score=171.13  Aligned_cols=172  Identities=19%  Similarity=0.164  Sum_probs=128.5

Q ss_pred             HHHHHHHHHhc-HHHHHHHHHHhHHHHHHHHHHhhCCCC-----CHHHHHHHHHHHHHH-hhhccCCcCCCchhhHHHHH
Q 009449          283 ERVLKQHLAFG-WYCREELIKSTRPLVLFLARNYRGLGI-----PFSDLLQAGNVGVLQ-GAERFDHTRGYKFSTYVQYW  355 (534)
Q Consensus       283 ~~~L~~~l~~G-~~A~e~LI~~nlrLV~sIArrY~~~g~-----~~eDLiQEG~lgL~r-A~ekFDp~kG~rFSTYA~~w  355 (534)
                      ...|...+..| ..|++.|+..|.+.|+.+|++|.++..     +++|++||+|+.+|+ ...+|++.  ..|.+|++.+
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            34566777777 679999999999999999999999877     899999999999998 78889764  3699999999


Q ss_pred             HHHHHHHHHHHhccccccccchHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHHhhhhcccccccccc
Q 009449          356 IRKSISKMVARHARGIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDC  435 (534)
Q Consensus       356 IR~aI~~~lr~~sr~iRlP~~~~~~i~ki~ka~~~L~~elGr~Pt~eEIA~~lgis~~kv~~~l~~~~~~~SLD~~i~~~  435 (534)
                      ++|.+.++++++.+..+....                                               ....++      
T Consensus        82 ~~n~~~d~~R~~~~~~~~~~~-----------------------------------------------~~~~~~------  108 (183)
T TIGR02999        82 MRRILVDHARRRRAQKRGGGA-----------------------------------------------VRVPLD------  108 (183)
T ss_pred             HHHHHHHHHHHHHHHhccCCc-----------------------------------------------cccccc------
Confidence            999999999875321000000                                               000000      


Q ss_pred             hhhhhhhccCCCCCCChHHHHHHHHHHHHHHHHHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 009449          436 LNAKYLEFAPDRSVKSPKEIVMRQHMKKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKA  515 (534)
Q Consensus       436 ~~~~l~e~i~d~~~~spee~v~~~el~e~L~~~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RA  515 (534)
                            +..++.   .++.. ......+.+...|+.|||++|+||.|+|    ++|+|++|||+.||+|.++|+..++||
T Consensus       109 ------~~~~~~---~~~~~-~~~~~l~~~~~~l~~Lp~~~r~v~~l~~----~~g~s~~EIA~~lgis~~tVk~~l~Ra  174 (183)
T TIGR02999       109 ------EVLPDA---EADLD-EELLDLDDALDKLAQVDPRQAEVVELRF----FAGLTVEEIAELLGVSVRTVERDWRFA  174 (183)
T ss_pred             ------cccCCC---CccHH-HHHHHHHHHHHHhhcCCHHHHHHHHHHH----HcCCCHHHHHHHhCCCHHHHHHHHHHH
Confidence                  000011   11111 1111123344556779999999999999    899999999999999999999999999


Q ss_pred             HHHHHhHh
Q 009449          516 MTKLRDSE  523 (534)
Q Consensus       516 L~KLR~~l  523 (534)
                      +++||+.+
T Consensus       175 r~~Lr~~l  182 (183)
T TIGR02999       175 RAWLADEL  182 (183)
T ss_pred             HHHHHHHh
Confidence            99999875

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.

>PRK09649 RNA polymerase sigma factor SigC; Reviewed

Probab=99.84  E-value=1.3e-19  Score=173.29  Aligned_cols=171  Identities=18%  Similarity=0.098  Sum_probs=132.5

Q ss_pred             HHHHHHHHhc-HHHHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCchhhHHHHHHHHHHHH
Q 009449          284 RVLKQHLAFG-WYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISK  362 (534)
Q Consensus       284 ~~L~~~l~~G-~~A~e~LI~~nlrLV~sIArrY~~~g~~~eDLiQEG~lgL~rA~ekFDp~kG~rFSTYA~~wIR~aI~~  362 (534)
                      ..|...+..| ..|++.|+..|.+.|+.+++ +.++..+++|++||+|+.+|+..++|++.  ..|.+|++.+++|.+.+
T Consensus        12 ~~l~~~~~~gd~~af~~l~~~~~~~l~~~~~-~~~~~~~AeDivQe~flkl~~~~~~~~~~--~~~~~Wl~~Iarn~~~d   88 (185)
T PRK09649         12 TALALSAAKGNGRALEAFIKATQQDVWRFVA-YLSDVGSADDLTQETFLRAIGAIPRFSAR--SSARTWLLAIARHVVAD   88 (185)
T ss_pred             HHHHHHHHccCHHHHHHHHHHHHHHHHHHHH-HhCCHHHHHHHHHHHHHHHHHhccccCcc--chHHHHHHHHHHHHHHH
Confidence            4566667777 77999999999999999995 68888999999999999999999999864  37999999999999999


Q ss_pred             HHHHhccccccccchHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHHhhhhcccccccccchhhhhhh
Q 009449          363 MVARHARGIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNAKYLE  442 (534)
Q Consensus       363 ~lr~~sr~iRlP~~~~~~i~ki~ka~~~L~~elGr~Pt~eEIA~~lgis~~kv~~~l~~~~~~~SLD~~i~~~~~~~l~e  442 (534)
                      ++++..+..+...                                                     +.    ..     +
T Consensus        89 ~~Rk~~~~~~~~~-----------------------------------------------------~~----~~-----~  106 (185)
T PRK09649         89 HIRHVRSRPRTTR-----------------------------------------------------GA----RP-----E  106 (185)
T ss_pred             HHHHhcccccccc-----------------------------------------------------cc----ch-----h
Confidence            9987542110000                                                     00    00     0


Q ss_pred             ccCCCCCCChHHHHHHHHHHHHHHHHHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhH
Q 009449          443 FAPDRSVKSPKEIVMRQHMKKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDS  522 (534)
Q Consensus       443 ~i~d~~~~spee~v~~~el~e~L~~~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~~  522 (534)
                      ...+.     +......+....|..+|..|||++|+||.|+|    ++++|++|||+.||+|.++|++.++||+++||+.
T Consensus       107 ~~~~~-----~~~~~~~e~~~~l~~~l~~Lp~~~r~v~~L~~----~~g~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~  177 (185)
T PRK09649        107 HLIDG-----DRHARGFEDLVEVTTMIADLTTDQREALLLTQ----LLGLSYADAAAVCGCPVGTIRSRVARARDALLAD  177 (185)
T ss_pred             hccCh-----hhhhhhHHHHHHHHHHHHhCCHHHhHHhhhHH----HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhh
Confidence            00000     00011112234588899999999999999999    9999999999999999999999999999999997


Q ss_pred             hhhhcc
Q 009449          523 ETCRDL  528 (534)
Q Consensus       523 l~~~~L  528 (534)
                      +....|
T Consensus       178 ~~~~~~  183 (185)
T PRK09649        178 AEPDDL  183 (185)
T ss_pred             CCcccc
Confidence            665544

>PRK12512 RNA polymerase sigma factor; Provisional

Probab=99.84  E-value=1.7e-19  Score=171.30  Aligned_cols=167  Identities=20%  Similarity=0.210  Sum_probs=131.0

Q ss_pred             HHHHHHHhc-HHHHHHHHHHhHHHHHHHHHHhhCC----CCCHHHHHHHHHHHHHHhhhccCCcCCCchhhHHHHHHHHH
Q 009449          285 VLKQHLAFG-WYCREELIKSTRPLVLFLARNYRGL----GIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKS  359 (534)
Q Consensus       285 ~L~~~l~~G-~~A~e~LI~~nlrLV~sIArrY~~~----g~~~eDLiQEG~lgL~rA~ekFDp~kG~rFSTYA~~wIR~a  359 (534)
                      .+...+..| ..|++.|+..|.+.|+.+|+++.++    ..+++|++||+++.+|+..++|++.  ..|.+|++..+|+.
T Consensus        11 ~l~~~~~~gd~~a~~~l~~~y~~~l~~~~~~~l~~~~~~~~~aeDlvQe~fl~l~~~~~~~~~~--~~~~~wl~~i~rn~   88 (184)
T PRK12512         11 DLMRSANAGDAAAYRRLLKAVTPVLRAAARRGLARAGQPADQAEDIVQEILLAVHLKRHTWDPG--APFAPWLFAIARNK   88 (184)
T ss_pred             HHHHHHHccCHHHHHHHHHHHHHHHHHHHHHHHHhccCCcccHHHHHHHHHHHHHHhHHhcCcc--ccHHHHHHHHHHHH
Confidence            345555655 7899999999999999999998753    4699999999999999999999874  37999999999999


Q ss_pred             HHHHHHHhccccccccchHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHHhhhhcccccccccchhhh
Q 009449          360 ISKMVARHARGIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNAK  439 (534)
Q Consensus       360 I~~~lr~~sr~iRlP~~~~~~i~ki~ka~~~L~~elGr~Pt~eEIA~~lgis~~kv~~~l~~~~~~~SLD~~i~~~~~~~  439 (534)
                      +.++++++.+....+                                                     ++.         
T Consensus        89 ~~d~~Rr~~~~~~~~-----------------------------------------------------~~~---------  106 (184)
T PRK12512         89 LIDALRRRGRRVFVD-----------------------------------------------------IDD---------  106 (184)
T ss_pred             HHHHHHhhcccccCC-----------------------------------------------------chh---------
Confidence            999998764311110                                                     000         


Q ss_pred             hhhccCCCCCCChHHHHHHHHHHHHHHHHHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Q 009449          440 YLEFAPDRSVKSPKEIVMRQHMKKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKL  519 (534)
Q Consensus       440 l~e~i~d~~~~spee~v~~~el~e~L~~~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KL  519 (534)
                      +.+.+++..   +.+    ....+.+..+|+.||+++++||.++|    .+++|++|||+.||+|..+|+..++||+++|
T Consensus       107 ~~~~~~~~~---~~~----~~~~~~l~~~l~~L~~~~r~v~~l~~----~~g~s~~eIA~~l~is~~tV~~~l~ra~~~L  175 (184)
T PRK12512        107 FAETLPAEP---ATE----TLPAGDVGRHLETLPPRQRDVVQSIS----VEGASIKETAAKLSMSEGAVRVALHRGLAAL  175 (184)
T ss_pred             ccccccccc---hhh----HHHHHHHHHHHHhCCHHHHHHHHHHH----HcCCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Confidence            000011110   011    12234678899999999999999999    8999999999999999999999999999999


Q ss_pred             HhHhhhh
Q 009449          520 RDSETCR  526 (534)
Q Consensus       520 R~~l~~~  526 (534)
                      |..+...
T Consensus       176 r~~l~~~  182 (184)
T PRK12512        176 AAKFRSE  182 (184)
T ss_pred             HHHhhcC
Confidence            9988754

>PRK12533 RNA polymerase sigma factor; Provisional

Probab=99.84  E-value=1.9e-19  Score=177.12  Aligned_cols=171  Identities=18%  Similarity=0.126  Sum_probs=137.9

Q ss_pred             cHHHHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCchhhHHHHHHHHHHHHHHHHhccccc
Q 009449          293 GWYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIK  372 (534)
Q Consensus       293 G~~A~e~LI~~nlrLV~sIArrY~~~g~~~eDLiQEG~lgL~rA~ekFDp~kG~rFSTYA~~wIR~aI~~~lr~~sr~iR  372 (534)
                      ...++..|+..|.+.++.++.++.++..+++|++||+|+.+|+..++|++.   .|.+|++.+++|.++++++++.+...
T Consensus        16 ~~~~f~~l~~~~~~~l~~~~~~~~~d~~dAEDlvQEvflkl~~~~~~~~~~---~~~aWL~~IarN~~~d~~Rk~~~~~~   92 (216)
T PRK12533         16 RGERFRQLVLPHLDAAYNLARWLCGNASDADDVVQEACMRALRFFDSFRGD---NARPWLLAIVRHTWYSEWRRRANAHE   92 (216)
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHHhCCHhhHHHHHHHHHHHHHHhHHhcCcc---chHhHHHHHHHHHHHHHHHhhccccc
Confidence            356999999999999999999999999999999999999999999999853   49999999999999999987643110


Q ss_pred             cccchHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHHhhhhcccccccccchhhhhhhccCCCCCCCh
Q 009449          373 IPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNAKYLEFAPDRSVKSP  452 (534)
Q Consensus       373 lP~~~~~~i~ki~ka~~~L~~elGr~Pt~eEIA~~lgis~~kv~~~l~~~~~~~SLD~~i~~~~~~~l~e~i~d~~~~sp  452 (534)
                      ....                         +                        .++    .+  ... +.. ++...+|
T Consensus        93 ~~~~-------------------------~------------------------~~~----~~--~~~-~~~-~~~~~~~  115 (216)
T PRK12533         93 VAAP-------------------------D------------------------TLD----DA--DSL-DDW-QPAGEDP  115 (216)
T ss_pred             cccc-------------------------c------------------------ccc----cc--ccc-ccc-ccCCCCH
Confidence            0000                         0                        000    00  000 000 1112467


Q ss_pred             HHHHHHHHHHHHHHHHHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHhhhhc
Q 009449          453 KEIVMRQHMKKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDSETCRD  527 (534)
Q Consensus       453 ee~v~~~el~e~L~~~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~~l~~~~  527 (534)
                      ++.+...+....|..+|..||+++|+||.|+|    .+++|++|||+.||||.++|+++++||+++||+.+....
T Consensus       116 e~~~~~~e~~~~l~~al~~Lp~~~R~v~~L~y----~eg~s~~EIAe~LgiS~~tVk~~L~RAr~~Lr~~l~~~~  186 (216)
T PRK12533        116 LALLLRAEDVRLVNAALAKLPVEYREVLVLRE----LEDMSYREIAAIADVPVGTVMSRLARARRRLAALLGGAS  186 (216)
T ss_pred             HHHHHHHHHHHHHHHHHHcCCHHHHhHhhhHH----hcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHcccc
Confidence            78888888888999999999999999999999    899999999999999999999999999999999886543

>PRK12536 RNA polymerase sigma factor; Provisional

Probab=99.83  E-value=1e-19  Score=172.95  Aligned_cols=169  Identities=16%  Similarity=0.151  Sum_probs=131.7

Q ss_pred             HHHHHHHHhc-HHHHHHHHHHhHHHHHHHHHHhhC-CCCCHHHHHHHHHHHHHHhhhccCCcCCCchhhHHHHHHHHHHH
Q 009449          284 RVLKQHLAFG-WYCREELIKSTRPLVLFLARNYRG-LGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSIS  361 (534)
Q Consensus       284 ~~L~~~l~~G-~~A~e~LI~~nlrLV~sIArrY~~-~g~~~eDLiQEG~lgL~rA~ekFDp~kG~rFSTYA~~wIR~aI~  361 (534)
                      ..++.....| ..|++.++..|.+.|+.++.++.+ ...+++|++||+++.+|+..+.|++.  ..|.+|++..++|.++
T Consensus         9 ~~~~~~~~~~d~~a~~~l~~~~~~~l~~~~~~~~~~~~~~aeDlvQevfl~l~~~~~~~~~~--~~~~~wl~~iarN~~~   86 (181)
T PRK12536          9 RALLLRGLAGDAAAYRQFLSELAAHLRGFLRRRLPQLPDEVEDLVQEILLAVHNARHTYRAD--QPLTAWVHAIARYKLM   86 (181)
T ss_pred             HHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHcCCChhhHHHHHHHHHHHHHHhHHhcCCC--CchHHHHHHHHHHHHH
Confidence            3455555555 789999999999999999998764 57899999999999999999999975  3699999999999999


Q ss_pred             HHHHHhccccccccchHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHHhhhhcccccccccchhhhhh
Q 009449          362 KMVARHARGIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNAKYL  441 (534)
Q Consensus       362 ~~lr~~sr~iRlP~~~~~~i~ki~ka~~~L~~elGr~Pt~eEIA~~lgis~~kv~~~l~~~~~~~SLD~~i~~~~~~~l~  441 (534)
                      +++++..+....  +                                                 .+++.    .     .
T Consensus        87 d~~Rk~~~~~~~--~-------------------------------------------------~~~~~----~-----~  106 (181)
T PRK12536         87 DFLRSRARREAL--H-------------------------------------------------DPLDD----E-----S  106 (181)
T ss_pred             HHHHHHhccccc--c-------------------------------------------------CCccc----h-----h
Confidence            999986431100  0                                                 00000    0     0


Q ss_pred             hccCCCCCCChHHHHHHHHHHHHHHHHHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHh
Q 009449          442 EFAPDRSVKSPKEIVMRQHMKKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRD  521 (534)
Q Consensus       442 e~i~d~~~~spee~v~~~el~e~L~~~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~  521 (534)
                      +...+.. ..+      .+....+..+|..||++++.||.++|    .+++|++|||+.||+|+++|+..+++|+++||+
T Consensus       107 ~~~~~~~-~~~------~~~~~~l~~~l~~L~~~~r~v~~l~~----~~g~s~~EIA~~l~is~~tV~~~l~rar~~Lr~  175 (181)
T PRK12536        107 ELFATSD-DEA------AEARRDLGKLLEQLPDRQRLPIVHVK----LEGLSVAETAQLTGLSESAVKVGIHRGLKALAA  175 (181)
T ss_pred             hhcCCCC-cch------HHHHHHHHHHHHHCCHHHHHHHHHHH----HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence            0001111 111      13345689999999999999999999    899999999999999999999999999999999


Q ss_pred             Hhhh
Q 009449          522 SETC  525 (534)
Q Consensus       522 ~l~~  525 (534)
                      .+..
T Consensus       176 ~l~~  179 (181)
T PRK12536        176 KIRG  179 (181)
T ss_pred             HhcC
Confidence            8764

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

Probab=99.83  E-value=2.6e-19  Score=170.44  Aligned_cols=170  Identities=22%  Similarity=0.247  Sum_probs=136.7

Q ss_pred             HHHhcHHHHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCchhhHHHHHHHHHHHHHHHHhc
Q 009449          289 HLAFGWYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHA  368 (534)
Q Consensus       289 ~l~~G~~A~e~LI~~nlrLV~sIArrY~~~g~~~eDLiQEG~lgL~rA~ekFDp~kG~rFSTYA~~wIR~aI~~~lr~~s  368 (534)
                      .......++..++..+.+.++.+|+++.++..+++||+||+|+.+|+++..| +. +..|.||++.+++|.+++.+++..
T Consensus         9 ~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~dAeDlvQE~~lr~~~~~~~~-~~-~~~~~~wl~~Ia~n~~iD~~R~~~   86 (182)
T COG1595           9 ALRGDRAAFEELLERLRPRLRRLARRLLGDRADAEDLVQETFLRAWRAIDSF-RG-RSSFKAWLYRIARNLAIDRLRKRK   86 (182)
T ss_pred             HHhcchHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHhhc-CC-CCchHHHHHHHHHHHHHHHHHHhc
Confidence            3444578999999999999999999999998899999999999999999999 33 348999999999999999999876


Q ss_pred             cccccccchHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHHhhhhcccccccccchhhhhhhccCCCC
Q 009449          369 RGIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNAKYLEFAPDRS  448 (534)
Q Consensus       369 r~iRlP~~~~~~i~ki~ka~~~L~~elGr~Pt~eEIA~~lgis~~kv~~~l~~~~~~~SLD~~i~~~~~~~l~e~i~d~~  448 (534)
                      +.......                                                   .+          ......++.
T Consensus        87 r~~~~~~~---------------------------------------------------~~----------~~~~~~~~~  105 (182)
T COG1595          87 RRRARVEE---------------------------------------------------AD----------LLPEEADPA  105 (182)
T ss_pred             cccccccc---------------------------------------------------cc----------ccccccCcc
Confidence            43221000                                                   00          000001111


Q ss_pred             CCChHHHHHHHHHHHHHHHHHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHhhhh
Q 009449          449 VKSPKEIVMRQHMKKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDSETCR  526 (534)
Q Consensus       449 ~~spee~v~~~el~e~L~~~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~~l~~~  526 (534)
                      .+.+ +.+...+....|..+|..||+++|+||.|+|    .+|+|++|||+.||||.+||+..+++|+.+||..+...
T Consensus       106 ~~~~-~~~~~~~~~~~l~~al~~Lp~~~R~~~~l~~----~~gls~~EIA~~l~i~~~tVks~l~ra~~~l~~~l~~~  178 (182)
T COG1595         106 PDLA-ELLLAEEELERLRRALARLPPRQREAFLLRY----LEGLSYEEIAEILGISVGTVKSRLHRARKKLREQLEEA  178 (182)
T ss_pred             cccc-hHHHHHHHHHHHHHHHHhCCHHHhHHhhhHh----hcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHhhc
Confidence            0111 2456667778899999999999999999999    99999999999999999999999999999999987654

>PRK12529 RNA polymerase sigma factor; Provisional

Probab=99.83  E-value=2.4e-19  Score=170.26  Aligned_cols=164  Identities=10%  Similarity=0.034  Sum_probs=131.2

Q ss_pred             cHHHHHHHHHHhHHHHHHHHHHhhC--CCCCHHHHHHHHHHHHHHhhhccCCcCCCchhhHHHHHHHHHHHHHHHHhccc
Q 009449          293 GWYCREELIKSTRPLVLFLARNYRG--LGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARG  370 (534)
Q Consensus       293 G~~A~e~LI~~nlrLV~sIArrY~~--~g~~~eDLiQEG~lgL~rA~ekFDp~kG~rFSTYA~~wIR~aI~~~lr~~sr~  370 (534)
                      +..|++.|+..|.+.|+.++.++.+  +..+++|++||+|+.+|+..++|++.....|.||++..++|.+.++++++.+.
T Consensus        11 d~~af~~ly~~~~~~l~~~~~~~~~~~~~~~AeDivQevFl~~~~~~~~~~~~~~~~~~~wL~~ia~n~~~d~~Rk~~~~   90 (178)
T PRK12529         11 DRDKVATLYRENHAWLRNWLAYRLRSWGRGVADDLAHDIFLRILASRDGGQREAIRQPRAYLARIANCVLVSWRRRQSLE   90 (178)
T ss_pred             CHHHHHHHHHHHHHHHHHHHHHHhCCCChHHHHHHHHHHHHHHHhcccccccccccCHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3679999999999999998766665  46789999999999999999999854445799999999999999998765310


Q ss_pred             cccccchHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHHhhhhcccccccccchhhhhhhccCCCCCC
Q 009449          371 IKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNAKYLEFAPDRSVK  450 (534)
Q Consensus       371 iRlP~~~~~~i~ki~ka~~~L~~elGr~Pt~eEIA~~lgis~~kv~~~l~~~~~~~SLD~~i~~~~~~~l~e~i~d~~~~  450 (534)
                         +.                                                   ..+.         ..+ ..+...+
T Consensus        91 ---~~---------------------------------------------------~~~~---------~~~-~~~~~~~  106 (178)
T PRK12529         91 ---LA---------------------------------------------------WLEA---------LAT-LPEPLHP  106 (178)
T ss_pred             ---hh---------------------------------------------------hhhH---------hhh-ccCcCCC
Confidence               00                                                   0000         000 0111123


Q ss_pred             ChHHHHHHHHHHHHHHHHHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHhh
Q 009449          451 SPKEIVMRQHMKKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDSET  524 (534)
Q Consensus       451 spee~v~~~el~e~L~~~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~~l~  524 (534)
                      +|++.+...+....|..+|..|||++|+||.|+|    .+|+|++|||+.||+|.++|+..+++|+.++++.+.
T Consensus       107 ~~e~~~~~~~~~~~l~~~l~~Lp~~~R~v~~L~~----~~g~s~~EIA~~lgis~~tVk~~l~rAl~~~~~~~~  176 (178)
T PRK12529        107 SPEQQSVILETLHEIDALLDTLRPRVKQAFLMAT----LDGMKQKDIAQALDIALPTVKKYIHQAYVTCLSLMP  176 (178)
T ss_pred             CHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHH----HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHhCC
Confidence            6677666667777899999999999999999999    899999999999999999999999999999998743

>PRK12518 RNA polymerase sigma factor; Provisional

Probab=99.83  E-value=1.7e-19  Score=169.63  Aligned_cols=168  Identities=20%  Similarity=0.197  Sum_probs=130.0

Q ss_pred             HHHhc-HHHHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCchhhHHHHHHHHHHHHHHHHh
Q 009449          289 HLAFG-WYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARH  367 (534)
Q Consensus       289 ~l~~G-~~A~e~LI~~nlrLV~sIArrY~~~g~~~eDLiQEG~lgL~rA~ekFDp~kG~rFSTYA~~wIR~aI~~~lr~~  367 (534)
                      .++.| ..|++.++..|.+.|+.+++++.+ ..+++|++||+|+.+|+..++|++.  ..|.+|++..+++.+.+++++.
T Consensus         4 ~~~~gd~~a~~~l~~~~~~~l~~~~~~~~~-~~~aeDivQe~~l~l~~~~~~~~~~--~~~~~wl~~ia~n~~~d~~R~~   80 (175)
T PRK12518          4 RCQRGDRQSFRQLYRRYQQKVRSTLYQLCG-RELLDDLVQEVFLRVWKGLPKLRNP--AYFSTWLYRITWNVATDARRQF   80 (175)
T ss_pred             HHHcCCHHHHHHHHHHHHHHHHHHHHHHcC-HhHHHHHHHHHHHHHHHhHHhhCCc--ccHHHHHHHHHHHHHHHHHHHh
Confidence            34455 779999999999999999999875 4789999999999999999999974  4799999999999999999865


Q ss_pred             ccccccccchHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHHhhhhcccccccccchhhhhhhccCCC
Q 009449          368 ARGIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNAKYLEFAPDR  447 (534)
Q Consensus       368 sr~iRlP~~~~~~i~ki~ka~~~L~~elGr~Pt~eEIA~~lgis~~kv~~~l~~~~~~~SLD~~i~~~~~~~l~e~i~d~  447 (534)
                      .+.   +..                                                   .+... ..      +. +..
T Consensus        81 ~~~---~~~---------------------------------------------------~~~~~-~~------~~-~~~   98 (175)
T PRK12518         81 AQR---PSR---------------------------------------------------IQDDS-LN------DQ-PSR   98 (175)
T ss_pred             hcc---ccc---------------------------------------------------hhccc-cc------cc-ccC
Confidence            321   000                                                   00000 00      00 000


Q ss_pred             CCCChHHHHHHHHHHHHHHHHHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHhhhhc
Q 009449          448 SVKSPKEIVMRQHMKKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDSETCRD  527 (534)
Q Consensus       448 ~~~spee~v~~~el~e~L~~~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~~l~~~~  527 (534)
                      ....|  .....+....+..+|+.||+++|+||.|+|    ++|+|++|||+.||+|..+|++.++||+++||..+...+
T Consensus        99 ~~~~~--~~~~~~~~~~l~~~l~~L~~~~r~vl~l~~----~~g~s~~eIA~~lg~s~~tv~~~l~Rar~~L~~~l~~~~  172 (175)
T PRK12518         99 PSDTP--DLMQLHYQDLVQQGLQTLSLEHRAVLVLHD----LEDLPQKEIAEILNIPVGTVKSRLFYARRQLRKFLQQQG  172 (175)
T ss_pred             CCCcH--HHHHHHHHHHHHHHHHhCCHHHeeeeeehH----hcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHhcc
Confidence            00122  222233445688999999999999999999    899999999999999999999999999999999987644

>PRK09642 RNA polymerase sigma factor SigW; Reviewed

Probab=99.83  E-value=1.7e-19  Score=167.48  Aligned_cols=156  Identities=13%  Similarity=0.078  Sum_probs=127.2

Q ss_pred             HHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCchhhHHHHHHHHHHHHHHHHhccccccccchHHHH
Q 009449          302 KSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIPCKLNREI  381 (534)
Q Consensus       302 ~~nlrLV~sIArrY~~~g~~~eDLiQEG~lgL~rA~ekFDp~kG~rFSTYA~~wIR~aI~~~lr~~sr~iRlP~~~~~~i  381 (534)
                      +.|.+.|+.+|.++.++..+++|++||+|+.+|++.++|++.   .|.+|++..++|.+.++++++.+.....       
T Consensus         2 ~~y~~~l~~~~~~~~~~~~~AeDlvQe~fl~~~~~~~~~~~~---~~~~wl~~ia~n~~~d~~Rk~~~~~~~~-------   71 (160)
T PRK09642          2 QTYRHYIFQVIFSILRHEEDAKDVTQEVFVKIHASLPNYQFR---GLKTWMARIATNHAIDYKRKKARENEEL-------   71 (160)
T ss_pred             chHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHhcccccccc---hhHHHHHHHHHHHHHHHHHHhccccccc-------
Confidence            578999999999999999999999999999999999999863   4999999999999999998764211000       


Q ss_pred             HHHHHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHHhhhhcccccccccchhhhhhhccCCCCCCChHHHHHHHHH
Q 009449          382 SKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNAKYLEFAPDRSVKSPKEIVMRQHM  461 (534)
Q Consensus       382 ~ki~ka~~~L~~elGr~Pt~eEIA~~lgis~~kv~~~l~~~~~~~SLD~~i~~~~~~~l~e~i~d~~~~spee~v~~~el  461 (534)
                                                                   .+.    .+.    .+...  ..++|++.+...+.
T Consensus        72 ---------------------------------------------~~~----~~~----~~~~~--~~~~~~~~~~~~e~   96 (160)
T PRK09642         72 ---------------------------------------------SLC----KET----EENIK--SSHNIEDLLLTKEQ   96 (160)
T ss_pred             ---------------------------------------------ccc----hhh----hhhcc--CCCChHHHHHHHHH
Confidence                                                         000    000    00000  11256666777777


Q ss_pred             HHHHHHHHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHhhhh
Q 009449          462 KKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDSETCR  526 (534)
Q Consensus       462 ~e~L~~~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~~l~~~  526 (534)
                      ...|..+|+.|||++|+||.|+|    .+|+|++|||+.||+|.++|+++++||+++||+.+...
T Consensus        97 ~~~l~~~l~~Lp~~~r~v~~l~~----~~g~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~~~  157 (160)
T PRK09642         97 KLLIAQKLRELPENYRDVVLAHY----LEEKSYQEIALQEKIEVKTVEMKLYRARKWIKKHWKEE  157 (160)
T ss_pred             HHHHHHHHHhCCHHHHHHHHHHH----HhCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHhhh
Confidence            78899999999999999999999    89999999999999999999999999999999988654

>PRK12523 RNA polymerase sigma factor; Reviewed

Probab=99.83  E-value=2.1e-19  Score=169.26  Aligned_cols=163  Identities=17%  Similarity=0.097  Sum_probs=129.8

Q ss_pred             hc-HHHHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCchhhHHHHHHHHHHHHHHHHhccc
Q 009449          292 FG-WYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARG  370 (534)
Q Consensus       292 ~G-~~A~e~LI~~nlrLV~sIArrY~~~g~~~eDLiQEG~lgL~rA~ekFDp~kG~rFSTYA~~wIR~aI~~~lr~~sr~  370 (534)
                      .| ..|+..++..|.+.|+.+|.++.++..+++|++||+|+.+|+. ..|+..  ..|.+|++.+++|.+.++++++.+.
T Consensus         6 ~~~~~a~~~l~~~~~~~l~~~~~~~~~~~~~AeDlvQevflk~~~~-~~~~~~--~~~~~wL~~Iarn~~~d~~Rk~~~~   82 (172)
T PRK12523          6 SPHSELVGALYRDHRGWLLAWLRRNVACRQRAEDLSQDTFVRLLGR-PELPTP--REPRAFLAAVAKGLMFDHFRRAALE   82 (172)
T ss_pred             CCCcHHHHHHHHHHHHHHHHHHHHHcCCHhhHHHHHHHHHHHHHcc-cccCcc--hhHHHHHHHHHHHHHHHHHHHHHHH
Confidence            45 6799999999999999999999999999999999999999987 446543  3699999999999999999876420


Q ss_pred             cccccchHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHHhhhhcccccccccchhhhhhhccCCCCCC
Q 009449          371 IKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNAKYLEFAPDRSVK  450 (534)
Q Consensus       371 iRlP~~~~~~i~ki~ka~~~L~~elGr~Pt~eEIA~~lgis~~kv~~~l~~~~~~~SLD~~i~~~~~~~l~e~i~d~~~~  450 (534)
                      .                  ...         +++                        +            . .......
T Consensus        83 ~------------------~~~---------~~~------------------------~------------~-~~~~~~~   98 (172)
T PRK12523         83 Q------------------AYL---------AEL------------------------A------------L-VPEAEQP   98 (172)
T ss_pred             H------------------HHH---------HHH------------------------h------------h-cccccCC
Confidence            0                  000         000                        0            0 0001112


Q ss_pred             ChHHHHHHHHHHHHHHHHHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHhhh
Q 009449          451 SPKEIVMRQHMKKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDSETC  525 (534)
Q Consensus       451 spee~v~~~el~e~L~~~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~~l~~  525 (534)
                      +|++.....+....+..+|..||+++|+||.|+|    .+|+|++|||+.||+|.++|++.+++|+++||..+..
T Consensus        99 ~~~~~~~~~~~~~~l~~~l~~Lp~~~r~v~~L~~----~~g~s~~EIA~~lgis~~tV~~~l~ra~~~~~~~l~~  169 (172)
T PRK12523         99 SPEEQHLILEDLKAIDRLLGKLSSKARAAFLYNR----LDGMGHAEIAERLGVSVSRVRQYLAQGLRQCYIALYG  169 (172)
T ss_pred             ChHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHH----HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHhcC
Confidence            4555555555556899999999999999999999    8999999999999999999999999999999987653

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

Probab=99.82  E-value=1.8e-19  Score=172.87  Aligned_cols=172  Identities=12%  Similarity=0.042  Sum_probs=132.6

Q ss_pred             HHHHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCchhhHHHHHHHHHHHHHHHHhcccccc
Q 009449          294 WYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKI  373 (534)
Q Consensus       294 ~~A~e~LI~~nlrLV~sIArrY~~~g~~~eDLiQEG~lgL~rA~ekFDp~kG~rFSTYA~~wIR~aI~~~lr~~sr~iRl  373 (534)
                      ..+|+.|+..|.+.|+.+|.++.++..+++|++||+|+.+|++..+|++.  ..|.+|++..++|.+.++++++.+....
T Consensus        10 ~~~f~~l~~~~~~~l~~~~~~~~~~~~~AEDlvQevfl~~~~~~~~~~~~--~~~~~wL~~iarN~~~d~~Rk~~~~~~~   87 (193)
T TIGR02947        10 AQRFERDALEYLDQLYGAALRMTRNPADAEDLVQEAYAKAFSSFHQFKPG--TNLKAWLYRILTNTYINSYRKAQRRPQQ   87 (193)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhhcccCCC--CcchHHHHHHHHHHHHHHHHHhcCCccc
Confidence            56999999999999999999999999999999999999999999999864  3699999999999999999876431100


Q ss_pred             ccchHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHHhhhhcccccccccchhhhhhhccCCCCCCChH
Q 009449          374 PCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNAKYLEFAPDRSVKSPK  453 (534)
Q Consensus       374 P~~~~~~i~ki~ka~~~L~~elGr~Pt~eEIA~~lgis~~kv~~~l~~~~~~~SLD~~i~~~~~~~l~e~i~d~~~~spe  453 (534)
                      ..                         .+++..           .        .+..    .      .....+....++
T Consensus        88 ~~-------------------------~~~~~~-----------~--------~~~~----~------~~~~~~~~~~~e  113 (193)
T TIGR02947        88 SD-------------------------DDDIED-----------W--------QLAK----A------ASHTSNGLRSAE  113 (193)
T ss_pred             cc-------------------------chhhhh-----------h--------hhcc----c------cccccccccchh
Confidence            00                         000000           0        0000    0      000001112344


Q ss_pred             HHHHHHHHHHHHHHHHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHhhh
Q 009449          454 EIVMRQHMKKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDSETC  525 (534)
Q Consensus       454 e~v~~~el~e~L~~~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~~l~~  525 (534)
                      ......+....|..+|..||+++|+||.|+|    .+++|++|||+.||+|.++|+.+++||+++||+.+..
T Consensus       114 ~~~~~~~~~~~l~~~l~~Lp~~~r~i~~L~~----~~g~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~l~~  181 (193)
T TIGR02947       114 LEALDGLPDQDIKDALQGLPEEFRQAVYLAD----VEGFAYKEIAEIMGTPIGTVMSRLHRGRKQLRKQLVD  181 (193)
T ss_pred             HHHHhhhhHHHHHHHHHhCCHHHhhheeehh----hcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH
Confidence            4444445566899999999999999999999    8999999999999999999999999999999998864

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.

>PRK09644 RNA polymerase sigma factor SigM; Provisional

Probab=99.82  E-value=3.1e-19  Score=166.89  Aligned_cols=157  Identities=17%  Similarity=0.110  Sum_probs=131.6

Q ss_pred             HHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCchhhHHHHHHHHHHHHHHHHhccccccccc
Q 009449          297 REELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIPCK  376 (534)
Q Consensus       297 ~e~LI~~nlrLV~sIArrY~~~g~~~eDLiQEG~lgL~rA~ekFDp~kG~rFSTYA~~wIR~aI~~~lr~~sr~iRlP~~  376 (534)
                      ++.|+..|.+.|+.+|+++.++..+++|++||+++.+|+++++|++.   .|.+|++..++|.+.+++++..+.....  
T Consensus         3 ~~~l~~~y~~~l~~~~~~~~~~~~~AeDlvQe~fl~~~~~~~~~~~~---~~~~wL~~i~~n~~~d~~R~~~~~~~~~--   77 (165)
T PRK09644          3 IEEIYKMYINDVYRYLFSLTKSHHAAEDLLQETFYRAYIYLEDYDNQ---KVKPWLFKVAYHTFIDFVRKEKKVSFVG--   77 (165)
T ss_pred             HHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhHHhcccc---chHHHHHHHHHHHHHHHHHhhhhccccc--
Confidence            67899999999999999999999999999999999999999999863   5999999999999999998764311000  


Q ss_pred             hHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHHhhhhcccccccccchhhhhhhccCCCCCCChHHHH
Q 009449          377 LNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNAKYLEFAPDRSVKSPKEIV  456 (534)
Q Consensus       377 ~~~~i~ki~ka~~~L~~elGr~Pt~eEIA~~lgis~~kv~~~l~~~~~~~SLD~~i~~~~~~~l~e~i~d~~~~spee~v  456 (534)
                                              .+++                                     +.+.   ..+|++.+
T Consensus        78 ------------------------~~~~-------------------------------------~~~~---~~~~~~~~   93 (165)
T PRK09644         78 ------------------------TDEI-------------------------------------EAIQ---AESTEEYV   93 (165)
T ss_pred             ------------------------hhHH-------------------------------------hhhc---ccChHHHH
Confidence                                    0000                                     0000   12456666


Q ss_pred             HHHHHHHHHHHHHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHhhhh
Q 009449          457 MRQHMKKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDSETCR  526 (534)
Q Consensus       457 ~~~el~e~L~~~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~~l~~~  526 (534)
                      ...+....+..+|..||+++|+||.|+|    .+++|++|||+.||+|.++|++.++||+++||+.+...
T Consensus        94 ~~~~~~~~l~~~l~~L~~~~r~v~~l~~----~~g~s~~eIA~~lgis~~tv~~~l~Rar~~Lr~~l~~~  159 (165)
T PRK09644         94 VAKNSYEKLIQIIHTLPVIEAQAILLCD----VHELTYEEAASVLDLKLNTYKSHLFRGRKRLKALLKEE  159 (165)
T ss_pred             HHHHHHHHHHHHHHhCCHHHHHHHHhHH----HhcCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHhh
Confidence            6667778899999999999999999999    89999999999999999999999999999999988654

>PRK12528 RNA polymerase sigma factor; Provisional

Probab=99.82  E-value=6e-19  Score=164.11  Aligned_cols=157  Identities=15%  Similarity=0.108  Sum_probs=126.3

Q ss_pred             HHHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCchhhHHHHHHHHHHHHHHHHhccccccc
Q 009449          295 YCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIP  374 (534)
Q Consensus       295 ~A~e~LI~~nlrLV~sIArrY~~~g~~~eDLiQEG~lgL~rA~ekFDp~kG~rFSTYA~~wIR~aI~~~lr~~sr~iRlP  374 (534)
                      .|+++|+..|.+.|+.+|.++.++..+++|++||+|+.+|+..+.|++.   .|.+|++.+++|.+.+++++..+..   
T Consensus         4 ~a~~~l~~~~~~~l~~~~~~~~~~~~~AeDivQe~flk~~~~~~~~~~~---~~~~wl~~i~~n~~~d~~R~~~~~~---   77 (161)
T PRK12528          4 ATVEGLYSAHHHWLTGWLRRRLGCPQSAADLAQDTFVKVLVARETAQII---EPRAFLTTIAKRVLCNHYRRQDLER---   77 (161)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHcCCcccHHHHHHHHHHHHHhcccccccc---CHHHHHHHHHHHHHHHHHHHHHHHH---
Confidence            5899999999999999999999999999999999999999998888652   6999999999999999998753100   


Q ss_pred             cchHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHHhhhhcccccccccchhhhhhhccCCCCCCChHH
Q 009449          375 CKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNAKYLEFAPDRSVKSPKE  454 (534)
Q Consensus       375 ~~~~~~i~ki~ka~~~L~~elGr~Pt~eEIA~~lgis~~kv~~~l~~~~~~~SLD~~i~~~~~~~l~e~i~d~~~~spee  454 (534)
                       .              .         .++                        ++            + .++...+.+++
T Consensus        78 -~--------------~---------~~~------------------------~~------------~-~~~~~~~~~~~   96 (161)
T PRK12528         78 -A--------------Y---------LEA------------------------LA------------Q-LPERVAPSEEE   96 (161)
T ss_pred             -h--------------h---------HHH------------------------hh------------c-cccccCCCHHH
Confidence             0              0         000                        00            0 00111123444


Q ss_pred             HHHHHHHHHHHHHHHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhH
Q 009449          455 IVMRQHMKKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDS  522 (534)
Q Consensus       455 ~v~~~el~e~L~~~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~~  522 (534)
                      .....+....|..+|..||+++|+||.|+|    .+|+|++|||+.||+|.++|++.+++|+++||..
T Consensus        97 ~~~~~~~~~~l~~~l~~L~~~~r~v~~L~~----~~g~s~~EIA~~l~is~~tV~~~l~ra~~~~~~~  160 (161)
T PRK12528         97 RAIILETLVELDQLLDGLPPLVKRAFLLAQ----VDGLGYGEIATELGISLATVKRYLNKAAMRCYFA  160 (161)
T ss_pred             HHHHHHHHHHHHHHHHHCCHHHHHHHHHHH----HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhc
Confidence            444445556899999999999999999999    8999999999999999999999999999999964

>PRK12516 RNA polymerase sigma factor; Provisional

Probab=99.82  E-value=3.5e-19  Score=171.01  Aligned_cols=160  Identities=14%  Similarity=0.113  Sum_probs=128.6

Q ss_pred             HHHHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCchhhHHHHHHHHHHHHHHHHhcccccc
Q 009449          294 WYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKI  373 (534)
Q Consensus       294 ~~A~e~LI~~nlrLV~sIArrY~~~g~~~eDLiQEG~lgL~rA~ekFDp~kG~rFSTYA~~wIR~aI~~~lr~~sr~iRl  373 (534)
                      ..++..++..|.+.|+.+|.++.++..+++|++||+|+.+|+..++|++..  .|.+|++..++|.+.++++++.+..  
T Consensus         9 ~~~f~~l~~~~~~~L~~~a~~~~~~~~~AEDivQevfl~~~~~~~~~~~~~--~~~awL~~Ia~n~~~d~~R~~~~~~--   84 (187)
T PRK12516          9 TPPFKRELLAALPSLRAFAVSLIGRHDRADDLVQDTIMKAWAKQDHFEVGT--NMKAWLFTILRNEFYSQMRKRGREV--   84 (187)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHcCCHhHHHHHHHHHHHHHHHhhhccCCcc--cHHHHHHHHHHHHHHHHHHhhcCCc--
Confidence            579999999999999999999999999999999999999999999998643  6999999999999999998764311  


Q ss_pred             ccchHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHHhhhhcccccccccchhhhhhhccCCCCCCChH
Q 009449          374 PCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNAKYLEFAPDRSVKSPK  453 (534)
Q Consensus       374 P~~~~~~i~ki~ka~~~L~~elGr~Pt~eEIA~~lgis~~kv~~~l~~~~~~~SLD~~i~~~~~~~l~e~i~d~~~~spe  453 (534)
                       ..                                                   .+..        +.+.....  +...
T Consensus        85 -~~---------------------------------------------------~~~~--------~~~~~~~~--~~~~  102 (187)
T PRK12516         85 -QD---------------------------------------------------TDGM--------FTEQLAVH--PSQY  102 (187)
T ss_pred             -cc---------------------------------------------------cccc--------cccccCCC--cchh
Confidence             00                                                   0000        00000000  0111


Q ss_pred             HHHHHHHHHHHHHHHHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHhhhhc
Q 009449          454 EIVMRQHMKKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDSETCRD  527 (534)
Q Consensus       454 e~v~~~el~e~L~~~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~~l~~~~  527 (534)
                          .......|..+|..||+++|+||.|+|    .+++|++|||+.||+|.++|+++++||+++||+.+....
T Consensus       103 ----~~~~~~~l~~~L~~Lp~~~r~i~~L~~----~~g~s~~EIA~~Lgis~~tVk~~l~Rar~~Lr~~l~~~~  168 (187)
T PRK12516        103 ----GTLDLQDFRAALDQLPDDQREAIILVG----ASGFAYEEAAEICGCAVGTIKSRVNRARQRLQEILQIEG  168 (187)
T ss_pred             ----hHHHHHHHHHHHHhCCHHHHHHHHHHH----HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHhhc
Confidence                112235689999999999999999999    899999999999999999999999999999999987654

>TIGR02943 Sig70_famx1 RNA polymerase sigma-70 factor, TIGR02943 family

Probab=99.81  E-value=7.3e-19  Score=168.65  Aligned_cols=178  Identities=14%  Similarity=0.111  Sum_probs=135.0

Q ss_pred             HHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCchhhHHHHHHHHHHHHHHHHhccccccccchH
Q 009449          299 ELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIPCKLN  378 (534)
Q Consensus       299 ~LI~~nlrLV~sIArrY~~~g~~~eDLiQEG~lgL~rA~ekFDp~kG~rFSTYA~~wIR~aI~~~lr~~sr~iRlP~~~~  378 (534)
                      +.+..|.+.|+.+|+++.++..+++|++||+|+.+|+...+|++.  .+|.+|++..++|.++++++++.+....+.-  
T Consensus         6 ~~~~~~~~~l~~~~~~~~~~~~dAeDivQevfl~l~~~~~~~~~~--~~~~~wL~~iarn~~~d~~R~~~r~~~~~~~--   81 (188)
T TIGR02943         6 QELEQLRRDLLRFARLQLRDRDLAEDAVQETLLAALSHRDSFAGR--SALKTWLFAILKNKIIDALRAKGREVKVSDL--   81 (188)
T ss_pred             HHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhhhhhccc--cHHHHHHHHHHHHHHHHHHHhhcccCCcccc--
Confidence            568889999999999999999999999999999999999999875  3799999999999999999876542211100  


Q ss_pred             HHHHHHHHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHHhhhhcccccccccchhhhhhhccCCCCCCChHHHHHH
Q 009449          379 REISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNAKYLEFAPDRSVKSPKEIVMR  458 (534)
Q Consensus       379 ~~i~ki~ka~~~L~~elGr~Pt~eEIA~~lgis~~kv~~~l~~~~~~~SLD~~i~~~~~~~l~e~i~d~~~~spee~v~~  458 (534)
                                       ...+..                        ..++......  ..+.........++|++.+..
T Consensus        82 -----------------~~~~~~------------------------~~~~~~~~~~--~~~~~~~~~~~~~~~e~~~~~  118 (188)
T TIGR02943        82 -----------------DDELDD------------------------EAFNALFTQN--GHWAQHGQPQHWNTPEKQLEN  118 (188)
T ss_pred             -----------------cccccc------------------------chhhhhhccc--cchhccccccccCCHHHHHHH
Confidence                             000000                        0000000000  000000111122467777888


Q ss_pred             HHHHHHHHHHHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHhhhhc
Q 009449          459 QHMKKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDSETCRD  527 (534)
Q Consensus       459 ~el~e~L~~~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~~l~~~~  527 (534)
                      ++....+..+|..||+++|+||.|+|    .+++|++|||+.||+|.++|++++.||+++||+.+....
T Consensus       119 ~e~~~~l~~~l~~L~~~~r~v~~l~~----~~g~s~~EIA~~lgis~~tvk~rl~Rar~~Lr~~l~~~~  183 (188)
T TIGR02943       119 KEFWEVFEACLYHLPEQTARVFMMRE----VLGFESDEICQELEISTSNCHVLLYRARLSLRACLSINW  183 (188)
T ss_pred             HHHHHHHHHHHHhCCHHHHHHHHHHH----HhCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHHHHh
Confidence            88888899999999999999999999    899999999999999999999999999999999987554

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

>PRK12532 RNA polymerase sigma factor; Provisional

Probab=99.81  E-value=8e-19  Score=168.59  Aligned_cols=181  Identities=17%  Similarity=0.112  Sum_probs=134.6

Q ss_pred             HHHHHHhHHHHHHHHHHhhCCCCC-HHHHHHHHHHHHHHhhhccCCcCCCchhhHHHHHHHHHHHHHHHHhccccccccc
Q 009449          298 EELIKSTRPLVLFLARNYRGLGIP-FSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIPCK  376 (534)
Q Consensus       298 e~LI~~nlrLV~sIArrY~~~g~~-~eDLiQEG~lgL~rA~ekFDp~kG~rFSTYA~~wIR~aI~~~lr~~sr~iRlP~~  376 (534)
                      ++.+..|.+.|+.+|+++.++..+ ++|++||+|+.+|++.++|++.  ..|.+|++..++|.++++++++.+.......
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            356788999999999999999888 9999999999999999999864  3799999999999999999976532111000


Q ss_pred             hHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHHhhhhcccccccccchhhhhhhccCCCCCCChHHHH
Q 009449          377 LNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNAKYLEFAPDRSVKSPKEIV  456 (534)
Q Consensus       377 ~~~~i~ki~ka~~~L~~elGr~Pt~eEIA~~lgis~~kv~~~l~~~~~~~SLD~~i~~~~~~~l~e~i~d~~~~spee~v  456 (534)
                      .                   .....++..                    .+..   ..+ .....+..+ ....+|++.+
T Consensus        86 ~-------------------~~~~~~~~~--------------------~~~~---~~~-~~~~~~~~~-~~~~~~e~~~  121 (195)
T PRK12532         86 L-------------------DDELLDEAF--------------------ESHF---SQN-GHWTPEGQP-QHWNTPEKSL  121 (195)
T ss_pred             c-------------------cccccchhh--------------------hhhh---ccc-cccccccCc-cccCCHHHHH
Confidence            0                   000000000                    0000   000 000000001 1124678888


Q ss_pred             HHHHHHHHHHHHHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHhhhhcc
Q 009449          457 MRQHMKKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDSETCRDL  528 (534)
Q Consensus       457 ~~~el~e~L~~~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~~l~~~~L  528 (534)
                      ...+....+..+|..||+++|+||.|+|    .+++|++|||+.||+|..+|+++++||+++||+++....+
T Consensus       122 ~~~e~~~~l~~~l~~L~~~~r~i~~L~~----~~g~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~l~~~~~  189 (195)
T PRK12532        122 NNNEFQKILQSCLYNLPENTARVFTLKE----ILGFSSDEIQQMCGISTSNYHTIMHRARESLRQCLQIKWF  189 (195)
T ss_pred             HHHHHHHHHHHHHHhCCHHHHHHhhhHH----HhCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHhhc
Confidence            7788888899999999999999999999    8999999999999999999999999999999999876654

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

Probab=99.81  E-value=5.5e-19  Score=164.13  Aligned_cols=156  Identities=19%  Similarity=0.203  Sum_probs=127.4

Q ss_pred             cHHHHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCchhhHHHHHHHHHHHHHHHHhccccc
Q 009449          293 GWYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIK  372 (534)
Q Consensus       293 G~~A~e~LI~~nlrLV~sIArrY~~~g~~~eDLiQEG~lgL~rA~ekFDp~kG~rFSTYA~~wIR~aI~~~lr~~sr~iR  372 (534)
                      +..|++.++..|.+.|+++|.++.++..+++|++||+|+.+|++.++|+.  ...|.+|++..+++.+.+++++..+. .
T Consensus         4 ~~~~~~~l~~~~~~~l~~~~~~~~~~~~~aeDivQe~f~~~~~~~~~~~~--~~~~~~wl~~i~~n~~~d~~rk~~~~-~   80 (162)
T TIGR02983         4 TEEEFTAFVAARYPRLLRTAYLLTGDPHEAEDLVQEALVRTYVRWDRIRD--PDAPDAYVRRVLVNLARSRWRRRRLL-E   80 (162)
T ss_pred             cHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHhhcCC--cccHHHHHHHHHHHHHHHHHHhhccc-c
Confidence            36799999999999999999999999999999999999999999999964  34899999999999999999866420 0


Q ss_pred             cccchHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHHhhhhcccccccccchhhhhhhccCCCCCCCh
Q 009449          373 IPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNAKYLEFAPDRSVKSP  452 (534)
Q Consensus       373 lP~~~~~~i~ki~ka~~~L~~elGr~Pt~eEIA~~lgis~~kv~~~l~~~~~~~SLD~~i~~~~~~~l~e~i~d~~~~sp  452 (534)
                      .+                                                      +...            ++..   +
T Consensus        81 ~~------------------------------------------------------~~~~------------~~~~---~   91 (162)
T TIGR02983        81 LP------------------------------------------------------TREL------------PDAA---A   91 (162)
T ss_pred             cc------------------------------------------------------cccc------------Cccc---C
Confidence            00                                                      0000            0000   0


Q ss_pred             HHHHHHHHHHHHHHHHHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHhh
Q 009449          453 KEIVMRQHMKKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDSET  524 (534)
Q Consensus       453 ee~v~~~el~e~L~~~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~~l~  524 (534)
                      .+........+.|..++..||+++++||.|+|    .+++|.+|||+.||+|.++|++++.||+++||+.+.
T Consensus        92 ~~~~~~~~~~~~l~~~l~~L~~~~r~i~~l~~----~~g~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~l~  159 (162)
T TIGR02983        92 PDPAPDVALRAALARALRRLPARQRAVVVLRY----YEDLSEAQVAEALGISVGTVKSRLSRALARLRELLE  159 (162)
T ss_pred             CccchhHHHHHHHHHHHHhCCHHHHHHhhhHH----HhcCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhc
Confidence            01112334456789999999999999999999    899999999999999999999999999999998865

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.

>PRK12545 RNA polymerase sigma factor; Provisional

Probab=99.81  E-value=9.6e-19  Score=169.54  Aligned_cols=180  Identities=18%  Similarity=0.195  Sum_probs=133.0

Q ss_pred             HHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCchhhHHHHHHHHHHHHHHHHhccccccccchH
Q 009449          299 ELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIPCKLN  378 (534)
Q Consensus       299 ~LI~~nlrLV~sIArrY~~~g~~~eDLiQEG~lgL~rA~ekFDp~kG~rFSTYA~~wIR~aI~~~lr~~sr~iRlP~~~~  378 (534)
                      .++..|.+.|+.+|++++++..+++|++||+|+.+|+..++|++..  .|.||++.+++|.+.++++++.+...++..  
T Consensus        12 ~~~~~~~~~l~~~~~~~~~d~~~AEDivQe~fl~~~~~~~~~~~~~--~~~~WL~~IarN~~~d~~Rk~~r~~~~~~~--   87 (201)
T PRK12545         12 AYLAQLRHDLLRFARLQLRDADAAEDAVQEALAAAWSQAGRFAGQS--AHKTWVFGILRNKLIDTLRARQRTVNLSAL--   87 (201)
T ss_pred             HHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhhhhccccc--hHHHHHHHHHHHHHHHHHHhhccccccccc--
Confidence            4488999999999999999999999999999999999999999753  699999999999999999987532111100  


Q ss_pred             HHHHHHHHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHHhhhhcccccccccchhhhh-hhccCCCCCCChHHHHH
Q 009449          379 REISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNAKY-LEFAPDRSVKSPKEIVM  457 (534)
Q Consensus       379 ~~i~ki~ka~~~L~~elGr~Pt~eEIA~~lgis~~kv~~~l~~~~~~~SLD~~i~~~~~~~l-~e~i~d~~~~spee~v~  457 (534)
                                            .+++..                  ...++...... ...+ .+..++ ...+|++...
T Consensus        88 ----------------------~~~~~~------------------~~~~~~~~~~~-~~~~~~~~~~~-~~~~~~~~~~  125 (201)
T PRK12545         88 ----------------------DAELDG------------------EALLDRELFKD-NGHWAAHAKPR-PWPKPETILQ  125 (201)
T ss_pred             ----------------------ccccch------------------hhhhhhhhhcc-cccccccccCc-CCCCHHHHHH
Confidence                                  000000                  00000000000 0000 000111 1235666666


Q ss_pred             HHHHHHHHHHHHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHhhhhcc
Q 009449          458 RQHMKKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDSETCRDL  528 (534)
Q Consensus       458 ~~el~e~L~~~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~~l~~~~L  528 (534)
                      ..+....+..+|..|||++|+||.|+|    ++++|++|||+.||+|.++|++.++||+++||+.+...++
T Consensus       126 ~~~~~~~l~~~L~~Lp~~~r~v~~L~~----~eg~s~~EIA~~lgis~~tVk~~l~RAr~~Lr~~l~~~~~  192 (201)
T PRK12545        126 QQQFWTLFETCLDHLPEQIGRVFMMRE----FLDFEIDDICTELTLTANHCSVLLYRARTRLRTCLSEKGL  192 (201)
T ss_pred             HHHHHHHHHHHHHhCCHHHHHHHHHHH----HcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHHhc
Confidence            666667899999999999999999999    8999999999999999999999999999999999876554

>PRK12547 RNA polymerase sigma factor; Provisional

Probab=99.81  E-value=1e-18  Score=163.63  Aligned_cols=158  Identities=13%  Similarity=0.107  Sum_probs=126.3

Q ss_pred             HHHHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCchhhHHHHHHHHHHHHHHHHhcccccc
Q 009449          294 WYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKI  373 (534)
Q Consensus       294 ~~A~e~LI~~nlrLV~sIArrY~~~g~~~eDLiQEG~lgL~rA~ekFDp~kG~rFSTYA~~wIR~aI~~~lr~~sr~iRl  373 (534)
                      ...+.+++..|.+.|+.+|+++.++..+++|++||+++.+|+..++|++..  .|.+|++..++|.+.+.+++..+..  
T Consensus         5 ~~~f~~~~~~~~~~l~~~a~~~~~~~~~AeDivQe~fl~l~~~~~~~~~~~--~~~~wl~~i~~n~~~d~~R~~~~~~--   80 (164)
T PRK12547          5 SKNFKQELLLALPALRAFAVSLSSKHDKAEDLVQDTLMKAWAKQDSFEMGT--NLKAWLFTILRNEFYSQMRKRGREV--   80 (164)
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHcCCHhhHHHHHHHHHHHHHHhhhhcCCcc--cHHHHHHHHHHHHHHHHHHhhcccc--
Confidence            357899999999999999999999999999999999999999999998643  6999999999999999998764210  


Q ss_pred             ccchHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHHhhhhcccccccccchhhhhhhccCCCCCCChH
Q 009449          374 PCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNAKYLEFAPDRSVKSPK  453 (534)
Q Consensus       374 P~~~~~~i~ki~ka~~~L~~elGr~Pt~eEIA~~lgis~~kv~~~l~~~~~~~SLD~~i~~~~~~~l~e~i~d~~~~spe  453 (534)
                       ..                                                   .+......         .+   .+++
T Consensus        81 -~~---------------------------------------------------~~~~~~~~---------~~---~~~~   96 (164)
T PRK12547         81 -QD---------------------------------------------------SDGVFTAR---------VA---VHPA   96 (164)
T ss_pred             -cc---------------------------------------------------cccccccc---------CC---CCch
Confidence             00                                                   00000000         00   0111


Q ss_pred             HHHHHHHHHHHHHHHHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHhhh
Q 009449          454 EIVMRQHMKKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDSETC  525 (534)
Q Consensus       454 e~v~~~el~e~L~~~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~~l~~  525 (534)
                      ..  .....+.+..+|..|||++|+||.|+|    .+|+|++|||+.||+|.++|++.++||+++||..+.-
T Consensus        97 ~~--~~~~~~~l~~~l~~L~~~~r~v~~l~~----~~g~s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~l~~  162 (164)
T PRK12547         97 QY--GSLDLQDFKKALNLLSADQREAIILIG----ASGFSYEDAAAICGCAVGTIKSRVSRARNRLQELLKV  162 (164)
T ss_pred             hh--hHHHHHHHHHHHHhCCHHHHHHHHHHH----HcCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHhc
Confidence            11  112245788999999999999999999    8999999999999999999999999999999998754

>PRK09639 RNA polymerase sigma factor SigX; Provisional

Probab=99.81  E-value=1.4e-18  Score=161.78  Aligned_cols=160  Identities=19%  Similarity=0.138  Sum_probs=131.2

Q ss_pred             HHHHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCchhhHHHHHHHHHHHHHHHHhcccccc
Q 009449          294 WYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKI  373 (534)
Q Consensus       294 ~~A~e~LI~~nlrLV~sIArrY~~~g~~~eDLiQEG~lgL~rA~ekFDp~kG~rFSTYA~~wIR~aI~~~lr~~sr~iRl  373 (534)
                      ..|++.++..|.+.|+.+|+++.++..+++|++||+|+.+|++  .|+.  +..|.+|++..+++.+.+++++..+..+.
T Consensus         2 ~~~f~~l~~~y~~~l~~~~~~~~~~~~~aeDlvQe~fi~~~~~--~~~~--~~~~~~wl~~i~rn~~~d~~rk~~~~~~~   77 (166)
T PRK09639          2 DETFEDLFEQYYPDVVQQIFYIVKDRTQAEDLAQEVFLRLYRS--DFKG--IENEKGWLIKSARNVAYNYLRSEKRRRAR   77 (166)
T ss_pred             chHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHH--hccc--ccchHHHHHHHHHHHHHHHHHHhcccccc
Confidence            3589999999999999999999999999999999999999999  6764  34799999999999999999876432111


Q ss_pred             ccchHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHHhhhhcccccccccchhhhhhhccCCCCCCChH
Q 009449          374 PCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNAKYLEFAPDRSVKSPK  453 (534)
Q Consensus       374 P~~~~~~i~ki~ka~~~L~~elGr~Pt~eEIA~~lgis~~kv~~~l~~~~~~~SLD~~i~~~~~~~l~e~i~d~~~~spe  453 (534)
                      ...                                                          .  ....+.   ....+|+
T Consensus        78 ~~~----------------------------------------------------------~--~~~~~~---~~~~~~e   94 (166)
T PRK09639         78 ILG----------------------------------------------------------E--FQWQEV---DNEPSPE   94 (166)
T ss_pred             ccc----------------------------------------------------------h--hhhhhc---cCCCChH
Confidence            000                                                          0  000000   1123677


Q ss_pred             HHHHHHHHHHHHHHHHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHhhh
Q 009449          454 EIVMRQHMKKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDSETC  525 (534)
Q Consensus       454 e~v~~~el~e~L~~~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~~l~~  525 (534)
                      +.+...+....+..+|..||++++.||.++|     +|+|++|||+.||+|..+|+..++||+++||..+..
T Consensus        95 ~~~~~~~~~~~l~~~l~~L~~~~r~il~l~~-----~g~s~~eIA~~lgis~~tV~~~i~ra~~~Lr~~l~~  161 (166)
T PRK09639         95 EIWIRKEEITKVQEVLAKMTERDRTVLLLRF-----SGYSYKEIAEALGIKESSVGTTLARAKKKFRKIYEQ  161 (166)
T ss_pred             HHHHHHHHHHHHHHHHHcCCHHHHHHHHHHH-----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH
Confidence            7777777778899999999999999999998     689999999999999999999999999999998764

>PRK12530 RNA polymerase sigma factor; Provisional

Probab=99.81  E-value=1.2e-18  Score=167.20  Aligned_cols=175  Identities=17%  Similarity=0.090  Sum_probs=132.2

Q ss_pred             HHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCchhhHHHHHHHHHHHHHHHHhccccccccchH
Q 009449          299 ELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIPCKLN  378 (534)
Q Consensus       299 ~LI~~nlrLV~sIArrY~~~g~~~eDLiQEG~lgL~rA~ekFDp~kG~rFSTYA~~wIR~aI~~~lr~~sr~iRlP~~~~  378 (534)
                      ..|..|.+.|+.+|.+|.++..+++|++||+|+.+|+...+|++..  +|.+|++..++|.+.++++++.+..... .. 
T Consensus        11 ~~~~~~~~~l~~~~~~~~~d~~~AeDivQe~flk~~~~~~~~~~~~--~~~~wL~~Ia~n~~~d~~Rk~~~~~~~~-~~-   86 (189)
T PRK12530         11 LEIEEIRLQMLKFATLQLKDADLAEDVVQEALVSAYKNADSFKGQS--ALKTWIFAILKNKIIDLIRYRKRFVNES-EL-   86 (189)
T ss_pred             HHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHhchhccCCc--cHHHHHHHHHHHHHHHHHHhhccCCCcc-cc-
Confidence            4578889999999999999999999999999999999999998753  6999999999999999999765321110 00 


Q ss_pred             HHHHHHHHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHHhhhhcccccccccchhhhhhhccCCCCCCChHHHHHH
Q 009449          379 REISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNAKYLEFAPDRSVKSPKEIVMR  458 (534)
Q Consensus       379 ~~i~ki~ka~~~L~~elGr~Pt~eEIA~~lgis~~kv~~~l~~~~~~~SLD~~i~~~~~~~l~e~i~d~~~~spee~v~~  458 (534)
                                            .++.                   .+....    +.......+........+|++.+..
T Consensus        87 ----------------------~~~~-------------------~~~~~~----~~~~~~~~~~~~~~~~~~~~~~~~~  121 (189)
T PRK12530         87 ----------------------IEED-------------------SPNSFF----DEKGHWKPEYYEPSEWQEVENTVYK  121 (189)
T ss_pred             ----------------------cccc-------------------cchhhh----cccccccccccCCccccCHHHHHHH
Confidence                                  0000                   000000    0000000000001112467777777


Q ss_pred             HHHHHHHHHHHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHhhhh
Q 009449          459 QHMKKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDSETCR  526 (534)
Q Consensus       459 ~el~e~L~~~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~~l~~~  526 (534)
                      .+....+..+|+.||+++|+||.|+|    .+++|++|||+.||+|.++|+++++||+++||+++...
T Consensus       122 ~~~~~~l~~~l~~Lp~~~R~v~~L~~----~~g~s~~EIA~~lgis~~tVk~~l~RAr~~Lr~~l~~~  185 (189)
T PRK12530        122 EEFWLIFEACLNHLPAQQARVFMMRE----YLELSSEQICQECDISTSNLHVLLYRARLQLQACLSKN  185 (189)
T ss_pred             HHHHHHHHHHHHhCCHHHHHHHhHHH----HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHH
Confidence            78888899999999999999999999    89999999999999999999999999999999988643

>PRK12544 RNA polymerase sigma factor; Provisional

Probab=99.81  E-value=1.5e-18  Score=169.23  Aligned_cols=181  Identities=16%  Similarity=0.182  Sum_probs=135.9

Q ss_pred             HHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCchhhHHHHHHHHHHHHHHHHhccccccccc
Q 009449          297 REELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIPCK  376 (534)
Q Consensus       297 ~e~LI~~nlrLV~sIArrY~~~g~~~eDLiQEG~lgL~rA~ekFDp~kG~rFSTYA~~wIR~aI~~~lr~~sr~iRlP~~  376 (534)
                      -..++..|.+.|+.+|+++.++..+++|++||+|+.+|+.+.+|++.  .+|++|++.+++|.+++++++..+....+..
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            36789999999999999999999999999999999999999999864  3799999999999999999977542211100


Q ss_pred             hHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHHhhhhcccccccccchhhhhhhccCCCCCCChHHHH
Q 009449          377 LNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNAKYLEFAPDRSVKSPKEIV  456 (534)
Q Consensus       377 ~~~~i~ki~ka~~~L~~elGr~Pt~eEIA~~lgis~~kv~~~l~~~~~~~SLD~~i~~~~~~~l~e~i~d~~~~spee~v  456 (534)
                      .                  ........+                        +... +. ...+..........+|++.+
T Consensus        98 ~------------------~~~~~~~~~------------------------~~~~-~~-~~~~~~~~~~~~~~~~e~~~  133 (206)
T PRK12544         98 L------------------RDEEEEEDF------------------------EELF-DE-SGHWQKDERPQAWGNPEESL  133 (206)
T ss_pred             c------------------cccchhhHH------------------------HHhh-cc-cccccccccccccCCHHHHH
Confidence            0                  000000000                        0000 00 00000000011124677777


Q ss_pred             HHHHHHHHHHHHHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHhhhhc
Q 009449          457 MRQHMKKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDSETCRD  527 (534)
Q Consensus       457 ~~~el~e~L~~~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~~l~~~~  527 (534)
                      ...+....+..+|..|||++|+||.|+|    ++++|++|||+.||+|..+|++.++||+++||+.+....
T Consensus       134 ~~~e~~~~l~~~L~~L~~~~r~v~~L~~----~~g~s~~EIAe~lgis~~tV~~~l~RAr~~Lr~~l~~~~  200 (206)
T PRK12544        134 EQEQFWRIFEACLDGLPAKYARVFMMRE----FIELETNEICHAVDLSVSNLNVLLYRARLRLRECLENKW  200 (206)
T ss_pred             HHHHHHHHHHHHHHhCCHHHHHHHHHHH----HcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHHh
Confidence            7777778899999999999999999999    899999999999999999999999999999999987543

>PRK09647 RNA polymerase sigma factor SigE; Reviewed

Probab=99.81  E-value=1.8e-18  Score=168.34  Aligned_cols=164  Identities=23%  Similarity=0.294  Sum_probs=136.5

Q ss_pred             HHHHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCchhhHHHHHHHHHHHHHHHHhcccccc
Q 009449          294 WYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKI  373 (534)
Q Consensus       294 ~~A~e~LI~~nlrLV~sIArrY~~~g~~~eDLiQEG~lgL~rA~ekFDp~kG~rFSTYA~~wIR~aI~~~lr~~sr~iRl  373 (534)
                      ..++++|+..|.+.++.++.+|.++..+++|++||+|+.+|++..+|++  + .|.+|++..+|+.+.+++++..+ .+.
T Consensus        27 ~~a~~~l~~~~~~~L~~~~~~~~~~~~~AEDivQEvflkl~~~~~~~~~--~-~~~~wL~~iarn~~~d~~Rk~~~-~~~  102 (203)
T PRK09647         27 MPSWEELVRQHADRVYRLAYRLSGNQHDAEDLTQETFIRVFRSLQNYQP--G-TFEGWLHRITTNLFLDMVRRRAR-IRM  102 (203)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHhCCHhHHHHHHHHHHHHHHHhHHhcCC--c-ccHHHHHHHHHHHHHHHHHhccc-Ccc
Confidence            5799999999999999999999999999999999999999999999985  3 69999999999999999987642 110


Q ss_pred             ccchHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHHhhhhcccccccccchhhhhhhccCCCCCCChH
Q 009449          374 PCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNAKYLEFAPDRSVKSPK  453 (534)
Q Consensus       374 P~~~~~~i~ki~ka~~~L~~elGr~Pt~eEIA~~lgis~~kv~~~l~~~~~~~SLD~~i~~~~~~~l~e~i~d~~~~spe  453 (534)
                        .                                                  .++.    +    + +... ...++|+
T Consensus       103 --~--------------------------------------------------~~~~----~----~-~~~~-~~~~~~~  120 (203)
T PRK09647        103 --E--------------------------------------------------ALPE----D----Y-DRVP-GDEPNPE  120 (203)
T ss_pred             --c--------------------------------------------------cccc----c----c-cccC-CCCCCHH
Confidence              0                                                  0000    0    0 0011 1123566


Q ss_pred             HHHHHHHHHHHHHHHHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHhhhhc
Q 009449          454 EIVMRQHMKKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDSETCRD  527 (534)
Q Consensus       454 e~v~~~el~e~L~~~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~~l~~~~  527 (534)
                      ..+...++.+.|..+|..||+++++||.|+|    .++++++|||+.||+|..+|++.++||+++||+.+...+
T Consensus       121 ~~~~~~~~~~~l~~~L~~L~~~~r~v~~L~~----~~g~s~~EIA~~Lgis~~tV~~~l~RArk~Lr~~l~~~~  190 (203)
T PRK09647        121 QIYHDARLDPDLQAALDSLPPEFRAAVVLCD----IEGLSYEEIAATLGVKLGTVRSRIHRGRQQLRAALAAHA  190 (203)
T ss_pred             HHHHHHHHHHHHHHHHHhCCHHHHHHHHHHH----HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHhc
Confidence            6677777788899999999999999999999    899999999999999999999999999999999887543

>PRK12541 RNA polymerase sigma factor; Provisional

Probab=99.80  E-value=1.9e-18  Score=160.83  Aligned_cols=156  Identities=13%  Similarity=0.117  Sum_probs=124.6

Q ss_pred             HHHHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCchhhHHHHHHHHHHHHHHHHhcccccc
Q 009449          294 WYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKI  373 (534)
Q Consensus       294 ~~A~e~LI~~nlrLV~sIArrY~~~g~~~eDLiQEG~lgL~rA~ekFDp~kG~rFSTYA~~wIR~aI~~~lr~~sr~iRl  373 (534)
                      ..|+++++..|.+.|+.+|.++.++..+++|++||+++.+|+..++|++.   .|.||++..++|.+.+++++..+....
T Consensus         4 ~~a~~~l~~~~~~~l~~~~~~~~~~~~~AeDv~Qe~f~~~~~~~~~~~~~---~~~~wl~~i~~n~~~d~~R~~~~~~~~   80 (161)
T PRK12541          4 KQSLEEIYSEHMQDLFRYLLSLTGDSHFAEDLMQETFYRMLVHIDYYKGE---EIRPWLFTIAYNAFIDWYRKEKKYKTT   80 (161)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHhHHHccCC---ChHHHHHHHHHHHHHHHHHhccccccc
Confidence            46999999999999999999999999999999999999999999999863   599999999999999999876431100


Q ss_pred             ccchHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHHhhhhcccccccccchhhhhhhccCCCCCCChH
Q 009449          374 PCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNAKYLEFAPDRSVKSPK  453 (534)
Q Consensus       374 P~~~~~~i~ki~ka~~~L~~elGr~Pt~eEIA~~lgis~~kv~~~l~~~~~~~SLD~~i~~~~~~~l~e~i~d~~~~spe  453 (534)
                                                                           ..+.         + .  .......++
T Consensus        81 -----------------------------------------------------~~~~---------~-~--~~~~~~~~~   95 (161)
T PRK12541         81 -----------------------------------------------------TIEE---------F-H--LPNVPSTEH   95 (161)
T ss_pred             -----------------------------------------------------chhh---------h-h--ccCCCCcHH
Confidence                                                                 0000         0 0  000001122


Q ss_pred             HHHHHHHHHHHHHHHHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhH
Q 009449          454 EIVMRQHMKKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDS  522 (534)
Q Consensus       454 e~v~~~el~e~L~~~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~~  522 (534)
                      +.....+. ..+..+|..||+++|.||.|+|    .+++|++|||+.||+|..+|++.++||+++||+.
T Consensus        96 ~~~~~~~~-~~~~~~l~~L~~~~r~v~~l~~----~~~~s~~eIA~~lgis~~tv~~~l~Rar~~L~~~  159 (161)
T PRK12541         96 EYFIKHEI-ASWLDSLSSLPLERRNVLLLRD----YYGFSYKEIAEMTGLSLAKVKIELHRGRKETKSI  159 (161)
T ss_pred             HHHHHhHH-HHHHHHHHHCCHHHHHHhhhHH----hcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhh
Confidence            32333333 4556789999999999999999    8999999999999999999999999999999975

>PRK12535 RNA polymerase sigma factor; Provisional

Probab=99.80  E-value=2.6e-18  Score=166.22  Aligned_cols=171  Identities=18%  Similarity=0.097  Sum_probs=132.2

Q ss_pred             HHHHHHHHhc-HHHHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCchhhHHHHHHHHHHHH
Q 009449          284 RVLKQHLAFG-WYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISK  362 (534)
Q Consensus       284 ~~L~~~l~~G-~~A~e~LI~~nlrLV~sIArrY~~~g~~~eDLiQEG~lgL~rA~ekFDp~kG~rFSTYA~~wIR~aI~~  362 (534)
                      .+|...+..| ..|++.++..|.+.++.+++ +.++..+++|++||.|+.+|+..++|++.  ..|.+|++..++|.+++
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            4455666666 77999999999999999975 67888999999999999999999999864  37999999999999999


Q ss_pred             HHHHhccccccccchHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHHhhhhcccccccccchhhhhhh
Q 009449          363 MVARHARGIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNAKYLE  442 (534)
Q Consensus       363 ~lr~~sr~iRlP~~~~~~i~ki~ka~~~L~~elGr~Pt~eEIA~~lgis~~kv~~~l~~~~~~~SLD~~i~~~~~~~l~e  442 (534)
                      ++++..+..+.  +                                                   .+ ... .    .  
T Consensus        90 ~~Rk~~~~~~~--~---------------------------------------------------~~-~~~-~----~--  108 (196)
T PRK12535         90 NIRHDMARPRK--S---------------------------------------------------AT-EYE-D----A--  108 (196)
T ss_pred             HHHhhccCCCc--c---------------------------------------------------cc-ccc-c----c--
Confidence            99976431110  0                                                   00 000 0    0  


Q ss_pred             ccCCCCCCChHHHHHHHHHHHHHHHHHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhH
Q 009449          443 FAPDRSVKSPKEIVMRQHMKKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDS  522 (534)
Q Consensus       443 ~i~d~~~~spee~v~~~el~e~L~~~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~~  522 (534)
                        .+.. ..|+.... ......|..+|+.|||++++||.|+|    ++++|++|||+.||+|.++|++.++||+++||+.
T Consensus       109 --~~~~-~~~~~~~~-~~~~~~l~~~l~~Lp~~~r~v~~l~~----~~g~s~~EIAe~lgis~~tV~~~l~Rar~~Lr~~  180 (196)
T PRK12535        109 --AATT-ASNETTGS-WSEWIDVRTLIDALPPERREALILTQ----VLGYTYEEAAKIADVRVGTIRSRVARARADLIAA  180 (196)
T ss_pred             --cccc-CCcchhHH-HHHHHHHHHHHHcCCHHHHHHhhhHH----HhCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence              0000 11221111 12234789999999999999999999    9999999999999999999999999999999998


Q ss_pred             hhhh
Q 009449          523 ETCR  526 (534)
Q Consensus       523 l~~~  526 (534)
                      +...
T Consensus       181 l~~~  184 (196)
T PRK12535        181 TATG  184 (196)
T ss_pred             hccc
Confidence            7644

>PRK08241 RNA polymerase factor sigma-70; Validated

Probab=99.80  E-value=3.1e-18  Score=178.25  Aligned_cols=188  Identities=20%  Similarity=0.235  Sum_probs=140.0

Q ss_pred             HHHHHHHHhc-HHHHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCchhhHHHHHHHHHHHH
Q 009449          284 RVLKQHLAFG-WYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISK  362 (534)
Q Consensus       284 ~~L~~~l~~G-~~A~e~LI~~nlrLV~sIArrY~~~g~~~eDLiQEG~lgL~rA~ekFDp~kG~rFSTYA~~wIR~aI~~  362 (534)
                      .+|+..+..| ..|+++|+..|.+.|+.+|.++.++..+++|++||+|+.+|+.+++|++.  ..|.+|++..++|.+++
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            4577777777 77999999999999999999999999999999999999999999999853  37999999999999999


Q ss_pred             HHHHhccccccccchHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHHhhhhcccccccccchhhhhhh
Q 009449          363 MVARHARGIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNAKYLE  442 (534)
Q Consensus       363 ~lr~~sr~iRlP~~~~~~i~ki~ka~~~L~~elGr~Pt~eEIA~~lgis~~kv~~~l~~~~~~~SLD~~i~~~~~~~l~e  442 (534)
                      +++++.+.. .+..                  .+. +..                         ........+.+..+.+
T Consensus        85 ~~Rk~~~~~-~~~~------------------~~~-~~~-------------------------~~~~~~~~~~~~~~~~  119 (339)
T PRK08241         85 ALEGRARRP-LPTD------------------LGA-PAA-------------------------DPVDELVERPEVPWLE  119 (339)
T ss_pred             HHHhhcccc-Cccc------------------cCC-CcC-------------------------cccccccccccccccC
Confidence            998764311 0000                  000 000                         0000000000000111


Q ss_pred             ccCCC----CCCChHHHHHHHH-HHHHHHHHHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 009449          443 FAPDR----SVKSPKEIVMRQH-MKKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMT  517 (534)
Q Consensus       443 ~i~d~----~~~spee~v~~~e-l~e~L~~~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~  517 (534)
                      .+++.    ...+|++.+...+ ....|..+|..||+++|+||.|+|    .+++|++|||+.||+|..+|+++++||++
T Consensus       120 ~~~~~~~~~~~~~~e~~~~~~e~~~~~l~~~l~~Lp~~~R~v~~L~~----~~g~s~~EIA~~lgis~~tVk~~l~RAr~  195 (339)
T PRK08241        120 PYPDALLDPAAADPAARVVARESVRLAFVAALQHLPPRQRAVLILRD----VLGWSAAEVAELLDTSVAAVNSALQRARA  195 (339)
T ss_pred             CCCcccccccCCChHHHHHHHHHHHHHHHHHHHhCCHHHhhhhhhHH----hhCCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence            11111    1246777666554 345689999999999999999999    89999999999999999999999999999


Q ss_pred             HHHhH
Q 009449          518 KLRDS  522 (534)
Q Consensus       518 KLR~~  522 (534)
                      +||+.
T Consensus       196 ~Lr~~  200 (339)
T PRK08241        196 TLAER  200 (339)
T ss_pred             HHhhc
Confidence            99983

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

Probab=99.79  E-value=2.9e-18  Score=176.91  Aligned_cols=181  Identities=16%  Similarity=0.146  Sum_probs=135.0

Q ss_pred             HHHHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCchhhHHHHHHHHHHHHHHHHhcccccc
Q 009449          294 WYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKI  373 (534)
Q Consensus       294 ~~A~e~LI~~nlrLV~sIArrY~~~g~~~eDLiQEG~lgL~rA~ekFDp~kG~rFSTYA~~wIR~aI~~~lr~~sr~iRl  373 (534)
                      ..|++.|+..|.+.|+++|.++.++..+++|++||+|+.+|+..++|++.  ..|.+|++..++|.++++++++.+....
T Consensus         4 ~~af~~l~~~~~~~l~~~a~~~~~~~~~AEDivQe~fl~~~~~~~~~~~~--~~~~~WL~~Ia~n~~~d~~Rk~~~~~~~   81 (324)
T TIGR02960         4 GAAFTALAEPHRRELLAHCYRMLGSLHEAEDLVQETLLRAWRARDRFEGR--SSVRTWLYRIATNACLDALEARQRRPRP   81 (324)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHhcCChhhHHHHHHHHHHHHHhhhhccCcc--cchHHHHHHHHHHHHHHHHHhccCCcCc
Confidence            57999999999999999999999999999999999999999999999864  3699999999999999999876431100


Q ss_pred             ccchHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHHhhhhcccccccccchhhhhhhccC-------C
Q 009449          374 PCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNAKYLEFAP-------D  446 (534)
Q Consensus       374 P~~~~~~i~ki~ka~~~L~~elGr~Pt~eEIA~~lgis~~kv~~~l~~~~~~~SLD~~i~~~~~~~l~e~i~-------d  446 (534)
                      ...                  .. ....                         ..+. ...+....+.+.++       .
T Consensus        82 ~~~------------------~~-~~~~-------------------------~~~~-~~~~~~~~~~~~~~~~~~~~~~  116 (324)
T TIGR02960        82 VGL------------------GA-PSAD-------------------------GTAA-ASEAAEVTWLEPLPDLTLDLDD  116 (324)
T ss_pred             ccc------------------CC-CCCc-------------------------cccc-ccccccccccCCCCcccccccc
Confidence            000                  00 0000                         0000 00000000000000       1


Q ss_pred             CCCCChHHHHHHHH-HHHHHHHHHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHhhh
Q 009449          447 RSVKSPKEIVMRQH-MKKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDSETC  525 (534)
Q Consensus       447 ~~~~spee~v~~~e-l~e~L~~~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~~l~~  525 (534)
                      ....+|++.+...+ +...+..+|..|||++|+||.|+|    .+++|++|||+.||+|.++|+++++||+++||+.+..
T Consensus       117 ~~~~~~~~~~~~~e~~~~~l~~~l~~Lp~~~R~v~~L~~----~~g~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~~  192 (324)
T TIGR02960       117 PAAADPSVAAGSRESVRLAFVAAIQYLPPRQRAVLLLRD----VLGWRAAETAELLGTSTASVNSALQRARATLDEVGPS  192 (324)
T ss_pred             CCCCCHHHHHHHHHHHHHHHHHHHHhCCHHHhhHhhhHH----HhCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHhccc
Confidence            11235776665554 456788999999999999999999    8999999999999999999999999999999998774

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.

>TIGR02950 SigM_subfam RNA polymerase sigma factor, SigM family

Probab=99.79  E-value=1e-18  Score=160.63  Aligned_cols=153  Identities=16%  Similarity=0.142  Sum_probs=124.9

Q ss_pred             HHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCchhhHHHHHHHHHHHHHHHHhccccccccchHHH
Q 009449          301 IKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIPCKLNRE  380 (534)
Q Consensus       301 I~~nlrLV~sIArrY~~~g~~~eDLiQEG~lgL~rA~ekFDp~kG~rFSTYA~~wIR~aI~~~lr~~sr~iRlP~~~~~~  380 (534)
                      +..|.+.|+.++.++.++..+++|++||+++.+|+++++|++   .+|.||++..+++.+.++++++.+....+      
T Consensus         1 y~~~~~~l~~~~~~~~~~~~~aeD~~Qe~~~~l~~~~~~~~~---~~f~~wl~~i~~~~~~d~~r~~~~~~~~~------   71 (154)
T TIGR02950         1 YREYMHDVFRYLYRLTKDKHLAEDLLQETFLKAYIHLHSFKD---SSIKPWLFRIARNAFIDWYRKDKKIQTID------   71 (154)
T ss_pred             CchHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhHHHhcC---CchHHHHHHHHHHHHHHHHHHhhhhcccc------
Confidence            357899999999999999899999999999999999999997   37999999999999999998764211000      


Q ss_pred             HHHHHHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHHhhhhcccccccccchhhhhhhccCCCCCCChHHHHHHHH
Q 009449          381 ISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNAKYLEFAPDRSVKSPKEIVMRQH  460 (534)
Q Consensus       381 i~ki~ka~~~L~~elGr~Pt~eEIA~~lgis~~kv~~~l~~~~~~~SLD~~i~~~~~~~l~e~i~d~~~~spee~v~~~e  460 (534)
                                           .+                                   .+.+... +....|++.+...+
T Consensus        72 ---------------------~~-----------------------------------~~~~~~~-~~~~~~~~~~~~~~   94 (154)
T TIGR02950        72 ---------------------DD-----------------------------------AIGDLEQ-HPVESPEHHLLIKI   94 (154)
T ss_pred             ---------------------Hh-----------------------------------hhhhccc-cccCChhHHHHHHH
Confidence                                 00                                   0000000 11125666666667


Q ss_pred             HHHHHHHHHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHh
Q 009449          461 MKKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDSE  523 (534)
Q Consensus       461 l~e~L~~~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~~l  523 (534)
                      ....|..+|..||+++++||.++|    .+|+|++|||+.||+|..+|++.++||+++||+.+
T Consensus        95 ~~~~l~~~l~~L~~~~r~i~~l~~----~~g~s~~eIA~~lgis~~tv~~~l~Ra~~~Lr~~l  153 (154)
T TIGR02950        95 EQEEITHHLSRLPENYRTVLILRE----FKEFSYKEIAELLNLSLAKVKSNLFRARKELKKLL  153 (154)
T ss_pred             HHHHHHHHHHhCCHhheeeeeehh----hccCcHHHHHHHHCCCHHHHHHHHHHHHHHHHHHh
Confidence            777899999999999999999999    89999999999999999999999999999999865

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.

>PRK09637 RNA polymerase sigma factor SigZ; Provisional

Probab=99.79  E-value=5.6e-18  Score=161.72  Aligned_cols=154  Identities=12%  Similarity=0.106  Sum_probs=127.2

Q ss_pred             HHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCchhhHHHHHHHHHHHHHHHHhccccccccc
Q 009449          297 REELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIPCK  376 (534)
Q Consensus       297 ~e~LI~~nlrLV~sIArrY~~~g~~~eDLiQEG~lgL~rA~ekFDp~kG~rFSTYA~~wIR~aI~~~lr~~sr~iRlP~~  376 (534)
                      ++.+++.|.+.|+.+|.++.++..+++|++||+++.+|+.+..|++.  ..|.+|++..+++.+.+++++..+...++. 
T Consensus         3 ~~~l~~~y~~~l~~~~~~~~~~~~~aeDi~QEvflkl~~~~~~~~~~--~~~~~wL~~i~~n~~~d~~Rk~~~~~~~~~-   79 (181)
T PRK09637          3 LESIWSEYKAQLKAFLHSRVSNEADVDDLLQEVLIKTHSNLHSLKDG--SSIKSWLYQIANNTIIDFYRKKNRSEELPD-   79 (181)
T ss_pred             HHHHHHHHHHHHHHHHHHHhCChhhHHHHHHHHHHHHHHhHHHhccc--cchHHHHHHHHHHHHHHHHHhccccCCcch-
Confidence            67899999999999999999999999999999999999999999853  379999999999999999987643111000 


Q ss_pred             hHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHHhhhhcccccccccchhhhhhhccCCCCCCChHHHH
Q 009449          377 LNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNAKYLEFAPDRSVKSPKEIV  456 (534)
Q Consensus       377 ~~~~i~ki~ka~~~L~~elGr~Pt~eEIA~~lgis~~kv~~~l~~~~~~~SLD~~i~~~~~~~l~e~i~d~~~~spee~v  456 (534)
                                                                                +      +...+    .+++..
T Consensus        80 ----------------------------------------------------------~------~~~~~----~~~~~~   91 (181)
T PRK09637         80 ----------------------------------------------------------D------LLFED----EEREEN   91 (181)
T ss_pred             ----------------------------------------------------------h------hhccC----CChhHH
Confidence                                                                      0      00000    112223


Q ss_pred             HHHHHHHHHHHHHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHhhh
Q 009449          457 MRQHMKKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDSETC  525 (534)
Q Consensus       457 ~~~el~e~L~~~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~~l~~  525 (534)
                      ...+....+..+|+.||+++|+||.|+|    .+|++++|||+.||+|..+|+..+.||+++||+.+..
T Consensus        92 ~~~e~~~~l~~~l~~L~~~~r~i~~l~~----~~g~~~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~~  156 (181)
T PRK09637         92 AKKELAPCLRPFIDALPEKYAEALRLTE----LEGLSQKEIAEKLGLSLSGAKSRVQRGRVKLKELLEG  156 (181)
T ss_pred             HHHHHHHHHHHHHHhCCHHHHHHHHHHH----hcCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHHH
Confidence            3445667899999999999999999999    8999999999999999999999999999999998753

>PRK12540 RNA polymerase sigma factor; Provisional

Probab=99.79  E-value=3.8e-18  Score=163.12  Aligned_cols=160  Identities=16%  Similarity=0.156  Sum_probs=128.0

Q ss_pred             HHHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCchhhHHHHHHHHHHHHHHHHhccccccc
Q 009449          295 YCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIP  374 (534)
Q Consensus       295 ~A~e~LI~~nlrLV~sIArrY~~~g~~~eDLiQEG~lgL~rA~ekFDp~kG~rFSTYA~~wIR~aI~~~lr~~sr~iRlP  374 (534)
                      .++..++..+.+.|+.+|.++.++..+++|++||+|+.+|+..++|++..  .|.+|++..++|.+.+.++++.+.... 
T Consensus         5 ~~~~~~~~~~~~~l~~~~~~~~~~~~~AEDivQevflkl~~~~~~~~~~~--~~~~WL~~Ia~n~~~d~~Rk~~~~~~~-   81 (182)
T PRK12540          5 DSLRDDILAAVPSLRAFAISLSGNGDRADDLVQETLLRALANIDSFQPGS--NLPAWLFTILRNLFRSDYRKRRREVED-   81 (182)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhHHhcCCCc--hHHHHHHHHHHHHHHHHHHhccccccc-
Confidence            47789999999999999999999999999999999999999999998753  699999999999999999876431000 


Q ss_pred             cchHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHHhhhhcccccccccchhhhhhhccCCCCCCChHH
Q 009449          375 CKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNAKYLEFAPDRSVKSPKE  454 (534)
Q Consensus       375 ~~~~~~i~ki~ka~~~L~~elGr~Pt~eEIA~~lgis~~kv~~~l~~~~~~~SLD~~i~~~~~~~l~e~i~d~~~~spee  454 (534)
                                                                           .+.        .+.+.. ++   .++.
T Consensus        82 -----------------------------------------------------~~~--------~~~~~~-~~---~~~~   96 (182)
T PRK12540         82 -----------------------------------------------------ADG--------SYAKTL-KS---QPGQ   96 (182)
T ss_pred             -----------------------------------------------------ccc--------cccccc-cC---CCch
Confidence                                                                 000        000000 00   1111


Q ss_pred             HHHHHHHHHHHHHHHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHhhhhcc
Q 009449          455 IVMRQHMKKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDSETCRDL  528 (534)
Q Consensus       455 ~v~~~el~e~L~~~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~~l~~~~L  528 (534)
                      ..  ......|..+|+.|||++|+||.|+|    .+++|++|||+.||+|..+|++.++||+++||+.+.....
T Consensus        97 ~~--~~~~~~l~~~l~~Lp~~~R~v~~L~~----~~g~s~~EIA~~Lgis~~tV~~~l~RAr~~Lr~~l~~~~~  164 (182)
T PRK12540         97 NA--HLEFEEFRAALDKLPQDQREALILVG----ASGFSYEDAAAICGCAVGTIKSRVNRARSKLSALLYVDGA  164 (182)
T ss_pred             HH--HHHHHHHHHHHHhCCHHHHHHhhHHH----HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHhccc
Confidence            11  11234689999999999999999999    8999999999999999999999999999999999886654

>PRK12527 RNA polymerase sigma factor; Reviewed

Probab=99.79  E-value=5.3e-18  Score=157.44  Aligned_cols=155  Identities=14%  Similarity=0.064  Sum_probs=125.8

Q ss_pred             HHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCchhhHHHHHHHHHHHHHHHHhccccccccchHHH
Q 009449          301 IKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIPCKLNRE  380 (534)
Q Consensus       301 I~~nlrLV~sIArrY~~~g~~~eDLiQEG~lgL~rA~ekFDp~kG~rFSTYA~~wIR~aI~~~lr~~sr~iRlP~~~~~~  380 (534)
                      +..|.+.++.++.++.++..+++|++||+|+.+|+..+.|++.   +|.||++..++|.+.++++++.+....       
T Consensus         1 ~~~~~~~l~~~~~~~~~~~~~aeDi~Qevf~~l~~~~~~~~~~---~~~~wL~~ia~n~~~d~~R~~~~~~~~-------   70 (159)
T PRK12527          1 MENYYRELVRFLSARLGNRQAAEDVAHDAYLRVLERSSSAQIE---HPRAFLYRTALNLVVDRHRRHRVRQAE-------   70 (159)
T ss_pred             ChhHHHHHHHHHHHHcCCHhhHHHHHHHHHHHHHhcccccccc---chHHHHHHHHHHHHHHHHHHHhccccc-------
Confidence            3578889999999999998999999999999999999998752   799999999999999999865321000       


Q ss_pred             HHHHHHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHHhhhhcccccccccchhhhhhhccCCCCCCChHHHHHHHH
Q 009449          381 ISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNAKYLEFAPDRSVKSPKEIVMRQH  460 (534)
Q Consensus       381 i~ki~ka~~~L~~elGr~Pt~eEIA~~lgis~~kv~~~l~~~~~~~SLD~~i~~~~~~~l~e~i~d~~~~spee~v~~~e  460 (534)
                                                                    +++. .. +.        .....++|++.+..++
T Consensus        71 ----------------------------------------------~~~~-~~-~~--------~~~~~~~~~~~~~~~~   94 (159)
T PRK12527         71 ----------------------------------------------PLEV-LD-EE--------ERLHSPSPQTRLDLGQ   94 (159)
T ss_pred             ----------------------------------------------chhh-hh-cc--------ccccCCCHHHHHHHHH
Confidence                                                          0000 00 00        0011235677777777


Q ss_pred             HHHHHHHHHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHhhh
Q 009449          461 MKKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDSETC  525 (534)
Q Consensus       461 l~e~L~~~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~~l~~  525 (534)
                      ....+..+|..|||++++||.|+|    ++++|++|||+.||+|.++|+..+.||+++||+.+..
T Consensus        95 ~~~~l~~~l~~L~~~~r~v~~l~~----~~~~s~~eIA~~lgis~~tv~~~l~ra~~~Lr~~l~~  155 (159)
T PRK12527         95 RLALLQRALAELPPACRDSFLLRK----LEGLSHQQIAEHLGISRSLVEKHIVNAMKHCRVRMRQ  155 (159)
T ss_pred             HHHHHHHHHHhCCHHHHHHHHHHH----HcCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHHh
Confidence            778899999999999999999999    8999999999999999999999999999999998764

>TIGR02895 spore_sigI RNA polymerase sigma-I factor

Probab=99.78  E-value=5.2e-18  Score=167.19  Aligned_cols=118  Identities=17%  Similarity=0.267  Sum_probs=106.0

Q ss_pred             HHHhcHHHHHHHHHHhHHHHHHHHHHhhCCC--CCHHHHHHHHHHHHHHhhhccCCcCCCchhhHHHHHHHHHHHHHHHH
Q 009449          289 HLAFGWYCREELIKSTRPLVLFLARNYRGLG--IPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVAR  366 (534)
Q Consensus       289 ~l~~G~~A~e~LI~~nlrLV~sIArrY~~~g--~~~eDLiQEG~lgL~rA~ekFDp~kG~rFSTYA~~wIR~aI~~~lr~  366 (534)
                      .++.|...+++||..|.|+|.++|.+|.++.  .+.+|++|+|++|||+|+++|||++|.+|.|||.+||++.|.+++++
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            3566755599999999999999999998764  58999999999999999999999999999999999999999999998


Q ss_pred             hc---cccccccchHHHHHHHHHHHHHHHHhcCCCCCHHHHHH
Q 009449          367 HA---RGIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAK  406 (534)
Q Consensus       367 ~s---r~iRlP~~~~~~i~ki~ka~~~L~~elGr~Pt~eEIA~  406 (534)
                      ..   +.+++|....+....+..+..++..++++.|+.+||+.
T Consensus        83 ~~k~~~~v~~~~~~~e~~~~~~~~~~~~~~~~~~~~~~eEI~~  125 (218)
T TIGR02895        83 NQKYQNLLYLDEDYDENPLEFNKSMEEYRNEIENENRRLEILE  125 (218)
T ss_pred             cccccCeeeCCchHHHHHHHHHHHHHHHHHHHccccHHHHHHH
Confidence            87   56788876666677888888899999999999999976

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).

>PRK07037 extracytoplasmic-function sigma-70 factor; Validated

Probab=99.78  E-value=8e-18  Score=156.49  Aligned_cols=158  Identities=15%  Similarity=0.184  Sum_probs=126.8

Q ss_pred             HHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCchhhHHHHHHHHHHHHHHHHhccccccccchH
Q 009449          299 ELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIPCKLN  378 (534)
Q Consensus       299 ~LI~~nlrLV~sIArrY~~~g~~~eDLiQEG~lgL~rA~ekFDp~kG~rFSTYA~~wIR~aI~~~lr~~sr~iRlP~~~~  378 (534)
                      .++..+.+.++.+|.++.++..+++|++||+++.+|+....|++.   .|.+|++..+++.+.++++++.+.....    
T Consensus         2 ~~~~~~~~~l~~~~~~~~~~~~~aeDivQe~~l~l~~~~~~~~~~---~~~~wl~~iarn~~~d~~R~~~~~~~~~----   74 (163)
T PRK07037          2 DVFVDNRSMLVKIAARIVGCRSRAEDVVQDAFVKLVEAPNQDAVK---QPVAYLFRIVRNLAIDHYRRQALENKYH----   74 (163)
T ss_pred             hHHHHHHHHHHHHHHHHcCCHhHHHHHHHHHHHHHHhccccCCcc---cHHHHHHHHHHHHHHHHHHhhccccccc----
Confidence            357888999999999999999999999999999999998888763   4889999999999999998765211000    


Q ss_pred             HHHHHHHHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHHhhhhcccccccccchhhhhhhccCCCCCCChHHHHHH
Q 009449          379 REISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNAKYLEFAPDRSVKSPKEIVMR  458 (534)
Q Consensus       379 ~~i~ki~ka~~~L~~elGr~Pt~eEIA~~lgis~~kv~~~l~~~~~~~SLD~~i~~~~~~~l~e~i~d~~~~spee~v~~  458 (534)
                                                                      ..+     +.  .. + .++. ..+|++.+..
T Consensus        75 ------------------------------------------------~~~-----~~--~~-~-~~~~-~~~~~~~~~~   96 (163)
T PRK07037         75 ------------------------------------------------GDE-----ED--GL-D-VPSP-EASPEAALIN   96 (163)
T ss_pred             ------------------------------------------------ccc-----cc--cc-c-cCCC-CCCHHHHHHH
Confidence                                                            000     00  00 0 0111 1356666666


Q ss_pred             HHHHHHHHHHHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHhhh
Q 009449          459 QHMKKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDSETC  525 (534)
Q Consensus       459 ~el~e~L~~~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~~l~~  525 (534)
                      .+..+.+..+|+.|||++|+||.++|    .+++|++|||+.||+|.++|++.+.||+++||..+..
T Consensus        97 ~~~~~~l~~~l~~L~~~~r~v~~l~~----~~~~s~~EIA~~lgis~~tV~~~l~ra~~~lr~~l~~  159 (163)
T PRK07037         97 RDTLRHVADALSELPARTRYAFEMYR----LHGETQKDIARELGVSPTLVNFMIRDALVHCRKCLDA  159 (163)
T ss_pred             HHHHHHHHHHHHhCCHHHHHHHHHHH----HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHhc
Confidence            67778899999999999999999999    8999999999999999999999999999999998754

>PRK09651 RNA polymerase sigma factor FecI; Provisional

Probab=99.78  E-value=1.1e-17  Score=157.90  Aligned_cols=161  Identities=15%  Similarity=0.099  Sum_probs=126.9

Q ss_pred             HHHHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCchhhHHHHHHHHHHHHHHHHhcccccc
Q 009449          294 WYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKI  373 (534)
Q Consensus       294 ~~A~e~LI~~nlrLV~sIArrY~~~g~~~eDLiQEG~lgL~rA~ekFDp~kG~rFSTYA~~wIR~aI~~~lr~~sr~iRl  373 (534)
                      ..|++.++..|.+.++.++.++.++..+++|++||.|+.+|+. ..|++-.  .|.+|++..++|.+.+++++..+..  
T Consensus         9 ~~af~~l~~~~~~~l~~~~~~~~~~~~~AEDlvQe~flkl~~~-~~~~~~~--~~~~wL~~iarn~~~d~~R~~~~~~--   83 (172)
T PRK09651          9 SLTFESLYGTHHGWLKSWLTRKLQSAFDADDIAQDTFLRVMVS-ETLSTIR--DPRSFLCTIAKRVMVDLFRRNALEK--   83 (172)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHcCCHhHHHHHHHHHHHHHHhh-ccccccc--CHHHHHHHHHHHHHHHHHHHHHHHh--
Confidence            4699999999999999999999999999999999999999998 3554432  5899999999999999998653100  


Q ss_pred             ccchHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHHhhhhcccccccccchhhhhhhccCCCCCCChH
Q 009449          374 PCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNAKYLEFAPDRSVKSPK  453 (534)
Q Consensus       374 P~~~~~~i~ki~ka~~~L~~elGr~Pt~eEIA~~lgis~~kv~~~l~~~~~~~SLD~~i~~~~~~~l~e~i~d~~~~spe  453 (534)
                       ..                        .+.                        ++            + +++...++|+
T Consensus        84 -~~------------------------~~~------------------------~~------------~-~~~~~~~~~~  101 (172)
T PRK09651         84 -AY------------------------LEM------------------------LA------------L-MPEGGAPSPE  101 (172)
T ss_pred             -hh------------------------hhH------------------------Hh------------h-ccccCCCChH
Confidence             00                        000                        00            0 0011112444


Q ss_pred             HHHHHHHHHHHHHHHHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHhhh
Q 009449          454 EIVMRQHMKKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDSETC  525 (534)
Q Consensus       454 e~v~~~el~e~L~~~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~~l~~  525 (534)
                      ......+....|..+|..|||++|+||.|+|    ++++|++|||+.||+|.++|+..++||+++|+.....
T Consensus       102 ~~~~~~e~~~~l~~~l~~L~~~~r~i~~l~~----~~g~s~~EIA~~lgis~~tV~~~l~Ra~~~~~~~~~~  169 (172)
T PRK09651        102 ERESQLETLQLLDSMLDGLNGKTREAFLLSQ----LDGLTYSEIAHKLGVSVSSVKKYVAKATEHCLLFRLE  169 (172)
T ss_pred             HHHHHHHHHHHHHHHHHhCCHHHhHHhhhhh----ccCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHHH
Confidence            4454555567799999999999999999999    8999999999999999999999999999999976543

>TIGR02959 SigZ RNA polymerase sigma factor, SigZ family

Probab=99.77  E-value=9.1e-18  Score=158.33  Aligned_cols=148  Identities=14%  Similarity=0.175  Sum_probs=121.9

Q ss_pred             HHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCchhhHHHHHHHHHHHHHHHHhccccccccchHHHH
Q 009449          302 KSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIPCKLNREI  381 (534)
Q Consensus       302 ~~nlrLV~sIArrY~~~g~~~eDLiQEG~lgL~rA~ekFDp~kG~rFSTYA~~wIR~aI~~~lr~~sr~iRlP~~~~~~i  381 (534)
                      ..|.+.|+.++.++.++..+++|++||+++.+|+++.+|++.  .+|.+|++..+++.+.+++++..+...++.      
T Consensus         2 ~~~~~~l~~~~~~~~~~~~~AeDlvQe~fl~l~~~~~~~~~~--~~f~~wl~~iarn~~~d~~Rk~~~~~~~~~------   73 (170)
T TIGR02959         2 DEFRSELKAFIKSRVSDASDVEDLLQEVFIKIHRNLPSLKDG--QKIQSWLYQIARNTIIDFYRSKSRSVELPE------   73 (170)
T ss_pred             chHHHHHHHHHHHHcCCHhhHHHHHHHHHHHHHHHHHhcCCc--ccHHHHHHHHHHHHHHHHHHhccCccccch------
Confidence            468899999999999999999999999999999999999864  489999999999999999988753111100      


Q ss_pred             HHHHHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHHhhhhcccccccccchhhhhhhccCCCCCCChHHHHHHHHH
Q 009449          382 SKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNAKYLEFAPDRSVKSPKEIVMRQHM  461 (534)
Q Consensus       382 ~ki~ka~~~L~~elGr~Pt~eEIA~~lgis~~kv~~~l~~~~~~~SLD~~i~~~~~~~l~e~i~d~~~~spee~v~~~el  461 (534)
                                                                      .            ....   .++++.....+.
T Consensus        74 ------------------------------------------------~------------~~~~---~~~~~~~~~~e~   90 (170)
T TIGR02959        74 ------------------------------------------------S------------LLAA---DSAREETFVKEL   90 (170)
T ss_pred             ------------------------------------------------h------------hccc---CCccHHHHHHHH
Confidence                                                            0            0000   012223334455


Q ss_pred             HHHHHHHHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHhh
Q 009449          462 KKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDSET  524 (534)
Q Consensus       462 ~e~L~~~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~~l~  524 (534)
                      ...+..+|..||+++|+||.|+|    .+++|++|||+.||+|..+|++.++||+++||..+.
T Consensus        91 ~~~l~~~l~~L~~~~r~v~~l~~----~~g~s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~l~  149 (170)
T TIGR02959        91 SQCIPPMIKELPDEYREAIRLTE----LEGLSQQEIAEKLGLSLSGAKSRVQRGRKKLKELLE  149 (170)
T ss_pred             HHHHHHHHHhCCHHHHHHHHHHH----HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence            66799999999999999999999    899999999999999999999999999999999875

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).

>PRK12517 RNA polymerase sigma factor; Provisional

Probab=99.77  E-value=1.5e-17  Score=159.67  Aligned_cols=163  Identities=17%  Similarity=0.132  Sum_probs=128.2

Q ss_pred             HHhcHHHHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCchhhHHHHHHHHHHHHHHHHhcc
Q 009449          290 LAFGWYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHAR  369 (534)
Q Consensus       290 l~~G~~A~e~LI~~nlrLV~sIArrY~~~g~~~eDLiQEG~lgL~rA~ekFDp~kG~rFSTYA~~wIR~aI~~~lr~~sr  369 (534)
                      +.....+++.++..|.+.|+.+|+++.++..+++|++||+|+.+|+....|++.  ..|.+|++..++|.+.+..++..+
T Consensus        18 ~~~~~~~f~~l~~~y~~~l~~~~~~~~~~~~~AeDlvQdvflkl~~~~~~~~~~--~~~~~wL~~Iarn~~~~~~r~~~~   95 (188)
T PRK12517         18 MLSKQRRYEALVKALHADIYRYAYWLCKDKHIAEDLVQETFLRAWRSLDSLKDE--KAAKAWLITILRRENARRFERKQF   95 (188)
T ss_pred             hhccHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhHHhhcCc--cchHHHHHHHHHHHHHHHHHHhcc
Confidence            344578999999999999999999999999999999999999999999999865  369999999999987766543221


Q ss_pred             ccccccchHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHHhhhhcccccccccchhhhhhhccCCCCC
Q 009449          370 GIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNAKYLEFAPDRSV  449 (534)
Q Consensus       370 ~iRlP~~~~~~i~ki~ka~~~L~~elGr~Pt~eEIA~~lgis~~kv~~~l~~~~~~~SLD~~i~~~~~~~l~e~i~d~~~  449 (534)
                      .  ..                                                    ..+.           +...+...
T Consensus        96 ~--~~----------------------------------------------------~~~~-----------~~~~~~~~  110 (188)
T PRK12517         96 D--LV----------------------------------------------------DIED-----------DSIEDDAS  110 (188)
T ss_pred             C--cc----------------------------------------------------Cccc-----------ccccCccc
Confidence            0  00                                                    0000           00011111


Q ss_pred             CChHHHHHHHHHHHHHHHHHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHhhhhc
Q 009449          450 KSPKEIVMRQHMKKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDSETCRD  527 (534)
Q Consensus       450 ~spee~v~~~el~e~L~~~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~~l~~~~  527 (534)
                      .+|+...    ..+.|..+|..||+++|.||.++|    .+++|++|||+.||||..+|+.+++||+++||..+....
T Consensus       111 ~~~e~~~----~~~~l~~~l~~Lp~~~r~v~~l~~----~~g~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~~~~  180 (188)
T PRK12517        111 HSSEEEM----EQEWLRRQIAKLDPEYREPLLLQV----IGGFSGEEIAEILDLNKNTVMTRLFRARNQLKEALEKPD  180 (188)
T ss_pred             cChhHHH----HHHHHHHHHHhCCHHHHHHHHHHH----HhCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHH
Confidence            2333322    235689999999999999999999    899999999999999999999999999999999987543

>PRK12525 RNA polymerase sigma factor; Provisional

Probab=99.76  E-value=3.7e-17  Score=153.62  Aligned_cols=159  Identities=16%  Similarity=0.108  Sum_probs=128.3

Q ss_pred             HHHHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCchhhHHHHHHHHHHHHHHHHhcccccc
Q 009449          294 WYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKI  373 (534)
Q Consensus       294 ~~A~e~LI~~nlrLV~sIArrY~~~g~~~eDLiQEG~lgL~rA~ekFDp~kG~rFSTYA~~wIR~aI~~~lr~~sr~iRl  373 (534)
                      ..++.+++..|.+.++.+|.+|.++..+++|++||+|+.+|+..+.++.   ..|.+|++..++|.+.+++++....   
T Consensus         8 ~~~~~~~~~~~~~~l~~~~~~~~~~~~~aeDlvQevf~~l~~~~~~~~~---~~~~~wl~~Iarn~~~d~~Rr~~~~---   81 (168)
T PRK12525          8 NTLIGQMFQQDYDWLCKKLSRQLGCPHSAEDIASETFLQVLALPDPASI---REPRALLTTIARRLMYEGWRRQDLE---   81 (168)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHcCCcCcHHHHHHHHHHHHHhCCCcccc---cCHHHHHHHHHHHHHHHHHHHHHHH---
Confidence            3588999999999999999999999999999999999999987665543   2699999999999999998764210   


Q ss_pred             ccchHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHHhhhhcccccccccchhhhhhhccCCCCCCChH
Q 009449          374 PCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNAKYLEFAPDRSVKSPK  453 (534)
Q Consensus       374 P~~~~~~i~ki~ka~~~L~~elGr~Pt~eEIA~~lgis~~kv~~~l~~~~~~~SLD~~i~~~~~~~l~e~i~d~~~~spe  453 (534)
                                  +   ....                                 +.+            + .+.+..++|+
T Consensus        82 ------------~---~~~~---------------------------------~~~------------~-~~~~~~~~~~  100 (168)
T PRK12525         82 ------------R---AYLQ---------------------------------SLA------------E-APEAVQPSPE  100 (168)
T ss_pred             ------------H---HHHH---------------------------------HHh------------c-ccccccCChH
Confidence                        0   0000                                 000            0 0011123666


Q ss_pred             HHHHHHHHHHHHHHHHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHh
Q 009449          454 EIVMRQHMKKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDSE  523 (534)
Q Consensus       454 e~v~~~el~e~L~~~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~~l  523 (534)
                      +.....+..+.|..+|..|||++|+||.|+|    .+++|++|||+.||+|..+|+..+.+|+++||..+
T Consensus       101 ~~~~~~~~~~~l~~~l~~L~~~~r~v~~L~~----~eg~s~~EIA~~l~is~~tV~~~l~ra~~~~~~~~  166 (168)
T PRK12525        101 EQWMVIETLLAIDRLLDGLSGKARAAFLMSQ----LEGLTYVEIGERLGVSLSRIHQYMVEAFKCCYQGF  166 (168)
T ss_pred             HHHHHHHHHHHHHHHHHhCCHHHHHHHHHHH----HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHhh
Confidence            6666667778899999999999999999999    89999999999999999999999999999999765

>PRK12546 RNA polymerase sigma factor; Provisional

Probab=99.75  E-value=2.9e-17  Score=158.06  Aligned_cols=157  Identities=15%  Similarity=0.143  Sum_probs=122.3

Q ss_pred             HHHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCchhhHHHHHHHHHHHHHHHHhccccccc
Q 009449          295 YCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIP  374 (534)
Q Consensus       295 ~A~e~LI~~nlrLV~sIArrY~~~g~~~eDLiQEG~lgL~rA~ekFDp~kG~rFSTYA~~wIR~aI~~~lr~~sr~iRlP  374 (534)
                      .+++.|+. |.+.|+++|.++.++..+++|++||+|+.+|+.+..|+..  ..|.+|++..++|.+.+++++..+..   
T Consensus         8 ~~~~~l~~-~~~~l~~~a~~~l~~~~~AEDivQevfl~l~~~~~~~~~~--~~~~awL~~ia~n~~~d~~Rk~~r~~---   81 (188)
T PRK12546          8 DPRDELVE-HLPALRAFAISLTRNVAVADDLVQDTIVKAWTNFDKFQEG--TNLRAWLFTILRNTFYSDRRKHKREV---   81 (188)
T ss_pred             hHHHHHHH-HHHHHHHHHHHHcCChhhHHHHHHHHHHHHHHHHhccCCC--cchHHHHHHHHHHHHHHHHHHhcccc---
Confidence            35566655 7799999999999999999999999999999999999864  37999999999999999998764210   


Q ss_pred             cchHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHHhhhhcccccccccchhhhhhhccCCCCCCChHH
Q 009449          375 CKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNAKYLEFAPDRSVKSPKE  454 (534)
Q Consensus       375 ~~~~~~i~ki~ka~~~L~~elGr~Pt~eEIA~~lgis~~kv~~~l~~~~~~~SLD~~i~~~~~~~l~e~i~d~~~~spee  454 (534)
                      ..                                                   .+.        ...+...+..  ..+.
T Consensus        82 ~~---------------------------------------------------~~~--------~~~~~~~~~~--~~~~  100 (188)
T PRK12546         82 PD---------------------------------------------------PEG--------VHAASLAVKP--AHDG  100 (188)
T ss_pred             cC---------------------------------------------------ccc--------ccccccccCC--cchh
Confidence            00                                                   000        0000000000  1111


Q ss_pred             HHHHHHHHHHHHHHHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHhhhh
Q 009449          455 IVMRQHMKKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDSETCR  526 (534)
Q Consensus       455 ~v~~~el~e~L~~~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~~l~~~  526 (534)
                          ......+..+|..|||++++||.|+|    .+++|.+|||+.||||..+|++++.||+++||+.+...
T Consensus       101 ----~~~~~~l~~~L~~Lp~~~r~v~~L~~----~~g~s~~EIA~~LgiS~~tVk~~l~Rar~~Lr~~l~~~  164 (188)
T PRK12546        101 ----RLAMSDFRAAFAQLPDEQREALILVG----ASGFSYEEAAEMCGVAVGTVKSRANRARARLAELLQLE  164 (188)
T ss_pred             ----HHHHHHHHHHHHhCCHHHhHHhhhHH----hcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHhcc
Confidence                12234688999999999999999999    89999999999999999999999999999999988653

>PRK12511 RNA polymerase sigma factor; Provisional

Probab=99.75  E-value=2.9e-17  Score=157.10  Aligned_cols=158  Identities=15%  Similarity=0.094  Sum_probs=123.4

Q ss_pred             HHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCchhhHHHHHHHHHHHHHHHHhcccccccc
Q 009449          296 CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIPC  375 (534)
Q Consensus       296 A~e~LI~~nlrLV~sIArrY~~~g~~~eDLiQEG~lgL~rA~ekFDp~kG~rFSTYA~~wIR~aI~~~lr~~sr~iRlP~  375 (534)
                      ..+..+..+.+.|+.+|.++.++..+++|++||+|+.+|+....|++.  ..|.+|++..+++.++++++++.+..... 
T Consensus         5 ~~~~~~~~~~~~l~~~~~~~~~~~~dAEDivQe~flkl~~~~~~~~~~--~~~~~WL~~Iarn~~id~~Rk~~~~~~~~-   81 (182)
T PRK12511          5 SKRFDVLDQLVPLRRYARSLTRDSAEAEDLVHDALVRALERRASFRSG--GNLRTWLMSILHNAFIDELRRRRVEARRA-   81 (182)
T ss_pred             chhhhHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhHHhcCCc--cchHHHHHHHHHHHHHHHHHhhccccccc-
Confidence            345557889999999999999999999999999999999999999864  37999999999999999998764311000 


Q ss_pred             chHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHHhhhhcccccccccchhhhhhhccCCCCCCChHHH
Q 009449          376 KLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNAKYLEFAPDRSVKSPKEI  455 (534)
Q Consensus       376 ~~~~~i~ki~ka~~~L~~elGr~Pt~eEIA~~lgis~~kv~~~l~~~~~~~SLD~~i~~~~~~~l~e~i~d~~~~spee~  455 (534)
                                                +++                        +            +. .+...+.+.+ 
T Consensus        82 --------------------------~~~------------------------~------------~~-~~~~~~~~~~-   97 (182)
T PRK12511         82 --------------------------DEL------------------------A------------VL-ADASLPAAQE-   97 (182)
T ss_pred             --------------------------cch------------------------h------------hc-cccCCCcchH-
Confidence                                      000                        0            00 0000011111 


Q ss_pred             HHHHHHHHHHHHHHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHhhhh
Q 009449          456 VMRQHMKKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDSETCR  526 (534)
Q Consensus       456 v~~~el~e~L~~~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~~l~~~  526 (534)
                        .......|..+|..||+++|+||.|+|    .+++|++|||+.||||.++|++.++||+++||..+...
T Consensus        98 --~~~~~~~l~~~l~~Lp~~~R~v~~L~~----~eg~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~~~~~  162 (182)
T PRK12511         98 --HAVRLAQIRDAFFDLPEEQRAALHLVA----IEGLSYQEAAAVLGIPIGTLMSRIGRARAALRAFEEGT  162 (182)
T ss_pred             --HHHHHHHHHHHHHhCCHHHHHHHHHHH----HcCCCHHHHHHHhCcCHHHHHHHHHHHHHHHHHHHHhc
Confidence              122345788999999999999999999    89999999999999999999999999999999987643

>PRK09047 RNA polymerase factor sigma-70; Validated

Probab=99.73  E-value=6.5e-17  Score=149.71  Aligned_cols=155  Identities=14%  Similarity=0.137  Sum_probs=114.2

Q ss_pred             CCCCCHHHHHHHHHHHHHHhhhccCCcCCCchhhHHHHHHHHHHHHHHHHhccccccccchHHHHHHHHHHHHHHHHhcC
Q 009449          317 GLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIPCKLNREISKIQKARKALTNSHG  396 (534)
Q Consensus       317 ~~g~~~eDLiQEG~lgL~rA~ekFDp~kG~rFSTYA~~wIR~aI~~~lr~~sr~iRlP~~~~~~i~ki~ka~~~L~~elG  396 (534)
                      ++..+++|++||+|+.+|+.... ++  +..|.+|++..++|.++++++++.+.......                    
T Consensus         2 ~~~~~AeDivQe~fl~~~~~~~~-~~--~~~~~~wl~~ia~n~~~d~~Rk~~~~~~~~~~--------------------   58 (161)
T PRK09047          2 RDDDAALDIVQDAMIKLAEKYGD-RP--AAEWPPLFQRILQNRIHDWFRRQKVRNTWVSL--------------------   58 (161)
T ss_pred             CCHHHHHHHHHHHHHHHHHHHhh-cc--cCchHHHHHHHHHHHHHHHHHhhccccccccc--------------------
Confidence            34567999999999999999886 33  34799999999999999999876431111000                    


Q ss_pred             CCCCHHHHHHHcCCCHHHHHHHHHHhhhhcccccccccchhhhhhhccCCCC--CCChHHHHHHHHHHHHHHHHHhhCCH
Q 009449          397 KYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNAKYLEFAPDRS--VKSPKEIVMRQHMKKDVFRILESLDS  474 (534)
Q Consensus       397 r~Pt~eEIA~~lgis~~kv~~~l~~~~~~~SLD~~i~~~~~~~l~e~i~d~~--~~spee~v~~~el~e~L~~~L~~L~~  474 (534)
                                                  ..++..... +++....+.+.+..  .++|++.+...+....|..+|..||+
T Consensus        59 ----------------------------~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~Lp~  109 (161)
T PRK09047         59 ----------------------------FSSFSDDDD-DDDFDPLETLDSADEGAESPADKLERAQVLQLIEEAIQKLPA  109 (161)
T ss_pred             ----------------------------ccccccccc-cccccHHHHhccccccCCCHHHHHHHHHHHHHHHHHHHhCCH
Confidence                                        000000000 00011111122211  24678888888888899999999999


Q ss_pred             HHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHhhhhc
Q 009449          475 RERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDSETCRD  527 (534)
Q Consensus       475 rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~~l~~~~  527 (534)
                      ++|+||.|+|    ++++|++|||+.||+|..+|+++++||+++||+.+...+
T Consensus       110 ~~r~v~~l~~----~~g~s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~l~~~~  158 (161)
T PRK09047        110 RQREAFLLRY----WEDMDVAETAAAMGCSEGSVKTHCSRATHALAKALEAKG  158 (161)
T ss_pred             HHHHHHHHHH----HhcCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHhcC
Confidence            9999999999    899999999999999999999999999999999987654

>PRK09636 RNA polymerase sigma factor SigJ; Provisional

Probab=99.72  E-value=1.3e-16  Score=163.24  Aligned_cols=159  Identities=16%  Similarity=0.164  Sum_probs=124.1

Q ss_pred             HHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCchhhHHHHHHHHHHHHHHHHhcccccccc
Q 009449          296 CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIPC  375 (534)
Q Consensus       296 A~e~LI~~nlrLV~sIArrY~~~g~~~eDLiQEG~lgL~rA~ekFDp~kG~rFSTYA~~wIR~aI~~~lr~~sr~iRlP~  375 (534)
                      .+.++++.|.+.++.+|+++.++..++||++||+|+. |.....|++   ..|.+|++..++|.+++++++..+..  ..
T Consensus         5 ~~~~l~~~~~~~l~~~a~~~~~~~~dAEDlvQe~fl~-~~~~~~~~~---~~~~~WL~~Ia~n~~~d~lR~~~~~~--~~   78 (293)
T PRK09636          5 DAAAEFEPLRPHLLSVAYRMLGSVADAEDIVQEAWLR-WNNADRAQI---RDPRAWLTRVVTRLCLDRLRSARHRR--ET   78 (293)
T ss_pred             HHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHH-HHhcccccc---cCHHHHHHHHHHHHHHHHHHhhhccc--cc
Confidence            4678999999999999999999999999999999999 666777763   47999999999999999998754210  00


Q ss_pred             chHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHHhhhhcccccccccchhhhhhhccCCCCCCChHHH
Q 009449          376 KLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNAKYLEFAPDRSVKSPKEI  455 (534)
Q Consensus       376 ~~~~~i~ki~ka~~~L~~elGr~Pt~eEIA~~lgis~~kv~~~l~~~~~~~SLD~~i~~~~~~~l~e~i~d~~~~spee~  455 (534)
                      ..                  +                             ..+..+            ..+.. .+|++.
T Consensus        79 ~~------------------~-----------------------------~~~~e~------------~~~~~-~~~~~~   98 (293)
T PRK09636         79 YV------------------G-----------------------------PWLPEP------------VVEEL-DDPLEA   98 (293)
T ss_pred             cc------------------C-----------------------------CcCCcC------------CCCCC-CChHHH
Confidence            00                  0                             000000            01111 134443


Q ss_pred             H-HHHHHHHHHHHHHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHhh
Q 009449          456 V-MRQHMKKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDSET  524 (534)
Q Consensus       456 v-~~~el~e~L~~~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~~l~  524 (534)
                      . ....+...+..+|+.|||++|+||.|+|    .+++|++|||+.||+|..+|+++++||+++||+...
T Consensus        99 ~~~~~~~~~~l~~~l~~L~~~~R~v~~L~~----~~g~s~~EIA~~lg~s~~tVk~~l~RAr~~Lr~~~~  164 (293)
T PRK09636         99 VVAAEDLSLALMLALERLSPLERAAFLLHD----VFGVPFDEIASTLGRSPAACRQLASRARKHVRAARP  164 (293)
T ss_pred             HHHHHHHHHHHHHHHHhCCHHHHHHHHHHH----HhCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhhCC
Confidence            3 3445556789999999999999999999    899999999999999999999999999999999764

>TIGR02957 SigX4 RNA polymerase sigma-70 factor, TIGR02957 family

Probab=99.68  E-value=8.4e-16  Score=156.72  Aligned_cols=156  Identities=20%  Similarity=0.192  Sum_probs=120.3

Q ss_pred             HHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCchhhHHHHHHHHHHHHHHHHhccccccccchH
Q 009449          299 ELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIPCKLN  378 (534)
Q Consensus       299 ~LI~~nlrLV~sIArrY~~~g~~~eDLiQEG~lgL~rA~ekFDp~kG~rFSTYA~~wIR~aI~~~lr~~sr~iRlP~~~~  378 (534)
                      +++..|.+.++.+|+++.++..++||++||+|+.+++.  .|+..  ..|.+|++.+++|.+++++++..+.......  
T Consensus         1 ~l~~~~~~~l~~~a~r~lg~~~dAEDvvQE~flk~~~~--~~~~~--~~~~awL~~Ia~n~~ld~lR~~~~~~~~~~~--   74 (281)
T TIGR02957         1 EEFEALRPLLFSLAYRMLGSVADAEDIVQETFLRWQEA--DRAQI--ENPKAYLTKVVTRRCIDVLRSARARREVYVG--   74 (281)
T ss_pred             ChHHHHHHHHHHHHHHHhCCHhHHHHHHHHHHHHHHhC--Ccccc--cCHHHHHHHHHHHHHHHHHHHhhhcccccCC--
Confidence            36899999999999999999999999999999997775  45432  3699999999999999999875321000000  


Q ss_pred             HHHHHHHHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHHhhhhcccccccccchhhhhhhccCCCCCCChHHHHHH
Q 009449          379 REISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNAKYLEFAPDRSVKSPKEIVMR  458 (534)
Q Consensus       379 ~~i~ki~ka~~~L~~elGr~Pt~eEIA~~lgis~~kv~~~l~~~~~~~SLD~~i~~~~~~~l~e~i~d~~~~spee~v~~  458 (534)
                                          +                           -+..+            ..+. ..+|++.+..
T Consensus        75 --------------------~---------------------------~~~e~------------~~~~-~~~~~~~~~~   94 (281)
T TIGR02957        75 --------------------P---------------------------WLPEP------------LLTT-SADPAESVEL   94 (281)
T ss_pred             --------------------C---------------------------CCCcc------------cCCC-CCChHHHHHH
Confidence                                0                           00000            0011 1345555443


Q ss_pred             H-HHHHHHHHHHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHhh
Q 009449          459 Q-HMKKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDSET  524 (534)
Q Consensus       459 ~-el~e~L~~~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~~l~  524 (534)
                      . .+...+..+|+.|||+||.||.|+|    ..++|++|||+.||+|..+|+++++||+++||+...
T Consensus        95 ~e~~~~~l~~~l~~L~~~~R~v~~L~~----~~g~s~~EIA~~lg~s~~tVr~~l~RAr~~Lr~~~~  157 (281)
T TIGR02957        95 AESLSMAYLLLLERLSPLERAVFVLRE----VFDYPYEEIASIVGKSEANCRQLVSRARRHLDARRP  157 (281)
T ss_pred             HHHHHHHHHHHHhhCCHHHHHHHHHHH----HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhhCC
Confidence            3 4556788899999999999999999    899999999999999999999999999999998654

This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building and bidirectional best hits, to represent a conserved family. This family is found in a limited number of bacterial lineages. This family includes apparent paralogous expansion in Streptomyces coelicolor A3(2), and multiple copies in Mycobacterium smegmatis MC2, Streptomyces avermitilis MA-4680 and Nocardia farcinica IFM10152.

>PRK09635 sigI RNA polymerase sigma factor SigI; Provisional

Probab=99.68  E-value=1e-15  Score=157.04  Aligned_cols=161  Identities=16%  Similarity=0.095  Sum_probs=124.9

Q ss_pred             HHHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCchhhHHHHHHHHHHHHHHHHhccccccc
Q 009449          295 YCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIP  374 (534)
Q Consensus       295 ~A~e~LI~~nlrLV~sIArrY~~~g~~~eDLiQEG~lgL~rA~ekFDp~kG~rFSTYA~~wIR~aI~~~lr~~sr~iRlP  374 (534)
                      ..+..+++.|.+.++.+|+++.++..++||++||+|+.+|++...+ .   ..|.+|++...+|.+++++++..+.-..+
T Consensus         5 ~~~~~l~~~~~~~L~~~a~r~lgs~~dAEDvvQE~flr~~~~~~~~-~---~~~~aWL~~Ia~n~~id~lRk~~~rr~~~   80 (290)
T PRK09635          5 DPVSAAWRAHRAYLVDLAFRMVGDIGVAEDMVQEAFSRLLRAPVGD-I---DDERGWLIVVTSRLCLDHIKSASTRRERP   80 (290)
T ss_pred             cHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHhcCccc-c---ccHHHHHHHHHHHHHHHHHhhhhccCcCc
Confidence            4688999999999999999999999999999999999999987543 1   26999999999999999998753210000


Q ss_pred             cchHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHHhhhhcccccccccchhhhhhhccCCCCCCChHH
Q 009449          375 CKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNAKYLEFAPDRSVKSPKE  454 (534)
Q Consensus       375 ~~~~~~i~ki~ka~~~L~~elGr~Pt~eEIA~~lgis~~kv~~~l~~~~~~~SLD~~i~~~~~~~l~e~i~d~~~~spee  454 (534)
                      .                                                   ..+...  .     .+..+  ...+|++
T Consensus        81 ~---------------------------------------------------~~~~~~--~-----~~~~~--~~~~~~~  100 (290)
T PRK09635         81 Q---------------------------------------------------DIAAWH--D-----GDASV--SSVDPAD  100 (290)
T ss_pred             c---------------------------------------------------cccccC--c-----cccCC--CCCCcHH
Confidence            0                                                   000000  0     00001  1123443


Q ss_pred             -HHHHHHHHHHHHHHHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHh
Q 009449          455 -IVMRQHMKKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDSE  523 (534)
Q Consensus       455 -~v~~~el~e~L~~~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~~l  523 (534)
                       .....+....+..+|..|||++|.||.|+|    ..++|++|||+.||+|..+|+++++||+++||...
T Consensus       101 ~~~~~~e~~~al~~~L~~L~p~~R~vf~L~~----~~g~s~~EIA~~Lgis~~tVr~~l~RAr~~Lr~~~  166 (290)
T PRK09635        101 RVTLDDEVRLALLIMLERLGPAERVVFVLHE----IFGLPYQQIATTIGSQASTCRQLAHRARRKINESR  166 (290)
T ss_pred             HHHHHHHHHHHHHHHHHhCCHHHHHHhhHHH----HhCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHhhC
Confidence             344556667899999999999999999999    89999999999999999999999999999999854

>PRK06704 RNA polymerase factor sigma-70; Validated

Probab=99.68  E-value=1e-15  Score=152.08  Aligned_cols=158  Identities=20%  Similarity=0.167  Sum_probs=121.6

Q ss_pred             HHHHHHhcHHHHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCchhhHHHHHHHHHHHHHHH
Q 009449          286 LKQHLAFGWYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVA  365 (534)
Q Consensus       286 L~~~l~~G~~A~e~LI~~nlrLV~sIArrY~~~g~~~eDLiQEG~lgL~rA~ekFDp~kG~rFSTYA~~wIR~aI~~~lr  365 (534)
                      |.+.+.....+++.+++.| +.++.+|.++.++..+++|++||+|+.+|+.   |+...  .|.+|++.+++|.+++.++
T Consensus         9 ~~~~~~~~~~~~~~l~~~y-~~L~r~~~~~~~d~~dAEDlvQE~flk~~~~---~~~~~--~~~~WL~~IarN~~id~~R   82 (228)
T PRK06704          9 LKNHIDMNHSNINFLIEQY-GELKRYCTFLTKNKWDGEDLAQETVCKVLQK---YSNKD--ICMTLVYKIARNRWLDQIK   82 (228)
T ss_pred             HhcccCCCHHHHHHHHHHH-HHHHHHHHHHhCCHHHHHHHHHHHHHHHHHH---cCccc--cHHHHHHHHHHHHHHHHHh
Confidence            3344444456888777777 7899999999999999999999999999986   55432  5999999999999999998


Q ss_pred             HhccccccccchHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHHhhhhcccccccccchhhhhhhccC
Q 009449          366 RHARGIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNAKYLEFAP  445 (534)
Q Consensus       366 ~~sr~iRlP~~~~~~i~ki~ka~~~L~~elGr~Pt~eEIA~~lgis~~kv~~~l~~~~~~~SLD~~i~~~~~~~l~e~i~  445 (534)
                      ++.+...+                                                      .+     +        ..
T Consensus        83 k~k~~~~~------------------------------------------------------~~-----~--------~~   95 (228)
T PRK06704         83 SKSVHEKI------------------------------------------------------RD-----Q--------IT   95 (228)
T ss_pred             cccccccc------------------------------------------------------cc-----c--------cc
Confidence            76421000                                                      00     0        00


Q ss_pred             CCCCCChHHHHHHHHHHHHHHHHHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHhhh
Q 009449          446 DRSVKSPKEIVMRQHMKKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDSETC  525 (534)
Q Consensus       446 d~~~~spee~v~~~el~e~L~~~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~~l~~  525 (534)
                         ..++.+..  .+..+.+..+|+.||+++|+|+.|+|    .+++|++|||+.||+|.++|++.++||+++||+.+..
T Consensus        96 ---~~~~~~~~--~~~~~~l~~~L~~Lp~~~R~v~lL~~----~eg~S~~EIAe~LgiS~~tVksrL~Rark~Lr~~l~~  166 (228)
T PRK06704         96 ---FEEPHEKI--ADLHEMVGKVLSSLNVQQSAILLLKD----VFQYSIADIAKVCSVSEGAVKASLFRSRNRLKTVSEE  166 (228)
T ss_pred             ---cCChHHHH--HHHHHHHHHHHHhCCHHHhhHhhhHH----hhCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHh
Confidence               00111111  12345688999999999999999999    8999999999999999999999999999999998754

>TIGR03209 P21_Cbot clostridium toxin-associated regulator BotR

Probab=99.57  E-value=3e-14  Score=130.03  Aligned_cols=136  Identities=14%  Similarity=0.233  Sum_probs=100.8

Q ss_pred             HHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhc-----cCCcCCCchhhHHHHHHHHHHHHHHHHhcccc
Q 009449          297 REELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAER-----FDHTRGYKFSTYVQYWIRKSISKMVARHARGI  371 (534)
Q Consensus       297 ~e~LI~~nlrLV~sIArrY~~~g~~~eDLiQEG~lgL~rA~ek-----FDp~kG~rFSTYA~~wIR~aI~~~lr~~sr~i  371 (534)
                      ++.++..|.++++++|++|...    +| +||.++.+|....+     |++.  ..|.||++..++|.++++++++.+..
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            4689999999999999999652    34 49999999999865     5543  47999999999999999998764210


Q ss_pred             ccccchHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHHhhhhcccccccccchhhhhhhccCCCCCCC
Q 009449          372 KIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNAKYLEFAPDRSVKS  451 (534)
Q Consensus       372 RlP~~~~~~i~ki~ka~~~L~~elGr~Pt~eEIA~~lgis~~kv~~~l~~~~~~~SLD~~i~~~~~~~l~e~i~d~~~~s  451 (534)
                      ...                 .        ..+                        .+                +.. ..
T Consensus        74 ~~~-----------------~--------~~~------------------------~~----------------~~~-~~   87 (142)
T TIGR03209        74 KII-----------------Y--------NSE------------------------IT----------------DIK-LS   87 (142)
T ss_pred             hhh-----------------h--------hhh------------------------hh----------------ccc-cc
Confidence            000                 0        000                        00                000 01


Q ss_pred             hHHHHHHHHHHHHHHHHHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHH
Q 009449          452 PKEIVMRQHMKKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIR  509 (534)
Q Consensus       452 pee~v~~~el~e~L~~~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVR  509 (534)
                      +.+.+...+....+..+|+.|||.+|+||.|+|    .+++|++|||+.||+|.+||+
T Consensus        88 ~~~~~~~~~~~~~l~~~l~~Lp~~~r~v~~l~~----~~~~s~~EIA~~l~is~~tV~  141 (142)
T TIGR03209        88 LINVYSSNDLEFEFNDLISILPNKQKKIIYMKF----FEDMKEIDIAKKLHISRQSVY  141 (142)
T ss_pred             hhHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHH----HcCCCHHHHHHHHCcCHHhhc
Confidence            122333444556788999999999999999999    899999999999999999997

Similarly, tetanus toxin production of Clostridium tetani is regulated by TetR which is a very close relative of BotR. Both BotR and TetR are members of the TIGR02937 subfamily of sigma-70 RNA polymerase sigma factors. Functional complementation experiments have been done for botR and tetR in highly transformable strain of Clostridium perfringens host cells to assess functional interchangeability of sigma factors and it has been confirmed that they are interchangeable in vivo.

>PRK09191 two-component response regulator; Provisional

Probab=99.56  E-value=3.6e-14  Score=140.44  Aligned_cols=137  Identities=18%  Similarity=0.124  Sum_probs=112.4

Q ss_pred             HHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCchhhHHHHHHHHHHHHHHHHhcccccccc
Q 009449          296 CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIPC  375 (534)
Q Consensus       296 A~e~LI~~nlrLV~sIArrY~~~g~~~eDLiQEG~lgL~rA~ekFDp~kG~rFSTYA~~wIR~aI~~~lr~~sr~iRlP~  375 (534)
                      |+..++..|.+.|+++|.++.++..+++|++||+++.+|+...+|++.  ..|.+|++.++++......          .
T Consensus         2 ~~~~l~~~~~~~l~~~~~~~~~~~~~aeDi~qd~~~~~~~~~~~~~~~--~~~~~wl~~~~~~~~~~~~----------~   69 (261)
T PRK09191          2 SLSQRIAPHLPYLRRYARALTGSQSSGDAYVAATLEALLADPSIFPEA--SSPRVGLYRLFHRLWSSAG----------A   69 (261)
T ss_pred             chHHHHHHHhHHHHHHHHHhcCChhhHHHHHHHHHHHHHHhHHhcCCC--cchhhHHHHHHHHHhcccc----------c
Confidence            578999999999999999999999999999999999999999999874  3689999987765321000          0


Q ss_pred             chHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHHhhhhcccccccccchhhhhhhccCCCCCCChHHH
Q 009449          376 KLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNAKYLEFAPDRSVKSPKEI  455 (534)
Q Consensus       376 ~~~~~i~ki~ka~~~L~~elGr~Pt~eEIA~~lgis~~kv~~~l~~~~~~~SLD~~i~~~~~~~l~e~i~d~~~~spee~  455 (534)
                                                                           +     .         ...  ..+.. 
T Consensus        70 -----------------------------------------------------~-----~---------~~~--~~~~~-   79 (261)
T PRK09191         70 -----------------------------------------------------N-----D---------PEP--GSPFE-   79 (261)
T ss_pred             -----------------------------------------------------c-----C---------CCC--CCCch-
Confidence                                                                 0     0         000  01111 


Q ss_pred             HHHHHHHHHHHHHHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHhhh
Q 009449          456 VMRQHMKKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDSETC  525 (534)
Q Consensus       456 v~~~el~e~L~~~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~~l~~  525 (534)
                             ..+..+|+.||+++|+|+.|+|    .+++|++|||+.||+|.++|+.+.++|+++||..+..
T Consensus        80 -------~~l~~~l~~L~~~~r~v~~l~~----~~~~s~~eIA~~l~~s~~tV~~~l~ra~~~l~~~~~~  138 (261)
T PRK09191         80 -------ARAERRLAGLTPLPRQAFLLTA----LEGFSVEEAAEILGVDPAEAEALLDDARAEIARQVAT  138 (261)
T ss_pred             -------HHHHHHHHhCCHHHhHHHHHHH----HhcCCHHHHHHHHCCCHHHHHHHHHHHHHHHhccCCC
Confidence                   1688899999999999999999    8999999999999999999999999999999987653

>PRK08311 putative RNA polymerase sigma factor SigI; Reviewed

Probab=99.45  E-value=3.9e-12  Score=127.18  Aligned_cols=89  Identities=19%  Similarity=0.321  Sum_probs=80.2

Q ss_pred             CHHHHHHHHHhc-HHHHHHHHHHhHHHHHHHHHHhhCCCC--CHHHHHHHHHHHHHHhhhccCCcCCCchhhHHHHHHHH
Q 009449          282 SERVLKQHLAFG-WYCREELIKSTRPLVLFLARNYRGLGI--PFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRK  358 (534)
Q Consensus       282 d~~~L~~~l~~G-~~A~e~LI~~nlrLV~sIArrY~~~g~--~~eDLiQEG~lgL~rA~ekFDp~kG~rFSTYA~~wIR~  358 (534)
                      +.+.|+..++.| ..|++.|+..|.++|+++|.+|.++..  +.+|++|||++++|+++++||+.+|..|.+|++++|++
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            455677777777 679999999999999999999998865  59999999999999999999999888999999999999


Q ss_pred             HHHHHHHHhccc
Q 009449          359 SISKMVARHARG  370 (534)
Q Consensus       359 aI~~~lr~~sr~  370 (534)
                      .+.+++++..+.
T Consensus        84 ~~iDylRk~~~~   95 (237)
T PRK08311         84 RLIDYFRKESKH   95 (237)
T ss_pred             HHHHHHHHhhcc
Confidence            999999987653

>PF07638 Sigma70_ECF: ECF sigma factor

Probab=99.44  E-value=7.3e-12  Score=120.30  Aligned_cols=175  Identities=19%  Similarity=0.253  Sum_probs=124.1

Q ss_pred             HHHHHHHHHhc-HHHHHHHHHHhHHHHHHHHHHhhCC---CCCHHHH--HHHHHHHHHHhhhccCCcCCCchhhHHHHHH
Q 009449          283 ERVLKQHLAFG-WYCREELIKSTRPLVLFLARNYRGL---GIPFSDL--LQAGNVGVLQGAERFDHTRGYKFSTYVQYWI  356 (534)
Q Consensus       283 ~~~L~~~l~~G-~~A~e~LI~~nlrLV~sIArrY~~~---g~~~eDL--iQEG~lgL~rA~ekFDp~kG~rFSTYA~~wI  356 (534)
                      ...|+..++.| ..|.+.|+..|++.++.+|+++...   +.+.+|.  ++|+|+.+++.-...+++....|-.|+...+
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            35677888888 6799999999999999999987633   3455554  6777887776433323333346888999999


Q ss_pred             HHHHHHHHHHhccccccccchHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHHhhhhcccccccccch
Q 009449          357 RKSISKMVARHARGIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCL  436 (534)
Q Consensus       357 R~aI~~~lr~~sr~iRlP~~~~~~i~ki~ka~~~L~~elGr~Pt~eEIA~~lgis~~kv~~~l~~~~~~~SLD~~i~~~~  436 (534)
                      ++.+.+.++.+.+..|-...                                               ...+||....   
T Consensus        84 rr~lid~~R~~~a~KRg~~~-----------------------------------------------~~~~l~~~~~---  113 (185)
T PF07638_consen   84 RRKLIDHARRRQAQKRGGDQ-----------------------------------------------VRVELDERAD---  113 (185)
T ss_pred             HHHHHHHHHHHHHHhcCCCC-----------------------------------------------cccchhhhhc---
Confidence            99999999876532221110                                               0012221110   


Q ss_pred             hhhhhhccCCCCCCChHHHHHHHHHHHHHHHHHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHH
Q 009449          437 NAKYLEFAPDRSVKSPKEIVMRQHMKKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAM  516 (534)
Q Consensus       437 ~~~l~e~i~d~~~~spee~v~~~el~e~L~~~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL  516 (534)
                               +...++|++.+   ++.+.+..+.. |+|++++||.++|    +.|+|.+|||+.||||+.||+.....|.
T Consensus       114 ---------~~~~~~~~~~~---~l~e~l~~L~~-l~~~~~~~v~l~~----~~Gls~~EIA~~lgiS~~tV~r~l~~aR  176 (185)
T PF07638_consen  114 ---------SGDEPSPEELL---ELEEALERLLA-LDPRQRRVVELRF----FEGLSVEEIAERLGISERTVRRRLRRAR  176 (185)
T ss_pred             ---------cccCCCHHHHH---HHHHHHHHHHc-cCHHHHHHHHHHH----HCCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence                     01113555544   34445555555 9999999999999    8999999999999999999999999999


Q ss_pred             HHHHhHhh
Q 009449          517 TKLRDSET  524 (534)
Q Consensus       517 ~KLR~~l~  524 (534)
                      .+|+..+.
T Consensus       177 ~~l~~~l~  184 (185)
T PF07638_consen  177 AWLRRELR  184 (185)
T ss_pred             HHHHHHhc
Confidence            99998764

>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=99.27  E-value=1.2e-11  Score=99.00  Aligned_cols=70  Identities=24%  Similarity=0.375  Sum_probs=67.0

Q ss_pred             HHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCchhhHHHHHHHHHHHHHHHHhcc
Q 009449          300 LIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHAR  369 (534)
Q Consensus       300 LI~~nlrLV~sIArrY~~~g~~~eDLiQEG~lgL~rA~ekFDp~kG~rFSTYA~~wIR~aI~~~lr~~sr  369 (534)
                      |++.|.++|+.+|++|.+++.+++|++||+++++|+++++||++++..|.+|++..+++.+.+.++++.|
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            6899999999999999999999999999999999999999999999899999999999999999997754

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 ....

>PF04539 Sigma70_r3: Sigma-70 region 3; InterPro: IPR007624 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription

Probab=99.23  E-value=2.1e-11  Score=100.83  Aligned_cols=78  Identities=33%  Similarity=0.483  Sum_probs=67.2

Q ss_pred             HHHHHHHHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHHhhhhcccccccccchhhhhhhccCCCCCCChHHHH
Q 009449          379 REISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNAKYLEFAPDRSVKSPKEIV  456 (534)
Q Consensus       379 ~~i~ki~ka~~~L~~elGr~Pt~eEIA~~lgis~~kv~~~l~~~~~~~SLD~~i~~~~~~~l~e~i~d~~~~spee~v  456 (534)
                      +.+++|.+++++|.+++||.||.+|||+.|||++++|..++.+.+.+.|||.+++.+++..+.++++|+..++|++.+
T Consensus         1 E~l~~i~~a~~~L~~~lgr~Pt~eEiA~~lgis~~~v~~~l~~~~~~~Sl~~~~~~~~~~~l~~~i~d~~~~~P~e~~   78 (78)
T PF04539_consen    1 EKLRKIERARRELEQELGREPTDEEIAEELGISVEEVRELLQASRRPVSLDLPVGDEDDSTLGDFIEDDDAPSPEEEV   78 (78)
T ss_dssp             HHHHHHHHHHHHHHHHHSS--BHHHHHHHHTS-HHHHHHHHHHHSCCEESSHCCSSSSSEEGGGSSB-SSS--HHHH-
T ss_pred             ChHHHHHHHHHHHHHHhCCCCCHHHHHHHHcccHHHHHHHHHhCCCCeEEeeeecCCCCCchhheecCCCCCChhhcc
Confidence            468999999999999999999999999999999999999999999999999999988889999999999888998754

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 ....

>PF04545 Sigma70_r4: Sigma-70, region 4; InterPro: IPR007630 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription

Probab=99.21  E-value=3.7e-11  Score=91.39  Aligned_cols=50  Identities=40%  Similarity=0.650  Sum_probs=46.4

Q ss_pred             HHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHh
Q 009449          468 ILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRD  521 (534)
Q Consensus       468 ~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~  521 (534)
                      +|+.|||+|++||.++|    ++++|++|||+.||+|+++|++++.+|++|||+
T Consensus         1 Al~~L~~~er~vi~~~y----~~~~t~~eIa~~lg~s~~~V~~~~~~al~kLR~   50 (50)
T PF04545_consen    1 ALDQLPPREREVIRLRY----FEGLTLEEIAERLGISRSTVRRILKRALKKLRK   50 (50)
T ss_dssp             HHCTS-HHHHHHHHHHH----TST-SHHHHHHHHTSCHHHHHHHHHHHHHHHHH
T ss_pred             ChhhCCHHHHHHHHHHh----cCCCCHHHHHHHHCCcHHHHHHHHHHHHHHhcC
Confidence            58899999999999999    899999999999999999999999999999995

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 ....

>PF08281 Sigma70_r4_2: Sigma-70, region 4; InterPro: IPR013249 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription

Probab=98.95  E-value=2.3e-09  Score=82.52  Aligned_cols=54  Identities=26%  Similarity=0.500  Sum_probs=46.5

Q ss_pred             HHHHHHHHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Q 009449          462 KKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKL  519 (534)
Q Consensus       462 ~e~L~~~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KL  519 (534)
                      ++.|..++..|||++|+||.++|    .+++|++|||+.+|+|.++|++.+.+|+++|
T Consensus         1 r~~l~~~l~~L~~~~r~i~~l~~----~~g~s~~eIa~~l~~s~~~v~~~l~ra~~~L   54 (54)
T PF08281_consen    1 REALQQALAQLPERQREIFLLRY----FQGMSYAEIAEILGISESTVKRRLRRARKKL   54 (54)
T ss_dssp             HHHHHHHHHCS-HHHHHHHHHHH----TS---HHHHHHHCTS-HHHHHHHHHHHHHHH
T ss_pred             CHHHHHHHHCCCHHHHHHHHHHH----HHCcCHHHHHHHHCcCHHHHHHHHHHHHhhC
Confidence            35789999999999999999999    9999999999999999999999999999987

Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 promoter element via a helix-turn-helix motif [].; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 2LFW_A 1OR7_B 2H27_D 2O8X_B.

>PRK06930 positive control sigma-like factor; Validated

Probab=98.74  E-value=1.9e-07  Score=89.20  Aligned_cols=72  Identities=19%  Similarity=0.232  Sum_probs=64.1

Q ss_pred             ChHHHHHHHHHHHHHHHHHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHhhhh
Q 009449          451 SPKEIVMRQHMKKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDSETCR  526 (534)
Q Consensus       451 spee~v~~~el~e~L~~~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~~l~~~  526 (534)
                      .|.+.....+....|..++..|||++++||.|+|    .+++|++|||+.||+|.++|++++.||+++|+..+...
T Consensus        94 ~~~~~~~~~e~~~~l~~al~~L~~rer~V~~L~~----~eg~s~~EIA~~lgiS~~tVk~~l~Ra~~kLr~~l~~~  165 (170)
T PRK06930         94 EEPESVISEWDKIRIEDALSVLTEREKEVYLMHR----GYGLSYSEIADYLNIKKSTVQSMIERAEKKIARQINES  165 (170)
T ss_pred             CChhHHHHHHHHHHHHHHHHhCCHHHHHHHHHHH----HcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHh
Confidence            3445555666778899999999999999999999    89999999999999999999999999999999987644

>PRK00118 putative DNA-binding protein; Validated

Probab=98.43  E-value=9.6e-07  Score=77.74  Aligned_cols=61  Identities=26%  Similarity=0.195  Sum_probs=55.2

Q ss_pred             HHHHHHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHhhhhcc
Q 009449          464 DVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDSETCRDL  528 (534)
Q Consensus       464 ~L~~~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~~l~~~~L  528 (534)
                      .+.-....||+++++|+.++|    .+++|.+|||+.+|+|++||+.++.+|+++||+++..-++
T Consensus        10 l~d~~~~~L~ekqRevl~L~y----~eg~S~~EIAe~lGIS~~TV~r~L~RArkkLr~~~~~~~~   70 (104)
T PRK00118         10 LFDFYGSLLTEKQRNYMELYY----LDDYSLGEIAEEFNVSRQAVYDNIKRTEKLLEDYEEKLHL   70 (104)
T ss_pred             HHHHHhccCCHHHHHHHHHHH----HcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHHCh
Confidence            444466789999999999999    8999999999999999999999999999999998876654

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

Probab=98.31  E-value=1.9e-06  Score=64.17  Aligned_cols=54  Identities=33%  Similarity=0.547  Sum_probs=50.0

Q ss_pred             HHHHHHHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 009449          463 KDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLR  520 (534)
Q Consensus       463 e~L~~~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR  520 (534)
                      +.+..++..|++.++.++.++|    .+++|..+||+.+|+|..+|+++..++..+|+
T Consensus         2 ~~~~~~~~~l~~~~~~~~~~~~----~~~~~~~~ia~~~~~s~~~i~~~~~~~~~~l~   55 (55)
T cd06171           2 ERLEEALDKLPEREREVILLRF----GEGLSYEEIAEILGISRSTVRQRLHRALKKLR   55 (55)
T ss_pred             HHHHHHHHhCCHHHHHHHHHHH----hcCCCHHHHHHHHCcCHHHHHHHHHHHHHHcC
Confidence            3577889999999999999999    78999999999999999999999999998874

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

>TIGR00721 tfx DNA-binding protein, Tfx family

Probab=98.18  E-value=3.6e-06  Score=77.64  Aligned_cols=57  Identities=28%  Similarity=0.406  Sum_probs=49.5

Q ss_pred             hhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHhhhhcchhh
Q 009449          470 ESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDSETCRDLSHF  531 (534)
Q Consensus       470 ~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~~l~~~~L~~y  531 (534)
                      ..|+++|++|+.|++     +|+|++|||+.||+|+++|++++++|+++|+.....-.+-.+
T Consensus         5 ~~Lte~qr~VL~Lr~-----~GlTq~EIAe~LgiS~stV~~~e~ra~kkLr~a~~~~~l~~~   61 (137)
T TIGR00721         5 TFLTERQIKVLELRE-----KGLSQKEIAKELKTTRANVSAIEKRAMENIEKARNTLDFVKF   61 (137)
T ss_pred             CCCCHHHHHHHHHHH-----cCCCHHHHHHHHCcCHHHHHHHHHhHHHHHHHHhhHHHHHHH
Confidence            359999999999975     899999999999999999999999999999986555544433

Tfx from Methanobacterium thermoautotrophicum is associated with the operon for molybdenum formyl-methanofuran dehydrogenase and binds a DNA sequence near its promoter.

>PRK03975 tfx putative transcriptional regulator; Provisional

Probab=98.14  E-value=5.1e-06  Score=76.96  Aligned_cols=51  Identities=25%  Similarity=0.367  Sum_probs=47.0

Q ss_pred             hhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHhhh
Q 009449          470 ESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDSETC  525 (534)
Q Consensus       470 ~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~~l~~  525 (534)
                      ..|+|+|++||.+++     +++|++|||+.||+|+.+|++++++|+++||+....
T Consensus         5 ~~Lt~rqreVL~lr~-----~GlTq~EIAe~LGiS~~tVs~ie~ra~kkLr~~~~t   55 (141)
T PRK03975          5 SFLTERQIEVLRLRE-----RGLTQQEIADILGTSRANVSSIEKRARENIEKARET   55 (141)
T ss_pred             cCCCHHHHHHHHHHH-----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH
Confidence            469999999999965     899999999999999999999999999999987654

>PRK04217 hypothetical protein; Provisional

Probab=98.11  E-value=5.9e-06  Score=73.49  Aligned_cols=56  Identities=20%  Similarity=0.032  Sum_probs=51.5

Q ss_pred             hhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHhhhhcch
Q 009449          470 ESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDSETCRDLS  529 (534)
Q Consensus       470 ~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~~l~~~~L~  529 (534)
                      ..|++.|++|+.++|    .+++|++|||+.+|||+.||++++.+|+++|++.+......
T Consensus        41 ~~Lt~eereai~l~~----~eGlS~~EIAk~LGIS~sTV~r~L~RArkkLre~L~~~~~~   96 (110)
T PRK04217         41 IFMTYEEFEALRLVD----YEGLTQEEAGKRMGVSRGTVWRALTSARKKVAQMLVEGREL   96 (110)
T ss_pred             ccCCHHHHHHHHHHH----HcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHhccce
Confidence            569999999999999    89999999999999999999999999999999998765543

>PF04297 UPF0122: Putative helix-turn-helix protein, YlxM / p13 like; InterPro: IPR007394 Members of this family are predicted to contain a helix-turn-helix motif, for example residues 37-55 in Mycoplasma mycoides p13 (O05290 from SWISSPROT)

Probab=98.00  E-value=3.1e-05  Score=67.84  Aligned_cols=54  Identities=30%  Similarity=0.370  Sum_probs=43.5

Q ss_pred             hhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHhhhhc
Q 009449          470 ESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDSETCRD  527 (534)
Q Consensus       470 ~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~~l~~~~  527 (534)
                      .-|+++|++++.++|    .+++|+.|||+.+|||+.+|...+.||.++|...-..-+
T Consensus        16 ~LLT~kQ~~~l~lyy----~eDlSlsEIAe~~~iSRqaV~d~ikr~~~~L~~yE~kL~   69 (101)
T PF04297_consen   16 ELLTEKQREILELYY----EEDLSLSEIAEELGISRQAVYDSIKRAEKKLEEYEEKLG   69 (101)
T ss_dssp             GGS-HHHHHHHHHHC----TS---HHHHHHHCTS-HHHHHHHHHHHHHHHHHHHHHH-
T ss_pred             HHCCHHHHHHHHHHH----ccCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHh
Confidence            449999999999999    899999999999999999999999999999987654443

Genes encoding family members are often part of operons that encode components of the SRP pathway, and this protein may regulate the expression of an operon related to the SRP pathway [].; PDB: 1S7O_A 1XSV_B.

>TIGR01636 phage_rinA phage transcriptional activator, RinA family

Probab=97.88  E-value=5.9e-05  Score=69.29  Aligned_cols=60  Identities=13%  Similarity=0.227  Sum_probs=54.1

Q ss_pred             HHHHHHHHHHhhCCHHHHHHHhhHhcCCCCCC--CCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHh
Q 009449          460 HMKKDVFRILESLDSRERQVLVLRYGLNDHRP--KSLEEIGKLFHVSKEWIRKLEKKAMTKLRDSE  523 (534)
Q Consensus       460 el~e~L~~~L~~L~~rEReVL~LryGL~d~e~--~Sl~EIA~~LgISrerVRqi~~RAL~KLR~~l  523 (534)
                      ...+.|..+|+.|++.+++||.++|    +.+  +|..+||..||+|+.+|+++..+|+.+|+..+
T Consensus        71 ~~~~~I~~~l~~Ld~~er~II~~rY----~~~~~~t~~~Ia~~l~iS~~t~~r~r~~~l~kla~~l  132 (134)
T TIGR01636        71 RNRDAIENCLNEADEQTRVIIQELY----MKKRPLTLVGLAQQLFISKSTAYRLRNHIIEAVAEEL  132 (134)
T ss_pred             HHHHHHHHHHHhCCHHHHHHHHHHH----ccCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHh
Confidence            4566789999999999999999999    443  59999999999999999999999999999765

This model represents a family of phage proteins, including RinA, a transcriptional activator in staphylococcal phage phi 11. This family shows similarity to ArpU, a phage-related putative autolysin regulator, and to some sporulation-specific sigma factors.

>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon

Probab=97.83  E-value=3.7e-05  Score=58.25  Aligned_cols=47  Identities=30%  Similarity=0.309  Sum_probs=42.3

Q ss_pred             hhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHh
Q 009449          470 ESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRD  521 (534)
Q Consensus       470 ~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~  521 (534)
                      ..|+++|+.|+.+.+     .++|.+|||+.+|+|+.+|+++..+++.+|..
T Consensus         2 ~~l~~~e~~i~~~~~-----~g~s~~eia~~l~is~~tv~~~~~~~~~kl~~   48 (58)
T smart00421        2 ASLTPREREVLRLLA-----EGLTNKEIAERLGISEKTVKTHLSNIMRKLGV   48 (58)
T ss_pred             CCCCHHHHHHHHHHH-----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCC
Confidence            468999999987744     78999999999999999999999999999874

lux regulon (activates the bioluminescence operon

>PF00196 GerE: Bacterial regulatory proteins, luxR family; InterPro: IPR000792 This domain is a DNA-binding, helix-turn-helix (HTH) domain of about 65 amino acids, present in transcription regulators of the LuxR/FixJ family of response regulators

Probab=97.73  E-value=6.8e-05  Score=58.65  Aligned_cols=47  Identities=30%  Similarity=0.325  Sum_probs=41.7

Q ss_pred             hhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHh
Q 009449          470 ESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRD  521 (534)
Q Consensus       470 ~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~  521 (534)
                      ..|+++|.+|+.+..     .|+|.+|||+.+|||..||+.+..++++||.-
T Consensus         2 ~~LT~~E~~vl~~l~-----~G~~~~eIA~~l~is~~tV~~~~~~i~~Kl~~   48 (58)
T PF00196_consen    2 PSLTERELEVLRLLA-----QGMSNKEIAEELGISEKTVKSHRRRIMKKLGV   48 (58)
T ss_dssp             GSS-HHHHHHHHHHH-----TTS-HHHHHHHHTSHHHHHHHHHHHHHHHHT-
T ss_pred             CccCHHHHHHHHHHH-----hcCCcchhHHhcCcchhhHHHHHHHHHHHhCC
Confidence            469999999999987     89999999999999999999999999999874

The domain is named after Vibrio fischeri luxR, a transcriptional activator for quorum-sensing control of luminescence. LuxR-type HTH domain proteins occur in a variety of organisms. The DNA-binding HTH domain is usually located in the C-terminal region; the N-terminal region often containing an autoinducer-binding domain or a response regulatory domain. Most luxR-type regulators act as transcription activators, but some can be repressors or have a dual role for different sites. LuxR-type HTH regulators control a wide variety of activities in various biological processes. The luxR-type, DNA-binding HTH domain forms a four-helical bundle structure. The HTH motif comprises the second and third helices, known as the scaffold and recognition helix, respectively. The HTH binds DNA in the major groove, where the N-terminal part of the recognition helix makes most of the DNA contacts. The fourth helix is involved in dimerisation of gerE and traR. Signalling events by one of the four activation mechanisms described below lead to multimerisation of the regulator. The regulators bind DNA as multimers [, , ]. LuxR-type HTH proteins can be activated by one of four different mechanisms: 1) Regulators which belong to a two-component sensory transduction system where the protein is activated by its phosphorylation, generally on an aspartate residue, by a transmembrane kinase [, ]. Some proteins that belong to this category are: Rhizobiaceae fixJ (global regulator inducing expression of nitrogen-fixation genes in microaerobiosis) Escherichia coli and Salmonella typhimurium uhpA (activates hexose phosphate transport gene uhpT) E. coli narL and narP (activate nitrate reductase operon) Enterobacteria rcsB (regulation of exopolysaccharide biosynthesis in enteric and plant pathogenesis) Bordetella pertussis bvgA (virulence factor) Bacillus subtilis coma (involved in expression of late-expressing competence genes) 2) Regulators which are activated, or in very rare cases repressed, when bound to N-acyl homoserine lactones, which are used as quorum sensing molecules in a variety of Gram-negative bacteria []: V. fischeri luxR (activates bioluminescence operon) Agrobacterium tumefaciens traR (regulation of Ti plasmid transfer) Erwinia carotovora carR (control of carbapenem antibiotics biosynthesis) E. carotovora expR (virulence factor for soft rot disease; activates plant tissue macerating enzyme genes) Pseudomonas aeruginosa lasR (activates elastase gene lasB) Erwinia chrysanthemi echR and Erwinia stewartii esaR Pseudomonas chlororaphis phzR (positive regulator of phenazine antibiotic production) Pseudomonas aeruginosa rhlR (activates rhlAB operon and lasB gene) 3) Autonomous effector domain regulators, without a regulatory domain, represented by gerE []. B. subtilis gerE (transcription activator and repressor for the regulation of spore formation) 4) Multiple ligand-binding regulators, exemplified by malT []. E. coli malT (activates maltose operon; MalT binds ATP and maltotriose); GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3SZT_A 3CLO_A 1H0M_A 1L3L_A 3C57_B 1ZLK_B 1ZLJ_H 3C3W_B 1RNL_A 1ZG1_A ....

>cd06170 LuxR_C_like C-terminal DNA-binding domain of LuxR-like proteins

Probab=97.63  E-value=0.00013  Score=55.34  Aligned_cols=46  Identities=30%  Similarity=0.388  Sum_probs=41.7

Q ss_pred             CCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhH
Q 009449          472 LDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDS  522 (534)
Q Consensus       472 L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~~  522 (534)
                      |+++|++|+.+.+     .++|.+|||+.+|+|+.+|+.+..+++++|+..
T Consensus         1 l~~~e~~i~~~~~-----~~~s~~eia~~l~~s~~tv~~~~~~~~~~l~~~   46 (57)
T cd06170           1 LTPREREVLRLLA-----EGKTNKEIADILGISEKTVKTHLRNIMRKLGVK   46 (57)
T ss_pred             CCHHHHHHHHHHH-----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHhCCC
Confidence            6899999998854     789999999999999999999999999998864

This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many are active as homodimers. Many are two domain proteins in which the DNA binding property of the C-terminal DNA binding domain is modulated by modifications of the N-terminal domain. For example in the case of Lux R which participates in the regulation of gene expression in response to fluctuations in cell-population density (quorum-sensing), a signaling molecule, the pheromone Acyl HSL (N-acyl derivatives of homoserine lactone), binds to the N-terminal domain and leads to LuxR dimerization. For others phophorylation of the N-terminal domain leads to multimerization, for example Escherichia coli NarL and Sinorhizobium melilot FixJ. NarL controls gene expression of many respiratory-related operons when environmental

>PF07374 DUF1492: Protein of unknown function (DUF1492); InterPro: IPR010861 This entry is represented by Streptococcus phage 7201, Orf19

Probab=97.60  E-value=0.00031  Score=61.38  Aligned_cols=55  Identities=27%  Similarity=0.462  Sum_probs=49.9

Q ss_pred             HHHHHHHHHhhCC-HHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Q 009449          461 MKKDVFRILESLD-SRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKL  519 (534)
Q Consensus       461 l~e~L~~~L~~L~-~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KL  519 (534)
                      .+..+..+++.|+ +.+|.||.++|    ..+++..+||+.||+|+.+|..+..+|++.|
T Consensus        44 ~k~ei~~~I~~l~d~~~r~iL~~~Y----i~~~~~~~I~~~l~~S~~t~yr~~~~Al~~L   99 (100)
T PF07374_consen   44 EKLEIRRAINKLEDPDERLILRMRY----INKLTWEQIAEELNISRRTYYRIHKKALKEL   99 (100)
T ss_pred             HHHHHHHHHHHccChhHHHHHHHHH----HcCCCHHHHHHHHCCCHHHHHHHHHHHHHhc
Confidence            4456888888885 79999999999    8899999999999999999999999999876

The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This entry consists of several hypothetical, highly conserved Streptococcal and related phage proteins. The function of this family is unknown.

>TIGR03879 near_KaiC_dom probable regulatory domain

Probab=97.60  E-value=0.00012  Score=60.42  Aligned_cols=47  Identities=19%  Similarity=0.136  Sum_probs=41.9

Q ss_pred             HHHHHHhhCCHHHHHHHhhH-hcCCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 009449          464 DVFRILESLDSRERQVLVLR-YGLNDHRPKSLEEIGKLFHVSKEWIRKLEKK  514 (534)
Q Consensus       464 ~L~~~L~~L~~rEReVL~Lr-yGL~d~e~~Sl~EIA~~LgISrerVRqi~~R  514 (534)
                      .+.+-|+.||++.++++.|. |    .+++|++|||+.||+|..+|++++++
T Consensus         8 ~~~~~l~~l~~~~r~af~L~R~----~eGlS~kEIAe~LGIS~~TVk~~l~~   55 (73)
T TIGR03879         8 KLAERLTWVDSLAEAAAALARE----EAGKTASEIAEELGRTEQTVRNHLKG   55 (73)
T ss_pred             hHHHHHhcCCHHHHHHHHHHHH----HcCCCHHHHHHHHCcCHHHHHHHHhc
Confidence            45667899999999999995 4    58999999999999999999998875

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.

>PF04967 HTH_10: HTH DNA binding domain; InterPro: IPR007050 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif

Probab=97.48  E-value=0.00039  Score=54.08  Aligned_cols=48  Identities=33%  Similarity=0.480  Sum_probs=42.1

Q ss_pred             CCHHHHHHHhhHh--cCCCC-CCCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Q 009449          472 LDSRERQVLVLRY--GLNDH-RPKSLEEIGKLFHVSKEWIRKLEKKAMTKL  519 (534)
Q Consensus       472 L~~rEReVL~Lry--GL~d~-e~~Sl~EIA~~LgISrerVRqi~~RAL~KL  519 (534)
                      |+++|++||..-|  |..|. .+.|+.|||+.||||+++|..++++|.+||
T Consensus         1 LT~~Q~e~L~~A~~~GYfd~PR~~tl~elA~~lgis~st~~~~LRrae~kl   51 (53)
T PF04967_consen    1 LTDRQREILKAAYELGYFDVPRRITLEELAEELGISKSTVSEHLRRAERKL   51 (53)
T ss_pred             CCHHHHHHHHHHHHcCCCCCCCcCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Confidence            7899999998766  44443 578999999999999999999999999987

This entry represents the HTH DNA binding domain found in Halobacterium salinarium (Halobacterium halobium) and described as a putative bacterio-opsin activator.

>TIGR01321 TrpR trp operon repressor, proteobacterial

Probab=97.44  E-value=0.0002  Score=61.96  Aligned_cols=48  Identities=27%  Similarity=0.173  Sum_probs=41.7

Q ss_pred             HHHHHH-hhCCHHHHHHHhhHhcCCC---CCCCCHHHHHHHhCCCHHHHHHH
Q 009449          464 DVFRIL-ESLDSRERQVLVLRYGLND---HRPKSLEEIGKLFHVSKEWIRKL  511 (534)
Q Consensus       464 ~L~~~L-~~L~~rEReVL~LryGL~d---~e~~Sl~EIA~~LgISrerVRqi  511 (534)
                      .+...| ..|+|+|+.+|.+||||.+   ..++|++|||+.+|||+.+|...
T Consensus        24 ~l~~~l~~lLTp~E~~~l~~R~~i~~~Ll~~~~tQrEIa~~lGiS~atIsR~   75 (94)
T TIGR01321        24 DMQLLLELILTRSEREDLGDRIRIVNELLNGNMSQREIASKLGVSIATITRG   75 (94)
T ss_pred             HHHHHHHHhCCHHHHHHHHHHHHHHHHHHhCCCCHHHHHHHhCCChhhhhHH
Confidence            455566 4599999999999999987   57899999999999999999754

This model represents TrpR, the repressor of the trp operon. It is found so far only in the gamma subdivision of the proteobacteria and in Chlamydia trachomatis. All members belong to species capable of tryptophan biosynthesis.

>PRK15411 rcsA colanic acid capsular biosynthesis activation protein A; Provisional

Probab=97.42  E-value=0.00024  Score=69.54  Aligned_cols=46  Identities=13%  Similarity=0.196  Sum_probs=43.8

Q ss_pred             hCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHh
Q 009449          471 SLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRD  521 (534)
Q Consensus       471 ~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~  521 (534)
                      .|+|+|++|+.+.-     +|+|.+|||+.||+|..||+.+..+.++||.-
T Consensus       137 ~LT~RE~eVL~lla-----~G~snkeIA~~L~iS~~TVk~h~~~I~~KL~v  182 (207)
T PRK15411        137 SLSRTESSMLRMWM-----AGQGTIQISDQMNIKAKTVSSHKGNIKRKIKT  182 (207)
T ss_pred             cCCHHHHHHHHHHH-----cCCCHHHHHHHcCCCHHHHHHHHHHHHHHhCC
Confidence            49999999999996     89999999999999999999999999999984

>PRK15201 fimbriae regulatory protein FimW; Provisional

Probab=97.40  E-value=0.00031  Score=67.26  Aligned_cols=48  Identities=27%  Similarity=0.330  Sum_probs=44.6

Q ss_pred             hhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhH
Q 009449          470 ESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDS  522 (534)
Q Consensus       470 ~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~~  522 (534)
                      ..|+|+|++|+.+.-     +|+|.+|||+.|++|..||+....++++||.-.
T Consensus       132 ~~LSpRErEVLrLLA-----qGkTnKEIAe~L~IS~rTVkth~srImkKLgV~  179 (198)
T PRK15201        132 RHFSVTERHLLKLIA-----SGYHLSETAALLSLSEEQTKSLRRSIMRKLHVK  179 (198)
T ss_pred             CCCCHHHHHHHHHHH-----CCCCHHHHHHHhCCCHHHHHHHHHHHHHHhCCC
Confidence            459999999999996     899999999999999999999999999999753

>PRK10840 transcriptional regulator RcsB; Provisional

Probab=97.37  E-value=0.0003  Score=68.09  Aligned_cols=47  Identities=32%  Similarity=0.265  Sum_probs=43.9

Q ss_pred             hhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHh
Q 009449          470 ESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRD  521 (534)
Q Consensus       470 ~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~  521 (534)
                      ..|++||++|+.+.-     +|+|.+|||+.|+||..||+.+..+.++||--
T Consensus       149 ~~Lt~rE~evl~~~~-----~G~s~~eIA~~l~iS~~TV~~h~~~i~~Kl~v  195 (216)
T PRK10840        149 KRLSPKESEVLRLFA-----EGFLVTEIAKKLNRSIKTISSQKKSAMMKLGV  195 (216)
T ss_pred             ccCCHHHHHHHHHHH-----CCCCHHHHHHHHCCCHHHHHHHHHHHHHHcCC
Confidence            359999999999986     89999999999999999999999999999953

>PRK13719 conjugal transfer transcriptional regulator TraJ; Provisional

Probab=97.34  E-value=0.00033  Score=69.18  Aligned_cols=52  Identities=13%  Similarity=0.091  Sum_probs=47.6

Q ss_pred             HHHHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhH
Q 009449          466 FRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDS  522 (534)
Q Consensus       466 ~~~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~~  522 (534)
                      .++...|+|+|++|+.+.-     +|+|.+|||+.|++|..||+.+..+.++||.-.
T Consensus       138 ~~~~~~LS~RE~eVL~Lia-----~G~SnkEIA~~L~IS~~TVk~hvs~I~~KLgv~  189 (217)
T PRK13719        138 LEAKNKVTKYQNDVFILYS-----FGFSHEYIAQLLNITVGSSKNKISEILKFFGIS  189 (217)
T ss_pred             hhccCCCCHHHHHHHHHHH-----CCCCHHHHHHHhCCCHHHHHHHHHHHHHHhCCC
Confidence            4566889999999999986     899999999999999999999999999999743

>PRK11475 DNA-binding transcriptional activator BglJ; Provisional

Probab=97.33  E-value=0.00037  Score=68.49  Aligned_cols=47  Identities=26%  Similarity=0.283  Sum_probs=44.1

Q ss_pred             hhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHh
Q 009449          470 ESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRD  521 (534)
Q Consensus       470 ~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~  521 (534)
                      ..|++||++|+.+..     +|+|.+|||+.|+||..||+.+..+.++||--
T Consensus       133 ~~LT~RE~eVL~ll~-----~G~snkeIA~~L~iS~~TV~~h~~~I~~KLgv  179 (207)
T PRK11475        133 RMLSPTEREILRFMS-----RGYSMPQIAEQLERNIKTIRAHKFNVMSKLGV  179 (207)
T ss_pred             CCCCHHHHHHHHHHH-----CCCCHHHHHHHHCCCHHHHHHHHHHHHHHcCC
Confidence            469999999999986     89999999999999999999999999999963

>PRK13870 transcriptional regulator TraR; Provisional

Probab=97.31  E-value=0.00037  Score=69.76  Aligned_cols=47  Identities=26%  Similarity=0.228  Sum_probs=43.9

Q ss_pred             hCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhH
Q 009449          471 SLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDS  522 (534)
Q Consensus       471 ~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~~  522 (534)
                      .|++||++||.+--     +|+|..|||.+||||..||..++..|++||--.
T Consensus       173 ~LT~RE~E~L~W~A-----~GKT~~EIa~ILgISe~TV~~Hl~na~~KLga~  219 (234)
T PRK13870        173 WLDPKEATYLRWIA-----VGKTMEEIADVEGVKYNSVRVKLREAMKRFDVR  219 (234)
T ss_pred             CCCHHHHHHHHHHH-----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHcCCC
Confidence            59999999999986     999999999999999999999999999999643

>TIGR03541 reg_near_HchA LuxR family transcriptional regulatory, chaperone HchA-associated

Probab=97.29  E-value=0.0004  Score=69.22  Aligned_cols=51  Identities=24%  Similarity=0.271  Sum_probs=46.0

Q ss_pred             HhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHhh
Q 009449          469 LESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDSET  524 (534)
Q Consensus       469 L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~~l~  524 (534)
                      ...|+++|++||.+..     +|+|.+|||++||||..||+.++.+|++||+..-.
T Consensus       169 ~~~Lt~re~evl~~~a-----~G~t~~eIa~~l~is~~Tv~~~l~~~~~kl~~~~~  219 (232)
T TIGR03541       169 AGVLSEREREVLAWTA-----LGRRQADIAAILGISERTVENHLRSARRKLGVATT  219 (232)
T ss_pred             hccCCHHHHHHHHHHH-----CCCCHHHHHHHHCcCHHHHHHHHHHHHHHHCCCCH
Confidence            3479999999999965     89999999999999999999999999999985433

Members of this protein family belong to the LuxR transcriptional regulator family, and contain both autoinducer binding (pfam03472) and transcriptional regulator (pfam00196) domains. Members, however, occur only in a few members of the Gammaproteobacteria that have the chaperone/aminopeptidase HchA, and are always encoded by the adjacent gene.

>TIGR03020 EpsA transcriptional regulator EpsA

Probab=97.28  E-value=0.00044  Score=69.99  Aligned_cols=50  Identities=20%  Similarity=0.236  Sum_probs=45.7

Q ss_pred             HhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHh
Q 009449          469 LESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDSE  523 (534)
Q Consensus       469 L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~~l  523 (534)
                      +..|+++|++|+.+..     +|+|.+|||+.||||..||+.++.++++||.-.-
T Consensus       188 ~~~LT~RE~evl~l~a-----~G~s~~eIA~~L~IS~~TVk~hl~~i~~KL~v~n  237 (247)
T TIGR03020       188 AGLITAREAEILAWVR-----DGKTNEEIAAILGISSLTVKNHLQHIFKKLDVRN  237 (247)
T ss_pred             ccCCCHHHHHHHHHHH-----CCCCHHHHHHHHCcCHHHHHHHHHHHHHHhCCCC
Confidence            4579999999999975     8999999999999999999999999999998543

Proteins in this family include a C-terminal LuxR transcriptional regulator domain (pfam00196). These proteins are positioned proximal to either EpsH-containing exopolysaccharide biosynthesis operons of the Methylobacillus type, or the associated PEP-CTERM-containing genes.

>PRK10100 DNA-binding transcriptional regulator CsgD; Provisional

Probab=97.26  E-value=0.00048  Score=68.15  Aligned_cols=47  Identities=19%  Similarity=0.188  Sum_probs=44.5

Q ss_pred             hhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHh
Q 009449          470 ESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRD  521 (534)
Q Consensus       470 ~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~  521 (534)
                      ..|+++|++|+.+.+     +|+|.+|||+.|++|..||+.+..++++||.-
T Consensus       154 ~~Lt~rE~~Vl~l~~-----~G~s~~eIA~~L~iS~~TVk~~~~~i~~Kl~v  200 (216)
T PRK10100        154 ALLTHREKEILNKLR-----IGASNNEIARSLFISENTVKTHLYNLFKKIAV  200 (216)
T ss_pred             CCCCHHHHHHHHHHH-----cCCCHHHHHHHhCCCHHHHHHHHHHHHHHhCC
Confidence            469999999999998     69999999999999999999999999999975

>PRK10188 DNA-binding transcriptional activator SdiA; Provisional

Probab=97.25  E-value=0.0005  Score=69.07  Aligned_cols=47  Identities=19%  Similarity=0.306  Sum_probs=44.2

Q ss_pred             hCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhH
Q 009449          471 SLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDS  522 (534)
Q Consensus       471 ~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~~  522 (534)
                      .|+++|++||.+..     +|+|..|||++||||..||+.++.++++||--.
T Consensus       179 ~LT~rE~evl~~~a-----~G~t~~eIa~~l~is~~TV~~h~~~~~~KL~~~  225 (240)
T PRK10188        179 NFSKREKEILKWTA-----EGKTSAEIAMILSISENTVNFHQKNMQKKFNAP  225 (240)
T ss_pred             CCCHHHHHHHHHHH-----cCCCHHHHHHHhCCCHHHHHHHHHHHHHHhCCC
Confidence            59999999999997     899999999999999999999999999999743

>COG4566 TtrR Response regulator [Signal transduction mechanisms]

Probab=97.25  E-value=0.0011  Score=64.19  Aligned_cols=66  Identities=21%  Similarity=0.183  Sum_probs=56.6

Q ss_pred             HHHHHHHHHHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHhhhhcchh
Q 009449          460 HMKKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDSETCRDLSH  530 (534)
Q Consensus       460 el~e~L~~~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~~l~~~~L~~  530 (534)
                      .....+...+.+|+||||+|+...-     .|+..++||..||||.-||..+..+.++|++......-++-
T Consensus       131 ~~~~~~~~~l~tLT~RERqVl~~vV-----~G~~NKqIA~dLgiS~rTVe~HRanvM~Km~a~SlaeLvr~  196 (202)
T COG4566         131 DRQAAIRARLATLTPRERQVLDLVV-----RGLMNKQIAFDLGISERTVELHRANVMEKMQARSLAELVRM  196 (202)
T ss_pred             HHHHHHHHHHHhcCHHHHHHHHHHH-----cCcccHHHHHHcCCchhhHHHHHHHHHHHHhhccHHHHHHH
Confidence            3456788899999999999999886     89999999999999999999999999999987654444443

>COG2197 CitB Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]

Probab=97.24  E-value=0.00047  Score=67.86  Aligned_cols=48  Identities=27%  Similarity=0.254  Sum_probs=44.6

Q ss_pred             hhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhH
Q 009449          470 ESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDS  522 (534)
Q Consensus       470 ~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~~  522 (534)
                      ..|++||++|+++.-     +|+|.+|||+.|++|..||+.+.++.++||.-.
T Consensus       147 ~~LT~RE~eVL~lla-----~G~snkeIA~~L~iS~~TVk~h~~~i~~KL~v~  194 (211)
T COG2197         147 ELLTPRELEVLRLLA-----EGLSNKEIAEELNLSEKTVKTHVSNILRKLGVR  194 (211)
T ss_pred             CCCCHHHHHHHHHHH-----CCCCHHHHHHHHCCCHhHHHHHHHHHHHHcCCC
Confidence            469999999999985     899999999999999999999999999999743

>COG2771 CsgD DNA-binding HTH domain-containing proteins [Transcription]

Probab=97.13  E-value=0.0014  Score=51.36  Aligned_cols=50  Identities=28%  Similarity=0.377  Sum_probs=44.7

Q ss_pred             hhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHhh
Q 009449          470 ESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDSET  524 (534)
Q Consensus       470 ~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~~l~  524 (534)
                      ..|+++|.+|+.+.-     .|+|..|||..+|+|..||+....++.+||.-.-+
T Consensus         3 ~~Lt~rE~~v~~l~~-----~G~s~~eia~~l~is~~tV~~h~~~i~~Kl~~~~r   52 (65)
T COG2771           3 ADLTPREREILRLVA-----QGKSNKEIARILGISEETVKTHLRNIYRKLGVKNR   52 (65)
T ss_pred             ccCCHHHHHHHHHHH-----CCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCCCH
Confidence            359999999998886     78999999999999999999999999999975443

>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A

Probab=97.11  E-value=0.00063  Score=50.64  Aligned_cols=41  Identities=22%  Similarity=0.248  Sum_probs=25.0

Q ss_pred             hhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 009449          470 ESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKK  514 (534)
Q Consensus       470 ~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~R  514 (534)
                      ..|++.||..|...+    .+|+|..+||+.||++++||...+.|
T Consensus         3 ~~Lt~~eR~~I~~l~----~~G~s~~~IA~~lg~s~sTV~relkR   43 (44)
T PF13936_consen    3 KHLTPEERNQIEALL----EQGMSIREIAKRLGRSRSTVSRELKR   43 (44)
T ss_dssp             ---------HHHHHH----CS---HHHHHHHTT--HHHHHHHHHH
T ss_pred             cchhhhHHHHHHHHH----HcCCCHHHHHHHHCcCcHHHHHHHhc
Confidence            468999999999988    79999999999999999999988776

>PF02001 DUF134: Protein of unknown function DUF134; InterPro: IPR002852 The bacterial and archaeal proteins in this family have no known function

Probab=97.10  E-value=0.0011  Score=58.68  Aligned_cols=52  Identities=21%  Similarity=0.153  Sum_probs=48.4

Q ss_pred             CCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHhhhhc
Q 009449          472 LDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDSETCRD  527 (534)
Q Consensus       472 L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~~l~~~~  527 (534)
                      |+..|-+.|+|.+    .+++|++|-|+.||||+.|+..++..|.+|+-..+....
T Consensus        42 L~~dElEAiRL~D----~egl~QeeaA~~MgVSR~T~~ril~~ARkKiA~ALv~Gk   93 (106)
T PF02001_consen   42 LTVDELEAIRLVD----YEGLSQEEAAERMGVSRPTFQRILESARKKIADALVEGK   93 (106)
T ss_pred             eeHHHHHHHHHHH----HcCCCHHHHHHHcCCcHHHHHHHHHHHHHHHHHHHHCCC
Confidence            8889999999999    899999999999999999999999999999998876544

>PRK09483 response regulator; Provisional

Probab=96.98  E-value=0.0013  Score=62.55  Aligned_cols=46  Identities=22%  Similarity=0.390  Sum_probs=42.8

Q ss_pred             hhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 009449          470 ESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLR  520 (534)
Q Consensus       470 ~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR  520 (534)
                      ..|+++|++|+.+..     +|+|.+|||+.|++|..||+.+.++.++||-
T Consensus       147 ~~Lt~rE~~vl~~~~-----~G~~~~~Ia~~l~is~~TV~~~~~~i~~Kl~  192 (217)
T PRK09483        147 ASLSERELQIMLMIT-----KGQKVNEISEQLNLSPKTVNSYRYRMFSKLN  192 (217)
T ss_pred             cccCHHHHHHHHHHH-----CCCCHHHHHHHhCCCHHHHHHHHHHHHHHcC
Confidence            469999999998865     8999999999999999999999999999995

>COG3413 Predicted DNA binding protein [General function prediction only]

Probab=96.93  E-value=0.0019  Score=63.64  Aligned_cols=52  Identities=33%  Similarity=0.440  Sum_probs=45.5

Q ss_pred             hCCHHHHHHHhhHh--cCCCC-CCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhH
Q 009449          471 SLDSRERQVLVLRY--GLNDH-RPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDS  522 (534)
Q Consensus       471 ~L~~rEReVL~Lry--GL~d~-e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~~  522 (534)
                      .|+|+|++||+.-|  |..|. ...+++|||+.||||++++.+++++|.+||=..
T Consensus       155 ~LTdrQ~~vL~~A~~~GYFd~PR~~~l~dLA~~lGISkst~~ehLRrAe~Kl~~~  209 (215)
T COG3413         155 DLTDRQLEVLRLAYKMGYFDYPRRVSLKDLAKELGISKSTLSEHLRRAERKLIEA  209 (215)
T ss_pred             cCCHHHHHHHHHHHHcCCCCCCccCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence            59999999999876  44444 678999999999999999999999999998654

>COG4941 Predicted RNA polymerase sigma factor containing a TPR repeat domain [Transcription]

Probab=96.86  E-value=0.023  Score=59.61  Aligned_cols=158  Identities=20%  Similarity=0.143  Sum_probs=101.0

Q ss_pred             HHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCchhhHHHHHHHHHHHHHHHHhccccccccchH
Q 009449          299 ELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIPCKLN  378 (534)
Q Consensus       299 ~LI~~nlrLV~sIArrY~~~g~~~eDLiQEG~lgL~rA~ekFDp~kG~rFSTYA~~wIR~aI~~~lr~~sr~iRlP~~~~  378 (534)
                      ..+..-.+.++.---+|+++-...||.+||+|+...+.-.+=-|-+  .-..|++..-|+.-++.+++..+.-..|.+. 
T Consensus         9 ~~~r~~~~r~~a~L~r~~rd~dlAEEa~~dA~~~Ale~WPr~G~P~--~PaAWL~~v~R~~aiD~~Rr~~~~~~~~~el-   85 (415)
T COG4941           9 AAARIERPRAMAALARYLRDLDLAEEALQDAFAAALERWPRAGPPR--NPAAWLIAVGRNRAIDRVRRRARRDAAPPEL-   85 (415)
T ss_pred             HHHHHhhhHHHHHHHHHhcccchHHHHHHHHHHHHHHhCcccCCCC--ChHHHHHHHHhhhHHHHHHHHHHhccCChhh-
Confidence            3344444555555556777767899999999986544433322222  3578999999999999999887544444321 


Q ss_pred             HHHHHHHHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHHhhhhcccccccccchhhhhhhccCCCCCCChHHHHHH
Q 009449          379 REISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNAKYLEFAPDRSVKSPKEIVMR  458 (534)
Q Consensus       379 ~~i~ki~ka~~~L~~elGr~Pt~eEIA~~lgis~~kv~~~l~~~~~~~SLD~~i~~~~~~~l~e~i~d~~~~spee~v~~  458 (534)
                                                                    .++.+     +...+   ..+     .+++....
T Consensus        86 ----------------------------------------------~~~~e-----~~e~~---~a~-----~~~d~~i~  106 (415)
T COG4941          86 ----------------------------------------------LLSDE-----DEEME---EAE-----ALDDEHIR  106 (415)
T ss_pred             ----------------------------------------------ccccc-----chhhh---ccc-----cccccccc
Confidence                                                          00110     00000   000     01111111


Q ss_pred             HHHHHHHHHHH-hhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhH
Q 009449          459 QHMKKDVFRIL-ESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDS  522 (534)
Q Consensus       459 ~el~e~L~~~L-~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~~  522 (534)
                      .+....|.-|. -.|++.+|-.+.||.    .-|+|..|||..|=|+..++-|.+.||+++++..
T Consensus       107 Dd~LRLiFvccHPal~~~~riALtLR~----v~GLs~~eIArAFLv~e~am~QRivRAK~ri~~a  167 (415)
T COG4941         107 DDRLRLIFVCCHPALPPEQRIALTLRL----VGGLSTAEIARAFLVPEAAMAQRIVRAKARIREA  167 (415)
T ss_pred             hhhHHhhhhhcCCCCChhhHHHHHHHH----HcCCcHHHHHHHHcCCcHHHHHHHHHHHHHHHhc
Confidence            11112222222 469999999999999    8899999999999999999999999999999964

>PRK15369 two component system sensor kinase SsrB; Provisional

Probab=96.77  E-value=0.0025  Score=59.04  Aligned_cols=47  Identities=26%  Similarity=0.268  Sum_probs=43.1

Q ss_pred             hhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHh
Q 009449          470 ESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRD  521 (534)
Q Consensus       470 ~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~  521 (534)
                      ..|+++|++|+.+.     .++++.+|||+.+++|..||+.+..++++||.-
T Consensus       148 ~~lt~~e~~vl~l~-----~~g~~~~~Ia~~l~~s~~tv~~~~~~~~~kl~~  194 (211)
T PRK15369        148 PLLTPRERQILKLI-----TEGYTNRDIAEQLSISIKTVETHRLNMMRKLDV  194 (211)
T ss_pred             cCCCHHHHHHHHHH-----HCCCCHHHHHHHhCCCHHHHHHHHHHHHHHhCC
Confidence            45999999999984     489999999999999999999999999999963

>TIGR01637 phage_arpU phage transcriptional regulator, ArpU family

Probab=96.64  E-value=0.012  Score=53.45  Aligned_cols=61  Identities=18%  Similarity=0.207  Sum_probs=53.6

Q ss_pred             HHHHHHHHHH-hhCCHHHHHHHhhHhcCCCCC--CCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHhh
Q 009449          460 HMKKDVFRIL-ESLDSRERQVLVLRYGLNDHR--PKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDSET  524 (534)
Q Consensus       460 el~e~L~~~L-~~L~~rEReVL~LryGL~d~e--~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~~l~  524 (534)
                      .....+..++ +.|++.+|+||..+|    ..  +++..+|+..+|+|+.+...+..+|+.++-..+.
T Consensus        67 ~~~~~i~~ai~~~l~~~~r~Il~~~Y----l~~~~~~~~~I~~~l~~s~~~~y~~k~~Al~~fA~~l~  130 (132)
T TIGR01637        67 QEARAIVNAIVNQLDEISRQILYDKY----LEPDQKYDYQIMMELGYSHRQYYRIKKRALLRFATLYG  130 (132)
T ss_pred             HHHHHHHHHHHHhCCHHHHHHHHHHH----cCccccchHHHHHHhCCcHHHHHHHHHHHHHHHHHHhC
Confidence            3445677777 999999999999999    55  8899999999999999999999999999887654

This model represents a family of phage proteins, including ArpU, called a putative autolysin regulatory protein. ArpU was described as a regulator of cellular muramidase-2 of Enterococcus hirae but appears to have been cloned from a prophage. This family appears related to the RinA family of bacteriophage transcriptional activators and to some sporulation-specific sigma factors. We propose that this is a phage transcriptional activator family.

>PRK10651 transcriptional regulator NarL; Provisional

Probab=96.59  E-value=0.0036  Score=58.73  Aligned_cols=47  Identities=19%  Similarity=0.282  Sum_probs=43.4

Q ss_pred             hhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHh
Q 009449          470 ESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRD  521 (534)
Q Consensus       470 ~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~  521 (534)
                      ..|+++|++|+.+..     ++++.++||+.+++|..||+.+..+.++||.-
T Consensus       154 ~~Lt~rE~~vl~~l~-----~g~~~~~ia~~l~is~~tV~~~~~~l~~Kl~~  200 (216)
T PRK10651        154 NQLTPRERDILKLIA-----QGLPNKMIARRLDITESTVKVHVKHMLKKMKL  200 (216)
T ss_pred             ccCCHHHHHHHHHHH-----cCCCHHHHHHHcCCCHHHHHHHHHHHHHHcCC
Confidence            459999999999875     88999999999999999999999999999964

>PRK01381 Trp operon repressor; Provisional

Probab=96.56  E-value=0.0023  Score=55.80  Aligned_cols=48  Identities=23%  Similarity=0.187  Sum_probs=40.0

Q ss_pred             HHHHHHHHhh-CCHHHHHHHhhHhcCCC---CCCCCHHHHHHHhCCCHHHHH
Q 009449          462 KKDVFRILES-LDSRERQVLVLRYGLND---HRPKSLEEIGKLFHVSKEWIR  509 (534)
Q Consensus       462 ~e~L~~~L~~-L~~rEReVL~LryGL~d---~e~~Sl~EIA~~LgISrerVR  509 (534)
                      .+.+...|.. |+|+|+.+|..||++..   ..++|+.|||+.+|||..||.
T Consensus        22 ~~~~~~~l~~llTp~Er~al~~R~~I~~~L~~g~~sQREIa~~lGvSiaTIT   73 (99)
T PRK01381         22 EDLHLPLLTLLLTPDEREALGTRVRIVEELLRGELSQREIKQELGVGIATIT   73 (99)
T ss_pred             HHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHcCCcCHHHHHHHhCCceeeeh
Confidence            3455556654 99999999999999975   346999999999999999885

>COG1356 tfx Transcriptional regulator [DNA replication, recombination and repair]

Probab=96.51  E-value=0.0022  Score=57.99  Aligned_cols=48  Identities=23%  Similarity=0.457  Sum_probs=44.8

Q ss_pred             CCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHhh
Q 009449          472 LDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDSET  524 (534)
Q Consensus       472 L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~~l~  524 (534)
                      |+++|-+||.||-     +|.|++|||++||-|+..|+-++.+|+.++.+...
T Consensus         9 lte~qikvl~lRe-----kG~tQ~eIA~~L~TTraNvSaIEkrA~enIekarn   56 (143)
T COG1356           9 LTEQQIKVLVLRE-----KGLTQSEIARILKTTRANVSAIEKRALENIEKARN   56 (143)
T ss_pred             eehhheeeeehhh-----ccccHHHHHHHHccchhhHHHHHHHHHHHHHHHHH
Confidence            8999999999996     99999999999999999999999999999987644

>COG2739 Uncharacterized protein conserved in bacteria [Function unknown]

Probab=96.50  E-value=0.0098  Score=51.90  Aligned_cols=49  Identities=31%  Similarity=0.343  Sum_probs=44.7

Q ss_pred             hhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhH
Q 009449          470 ESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDS  522 (534)
Q Consensus       470 ~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~~  522 (534)
                      .-|+.+|+..+.++|    ..++|+.|||+.++||+++|...+.|+-..|-..
T Consensus        16 sLLT~KQ~~Y~~lyy----~dDlSl~EIAee~~VSRqAIyDnIKr~~~~L~~Y   64 (105)
T COG2739          16 SLLTKKQKNYLELYY----LDDLSLSEIAEEFNVSRQAIYDNIKRTEKILEDY   64 (105)
T ss_pred             HHHhHHHHHHHHHHH----HhhccHHHHHHHhCccHHHHHHHHHHHHHHHHHH
Confidence            448999999999999    8899999999999999999999999998877654

>PRK09390 fixJ response regulator FixJ; Provisional

Probab=96.47  E-value=0.0078  Score=55.46  Aligned_cols=55  Identities=25%  Similarity=0.252  Sum_probs=48.0

Q ss_pred             HHHHHHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHh
Q 009449          464 DVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDSE  523 (534)
Q Consensus       464 ~L~~~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~~l  523 (534)
                      .+...+..|+++|++|+.+.+     .+++.++||+.+|+|..+|+.+..++++||+..-
T Consensus       134 ~~~~~~~~l~~~e~~vl~~~~-----~~~~~~~ia~~l~~s~~tv~~~~~~~~~kl~~~~  188 (202)
T PRK09390        134 DIRARIASLSERERQVMDGLV-----AGLSNKVIARDLDISPRTVEVYRANVMTKMQAGS  188 (202)
T ss_pred             HHHHHHHhhhhhHHHHHHHHH-----ccCchHHHHHHcCCCHHHHHHHHHHHHHHHcccc
Confidence            455667889999999999754     6899999999999999999999999999997543

>PF00140 Sigma70_r1_2: Sigma-70 factor, region 1

Probab=96.31  E-value=0.0031  Score=45.38  Aligned_cols=32  Identities=22%  Similarity=0.213  Sum_probs=24.1

Q ss_pred             HHHHHhhccC-CCCCCchHHHHHHhhchHHHHH
Q 009449          224 SAERALNSRG-RRLTIARNEAEMSKGVQVVANL  255 (534)
Q Consensus       224 ~~~~~~~~~~-~~lLt~~eE~~L~~~iq~~~~l  255 (534)
                      .++-|++..+ .||||++||++|+++|+.+...
T Consensus         3 ~l~~Yl~ei~~~~LLt~eeE~~LA~~i~~g~~~   35 (37)
T PF00140_consen    3 SLRLYLKEIGRYPLLTAEEEIELARRIRKGDEA   35 (37)
T ss_dssp             HHHHHHHHHHHS-EETTHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHcCCCCCCHHHHHHHHHHHHHhHHh
Confidence            3455555444 6999999999999999988654

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 ....

>PRK15320 transcriptional activator SprB; Provisional

Probab=96.25  E-value=0.0077  Score=58.82  Aligned_cols=66  Identities=17%  Similarity=0.270  Sum_probs=51.8

Q ss_pred             CChHHHHHHHHHHHHHHHHHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHh
Q 009449          450 KSPKEIVMRQHMKKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRD  521 (534)
Q Consensus       450 ~spee~v~~~el~e~L~~~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~  521 (534)
                      ++||+.+..-. .-....+--.|+++|.+|+.+--     +|+|.+|||+.|++|..||+....+.+.||.-
T Consensus       144 ~~~~~~~~~~~-~~~~~~~~~~LSdREIEVL~LLA-----kG~SNKEIAekL~LS~KTVSTYKnRLLeKLgA  209 (251)
T PRK15320        144 ETPEEVLFNIN-QYAWWNLPPGVTQAKYALLILLS-----SGHPAIELAKKFGLGTKTVSIYRKKVMYRLGM  209 (251)
T ss_pred             CChHHHhhhcc-ceeeecCCCCCCHHHHHHHHHHH-----cCCCHHHHHHHhccchhhHHHHHHHHHHHcCC
Confidence            46776554321 11223333679999999999986     89999999999999999999999999999873

>COG1342 Predicted DNA-binding proteins [General function prediction only]

Probab=96.24  E-value=0.0099  Score=51.38  Aligned_cols=52  Identities=21%  Similarity=0.121  Sum_probs=47.4

Q ss_pred             CCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHhhhhc
Q 009449          472 LDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDSETCRD  527 (534)
Q Consensus       472 L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~~l~~~~  527 (534)
                      |+..|-+.|+|..    +++++++|-|.+||||+.|+...+..|++|+-.++....
T Consensus        34 lt~eElEAlRLvD----~~~l~QeeAA~rMgISr~Tfwr~l~sAR~KvA~aLveGk   85 (99)
T COG1342          34 LTIEELEALRLVD----YEGLTQEEAALRMGISRQTFWRLLTSARKKVADALVEGK   85 (99)
T ss_pred             ecHHHHHHHHHHh----HhhccHHHHHHHhcccHHHHHHHHHHHHHHHHHHHhcCC
Confidence            7788888999998    999999999999999999999999999999998876543

>PRK10403 transcriptional regulator NarP; Provisional

Probab=96.03  E-value=0.012  Score=55.15  Aligned_cols=48  Identities=21%  Similarity=0.221  Sum_probs=43.5

Q ss_pred             hhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhH
Q 009449          470 ESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDS  522 (534)
Q Consensus       470 ~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~~  522 (534)
                      ..|+++|.+|+.+..     +++|.+|||+.+|+|..||+.+..+.++||.-.
T Consensus       152 ~~Lt~~e~~vl~~~~-----~g~s~~~ia~~l~~s~~tv~~~~~~i~~kl~~~  199 (215)
T PRK10403        152 SVLTERELDVLHELA-----QGLSNKQIASVLNISEQTVKVHIRNLLRKLNVR  199 (215)
T ss_pred             ccCCHHHHHHHHHHH-----CCCCHHHHHHHcCCCHHHHHHHHHHHHHHcCCC
Confidence            359999999999875     789999999999999999999999999999643

>PRK10360 DNA-binding transcriptional activator UhpA; Provisional

Probab=95.77  E-value=0.017  Score=53.89  Aligned_cols=50  Identities=26%  Similarity=0.243  Sum_probs=44.5

Q ss_pred             hhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHhh
Q 009449          470 ESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDSET  524 (534)
Q Consensus       470 ~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~~l~  524 (534)
                      ..|+++|.+|+.+..     +++|.++||+.+++|..||+.+..+.++||.-.-+
T Consensus       136 ~~Lt~~E~~il~~l~-----~g~~~~~Ia~~l~~s~~tv~~~~~~l~~Kl~~~~~  185 (196)
T PRK10360        136 DPLTKRERQVAEKLA-----QGMAVKEIAAELGLSPKTVHVHRANLMEKLGVSND  185 (196)
T ss_pred             cCCCHHHHHHHHHHH-----CCCCHHHHHHHhCCCHHHHHHHHHHHHHHhCCCCH
Confidence            369999999999976     68999999999999999999999999999974433

>PRK09935 transcriptional regulator FimZ; Provisional

Probab=95.65  E-value=0.022  Score=53.36  Aligned_cols=46  Identities=22%  Similarity=0.157  Sum_probs=41.5

Q ss_pred             hCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHh
Q 009449          471 SLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRD  521 (534)
Q Consensus       471 ~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~  521 (534)
                      .|+++|.+|+.+..     +++|.+|||+.+++|..||+.+..++++||.-
T Consensus       149 ~lt~re~~vl~~l~-----~g~s~~eIa~~l~~s~~tv~~~~~~~~~kl~~  194 (210)
T PRK09935        149 VLSNREVTILRYLV-----SGLSNKEIADQLLLSNKTVSAHKSNIYGKLGL  194 (210)
T ss_pred             cCCHHHHHHHHHHH-----cCCCHHHHHHHhCCCHHHHHHHHHHHHHHcCC
Confidence            48999999988654     78999999999999999999999999999963

>PRK13558 bacterio-opsin activator; Provisional

Probab=95.65  E-value=0.02  Score=65.05  Aligned_cols=50  Identities=20%  Similarity=0.180  Sum_probs=45.1

Q ss_pred             HhhCCHHHHHHHhhHhcCCCCCCC-------CHHHHHHHhCCCHHHHHHHHHHHHHHHHhH
Q 009449          469 LESLDSRERQVLVLRYGLNDHRPK-------SLEEIGKLFHVSKEWIRKLEKKAMTKLRDS  522 (534)
Q Consensus       469 L~~L~~rEReVL~LryGL~d~e~~-------Sl~EIA~~LgISrerVRqi~~RAL~KLR~~  522 (534)
                      ...|+++|+++|..-|    ..||       |.+|||+.||||+.|+.+++++|.+||=..
T Consensus       605 ~~~lt~~q~e~l~~a~----~~gyf~~pr~~~~~e~a~~l~is~~t~~~~lr~a~~~l~~~  661 (665)
T PRK13558        605 ENDLTDRQLTALQKAY----VSGYFEWPRRVEGEELAESMGISRSTFHQHLRAAERKLVGA  661 (665)
T ss_pred             hhhCCHHHHHHHHHHH----HcCCCCCCccCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence            4679999999999998    5566       999999999999999999999999998644

>PRK09958 DNA-binding transcriptional activator EvgA; Provisional

Probab=95.64  E-value=0.022  Score=53.44  Aligned_cols=47  Identities=23%  Similarity=0.335  Sum_probs=43.2

Q ss_pred             HhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 009449          469 LESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLR  520 (534)
Q Consensus       469 L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR  520 (534)
                      +..|+++|.+|+.+..     .+.|.+|||+.+++|..||+.+..+.++||.
T Consensus       141 ~~~lt~~E~~vl~~l~-----~g~~~~~I~~~l~~s~~tv~~~~~~l~~Kl~  187 (204)
T PRK09958        141 LDSLSKQEISVMRYIL-----DGKDNNDIAEKMFISNKTVSTYKSRLMEKLE  187 (204)
T ss_pred             cccCCHHHHHHHHHHH-----cCCCHHHHHHHhCCCHHHHHHHHHHHHHHcC
Confidence            3569999999999887     7889999999999999999999999999994

>PRK04841 transcriptional regulator MalT; Provisional

Probab=95.61  E-value=0.018  Score=67.35  Aligned_cols=48  Identities=31%  Similarity=0.277  Sum_probs=44.4

Q ss_pred             hhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhH
Q 009449          470 ESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDS  522 (534)
Q Consensus       470 ~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~~  522 (534)
                      ..|+++|.+|+.+..     +|+|.+|||..|+||..||+.++++...||.-.
T Consensus       837 ~~lt~~e~~v~~~~~-----~g~~~~~ia~~l~~s~~tv~~h~~~~~~kl~v~  884 (903)
T PRK04841        837 SPLTQREWQVLGLIY-----SGYSNEQIAGELDVAATTIKTHIRNLYQKLGIA  884 (903)
T ss_pred             CCCCHHHHHHHHHHH-----cCCCHHHHHHHhCCCHHHHHHHHHHHHHHhCCC
Confidence            349999999999986     899999999999999999999999999999743

>PRK05658 RNA polymerase sigma factor RpoD; Validated

Probab=95.60  E-value=2.9  Score=47.90  Aligned_cols=34  Identities=15%  Similarity=0.135  Sum_probs=28.7

Q ss_pred             CCCchhHHHHHHhhccCCCCCCchHHHHHHhhchHHH
Q 009449          217 LKQPTIFSAERALNSRGRRLTIARNEAEMSKGVQVVA  253 (534)
Q Consensus       217 ~~~~~~~~~~~~~~~~~~~lLt~~eE~~L~~~iq~~~  253 (534)
                      ..||.+-|+   ..+...+|||.++||++|++|..+.
T Consensus       102 t~DPVRMYL---REMG~V~LLTREgEIeIAKRIE~G~  135 (619)
T PRK05658        102 TDDPVRMYL---REMGTVELLTREGEIEIAKRIEAGE  135 (619)
T ss_pred             CCChHHHHH---HHhccCcCCCcHHHHHHHHHHHHHH
Confidence            368888877   4677889999999999999998764

>TIGR02531 yecD_yerC TrpR-related protein YerC/YecD

Probab=94.90  E-value=0.054  Score=46.51  Aligned_cols=40  Identities=25%  Similarity=0.271  Sum_probs=32.8

Q ss_pred             HhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 009449          469 LESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKA  515 (534)
Q Consensus       469 L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RA  515 (534)
                      +..|++| .+|+.+.-     .++|..|||+.+|||+.||..+ .++
T Consensus        34 ~~~Ls~R-~~I~~ll~-----~G~S~~eIA~~LgISrsTIyRi-~R~   73 (88)
T TIGR02531        34 IQSLAQR-LQVAKMLK-----QGKTYSDIEAETGASTATISRV-KRC   73 (88)
T ss_pred             HHhhhHH-HHHHHHHH-----CCCCHHHHHHHHCcCHHHHHHH-HHh
Confidence            3458999 78887764     7899999999999999999984 444

This model represents a protein subfamily found mostly in the Firmicutes (Bacillus and allies). This family is similar in sequence to the trp operon repressor TrpR described by TIGR01321, and represents a distinct clade within the broader family described by pfam01371. At least one species, Xylella fastidiosa, in the Proteobacteria, has a member of both this family and TIGR01321. Several genomes with a member of this family do not synthesize tryptophan, and members of this family should not be considered trp operon repressors without new evidence.

>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C

Probab=94.86  E-value=0.024  Score=42.54  Aligned_cols=33  Identities=27%  Similarity=0.267  Sum_probs=23.3

Q ss_pred             HHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 009449          478 QVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKA  515 (534)
Q Consensus       478 eVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RA  515 (534)
                      +||.++.     +++|..+||+.||||+.||+++..+-
T Consensus         9 ~ii~l~~-----~G~s~~~ia~~lgvs~~Tv~~w~kr~   41 (50)
T PF13384_consen    9 QIIRLLR-----EGWSIREIAKRLGVSRSTVYRWIKRY   41 (50)
T ss_dssp             -HHHHHH-----HT--HHHHHHHHTS-HHHHHHHHT--
T ss_pred             HHHHHHH-----CCCCHHHHHHHHCcCHHHHHHHHHHc
Confidence            3566665     59999999999999999999987663

>PF13613 HTH_Tnp_4: Helix-turn-helix of DDE superfamily endonuclease

Probab=94.57  E-value=0.085  Score=40.64  Aligned_cols=50  Identities=16%  Similarity=0.264  Sum_probs=42.2

Q ss_pred             hCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHh
Q 009449          471 SLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDSE  523 (534)
Q Consensus       471 ~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~~l  523 (534)
                      +|+..++-++.|.| |  -.+.+++.+|..+|||+++|.++.+....-|-..+
T Consensus         2 kLs~~d~lll~L~~-L--R~~~~~~~La~~FgIs~stvsri~~~~~~~L~~~l   51 (53)
T PF13613_consen    2 KLSLEDQLLLTLMY-L--RLNLTFQDLAYRFGISQSTVSRIFHEWIPLLYQVL   51 (53)
T ss_pred             CCCHHHHHHHHHHH-H--HcCCcHhHHhhheeecHHHHHHHHHHHHHHHHHhc
Confidence            57888888888777 2  37899999999999999999999999888776543

>PRK15418 transcriptional regulator LsrR; Provisional

Probab=94.47  E-value=0.049  Score=57.17  Aligned_cols=37  Identities=19%  Similarity=0.306  Sum_probs=33.9

Q ss_pred             HHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 009449          477 RQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMT  517 (534)
Q Consensus       477 ReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~  517 (534)
                      -.|-.|||    .+++|++|||+.|||||.+|.+++.+|++
T Consensus        19 ~~vA~lYY----~~g~tQ~eIA~~lgiSR~~VsRlL~~Ar~   55 (318)
T PRK15418         19 ARIAWFYY----HDGLTQSEIGERLGLTRLKVSRLLEKGRQ   55 (318)
T ss_pred             HHHHHHHH----hcCCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence            34778999    89999999999999999999999999976

>PF05263 DUF722: Protein of unknown function (DUF722); InterPro: IPR007927 This entry is represented by Bacteriophage bIL285, Orf38

Probab=94.47  E-value=0.13  Score=47.30  Aligned_cols=57  Identities=23%  Similarity=0.399  Sum_probs=46.2

Q ss_pred             HHHHHHHHHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Q 009449          461 MKKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKL  519 (534)
Q Consensus       461 l~e~L~~~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KL  519 (534)
                      .++.|...++.|.+.++.||.+||+=  ..++|..+||..|+++..+++.....-...+
T Consensus        71 ~k~~id~~~~~l~de~k~Ii~lry~~--r~~~TW~~IA~~l~i~erta~r~~~~fK~~i  127 (130)
T PF05263_consen   71 QKEAIDRWLETLIDEEKRIIKLRYDR--RSRRTWYQIAQKLHISERTARRWRDRFKNDI  127 (130)
T ss_pred             HHHHHHHHHHhhCHHHHHHHHHHHcc--cccchHHHHHHHhCccHHHHHHHHHHHHHHh
Confidence            34567788899999999999999932  2359999999999999999988766554433

The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.

>PF00325 Crp: Bacterial regulatory proteins, crp family; InterPro: IPR001808 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif

Probab=94.44  E-value=0.05  Score=38.04  Aligned_cols=27  Identities=19%  Similarity=0.453  Sum_probs=20.2

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHHHHHHHHHHh
Q 009449          491 PKSLEEIGKLFHVSKEWIRKLEKKAMTKLRD  521 (534)
Q Consensus       491 ~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~  521 (534)
                      ++|.+|||+.+|+|+++|+    |++++|++
T Consensus         2 ~mtr~diA~~lG~t~ETVS----R~l~~l~~   28 (32)
T PF00325_consen    2 PMTRQDIADYLGLTRETVS----RILKKLER   28 (32)
T ss_dssp             E--HHHHHHHHTS-HHHHH----HHHHHHHH
T ss_pred             CcCHHHHHHHhCCcHHHHH----HHHHHHHH
Confidence            4789999999999999996    66677764

These proteins are very diverse, but for convenience may be grouped into subfamilies on the basis of sequence similarity. This family groups together a range of proteins, including anr, crp, clp, cysR, fixK, flp, fnr, fnrN, hlyX and ntcA [, ]. Within this family, the HTH motif is situated towards the C terminus.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 2OZ6_A 1CGP_B 2GZW_C 1O3T_B 3ROU_A 2CGP_A 3RDI_A 1I5Z_A 3IYD_H 3FWE_B ....

>PF13412 HTH_24: Winged helix-turn-helix DNA-binding; PDB: 1I1G_B 2IA0_B 3I4P_A 2GQQ_A 2L4A_A 2CFX_B 2DBB_B 2EFO_A 2EFQ_A 2PN6_A

Probab=94.35  E-value=0.095  Score=39.10  Aligned_cols=41  Identities=20%  Similarity=0.314  Sum_probs=30.1

Q ss_pred             CCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 009449          472 LDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKA  515 (534)
Q Consensus       472 L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RA  515 (534)
                      |++.++.||..-+   ...+.|..|||+.+|+|..+|++++.+-
T Consensus         1 l~~~~~~Il~~l~---~~~~~t~~ela~~~~is~~tv~~~l~~L   41 (48)
T PF13412_consen    1 LDETQRKILNYLR---ENPRITQKELAEKLGISRSTVNRYLKKL   41 (48)
T ss_dssp             --HHHHHHHHHHH---HCTTS-HHHHHHHHTS-HHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHH---HcCCCCHHHHHHHhCCCHHHHHHHHHHH
Confidence            5678888887766   2467999999999999999998766543

...

>PF12645 HTH_16: Helix-turn-helix domain; InterPro: IPR024760 This domain appears to be a helix-turn-helix domain, suggesting a transcriptional regulatory protein

Probab=94.14  E-value=0.21  Score=40.47  Aligned_cols=55  Identities=22%  Similarity=0.259  Sum_probs=44.7

Q ss_pred             HHHHHhc-HHHHHHHHHHhHHHHHHHHHHh----hC--CCCCHHHHHHHHHHHHHHhhhccC
Q 009449          287 KQHLAFG-WYCREELIKSTRPLVLFLARNY----RG--LGIPFSDLLQAGNVGVLQGAERFD  341 (534)
Q Consensus       287 ~~~l~~G-~~A~e~LI~~nlrLV~sIArrY----~~--~g~~~eDLiQEG~lgL~rA~ekFD  341 (534)
                      +.....| ..|.+++++.|.+++.+.+.+-    .+  .+.--+|+-|+--..|++++.+|+
T Consensus         4 I~~A~~GD~~A~~~IL~~y~~yI~kls~r~~~d~~g~~~~~vDedl~q~l~~kLi~~I~~F~   65 (65)
T PF12645_consen    4 IKAAKQGDPEAMEEILKHYEPYISKLSTRTLYDEYGNVYGYVDEDLKQRLEIKLIEAILKFE   65 (65)
T ss_pred             HHHHHcCCHHHHHHHHHHHHHHHHHHHHhhcccccCCcCceeCHHHHHHHHHHHHHHHHccC
Confidence            4445555 7899999999999999988762    22  245569999999999999999996

Some proteins with this domain are annotated as conjugative transposon proteins.

>PF02796 HTH_7: Helix-turn-helix domain of resolvase; InterPro: IPR006120 Site-specific recombination plays an important role in DNA rearrangement in prokaryotic organisms

Probab=94.02  E-value=0.049  Score=40.59  Aligned_cols=33  Identities=24%  Similarity=0.236  Sum_probs=24.2

Q ss_pred             HHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 009449          476 ERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEK  513 (534)
Q Consensus       476 EReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~  513 (534)
                      ..+|+.|+-     +|+|..+||+.+|||+.||..++.
T Consensus        11 ~~~i~~l~~-----~G~si~~IA~~~gvsr~TvyR~l~   43 (45)
T PF02796_consen   11 IEEIKELYA-----EGMSIAEIAKQFGVSRSTVYRYLN   43 (45)
T ss_dssp             HHHHHHHHH-----TT--HHHHHHHTTS-HHHHHHHHC
T ss_pred             HHHHHHHHH-----CCCCHHHHHHHHCcCHHHHHHHHh
Confidence            455666664     789999999999999999988753

Two types of site-specific recombination are known to occur: Recombination between inverted repeats resulting in the reversal of a DNA segment. Recombination between repeat sequences on two DNA molecules resulting in their cointegration, or between repeats on one DNA molecule resulting in the excision of a DNA fragment. Site-specific recombination is characterised by a strand exchange mechanism that requires no DNA synthesis or high energy cofactor; the phosphodiester bond energy is conserved in a phospho-protein linkage during strand cleavage and re-ligation. Two unrelated families of recombinases are currently known []. The first, called the 'phage integrase' family, groups a number of bacterial phage and yeast plasmid enzymes. The second [], called the 'resolvase' family, groups enzymes which share the following structural characteristics: an N-terminal catalytic and dimerization domain that contains a conserved serine residue involved in the transient covalent attachment to DNA IPR006119 from INTERPRO, and a C-terminal helix-turn-helix DNA-binding domain. ; GO: 0000150 recombinase activity, 0003677 DNA binding, 0006310 DNA recombination; PDB: 1ZR2_A 2GM4_B 1RES_A 1ZR4_A 1RET_A 1GDT_B 2R0Q_C 1JKP_C 1IJW_C 1JJ6_C ....

>cd00569 HTH_Hin_like Helix-turn-helix domain of Hin and related proteins, a family of DNA-binding domains unique to bacteria and represented by the Hin protein of Salmonella

Probab=93.94  E-value=0.1  Score=34.55  Aligned_cols=36  Identities=17%  Similarity=0.154  Sum_probs=28.4

Q ss_pred             CCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHH
Q 009449          472 LDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKL  511 (534)
Q Consensus       472 L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi  511 (534)
                      +++.++..+...|    ..+.|..+||+.+|+++.+|..+
T Consensus         6 ~~~~~~~~i~~~~----~~~~s~~~ia~~~~is~~tv~~~   41 (42)
T cd00569           6 LTPEQIEEARRLL----AAGESVAEIARRLGVSRSTLYRY   41 (42)
T ss_pred             CCHHHHHHHHHHH----HcCCCHHHHHHHHCCCHHHHHHh
Confidence            4555666665566    46789999999999999999875

The basic HTH domain is a simple fold comprised of three core helices that form a right-handed helical bundle. The principal DNA-protein interface is formed by the third helix, the recognition helix, inserting itself into the major groove of the DNA. A diverse array of HTH domains participate in a variety of functions that depend on their DNA-binding properties. HTH_Hin represents one of the simplest versions of the HTH domains; the characterization of homologous relationships between various sequence-diverse HTH domain families remains difficult. The Hin recombinase induces the site-specific inversion of a chromosomal DNA segment containing a promoter, which controls the alternate expression of two genes by reversibly switching orientation. The Hin recombinase consists of a single polypeptide chain containing a D

>PF06530 Phage_antitermQ: Phage antitermination protein Q; InterPro: IPR010534 This entry is represented by Bacteriophage 933W, GpQ

Probab=93.49  E-value=0.43  Score=43.38  Aligned_cols=55  Identities=24%  Similarity=0.204  Sum_probs=49.2

Q ss_pred             HHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHhhhh
Q 009449          468 ILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDSETCR  526 (534)
Q Consensus       468 ~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~~l~~~  526 (534)
                      .|..-.|.+-++|.++|    ..+.|...||..+++|...|++.+.+|-..+..++...
T Consensus        59 ~L~~~~~~~~~ll~~~Y----v~g~s~r~IA~~~~~s~~~ir~~l~~ae~~i~g~l~~~  113 (125)
T PF06530_consen   59 RLKKRDPEEYDLLILYY----VYGWSKRQIARKLKCSEGKIRKRLQRAEGFIDGCLSML  113 (125)
T ss_pred             HHHccCHHHHHHHHHHH----HcCCCHHHHHHHHCCCHHHHHHHHHHhhhhHhhhhHHh
Confidence            34557999999999999    89999999999999999999999999999999876543

The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This family consists of several phage antitermination protein Q and related bacterial sequences. Phage 993W gene Q encodes a phage-specific positive regulator of late gene expression, thought, by analogy to the corresponding gene of phage lambda, to be a transcription antiterminator. GpQ positively regulates expression of the phage late gene operons. Bacterial host RNA polymerase modified by antitermination proteins transcribes through termination sites that otherwise prevent expression of the regulated genes [, ].; GO: 0003677 DNA binding, 0060567 negative regulation of transcription termination, DNA-dependent

>PRK07598 RNA polymerase sigma factor SigC; Validated

Probab=93.28  E-value=0.91  Score=49.50  Aligned_cols=38  Identities=26%  Similarity=0.380  Sum_probs=30.0

Q ss_pred             HHHHHHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHH
Q 009449          381 ISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSA  418 (534)
Q Consensus       381 i~ki~ka~~~L~~elGr~Pt~eEIA~~lgis~~kv~~~  418 (534)
                      ...+.+.+..|..++|++||.+|.|..+|+++..++..
T Consensus       110 ~~~l~~~~~~l~~~~g~~pt~~ewa~~~~~~~~~l~~~  147 (415)
T PRK07598        110 YLRLIEVRERLTSELGHRPSLERWAKTADISLADLKPT  147 (415)
T ss_pred             HHHHHHHHHHHHHHhCCCCCHHHHHHHhCCcHHHHHHh
Confidence            34566778889999999999999998888776655544

>PRK09210 RNA polymerase sigma factor RpoD; Validated

Probab=92.65  E-value=1.6  Score=46.64  Aligned_cols=130  Identities=12%  Similarity=0.165  Sum_probs=71.2

Q ss_pred             HHHHHHHHHHHHhCCCCchHHHHHHcCCCHHHHHHHHHhcHHHHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHH-HHH
Q 009449          254 NLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQHLAFGWYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAG-NVG  332 (534)
Q Consensus       254 ~le~~~~~l~~~~g~~ps~~ewa~a~g~d~~~L~~~l~~G~~A~e~LI~~nlrLV~sIArrY~~~g~~~eDLiQEG-~lg  332 (534)
                      ++.+....|..++|+.||..+.|+..|++.+.+...+...                   ..    ..++++.+.++ -..
T Consensus       217 ~~~~~~~~l~~~lgr~pt~~EiA~~l~~~~~~v~~~~~~~-------------------~~----~~SLd~~~~~~~~~~  273 (367)
T PRK09210        217 KLIRVQRQLLQELGREPTPEEIAEEMDMPPEKVREILKIA-------------------QE----PVSLETPIGEEDDSH  273 (367)
T ss_pred             HHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHHh-------------------cC----CCCcCCCCCCCCcch
Confidence            3455667788889999999999999999998876543211                   00    01111111100 001


Q ss_pred             HHHhhhccCCcCCCchhhHHHHHHHHHHHHHHHHhccccccccchHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHcCCCH
Q 009449          333 VLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSL  412 (534)
Q Consensus       333 L~rA~ekFDp~kG~rFSTYA~~wIR~aI~~~lr~~sr~iRlP~~~~~~i~ki~ka~~~L~~elGr~Pt~eEIA~~lgis~  412 (534)
                      +...+.  |+.............++..+.+++.      .+|..-...+    .  ..+.-..|..-|.+|||+.+|+|.
T Consensus       274 l~d~i~--d~~~~~p~~~~~~~~~~~~l~~~l~------~L~~rEr~Vl----~--lrygl~~~~~~tl~EIa~~lgvs~  339 (367)
T PRK09210        274 LGDFIE--DQDATSPADHAAYELLKEQLEDVLD------TLTDREENVL----R--LRFGLDDGRTRTLEEVGKVFGVTR  339 (367)
T ss_pred             hhhhcc--CCCCCCHHHHHHHHHHHHHHHHHHH------hCCHHHHHHH----H--HHhccCCCCCccHHHHHHHHCCCH
Confidence            111111  1111223444556666777776664      2443211111    1  011111236789999999999999


Q ss_pred             HHHHHHHH
Q 009449          413 AEIRSASE  420 (534)
Q Consensus       413 ~kv~~~l~  420 (534)
                      ++|+++..
T Consensus       340 erVrQi~~  347 (367)
T PRK09210        340 ERIRQIEA  347 (367)
T ss_pred             HHHHHHHH
Confidence            99998754

>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins

Probab=92.52  E-value=0.28  Score=44.03  Aligned_cols=50  Identities=20%  Similarity=0.206  Sum_probs=44.0

Q ss_pred             HHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHh
Q 009449          468 ILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRD  521 (534)
Q Consensus       468 ~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~  521 (534)
                      .+..|++.+.+-|....    ...=+++|+++.||||..|||..+.+.+.+|--
T Consensus        30 ~~~~L~~E~~~Fi~~Fi----~~rGnlKe~e~~lgiSYPTvR~rLd~ii~~lg~   79 (113)
T PF09862_consen   30 WFARLSPEQLEFIKLFI----KNRGNLKEMEKELGISYPTVRNRLDKIIEKLGY   79 (113)
T ss_pred             hhhcCCHHHHHHHHHHH----HhcCCHHHHHHHHCCCcHHHHHHHHHHHHHhCC
Confidence            36789999998888777    455599999999999999999999999999975

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

Probab=92.35  E-value=2.2  Score=42.45  Aligned_cols=35  Identities=17%  Similarity=0.311  Sum_probs=29.0

Q ss_pred             HHHHHHHHHHHHhCCCCchHHHHHHcCCCHHHHHH
Q 009449          254 NLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQ  288 (534)
Q Consensus       254 ~le~~~~~l~~~~g~~ps~~ewa~a~g~d~~~L~~  288 (534)
                      ++.+....+....|++||.++-|+..|++.+.+..
T Consensus        88 ~~~~~~~~l~~~~g~~pt~~eia~~l~~~~~~v~~  122 (238)
T TIGR02393        88 KLIKAERQLTQELGREPTDEELAERMGMPAEKVRE  122 (238)
T ss_pred             HHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHH
Confidence            44456677888899999999999999999988654

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.

>PRK05901 RNA polymerase sigma factor; Provisional

Probab=92.33  E-value=3.5  Score=46.17  Aligned_cols=36  Identities=22%  Similarity=0.348  Sum_probs=29.9

Q ss_pred             HHHHHHHHHHHHhCCCCchHHHHHHcCCCHHHHHHH
Q 009449          254 NLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQH  289 (534)
Q Consensus       254 ~le~~~~~l~~~~g~~ps~~ewa~a~g~d~~~L~~~  289 (534)
                      ++.+....|...+|+.||..+.|+..|++.+.+...
T Consensus       359 kl~~~~~~L~~~lgr~PT~eELAe~Lgis~e~V~~~  394 (509)
T PRK05901        359 KLGRIERELLQELGREPTPEELAKEMGFTPEKVREI  394 (509)
T ss_pred             HHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHH
Confidence            455567788888999999999999999999876553

>COG2909 MalT ATP-dependent transcriptional regulator [Transcription]

Probab=92.02  E-value=0.17  Score=58.90  Aligned_cols=47  Identities=28%  Similarity=0.239  Sum_probs=43.9

Q ss_pred             hCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhH
Q 009449          471 SLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDS  522 (534)
Q Consensus       471 ~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~~  522 (534)
                      .|+.||.+|+.+.|     +|+|.+|||+.+.||-.||+.+++....||.-.
T Consensus       831 ~Ls~RE~eVL~Lia-----~G~SN~eIa~~L~isl~TVKtH~rniy~KLgV~  877 (894)
T COG2909         831 PLSQRELEVLGLIA-----QGLSNEEIAQELFISLTTVKTHIRNIYQKLGVA  877 (894)
T ss_pred             CccHHHHHHHHHHH-----ccCCHHHHHHHHHHHHHHHHHHHHHHHHHhCcc
Confidence            38999999999999     899999999999999999999999999998643

>PF06056 Terminase_5: Putative ATPase subunit of terminase (gpP-like); InterPro: IPR010332 This family of proteins are annotated as ATPase subunits of phage terminase after []

Probab=91.82  E-value=0.27  Score=38.90  Aligned_cols=27  Identities=15%  Similarity=0.174  Sum_probs=24.6

Q ss_pred             CCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 009449          489 HRPKSLEEIGKLFHVSKEWIRKLEKKA  515 (534)
Q Consensus       489 ~e~~Sl~EIA~~LgISrerVRqi~~RA  515 (534)
                      .+|++..|||+.||+++.||.+...+-
T Consensus        11 ~~G~~~~eIA~~Lg~~~~TV~~W~~r~   37 (58)
T PF06056_consen   11 LQGWSIKEIAEELGVPRSTVYSWKDRY   37 (58)
T ss_pred             HcCCCHHHHHHHHCCChHHHHHHHHhh
Confidence            489999999999999999999988764

Terminases are viral proteins that are involved in packaging viral DNA into the capsid.; GO: 0005524 ATP binding, 0019069 viral capsid assembly

>PF13518 HTH_28: Helix-turn-helix domain

Probab=91.77  E-value=0.25  Score=36.96  Aligned_cols=27  Identities=22%  Similarity=0.314  Sum_probs=23.5

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHHHHH
Q 009449          490 RPKSLEEIGKLFHVSKEWIRKLEKKAM  516 (534)
Q Consensus       490 e~~Sl~EIA~~LgISrerVRqi~~RAL  516 (534)
                      ++.|+.+||..+|||+.+|+.+..+-.
T Consensus        11 ~g~s~~~~a~~~gis~~tv~~w~~~y~   37 (52)
T PF13518_consen   11 EGESVREIAREFGISRSTVYRWIKRYR   37 (52)
T ss_pred             cCCCHHHHHHHHCCCHhHHHHHHHHHH
Confidence            567999999999999999998876654

>smart00351 PAX Paired Box domain

Probab=91.73  E-value=0.39  Score=43.57  Aligned_cols=42  Identities=21%  Similarity=0.188  Sum_probs=34.2

Q ss_pred             CCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 009449          472 LDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMT  517 (534)
Q Consensus       472 L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~  517 (534)
                      ++..+|.-|...|    .++.|..+||+.||||+.+|..++.+...
T Consensus        18 ~s~~~R~riv~~~----~~G~s~~~iA~~~gvs~~tV~kwi~r~~~   59 (125)
T smart00351       18 LPDEERQRIVELA----QNGVRPCDISRQLCVSHGCVSKILGRYYE   59 (125)
T ss_pred             CCHHHHHHHHHHH----HcCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence            5565666666666    57899999999999999999999988753

>PRK10430 DNA-binding transcriptional activator DcuR; Provisional

Probab=91.71  E-value=0.28  Score=48.29  Aligned_cols=46  Identities=15%  Similarity=0.099  Sum_probs=36.2

Q ss_pred             hCCHHHHHHHhhHh-cCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 009449          471 SLDSRERQVLVLRY-GLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMT  517 (534)
Q Consensus       471 ~L~~rEReVL~Lry-GL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~  517 (534)
                      .|+++|.+++.... +. ..+|+|.+|||+.||+|..||+.+..++..
T Consensus       158 ~Lt~re~~~l~~~i~~~-~~~g~s~~eIA~~l~iS~~Tv~~~~~~~~~  204 (239)
T PRK10430        158 GLTPQTLRTLCQWIDAH-QDYEFSTDELANAVNISRVSCRKYLIWLVN  204 (239)
T ss_pred             CCCHHHHHHHHHHHHhC-CCCCcCHHHHHHHhCchHHHHHHHHHHHHh
Confidence            48899977764433 22 148999999999999999999999887744

>COG2390 DeoR Transcriptional regulator, contains sigma factor-related N-terminal domain [Transcription]

Probab=91.64  E-value=0.22  Score=52.43  Aligned_cols=36  Identities=22%  Similarity=0.233  Sum_probs=32.5

Q ss_pred             HHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 009449          478 QVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMT  517 (534)
Q Consensus       478 eVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~  517 (534)
                      .+-.+||    .+++|+.|||++||||+.+|+..+.+|++
T Consensus        17 ~~A~lYY----~~gltQ~eIA~~LgiSR~~v~rlL~~Ar~   52 (321)
T COG2390          17 RAAWLYY----VEGLTQSEIAERLGISRATVSRLLAKARE   52 (321)
T ss_pred             HHHHHHH----hcCCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence            3557899    89999999999999999999999998875

>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=91.49  E-value=0.26  Score=39.87  Aligned_cols=45  Identities=18%  Similarity=0.318  Sum_probs=27.8

Q ss_pred             HhhCCHHHHHHHhhHhc--CCCCCCCCHHHHHHHhCCC-HHHHHHHHH
Q 009449          469 LESLDSRERQVLVLRYG--LNDHRPKSLEEIGKLFHVS-KEWIRKLEK  513 (534)
Q Consensus       469 L~~L~~rEReVL~LryG--L~d~e~~Sl~EIA~~LgIS-rerVRqi~~  513 (534)
                      +..|+++|++||...--  -..+-+-|..|||+.||++ .++|.+++.
T Consensus         1 M~~LT~rQ~~vL~~I~~~~~~~G~~Pt~rEIa~~~g~~S~~tv~~~L~   48 (65)
T PF01726_consen    1 MKELTERQKEVLEFIREYIEENGYPPTVREIAEALGLKSTSTVQRHLK   48 (65)
T ss_dssp             -----HHHHHHHHHHHHHHHHHSS---HHHHHHHHTSSSHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCChHHHHHHHH
Confidence            35799999999876321  1124567999999999996 999977653

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.

>PF04539 Sigma70_r3: Sigma-70 region 3; InterPro: IPR007624 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription

Probab=91.48  E-value=0.49  Score=38.67  Aligned_cols=38  Identities=26%  Similarity=0.408  Sum_probs=30.2

Q ss_pred             HHHHHHHHHHHHHhCCCCchHHHHHHcCCCHHHHHHHH
Q 009449          253 ANLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQHL  290 (534)
Q Consensus       253 ~~le~~~~~l~~~~g~~ps~~ewa~a~g~d~~~L~~~l  290 (534)
                      .++.+++..|..++||.||..+.|+..|++.+.+...+
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            46778889999999999999999999999998876644

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 ....

>PF04218 CENP-B_N: CENP-B N-terminal DNA-binding domain; InterPro: IPR006695 Centromere Protein B (CENP-B) is a DNA-binding protein localized to the centromere

Probab=91.32  E-value=0.2  Score=38.83  Aligned_cols=40  Identities=25%  Similarity=0.346  Sum_probs=28.1

Q ss_pred             hCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 009449          471 SLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKK  514 (534)
Q Consensus       471 ~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~R  514 (534)
                      .|+..|+.=|.-+|    ..|.+..+||..|||+++||+.++..
T Consensus         6 ~LTl~eK~~iI~~~----e~g~s~~~ia~~fgv~~sTv~~I~K~   45 (53)
T PF04218_consen    6 SLTLEEKLEIIKRL----EEGESKRDIAREFGVSRSTVSTILKN   45 (53)
T ss_dssp             S--HHHHHHHHHHH----HCTT-HHHHHHHHT--CCHHHHHHHC
T ss_pred             cCCHHHHHHHHHHH----HcCCCHHHHHHHhCCCHHHHHHHHHh
Confidence            46666666555566    57889999999999999999998865

Within the N-terminal 125 residues, there is a DNA-binding region, which binds to a corresponding 17bp CENP-B box sequence. CENP-B dimers either bind two separate DNA molecules or alternatively, they may bind two CENP-B boxes on one DNA molecule, with the intervening stretch of DNA forming a loop structure. The CENP-B DNA-binding domain consists of two repeating domains, RP1 and RP2. This family corresponds to RP1 has been shown to consist of four helices in a helix-turn-helix structure [].; GO: 0003677 DNA binding, 0000775 chromosome, centromeric region; PDB: 1BW6_A 1HLV_A 2ELH_A.

>PF10668 Phage_terminase: Phage terminase small subunit; InterPro: IPR018925 This entry describes the terminase small subunit from Enterococcus phage phiFL1A, related proteins in other bacteriophage, and prophage regions of bacterial genomes

Probab=91.25  E-value=0.32  Score=38.85  Aligned_cols=35  Identities=20%  Similarity=0.250  Sum_probs=26.6

Q ss_pred             HHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 009449          478 QVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKK  514 (534)
Q Consensus       478 eVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~R  514 (534)
                      ..+.++...  ...+++.|||+.||||..+|+....+
T Consensus        11 kA~e~y~~~--~g~i~lkdIA~~Lgvs~~tIr~WK~~   45 (60)
T PF10668_consen   11 KAFEIYKES--NGKIKLKDIAEKLGVSESTIRKWKSR   45 (60)
T ss_pred             HHHHHHHHh--CCCccHHHHHHHHCCCHHHHHHHhhh
Confidence            344444422  45899999999999999999987654

Packaging of double-stranded viral DNA concatemers requires interaction of the prohead with virus DNA. This process is mediated by a phage-encoded DNA recognition and terminase protein. The terminase enzymes described so far, which are hetero-oligomers composed of a small and a large subunit, do not have a significant level of sequence homology. The small terminase subunit is thought to form a nucleoprotein structure that helps to position the terminase large subunit at the packaging initiation site [].

>PF13730 HTH_36: Helix-turn-helix domain

Probab=90.87  E-value=0.69  Score=35.27  Aligned_cols=47  Identities=19%  Similarity=0.292  Sum_probs=34.4

Q ss_pred             hCCHHHHHHHhhHhcCCCCCCC---CHHHHHHHhCCCHHHHHHHHHHHHHHHHh
Q 009449          471 SLDSRERQVLVLRYGLNDHRPK---SLEEIGKLFHVSKEWIRKLEKKAMTKLRD  521 (534)
Q Consensus       471 ~L~~rEReVL~LryGL~d~e~~---Sl~EIA~~LgISrerVRqi~~RAL~KLR~  521 (534)
                      .|++.++.|+....-..+..+.   |.+.||+.+|+|+.||+    ++++.|.+
T Consensus         2 ~Ls~~~~~v~~~l~~~~~~~~~~~pS~~~la~~~g~s~~Tv~----~~i~~L~~   51 (55)
T PF13730_consen    2 NLSPTAKLVYLYLASYANKNGGCFPSQETLAKDLGVSRRTVQ----RAIKELEE   51 (55)
T ss_pred             CCCHHHHHHHHHHHHhcCCCCCCCcCHHHHHHHHCcCHHHHH----HHHHHHHH
Confidence            5888888887665544322333   89999999999999996    56666654

>PHA00675 hypothetical protein

Probab=90.86  E-value=0.43  Score=39.87  Aligned_cols=41  Identities=20%  Similarity=0.101  Sum_probs=31.1

Q ss_pred             hhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 009449          470 ESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEK  513 (534)
Q Consensus       470 ~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~  513 (534)
                      ..|++.+-+.|+..+-   ..+.|+.+||+.||||+++|.+|..
T Consensus        21 AKLt~~qV~~IR~l~~---r~G~s~~~IA~~fGVsrstV~~I~~   61 (78)
T PHA00675         21 AKLTDAEVERIRELHE---VEGMSYAVLAEKFEQSKGAIAKICR   61 (78)
T ss_pred             cccCHHHHHHHHHHHH---hcCccHHHHHHHhCCCHHHHHHHHc
Confidence            3466666665555541   2678999999999999999999865

>PF13404 HTH_AsnC-type: AsnC-type helix-turn-helix domain; PDB: 2ZNY_E 2ZNZ_G 1RI7_A 2CYY_A 2E1C_A 2VC1_B 2QZ8_A 2W29_C 2IVM_B 2VBX_B

Probab=90.78  E-value=0.63  Score=34.37  Aligned_cols=39  Identities=21%  Similarity=0.328  Sum_probs=26.6

Q ss_pred             CHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 009449          473 DSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKK  514 (534)
Q Consensus       473 ~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~R  514 (534)
                      ++-.+.||...-.   ....|+.+||+.+|+|..+|...+.+
T Consensus         2 D~~D~~Il~~Lq~---d~r~s~~~la~~lglS~~~v~~Ri~r   40 (42)
T PF13404_consen    2 DELDRKILRLLQE---DGRRSYAELAEELGLSESTVRRRIRR   40 (42)
T ss_dssp             -HHHHHHHHHHHH----TTS-HHHHHHHHTS-HHHHHHHHHH
T ss_pred             CHHHHHHHHHHHH---cCCccHHHHHHHHCcCHHHHHHHHHH
Confidence            4455566655541   35789999999999999999887654

...

>PRK07921 RNA polymerase sigma factor SigB; Reviewed

Probab=90.33  E-value=4  Score=43.04  Aligned_cols=36  Identities=28%  Similarity=0.454  Sum_probs=30.1

Q ss_pred             HHHHHHHHHHHHHhCCCCchHHHHHHcCCCHHHHHH
Q 009449          253 ANLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQ  288 (534)
Q Consensus       253 ~~le~~~~~l~~~~g~~ps~~ewa~a~g~d~~~L~~  288 (534)
                      .++.++...|...+|+.||..+.|+..|++.+.+..
T Consensus       173 ~~l~~~~~~l~~~lgr~pt~~EiA~~lgi~~~~v~~  208 (324)
T PRK07921        173 NKLARIKRELHQQLGREATDEELAEESGIPEEKIAD  208 (324)
T ss_pred             HHHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHH
Confidence            345567778888899999999999999999987654

>PF02650 HTH_WhiA: WhiA C-terminal HTH domain; InterPro: IPR023054 This domain is found at the C terminus of the sporulation regulator WhiA

Probab=89.82  E-value=0.55  Score=40.09  Aligned_cols=44  Identities=30%  Similarity=0.449  Sum_probs=34.3

Q ss_pred             HhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHh--CCCHHHHHHHHHHH
Q 009449          469 LESLDSRERQVLVLRYGLNDHRPKSLEEIGKLF--HVSKEWIRKLEKKA  515 (534)
Q Consensus       469 L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~L--gISrerVRqi~~RA  515 (534)
                      ++.||+..+++..+|.   ...+.|+.|+|+.|  .||++.|..+..+-
T Consensus        35 ~~~l~~~l~~~a~lRl---~~Pd~SL~EL~~~~~~~iSKSgvnhrlrKl   80 (85)
T PF02650_consen   35 LDKLPEKLREFAELRL---ENPDASLKELGELLEPPISKSGVNHRLRKL   80 (85)
T ss_dssp             GGGS-HHHHHHHHHHH---H-TTS-HHHHHHTT--T--HHHHHHHHHHH
T ss_pred             cccCCHHHHHHHHHHH---HCccccHHHHHHHHcCcCcHHHHHHHHHHH
Confidence            5789999999999998   35899999999999  99999998877654

It is predicted to form a DNA binding helix-turn-helix structure []. ; PDB: 3HYI_A.

>PHA02591 hypothetical protein; Provisional

Probab=89.52  E-value=0.56  Score=39.29  Aligned_cols=25  Identities=24%  Similarity=0.340  Sum_probs=22.8

Q ss_pred             CCCCCHHHHHHHhCCCHHHHHHHHH
Q 009449          489 HRPKSLEEIGKLFHVSKEWIRKLEK  513 (534)
Q Consensus       489 ~e~~Sl~EIA~~LgISrerVRqi~~  513 (534)
                      ..|+|.++||+.||++.++|++...
T Consensus        57 eqGlSqeqIA~~LGVsqetVrKYL~   81 (83)
T PHA02591         57 RKGFTVEKIASLLGVSVRKVRRYLE   81 (83)
T ss_pred             HcCCCHHHHHHHhCCCHHHHHHHHh
Confidence            4789999999999999999999865

>PF01022 HTH_5: Bacterial regulatory protein, arsR family; InterPro: IPR001845 Bacterial transcription regulatory proteins that bind DNA via a helix-turn-helix (HTH) motif can be grouped into families on the basis of sequence similarities

Probab=89.24  E-value=0.75  Score=34.31  Aligned_cols=37  Identities=19%  Similarity=0.244  Sum_probs=28.7

Q ss_pred             HHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 009449          474 SRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKK  514 (534)
Q Consensus       474 ~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~R  514 (534)
                      |.-.+|+.+-.    ..+++..||++.+|+|+++|++.+..
T Consensus         2 ~~R~~Il~~L~----~~~~~~~el~~~l~~s~~~vs~hL~~   38 (47)
T PF01022_consen    2 PTRLRILKLLS----EGPLTVSELAEELGLSQSTVSHHLKK   38 (47)
T ss_dssp             HHHHHHHHHHT----TSSEEHHHHHHHHTS-HHHHHHHHHH
T ss_pred             HHHHHHHHHHH----hCCCchhhHHHhccccchHHHHHHHH
Confidence            44556776666    57899999999999999999977643

One such group, termed arsR, includes several proteins that appear to dissociate from DNA in the presence of metal ions: arsR, which functions as a transcriptional repressor of an arsenic resistance operon; smtB from Synechococcus sp. (strain PCC 7942), which acts as a transcriptional repressor of the smtA gene that codes for a metallothionein; cadC, a protein required for cadmium-resistance; and hypothetical protein yqcJ from Bacillus subtilis. The HTH motif is thought to be located in the central part of these proteins []. The motif is characterised by a number of well-conserved residues: at its N-terminal extremity is a cysteine residue; a second Cys is found in arsR and cadC, but not in smtA; and at the C terminus lie one or two histidines. These residues may be involved in metal-binding (Zn in smtB; metal-oxyanions such as arsenite, antimonite and arsenate for arsR; and cadmium for cadC) []. It is believed that binding of a metal ion could induce a conformational change that would prevent the protein from binding DNA []. The crystal structure of the cyanobacterial smtB shows a fold of five alpha-helices (H) and a pair of antiparallel beta-strands (B) in the topology H1-H2-H3-H4-B1-B2-H5. Helices 3 and 4 comprise the helix-turn-helix motif and the beta-sheet is called the wing as in other wHTH, such as the dtxR-type or the merR-type. Helix 4 is termed the recognition helix, like in other HTHs where it binds the DNA major groove. Most arsR/smtB-like metalloregulators form homodimers []. The dimer interface is formed by helix 5 and an N-terminal part []. Two distinct metal-binding sites have been identified. The first site comprises cysteine thiolates located in the HTH in helix 3 and for some cases in the N terminus, called the alpha3(N) site []. The second metal-binding site is located in helix 5 (and C terminus) and is called the alpha5(C) site. The alpha3N site binds large thiophilic, toxic metals including Cd, Pb, and Bi, as in S. aureus cadC. ArsR lacks the N-terminal arm and its alpha3 site coordinates smaller thiophilic ions like As and Sb. The alpha5 site contains carboxylate and imidazole ligands and interacts preferentially with biologically required metal ions including Zn, Co, and Ni. ArsR-type metalloregulators contain one of these sites, both, or other potential metal-binding sites [, ]. Binding of metal ions to these sites leads to allosteric changes that can derepress the operator/promotor DNA. The metal-inducible operons contain one or two imperfect 12-2-12 inverted repeats, which can be recognised by multimeric arsR-type metalloregulators. ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3CUO_A 1U2W_C 3F72_C 3F6V_A 3JTH_B 2P4W_B 1KU9_B 2LKP_B 1SMT_A 1R22_B ....

>cd00131 PAX Paired Box domain

Probab=89.16  E-value=0.88  Score=41.54  Aligned_cols=42  Identities=19%  Similarity=0.156  Sum_probs=33.3

Q ss_pred             CCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 009449          472 LDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMT  517 (534)
Q Consensus       472 L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~  517 (534)
                      |+...|.-|...|    .+|+|..+||+.||||+.+|..+..+-..
T Consensus        18 lS~d~R~rIv~~~----~~G~s~~~iA~~~~Vs~~tV~r~i~r~~e   59 (128)
T cd00131          18 LPDSIRQRIVELA----QSGIRPCDISRQLRVSHGCVSKILNRYYE   59 (128)
T ss_pred             CCHHHHHHHHHHH----HcCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence            5555555555666    57999999999999999999999887553

>TIGR02395 rpoN_sigma RNA polymerase sigma-54 factor

Probab=88.78  E-value=21  Score=39.26  Aligned_cols=29  Identities=17%  Similarity=0.234  Sum_probs=24.3

Q ss_pred             hcCCCCCCCCHHHHHHHhCCCHHHHHHHH
Q 009449          484 YGLNDHRPKSLEEIGKLFHVSKEWIRKLE  512 (534)
Q Consensus       484 yGL~d~e~~Sl~EIA~~LgISrerVRqi~  512 (534)
                      +|-....++|+++||+.+|++.+||+...
T Consensus       311 ~G~~~LkPLtlkdiA~~lglheSTVSRav  339 (429)
T TIGR02395       311 GGPAALKPLTLREVAEELGLHESTISRAI  339 (429)
T ss_pred             cCcccCcCCcHHHHHHHhCCCccchhhhh
Confidence            45444689999999999999999998654

A sigma factor is a DNA-binding protein protein that binds to the DNA-directed RNA polymerase core to produce the holoenzyme capable of initiating transcription at specific sites. Different sigma factors act in vegetative growth, heat shock, extracytoplasmic functions (ECF), etc. This model represents the clade of sigma factors called sigma-54, or RpoN (unrelated to sigma 70-type factors such as RpoD/SigA). RpoN is responsible for enhancer-dependent transcription, and its presence characteristically is associated with varied panels of activators, most of which are enhancer-binding proteins (but see Brahmachary, et al., PubMed:15231786). RpoN may be responsible for transcription of nitrogen fixation genes, flagellins, pilins, etc., and synonyms for the gene symbol rpoN, such as ntrA, reflect these observations

>TIGR02147 Fsuc_second hypothetical protein, TIGR02147

Probab=88.51  E-value=9.7  Score=39.29  Aligned_cols=98  Identities=19%  Similarity=0.225  Sum_probs=55.6

Q ss_pred             CCCCHHHHHHHcC--CCHHHHHHHHHHhhhhcccccccccchhhhhh---hccCCCCCCChH-HHHHHHHHHHHHHHHHh
Q 009449          397 KYPEDIEIAKYTG--LSLAEIRSASECLRIVGSIDQKIGDCLNAKYL---EFAPDRSVKSPK-EIVMRQHMKKDVFRILE  470 (534)
Q Consensus       397 r~Pt~eEIA~~lg--is~~kv~~~l~~~~~~~SLD~~i~~~~~~~l~---e~i~d~~~~spe-e~v~~~el~e~L~~~L~  470 (534)
                      -.++.++||+.++  ||+++++..+......--+.. .+   ++.+.   ..+..+....|. -.-.+..+.+.-.++|+
T Consensus       136 ~~~~~~~ia~~l~p~is~~ev~~sL~~L~~~glikk-~~---~g~y~~t~~~l~~~~~~~~~avr~~h~q~l~lA~~al~  211 (271)
T TIGR02147       136 FADDPEELAKRCFPKISAEQVKESLDLLERLGLIKK-NE---DGFYKQTDKAVSTGDEVIPLAVRQYQKQMIDLAKEALD  211 (271)
T ss_pred             CCCCHHHHHHHhCCCCCHHHHHHHHHHHHHCCCeeE-CC---CCcEEeecceeecCCccchHHHHHHHHHHHHHHHHHHH
Confidence            4567889999999  999999998887654322221 11   11111   111111111111 11223334445567888


Q ss_pred             hCCHHHHHHHhhHhcCCCCCCCCHHHHHHHh
Q 009449          471 SLDSRERQVLVLRYGLNDHRPKSLEEIGKLF  501 (534)
Q Consensus       471 ~L~~rEReVL~LryGL~d~e~~Sl~EIA~~L  501 (534)
                      ..|+.+|.+=.+-+|++   ..++++|.+.+
T Consensus       212 ~~p~~eR~~S~lT~~i~---~~~~~~i~~~i  239 (271)
T TIGR02147       212 ALPPSERDVSTVTFGIS---EEAYKEIVKKI  239 (271)
T ss_pred             hCCccccccceeeEecC---HHHHHHHHHHH
Confidence            99999999888877654   24555555443

This family consists of the 40 members of a paralogous protein family in the rumen anaerobe Fibrobacter succinogenes S85. Member proteins are about 270 residues long and appear to lack signal sequences and transmembrane helices. The only perfectly conserved residue is a glycine in an otherwise poorly conserved region, suggesting members are not enzymes. The family is not characterized.

>PF08279 HTH_11: HTH domain; InterPro: IPR013196 Winged helix DNA-binding proteins share a related winged helix-turn-helix DNA-binding motif, where the "wings", or loops, are small beta-sheets

Probab=88.50  E-value=0.77  Score=34.98  Aligned_cols=38  Identities=29%  Similarity=0.427  Sum_probs=26.7

Q ss_pred             HHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 009449          475 RERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKK  514 (534)
Q Consensus       475 rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~R  514 (534)
                      |+.+|+.+.+  ....+.|.+|||+.||||+.||+..+..
T Consensus         1 R~~~il~~L~--~~~~~it~~eLa~~l~vS~rTi~~~i~~   38 (55)
T PF08279_consen    1 RQKQILKLLL--ESKEPITAKELAEELGVSRRTIRRDIKE   38 (55)
T ss_dssp             HHHHHHHHHH--HTTTSBEHHHHHHHCTS-HHHHHHHHHH
T ss_pred             CHHHHHHHHH--HcCCCcCHHHHHHHhCCCHHHHHHHHHH
Confidence            4556666653  1134599999999999999999865544

The winged helix motif consists of two wings (W1, W2), three alpha helices (H1, H2, H3) and three beta-sheets (S1, S2, S3) arranged in the order H1-S1-H2-H3-S2-W1-S3-W2 []. The DNA-recognition helix makes sequence-specific DNA contacts with the major groove of DNA, while the wings make different DNA contacts, often with the minor groove or the backbone of DNA. Several winged-helix proteins display an exposed patch of hydrophobic residues thought to mediate protein-protein interactions. This entry represents a subset of the winged helix domain superfamily which is predominantly found in bacterial proteins, though there are also some archaeal and eukaryotic examples. This domain is commonly found in the biotin (vitamin H) repressor protein BirA which regulates transcription of the biotin operon []. It is also found in other proteins including regulators of amino acid biosynthsis such as LysM [], and regulators of carbohydrate metabolisms such as LicR and FrvR [, ].; PDB: 1HXD_B 2EWN_B 1BIA_A 1BIB_A 1J5Y_A 3V7S_A 3V7C_A 3RKW_A 3RIR_A 3RKX_A ....

>PF12840 HTH_20: Helix-turn-helix domain; PDB: 1ULY_A 2CWE_A 1Y0U_B 2QUF_B 2QLZ_C 2OQG_B 2ZKZ_C 3PQK_A 3PQJ_D 3F6O_B

Probab=88.42  E-value=1.5  Score=34.40  Aligned_cols=43  Identities=21%  Similarity=0.346  Sum_probs=31.9

Q ss_pred             HHHHHhhCCHHHHHHHhhH-hcCCCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 009449          465 VFRILESLDSRERQVLVLR-YGLNDHRPKSLEEIGKLFHVSKEWIRKLEK  513 (534)
Q Consensus       465 L~~~L~~L~~rEReVL~Lr-yGL~d~e~~Sl~EIA~~LgISrerVRqi~~  513 (534)
                      +.++|.  +|.-..|+.+- -    ..++|..|||+.+|++.++|+.++.
T Consensus         3 i~~aL~--~p~R~~Il~~L~~----~~~~t~~ela~~l~~~~~t~s~hL~   46 (61)
T PF12840_consen    3 IFKALS--DPTRLRILRLLAS----NGPMTVSELAEELGISQSTVSYHLK   46 (61)
T ss_dssp             HHHHHT--SHHHHHHHHHHHH----CSTBEHHHHHHHHTS-HHHHHHHHH
T ss_pred             HHHHhC--CHHHHHHHHHHhc----CCCCCHHHHHHHHCCCHHHHHHHHH
Confidence            444553  46667777766 4    6899999999999999999986543

...

>PRK07406 RNA polymerase sigma factor RpoD; Validated

Probab=88.05  E-value=8.7  Score=41.42  Aligned_cols=126  Identities=21%  Similarity=0.261  Sum_probs=70.8

Q ss_pred             HHHHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHH------------hhhhccc-----------ccccccchhhh
Q 009449          383 KIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASEC------------LRIVGSI-----------DQKIGDCLNAK  439 (534)
Q Consensus       383 ki~ka~~~L~~elGr~Pt~eEIA~~lgis~~kv~~~l~~------------~~~~~SL-----------D~~i~~~~~~~  439 (534)
                      .+.+.+..|..++|+.|+..+.|...|++...+...+..            .+.+.++           +..+. ++...
T Consensus        95 ~~~~~~~~l~~~~g~~~~~~~~~~~~~~~~~~l~~~~~~g~~A~~~Li~~~l~lV~~iA~ry~~~~~~~eDLiQ-EG~ig  173 (373)
T PRK07406         95 ELEELREQFESELGREPSDKEWAELVDMPLPKFRRRLMLGRRAKEKMVQSNLRLVVSIAKKYMNRGLSFQDLIQ-EGSLG  173 (373)
T ss_pred             HHHHHHHHHHHhcccccchhhHhhhccccHHHHHHHHhcCHHHHHHHHHHHHHHHHHHHHHHcCCCCCHHHHHH-HHHHH
Confidence            345567788888999999999999999998766654321            1111111           11111 11111


Q ss_pred             hhhccC--CCCCCChHHHHHHHHHHHHHHHHHhh------CCHHHHH----------HHhhHhcCCCCCCCCHHHHHHHh
Q 009449          440 YLEFAP--DRSVKSPKEIVMRQHMKKDVFRILES------LDSRERQ----------VLVLRYGLNDHRPKSLEEIGKLF  501 (534)
Q Consensus       440 l~e~i~--d~~~~spee~v~~~el~e~L~~~L~~------L~~rERe----------VL~LryGL~d~e~~Sl~EIA~~L  501 (534)
                      +...+.  |+.-..+.......-+++.|.++|..      ||-.-..          -+...+    +..-|.+|||+.+
T Consensus       174 L~~Ai~kFd~~kg~~FsTYA~wWIRqaI~~~I~~~~r~IRlP~~~~~~~~~i~~a~~~l~~~l----gr~Pt~~EIA~~l  249 (373)
T PRK07406        174 LIRAAEKFDHEKGYKFSTYATWWIRQAITRAIADQSRTIRLPVHLYETISRIKKTTKVLSQEF----GRKPTEEEIAESM  249 (373)
T ss_pred             HHHHHHhcCCccCCCHHHHHHHHHHHHHHHHHHhcCCceeCCHHHHHHHHHHHHHHHHHHHHh----CCCCCHHHHHHHh
Confidence            111111  22222344455444555556555532      5543322          223344    4566899999999


Q ss_pred             CCCHHHHHHHHH
Q 009449          502 HVSKEWIRKLEK  513 (534)
Q Consensus       502 gISrerVRqi~~  513 (534)
                      |++.+.|+.+..
T Consensus       250 g~~~e~v~~~~~  261 (373)
T PRK07406        250 EMTIEKLRFIAK  261 (373)
T ss_pred             CCCHHHHHHHHH
Confidence            999999987643

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

Probab=87.66  E-value=11  Score=38.56  Aligned_cols=124  Identities=15%  Similarity=0.095  Sum_probs=71.0

Q ss_pred             HHHHHHHHHHHHhCCCCchHHHHHHcCCCHHHHHHHHHhcHHHHHHHHHHhHHHHHHHHHHhhCCCCC-HHHHHHHHHHH
Q 009449          254 NLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQHLAFGWYCREELIKSTRPLVLFLARNYRGLGIP-FSDLLQAGNVG  332 (534)
Q Consensus       254 ~le~~~~~l~~~~g~~ps~~ewa~a~g~d~~~L~~~l~~G~~A~e~LI~~nlrLV~sIArrY~~~g~~-~eDLiQEG~lg  332 (534)
                      +++.+...|+.++|++||..+-|+..|++.+++...+.          ..+...+.++--.....+.+ ..|        
T Consensus       111 ~i~~~~~~l~~el~r~pt~~EIA~~L~i~~ee~~~~~~----------~~~~~~~~sld~~~~~~~d~~~~~--------  172 (247)
T COG1191         111 RIEEAIDELEQELGREPTDEEIAEELGIDKEEYIEALL----------AINGSQLLSLDEDVLKDDDDDVDD--------  172 (247)
T ss_pred             HHHHHHHHHHHHhCCCCcHHHHHHHhCCCHHHHHHHHH----------Hhccccccchhhhhccccccchhh--------
Confidence            34567778899999999999999999999988665332          22222222222221111111 111        


Q ss_pred             HHHhhhccCCcCCCchhhHHHHHHHHHHHHHHHHhccccccccchHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHcCCCH
Q 009449          333 VLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSL  412 (534)
Q Consensus       333 L~rA~ekFDp~kG~rFSTYA~~wIR~aI~~~lr~~sr~iRlP~~~~~~i~ki~ka~~~L~~elGr~Pt~eEIA~~lgis~  412 (534)
                                ..+..+..+-.|-..+.+..++.      .+|..-..          -+.-....+-|--|||+.+||+.
T Consensus       173 ----------~~~~~~~~~~~~~~~~~l~~ai~------~L~EREk~----------Vl~l~y~eelt~kEI~~~LgISe  226 (247)
T COG1191         173 ----------QIENPDDGVEKEELLEILKEAIE------PLPEREKL----------VLVLRYKEELTQKEIAEVLGISE  226 (247)
T ss_pred             ----------ccccchhHHHHHHHHHHHHHHHH------ccCHHHHH----------HHHHHHHhccCHHHHHHHhCccH
Confidence                      12224455566666677766664      12322100          01111123457789999999999


Q ss_pred             HHHHHHHHH
Q 009449          413 AEIRSASEC  421 (534)
Q Consensus       413 ~kv~~~l~~  421 (534)
                      .+|.++...
T Consensus       227 s~VSql~kk  235 (247)
T COG1191         227 SRVSRLHKK  235 (247)
T ss_pred             HHHHHHHHH
Confidence            999877543

>PF12802 MarR_2: MarR family; PDB: 3ECO_B 2QWW_B 3KP6_B 3KP4_B 3KP2_A 3KP5_A 3KP3_B 3KP7_A 3NQO_B 3K0L_B

Probab=87.59  E-value=1.1  Score=34.70  Aligned_cols=43  Identities=16%  Similarity=0.206  Sum_probs=31.9

Q ss_pred             hCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 009449          471 SLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKK  514 (534)
Q Consensus       471 ~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~R  514 (534)
                      .|++.|..||...+.-++ .+.|..|||+.+++++.+|..++.+
T Consensus         2 glt~~q~~vL~~l~~~~~-~~~t~~~la~~l~~~~~~vs~~v~~   44 (62)
T PF12802_consen    2 GLTPSQFRVLMALARHPG-EELTQSELAERLGISKSTVSRIVKR   44 (62)
T ss_dssp             TSTHHHHHHHHHHHHSTT-SGEEHHHHHHHHTS-HHHHHHHHHH
T ss_pred             ccCHHHHHHHHHHHHCCC-CCcCHHHHHHHHCcCHHHHHHHHHH
Confidence            478888888877764322 2389999999999999999765544

...

>COG3355 Predicted transcriptional regulator [Transcription]

Probab=87.55  E-value=1.8  Score=39.61  Aligned_cols=53  Identities=15%  Similarity=0.354  Sum_probs=42.1

Q ss_pred             HHHHHHHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHh
Q 009449          463 KDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRD  521 (534)
Q Consensus       463 e~L~~~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~  521 (534)
                      +++..++-.|++.+.+|+....-  ...+.|..|||+.+|++++||.    ||+++|=.
T Consensus        16 ~dvl~c~~GLs~~Dv~v~~~LL~--~~~~~tvdelae~lnr~rStv~----rsl~~L~~   68 (126)
T COG3355          16 EDVLKCVYGLSELDVEVYKALLE--ENGPLTVDELAEILNRSRSTVY----RSLQNLLE   68 (126)
T ss_pred             HHHHHHHhCCcHHHHHHHHHHHh--hcCCcCHHHHHHHHCccHHHHH----HHHHHHHH
Confidence            35667888899999998876542  2469999999999999999995    66766643

>PF01726 LexA_DNA_bind: LexA DNA binding domain; InterPro: IPR006199 This is the DNA binding domain of the LexA SOS regulon repressor which prevents expression of DNA repair proteins in bacteria

Probab=86.57  E-value=2.2  Score=34.51  Aligned_cols=42  Identities=19%  Similarity=0.264  Sum_probs=31.9

Q ss_pred             HHHHHHHHHHHHhcCCCCCHHHHHHHcCCC-HHHHHHHHHHhh
Q 009449          382 SKIQKARKALTNSHGKYPEDIEIAKYTGLS-LAEIRSASECLR  423 (534)
Q Consensus       382 ~ki~ka~~~L~~elGr~Pt~eEIA~~lgis-~~kv~~~l~~~~  423 (534)
                      .+|-.....+..+.|..||..|||+.+|+. ...|...+....
T Consensus         9 ~~vL~~I~~~~~~~G~~Pt~rEIa~~~g~~S~~tv~~~L~~Le   51 (65)
T PF01726_consen    9 KEVLEFIREYIEENGYPPTVREIAEALGLKSTSTVQRHLKALE   51 (65)
T ss_dssp             HHHHHHHHHHHHHHSS---HHHHHHHHTSSSHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCCCCCHHHHHHHhCCCChHHHHHHHHHHH
Confidence            455566677788999999999999999997 888988877664

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.

>PRK11083 DNA-binding response regulator CreB; Provisional

Probab=86.28  E-value=0.96  Score=42.78  Aligned_cols=50  Identities=18%  Similarity=0.063  Sum_probs=42.7

Q ss_pred             hCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCC-----HHHHHHHHHHHHHHHHh
Q 009449          471 SLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVS-----KEWIRKLEKKAMTKLRD  521 (534)
Q Consensus       471 ~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgIS-----rerVRqi~~RAL~KLR~  521 (534)
                      .|+++|.+|+.+..- +.++++|.+||++.++.+     ..||+.+..+.++||..
T Consensus       154 ~Lt~~E~~il~~l~~-~~~~~~s~~~i~~~l~~~~~~~~~~tv~~~i~~l~~Kl~~  208 (228)
T PRK11083        154 TLTRYEFLLLKTLLL-SPGRVFSRQQLMDIVWEDAQDSYDRTVDTHIKTLRAKLRA  208 (228)
T ss_pred             ecCHHHHHHHHHHHh-CCCceECHHHHHHHhcCCCCCCCccCHHHHHHHHHHHhcc
Confidence            499999999988772 223569999999999986     78999999999999974

>PF03444 HrcA_DNA-bdg: Winged helix-turn-helix transcription repressor, HrcA DNA-binding; InterPro: IPR005104 Prokaryotic cells have a defence mechanism against a sudden heat-shock stress

Probab=86.00  E-value=1.4  Score=37.03  Aligned_cols=42  Identities=24%  Similarity=0.241  Sum_probs=33.5

Q ss_pred             CCHHHHHHHhhHhcC--CCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 009449          472 LDSRERQVLVLRYGL--NDHRPKSLEEIGKLFHVSKEWIRKLEK  513 (534)
Q Consensus       472 L~~rEReVL~LryGL--~d~e~~Sl~EIA~~LgISrerVRqi~~  513 (534)
                      |+++|++||...--+  ..+++-.-++||+.+++|..|||+.+.
T Consensus         2 Lt~rq~~IL~alV~~Y~~~~~PVgSk~ia~~l~~s~aTIRN~M~   45 (78)
T PF03444_consen    2 LTERQREILKALVELYIETGEPVGSKTIAEELGRSPATIRNEMA   45 (78)
T ss_pred             CCHHHHHHHHHHHHHHHhcCCCcCHHHHHHHHCCChHHHHHHHH
Confidence            789999987654322  346888999999999999999998653

Commonly, they induce a set of proteins that protect cellular proteins from being denatured by heat. Among such proteins are the GroE and DnaK chaperones whose transcription is regulated by a heat-shock repressor protein HrcA. HrcA is a winged helix-turn-helix repressor that negatively regulates the transcription of dnaK and groE operons by binding the upstream CIRCE (controlling inverted repeat of chaperone expression) element. In Bacillus subtilis this element is a perfect 9 base pair inverted repeat separated by a 9 base pair spacer. The crystal structure of a heat-inducible transcriptional repressor, HrcA, from Thermotoga maritima has been reported at 2.2A resolution. HrcA is composed of three domains: an N-terminal winged helix-turn-helix domain (WHTH), a GAF-like domain, and an inserted dimerizing domain (IDD). The IDD shows a unique structural fold with an anti-parallel beta-sheet composed of three beta-strands sided by four alpha-helices. HrcA crystallises as a dimer, which is formed through hydrophobic contact between the IDDs and a limited contact that involves conserved residues between the GAF-like domains []. The structural studies suggest that the inactive form of HrcA is the dimer and this is converted to its DNA-binding form by interaction with GroEL, which binds to a conserved C-terminal sequence region [, ]. Comparison of the HrcA-CIRCE complexes from B. subtilis and Bacillus thermoglucosidasius (Geobacillus thermoglucosidasius), which grow at vastly different ranges of temperature shows that the thermostability profiles were consistent with the difference in the growth temperatures suggesting that HrcA can function as a thermosensor to detect temperature changes in cells []. Any increase in temperature causes the dissociation of the HrcA from the CIRCE complex with the concomitant activation of transcription of the groE and dnaK operons. This domain represents the winged helix-turn-helix DNA-binding domain which is located close to the N terminus of HrcA. This domain is also found at the N terminus of a set of uncharacterised proteins that have two C-terminal CBS domains. ; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent

>PHA02547 55 RNA polymerase sigma factor; Provisional

Probab=85.99  E-value=2.5  Score=40.51  Aligned_cols=65  Identities=15%  Similarity=0.186  Sum_probs=50.6

Q ss_pred             HhHHHHHHHHHHhhCCCCC---HHHHHHHHHHHHHHhhhccCCcCCCchhhHHHHHHHHHHHHHHHHh
Q 009449          303 STRPLVLFLARNYRGLGIP---FSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARH  367 (534)
Q Consensus       303 ~nlrLV~sIArrY~~~g~~---~eDLiQEG~lgL~rA~ekFDp~kG~rFSTYA~~wIR~aI~~~lr~~  367 (534)
                      +-+..+..++++|.-++..   -+|.|.+|.-..++.+..|||++...+-+|++..+-++..+-|...
T Consensus        45 ~imkIa~glS~r~nF~~Yt~~wKedMI~DgIe~~i~ylhNFD~~k~~Np~aYiT~~~~~AF~~RI~kE  112 (179)
T PHA02547         45 AIMKIAEGLSRRPNFSGYTQTWKEDMIADGIEACIKGLHNFDETKYKNPHAYITQACFNAFVQRIKKE  112 (179)
T ss_pred             HHHHHHhccccCCccccchHHHHHHHHHHHHHHHHHHhhcCCcccccChHHHHHHHHHHHHHHHHHHH
Confidence            3445555666666555555   6899999999999999999999988888888888888877777644

>PF01325 Fe_dep_repress: Iron dependent repressor, N-terminal DNA binding domain; InterPro: IPR022687 The DtxR-type HTH domain is a DNA-binding, winged helix-turn-helix (wHTH) domain of about 65 residues present in metalloregulators of the DtxR/MntR family

Probab=85.98  E-value=0.96  Score=35.88  Aligned_cols=46  Identities=22%  Similarity=0.343  Sum_probs=30.7

Q ss_pred             CCHHHHHHHhhHhcCC-CCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHh
Q 009449          472 LDSRERQVLVLRYGLN-DHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRD  521 (534)
Q Consensus       472 L~~rEReVL~LryGL~-d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~  521 (534)
                      |++....-|...|-|. ++...+..+||+.||||+.+|..    ++++|.+
T Consensus         2 Lt~~~e~YL~~Iy~l~~~~~~v~~~~iA~~L~vs~~tvt~----ml~~L~~   48 (60)
T PF01325_consen    2 LTESEEDYLKAIYELSEEGGPVRTKDIAERLGVSPPTVTE----MLKRLAE   48 (60)
T ss_dssp             CSCHHHHHHHHHHHHHHCTSSBBHHHHHHHHTS-HHHHHH----HHHHHHH
T ss_pred             CCcHHHHHHHHHHHHHcCCCCccHHHHHHHHCCChHHHHH----HHHHHHH
Confidence            3444444444444443 45789999999999999999964    5556653

The family is named after Corynebacterium diphtheriae DtxR, an iron-specific diphtheria toxin repressor, and Bacillus subtilis MntR, a manganese transport regulator. Iron-responsive metalloregulators such as DtxR and IdeR occur in Gram-positive bacteria of the high GC branch, while manganese-responsive metalloregulators like MntR are described in diverse genera of Gram-positive and Gram-negative bacteria and also in Archaea [].The metalloregulators like DtxR/MntR contain the DNA-binding DtxR-type HTH domain usually in the N-terminal part. The C-terminal part contains a dimerisation domain with two metal-binding sites, although the primary metal-binding site is less conserved in the Mn(II)-regulators. Fe(II)-regulated proteins contain an SH3-like domain as a C-terminal extension, which is absent in Mn(II)-regulated MntR [, ]. Metal-ion dependent regulators orchestrate the virulence of several important human pathogens. The DtxR protein regulates the expression of diphtheria toxinin response to environmental iron concentrations. Furthermore, DtxR and IdeR control iron uptake []. Homeostasis of manganese, which is an essential nutrient, is regulated by MntR. A typical DtxR-type metalloregulator binds two divalent metal effectors per monomer, upon which allosteric changes occur that moderate binding to the cognate DNA operators. Iron-bound DtxR homodimers bind to an interrupted palindrome of 19 bp, protecting a sequence of ~30 bp. The crystal structures of iron-regulated and manganese-regulated repressors show that the DNA binding domain contains three alpha-helices and a pair of antiparallel beta-strands. Helices 2 and 3 comprise the helix-turn-helix motif and the beta-strands are called the wing []. This wHTH topology is similar to the lysR-type HTH (see PDOC00043 from PROSITEDOC). Most DtxR-type metalloregulators bind as dimers to the DNA major groove. Several proteins are known to contain a DtxR-type HTH domain. These include- Corynebacterium diphtheriae DtxR, a diphtheria toxin repressor [], which regulates the expression of the high-affinity iron uptake system, other iron-sensitive genes, and the bacteriophage tox gene. Metal-bound DtxR represses transcription by binding the tox operator; if iron is limiting, conformational changes of the wHTH disrupt DNA-binding and the diphtheria toxin is produced. Mycobacterium tuberculosis IdeR, an iron-dependent regulator that is essential for this pathogen. The regulator represses genes for iron acquisition and activates iron storage genes, and is a positive regulator of oxidative stress responses []. Bacillus subtilis MntR, a manganese transport regulator, binds Mn2+ as an effector and is a transcriptional repressor of transporters for the import of manganese. Treponema pallidum troR, a metal-dependent transcriptional repressor. Archaeoglobus fulgidus MDR1 (troR), a metal-dependent transcriptional repressor, which negatively regulates its own transcription. This entry covers the entire DtxR-type HTH domain.; GO: 0005506 iron ion binding; PDB: 3HRT_B 3HRS_A 3HRU_B 2X4H_D 1ON1_B 2HYF_C 2F5E_A 3R60_B 1ON2_B 2F5F_A ....

>PRK10710 DNA-binding transcriptional regulator BaeR; Provisional

Probab=85.93  E-value=1.1  Score=43.02  Aligned_cols=50  Identities=20%  Similarity=0.088  Sum_probs=44.0

Q ss_pred             hCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhC-----CCHHHHHHHHHHHHHHHHh
Q 009449          471 SLDSRERQVLVLRYGLNDHRPKSLEEIGKLFH-----VSKEWIRKLEKKAMTKLRD  521 (534)
Q Consensus       471 ~L~~rEReVL~LryGL~d~e~~Sl~EIA~~Lg-----ISrerVRqi~~RAL~KLR~  521 (534)
                      .|+++|.+|+.+... +.+++.|.++|++.+.     ++..||..+..+.++||..
T Consensus       160 ~Lt~~e~~il~~l~~-~~~~~~s~~~i~~~~~~~~~~~~~~tv~~~i~~lr~kl~~  214 (240)
T PRK10710        160 DLTPAEFRLLKTLSH-EPGKVFSREQLLNHLYDDYRVVTDRTIDSHIKNLRRKLES  214 (240)
T ss_pred             ecCHHHHHHHHHHHh-CCCceEcHHHHHHHhcCcCcCCCccCHHHHHHHHHHHhhc
Confidence            499999999998873 3456899999999998     9999999999999999974

>PRK10046 dpiA two-component response regulator DpiA; Provisional

Probab=85.89  E-value=0.75  Score=44.94  Aligned_cols=39  Identities=15%  Similarity=0.144  Sum_probs=29.5

Q ss_pred             hCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 009449          471 SLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEK  513 (534)
Q Consensus       471 ~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~  513 (534)
                      .|+++  +|+.+.-  .+..++|.+|||+.||||+.||+.+..
T Consensus       161 ~Lt~r--~Vl~~~~--~g~~g~s~~eIa~~l~iS~~Tv~~~~~  199 (225)
T PRK10046        161 PLTLN--AVRKLFK--EPGVQHTAETVAQALTISRTTARRYLE  199 (225)
T ss_pred             HHHHH--HHHHHHH--cCCCCcCHHHHHHHhCccHHHHHHHHH
Confidence            35665  6766554  122379999999999999999998875

>PRK05932 RNA polymerase factor sigma-54; Reviewed

Probab=85.75  E-value=35  Score=37.79  Aligned_cols=46  Identities=20%  Similarity=0.366  Sum_probs=33.1

Q ss_pred             HHHhhCCHHHHHHHhh------------HhcCCCCCCCCHHHHHHHhCCCHHHHHHHH
Q 009449          467 RILESLDSRERQVLVL------------RYGLNDHRPKSLEEIGKLFHVSKEWIRKLE  512 (534)
Q Consensus       467 ~~L~~L~~rEReVL~L------------ryGL~d~e~~Sl~EIA~~LgISrerVRqi~  512 (534)
                      .++..|.-|.+.+++.            .+|-....++|+++||+.+|+..+||+...
T Consensus       307 ~li~~i~~R~~TL~~v~~~Iv~~Q~~Ff~~G~~~LkPLtlkdvAe~lglheSTVSRav  364 (455)
T PRK05932        307 WLIKSLEQRKETLLKVARCIVEQQRDFFEHGEEALKPLVLKDIAEELGMHESTISRAT  364 (455)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCcccCcCccHHHHHHHhCCCccchhhhh
Confidence            3445566666555432            346545689999999999999999998654

>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases

Probab=85.60  E-value=2  Score=34.80  Aligned_cols=37  Identities=11%  Similarity=0.171  Sum_probs=25.3

Q ss_pred             HHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 009449          476 ERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEK  513 (534)
Q Consensus       476 EReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~  513 (534)
                      +..|+.+... .+.++.|..|||+.+|+++.+|++++.
T Consensus         8 ~~~IL~~L~~-~g~~~~ta~eLa~~lgl~~~~v~r~L~   44 (68)
T smart00550        8 EEKILEFLEN-SGDETSTALQLAKNLGLPKKEVNRVLY   44 (68)
T ss_pred             HHHHHHHHHH-CCCCCcCHHHHHHHHCCCHHHHHHHHH
Confidence            3445444442 122359999999999999999975543

Helix-turn-helix-containing domain. Also known as Zab.

>PRK05911 RNA polymerase sigma factor sigma-28; Reviewed

Probab=85.28  E-value=9.5  Score=38.64  Aligned_cols=34  Identities=18%  Similarity=0.200  Sum_probs=27.1

Q ss_pred             HHHHHHHHHHHhCCCCchHHHHHHcCCCHHHHHH
Q 009449          255 LERIKTTLEKESGKAASLNCWAQAAGVSERVLKQ  288 (534)
Q Consensus       255 le~~~~~l~~~~g~~ps~~ewa~a~g~d~~~L~~  288 (534)
                      +......+...+|++|+..+-|+..|++.+.+..
T Consensus       112 l~~~~~~l~~~~gr~pt~~eiA~~l~i~~~~v~~  145 (257)
T PRK05911        112 LADAMDSLRQSLGKEPTDGELCEYLNISQQELSG  145 (257)
T ss_pred             HHHHHHHHHHHHCcCCCHHHHHHHhCcCHHHHHH
Confidence            3344556777889999999999999999887644

>PRK07408 RNA polymerase sigma factor SigF; Reviewed

Probab=85.27  E-value=3.4  Score=41.76  Aligned_cols=35  Identities=20%  Similarity=0.280  Sum_probs=29.6

Q ss_pred             HHHHHHHHHHHHhCCCCchHHHHHHcCCCHHHHHH
Q 009449          254 NLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQ  288 (534)
Q Consensus       254 ~le~~~~~l~~~~g~~ps~~ewa~a~g~d~~~L~~  288 (534)
                      ++.+.+..|...+|++|+..+.|+..|++.+.+..
T Consensus       114 ~~~~~~~~l~~~lgr~pt~~elA~~lgi~~~~v~~  148 (256)
T PRK07408        114 QAKKVRQELRQELGRQPTDQEIAQALDISLEEWQE  148 (256)
T ss_pred             HHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHH
Confidence            45566778888999999999999999999987654

>PRK06288 RNA polymerase sigma factor WhiG; Reviewed

Probab=84.96  E-value=27  Score=35.38  Aligned_cols=35  Identities=26%  Similarity=0.284  Sum_probs=29.3

Q ss_pred             HHHHHHHHHHHHhCCCCchHHHHHHcCCCHHHHHH
Q 009449          254 NLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQ  288 (534)
Q Consensus       254 ~le~~~~~l~~~~g~~ps~~ewa~a~g~d~~~L~~  288 (534)
                      ++.+.+..|+..+|++||..+-|...|++.+.+..
T Consensus       119 ~i~~~~~~l~~~~~~~pt~~eia~~lg~~~~~v~~  153 (268)
T PRK06288        119 QIERAIAMLEARLGRTPSDEEIADELGISLEEYNS  153 (268)
T ss_pred             HHHHHHHHHHHHHCCCCCHHHHHHHcCCCHHHHHH
Confidence            45566778888899999999999999999877654

>PF13542 HTH_Tnp_ISL3: Helix-turn-helix domain of transposase family ISL3

Probab=84.92  E-value=2.1  Score=32.18  Aligned_cols=33  Identities=18%  Similarity=0.290  Sum_probs=26.4

Q ss_pred             HHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 009449          478 QVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKA  515 (534)
Q Consensus       478 eVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RA  515 (534)
                      .|+.+..     +..|.++||+.+|||..+|+.+..+.
T Consensus        19 ~i~~~~~-----~~~s~~~vA~~~~vs~~TV~ri~~~~   51 (52)
T PF13542_consen   19 YILKLLR-----ESRSFKDVARELGVSWSTVRRIFDRY   51 (52)
T ss_pred             HHHHHHh-----hcCCHHHHHHHHCCCHHHHHHHHHhh
Confidence            4555554     34699999999999999999988764

>PRK10336 DNA-binding transcriptional regulator QseB; Provisional

Probab=84.92  E-value=1.1  Score=42.09  Aligned_cols=49  Identities=20%  Similarity=0.130  Sum_probs=41.2

Q ss_pred             hCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhC-----CCHHHHHHHHHHHHHHHH
Q 009449          471 SLDSRERQVLVLRYGLNDHRPKSLEEIGKLFH-----VSKEWIRKLEKKAMTKLR  520 (534)
Q Consensus       471 ~L~~rEReVL~LryGL~d~e~~Sl~EIA~~Lg-----ISrerVRqi~~RAL~KLR  520 (534)
                      .|+++|.+|+.+.. -+.+..+|.++|++.+.     ++..+|+.+..+.++||.
T Consensus       149 ~Lt~~E~~il~~l~-~~~~~~~s~~~i~~~l~~~~~~~~~~tv~~~i~~lr~Kl~  202 (219)
T PRK10336        149 TLKPKEFALLELLM-RNAGRVLPRKLIEEKLYTWDEEVTSNAVEVHVHHLRRKLG  202 (219)
T ss_pred             ecCHHHHHHHHHHH-hCCCccCcHHHHHHHhcCCCCCCCccCHHHHHHHHHHhcC
Confidence            49999999998765 22234599999999996     999999999999999985

>smart00342 HTH_ARAC helix_turn_helix, arabinose operon control protein

Probab=84.41  E-value=17  Score=28.63  Aligned_cols=73  Identities=16%  Similarity=0.109  Sum_probs=46.1

Q ss_pred             CCCHHHHHHHcCCCHHHHHHHHHHhhhhcccccccccchhhhhhhccCCCCCCChHHHHHHHHHHHHHHHHHhhCCHHHH
Q 009449          398 YPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNAKYLEFAPDRSVKSPKEIVMRQHMKKDVFRILESLDSRER  477 (534)
Q Consensus       398 ~Pt~eEIA~~lgis~~kv~~~l~~~~~~~SLD~~i~~~~~~~l~e~i~d~~~~spee~v~~~el~e~L~~~L~~L~~rER  477 (534)
                      +++.++||+.+|++...+..+......                         .+|.+.+.. .   .+           .
T Consensus         1 ~~~~~~la~~~~~s~~~l~~~f~~~~~-------------------------~s~~~~~~~-~---r~-----------~   40 (84)
T smart00342        1 PLTLEDLAEALGMSPRHLQRLFKKETG-------------------------TTPKQYLRD-R---RL-----------E   40 (84)
T ss_pred             CCCHHHHHHHhCCCHHHHHHHHHHHhC-------------------------cCHHHHHHH-H---HH-----------H
Confidence            368899999999999998877653310                         122222111 0   11           1


Q ss_pred             HHHhhHhcCCCCCCCCHHHHHHHhCC-CHHHHHHHHHH
Q 009449          478 QVLVLRYGLNDHRPKSLEEIGKLFHV-SKEWIRKLEKK  514 (534)
Q Consensus       478 eVL~LryGL~d~e~~Sl~EIA~~LgI-SrerVRqi~~R  514 (534)
                      .++.+..    ..+.++.|||..+|+ +.....+...+
T Consensus        41 ~a~~~l~----~~~~~~~~ia~~~g~~s~~~f~r~Fk~   74 (84)
T smart00342       41 RARRLLR----DTDLSVTEIALRVGFSSQSYFSRAFKK   74 (84)
T ss_pred             HHHHHHH----cCCCCHHHHHHHhCCCChHHHHHHHHH
Confidence            2333333    237899999999999 99888766544

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

Probab=84.12  E-value=15  Score=38.00  Aligned_cols=34  Identities=35%  Similarity=0.488  Sum_probs=27.0

Q ss_pred             HHHHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHH
Q 009449          383 KIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIR  416 (534)
Q Consensus       383 ki~ka~~~L~~elGr~Pt~eEIA~~lgis~~kv~  416 (534)
                      .+......|...+|++||..+.|+..|++...+.
T Consensus        33 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~   66 (298)
T TIGR02997        33 VLEELREELEEQLGREPSKEEWAAAAGLSEAELR   66 (298)
T ss_pred             HHHHHHHHHHHhhcCCCcHHHHHHhccCCHHHHH
Confidence            3445667788889999999999999998865443

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).

>COG3415 Transposase and inactivated derivatives [DNA replication, recombination, and repair]

Probab=84.04  E-value=1.8  Score=40.34  Aligned_cols=28  Identities=21%  Similarity=0.114  Sum_probs=25.4

Q ss_pred             CCCCCHHHHHHHhCCCHHHHHHHHHHHH
Q 009449          489 HRPKSLEEIGKLFHVSKEWIRKLEKKAM  516 (534)
Q Consensus       489 ~e~~Sl~EIA~~LgISrerVRqi~~RAL  516 (534)
                      .+|+|..|||++||||.+||..+..+..
T Consensus        19 ~~G~S~re~Ak~~gvs~sTvy~wv~r~~   46 (138)
T COG3415          19 GEGLSCREAAKRFGVSISTVYRWVRRYR   46 (138)
T ss_pred             HcCccHHHHHHHhCccHHHHHHHHHHhc
Confidence            4899999999999999999999888754

>TIGR02885 spore_sigF RNA polymerase sigma-F factor

Probab=84.03  E-value=6.1  Score=38.97  Aligned_cols=34  Identities=32%  Similarity=0.446  Sum_probs=27.2

Q ss_pred             HHHHHHHHHHHhCCCCchHHHHHHcCCCHHHHHH
Q 009449          255 LERIKTTLEKESGKAASLNCWAQAAGVSERVLKQ  288 (534)
Q Consensus       255 le~~~~~l~~~~g~~ps~~ewa~a~g~d~~~L~~  288 (534)
                      +.+....+...+|+.||..+.|+..|++.+.+..
T Consensus        99 ~~~~~~~l~~~~~r~pt~~ela~~l~~~~~~v~~  132 (231)
T TIGR02885        99 IRYMKEELSKELGREPTINELAEALGVSPEEIVM  132 (231)
T ss_pred             HHHHHHHHHHHHCcCCCHHHHHHHHCcCHHHHHH
Confidence            3445567777889999999999999999887654

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.

>PRK12469 RNA polymerase factor sigma-54; Provisional

Probab=84.03  E-value=36  Score=38.00  Aligned_cols=47  Identities=15%  Similarity=0.278  Sum_probs=34.3

Q ss_pred             HHHhhCCHHHHHHHh------------hHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 009449          467 RILESLDSRERQVLV------------LRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEK  513 (534)
Q Consensus       467 ~~L~~L~~rEReVL~------------LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~  513 (534)
                      .++..|.-|.+.+++            +.+|.....++|+++||+.+|+..+||+...+
T Consensus       333 wli~si~qR~~TllkV~~~Iv~~Q~~Ff~~G~~~LkPLtlkdVAe~lglHeSTVSRa~~  391 (481)
T PRK12469        333 WLIRNAQQRFDTIQRVAECIVARQRDFFRYGEIALKPLVLRDVAEELGLHESTISRATG  391 (481)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCcccCcCCcHHHHHHHhCCCcchhhHHhc
Confidence            344566666665554            23565556899999999999999999986543

>PRK07122 RNA polymerase sigma factor SigF; Reviewed

Probab=83.86  E-value=15  Score=37.37  Aligned_cols=36  Identities=19%  Similarity=0.284  Sum_probs=29.1

Q ss_pred             HHHHHHHHHHHHhCCCCchHHHHHHcCCCHHHHHHH
Q 009449          254 NLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQH  289 (534)
Q Consensus       254 ~le~~~~~l~~~~g~~ps~~ewa~a~g~d~~~L~~~  289 (534)
                      ++.+....+...+|+.||..+.|+..|++.+++...
T Consensus       128 ~i~~~~~~l~~~lg~~pt~~eiA~~lg~~~~~v~~~  163 (264)
T PRK07122        128 RLGRATAELSQRLGRAPTASELAAELGMDREEVVEG  163 (264)
T ss_pred             HHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHH
Confidence            344556677788899999999999999999887553

>PF12728 HTH_17: Helix-turn-helix domain

Probab=83.81  E-value=1.2  Score=33.53  Aligned_cols=24  Identities=13%  Similarity=0.300  Sum_probs=21.4

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHHHH
Q 009449          492 KSLEEIGKLFHVSKEWIRKLEKKA  515 (534)
Q Consensus       492 ~Sl~EIA~~LgISrerVRqi~~RA  515 (534)
                      +|.+|+|+.||||+.+|+++..+.
T Consensus         2 lt~~e~a~~l~is~~tv~~~~~~g   25 (51)
T PF12728_consen    2 LTVKEAAELLGISRSTVYRWIRQG   25 (51)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHcC
Confidence            589999999999999999987653

>PRK05949 RNA polymerase sigma factor; Validated

Probab=83.70  E-value=13  Score=39.20  Aligned_cols=35  Identities=11%  Similarity=0.275  Sum_probs=28.1

Q ss_pred             HHHHHHHHHHHHhCCCCchHHHHHHcCCCHHHHHH
Q 009449          254 NLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQ  288 (534)
Q Consensus       254 ~le~~~~~l~~~~g~~ps~~ewa~a~g~d~~~L~~  288 (534)
                      ++.+....+..++|++|+..+.|+..|++.+.+..
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            34455667777889999999999999999887655

>PF13463 HTH_27: Winged helix DNA-binding domain; PDB: 3GFL_A 2YR2_B 3GFM_A 3GFJ_A 3GF2_A 3GEZ_A 2GXG_A 3GFI_A 2EB7_A

Probab=83.56  E-value=2.1  Score=33.66  Aligned_cols=41  Identities=22%  Similarity=0.293  Sum_probs=26.2

Q ss_pred             CCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 009449          472 LDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKK  514 (534)
Q Consensus       472 L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~R  514 (534)
                      |++.|..||..-.  ....+++..+||+.+++++.+|...+.+
T Consensus         1 lt~~q~~vL~~l~--~~~~~~t~~~l~~~~~~~~~~vs~~i~~   41 (68)
T PF13463_consen    1 LTRPQWQVLRALA--HSDGPMTQSDLAERLGISKSTVSRIIKK   41 (68)
T ss_dssp             --HHHHHHHHHHT----TS-BEHHHHHHHTT--HHHHHHHHHH
T ss_pred             CCHHHHHHHHHHH--ccCCCcCHHHHHHHHCcCHHHHHHHHHH
Confidence            4666777765554  2457999999999999999999754443

>PF00356 LacI: Bacterial regulatory proteins, lacI family; InterPro: IPR000843 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif

Probab=83.40  E-value=1.2  Score=33.68  Aligned_cols=22  Identities=18%  Similarity=0.285  Sum_probs=19.7

Q ss_pred             CHHHHHHHhCCCHHHHHHHHHH
Q 009449          493 SLEEIGKLFHVSKEWIRKLEKK  514 (534)
Q Consensus       493 Sl~EIA~~LgISrerVRqi~~R  514 (534)
                      |++|||+..|||..||+..++.
T Consensus         1 Ti~dIA~~agvS~~TVSr~ln~   22 (46)
T PF00356_consen    1 TIKDIAREAGVSKSTVSRVLNG   22 (46)
T ss_dssp             CHHHHHHHHTSSHHHHHHHHTT
T ss_pred             CHHHHHHHHCcCHHHHHHHHhC
Confidence            7899999999999999987763

These proteins are very diverse, but for convenience may be grouped into subfamilies on the basis of sequence similarity. One such family groups together a range of proteins, including ascG, ccpA, cytR, ebgR, fruR, galR, galS, lacI, malI, opnR, purF, rafR, rbtR and scrR [, ]. Within this family, the HTH motif is situated towards the N terminus.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3KJX_C 1ZAY_A 1VPW_A 2PUA_A 1QQA_A 1PNR_A 1JFT_A 1QP4_A 2PUD_A 1JH9_A ....

>PF01710 HTH_Tnp_IS630: Transposase; InterPro: IPR002622 Transposase proteins are necessary for efficient DNA transposition

Probab=83.35  E-value=10  Score=33.91  Aligned_cols=24  Identities=21%  Similarity=0.202  Sum_probs=20.7

Q ss_pred             CCCCCHHHHHHHhCCCHHHHHHHH
Q 009449          489 HRPKSLEEIGKLFHVSKEWIRKLE  512 (534)
Q Consensus       489 ~e~~Sl~EIA~~LgISrerVRqi~  512 (534)
                      ..+.|+.|||+.||||.++|...+
T Consensus        69 ~pd~tl~Ela~~l~Vs~~ti~~~L   92 (119)
T PF01710_consen   69 NPDATLRELAERLGVSPSTIWRAL   92 (119)
T ss_pred             CCCcCHHHHHHHcCCCHHHHHHHH
Confidence            378999999999999999997443

This entry includes insertion sequences from Synechocystis sp. (strain PCC 6803) three of which are characterised as homologous to bacterial IS5- and IS4- and to several members of the IS630-Tc1-mariner superfamily []. More information about these proteins can be found at Protein of the Month: Transposase [].

>PF01418 HTH_6: Helix-turn-helix domain, rpiR family; InterPro: IPR000281 This domain contains a helix-turn-helix motif []

Probab=83.13  E-value=2  Score=35.47  Aligned_cols=53  Identities=17%  Similarity=0.142  Sum_probs=36.3

Q ss_pred             HHHHHHHHHhhCCHHHHHHHhhHhc-CCCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 009449          461 MKKDVFRILESLDSRERQVLVLRYG-LNDHRPKSLEEIGKLFHVSKEWIRKLEK  513 (534)
Q Consensus       461 l~e~L~~~L~~L~~rEReVL~LryG-L~d~e~~Sl~EIA~~LgISrerVRqi~~  513 (534)
                      +.+.|......|++.|+.|.....- .++...+|..|||+..|||+.+|....+
T Consensus         3 l~~~i~~~~~~ls~~e~~Ia~yil~~~~~~~~~si~elA~~~~vS~sti~Rf~k   56 (77)
T PF01418_consen    3 LLEKIRSQYNSLSPTEKKIADYILENPDEIAFMSISELAEKAGVSPSTIVRFCK   56 (77)
T ss_dssp             HHHHHHHHGGGS-HHHHHHHHHHHH-HHHHCT--HHHHHHHCTS-HHHHHHHHH
T ss_pred             HHHHHHHHHhhCCHHHHHHHHHHHhCHHHHHHccHHHHHHHcCCCHHHHHHHHH
Confidence            3456777789999999998765441 1134579999999999999999975443

Every member of this family is N-terminal to a SIS domain IPR001347 from INTERPRO. Members of this family are probably regulators of genes involved in phosphosugar metobolism.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 2O3F_B 3IWF_B.

>smart00344 HTH_ASNC helix_turn_helix ASNC type

Probab=82.99  E-value=2.5  Score=36.58  Aligned_cols=40  Identities=25%  Similarity=0.243  Sum_probs=31.1

Q ss_pred             CCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 009449          472 LDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKK  514 (534)
Q Consensus       472 L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~R  514 (534)
                      |++.++.|+....-   ....|..|||+.+|+|+.+|+..+.+
T Consensus         1 ld~~D~~il~~L~~---~~~~~~~~la~~l~~s~~tv~~~l~~   40 (108)
T smart00344        1 LDEIDRKILEELQK---DARISLAELAKKVGLSPSTVHNRVKR   40 (108)
T ss_pred             CCHHHHHHHHHHHH---hCCCCHHHHHHHHCcCHHHHHHHHHH
Confidence            46677888776651   24689999999999999999865544

AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli

>PF11427 HTH_Tnp_Tc3_1: Tc3 transposase; PDB: 1U78_A 1TC3_C

Probab=82.99  E-value=2.3  Score=32.76  Aligned_cols=39  Identities=26%  Similarity=0.266  Sum_probs=26.3

Q ss_pred             hCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 009449          471 SLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEK  513 (534)
Q Consensus       471 ~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~  513 (534)
                      .|++.|+--|....    ..++++.|||..+|-|+..|+..+.
T Consensus         4 ~Lt~~Eqaqid~m~----qlG~s~~~isr~i~RSr~~Ir~yl~   42 (50)
T PF11427_consen    4 TLTDAEQAQIDVMH----QLGMSLREISRRIGRSRTCIRRYLK   42 (50)
T ss_dssp             ---HHHHHHHHHHH----HTT--HHHHHHHHT--HHHHHHHHH
T ss_pred             cCCHHHHHHHHHHH----HhchhHHHHHHHhCccHHHHHHHhc
Confidence            47777777776666    6799999999999999999987653

>PRK00423 tfb transcription initiation factor IIB; Reviewed

Probab=82.89  E-value=65  Score=33.71  Aligned_cols=178  Identities=14%  Similarity=0.045  Sum_probs=87.6

Q ss_pred             HHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCchhhHHHHHHHHHHHHHHHHhccccccccchH
Q 009449          299 ELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIPCKLN  378 (534)
Q Consensus       299 ~LI~~nlrLV~sIArrY~~~g~~~eDLiQEG~lgL~rA~ekFDp~kG~rFSTYA~~wIR~aI~~~lr~~sr~iRlP~~~~  378 (534)
                      +-+......|-.++.+.     .+.+-+.|....+++.+..-..-+|.....++.-.|.-++.    .            
T Consensus       120 r~l~~a~~~I~~~~~~L-----~Lp~~v~e~A~~iyk~~~~~~~~rgrs~~~i~AAclYiACR----~------------  178 (310)
T PRK00423        120 RNLAFALSELDRIASQL-----GLPRSVREEAAVIYRKAVEKGLIRGRSIEGVVAAALYAACR----R------------  178 (310)
T ss_pred             HHHHHHHHHHHHHHHHc-----CCCHHHHHHHHHHHHHHHhcCcccCCCHHHHHHHHHHHHHH----H------------
Confidence            33344456677777665     22356667777777777655666776655544444443332    1            


Q ss_pred             HHHHHHHHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHHhhhhcccccccccchhhhhhhccCCCCCCChHHHHHH
Q 009449          379 REISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNAKYLEFAPDRSVKSPKEIVMR  458 (534)
Q Consensus       379 ~~i~ki~ka~~~L~~elGr~Pt~eEIA~~lgis~~kv~~~l~~~~~~~SLD~~i~~~~~~~l~e~i~d~~~~spee~v~~  458 (534)
                                      .|-+-|..||+..++++..++..........+.++.+..+  ...+..-+.+.- .-|.+..  
T Consensus       179 ----------------~~~prtl~eI~~~~~v~~k~i~~~~~~l~k~L~~~~~~~~--p~~~i~r~~~~L-~L~~~v~--  237 (310)
T PRK00423        179 ----------------CKVPRTLDEIAEVSRVSRKEIGRCYRFLLRELNLKLPPTD--PIDYVPRFASEL-GLSGEVQ--  237 (310)
T ss_pred             ----------------cCCCcCHHHHHHHhCCCHHHHHHHHHHHHHHhCCCCCCCC--HHHHHHHHHHHc-CCCHHHH--
Confidence                            1222356677777777777776654444433333332211  111111111000 0111111  


Q ss_pred             HHHHHHHHHHHh-hC----CHHH--HHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Q 009449          459 QHMKKDVFRILE-SL----DSRE--RQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKL  519 (534)
Q Consensus       459 ~el~e~L~~~L~-~L----~~rE--ReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KL  519 (534)
                      +.....+..+.+ .|    +|.-  .-+|.+-.=+. +.+.|++|||...||+..+|++....-.+.|
T Consensus       238 ~~A~~i~~~a~~~~l~~Gr~P~sIAAAaIYlA~~~~-g~~~t~keIa~v~~Vs~~tI~~~ykel~~~l  304 (310)
T PRK00423        238 KKAIEILQKAKEKGLTSGKGPTGLAAAAIYIASLLL-GERRTQREVAEVAGVTEVTVRNRYKELAEKL  304 (310)
T ss_pred             HHHHHHHHHHHhcCcccCCCHHHHHHHHHHHHHHHh-CCCCCHHHHHHHcCCCHHHHHHHHHHHHHHh
Confidence            111111222211 11    2211  11222211112 4679999999999999999998776666554

>PRK15479 transcriptional regulatory protein TctD; Provisional

Probab=82.84  E-value=1.9  Score=40.53  Aligned_cols=50  Identities=26%  Similarity=0.304  Sum_probs=41.3

Q ss_pred             hCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhC-----CCHHHHHHHHHHHHHHHHh
Q 009449          471 SLDSRERQVLVLRYGLNDHRPKSLEEIGKLFH-----VSKEWIRKLEKKAMTKLRD  521 (534)
Q Consensus       471 ~L~~rEReVL~LryGL~d~e~~Sl~EIA~~Lg-----ISrerVRqi~~RAL~KLR~  521 (534)
                      .|+++|.+|+.+.. -..+...|.++|++.+.     +|..+|..+..+.++||..
T Consensus       148 ~Lt~~E~~il~~l~-~~~~~~~~~~~i~~~l~~~~~~~~~~tv~~~i~~ir~kl~~  202 (221)
T PRK15479        148 ALTPREQALLTVLM-YRRTRPVSRQQLFEQVFSLNDEVSPESIELYIHRLRKKLQG  202 (221)
T ss_pred             ecCHHHHHHHHHHH-hCCCCcCcHHHHHHHhcCCCCCCCcccHHHHHHHHHHhcCC
Confidence            49999999998775 11134579999999986     9999999999999999963

>PRK12423 LexA repressor; Provisional

Probab=82.77  E-value=1.7  Score=42.46  Aligned_cols=47  Identities=26%  Similarity=0.378  Sum_probs=34.1

Q ss_pred             hCCHHHHHHHhhHhcC-C-CCCCCCHHHHHHHhC-CCHHHHHHHHHHHHHHHHh
Q 009449          471 SLDSRERQVLVLRYGL-N-DHRPKSLEEIGKLFH-VSKEWIRKLEKKAMTKLRD  521 (534)
Q Consensus       471 ~L~~rEReVL~LryGL-~-d~e~~Sl~EIA~~Lg-ISrerVRqi~~RAL~KLR~  521 (534)
                      .|++++++|+..---. . .+-..|..|||+.|| +|+.+|+.    ++++|++
T Consensus         3 ~lt~~q~~il~~l~~~i~~~g~~Ps~~eia~~~g~~s~~~v~~----~l~~L~~   52 (202)
T PRK12423          3 TLTPKRAAILAFIRERIAQAGQPPSLAEIAQAFGFASRSVARK----HVQALAE   52 (202)
T ss_pred             cCCHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCChHHHHH----HHHHHHH
Confidence            4899999998755421 1 122469999999999 59999984    6666665

>TIGR02850 spore_sigG RNA polymerase sigma-G factor

Probab=82.54  E-value=15  Score=37.01  Aligned_cols=37  Identities=16%  Similarity=0.179  Sum_probs=29.6

Q ss_pred             HHHHHHHHHHHHhCCCCchHHHHHHcCCCHHHHHHHH
Q 009449          254 NLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQHL  290 (534)
Q Consensus       254 ~le~~~~~l~~~~g~~ps~~ewa~a~g~d~~~L~~~l  290 (534)
                      ++.+....+..++|++|+..+.|+..|++.+.+...+
T Consensus       121 ~~~~~~~~l~~~l~~~pt~~elA~~l~~~~e~v~~~~  157 (254)
T TIGR02850       121 KALQVRDKLISENSKEPTVSEIAKELKVPQEEVVFAL  157 (254)
T ss_pred             HHHHHHHHHHHHhCCCCCHHHHHHHHCcCHHHHHHHH
Confidence            3445566777888999999999999999998876543

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.

>PF13744 HTH_37: Helix-turn-helix domain; PDB: 2A6C_B 2O38_A

Probab=82.48  E-value=2.7  Score=34.99  Aligned_cols=44  Identities=18%  Similarity=0.208  Sum_probs=29.4

Q ss_pred             HHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHH-----HHHHHHHhHhhhh
Q 009449          479 VLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEK-----KAMTKLRDSETCR  526 (534)
Q Consensus       479 VL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~-----RAL~KLR~~l~~~  526 (534)
                      |..++-    ..++|+.|+|+.+|+++++|+.+++     -.+.+|...+..-
T Consensus        23 i~~~~~----~~~ltQ~e~A~~lgisq~~vS~l~~g~~~~~sl~~L~~~l~aL   71 (80)
T PF13744_consen   23 IRELRE----ERGLTQAELAERLGISQPRVSRLENGKIDDFSLDTLLRYLEAL   71 (80)
T ss_dssp             HHHHHH----CCT--HHHHHHHHTS-HHHHHHHHTT-GCC--HHHHHHHHHHT
T ss_pred             HHHHHH----HcCCCHHHHHHHHCCChhHHHHHHcCcccCCCHHHHHHHHHHc
Confidence            445555    6899999999999999999999884     2355555554443

>TIGR02154 PhoB phosphate regulon transcriptional regulatory protein PhoB

Probab=82.29  E-value=1.1  Score=42.35  Aligned_cols=50  Identities=20%  Similarity=0.180  Sum_probs=42.0

Q ss_pred             hCCHHHHHHHhhHhcCCCCCCCCHHHH-----HHHhCCCHHHHHHHHHHHHHHHHh
Q 009449          471 SLDSRERQVLVLRYGLNDHRPKSLEEI-----GKLFHVSKEWIRKLEKKAMTKLRD  521 (534)
Q Consensus       471 ~L~~rEReVL~LryGL~d~e~~Sl~EI-----A~~LgISrerVRqi~~RAL~KLR~  521 (534)
                      .|+++|.+|+.+... +.+++.|.++|     |..++++..||+.+..+.++||..
T Consensus       154 ~Lt~~E~~il~~l~~-~~~~~~s~~~i~~~~~~~~~~~~~~tv~~~i~~l~~Kl~~  208 (226)
T TIGR02154       154 SLGPTEFRLLHFFMT-HPERVYSREQLLDRVWGRDVYVEERTVDVHIRRLRKALNP  208 (226)
T ss_pred             EcCHHHHHHHHHHHh-CCCceEcHHHHHHHhcCCCCCCCCccHHHHHHHHHHhhcc
Confidence            499999999988872 22347788888     888999999999999999999963

PhoB is a DNA-binding response regulator protein acting with PhoR in a 2-component system responding to phosphate ion. PhoB acts as a positive regulator of gene expression for phosphate-related genes such as phoA, phoS, phoE and ugpAB as well as itself. It is often found proximal to genes for the high-affinity phosphate ABC transporter (pstSCAB; GenProp0190) and presumably regulates these as well.

>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor

Probab=82.15  E-value=2.4  Score=32.04  Aligned_cols=29  Identities=24%  Similarity=0.324  Sum_probs=23.3

Q ss_pred             CCCC-CHHHHHHHhCCCHHHHHHHHHHHHHHHHh
Q 009449          489 HRPK-SLEEIGKLFHVSKEWIRKLEKKAMTKLRD  521 (534)
Q Consensus       489 ~e~~-Sl~EIA~~LgISrerVRqi~~RAL~KLR~  521 (534)
                      +... |..|||+.+|+|+.+|+    +++++|.+
T Consensus        17 ~~~l~s~~~la~~~~vs~~tv~----~~l~~L~~   46 (60)
T smart00345       17 GDKLPSERELAAQLGVSRTTVR----EALSRLEA   46 (60)
T ss_pred             CCcCcCHHHHHHHHCCCHHHHH----HHHHHHHH
Confidence            4456 89999999999999997    56666664

>PF01371 Trp_repressor: Trp repressor protein; InterPro: IPR000831 The Trp repressor (TrpR) binds to at least five operators in the Escherichia coli genome, repressing gene expression

Probab=81.74  E-value=1.8  Score=37.14  Aligned_cols=45  Identities=22%  Similarity=0.245  Sum_probs=31.1

Q ss_pred             CCHHHHHHHhhHhcCCC---CCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 009449          472 LDSRERQVLVLRYGLND---HRPKSLEEIGKLFHVSKEWIRKLEKKAMT  517 (534)
Q Consensus       472 L~~rEReVL~LryGL~d---~e~~Sl~EIA~~LgISrerVRqi~~RAL~  517 (534)
                      ++|.|++-|..|+-+-.   .+++|+.||++.+|+|..||.. .+|+++
T Consensus        27 ~T~~E~~~l~~R~~va~~lL~~g~syreIa~~tgvS~aTItR-vsr~Lk   74 (87)
T PF01371_consen   27 CTPDELEALAQRWQVAKELLDEGKSYREIAEETGVSIATITR-VSRCLK   74 (87)
T ss_dssp             SSHHHHHHHHHHHHHHHHHHHTTSSHHHHHHHHTSTHHHHHH-HHHHHH
T ss_pred             CCHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHhCCCHHHHHH-HHHHHH
Confidence            67777665555443221   2689999999999999999964 344444

The operators at which it binds vary considerably in DNA sequence and location within the promoter; when bound to the Trp operon it recognises the sequence 5'-ACTAGT-3' and acts to prevent the initiation of transcription. The TrpR controls the trpEDCBA (trpO) operon and the genes for trpR, aroH, mtr and aroL, which are involved in the biosynthesis and uptake of the amino acid tryptophan []. The repressor binds to the operators only in the presence of L-tryptophan, thereby controlling the intracellular level of its effector; the complex also regulates Trp repressor biosynthesis by binding to its own regulatory region. TrpR acts as a dimer that is composed of identical 6-helical subunits, where four of the helices form the core of the protein and intertwine with the corresponding helices from the other subunit.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3FRW_H 3KOR_A 3SSW_N 1P6Z_N 1CO0_B 1JHG_A 1WRT_S 1WRS_R 1WRP_R 1RCS_B ....

>cd04762 HTH_MerR-trunc Helix-Turn-Helix DNA binding domain of truncated MerR-like proteins

Probab=81.63  E-value=1.4  Score=31.68  Aligned_cols=25  Identities=24%  Similarity=0.284  Sum_probs=22.4

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHHHHH
Q 009449          492 KSLEEIGKLFHVSKEWIRKLEKKAM  516 (534)
Q Consensus       492 ~Sl~EIA~~LgISrerVRqi~~RAL  516 (534)
                      +|..|+|+.+|||+.+|+.+...+.
T Consensus         1 ~s~~e~a~~lgvs~~tl~~~~~~g~   25 (49)
T cd04762           1 LTTKEAAELLGVSPSTLRRWVKEGK   25 (49)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHcCC
Confidence            5889999999999999999988764

Proteins in this family mostly have a truncated helix-turn-helix (HTH) MerR-like domain. They lack a portion of the C-terminal region, called Wing 2 and the long dimerization helix that is typically present in MerR-like proteins. These truncated domains are found in response regulator receiver (REC) domain proteins (i.e., CheY), cytosine-C5 specific DNA methylases, IS607 transposase-like proteins, and RacA, a bacterial protein that anchors chromosomes to cell poles.

>PRK13413 mpi multiple promoter invertase; Provisional

Probab=81.44  E-value=2.5  Score=41.05  Aligned_cols=34  Identities=24%  Similarity=0.295  Sum_probs=27.6

Q ss_pred             HHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 009449          476 ERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKK  514 (534)
Q Consensus       476 EReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~R  514 (534)
                      ++.|..++     ..++|..+||+.||||+.||.++...
T Consensus       162 ~~~i~~~~-----~~g~s~~~iak~lgis~~Tv~r~~k~  195 (200)
T PRK13413        162 EEKIKKLL-----DKGTSKSEIARKLGVSRTTLARFLKT  195 (200)
T ss_pred             HHHHHHHH-----HCCCCHHHHHHHHCCCHHHHHHHHHh
Confidence            34566664     36899999999999999999988763

>TIGR01764 excise DNA binding domain, excisionase family

Probab=81.33  E-value=1.8  Score=31.45  Aligned_cols=24  Identities=25%  Similarity=0.356  Sum_probs=21.6

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHHHH
Q 009449          492 KSLEEIGKLFHVSKEWIRKLEKKA  515 (534)
Q Consensus       492 ~Sl~EIA~~LgISrerVRqi~~RA  515 (534)
                      +|.+|+|+.||||+.+|+++....
T Consensus         2 lt~~e~a~~lgis~~ti~~~~~~g   25 (49)
T TIGR01764         2 LTVEEAAEYLGVSKDTVYRLIHEG   25 (49)
T ss_pred             CCHHHHHHHHCCCHHHHHHHHHcC
Confidence            589999999999999999988654

An excisionase, or Xis protein, is a small protein that binds and promotes excisive recombination; it is not enzymatically active. This model represents a number of putative excisionases and related proteins from temperate phage, plasmids, and transposons, as well as DNA binding domains of other proteins, such as a DNA modification methylase. This model identifies mostly small proteins and N-terminal regions of large proteins, but some proteins appear to have two copies. This domain appears similar, in both sequence and predicted secondary structure (PSIPRED) to the MerR family of transcriptional regulators (pfam00376).

>TIGR01610 phage_O_Nterm phage replication protein O, N-terminal domain

Probab=81.32  E-value=3.3  Score=35.69  Aligned_cols=49  Identities=27%  Similarity=0.350  Sum_probs=37.0

Q ss_pred             HhhCCHHHHHHHhhH----hcCC-CCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHh
Q 009449          469 LESLDSRERQVLVLR----YGLN-DHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRD  521 (534)
Q Consensus       469 L~~L~~rEReVL~Lr----yGL~-d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~  521 (534)
                      ...+++++..||...    ||.. ...+.|..|||+.+|+++++|+    |++++|.+
T Consensus        20 ~~~l~~r~~~vLl~L~~~~~G~~~~~~~is~~eLa~~~g~sr~tVs----r~L~~Le~   73 (95)
T TIGR01610        20 GADLSGREFRVLLAIIRLTYGWNKKQDRVTATVIAELTGLSRTHVS----DAIKSLAR   73 (95)
T ss_pred             hCCCCHHHHHHHHHHHHHHhCccccCCccCHHHHHHHHCcCHHHHH----HHHHHHHH
Confidence            467899999877633    3422 2468999999999999999996    56666654

This model represents the N-terminal region of the phage lambda replication protein O and homologous regions of other phage proteins.

>COG2973 TrpR Trp operon repressor [Transcription]

Probab=81.29  E-value=3.5  Score=36.06  Aligned_cols=45  Identities=27%  Similarity=0.289  Sum_probs=34.6

Q ss_pred             CCHHHHHHHhhHhcCCC---CCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 009449          472 LDSRERQVLVLRYGLND---HRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLR  520 (534)
Q Consensus       472 L~~rEReVL~LryGL~d---~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR  520 (534)
                      |+|.||+-+-.|+-+-.   ...+|..||+..||+|..+|    .|+-+-|+
T Consensus        38 LTpdEReal~~Rv~Iv~eLL~ge~sQREi~~~LgvsiAtI----TRGSN~LK   85 (103)
T COG2973          38 LTPDEREALGTRVRIVEELLRGELSQREIAQKLGVSIATI----TRGSNSLK   85 (103)
T ss_pred             cCHhHHHHHHHHHHHHHHHHhccccHHHHHHHhCcchhhh----ccchhhhc
Confidence            89999988887775431   15899999999999999998    35555544

>PRK07670 RNA polymerase sigma factor SigD; Validated

Probab=80.94  E-value=26  Score=35.16  Aligned_cols=37  Identities=16%  Similarity=0.198  Sum_probs=29.3

Q ss_pred             HHHHHHHHHHHHhCCCCchHHHHHHcCCCHHHHHHHH
Q 009449          254 NLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQHL  290 (534)
Q Consensus       254 ~le~~~~~l~~~~g~~ps~~ewa~a~g~d~~~L~~~l  290 (534)
                      .+.+....+...+|+.|+..++|+..|++.+.+...+
T Consensus       110 ~~~~~~~~~~~~~~~~~~~~eia~~l~~~~~~v~~~~  146 (251)
T PRK07670        110 KVEAAIEKLEQRYMRNVTPKEVAAELGMTEEEVEATM  146 (251)
T ss_pred             HHHHHHHHHHHHHCCCCCHHHHHHHhCcCHHHHHHHH
Confidence            3445556677788999999999999999998876543

>TIGR03787 marine_sort_RR proteobacterial dedicated sortase system response regulator

Probab=80.57  E-value=2.3  Score=40.44  Aligned_cols=50  Identities=16%  Similarity=0.064  Sum_probs=41.5

Q ss_pred             hCCHHHHHHHhhHhcCCCCCCCCHHHH--HHHhCCCHHHHHHHHHHHHHHHHh
Q 009449          471 SLDSRERQVLVLRYGLNDHRPKSLEEI--GKLFHVSKEWIRKLEKKAMTKLRD  521 (534)
Q Consensus       471 ~L~~rEReVL~LryGL~d~e~~Sl~EI--A~~LgISrerVRqi~~RAL~KLR~  521 (534)
                      .|+++|.+||.+.. -+.+.-.|.++|  |..++++..||+.+..+.++||..
T Consensus       156 ~Lt~~E~~il~~l~-~~~g~v~s~~~i~~~~~~~~~~~tv~~~v~rlr~Kl~~  207 (227)
T TIGR03787       156 DLTVTEFWMVHALA-KHPGHVKSRQQLMDAAKIVVDDSTITSHIKRIRKKFQA  207 (227)
T ss_pred             cCCHHHHHHHHHHH-hCCCccccHHHHHHHhhhcCCccCHHHHHHHHHHHhcc
Confidence            39999999998887 111233599999  888999999999999999999974

This model describes a family of DNA-binding response regulator proteins, associated with an adjacent histidine kinase (TIGR03785) to form a two-component system. This system co-occurs with, and often is adjacent to, a proteobacterial variant form of the protein sorting transpeptidase called sortase (TIGR03784), and a single target protein for the sortase. We give this protein the gene symbol pdsR, for Proteobacterial Dedicated Sortase system Response regulator.

>PF01047 MarR: MarR family; InterPro: IPR000835 The MarR-type HTH domain is a DNA-binding, winged helix-turn-helix (wHTH) domain of about 135 amino acids present in transcription regulators of the MarR/SlyA family, involved in the development of antibiotic resistance

Probab=80.35  E-value=2.4  Score=32.50  Aligned_cols=40  Identities=15%  Similarity=0.334  Sum_probs=29.2

Q ss_pred             CCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 009449          472 LDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKK  514 (534)
Q Consensus       472 L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~R  514 (534)
                      |++.|-.||..-+   ...+.|..|||+.+++++.+|.++..+
T Consensus         1 lt~~q~~iL~~l~---~~~~~~~~~la~~~~~~~~~~t~~i~~   40 (59)
T PF01047_consen    1 LTPSQFRILRILY---ENGGITQSELAEKLGISRSTVTRIIKR   40 (59)
T ss_dssp             STHHHHHHHHHHH---HHSSEEHHHHHHHHTS-HHHHHHHHHH
T ss_pred             CCHHHHHHHHHHH---HcCCCCHHHHHHHHCCChhHHHHHHHH
Confidence            4556666666655   246799999999999999999766554

This family of transcription regulators is named after Escherichia coli MarR, a repressor of genes which activate the multiple antibiotic resistance and oxidative stress regulons, and after slyA from Salmonella typhimurium and E. coli, a transcription regulator that is required for virulence and survival in the macrophage environment. Regulators with the MarR-type HTH domain are present in bacteria and archaea and control a variety of biological functions, including resistance to multiple antibiotics, household disinfectants, organic solvents, oxidative stress agents and regulation of the virulence factor synthesis in pathogens of humans and plants. Many of the MarR-like regulators respond to aromatic compounds [, , ]. The crystal structures of MarR, MexR and SlyA have been determined and show a winged HTH DNA-binding core flanked by helices involved in dimerisation. The DNA-binding domains are ascribed to the superfamily of winged helix proteins, containing a three (four)-helix (H) bundle and a three-stranded antiparallel beta-sheet (B) in the topology: H1-(H1')-H2-B1-H3-H4-B2-B3-H5-H6. Helices 3 and 4 comprise the helix-turn-helix motif and the beta-sheet is called the wing. Helix 4 is termed the recognition helix, like in other HTHs where it binds the DNA major groove. The helices 1, 5 and 6 are involved in dimerisation, as most MarR-like transcription regulators form dimers [, ]. ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 1JGS_A 2NYX_D 2PEX_B 2PFB_A 3BPX_A 3BPV_A 2BV6_A 3BJA_A 3E6M_B 2ETH_A ....

>PF13551 HTH_29: Winged helix-turn helix

Probab=80.20  E-value=3.1  Score=35.70  Aligned_cols=33  Identities=21%  Similarity=0.314  Sum_probs=26.6

Q ss_pred             HHHhhHhcCCCCCCC-CHHHHHHHhCCCHHHHHHHHHHH
Q 009449          478 QVLVLRYGLNDHRPK-SLEEIGKLFHVSKEWIRKLEKKA  515 (534)
Q Consensus       478 eVL~LryGL~d~e~~-Sl~EIA~~LgISrerVRqi~~RA  515 (534)
                      .||.+..     ++. |..+||+.+|+|+.||+.++.+-
T Consensus         3 ~~l~l~~-----~g~~~~~~ia~~lg~s~~Tv~r~~~~~   36 (112)
T PF13551_consen    3 QILLLLA-----EGVSTIAEIARRLGISRRTVYRWLKRY   36 (112)
T ss_pred             HHHHHHH-----cCCCcHHHHHHHHCcCHHHHHHHHHHH
Confidence            3455544     677 59999999999999999988773

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	534
1l9u_H	332	Thermus Aquaticus Rna Polymerase Holoenzyme At 4 A		6e-38
1l9z_H	438	Thermus Aquaticus Rna Polymerase HoloenzymeFORK-Jun		1e-37
3dxj_F	423	Crystal Structure Of Thermus Thermophilus Rna Polym		3e-37
1iw7_F	423	Crystal Structure Of The Rna Polymerase Holoenzyme		3e-37
4g7h_F	443	Crystal Structure Of Thermus Thermophilus Transcrip		3e-37
3iyd_F	613	Three-Dimensional Em Structure Of An Intact Activat		2e-35
4igc_X	613	X-ray Crystal Structure Of Escherichia Coli Sigma70		2e-35
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		4e-14
1l0o_C	243	Crystal Structure Of The Bacillus Stearothermophilu		4e-14
1tty_A	87	Solution Structure Of Sigma A Region 4 From Thermot		2e-11
4g6d_A	73	G1 Orf67 / Staphyloccus Aureus Sigmaa Domain 4 Comp		1e-10
4g94_A	62	G1 Orf67 / Staphyloccus Aureus Sigmaa Domain 4 Comp		4e-09
1tlh_B	81	T4 Asia Bound To Sigma70 Region 4 Length = 81		7e-07
2p7v_B	68	Crystal Structure Of The Escherichia Coli Regulator		1e-06
3t72_q	99	Phob(E)-Sigma70(4)-(Rnap-Betha-Flap-Tip-Helix)-Dna		1e-06
3n97_A	72	Rna Polymerase Alpha C-Terminal Domain (E. Coli) An		2e-06
1rio_H	73	Structure Of Bacteriophage Lambda Ci-Ntd In Complex		3e-06
1ku3_A	73	Crystal Structure Of Thermus Aquaticus Rna Polymera		4e-06
1rp3_A	239	Cocrystal Structure Of The Flagellar SigmaANTI-Sigm		4e-05

>pdb|1L9U|H Chain H, Thermus Aquaticus Rna Polymerase Holoenzyme At 4 A Resolution Length = 332

Iteration: 1
 Score =  155 bits (392), Expect = 6e-38,   Method: Compositional matrix adjust.
 Identities = 89/244 (36%), Positives = 143/244 (58%), Gaps = 5/244 (2%)
Query: 293 GWYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYV 352
           G   R+ LI++   LV+ +A+ Y G G+ F DL+Q GN G+++  E+F++ R +KFSTY 
Sbjct: 89  GEAARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQEGNQGLIRAVEKFEYKRRFKFSTYA 148
Query: 353 QYWIRKSISKMVARHARGIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSL 412
            +WIR++I++ +A  AR I+IP  +   I+K+ +  + L    G+ P   EIA+  G   
Sbjct: 149 TWWIRQAINRAIADQARTIRIPVHMVETINKLSRTARQLQQELGREPSYEEIAEAMGPGW 208
Query: 413 AEIRSASECLRIVG---SIDQKIGDCLNAKYLEFAPDRSVKSPKEIVMRQHMKKDVFRIL 469
            + +   E L+I     S++  IGD  ++ Y +F PD ++ SP E   +  + +++ + L
Sbjct: 209 -DAKRVEETLKIAQEPVSLETPIGDEKDSFYGDFIPDENLPSPVEAAAQSLLSEELEKAL 267
Query: 470 ESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDSET-CRDL 528
             L  RE  VL LR GL D R  +LEE+G  F V++E IR++E KA+ KL+  E+  R L
Sbjct: 268 SKLSEREAMVLKLRKGLIDGREHTLEEVGAYFGVTRERIRQIENKALRKLKYHESRTRKL 327
Query: 529 SHFL 532
             FL
Sbjct: 328 RDFL 331

>pdb|1L9Z|H Chain H, Thermus Aquaticus Rna Polymerase HoloenzymeFORK-Junction Promoter Dna Complex At 6.5 A Resolution Length = 438

Iteration: 1
 Score =  154 bits (390), Expect = 1e-37,   Method: Compositional matrix adjust.
 Identities = 98/279 (35%), Positives = 157/279 (56%), Gaps = 18/279 (6%)
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 CLNAKYLEFAPDRSVKSPKEIVMRQHMKKDVFRILESLDSRERQVLVLRYGLNDHRPKSL 494
             ++ Y +F PD ++ SP E   +  + +++ + L  L  RE  VL LR GL D R  +L
Sbjct: 339 EKDSFYGDFIPDENLPSPVEAAAQSLLSEELEKALSKLSEREAMVLKLRKGLIDGREHTL 398
Query: 495 EEIGKLFHVSKEWIRKLEKKAMTKLRDSET-CRDLSHFL 532
           EE+G  F V++E IR++E KA+ KL+  E+  R L  FL
Sbjct: 399 EEVGAYFGVTRERIRQIENKALRKLKYHESRTRKLRDFL 437

>pdb|3DXJ|F Chain F, Crystal Structure Of Thermus Thermophilus Rna Polymerase Holoenzyme In Complex With The Antibiotic Myxopyronin Length = 423

Iteration: 1
 Score =  152 bits (385), Expect = 3e-37,   Method: Compositional matrix adjust.
 Identities = 88/244 (36%), Positives = 142/244 (58%), Gaps = 5/244 (2%)
Query: 293 GWYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYV 352
           G   R+ LI++   LV+ +A+ Y G G+ F DL+Q GN G+++  E+F++ R +KFSTY 
Sbjct: 180 GEAARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQEGNQGLIRAVEKFEYKRRFKFSTYA 239
Query: 353 QYWIRKSISKMVARHARGIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSL 412
            +WIR++I++ +A  AR I+IP  +   I+K+ +  + L    G+ P   EIA+  G   
Sbjct: 240 TWWIRQAINRAIADQARTIRIPVHMVETINKLSRTARQLQQELGREPTYEEIAEAMGPGW 299
Query: 413 AEIRSASECLRIVG---SIDQKIGDCLNAKYLEFAPDRSVKSPKEIVMRQHMKKDVFRIL 469
            + +   E L+I     S++  IGD  ++ Y +F PD  + SP +   +  + +++ + L
Sbjct: 300 -DAKRVEETLKIAQEPVSLETPIGDEKDSFYGDFIPDEHLPSPVDAATQSLLSEELEKAL 358
Query: 470 ESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDSET-CRDL 528
             L  RE  VL LR GL D R  +LEE+G  F V++E IR++E KA+ KL+  E+  R L
Sbjct: 359 SKLSEREAMVLKLRKGLIDGREHTLEEVGAFFGVTRERIRQIENKALRKLKYHESRTRKL 418
Query: 529 SHFL 532
             FL
Sbjct: 419 RDFL 422

>pdb|1IW7|F Chain F, Crystal Structure Of The Rna Polymerase Holoenzyme From Thermus Thermophilus At 2.6a Resolution Length = 423

Iteration: 1
 Score =  152 bits (385), Expect = 3e-37,   Method: Compositional matrix adjust.
 Identities = 88/244 (36%), Positives = 142/244 (58%), Gaps = 5/244 (2%)
Query: 293 GWYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYV 352
           G   R+ LI++   LV+ +A+ Y G G+ F DL+Q GN G+++  E+F++ R +KFSTY 
Sbjct: 180 GEAARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQEGNQGLIRAVEKFEYKRRFKFSTYA 239
Query: 353 QYWIRKSISKMVARHARGIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSL 412
            +WIR++I++ +A  AR I+IP  +   I+K+ +  + L    G+ P   EIA+  G   
Sbjct: 240 TWWIRQAINRAIADQARTIRIPVHMVETINKLSRTARQLQQELGREPTYEEIAEAMGPGW 299
Query: 413 AEIRSASECLRIVG---SIDQKIGDCLNAKYLEFAPDRSVKSPKEIVMRQHMKKDVFRIL 469
            + +   E L+I     S++  IGD  ++ Y +F PD  + SP +   +  + +++ + L
Sbjct: 300 -DAKRVEETLKIAQEPVSLETPIGDEKDSFYGDFIPDEHLPSPVDAATQSLLSEELEKAL 358
Query: 470 ESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDSET-CRDL 528
             L  RE  VL LR GL D R  +LEE+G  F V++E IR++E KA+ KL+  E+  R L
Sbjct: 359 SKLSEREAMVLKLRKGLIDGREHTLEEVGAFFGVTRERIRQIENKALRKLKYHESRTRKL 418
Query: 529 SHFL 532
             FL
Sbjct: 419 RDFL 422

>pdb|4G7H|F Chain F, Crystal Structure Of Thermus Thermophilus Transcription Initiation Complex Length = 443

Iteration: 1
 Score =  152 bits (385), Expect = 3e-37,   Method: Compositional matrix adjust.
 Identities = 88/244 (36%), Positives = 142/244 (58%), Gaps = 5/244 (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---SIDQKIGDCLNAKYLEFAPDRSVKSPKEIVMRQHMKKDVFRIL 469
            + +   E L+I     S++  IGD  ++ Y +F PD  + SP +   +  + +++ + L
Sbjct: 320 -DAKRVEETLKIAQEPVSLETPIGDEKDSFYGDFIPDEHLPSPVDAATQSLLSEELEKAL 378
Query: 470 ESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDSET-CRDL 528
             L  RE  VL LR GL D R  +LEE+G  F V++E IR++E KA+ KL+  E+  R L
Sbjct: 379 SKLSEREAMVLKLRKGLIDGREHTLEEVGAFFGVTRERIRQIENKALRKLKYHESRTRKL 438
Query: 529 SHFL 532
             FL
Sbjct: 439 RDFL 442

>pdb|3IYD|F Chain F, Three-Dimensional Em Structure Of An Intact Activator-Dependent Transcription Initiation Complex Length = 613

Iteration: 1
 Score =  147 bits (370), Expect = 2e-35,   Method: Compositional matrix adjust.
 Identities = 74/237 (31%), Positives = 140/237 (59%)
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 RSASECLRIVGSIDQKIGDCLNAKYLEFAPDRSVKSPKEIVMRQHMKKDVFRILESLDSR 475
           R   +  +   S++  IGD  ++   +F  D +++ P +    + ++     +L  L +R
Sbjct: 495 RKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATTESLRAATHDVLAGLTAR 554
Query: 476 ERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDSETCRDLSHFL 532
           E +VL +R+G++ +   +LEE+GK F V++E IR++E KA+ KLR       L  FL
Sbjct: 555 EAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRSFL 611

>pdb|4IGC|X Chain X, X-ray Crystal Structure Of Escherichia Coli Sigma70 Holoenzyme Length = 613

Iteration: 1
 Score =  146 bits (369), Expect = 2e-35,   Method: Compositional matrix adjust.
 Identities = 74/237 (31%), Positives = 140/237 (59%)
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 RSASECLRIVGSIDQKIGDCLNAKYLEFAPDRSVKSPKEIVMRQHMKKDVFRILESLDSR 475
           R   +  +   S++  IGD  ++   +F  D +++ P +    + ++     +L  L +R
Sbjct: 495 RKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATTESLRAATHDVLAGLTAR 554
Query: 476 ERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDSETCRDLSHFL 532
           E +VL +R+G++ +   +LEE+GK F V++E IR++E KA+ KLR       L  FL
Sbjct: 555 EAKVLRMRFGIDMNTDYTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRSFL 611

>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 = 94.7 bits (234), 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 = 78.2 bits (191), 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 = 4e-14,   Method: Compositional matrix adjust.
 Identities = 32/77 (41%), Positives = 53/77 (68%)
Query: 293 GWYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYV 352
           G   R+ LI++   LV+ +A+ Y G G+ F DL+Q GN G+++  E+F++ RG+ FSTY 
Sbjct: 103 GEAARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQEGNQGLIRAVEKFEYKRGFAFSTYA 162
Query: 353 QYWIRKSISKMVARHAR 369
            +WIR++I++ +A  AR
Sbjct: 163 TWWIRQAINRAIADQAR 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 = 76.3 bits (186), Expect = 4e-14,   Method: Compositional matrix adjust.
 Identities = 63/229 (27%), Positives = 113/229 (49%), Gaps = 18/229 (7%)
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----GDCLNAKYLEFAPDRSVKSPKEIVMRQHMKKDVFRILES 471
             A E +R+  SI + +    GD +    L+   D    S  + +    +KK     +E 
Sbjct: 148 VLAQEAVRLPTSIHETVYENDGDPIT--LLDQIADADEASWFDKIA---LKK----AIEE 198
Query: 472 LDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLR 520
           LD RER ++ LRY    ++ ++  E+     +S+  + +LEKK +  ++
Sbjct: 199 LDERERLIVYLRY----YKDQTQSEVASRLGISQVQMSRLEKKILQHIK 243

>pdb|1TTY|A Chain A, Solution Structure Of Sigma A Region 4 From Thermotoga Maritima Length = 87

Iteration: 1
 Score = 67.4 bits (163), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 34/78 (43%), Positives = 54/78 (69%)
Query: 457 MRQHMKKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAM 516
           MR  M++++ ++L++L  RE  VL +RYGL D +PK+LEE+G+ F+V++E IR++E KA+
Sbjct: 4   MRMLMREELEKVLKTLSPREAMVLRMRYGLLDGKPKTLEEVGQYFNVTRERIRQIEVKAL 63
Query: 517 TKLRDSETCRDLSHFLVL 534
            KLR     + L   L L
Sbjct: 64  RKLRHPSRSKYLKSLLSL 81

>pdb|4G6D|A Chain A, G1 Orf67 / Staphyloccus Aureus Sigmaa Domain 4 Complex Length = 73

Iteration: 1
 Score = 64.3 bits (155), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 32/72 (44%), Positives = 50/72 (69%)
Query: 461 MKKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLR 520
           MK+ +  +L++L  RE  VL LR+GL+D R ++LEE+GK+F V++E IR++E KA+ KLR
Sbjct: 1   MKEQLEDVLDTLTDREENVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLR 60
Query: 521 DSETCRDLSHFL 532
                + L  F+
Sbjct: 61  HPSRSKRLKDFM 72

>pdb|4G94|A Chain A, G1 Orf67 / Staphyloccus Aureus Sigmaa Domain 4 Complex Length = 62

Iteration: 1
 Score = 59.7 bits (143), Expect = 4e-09,   Method: Composition-based stats.
 Identities = 30/60 (50%), Positives = 46/60 (76%)
Query: 461 MKKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLR 520
           MK+ +  +L++L  RE  VL LR+GL+D R ++LEE+GK+F V++E IR++E KA+ KLR
Sbjct: 1   MKEQLEDVLDTLTDREENVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLR 60

>pdb|1TLH|B Chain B, T4 Asia Bound To Sigma70 Region 4 Length = 81

Iteration: 1
 Score = 52.0 bits (123), Expect = 7e-07,   Method: Compositional matrix adjust.
 Identities = 27/65 (41%), Positives = 42/65 (64%)
Query: 468 ILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDSETCRD 527
           +L  L +RE +VL +R+G++ +   +LEE+GK F V++E IR++E KA+ KLR       
Sbjct: 15  VLAGLTAREAKVLRMRFGIDMNTDYTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEV 74
Query: 528 LSHFL 532
           L  FL
Sbjct: 75  LRSFL 79

>pdb|2P7V|B Chain B, Crystal Structure Of The Escherichia Coli Regulator Of Sigma 70, Rsd, In Complex With Sigma 70 Domain 4 Length = 68

Iteration: 1
 Score = 51.6 bits (122), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 27/65 (41%), Positives = 42/65 (64%)
Query: 468 ILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDSETCRD 527
           +L  L +RE +VL +R+G++ +   +LEE+GK F V++E IR++E KA+ KLR       
Sbjct: 2   VLAGLTAREAKVLRMRFGIDMNTDYTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEV 61
Query: 528 LSHFL 532
           L  FL
Sbjct: 62  LRSFL 66

>pdb|3T72|QQ Chain q, Phob(E)-Sigma70(4)-(Rnap-Betha-Flap-Tip-Helix)-Dna Transcription Activation Sub-Complex Length = 99

Iteration: 1
 Score = 51.6 bits (122), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 24/53 (45%), Positives = 39/53 (73%)
Query: 468 ILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLR 520
           +L  L +RE +VL +R+G++ +   +LEE+GK F V++E IR++E KA+ KLR
Sbjct: 16  VLAGLTAREAKVLRMRFGIDMNTDYTLEEVGKQFDVTRERIRQIEAKALRKLR 68

>pdb|3N97|A Chain A, Rna Polymerase Alpha C-Terminal Domain (E. Coli) And Sigma Region 4 (T. Aq. Mutant) Bound To (Up,-35 Element) Dna Length = 72

Iteration: 1
 Score = 50.8 bits (120), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 29/64 (45%), Positives = 37/64 (57%)
Query: 469 LESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDSETCRDL 528
           L  L  RE  VL +R GL D R  +LEE+G  F V++E IR++E KA+ KLR       L
Sbjct: 8   LSKLSEREAMVLKMRKGLIDGREHTLEEVGAYFGVTRERIRQIENKALRKLRHPSRSEKL 67
Query: 529 SHFL 532
             FL
Sbjct: 68  RDFL 71

>pdb|1RIO|H Chain H, Structure Of Bacteriophage Lambda Ci-Ntd In Complex With Sigma-Region4 Of Thermus Aquaticus Bound To Dna Length = 73

Iteration: 1
 Score = 50.1 bits (118), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 31/65 (47%), Positives = 40/65 (61%), Gaps = 1/65 (1%)
Query: 469 LESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDSET-CRD 527
           L  L  RE  VL LR GL D R  +LEE+G  F V++E IR++E KA+ KL+  E+  R 
Sbjct: 8   LSKLSEREAMVLKLRKGLIDGREHTLEEVGAYFGVTRERIRQIENKALRKLKYHESRTRK 67
Query: 528 LSHFL 532
           L  FL
Sbjct: 68  LRDFL 72

>pdb|1KU3|A Chain A, Crystal Structure Of Thermus Aquaticus Rna Polymerase Sigma Subunit Fragment, Region 4 Length = 73

Iteration: 1
 Score = 49.7 bits (117), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 30/65 (46%), Positives = 40/65 (61%), Gaps = 1/65 (1%)
Query: 469 LESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDSET-CRD 527
           L  L  RE  VL +R GL D R  +LEE+G  F V++E IR++E KA+ KL+  E+  R 
Sbjct: 8   LSKLSEREAMVLKMRKGLIDGREHTLEEVGAYFGVTRERIRQIENKALRKLKYHESRTRK 67
Query: 528 LSHFL 532
           L  FL
Sbjct: 68  LRDFL 72

>pdb|1RP3|A Chain A, Cocrystal Structure Of The Flagellar SigmaANTI-Sigma Complex, Sigma-28FLGM Length = 239

Iteration: 1
 Score = 46.2 bits (108), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 55/234 (23%), Positives = 103/234 (44%), Gaps = 23/234 (9%)
Query: 297 REELIKSTRPLVLFLARNYR---GLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQ 353
           REELI    PLV  +A N +      +   DL+  G +G+++  +        +   Y++
Sbjct: 14  REELILKYLPLVKAIATNIKKHLPEDVDIRDLISYGVIGLIKAVDNLSTENPKRAEAYIK 73
Query: 354 YWIRKSISKMVARHARGIKIPCKLNREISK-IQKARKALTNSHGKYPEDIEIAKYTGLSL 412
             I+ +I      + R +    +  RE  + I++  + L    G+ P D E+AK  G+  
Sbjct: 74  LRIKGAIYD----YLRSLDFGSRQVREKERRIKEVVEKLKEKLGREPTDEEVAKELGI-- 127
Query: 413 AEIRSASECLRIVGSIDQKIGDCLNAKYLEFAPDRSVKSP-----KEIVMRQHMKKDVFR 467
               S  E  + +  I+      L   + +FA D S   P     +E V+++ + + V  
Sbjct: 128 ----STEELFKTLDKINFSYILSLEEVFRDFARDYSELIPSSTNVEEEVIKRELTEKVKE 183
Query: 468 ILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRD 521
            +  L  RE+  LV++    +  P    E+ K+   S   + +L+ KA+ +LR+
Sbjct: 184 AVSKLPEREK--LVIQLIFYEELPAK--EVAKILETSVSRVSQLKAKALERLRE 233

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	534
3iyd_F	613	RNA polymerase sigma factor RPOD; transcription, i	2e-50
2a6h_F	423	RNA polymerase sigma factor RPOD; RNA polymerase h	1e-47
1l9z_H	438	Sigma factor SIGA; helix-turn-helix, coiled-coil,	3e-47
1l0o_C	243	Sigma factor; bergerat fold, helix-turn-helix, pro	1e-42
1rp3_A	239	RNA polymerase sigma factor sigma-28 (FLIA); trans	2e-41
3ugo_A	245	RNA polymerase sigma factor; protein-DNA complex,	9e-23
1tty_A	87	Sigma-A, RNA polymerase sigma factor RPOD; helix-t	4e-17
3t72_q	99	RNA polymerase sigma factor RPOD, DNA-directed RN	1e-16
2p7v_B	68	Sigma-70, RNA polymerase sigma factor RPOD; RSD, r	3e-15
1sig_A	339	Sigma70, RNA polymerase primary sigma factor; RNA	6e-15
1ku3_A	73	Sigma factor SIGA; helix-turn-helix, transcription	2e-14
3mzy_A	164	RNA polymerase sigma-H factor; PSI, MCSG, structur	2e-05
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	3e-05

>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 =  181 bits (461), Expect = 2e-50
 Identities = 74/236 (31%), Positives = 140/236 (59%)

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 SASECLRIVGSIDQKIGDCLNAKYLEFAPDRSVKSPKEIVMRQHMKKDVFRILESLDSRE 476
              +  +   S++  IGD  ++   +F  D +++ P +    + ++     +L  L +RE
Sbjct: 496 KVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATTESLRAATHDVLAGLTARE 555

Query: 477 RQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDSETCRDLSHFL 532
            +VL +R+G++ +   +LEE+GK F V++E IR++E KA+ KLR       L  FL
Sbjct: 556 AKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRSFL 611

>2a6h_F RNA polymerase sigma factor RPOD; RNA polymerase holoenzyme, streptolydigin, antibiotic, transcription regulation; HET: STD; 2.40A {Thermus thermophilus} SCOP: a.4.13.1 a.4.13.2 a.177.1.1 PDB: 1smy_F* 1zyr_F* 1iw7_F* 2a69_F* 2a6e_F 2a68_F* 2be5_F* 2cw0_F 3eql_F* 3dxj_F* 1l9u_H Length = 423

 Score =  170 bits (432), Expect = 1e-47
 Identities = 83/243 (34%), Positives = 136/243 (55%), Gaps = 8/243 (3%)

Query: 284 RVLKQHLAFGWYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHT 343
           +        G   R+ LI++   LV+ +A+ Y G G+ F DL+Q GN G+++  E+F++ 
Sbjct: 171 KRYLHIAREGEAARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQEGNQGLIRAVEKFEYK 230

Query: 344 RGYKFSTYVQYWIRKSISKMVARHARGIKIPCKLNREISKIQKARKALTNSHGKYPEDIE 403
           R +KFSTY  +WIR++I++ +A  AR I+IP  +   I+K+ +  + L    G+ P   E
Sbjct: 231 RRFKFSTYATWWIRQAINRAIADQARTIRIPVHMVETINKLSRTARQLQQELGREPTYEE 290

Query: 404 IAK--YTGLSLAEIRSASECLRIVG---SIDQKIGDCLNAKYLEFAPDRSVKSPKEIVMR 458
           IA+    G     +    E L+I     S++  IGD  ++ Y +F PD  + SP +   +
Sbjct: 291 IAEAMGPGWDAKRVE---ETLKIAQEPVSLETPIGDEKDSFYGDFIPDEHLPSPVDAATQ 347

Query: 459 QHMKKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTK 518
             + +++ + L  L  RE  VL LR GL D R  +LEE+G  F V++E IR++E KA+ K
Sbjct: 348 SLLSEELEKALSKLSEREAMVLKLRKGLIDGREHTLEEVGAFFGVTRERIRQIENKALRK 407

Query: 519 LRD 521
           L+ 
Sbjct: 408 LKY 410

>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 =  169 bits (429), Expect = 3e-47
 Identities = 83/229 (36%), Positives = 135/229 (58%), Gaps = 8/229 (3%)

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---SIDQKIGDCLNAKYLEFAPDRSVKSPKEIVMRQHMKKDVFRILES 471
           +    E L+I     S++  IGD  ++ Y +F PD ++ SP E   +  + +++ + L  
Sbjct: 319 VE---ETLKIAQEPVSLETPIGDEKDSFYGDFIPDENLPSPVEAAAQSLLSEELEKALSK 375

Query: 472 LDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLR 520
           L  RE  VL LR GL D R  +LEE+G  F V++E IR++E KA+ KL+
Sbjct: 376 LSEREAMVLKLRKGLIDGREHTLEEVGAYFGVTRERIRQIENKALRKLK 424

>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 =  151 bits (383), Expect = 1e-42
 Identities = 60/228 (26%), Positives = 108/228 (47%), Gaps = 18/228 (7%)

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 EIRSASECLRIVGSIDQKIG-DCLNAKYLEFAPDRSVKSPKEIVMRQHMKKDVFRILESL 472
           ++  A E +R+  SI + +  +  +   L    D+   + +     +   K     +E L
Sbjct: 146 DVVLAQEAVRLPTSIHETVYENDGDPITLL---DQIADADEASWFDKIALKKA---IEEL 199

Query: 473 DSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLR 520
           D RER ++ LRY  +    ++  E+     +S+  + +LEKK +  ++
Sbjct: 200 DERERLIVYLRYYKD----QTQSEVASRLGISQVQMSRLEKKILQHIK 243

>1rp3_A RNA polymerase sigma factor sigma-28 (FLIA); transcription; 2.30A {Aquifex aeolicus} SCOP: a.4.13.1 a.4.13.2 a.177.1.1 PDB: 1sc5_A Length = 239

 Score =  148 bits (375), Expect = 2e-41
 Identities = 52/231 (22%), Positives = 103/231 (44%), Gaps = 17/231 (7%)

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--VGSIDQKIGDCLNAKYLEFAPDRSVKSPKEIVMRQHMKKDVFRILE 470
            E+    + +    + S+++   D     Y E  P     + +E V+++ + + V   + 
Sbjct: 130 EELFKTLDKINFSYILSLEEVFRD-FARDYSELIPS--STNVEEEVIKRELTEKVKEAVS 186

Query: 471 SLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRD 521
            L  RE+ V+ L +          +E+ K+   S   + +L+ KA+ +LR+
Sbjct: 187 KLPEREKLVIQLIFYEE----LPAKEVAKILETSVSRVSQLKAKALERLRE 233

>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 = 96.5 bits (240), Expect = 9e-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

>1tty_A Sigma-A, RNA polymerase sigma factor RPOD; helix-turn-helix, transcription; NMR {Thermotoga maritima} SCOP: a.4.13.2 Length = 87

 Score = 75.5 bits (186), Expect = 4e-17
 Identities = 33/79 (41%), Positives = 54/79 (68%)

Query: 454 EIVMRQHMKKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEK 513
           +  MR  M++++ ++L++L  RE  VL +RYGL D +PK+LEE+G+ F+V++E IR++E 
Sbjct: 1   KEAMRMLMREELEKVLKTLSPREAMVLRMRYGLLDGKPKTLEEVGQYFNVTRERIRQIEV 60

Query: 514 KAMTKLRDSETCRDLSHFL 532
           KA+ KLR     + L   L
Sbjct: 61  KALRKLRHPSRSKYLKSLL 79

>3t72_q RNA polymerase sigma factor RPOD, DNA-directed RN polymerase subunit beta; winged-helix motif, transcription activation, DNA-binding; 4.33A {Escherichia coli} PDB: 1tlh_B Length = 99

 Score = 74.4 bits (183), Expect = 1e-16
 Identities = 25/79 (31%), Positives = 44/79 (55%)

Query: 454 EIVMRQHMKKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEK 513
           +    + ++     +L  L +RE +VL +R+G++ +   +LEE+GK F V++E IR++E 
Sbjct: 2   DSATTESLRAATHDVLAGLTAREAKVLRMRFGIDMNTDYTLEEVGKQFDVTRERIRQIEA 61

Query: 514 KAMTKLRDSETCRDLSHFL 532
           KA+ KLR       L    
Sbjct: 62  KALRKLRHPSRSEVLRSGS 80

>2p7v_B Sigma-70, RNA polymerase sigma factor RPOD; RSD, regulator of sigma 70, sigma 70 domain 4, transcription, regulation, helix-turn-helix; 2.60A {Escherichia coli} SCOP: a.4.13.2 Length = 68

 Score = 69.2 bits (170), Expect = 3e-15
 Identities = 27/65 (41%), Positives = 42/65 (64%)

Query: 468 ILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDSETCRD 527
           +L  L +RE +VL +R+G++ +   +LEE+GK F V++E IR++E KA+ KLR       
Sbjct: 2   VLAGLTAREAKVLRMRFGIDMNTDYTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEV 61

Query: 528 LSHFL 532
           L  FL
Sbjct: 62  LRSFL 66

>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 = 74.9 bits (184), Expect = 6e-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

>1ku3_A Sigma factor SIGA; helix-turn-helix, transcription; 1.80A {Thermus aquaticus} SCOP: a.4.13.2 PDB: 1ku7_A 1rio_H 3n97_A* Length = 73

 Score = 67.0 bits (164), Expect = 2e-14
 Identities = 30/67 (44%), Positives = 41/67 (61%), Gaps = 1/67 (1%)

Query: 467 RILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDSET-C 525
           + L  L  RE  VL +R GL D R  +LEE+G  F V++E IR++E KA+ KL+  E+  
Sbjct: 6   KALSKLSEREAMVLKMRKGLIDGREHTLEEVGAYFGVTRERIRQIENKALRKLKYHESRT 65

Query: 526 RDLSHFL 532
           R L  FL
Sbjct: 66  RKLRDFL 72

>3mzy_A RNA polymerase sigma-H factor; PSI, MCSG, structural genomics, midwest center for structura genomics, protein structure initiative; 2.50A {Fusobacterium nucleatum subsp} Length = 164

 Score = 44.1 bits (104), Expect = 2e-05
 Identities = 32/210 (15%), Positives = 69/210 (32%), Gaps = 55/210 (26%)

Query: 319 GIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIPCKLN 378
           G    DL+Q G +G+L+  + +D T+   FS++    IR+ +   + +      +   LN
Sbjct: 1   GAEKEDLVQEGILGLLKAIKFYDETKS-SFSSFAFLCIRREMISAIRKANTQKHMV--LN 57

Query: 379 REISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNA 438
             +                  ED       G ++   +S+                    
Sbjct: 58  EAL------------KTNAILEDSAYFDDEGHNINNYKSSES------------------ 87

Query: 439 KYLEFAPDRSVKSPKEIVMRQHMKKDVF-RILESLDSRERQVLVLRYGLNDHRPKSLEEI 497
                       +P+E  + +   ++       +    E++VL         R  S  EI
Sbjct: 88  ------------NPEEAYLLKEEIEEFKKFSENNFSKFEKEVLTYLI-----RGYSYREI 130

Query: 498 GKLFHVS----KEWIRKLEKKAMTKLRDSE 523
             +   +       I+++ KK+   +++ E
Sbjct: 131 ATILSKNLKSIDNTIQRIRKKSEEWIKEEE 160

>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 = 3e-05
 Identities = 64/466 (13%), Positives = 128/466 (27%), Gaps = 130/466 (27%)

Query: 74  TVENDYSETEEIRQKSTSC--IGQDASSRSDFRLLMENLDVLESTFADSDALRLEREILQ 131
            ++N  S    +         I  + +SRSD      N+ +   +        L R +  
Sbjct: 188 NLKNCNSPETVLEMLQKLLYQIDPNWTSRSDH---SSNIKLRIHSIQA----ELRRLLKS 240

Query: 132 QLGKLGALKLFNSHLSRIVKTSNVLDLSDVH------TEEQKMNDSRD-YHMGKILVPSK 184
           +  +   L L N      V+ +   +  ++       T  +++ D         I +   
Sbjct: 241 KPYENCLLVLLN------VQNAKAWNAFNLSCKILLTTRFKQVTDFLSAATTTHISLDHH 294

Query: 185 RKGKRKLKTARVSEESIETSLLSLPSEALQEGLKQPTIFSAERALNSRGRRLTIARNEAE 244
                  +   +  + ++     LP E L      P      R L+     +   R+   
Sbjct: 295 SMTLTPDEVKSLLLKYLDCRPQDLPREVLTTN---P------RRLSIIAESI---RDGLA 342

Query: 245 MSKGVQVVANLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQHLAFGWYCREELIKST 304
                + V N +++ T +E      +SLN       +     ++      +         
Sbjct: 343 TWDNWKHV-NCDKLTTIIE------SSLNV------LEPAEYRKM-----F--------- 375

Query: 305 RPLVLFLARNYRGLGIPFSDLLQAGNVGVL------QGAERFDHT--------RGYKFST 350
             L +F         IP + LL      ++             +         +  K ST
Sbjct: 376 DRLSVFPP----SAHIP-TILLS-----LIWFDVIKSDVMVVVNKLHKYSLVEKQPKEST 425

Query: 351 Y----VQYWIRKSISKMVARHARGIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAK 406
                +   ++  +    A H     I       +      +   ++       D     
Sbjct: 426 ISIPSIYLELKVKLENEYALHR---SI-------VDHYNIPKTFDSDDLIPPYLDQYFYS 475

Query: 407 YTGLSLAEIRSA--SECLRIV----GSIDQKI----------GDCLNA-----KYLEFAP 445
           + G  L  I         R+V      ++QKI          G  LN       Y  +  
Sbjct: 476 HIGHHLKNIEHPERMTLFRMVFLDFRFLEQKIRHDSTAWNASGSILNTLQQLKFYKPYIC 535

Query: 446 DRSVKSPKEIVMRQHMKKDVFRILESLDS---RERQVLVLRYGLND 488
           D     PK     + +   +   L  ++      +   +LR  L  
Sbjct: 536 D---NDPK----YERLVNAILDFLPKIEENLICSKYTDLLRIALMA 574

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	534
1l9z_H	438	Sigma factor SIGA; helix-turn-helix, coiled-coil,	100.0
2a6h_F	423	RNA polymerase sigma factor RPOD; RNA polymerase h	100.0
3iyd_F	613	RNA polymerase sigma factor RPOD; transcription, i	100.0
3ugo_A	245	RNA polymerase sigma factor; protein-DNA complex,	100.0
1rp3_A	239	RNA polymerase sigma factor sigma-28 (FLIA); trans	100.0
1l0o_C	243	Sigma factor; bergerat fold, helix-turn-helix, pro	99.97
1or7_A	194	Sigma-24, RNA polymerase sigma-E factor; regulatio	99.9
2q1z_A	184	RPOE, ECF SIGE; ECF sigma factor, cupin fold, zinc	99.9
3mzy_A	164	RNA polymerase sigma-H factor; PSI, MCSG, structur	99.88
2lfw_A	157	PHYR sigma-like domain; signal transduction, respo	99.74
1sig_A	339	Sigma70, RNA polymerase primary sigma factor; RNA	99.66
3n0r_A	286	Response regulator; sigma factor, receiver, two-co	99.6
3t72_q	99	RNA polymerase sigma factor RPOD, DNA-directed RN	99.53
2p7v_B	68	Sigma-70, RNA polymerase sigma factor RPOD; RSD, r	99.32
3hug_A	92	RNA polymerase sigma factor; ECF sigma factor, zin	99.32
1tty_A	87	Sigma-A, RNA polymerase sigma factor RPOD; helix-t	99.31
1ku3_A	73	Sigma factor SIGA; helix-turn-helix, transcription	99.3
2o7g_A	112	Probable RNA polymerase sigma-C factor; sigma fact	99.02
2o8x_A	70	Probable RNA polymerase sigma-C factor; promoter r	99.0
1h3l_A	87	RNA polymerase sigma factor; transcription, DNA-bi	98.91
1xsv_A	113	Hypothetical UPF0122 protein SAV1236; helix-turn-h	98.85
3clo_A	258	Transcriptional regulator; NP_811094.1, bacterial	98.75
1s7o_A	113	Hypothetical UPF0122 protein SPY1201/SPYM3_0842/SP	98.68
2rnj_A	91	Response regulator protein VRAR; HTH LUXR-type dom	98.57
1x3u_A	79	Transcriptional regulatory protein FIXJ; helix-tur	98.5
3c57_A	95	Two component transcriptional regulatory protein;	98.5
1jhg_A	101	Trp operon repressor; complex (regulatory protein-	98.43
1je8_A	82	Nitrate/nitrite response regulator protein NARL; p	98.39
1fse_A	74	GERE; helix-turn-helix DNA-binding protein transcr	98.24
3ulq_B	90	Transcriptional regulatory protein COMA; tetratric	98.08
2jpc_A	61	SSRB; DNA binding protein, structural genomics, PS	97.93
1p4w_A	99	RCSB; solution structure, DNA binding domain, DNA	97.9
2q0o_A	236	Probable transcriptional activator protein TRAR; h	97.52
1l3l_A	234	Transcriptional activator protein TRAR; helix-turn	97.5
3szt_A	237	QCSR, quorum-sensing control repressor; quorum sen	97.4
3qp6_A	265	CVIR transcriptional regulator; quorum sensing, ag	97.24
1tc3_C	51	Protein (TC3 transposase); DNA binding, helix-turn	96.99
2w7n_A	101	TRFB transcriptional repressor protein; INCP, plas	96.73
1yio_A	208	Response regulatory protein; transcription regulat	96.58
1a04_A	215	Nitrate/nitrite response regulator protein NARL; s	96.31
2x48_A	55	CAG38821; archeal virus, viral protein; 2.60A {Sul	96.21
3c3w_A	225	Two component transcriptional regulatory protein;	96.02
3klo_A	225	Transcriptional regulator VPST; REC domain, HTH do	95.39
3p7n_A	258	Sensor histidine kinase; LOV domain, light-activat	95.04
1p2f_A	220	Response regulator; DRRB, OMPR/PHOB, transcription	93.45
1jko_C	52	HIN recombinase, DNA-invertase HIN; water-mediated	93.21
2gwr_A	238	DNA-binding response regulator MTRA; two-component	93.18
2oqr_A	230	Sensory transduction protein REGX3; response regul	92.92
1kgs_A	225	DRRD, DNA binding response regulator D; DNA-bindin	92.53
1qgp_A	77	Protein (double stranded RNA adenosine deaminase);	92.25
1ys7_A	233	Transcriptional regulatory protein PRRA; response	92.09
1qbj_A	81	Protein (double-stranded RNA specific adenosine D	91.63
3ugo_A	245	RNA polymerase sigma factor; protein-DNA complex,	91.54
1u78_A	141	TC3 transposase, transposable element TC3 transpos	91.38
3kor_A	119	Possible Trp repressor; putative DNA-binding Trp r	91.33
1pdn_C	128	Protein (PRD paired); protein-DNA complex, double	91.2
1zx4_A	192	P1 PARB, plasmid partition PAR B protein, PARB; tr	90.58
2hqr_A	223	Putative transcriptional regulator; phosporylation	90.42
3q9s_A	249	DNA-binding response regulator; DNA binding protei	90.33
1k78_A	149	Paired box protein PAX5; paired domain, ETS domain	89.42
3r0j_A	250	Possible two component system response transcript	89.34
1oyi_A	82	Double-stranded RNA-binding protein; (alpha+beta)	89.0
2elh_A	87	CG11849-PA, LD40883P; structural genomics, NPPSFA,	88.74
2heo_A	67	Z-DNA binding protein 1; protein DLM1-Z-DNA comple	87.62
3r0a_A	123	Putative transcriptional regulator; structural gen	87.6
2w48_A	315	Sorbitol operon regulator; SORC, activator, repres	87.36
2d1h_A	109	ST1889, 109AA long hypothetical transcriptional re	86.49
2jn6_A	97	Protein CGL2762, transposase; GFT PSI-2, protein s	86.18
3k2z_A	196	LEXA repressor; winged helix-turn-helix, SOS syste	85.74
3tgn_A	146	ADC operon repressor ADCR; helix-turn-helix, trans	85.57
2o3f_A	111	Putative HTH-type transcriptional regulator YBBH;	85.57
1r1u_A	106	CZRA, repressor protein; zinc, DNA binding, transc	85.38
3mn2_A	108	Probable ARAC family transcriptional regulator; st	85.37
3jth_A	98	Transcription activator HLYU; transcription factor	84.81
3cuo_A	99	Uncharacterized HTH-type transcriptional regulato;	84.7
2cfx_A	144	HTH-type transcriptional regulator LRPC; transcrip	84.35
2k27_A	159	Paired box protein PAX-8; paired domain, solution	83.92
3pqk_A	102	Biofilm growth-associated repressor; helix-turn-he	83.81
2gxg_A	146	146AA long hypothetical transcriptional regulator;	83.77
2k9s_A	107	Arabinose operon regulatory protein; activator, ar	83.6
3oio_A	113	Transcriptional regulator (ARAC-type DNA-binding c	83.6
2dbb_A	151	Putative HTH-type transcriptional regulator PH006;	83.58
2glo_A	59	Brinker CG9653-PA; protein-DNA complex, helix-turn	83.54
1sfx_A	109	Conserved hypothetical protein AF2008; structural	83.33
3oou_A	108	LIN2118 protein; protein structure initiative, PSI	83.17
2cyy_A	151	Putative HTH-type transcriptional regulator PH151;	82.45
2w25_A	150	Probable transcriptional regulatory protein; trans	82.38
2p5v_A	162	Transcriptional regulator, LRP/ASNC family; NMB057	82.32
2pn6_A	150	ST1022, 150AA long hypothetical transcriptional re	82.2
3ech_A	142	MEXR, multidrug resistance operon repressor; winge	82.07
2cg4_A	152	Regulatory protein ASNC; DNA binding, FFRP, LRP fa	81.89
2oqg_A	114	Possible transcriptional regulator, ARSR family P;	81.64
1i1g_A	141	Transcriptional regulator LRPA; helix-turn-helix,	81.63
3lsg_A	103	Two-component response regulator YESN; structural	81.59
1sfu_A	75	34L protein; protein/Z-DNA complex, DNA binding pr	81.58
2x4h_A	139	Hypothetical protein SSO2273; transcription; 2.30A	81.48
3bpv_A	138	Transcriptional regulator; MARR, DNA binding, tran	81.47
3frw_A	107	Putative Trp repressor protein; structural genomic	81.42
3nqo_A	189	MARR-family transcriptional regulator; structural	81.38
2lkp_A	119	Transcriptional regulator, ARSR family; symmetric	81.33
3i4p_A	162	Transcriptional regulator, ASNC family; PSI, struc	81.16
2zkz_A	99	Transcriptional repressor PAGR; protein-DNA, HTH m	81.06
3o9x_A	133	Uncharacterized HTH-type transcriptional regulato;	81.05
3bdd_A	142	Regulatory protein MARR; putative multiple antibio	80.82
1y0u_A	96	Arsenical resistance operon repressor, putative; s	80.73
1uly_A	192	Hypothetical protein PH1932; helix-turn-helix, str	80.5
2l0k_A	93	Stage III sporulation protein D; SPOIIID, solution	80.38
1r1t_A	122	Transcriptional repressor SMTB; zinc, transcriptio	80.26
2nnn_A	140	Probable transcriptional regulator; structural gen	80.19

>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=5.4e-53  Score=450.95  Aligned_cols=309  Identities=30%  Similarity=0.472  Sum_probs=276.8

Q ss_pred             HHHHhhccC-CCCCCchHHHHHHhhchHHHHHHHHHHH------------------HHHHhCCCCchHHHHHH-------
Q 009449          225 AERALNSRG-RRLTIARNEAEMSKGVQVVANLERIKTT------------------LEKESGKAASLNCWAQA-------  278 (534)
Q Consensus       225 ~~~~~~~~~-~~lLt~~eE~~L~~~iq~~~~le~~~~~------------------l~~~~g~~ps~~ewa~a-------  278 (534)
                      ++-|++..+ .||||++||++|+++|+.+..++.....                  .....++.|+..+|+..       
T Consensus        96 ~~~Yl~ei~~~pLLt~eEE~~La~~i~~g~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  175 (438)
T 1l9z_H           96 VRQYLHEIGQVPLLTLEEEIDLARKVEEGMEAIKKLSEATGLDQELIREVVRAKILGTARIQKIPGLKEKPDPKTVEEVD  175 (438)
T ss_pred             HHHHHHHhccCCCCCHHHHHHHHHHHHHhhhHHHHHHhhhccchhhhhhhhhhhhhhcccccccccccccccchhhhhhh
Confidence            344554444 6999999999999999998655432211                  12234677888887432       


Q ss_pred             -----cCCCHHHHHHHHHhcHHHHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCchhhHHH
Q 009449          279 -----AGVSERVLKQHLAFGWYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQ  353 (534)
Q Consensus       279 -----~g~d~~~L~~~l~~G~~A~e~LI~~nlrLV~sIArrY~~~g~~~eDLiQEG~lgL~rA~ekFDp~kG~rFSTYA~  353 (534)
                           .+++...|...++.|..|+++||.+|+++|++||++|.++|.+++|||||||+|||+|+++|||.+|++|+|||+
T Consensus       176 ~~~~~~~~~~~eLi~~~~~d~~A~~~Li~~nlrlVv~iA~ry~~~g~~aeDLIQEg~IgL~kAvekFDp~kG~rFsTYA~  255 (438)
T 1l9z_H          176 GKLKSLPKELKRYLHIAREGEAARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQEGNQGLIRAVEKFEYKRRFKFSTYAT  255 (438)
T ss_pred             hhhhcccchHHHHHHHHhcCHHHHHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHhcCcccCCChHHHHH
Confidence                 245667888888888999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHhccccccccchHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHcC--CCHHHHHHHHHHhhhhcccccc
Q 009449          354 YWIRKSISKMVARHARGIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTG--LSLAEIRSASECLRIVGSIDQK  431 (534)
Q Consensus       354 ~wIR~aI~~~lr~~sr~iRlP~~~~~~i~ki~ka~~~L~~elGr~Pt~eEIA~~lg--is~~kv~~~l~~~~~~~SLD~~  431 (534)
                      ||||+.|.++++++.|++++|.|+.+.+++++++.+.+.+.+||.|+.+|||+.+|  +++++|..++.....++|+|.+
T Consensus       256 ~wIR~~I~~~i~~~~R~irlp~~~~~~l~~lrr~~r~l~~~lgr~pt~eeiA~~l~~~v~~e~V~~~~~~~~~~~SLd~~  335 (438)
T 1l9z_H          256 WWIRQAINRAIADQARTIRIPVHMVETINKLSRTARQLQQELGREPSYEEIAEAMGPGWDAKRVEETLKIAQEPVSLETP  335 (438)
T ss_pred             HHHHHHHHHHHHHhcchhccchHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCCCHHHHHHHHHhcccccccccc
Confidence            99999999999999999999999999999999999999999999999999999999  9999999999888889999999


Q ss_pred             cccchhhhhhhccCCCCCCChHHHHHHHHHHHHHHHHHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHH
Q 009449          432 IGDCLNAKYLEFAPDRSVKSPKEIVMRQHMKKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKL  511 (534)
Q Consensus       432 i~~~~~~~l~e~i~d~~~~spee~v~~~el~e~L~~~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi  511 (534)
                      ++++++..+.+.+++....+|++.+....+...|..+|+.||++||+||.+||||+|++++|++|||+.||||++||||+
T Consensus       336 ~~~d~d~~l~d~l~d~~~~~pee~~~~~~~~~~L~~aL~~L~ereR~VI~LRygL~~~e~~TleEIAe~LgIS~erVRqi  415 (438)
T 1l9z_H          336 IGDEKDSFYGDFIPDENLPSPVEAAAQSLLSEELEKALSKLSEREAMVLKLRKGLIDGREHTLEEVGAYFGVTRERIRQI  415 (438)
T ss_pred             cccccchhhhhhhcccccCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHhccCCCCCCHHHHHHHHCcCHHHHHHH
Confidence            98777777888888776678999998889999999999999999999999999999989999999999999999999999


Q ss_pred             HHHHHHHHH-hHhhhhcchhhhc
Q 009449          512 EKKAMTKLR-DSETCRDLSHFLV  533 (534)
Q Consensus       512 ~~RAL~KLR-~~l~~~~L~~yl~  533 (534)
                      +++|++||| +.+....|++|+.
T Consensus       416 ~~RAlkKLR~~~~~~~~l~~yl~  438 (438)
T 1l9z_H          416 ENKALRKLKYHESRTRKLRDFLE  438 (438)
T ss_pred             HHHHHHHHHHhHhhHHHHHHhhC
Confidence            999999999 8888889999974

>2a6h_F RNA polymerase sigma factor RPOD; RNA polymerase holoenzyme, streptolydigin, antibiotic, transcription regulation; HET: STD; 2.40A {Thermus thermophilus} SCOP: a.4.13.1 a.4.13.2 a.177.1.1 PDB: 1smy_F* 1zyr_F* 1iw7_F* 2a69_F* 2a6e_F 2a68_F* 2be5_F* 2cw0_F 3eql_F* 3dxj_F* 1l9u_H

Probab=100.00  E-value=6.8e-53  Score=449.83  Aligned_cols=311  Identities=30%  Similarity=0.476  Sum_probs=271.0

Q ss_pred             HHHHHHhhccC-CCCCCchHHHHHHhhchHHHHHHHHHHHH------------------HHHhCCCCchHHHH-------
Q 009449          223 FSAERALNSRG-RRLTIARNEAEMSKGVQVVANLERIKTTL------------------EKESGKAASLNCWA-------  276 (534)
Q Consensus       223 ~~~~~~~~~~~-~~lLt~~eE~~L~~~iq~~~~le~~~~~l------------------~~~~g~~ps~~ewa-------  276 (534)
                      +.++-|+...+ .||||++||++|+++|+.+..+.......                  ....++.|+..+|+       
T Consensus        79 d~~~~Yl~ei~~~plLt~eEE~~La~ri~~g~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  158 (423)
T 2a6h_F           79 DPVRQYLHEIGQVPLLTLEEEVELARKVEEGMEAIKKLSEITGLDPDLIREVVRAKILGSARVRHIPGLKETLDPKTVEE  158 (423)
T ss_dssp             HHHHHHHHHHHHCCCCTTHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHCCHHHHHTTSCSSSCTTHHHHH
T ss_pred             cHHHHHHHHhcccCCCCHHHHHHHHHHHHhchhHHHHHHHhhccchhhhhhhHhhhhhhhhhcccccchhhhhhhhhhhh
Confidence            44555664444 69999999999999999986544322110                  01223556654433       


Q ss_pred             --H---HcCCCHHHHHHHHHhcHHHHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCchhhH
Q 009449          277 --Q---AAGVSERVLKQHLAFGWYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTY  351 (534)
Q Consensus       277 --~---a~g~d~~~L~~~l~~G~~A~e~LI~~nlrLV~sIArrY~~~g~~~eDLiQEG~lgL~rA~ekFDp~kG~rFSTY  351 (534)
                        .   +.+++...|...++.|..|+++||.+|+++|++||++|.++|.+++||+||||+|||+|+++|||.+|++|+||
T Consensus       159 ~~~~~~~~~~~~~~L~~~~~~d~~A~~~Li~~~lrlV~~iA~~y~~~~~~~eDLiQEg~igL~kav~kFd~~~g~~FstY  238 (423)
T 2a6h_F          159 IDQKLKSLPKEHKRYLHIAREGEAARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQEGNQGLIRAVEKFEYKRRFKFSTY  238 (423)
T ss_dssp             HHHHHHHSCHHHHHHHHHHHHHHHHHHHHHHHTHHHHHHHHTTTCTTTSCHHHHHHHHHHHHHHHHHHCCTTSCCCHHHH
T ss_pred             hhhhhhcccccHHHHHHHHhcCHHHHHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHhcCcccCCCHHHH
Confidence              2   34566788888888889999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHhccccccccchHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHcC--CCHHHHHHHHHHhhhhcccc
Q 009449          352 VQYWIRKSISKMVARHARGIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTG--LSLAEIRSASECLRIVGSID  429 (534)
Q Consensus       352 A~~wIR~aI~~~lr~~sr~iRlP~~~~~~i~ki~ka~~~L~~elGr~Pt~eEIA~~lg--is~~kv~~~l~~~~~~~SLD  429 (534)
                      |+||||++|.++++++.|++++|.|+.+.+++++++.+.+.+.+||.|+.+|||+.+|  +++++|..++.....++|+|
T Consensus       239 a~~wIr~~i~~~i~~~~r~ir~p~~~~~~~~~lrr~~~~l~~~~~r~p~~~eiA~~l~~~~~~~~v~~~~~~~~~~~Sld  318 (423)
T 2a6h_F          239 ATWWIRQAINRAIADQARTIRIPVHMVETINKLSRTARQLQQELGREPTYEEIAEAMGPGWDAKRVEETLKIAQEPVSLE  318 (423)
T ss_dssp             HHHHHHHHHHHHHHHHSSSSCCCHHHHHHHHHHHHHHHHHHHHHSSCCCHHHHHHHHCTTCCHHHHHHHHHHHSCCEESS
T ss_pred             HHHHHHHHHHHHHHHccceeeccHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCCCHHHHHHHHHhccCCcccc
Confidence            9999999999999999999999999999999999999999999999999999999999  99999999998888899999


Q ss_pred             cccccchhhhhhhccCCCCCCChHHHHHHHHHHHHHHHHHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHH
Q 009449          430 QKIGDCLNAKYLEFAPDRSVKSPKEIVMRQHMKKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIR  509 (534)
Q Consensus       430 ~~i~~~~~~~l~e~i~d~~~~spee~v~~~el~e~L~~~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVR  509 (534)
                      .+++++++..+.+.+++....+|++.+....+...|..+|+.||++||+||.+||||+|++++|++|||+.||||++||+
T Consensus       319 ~~~~~~~~~~l~d~l~d~~~~~pe~~~~~~~~~~~L~~aL~~L~~rer~Vl~lr~~L~~~e~~Tl~EIA~~lgiS~erVr  398 (423)
T 2a6h_F          319 TPIGDEKDSFYGDFIPDEHLPSPVDAATQSLLSEELEKALSKLSEREAMVLKLRKGLIDGREHTLEEVGAFFGVTRERIR  398 (423)
T ss_dssp             CBCSSSSSCBGGGSSCCSSSCCHHHHHHHHHHHHHHHHHHHSSCHHHHHHHHHHHHTTCC-----CHHHHSSSSCHHHHH
T ss_pred             cccCCCCccchhhhhccccCCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHhccCCCCCCCHHHHHHHHCcCHHHHH
Confidence            99988777778888888766789999998899999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHH-hHhhhhcchhhhc
Q 009449          510 KLEKKAMTKLR-DSETCRDLSHFLV  533 (534)
Q Consensus       510 qi~~RAL~KLR-~~l~~~~L~~yl~  533 (534)
                      |++++|++||| +......|++|++
T Consensus       399 qi~~rAl~kLR~~~~~~~~l~~~l~  423 (423)
T 2a6h_F          399 QIENKALRKLKYHESRTRKLRDFLD  423 (423)
T ss_dssp             HHHHHHHHHHHHHHHHTTSSSSCCC
T ss_pred             HHHHHHHHHHHhhhhhhHHHHHhhC
Confidence            99999999999 8888899999974

>3iyd_F RNA polymerase sigma factor RPOD; transcription, initiation, class I, activator, RNA polymeras holoenzyme, sigma70, open complex, CAP, CRP; HET: DNA CMP; 19.80A {Escherichia coli k-12}

Probab=100.00  E-value=4.3e-43  Score=389.91  Aligned_cols=251  Identities=30%  Similarity=0.576  Sum_probs=238.6

Q ss_pred             HHHHHHHHHhc-HHH---HHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCchhhHHHHHHHH
Q 009449          283 ERVLKQHLAFG-WYC---REELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRK  358 (534)
Q Consensus       283 ~~~L~~~l~~G-~~A---~e~LI~~nlrLV~sIArrY~~~g~~~eDLiQEG~lgL~rA~ekFDp~kG~rFSTYA~~wIR~  358 (534)
                      ...|..+++.| ..|   ++.||..|.++|+++|++|.+++.+++||+||||+|||+++++|||.+|++|+||++|||||
T Consensus       358 ~~~Li~~~~~Gd~~A~~A~~~L~~~y~~~v~~ia~r~~~~~~~aeDlvQE~fi~l~~a~~~fd~~~g~~Fstyl~~~irn  437 (613)
T 3iyd_F          358 VKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQ  437 (613)
T ss_dssp             HHHHHHTHHHHHHHHHHHHTTTTTTTTHHHHHGGGSSSTTSSCSTTTTHHHHHHHHHHTTSCCTTSSSCSTTTHHHHHHH
T ss_pred             HHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHcCccccCcHHHHHHHHHHH
Confidence            45677788888 445   99999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHhccccccccchHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHHhhhhcccccccccchhh
Q 009449          359 SISKMVARHARGIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNA  438 (534)
Q Consensus       359 aI~~~lr~~sr~iRlP~~~~~~i~ki~ka~~~L~~elGr~Pt~eEIA~~lgis~~kv~~~l~~~~~~~SLD~~i~~~~~~  438 (534)
                      +|.++++++.+++|+|.|+.+.+++++++.+.+.+++||.||.+|||+.+|+++++++.++...+.++|+|.+++++.+.
T Consensus       438 ~i~~~lr~~~r~~rip~~~~~~~~k~~r~~~~l~~~~gr~pt~eela~~l~~~~~~v~~~~~~~~~~~sld~~~~~~~~~  517 (613)
T 3iyd_F          438 AITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDS  517 (613)
T ss_dssp             HHHHHTTTSCSSSCCCSHHHHTTTTTTTTTTTTTTTTCSCCCTTTTTTTSSCCSSHHHHHHHHSCCCCCSSCCCSSSSSC
T ss_pred             HHHHHHHhcCcceeCcHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhccCCcccCCCCCCCCCc
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999988778


Q ss_pred             hhhhccCCCCCCChHHHHHHHHHHHHHHHHHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHH
Q 009449          439 KYLEFAPDRSVKSPKEIVMRQHMKKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTK  518 (534)
Q Consensus       439 ~l~e~i~d~~~~spee~v~~~el~e~L~~~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~K  518 (534)
                      .+.+.+++....+|++.+...++...|..+|+.|||++|+||.|+||+++++++|++|||+.||||++||++++++|+++
T Consensus       518 ~l~d~i~d~~~~~p~~~~~~~e~~~~l~~aL~~Lp~~er~Vl~Lr~~~~~~e~~s~~EIA~~lgis~~tVk~~~~rAl~k  597 (613)
T 3iyd_F          518 HLGDFIEDTTLELPLDSATTESLRAATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRK  597 (613)
T ss_dssp             CGGGSCCCSSSCCHHHHHHHHTTSSSHHHHTTSSCHHHHHHHHHHHTSSSCCCCSTTGGGTTTSSCSSHHHHHHHHHHTT
T ss_pred             cHHHHhcCCCCCCHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHhccCCCCCcCHHHHHHHhCCCHHHHHHHHHHHHHH
Confidence            88899988877899999998888889999999999999999999999888799999999999999999999999999999


Q ss_pred             HHhHhhhhcchhhhc
Q 009449          519 LRDSETCRDLSHFLV  533 (534)
Q Consensus       519 LR~~l~~~~L~~yl~  533 (534)
                      ||+++....|+.|++
T Consensus       598 LR~~~~~~~l~~~l~  612 (613)
T 3iyd_F          598 LRHPSRSEVLRSFLD  612 (613)
T ss_dssp             TTSCSSSCSSTTCC-
T ss_pred             hhCcchhhHHHHHhc
Confidence            999999999999986

>3ugo_A RNA polymerase sigma factor; protein-DNA complex, bacterial promoter opening, G-quartet, quadruplex, DNA binding; 2.10A {Thermus aquaticus} PDB: 3ugp_A 4gor_A 1ku2_A 3lev_A* 3les_A*

Probab=100.00  E-value=1.5e-34  Score=287.69  Aligned_cols=207  Identities=25%  Similarity=0.384  Sum_probs=124.8

Q ss_pred             hHHHHHHhhccC-CCCCCchHHHHHHhhchHHHHHH-HHHHHH-------HHH------------------hCCCCchHH
Q 009449          222 IFSAERALNSRG-RRLTIARNEAEMSKGVQVVANLE-RIKTTL-------EKE------------------SGKAASLNC  274 (534)
Q Consensus       222 ~~~~~~~~~~~~-~~lLt~~eE~~L~~~iq~~~~le-~~~~~l-------~~~------------------~g~~ps~~e  274 (534)
                      .|.++-|++..+ .||||++||++|+++|+.++... .+....       .+.                  .+.+|+..+
T Consensus         6 ~d~~~~yl~~i~~~~llt~~~e~~la~~i~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~~~~~g~~~~~~~~~~~   85 (245)
T 3ugo_A            6 SDPVRQYLHEIGQVPLLTLEEEIDLARKVEEGMEAIKKLSEATGLDQELIREVVRAKILGTARIQKIPGLKEKPDPKTVE   85 (245)
T ss_dssp             CHHHHHHHHHHTTSCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHTTGGGCSCCCCTTCCCCCCHHHHH
T ss_pred             CCcHHHHHHHcccccCCCHHHHHHHHHHHHHHHHHHHHHHhccCCcHHHHHHhhhhhhhccchhcccccccccccchhHH
Confidence            455666776666 69999999999999999987633 222110       000                  136788999


Q ss_pred             HHHHcCCCH----HHHHHHHHhcHHHHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCchhh
Q 009449          275 WAQAAGVSE----RVLKQHLAFGWYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFST  350 (534)
Q Consensus       275 wa~a~g~d~----~~L~~~l~~G~~A~e~LI~~nlrLV~sIArrY~~~g~~~eDLiQEG~lgL~rA~ekFDp~kG~rFST  350 (534)
                      ||.+.+++.    ..|.+.++.|..|+++||+.|.++|+++|++|.+++.+++||+||||+|||+++++|||++|++|+|
T Consensus        86 ~~~~~~~~~~~~~~~L~~~~~~d~~A~~~L~~~y~~lV~~ia~r~~~~~~~aeDLvQegfi~L~~a~~~fd~~~g~~F~t  165 (245)
T 3ugo_A           86 EVDGKLKSLPKELKRYLHIAREGEAARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQEGNQGLIRAVEKFEYKRRFKFST  165 (245)
T ss_dssp             HHHHHHHTSCHHHHHHHHHHHHHHHHHHHHHHTTHHHHHHHHGGGTTSSSCHHHHHHHHHHHHHHHHHHCCGGGCCCHHH
T ss_pred             HHHHhhccchHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHcCCCCcHHHHHHHHHHHHHHHHHHcCcccCCcHHH
Confidence            999988753    4556667778899999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHHhccccccccchHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHcC--CCHHHHHHHHHHhhhhccc
Q 009449          351 YVQYWIRKSISKMVARHARGIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTG--LSLAEIRSASECLRIVGSI  428 (534)
Q Consensus       351 YA~~wIR~aI~~~lr~~sr~iRlP~~~~~~i~ki~ka~~~L~~elGr~Pt~eEIA~~lg--is~~kv~~~l~~~~~~~SL  428 (534)
                      |++||||++|.++++++.+.+++|.++.+.++++.++.+.+.+.+|+.||.+|||+.||  ||+++|...+..++.++||
T Consensus       166 ya~~~ir~~i~~~ir~~~r~~r~p~~l~e~i~~l~~~~~~L~~~~~~~ps~~EIAe~Lg~~is~~tVk~~l~~ar~~lsl  245 (245)
T 3ugo_A          166 YATWWIRQAINRAIADQARTIRIPVHMVETINKLSRTARQLQQELGREPSYEEIAEAMGPGWDAKRVEETLKIAQEPVSL  245 (245)
T ss_dssp             HHHHHHHHHHHHHHHHHTC-------------------------------------------------------------
T ss_pred             HHHHHHHHHHHHHHHHhcccccccHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHCCCCCHHHHHHHHHHHhhccCC
Confidence            99999999999999999999999999999999999999999999999999999999999  9999999999888877775

>1rp3_A RNA polymerase sigma factor sigma-28 (FLIA); transcription; 2.30A {Aquifex aeolicus} SCOP: a.4.13.1 a.4.13.2 a.177.1.1 PDB: 1sc5_A

Probab=100.00  E-value=1.4e-32  Score=265.56  Aligned_cols=222  Identities=21%  Similarity=0.315  Sum_probs=197.4

Q ss_pred             HHHHHHHHHHhHHHHHHHHHHhh---CCCCCHHHHHHHHHHHHHHhhhccCCcCCCchhhHHHHHHHHHHHHHHHHhccc
Q 009449          294 WYCREELIKSTRPLVLFLARNYR---GLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARG  370 (534)
Q Consensus       294 ~~A~e~LI~~nlrLV~sIArrY~---~~g~~~eDLiQEG~lgL~rA~ekFDp~kG~rFSTYA~~wIR~aI~~~lr~~sr~  370 (534)
                      ..|++.|+..|.++|+++|++|.   +++.+++||+|||++++|+++++|||.+|.+|+||+++||++.+.++++++.  
T Consensus        11 ~~a~~~l~~~~~~~v~~~a~~~~~~~~~~~~aeDl~Qe~~l~l~~~~~~~~~~~~~~f~~~l~~~~~~~~~d~~r~~~--   88 (239)
T 1rp3_A           11 QIEREELILKYLPLVKAIATNIKKHLPEDVDIRDLISYGVIGLIKAVDNLSTENPKRAEAYIKLRIKGAIYDYLRSLD--   88 (239)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHTTSCTTSCHHHHHHHHHHHHHHHHHTCCCCCTHHHHHHHHHHHHHHHHHHHHTSS--
T ss_pred             chHHHHHHHHhHHHHHHHHHHHHHhccCCCCHHHHHHHHHHHHHHHHHHcCcccCCCHHHHHHHHHHHHHHHHHHhcC--
Confidence            34899999999999999999998   6789999999999999999999999999999999999999999999999875  


Q ss_pred             cccccchHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHHhh--hhcccccccccchhhhhhhccCCCC
Q 009449          371 IKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLR--IVGSIDQKIGDCLNAKYLEFAPDRS  448 (534)
Q Consensus       371 iRlP~~~~~~i~ki~ka~~~L~~elGr~Pt~eEIA~~lgis~~kv~~~l~~~~--~~~SLD~~i~~~~~~~l~e~i~d~~  448 (534)
                       +.|.++.....++.++...+.+.+|+.|+.+++|+.+|++++++..++....  ...|+|.++.++++.. .+. +++ 
T Consensus        89 -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~sl~~~~~~~~~~~-~~~-~~~-  164 (239)
T 1rp3_A           89 -FGSRQVREKERRIKEVVEKLKEKLGREPTDEEVAKELGISTEELFKTLDKINFSYILSLEEVFRDFARDY-SEL-IPS-  164 (239)
T ss_dssp             -TTCHHHHHHHHHHHHHHHHHHHHHSSCCCHHHHHHHHTSCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-TTT-GGG-
T ss_pred             -ccchHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHHhccCCCccccccccCCCccc-ccc-cCC-
Confidence             5788888899999999999999999999999999999999999998876553  4467777665443333 444 333 


Q ss_pred             CCChHHHHHHHHHHHHHHHHHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHhhh
Q 009449          449 VKSPKEIVMRQHMKKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDSETC  525 (534)
Q Consensus       449 ~~spee~v~~~el~e~L~~~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~~l~~  525 (534)
                      ..+|++.+...+....|..+|..|||++|+||.++|    ++++|++|||+.||||.++|++++++|+++||+.+..
T Consensus       165 ~~~~~~~~~~~e~~~~l~~~l~~L~~~~r~vl~l~~----~~g~s~~EIA~~lgis~~~V~~~~~ra~~~Lr~~l~~  237 (239)
T 1rp3_A          165 STNVEEEVIKRELTEKVKEAVSKLPEREKLVIQLIF----YEELPAKEVAKILETSVSRVSQLKAKALERLREMLSN  237 (239)
T ss_dssp             SCHHHHHHHHHHHHHHHHHHHTTSCHHHHHHHHHHH----TSCCCHHHHHHHTTSCHHHHHHHHHHHHHHHHHHHHC
T ss_pred             CCCHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHH----hcCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHhc
Confidence            357888888888899999999999999999999999    8999999999999999999999999999999998753

>1l0o_C Sigma factor; bergerat fold, helix-turn-helix, protein binding; HET: ADP; 2.90A {Geobacillus stearothermophilus} SCOP: a.4.13.2

Probab=99.97  E-value=1.4e-31  Score=258.23  Aligned_cols=227  Identities=26%  Similarity=0.383  Sum_probs=53.5

Q ss_pred             CHHHHHHHHHhc-HHHHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCchhhHHHHHHHHHH
Q 009449          282 SERVLKQHLAFG-WYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSI  360 (534)
Q Consensus       282 d~~~L~~~l~~G-~~A~e~LI~~nlrLV~sIArrY~~~g~~~eDLiQEG~lgL~rA~ekFDp~kG~rFSTYA~~wIR~aI  360 (534)
                      +...|...++.| ..|++.|+..|.++|+++|++|.++..+++|++|||++++|+++++|||.+|..|.||+++|+++.+
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            345677777777 6799999999999999999999999999999999999999999999999988899999999999999


Q ss_pred             HHHHHHhccccccccchHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHHhhhhcccccccccchh--h
Q 009449          361 SKMVARHARGIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLN--A  438 (534)
Q Consensus       361 ~~~lr~~sr~iRlP~~~~~~i~ki~ka~~~L~~elGr~Pt~eEIA~~lgis~~kv~~~l~~~~~~~SLD~~i~~~~~--~  438 (534)
                      .++++++. .+++|.++.....+++++...+.+..|+.|+.++++..+|++.+.+...+.....+.|++.++.++++  .
T Consensus        94 ~d~~r~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~~~~~~~  172 (243)
T 1l0o_C           94 QRFLRDDG-TVKVSRSLKEMGNKIRKAKDELSKTRGRAPTVTEIADHLGISPEDVVLAQEAVRLPTSIHETVYENDGDPI  172 (243)
T ss_dssp             ------CC-CCTTHHHHHHHHHHHHHHHHHHHHHHTSCCBHHHHHHHHTSCHHHHHHHHHHHHC----------------
T ss_pred             HHHHHhcC-CccCcHHHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHHCCCHHHHHHHHHHhccccCccccccccCCccc
Confidence            99999986 78999999999999999999999999999999999999999999999888777778888877654322  2


Q ss_pred             hhhhccCCCCCCChHHHHHHHHHHHHHHHHHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHH
Q 009449          439 KYLEFAPDRSVKSPKEIVMRQHMKKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTK  518 (534)
Q Consensus       439 ~l~e~i~d~~~~spee~v~~~el~e~L~~~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~K  518 (534)
                      ++.+.+       |++.+...+....|..+|..||+++|+||.|+|    ++++|++|||+.||||.++|++++++|+++
T Consensus       173 ~~~~~~-------~~~~~~~~~~~~~l~~~l~~L~~~~r~vl~l~~----~~g~s~~EIA~~lgis~~tV~~~~~ra~~~  241 (243)
T 1l0o_C          173 TLLDQI-------ADADEASWFDKIALKKAIEELDERERLIVYLRY----YKDQTQSEVASRLGISQVQMSRLEKKILQH  241 (243)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             chhhcc-------CcchhHHHHHHHHHHHHHHhCCHHHHHHHHHHH----hcCCCHHHHHHHHCcCHHHHHHHHHHHHHH
Confidence            223322       233344445667889999999999999999999    799999999999999999999999999999


Q ss_pred             HH
Q 009449          519 LR  520 (534)
Q Consensus       519 LR  520 (534)
                      ||
T Consensus       242 Lr  243 (243)
T 1l0o_C          242 IK  243 (243)
T ss_dssp             --
T ss_pred             cC
Confidence            97

>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=99.90  E-value=1.8e-23  Score=196.32  Aligned_cols=179  Identities=16%  Similarity=0.221  Sum_probs=139.1

Q ss_pred             HHHHHHHHHhc-HHHHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCchhhHHHHHHHHHHH
Q 009449          283 ERVLKQHLAFG-WYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSIS  361 (534)
Q Consensus       283 ~~~L~~~l~~G-~~A~e~LI~~nlrLV~sIArrY~~~g~~~eDLiQEG~lgL~rA~ekFDp~kG~rFSTYA~~wIR~aI~  361 (534)
                      +..|...++.| ..|++.|+..|.+.|+++|++|.+ ..+++|++||+++++|+++++|++..  .|.+|++.+++|.+.
T Consensus        10 ~~~l~~~~~~gd~~a~~~l~~~~~~~l~~~~~~~~~-~~~aeDl~Qe~~l~~~~~~~~~~~~~--~~~~~l~~i~~n~~~   86 (194)
T 1or7_A           10 DQVLVERVQKGDQKAFNLLVVRYQHKVASLVSRYVP-SGDVPDVVQEAFIKAYRALDSFRGDS--AFYTWLYRIAVNTAK   86 (194)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHHHHHHHHHHTTTSC-GGGHHHHHHHHHHHHHHHGGGCCSSS--CHHHHHHHHHHHHHH
T ss_pred             hHHHHHHHHccCHHHHHHHHHHHHHHHHHHHHHHcC-HHhHHHHHHHHHHHHHHhHHhcCCcc--chHHHHHHHHHHHHH
Confidence            56677888888 789999999999999999999999 99999999999999999999999875  599999999999999


Q ss_pred             HHHHHhccccccccchHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHHhhhhcccccccccchhhhhh
Q 009449          362 KMVARHARGIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNAKYL  441 (534)
Q Consensus       362 ~~lr~~sr~iRlP~~~~~~i~ki~ka~~~L~~elGr~Pt~eEIA~~lgis~~kv~~~l~~~~~~~SLD~~i~~~~~~~l~  441 (534)
                      +++++..+.....                            ++..           .     ....++.+          
T Consensus        87 d~~R~~~~~~~~~----------------------------~~~~-----------~-----~~~~~~~~----------  112 (194)
T 1or7_A           87 NYLVAQGRRPPSS----------------------------DVDA-----------I-----EAENFESG----------  112 (194)
T ss_dssp             HHHHHHTTCCTHH----------------------------HHHH-----------H-----HHHSCCSS----------
T ss_pred             HHHHHHhccCccc----------------------------cccc-----------c-----cccccccc----------
Confidence            9999875422110                            0000           0     00011100          


Q ss_pred             hccCCCCCCChHHHHHHHHHHHHHHHHHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHh
Q 009449          442 EFAPDRSVKSPKEIVMRQHMKKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRD  521 (534)
Q Consensus       442 e~i~d~~~~spee~v~~~el~e~L~~~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~  521 (534)
                      +.+++  ..+|++.+...+....|..+|..||+++|+||.|+|    .+++|++|||+.||+|..+|+++++||+++||+
T Consensus       113 ~~~~~--~~~~~~~~~~~e~~~~l~~~l~~L~~~~r~vl~l~~----~~g~s~~EIA~~lgis~~tV~~~l~ra~~~Lr~  186 (194)
T 1or7_A          113 GALKE--ISNPENLMLSEELRQIVFRTIESLPEDLRMAITLRE----LDGLSYEEIAAIMDCPVGTVRSRIFRAREAIDN  186 (194)
T ss_dssp             CC----------CEEEHHHHHHHHHHHHHHSCHHHHHHHHHHH----TTCCCHHHHHHHTTSCHHHHHHHHHHHHHHHHH
T ss_pred             ccccC--CCChHHHHHHHHHHHHHHHHHHhCCHHHHHHhHHHH----HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence            00111  123444444455667888999999999999999999    899999999999999999999999999999998


Q ss_pred             Hhh
Q 009449          522 SET  524 (534)
Q Consensus       522 ~l~  524 (534)
                      .+.
T Consensus       187 ~l~  189 (194)
T 1or7_A          187 KVQ  189 (194)
T ss_dssp             HHC
T ss_pred             HHH
Confidence            864

>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=99.88  E-value=3.4e-22  Score=181.49  Aligned_cols=155  Identities=17%  Similarity=0.207  Sum_probs=109.5

Q ss_pred             CCCHHHHHHHHHHHHHHhhhccCCcCCCchhhHHHHHHHHHHHHHHHHhccccccccchHHHHHHHHHHHHHHHHhcCCC
Q 009449          319 GIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIPCKLNREISKIQKARKALTNSHGKY  398 (534)
Q Consensus       319 g~~~eDLiQEG~lgL~rA~ekFDp~kG~rFSTYA~~wIR~aI~~~lr~~sr~iRlP~~~~~~i~ki~ka~~~L~~elGr~  398 (534)
                      |.+++|++|||++++|+++.+||+.+ .+|.||+++++++.+.++++++.+..+.|..                      
T Consensus         1 g~daeDl~Qe~~~~l~~~~~~~~~~~-~~f~~~l~~i~~n~~~d~~r~~~~~~~~~~~----------------------   57 (164)
T 3mzy_A            1 GAEKEDLVQEGILGLLKAIKFYDETK-SSFSSFAFLCIRREMISAIRKANTQKHMVLN----------------------   57 (164)
T ss_dssp             ----CTTHHHHHHHHHHHHHHCCTTT-SCHHHHHHHHHHHHHHHHHHHHHHCC---------------------------
T ss_pred             CCcHHHHHHHHHHHHHHHHHHhCccC-CChHHHhHHHHHHHHHHHHHHhhcccchhhH----------------------
Confidence            57899999999999999999999987 6999999999999999999987643333211                      


Q ss_pred             CCHHHHHHHcCCCHHHHHHHHHHhhhhcccccccccchhhhhh----hccCCCCCCChHHHHHHHHHHHHHHHHHh-hCC
Q 009449          399 PEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNAKYL----EFAPDRSVKSPKEIVMRQHMKKDVFRILE-SLD  473 (534)
Q Consensus       399 Pt~eEIA~~lgis~~kv~~~l~~~~~~~SLD~~i~~~~~~~l~----e~i~d~~~~spee~v~~~el~e~L~~~L~-~L~  473 (534)
                                               .+.+.+.+..++....+.    +.+. ....+|++.+...+....|..+|. .||
T Consensus        58 -------------------------~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~e~~~~l~~~l~~~L~  111 (164)
T 3mzy_A           58 -------------------------EALKTNAILEDSAYFDDEGHNINNYK-SSESNPEEAYLLKEEIEEFKKFSENNFS  111 (164)
T ss_dssp             ----------------------------------------------------------CHHHHHHHHHHHHHHHHHHHSC
T ss_pred             -------------------------HHhhhhhhhccCCCCCcccchhhhhc-ccCCCHHHHHHHHHHHHHHHHHHHhhCC
Confidence                                     011222222111111111    1111 122467888888888899999999 999


Q ss_pred             HHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHhhhhc
Q 009449          474 SRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDSETCRD  527 (534)
Q Consensus       474 ~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~~l~~~~  527 (534)
                      |++|+||. +|    .+|+|++|||+.||||.++|+++++||+++||+.+...+
T Consensus       112 ~~~r~v~~-~~----~~g~s~~EIA~~lgis~~tV~~~~~ra~~~Lr~~l~~~~  160 (164)
T 3mzy_A          112 KFEKEVLT-YL----IRGYSYREIATILSKNLKSIDNTIQRIRKKSEEWIKEEE  160 (164)
T ss_dssp             HHHHHHHH-HH----TTTCCHHHHHHHHTCCHHHHHHHHHHHHHHHHHHHHHHT
T ss_pred             HHHHHHHH-HH----HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHcC
Confidence            99999999 67    799999999999999999999999999999999887654

>2lfw_A PHYR sigma-like domain; signal transduction, response regulator, sigma factor mimicr sigma factor, general stress response, signaling protein; NMR {Sphingomonas SP}

Probab=99.74  E-value=4.9e-20  Score=169.78  Aligned_cols=143  Identities=13%  Similarity=0.103  Sum_probs=120.1

Q ss_pred             HHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCchhhHHHHHHHHHHHHHHHHhccccccccc
Q 009449          297 REELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIPCK  376 (534)
Q Consensus       297 ~e~LI~~nlrLV~sIArrY~~~g~~~eDLiQEG~lgL~rA~ekFDp~kG~rFSTYA~~wIR~aI~~~lr~~sr~iRlP~~  376 (534)
                      ++.|+..|.+.|+.+|.++.++..+++|++||+|+.+|++.++|++..  .|.+|++..++|.+.+++++...       
T Consensus         3 f~~l~~~~~~~l~~~~~~~~~~~~~AeDlvQe~fl~~~~~~~~~~~~~--~~~~wl~~ia~n~~~d~~R~~~~-------   73 (157)
T 2lfw_A            3 LGQQLAPHLPFLRRYGRALTGSQNQGDKYVRATLEAIVAAPDQFPRDV--DPRLGLYRMFQGIWASANADGEA-------   73 (157)
T ss_dssp             GGGGTGGGGGGGTTTGGGTTSCHHHHHHHHHHHHHTTTTCGGGCCCSS--CTTHHHHHHHHHHHHHHTTTTSC-------
T ss_pred             HHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhHHHcCCCC--cHHHHHHHHHHHHHHHHhhccCc-------
Confidence            567899999999999999999999999999999999999999999764  69999999999999999865310       


Q ss_pred             hHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHHhhhhcccccccccchhhhhhhccCCCCCCChHHHH
Q 009449          377 LNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNAKYLEFAPDRSVKSPKEIV  456 (534)
Q Consensus       377 ~~~~i~ki~ka~~~L~~elGr~Pt~eEIA~~lgis~~kv~~~l~~~~~~~SLD~~i~~~~~~~l~e~i~d~~~~spee~v  456 (534)
                                            +                             +.+             ++.         
T Consensus        74 ----------------------~-----------------------------~~~-------------~e~---------   80 (157)
T 2lfw_A           74 ----------------------Q-----------------------------TSQ-------------SDA---------   80 (157)
T ss_dssp             ----------------------C-----------------------------CCC-------------CSC---------
T ss_pred             ----------------------c-----------------------------cCC-------------cch---------
Confidence                                  0                             000             000         


Q ss_pred             HHHHHHHHHHHHHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHhhhhc
Q 009449          457 MRQHMKKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDSETCRD  527 (534)
Q Consensus       457 ~~~el~e~L~~~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~~l~~~~  527 (534)
                        .+....|..+|..||+++|+||.|+|    .+|+|++|||+.||||..+|++.+.||+++||+.+....
T Consensus        81 --~~~~~~l~~~l~~Lp~~~r~vl~L~~----~~g~s~~EIA~~lgis~~tV~~~l~rar~~Lr~~l~~~~  145 (157)
T 2lfw_A           81 --EGTEAVARARLARMTPLSRQALLLTA----MEGFSPEDAAYLIEVDTSEVETLVTEALAEIEKQTRALE  145 (157)
T ss_dssp             --SSSSSTTTTTTTTSCTTHHHHHTTTS----SSCCCHHHHHHTTTSCHHHHHHHHHHHHHHHHTTSSCCC
T ss_pred             --HHHHHHHHHHHHhCCHHHHHHHHHHH----HcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHhcc
Confidence              00112466788999999999999999    899999999999999999999999999999999876543

>1sig_A Sigma70, RNA polymerase primary sigma factor; RNA polymerase sigma factor, transcription regulation; 2.60A {Escherichia coli} SCOP: a.177.1.1

Probab=99.66  E-value=5.2e-16  Score=160.38  Aligned_cols=85  Identities=34%  Similarity=0.792  Sum_probs=79.1

Q ss_pred             HHHHHHHHhc-H---HHHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCchhhHHHHHHHHH
Q 009449          284 RVLKQHLAFG-W---YCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKS  359 (534)
Q Consensus       284 ~~L~~~l~~G-~---~A~e~LI~~nlrLV~sIArrY~~~g~~~eDLiQEG~lgL~rA~ekFDp~kG~rFSTYA~~wIR~a  359 (534)
                      ..|..+++.| .   .|++.||..|.++|+++|++|.+++.+++||+||||+|||+++++|||.+|++|+||++|||+|.
T Consensus       250 ~~l~~~~~~gd~~~~~A~~~L~~~~~~~v~~~a~~~~~~~~~aeDlvQe~~i~l~~a~~~f~~~~g~~f~twl~~iirn~  329 (339)
T 1sig_A          250 KDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQA  329 (339)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHTHHHHHHHHTTSTTSSSCHHHHHHHHHHHHHHHHHHCCGGGCCCHHHHHHHHHHHH
T ss_pred             HHHHHHHHhccccchhhhHHHHHHHHHHHHHHHHHHhcCCCCHhHHHHHHHHHHHHHHHHhCCccCCCHHHHHHHHHHHH
Confidence            4567777777 5   79999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHhc
Q 009449          360 ISKMVARHA  368 (534)
Q Consensus       360 I~~~lr~~s  368 (534)
                      |+++++++.
T Consensus       330 ~~~~lr~~~  338 (339)
T 1sig_A          330 ITRSIADQA  338 (339)
T ss_dssp             HHHHHHHC-
T ss_pred             HHHHHHHhc
Confidence            999999865

>3n0r_A Response regulator; sigma factor, receiver, two-component SI transduction, signaling protein; HET: MSE GOL; 1.25A {Caulobacter vibrioides} PDB: 3t0y_A

Probab=99.60  E-value=7.7e-16  Score=155.45  Aligned_cols=141  Identities=11%  Similarity=0.014  Sum_probs=119.4

Q ss_pred             HHHHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCchhhHHHHHHHHHHHHHHHHhcccccc
Q 009449          294 WYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKI  373 (534)
Q Consensus       294 ~~A~e~LI~~nlrLV~sIArrY~~~g~~~eDLiQEG~lgL~rA~ekFDp~kG~rFSTYA~~wIR~aI~~~lr~~sr~iRl  373 (534)
                      ..+|+.|+..|.+.++.+|.+|.++..+++|++||+|+.+|+...+|++.  ..|.+|++.+++|.+.++++....    
T Consensus        20 ~~~f~~l~~~~~~~l~~~a~~~~~~~~~AeD~vQe~fl~~~~~~~~~~~~--~~~~~wL~~ia~n~~~d~~r~~~~----   93 (286)
T 3n0r_A           20 EMHLLARLAPHLPYIRRYARALTGDQATGDHYVRVALEALAAGELVLDAN--LSPRVALYRVFHAIWLSSGAQLEV----   93 (286)
T ss_dssp             CCCHHHHHGGGHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHTTSSCCCSS--SCHHHHHHHHHHHHHSCTTC--------
T ss_pred             cCCHHHHHHHHHHHHHHHHHHHhCCHhhHHHHHHHHHHHHHhCchhcCCC--cChHHHHHHHHHHHHHhhcccccc----
Confidence            45899999999999999999999999999999999999999999999875  369999999999999887652100    


Q ss_pred             ccchHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHHhhhhcccccccccchhhhhhhccCCCCCCChH
Q 009449          374 PCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNAKYLEFAPDRSVKSPK  453 (534)
Q Consensus       374 P~~~~~~i~ki~ka~~~L~~elGr~Pt~eEIA~~lgis~~kv~~~l~~~~~~~SLD~~i~~~~~~~l~e~i~d~~~~spe  453 (534)
                                                                           ..      .         .+..     
T Consensus        94 -----------------------------------------------------~~------~---------~~~~-----  100 (286)
T 3n0r_A           94 -----------------------------------------------------GH------D---------QGLH-----  100 (286)
T ss_dssp             -----------------------------------------------------CC------C---------CCCC-----
T ss_pred             -----------------------------------------------------CC------C---------cccc-----
Confidence                                                                 00      0         0000     


Q ss_pred             HHHHHHHHHHHHHHHHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHhh
Q 009449          454 EIVMRQHMKKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDSET  524 (534)
Q Consensus       454 e~v~~~el~e~L~~~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~~l~  524 (534)
                             ....|..+|+.||+++|+||.|+|    .+++|++|||+.+|++..+|+....+|+++|+..+.
T Consensus       101 -------~~~~l~~al~~Lp~~~R~v~~L~~----~eg~s~~EIA~~lgis~~tVks~l~rA~~~Lr~~l~  160 (286)
T 3n0r_A          101 -------AGDDAAQRLMRIAPRSRQAFLLTA----LEGFTPTEAAQILDCDFGEVERLIGDAQAEIDAELA  160 (286)
T ss_dssp             -------TTSHHHHHHHHHSCHHHHHHHHHH----TTCCCHHHHHHHHTCCHHHHHHHHHHHHHHHHTSCC
T ss_pred             -------hHHHHHHHHHhCCHHHeeEEEEEe----eCCCCHHHHHHHhCcCHHHHHHHHHHHHhhhhccCC
Confidence                   012478899999999999999999    999999999999999999999999999999997654

>3t72_q RNA polymerase sigma factor RPOD, DNA-directed RN polymerase subunit beta; winged-helix motif, transcription activation, DNA-binding; 4.33A {Escherichia coli} PDB: 1tlh_B

Probab=99.53  E-value=2.2e-14  Score=123.67  Aligned_cols=80  Identities=31%  Similarity=0.516  Sum_probs=74.7

Q ss_pred             HHHHHHHHHHHHHHHHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHhhhhcchhhhc
Q 009449          454 EIVMRQHMKKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDSETCRDLSHFLV  533 (534)
Q Consensus       454 e~v~~~el~e~L~~~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~~l~~~~L~~yl~  533 (534)
                      +.+...++...|..+|+.|||+||+||.|+||++|.+++|++|||+.||||++||++++.+|+++||..+....|++|+.
T Consensus         2 ~~~~~~el~~~l~~aL~~Lp~reR~Vi~Lry~l~~~e~~s~~EIA~~lgiS~~tVr~~~~rAlkkLR~~~~~~~l~~~~~   81 (99)
T 3t72_q            2 DSATTESLRAATHDVLAGLTAREAKVLRMRFGIDMNTDYTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRSGSS   81 (99)
T ss_pred             HHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            34567788889999999999999999999999998899999999999999999999999999999999999999999974

>2p7v_B Sigma-70, RNA polymerase sigma factor RPOD; RSD, regulator of sigma 70, sigma 70 domain 4, transcription, regulation, helix-turn-helix; 2.60A {Escherichia coli} SCOP: a.4.13.2

Probab=99.32  E-value=1e-12  Score=104.61  Aligned_cols=66  Identities=41%  Similarity=0.677  Sum_probs=62.3

Q ss_pred             HHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHhhhhcchhhhc
Q 009449          468 ILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDSETCRDLSHFLV  533 (534)
Q Consensus       468 ~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~~l~~~~L~~yl~  533 (534)
                      +|+.|||+|++||.++||+++++++|++|||+.||+|+++|++++.+|+++||..+....+..|++
T Consensus         2 ~l~~L~~~er~il~l~~~l~~~~g~s~~eIA~~lgis~~tV~~~~~ra~~kLr~~~~~~~~~~~~~   67 (68)
T 2p7v_B            2 VLAGLTAREAKVLRMRFGIDMNTDYTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRSFLD   67 (68)
T ss_dssp             CSCCCCHHHHHHHHHHTTTTSSSCCCHHHHHHHHTCCHHHHHHHHHHHHHGGGSCCGGGGGSCTTC
T ss_pred             HHHcCCHHHHHHHHHHHccCCCCCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence            467899999999999999998899999999999999999999999999999999999999988874

>3hug_A RNA polymerase sigma factor; ECF sigma factor, zinc binding anti-sigma factor, oxidative transcription regulation; 2.35A {Mycobacterium tuberculosis}

Probab=99.32  E-value=9.5e-12  Score=104.72  Aligned_cols=75  Identities=17%  Similarity=0.099  Sum_probs=70.8

Q ss_pred             CCChHHHHHHHHHHHHHHHHHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHhhhhc
Q 009449          449 VKSPKEIVMRQHMKKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDSETCRD  527 (534)
Q Consensus       449 ~~spee~v~~~el~e~L~~~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~~l~~~~  527 (534)
                      ..+|++.+...+....|..+|..||+++|+||.|+|    .+++|++|||+.||||..+|++++++|+++||..+...+
T Consensus        15 ~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~vl~l~~----~~g~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~l~~~~   89 (92)
T 3hug_A           15 EQSTPDEVNAALDRLLIADALAQLSAEHRAVIQRSY----YRGWSTAQIATDLGIAEGTVKSRLHYAVRALRLTLQELG   89 (92)
T ss_dssp             CCCHHHHHHHHHHHHHHHHHHHTSCHHHHHHHHHHH----TSCCCHHHHHHHHTSCHHHHHHHHHHHHHHHHHHHHHHT
T ss_pred             CCCchHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHH----HcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHhC
Confidence            358999999999999999999999999999999999    899999999999999999999999999999999987654

>1tty_A Sigma-A, RNA polymerase sigma factor RPOD; helix-turn-helix, transcription; NMR {Thermotoga maritima} SCOP: a.4.13.2

Probab=99.31  E-value=2.9e-12  Score=107.05  Aligned_cols=70  Identities=43%  Similarity=0.754  Sum_probs=65.0

Q ss_pred             HHHHHHHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHhhhhcchhhh
Q 009449          463 KDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDSETCRDLSHFL  532 (534)
Q Consensus       463 e~L~~~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~~l~~~~L~~yl  532 (534)
                      ..|..+|+.|||++|+||.++|+|++.+++|++|||+.||+|+++|++++.+|+++||..+....+..|+
T Consensus        10 ~~l~~~l~~L~~~er~vl~l~~~l~~~~~~s~~EIA~~lgis~~tV~~~~~ra~~kLr~~l~~~~~~~~~   79 (87)
T 1tty_A           10 EELEKVLKTLSPREAMVLRMRYGLLDGKPKTLEEVGQYFNVTRERIRQIEVKALRKLRHPSRSKYLKSLL   79 (87)
T ss_dssp             SHHHHHHTTSCHHHHHHHHHHHTTTTSSCCCHHHHHHHHTCCHHHHHHHHHHHHHHHBTTBSSHHHHHHH
T ss_pred             HHHHHHHHhCCHHHHHHHHHHHccCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHhHHHHHH
Confidence            3678899999999999999999888779999999999999999999999999999999999888887775

>1ku3_A Sigma factor SIGA; helix-turn-helix, transcription; 1.80A {Thermus aquaticus} SCOP: a.4.13.2 PDB: 1ku7_A 1rio_H 3n97_A*

Probab=99.30  E-value=1.1e-12  Score=105.83  Aligned_cols=70  Identities=41%  Similarity=0.650  Sum_probs=56.0

Q ss_pred             HHHHHHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH-hHhhhhcchhhhc
Q 009449          464 DVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLR-DSETCRDLSHFLV  533 (534)
Q Consensus       464 ~L~~~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR-~~l~~~~L~~yl~  533 (534)
                      .|..+|+.|||+|++||.++|+|+|.+++|++|||+.||+|+++|++++.+|+++|| ..+....+++|+.
T Consensus         3 ~l~~~l~~L~~~er~il~l~~~l~~~~~~s~~eIA~~l~is~~tV~~~~~ra~~kLr~~~~~~~~~~~~~~   73 (73)
T 1ku3_A            3 ELEKALSKLSEREAMVLKMRKGLIDGREHTLEEVGAYFGVTRERIRQIENKALRKLKYHESRTRKLRDFLE   73 (73)
T ss_dssp             CCSSSTTTSCHHHHHHHHHHHTTTTSSCCCHHHHHHHHTCCHHHHHHHHHHHHHHHHHTTC----------
T ss_pred             HHHHHHHhCCHHHHHHHHHHHhcccCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhhHhhHHHHHHhhC
Confidence            345678899999999999999888779999999999999999999999999999999 8888888888863

>2o7g_A Probable RNA polymerase sigma-C factor; sigma factor, transcription regulation, -10 element recognit domain, transcription; 2.70A {Mycobacterium tuberculosis}

Probab=99.02  E-value=6.5e-10  Score=95.83  Aligned_cols=82  Identities=18%  Similarity=0.100  Sum_probs=71.6

Q ss_pred             HHHHHHHhc-HHHHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCchhhHHHHHHHHHHHHH
Q 009449          285 VLKQHLAFG-WYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKM  363 (534)
Q Consensus       285 ~L~~~l~~G-~~A~e~LI~~nlrLV~sIArrY~~~g~~~eDLiQEG~lgL~rA~ekFDp~kG~rFSTYA~~wIR~aI~~~  363 (534)
                      .|...+..| ..|++.|+..|.+.|+.+|.++ ++..+++|++||+++.+|+.+.+|++.  ..|.+|++..++|.+.++
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            566677777 7899999999999999999999 888999999999999999999999974  379999999999999999


Q ss_pred             HHHhcc
Q 009449          364 VARHAR  369 (534)
Q Consensus       364 lr~~sr  369 (534)
                      +++..+
T Consensus        90 ~R~~~~   95 (112)
T 2o7g_A           90 IRHVRS   95 (112)
T ss_dssp             TC----
T ss_pred             HHHhhc
Confidence            987654

>2o8x_A Probable RNA polymerase sigma-C factor; promoter recognition, transcription regulation, helix-turn-H motif, transcription; 3.00A {Mycobacterium tuberculosis}

Probab=99.00  E-value=6.7e-10  Score=87.64  Aligned_cols=65  Identities=18%  Similarity=0.152  Sum_probs=54.4

Q ss_pred             HHHHHHHHHHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHhhhhcc
Q 009449          460 HMKKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDSETCRDL  528 (534)
Q Consensus       460 el~e~L~~~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~~l~~~~L  528 (534)
                      +....+..+++.|||++++||.++|    .+++|++|||+.||+|+.+|+++.++|+++||..+....+
T Consensus         4 e~~~~l~~~l~~L~~~~r~il~l~~----~~g~s~~eIA~~lgis~~tv~~~~~ra~~~l~~~l~~~~~   68 (70)
T 2o8x_A            4 EDLVEVTTMIADLTTDQREALLLTQ----LLGLSYADAAAVCGCPVGTIRSRVARARDALLADAEPDDL   68 (70)
T ss_dssp             HHHHHHHTTTTSSCHHHHHHHHHHH----TSCCCHHHHHHHHTSCHHHHHHHHHHHHHHHHC-------
T ss_pred             HHHHHHHHHHHhCCHHHHHHHHHHH----HcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHhhcccC
Confidence            3445788899999999999999999    8999999999999999999999999999999998876543

>1h3l_A RNA polymerase sigma factor; transcription, DNA-binding, transcription regulation; 2.37A {Streptomyces coelicolor A3} SCOP: a.177.1.1

Probab=98.91  E-value=1.1e-09  Score=90.26  Aligned_cols=73  Identities=8%  Similarity=-0.039  Sum_probs=66.4

Q ss_pred             HHHHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCchhhHHHHHHHHHHHHHHHHhc
Q 009449          294 WYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHA  368 (534)
Q Consensus       294 ~~A~e~LI~~nlrLV~sIArrY~~~g~~~eDLiQEG~lgL~rA~ekFDp~kG~rFSTYA~~wIR~aI~~~lr~~s  368 (534)
                      ..|++.|+..|.+.|+.+|.++.++..+++|++||+++.+|+...+|++.  ..|.+|++.+++|.+.++++++.
T Consensus        11 ~~af~~l~~~~~~~l~~~~~~~~~~~~~aeD~vQe~fl~~~~~~~~~~~~--~~~~~wl~~i~~n~~~d~~R~~~   83 (87)
T 1h3l_A           11 SARFERDALEFLDQMYSAALRMTRNPADAEDLVQETYAKAYASFHQFREG--TNLKAWLYRILTNTFINSYRKKQ   83 (87)
T ss_dssp             HHHHHHHHHHTHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHGGGCCSS--SCHHHHHHHHHHHHHHHTCC---
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHhcCCC--ccHHHHHHHHHHHHHHHHHHHhc
Confidence            67999999999999999999999999999999999999999999999875  37999999999999999987654

>1xsv_A Hypothetical UPF0122 protein SAV1236; helix-turn-helix, putative DNA-binding protein, signal recognition particle, unknown function; 1.70A {Staphylococcus aureus subsp} SCOP: a.4.13.3

Probab=98.85  E-value=8.1e-09  Score=90.62  Aligned_cols=69  Identities=23%  Similarity=0.300  Sum_probs=61.6

Q ss_pred             HHHHHHHHHHHHHH-hhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHhhhhcc
Q 009449          456 VMRQHMKKDVFRIL-ESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDSETCRDL  528 (534)
Q Consensus       456 v~~~el~e~L~~~L-~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~~l~~~~L  528 (534)
                      +........+..++ ..|||++++||.++|    .+++|++|||+.||+|..+|+.+++||+++||..+...++
T Consensus         9 ~e~~~~~~~l~~~l~~~L~~~~r~vl~l~~----~~g~s~~EIA~~lgiS~~tV~~~l~ra~~kLr~~l~~~~~   78 (113)
T 1xsv_A            9 LVKTLRMNYLFDFYQSLLTNKQRNYLELFY----LEDYSLSEIADTFNVSRQAVYDNIRRTGDLVEDYEKKLEL   78 (113)
T ss_dssp             HHHHHHHHHHHHHHGGGSCHHHHHHHHHHH----TSCCCHHHHHHHTTCCHHHHHHHHHHHHHHHHHHHHHHCH
T ss_pred             HHHHHHHHHHHHHHHhcCCHHHHHHHHHHH----HcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHHhH
Confidence            34445566788899 999999999999999    8999999999999999999999999999999998876554

>3clo_A Transcriptional regulator; NP_811094.1, bacterial regulatory proteins, LUXR family, structural genomics; 2.04A {Bacteroides thetaiotaomicron vpi-5482}

Probab=98.75  E-value=8.5e-12  Score=123.78  Aligned_cols=155  Identities=10%  Similarity=-0.001  Sum_probs=113.3

Q ss_pred             HHHHHHHhc-HHHHHHHHHHhHHHHHHHHHHhhCCCCCHHHHH----HHHHHHHHHhhhccCCcCCCchhhHHHHHHHHH
Q 009449          285 VLKQHLAFG-WYCREELIKSTRPLVLFLARNYRGLGIPFSDLL----QAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKS  359 (534)
Q Consensus       285 ~L~~~l~~G-~~A~e~LI~~nlrLV~sIArrY~~~g~~~eDLi----QEG~lgL~rA~ekFDp~kG~rFSTYA~~wIR~a  359 (534)
                      .|..++..+ ..+++.+...+.++++.+............|+.    ||.++.+|+....|++..  .|.+|++..+++.
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            455555555 568999999999999999988877777888886    999999999999998754  6888888777665


Q ss_pred             HHHHHHHhccccccccchHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHHhhhhcccccccccchhhh
Q 009449          360 ISKMVARHARGIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNAK  439 (534)
Q Consensus       360 I~~~lr~~sr~iRlP~~~~~~i~ki~ka~~~L~~elGr~Pt~eEIA~~lgis~~kv~~~l~~~~~~~SLD~~i~~~~~~~  439 (534)
                      +.+..+...    +                                                       ...+...... 
T Consensus       164 ~~d~~r~~~----~-------------------------------------------------------~~~~~~~~~~-  183 (258)
T 3clo_A          164 SADQRPEQG----I-------------------------------------------------------YATITQMERG-  183 (258)
T ss_dssp             CSCCCCCSS----C-------------------------------------------------------CCEEEETTTT-
T ss_pred             HcchhhhhH----H-------------------------------------------------------HHHHHhhccc-
Confidence            554421100    0                                                       0000000000 


Q ss_pred             hhhccCCCCCCChHHHHHHHHHHHHHHHHHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Q 009449          440 YLEFAPDRSVKSPKEIVMRQHMKKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKL  519 (534)
Q Consensus       440 l~e~i~d~~~~spee~v~~~el~e~L~~~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KL  519 (534)
                        +...     .+           .+..++..||++||+||.|++     +|+|.+|||+.||+|..||+.+++||++||
T Consensus       184 --~~~~-----~~-----------~~~~~~~~L~~~erevl~L~~-----~G~s~~EIA~~L~iS~~TVk~~l~ra~~kL  240 (258)
T 3clo_A          184 --EVET-----LS-----------LSEEHRNILSEREKEILRCIR-----KGLSSKEIAATLYISVNTVNRHRQNILEKL  240 (258)
T ss_dssp             --EEEE-----CC-----------CHHHHTTSSCHHHHHHHHHHH-----TTCCHHHHHHHHTCCHHHHHHHHHHHHHHT
T ss_pred             --cccc-----ch-----------hhHHHHccCCHHHHHHHHHHH-----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHH
Confidence              0000     00           134567899999999999976     899999999999999999999999999999


Q ss_pred             HhHhh
Q 009449          520 RDSET  524 (534)
Q Consensus       520 R~~l~  524 (534)
                      |....
T Consensus       241 ~~~~~  245 (258)
T 3clo_A          241 SVGNS  245 (258)
T ss_dssp             TCSSH
T ss_pred             cCCCH
Confidence            97544

>1s7o_A Hypothetical UPF0122 protein SPY1201/SPYM3_0842/SPS1042/SPYM18_1152; putative DNA binding protein, structural genomics; 2.31A {Streptococcus pyogenes serotype M3} SCOP: a.4.13.3

Probab=98.68  E-value=4.8e-08  Score=85.78  Aligned_cols=63  Identities=22%  Similarity=0.252  Sum_probs=57.3

Q ss_pred             HHHHHHHH-hhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHhhhhcc
Q 009449          462 KKDVFRIL-ESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDSETCRDL  528 (534)
Q Consensus       462 ~e~L~~~L-~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~~l~~~~L  528 (534)
                      ...+..++ ..|||++++|+.++|    .+|+|++|||+.+|+|+.+|+.++++|+++||..+...++
T Consensus        12 ~~~l~~~l~~~L~~~~r~vl~l~y----~~g~s~~EIA~~lgiS~~tV~~~l~ra~~kLr~~l~~~~~   75 (113)
T 1s7o_A           12 MNALFEFYAALLTDKQMNYIELYY----ADDYSLAEIADEFGVSRQAVYDNIKRTEKILETYEMKLHM   75 (113)
T ss_dssp             HHHHHHHHGGGSCHHHHHHHHHHH----HTCCCHHHHHHHHTCCHHHHHHHHHHHHHHHHHHHHHHCH
T ss_pred             HHHHHHHHHhcCCHHHHHHHHHHH----HcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHhhH
Confidence            44677788 899999999999999    8999999999999999999999999999999998876554

>2rnj_A Response regulator protein VRAR; HTH LUXR-type domain, DNA binding domain, activator, antibiotic resistance, cytoplasm, DNA-binding; NMR {Staphylococcus aureus}

Probab=98.57  E-value=2.4e-08  Score=83.63  Aligned_cols=63  Identities=22%  Similarity=0.257  Sum_probs=49.0

Q ss_pred             HHHHHHHHHHHHHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHhh
Q 009449          457 MRQHMKKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDSET  524 (534)
Q Consensus       457 ~~~el~e~L~~~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~~l~  524 (534)
                      ........+..++..|+++|++||.+++     +|+|.+|||+.||||..||+.++.+|++||+....
T Consensus        15 ~~~~~~~~l~~~l~~Lt~~e~~vl~l~~-----~g~s~~eIA~~l~is~~tV~~~l~r~~~kL~~~~~   77 (91)
T 2rnj_A           15 PRGSHMKKRAELYEMLTEREMEILLLIA-----KGYSNQEIASASHITIKTVKTHVSNILSKLEVQDR   77 (91)
T ss_dssp             ----------CTGGGCCSHHHHHHHHHH-----TTCCTTHHHHHHTCCHHHHHHHHHHHHHHTTCCSS
T ss_pred             CcHHHHHHHHHHHhcCCHHHHHHHHHHH-----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHCCCCH
Confidence            3334455788899999999999999954     89999999999999999999999999999986543

>1x3u_A Transcriptional regulatory protein FIXJ; helix-turn-helix; NMR {Sinorhizobium meliloti}

Probab=98.50  E-value=1.5e-07  Score=76.02  Aligned_cols=57  Identities=23%  Similarity=0.248  Sum_probs=51.3

Q ss_pred             HHHHHHHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHhh
Q 009449          463 KDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDSET  524 (534)
Q Consensus       463 e~L~~~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~~l~  524 (534)
                      +.+..++..||++|++|+.+ |    .+++|.+|||+.||+|..+|+++..++++||+....
T Consensus         8 ~~l~~~l~~L~~~e~~vl~l-~----~~g~s~~eIA~~l~is~~tV~~~~~r~~~kl~~~~~   64 (79)
T 1x3u_A            8 NDIRARLQTLSERERQVLSA-V----VAGLPNKSIAYDLDISPRTVEVHRANVMAKMKAKSL   64 (79)
T ss_dssp             HHHHHHHHHHCHHHHHHHHH-H----TTTCCHHHHHHHTTSCHHHHHHHHHHHHHHTTCCSH
T ss_pred             HHHHHHHHhCCHHHHHHHHH-H----HcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHcCCCH
Confidence            35778899999999999999 5    489999999999999999999999999999996543

>3c57_A Two component transcriptional regulatory protein; response regulator, two-component regulatory system, DNA-BIN protein; 1.70A {Mycobacterium tuberculosis} PDB: 1zlk_A 1zlj_A

Probab=98.50  E-value=1.4e-07  Score=79.83  Aligned_cols=60  Identities=15%  Similarity=0.180  Sum_probs=46.2

Q ss_pred             HHHHHHHHHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHhhh
Q 009449          461 MKKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDSETC  525 (534)
Q Consensus       461 l~e~L~~~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~~l~~  525 (534)
                      ....|..++..|+++|++||.+++     +|+|++|||+.||+|..||+.++.++++||+.....
T Consensus        17 ~~~~l~~~l~~Lt~~e~~vl~l~~-----~g~s~~eIA~~l~is~~tV~~~l~r~~~kL~~~~~~   76 (95)
T 3c57_A           17 RGSHMQDPLSGLTDQERTLLGLLS-----EGLTNKQIADRMFLAEKTVKNYVSRLLAKLGMERRT   76 (95)
T ss_dssp             ----------CCCHHHHHHHHHHH-----TTCCHHHHHHHHTCCHHHHHHHHHHHHHHHTCCCCC
T ss_pred             HHHHHHHHHhcCCHHHHHHHHHHH-----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHcCCCHH
Confidence            344678899999999999999965     899999999999999999999999999999975443

>1jhg_A Trp operon repressor; complex (regulatory protein-peptide), DNA-binding regulatory complex (regulatory protein-peptide) complex; HET: TRP; 1.30A {Escherichia coli} SCOP: a.4.12.1 PDB: 1co0_A* 1mi7_R 1p6z_R 1wrp_R* 1zt9_A* 2oz9_R* 3ssw_R 3wrp_A 1rcs_A* 1wrs_R* 1wrt_R 2xdi_A 3ssx_R* 1trr_A* 1tro_A*

Probab=98.43  E-value=1.5e-07  Score=81.22  Aligned_cols=68  Identities=13%  Similarity=0.059  Sum_probs=56.0

Q ss_pred             HHHHHHHHHHHHHH-hhCCHHHHHHHhhHhcCCC---CCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHhh
Q 009449          456 VMRQHMKKDVFRIL-ESLDSRERQVLVLRYGLND---HRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDSET  524 (534)
Q Consensus       456 v~~~el~e~L~~~L-~~L~~rEReVL~LryGL~d---~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~~l~  524 (534)
                      +......+.+...+ ..|+|+|+++|.+||||.+   ..++|+.|||+.+|+|+++|+.+ .|++++|...+.
T Consensus        19 i~~~~~~~~l~~~l~~lLT~~Er~~l~~R~~l~~~L~~ge~TQREIA~~lGiS~stISRi-~r~L~~l~~~~k   90 (101)
T 1jhg_A           19 LKNAYQNDLHLPLLNLMLTPDEREALGTRVRIIEELLRGEMSQRELKNELGAGIATITRG-SNSLKAAPVELR   90 (101)
T ss_dssp             HHHHHHTTCHHHHHHHHSCHHHHHHHHHHHHHHHHHHHCCSCHHHHHHHHCCCHHHHHHH-HHHHHHSCHHHH
T ss_pred             HHhcCCHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHcCCcCHHHHHHHHCCChhhhhHH-HHHHHHccHHHH
Confidence            33334445566777 5799999999999999974   44699999999999999999999 899999887654

>1je8_A Nitrate/nitrite response regulator protein NARL; protein-DNA complex, two-component response regulator, helix-turn-helix, DNA bending; 2.12A {Escherichia coli} SCOP: a.4.6.2 PDB: 1zg1_A 1zg5_A

Probab=98.39  E-value=1.8e-07  Score=77.05  Aligned_cols=57  Identities=18%  Similarity=0.244  Sum_probs=49.3

Q ss_pred             HHHHHHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHhhh
Q 009449          464 DVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDSETC  525 (534)
Q Consensus       464 ~L~~~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~~l~~  525 (534)
                      .+..++..|+++|++||.+ |    .+|+|.+|||+.||||..+|+.++.+|++||+.....
T Consensus        14 ~~~~~~~~Lt~~e~~vl~l-~----~~g~s~~eIA~~l~is~~tV~~~l~r~~~kL~~~~~~   70 (82)
T 1je8_A           14 TTERDVNQLTPRERDILKL-I----AQGLPNKMIARRLDITESTVKVHVKHMLKKMKLKSRV   70 (82)
T ss_dssp             ---CCGGGSCHHHHHHHHH-H----TTTCCHHHHHHHHTSCHHHHHHHHHHHHHHTTCSSHH
T ss_pred             HHHHHHccCCHHHHHHHHH-H----HcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHcCCCHH
Confidence            4567789999999999999 4    4899999999999999999999999999999876543

>1fse_A GERE; helix-turn-helix DNA-binding protein transcriptional regulat transcription; 2.05A {Bacillus subtilis} SCOP: a.4.6.2

Probab=98.24  E-value=7.9e-07  Score=70.51  Aligned_cols=56  Identities=29%  Similarity=0.334  Sum_probs=47.3

Q ss_pred             HHHHHHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHhh
Q 009449          464 DVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDSET  524 (534)
Q Consensus       464 ~L~~~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~~l~  524 (534)
                      .....+..|+++|++|+.+ |    .+++|.+|||+.||+|+.+|+++..++++||+....
T Consensus         4 ~~~~~~~~L~~~e~~il~~-~----~~g~s~~eIA~~l~is~~tV~~~~~~~~~kl~~~~~   59 (74)
T 1fse_A            4 KEFQSKPLLTKREREVFEL-L----VQDKTTKEIASELFISEKTVRNHISNAMQKLGVKGR   59 (74)
T ss_dssp             ----CCCCCCHHHHHHHHH-H----TTTCCHHHHHHHHTSCHHHHHHHHHHHHHHHTCSSH
T ss_pred             CcCCCCCCCCHHHHHHHHH-H----HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCCCH
Confidence            3445678899999999999 5    478999999999999999999999999999986544

>3ulq_B Transcriptional regulatory protein COMA; tetratricopeptide repeat, response regulator helix-turn-HELX binding, 3-helix bundle; 2.30A {Bacillus subtilis} PDB: 2krf_A

Probab=98.08  E-value=4.6e-06  Score=70.11  Aligned_cols=51  Identities=24%  Similarity=0.189  Sum_probs=44.3

Q ss_pred             HHHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhH
Q 009449          467 RILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDS  522 (534)
Q Consensus       467 ~~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~~  522 (534)
                      .....|+++|++|+.+.+     +|+|.+|||+.||||..||+.++.++++||.-.
T Consensus        25 ~~~~~Lt~rE~~Vl~l~~-----~G~s~~eIA~~L~iS~~TV~~~~~~i~~Klgv~   75 (90)
T 3ulq_B           25 KEQDVLTPRECLILQEVE-----KGFTNQEIADALHLSKRSIEYSLTSIFNKLNVG   75 (90)
T ss_dssp             ----CCCHHHHHHHHHHH-----TTCCHHHHHHHHTCCHHHHHHHHHHHHHHTTCS
T ss_pred             ccccCCCHHHHHHHHHHH-----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHCCC
Confidence            346789999999999987     899999999999999999999999999999743

>2jpc_A SSRB; DNA binding protein, structural genomics, PSI-2, protein structure initiative; NMR {Salmonella typhimurium}

Probab=97.93  E-value=5.8e-06  Score=63.30  Aligned_cols=45  Identities=29%  Similarity=0.312  Sum_probs=41.0

Q ss_pred             HHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHh
Q 009449          474 SRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDSE  523 (534)
Q Consensus       474 ~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~~l  523 (534)
                      |+|++|+.+ +    .+|+|.+|||+.||+|..+|+.+..++++||+..-
T Consensus         1 ~re~~vl~l-~----~~g~s~~eIA~~l~is~~tV~~~~~~~~~kl~~~~   45 (61)
T 2jpc_A            1 LRERQVLKL-I----DEGYTNHGISEKLHISIKTVETHRMNMMRKLQVHK   45 (61)
T ss_dssp             CHHHHHHHH-H----HTSCCSHHHHHHTCSCHHHHHHHHHHHHHHHTCSS
T ss_pred             CHHHHHHHH-H----HcCCCHHHHHHHhCCCHHHHHHHHHHHHHHHCCCC
Confidence            579999999 5    58999999999999999999999999999998643

>1p4w_A RCSB; solution structure, DNA binding domain, DNA binding protein; NMR {Erwinia amylovora} SCOP: a.4.6.2

Probab=97.90  E-value=1.4e-05  Score=68.50  Aligned_cols=48  Identities=31%  Similarity=0.263  Sum_probs=44.4

Q ss_pred             hhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhH
Q 009449          470 ESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDS  522 (534)
Q Consensus       470 ~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~~  522 (534)
                      ..|+++|++||.+.+     +++|.+|||+.||||..||+..+.++++||.-.
T Consensus        33 ~~Lt~re~~Vl~l~~-----~G~s~~EIA~~L~iS~~TV~~~l~ri~~KLgv~   80 (99)
T 1p4w_A           33 KRLSPKESEVLRLFA-----EGFLVTEIAKKLNRSIKTISSQKKSAMMKLGVD   80 (99)
T ss_dssp             SSCCHHHHHHHHHHH-----HTCCHHHHHHHHTSCHHHHHHHHHHHHHHHTCS
T ss_pred             CCCCHHHHHHHHHHH-----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHCCC
Confidence            669999999999965     799999999999999999999999999999753

>2q0o_A Probable transcriptional activator protein TRAR; helix-turn-helix, two-helix coiled coil; HET: LAE; 2.00A {Rhizobium SP}

Probab=97.52  E-value=0.00012  Score=70.99  Aligned_cols=47  Identities=23%  Similarity=0.225  Sum_probs=43.8

Q ss_pred             hCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhH
Q 009449          471 SLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDS  522 (534)
Q Consensus       471 ~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~~  522 (534)
                      .|+++|++|+.+.+     +|+|.+|||++||||..||+.++.++++||.-.
T Consensus       175 ~Lt~~e~~vl~~~~-----~g~s~~eIa~~l~is~~tV~~~~~~~~~kl~~~  221 (236)
T 2q0o_A          175 MLSPREMLCLVWAS-----KGKTASVTANLTGINARTVQHYLDKARAKLDAE  221 (236)
T ss_dssp             SCCHHHHHHHHHHH-----TTCCHHHHHHHHCCCHHHHHHHHHHHHHHHTCS
T ss_pred             CCCHHHHHHHHHHH-----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHhCCC
Confidence            59999999999965     899999999999999999999999999999753

>1l3l_A Transcriptional activator protein TRAR; helix-turn-helix DNA binding motif, alpha/beta/alpha sandwich; HET: LAE; 1.66A {Agrobacterium tumefaciens} SCOP: a.4.6.2 d.110.5.1 PDB: 1h0m_A*

Probab=97.50  E-value=0.00013  Score=70.77  Aligned_cols=47  Identities=26%  Similarity=0.228  Sum_probs=43.5

Q ss_pred             hCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhH
Q 009449          471 SLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDS  522 (534)
Q Consensus       471 ~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~~  522 (534)
                      .|+++|++|+.+.+     +|+|.+|||++||||..||+.++.++++||.-.
T Consensus       173 ~Lt~~e~~vl~~~~-----~g~s~~eIa~~l~is~~tV~~~~~~~~~kl~~~  219 (234)
T 1l3l_A          173 WLDPKEATYLRWIA-----VGKTMEEIADVEGVKYNSVRVKLREAMKRFDVR  219 (234)
T ss_dssp             CCCHHHHHHHHHHT-----TTCCHHHHHHHHTCCHHHHHHHHHHHHHHHTCS
T ss_pred             CCCHHHHHHHHHHH-----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHhCCC
Confidence            59999999999964     899999999999999999999999999999743

>3szt_A QCSR, quorum-sensing control repressor; quorum sensing acyl-homoserine lactone, helix-turn-helix, transcription factor, 3-OXO-C12 HSL; HET: OHN; 2.55A {Pseudomonas aeruginosa}

Probab=97.40  E-value=0.00038  Score=67.84  Aligned_cols=48  Identities=27%  Similarity=0.323  Sum_probs=44.3

Q ss_pred             hhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhH
Q 009449          470 ESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDS  522 (534)
Q Consensus       470 ~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~~  522 (534)
                      ..|+++|++|+.+..     +|+|.+|||+.||||..||+.++.++++||.-.
T Consensus       174 ~~Lt~re~~vl~~~~-----~G~s~~eIa~~l~is~~tV~~~~~~~~~kl~~~  221 (237)
T 3szt_A          174 VRLTARETEMLKWTA-----VGKTYGEIGLILSIDQRTVKFHIVNAMRKLNSS  221 (237)
T ss_dssp             CCCCHHHHHHHHHHH-----TTCCHHHHHHHHTSCHHHHHHHHHHHHHHTTCS
T ss_pred             CCCCHHHHHHHHHHH-----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHhCCC
Confidence            469999999999976     899999999999999999999999999998643

>3qp6_A CVIR transcriptional regulator; quorum sensing, agonist, antagonist, LUXR, acylated homoseri lactone, transcription factor; HET: HL6; 2.00A {Chromobacterium violaceum} PDB: 3qp5_A*

Probab=97.24  E-value=0.0003  Score=69.88  Aligned_cols=47  Identities=21%  Similarity=0.278  Sum_probs=44.2

Q ss_pred             hCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhH
Q 009449          471 SLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDS  522 (534)
Q Consensus       471 ~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~~  522 (534)
                      .|+++|++|+.+..     +|+|.+|||++||||..||+.++.++++||.-.
T Consensus       197 ~Lt~re~~vl~~~~-----~G~s~~eIA~~l~is~~TV~~~~~~~~~kl~~~  243 (265)
T 3qp6_A          197 PLSQREYDIFHWMS-----RGKTNWEIATILNISERTVKFHVANVIRKLNAN  243 (265)
T ss_dssp             CCCHHHHHHHHHHH-----TTCCHHHHHHHHTSCHHHHHHHHHHHHHHTTCS
T ss_pred             CCCHHHHHHHHHHH-----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHhCCC
Confidence            69999999999987     899999999999999999999999999999753

>1tc3_C Protein (TC3 transposase); DNA binding, helix-turn-helix, TC1/mariner family, complex (transposase/DNA), DNA binding protein/DNA complex; HET: DNA; 2.45A {Caenorhabditis elegans} SCOP: a.4.1.2

Probab=96.99  E-value=0.00078  Score=48.05  Aligned_cols=40  Identities=28%  Similarity=0.248  Sum_probs=33.3

Q ss_pred             hCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 009449          471 SLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKK  514 (534)
Q Consensus       471 ~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~R  514 (534)
                      .|++.++..+...|    .+++|..|||+.||||+.||+.++.+
T Consensus         5 ~l~~~~~~~i~~~~----~~g~s~~~IA~~lgis~~Tv~~~~~~   44 (51)
T 1tc3_C            5 ALSDTERAQLDVMK----LLNVSLHEMSRKISRSRHCIRVYLKD   44 (51)
T ss_dssp             CCCHHHHHHHHHHH----HTTCCHHHHHHHHTCCHHHHHHHHHC
T ss_pred             CCCHHHHHHHHHHH----HcCCCHHHHHHHHCcCHHHHHHHHhh
Confidence            47888886666666    57899999999999999999987754

>2w7n_A TRFB transcriptional repressor protein; INCP, plasmid, repressor, DNA-binding, transcription/DNA; HET: BRU; 1.85A {Escherichia coli}

Probab=96.73  E-value=0.003  Score=54.27  Aligned_cols=46  Identities=2%  Similarity=0.021  Sum_probs=43.0

Q ss_pred             hCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 009449          471 SLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLR  520 (534)
Q Consensus       471 ~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR  520 (534)
                      .+++.-..|-.++|    .+|+|+.|||+.||||+.+|.+++.+|...+-
T Consensus        18 ~~~~~~~~~A~lyY----v~g~tQ~eIA~~lGiSR~~VsrlL~~Ar~~~~   63 (101)
T 2w7n_A           18 EVGQQTIEIARGVL----VDGKPQATFATSLGLTRGAVSQAVHRVWAAFE   63 (101)
T ss_dssp             CCCHHHHHHHHHHH----TTCCCHHHHHHHHTCCHHHHHHHHHHHHHHHH
T ss_pred             ChHHHHHHHHHHHH----HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHh
Confidence            68888899999999    99999999999999999999999999998764

>1yio_A Response regulatory protein; transcription regulation, DNA binding protein; 2.20A {Pseudomonas fluorescens} SCOP: a.4.6.2 c.23.1.1 PDB: 1zn2_A

Probab=96.58  E-value=0.0045  Score=57.25  Aligned_cols=51  Identities=25%  Similarity=0.286  Sum_probs=45.6

Q ss_pred             HHHHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHh
Q 009449          466 FRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRD  521 (534)
Q Consensus       466 ~~~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~  521 (534)
                      ...+..|+++|++|+.+..     +++|.+|||+.+|+|..||+.+..++++||..
T Consensus       137 ~~~~~~Lt~rE~~vl~~l~-----~g~s~~~Ia~~l~is~~TV~~~~~~i~~Kl~~  187 (208)
T 1yio_A          137 EQLFSSLTGREQQVLQLTI-----RGLMNKQIAGELGIAEVTVKVHRHNIMQKLNV  187 (208)
T ss_dssp             HHHHHTSCHHHHHHHHHHT-----TTCCHHHHHHHHTCCHHHHHHHHHHHHHHTTC
T ss_pred             HHHHHhcCHHHHHHHHHHH-----cCCcHHHHHHHcCCCHHHHHHHHHHHHHHhCC
Confidence            4445679999999998875     78999999999999999999999999999964

>1a04_A Nitrate/nitrite response regulator protein NARL; signal transduction protein, response regulators, two- component systems; 2.20A {Escherichia coli} SCOP: a.4.6.2 c.23.1.1 PDB: 1rnl_A

Probab=96.31  E-value=0.0061  Score=56.76  Aligned_cols=47  Identities=19%  Similarity=0.282  Sum_probs=43.5

Q ss_pred             hhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHh
Q 009449          470 ESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRD  521 (534)
Q Consensus       470 ~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~  521 (534)
                      ..|+++|.+|+.+..     +++|.+|||+.+++|..||+.+..+.++||.-
T Consensus       153 ~~Lt~rE~~vl~~l~-----~g~s~~~Ia~~l~is~~TV~~hi~~i~~Kl~~  199 (215)
T 1a04_A          153 NQLTPRERDILKLIA-----QGLPNKMIARRLDITESTVKVHVKHMLKKMKL  199 (215)
T ss_dssp             GGSCHHHHHHHHHHH-----TTCCHHHHHHHHTCCHHHHHHHHHHHHHHHTC
T ss_pred             cCCCHHHHHHHHHHH-----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHcCC
Confidence            459999999999886     78999999999999999999999999999964

>2x48_A CAG38821; archeal virus, viral protein; 2.60A {Sulfolobus islandicus rod-shaped virusorganism_taxid}

Probab=96.21  E-value=0.0033  Score=46.82  Aligned_cols=38  Identities=16%  Similarity=0.154  Sum_probs=29.9

Q ss_pred             CHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 009449          473 DSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKA  515 (534)
Q Consensus       473 ~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RA  515 (534)
                      ++..+.|+.+ +    ..++|..|||+.||||+.||+.++.+|
T Consensus        18 ~~~~~~i~~l-~----~~g~s~~eIA~~lgis~~TV~~~l~~a   55 (55)
T 2x48_A           18 DDLVSVAHEL-A----KMGYTVQQIANALGVSERKVRRYLESC   55 (55)
T ss_dssp             HHHHHHHHHH-H----HTTCCHHHHHHHHTSCHHHHHHHHTC-
T ss_pred             HHHHHHHHHH-H----HcCCCHHHHHHHHCcCHHHHHHHHHhC
Confidence            4455666666 5    478999999999999999999987654

>3c3w_A Two component transcriptional regulatory protein; response regulator, two-component regulatory system, DNA-BIN protein; 2.20A {Mycobacterium tuberculosis}

Probab=96.02  E-value=0.0084  Score=56.72  Aligned_cols=47  Identities=17%  Similarity=0.246  Sum_probs=43.2

Q ss_pred             hhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHh
Q 009449          470 ESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRD  521 (534)
Q Consensus       470 ~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~  521 (534)
                      ..|+++|++|+.+..     +++|.+|||+.+++|..||+....+.++||.-
T Consensus       148 ~~LT~rE~~vL~~l~-----~g~s~~eIa~~l~is~~TV~~hi~~l~~KL~~  194 (225)
T 3c3w_A          148 SGLTDQERTLLGLLS-----EGLTNKQIADRMFLAEKTVKNYVSRLLAKLGM  194 (225)
T ss_dssp             TTSCHHHHHHHHHHH-----TTCCHHHHHHHHTCCHHHHHHHHHHHHHHTTC
T ss_pred             CCCCHHHHHHHHHHH-----CCCCHHHHHHHhCCCHHHHHHHHHHHHHHhCC
Confidence            469999999999876     78999999999999999999999999999864

>3klo_A Transcriptional regulator VPST; REC domain, HTH domain, DNA-binding, transcription regulation; HET: C2E TAR; 2.80A {Vibrio cholerae} PDB: 3kln_A*

Probab=95.39  E-value=0.014  Score=55.06  Aligned_cols=47  Identities=23%  Similarity=0.257  Sum_probs=42.7

Q ss_pred             hhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHh
Q 009449          470 ESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRD  521 (534)
Q Consensus       470 ~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~  521 (534)
                      ..|+++|.+|+.+..     +++|.+|||+.+++|..||+.+..+.++||.-
T Consensus       158 ~~Lt~rE~~vL~~l~-----~g~s~~~Ia~~l~~s~~Tv~~~i~~l~~KL~~  204 (225)
T 3klo_A          158 AKLTKREQQIIKLLG-----SGASNIEIADKLFVSENTVKTHLHNVFKKINA  204 (225)
T ss_dssp             HTSCHHHHHHHHHHT-----TTCCHHHHHHHTTCCHHHHHHHHHHHTTTSCC
T ss_pred             ccCCHHHHHHHHHHH-----cCCCHHHHHHHhCCCHHHHHHHHHHHHHHhCC
Confidence            469999999999864     78999999999999999999999999999853

>3p7n_A Sensor histidine kinase; LOV domain, light-activated transcription factor, DNA bindin; HET: FMN; 2.10A {Erythrobacter litoralis}

Probab=95.04  E-value=0.056  Score=51.38  Aligned_cols=57  Identities=18%  Similarity=0.188  Sum_probs=50.6

Q ss_pred             HHHHHHHHHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhH
Q 009449          461 MKKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDS  522 (534)
Q Consensus       461 l~e~L~~~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~~  522 (534)
                      ........+..|++++++|+.+..     .+++.++||..+|+|..+|+....++++||.-.
T Consensus       188 ~~~~~~~~l~~L~~r~~~i~~~~~-----~g~~~~eia~~l~~s~~tv~~~l~~i~~kl~~~  244 (258)
T 3p7n_A          188 RRERAAEMLKTLSPRQLEVTTLVA-----SGLRNKEVAARLGLSEKTVKMHRGLVMEKLNLK  244 (258)
T ss_dssp             HHHHHHHHHTTSCHHHHHHHHHHH-----TTCCHHHHHHHHTCCHHHHHHHHHHHHHHTTCS
T ss_pred             HHHHHHHHHhhcCHHHHHHHHHHH-----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHCCC
Confidence            345677888999999999999876     689999999999999999999999999998643

>1p2f_A Response regulator; DRRB, OMPR/PHOB, transcription; HET: MSE; 1.80A {Thermotoga maritima} SCOP: a.4.6.1 c.23.1.1 PDB: 3nns_A*

Probab=93.45  E-value=0.061  Score=50.00  Aligned_cols=50  Identities=20%  Similarity=0.251  Sum_probs=42.4

Q ss_pred             hCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhC---CCHHHHHHHHHHHHHHHHh
Q 009449          471 SLDSRERQVLVLRYGLNDHRPKSLEEIGKLFH---VSKEWIRKLEKKAMTKLRD  521 (534)
Q Consensus       471 ~L~~rEReVL~LryGL~d~e~~Sl~EIA~~Lg---ISrerVRqi~~RAL~KLR~  521 (534)
                      .|+++|.+|+.+.. -+.++.+|.+|||+.++   +|..||+.+..+.++||..
T Consensus       145 ~Lt~rE~~vl~~l~-~~~~~~~s~~~Ia~~l~~~~~s~~tv~~~i~~l~~Kl~~  197 (220)
T 1p2f_A          145 HLPKKEFEILLFLA-ENAGKVVTREKLLETFWEDPVSPRVVDTVIKRIRKAIED  197 (220)
T ss_dssp             CCCHHHHHHHHHHH-HTTTSCEEHHHHHHHHCSSCCCTHHHHHHHHHHHHHHCS
T ss_pred             ecCHHHHHHHHHHH-HCCCceEcHHHHHHHHhCCCCCcchHHHHHHHHHHHHhc
Confidence            49999999998765 11123499999999999   9999999999999999974

>1jko_C HIN recombinase, DNA-invertase HIN; water-mediated recognition, protein-DNA complex, A10G mutant, DNA binding protein/DNA complex; 2.24A {Synthetic} SCOP: a.4.1.2 PDB: 1ijw_C* 1jj6_C* 1jj8_C* 1hcr_A 1jkp_C 1jkq_C 1jkr_C

Probab=93.21  E-value=0.058  Score=38.51  Aligned_cols=33  Identities=9%  Similarity=0.171  Sum_probs=25.9

Q ss_pred             HHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 009449          477 RQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKK  514 (534)
Q Consensus       477 ReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~R  514 (534)
                      +.|+.+ +    ..+.|..|||+.+|||+.||..++.+
T Consensus        12 ~~i~~l-~----~~g~s~~~ia~~lgvs~~Tv~r~l~~   44 (52)
T 1jko_C           12 EQISRL-L----EKGHPRQQLAIIFGIGVSTLYRYFPA   44 (52)
T ss_dssp             HHHHHH-H----HTTCCHHHHHHTTSCCHHHHHHHSCT
T ss_pred             HHHHHH-H----HcCCCHHHHHHHHCCCHHHHHHHHHH
Confidence            345555 4    35699999999999999999987653

>2gwr_A DNA-binding response regulator MTRA; two-component regulatory system, transcription regulation, phosphorylation, OMPR family; 2.10A {Mycobacterium tuberculosis} PDB: 3nhz_A

Probab=93.18  E-value=0.085  Score=49.94  Aligned_cols=50  Identities=12%  Similarity=0.052  Sum_probs=41.5

Q ss_pred             hCCHHHHHHHhhHhcCCCCCCCCHHHHHHHh-----CCCHHHHHHHHHHHHHHHHh
Q 009449          471 SLDSRERQVLVLRYGLNDHRPKSLEEIGKLF-----HVSKEWIRKLEKKAMTKLRD  521 (534)
Q Consensus       471 ~L~~rEReVL~LryGL~d~e~~Sl~EIA~~L-----gISrerVRqi~~RAL~KLR~  521 (534)
                      .|+++|.+||.+.. -+.++.+|.+|||+.+     ++|..||+....+.++||..
T Consensus       153 ~LT~rE~~vL~~l~-~~~~~~~s~~eIa~~lw~~~~~~s~~tV~~hi~~lr~KL~~  207 (238)
T 2gwr_A          153 SLTPLEFDLLVALA-RKPRQVFTRDVLLEQVWGYRHPADTRLVNVHVQRLRAKVEK  207 (238)
T ss_dssp             CCCHHHHHHHHHHH-HSTTCCBCHHHHHHHHTCCC--CCTHHHHHHHHHHHHHHCS
T ss_pred             ccCHHHHHHHHHHH-HCCCceecHHHHHHHHcCCCCCCCcccHHHHHHHHHHHhcc
Confidence            49999999998776 1112349999999999     99999999999999999964

>2oqr_A Sensory transduction protein REGX3; response regulator, winged-helix-turn-helix, DNA-binding, 3D swapping, two component system; 2.03A {Mycobacterium tuberculosis H37RV}

Probab=92.92  E-value=0.075  Score=49.65  Aligned_cols=50  Identities=14%  Similarity=0.050  Sum_probs=42.6

Q ss_pred             hCCHHHHHHHhhHhcCCCCCCCCHHHHHHHh-----CCCHHHHHHHHHHHHHHHHh
Q 009449          471 SLDSRERQVLVLRYGLNDHRPKSLEEIGKLF-----HVSKEWIRKLEKKAMTKLRD  521 (534)
Q Consensus       471 ~L~~rEReVL~LryGL~d~e~~Sl~EIA~~L-----gISrerVRqi~~RAL~KLR~  521 (534)
                      .|+++|.+|+.+.. -+.++.+|.+|||+.+     ++|..||+.+..+.++||..
T Consensus       156 ~Lt~rE~~vL~~l~-~~~~~~~s~~~Ia~~lw~~~~~~s~~tv~~hi~~i~~Kl~~  210 (230)
T 2oqr_A          156 TLPLKEFDLLEYLM-RNSGRVLTRGQLIDRVWGADYVGDTKTLDVHVKRLRSKIEA  210 (230)
T ss_dssp             CCCHHHHHHHHHHH-HTTTSCEEHHHHHHHHTSSCCTTHHHHHHHHHHHHHHHHCS
T ss_pred             ecCHHHHHHHHHHH-hCCCceEcHHHHHHHhcCCCCCCCCcCHHHHHHHHHHHHhh
Confidence            49999999998776 1123459999999999     99999999999999999964

>1kgs_A DRRD, DNA binding response regulator D; DNA-binding protein, ALPH-beta sandwich, winged-helix, helix helix, DNA binding protein; HET: DNA MSE; 1.50A {Thermotoga maritima} SCOP: a.4.6.1 c.23.1.1 PDB: 3nnn_A*

Probab=92.53  E-value=0.09  Score=48.81  Aligned_cols=50  Identities=24%  Similarity=0.284  Sum_probs=42.2

Q ss_pred             hCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhC-----CCHHHHHHHHHHHHHHHHh
Q 009449          471 SLDSRERQVLVLRYGLNDHRPKSLEEIGKLFH-----VSKEWIRKLEKKAMTKLRD  521 (534)
Q Consensus       471 ~L~~rEReVL~LryGL~d~e~~Sl~EIA~~Lg-----ISrerVRqi~~RAL~KLR~  521 (534)
                      .|+++|.+|+.+.. -+.+..+|.+|||+.++     +|..||+.+..+.++||..
T Consensus       151 ~Lt~rE~~vL~~l~-~~~~~~~s~~eIa~~l~~~~~~~s~~tv~~hi~~l~~Kl~~  205 (225)
T 1kgs_A          151 DLTKKEYQILEYLV-MNKNRVVTKEELQEHLWSFDDEVFSDVLRSHIKNLRKKVDK  205 (225)
T ss_dssp             CCCHHHHHHHHHHH-HTTTSCEEHHHHHHHCC-----CHHHHHHHHHHHHHHHHHT
T ss_pred             ecCHHHHHHHHHHH-hCCCcccCHHHHHHHhcCCCCCCCcchHHHHHHHHHHHhhC
Confidence            49999999998765 11123499999999998     9999999999999999974

>1qgp_A Protein (double stranded RNA adenosine deaminase); Z-alpha-Z-DNA binding domain, RNA-editing, Z-DNA recognition, ADAR1, helix- turn-helix; NMR {Homo sapiens} SCOP: a.4.5.19

Probab=92.25  E-value=0.11  Score=41.90  Aligned_cols=40  Identities=13%  Similarity=0.231  Sum_probs=29.3

Q ss_pred             HHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 009449          474 SRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEK  513 (534)
Q Consensus       474 ~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~  513 (534)
                      +.++.||.+..-...+++.|..|||+.+|||+.+|++++.
T Consensus        14 ~~~~~IL~~L~~~~~~~~~t~~eLA~~Lgvs~~tV~~~L~   53 (77)
T 1qgp_A           14 DQEQRILKFLEELGEGKATTAHDLSGKLGTPKKEINRVLY   53 (77)
T ss_dssp             HHHHHHHHHHHHHCSSSCEEHHHHHHHHCCCHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCCCCcCHHHHHHHHCcCHHHHHHHHH
Confidence            3456676665544434579999999999999999976543

>1ys7_A Transcriptional regulatory protein PRRA; response regulator, DNA binding domain, phosphorylation; 1.58A {Mycobacterium tuberculosis} SCOP: a.4.6.1 c.23.1.1 PDB: 1ys6_A

Probab=92.09  E-value=0.088  Score=49.17  Aligned_cols=50  Identities=16%  Similarity=0.102  Sum_probs=41.4

Q ss_pred             hCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhC-----CCHHHHHHHHHHHHHHHHh
Q 009449          471 SLDSRERQVLVLRYGLNDHRPKSLEEIGKLFH-----VSKEWIRKLEKKAMTKLRD  521 (534)
Q Consensus       471 ~L~~rEReVL~LryGL~d~e~~Sl~EIA~~Lg-----ISrerVRqi~~RAL~KLR~  521 (534)
                      .|+++|.+|+.+..- +.+..+|.+|||+.++     +|..||+.+..+.++||..
T Consensus       159 ~Lt~rE~~vL~~l~~-g~~~~~s~~~Ia~~l~~~~~~~s~~tv~~hi~~l~~Kl~~  213 (233)
T 1ys7_A          159 DLTKREFDLLAVLAE-HKTAVLSRAQLLELVWGYDFAADTNVVDVFIGYLRRKLEA  213 (233)
T ss_dssp             CCCHHHHHHHHHHHH-TTTCCBCHHHHHHHHHCCCCC-CCCHHHHHHHHHHHHHHC
T ss_pred             ccCHHHHHHHHHHHh-CCCCeEcHHHHHHHhcCcccCCCccCHHHHHHHHHHHhcc
Confidence            499999999988761 1123399999999998     9999999999999999975

>1qbj_A Protein (double-stranded RNA specific adenosine D (ADAR1)); protein-Z-DNA complex, hydrolase-DNA complex; HET: DNA; 2.10A {Homo sapiens} SCOP: a.4.5.19 PDB: 3f21_A* 3f22_A* 3f23_A* 3irr_A* 3irq_D* 2gxb_A 2acj_A 2l54_A

Probab=91.63  E-value=0.24  Score=40.52  Aligned_cols=43  Identities=14%  Similarity=0.274  Sum_probs=31.1

Q ss_pred             HHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHh
Q 009449          475 RERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRD  521 (534)
Q Consensus       475 rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~  521 (534)
                      .++.||.+......+...|..|||+.||||+.+|+    +++.+|.+
T Consensus        11 ~~~~IL~~L~~~~pg~~~t~~eLA~~Lgvsr~tV~----~~L~~Le~   53 (81)
T 1qbj_A           11 QEQRILKFLEELGEGKATTAHDLSGKLGTPKKEIN----RVLYSLAK   53 (81)
T ss_dssp             HHHHHHHHHHHHCTTCCBCHHHHHHHHTCCHHHHH----HHHHHHHH
T ss_pred             HHHHHHHHHHHcCCCCCcCHHHHHHHHCcCHHHHH----HHHHHHHH
Confidence            35556665554444568999999999999999986    45666654

>3ugo_A RNA polymerase sigma factor; protein-DNA complex, bacterial promoter opening, G-quartet, quadruplex, DNA binding; 2.10A {Thermus aquaticus} PDB: 3ugp_A 4gor_A 1ku2_A 3lev_A* 3les_A*

Probab=91.54  E-value=0.034  Score=54.63  Aligned_cols=52  Identities=19%  Similarity=0.218  Sum_probs=0.0

Q ss_pred             HHHHHHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhC--CCHHHHHHHHHHHHHHHH
Q 009449          464 DVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFH--VSKEWIRKLEKKAMTKLR  520 (534)
Q Consensus       464 ~L~~~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~Lg--ISrerVRqi~~RAL~KLR  520 (534)
                      .+...+..|++.++.+ ...|    +.+.|.+|||+.||  ||.++|+.++.+|++.|.
T Consensus       191 ~l~e~i~~l~~~~~~L-~~~~----~~~ps~~EIAe~Lg~~is~~tVk~~l~~ar~~ls  244 (245)
T 3ugo_A          191 HMVETINKLSRTARQL-QQEL----GREPSYEEIAEAMGPGWDAKRVEETLKIAQEPVS  244 (245)
T ss_dssp             -----------------------------------------------------------
T ss_pred             HHHHHHHHHHHHHHHH-HHHh----CCCCCHHHHHHHHCCCCCHHHHHHHHHHHhhccC
Confidence            3455667788888874 4566    57889999999999  999999999999988763

>1u78_A TC3 transposase, transposable element TC3 transposase; transposon DNA, bipartite DNA-binding, HTH- motif, DNA binding protein/DNA complex; 2.69A {Caenorhabditis elegans} SCOP: a.4.1.2 a.4.1.2

Probab=91.38  E-value=0.19  Score=43.55  Aligned_cols=40  Identities=28%  Similarity=0.248  Sum_probs=33.4

Q ss_pred             hCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 009449          471 SLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKK  514 (534)
Q Consensus       471 ~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~R  514 (534)
                      .|++.++..|...+    ..|.|..+||+.||||+.||+.+..+
T Consensus         6 ~~s~~~r~~i~~~~----~~G~s~~~ia~~lgis~~Tv~r~~~~   45 (141)
T 1u78_A            6 ALSDTERAQLDVMK----LLNVSLHEMSRKISRSRHCIRVYLKD   45 (141)
T ss_dssp             CCCHHHHHHHHHHH----HTTCCHHHHHHHHTCCHHHHHHHHHS
T ss_pred             cCCHHHHHHHHHHH----HcCCCHHHHHHHHCcCHHHHHHHHHc
Confidence            46777777666666    57899999999999999999988765

>3kor_A Possible Trp repressor; putative DNA-binding Trp repressor, TRPR like protein, struc genomics, transcription; 1.60A {Staphylococcus aureus}

Probab=91.33  E-value=0.17  Score=44.58  Aligned_cols=35  Identities=23%  Similarity=0.144  Sum_probs=29.2

Q ss_pred             hhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHH
Q 009449          470 ESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRK  510 (534)
Q Consensus       470 ~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRq  510 (534)
                      ..|+.| .+|+.+..     +++|+.|||+.+|+|..||..
T Consensus        60 ~aLs~R-~eV~klL~-----~G~syreIA~~~g~S~aTIsR   94 (119)
T 3kor_A           60 QSLSQR-LQVAKMIK-----QGYTYATIEQESGASTATISR   94 (119)
T ss_dssp             HHHHHH-HHHHHHHH-----HTCCHHHHHHHHCCCHHHHHH
T ss_pred             HHHHHH-HHHHHHHH-----cCCCHHHHHHHHCCCHHHHHH
Confidence            456666 67888865     789999999999999999975

>1pdn_C Protein (PRD paired); protein-DNA complex, double helix, PAX, paired domain, DNA-binding protein, gene regulation/DNA complex; HET: DNA; 2.50A {Drosophila melanogaster} SCOP: a.4.1.5

Probab=91.20  E-value=0.27  Score=41.50  Aligned_cols=42  Identities=17%  Similarity=0.080  Sum_probs=32.3

Q ss_pred             hCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHH
Q 009449          471 SLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAM  516 (534)
Q Consensus       471 ~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL  516 (534)
                      .+++.++.-+...+    ..++|..+||+.||||+.||+.++.+..
T Consensus        17 ~~s~~~r~~i~~~~----~~g~s~~~ia~~lgis~~Tv~~w~~~~~   58 (128)
T 1pdn_C           17 PLPNNIRLKIVEMA----ADGIRPCVISRQLRVSHGCVSKILNRYQ   58 (128)
T ss_dssp             CCCHHHHHHHHHHH----HTTCCHHHHHHHHTCCHHHHHHHHHHHH
T ss_pred             cCCHHHHHHHHHHH----HcCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence            35665555554445    4689999999999999999999987753

>1zx4_A P1 PARB, plasmid partition PAR B protein, PARB; translation; HET: CIT; 2.98A {Enterobacteria phage P1} PDB: 2ntz_A

Probab=90.58  E-value=0.26  Score=46.81  Aligned_cols=35  Identities=11%  Similarity=0.073  Sum_probs=29.6

Q ss_pred             HHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHH
Q 009449          477 RQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAM  516 (534)
Q Consensus       477 ReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL  516 (534)
                      ..+..+ |    ..|+|+.|||+.||||+.+|.+++..|.
T Consensus        15 ~ria~~-y----~~g~tQ~eIA~~lGiSr~~VSR~L~~A~   49 (192)
T 1zx4_A           15 LRLMRM-K----NDGMSQKDIAAKEGLSQAKVTRALQAAS   49 (192)
T ss_dssp             HHHHHH-H----HTTCCHHHHHHHHTCCHHHHHHHHHHHT
T ss_pred             HHHHHH-H----HcCCCHHHHHHHhCcCHHHHHHHHHHhc
Confidence            445555 6    5789999999999999999999988875

>2hqr_A Putative transcriptional regulator; phosporylation-independent response regulator, H. pylori, SY dimer, signaling protein; NMR {Helicobacter pylori}

Probab=90.42  E-value=0.077  Score=49.43  Aligned_cols=51  Identities=14%  Similarity=0.089  Sum_probs=42.5

Q ss_pred             hCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhC-----CCHHHHHHHHHHHHHHHHhH
Q 009449          471 SLDSRERQVLVLRYGLNDHRPKSLEEIGKLFH-----VSKEWIRKLEKKAMTKLRDS  522 (534)
Q Consensus       471 ~L~~rEReVL~LryGL~d~e~~Sl~EIA~~Lg-----ISrerVRqi~~RAL~KLR~~  522 (534)
                      .|+++|.+|+.+..- +.++..|.+|||+.++     +|..||+.+..+.++||...
T Consensus       143 ~Lt~rE~~vL~~l~~-~~~~~~s~~~Ia~~l~~~~~~~s~~tv~~~i~~lr~KL~~~  198 (223)
T 2hqr_A          143 EVKGKPFEVLTHLAR-HRDQIVSKEQLLDAIWEEPEMVTPNVIEVAINQIRQKMDKP  198 (223)
T ss_dssp             CCCSTTTHHHHHHHH-TCSEEEEHHHHHHHHCCSSCSCGGGTHHHHHHHHHHHHHTT
T ss_pred             ecCHHHHHHHHHHHh-CCCCcCCHHHHHHHhcCCccCCCCcCHHHHHHHHHHHHhcC
Confidence            499999999988750 0012299999999999     99999999999999999853

>3q9s_A DNA-binding response regulator; DNA binding protein; 2.40A {Deinococcus radiodurans}

Probab=90.33  E-value=0.16  Score=48.80  Aligned_cols=51  Identities=25%  Similarity=0.244  Sum_probs=42.6

Q ss_pred             hCCHHHHHHHhhHhcCCCCCCCCHHHHHH-----HhCCCHHHHHHHHHHHHHHHHhH
Q 009449          471 SLDSRERQVLVLRYGLNDHRPKSLEEIGK-----LFHVSKEWIRKLEKKAMTKLRDS  522 (534)
Q Consensus       471 ~L~~rEReVL~LryGL~d~e~~Sl~EIA~-----~LgISrerVRqi~~RAL~KLR~~  522 (534)
                      .|+++|.+||.+.. -+.++.+|.+|||+     .++++..||+.+..+.++||...
T Consensus       182 ~LT~rE~evL~ll~-~g~~~~~s~~eIa~~l~~~~l~~s~~TV~~hi~~lr~KL~~~  237 (249)
T 3q9s_A          182 RLSPKEFDILALLI-RQPGRVYSRQEIGQEIWQGRLPEGSNVVDVHMANLRAKLRDL  237 (249)
T ss_dssp             CCCHHHHHHHHHHH-HSTTCCCCHHHHHHHHHTTCSCTTCSHHHHHHHHHHHHHCCC
T ss_pred             ecCHHHHHHHHHHH-HCCCceEcHHHHHHHhcCCCCCCCccCHHHHHHHHHHHhhcC
Confidence            49999999999886 11234599999999     58889999999999999999743

>1k78_A Paired box protein PAX5; paired domain, ETS domain, transcription factor, transcription/DNA complex; 2.25A {Homo sapiens} SCOP: a.4.1.5 a.4.1.5 PDB: 1mdm_A 6pax_A

Probab=89.42  E-value=0.44  Score=42.16  Aligned_cols=42  Identities=21%  Similarity=0.192  Sum_probs=32.9

Q ss_pred             hCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHH
Q 009449          471 SLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAM  516 (534)
Q Consensus       471 ~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL  516 (534)
                      .+++.++.-|...+    ..+.|..+||+.||||+.||+.++.+..
T Consensus        32 ~~s~e~r~~iv~~~----~~G~s~~~iA~~lgis~~TV~rw~~~~~   73 (149)
T 1k78_A           32 PLPDVVRQRIVELA----HQGVRPCDISRQLRVSHGCVSKILGRYY   73 (149)
T ss_dssp             CCCHHHHHHHHHHH----HTTCCHHHHHHHHTCCHHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHH----HcCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence            35666665555555    4689999999999999999999988754

>3r0j_A Possible two component system response transcript positive regulator PHOP; beta-alpha fold, winged helix-turn-helix; 2.50A {Mycobacterium tuberculosis}

Probab=89.34  E-value=0.48  Score=45.08  Aligned_cols=50  Identities=16%  Similarity=0.012  Sum_probs=43.5

Q ss_pred             hCCHHHHHHHhhHhcCCCCCCCCHHHHHHHh-----CCCHHHHHHHHHHHHHHHHh
Q 009449          471 SLDSRERQVLVLRYGLNDHRPKSLEEIGKLF-----HVSKEWIRKLEKKAMTKLRD  521 (534)
Q Consensus       471 ~L~~rEReVL~LryGL~d~e~~Sl~EIA~~L-----gISrerVRqi~~RAL~KLR~  521 (534)
                      .|+++|.+||.+.. -+.++..|.+||++.+     +++..+|+.+..+.++||..
T Consensus       176 ~LT~rE~~iL~~l~-~~~~~~~s~~~i~~~lw~~~~~~~~~tv~~~i~~lr~KL~~  230 (250)
T 3r0j_A          176 SLSPTEFTLLRYFV-INAGTVLSKPKILDHVWRYDFGGDVNVVESYVSYLRRKIDT  230 (250)
T ss_dssp             CCCHHHHHHHHHHH-HTTTCCBCHHHHHHHHTTTSCCSCTHHHHHHHHHHHHHHCC
T ss_pred             ecCHHHHHHHHHHH-HCCCceEcHHHHHHHHcCCCCCCCccCHHHHHHHHHHhhcC
Confidence            49999999998886 2335679999999999     78999999999999999964

>1oyi_A Double-stranded RNA-binding protein; (alpha+beta) helix-turn-helix, viral protein; NMR {Vaccinia virus} SCOP: a.4.5.19

Probab=89.00  E-value=0.32  Score=40.09  Aligned_cols=25  Identities=8%  Similarity=0.116  Sum_probs=21.7

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHHH
Q 009449          490 RPKSLEEIGKLFHVSKEWIRKLEKK  514 (534)
Q Consensus       490 e~~Sl~EIA~~LgISrerVRqi~~R  514 (534)
                      .+.|..|||+.||||+.+|++++.+
T Consensus        29 ~g~sa~eLAk~LgiSk~aVr~~L~~   53 (82)
T 1oyi_A           29 EGATAAQLTRQLNMEKREVNKALYD   53 (82)
T ss_dssp             STEEHHHHHHHSSSCHHHHHHHHHH
T ss_pred             cCCCHHHHHHHHCcCHHHHHHHHHH
Confidence            3499999999999999999887654

>2elh_A CG11849-PA, LD40883P; structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Drosophila melanogaster}

Probab=88.74  E-value=0.57  Score=38.13  Aligned_cols=27  Identities=15%  Similarity=0.088  Sum_probs=23.5

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHHHHH
Q 009449          490 RPKSLEEIGKLFHVSKEWIRKLEKKAM  516 (534)
Q Consensus       490 e~~Sl~EIA~~LgISrerVRqi~~RAL  516 (534)
                      .+.|..+||+.+||++.+|+++..+..
T Consensus        37 ~g~s~~~iA~~~gIs~sTl~rW~k~~~   63 (87)
T 2elh_A           37 DGESKASVARDIGVPESTLRGWCKNED   63 (87)
T ss_dssp             HTCCHHHHHHHHTCCHHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence            468999999999999999999886544

>2heo_A Z-DNA binding protein 1; protein DLM1-Z-DNA complex, immune system-DNA complex; 1.70A {Mus musculus} PDB: 1j75_A

Probab=87.62  E-value=0.55  Score=36.58  Aligned_cols=44  Identities=20%  Similarity=0.321  Sum_probs=29.6

Q ss_pred             CCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHh
Q 009449          472 LDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRD  521 (534)
Q Consensus       472 L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~  521 (534)
                      +++...+||.+.-  .+..+.|..|||+.+|+|+.+|.+    .++.|++
T Consensus         8 m~~~~~~IL~~L~--~~~~~~s~~eLA~~lglsr~tv~~----~l~~L~~   51 (67)
T 2heo_A            8 GDNLEQKILQVLS--DDGGPVAIFQLVKKCQVPKKTLNQ----VLYRLKK   51 (67)
T ss_dssp             -CHHHHHHHHHHH--HHCSCEEHHHHHHHHCSCHHHHHH----HHHHHHH
T ss_pred             ccHHHHHHHHHHH--HcCCCcCHHHHHHHHCcCHHHHHH----HHHHHHH
Confidence            3444555655543  113578999999999999999964    5556664

>3r0a_A Putative transcriptional regulator; structural genomics, PSI-biology, midwest center for structu genomics, MCSG; 2.31A {Methanosarcina mazei}

Probab=87.60  E-value=0.92  Score=39.30  Aligned_cols=49  Identities=10%  Similarity=0.154  Sum_probs=37.3

Q ss_pred             HHHhhCCHHHHHHHhhHhcCCCCCC-CCHHHHHHHhCCCHHHHHHHHHHHHHHHHh
Q 009449          467 RILESLDSRERQVLVLRYGLNDHRP-KSLEEIGKLFHVSKEWIRKLEKKAMTKLRD  521 (534)
Q Consensus       467 ~~L~~L~~rEReVL~LryGL~d~e~-~Sl~EIA~~LgISrerVRqi~~RAL~KLR~  521 (534)
                      ...-.|++.+..|+.....-  ..+ .|..|||+.+|++++||.    |++++|.+
T Consensus        19 ~~~~gLt~~e~~il~~L~~~--~~~~~t~~eLa~~l~~s~sTV~----r~L~~L~~   68 (123)
T 3r0a_A           19 KCALNLTKADLNVMKSFLNE--PDRWIDTDALSKSLKLDVSTVQ----RSVKKLHE   68 (123)
T ss_dssp             HHHHTCCHHHHHHHHHHHHS--TTCCEEHHHHHHHHTSCHHHHH----HHHHHHHH
T ss_pred             HHHcCCCHHHHHHHHHHHHC--CCCCcCHHHHHHHHCcCHHHHH----HHHHHHHH
Confidence            44567999999999876621  223 899999999999999996    55566654

>2w48_A Sorbitol operon regulator; SORC, activator, repressor, DNA-binding, transcription, transcription regulator, transcription regulation; 3.20A {Klebsiella pneumoniae}

Probab=87.36  E-value=0.63  Score=46.82  Aligned_cols=37  Identities=16%  Similarity=0.262  Sum_probs=31.8

Q ss_pred             HHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 009449          477 RQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMT  517 (534)
Q Consensus       477 ReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~  517 (534)
                      ..|..|+|    .++.|.+|||+.||||+.|||..+..+.+
T Consensus        11 ~~ia~l~~----~~~~~~~ela~~l~vS~~tIrRdL~~l~~   47 (315)
T 2w48_A           11 VKIAQLYY----EQDMTQAQIARELGIYRTTISRLLKRGRE   47 (315)
T ss_dssp             HHHHHHHH----TSCCCHHHHHHHTTCCHHHHHHHHHHHHH
T ss_pred             HHHHHHHH----cCCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence            34778888    78999999999999999999988776644

>2d1h_A ST1889, 109AA long hypothetical transcriptional regulator; helix-turn-helix, intermolecular and intramolecular S-S bond structural genomics; 2.05A {Sulfolobus tokodaii} SCOP: a.4.5.50

Probab=86.49  E-value=1.1  Score=36.56  Aligned_cols=42  Identities=19%  Similarity=0.253  Sum_probs=32.7

Q ss_pred             HhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHH
Q 009449          469 LESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLE  512 (534)
Q Consensus       469 L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~  512 (534)
                      ...|++.+..+|...+.  ...+.|..|||+.+|+|+.+|++++
T Consensus        16 ~~~l~~~~~~~l~~l~~--~~~~~t~~ela~~l~is~~tv~~~l   57 (109)
T 2d1h_A           16 CYKITDTDVAVLLKMVE--IEKPITSEELADIFKLSKTTVENSL   57 (109)
T ss_dssp             HHTCCHHHHHHHHHHHH--HCSCEEHHHHHHHHTCCHHHHHHHH
T ss_pred             hhcCCHHHHHHHHHHHH--cCCCCCHHHHHHHHCcCHHHHHHHH
Confidence            45789998888765541  1357999999999999999997544

>2jn6_A Protein CGL2762, transposase; GFT PSI-2, protein structure, structural genomics, protein structure initiative; NMR {Corynebacterium glutamicum} SCOP: a.4.1.19

Probab=86.18  E-value=1.2  Score=36.62  Aligned_cols=40  Identities=13%  Similarity=0.140  Sum_probs=29.6

Q ss_pred             CCHHHHH-HHhhHhcCCCCC-CCCHHHHHHHhCCCHHHHHHHHHHH
Q 009449          472 LDSRERQ-VLVLRYGLNDHR-PKSLEEIGKLFHVSKEWIRKLEKKA  515 (534)
Q Consensus       472 L~~rERe-VL~LryGL~d~e-~~Sl~EIA~~LgISrerVRqi~~RA  515 (534)
                      .++..+. |+.++.    .. +.|..+||..+|||+.+|+++..+.
T Consensus         6 ys~e~k~~~v~~~~----~~~g~s~~~ia~~~gIs~~tl~rW~~~~   47 (97)
T 2jn6_A            6 YSEEFKRDAVALYE----NSDGASLQQIANDLGINRVTLKNWIIKY   47 (97)
T ss_dssp             CCHHHHHHHHHHHT----TGGGSCHHHHHHHHTSCHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHH----HcCCChHHHHHHHHCcCHHHHHHHHHHH
Confidence            4555554 444443    23 7899999999999999999987654

>3k2z_A LEXA repressor; winged helix-turn-helix, SOS system, autoca cleavage, DNA damage, DNA repair, DNA replication, DNA-BIND hydrolase; 1.37A {Thermotoga maritima}

Probab=85.74  E-value=0.68  Score=43.30  Aligned_cols=42  Identities=24%  Similarity=0.311  Sum_probs=32.5

Q ss_pred             hCCHHHHHHHhhHhcCC--CCCCCCHHHHHHHhCCCHHHHHHHH
Q 009449          471 SLDSRERQVLVLRYGLN--DHRPKSLEEIGKLFHVSKEWIRKLE  512 (534)
Q Consensus       471 ~L~~rEReVL~LryGL~--d~e~~Sl~EIA~~LgISrerVRqi~  512 (534)
                      .|+++|++|+....-.-  .+.+.|..|||+.||++..+|+.++
T Consensus         2 ~lt~~q~~il~~I~~~~~~~g~~~s~~eia~~lgl~~~tv~~~l   45 (196)
T 3k2z_A            2 DLTERQRKVLLFIEEFIEKNGYPPSVREIARRFRITPRGALLHL   45 (196)
T ss_dssp             CCCHHHHHHHHHHHHHHHHHSSCCCHHHHHHHHTSCHHHHHHHH
T ss_pred             CcCHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCcHHHHHHH
Confidence            58999999998754221  1357899999999999999876544

>3tgn_A ADC operon repressor ADCR; helix-turn-helix, transcriptional regulator, transcription; 2.00A {Streptococcus pneumoniae}

Probab=85.57  E-value=1.3  Score=38.21  Aligned_cols=40  Identities=20%  Similarity=0.294  Sum_probs=32.1

Q ss_pred             hCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 009449          471 SLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKK  514 (534)
Q Consensus       471 ~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~R  514 (534)
                      .|++.+..||...+    ..+.|..|||+.+|+++.+|++++.+
T Consensus        35 ~lt~~~~~iL~~l~----~~~~t~~eLa~~l~~s~~tvs~~l~~   74 (146)
T 3tgn_A           35 ALTNTQEHILMLLS----EESLTNSELARRLNVSQAAVTKAIKS   74 (146)
T ss_dssp             CCCHHHHHHHHHHT----TCCCCHHHHHHHHTCCHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHH----hCCCCHHHHHHHHCCCHHHHHHHHHH
Confidence            47888888887776    33499999999999999999765443

>2o3f_A Putative HTH-type transcriptional regulator YBBH; APC85504, putative transcriptional regulator YBBH; HET: MLY; 1.75A {Bacillus subtilis} SCOP: a.4.1.20

Probab=85.57  E-value=1.7  Score=37.16  Aligned_cols=51  Identities=16%  Similarity=0.139  Sum_probs=39.1

Q ss_pred             HHHHHHHhhCCHHHHHHHhhHhcC-CCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 009449          463 KDVFRILESLDSRERQVLVLRYGL-NDHRPKSLEEIGKLFHVSKEWIRKLEK  513 (534)
Q Consensus       463 e~L~~~L~~L~~rEReVL~LryGL-~d~e~~Sl~EIA~~LgISrerVRqi~~  513 (534)
                      ..|......|++.|+.|......= +....+|..|||+..|||..||...-+
T Consensus        10 ~~i~~~~~~ls~~e~~ia~yil~~~~~~~~~si~elA~~~~vS~aTv~Rf~k   61 (111)
T 2o3f_A           10 AIIQSMXHXLPPSERKLADYILAHPHXAIESTVNEISALANSSDAAVIRLCX   61 (111)
T ss_dssp             HHHHHHGGGSCHHHHHHHHHHHHCHHHHHTCCHHHHHHHTTCCHHHHHHHHH
T ss_pred             HHHHHHhccCCHHHHHHHHHHHHChHHHHhcCHHHHHHHHCCCHHHHHHHHH
Confidence            456777789999999998766510 011369999999999999999986553

>1r1u_A CZRA, repressor protein; zinc, DNA binding, transcriptional regulation, winged HTH protein, transcription repressor; 2.00A {Staphylococcus aureus} SCOP: a.4.5.5 PDB: 1r1v_A 2kjb_A 2kjc_A

Probab=85.38  E-value=2.2  Score=35.55  Aligned_cols=46  Identities=17%  Similarity=0.197  Sum_probs=33.0

Q ss_pred             HHHHHHhhCC-HHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 009449          464 DVFRILESLD-SRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEK  513 (534)
Q Consensus       464 ~L~~~L~~L~-~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~  513 (534)
                      .+...+..|. +....||.+..    ..+.|..|||+.+|+|+.+|++++.
T Consensus        15 ~~~~~~~~l~~~~r~~IL~~L~----~~~~~~~ela~~l~is~stvs~~L~   61 (106)
T 1r1u_A           15 RVTEIFKALGDYNRIRIMELLS----VSEASVGHISHQLNLSQSNVSHQLK   61 (106)
T ss_dssp             HHHHHHHHTCSHHHHHHHHHHH----HCCBCHHHHHHHHTCCHHHHHHHHH
T ss_pred             HHHHHHHHhCCHHHHHHHHHHH----hCCCCHHHHHHHHCcCHHHHHHHHH
Confidence            3444555554 55667776655    3578999999999999999976543

>3mn2_A Probable ARAC family transcriptional regulator; structural genomics, PSI-2, protein structure initiative; 1.80A {Rhodopseudomonas palustris}

Probab=85.37  E-value=10  Score=31.25  Aligned_cols=38  Identities=13%  Similarity=0.088  Sum_probs=29.8

Q ss_pred             HHHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHH
Q 009449          384 IQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASEC  421 (534)
Q Consensus       384 i~ka~~~L~~elGr~Pt~eEIA~~lgis~~kv~~~l~~  421 (534)
                      +.++..-+.......++.++||+.+|+++..+......
T Consensus         4 i~~~~~~i~~~~~~~~~~~~lA~~~~~s~~~l~r~fk~   41 (108)
T 3mn2_A            4 VRQVEEYIEANWMRPITIEKLTALTGISSRGIFKAFQR   41 (108)
T ss_dssp             HHHHHHHHHHHTTSCCCHHHHHHHHTCCHHHHHHHHHH
T ss_pred             HHHHHHHHHHcccCCCCHHHHHHHHCCCHHHHHHHHHH
Confidence            44555556666777899999999999999999877653

>3jth_A Transcription activator HLYU; transcription factor, RTXA, DNA-binding, transcription regulation; 2.00A {Vibrio vulnificus}

Probab=84.81  E-value=2.8  Score=34.14  Aligned_cols=49  Identities=18%  Similarity=0.305  Sum_probs=33.3

Q ss_pred             HHHHHhhC-CHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHh
Q 009449          465 VFRILESL-DSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRD  521 (534)
Q Consensus       465 L~~~L~~L-~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~  521 (534)
                      +..++..| +|....||.+-.    ..+.|..|||+.+|+|+.+|+++    +++|++
T Consensus        13 ~~~~~~~l~~~~r~~Il~~L~----~~~~~~~ela~~l~is~~tvs~~----L~~L~~   62 (98)
T 3jth_A           13 AVVLLKAMANERRLQILCMLH----NQELSVGELCAKLQLSQSALSQH----LAWLRR   62 (98)
T ss_dssp             HHHHHHHHCSHHHHHHHHHTT----TSCEEHHHHHHHHTCCHHHHHHH----HHHHHH
T ss_pred             HHHHHHHcCCHHHHHHHHHHh----cCCCCHHHHHHHHCcCHHHHHHH----HHHHHH
Confidence            33444444 455566665544    26899999999999999999754    455554

>3cuo_A Uncharacterized HTH-type transcriptional regulato; DNA-binding transcriptional regulator, structural genomics, MCSG; 2.00A {Escherichia coli K12}

Probab=84.70  E-value=1.5  Score=35.49  Aligned_cols=38  Identities=11%  Similarity=0.060  Sum_probs=29.3

Q ss_pred             CHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 009449          473 DSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEK  513 (534)
Q Consensus       473 ~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~  513 (534)
                      ++.+..|+....   .+.+.|..|||+.+|+|+.+|++++.
T Consensus        23 ~~~~~~il~~l~---~~~~~s~~ela~~l~is~~tvs~~l~   60 (99)
T 3cuo_A           23 HPKRLLILCMLS---GSPGTSAGELTRITGLSASATSQHLA   60 (99)
T ss_dssp             SHHHHHHHHHHT---TCCSEEHHHHHHHHCCCHHHHHHHHH
T ss_pred             ChHHHHHHHHHH---hCCCcCHHHHHHHHCcCHHHHHHHHH
Confidence            467777776554   24579999999999999999976543

>2cfx_A HTH-type transcriptional regulator LRPC; transcriptional regulation, DNA binding, FFRP; 2.4A {Bacillus subtilis} SCOP: a.4.5.32 d.58.4.2

Probab=84.35  E-value=1.5  Score=38.73  Aligned_cols=40  Identities=15%  Similarity=0.199  Sum_probs=31.7

Q ss_pred             hCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 009449          471 SLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEK  513 (534)
Q Consensus       471 ~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~  513 (534)
                      .|++.++.||.+...   ....|..|||+.+|+|+.+|+.++.
T Consensus         2 ~ld~~d~~il~~L~~---~~~~s~~ela~~lg~s~~tv~~~l~   41 (144)
T 2cfx_A            2 KLDQIDLNIIEELKK---DSRLSMRELGRKIKLSPPSVTERVR   41 (144)
T ss_dssp             CCCHHHHHHHHHHHH---CSCCCHHHHHHHHTCCHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHH---cCCCCHHHHHHHHCcCHHHHHHHHH
Confidence            378888888876541   3579999999999999999975543

>2k27_A Paired box protein PAX-8; paired domain, solution structure, triple frequency, 3D NMR, induced FIT, alternative splicing, developmental protein; NMR {Homo sapiens}

Probab=83.92  E-value=0.47  Score=42.57  Aligned_cols=39  Identities=23%  Similarity=0.210  Sum_probs=30.3

Q ss_pred             CCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 009449          472 LDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKK  514 (534)
Q Consensus       472 L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~R  514 (534)
                      ++..++.-|...+    ..+.|..+||+.||||+.||+.++.+
T Consensus        26 ~s~e~r~~ii~l~----~~G~s~~~IA~~lgis~~TV~rwl~r   64 (159)
T 2k27_A           26 LPEVVRQRIVDLA----HQGVRPCDISRQLRVSHGCVSKILGR   64 (159)
T ss_dssp             SCHHHHHHHHHHH----HHTCCHHHHHHHHTCCSHHHHHHHCC
T ss_pred             CCHHHHHHHHHHH----HcCCCHHHHHHHHCcCHHHHHHHHHH
Confidence            5555555554455    36799999999999999999998765

>3pqk_A Biofilm growth-associated repressor; helix-turn-helix motif, winged-helix fold, transcriptional R DNA binding, transcription; 2.09A {Xylella fastidiosa} PDB: 3pqj_A

Probab=83.81  E-value=2.4  Score=34.87  Aligned_cols=49  Identities=14%  Similarity=0.197  Sum_probs=33.5

Q ss_pred             HHHHHhhC-CHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHh
Q 009449          465 VFRILESL-DSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRD  521 (534)
Q Consensus       465 L~~~L~~L-~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~  521 (534)
                      +..++..| +|.-..||.+..    ..+.|..|||+.+|+|+.+|+++    +++|++
T Consensus        13 ~~~~~~~l~~~~r~~Il~~L~----~~~~~~~ela~~l~is~~tvs~~----L~~L~~   62 (102)
T 3pqk_A           13 VANLLKTLSHPVRLMLVCTLV----EGEFSVGELEQQIGIGQPTLSQQ----LGVLRE   62 (102)
T ss_dssp             HHHHHHHHCSHHHHHHHHHHH----TCCBCHHHHHHHHTCCTTHHHHH----HHHHHH
T ss_pred             HHHHHHHcCCHHHHHHHHHHH----hCCCCHHHHHHHHCcCHHHHHHH----HHHHHH
Confidence            34444444 455566666554    35799999999999999999764    445543

>2gxg_A 146AA long hypothetical transcriptional regulator; winged helix; 1.45A {Sulfolobus tokodaii} PDB: 2eb7_A 2yr2_A 3gez_A 3gf2_A* 3gfi_A 3gfm_A 3gfj_A 3gfl_A

Probab=83.77  E-value=3.5  Score=35.32  Aligned_cols=47  Identities=21%  Similarity=0.222  Sum_probs=36.6

Q ss_pred             HHHHHH--hhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 009449          464 DVFRIL--ESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKK  514 (534)
Q Consensus       464 ~L~~~L--~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~R  514 (534)
                      .+...+  ..|++.+..||...+    ..+.|..|||+.+|+++.+|..++.+
T Consensus        25 ~~~~~~~~~~l~~~~~~iL~~l~----~~~~~~~ela~~l~~s~~tvs~~l~~   73 (146)
T 2gxg_A           25 ELNRRLGELNLSYLDFLVLRATS----DGPKTMAYLANRYFVTQSAITASVDK   73 (146)
T ss_dssp             HHHHHHHTTTCCHHHHHHHHHHT----TSCBCHHHHHHHTTCCHHHHHHHHHH
T ss_pred             HHHHHHHhcCCCHHHHHHHHHHh----cCCcCHHHHHHHhCCCchhHHHHHHH
Confidence            344444  359999999988776    46899999999999999999765443

>2k9s_A Arabinose operon regulatory protein; activator, arabinose catabolism, carbohydrate metabolism, cytoplasm, DNA-binding, repressor, transcription; NMR {Escherichia coli}

Probab=83.60  E-value=13  Score=30.60  Aligned_cols=38  Identities=11%  Similarity=0.073  Sum_probs=30.0

Q ss_pred             HHHHHHHHHHhcC-CCCCHHHHHHHcCCCHHHHHHHHHH
Q 009449          384 IQKARKALTNSHG-KYPEDIEIAKYTGLSLAEIRSASEC  421 (534)
Q Consensus       384 i~ka~~~L~~elG-r~Pt~eEIA~~lgis~~kv~~~l~~  421 (534)
                      +.++..-+.+... ..++.++||+.+|+++..+......
T Consensus         5 i~~~~~~i~~~~~~~~~~~~~lA~~~~~S~~~l~r~fk~   43 (107)
T 2k9s_A            5 VREACQYISDHLADSNFDIASVAQHVCLSPSRLSHLFRQ   43 (107)
T ss_dssp             HHHHHHHHHHTSSCSSCCHHHHHHHTTSCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhccCCCCHHHHHHHHCCCHHHHHHHHHH
Confidence            4555556666676 7899999999999999999877653

>3oio_A Transcriptional regulator (ARAC-type DNA-binding containing proteins); PSI-2, midwest center for structural genomics; 1.65A {Chromobacterium violaceum}

Probab=83.60  E-value=10  Score=31.51  Aligned_cols=40  Identities=18%  Similarity=0.178  Sum_probs=30.6

Q ss_pred             HHHHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHHh
Q 009449          383 KIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECL  422 (534)
Q Consensus       383 ki~ka~~~L~~elGr~Pt~eEIA~~lgis~~kv~~~l~~~  422 (534)
                      .+.++..-+.......++.++||+.+|+++..+.......
T Consensus         8 ~i~~~~~~i~~~~~~~~~~~~lA~~~~~S~~~l~r~fk~~   47 (113)
T 3oio_A            8 KLTEAVSLMEANIEEPLSTDDIAYYVGVSRRQLERLFKQY   47 (113)
T ss_dssp             HHHHHHHHHHTCSSSCCCHHHHHHHHTSCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhhhcCCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence            3455555566666778999999999999999998876533

>2dbb_A Putative HTH-type transcriptional regulator PH006; ASNC family, helix-turn-helix (HTH) domain, structural genom NPPSFA; 2.00A {Pyrococcus horikoshii}

Probab=83.58  E-value=1.9  Score=38.07  Aligned_cols=41  Identities=12%  Similarity=0.272  Sum_probs=32.2

Q ss_pred             hhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 009449          470 ESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEK  513 (534)
Q Consensus       470 ~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~  513 (534)
                      ..|++.++.||.+..   .....|..|||+.+|+|+.+|+.++.
T Consensus         5 ~~ld~~d~~il~~L~---~~~~~s~~ela~~lg~s~~tv~~~l~   45 (151)
T 2dbb_A            5 RKLDRVDMQLVKILS---ENSRLTYRELADILNTTRQRIARRID   45 (151)
T ss_dssp             -CCCHHHHHHHHHHH---HCTTCCHHHHHHHTTSCHHHHHHHHH
T ss_pred             hhCCHHHHHHHHHHH---HcCCCCHHHHHHHHCcCHHHHHHHHH
Confidence            348899999887654   13579999999999999999975543

>2glo_A Brinker CG9653-PA; protein-DNA complex, helix-turn-helix motif, transcription/DNA complex; NMR {Drosophila melanogaster}

Probab=83.54  E-value=1.1  Score=33.65  Aligned_cols=33  Identities=15%  Similarity=0.239  Sum_probs=25.8

Q ss_pred             CCCC----HHHHHHHhCCCHHHHHHHHHHHHHHHHhHh
Q 009449          490 RPKS----LEEIGKLFHVSKEWIRKLEKKAMTKLRDSE  523 (534)
Q Consensus       490 e~~S----l~EIA~~LgISrerVRqi~~RAL~KLR~~l  523 (534)
                      .+.|    ..+||..+||++++|+++... ...+|..+
T Consensus        20 ~g~s~~~~~~~vA~~~gIs~~tl~~W~~~-~~~~~~~~   56 (59)
T 2glo_A           20 NDNDCKGNQRATARKYNIHRRQIQKWLQC-ESNLRSSV   56 (59)
T ss_dssp             HCTTTTTCHHHHHHHTTSCHHHHHHHHTT-HHHHHHHH
T ss_pred             cCCCcchHHHHHHHHHCcCHHHHHHHHHH-HHHHHHHH
Confidence            4568    999999999999999999764 45555443

>1sfx_A Conserved hypothetical protein AF2008; structural genomics, HTH MOT protein structure initiative, midwest center for structural genomics; 1.55A {Archaeoglobus fulgidus} SCOP: a.4.5.50

Probab=83.33  E-value=1.5  Score=35.52  Aligned_cols=40  Identities=18%  Similarity=0.277  Sum_probs=32.2

Q ss_pred             hCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 009449          471 SLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEK  513 (534)
Q Consensus       471 ~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~  513 (534)
                      .|++.+..|+.....   ..+.|..|||+.+|+++.+|++++.
T Consensus        17 ~l~~~~~~il~~l~~---~~~~s~~ela~~l~is~~tv~~~l~   56 (109)
T 1sfx_A           17 SFKPSDVRIYSLLLE---RGGMRVSEIARELDLSARFVRDRLK   56 (109)
T ss_dssp             CCCHHHHHHHHHHHH---HCCBCHHHHHHHHTCCHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHH---cCCCCHHHHHHHHCCCHHHHHHHHH
Confidence            578988888876641   3579999999999999999975543

>3oou_A LIN2118 protein; protein structure initiative, PSI-2, structural genomics, MI center for structural genomics, MCSG, unknown function; HET: BTB; 1.57A {Listeria innocua}

Probab=83.17  E-value=14  Score=30.54  Aligned_cols=39  Identities=8%  Similarity=-0.082  Sum_probs=29.8

Q ss_pred             HHHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHHh
Q 009449          384 IQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECL  422 (534)
Q Consensus       384 i~ka~~~L~~elGr~Pt~eEIA~~lgis~~kv~~~l~~~  422 (534)
                      +.++..-+.......++.++||+.+|+++..+.......
T Consensus         7 i~~~~~~i~~~~~~~~~~~~lA~~~~~S~~~l~r~fk~~   45 (108)
T 3oou_A            7 IQNVLSYITEHFSEGMSLKTLGNDFHINAVYLGQLFQKE   45 (108)
T ss_dssp             HHHHHHHHHHHTTSCCCHHHHHHHHTSCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhcCCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence            344555556666778999999999999999998876533

>2cyy_A Putative HTH-type transcriptional regulator PH151; structural genomics, pyrococcus horikosii OT3, NPPSFA; HET: MSE GLN; 1.80A {Pyrococcus horikoshii} SCOP: a.4.5.32 d.58.4.2

Probab=82.45  E-value=1.9  Score=38.24  Aligned_cols=40  Identities=18%  Similarity=0.296  Sum_probs=31.8

Q ss_pred             hCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 009449          471 SLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEK  513 (534)
Q Consensus       471 ~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~  513 (534)
                      .|++.++.||.+...   ....|..|||+.+|+|+.+|++++.
T Consensus         4 ~ld~~~~~il~~L~~---~~~~s~~ela~~lg~s~~tv~~~l~   43 (151)
T 2cyy_A            4 PLDEIDKKIIKILQN---DGKAPLREISKITGLAESTIHERIR   43 (151)
T ss_dssp             CCCHHHHHHHHHHHH---CTTCCHHHHHHHHCSCHHHHHHHHH
T ss_pred             CcCHHHHHHHHHHHH---cCCCCHHHHHHHHCcCHHHHHHHHH
Confidence            478888888875541   3578999999999999999976544

>2w25_A Probable transcriptional regulatory protein; transcription regulation, mutant, RV3291C, Glu104Ala, DNA-binding; 2.15A {Mycobacterium tuberculosis} PDB: 2vbw_A* 2vbx_A* 2vby_A* 2vbz_A* 2vc0_A 2vc1_A 2w24_A 2ivm_A 2w29_A 2qz8_A

Probab=82.38  E-value=1.9  Score=38.16  Aligned_cols=40  Identities=15%  Similarity=0.124  Sum_probs=32.1

Q ss_pred             hCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 009449          471 SLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEK  513 (534)
Q Consensus       471 ~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~  513 (534)
                      .|++.++.||.+-.   .....|..|||+.+|+|+.+|++++.
T Consensus         4 ~ld~~~~~iL~~L~---~~~~~s~~ela~~lg~s~~tv~~~l~   43 (150)
T 2w25_A            4 ALDDIDRILVRELA---ADGRATLSELATRAGLSVSAVQSRVR   43 (150)
T ss_dssp             CCCHHHHHHHHHHH---HCTTCCHHHHHHHHTSCHHHHHHHHH
T ss_pred             ccCHHHHHHHHHHH---HcCCCCHHHHHHHHCcCHHHHHHHHH
Confidence            48888888887654   13579999999999999999976543

>2p5v_A Transcriptional regulator, LRP/ASNC family; NMB0573, structu genomics; 1.99A {Neisseria meningitidis} PDB: 2p6s_A 2p6t_A

Probab=82.32  E-value=1.9  Score=38.75  Aligned_cols=40  Identities=15%  Similarity=0.083  Sum_probs=32.1

Q ss_pred             hCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 009449          471 SLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEK  513 (534)
Q Consensus       471 ~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~  513 (534)
                      .|++.++.||.+...   ....|..|||+.+|+|+.+|+.++.
T Consensus         7 ~ld~~~~~il~~L~~---~~~~s~~ela~~lg~s~~tv~~~l~   46 (162)
T 2p5v_A            7 TLDKTDIKILQVLQE---NGRLTNVELSERVALSPSPCLRRLK   46 (162)
T ss_dssp             CCCHHHHHHHHHHHH---CTTCCHHHHHHHHTSCHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHH---cCCCCHHHHHHHHCcCHHHHHHHHH
Confidence            488888888876541   3568999999999999999976544

>2pn6_A ST1022, 150AA long hypothetical transcriptional regulator; LRP/ASNC family Gln binding, structural genomics, NPPSFA; HET: GLN; 1.44A {Sulfolobus tokodaii} PDB: 2efn_A* 2e7x_A* 2e7w_A* 2yx4_A* 2efq_A* 2pmh_A* 2yx7_A* 2efp_A* 2efo_A*

Probab=82.20  E-value=2.1  Score=37.70  Aligned_cols=39  Identities=21%  Similarity=0.234  Sum_probs=30.1

Q ss_pred             CCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 009449          472 LDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEK  513 (534)
Q Consensus       472 L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~  513 (534)
                      |++.+..||.+..   .....|..|||+.+|+|+.+|+.++.
T Consensus         1 ld~~~~~il~~L~---~~~~~~~~ela~~lg~s~~tv~~~l~   39 (150)
T 2pn6_A            1 MDEIDLRILKILQ---YNAKYSLDEIAREIRIPKATLSYRIK   39 (150)
T ss_dssp             CCHHHHHHHHHHT---TCTTSCHHHHHHHHTSCHHHHHHHHH
T ss_pred             CChHHHHHHHHHH---HcCCCCHHHHHHHHCcCHHHHHHHHH
Confidence            5677778877554   23479999999999999999975543

>3ech_A MEXR, multidrug resistance operon repressor; winged helix, helix-turn-helix, protein-peptide complex; 1.80A {Pseudomonas aeruginosa} SCOP: a.4.5.28 PDB: 1lnw_A 3mex_A

Probab=82.07  E-value=3.3  Score=35.58  Aligned_cols=51  Identities=20%  Similarity=0.305  Sum_probs=36.5

Q ss_pred             HHHHHHHHHhh----CCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 009449          461 MKKDVFRILES----LDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKK  514 (534)
Q Consensus       461 l~e~L~~~L~~----L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~R  514 (534)
                      +...+...+..    |++.|-.||..-+.   ..+.|..|||+.+|+++++|..++.+
T Consensus        20 ~~~~~~~~l~~~~~~lt~~~~~vL~~l~~---~~~~t~~eLa~~l~~~~~tvs~~l~~   74 (142)
T 3ech_A           20 VRTRIQSELDCQRLDLTPPDVHVLKLIDE---QRGLNLQDLGRQMCRDKALITRKIRE   74 (142)
T ss_dssp             HHHHHHHHHHHTTCCCCHHHHHHHHHHHH---TTTCCHHHHHHHHC---CHHHHHHHH
T ss_pred             HHHHHHHHHhhccCCCCHHHHHHHHHHHh---CCCcCHHHHHHHhCCCHHHHHHHHHH
Confidence            33455566654    99999999887763   35899999999999999999865544

>2cg4_A Regulatory protein ASNC; DNA binding, FFRP, LRP family, transcription, DNA- binding, transcription regulation; 2.4A {Escherichia coli} SCOP: a.4.5.32 d.58.4.2

Probab=81.89  E-value=2  Score=38.08  Aligned_cols=41  Identities=27%  Similarity=0.290  Sum_probs=32.2

Q ss_pred             hCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 009449          471 SLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKK  514 (534)
Q Consensus       471 ~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~R  514 (534)
                      .|++.++.||.+..   .....|..|||+.+|+|+.+|+.++.+
T Consensus         5 ~ld~~d~~il~~L~---~~~~~s~~ela~~lg~s~~tv~~~l~~   45 (152)
T 2cg4_A            5 LIDNLDRGILEALM---GNARTAYAELAKQFGVSPETIHVRVEK   45 (152)
T ss_dssp             CCCHHHHHHHHHHH---HCTTSCHHHHHHHHTSCHHHHHHHHHH
T ss_pred             ccCHHHHHHHHHHH---HcCCCCHHHHHHHHCcCHHHHHHHHHH
Confidence            47888888887554   135789999999999999999865443

>2oqg_A Possible transcriptional regulator, ARSR family P; winged-helix-turn-helix, structural genomics, PSI-2, protein structure initiative; 1.54A {Rhodococcus SP}

Probab=81.64  E-value=2.6  Score=35.01  Aligned_cols=45  Identities=18%  Similarity=0.196  Sum_probs=31.7

Q ss_pred             HHHHHhhC-CHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 009449          465 VFRILESL-DSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEK  513 (534)
Q Consensus       465 L~~~L~~L-~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~  513 (534)
                      +..++..| ++....||....    ..+.|..|||+.+|+|+.+|+.++.
T Consensus        11 ~~~~~~~l~~~~r~~IL~~L~----~~~~~~~ela~~l~is~~tv~~~l~   56 (114)
T 2oqg_A           11 LASVFAALSDETRWEILTELG----RADQSASSLATRLPVSRQAIAKHLN   56 (114)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHH----HSCBCHHHHHHHSSSCHHHHHHHHH
T ss_pred             HHHHHHHhCChHHHHHHHHHH----cCCCCHHHHHHHHCcCHHHHHHHHH
Confidence            33444444 456666766543    3579999999999999999976544

>1i1g_A Transcriptional regulator LRPA; helix-turn-helix, LRP/ASNC family; 2.90A {Pyrococcus furiosus} SCOP: a.4.5.32 d.58.4.2

Probab=81.63  E-value=1.7  Score=37.78  Aligned_cols=39  Identities=26%  Similarity=0.373  Sum_probs=30.0

Q ss_pred             CCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 009449          472 LDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEK  513 (534)
Q Consensus       472 L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~  513 (534)
                      |++.++.||....   .....|..|||+.+|+|+.+|++.+.
T Consensus         2 ld~~~~~il~~L~---~~~~~~~~ela~~lg~s~~tv~~~l~   40 (141)
T 1i1g_A            2 IDERDKIILEILE---KDARTPFTEIAKKLGISETAVRKRVK   40 (141)
T ss_dssp             CCSHHHHHHHHHH---HCTTCCHHHHHHHHTSCHHHHHHHHH
T ss_pred             CCHHHHHHHHHHH---HcCCCCHHHHHHHHCcCHHHHHHHHH
Confidence            6777888877543   13568999999999999999975443

>3lsg_A Two-component response regulator YESN; structural genomics, PSI-2, protein structure initiative, MCSG; 2.05A {Fusobacterium nucleatum}

Probab=81.59  E-value=19  Score=29.20  Aligned_cols=37  Identities=8%  Similarity=-0.135  Sum_probs=27.3

Q ss_pred             HHHHHHHHhcCC-CCCHHHHHHHcCCCHHHHHHHHHHh
Q 009449          386 KARKALTNSHGK-YPEDIEIAKYTGLSLAEIRSASECL  422 (534)
Q Consensus       386 ka~~~L~~elGr-~Pt~eEIA~~lgis~~kv~~~l~~~  422 (534)
                      ++..-+...... .++.++||+.+|+++..+.......
T Consensus         6 ~i~~~i~~~~~~~~~~~~~lA~~~~~S~~~l~r~fk~~   43 (103)
T 3lsg_A            6 LIQNIIEESYTDSQFTLSVLSEKLDLSSGYLSIMFKKN   43 (103)
T ss_dssp             HHHHHHHHHTTCTTCCHHHHHHHTTCCHHHHHHHHHHH
T ss_pred             HHHHHHHHHccCCCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence            333444455555 7899999999999999998876533

>1sfu_A 34L protein; protein/Z-DNA complex, DNA binding protein/DNA complex; 2.00A {Yaba-like disease virus} SCOP: a.4.5.19

Probab=81.58  E-value=2.2  Score=34.48  Aligned_cols=28  Identities=14%  Similarity=0.146  Sum_probs=21.5

Q ss_pred             CCCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 009449          486 LNDHRPKSLEEIGKLFHVSKEWIRKLEK  513 (534)
Q Consensus       486 L~d~e~~Sl~EIA~~LgISrerVRqi~~  513 (534)
                      |..++..|..+||+.||+++..|.+.+.
T Consensus        24 L~~~~~~Ta~~IAkkLg~sK~~vNr~LY   51 (75)
T 1sfu_A           24 LNTNDYTTAISLSNRLKINKKKINQQLY   51 (75)
T ss_dssp             SCTTCEECHHHHHHHTTCCHHHHHHHHH
T ss_pred             CCCCcchHHHHHHHHHCCCHHHHHHHHH
Confidence            3334558999999999999988865443

>2x4h_A Hypothetical protein SSO2273; transcription; 2.30A {Sulfolobus solfataricus}

Probab=81.48  E-value=2  Score=37.08  Aligned_cols=45  Identities=13%  Similarity=0.124  Sum_probs=32.6

Q ss_pred             hhCCHHHHHHHhhHhcC-CCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 009449          470 ESLDSRERQVLVLRYGL-NDHRPKSLEEIGKLFHVSKEWIRKLEKK  514 (534)
Q Consensus       470 ~~L~~rEReVL~LryGL-~d~e~~Sl~EIA~~LgISrerVRqi~~R  514 (534)
                      ..|++.+..+|...+-+ ....+.|..|||+.+|+++.+|+.++.+
T Consensus         9 ~~lt~~~~~~L~~l~~l~~~~~~~s~~ela~~l~is~~tv~~~l~~   54 (139)
T 2x4h_A            9 SNLSRREFSYLLTIKRYNDSGEGAKINRIAKDLKIAPSSVFEEVSH   54 (139)
T ss_dssp             --CCHHHHHHHHHHHHHHTTTSCBCHHHHHHHHTCCHHHHHHHHHH
T ss_pred             hhcCHHHHHHHHHHHHHHhcCCCcCHHHHHHHhCCChHHHHHHHHH
Confidence            46888888777665533 2246789999999999999999755443

>3bpv_A Transcriptional regulator; MARR, DNA binding, transcription factor, winged helix motif, DNA-binding; 1.40A {Methanobacterium thermoautotrophicum} PDB: 3bpx_A*

Probab=81.47  E-value=4  Score=34.58  Aligned_cols=49  Identities=20%  Similarity=0.195  Sum_probs=37.3

Q ss_pred             HHHHHHHh--hCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 009449          463 KDVFRILE--SLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKK  514 (534)
Q Consensus       463 e~L~~~L~--~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~R  514 (534)
                      ..+...+.  .|++.+-.||...+.   ..+.|..|||+.+|+++.+|..++.+
T Consensus        16 ~~~~~~~~~~~l~~~~~~iL~~l~~---~~~~~~~ela~~l~~s~~tvs~~l~~   66 (138)
T 3bpv_A           16 VFIGRELGHLNLTDAQVACLLRIHR---EPGIKQDELATFFHVDKGTIARTLRR   66 (138)
T ss_dssp             HHHHHHSGGGTCCHHHHHHHHHHHH---STTCBHHHHHHHHTCCHHHHHHHHHH
T ss_pred             HHHHHHHHhcCCCHHHHHHHHHHHH---cCCCCHHHHHHHHCCCHHHHHHHHHH
Confidence            34444443  589999998887762   36899999999999999999765443

>3frw_A Putative Trp repressor protein; structural genomics, APC21159, PSI-2, P structure initiative; 2.05A {Ruminococcus obeum atcc 29174} PDB: 3g1c_A

Probab=81.42  E-value=2  Score=36.99  Aligned_cols=39  Identities=15%  Similarity=0.142  Sum_probs=28.5

Q ss_pred             CCHHHHHHHhhHhcCCC--CCCCCHHHHHHHhCCCHHHHHH
Q 009449          472 LDSRERQVLVLRYGLND--HRPKSLEEIGKLFHVSKEWIRK  510 (534)
Q Consensus       472 L~~rEReVL~LryGL~d--~e~~Sl~EIA~~LgISrerVRq  510 (534)
                      ++|.|+.-|-.|+-+-.  .+|+|+.||++.+|+|..||..
T Consensus        37 ~T~~E~~alaqR~~Ia~lL~~G~SyreIa~~tG~StaTIsR   77 (107)
T 3frw_A           37 CTINELLSLSQRFEVAKMLTDKRTYLDISEKTGASTATISR   77 (107)
T ss_dssp             SCHHHHHHHHHHHHHHHHHHTTCCHHHHHHHHCCCHHHHHH
T ss_pred             CCHHHHHHHHHHHHHHHHHHcCCCHHHHHHHHCccHHHHHH
Confidence            67777665554443220  2689999999999999999965

>3nqo_A MARR-family transcriptional regulator; structural genomics, joint center for structural genomics, J protein structure initiative, PSI-2; HET: MSE PG4; 2.20A {Clostridium difficile}

Probab=81.38  E-value=3.6  Score=37.70  Aligned_cols=53  Identities=19%  Similarity=0.227  Sum_probs=40.1

Q ss_pred             HHHHHHHHHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 009449          461 MKKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKK  514 (534)
Q Consensus       461 l~e~L~~~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~R  514 (534)
                      +...+...+..|++.|-.||...+-.. ..+.|..+||+.+|+++++|..++.+
T Consensus        28 ~~~~~~~~~~~lt~~q~~vL~~L~~~~-~~~~t~~eLa~~l~is~~tvs~~l~~   80 (189)
T 3nqo_A           28 IQIEGDKYFGILTSRQYMTILSILHLP-EEETTLNNIARKMGTSKQNINRLVAN   80 (189)
T ss_dssp             HHHHHHHHHCSSCHHHHHHHHHHHHSC-GGGCCHHHHHHHHTSCHHHHHHHHHH
T ss_pred             HHHHHHHHHccCCHHHHHHHHHHHhcc-CCCcCHHHHHHHHCCCHHHHHHHHHH
Confidence            344555666779999999998776221 24799999999999999999765443

>2lkp_A Transcriptional regulator, ARSR family; symmetric homodimer, NI(II) binding protein, DNA binding Pro transcription regulator; NMR {Mycobacterium tuberculosis}

Probab=81.33  E-value=2.2  Score=36.08  Aligned_cols=39  Identities=5%  Similarity=0.097  Sum_probs=31.4

Q ss_pred             CCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 009449          472 LDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKK  514 (534)
Q Consensus       472 L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~R  514 (534)
                      .++.+..||.+..    ..+.|..|||+.+|+|+.+|++++.+
T Consensus        30 ~~~~~~~il~~L~----~~~~s~~ela~~l~is~stvsr~l~~   68 (119)
T 2lkp_A           30 ATPSRLMILTQLR----NGPLPVTDLAEAIGMEQSAVSHQLRV   68 (119)
T ss_dssp             CCHHHHHHHHHHH----HCCCCHHHHHHHHSSCHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHH----HCCCCHHHHHHHHCcCHHHHHHHHHH
Confidence            4677888887766    24799999999999999999865543

>3i4p_A Transcriptional regulator, ASNC family; PSI, structural genom protein structure initiative, midwest center for structural genomics; 2.30A {Agrobacterium tumefaciens str}

Probab=81.16  E-value=2.4  Score=38.28  Aligned_cols=40  Identities=15%  Similarity=0.222  Sum_probs=31.0

Q ss_pred             CCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 009449          472 LDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKK  514 (534)
Q Consensus       472 L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~R  514 (534)
                      |++.++.||.+.-   .....|..|||+.+|+|+.+|+..+.+
T Consensus         1 lD~~d~~il~~L~---~~~~~s~~~la~~lg~s~~tv~~rl~~   40 (162)
T 3i4p_A            1 MDRLDRKILRILQ---EDSTLAVADLAKKVGLSTTPCWRRIQK   40 (162)
T ss_dssp             CCHHHHHHHHHHT---TCSCSCHHHHHHHHTCCHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHH---HCCCCCHHHHHHHHCcCHHHHHHHHHH
Confidence            5677788877654   135789999999999999999865543

>2zkz_A Transcriptional repressor PAGR; protein-DNA, HTH motif, dimer, DN binding, transcription regulation; 2.00A {Bacillus anthracis}

Probab=81.06  E-value=1.9  Score=35.66  Aligned_cols=38  Identities=8%  Similarity=0.139  Sum_probs=29.2

Q ss_pred             CCHHHHHHH-hhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 009449          472 LDSRERQVL-VLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEK  513 (534)
Q Consensus       472 L~~rEReVL-~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~  513 (534)
                      -+|....|| .+.-    ..+.|..|||+.+|+|+++|++++.
T Consensus        25 ~~~~Rl~IL~~l~~----~~~~~~~ela~~l~is~stvs~hL~   63 (99)
T 2zkz_A           25 AHPMRLKIVNELYK----HKALNVTQIIQILKLPQSTVSQHLC   63 (99)
T ss_dssp             CSHHHHHHHHHHHH----HSCEEHHHHHHHHTCCHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHH----CCCcCHHHHHHHHCcCHHHHHHHHH
Confidence            356667777 3332    3579999999999999999987655

>3o9x_A Uncharacterized HTH-type transcriptional regulato; HTH-XRE DNA binding motif, transcriptional regulator, bacter antitoxin, Zn binding protein, transcription regulator-DNA; HET: DNA; 2.10A {Escherichia coli} PDB: 3gn5_A* 3gn5_B* 2kz8_A

Probab=81.05  E-value=4.1  Score=35.13  Aligned_cols=39  Identities=13%  Similarity=0.108  Sum_probs=31.1

Q ss_pred             hhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 009449          470 ESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKK  514 (534)
Q Consensus       470 ~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~R  514 (534)
                      ..+++.+-.-++...      ++|++|+|+.+|||+.+|++++.-
T Consensus        69 ~~~~~~~l~~~R~~~------glsq~~la~~~g~s~~~i~~~E~g  107 (133)
T 3o9x_A           69 ETVAPEFIVKVRKKL------SLTQKEASEIFGGGVNAFSRYEKG  107 (133)
T ss_dssp             TTCCHHHHHHHHHHT------TCCHHHHHHHHCSCTTHHHHHHHT
T ss_pred             cCCCHHHHHHHHHHc------CCCHHHHHHHHCCCHHHHHHHHCC
Confidence            346776655555554      789999999999999999999874

>3bdd_A Regulatory protein MARR; putative multiple antibiotic-resistance repressor, structura genomics, joint center for structural genomics, JCSG; 2.20A {Streptococcus suis}

Probab=80.82  E-value=4.2  Score=34.51  Aligned_cols=41  Identities=7%  Similarity=0.088  Sum_probs=33.8

Q ss_pred             hCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 009449          471 SLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKK  514 (534)
Q Consensus       471 ~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~R  514 (534)
                      .|++.+..||...+.   ..+.|..|||+.+|+|+.+|..++.+
T Consensus        28 ~l~~~~~~iL~~l~~---~~~~~~~ela~~l~is~~~vs~~l~~   68 (142)
T 3bdd_A           28 GISLTRYSILQTLLK---DAPLHQLALQERLQIDRAAVTRHLKL   68 (142)
T ss_dssp             SSCHHHHHHHHHHHH---HCSBCHHHHHHHHTCCHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHh---CCCCCHHHHHHHHCCCHHHHHHHHHH
Confidence            699999999887762   35799999999999999999765443

>1y0u_A Arsenical resistance operon repressor, putative; structural genomics, protein structure initiative, PSI; HET: MSE; 1.60A {Archaeoglobus fulgidus} SCOP: a.4.5.5

Probab=80.73  E-value=6.8  Score=31.81  Aligned_cols=36  Identities=25%  Similarity=0.303  Sum_probs=27.7

Q ss_pred             CHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 009449          473 DSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEK  513 (534)
Q Consensus       473 ~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~  513 (534)
                      ++....||.+.   +  .+.|..|||+.+|+|+.+|++++.
T Consensus        30 ~~~r~~Il~~L---~--~~~~~~eLa~~l~is~~tv~~~L~   65 (96)
T 1y0u_A           30 NPVRRKILRML---D--KGRSEEEIMQTLSLSKKQLDYHLK   65 (96)
T ss_dssp             CHHHHHHHHHH---H--TTCCHHHHHHHHTCCHHHHHHHHH
T ss_pred             CHHHHHHHHHH---c--CCCCHHHHHHHHCcCHHHHHHHHH
Confidence            56666676654   2  469999999999999999976543

>1uly_A Hypothetical protein PH1932; helix-turn-helix, structural genomics, DNA binding protein; 2.50A {Pyrococcus horikoshii} SCOP: a.4.5.58 PDB: 2cwe_A

Probab=80.50  E-value=2.6  Score=39.56  Aligned_cols=39  Identities=15%  Similarity=0.301  Sum_probs=32.4

Q ss_pred             CCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 009449          472 LDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKK  514 (534)
Q Consensus       472 L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~R  514 (534)
                      +++.+..||.+..    ..+.|..|||+.+|+|+.+|++++.+
T Consensus        18 ~d~~~~~IL~~L~----~~~~s~~eLA~~lglS~stv~~~l~~   56 (192)
T 1uly_A           18 LEDTRRKILKLLR----NKEMTISQLSEILGKTPQTIYHHIEK   56 (192)
T ss_dssp             HSHHHHHHHHHHT----TCCBCHHHHHHHHTCCHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHH----cCCCCHHHHHHHHCcCHHHHHHHHHH
Confidence            6788888988775    25799999999999999999866543

>2l0k_A Stage III sporulation protein D; SPOIIID, solution structure, DNA binding, bacillus subti transcription factor, transcription; NMR {Bacillus subtilis}

Probab=80.38  E-value=1.3  Score=37.08  Aligned_cols=37  Identities=24%  Similarity=0.177  Sum_probs=28.6

Q ss_pred             HHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 009449          474 SRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKK  514 (534)
Q Consensus       474 ~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~R  514 (534)
                      +|...|+.+..    ..+.|..+||+.+|||..||+..+..
T Consensus         7 ~R~~~I~~~l~----~~~~ti~dlA~~~gVS~~TVsR~L~~   43 (93)
T 2l0k_A            7 ERTIKIGKYIV----ETKKTVRVIAKEFGVSKSTVHKDLTE   43 (93)
T ss_dssp             HHHHHHHHHHH----HHCCCHHHHHHHHTSCHHHHHHHHTT
T ss_pred             HHHHHHHHHHH----HcCCCHHHHHHHHCCCHHHHHHHHcC
Confidence            35555665554    34589999999999999999988765

>1r1t_A Transcriptional repressor SMTB; zinc, transcriptional regulation, winged HTH protein, DNA binding, transcription repressor; 1.70A {Synechococcus elongatus pcc 7942} SCOP: a.4.5.5 PDB: 1r23_A 1smt_A 1r22_A

Probab=80.26  E-value=4.1  Score=35.10  Aligned_cols=37  Identities=14%  Similarity=0.178  Sum_probs=29.3

Q ss_pred             CHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 009449          473 DSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEK  513 (534)
Q Consensus       473 ~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~  513 (534)
                      ++....||.+..    ..+.+..|||+.+|+|+.+|++++.
T Consensus        45 ~~~rl~IL~~L~----~~~~s~~ela~~lgis~stvs~~L~   81 (122)
T 1r1t_A           45 DPNRLRLLSLLA----RSELCVGDLAQAIGVSESAVSHQLR   81 (122)
T ss_dssp             CHHHHHHHHHHT----TCCBCHHHHHHHHTCCHHHHHHHHH
T ss_pred             CHHHHHHHHHHH----cCCCCHHHHHHHHCcCHHHHHHHHH
Confidence            566667777655    3578999999999999999986543

>2nnn_A Probable transcriptional regulator; structural genomics, PSI-2, protein structure initiative, M center for structural genomics, MCSG; 2.40A {Pseudomonas aeruginosa}

Probab=80.19  E-value=3.1  Score=35.26  Aligned_cols=48  Identities=15%  Similarity=0.141  Sum_probs=36.3

Q ss_pred             HHHHHHh-hCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 009449          464 DVFRILE-SLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKK  514 (534)
Q Consensus       464 ~L~~~L~-~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~R  514 (534)
                      .+...+. .|++.+-.||...+.   ..+.|..|||+.+|+++.+|..++.+
T Consensus        27 ~~~~~~~~~l~~~~~~iL~~l~~---~~~~t~~ela~~l~~~~~tvs~~l~~   75 (140)
T 2nnn_A           27 LFANGIGNGLTPTQWAALVRLGE---TGPCPQNQLGRLTAMDAATIKGVVER   75 (140)
T ss_dssp             HHHHHCSSCCCHHHHHHHHHHHH---HSSBCHHHHHHHTTCCHHHHHHHHHH
T ss_pred             HHHHHHHCCCCHHHHHHHHHHHH---cCCCCHHHHHHHHCCCHHHHHHHHHH
Confidence            3444333 799999998877652   34899999999999999999765443

---

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	534
d1ttya_	87	a.4.13.2 (A:) Sigma70 (SigA, RpoD) {Thermotoga mar	2e-20
d1siga_	334	a.177.1.1 (A:) Sigma70 {Escherichia coli [TaxId: 5	4e-19
d2p7vb1	68	a.4.13.2 (B:546-613) Sigma70 (SigA, RpoD) {Escheri	4e-17
d1ku3a_	61	a.4.13.2 (A:) Sigma70 (SigA, RpoD) {Thermus aquati	5e-16
d1ku2a2	180	a.177.1.1 (A:93-272) Sigma factor SigA {Thermus aq	2e-15
d1rp3a3	87	a.177.1.1 (A:0-86) Sigma factor sigma-28 (FliA) {A	6e-14
d1rp3a2	71	a.4.13.2 (A:164-234) Sigma factor sigma-28 (FliA)	4e-09
d1l0oc_	57	a.4.13.2 (C:) SigmaF {Bacillus stearothermophilus	4e-06
d1or7a1	68	a.4.13.2 (A:120-187) SigmaE factor (RpoE) {Escheri	2e-05
d1rp3a1	77	a.4.13.1 (A:87-163) Sigma factor sigma-28 (FliA) {	2e-05
d1ku2a1	60	a.4.13.1 (A:273-332) Sigma factor SigA {Thermus aq	0.001

>d1ttya_ a.4.13.2 (A:) Sigma70 (SigA, RpoD) {Thermotoga maritima [TaxId: 2336]} Length = 87

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Sigma3 and sigma4 domains of RNA polymerase sigma factors
family: Sigma4 domain
domain: Sigma70 (SigA, RpoD)
species: Thermotoga maritima [TaxId: 2336]

 Score = 83.6 bits (207), Expect = 2e-20
 Identities = 33/77 (42%), Positives = 53/77 (68%)

Query: 456 VMRQHMKKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKA 515
            MR  M++++ ++L++L  RE  VL +RYGL D +PK+LEE+G+ F+V++E IR++E KA
Sbjct: 3   AMRMLMREELEKVLKTLSPREAMVLRMRYGLLDGKPKTLEEVGQYFNVTRERIRQIEVKA 62

Query: 516 MTKLRDSETCRDLSHFL 532
           + KLR     + L   L
Sbjct: 63  LRKLRHPSRSKYLKSLL 79

>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 = 86.5 bits (213), Expect = 4e-19
 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

>d2p7vb1 a.4.13.2 (B:546-613) Sigma70 (SigA, RpoD) {Escherichia coli [TaxId: 562]} Length = 68

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Sigma3 and sigma4 domains of RNA polymerase sigma factors
family: Sigma4 domain
domain: Sigma70 (SigA, RpoD)
species: Escherichia coli [TaxId: 562]

 Score = 73.6 bits (181), Expect = 4e-17
 Identities = 27/65 (41%), Positives = 42/65 (64%)

Query: 468 ILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDSETCRD 527
           +L  L +RE +VL +R+G++ +   +LEE+GK F V++E IR++E KA+ KLR       
Sbjct: 2   VLAGLTAREAKVLRMRFGIDMNTDYTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEV 61

Query: 528 LSHFL 532
           L  FL
Sbjct: 62  LRSFL 66

>d1ku3a_ a.4.13.2 (A:) Sigma70 (SigA, RpoD) {Thermus aquaticus [TaxId: 271]} Length = 61

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Sigma3 and sigma4 domains of RNA polymerase sigma factors
family: Sigma4 domain
domain: Sigma70 (SigA, RpoD)
species: Thermus aquaticus [TaxId: 271]

 Score = 70.1 bits (172), Expect = 5e-16
 Identities = 26/61 (42%), Positives = 39/61 (63%)

Query: 464 DVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDSE 523
           ++ + L  L  RE  VL +R GL D R  +LEE+G  F V++E IR++E KA+ KL+  E
Sbjct: 1   ELEKALSKLSEREAMVLKMRKGLIDGREHTLEEVGAYFGVTRERIRQIENKALRKLKYHE 60

Query: 524 T 524
           +
Sbjct: 61  S 61

>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 = 72.5 bits (177), Expect = 2e-15
 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 = 65.3 bits (159), Expect = 6e-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

>d1rp3a2 a.4.13.2 (A:164-234) Sigma factor sigma-28 (FliA) {Aquifex aeolicus [TaxId: 63363]} Length = 71

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Sigma3 and sigma4 domains of RNA polymerase sigma factors
family: Sigma4 domain
domain: Sigma factor sigma-28 (FliA)
species: Aquifex aeolicus [TaxId: 63363]

 Score = 51.0 bits (122), Expect = 4e-09
 Identities = 16/71 (22%), Positives = 36/71 (50%), Gaps = 4/71 (5%)

Query: 451 SPKEIVMRQHMKKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRK 510
           + +E V+++ + + V   +  L  RE+ V+ L +          +E+ K+   S   + +
Sbjct: 1   NVEEEVIKRELTEKVKEAVSKLPEREKLVIQLIFY----EELPAKEVAKILETSVSRVSQ 56

Query: 511 LEKKAMTKLRD 521
           L+ KA+ +LR+
Sbjct: 57  LKAKALERLRE 67

>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 = 42.0 bits (99), Expect = 4e-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

>d1or7a1 a.4.13.2 (A:120-187) SigmaE factor (RpoE) {Escherichia coli [TaxId: 562]} Length = 68

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Sigma3 and sigma4 domains of RNA polymerase sigma factors
family: Sigma4 domain
domain: SigmaE factor (RpoE)
species: Escherichia coli [TaxId: 562]

 Score = 40.4 bits (95), Expect = 2e-05
 Identities = 15/67 (22%), Positives = 29/67 (43%), Gaps = 4/67 (5%)

Query: 455 IVMRQHMKKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKK 514
           +++ + +++ VFR +ESL    R  + LR         S EEI  +       +R    +
Sbjct: 2   LMLSEELRQIVFRTIESLPEDLRMAITLRELDG----LSYEEIAAIMDCPVGTVRSRIFR 57

Query: 515 AMTKLRD 521
           A   + +
Sbjct: 58  AREAIDN 64

>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 = 40.5 bits (95), Expect = 2e-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 = 35.0 bits (81), Expect = 0.001
 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	534
d1ku2a2	180	Sigma factor SigA {Thermus aquaticus [TaxId: 271]}	99.96
d1siga_	334	Sigma70 {Escherichia coli [TaxId: 562]}	99.83
d1rp3a3	87	Sigma factor sigma-28 (FliA) {Aquifex aeolicus [Ta	99.74
d1ttya_	87	Sigma70 (SigA, RpoD) {Thermotoga maritima [TaxId:	99.62
d2p7vb1	68	Sigma70 (SigA, RpoD) {Escherichia coli [TaxId: 562	99.62
d1ku3a_	61	Sigma70 (SigA, RpoD) {Thermus aquaticus [TaxId: 27	99.53
d1rp3a2	71	Sigma factor sigma-28 (FliA) {Aquifex aeolicus [Ta	99.39
d1or7a2	113	SigmaE factor (RpoE) {Escherichia coli [TaxId: 562	99.25
d1or7a1	68	SigmaE factor (RpoE) {Escherichia coli [TaxId: 562	99.19
d1ku2a1	60	Sigma factor SigA {Thermus aquaticus [TaxId: 271]}	99.17
d1l0oc_	57	SigmaF {Bacillus stearothermophilus [TaxId: 1422]}	98.97
d1xsva_	106	Hypothetical protein SAV1236 {Staphylococcus aureu	98.79
d1s7oa_	106	Hypothetical protein SPy1201 {Streptococcus pyogen	98.75
d1rp3a1	77	Sigma factor sigma-28 (FliA) {Aquifex aeolicus [Ta	98.71
d1h3la_	75	Sigma factor SigR {Streptomyces coelicolor a3(2) [	98.69
d1yioa1	70	Response regulatory protein StyR, C-terminal domai	98.35
d1a04a1	67	Nitrate/nitrite response regulator (NarL) {Escheri	98.13
d1l3la1	65	Quorum-sensing transcription factor TraR, C-termin	97.98
d1fsea_	67	Germination protein GerE {Bacillus subtilis [TaxId	97.92
d1p4wa_	87	Transcriptional regulator RcsB {Erwinia amylovora	97.6
d1ijwc_	47	HIN recombinase (DNA-binding domain) {Synthetic}	95.0
d1l0oc_	57	SigmaF {Bacillus stearothermophilus [TaxId: 1422]}	94.48
d1rp3a1	77	Sigma factor sigma-28 (FliA) {Aquifex aeolicus [Ta	93.18
d1jhfa1	71	LexA repressor, N-terminal DNA-binding domain {Esc	93.0
d1gdta1	43	gamma,delta resolvase (C-terminal domain) {Escheri	92.05
d1hlva1	66	DNA-binding domain of centromere binding protein B	90.89
d1i1ga1	60	LprA {Archaeon Pyrococcus furiosus [TaxId: 2261]}	90.22
d2cg4a1	63	Regulatory protein AsnC {Escherichia coli [TaxId:	90.19
d2cfxa1	63	Transcriptional regulator LrpC {Bacillus subtilis	89.65
d1ku2a1	60	Sigma factor SigA {Thermus aquaticus [TaxId: 271]}	89.22
d1jhfa1	71	LexA repressor, N-terminal DNA-binding domain {Esc	89.0
d2jn6a1	89	Uncharacterized protein Cgl2762 {Corynebacterium g	88.53
d1pdnc_	123	Paired protein (prd) {Fruit fly (Drosophila melano	87.43
d2cyya1	60	Putative transcriptional regulator PH1519 {Archaeo	87.41
d1biaa1	63	Biotin repressor, N-terminal domain {Escherichia c	87.32
d1dpua_	69	C-terminal domain of RPA32 {Human (Homo sapiens) [	87.17
d1nr3a_	122	DNA-binding protein Tfx {Archaeon Methanobacterium	86.74
d2ppxa1	62	Uncharacterized protein Atu1735 {Agrobacterium tum	86.61
d1r1ta_	98	SmtB repressor {Cyanobacteria (Synechococcus), pcc	84.81
d1ft9a1	80	CO-sensing protein CooA, C-terminal domain {Rhodos	84.63
d2a6ca1	69	HTH-motif protein NE1354 {Nitrosomonas europaea [T	84.13
d1r1ua_	94	Metal-sensing transcriptional repressor CzrA {Stap	83.95
d1ku9a_	151	DNA-binding protein Mj223 {Archaeon Methanococcus	83.18
d2d1ha1	109	Hypothetical transcriptional regulator ST1889 {Sul	82.93
d3e5ua1	80	Chlorophenol reduction protein CprK {Desulfitobact	82.66
d1k78a1	63	Pax-5 {Human (Homo sapiens) [TaxId: 9606]}	82.46
d1utxa_	66	Putative transcription regulator CylR2 {Enterococc	82.36
d2o38a1	89	Hypothetical protein RPA3824 {Rhodopseudomonas pal	81.97
d2auwa1	67	Hypothetical protein NE0471 C-terminal domain {Nit	81.89
d2gaua1	81	Transcriptional regulator PG0396, C-terminal domai	81.78
d2o3fa1	83	Putative transcriptional regulator YbbH {Bacillus	81.45
d1zyba1	73	Probable transcription regulator BT4300, C-termina	81.44
d1j5ya1	65	Putative transcriptional regulator TM1602, N-termi	81.26
d1stza1	87	Heat-inducible transcription repressor HrcA, N-ter	81.03
d1r69a_	63	434 C1 repressor, DNA-binding domain {Bacteriophag	80.63
d1yz8p1	60	Pituitary homeobox 2 {Human (Homo sapiens) [TaxId:	80.44
d1y7ya1	69	Restriction-modification controller protein C.AhdI	80.41
d1i5za1	69	Catabolite gene activator protein (CAP), C-termina	80.32

>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=99.96  E-value=9.8e-31  Score=245.69  Aligned_cols=149  Identities=26%  Similarity=0.403  Sum_probs=117.9

Q ss_pred             CchhHHHHHHhhccCCCCCCchHHHHHHhhchHHHHHHHHHHHHH------------------HHhCCCCchHHHHHHcC
Q 009449          219 QPTIFSAERALNSRGRRLTIARNEAEMSKGVQVVANLERIKTTLE------------------KESGKAASLNCWAQAAG  280 (534)
Q Consensus       219 ~~~~~~~~~~~~~~~~~lLt~~eE~~L~~~iq~~~~le~~~~~l~------------------~~~g~~ps~~ewa~a~g  280 (534)
                      ||.+.|+   ..+...||||++||++|+++|+.+..+........                  ...+..|...+|.....
T Consensus         2 DpVr~YL---reig~v~LLT~EEEieLAr~Ie~g~~~~~~~~e~~~~~~~l~~e~~~~~~~~~~~~~~~~~~~e~~~~~~   78 (180)
T d1ku2a2           2 DPVRQYL---HEIGQVPLLTLEEEIDLARKVEEGMEAIKKLSEATGLDQELIREVVRAKILGTARIQKIPGLKEKPDPKT   78 (180)
T ss_dssp             HHHHHHH---HHHTTSCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHTTCSSCCCTTSCCSSCTTT
T ss_pred             CcHHHHH---HHhcCcCCCCHHHHHHHHHHHHHHHHHHHHHHHhhhccHHHHHHHHHHHhhhHHHHhcchhhHHHhhHHH
Confidence            5665555   34566799999999999999998876654332221                  01223344444432221


Q ss_pred             C------------CHHHHHHHHHhcHHHHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCch
Q 009449          281 V------------SERVLKQHLAFGWYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKF  348 (534)
Q Consensus       281 ~------------d~~~L~~~l~~G~~A~e~LI~~nlrLV~sIArrY~~~g~~~eDLiQEG~lgL~rA~ekFDp~kG~rF  348 (534)
                      .            ....+.+.+..|+.|+++||.+|++||++||++|.+.|.+++||+|||++||++|+++|||++|++|
T Consensus        79 ~~~~~~~~~~~~~el~~l~~~~~~~~~a~~~li~~~~~lv~~~a~~~~~~~~~~~dl~q~g~~gl~~a~~~fd~~~g~~f  158 (180)
T d1ku2a2          79 VEEVDGKLKSLPKELKRYLHIAREGEAARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQEGNQGLIRAVEKFEYKRRFKF  158 (180)
T ss_dssp             HHHHHHHHHSCCHHHHHHHHHHHHHHHHHHHHHHTTHHHHHHHHHTTCSSSSCHHHHHHHHHHHHHHHHHHCCGGGCSCH
T ss_pred             HHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccCCCcCHHHHHHHHHHHHHHHHHHcCCCCCCCH
Confidence            1            1244566777889999999999999999999999999999999999999999999999999999999


Q ss_pred             hhHHHHHHHHHHHHHHHHhccc
Q 009449          349 STYVQYWIRKSISKMVARHARG  370 (534)
Q Consensus       349 STYA~~wIR~aI~~~lr~~sr~  370 (534)
                      +|||+||||++|.+++++++||
T Consensus       159 ~tya~~~i~~~i~~~~~~~~rt  180 (180)
T d1ku2a2         159 STYATWWIRQAINRAIADQART  180 (180)
T ss_dssp             HHHHHHHHHHHHHHHHTTSCCC
T ss_pred             HHHHHHHHHHHHHHHHHHhCCC
Confidence            9999999999999999998875

>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=99.83  E-value=1.1e-20  Score=191.34  Aligned_cols=90  Identities=32%  Similarity=0.772  Sum_probs=79.3

Q ss_pred             HcCCCHHH---HHHHHHhc----HHHHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCchhh
Q 009449          278 AAGVSERV---LKQHLAFG----WYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFST  350 (534)
Q Consensus       278 a~g~d~~~---L~~~l~~G----~~A~e~LI~~nlrLV~sIArrY~~~g~~~eDLiQEG~lgL~rA~ekFDp~kG~rFST  350 (534)
                      ..|++..+   +.+.+..|    ..|+++||++|++||++||++|.++|++++||+|+|++||++|+++|||.+|++|||
T Consensus       238 ~~gl~~~elk~i~~~i~~ge~~~~~ak~~~~~~~~~lv~~~~~~~~~~~~~~~dl~~~~~~~l~~~~~~~~~~~~~~f~~  317 (334)
T d1siga_         238 ETGLTIEQVKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFST  317 (334)
T ss_dssp             HHTSCHHHHHHHHHHHHHHHHHHHHHHHHHHHHTHHHHHHHHTTSTTSSSCHHHHHHHHHHHHHHHHHHCCGGGCCCHHH
T ss_pred             HhhhhHHHHHHHHHHHHHHHhhccchHHHHHHhHHHHHHHHHHhccCCCCCHHHHHHhhHHHHHHHHHhcCCCCCCchHh
Confidence            34554433   34445555    469999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHHh
Q 009449          351 YVQYWIRKSISKMVARH  367 (534)
Q Consensus       351 YA~~wIR~aI~~~lr~~  367 (534)
                      ||+||||++|.+++++|
T Consensus       318 ~~~~~~~~~~~~~~~~~  334 (334)
T d1siga_         318 YATWWIRQAITRSIADQ  334 (334)
T ss_dssp             HHHHHHHHHHHHHHHHC
T ss_pred             hhHHHHHHHHHHHHhCC
Confidence            99999999999999875

>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=99.74  E-value=1.8e-18  Score=143.95  Aligned_cols=73  Identities=23%  Similarity=0.385  Sum_probs=68.9

Q ss_pred             HHHHHHHHHhHHHHHHHHHHhhCC---CCCHHHHHHHHHHHHHHhhhccCCcCCCchhhHHHHHHHHHHHHHHHHh
Q 009449          295 YCREELIKSTRPLVLFLARNYRGL---GIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARH  367 (534)
Q Consensus       295 ~A~e~LI~~nlrLV~sIArrY~~~---g~~~eDLiQEG~lgL~rA~ekFDp~kG~rFSTYA~~wIR~aI~~~lr~~  367 (534)
                      ..+++||..|++||.++|++|.++   +++.+||+|+|++||++|+++|||++|.+|+|||.+|||++|.+++|+.
T Consensus        10 ~~re~li~~~~~LV~~ia~~~~~~~~~~~e~eDL~q~G~igL~~A~~~yd~~~g~~F~tYA~~~Irgai~d~lRk~   85 (87)
T d1rp3a3          10 IEREELILKYLPLVKAIATNIKKHLPEDVDIRDLISYGVIGLIKAVDNLSTENPKRAEAYIKLRIKGAIYDYLRSL   85 (87)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHTTSCTTSCHHHHHHHHHHHHHHHHHTCCCCCTHHHHHHHHHHHHHHHHHHHHTS
T ss_pred             HHHHHHHHHhHHHHHHHHHHHhccCCCCCCHHHHHHHHHHHHHHHHHhhCCCCCCCHHHHHHHHHHHHHHHHHHhC
Confidence            467999999999999999999764   7899999999999999999999999999999999999999999999875

>d1ttya_ a.4.13.2 (A:) Sigma70 (SigA, RpoD) {Thermotoga maritima [TaxId: 2336]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Sigma3 and sigma4 domains of RNA polymerase sigma factors
family: Sigma4 domain
domain: Sigma70 (SigA, RpoD)
species: Thermotoga maritima [TaxId: 2336]

Probab=99.62  E-value=1.1e-16  Score=132.94  Aligned_cols=75  Identities=43%  Similarity=0.740  Sum_probs=70.4

Q ss_pred             HHHHHHHHHHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHhhhhcchhhhcC
Q 009449          460 HMKKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDSETCRDLSHFLVL  534 (534)
Q Consensus       460 el~e~L~~~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~~l~~~~L~~yl~~  534 (534)
                      .+++.|..+|+.|+|+|+.||.+||||++++++|+.|||+.||||+++|||++.+|++|||.+.....|+.|+++
T Consensus         7 ~l~~~l~~~l~~L~~rE~~Ii~~rfGl~~~~~~tl~eI~~~lgiSrERVRQie~~al~kLr~~~~~~~L~~~l~~   81 (87)
T d1ttya_           7 LMREELEKVLKTLSPREAMVLRMRYGLLDGKPKTLEEVGQYFNVTRERIRQIEVKALRKLRHPSRSKYLKSLLSL   81 (87)
T ss_dssp             CCCSHHHHHHTTSCHHHHHHHHHHHTTTTSSCCCHHHHHHHHTCCHHHHHHHHHHHHHHHBTTBSSHHHHHHHHH
T ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHcCCCCCCcCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcHHHHHHHHHHHh
Confidence            345678999999999999999999999999999999999999999999999999999999999999999999863

>d2p7vb1 a.4.13.2 (B:546-613) Sigma70 (SigA, RpoD) {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Sigma3 and sigma4 domains of RNA polymerase sigma factors
family: Sigma4 domain
domain: Sigma70 (SigA, RpoD)
species: Escherichia coli [TaxId: 562]

Probab=99.62  E-value=1e-16  Score=127.14  Aligned_cols=66  Identities=41%  Similarity=0.677  Sum_probs=63.5

Q ss_pred             HHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHhhhhcchhhhc
Q 009449          468 ILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDSETCRDLSHFLV  533 (534)
Q Consensus       468 ~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~~l~~~~L~~yl~  533 (534)
                      +|+.|+|+|+.||.+||||++++++|++|||+.||||+++|||++.+|++|||+......|++|++
T Consensus         2 ~L~~L~~rE~~Ii~~rfGl~~~~~~tl~eI~~~lgiSrerVrqie~~al~kLr~~~~~~~L~~yl~   67 (68)
T d2p7vb1           2 VLAGLTAREAKVLRMRFGIDMNTDYTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRSFLD   67 (68)
T ss_dssp             CSCCCCHHHHHHHHHHTTTTSSSCCCHHHHHHHHTCCHHHHHHHHHHHHHGGGSCCGGGGGSCTTC
T ss_pred             hhhcCCHHHHHHHHHHcCCCCCCcCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhhHHHHHHHHHhc
Confidence            468899999999999999999999999999999999999999999999999999999999999986

>d1ku3a_ a.4.13.2 (A:) Sigma70 (SigA, RpoD) {Thermus aquaticus [TaxId: 271]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Sigma3 and sigma4 domains of RNA polymerase sigma factors
family: Sigma4 domain
domain: Sigma70 (SigA, RpoD)
species: Thermus aquaticus [TaxId: 271]

Probab=99.53  E-value=2.1e-15  Score=117.09  Aligned_cols=58  Identities=43%  Similarity=0.645  Sum_probs=54.9

Q ss_pred             HHHHHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhH
Q 009449          465 VFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDS  522 (534)
Q Consensus       465 L~~~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~~  522 (534)
                      |.++|+.|+++|+.||.+||||++++++|++|||+.||||+++|||++.+|++|||+.
T Consensus         2 l~~~L~~L~~rer~Ii~~ryGl~~~~~~tl~eIa~~lgiS~erVrqi~~~al~kLR~~   59 (61)
T d1ku3a_           2 LEKALSKLSEREAMVLKMRKGLIDGREHTLEEVGAYFGVTRERIRQIENKALRKLKYH   59 (61)
T ss_dssp             CSSSTTTSCHHHHHHHHHHHTTTTSSCCCHHHHHHHHTCCHHHHHHHHHHHHHHHHHT
T ss_pred             HHHHHhcCCHHHHHHHHHHhCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHhcC
Confidence            3457899999999999999999999999999999999999999999999999999975

>d1rp3a2 a.4.13.2 (A:164-234) Sigma factor sigma-28 (FliA) {Aquifex aeolicus [TaxId: 63363]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Sigma3 and sigma4 domains of RNA polymerase sigma factors
family: Sigma4 domain
domain: Sigma factor sigma-28 (FliA)
species: Aquifex aeolicus [TaxId: 63363]

Probab=99.39  E-value=5.7e-13  Score=105.12  Aligned_cols=70  Identities=23%  Similarity=0.392  Sum_probs=66.7

Q ss_pred             ChHHHHHHHHHHHHHHHHHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHhh
Q 009449          451 SPKEIVMRQHMKKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDSET  524 (534)
Q Consensus       451 spee~v~~~el~e~L~~~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~~l~  524 (534)
                      +|++.+...+..+.|..+|+.|||++|+||.++|    ++++|++|||+.||+|+++|++++++|+++||+.+.
T Consensus         1 d~e~~~~~~e~~~~l~~~l~~L~~~~r~v~~l~~----~~~~s~~eIA~~lgis~~tv~~~~~ra~~~Lr~~L~   70 (71)
T d1rp3a2           1 NVEEEVIKRELTEKVKEAVSKLPEREKLVIQLIF----YEELPAKEVAKILETSVSRVSQLKAKALERLREMLS   70 (71)
T ss_dssp             HHHHHHHHHHHHHHHHHHHTTSCHHHHHHHHHHH----TSCCCHHHHHHHTTSCHHHHHHHHHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHH----hHhCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHcc
Confidence            3788899999999999999999999999999999    899999999999999999999999999999998864

>d1or7a1 a.4.13.2 (A:120-187) SigmaE factor (RpoE) {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Sigma3 and sigma4 domains of RNA polymerase sigma factors
family: Sigma4 domain
domain: SigmaE factor (RpoE)
species: Escherichia coli [TaxId: 562]

Probab=99.19  E-value=3.2e-11  Score=94.51  Aligned_cols=63  Identities=24%  Similarity=0.285  Sum_probs=59.0

Q ss_pred             HHHHHHHHHHHHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHhh
Q 009449          458 RQHMKKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDSET  524 (534)
Q Consensus       458 ~~el~e~L~~~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~~l~  524 (534)
                      .++....|..+|+.|||++|+||.++|    ++++|++|||+.||+|.++|++.++||+++||..++
T Consensus         5 ~~e~~~~l~~~l~~Lp~~~r~v~~l~~----~~~~s~~eIA~~lgis~~tv~~~l~ra~~~Lr~~l~   67 (68)
T d1or7a1           5 SEELRQIVFRTIESLPEDLRMAITLRE----LDGLSYEEIAAIMDCPVGTVRSRIFRAREAIDNKVQ   67 (68)
T ss_dssp             HHHHHHHHHHHHHHSCHHHHHHHHHHH----TTCCCHHHHHHHTTSCHHHHHHHHHHHHHHHHHHHC
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHH----HhCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHcC
Confidence            456677899999999999999999999    999999999999999999999999999999998764

>d1ku2a1 a.4.13.1 (A:273-332) Sigma factor SigA {Thermus aquaticus [TaxId: 271]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Sigma3 and sigma4 domains of RNA polymerase sigma factors
family: Sigma3 domain
domain: Sigma factor SigA
species: Thermus aquaticus [TaxId: 271]

Probab=99.17  E-value=1.3e-11  Score=94.98  Aligned_cols=58  Identities=22%  Similarity=0.354  Sum_probs=54.9

Q ss_pred             cccccchHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHcC--CCHHHHHHHHHHhhhhccc
Q 009449          371 IKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTG--LSLAEIRSASECLRIVGSI  428 (534)
Q Consensus       371 iRlP~~~~~~i~ki~ka~~~L~~elGr~Pt~eEIA~~lg--is~~kv~~~l~~~~~~~SL  428 (534)
                      ||+|.|+++.+++++++.++|.+++||+||.+|||+.+|  +++++|..++...+.++||
T Consensus         1 IRlPvH~~e~i~rv~r~~~~l~qe~gRePt~eEiA~~l~~~l~~ekV~~~l~~~~~p~SL   60 (60)
T d1ku2a1           1 IRIPVHMVETINKLSRTARQLQQELGREPSYEEIAEAMGPGWDAKRVEETLKIAQEPVSL   60 (60)
T ss_dssp             CCCCHHHHHHHHHHHHHHHHHHHHHTSCCCHHHHHHHHCSSCCHHHHHHHGGGSSSCCCC
T ss_pred             CccchhHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHCCCCCHHHHHHHHHHccCCCCC
Confidence            799999999999999999999999999999999999997  5589999999999988886

>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=98.97  E-value=3.4e-10  Score=86.03  Aligned_cols=55  Identities=31%  Similarity=0.446  Sum_probs=52.0

Q ss_pred             cccccccchHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHHhh
Q 009449          369 RGIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLR  423 (534)
Q Consensus       369 r~iRlP~~~~~~i~ki~ka~~~L~~elGr~Pt~eEIA~~lgis~~kv~~~l~~~~  423 (534)
                      .+||+|.|+.+.++|++++.++|.+++||+||.+|||+.+|+|+++|..++.+.+
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            4799999999999999999999999999999999999999999999999987654

>d1xsva_ a.4.13.3 (A:) Hypothetical protein SAV1236 {Staphylococcus aureus, strain Mu50 / ATCC 700699 [TaxId: 1280]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Sigma3 and sigma4 domains of RNA polymerase sigma factors
family: YlxM/p13-like
domain: Hypothetical protein SAV1236
species: Staphylococcus aureus, strain Mu50 / ATCC 700699 [TaxId: 1280]

Probab=98.79  E-value=9.9e-09  Score=87.31  Aligned_cols=55  Identities=27%  Similarity=0.324  Sum_probs=50.1

Q ss_pred             hhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHhhhhcc
Q 009449          470 ESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDSETCRDL  528 (534)
Q Consensus       470 ~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~~l~~~~L  528 (534)
                      .-|||+||+||.|+|    ++++|+.|||+.||||+++|+++++||+++||+....-+|
T Consensus        17 ~LLpe~QR~vl~L~~----~e~ls~~EIA~~lgiS~~aV~~~l~Ra~~~L~~ye~kL~l   71 (106)
T d1xsva_          17 SLLTNKQRNYLELFY----LEDYSLSEIADTFNVSRQAVYDNIRRTGDLVEDYEKKLEL   71 (106)
T ss_dssp             GGSCHHHHHHHHHHH----TSCCCHHHHHHHTTCCHHHHHHHHHHHHHHHHHHHHHHCH
T ss_pred             HhCCHHHHHHHHHHH----HhCCcHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHHCh
Confidence            349999999999999    9999999999999999999999999999999986554444

>d1s7oa_ a.4.13.3 (A:) Hypothetical protein SPy1201 {Streptococcus pyogenes [TaxId: 1314]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Sigma3 and sigma4 domains of RNA polymerase sigma factors
family: YlxM/p13-like
domain: Hypothetical protein SPy1201
species: Streptococcus pyogenes [TaxId: 1314]

Probab=98.75  E-value=1e-08  Score=87.25  Aligned_cols=55  Identities=24%  Similarity=0.232  Sum_probs=49.7

Q ss_pred             hhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHhhhhcc
Q 009449          470 ESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDSETCRDL  528 (534)
Q Consensus       470 ~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~~l~~~~L  528 (534)
                      +.|||+||.||.|+|    ++++|++|||+.||||+++|+++++||+++||+...+-++
T Consensus        15 ~lLp~~qR~v~~L~y----~~~ls~~EIA~~lgiS~~aV~~~l~RA~~~L~~~e~kL~l   69 (106)
T d1s7oa_          15 ALLTDKQMNYIELYY----ADDYSLAEIADEFGVSRQAVYDNIKRTEKILETYEMKLHM   69 (106)
T ss_dssp             GGSCHHHHHHHHHHH----HTCCCHHHHHHHHTCCHHHHHHHHHHHHHHHHHHHHHHCH
T ss_pred             hhCCHHHHHHHHHHH----HcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHHCh
Confidence            349999999999999    9999999999999999999999999999999986544443

>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=98.71  E-value=5.8e-09  Score=83.43  Aligned_cols=70  Identities=23%  Similarity=0.393  Sum_probs=59.5

Q ss_pred             hHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHHhh--hhcccccccccchhhhhhhccCCC
Q 009449          377 LNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLR--IVGSIDQKIGDCLNAKYLEFAPDR  447 (534)
Q Consensus       377 ~~~~i~ki~ka~~~L~~elGr~Pt~eEIA~~lgis~~kv~~~l~~~~--~~~SLD~~i~~~~~~~l~e~i~d~  447 (534)
                      +.+.++++.++...|.+++||.||.+|||+.|||++++|..++....  .++|||.++.+ ++..+.+++++.
T Consensus         5 ~r~~~~ki~~a~~~L~~~lGR~Pt~~EiA~~lg~s~~e~~~~l~~~~~~~~~SLD~~~~d-~~~~~~e~lpss   76 (77)
T d1rp3a1           5 VREKERRIKEVVEKLKEKLGREPTDEEVAKELGISTEELFKTLDKINFSYILSLEEVFRD-FARDYSELIPSS   76 (77)
T ss_dssp             HHHHHHHHHHHHHHHHHHHSSCCCHHHHHHHHTSCHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHTTTGGGS
T ss_pred             HHHHHHHHHHHHHHHHHHHCcCCCHHHHHHHHCcCHHHHHHHHHHHhcCCceecccCccC-CCCchhccCCCC
Confidence            45788999999999999999999999999999999999999987544  67899997764 455677777753

>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=98.69  E-value=9.5e-09  Score=81.28  Aligned_cols=69  Identities=9%  Similarity=-0.053  Sum_probs=64.2

Q ss_pred             HHHHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCchhhHHHHHHHHHHHHHH
Q 009449          294 WYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMV  364 (534)
Q Consensus       294 ~~A~e~LI~~nlrLV~sIArrY~~~g~~~eDLiQEG~lgL~rA~ekFDp~kG~rFSTYA~~wIR~aI~~~l  364 (534)
                      ..+|++++..|.+.++.+|.++.++..+++|++||+++.+|+..++|++.  .+|.+|++..++|.+++++
T Consensus         6 ~~~f~~~~~~y~~~l~~~~~~~~~d~~~aeDivQd~f~~~~~~~~~~~~~--~~~~~wl~~i~~n~~~d~~   74 (75)
T d1h3la_           6 SARFERDALEFLDQMYSAALRMTRNPADAEDLVQETYAKAYASFHQFREG--TNLKAWLYRILTNTFINSY   74 (75)
T ss_dssp             HHHHHHHHHHTHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHGGGCCSS--SCHHHHHHHHHHHHHHHTC
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhhhhcCCC--CCHHHHHHHHHHHHHHHHh
Confidence            35799999999999999999999999999999999999999999999874  4799999999999998865

>d1yioa1 a.4.6.2 (A:131-200) Response regulatory protein StyR, C-terminal domain {Pseudomonas fluorescens [TaxId: 294]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: C-terminal effector domain of the bipartite response regulators
family: GerE-like (LuxR/UhpA family of transcriptional regulators)
domain: Response regulatory protein StyR, C-terminal domain
species: Pseudomonas fluorescens [TaxId: 294]

Probab=98.35  E-value=5.6e-07  Score=70.44  Aligned_cols=56  Identities=23%  Similarity=0.285  Sum_probs=50.6

Q ss_pred             HHHHHHHHHhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHh
Q 009449          461 MKKDVFRILESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRD  521 (534)
Q Consensus       461 l~e~L~~~L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~  521 (534)
                      ..+.+...++.|+|+|++|+.+..     .|+|.+|||..||||..||+....++++||--
T Consensus         2 ~~~~~~~~~~~LT~rE~~vl~~l~-----~G~s~~eIA~~l~iS~~TV~~~~~~i~~Klgv   57 (70)
T d1yioa1           2 TQDQLEQLFSSLTGREQQVLQLTI-----RGLMNKQIAGELGIAEVTVKVHRHNIMQKLNV   57 (70)
T ss_dssp             HHHHHHHHHHTSCHHHHHHHHHHT-----TTCCHHHHHHHHTCCHHHHHHHHHHHHHHTTC
T ss_pred             cHHHHHHHHccCCHHHHHHHHHHH-----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHcCC
Confidence            345777888999999999999976     89999999999999999999999999999863

>d1a04a1 a.4.6.2 (A:150-216) Nitrate/nitrite response regulator (NarL) {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: C-terminal effector domain of the bipartite response regulators
family: GerE-like (LuxR/UhpA family of transcriptional regulators)
domain: Nitrate/nitrite response regulator (NarL)
species: Escherichia coli [TaxId: 562]

Probab=98.13  E-value=2e-06  Score=66.57  Aligned_cols=48  Identities=19%  Similarity=0.288  Sum_probs=45.0

Q ss_pred             HhhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHh
Q 009449          469 LESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRD  521 (534)
Q Consensus       469 L~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~  521 (534)
                      +..|+|+|.+|+.+..     +|+|.+|||+.||||..||+++..+++.||.-
T Consensus         4 l~~LT~rE~~vl~ll~-----~G~s~~eIA~~l~iS~~TV~~~~~~i~~Klgv   51 (67)
T d1a04a1           4 VNQLTPRERDILKLIA-----QGLPNKMIARRLDITESTVKVHVKHMLKKMKL   51 (67)
T ss_dssp             GGGSCHHHHHHHHHHH-----TTCCHHHHHHHHTCCHHHHHHHHHHHHHHHTC
T ss_pred             cccCCHHHHHHHHHHH-----hCCCHHHHHHHHCCCHHHHHHHHHHHHHHhCC
Confidence            5689999999999987     89999999999999999999999999999964

>d1l3la1 a.4.6.2 (A:170-234) Quorum-sensing transcription factor TraR, C-terminal domain {Agrobacterium tumefaciens [TaxId: 358]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: C-terminal effector domain of the bipartite response regulators
family: GerE-like (LuxR/UhpA family of transcriptional regulators)
domain: Quorum-sensing transcription factor TraR, C-terminal domain
species: Agrobacterium tumefaciens [TaxId: 358]

Probab=97.98  E-value=6.1e-06  Score=63.33  Aligned_cols=46  Identities=26%  Similarity=0.234  Sum_probs=43.3

Q ss_pred             hCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHh
Q 009449          471 SLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRD  521 (534)
Q Consensus       471 ~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~  521 (534)
                      .|+|+|++|+.+.-     +|+|.+|||+.||+|..||+.+..++++||.-
T Consensus         4 ~Lt~rE~~vl~l~~-----~G~s~~eIA~~l~iS~~TV~~~~~~i~~Klgv   49 (65)
T d1l3la1           4 WLDPKEATYLRWIA-----VGKTMEEIADVEGVKYNSVRVKLREAMKRFDV   49 (65)
T ss_dssp             CCCHHHHHHHHHHT-----TTCCHHHHHHHHTCCHHHHHHHHHHHHHHHTC
T ss_pred             ccCHHHHHHHHHHH-----hcCCHHHHHHHHCCCHHHHHHHHHHHHHHcCC
Confidence            59999999998885     89999999999999999999999999999964

>d1fsea_ a.4.6.2 (A:) Germination protein GerE {Bacillus subtilis [TaxId: 1423]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: C-terminal effector domain of the bipartite response regulators
family: GerE-like (LuxR/UhpA family of transcriptional regulators)
domain: Germination protein GerE
species: Bacillus subtilis [TaxId: 1423]

Probab=97.92  E-value=8.8e-06  Score=62.71  Aligned_cols=46  Identities=33%  Similarity=0.383  Sum_probs=42.9

Q ss_pred             hCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHh
Q 009449          471 SLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRD  521 (534)
Q Consensus       471 ~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~  521 (534)
                      .|+|+|++|+.+..     +|+|.+|||+.||+|..||+.+..++++||--
T Consensus         4 ~LT~rE~~vl~l~~-----~G~s~~eIA~~L~is~~TV~~~~~~i~~Kl~v   49 (67)
T d1fsea_           4 LLTKREREVFELLV-----QDKTTKEIASELFISEKTVRNHISNAMQKLGV   49 (67)
T ss_dssp             CCCHHHHHHHHHHT-----TTCCHHHHHHHHTSCHHHHHHHHHHHHHHHTC
T ss_pred             CCCHHHHHHHHHHH-----ccCCHHHHHHHHCCCHHHHHHHHHHHHHHcCC
Confidence            49999999999875     89999999999999999999999999999864

>d1p4wa_ a.4.6.2 (A:) Transcriptional regulator RcsB {Erwinia amylovora [TaxId: 552]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: C-terminal effector domain of the bipartite response regulators
family: GerE-like (LuxR/UhpA family of transcriptional regulators)
domain: Transcriptional regulator RcsB
species: Erwinia amylovora [TaxId: 552]

Probab=97.60  E-value=3.9e-05  Score=62.10  Aligned_cols=45  Identities=33%  Similarity=0.290  Sum_probs=43.1

Q ss_pred             hCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 009449          471 SLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLR  520 (534)
Q Consensus       471 ~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR  520 (534)
                      .|+++|.+|+.+..     .|++.+|||+.|++|..||+....++++||.
T Consensus        22 ~LT~rE~~vl~ll~-----~G~s~~eIA~~l~iS~~TV~~~~~~i~~Kl~   66 (87)
T d1p4wa_          22 RLSPKESEVLRLFA-----EGFLVTEIAKKLNRSIKTISSQKKSAMMKLG   66 (87)
T ss_dssp             SCCHHHHHHHHHHH-----HTCCHHHHHHHHTSCHHHHHHHHHHHHHHHT
T ss_pred             CCCHHHHHHHHHHH-----cCCCHHHHHHHhCCCHHHHHHHHHHHHHHcC
Confidence            59999999999987     8999999999999999999999999999996

>d1ijwc_ a.4.1.2 (C:) HIN recombinase (DNA-binding domain) {Synthetic}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Recombinase DNA-binding domain
domain: HIN recombinase (DNA-binding domain)
species: Synthetic

Probab=95.00  E-value=0.012  Score=41.83  Aligned_cols=37  Identities=5%  Similarity=0.227  Sum_probs=31.9

Q ss_pred             hCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHH
Q 009449          471 SLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKL  511 (534)
Q Consensus       471 ~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi  511 (534)
                      .|++.+.+-++-.+    ..|.|..+||+.||||+.||...
T Consensus         5 ~lt~~q~~~a~~l~----~~G~s~~~iA~~~gVSr~TiYry   41 (47)
T d1ijwc_           5 AINKHEQEQISRLL----EKGHPRQQLAIIFGIGVSTLYRY   41 (47)
T ss_dssp             SSCHHHHHHHHHHH----HTTCCHHHHHHHHTCCHHHHHHH
T ss_pred             cCCHHHHHHHHHHH----HCCCCHHHHHHHHCcCHHHHHhh
Confidence            47888877777777    68999999999999999999875

>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=94.48  E-value=0.037  Score=40.53  Aligned_cols=40  Identities=20%  Similarity=0.258  Sum_probs=34.6

Q ss_pred             HHHHHHHHHHHHHhCCCCchHHHHHHcCCCHHHHHHHHHh
Q 009449          253 ANLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQHLAF  292 (534)
Q Consensus       253 ~~le~~~~~l~~~~g~~ps~~ewa~a~g~d~~~L~~~l~~  292 (534)
                      .++.++..+|..++||+||.++.|++.|++.+++...+..
T Consensus        15 ~ki~~~~~~l~q~lgRePT~~EiA~~l~~~~e~V~~~l~a   54 (57)
T d1l0oc_          15 NKIRKAKDELSKTRGRAPTVTEIADHLGISPEDVVLAQEA   54 (57)
T ss_dssp             HHHHHHHHHHHHHHTSCCBHHHHHHHHTSCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCCCCCHHHHHHHHCcCHHHHHHHHHH
Confidence            4566778899999999999999999999999998876654

>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=93.18  E-value=0.079  Score=40.67  Aligned_cols=40  Identities=18%  Similarity=0.253  Sum_probs=34.7

Q ss_pred             HHHHHHHHHHHHHHhCCCCchHHHHHHcCCCHHHHHHHHH
Q 009449          252 VANLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQHLA  291 (534)
Q Consensus       252 ~~~le~~~~~l~~~~g~~ps~~ewa~a~g~d~~~L~~~l~  291 (534)
                      ..+++++...|..++||+||.++.|...||+.+++.+.+.
T Consensus         9 ~~ki~~a~~~L~~~lGR~Pt~~EiA~~lg~s~~e~~~~l~   48 (77)
T d1rp3a1           9 ERRIKEVVEKLKEKLGREPTDEEVAKELGISTEELFKTLD   48 (77)
T ss_dssp             HHHHHHHHHHHHHHHSSCCCHHHHHHHHTSCHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHCcCCCHHHHHHHHCcCHHHHHHHHH
Confidence            3467888999999999999999999999999998876543

>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=93.00  E-value=0.046  Score=41.72  Aligned_cols=43  Identities=21%  Similarity=0.207  Sum_probs=33.4

Q ss_pred             hCCHHHHHHHhhHhcC--CCCCCCCHHHHHHHhCC-CHHHHHHHHH
Q 009449          471 SLDSRERQVLVLRYGL--NDHRPKSLEEIGKLFHV-SKEWIRKLEK  513 (534)
Q Consensus       471 ~L~~rEReVL~LryGL--~d~e~~Sl~EIA~~LgI-SrerVRqi~~  513 (534)
                      .|+|+|++|+...-..  ..+-+-|++|||+.+|+ |.++|+.++.
T Consensus         2 ~LT~rQ~~vL~~I~~~~~~~G~~Ps~rei~~~~g~~S~stv~~~l~   47 (71)
T d1jhfa1           2 ALTARQQEVFDLIRDHISQTGMPPTRAEIAQRLGFRSPNAAEEHLK   47 (71)
T ss_dssp             CCCHHHHHHHHHHHHHHHHHSSCCCHHHHHHHTTCSSHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCCHHHHHHHHH
Confidence            5899999998754222  22567899999999999 8999987753

>d1gdta1 a.4.1.2 (A:141-183) gamma,delta resolvase (C-terminal domain) {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Recombinase DNA-binding domain
domain: gamma,delta resolvase (C-terminal domain)
species: Escherichia coli [TaxId: 562]

Probab=92.05  E-value=0.069  Score=36.99  Aligned_cols=32  Identities=16%  Similarity=0.214  Sum_probs=27.2

Q ss_pred             HHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 009449          478 QVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKK  514 (534)
Q Consensus       478 eVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~R  514 (534)
                      +|..|+-     +++.-.+||+.|||++.+|..++..
T Consensus        10 ~V~~L~~-----~G~gat~IAk~lgI~R~SVYR~L~~   41 (43)
T d1gdta1          10 AVLNMWQ-----QGLGASHISKTMNIARSTVYKVINE   41 (43)
T ss_dssp             HHHHHHH-----TTCCHHHHHHHHTCCHHHHHHHHHS
T ss_pred             HHHHHHH-----cCCCHHHHHHHHCCCHHHHHHHHhh
Confidence            4666764     8999999999999999999887653

>d1hlva1 a.4.1.7 (A:1-66) DNA-binding domain of centromere binding protein B (CENP-B) {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Centromere-binding
domain: DNA-binding domain of centromere binding protein B (CENP-B)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=90.89  E-value=0.17  Score=38.17  Aligned_cols=45  Identities=16%  Similarity=0.252  Sum_probs=33.0

Q ss_pred             hCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 009449          471 SLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMT  517 (534)
Q Consensus       471 ~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~  517 (534)
                      .|+..++.=|..+|  ++++.++..|||..|||+++||+.|+.+-=+
T Consensus         7 ~LT~~eK~~ii~~~--e~g~k~sq~eIA~~fGv~~STvs~IlKnK~k   51 (66)
T d1hlva1           7 QLTFREKSRIIQEV--EENPDLRKGEIARRFNIPPSTLSTILKNKRA   51 (66)
T ss_dssp             CCCHHHHHHHHHHH--HHCTTSCHHHHHHHHTCCHHHHHHHHHTHHH
T ss_pred             cCCHHHHHHHHHHH--HcCCcchHHHHHHHhCCChhHHHHHHHHHHH
Confidence            36666665555555  2234478999999999999999999877433

>d1i1ga1 a.4.5.32 (A:2-61) LprA {Archaeon Pyrococcus furiosus [TaxId: 2261]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Lrp/AsnC-like transcriptional regulator N-terminal domain
domain: LprA
species: Archaeon Pyrococcus furiosus [TaxId: 2261]

Probab=90.22  E-value=0.21  Score=36.54  Aligned_cols=40  Identities=25%  Similarity=0.347  Sum_probs=30.6

Q ss_pred             CCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 009449          472 LDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKK  514 (534)
Q Consensus       472 L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~R  514 (534)
                      |++.+++||.+.-.   ....|+.|||+.+|+|+++|..++.+
T Consensus         1 lD~~D~kIl~~L~~---n~r~s~~~lA~~~gls~~~v~~Ri~~   40 (60)
T d1i1ga1           1 IDERDKIILEILEK---DARTPFTEIAKKLGISETAVRKRVKA   40 (60)
T ss_dssp             CCSHHHHHHHHHHH---CTTCCHHHHHHHHTSCHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHH---cCCCCHHHHHHHHCcCHHHHHHHHHH
Confidence            45667778775551   35789999999999999999876543

>d2cg4a1 a.4.5.32 (A:4-66) Regulatory protein AsnC {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Lrp/AsnC-like transcriptional regulator N-terminal domain
domain: Regulatory protein AsnC
species: Escherichia coli [TaxId: 562]

Probab=90.19  E-value=0.25  Score=36.36  Aligned_cols=40  Identities=30%  Similarity=0.369  Sum_probs=32.4

Q ss_pred             CCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 009449          472 LDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKK  514 (534)
Q Consensus       472 L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~R  514 (534)
                      |++..++||...-.   ....|+.|||+.+|+|..+|+.++.+
T Consensus         3 lD~~D~~IL~~L~~---~~r~s~~eiA~~l~ls~~~v~~Ri~r   42 (63)
T d2cg4a1           3 IDNLDRGILEALMG---NARTAYAELAKQFGVSPETIHVRVEK   42 (63)
T ss_dssp             CCHHHHHHHHHHHH---CTTSCHHHHHHHHTSCHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHH---cCCCCHHHHHHHHCcCHHHHHHHHHH
Confidence            67778888877662   46889999999999999999876543

>d2cfxa1 a.4.5.32 (A:1-63) Transcriptional regulator LrpC {Bacillus subtilis [TaxId: 1423]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Lrp/AsnC-like transcriptional regulator N-terminal domain
domain: Transcriptional regulator LrpC
species: Bacillus subtilis [TaxId: 1423]

Probab=89.65  E-value=0.3  Score=35.98  Aligned_cols=40  Identities=15%  Similarity=0.199  Sum_probs=31.8

Q ss_pred             hCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 009449          471 SLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEK  513 (534)
Q Consensus       471 ~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~  513 (534)
                      .|++..+.||...-.   ....|+.|||+.+|+|+++|.+++.
T Consensus         2 klD~~D~~IL~~L~~---n~r~s~~~iA~~lgis~~tv~~Ri~   41 (63)
T d2cfxa1           2 KLDQIDLNIIEELKK---DSRLSMRELGRKIKLSPPSVTERVR   41 (63)
T ss_dssp             CCCHHHHHHHHHHHH---CSCCCHHHHHHHHTCCHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHH---cCCCCHHHHHHHHCcCHHHHHHHHH
Confidence            367778888876652   3578999999999999999987654

>d1ku2a1 a.4.13.1 (A:273-332) Sigma factor SigA {Thermus aquaticus [TaxId: 271]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Sigma3 and sigma4 domains of RNA polymerase sigma factors
family: Sigma3 domain
domain: Sigma factor SigA
species: Thermus aquaticus [TaxId: 271]

Probab=89.22  E-value=0.32  Score=35.76  Aligned_cols=40  Identities=25%  Similarity=0.395  Sum_probs=31.2

Q ss_pred             HHHHHHHHHHHHHHHhCCCCchHHHHHHcC--CCHHHHHHHH
Q 009449          251 VVANLERIKTTLEKESGKAASLNCWAQAAG--VSERVLKQHL  290 (534)
Q Consensus       251 ~~~~le~~~~~l~~~~g~~ps~~ewa~a~g--~d~~~L~~~l  290 (534)
                      .+-++.++..+|..++||+||.+|.|++.|  ++.+.+...+
T Consensus        10 ~i~rv~r~~~~l~qe~gRePt~eEiA~~l~~~l~~ekV~~~l   51 (60)
T d1ku2a1          10 TINKLSRTARQLQQELGREPSYEEIAEAMGPGWDAKRVEETL   51 (60)
T ss_dssp             HHHHHHHHHHHHHHHHTSCCCHHHHHHHHCSSCCHHHHHHHG
T ss_pred             HHHHHHHHHHHHHHHhCCCCCHHHHHHHHCCCCCHHHHHHHH
Confidence            344667788899999999999999999987  4566655544

>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=89.00  E-value=0.4  Score=36.20  Aligned_cols=46  Identities=17%  Similarity=0.154  Sum_probs=37.4

Q ss_pred             HHHHHHHHHHHHHHhcCCCCCHHHHHHHcCC-CHHHHHHHHHHhhhh
Q 009449          380 EISKIQKARKALTNSHGKYPEDIEIAKYTGL-SLAEIRSASECLRIV  425 (534)
Q Consensus       380 ~i~ki~ka~~~L~~elGr~Pt~eEIA~~lgi-s~~kv~~~l~~~~~~  425 (534)
                      .-.+|-.....+..+.|..||..|||+.+|+ +...+...+.....-
T Consensus         6 rQ~~vL~~I~~~~~~~G~~Ps~rei~~~~g~~S~stv~~~l~~Le~k   52 (71)
T d1jhfa1           6 RQQEVFDLIRDHISQTGMPPTRAEIAQRLGFRSPNAAEEHLKALARK   52 (71)
T ss_dssp             HHHHHHHHHHHHHHHHSSCCCHHHHHHHTTCSSHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCCHHHHHHHHHHHHHC
Confidence            3345666777788899999999999999999 799999888776543

>d2jn6a1 a.4.1.19 (A:1-89) Uncharacterized protein Cgl2762 {Corynebacterium glutamicum [TaxId: 1718]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Cgl2762-like
domain: Uncharacterized protein Cgl2762
species: Corynebacterium glutamicum [TaxId: 1718]

Probab=88.53  E-value=0.23  Score=39.01  Aligned_cols=35  Identities=17%  Similarity=0.198  Sum_probs=28.8

Q ss_pred             HHHHhhHhcCCCC-CCCCHHHHHHHhCCCHHHHHHHHHHH
Q 009449          477 RQVLVLRYGLNDH-RPKSLEEIGKLFHVSKEWIRKLEKKA  515 (534)
Q Consensus       477 ReVL~LryGL~d~-e~~Sl~EIA~~LgISrerVRqi~~RA  515 (534)
                      .+||.+..    . +|.|..+||+.|||+..+|+++..+.
T Consensus        12 ~~aV~l~~----~~~g~s~~~vA~~lGIs~~tl~~W~k~~   47 (89)
T d2jn6a1          12 RDAVALYE----NSDGASLQQIANDLGINRVTLKNWIIKY   47 (89)
T ss_dssp             HHHHHHHT----TGGGSCHHHHHHHHTSCHHHHHHHHHHH
T ss_pred             HHHHHHHH----HcCCCcHHHHHHHHCCCHHHHHHHHHHH
Confidence            35666665    3 47999999999999999999998765

>d1pdnc_ a.4.1.5 (C:) Paired protein (prd) {Fruit fly (Drosophila melanogaster) [TaxId: 7227]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Paired domain
domain: Paired protein (prd)
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

Probab=87.43  E-value=0.35  Score=40.40  Aligned_cols=40  Identities=18%  Similarity=0.089  Sum_probs=30.3

Q ss_pred             CCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 009449          472 LDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKA  515 (534)
Q Consensus       472 L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RA  515 (534)
                      |+...|+=|.-.|    ..+++..+||+.||||+.+|..++.+=
T Consensus        17 Ls~dlR~rIv~~~----~~G~s~r~iA~~~~VS~~tV~k~l~r~   56 (123)
T d1pdnc_          17 LPNNIRLKIVEMA----ADGIRPCVISRQLRVSHGCVSKILNRY   56 (123)
T ss_dssp             CCHHHHHHHHHHH----HTTCCHHHHHHHHTCCHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHH----HhcCCHHHHHHHHCcCHHHHHHHHHHH
Confidence            4555444444445    579999999999999999999887663

>d2cyya1 a.4.5.32 (A:5-64) Putative transcriptional regulator PH1519 {Archaeon Pyrococcus horikoshii [TaxId: 53953]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Lrp/AsnC-like transcriptional regulator N-terminal domain
domain: Putative transcriptional regulator PH1519
species: Archaeon Pyrococcus horikoshii [TaxId: 53953]

Probab=87.41  E-value=0.54  Score=34.07  Aligned_cols=40  Identities=20%  Similarity=0.319  Sum_probs=29.8

Q ss_pred             CCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 009449          472 LDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKK  514 (534)
Q Consensus       472 L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~R  514 (534)
                      |++..+.||...-.   ....|+.|||+.+|+|+.+|..++.+
T Consensus         1 lD~~D~~Il~~L~~---n~r~s~~eiA~~l~ls~~~v~~Ri~~   40 (60)
T d2cyya1           1 LDEIDKKIIKILQN---DGKAPLREISKITGLAESTIHERIRK   40 (60)
T ss_dssp             CCHHHHHHHHHHHH---CTTCCHHHHHHHHCSCHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHH---cCCCCHHHHHHHHCcCHHHHHHHHHH
Confidence            45566677765541   35779999999999999999865543

>d1biaa1 a.4.5.1 (A:1-63) Biotin repressor, N-terminal domain {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Biotin repressor-like
domain: Biotin repressor, N-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=87.32  E-value=0.53  Score=34.61  Aligned_cols=42  Identities=24%  Similarity=0.280  Sum_probs=30.9

Q ss_pred             CHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHh
Q 009449          473 DSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRD  521 (534)
Q Consensus       473 ~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~  521 (534)
                      +....+||.+--   +....|.+|+|+.||||+.||+..+    ++|++
T Consensus         4 ~~~~~~iL~~L~---~~~~~s~~eLa~~l~vS~~ti~r~i----~~L~~   45 (63)
T d1biaa1           4 NTVPLKLIALLA---NGEFHSGEQLGETLGMSRAAINKHI----QTLRD   45 (63)
T ss_dssp             CHHHHHHHHHHT---TSSCBCHHHHHHHHTSCHHHHHHHH----HHHHH
T ss_pred             cHHHHHHHHHHH---HCCcCCHHHHHHHHCcCHHHHHHHH----HHHHH
Confidence            445556666543   4577899999999999999998654    45654

>d1dpua_ a.4.5.16 (A:) C-terminal domain of RPA32 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: C-terminal domain of RPA32
domain: C-terminal domain of RPA32
species: Human (Homo sapiens) [TaxId: 9606]

Probab=87.17  E-value=0.31  Score=36.98  Aligned_cols=43  Identities=19%  Similarity=0.210  Sum_probs=38.5

Q ss_pred             hhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHh-CCCHHHHHHHH
Q 009449          470 ESLDSRERQVLVLRYGLNDHRPKSLEEIGKLF-HVSKEWIRKLE  512 (534)
Q Consensus       470 ~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~L-gISrerVRqi~  512 (534)
                      +.|+|.+++|+.+.-.-.+.+|.+..||+..| |++...|++..
T Consensus         2 nGLs~~q~~V~~~i~s~~~~eGi~~~el~~~l~~~~~~~i~~ai   45 (69)
T d1dpua_           2 NGLTVAQNQVLNLIKACPRPEGLNFQDLKNQLKHMSVSSIKQAV   45 (69)
T ss_dssp             CCSCHHHHHHHHHHHHCCCTTTEEHHHHHHHSTTSCHHHHHHHH
T ss_pred             CCCCHHHHHHHHHHHhCCCccCcCHHHHHHHccCCCHHHHHHHH
Confidence            46999999999999988888999999999999 89999997654

>d1nr3a_ d.236.1.1 (A:) DNA-binding protein Tfx {Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262]}

class: Alpha and beta proteins (a+b)
fold: DNA-binding protein Tfx
superfamily: DNA-binding protein Tfx
family: DNA-binding protein Tfx
domain: DNA-binding protein Tfx
species: Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262]

Probab=86.74  E-value=0.0069  Score=51.40  Aligned_cols=34  Identities=24%  Similarity=0.397  Sum_probs=31.4

Q ss_pred             CCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhH
Q 009449          489 HRPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDS  522 (534)
Q Consensus       489 ~e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~~  522 (534)
                      .+|+|++|||++||.|+..|+.++++|+..+++.
T Consensus         3 ~kGltQ~eIA~~LgTSraNIs~IEk~A~eNIekA   36 (122)
T d1nr3a_           3 ERGWSQKKIARELKTTRQNVSAIERKAMENIEKS   36 (122)
T ss_dssp             CCSCSSCSTHHHHHHCCSSSCCHHHHHHTTCSSS
T ss_pred             cccCCHHHHHHHHCccHHHHHHHHHHHHHHHHHH
Confidence            3799999999999999999999999999988764

>d2ppxa1 a.35.1.3 (A:30-91) Uncharacterized protein Atu1735 {Agrobacterium tumefaciens [TaxId: 358]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: SinR domain-like
domain: Uncharacterized protein Atu1735
species: Agrobacterium tumefaciens [TaxId: 358]

Probab=86.61  E-value=0.27  Score=36.02  Aligned_cols=25  Identities=20%  Similarity=0.279  Sum_probs=23.0

Q ss_pred             CCCCCHHHHHHHhCCCHHHHHHHHH
Q 009449          489 HRPKSLEEIGKLFHVSKEWIRKLEK  513 (534)
Q Consensus       489 ~e~~Sl~EIA~~LgISrerVRqi~~  513 (534)
                      ..++|.+|+|+.+|||+.+|+++++
T Consensus        10 ~~gltQ~elA~~lGvs~~tvs~~E~   34 (62)
T d2ppxa1          10 ALKLTQEEFSARYHIPLGTLRDWEQ   34 (62)
T ss_dssp             HTTCCHHHHHHHHTCCHHHHHHHHT
T ss_pred             HcCCCHHHHHHHhCCCHHHHHHHHC
Confidence            3489999999999999999999997

>d1r1ta_ a.4.5.5 (A:) SmtB repressor {Cyanobacteria (Synechococcus), pcc7942 [TaxId: 1129]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: ArsR-like transcriptional regulators
domain: SmtB repressor
species: Cyanobacteria (Synechococcus), pcc7942 [TaxId: 1129]

Probab=84.81  E-value=1.1  Score=35.74  Aligned_cols=45  Identities=13%  Similarity=0.190  Sum_probs=32.4

Q ss_pred             HHHHHhhC-CHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 009449          465 VFRILESL-DSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEK  513 (534)
Q Consensus       465 L~~~L~~L-~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~  513 (534)
                      +.+++..| +|.-.+||.+-.    ..+++..|||+.+|+|+++|++++.
T Consensus        13 la~~~kaL~~p~Rl~Il~~L~----~~~~~v~ela~~l~is~stvS~HL~   58 (98)
T d1r1ta_          13 LAEFFAVLADPNRLRLLSLLA----RSELCVGDLAQAIGVSESAVSHQLR   58 (98)
T ss_dssp             HHHHHHHHCCHHHHHHHHHHT----TCCBCHHHHHHHHTCCHHHHHHHHH
T ss_pred             HHHHHHHhCCHHHHHHHHHHH----cCCcCHHHHHHHHCcCHHHHHHHHH
Confidence            34444444 455556666554    4679999999999999999988754

>d1ft9a1 a.4.5.4 (A:134-213) CO-sensing protein CooA, C-terminal domain {Rhodospirillum rubrum [TaxId: 1085]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: CAP C-terminal domain-like
domain: CO-sensing protein CooA, C-terminal domain
species: Rhodospirillum rubrum [TaxId: 1085]

Probab=84.63  E-value=0.45  Score=36.29  Aligned_cols=28  Identities=25%  Similarity=0.298  Sum_probs=24.5

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhH
Q 009449          491 PKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDS  522 (534)
Q Consensus       491 ~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~~  522 (534)
                      ++|.+|||..+|+|+++|.    |++++|++.
T Consensus        30 ~~t~~eiA~~lG~sretvs----r~l~~l~~~   57 (80)
T d1ft9a1          30 DFTVEEIANLIGSSRQTTS----TALNSLIKE   57 (80)
T ss_dssp             CCCHHHHHHHHCSCHHHHH----HHHHHHHHT
T ss_pred             CCCHHHHHHHHCCCHHHHH----HHHHHHHHC
Confidence            6899999999999999995    777788764

>d2a6ca1 a.35.1.13 (A:1-69) HTH-motif protein NE1354 {Nitrosomonas europaea [TaxId: 915]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: NE1354
domain: HTH-motif protein NE1354
species: Nitrosomonas europaea [TaxId: 915]

Probab=84.13  E-value=0.53  Score=34.90  Aligned_cols=32  Identities=9%  Similarity=0.037  Sum_probs=27.9

Q ss_pred             HHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 009449          478 QVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEK  513 (534)
Q Consensus       478 eVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~  513 (534)
                      .|-.+|.    ..++|++|+|+.+||++.+|..+++
T Consensus        10 ~i~~~r~----~~gltq~elA~~~gv~~~~is~ie~   41 (69)
T d2a6ca1          10 VLQEHLR----NSGLTQFKAAELLGVTQPRVSDLMR   41 (69)
T ss_dssp             HHHHHHH----TTTCCHHHHHHHHTSCHHHHHHHHT
T ss_pred             HHHHHHH----HcCCCHHHHHHHHHcCHhHHHHHHc
Confidence            3555666    7899999999999999999999986

>d1r1ua_ a.4.5.5 (A:) Metal-sensing transcriptional repressor CzrA {Staphylococcus aureus [TaxId: 1280]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: ArsR-like transcriptional regulators
domain: Metal-sensing transcriptional repressor CzrA
species: Staphylococcus aureus [TaxId: 1280]

Probab=83.95  E-value=1.1  Score=35.52  Aligned_cols=47  Identities=19%  Similarity=0.258  Sum_probs=34.2

Q ss_pred             HHHHHHHhhCCHHHH-HHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 009449          463 KDVFRILESLDSRER-QVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEK  513 (534)
Q Consensus       463 e~L~~~L~~L~~rER-eVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~  513 (534)
                      +.+.+++..|...-| .||.+..    ..+++..||++.+|+|+++|++++.
T Consensus         6 e~~a~~fkaL~d~~Rl~Il~~L~----~~~~~v~el~~~l~~s~~~vS~HL~   53 (94)
T d1r1ua_           6 ERVTEIFKALGDYNRIRIMELLS----VSEASVGHISHQLNLSQSNVSHQLK   53 (94)
T ss_dssp             HHHHHHHHHTCSHHHHHHHHHHH----HCCBCHHHHHHHHTCCHHHHHHHHH
T ss_pred             HHHHHHHHHhCCHHHHHHHHHHH----cCCccHHHHHHHHCCCHHHHHHHHH
Confidence            345566677765544 5555544    4689999999999999999987653

>d1ku9a_ a.4.5.36 (A:) DNA-binding protein Mj223 {Archaeon Methanococcus jannaschii [TaxId: 2190]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: DNA-binding protein Mj223
domain: DNA-binding protein Mj223
species: Archaeon Methanococcus jannaschii [TaxId: 2190]

Probab=83.18  E-value=1.2  Score=37.08  Aligned_cols=51  Identities=20%  Similarity=0.288  Sum_probs=38.3

Q ss_pred             HHHHHHHHHh--hCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 009449          461 MKKDVFRILE--SLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEK  513 (534)
Q Consensus       461 l~e~L~~~L~--~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~  513 (534)
                      +.+.+...+.  .|++.+-.|+.+-+ +.+ +++|..|||+.+|+|+++|+..+.
T Consensus        11 ~~~~~~~~~~~~Gl~~~~~~i~~~L~-~~~-~plt~~ela~~l~vsk~~vs~~l~   63 (151)
T d1ku9a_          11 IIELFSELAKIHGLNKSVGAVYAILY-LSD-KPLTISDIMEELKISKGNVSMSLK   63 (151)
T ss_dssp             HHHHHHHHHHHTTCCHHHHHHHHHHH-HCS-SCEEHHHHHHHHTCCHHHHHHHHH
T ss_pred             HHHHHHHHHHHcCCCHHHHHHHHHHH-hCC-CCcCHHHHHHHhCCCcchHHHHHH
Confidence            3344444443  57999999998887 333 579999999999999999975443

>d2d1ha1 a.4.5.50 (A:1-109) Hypothetical transcriptional regulator ST1889 {Sulfolobus tokodaii [TaxId: 111955]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: TrmB-like
domain: Hypothetical transcriptional regulator ST1889
species: Sulfolobus tokodaii [TaxId: 111955]

Probab=82.93  E-value=0.59  Score=37.49  Aligned_cols=43  Identities=23%  Similarity=0.359  Sum_probs=33.6

Q ss_pred             hhCCHHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 009449          470 ESLDSRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKK  514 (534)
Q Consensus       470 ~~L~~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~R  514 (534)
                      -.|++.+..||...+--  ..++|..|||+.+|+++.+|+.++.+
T Consensus        17 ~gLs~~~~~iL~~L~~~--~~~~t~~eLa~~~~i~~~tvs~~l~~   59 (109)
T d2d1ha1          17 YKITDTDVAVLLKMVEI--EKPITSEELADIFKLSKTTVENSLKK   59 (109)
T ss_dssp             HTCCHHHHHHHHHHHHH--CSCEEHHHHHHHHTCCHHHHHHHHHH
T ss_pred             cCcCHHHHHHHHHHHHc--CCCCCHHHHHHHHCccHhHHHHHHHH
Confidence            36999999998655411  24689999999999999999865543

>d3e5ua1 a.4.5.4 (A:148-227) Chlorophenol reduction protein CprK {Desulfitobacterium hafniense [TaxId: 49338]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: CAP C-terminal domain-like
domain: Chlorophenol reduction protein CprK
species: Desulfitobacterium hafniense [TaxId: 49338]

Probab=82.66  E-value=0.61  Score=35.42  Aligned_cols=29  Identities=21%  Similarity=0.358  Sum_probs=24.7

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhH
Q 009449          490 RPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDS  522 (534)
Q Consensus       490 e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~~  522 (534)
                      -++|.+|||..+|+|+++|.    |++++|++.
T Consensus        29 ~~lt~~elA~~~g~sretvs----r~l~~l~~~   57 (80)
T d3e5ua1          29 MPLSQKSIGEITGVHHVTVS----RVLASLKRE   57 (80)
T ss_dssp             SCCCHHHHHHHHTCCHHHHH----HHHHHHHHT
T ss_pred             eCCCHHHHHHHHCCCHHHHH----HHHHHHHHC
Confidence            36899999999999999995    677777764

>d1k78a1 a.4.1.5 (A:19-81) Pax-5 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Paired domain
domain: Pax-5
species: Human (Homo sapiens) [TaxId: 9606]

Probab=82.46  E-value=1.1  Score=33.26  Aligned_cols=32  Identities=16%  Similarity=0.185  Sum_probs=26.8

Q ss_pred             HHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 009449          479 VLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKKA  515 (534)
Q Consensus       479 VL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~RA  515 (534)
                      ||.+..     ++.|..+||++|+||.++|..+..+-
T Consensus        23 iv~~~~-----~G~s~r~aA~rf~VS~s~v~k~l~r~   54 (63)
T d1k78a1          23 IVELAH-----QGVRPCDISRQLRVSHGCVSKILGRY   54 (63)
T ss_dssp             HHHHHH-----TTCCHHHHHHHHTCCHHHHHHHHHHH
T ss_pred             HHHHHH-----cCCCHHHHHHHhCCCHHHHHHHHHHH
Confidence            555543     78999999999999999999887764

>d1utxa_ a.35.1.3 (A:) Putative transcription regulator CylR2 {Enterococcus faecalis [TaxId: 1351]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: SinR domain-like
domain: Putative transcription regulator CylR2
species: Enterococcus faecalis [TaxId: 1351]

Probab=82.36  E-value=0.49  Score=34.72  Aligned_cols=25  Identities=32%  Similarity=0.449  Sum_probs=23.3

Q ss_pred             CCCCCHHHHHHHhCCCHHHHHHHHH
Q 009449          489 HRPKSLEEIGKLFHVSKEWIRKLEK  513 (534)
Q Consensus       489 ~e~~Sl~EIA~~LgISrerVRqi~~  513 (534)
                      ..++|++|+|+.+|||+.+|.++++
T Consensus        12 ~~g~tq~elA~~~gis~~~is~~e~   36 (66)
T d1utxa_          12 KKKISQSELAALLEVSRQTINGIEK   36 (66)
T ss_dssp             HTTCCHHHHHHHHTSCHHHHHHHHT
T ss_pred             HcCCCHHHHHHhcccCHHHHHHHHc
Confidence            5789999999999999999999986

>d2o38a1 a.35.1.13 (A:28-116) Hypothetical protein RPA3824 {Rhodopseudomonas palustris [TaxId: 1076]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: NE1354
domain: Hypothetical protein RPA3824
species: Rhodopseudomonas palustris [TaxId: 1076]

Probab=81.97  E-value=0.55  Score=36.70  Aligned_cols=31  Identities=6%  Similarity=0.003  Sum_probs=26.9

Q ss_pred             HHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 009449          479 VLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEK  513 (534)
Q Consensus       479 VL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~  513 (534)
                      |-.+|-    ..|+|++|+|+.+|||+.+|.++++
T Consensus        16 i~~~r~----~~gltq~~lA~~~gis~~~is~ie~   46 (89)
T d2o38a1          16 LNAVID----RARLSQAAAAARLGINQPKVSALRN   46 (89)
T ss_dssp             HHHHHH----HTTCCHHHHHHHHTCCHHHHHHHHT
T ss_pred             HHHHHH----HcCCCHHHHHHHHHhhHhHHHHHHc
Confidence            445555    6799999999999999999999997

>d2auwa1 a.35.1.10 (A:88-154) Hypothetical protein NE0471 C-terminal domain {Nitrosomonas europaea [TaxId: 915]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: NE0471 C-terminal domain-like
domain: Hypothetical protein NE0471 C-terminal domain
species: Nitrosomonas europaea [TaxId: 915]

Probab=81.89  E-value=0.6  Score=35.04  Aligned_cols=25  Identities=12%  Similarity=0.174  Sum_probs=22.9

Q ss_pred             CCCCCHHHHHHHhCCCHHHHHHHHH
Q 009449          489 HRPKSLEEIGKLFHVSKEWIRKLEK  513 (534)
Q Consensus       489 ~e~~Sl~EIA~~LgISrerVRqi~~  513 (534)
                      ..++|++|+|+.||||+.+|.+++.
T Consensus        12 ~~gltQ~elA~~LGvs~~ti~~yE~   36 (67)
T d2auwa1          12 RNNLSLTTAAEALGISRRMVSYYRT   36 (67)
T ss_dssp             HTTCCHHHHHHHHTSCHHHHHHHHT
T ss_pred             HcCCCHHHHHHHhCCCHHHHHHHHc
Confidence            4689999999999999999999876

>d2gaua1 a.4.5.4 (A:152-232) Transcriptional regulator PG0396, C-terminal domain {Porphyromonas gingivalis [TaxId: 837]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: CAP C-terminal domain-like
domain: Transcriptional regulator PG0396, C-terminal domain
species: Porphyromonas gingivalis [TaxId: 837]

Probab=81.78  E-value=0.65  Score=35.20  Aligned_cols=29  Identities=14%  Similarity=0.101  Sum_probs=24.6

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhH
Q 009449          490 RPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDS  522 (534)
Q Consensus       490 e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~~  522 (534)
                      -++|.+|||..+|+|+++|.    |++++|++.
T Consensus        28 ~~lt~~eLA~~~G~sretvs----r~L~~l~~~   56 (81)
T d2gaua1          28 IYLSREELATLSNMTVSNAI----RTLSTFVSE   56 (81)
T ss_dssp             CCCCHHHHHHHTTSCHHHHH----HHHHHHHHT
T ss_pred             ecCCHHHHHHHHCCCHHHHH----HHHHHHHHC
Confidence            46899999999999999995    677777764

>d2o3fa1 a.4.1.20 (A:1-83) Putative transcriptional regulator YbbH {Bacillus subtilis [TaxId: 1423]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: RpiR-like
domain: Putative transcriptional regulator YbbH
species: Bacillus subtilis [TaxId: 1423]

Probab=81.45  E-value=0.91  Score=35.18  Aligned_cols=51  Identities=18%  Similarity=0.150  Sum_probs=39.3

Q ss_pred             HHHHHHHhhCCHHHHHHHhhHhcC-CCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 009449          463 KDVFRILESLDSRERQVLVLRYGL-NDHRPKSLEEIGKLFHVSKEWIRKLEK  513 (534)
Q Consensus       463 e~L~~~L~~L~~rEReVL~LryGL-~d~e~~Sl~EIA~~LgISrerVRqi~~  513 (534)
                      ..|...+..|++.|+.|.....-= ++...+|.+|||+..|||+.+|-..-+
T Consensus         7 ~~i~~~~~~Ls~~e~~ia~yil~~~~~~~~~si~~lA~~~~vS~sTi~Rf~k   58 (83)
T d2o3fa1           7 AIIQSMKHKLPPSERKLADYILAHPHKAIESTVNEISALANSSDAAVIRLCK   58 (83)
T ss_dssp             HHHHHHGGGSCHHHHHHHHHHHHCHHHHHTCCHHHHHHHTTCCHHHHHHHHH
T ss_pred             HHHHHHHhhCCHHHHHHHHHHHcCHHHHHHccHHHHHHHHCCCHHHHHHHHH
Confidence            467778899999999987654310 123579999999999999999976544

>d1zyba1 a.4.5.4 (A:148-220) Probable transcription regulator BT4300, C-terminal domain {Bacteroides thetaiotaomicron [TaxId: 818]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: CAP C-terminal domain-like
domain: Probable transcription regulator BT4300, C-terminal domain
species: Bacteroides thetaiotaomicron [TaxId: 818]

Probab=81.44  E-value=0.59  Score=35.29  Aligned_cols=28  Identities=14%  Similarity=0.370  Sum_probs=24.2

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhH
Q 009449          491 PKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDS  522 (534)
Q Consensus       491 ~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~~  522 (534)
                      +.|.+|||..+|+|+++|.    |++++|++.
T Consensus        27 ~lt~~elA~~lg~sr~tvs----r~l~~l~~~   54 (73)
T d1zyba1          27 KVKMDDLARCLDDTRLNIS----KTLNELQDN   54 (73)
T ss_dssp             ECCHHHHHHHHTSCHHHHH----HHHHHHHHT
T ss_pred             ecCHHHHHHHHCCCHHHHH----HHHHHHHHC
Confidence            4799999999999999995    778888764

>d1j5ya1 a.4.5.1 (A:3-67) Putative transcriptional regulator TM1602, N-terminal domain {Thermotoga maritima [TaxId: 2336]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Biotin repressor-like
domain: Putative transcriptional regulator TM1602, N-terminal domain
species: Thermotoga maritima [TaxId: 2336]

Probab=81.26  E-value=1  Score=32.96  Aligned_cols=39  Identities=15%  Similarity=0.158  Sum_probs=28.2

Q ss_pred             HHHHHHHhhHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 009449          474 SRERQVLVLRYGLNDHRPKSLEEIGKLFHVSKEWIRKLEKK  514 (534)
Q Consensus       474 ~rEReVL~LryGL~d~e~~Sl~EIA~~LgISrerVRqi~~R  514 (534)
                      +|...|+.+..  ......|..|+|+.||||+.||++-+..
T Consensus         7 eR~~~Il~~L~--~~~~~vs~~~La~~l~VS~~TI~rdi~~   45 (65)
T d1j5ya1           7 ERLKSIVRILE--RSKEPVSGAQLAEELSVSRQVIVQDIAY   45 (65)
T ss_dssp             HHHHHHHHHHH--HCSSCBCHHHHHHHHTSCHHHHHHHHHH
T ss_pred             HHHHHHHHHHH--HcCCCCcHHHHHHHHCCCHHHHHHHHHH
Confidence            45566666543  1123579999999999999999876643

>d1stza1 a.4.5.51 (A:14-100) Heat-inducible transcription repressor HrcA, N-terminal domain {Thermotoga maritima [TaxId: 2336]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Heat-inducible transcription repressor HrcA, N-terminal domain
domain: Heat-inducible transcription repressor HrcA, N-terminal domain
species: Thermotoga maritima [TaxId: 2336]

Probab=81.03  E-value=0.65  Score=36.58  Aligned_cols=43  Identities=26%  Similarity=0.332  Sum_probs=33.0

Q ss_pred             hCCHHHHHHHhhHhc--CCCCCCCCHHHHHHHhC--CCHHHHHHHHH
Q 009449          471 SLDSRERQVLVLRYG--LNDHRPKSLEEIGKLFH--VSKEWIRKLEK  513 (534)
Q Consensus       471 ~L~~rEReVL~LryG--L~d~e~~Sl~EIA~~Lg--ISrerVRqi~~  513 (534)
                      .|++|+++||....-  +..+.+.+.++|++.+|  +|..|||..+.
T Consensus         1 ~Lt~Rq~~IL~~Ive~y~~~g~Pv~s~~i~~~~~l~~S~aTIRn~m~   47 (87)
T d1stza1           1 KLNDRQRKVLYCIVREYIENKKPVSSQRVLEVSNIEFSSATIRNDMK   47 (87)
T ss_dssp             CCCHHHHHHHHHHHHHHHHHCSCBCHHHHHHHSCCCSCHHHHHHHHH
T ss_pred             CcCHHHHHHHHHHHHHHHHcCCccCHHHHHHHhCCCCCHHHHHHHHH
Confidence            488999998864321  34578999999999966  58999998654

>d1r69a_ a.35.1.2 (A:) 434 C1 repressor, DNA-binding domain {Bacteriophage 434 [TaxId: 10712]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: Phage repressors
domain: 434 C1 repressor, DNA-binding domain
species: Bacteriophage 434 [TaxId: 10712]

Probab=80.63  E-value=0.71  Score=33.29  Aligned_cols=26  Identities=15%  Similarity=0.184  Sum_probs=23.9

Q ss_pred             CCCCCHHHHHHHhCCCHHHHHHHHHH
Q 009449          489 HRPKSLEEIGKLFHVSKEWIRKLEKK  514 (534)
Q Consensus       489 ~e~~Sl~EIA~~LgISrerVRqi~~R  514 (534)
                      ..++|++|+|+.+|||+.+|++++..
T Consensus        12 ~~g~sq~elA~~~gvs~~~is~~E~g   37 (63)
T d1r69a_          12 QLGLNQAELAQKVGTTQQSIEQLENG   37 (63)
T ss_dssp             HTTCCHHHHHHHHTSCHHHHHHHHTT
T ss_pred             HcCCcHHHHHHHhCcCHHHHHHHHCC
Confidence            57899999999999999999999863

>d1yz8p1 a.4.1.1 (P:1-60) Pituitary homeobox 2 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Pituitary homeobox 2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=80.44  E-value=2.2  Score=30.70  Aligned_cols=51  Identities=22%  Similarity=0.195  Sum_probs=42.4

Q ss_pred             hCCHHHHHHHhhHhcCCCC-CCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHh
Q 009449          471 SLDSRERQVLVLRYGLNDH-RPKSLEEIGKLFHVSKEWIRKLEKKAMTKLRD  521 (534)
Q Consensus       471 ~L~~rEReVL~LryGL~d~-e~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~  521 (534)
                      .+++.+..+|.-.|..+.+ ......+||..+|++...|..+......+.|.
T Consensus         7 ~ft~~Q~~~Le~~F~~~~yP~~~~r~~LA~~l~l~~~~V~~WFqNrR~k~kr   58 (60)
T d1yz8p1           7 HFTSQQLQQLEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRK   58 (60)
T ss_dssp             CCCHHHHHHHHHHHTTCSSCCTTTTTHHHHHTTSCHHHHHHHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHHHcCCCChHHHHHHHHHHCCChHHHHHHhHHHHHHHHh
Confidence            3678888999999976644 45677899999999999999999988888775

>d1y7ya1 a.35.1.3 (A:5-73) Restriction-modification controller protein C.AhdI {Aeromonas hydrophila [TaxId: 644]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: SinR domain-like
domain: Restriction-modification controller protein C.AhdI
species: Aeromonas hydrophila [TaxId: 644]

Probab=80.41  E-value=0.73  Score=33.98  Aligned_cols=25  Identities=16%  Similarity=0.275  Sum_probs=23.3

Q ss_pred             CCCCCHHHHHHHhCCCHHHHHHHHH
Q 009449          489 HRPKSLEEIGKLFHVSKEWIRKLEK  513 (534)
Q Consensus       489 ~e~~Sl~EIA~~LgISrerVRqi~~  513 (534)
                      ..++|++++|+.+|+|+.+|+++++
T Consensus        20 ~~gltq~~lA~~~gis~~~i~~~E~   44 (69)
T d1y7ya1          20 AKGLSQETLAFLSGLDRSYVGGVER   44 (69)
T ss_dssp             HTTCCHHHHHHHHTCCHHHHHHHHT
T ss_pred             HcCCCHHHHHhHhCCCHHHHHHHHC
Confidence            5789999999999999999999986

>d1i5za1 a.4.5.4 (A:138-206) Catabolite gene activator protein (CAP), C-terminal domain {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: CAP C-terminal domain-like
domain: Catabolite gene activator protein (CAP), C-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=80.32  E-value=0.6  Score=34.58  Aligned_cols=28  Identities=25%  Similarity=0.421  Sum_probs=23.4

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhH
Q 009449          491 PKSLEEIGKLFHVSKEWIRKLEKKAMTKLRDS  522 (534)
Q Consensus       491 ~~Sl~EIA~~LgISrerVRqi~~RAL~KLR~~  522 (534)
                      +.|.+|||..+|+|+++|.    |.+++|++.
T Consensus        29 ~lt~~~lA~~~G~sRetvs----r~L~~l~~~   56 (69)
T d1i5za1          29 KITRQEIGQIVGCSRETVG----RILKMLEDQ   56 (69)
T ss_dssp             ECCHHHHHHHHTCCHHHHH----HHHHHHHHT
T ss_pred             CCCHHHHHHHHCCCHHHHH----HHHHHHHHC
Confidence            4899999999999999996    566667653