Citrus Sinensis ID: 012638

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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-------46
Protein Sequence
MGMGFRLNLKWVSPVQSHFFTTSSCRLSSTSVRGREGSFNSARLSFLSTISEDSASYFQDPVKAYTCSFVNTQTVENDYSETEEIRQKSTSCIGQDASSRSDFRLLMENLDVLESTFADSDALRLEREILQQLGKLGALKLFNSHLSRIVKTSNVLDLSDVHTEEQKMNDSRDYHMGKILVPSKRKGKRKLKTARVSEESIETSLLSLPSEALQEGLKQPTIFSAERALNSRGRRLTIARNEAEMSKGVQVVANLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQHLAFGWYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNAKYLNIPPFFFPSFAIWEWEEY
Secondary Structure (PSIPRED)
cccccEEccccccccccccccccccccccccccccccccccccccHHHHHHHccccccccccccccccccccHHHHHHHHHHHHHHHHHccccccccccHHHHHHHHHHHHHHHHHHHcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccccccccHHHccccccccccccccccccHHHHHHHHHHHHHHHHHHHHcccccHHHHHHccccccccHHHHHHHHcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccHHHHHHHccccHHHHHHHHHHHHHHHHHHHHHcccEEEHHHHHcccccccHHHHHHHcHHHHHHHHHcccccccccccHHHHHHHHHHHHHHHHHccccccccHHHHHHHHHHHHHHHHHHHHccccccHHHHHHHHcccHHHHHHHHHcccccccccccccccccccccccccccccccccHHHccc
Secondary Structure Prediction (SSPRO)
ccccEEEccccccccccccccccccccccccccccEccccccEEccccccccccccccccccccEEccccccccEEcccccccccccccccEcccccccHHHHHHHHHHHHHHHHHHHcHHHHHHHHHHHHHHHHHcHHHHHHHHHccccccccccccccccccHcccccccHHccccEEEccccHHHHHHHHHHccccccccccccccHHHHHHHccccccHHHHHHHHHHccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccHHHHHHHccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccHHHHHHHHcccHHHHHHHHccccccccHHHHHHHHHHHHHHHHHHHHccccEccHHHHHHHHHHHHHHHHHHHHccccccHHHHHHHccccHHHHHHHHHHcccccEEcccccccccccHHHHcccccccHHccccccc
Coil and Loop (DISEMBL)
mgmgfrlnlkwvspvqshffttsscrlsstsvrgregsfnsARLSFLSTISedsasyfqdpvkayTCSFVntqtvendyseTEEIRQKstscigqdassrsDFRLLMENLDVlestfadsDALRLEREILQQLGKLGALKLFNSHLSRIvktsnvldlsdvhteeqkmndsrdyhmgkilvpskrkgkrklktaRVSEESIETSLlslpsealqeglkqptiFSAERALNSRGRRLTIARNEAEMSKGVQVVANLERIKTTLEkesgkaasLNCWAQAAGVSERVLKQHLAFGWYCREELIKSTRPLVLFLARNyrglgipfsdllqagnvgvlqgaerfdhtrgykfsTYVQYWIRKSISKMVARHArgikipcklNREISKIQKARKALtnshgkypedieiaKYTGLSLAEIRSASECLRIVGSIDQKIGdclnakylnippfffpsfaiweweey
Flexible Loop (DISEMBL)
MGMGFRLNLKWVSPVQSHFfttsscrlsstsvrgregsfNSARLSFLSTISEDSASYFQDPVKAYTCSFVNTQTVENDYSETEEirqkstscigqdassRSDFRLLMENLDVLESTFADSDALRLEREILQQLGKLGALKLFNSHLSRivktsnvldlsdvhteeqkmndsrdyhmgkilvpskrkgkrklktarvseesietsllslpsealqeglkqptifsaeralnsRGRRLtiarneaemskgvqvvaNLERIKTTLekesgkaasLNCWAQAAGVSERVLKQHLAFGWYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQgaerfdhtrgykfsTYVQYWIRKSISKMVARHARgikipcklnreiSKIQKARKaltnshgkypediEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNAKYLNIPPFFFPSFAIWEWEEY
Low Complexity Region (SEG)
MGMGFRLNLKWVSPVQSHFFTTSSCRLSSTSVRGREGSFNSARLSFLSTISEDSASYFQDPVKAYTCSFVNTQTVENDYSETEEIRQKSTSCIGQDASSRSDFRLLMENLDVLESTFADSDALRLEREIlqqlgklgalklFNSHLSRIVKTSNVLDLSDVHTEEQKMNDSRDYHMGKILVPSKRKGKRKLKTARVseesietsllslpseALQEGLKQPTIFSAERALNSRGRRLTIARNEAEMSKGVQVVANLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQHLAFGWYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNAKYLNIPPFFFPSFAIWEWEEY
Disordered region (IsUnstruct)
****FRLNLKWVSPVQSHFFTTSSCR*****************LSFLSTISEDSASYFQDPVKAYTCSFVNTQTV***************************FRLLMENLDVLESTFADSDALRLEREILQQLGKLGALKLFNSHLSRIVKTSNVLDL******************************************************************************************VQVVANLERIKTTL*****KAASLNCWAQAAGVSERVLKQHLAFGWYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNAKYLNIPPFFFPSFAIWEW***
Disordered Region (DISOPRED)
**MGFRLNLKWVSPV*********************************************PVKAYTCSFVNTQTV**********************SSRSDFRLLMENLDVLESTFAD****RLEREILQQLGKLGALKLFNS**********************************************************************************RALNSRGRRLTIARNEAEMSKGVQVVANLERIKTT***********NCWAQAAGVSERVLKQHLAFGWYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIPCKLNREISKIQKARK*********PEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNAKYLNIPPFFFPSF********
Disordered Region (DISEMBL)
MGMGFRLNLKWVSPVQSHFFTTSS**************FNSARLSFLSTISEDSASYFQDPVKAYTCSFVNTQTVE********************ASSRSDFRLLMENLDVLESTFADSDALRLEREILQQLGKLGALKLFNSHLSRIVKTSNVLDLSDVHTEEQKMNDSRDYHMGKILVPSK*******************SLLSLPSEALQEGLKQPTIFSAERALNSRGRRLTIARNEAEMSKGVQVVANLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQHLAFGWYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNAKYLNIPPFFFPSFAIWEWEEY
Disordered Region (DISPRO)
*GMGFRLNLKWVSPVQS*****************REGSFNSARLSFLSTISEDSASYFQDPVKAYTCSFVNTQTVENDYSETEEIRQKSTSCIGQDASSRSDFRLLMENLDVLESTFADSDALRLEREILQQLGKLGALKLFNSHLSR***********************************************************************PTIFSAERALNSRGRRLTIARNEAEMSKGVQVVANLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQHLAFGWYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNAKYLNIPPFF************
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
oooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MGMGFRLNLKWVSPVQSHFFTTSSCRLSSTSVRGREGSFNSARLSFLSTISEDSASYFQDPVKAYTCSFVNTQTVENDYSETEEIRQKSTSCIGQDASSRSDFRLLMENLDVLESTFADSDALRLEREILQQLGKLGALKLFNSHLSRIVKTSNVLDLSDVHTEEQKMNDSRDYHMGKILVPSKRKGKRKLKTARVSEESIETSLLSLPSEALQEGLKQPTIFSAERALNSRGRRLTIARNEAEMSKGVQVVANLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQHLAFGWYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNAKYLNIPPFFFPSFAIWEWEEY
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	459	2.2.26 [Sep-21-2011]
O24621	571	RNA polymerase sigma fact	yes	no	0.873	0.702	0.494	2e-97
O22056	572	RNA polymerase sigma fact	no	no	0.557	0.447	0.343	1e-39
P26683	390	RNA polymerase sigma fact	yes	no	0.433	0.510	0.311	1e-28
Q9LD95	547	RNA polymerase sigma fact	no	no	0.461	0.387	0.320	7e-28
Q31QG5	320	RNA polymerase sigma fact	yes	no	0.422	0.606	0.328	2e-26
P38023	399	RNA polymerase sigma fact	no	no	0.446	0.513	0.325	3e-26
P52322	416	RNA polymerase sigma fact	no	no	0.392	0.432	0.327	2e-24
Q31ME3	320	RNA polymerase sigma fact	no	no	0.450	0.646	0.307	4e-24
P0A602	528	RNA polymerase sigma fact	yes	no	0.307	0.267	0.367	7e-24
P0A603	528	RNA polymerase sigma fact	yes	no	0.307	0.267	0.367	7e-24

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

 Score =  357 bits (915), Expect = 2e-97,   Method: Compositional matrix adjust.
 Identities = 209/423 (49%), Positives = 283/423 (66%), Gaps = 22/423 (5%)

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

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

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

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

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

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

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

Query: 443 IPP 445
             P
Sbjct: 480 FTP 482

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

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

 Score =  164 bits (416), Expect = 1e-39,   Method: Compositional matrix adjust.
 Identities = 93/271 (34%), Positives = 159/271 (58%), Gaps = 15/271 (5%)

Query: 179 ILVPSKRKGKRKLKTARVSEESIETSLLSLPSEALQEGLKQPTIFSAE----------RA 228
           + V S R+ +RK + A+     +E +   +PS       K+  + + E          R 
Sbjct: 210 LAVRSTRQTERKARRAK----GLEKTASGIPSVKTGSSPKKKRLVAQEVDHNDPLRYLRM 265

Query: 229 LNSRGRRLTIARNEAEMSKGVQVVANLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQ 288
             S  + LT+ R E E+S G+Q +  LER++T L + SG+  +   WA AAGV ++ L+Q
Sbjct: 266 TTSSSKLLTV-REEHELSAGIQDLLKLERLQTELTERSGRQPTFAQWASAAGVDQKSLRQ 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 GLSLAEIRSASECLRIVGSIDQKIGDCLNAK 439
           GLS+  + +     +   S+DQKIG   N K
Sbjct: 445 GLSMKRLMAVLLSPKPPRSLDQKIGMNQNLK 475

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

Arabidopsis thaliana (taxid: 3702)

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

 Score =  128 bits (321), Expect = 1e-28,   Method: Compositional matrix adjust.
 Identities = 62/199 (31%), Positives = 119/199 (59%)

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

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

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

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

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

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

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

 Score =  125 bits (314), Expect = 7e-28,   Method: Compositional matrix adjust.
 Identities = 68/212 (32%), Positives = 118/212 (55%)

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 EIRSASECLRIVGSIDQKIGDCLNAKYLNIPP 445
           ++       R   S+ Q I    +  +  I P
Sbjct: 425 KLDKLLYNTRTPLSMQQPIWSDQDTTFQEITP 456

Sigma factors are initiation factors that promote the attachment of plastid-encoded RNA polymerase (PEP) to specific initiation sites and are then released. Regulates transcription in chloroplast in a DG1-dependent manner. Involved in light-dependent chloroplast development. Required during early plant development and primary leaf formation.

Arabidopsis thaliana (taxid: 3702)

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

 Score =  120 bits (301), Expect = 2e-26,   Method: Compositional matrix adjust.
 Identities = 64/195 (32%), Positives = 112/195 (57%), Gaps = 1/195 (0%)

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

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

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

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

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

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

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

 Score =  120 bits (300), Expect = 3e-26,   Method: Compositional matrix adjust.
 Identities = 67/206 (32%), Positives = 121/206 (58%), Gaps = 1/206 (0%)

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

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

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

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

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

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

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

 Score =  114 bits (284), Expect = 2e-24,   Method: Compositional matrix adjust.
 Identities = 59/180 (32%), Positives = 103/180 (57%)

Query: 254 NLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQHLAFGWYCREELIKSTRPLVLFLAR 313
            L  IK  L K    A  L  W   +       K+ L  G   +E++++S   LV+ +A+
Sbjct: 138 KLSDIKAYLGKTELTAPLLEEWLAKSKEYLSAFKRRLYHGRRAKEKMVQSNLRLVVSIAK 197

Query: 314 NYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKI 373
            Y   G+ F DL+Q G++G+++ AE+FDH +GYKFSTY  +WIR++I++ +A  +R I++
Sbjct: 198 KYMNRGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYATWWIRQAITRAIADQSRTIRL 257

Query: 374 PCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIG 433
           P  L   IS+I+K  K L+    + P + EIA    +++ ++R  ++  ++  S++  IG
Sbjct: 258 PVHLYETISRIKKTTKILSQEMRRKPTEEEIATKMEMTIEKLRFIAKSAQLPISLETPIG 317

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

Microcystis aeruginosa (taxid: 1126)

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

 Score =  113 bits (282), Expect = 4e-24,   Method: Compositional matrix adjust.
 Identities = 64/208 (30%), Positives = 115/208 (55%), Gaps = 1/208 (0%)

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

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

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

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

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

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

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

 Score =  112 bits (279), Expect = 7e-24,   Method: Compositional matrix adjust.
 Identities = 54/147 (36%), Positives = 90/147 (61%), Gaps = 6/147 (4%)

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

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

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

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

Mycobacterium tuberculosis (taxid: 1773)

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

 Score =  112 bits (279), Expect = 7e-24,   Method: Compositional matrix adjust.
 Identities = 54/147 (36%), Positives = 90/147 (61%), Gaps = 6/147 (4%)

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

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

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

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

Mycobacterium bovis (taxid: 1765)

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Length	Definition	Q cover	H cover	Identity	E-value
Query	459
225429414	561	PREDICTED: RNA polymerase sigma factor r	0.969	0.793	0.548	1e-142
147865632	611	hypothetical protein VITISV_036980 [Viti	0.901	0.677	0.546	1e-131
224088962	559	predicted protein [Populus trichocarpa]	0.982	0.806	0.516	1e-127
255550882	560	RNA polymerase sigma factor rpoD, putati	0.986	0.808	0.538	1e-125
39840783	548	sigma factor [Spinacia oleracea]	0.960	0.804	0.495	1e-116
356565804	551	PREDICTED: RNA polymerase sigma factor r	0.941	0.784	0.488	1e-106
449461399	559	PREDICTED: RNA polymerase sigma factor s	0.949	0.779	0.463	1e-105
7363220	567	sigma factor 3 [Sinapis alba]	0.851	0.689	0.491	1e-101
312281919	562	unnamed protein product [Thellungiella h	0.827	0.676	0.507	2e-97
297820128	568	predicted protein [Arabidopsis lyrata su	0.917	0.741	0.481	3e-96

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

 Score =  509 bits (1312), Expect = e-142,   Method: Compositional matrix adjust.
 Identities = 259/472 (54%), Positives = 328/472 (69%), Gaps = 27/472 (5%)

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

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

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

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

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

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

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

Query: 394 SHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNAKYLNIPP 445
           SHG+YP+D EIAK+TGLSLA+IRSA  CLR+VGS DQ   DC  A  L   P
Sbjct: 421 SHGRYPDDNEIAKFTGLSLAKIRSAGNCLRVVGSTDQSFQDCWGATILEFTP 472

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  474 bits (1219), Expect = e-131,   Method: Compositional matrix adjust.
 Identities = 241/441 (54%), Positives = 308/441 (69%), Gaps = 27/441 (6%)

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

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

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

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

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

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

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

Query: 425 VGSIDQKIGDCLNAKYLNIPP 445
           VGS DQ   DC  A  L   P
Sbjct: 502 VGSTDQSFQDCWGATILEFTP 522

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 =  461 bits (1185), Expect = e-127,   Method: Compositional matrix adjust.
 Identities = 251/486 (51%), Positives = 331/486 (68%), Gaps = 35/486 (7%)

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

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

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

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

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

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

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

Query: 393 NSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNAKYLNIPPFFFPSFA 452
           NSHG+YP+D E+AK+TGLSLA+I SA +CLR+V S+DQKIG+   AKY      F P  +
Sbjct: 418 NSHGRYPDDWEVAKFTGLSLAKIESAQKCLRVVASLDQKIGEGHYAKYSE----FIPDMS 473

Query: 453 IWEWEE 458
           I   EE
Sbjct: 474 IQNPEE 479

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  454 bits (1169), Expect = e-125,   Method: Compositional matrix adjust.
 Identities = 261/485 (53%), Positives = 343/485 (70%), Gaps = 32/485 (6%)

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 SHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNAKYLNIPPFFFPSFAI 453
           S+GKYP+D EIAKYTGLSLA+I SAS CLR+VGSIDQKIG+ LNAKYL     F P  ++
Sbjct: 420 SNGKYPDDDEIAKYTGLSLAKIESASRCLRVVGSIDQKIGESLNAKYLE----FLPDTSV 475

Query: 454 WEWEE 458
              EE
Sbjct: 476 QSPEE 480

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  426 bits (1094), Expect = e-116,   Method: Compositional matrix adjust.
 Identities = 230/464 (49%), Positives = 314/464 (67%), Gaps = 23/464 (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 IEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNAKYLNIPP 445
           +E++K TGLSL +I+SA  CLRIVGS+DQK+G  +N KYL   P
Sbjct: 417 VEVSKSTGLSLDKIKSADNCLRIVGSLDQKVGHFINMKYLECTP 460

Source: Spinacia oleracea

Species: Spinacia oleracea

Genus: Spinacia

Family: Amaranthaceae

Order: Caryophyllales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  390 bits (1003), Expect = e-106,   Method: Compositional matrix adjust.
 Identities = 231/473 (48%), Positives = 314/473 (66%), Gaps = 41/473 (8%)

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

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

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

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

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

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

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

Query: 393 NSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNAKYLNIPP 445
           ++H K P+D EIAK TGLSL +I+SAS CLRIV SIDQK+GD L  +Y+ + P
Sbjct: 410 STHKKCPDDYEIAKMTGLSLDKIKSASNCLRIVASIDQKVGDYLGVEYMELLP 462

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

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 =  390 bits (1001), Expect = e-105,   Method: Compositional matrix adjust.
 Identities = 219/472 (46%), Positives = 300/472 (63%), Gaps = 36/472 (7%)

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-------HTEEQKMNDSRDYHMGKILVPSKRKGKRKLKTARVSEESIETSLLSLP 209
           D S +       H   QK ND  D     + V S +K  R+    R  + + + +   L 
Sbjct: 181 DSSGLPIEGGEDHNVNQKTNDQND----NVTVYSAKKAGRRSVKKRAMDNADKIASRLLT 236

Query: 210 SEALQEGLKQPTIFSAERALNSRGRRLTIARNEAEMSKGVQVVANLERIKTTLEKESGKA 269
           + A++E + + T+FS +++ NS  RRL +A NEAEMS GV+VVANLERI+ TLEKESG+ 
Sbjct: 237 TRAVKEKIHRSTVFSRKKSSNSSKRRLIVAINEAEMSTGVKVVANLERIRETLEKESGRI 296

Query: 270 ASLNCWAQAAGVSERVLKQHLAFGWYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAG 329
           AS++CWA+AA V  + L++ L FG +CR+EL++ST  LV+FLA+ YR  G+P  DL+QAG
Sbjct: 297 ASMSCWAEAASVDIKDLQKQLQFGSFCRDELLRSTNSLVVFLAKKYRCSGLPMEDLVQAG 356

Query: 330 NVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIPCKLNREISKIQKARK 389
            +GVLQG ERFD  RG++ STY+QYWIRKS+S++VAR++RGI+IP  L + I++IQKARK
Sbjct: 357 ALGVLQGVERFDPKRGFRISTYIQYWIRKSMSRVVARNSRGIQIPRSLTKAINQIQKARK 416

Query: 390 ALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNAKYL 441
            L +S  +Y +D +IA+ TGL LA++R AS CL++VGS DQK+GD +N KY+
Sbjct: 417 VLNHSGRRYSDD-DIARATGLPLAKVRVASNCLKVVGSNDQKMGDGVNMKYM 467

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  376 bits (965), Expect = e-101,   Method: Compositional matrix adjust.
 Identities = 205/417 (49%), Positives = 281/417 (67%), Gaps = 26/417 (6%)

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

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

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

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

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

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

Query: 390 ALTNSHG-KYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNAKYLNIPP 445
            L  S G KYP D EI+K TG SL +IR+A++CL++VGSID+K+GDC   ++L   P
Sbjct: 422 TLKTSQGIKYPADEEISKLTGYSLKKIRAANQCLKVVGSIDKKVGDCFTTRFLEFTP 478

Source: Sinapis alba

Species: Sinapis alba

Genus: Sinapis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  362 bits (929), Expect = 2e-97,   Method: Compositional matrix adjust.
 Identities = 202/398 (50%), Positives = 271/398 (68%), Gaps = 18/398 (4%)

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

Query: 109 NLDVLESTFADSDALRLEREILQQLGKLGALKLFNSHLSRIVKTSNVLDLSDVHTEEQKM 168
           NL  LE TF   D+LR+ER+I+ Q+GKLGA +LF + LSR   +S    LSD  TE    
Sbjct: 144 NLLALEETFVSLDSLRMERDIMLQMGKLGATELFKTCLSRSRGSSVTSCLSDTGTELVVA 203

Query: 169 NDSRDYHMGKILVPSKRKGKRKLKTARVSEESIETSLLSLPSEALQEGLKQPTIFSAERA 228
            + +     +  VPS+RK K+K + + +S    +   L + S      +  P +    ++
Sbjct: 204 TEEQ-----QTFVPSRRKLKKKARRSSLSTGKGDQGSLLIGSRTTWNDIDAPRL---RKS 255

Query: 229 LNSRGRRLTIARNEAEMSKGVQVVANLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQ 288
              R +R  I+RNEAEMS G ++VA++ERI+T LE+ESGK AS++CWA+AAG++E +L +
Sbjct: 256 SKYRKKRERISRNEAEMSAGAKIVADMERIRTKLEEESGKVASMSCWAEAAGMNEILLMR 315

Query: 289 HLAFGWYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKF 348
           +L +GWYCR+EL+KSTR LVLFL+RNYRGLGI   DL+QAGNVGVLQGAERFDHTRGYKF
Sbjct: 316 NLHYGWYCRDELLKSTRSLVLFLSRNYRGLGIAHEDLIQAGNVGVLQGAERFDHTRGYKF 375

Query: 349 STYVQYWIRKSISKMVARHARGIKIPCKLNREISKIQKARKALTNSHG-KYPEDIEIAKY 407
           STYVQYWIRKS+S MV+RHARG+ IP  + R +S+IQKARK L  SHG KYP D EI+K 
Sbjct: 376 STYVQYWIRKSMSMMVSRHARGVYIPSSVIRTMSQIQKARKTLKTSHGIKYPADEEISKE 435

Query: 408 TGLSLAEIRSASECLRIVGSIDQKIGDCLNAKYLNIPP 445
           TG SL +IR+A++CL++VGSID+K+GDC   K+L   P
Sbjct: 436 TGYSLKKIRAANQCLKVVGSIDKKVGDCFTTKFLEFTP 473

Source: Thellungiella halophila

Species: Eutrema halophilum

Genus: Eutrema

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  358 bits (919), Expect = 3e-96,   Method: Compositional matrix adjust.
 Identities = 211/438 (48%), Positives = 292/438 (66%), Gaps = 17/438 (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 IDQKIGDCLNAKYLNIPP 445
           I++K+GDC + K+L   P
Sbjct: 462 IEKKVGDCFSTKFLEFTP 479

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	459
TAIR|locus:2084420	571	SIGC "AT3G53920" [Arabidopsis	0.862	0.693	0.480	8.3e-90
TAIR|locus:2025650	572	SIG2 "AT1G08540" [Arabidopsis	0.461	0.370	0.384	7e-38
TAIR|locus:2057996	547	SIGF "AT2G36990" [Arabidopsis	0.459	0.385	0.328	2.6e-27
UNIPROTKB|Q84LK8	572	SIG6 "Sig6" [Oryza sativa Japo	0.383	0.307	0.305	1.9e-21
UNIPROTKB|Q59563	323	mysB "RNA polymerase sigma fac	0.307	0.436	0.340	3.1e-21
TAIR|locus:2173249	419	SIG4 "AT5G13730" [Arabidopsis	0.381	0.417	0.342	3.9e-21
UNIPROTKB|P0A602	528	rpoD "RNA polymerase sigma fac	0.307	0.267	0.367	1.7e-20
TIGR_CMR|GSU_3089	577	GSU_3089 "RNA polymerase sigma	0.420	0.334	0.315	3.3e-20
TIGR_CMR|CHY_0455	370	CHY_0455 "RNA polymerase sigma	0.300	0.372	0.362	2.7e-19
TIGR_CMR|CJE_1081	622	CJE_1081 "RNA polymerase sigma	0.307	0.226	0.361	5.8e-19

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

 Score = 896 (320.5 bits), Expect = 8.3e-90, P = 8.3e-90
 Identities = 197/410 (48%), Positives = 263/410 (64%)

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

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

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

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

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

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

Query:   397 -KYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNAKYLNIPP 445
              KY  D EIAK TG S+ +IR+A++CL++VGSID+K+GDC   K+L   P
Sbjct:   433 IKYAADEEIAKLTGHSVKKIRAANQCLKVVGSIDKKVGDCFTTKFLEFTP 482

GO:0003677 "DNA binding" evidence=ISS

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

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

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

GO:0009507 "chloroplast" evidence=ISM;IDA

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

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

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

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

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

GO:0016987 "sigma factor activity" evidence=ISS

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

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

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

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

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

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

GO:0003677 "DNA binding" evidence=ISS

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

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

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

GO:0009507 "chloroplast" evidence=ISM;IDA

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

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

GO:0009658 "chloroplast organization" evidence=IMP

GO:0006399 "tRNA metabolic process" evidence=IMP

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

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

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

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

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

GO:0006364 "rRNA processing" evidence=RCA

GO:0009902 "chloroplast relocation" evidence=RCA

GO:0010027 "thylakoid membrane organization" evidence=RCA

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

GO:0016117 "carotenoid biosynthetic process" evidence=RCA

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

GO:0034660 "ncRNA metabolic process" evidence=RCA

GO:0016987 "sigma factor activity" evidence=ISS

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

 Score = 316 (116.3 bits), Expect = 2.6e-27, P = 2.6e-27
 Identities = 70/213 (32%), Positives = 120/213 (56%)

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 AEIRSASECLRIVGSIDQKIGDCLNAKYLNIPP 445
              ++       R   S+ Q I    +  +  I P
Sbjct:   424 EKLDKLLYNTRTPLSMQQPIWSDQDTTFQEITP 456

GO:0003677 "DNA binding" evidence=ISS

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

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

GO:0005634 "nucleus" evidence=ISM

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

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

GO:0009507 "chloroplast" evidence=IDA

GO:0009536 "plastid" evidence=IDA

GO:0016987 "sigma factor activity" evidence=ISS;IDA

GO:0071483 "cellular response to blue light" evidence=IEP

GO:0045893 "positive regulation of transcription, DNA-dependent" evidence=RCA;IMP

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

GO:0090351 "seedling development" evidence=IMP

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

GO:0005515 "protein binding" evidence=IPI

GO:0009902 "chloroplast relocation" evidence=RCA

GO:0009965 "leaf morphogenesis" evidence=RCA

GO:0010027 "thylakoid membrane organization" evidence=RCA

GO:0016117 "carotenoid biosynthetic process" evidence=RCA

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

GO:0030154 "cell differentiation" evidence=RCA

GO:0034660 "ncRNA metabolic process" evidence=RCA

UNIPROTKB|Q84LK8 SIG6 "Sig6" [Oryza sativa Japonica Group (taxid:39947)]

 Score = 275 (101.9 bits), Expect = 1.9e-21, P = 1.9e-21
 Identities = 54/177 (30%), Positives = 103/177 (58%)

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

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

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

GO:0009536 "plastid" evidence=RCA

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

 Score = 253 (94.1 bits), Expect = 3.1e-21, P = 3.1e-21
 Identities = 48/141 (34%), Positives = 88/141 (62%)

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

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

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

GO:0001666 "response to hypoxia" evidence=IEP

GO:0005829 "cytosol" evidence=IDA

GO:0005886 "plasma membrane" evidence=IDA

GO:0009408 "response to heat" evidence=IEP

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

GO:0016987 "sigma factor activity" evidence=IGI

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

GO:0040007 "growth" evidence=IMP

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

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

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

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

 Score = 265 (98.3 bits), Expect = 3.9e-21, Sum P(2) = 3.9e-21
 Identities = 61/178 (34%), Positives = 102/178 (57%)

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

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

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

GO:0003677 "DNA binding" evidence=ISS

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

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

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

GO:0009507 "chloroplast" evidence=ISM

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

GO:0016987 "sigma factor activity" evidence=ISS

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

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

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

GO:0000023 "maltose metabolic process" evidence=RCA

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

GO:0016556 "mRNA modification" evidence=RCA

GO:0019252 "starch biosynthetic process" evidence=RCA

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

 Score = 266 (98.7 bits), Expect = 1.7e-20, P = 1.7e-20
 Identities = 54/147 (36%), Positives = 90/147 (61%)

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

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

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

GO:0003677 "DNA binding" evidence=IDA

GO:0005515 "protein binding" evidence=IPI

GO:0005618 "cell wall" evidence=IDA

GO:0005886 "plasma membrane" evidence=IDA

GO:0009405 "pathogenesis" evidence=IMP

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

GO:0016987 "sigma factor activity" evidence=IDA

GO:0040007 "growth" evidence=IMP

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

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

 Score = 264 (98.0 bits), Expect = 3.3e-20, Sum P(2) = 3.3e-20
 Identities = 64/203 (31%), Positives = 115/203 (56%)

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

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

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

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

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

GO:0016987 "sigma factor activity" evidence=ISS

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

 Score = 249 (92.7 bits), Expect = 2.7e-19, P = 2.7e-19
 Identities = 50/138 (36%), Positives = 86/138 (62%)

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

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

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

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

GO:0016987 "sigma factor activity" evidence=ISS

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

 Score = 256 (95.2 bits), Expect = 5.8e-19, Sum P(2) = 5.8e-19
 Identities = 51/141 (36%), Positives = 87/141 (61%)

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 ECLRIVGSIDQKIGDCLNAKY 440
             +  +   S++  IG+  + K+
Sbjct:   505 KITKEPISLEAPIGNEDDGKF 525

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

GO:0016987 "sigma factor activity" evidence=ISS

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input: GSVIVG00032140001 SubName- Full=Chromosome chr4 scaffold_6, whole genome shotgun sequence; (561 aa) (Vitis vinifera)

Predicted Functional Partners:

Sorry, there are no predicted associations at the current settings.

---

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	459
TIGR02997	298	TIGR02997, Sig70-cyanoRpoD, RNA polymerase sigma f	9e-38
PRK05949	327	PRK05949, PRK05949, RNA polymerase sigma factor; V	1e-33
PRK07405	317	PRK07405, PRK07405, RNA polymerase sigma factor Si	3e-32
PRK07406	373	PRK07406, PRK07406, RNA polymerase sigma factor Rp	9e-32
TIGR02393	238	TIGR02393, RpoD_Cterm, RNA polymerase sigma factor	2e-31
COG0568	342	COG0568, RpoD, DNA-directed RNA polymerase, sigma	7e-31
TIGR02394	285	TIGR02394, rpoS_proteo, RNA polymerase sigma facto	4e-25
PRK07598	415	PRK07598, PRK07598, RNA polymerase sigma factor Si	2e-23
PRK07921	324	PRK07921, PRK07921, RNA polymerase sigma factor Si	5e-23
PRK09210	367	PRK09210, PRK09210, RNA polymerase sigma factor Rp	2e-20
PRK05901	509	PRK05901, PRK05901, RNA polymerase sigma factor; P	1e-19
TIGR02980	227	TIGR02980, SigBFG, RNA polymerase sigma-70 factor,	2e-19
PRK05658	619	PRK05658, PRK05658, RNA polymerase sigma factor Rp	1e-16
PRK05657	325	PRK05657, PRK05657, RNA polymerase sigma factor Rp	3e-16
pfam04542	71	pfam04542, Sigma70_r2, Sigma-70 region 2	1e-13
COG1191	247	COG1191, FliA, DNA-directed RNA polymerase special	3e-13
TIGR02392	270	TIGR02392, rpoH_proteo, alternative sigma factor R	4e-13
PRK07500	289	PRK07500, rpoH2, RNA polymerase factor sigma-32; R	1e-12
TIGR02479	224	TIGR02479, FliA_WhiG, RNA polymerase sigma factor,	3e-12
PRK07408	256	PRK07408, PRK07408, RNA polymerase sigma factor Si	5e-12
PRK06596	284	PRK06596, PRK06596, RNA polymerase factor sigma-32	1e-10
TIGR02885	231	TIGR02885, spore_sigF, RNA polymerase sigma-F fact	1e-09
TIGR02941	255	TIGR02941, Sigma_B, RNA polymerase sigma-B factor	2e-09
PRK06288	268	PRK06288, PRK06288, RNA polymerase sigma factor Wh	2e-09
PRK05572	252	PRK05572, PRK05572, sporulation sigma factor SigF;	5e-09
PRK06986	236	PRK06986, fliA, flagellar biosynthesis sigma facto	3e-08
PRK08583	257	PRK08583, PRK08583, RNA polymerase sigma factor Si	3e-07
TIGR02850	254	TIGR02850, spore_sigG, RNA polymerase sigma-G fact	1e-06
PRK07122	264	PRK07122, PRK07122, RNA polymerase sigma factor Si	1e-06
TIGR02937	158	TIGR02937, sigma70-ECF, RNA polymerase sigma facto	3e-06
PRK08215	258	PRK08215, PRK08215, sporulation sigma factor SigG;	7e-06
pfam04539	78	pfam04539, Sigma70_r3, Sigma-70 region 3	7e-04
PRK05911	257	PRK05911, PRK05911, RNA polymerase sigma factor si	0.001
PRK07670	251	PRK07670, PRK07670, RNA polymerase sigma factor Si	0.002

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

 Score =  139 bits (352), Expect = 9e-38
 Identities = 74/207 (35%), Positives = 124/207 (59%), Gaps = 1/207 (0%)

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

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

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

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

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

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

 Score =  128 bits (324), Expect = 1e-33
 Identities = 70/188 (37%), Positives = 115/188 (61%)

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

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

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

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

Length = 327

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

 Score =  124 bits (313), Expect = 3e-32
 Identities = 62/193 (32%), Positives = 115/193 (59%)

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

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

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

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

Length = 317

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

 Score =  124 bits (313), Expect = 9e-32
 Identities = 61/174 (35%), Positives = 104/174 (59%), Gaps = 1/174 (0%)

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

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

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

Length = 373

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

 Score =  120 bits (303), Expect = 2e-31
 Identities = 50/138 (36%), Positives = 89/138 (64%)

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

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

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

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

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

 Score =  121 bits (306), Expect = 7e-31
 Identities = 51/139 (36%), Positives = 88/139 (63%)

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

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

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

Length = 342

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

 Score =  104 bits (260), Expect = 4e-25
 Identities = 42/138 (30%), Positives = 79/138 (57%)

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

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

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

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

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

 Score =  101 bits (254), Expect = 2e-23
 Identities = 60/205 (29%), Positives = 106/205 (51%), Gaps = 23/205 (11%)

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

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

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

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

Length = 415

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

 Score = 99.0 bits (247), Expect = 5e-23
 Identities = 48/137 (35%), Positives = 87/137 (63%)

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

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

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

Length = 324

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

 Score = 92.4 bits (230), Expect = 2e-20
 Identities = 44/118 (37%), Positives = 76/118 (64%), Gaps = 3/118 (2%)

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

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

Length = 367

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

 Score = 90.8 bits (226), Expect = 1e-19
 Identities = 46/124 (37%), Positives = 76/124 (61%)

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

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

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

Length = 509

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

 Score = 86.1 bits (214), Expect = 2e-19
 Identities = 48/140 (34%), Positives = 72/140 (51%), Gaps = 2/140 (1%)

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

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

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

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

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

 Score = 82.1 bits (204), Expect = 1e-16
 Identities = 46/127 (36%), Positives = 76/127 (59%), Gaps = 18/127 (14%)

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

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

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

Length = 619

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

 Score = 79.2 bits (196), Expect = 3e-16
 Identities = 36/120 (30%), Positives = 70/120 (58%)

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

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

Length = 325

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

 Score = 65.7 bits (161), Expect = 1e-13
 Identities = 29/70 (41%), Positives = 40/70 (57%)

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

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

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

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

 Score = 68.9 bits (169), Expect = 3e-13
 Identities = 43/137 (31%), Positives = 67/137 (48%), Gaps = 4/137 (2%)

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

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

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

Length = 247

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

 Score = 68.8 bits (169), Expect = 4e-13
 Identities = 41/126 (32%), Positives = 70/126 (55%), Gaps = 13/126 (10%)

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

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

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

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

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

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

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

Length = 289

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

 Score = 65.8 bits (161), Expect = 3e-12
 Identities = 46/140 (32%), Positives = 71/140 (50%), Gaps = 12/140 (8%)

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

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

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

Most members of this family are the flagellar operon sigma factor FliA, controlling transcription of bacterial flagellar genes by RNA polymerase. An exception is the sigma factor WhiG in the genus Streptomyces, involved in the production of sporulating aerial mycelium. Length = 224

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

 Score = 65.3 bits (160), Expect = 5e-12
 Identities = 35/117 (29%), Positives = 62/117 (52%), Gaps = 4/117 (3%)

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

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

Length = 256

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

 Score = 61.3 bits (150), Expect = 1e-10
 Identities = 26/75 (34%), Positives = 48/75 (64%)

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

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

Length = 284

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

 Score = 57.8 bits (140), Expect = 1e-09
 Identities = 39/136 (28%), Positives = 65/136 (47%), Gaps = 1/136 (0%)

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

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

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

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

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

 Score = 58.0 bits (140), Expect = 2e-09
 Identities = 36/124 (29%), Positives = 60/124 (48%)

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

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

Query: 417 SASE 420
              E
Sbjct: 151 EIME 154

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

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

 Score = 58.2 bits (141), Expect = 2e-09
 Identities = 44/126 (34%), Positives = 62/126 (49%), Gaps = 10/126 (7%)

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

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

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

Length = 268

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

 Score = 56.5 bits (137), Expect = 5e-09
 Identities = 43/144 (29%), Positives = 66/144 (45%), Gaps = 17/144 (11%)

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

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

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

Length = 252

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

 Score = 54.1 bits (131), Expect = 3e-08
 Identities = 41/131 (31%), Positives = 64/131 (48%), Gaps = 18/131 (13%)

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

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

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

Length = 236

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

 Score = 51.2 bits (123), Expect = 3e-07
 Identities = 37/123 (30%), Positives = 56/123 (45%)

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

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

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

Length = 257

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

 Score = 49.4 bits (118), Expect = 1e-06
 Identities = 37/120 (30%), Positives = 59/120 (49%), Gaps = 3/120 (2%)

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

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

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

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

 Score = 49.4 bits (118), Expect = 1e-06
 Identities = 41/148 (27%), Positives = 64/148 (43%), Gaps = 18/148 (12%)

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

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

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

Length = 264

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

 Score = 46.6 bits (111), Expect = 3e-06
 Identities = 22/77 (28%), Positives = 32/77 (41%), Gaps = 2/77 (2%)

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

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

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

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

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

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

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

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

Length = 258

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

 Score = 38.0 bits (89), Expect = 7e-04
 Identities = 17/56 (30%), Positives = 31/56 (55%)

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

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

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

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

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

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

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

Length = 257

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

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

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

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

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

Length = 251

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	459
PRK07598	415	RNA polymerase sigma factor SigC; Validated	100.0
PRK05949	327	RNA polymerase sigma factor; Validated	100.0
TIGR02997	298	Sig70-cyanoRpoD RNA polymerase sigma factor, cyano	100.0
PRK07406	373	RNA polymerase sigma factor RpoD; Validated	100.0
PRK07405	317	RNA polymerase sigma factor SigD; Validated	100.0
COG0568	342	RpoD DNA-directed RNA polymerase, sigma subunit (s	100.0
PRK05901	509	RNA polymerase sigma factor; Provisional	100.0
PRK07921	324	RNA polymerase sigma factor SigB; Reviewed	100.0
PRK09210	367	RNA polymerase sigma factor RpoD; Validated	100.0
PRK05658	619	RNA polymerase sigma factor RpoD; Validated	100.0
PRK07122	264	RNA polymerase sigma factor SigF; Reviewed	99.98
TIGR02393	238	RpoD_Cterm RNA polymerase sigma factor RpoD, C-ter	99.98
PRK07408	256	RNA polymerase sigma factor SigF; Reviewed	99.97
PRK07500	289	rpoH2 RNA polymerase factor sigma-32; Reviewed	99.97
TIGR02850	254	spore_sigG RNA polymerase sigma-G factor. Members	99.97
PRK06596	284	RNA polymerase factor sigma-32; Reviewed	99.96
TIGR02392	270	rpoH_proteo alternative sigma factor RpoH. A sigma	99.96
PRK08215	258	sporulation sigma factor SigG; Reviewed	99.96
PRK05657	325	RNA polymerase sigma factor RpoS; Validated	99.96
PRK05911	257	RNA polymerase sigma factor sigma-28; Reviewed	99.95
TIGR02885	231	spore_sigF RNA polymerase sigma-F factor. Members	99.95
COG1191	247	FliA DNA-directed RNA polymerase specialized sigma	99.95
TIGR02980	227	SigBFG RNA polymerase sigma-70 factor, sigma-B/F/G	99.94
PRK06288	268	RNA polymerase sigma factor WhiG; Reviewed	99.93
TIGR02941	255	Sigma_B RNA polymerase sigma-B factor. This sigma	99.93
PRK07670	251	RNA polymerase sigma factor SigD; Validated	99.92
TIGR02394	285	rpoS_proteo RNA polymerase sigma factor RpoS. A si	99.92
PRK05572	252	sporulation sigma factor SigF; Validated	99.91
PRK12427	231	flagellar biosynthesis sigma factor; Provisional	99.9
TIGR02479	224	FliA_WhiG RNA polymerase sigma factor, FliA/WhiG f	99.9
PRK08583	257	RNA polymerase sigma factor SigB; Validated	99.9
PRK06986	236	fliA flagellar biosynthesis sigma factor; Validate	99.88
PRK05803	233	sporulation sigma factor SigK; Reviewed	99.79
TIGR02895	218	spore_sigI RNA polymerase sigma-I factor. Members	99.78
TIGR02846	227	spore_sigmaK RNA polymerase sigma-K factor. The sp	99.76
PRK08301	234	sporulation sigma factor SigE; Reviewed	99.75
TIGR02859	198	spore_sigH RNA polymerase sigma-H factor. Members	99.74
PRK08295	208	RNA polymerase factor sigma-70; Validated	99.74
PRK05602	186	RNA polymerase sigma factor; Reviewed	99.73
TIGR02835	234	spore_sigmaE RNA polymerase sigma-E factor. Member	99.73
PRK12513	194	RNA polymerase sigma factor; Provisional	99.72
PRK06811	189	RNA polymerase factor sigma-70; Validated	99.71
PRK09646	194	RNA polymerase sigma factor SigK; Reviewed	99.71
PRK09648	189	RNA polymerase sigma factor SigD; Reviewed	99.69
PRK13919	186	putative RNA polymerase sigma E protein; Provision	99.69
TIGR02954	169	Sig70_famx3 RNA polymerase sigma-70 factor, TIGR02	99.69
PRK12514	179	RNA polymerase sigma factor; Provisional	99.69
PRK09640	188	RNA polymerase sigma factor SigX; Reviewed	99.69
PRK12537	182	RNA polymerase sigma factor; Provisional	99.69
PRK12524	196	RNA polymerase sigma factor; Provisional	99.68
PRK06759	154	RNA polymerase factor sigma-70; Validated	99.68
TIGR02948	187	SigW_bacill RNA polymerase sigma-W factor. This si	99.68
PRK09638	176	RNA polymerase sigma factor SigY; Reviewed	99.68
PRK09643	192	RNA polymerase sigma factor SigM; Reviewed	99.67
TIGR02952	170	Sig70_famx2 RNA polymerase sigma-70 factor, TIGR02	99.67
PRK09641	187	RNA polymerase sigma factor SigW; Provisional	99.67
PRK12531	194	RNA polymerase sigma factor; Provisional	99.67
PRK12534	187	RNA polymerase sigma factor; Provisional	99.66
PRK12538	233	RNA polymerase sigma factor; Provisional	99.66
TIGR02939	190	RpoE_Sigma70 RNA polymerase sigma factor RpoE. A s	99.65
PRK12519	194	RNA polymerase sigma factor; Provisional	99.65
PRK12536	181	RNA polymerase sigma factor; Provisional	99.64
PRK12526	206	RNA polymerase sigma factor; Provisional	99.64
PRK11922	231	RNA polymerase sigma factor; Provisional	99.64
PRK11923	193	algU RNA polymerase sigma factor AlgU; Provisional	99.64
PRK09652	182	RNA polymerase sigma factor RpoE; Provisional	99.64
PRK12539	184	RNA polymerase sigma factor; Provisional	99.64
PRK12542	185	RNA polymerase sigma factor; Provisional	99.63
PRK12515	189	RNA polymerase sigma factor; Provisional	99.63
TIGR02999	183	Sig-70_X6 RNA polymerase sigma factor, TIGR02999 f	99.62
COG1595	182	RpoE DNA-directed RNA polymerase specialized sigma	99.62
PRK09649	185	RNA polymerase sigma factor SigC; Reviewed	99.61
TIGR03001	244	Sig-70_gmx1 RNA polymerase sigma-70 factor, Myxoco	99.61
TIGR02989	159	Sig-70_gvs1 RNA polymerase sigma-70 factor, Rhodop	99.6
PRK12512	184	RNA polymerase sigma factor; Provisional	99.6
PRK11924	179	RNA polymerase sigma factor; Provisional	99.58
PRK12522	173	RNA polymerase sigma factor; Provisional	99.58
PRK12520	191	RNA polymerase sigma factor; Provisional	99.57
PRK12543	179	RNA polymerase sigma factor; Provisional	99.57
TIGR02947	193	SigH_actino RNA polymerase sigma-70 factor, TIGR02	99.56
PRK12518	175	RNA polymerase sigma factor; Provisional	99.56
PRK09415	179	RNA polymerase factor sigma C; Reviewed	99.56
PRK12516	187	RNA polymerase sigma factor; Provisional	99.55
PRK09645	173	RNA polymerase sigma factor SigL; Provisional	99.55
TIGR02937	158	sigma70-ECF RNA polymerase sigma factor, sigma-70	99.55
TIGR02983	162	SigE-fam_strep RNA polymerase sigma-70 factor, sig	99.55
PRK08241	339	RNA polymerase factor sigma-70; Validated	99.54
PRK12529	178	RNA polymerase sigma factor; Provisional	99.54
PRK12547	164	RNA polymerase sigma factor; Provisional	99.53
TIGR02984	189	Sig-70_plancto1 RNA polymerase sigma-70 factor, Pl	99.53
PRK12541	161	RNA polymerase sigma factor; Provisional	99.53
PRK12535	196	RNA polymerase sigma factor; Provisional	99.52
PRK12523	172	RNA polymerase sigma factor; Reviewed	99.51
TIGR02985	161	Sig70_bacteroi1 RNA polymerase sigma-70 factor, Ba	99.51
PRK09644	165	RNA polymerase sigma factor SigM; Provisional	99.5
PRK12533	216	RNA polymerase sigma factor; Provisional	99.5
TIGR02960	324	SigX5 RNA polymerase sigma-70 factor, TIGR02960 fa	99.49
PRK08311	237	putative RNA polymerase sigma factor SigI; Reviewe	99.49
PRK12528	161	RNA polymerase sigma factor; Provisional	99.48
PRK09642	160	RNA polymerase sigma factor SigW; Reviewed	99.48
PRK12540	182	RNA polymerase sigma factor; Provisional	99.47
PRK09639	166	RNA polymerase sigma factor SigX; Provisional	99.46
PRK09647	203	RNA polymerase sigma factor SigE; Reviewed	99.45
PRK12532	195	RNA polymerase sigma factor; Provisional	99.45
PRK12545	201	RNA polymerase sigma factor; Provisional	99.45
PRK09637	181	RNA polymerase sigma factor SigZ; Provisional	99.44
PRK12530	189	RNA polymerase sigma factor; Provisional	99.44
TIGR02950	154	SigM_subfam RNA polymerase sigma factor, SigM fami	99.44
PRK12544	206	RNA polymerase sigma factor; Provisional	99.43
PRK12517	188	RNA polymerase sigma factor; Provisional	99.43
TIGR02959	170	SigZ RNA polymerase sigma factor, SigZ family. Thi	99.42
PF04542	71	Sigma70_r2: Sigma-70 region 2 ; InterPro: IPR00762	99.42
TIGR02943	188	Sig70_famx1 RNA polymerase sigma-70 factor, TIGR02	99.41
PRK12546	188	RNA polymerase sigma factor; Provisional	99.41
PRK09651	172	RNA polymerase sigma factor FecI; Provisional	99.38
PRK12511	182	RNA polymerase sigma factor; Provisional	99.38
PRK06704	228	RNA polymerase factor sigma-70; Validated	99.33
PRK07037	163	extracytoplasmic-function sigma-70 factor; Validat	99.33
PRK12527	159	RNA polymerase sigma factor; Reviewed	99.32
PRK12525	168	RNA polymerase sigma factor; Provisional	99.31
PRK09636	293	RNA polymerase sigma factor SigJ; Provisional	99.25
PF04539	78	Sigma70_r3: Sigma-70 region 3; InterPro: IPR007624	99.2
PRK09191	261	two-component response regulator; Provisional	99.18
TIGR02957	281	SigX4 RNA polymerase sigma-70 factor, TIGR02957 fa	99.18
TIGR03209	142	P21_Cbot clostridium toxin-associated regulator Bo	99.17
PRK09635	290	sigI RNA polymerase sigma factor SigI; Provisional	99.17
PRK09047	161	RNA polymerase factor sigma-70; Validated	99.07
PF07638	185	Sigma70_ECF: ECF sigma factor	98.85
TIGR02393	238	RpoD_Cterm RNA polymerase sigma factor RpoD, C-ter	96.46
PF00140	37	Sigma70_r1_2: Sigma-70 factor, region 1.2; InterPr	96.29
PRK07670	251	RNA polymerase sigma factor SigD; Validated	96.08
PRK09210	367	RNA polymerase sigma factor RpoD; Validated	95.95
PRK07408	256	RNA polymerase sigma factor SigF; Reviewed	95.82
PF12645	65	HTH_16: Helix-turn-helix domain; InterPro: IPR0247	95.82
PRK06288	268	RNA polymerase sigma factor WhiG; Reviewed	95.76
PRK05949	327	RNA polymerase sigma factor; Validated	95.7
PRK07122	264	RNA polymerase sigma factor SigF; Reviewed	95.38
PRK05911	257	RNA polymerase sigma factor sigma-28; Reviewed	95.37
COG1191	247	FliA DNA-directed RNA polymerase specialized sigma	95.3
TIGR02479	224	FliA_WhiG RNA polymerase sigma factor, FliA/WhiG f	95.16
TIGR02394	285	rpoS_proteo RNA polymerase sigma factor RpoS. A si	95.11
PRK05901	509	RNA polymerase sigma factor; Provisional	95.04
PRK07598	415	RNA polymerase sigma factor SigC; Validated	95.02
PRK07921	324	RNA polymerase sigma factor SigB; Reviewed	94.88
TIGR02885	231	spore_sigF RNA polymerase sigma-F factor. Members	94.67
TIGR02997	298	Sig70-cyanoRpoD RNA polymerase sigma factor, cyano	94.65
TIGR02850	254	spore_sigG RNA polymerase sigma-G factor. Members	94.25
PF04539	78	Sigma70_r3: Sigma-70 region 3; InterPro: IPR007624	94.05
PRK07500	289	rpoH2 RNA polymerase factor sigma-32; Reviewed	93.89
PRK07405	317	RNA polymerase sigma factor SigD; Validated	93.88
PRK06986	236	fliA flagellar biosynthesis sigma factor; Validate	93.87
PRK07406	373	RNA polymerase sigma factor RpoD; Validated	93.6
TIGR02941	255	Sigma_B RNA polymerase sigma-B factor. This sigma	93.37
PF08281	54	Sigma70_r4_2: Sigma-70, region 4; InterPro: IPR013	92.8
PRK05572	252	sporulation sigma factor SigF; Validated	92.79
PRK08215	258	sporulation sigma factor SigG; Reviewed	92.69
PRK12427	231	flagellar biosynthesis sigma factor; Provisional	91.9
TIGR02980	227	SigBFG RNA polymerase sigma-70 factor, sigma-B/F/G	91.64
PF01726	65	LexA_DNA_bind: LexA DNA binding domain; InterPro:	91.62
PHA02547	179	55 RNA polymerase sigma factor; Provisional	91.06
PRK05658	619	RNA polymerase sigma factor RpoD; Validated	90.83
PF04545	50	Sigma70_r4: Sigma-70, region 4; InterPro: IPR00763	90.75
PRK05657	325	RNA polymerase sigma factor RpoS; Validated	89.22
PRK08583	257	RNA polymerase sigma factor SigB; Validated	88.54
PRK06596	284	RNA polymerase factor sigma-32; Reviewed	86.3
COG4941	415	Predicted RNA polymerase sigma factor containing a	83.02
TIGR03879	73	near_KaiC_dom probable regulatory domain. This mod	80.79

>PRK07598 RNA polymerase sigma factor SigC; Validated

Probab=100.00  E-value=6.4e-48  Score=400.98  Aligned_cols=233  Identities=26%  Similarity=0.419  Sum_probs=217.9

Q ss_pred             CCCChhHHHHHHhccCCCCCCChHHHHHHHHHhHHHHH--------------------HHHHHHHHHHHhCCCCchHHHH
Q 012638          217 LKQPTIFSAERALNSRGRRLTIARNEAEMSKGVQVVAN--------------------LERIKTTLEKESGKAASLNCWA  276 (459)
Q Consensus       217 ~~~p~~~~~~~~~~~~~~~lLt~~eE~eL~~~i~~~~~--------------------le~~~~~l~~~~gr~pt~~ewa  276 (459)
                      ..||...|+   ...++.||||++||++|+++||.++.                    |++++..|++++|++||..+||
T Consensus        58 ~~d~v~~yl---~~igr~~lL~~~eEv~l~~~vq~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~l~~~~g~~pt~~ewa  134 (415)
T PRK07598         58 STDLVRLYL---QEIGRVRLLGRDEEVSEAQKVQRYMKLIVLANAAKEGDEVIKPYLRLIEVRERLTSELGHRPSLERWA  134 (415)
T ss_pred             CCChHHHHH---HhcccccCCCHHHHHHHHHHHHHHHHHhhhhhhhhcccchhhhHHHHHHHHHHHHHHhCCCCCHHHHH
Confidence            347777777   56677899999999999999999999                    8999999999999999999999


Q ss_pred             HH----------------------cCCCHHHHHHHHHhchHHHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHH
Q 012638          277 QA----------------------AGVSERVLKQHLAFGWYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVL  334 (459)
Q Consensus       277 ~a----------------------~g~deeeL~~~l~~G~~Are~LI~~nlrLV~sIAkry~g~g~d~EDLIQEG~IGLi  334 (459)
                      .+                      +|+++++|+..++.|..||++||.+|+++|+++|++|.++|++++||||||++|||
T Consensus       135 ~~~~~~~~~l~~~l~~~~~~~~~~~~l~~~eL~~~l~~G~~A~e~LI~~nlrLVvsiAkky~~~g~~~eDLiQEG~iGL~  214 (415)
T PRK07598        135 KTADISLADLKPTLAEGKRRWAEIAKLTVEELEQIQKQGLRAKEHMIKANLRLVVSVAKKYQNRGLELLDLVQEGTLGLE  214 (415)
T ss_pred             HHhCCcHHHHHHhhhhhhhhhhhhccCCHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHccCCCCHHHHHHHHHHHHH
Confidence            54                      45666777777889988999999999999999999999999999999999999999


Q ss_pred             HhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhhccccccccchHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHH
Q 012638          335 QGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAE  414 (459)
Q Consensus       335 rAieKFDp~kG~rFSTYa~~wIrnaI~d~Lrk~sr~irlP~~v~e~i~kI~ka~~~L~~~lgr~PT~eEIAe~LGIS~e~  414 (459)
                      +|+++|||.+|++|+||++||||++|.+++++++++|++|.|+.+.+++|+++...|.+.+|+.|+.+|||+.|||++++
T Consensus       215 ravekFDp~rG~rFSTYa~wwIRqaI~r~i~~~srtIrlP~~i~e~l~~lrk~~r~L~~~lgR~pt~~EiA~~l~is~~~  294 (415)
T PRK07598        215 RAVEKFDPTKGYRFSTYAYWWIRQGITRAIATQSRTIRLPVHITEKLNKIKKAQRKISQEKGRTPTIEDIAQELEMTPTQ  294 (415)
T ss_pred             HHHHHcCcccCCCHHHHHHHHHHHHHHHHHHHcCCceehhHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHhhccCCccccccCCCCCCccccCCCCCCCCcc
Q 012638          415 IRSASECLRIVGSIDQKIGDCLNAKYLNIPPFFFPSFA  452 (459)
Q Consensus       415 Vk~~l~~ar~~~SLD~~v~~d~~~~l~e~i~D~~~~~~  452 (459)
                      |+.++..++.++|||.+++++++.++.|+++++..+|+
T Consensus       295 vr~~l~~~~~~~SLd~~vg~~~d~~l~d~l~~~~~~pe  332 (415)
T PRK07598        295 VREVLLRVPRSVSLETKVGKDKDTELGDLLETDDISPE  332 (415)
T ss_pred             HHHHHHHccCCcccccccCCCccccHHHhccCCCCCHH
Confidence            99999999999999999999999999999988766654

>PRK05949 RNA polymerase sigma factor; Validated

Probab=100.00  E-value=8.6e-45  Score=368.75  Aligned_cols=232  Identities=32%  Similarity=0.471  Sum_probs=219.9

Q ss_pred             CCChhHHHHHHhccCCCCCCChHHHHHHHHHhHHHHHHHHHHHHHHHHhCCCCchHHHHHHcCCCHHHHHHHHHhchHHH
Q 012638          218 KQPTIFSAERALNSRGRRLTIARNEAEMSKGVQVVANLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQHLAFGWYCR  297 (459)
Q Consensus       218 ~~p~~~~~~~~~~~~~~~lLt~~eE~eL~~~i~~~~~le~~~~~l~~~~gr~pt~~ewa~a~g~deeeL~~~l~~G~~Ar  297 (459)
                      .++...|+   ......||||++||++|++.|+.++.+++.+..|+..+|+.|+..+||.++++++.+|+..++.|+.|+
T Consensus        17 ~d~~~~yl---~~i~~~~lLt~eeE~~l~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~eL~~~~~~g~~A~   93 (327)
T PRK05949         17 ADMVRTYL---HEIGRVPLLTHEQEIVYGKQVQQMMSLLEAKEALAKKLGREPSLPEWAEAVNLSETELKQTLKQGKRAK   93 (327)
T ss_pred             CCHHHHHH---HHcCCccCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhccCCchHHHHHhccCCHHHHHHHHHccHHHH
Confidence            35555555   355678999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhhccccccccch
Q 012638          298 EELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIPCKL  377 (459)
Q Consensus       298 e~LI~~nlrLV~sIAkry~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIrnaI~d~Lrk~sr~irlP~~v  377 (459)
                      +.||..|+++|+++|++|.+++.+++||+||||+|||+++++|||.+|++|+|||+||||++|.++|++++++||+|.|+
T Consensus        94 ~~Li~~~~~~V~~iA~~y~~~~~~~eDLvQEg~igL~~a~~kfd~~~G~rFsTYa~wwIrq~I~r~i~~~~r~iRlP~~~  173 (327)
T PRK05949         94 QKMIEANLRLVVAIAKKYQKRNMEFLDLIQEGTLGLERGVEKFDPTRGYKFSTYAYWWIRQAITRAIAQQARTIRLPIHI  173 (327)
T ss_pred             HHHHHHHHHHHHHHHHHHccCCCCHHHHHHHHHHHHHHHHHhcCCcCCCChhhhhHHHHHHHHHHHHHHcCCceeCCHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHhhccCCccccccCCCCCCccccCCCCCCCCcc
Q 012638          378 NREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNAKYLNIPPFFFPSFA  452 (459)
Q Consensus       378 ~e~i~kI~ka~~~L~~~lgr~PT~eEIAe~LGIS~e~Vk~~l~~ar~~~SLD~~v~~d~~~~l~e~i~D~~~~~~  452 (459)
                      .+.+++++++...+..++|+.||.+|||+.+||++++|..++..++.++|||.|++++++.++.|+++|+.++|+
T Consensus       174 ~~~~~~l~k~~~~l~~~lgr~pt~~eiA~~l~i~~~~v~~~~~~~~~~~SLd~~~~~~~~~~l~~~l~d~~~~pe  248 (327)
T PRK05949        174 TEKLNKIKKTQRELSQKLGRSATPAEIAKELELEPSQIREYLSMARQPISLDVRVGDNQDTELSELLEDEGPSPD  248 (327)
T ss_pred             HHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHHhccccccCCCcCCCCCccHHhhcCCCCCCHH
Confidence            999999999999999999999999999999999999999999999999999999998888899999998766655

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

Probab=100.00  E-value=1.1e-44  Score=362.75  Aligned_cols=229  Identities=31%  Similarity=0.505  Sum_probs=216.5

Q ss_pred             hhHHHHHHhccCCCCCCChHHHHHHHHHhHHHHHHHHHHHHHHHHhCCCCchHHHHHHcCCCHHHHHHHHHhchHHHHHH
Q 012638          221 TIFSAERALNSRGRRLTIARNEAEMSKGVQVVANLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQHLAFGWYCREEL  300 (459)
Q Consensus       221 ~~~~~~~~~~~~~~~lLt~~eE~eL~~~i~~~~~le~~~~~l~~~~gr~pt~~ewa~a~g~deeeL~~~l~~G~~Are~L  300 (459)
                      ...|+   ......||||++||++|++.++.++.+++.+.+|+++.|++|+..+||+++|+++.+|+.+++.|..|+++|
T Consensus         3 ~~~yl---~~~~~~~lLt~eeE~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~g~~A~~~L   79 (298)
T TIGR02997         3 VRLYL---QEIGRVPLLTPEEEIELARQVQQMMVLEELREELEEQLGREPSKEEWAAAAGLSEAELRQRLRQGQRAKEKM   79 (298)
T ss_pred             HHHHH---HHccccCCCCHHHHHHHHHHHHHHhHHHHHHHHHHHhhcCCCcHHHHHHhccCCHHHHHHHHhccHHHHHHH
Confidence            34455   345678999999999999999999999999999999999999999999999999999999999998899999


Q ss_pred             HHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhhccccccccchHHH
Q 012638          301 IKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIPCKLNRE  380 (459)
Q Consensus       301 I~~nlrLV~sIAkry~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIrnaI~d~Lrk~sr~irlP~~v~e~  380 (459)
                      |.+|+++|+++|++|.++|.+++|||||||+|||+|+++|||.+|++|+||++||||++|.+++.++++++|+|.++...
T Consensus        80 v~~~lrlV~~iA~~y~~~~~~~eDLiQEg~igL~~a~~kfd~~~g~rFsTya~~wIr~~I~r~i~~~~r~vr~p~~~~~~  159 (298)
T TIGR02997        80 IKANLRLVVSVAKKYQNRGLELLDLIQEGSLGLERAVEKFDPTRGYKFSTYAYWWIRQGITRAIANQSRTIRLPIHITEK  159 (298)
T ss_pred             HHHhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHhCccCCCChHHHHHHHHHHHHHHHHHhcCCCeeCcHHHHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHhhccCCccccccCCCCCCccccCCCCCCCCcc
Q 012638          381 ISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNAKYLNIPPFFFPSFA  452 (459)
Q Consensus       381 i~kI~ka~~~L~~~lgr~PT~eEIAe~LGIS~e~Vk~~l~~ar~~~SLD~~v~~d~~~~l~e~i~D~~~~~~  452 (459)
                      +++++++...+...+|+.||.+|||+.+|+++++|..++..+..++|||.+++++++.++.++++|+.+.|+
T Consensus       160 ~~~~rk~~~~l~~~~~~~pt~~eia~~l~~~~~~v~~~~~~~~~~~SLd~~~~~~~~~~~~~~~~~~~~~pe  231 (298)
T TIGR02997       160 LNKIKKVQRELSQKLGRTPSEAEIAEALELEPEQVRELLQRARQPVSLDAPVGDEEDTELGDLLEDDGESPE  231 (298)
T ss_pred             HHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHHcccCcccCCCcCCCCcchHHHhccCCCCCHH
Confidence            999999999999999999999999999999999999999999999999999987777788898888666554

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

>PRK07406 RNA polymerase sigma factor RpoD; Validated

Probab=100.00  E-value=1.2e-44  Score=373.11  Aligned_cols=231  Identities=27%  Similarity=0.502  Sum_probs=218.0

Q ss_pred             CChhHHHHHHhccCCCCCCChHHHHHHHHHhHHHHHHHHHHHHHHHHhCCCCchHHHHHHcCCCHHHHHHHHHhchHHHH
Q 012638          219 QPTIFSAERALNSRGRRLTIARNEAEMSKGVQVVANLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQHLAFGWYCRE  298 (459)
Q Consensus       219 ~p~~~~~~~~~~~~~~~lLt~~eE~eL~~~i~~~~~le~~~~~l~~~~gr~pt~~ewa~a~g~deeeL~~~l~~G~~Are  298 (459)
                      ++...|+   ......||||++||++|+++|+.++.+++++.+|+++.|++|+..+||.++|+++.+|.+++..|..|++
T Consensus        63 d~l~~Yl---~~i~~~~lLt~eEE~~La~~i~~~~~~~~~~~~l~~~~g~~~~~~~~~~~~~~~~~~l~~~~~~g~~A~~  139 (373)
T PRK07406         63 DSIRVYL---QEIGRIRLLRPDEEIELARKIADLLELEELREQFESELGREPSDKEWAELVDMPLPKFRRRLMLGRRAKE  139 (373)
T ss_pred             CHHHHHH---HHhcccCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhcccccchhhHhhhccccHHHHHHHHhcCHHHHH
Confidence            4444455   3445689999999999999999999999999999999999999999999999999999999999988999


Q ss_pred             HHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhhccccccccchH
Q 012638          299 ELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIPCKLN  378 (459)
Q Consensus       299 ~LI~~nlrLV~sIAkry~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIrnaI~d~Lrk~sr~irlP~~v~  378 (459)
                      +||.+|+++|+++|++|.+++.+++||+|||+||||+|+++|||.+|++|+|||+||||++|.++|++++++||+|.++.
T Consensus       140 ~Li~~~l~lV~~iA~ry~~~~~~~eDLiQEG~igL~~Ai~kFd~~kg~~FsTYA~wWIRqaI~~~I~~~~r~IRlP~~~~  219 (373)
T PRK07406        140 KMVQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYATWWIRQAITRAIADQSRTIRLPVHLY  219 (373)
T ss_pred             HHHHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHhcCCccCCCHHHHHHHHHHHHHHHHHHhcCCceeCCHHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHhhccCCccccccCCCCCCccccCCCCCCCCcc
Q 012638          379 REISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNAKYLNIPPFFFPSFA  452 (459)
Q Consensus       379 e~i~kI~ka~~~L~~~lgr~PT~eEIAe~LGIS~e~Vk~~l~~ar~~~SLD~~v~~d~~~~l~e~i~D~~~~~~  452 (459)
                      +.+++|+++...|.+.+|+.||.+|||+.||+++++|..++..+..++|||.|++++++.++.|+++|+.+.|+
T Consensus       220 ~~~~~i~~a~~~l~~~lgr~Pt~~EIA~~lg~~~e~v~~~~~~~~~~~SLd~~i~~~~~~~l~d~l~d~~~~pe  293 (373)
T PRK07406        220 ETISRIKKTTKVLSQEFGRKPTEEEIAESMEMTIEKLRFIAKSAQLPISLETPIGKEEDSRLGDFIEADGETPE  293 (373)
T ss_pred             HHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCcccHHHhcCCCCCCHH
Confidence            99999999999999999999999999999999999999999988899999999988888899999998765554

>PRK07405 RNA polymerase sigma factor SigD; Validated

Probab=100.00  E-value=1.6e-43  Score=357.97  Aligned_cols=231  Identities=28%  Similarity=0.423  Sum_probs=218.5

Q ss_pred             CChhHHHHHHhccCCCCCCChHHHHHHHHHhHHHHHHHHHHHHHHHHhCCCCchHHHHHHcCCCHHHHHHHHHhchHHHH
Q 012638          219 QPTIFSAERALNSRGRRLTIARNEAEMSKGVQVVANLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQHLAFGWYCRE  298 (459)
Q Consensus       219 ~p~~~~~~~~~~~~~~~lLt~~eE~eL~~~i~~~~~le~~~~~l~~~~gr~pt~~ewa~a~g~deeeL~~~l~~G~~Are  298 (459)
                      +|...|+   ......||||++||++|+++|+.++.+++++..|++++|+.|+..+||.++++++.+|+..++.|+.|++
T Consensus         8 ~~~~~yl---~~i~~~~lLt~eeE~~La~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~L~~~~~~g~~A~~   84 (317)
T PRK07405          8 DLVRTYL---REIGRVPLLTHEEEILYGKQVQRLVALQEIREELAEELGREPTDAEWAKAAKLSEEELRSAIAEGEAAKR   84 (317)
T ss_pred             cHHHHHH---HHccccCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhcccccchHHHhhhccCCHHHHHHHHhccHHHHH
Confidence            4555555   3456689999999999999999999999999999999999999999999999999999999999988999


Q ss_pred             HHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhhccccccccchH
Q 012638          299 ELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIPCKLN  378 (459)
Q Consensus       299 ~LI~~nlrLV~sIAkry~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIrnaI~d~Lrk~sr~irlP~~v~  378 (459)
                      +||..|+++|+++|++|.+++.+++||+||||+|||+++++|||.+|++|+|||+||||++|.++|++++++||+|.++.
T Consensus        85 ~L~~~~~~~V~~~a~~~~~~~~~~eDLvQEg~i~L~~a~~~fd~~~g~rf~tYa~~wIR~~I~~~i~~~~~~ir~p~~~~  164 (317)
T PRK07405         85 KMVEANLRLVVSVAKKYLKRNVDLLDLIQEGTIGMQRGVEKFDPTKGYRFSTYAYWWIRQAITRAIAEKSRTIRLPIHIT  164 (317)
T ss_pred             HHHHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHhCcCCCCChHHHHHHHHHHHHHHHHHhcCCCccCChHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHhhccCCccccccCCCCCCccccCCCCCCCCcc
Q 012638          379 REISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNAKYLNIPPFFFPSFA  452 (459)
Q Consensus       379 e~i~kI~ka~~~L~~~lgr~PT~eEIAe~LGIS~e~Vk~~l~~ar~~~SLD~~v~~d~~~~l~e~i~D~~~~~~  452 (459)
                      ..+++++++...+...+|+.||.+|||+.+|+++++|..++...+.++|||.|++++++.++.++++|+.+.|+
T Consensus       165 ~~~~~l~~~~~~l~~~~gr~pt~~eiA~~~~~~~~~v~~~~~~~~~~~SLd~~~~~~~~~~l~~~~~d~~~~pe  238 (317)
T PRK07405        165 EKLNKIKKAQRQLSQQLGRAATIGELAEELELTPKQVREYLERARQPLSLDLRVGDNQDTELGELLEDTGASPE  238 (317)
T ss_pred             HHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHHcCCCeeecCCCCCCCCccHHHhhcCCCCCHH
Confidence            99999999999999999999999999999999999999999988899999999988888899999998765554

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

Probab=100.00  E-value=3e-41  Score=342.15  Aligned_cols=224  Identities=29%  Similarity=0.440  Sum_probs=203.6

Q ss_pred             ccCCCCCCChHHHHHHHHHhHHHHHHHHHHHHHHH-HhCCCCchH---------------HHHHHcCCCH-HHHHHHHHh
Q 012638          230 NSRGRRLTIARNEAEMSKGVQVVANLERIKTTLEK-ESGKAASLN---------------CWAQAAGVSE-RVLKQHLAF  292 (459)
Q Consensus       230 ~~~~~~lLt~~eE~eL~~~i~~~~~le~~~~~l~~-~~gr~pt~~---------------ewa~a~g~de-eeL~~~l~~  292 (459)
                      .....++++.++|.++.+.++....+......+.. .++..|+..               +|+.....++ ..|..++..
T Consensus        17 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~Ee~~la~~~~~   96 (342)
T COG0568          17 EIGRIPLLVREAEVELAKQLEDEQLLVELGEDLTDLKLGREPSERARRPAGRLSFYIRAIEAAPLLTPEEEKALARRLKR   96 (342)
T ss_pred             HhcchhhhhHHHHHHHHHHHhHhhhhhHHHHHHHhcccccccchhhhhhhhhHHHHHHHHhhhcccChHHHHHHHHHHHc
Confidence            34456999999999999999988877777777766 667888876               5555555444 678889999


Q ss_pred             ch--H-HHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhhcc
Q 012638          293 GW--Y-CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHAR  369 (459)
Q Consensus       293 G~--~-Are~LI~~nlrLV~sIAkry~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIrnaI~d~Lrk~sr  369 (459)
                      |.  . |+.+||.+|+++|++||++|.|+|+++.||||||+||||+|++||||.+|++|||||+||||++|.++|.++.+
T Consensus        97 g~~~~~Ak~klv~snLRlVvsIAk~Y~~rGL~~~DLIQEGniGLmkAVekFdp~rG~kFsTYA~wWIrqaI~raI~~q~r  176 (342)
T COG0568          97 GERDLDAKKKLVESNLRLVVSIAKKYTGRGLPFLDLIQEGNIGLMKAVEKFDPEKGFKFSTYATWWIRQAITRAIADQAR  176 (342)
T ss_pred             CCccHHHHHHHHHHHHHHHHHHHHHhhcCCCcHHHHHhcccHHHHHHHHhcCcccCCcchhHHHHHHHHHHHHHHHHhcc
Confidence            94  3 99999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ccccccchHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHhhccCCccccccCCCCCCccccCCCCCCC
Q 012638          370 GIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNAKYLNIPPFFFP  449 (459)
Q Consensus       370 ~irlP~~v~e~i~kI~ka~~~L~~~lgr~PT~eEIAe~LGIS~e~Vk~~l~~ar~~~SLD~~v~~d~~~~l~e~i~D~~~  449 (459)
                      +||+|.|+.+.++++.++.+.|.+.+++.|+++|||+.||+++++|..++..++.++|||.|+|++++..++|+++|+.+
T Consensus       177 tIRipvh~~e~~nkl~r~~r~l~q~~~r~p~~eeia~~l~~~~~~V~~m~~~~~~~~SLd~~ig~ded~~l~d~leD~~~  256 (342)
T COG0568         177 TIRIPVHQVELINKLRRVKRELLQELGREPTPEEIAEELGVSPDKVREMLKRASEPISLDTPIGDDEDSELGDFLEDDKS  256 (342)
T ss_pred             hhhHhHHHHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHhCCCHHHHHHHHHhcccCcccCCcCCCCcccHHHHHhhcCCc
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999865


Q ss_pred             -Cccc
Q 012638          450 -SFAI  453 (459)
Q Consensus       450 -~~~~  453 (459)
                       .|++
T Consensus       257 ~~p~~  261 (342)
T COG0568         257 VSPED  261 (342)
T ss_pred             CCHHH
Confidence             5543

>PRK05901 RNA polymerase sigma factor; Provisional

Probab=100.00  E-value=4.8e-40  Score=349.52  Aligned_cols=215  Identities=28%  Similarity=0.419  Sum_probs=191.5

Q ss_pred             CCChhHHHHHHhccCCCCCCChHHHHHHHHHhHHHHHHHHHHHHHHHHhCCCCchHHHHHHcCCCHHHHHHHHHhchHHH
Q 012638          218 KQPTIFSAERALNSRGRRLTIARNEAEMSKGVQVVANLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQHLAFGWYCR  297 (459)
Q Consensus       218 ~~p~~~~~~~~~~~~~~~lLt~~eE~eL~~~i~~~~~le~~~~~l~~~~gr~pt~~ewa~a~g~deeeL~~~l~~G~~Ar  297 (459)
                      .+|...|+   ......||||++||++|+++|+.+..+++...          ....|+.+   ...+|...+..|..|+
T Consensus       210 ~d~l~~YL---~~i~~~~lLt~eEE~~La~~i~~g~~~~~~~~----------~~~~~~~~---~~~~l~~~~~~g~~Ar  273 (509)
T PRK05901        210 ADPVKAYL---KQIGKVKLLNAEEEVELAKRIEAGLYAEELLA----------EGEKLDPE---LRRDLQWIGRDGKRAK  273 (509)
T ss_pred             ccHHHHHH---HHhccCCCCCHHHHHHHHHHHHhCCchhhhhh----------hcccchhh---hhhhhhhhccchHHHH
Confidence            35555555   23456799999999999999998866555321          11234422   3567888899999999


Q ss_pred             HHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhhccccccccch
Q 012638          298 EELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIPCKL  377 (459)
Q Consensus       298 e~LI~~nlrLV~sIAkry~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIrnaI~d~Lrk~sr~irlP~~v  377 (459)
                      ++||.+|+|||+++|++|.++|++++||||||+|||++|+++|||++|++|+|||+||||++|.++|+++.+.||+|.++
T Consensus       274 ~~LI~sNLrLVvsIAkrY~~~Gl~~eDLIQEGnIGLikAvekFDp~rG~rFSTYA~wWIRqaI~raI~d~~r~IRvP~~~  353 (509)
T PRK05901        274 NHLLEANLRLVVSLAKRYTNRGLSFLDLIQEGNLGLIKAVEKFDYTKGYKFSTYATWWIRQAITRAMADQARTIRIPVHM  353 (509)
T ss_pred             HHHHHHhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHhCcccCCCchhhhHHHHHHHHHHHHHHcCCceecCHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHhhccCCccccccCCCCCCccccCCCCCC
Q 012638          378 NREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNAKYLNIPPFFF  448 (459)
Q Consensus       378 ~e~i~kI~ka~~~L~~~lgr~PT~eEIAe~LGIS~e~Vk~~l~~ar~~~SLD~~v~~d~~~~l~e~i~D~~  448 (459)
                      .+.+++|.++.+.|.+.+|+.||.+|||+.|||++++|..++...+.++|||.|++++++.++.|+|+|+.
T Consensus       354 ~e~i~kl~~~~~~L~~~lgr~PT~eELAe~Lgis~e~V~~~~~~~~~~~SLD~~i~~d~~~~l~d~l~D~~  424 (509)
T PRK05901        354 VETINKLGRIERELLQELGREPTPEELAKEMGFTPEKVREIQKYNREPISLDKTIGKEGDSQFGDFIEDSE  424 (509)
T ss_pred             HHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccccccccCCcccHHHhccCCC
Confidence            99999999999999999999999999999999999999999999999999999999888888999999874

>PRK07921 RNA polymerase sigma factor SigB; Reviewed

Probab=100.00  E-value=1.5e-39  Score=330.01  Aligned_cols=215  Identities=27%  Similarity=0.411  Sum_probs=191.5

Q ss_pred             CCChhHHHHHHhccCCCCCCChHHHHHHHHHhHHHHHHHHHHHHHHHHhCCCCchHHHHHHcCCCHHHHHHHHHhchHHH
Q 012638          218 KQPTIFSAERALNSRGRRLTIARNEAEMSKGVQVVANLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQHLAFGWYCR  297 (459)
Q Consensus       218 ~~p~~~~~~~~~~~~~~~lLt~~eE~eL~~~i~~~~~le~~~~~l~~~~gr~pt~~ewa~a~g~deeeL~~~l~~G~~Ar  297 (459)
                      +++...|+   ......||||++||++|+++|+.+..++..           |+..+|+...  ...+|...++.|..|+
T Consensus        25 ~~~~~~Yl---~~i~~~~lLt~eeE~~La~~~~~g~~~~~~-----------~~~~~~~~~~--~~~~l~~~~~~~~~A~   88 (324)
T PRK07921         25 ADLVRVYL---NGIGKTALLTAADEVELAKRIEAGLYAEHL-----------LETRKRLSEA--RKRDLAAVVRDGEAAR   88 (324)
T ss_pred             CChHHHHH---HHhcccCCCCHHHHHHHHHHHHhhhhhhhh-----------hccccccchh--HHHHHHHHHhcCHHHH
Confidence            35555555   345668999999999999999988776654           1122232111  3567889999999999


Q ss_pred             HHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhhccccccccch
Q 012638          298 EELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIPCKL  377 (459)
Q Consensus       298 e~LI~~nlrLV~sIAkry~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIrnaI~d~Lrk~sr~irlP~~v  377 (459)
                      ++||..|+++|+++|++|.+++.+++||+|||+||||+|+++|||++|++|+|||+||||++|.++|+++++.|++|.++
T Consensus        89 ~~Lv~~~~~lV~~iA~r~~~~~~~~eDLvQEg~igL~~a~~~fdp~~G~rFsTYA~~wIr~aI~~~i~~~~r~vrlP~~~  168 (324)
T PRK07921         89 RHLLEANLRLVVSLAKRYTGRGMPLLDLIQEGNLGLIRAMEKFDYTKGFKFSTYATWWIRQAITRGMADQSRTIRLPVHL  168 (324)
T ss_pred             HHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHcCCccCCCHHHHHHHHHHHHHHHHHHHcCCCccCCHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHhhccCCccccccCCCCCCccccCCCCCC
Q 012638          378 NREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNAKYLNIPPFFF  448 (459)
Q Consensus       378 ~e~i~kI~ka~~~L~~~lgr~PT~eEIAe~LGIS~e~Vk~~l~~ar~~~SLD~~v~~d~~~~l~e~i~D~~  448 (459)
                      .+.++++.++...|...+|+.||.+|||+.||+++++|..++..+..++|||.|++++++.++.|+++|+.
T Consensus       169 ~~~~~~l~~~~~~l~~~lgr~pt~~EiA~~lgi~~~~v~~~~~~~~~~~SLd~~~~~~~~~~l~d~l~d~~  239 (324)
T PRK07921        169 VEQVNKLARIKRELHQQLGREATDEELAEESGIPEEKIADLLEHSRDPVSLDMPVGSDEEAPLGDFIEDSE  239 (324)
T ss_pred             HHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHHcCCCceecCCCCCCCCchHHHHhcCCC
Confidence            99999999999999999999999999999999999999999988888999999998877788999999863

>PRK09210 RNA polymerase sigma factor RpoD; Validated

Probab=100.00  E-value=3.1e-34  Score=295.50  Aligned_cols=187  Identities=27%  Similarity=0.449  Sum_probs=171.1

Q ss_pred             CChhHHHHHHhccCCCCCCChHHHHHHHHHhHHHHHHHHHHHHHHHHhCCCCchHHHHHHcCCCHHHHHHHHHhchHHHH
Q 012638          219 QPTIFSAERALNSRGRRLTIARNEAEMSKGVQVVANLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQHLAFGWYCRE  298 (459)
Q Consensus       219 ~p~~~~~~~~~~~~~~~lLt~~eE~eL~~~i~~~~~le~~~~~l~~~~gr~pt~~ewa~a~g~deeeL~~~l~~G~~Are  298 (459)
                      ++...|+   ......|+||++||.+|++.++.+                                        +..|++
T Consensus        96 d~~~~yl---~~i~~~~~l~~~ee~~L~~~~~~G----------------------------------------d~~A~~  132 (367)
T PRK09210         96 DPVRMYL---KEIGRVPLLTAEEEIELAKRIEEG----------------------------------------DEEAKQ  132 (367)
T ss_pred             cHHHHHH---HHhhccCCCCHHHHHHHHHHHHhh----------------------------------------HHHHHH
Confidence            4444444   344568999999999998866432                                        123899


Q ss_pred             HHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhhccccccccchH
Q 012638          299 ELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIPCKLN  378 (459)
Q Consensus       299 ~LI~~nlrLV~sIAkry~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIrnaI~d~Lrk~sr~irlP~~v~  378 (459)
                      +||..|+++|+++|++|.+++.+++||+|||+||||+|+++|||.+|++|+|||+|||+++|.++|+++.+++|+|.|+.
T Consensus       133 ~Li~~~~~lV~~iA~~~~~~~~~~eDLiQEg~igL~~a~~~fd~~~g~~FsTyA~~wIr~aI~~~i~~~~r~irip~~~~  212 (367)
T PRK09210        133 RLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNMGLMKAVEKFDYRKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMV  212 (367)
T ss_pred             HHHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHhcCCCCCCchHHHHHHHHHHHHHHHHHHcCCceeccHHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHhhccCCccccccCCCCCCccccCCCCCC
Q 012638          379 REISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNAKYLNIPPFFF  448 (459)
Q Consensus       379 e~i~kI~ka~~~L~~~lgr~PT~eEIAe~LGIS~e~Vk~~l~~ar~~~SLD~~v~~d~~~~l~e~i~D~~  448 (459)
                      +.++++.++.+.|...+|+.||.+|||+.|||++++|..++..++.++|||.|++++++.++.|+++|+.
T Consensus       213 ~~~~~~~~~~~~l~~~lgr~pt~~EiA~~l~~~~~~v~~~~~~~~~~~SLd~~~~~~~~~~l~d~i~d~~  282 (367)
T PRK09210        213 ETINKLIRVQRQLLQELGREPTPEEIAEEMDMPPEKVREILKIAQEPVSLETPIGEEDDSHLGDFIEDQD  282 (367)
T ss_pred             HHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHHhcCCCCcCCCCCCCCcchhhhhccCCC
Confidence            9999999999999999999999999999999999999999999989999999999888889999998874

>PRK05658 RNA polymerase sigma factor RpoD; Validated

Probab=100.00  E-value=8.1e-34  Score=309.76  Aligned_cols=173  Identities=27%  Similarity=0.533  Sum_probs=161.0

Q ss_pred             HHHcCCCH---HHHHHHHHhch----HHHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCch
Q 012638          276 AQAAGVSE---RVLKQHLAFGW----YCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKF  348 (459)
Q Consensus       276 a~a~g~de---eeL~~~l~~G~----~Are~LI~~nlrLV~sIAkry~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rF  348 (459)
                      ....+++.   ..+.++++.|+    .|+++||.+|++||++||++|.++|++++||||||+|||++|+++|||.+|++|
T Consensus       354 e~~~~Ls~eElk~l~~~i~~g~~~~~~a~~~Li~~nlrlV~~iA~ky~~~gl~~~DLiQeG~iGL~~Av~kfd~~~G~~F  433 (619)
T PRK05658        354 EEETGLTIEELKEINRQISKGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF  433 (619)
T ss_pred             HHHhCCCHHHHHHHHHHHhccchhhhHHHHHHHHHHHHHHHHHHHHHhhCCCCHHHHHHHHHHHHHHHHHhcCccCCCch
Confidence            33445554   34567778885    389999999999999999999999999999999999999999999999999999


Q ss_pred             hhHHHHHHHHHHHHHHHhhccccccccchHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHhhccCCcc
Q 012638          349 STYVQYWIRKSISKMVARHARGIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSI  428 (459)
Q Consensus       349 STYa~~wIrnaI~d~Lrk~sr~irlP~~v~e~i~kI~ka~~~L~~~lgr~PT~eEIAe~LGIS~e~Vk~~l~~ar~~~SL  428 (459)
                      +|||+||||++|.++|+++.++||+|.|+.+.+++++++...+.+++|+.||.+|||+.||+|+++|..++..+..++||
T Consensus       434 stYA~~wIr~aI~~~i~~~~r~irip~~~~~~~~k~~~~~~~~~~~~gr~pt~~eiA~~l~~~~~~v~~~~~~~~~~~Sl  513 (619)
T PRK05658        434 STYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEIGREPTPEELAERLGMPEDKVRKVLKIAKEPISL  513 (619)
T ss_pred             HHHhHHHHHHHHHHHHHHcCCceecCHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCCcC
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ccccCCCCCCccccCCCCCC
Q 012638          429 DQKIGDCLNAKYLNIPPFFF  448 (459)
Q Consensus       429 D~~v~~d~~~~l~e~i~D~~  448 (459)
                      |.|++++++.++.|+++|+.
T Consensus       514 d~~i~~~~~~~l~d~i~d~~  533 (619)
T PRK05658        514 ETPIGDDEDSHLGDFIEDKN  533 (619)
T ss_pred             CCCCCCCCCCchhhhcCCCC
Confidence            99999888889999999863

>PRK07122 RNA polymerase sigma factor SigF; Reviewed

Probab=99.98  E-value=4.4e-32  Score=267.96  Aligned_cols=154  Identities=22%  Similarity=0.309  Sum_probs=142.0

Q ss_pred             HHHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhhccccccc
Q 012638          295 YCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIP  374 (459)
Q Consensus       295 ~Are~LI~~nlrLV~sIAkry~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIrnaI~d~Lrk~sr~irlP  374 (459)
                      .++++||.+|++||+++|++|.++|++++||||||+|||++|+++|||++|++|+|||+|||+++|.++++++.+.|++|
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            38899999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cchHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHh--hccCCccccccCCCCC--CccccCCCCCC
Q 012638          375 CKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASEC--LRIVGSIDQKIGDCLN--AKYLNIPPFFF  448 (459)
Q Consensus       375 ~~v~e~i~kI~ka~~~L~~~lgr~PT~eEIAe~LGIS~e~Vk~~l~~--ar~~~SLD~~v~~d~~--~~l~e~i~D~~  448 (459)
                      .++.+..++++++...|.+.+|+.||.+|||+.||+++++|..++..  ...++|||.+++++++  ..+.+.++|++
T Consensus       120 r~~~~~~~~i~~~~~~l~~~lg~~pt~~eiA~~lg~~~~~v~~~~~~~~~~~~~SLd~~~~~~~~~~~~~~d~~~~~~  197 (264)
T PRK07122        120 RRLKELHLRLGRATAELSQRLGRAPTASELAAELGMDREEVVEGLVAGSAYNTLSIDSGGGSGDDDARAIADTLGDVD  197 (264)
T ss_pred             HHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHHhhcCCCCcccccccCCCCCcccchhccCCcH
Confidence            99999999999999999999999999999999999999999998764  4568999999875433  35666766654

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

Probab=99.98  E-value=1.1e-31  Score=260.18  Aligned_cols=153  Identities=33%  Similarity=0.592  Sum_probs=146.9

Q ss_pred             HHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhhcccccccc
Q 012638          296 CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIPC  375 (459)
Q Consensus       296 Are~LI~~nlrLV~sIAkry~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIrnaI~d~Lrk~sr~irlP~  375 (459)
                      |+++||..|+++|+++|++|.+++.+++||+|||++||++|+++|||.+|++|+|||+||||++|.++++++.+.+++|.
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             chHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHhhccCCccccccCCCCCCccccCCCCCC
Q 012638          376 KLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNAKYLNIPPFFF  448 (459)
Q Consensus       376 ~v~e~i~kI~ka~~~L~~~lgr~PT~eEIAe~LGIS~e~Vk~~l~~ar~~~SLD~~v~~d~~~~l~e~i~D~~  448 (459)
                      ++.+.++++.++...|...+|+.||.+|||+.||+++++|..++.....++|||.+++++++.++.|+++|+.
T Consensus        81 ~~~~~~~~~~~~~~~l~~~~g~~pt~~eia~~l~~~~~~v~~~~~~~~~~~SLd~~~~~~~~~~l~d~l~d~~  153 (238)
T TIGR02393        81 HMVETINKLIKAERQLTQELGREPTDEELAERMGMPAEKVREIKKIAQEPISLETPIGEEEDSFLGDFIEDTS  153 (238)
T ss_pred             HHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHHhccCCCcCCCCCCCCcccHHHHhcCCC
Confidence            9999999999999999999999999999999999999999999888888999999998777778999998875

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.

>PRK07408 RNA polymerase sigma factor SigF; Reviewed

Probab=99.97  E-value=1.5e-30  Score=255.66  Aligned_cols=160  Identities=24%  Similarity=0.339  Sum_probs=145.0

Q ss_pred             HhchH-HHHHHHHHhHHHHHHHHHHhhCC-CCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhhc
Q 012638          291 AFGWY-CREELIKSTRPLVLFLARNYRGL-GIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHA  368 (459)
Q Consensus       291 ~~G~~-Are~LI~~nlrLV~sIAkry~g~-g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIrnaI~d~Lrk~s  368 (459)
                      ..|+. |+++||..|+++|+++|++|.+. +.+++||+|||+||||+|+++|||++|++|+|||+|||+|+|.++++++.
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            46665 99999999999999999999876 66799999999999999999999999999999999999999999999999


Q ss_pred             cccccccchHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHH--hhccCCccccccCCCCC--CccccCC
Q 012638          369 RGIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASE--CLRIVGSIDQKIGDCLN--AKYLNIP  444 (459)
Q Consensus       369 r~irlP~~v~e~i~kI~ka~~~L~~~lgr~PT~eEIAe~LGIS~e~Vk~~l~--~ar~~~SLD~~v~~d~~--~~l~e~i  444 (459)
                      +.+|+|.++.+.+++++++...|.+.+|+.||.+|||+.||+++++|..++.  ....++|||.+++++++  .++.+.+
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            9999999999999999999999999999999999999999999999999865  34568999999865433  4678888


Q ss_pred             CCCCCC
Q 012638          445 PFFFPS  450 (459)
Q Consensus       445 ~D~~~~  450 (459)
                      +|+...
T Consensus       180 ~d~~~~  185 (256)
T PRK07408        180 PDPRYR  185 (256)
T ss_pred             CCcccc
Confidence            887543

>PRK07500 rpoH2 RNA polymerase factor sigma-32; Reviewed

Probab=99.97  E-value=3.5e-30  Score=257.60  Aligned_cols=183  Identities=22%  Similarity=0.292  Sum_probs=154.2

Q ss_pred             ccCCCCCCChHHHHHHHHHhHHHHHHHHHHHHHHHHhCCCCchHHHHHHcCCCHHHHHHHHHhchH-HHHHHHHHhHHHH
Q 012638          230 NSRGRRLTIARNEAEMSKGVQVVANLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQHLAFGWY-CREELIKSTRPLV  308 (459)
Q Consensus       230 ~~~~~~lLt~~eE~eL~~~i~~~~~le~~~~~l~~~~gr~pt~~ewa~a~g~deeeL~~~l~~G~~-Are~LI~~nlrLV  308 (459)
                      +..+.|+||+++|.+|+++++                                        ..|+. |+++||..|+++|
T Consensus        14 ~~~~~~~l~~~~e~~L~~~~~----------------------------------------~~gd~~A~~~Lv~~~~~lV   53 (289)
T PRK07500         14 SAMKAPYLEREEEHALAYRWK----------------------------------------DHRDEDALHRIISAHMRLV   53 (289)
T ss_pred             HHhcCCCCCHHHHHHHHHHHH----------------------------------------HCCCHHHHHHHHHHhHHHH
Confidence            345679999999998887542                                        12444 9999999999999


Q ss_pred             HHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhhccccccccchHH--HHHHHHH
Q 012638          309 LFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIPCKLNR--EISKIQK  386 (459)
Q Consensus       309 ~sIAkry~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIrnaI~d~Lrk~sr~irlP~~v~e--~i~kI~k  386 (459)
                      +++|++|.+++.+++||+||||+|||+|+++|||.+|.+|+|||+|||+++|.++|+++.+.+|+|.+..+  ...++.+
T Consensus        54 ~~~a~~~~~~~~~~eDLvQeg~i~L~~a~~~fd~~~~~~f~tya~~~Ir~~I~~~lr~~~~~iR~p~~~~~~~~~~~~~~  133 (289)
T PRK07500         54 ISMAGKFRRFGLPMNDLIQEGYVGLLEAAARFEPDREVRFSTYATWWIRASIQDYILRNWSIVRGGTSSAQKALFFNLRR  133 (289)
T ss_pred             HHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHcCCCCCCChHHHHHHHHHHHHHHHHHHCCCceecCccHHHHHHHHHHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999998655  3345555


Q ss_pred             HHHHHHH---HcCCCCCHHHHHHHhCCCHHHHHHHHH-hhccCCccccccCCCCC--CccccCCCCCCCCcc
Q 012638          387 ARKALTN---SHGKYPEDIEIAKYTGLSLAEIRSASE-CLRIVGSIDQKIGDCLN--AKYLNIPPFFFPSFA  452 (459)
Q Consensus       387 a~~~L~~---~lgr~PT~eEIAe~LGIS~e~Vk~~l~-~ar~~~SLD~~v~~d~~--~~l~e~i~D~~~~~~  452 (459)
                      +...+..   .+++.||.+|||+.||+++++|..+.. ....++|||.+++++++  .++.|+++|+.+.|+
T Consensus       134 ~~~~~~~~~~~l~~~pt~~eiA~~l~~~~~~v~~~~~~~~~~~~SLd~~~~~~~~~~~~l~d~i~d~~~~pe  205 (289)
T PRK07500        134 LRARLAQADEELTKQEIHREIATALGVSLSDVEMMDARLSGPDASLNAPQSEEDEGRSERMDFLVDDSPLPD  205 (289)
T ss_pred             HHHHHHhhhcccCCCCCHHHHHHHhCcCHHHHHHHHHHhcCCCccccCCCCCCCCCcccHHHhccCCCCCch
Confidence            5555544   679999999999999999999987753 34578999999976554  368999998866554

>TIGR02850 spore_sigG RNA polymerase sigma-G factor

Probab=99.97  E-value=3.5e-29  Score=245.10  Aligned_cols=154  Identities=24%  Similarity=0.257  Sum_probs=142.7

Q ss_pred             HHHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhhccccccc
Q 012638          295 YCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIP  374 (459)
Q Consensus       295 ~Are~LI~~nlrLV~sIAkry~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIrnaI~d~Lrk~sr~irlP  374 (459)
                      .|+++||..|.++|+++|++|.+++.+++||+|||++|||+++++||+.+|.+|+||+++||+|.|.++++++. .+++|
T Consensus        34 ~a~~~L~~~~~~~v~~~a~~~~~~~~~aeDlvQe~~i~l~~a~~~fd~~~~~~f~tyl~~~irn~~~~~lr~~~-~ir~p  112 (254)
T TIGR02850        34 TAREKLINGNLRLVLSVIQRFNNRGEYVDDLFQVGCIGLMKSIDNFDLSQNVKFSTYAVPMIIGEIRRYLRDNN-PIRVS  112 (254)
T ss_pred             HHHHHHHHHhHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCChHHHHHHHHHHHHHHHHHhCC-CccCc
Confidence            39999999999999999999999999999999999999999999999999999999999999999999999874 78999


Q ss_pred             cchHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHhhccCCccccccCCCCC--CccccCCCCCCC
Q 012638          375 CKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLN--AKYLNIPPFFFP  449 (459)
Q Consensus       375 ~~v~e~i~kI~ka~~~L~~~lgr~PT~eEIAe~LGIS~e~Vk~~l~~ar~~~SLD~~v~~d~~--~~l~e~i~D~~~  449 (459)
                      .++.+...++.++...+..++|+.||.+|||+.||+++++|..++.....++|||.++.++++  .++.+.++|+..
T Consensus       113 ~~~~~~~~~~~~~~~~l~~~l~~~pt~~elA~~l~~~~e~v~~~~~~~~~~~Sld~~~~~~~~~~~~~~~~~~d~~~  189 (254)
T TIGR02850       113 RSLRDIAYKALQVRDKLISENSKEPTVSEIAKELKVPQEEVVFALDAIQDPVSLFEPIYNDGGDPIYVMDQISDEKN  189 (254)
T ss_pred             hHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHCcCHHHHHHHHHhcCCCCcccCCCCCCCCCcchhhhhcCCccc
Confidence            999999999999999999999999999999999999999999999988889999999864433  457888887644

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

>PRK06596 RNA polymerase factor sigma-32; Reviewed

Probab=99.96  E-value=6.2e-29  Score=247.92  Aligned_cols=159  Identities=27%  Similarity=0.380  Sum_probs=133.9

Q ss_pred             hchH-HHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhhccc
Q 012638          292 FGWY-CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARG  370 (459)
Q Consensus       292 ~G~~-Are~LI~~nlrLV~sIAkry~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIrnaI~d~Lrk~sr~  370 (459)
                      .|+. |+++||..|+++|+++|++|.+.+.+++||+|||++||++|+++|||.+|++|+|||+|||+++|.++++++.+.
T Consensus        44 ~Gd~~a~~~Lv~~~~~lV~~ia~~~~~~~~~~eDLvQeg~igL~~a~~~fd~~~~~~FstYA~~~Ir~~i~~~l~~~~~~  123 (284)
T PRK06596         44 HGDLEAAKQLVLSHLRFVVHIARGYRGYGLPQADLIQEGNIGLMKAVKRFDPEVGVRLVSFAVHWIKAEIHEYILRNWRI  123 (284)
T ss_pred             cCCHHHHHHHHHHhHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHHHhCcccCCCHHHHHHHHHHHHHHHHHHHcCCe
Confidence            3554 999999999999999999999999999999999999999999999999999999999999999999999998778


Q ss_pred             cccccchHH--HHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHhh-ccCCccccccCCCC--CCccccCCC
Q 012638          371 IKIPCKLNR--EISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECL-RIVGSIDQKIGDCL--NAKYLNIPP  445 (459)
Q Consensus       371 irlP~~v~e--~i~kI~ka~~~L~~~lgr~PT~eEIAe~LGIS~e~Vk~~l~~a-r~~~SLD~~v~~d~--~~~l~e~i~  445 (459)
                      +++|.+...  ...++.+....+.  .++.||.+|||+.||+++++|..++... ..++|||.++++++  +.++.++++
T Consensus       124 vr~p~~~~~~~~~~~~~~~~~~l~--~~~~~t~~eiA~~l~~~~~~v~~~~~~~~~~~~SLd~~~~~~~~~~~~l~~~l~  201 (284)
T PRK06596        124 VKVATTKAQRKLFFNLRKAKKRLG--WLNPEEVEMVAEELGVSEEEVREMESRLSGQDASLDAPIDDDDEESGAPQDYLE  201 (284)
T ss_pred             eeccchHHHHHHHHHHHHHHHHhc--cCCCCCHHHHHHHhCcCHHHHHHHHHHhcCCCcCcCCCCCCCCCCcchHHHHcC
Confidence            999987542  3334444444443  3489999999999999999999987543 46899999987553  356889999


Q ss_pred             CCCCCcc
Q 012638          446 FFFPSFA  452 (459)
Q Consensus       446 D~~~~~~  452 (459)
                      |+.+.|+
T Consensus       202 d~~~~p~  208 (284)
T PRK06596        202 DKSSDPA  208 (284)
T ss_pred             CCCCCch
Confidence            8865554

>TIGR02392 rpoH_proteo alternative sigma factor RpoH

Probab=99.96  E-value=2.6e-28  Score=241.26  Aligned_cols=160  Identities=27%  Similarity=0.386  Sum_probs=132.3

Q ss_pred             hchH-HHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhhccc
Q 012638          292 FGWY-CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARG  370 (459)
Q Consensus       292 ~G~~-Are~LI~~nlrLV~sIAkry~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIrnaI~d~Lrk~sr~  370 (459)
                      .|+. |+++||..|+++|+++|++|.+++.+++||+|||++||++|+++|||++|++|+|||+|||+++|.++++++.+.
T Consensus        31 ~gd~~a~~~Lv~~~~~lV~~~a~~~~~~~~~~eDLvQeg~igl~~a~~~fd~~~~~~FsTYA~~~Ir~~i~~~l~~~~~~  110 (270)
T TIGR02392        31 HGDLDAAKKLVLSHLRFVVKIARGYRGYGLPQADLIQEGNIGLMKAVKRFDPERGVRLVSFAVHWIKAEIHEYILRNWRL  110 (270)
T ss_pred             CCCHHHHHHHHHHhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHhCcccCCChHHhhHHHHHHHHHHHHHHcCCc
Confidence            4554 999999999999999999999999999999999999999999999999999999999999999999999988778


Q ss_pred             cccccchH--HHHHHHHHHHHHHHHHcCCCC-CHHHHHHHhCCCHHHHHHHHHhhc-cCCccccccCCCCC--CccccCC
Q 012638          371 IKIPCKLN--REISKIQKARKALTNSHGKYP-EDIEIAKYTGLSLAEIRSASECLR-IVGSIDQKIGDCLN--AKYLNIP  444 (459)
Q Consensus       371 irlP~~v~--e~i~kI~ka~~~L~~~lgr~P-T~eEIAe~LGIS~e~Vk~~l~~ar-~~~SLD~~v~~d~~--~~l~e~i  444 (459)
                      +++|.+..  +...++.++...+.  ..+.| +.+|||+.||+++++|..++.... .++|||.+++++++  .++.+++
T Consensus       111 ir~p~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~eiA~~l~~~~~~v~~~~~~~~~~~~Sld~~~~~~~~~~~~~~~~l  188 (270)
T TIGR02392       111 VKVATTKAQRKLFFNLRKMKKRLQ--GWLNPEEVEAIAEELGVSEREVREMESRLSGQDMSLNASIDDDEDDGGAPIAYL  188 (270)
T ss_pred             eecCchHHHHHHHHHHHHHHHHHh--cCCCCCCHHHHHHHhCCCHHHHHHHHHHccCCCccCCCCCCCCCCccccHHHHh
Confidence            99997643  34445555554442  12455 699999999999999999865443 47999999976544  3678888


Q ss_pred             CCCCCCccc
Q 012638          445 PFFFPSFAI  453 (459)
Q Consensus       445 ~D~~~~~~~  453 (459)
                      +|+.++|+.
T Consensus       189 ~d~~~~pe~  197 (270)
T TIGR02392       189 VDKTSDPED  197 (270)
T ss_pred             cCCCCChHH
Confidence            887655543

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.

>PRK08215 sporulation sigma factor SigG; Reviewed

Probab=99.96  E-value=8.2e-28  Score=235.78  Aligned_cols=156  Identities=24%  Similarity=0.249  Sum_probs=142.8

Q ss_pred             HHHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhhccccccc
Q 012638          295 YCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIP  374 (459)
Q Consensus       295 ~Are~LI~~nlrLV~sIAkry~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIrnaI~d~Lrk~sr~irlP  374 (459)
                      .|+++||..|.++|+++|++|.+++.+++||+|||++|||+|+++||+.+|.+|+||+++||+|+|.++++++. .+++|
T Consensus        37 ~a~~~l~~~~~~~v~~~a~~~~~~~~~aeDlvQe~~i~l~~a~~~fd~~~~~~f~t~l~~~ir~~i~~~lr~~~-~vrip  115 (258)
T PRK08215         37 EAREKLINGNLRLVLSVIQRFNNRGENVDDLFQVGCIGLMKAIDNFDLSQNVKFSTYAVPMIIGEIRRYLRDNN-PIRVS  115 (258)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCCcHHHHHHHHHHHHHHHHHhCC-ceEec
Confidence            38999999999999999999999999999999999999999999999999999999999999999999999884 88999


Q ss_pred             cchHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHhhccCCccccccCCCCC--CccccCCCCCCCCc
Q 012638          375 CKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLN--AKYLNIPPFFFPSF  451 (459)
Q Consensus       375 ~~v~e~i~kI~ka~~~L~~~lgr~PT~eEIAe~LGIS~e~Vk~~l~~ar~~~SLD~~v~~d~~--~~l~e~i~D~~~~~  451 (459)
                      .++.....++.++...+..++|+.|+.+|||+.|||++++|..++.....++|||.+++++++  .++.|.++|+...+
T Consensus       116 ~~~~~~~~~~~~~~~~l~~~~~r~p~~~eia~~l~v~~~~v~~~~~~~~~~~sl~~~~~~~~~~~~~~~~~~~~~~~~~  194 (258)
T PRK08215        116 RSLRDIAYKALQVREKLINENSKEPTVEEIAKELEVPREEVVFALDAIQDPVSLFEPIYHDGGDPIYVMDQISDEKNKD  194 (258)
T ss_pred             HHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHCcCHHHHHHHHHhcCCCccccCCCCCCCCcchhhhhhccCccccH
Confidence            999999999999999999999999999999999999999999998888888999999865543  34677887765433

>PRK05657 RNA polymerase sigma factor RpoS; Validated

Probab=99.96  E-value=1.5e-27  Score=242.48  Aligned_cols=185  Identities=25%  Similarity=0.439  Sum_probs=164.9

Q ss_pred             HHHHHHhc-cCCCCCCChHHHHHHHHHhHHHHHHHHHHHHHHHHhCCCCchHHHHHHcCCCHHHHHHHHHhchH-HHHHH
Q 012638          223 FSAERALN-SRGRRLTIARNEAEMSKGVQVVANLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQHLAFGWY-CREEL  300 (459)
Q Consensus       223 ~~~~~~~~-~~~~~lLt~~eE~eL~~~i~~~~~le~~~~~l~~~~gr~pt~~ewa~a~g~deeeL~~~l~~G~~-Are~L  300 (459)
                      +.++.|.+ ++..|+||+++|.+|.+.                                         ++.|+. |+++|
T Consensus        53 ~~~~~y~~~~~~~~~l~~~ee~~li~~-----------------------------------------~~~Gd~~A~~~L   91 (325)
T PRK05657         53 DATQLYLNEIGYSPLLTAEEEVYFARR-----------------------------------------ALRGDFAARQRM   91 (325)
T ss_pred             cHHHHHHHHHhcCCCCCHHHHHHHHHH-----------------------------------------HHcCCHHHHHHH
Confidence            33444554 345788888888776663                                         334544 99999


Q ss_pred             HHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhhccccccccchHHH
Q 012638          301 IKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIPCKLNRE  380 (459)
Q Consensus       301 I~~nlrLV~sIAkry~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIrnaI~d~Lrk~sr~irlP~~v~e~  380 (459)
                      |..|.++|+++|++|++++.+++||+||||+|+|+++++||+.+|++|+||++||||++|.++++++.+.+++|.++...
T Consensus        92 i~~y~~~V~~~a~~~~~~~~~aeDLvQE~fi~l~~ai~~fd~~rg~~Fstyatw~iR~ai~~~i~~~~r~ir~p~~~~~~  171 (325)
T PRK05657         92 IESNLRLVVKIAKRYLNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPVHVVKE  171 (325)
T ss_pred             HHHhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHhCCccCCCHHHHHHHHHHHHHHHHHHHcCCccccCHHHHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999988


Q ss_pred             HHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHhhccCCccccccCCCCCCccccCCCCCC
Q 012638          381 ISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNAKYLNIPPFFF  448 (459)
Q Consensus       381 i~kI~ka~~~L~~~lgr~PT~eEIAe~LGIS~e~Vk~~l~~ar~~~SLD~~v~~d~~~~l~e~i~D~~  448 (459)
                      ++.+.++...|...+++.|+.+|||+.||+++++|..++.....++|||.+++++...++.|.++|+.
T Consensus       172 l~~~~R~~~~l~~~l~r~~t~~eiA~~l~~~~~~v~~~l~~~~~~~sld~~~~~~~~~~l~d~l~d~~  239 (325)
T PRK05657        172 LNVYLRAARELEHKLDHEPSAEEIAELLDKPVDDVSRMLALNERITSLDTPLGGDPEKSLLDILADEQ  239 (325)
T ss_pred             HHHHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHhccCCcccCCCCCCCCCcchhhhccCCC
Confidence            88888999999999999999999999999999999999988778899999998777788999988764

>PRK05911 RNA polymerase sigma factor sigma-28; Reviewed

Probab=99.95  E-value=3.7e-27  Score=231.86  Aligned_cols=157  Identities=22%  Similarity=0.281  Sum_probs=138.5

Q ss_pred             HhchH-HHHHHHHHhHHHHHHHHHHhhC---CCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHh
Q 012638          291 AFGWY-CREELIKSTRPLVLFLARNYRG---LGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVAR  366 (459)
Q Consensus       291 ~~G~~-Are~LI~~nlrLV~sIAkry~g---~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIrnaI~d~Lrk  366 (459)
                      ..|+. |+++||..|+|+|+++|++|.+   .+.+.+||+|||+||||+|+++|||++|++|+|||+|||+++|.+++|+
T Consensus        18 ~~~~~~ar~~Li~~~~~lV~~ia~~~~~~~~~~~~~eDL~QeG~igL~~ai~~fd~~~g~~F~tya~~~Ir~~i~~~lr~   97 (257)
T PRK05911         18 STQEIEYRDVLIEFYLPLVKNVAHRLISGMPSHVKTEDLYASGVEGLVRAVERFDPEKSRRFEGYALFLIKAAIIDDLRK   97 (257)
T ss_pred             hcCCHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHHHHHhcCCccCCCHHHHHHHHHHHHHHHHHHh
Confidence            34654 9999999999999999999863   3568999999999999999999999999999999999999999999998


Q ss_pred             hccccccccchHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHhhc--cCCccccccCC--C--CCCcc
Q 012638          367 HARGIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLR--IVGSIDQKIGD--C--LNAKY  440 (459)
Q Consensus       367 ~sr~irlP~~v~e~i~kI~ka~~~L~~~lgr~PT~eEIAe~LGIS~e~Vk~~l~~ar--~~~SLD~~v~~--d--~~~~l  440 (459)
                      +.   ++|.++.+..+++.++...|.+.+|+.|+.+|||+.|||++++|..++..++  .++|||.++..  +  ++.++
T Consensus        98 ~~---~~pr~~~~~~~~l~~~~~~l~~~~gr~pt~~eiA~~l~i~~~~v~~~~~~~~~~~~~Sld~~~~~~~~~~~~~~l  174 (257)
T PRK05911         98 QD---WVPRSVHQKANKLADAMDSLRQSLGKEPTDGELCEYLNISQQELSGWFSSARPALILSLNEEFPCQSDDEAGLAL  174 (257)
T ss_pred             cC---CCCHHHHHHHHHHHHHHHHHHHHHCcCCCHHHHHHHhCcCHHHHHHHHHHhhccceeeccccCCCCCCCccccch
Confidence            74   4899999999999999999999999999999999999999999999887664  36899998743  2  23568


Q ss_pred             ccCCCCCCCC
Q 012638          441 LNIPPFFFPS  450 (459)
Q Consensus       441 ~e~i~D~~~~  450 (459)
                      .+.++|+.+.
T Consensus       175 ~~~l~d~~~~  184 (257)
T PRK05911        175 EERIADERAE  184 (257)
T ss_pred             hhhccCCCCC
Confidence            8889887543

>TIGR02885 spore_sigF RNA polymerase sigma-F factor

Probab=99.95  E-value=5.1e-27  Score=225.84  Aligned_cols=160  Identities=25%  Similarity=0.276  Sum_probs=146.8

Q ss_pred             HHHHhchH-HHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHh
Q 012638          288 QHLAFGWY-CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVAR  366 (459)
Q Consensus       288 ~~l~~G~~-Are~LI~~nlrLV~sIAkry~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIrnaI~d~Lrk  366 (459)
                      .+++.|+. |+++||..|.++|+++|++|.+++.+++||+|||++|||+++++||+.+|.+|+||+++||+|.|.+++|+
T Consensus         3 ~~~~~gd~~a~~~l~~~y~~~v~~~a~~~~~~~~~aeDl~Qe~~i~l~~a~~~f~~~~~~~f~tyl~~~i~~~i~~~lr~   82 (231)
T TIGR02885         3 KLAQNGDKEARDKLIECNLRLVWSIVKRFLNRGYEPEDLFQIGCIGLVKAIDKFDLSYDVKFSTYAVPMIMGEIKRFLRD   82 (231)
T ss_pred             HHHHcCCHHHHHHHHHHhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHhcCCCCCCCcHHHHHHHHHHHHHHHHHh
Confidence            44566766 99999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             hccccccccchHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHhhccCCccccccCCCCC--CccccCC
Q 012638          367 HARGIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLN--AKYLNIP  444 (459)
Q Consensus       367 ~sr~irlP~~v~e~i~kI~ka~~~L~~~lgr~PT~eEIAe~LGIS~e~Vk~~l~~ar~~~SLD~~v~~d~~--~~l~e~i  444 (459)
                      +. .+++|.++.+...++.++...|..++|+.||.+|||+.||+++++|..++..+..+.|||.+++++++  .++.|.+
T Consensus        83 ~~-~i~~p~~~~~~~~~~~~~~~~l~~~~~r~pt~~ela~~l~~~~~~v~~~~~~~~~~~sl~~~~~~~~~~~~~~~d~~  161 (231)
T TIGR02885        83 DG-IIKVSRSLKELARKIRYMKEELSKELGREPTINELAEALGVSPEEIVMALESARSPQSLYDTVHQDDGDPIYLLDQI  161 (231)
T ss_pred             CC-CeECCHHHHHHHHHHHHHHHHHHHHHCcCCCHHHHHHHHCcCHHHHHHHHHHccCCcCcccCCCCCCCCcchhhhhc
Confidence            85 78999999999999999999999999999999999999999999999999888889999999875543  3567778


Q ss_pred             CCCC
Q 012638          445 PFFF  448 (459)
Q Consensus       445 ~D~~  448 (459)
                      +|+.
T Consensus       162 ~~~~  165 (231)
T TIGR02885       162 ADKG  165 (231)
T ss_pred             CCCC
Confidence            7764

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

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

Probab=99.95  E-value=4.1e-27  Score=230.74  Aligned_cols=170  Identities=28%  Similarity=0.337  Sum_probs=149.8

Q ss_pred             HHHHHHHHhchH-HHHHHHHHhHHHHHHHHHHhhCCCC-CHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHH
Q 012638          284 RVLKQHLAFGWY-CREELIKSTRPLVLFLARNYRGLGI-PFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSIS  361 (459)
Q Consensus       284 eeL~~~l~~G~~-Are~LI~~nlrLV~sIAkry~g~g~-d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIrnaI~  361 (459)
                      +.+....+.|+. ++ .||+.|+|||.++|++|.+++. +.+||+|.|+|||++|+++|||++|.+|+|||...|+++|+
T Consensus        12 ~~~~~~~~~g~~~~~-~Li~~ylpLV~~ia~k~~~r~~~~~dDLiqiG~iGLi~Aieryd~~kg~kF~tyA~~~I~Gei~   90 (247)
T COG1191          12 EKLLEYYAEGDEEAR-RLIERYLPLVKSIARKFENRGPSEYDDLIQIGMIGLIKAIERYDPSKGTKFSTYAVRRIRGEIL   90 (247)
T ss_pred             HHHHHHHHhcCHHHH-HHHHHHHHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHHHHHcCcccCcchHHHHHHHHHHHHH
Confidence            456667778877 88 9999999999999999998877 99999999999999999999999999999999999999999


Q ss_pred             HHHHhhccccccccchHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHhhc--cCCccccccCCCCCCc
Q 012638          362 KMVARHARGIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLR--IVGSIDQKIGDCLNAK  439 (459)
Q Consensus       362 d~Lrk~sr~irlP~~v~e~i~kI~ka~~~L~~~lgr~PT~eEIAe~LGIS~e~Vk~~l~~ar--~~~SLD~~v~~d~~~~  439 (459)
                      +++|++. .+++|+.+++..+++..+..+|..++|+.||++|||+.|||+.++|...+....  ..+|+|..+..+++..
T Consensus        91 d~LR~~~-~v~vpR~~~~~~~~i~~~~~~l~~el~r~pt~~EIA~~L~i~~ee~~~~~~~~~~~~~~sld~~~~~~~d~~  169 (247)
T COG1191          91 DYLRKND-SVKVPRSLRELGRRIEEAIDELEQELGREPTDEEIAEELGIDKEEYIEALLAINGSQLLSLDEDVLKDDDDD  169 (247)
T ss_pred             HHHHhCC-CccCcHHHHHHHHHHHHHHHHHHHHhCCCCcHHHHHHHhCCCHHHHHHHHHHhccccccchhhhhccccccc
Confidence            9999998 999999999999999999999999999999999999999999999999988764  6789998776444444


Q ss_pred             cccCCCCCCCCccchh
Q 012638          440 YLNIPPFFFPSFAIWE  455 (459)
Q Consensus       440 l~e~i~D~~~~~~~~e  455 (459)
                      ..+.+.++....+.|+
T Consensus       170 ~~~~~~~~~~~~~~~~  185 (247)
T COG1191         170 VDDQIENPDDGVEKEE  185 (247)
T ss_pred             hhhccccchhHHHHHH
Confidence            5555555544444444

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

Probab=99.94  E-value=1.2e-25  Score=215.49  Aligned_cols=154  Identities=32%  Similarity=0.399  Sum_probs=140.7

Q ss_pred             HHHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhhccccccc
Q 012638          295 YCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIP  374 (459)
Q Consensus       295 ~Are~LI~~nlrLV~sIAkry~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIrnaI~d~Lrk~sr~irlP  374 (459)
                      .|+++||..|.++|+++|++|.+++.+++||+|||++|||+|+++||+.+|.+|+||+++||+|.|.++++++.+.+++|
T Consensus         3 ~a~~~lv~~y~~~v~~~a~~~~~~~~~~eDl~Qe~~i~l~~a~~~f~~~~~~~F~ty~~~~i~~~~~~~~r~~~~~~ri~   82 (227)
T TIGR02980         3 EAREKLVELNLPLVRSIARRFRNRGEPHEDLVQVGTIGLVKAIDRFDPSYGVKFSTFAVPTIMGEIKRFFRDDTWAVRVP   82 (227)
T ss_pred             HHHHHHHHHhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHhcCcccCCCcHHHHHHHHHHHHHHHHHHcCCceecC
Confidence            48999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cchHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHhhcc--CCccccccCCCC--CCccccCCCCCC
Q 012638          375 CKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRI--VGSIDQKIGDCL--NAKYLNIPPFFF  448 (459)
Q Consensus       375 ~~v~e~i~kI~ka~~~L~~~lgr~PT~eEIAe~LGIS~e~Vk~~l~~ar~--~~SLD~~v~~d~--~~~l~e~i~D~~  448 (459)
                      .++.+...+++++...+...+|+.|+.+|+|+.||+++++|..++.....  +.|||.++++++  +.++.+.+++++
T Consensus        83 ~~~~~~~~~~~~~~~~l~~~~~~~p~~~ela~~l~~~~~~v~~~~~~~~~~~~~sld~~~~~~~~~~~~~~d~~~~~~  160 (227)
T TIGR02980        83 RRLKELGLKINKATEELTQRLGRSPTIAEIAEELGVSEEEVVEALEAGNSYSALSLDAPIEDDDGDPIALLDTLGDED  160 (227)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHhCCCHHHHHHHHHhhccCCCeeccccCCCCCCCCcccccccCCcc
Confidence            99999999999999999999999999999999999999999998887665  899999986332  334556665543

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.

>PRK06288 RNA polymerase sigma factor WhiG; Reviewed

Probab=99.93  E-value=1.2e-24  Score=214.77  Aligned_cols=149  Identities=30%  Similarity=0.353  Sum_probs=132.8

Q ss_pred             HHHHHHHHhHHHHHHHHHHhh-C--CCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhhccccc
Q 012638          296 CREELIKSTRPLVLFLARNYR-G--LGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIK  372 (459)
Q Consensus       296 Are~LI~~nlrLV~sIAkry~-g--~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIrnaI~d~Lrk~sr~ir  372 (459)
                      |++.|+..|.++|+.+|++|. +  .+.+++||+|||++|||+|+++||+.+|++|+||++|||+|.|++++|+.   ++
T Consensus        32 a~~~l~~~y~~lv~~~a~~~~~~~~~~~~~eDl~Qeg~l~L~~a~~~fd~~~~~~f~ty~~~~ir~~i~d~~R~~---~~  108 (268)
T PRK06288         32 IREYLILKYSPLVKYVAGRIAVGMPQNVEFDDLVSYGVFGLIDAIEKFDPEREIKFKTYAVTRIRGAIFDELRSI---DW  108 (268)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHHHHHHcCcccCCCHHHHHHHHHHHHHHHHHHhc---Cc
Confidence            899999999999999999986 3  46789999999999999999999999899999999999999999999965   56


Q ss_pred             cccchHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHhh--ccCCccccccCC-C--CCCccccCCCCC
Q 012638          373 IPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECL--RIVGSIDQKIGD-C--LNAKYLNIPPFF  447 (459)
Q Consensus       373 lP~~v~e~i~kI~ka~~~L~~~lgr~PT~eEIAe~LGIS~e~Vk~~l~~a--r~~~SLD~~v~~-d--~~~~l~e~i~D~  447 (459)
                      +|.++.....+++++...|...+++.||.+|||+.+|++++.|..++...  ..++|||.++.. +  +..++.+.++++
T Consensus       109 ~p~~~~~~~~~i~~~~~~l~~~~~~~pt~~eia~~lg~~~~~v~~~~~~~~~~~~~sld~~~~~~~~~~~~~l~~~~~~~  188 (268)
T PRK06288        109 IPRSVRQKARQIERAIAMLEARLGRTPSDEEIADELGISLEEYNSLLSKLSGTSVVSLNDLWFGGDEGDEVSLMDTLESP  188 (268)
T ss_pred             cCHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHcCCCHHHHHHHHHHHhcccccchhhhhccCCCcccchhhhhccCC
Confidence            89999999999999999999999999999999999999999999988765  457899998742 2  235677888765

>TIGR02941 Sigma_B RNA polymerase sigma-B factor

Probab=99.93  E-value=1.2e-24  Score=212.63  Aligned_cols=156  Identities=25%  Similarity=0.270  Sum_probs=143.1

Q ss_pred             HHHHHHHHHh-chH-HHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHH
Q 012638          283 ERVLKQHLAF-GWY-CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSI  360 (459)
Q Consensus       283 eeeL~~~l~~-G~~-Are~LI~~nlrLV~sIAkry~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIrnaI  360 (459)
                      +.+|+.+++. |+. |+++||..|.++|+.+|++|.+++.+++||+|||++|||+++++||+..|.+|.||+++||+|.|
T Consensus        15 ~~~li~~~~~~gd~~a~~~l~~~y~~~v~~~a~~~~~~~~~aeDlvQe~~i~l~~a~~~~~~~~~~~f~tyl~~~i~n~~   94 (255)
T TIGR02941        15 VIQWIAEFQQNQNGEAQEKLVDHYQNLVYSIAYKYSKGGPMHEDLVQVGMLGLLGAIRRYDYSIGNAFEPFAIPTIIGEI   94 (255)
T ss_pred             HHHHHHHHHHCCCHHHHHHHHHHhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHcCCcCCCCcHhHHHHHHHHHH
Confidence            4557777777 565 99999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHhhccccccccchHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHhh--ccCCccccccCCCCCC
Q 012638          361 SKMVARHARGIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECL--RIVGSIDQKIGDCLNA  438 (459)
Q Consensus       361 ~d~Lrk~sr~irlP~~v~e~i~kI~ka~~~L~~~lgr~PT~eEIAe~LGIS~e~Vk~~l~~a--r~~~SLD~~v~~d~~~  438 (459)
                      .++++++...+++|.++.+..++++.+...+...+|+.|+.+|||+.+||+.+.+..++...  ..+.|||.+++.+++.
T Consensus        95 ~~~lr~~~~~iri~~~~~~~~~~~~~~~~~l~~~~~r~p~~~eia~~l~i~~~~~~~~~~~~~~~~~~sl~~~~~~~~~~  174 (255)
T TIGR02941        95 KRYLRDKTWSVHVPRRIKELGPKIKKAIDELTDHLQRSPKIIEIADHLGLSEEEVLEIMEMGQSYRALSVDDVIEADSDG  174 (255)
T ss_pred             HHHHHHcCCCcCCCHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHHHhccCCccccccccCCCCC
Confidence            99999998899999999999999999999999999999999999999999999999887654  3578999998755443

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

>PRK07670 RNA polymerase sigma factor SigD; Validated

Probab=99.92  E-value=3.4e-24  Score=209.41  Aligned_cols=162  Identities=22%  Similarity=0.265  Sum_probs=140.6

Q ss_pred             CHHHHHHHHH-hchH-HHHHHHHHhHHHHHHHHHHhhC---CCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHH
Q 012638          282 SERVLKQHLA-FGWY-CREELIKSTRPLVLFLARNYRG---LGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWI  356 (459)
Q Consensus       282 deeeL~~~l~-~G~~-Are~LI~~nlrLV~sIAkry~g---~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wI  356 (459)
                      ++..|+++++ .|+. |+++||..|.++|+++|++|.+   ++.+++||+|||++|||+++++||+.+|.+|+||+++||
T Consensus         7 ~e~~l~~~~~~~~d~~a~~~L~~~y~~~v~~~~~~~~~~~~~~~~~eDl~Qe~~i~l~~~~~~f~~~~~~~f~tyl~~~i   86 (251)
T PRK07670          7 EEQKLWDRWKEERDPDAADELIRRYMPLVHYHVQRISVGLPKSVSKDDLKSLGMLGLYDALEKFDPSRDLKFDTYASFRI   86 (251)
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHHHHHHHHHcCcccCCCHHHHHHHHH
Confidence            3566777744 4566 9999999999999999999976   688999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHhhccccccccchHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHH--hhccCCccccccCC
Q 012638          357 RKSISKMVARHARGIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASE--CLRIVGSIDQKIGD  434 (459)
Q Consensus       357 rnaI~d~Lrk~sr~irlP~~v~e~i~kI~ka~~~L~~~lgr~PT~eEIAe~LGIS~e~Vk~~l~--~ar~~~SLD~~v~~  434 (459)
                      +|.|++++|++.   ++|.++.+.+++++++...+.+.+|+.|+.+|||+.||+++++|..++.  ....++|||.++.+
T Consensus        87 rn~~~d~lR~~~---~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~eia~~l~~~~~~v~~~~~~~~~~~~~sld~~~~~  163 (251)
T PRK07670         87 RGAIIDGLRKED---WLPRSMREKTKKVEAAIEKLEQRYMRNVTPKEVAAELGMTEEEVEATMNEGFFANLLSIDEKTHD  163 (251)
T ss_pred             HHHHHHHHHhcC---CCCHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHhCcCHHHHHHHHHHHhccCccccCccccC
Confidence            999999999864   6899999999999999999999999999999999999999999999876  34578999999865


Q ss_pred             CCC-CccccCCCC
Q 012638          435 CLN-AKYLNIPPF  446 (459)
Q Consensus       435 d~~-~~l~e~i~D  446 (459)
                      +++ .++.+.++|
T Consensus       164 ~~~~~~~~~~~~~  176 (251)
T PRK07670        164 QDDGENVSVTIRD  176 (251)
T ss_pred             CCCcchhhhhhcC
Confidence            443 334444444

>TIGR02394 rpoS_proteo RNA polymerase sigma factor RpoS

Probab=99.92  E-value=9.2e-24  Score=210.29  Aligned_cols=166  Identities=27%  Similarity=0.498  Sum_probs=153.3

Q ss_pred             HHHHHHHHHhchH-HHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHH
Q 012638          283 ERVLKQHLAFGWY-CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSIS  361 (459)
Q Consensus       283 eeeL~~~l~~G~~-Are~LI~~nlrLV~sIAkry~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIrnaI~  361 (459)
                      +.+|+..++.|+. |++.||..|.++|+++|++|.+++.+++||+|||+||||+|+++||+.+|++|+||+.|||+.++.
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            4678888999977 999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHhhccccccccchHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHhhccCCccccccCCCCCCccc
Q 012638          362 KMVARHARGIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNAKYL  441 (459)
Q Consensus       362 d~Lrk~sr~irlP~~v~e~i~kI~ka~~~L~~~lgr~PT~eEIAe~LGIS~e~Vk~~l~~ar~~~SLD~~v~~d~~~~l~  441 (459)
                      ++++++.+.+++|.++....+.+.+....+...+|+.|+.+++|+.+|+++..|..++..+...+|||.++.+++..++.
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            99999999999999999999988888888888889999999999999999999999999888899999988766666777


Q ss_pred             cCCCCCC
Q 012638          442 NIPPFFF  448 (459)
Q Consensus       442 e~i~D~~  448 (459)
                      +.++++.
T Consensus       193 ~~~~~~~  199 (285)
T TIGR02394       193 DTIADEQ  199 (285)
T ss_pred             hhhcCCC
Confidence            7776553

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).

>PRK05572 sporulation sigma factor SigF; Validated

Probab=99.91  E-value=1.3e-23  Score=205.44  Aligned_cols=164  Identities=25%  Similarity=0.340  Sum_probs=146.8

Q ss_pred             HHHHHHHHhchH-HHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHH
Q 012638          284 RVLKQHLAFGWY-CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISK  362 (459)
Q Consensus       284 eeL~~~l~~G~~-Are~LI~~nlrLV~sIAkry~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIrnaI~d  362 (459)
                      ..|+..+..|+. |+++||..|.++|+++|++|.+++.+++||+|||++++|+++++||+.+|.+|.||+++||++.|.+
T Consensus        20 ~~li~~~~~gd~~a~~~L~~~y~~~v~~~a~~~~~~~~~aeDl~Qe~~l~l~~~~~~f~~~~~~~f~twl~~~i~~~i~~   99 (252)
T PRK05572         20 KELIKKSQDGDQEARDTLVEKNLRLVWSVVQRFLNRGYEPDDLFQIGCIGLLKAVDKFDLSYDVKFSTYAVPMIIGEIQR   99 (252)
T ss_pred             HHHHHHHHcCCHHHHHHHHHHhHHHHHHHHHHHccCCCCHHHHHHHHHHHHHHHHHHcCCCCCCChHHHHHHHHHHHHHH
Confidence            445666777876 9999999999999999999999999999999999999999999999988889999999999999999


Q ss_pred             HHHhhccccccccchHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHhhccCCccccccCCCCC--Ccc
Q 012638          363 MVARHARGIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLN--AKY  440 (459)
Q Consensus       363 ~Lrk~sr~irlP~~v~e~i~kI~ka~~~L~~~lgr~PT~eEIAe~LGIS~e~Vk~~l~~ar~~~SLD~~v~~d~~--~~l  440 (459)
                      ++++. ..+++|..+.+...+++++...+..++|+.|+.+|||+.+|++++.|..++.....+.||+.++.+++.  .++
T Consensus       100 ~lr~~-~~~r~~~~~~~~~~~~~~~~~~l~~~~~r~p~~~eia~~l~~~~~~v~~~~~~~~~~~sl~~~~~~~~~~~~~~  178 (252)
T PRK05572        100 FLRDD-GTVKVSRSLKETANKIRKDKDELSKELGREPTIEELAEYLGVTPEEVVLAQEASRSPQSIHETVHENDGDPITL  178 (252)
T ss_pred             HHHhC-CCCCCCHHHHHHHHHHHHHHHHHHHHHCcCCCHHHHHHHhCcCHHHHHHHHHhcCCCcCcccCcccCCCCcchh
Confidence            99987 478999999999999999999999999999999999999999999999998888889999998865443  245


Q ss_pred             ccCCCCCC
Q 012638          441 LNIPPFFF  448 (459)
Q Consensus       441 ~e~i~D~~  448 (459)
                      .|.++++.
T Consensus       179 ~d~~~~~~  186 (252)
T PRK05572        179 LDQIADQS  186 (252)
T ss_pred             hhhcCCCc
Confidence            56665543

>PRK12427 flagellar biosynthesis sigma factor; Provisional

Probab=99.90  E-value=3.7e-23  Score=200.68  Aligned_cols=138  Identities=20%  Similarity=0.223  Sum_probs=123.6

Q ss_pred             HHHHHHHHhHHHHHHHHHHhhC---CCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhhccccc
Q 012638          296 CREELIKSTRPLVLFLARNYRG---LGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIK  372 (459)
Q Consensus       296 Are~LI~~nlrLV~sIAkry~g---~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIrnaI~d~Lrk~sr~ir  372 (459)
                      ....|+..|+|+|+++|++|..   .+.+.+||+|||++|||+|+++||+.+| +|+||++|||+|+|.+++++..   +
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            3557899999999999999875   4679999999999999999999998666 8999999999999999999753   5


Q ss_pred             cccchHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHh--hccCCccccccCCCCC
Q 012638          373 IPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASEC--LRIVGSIDQKIGDCLN  437 (459)
Q Consensus       373 lP~~v~e~i~kI~ka~~~L~~~lgr~PT~eEIAe~LGIS~e~Vk~~l~~--ar~~~SLD~~v~~d~~  437 (459)
                      .|+.+....++++++...+.+++|+.||.+|||+.||+++++|..++..  +..++|||.+++++++
T Consensus        92 ~~r~vr~~~~~i~~~~~~l~~~~g~~pt~~eiA~~lg~~~~~v~~~~~~~~~~~~~SLd~~~~~~~~  158 (231)
T PRK12427         92 RPRRLRQKTHKTNDAIREIAKRLGHEPNFEEISAELNLTAEEYQEYLLLENAGTLESLDELLALEAH  158 (231)
T ss_pred             CCHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHhCCCHHHHHHHHHHhccCCceeccCcccCCCc
Confidence            7888999999999999999999999999999999999999999998764  4568999999876544

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

Probab=99.90  E-value=3.7e-23  Score=198.36  Aligned_cols=145  Identities=29%  Similarity=0.393  Sum_probs=129.8

Q ss_pred             HHHHhHHHHHHHHHHhhC---CCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhhccccccccc
Q 012638          300 LIKSTRPLVLFLARNYRG---LGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIPCK  376 (459)
Q Consensus       300 LI~~nlrLV~sIAkry~g---~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIrnaI~d~Lrk~sr~irlP~~  376 (459)
                      |+..|.++|+.+|++|.+   ++.+++||+|||++|||+|+++|||.+|++|+||+++||+|.+++++|+..   ++|.+
T Consensus         1 L~~~~~~lv~~~a~~~~~~~~~~~~~eDl~Qe~~~~l~~a~~~fd~~~~~~f~t~~~~~i~~~~~~~lr~~~---~~p~~   77 (224)
T TIGR02479         1 LIRRYLPLVKRIAGRLSVGLPSSVELDDLIQAGMFGLLDAIERYDPSRGAKFETYAVQRIRGAMLDELRRLD---WVPRS   77 (224)
T ss_pred             CHHHHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHHHHHHHHhcCCccCCCHHHHHHHHHHHHHHHHHHHcC---ccCHH
Confidence            688999999999999986   789999999999999999999999999999999999999999999999763   68999


Q ss_pred             hHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHhh--ccCCccccccCCC-CCCccccCCCCC
Q 012638          377 LNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECL--RIVGSIDQKIGDC-LNAKYLNIPPFF  447 (459)
Q Consensus       377 v~e~i~kI~ka~~~L~~~lgr~PT~eEIAe~LGIS~e~Vk~~l~~a--r~~~SLD~~v~~d-~~~~l~e~i~D~  447 (459)
                      +...++++.++...|...+|+.|+.+|||+.||++++.|..++..+  ..++|+|.++.++ +..++.+.++++
T Consensus        78 ~~~~~~~l~~~~~~l~~~~~~~~~~~ela~~l~~~~~~v~~~~~~~~~~~~~sl~~~~~~~~~~~~~~~~~~~~  151 (224)
T TIGR02479        78 LRQKARKLERAIRELEARLGREPTEEEIAEELGMDLKEYRQALNEINALSLVSLDELLESGDDGGSLIDRIEDD  151 (224)
T ss_pred             HHHHHHHHHHHHHHHHHHHCcCCCHHHHHHHhCCCHHHHHHHHHHHhcCCccccCCcccCCCccchhhhhcccc
Confidence            9999999999999999999999999999999999999999998654  3568999877643 445677777643

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.

>PRK08583 RNA polymerase sigma factor SigB; Validated

Probab=99.90  E-value=9.1e-23  Score=199.67  Aligned_cols=167  Identities=25%  Similarity=0.238  Sum_probs=146.8

Q ss_pred             HHHHHHHHHh-chH-HHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHH
Q 012638          283 ERVLKQHLAF-GWY-CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSI  360 (459)
Q Consensus       283 eeeL~~~l~~-G~~-Are~LI~~nlrLV~sIAkry~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIrnaI  360 (459)
                      +..|+..++. |+. |+++||..|.++|+++|++|.+++.+++||+||||+|||+++++||+.+|.+|+||+++||+|.|
T Consensus        15 ~~~li~~~~~~gd~~a~~~l~~~~~~~v~~~a~~~~~~~~~aeDlvQe~~l~l~~~~~~f~~~~~~~f~tyl~~~i~n~~   94 (257)
T PRK08583         15 VNKWIAEYQENQDEEAQEKLVKHYKNLVESLAYKYSKGQSHHEDLVQVGMVGLLGAIRRYDPSFGRSFEAFAVPTIIGEI   94 (257)
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHcCccCCCChHHHHHHHHHHHH
Confidence            4557777764 665 99999999999999999999999999999999999999999999999988899999999999999


Q ss_pred             HHHHHhhccccccccchHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHhh--ccCCccccccCCCCC-
Q 012638          361 SKMVARHARGIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECL--RIVGSIDQKIGDCLN-  437 (459)
Q Consensus       361 ~d~Lrk~sr~irlP~~v~e~i~kI~ka~~~L~~~lgr~PT~eEIAe~LGIS~e~Vk~~l~~a--r~~~SLD~~v~~d~~-  437 (459)
                      .++++++...+++|.++.+..+++..+...+...+++.|+.+|+|+.+|++.+.|..++...  ..++|||.+++.+++ 
T Consensus        95 ~~~lr~~~~~~~i~r~~~~~~~~~~~~~~~~~~~~~r~~~~~e~a~~~~~~~~~~~~~~~~~~~~~~~sld~~~~~~~~~  174 (257)
T PRK08583         95 KRYLRDKTWSVHVPRRIKELGPKIKKAVDELTTELQRSPKISEIADRLGVSEEEVLEAMEMGKSYQALSVDHSIEADSDG  174 (257)
T ss_pred             HHHHHhcCCCcCCCHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHHhccCCceecCccccCCCCC
Confidence            99999999999999999999999999999999999999999999999999999998877654  357899999865433 


Q ss_pred             --CccccCCCCCCC
Q 012638          438 --AKYLNIPPFFFP  449 (459)
Q Consensus       438 --~~l~e~i~D~~~  449 (459)
                        ..+.+.++++..
T Consensus       175 ~~~~~~~~~~~~e~  188 (257)
T PRK08583        175 STVTLLDIVGQQED  188 (257)
T ss_pred             ccchHhhhcCCcch
Confidence              334555555543

>PRK06986 fliA flagellar biosynthesis sigma factor; Validated

Probab=99.88  E-value=6.1e-22  Score=191.57  Aligned_cols=143  Identities=29%  Similarity=0.422  Sum_probs=128.6

Q ss_pred             hchHHHHHHHHHhHHHHHHHHHHhh---CCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhhc
Q 012638          292 FGWYCREELIKSTRPLVLFLARNYR---GLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHA  368 (459)
Q Consensus       292 ~G~~Are~LI~~nlrLV~sIAkry~---g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIrnaI~d~Lrk~s  368 (459)
                      .|.-++++|+..|.++|+++|++|+   +++.+++||+||||+|||+++++||+.+|.+|+||+++||+|.|.+++|++.
T Consensus         5 ~~~~~~~~L~~~~~~~v~~~a~~~~~~~~~~~~aeDlvQe~~i~l~~~~~~f~~~~~~~f~tyl~~~irn~~~~~lR~~~   84 (236)
T PRK06986          5 EGKMDQDELVEQYAPLVKRIALRLKARLPASVDLDDLIQAGMIGLLEAARRYDGEQGASFETYAGQRIRGAMLDELRSLD   84 (236)
T ss_pred             cccccHHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHHHHHhcCcccCCChHHHHHHHHHHHHHHHHHHcC
Confidence            4666999999999999999999997   6789999999999999999999999998999999999999999999999875


Q ss_pred             cccccccchHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHhh--ccCCccccccCCCCC
Q 012638          369 RGIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECL--RIVGSIDQKIGDCLN  437 (459)
Q Consensus       369 r~irlP~~v~e~i~kI~ka~~~L~~~lgr~PT~eEIAe~LGIS~e~Vk~~l~~a--r~~~SLD~~v~~d~~  437 (459)
                      +   +|..+......+.++...+.+.+++.|+.+|||+.||+++++|..++...  ..++|+|.+++++++
T Consensus        85 ~---~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ela~~l~i~~~~v~~~~~~~~~~~~~sl~~~~~~~~~  152 (236)
T PRK06986         85 W---VPRSVRRNAREVAQAIRQLEQELGREPTDTEVAEKLGLSLEEYREMLLDTNISQLFSIDELRGEHGD  152 (236)
T ss_pred             C---CCHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHcCCCHHHHHHHHHHHhccCCccccccccCCCc
Confidence            3   68888888888899999999999999999999999999999999888753  356799998876554

>PRK05803 sporulation sigma factor SigK; Reviewed

Probab=99.79  E-value=8.1e-18  Score=162.71  Aligned_cols=170  Identities=22%  Similarity=0.252  Sum_probs=127.6

Q ss_pred             HHHHhHHHHHHHHHHHHHHHHhCCCCchHHHHHHcCCCHHHHHHHHHhchH-HHHHHHHHhHHHHHHHHHHhhCCCCCHH
Q 012638          245 MSKGVQVVANLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQHLAFGWY-CREELIKSTRPLVLFLARNYRGLGIPFS  323 (459)
Q Consensus       245 L~~~i~~~~~le~~~~~l~~~~gr~pt~~ewa~a~g~deeeL~~~l~~G~~-Are~LI~~nlrLV~sIAkry~g~g~d~E  323 (459)
                      |.--++..+.|.+....+    ++.|.+..      .++..|+..+..|+. |++.|+..|.++|+++|.+|.+++.+++
T Consensus         8 ~~~~~~~~~~~~~~~~~~----~~~~~~~~------~~e~~l~~~~~~gd~~a~~~l~~~y~~~l~~~a~~~~~~~~dae   77 (233)
T PRK05803          8 LLYIVKEILFLVSYVKNN----SFPQPLSE------EEERKYLELMKEGDEEARNILIERNLRLVAHIVKKFENTGEDVD   77 (233)
T ss_pred             HHHHHHHHHHHHHHHHHh----cccCCCCH------HHHHHHHHHHHcCCHHHHHHHHHHhHHHHHHHHHHHhcCCCCHH
Confidence            334456666766666554    44444332      124567888888877 9999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhhcccc---cc-------------------cc---chH
Q 012638          324 DLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGI---KI-------------------PC---KLN  378 (459)
Q Consensus       324 DLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIrnaI~d~Lrk~sr~i---rl-------------------P~---~v~  378 (459)
                      |++|||++++|+++++||+.+|.+|.||+++|++|.+++++|+..+..   .+                   +.   ...
T Consensus        78 DlvQE~fi~l~~~~~~f~~~~~~~f~~wl~~i~rn~~id~~Rk~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  157 (233)
T PRK05803         78 DLISIGTIGLIKAIESFDAGKGTKLATYAARCIENEILMHLRNLKKTKKEVSLQDPIGVDKEGNEISLIDILGSEEDDVI  157 (233)
T ss_pred             HHHHHHHHHHHHHHHhcCcccCCChHHHHHHHHHHHHHHHHHHHhccccCCCccccccCCCCcCcccHHHHccCCCCCHH
Confidence            999999999999999999988889999999999999999999764321   00                   00   000


Q ss_pred             ------HHHHHHHHHHHHHHHHc------------CCCCCHHHHHHHhCCCHHHHHHHHHhhcc
Q 012638          379 ------REISKIQKARKALTNSH------------GKYPEDIEIAKYTGLSLAEIRSASECLRI  424 (459)
Q Consensus       379 ------e~i~kI~ka~~~L~~~l------------gr~PT~eEIAe~LGIS~e~Vk~~l~~ar~  424 (459)
                            +....+.++...|+...            ..+.|++|||+.||||.++|+..+++++.
T Consensus       158 ~~~~~~~~~~~l~~~l~~Lp~~~R~i~~l~y~~~~~e~~S~~EIA~~lgis~~tV~~~~~rA~~  221 (233)
T PRK05803        158 EQVELKMEVEKLYKKIDILDEREKEVIEMRYGLGNGKEKTQREIAKALGISRSYVSRIEKRALK  221 (233)
T ss_pred             HHHHHHHHHHHHHHHHHhCCHHHHHHHHHHhCCCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence                  11223555555444332            25679999999999999999999877764

>TIGR02895 spore_sigI RNA polymerase sigma-I factor

Probab=99.78  E-value=3.1e-18  Score=165.70  Aligned_cols=129  Identities=17%  Similarity=0.276  Sum_probs=114.5

Q ss_pred             HHHhchHHHHHHHHHhHHHHHHHHHHhhCCC--CCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHh
Q 012638          289 HLAFGWYCREELIKSTRPLVLFLARNYRGLG--IPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVAR  366 (459)
Q Consensus       289 ~l~~G~~Are~LI~~nlrLV~sIAkry~g~g--~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIrnaI~d~Lrk  366 (459)
                      .++.|+..+++||..|.|+|.++|.+|.++.  .+.+|++|+|++|||+|+++||+++|.+|.|||.++|++.|++++|+
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            5678888899999999999999999998775  58999999999999999999999999999999999999999999998


Q ss_pred             hc---cccccccchHHHHHHHHHHHHHHHHHcCCCCCHHHHHH------HhCCCHHHHHH
Q 012638          367 HA---RGIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAK------YTGLSLAEIRS  417 (459)
Q Consensus       367 ~s---r~irlP~~v~e~i~kI~ka~~~L~~~lgr~PT~eEIAe------~LGIS~e~Vk~  417 (459)
                      ..   ..+++|....+....+..+..++..++++.|+.+||+.      ..||+.+.+.+
T Consensus        83 ~~k~~~~v~~~~~~~e~~~~~~~~~~~~~~~~~~~~~~eEI~~~~~~L~~~gi~~~dLv~  142 (218)
T TIGR02895        83 NQKYQNLLYLDEDYDENPLEFNKSMEEYRNEIENENRRLEILEYKKLLKQFGIEFVELVK  142 (218)
T ss_pred             cccccCeeeCCchHHHHHHHHHHHHHHHHHHHccccHHHHHHHHHHHHHHcCCcHHHHhh
Confidence            87   45688876666677888888899999999999999997      45888877653

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

>TIGR02846 spore_sigmaK RNA polymerase sigma-K factor

Probab=99.76  E-value=3.7e-17  Score=157.66  Aligned_cols=142  Identities=24%  Similarity=0.356  Sum_probs=115.0

Q ss_pred             HHHHHHHHHhchH-HHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHH
Q 012638          283 ERVLKQHLAFGWY-CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSIS  361 (459)
Q Consensus       283 eeeL~~~l~~G~~-Are~LI~~nlrLV~sIAkry~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIrnaI~  361 (459)
                      +..|+..++.|+. |++.|+..|.++|+++|.+|.++..+++|++||+|+++|+++++|++.++.+|.||+++|++|.|+
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            5678888999987 999999999999999999999999999999999999999999999998888899999999999999


Q ss_pred             HHHHhhccccc-c---------------------cc---c------hHHHHHHHHHHHHHHHHHc------------CCC
Q 012638          362 KMVARHARGIK-I---------------------PC---K------LNREISKIQKARKALTNSH------------GKY  398 (459)
Q Consensus       362 d~Lrk~sr~ir-l---------------------P~---~------v~e~i~kI~ka~~~L~~~l------------gr~  398 (459)
                      +++|+..+..+ .                     +.   .      ..+....|.+++..|+...            ..+
T Consensus       115 d~~Rk~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~L~~~~r~il~l~y~~~~~e~  194 (227)
T TIGR02846       115 MHLRALKKTKGEVSLQDPIGVDKEGNEISLIDILGSDGDSVIEQVELNLEIKKLYKKLSVLDGREREVIEMRYGLGDGRR  194 (227)
T ss_pred             HHHHHHhccccceeccccccCCcccCcccHHHHhcCCCCChHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHcCCCCCC
Confidence            99997654211 0                     00   0      0012233555555554432            156


Q ss_pred             CCHHHHHHHhCCCHHHHHHHHHhhcc
Q 012638          399 PEDIEIAKYTGLSLAEIRSASECLRI  424 (459)
Q Consensus       399 PT~eEIAe~LGIS~e~Vk~~l~~ar~  424 (459)
                      .|++|||+.||+|+++|+..+++++.
T Consensus       195 ~S~~EIAe~lgis~~tV~~~~~rAl~  220 (227)
T TIGR02846       195 KTQREIAKILGISRSYVSRIEKRALM  220 (227)
T ss_pred             cCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            79999999999999999999887764

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

>PRK08301 sporulation sigma factor SigE; Reviewed

Probab=99.75  E-value=1.5e-17  Score=160.35  Aligned_cols=143  Identities=24%  Similarity=0.392  Sum_probs=116.3

Q ss_pred             CHHHHHHHHHhchH-HHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHH
Q 012638          282 SERVLKQHLAFGWY-CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSI  360 (459)
Q Consensus       282 deeeL~~~l~~G~~-Are~LI~~nlrLV~sIAkry~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIrnaI  360 (459)
                      .+..|+..++.|+. |++.|+..|.++|+.+|++|.+++.+++|++||+|+++|+++++|++..+++|.||++++++|.+
T Consensus        38 ~~~~L~~~~~~gd~~af~~l~~~y~~~l~~~a~~~~~~~~~AeDlvQevfl~l~~~~~~f~~~~~~~f~twl~~iarn~~  117 (234)
T PRK08301         38 EEEYLLNKLPKGDEAVRSLLIERNLRLVVYIARKFENTGINIEDLISIGTIGLIKAVNTFNPEKKIKLATYASRCIENEI  117 (234)
T ss_pred             HHHHHHHHHHccCHHHHHHHHHHhHHHHHHHHHHhhcCCCCHHHHHHHHHHHHHHHHHhcCcccCCCHHHHHHHHHHHHH
Confidence            36778888999987 99999999999999999999999999999999999999999999999877889999999999999


Q ss_pred             HHHHHhhccccc-c----c-----------------c--ch----H---HHHHHHHHHHHHHHHHc------------CC
Q 012638          361 SKMVARHARGIK-I----P-----------------C--KL----N---REISKIQKARKALTNSH------------GK  397 (459)
Q Consensus       361 ~d~Lrk~sr~ir-l----P-----------------~--~v----~---e~i~kI~ka~~~L~~~l------------gr  397 (459)
                      ++++|++.+... .    +                 .  ..    .   .....+.++...|+...            ..
T Consensus       118 ~d~lRk~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~al~~Lp~~~R~v~~L~y~l~~~e  197 (234)
T PRK08301        118 LMYLRRNNKVKAEVSFDEPLNIDWDGNELLLSDVLGTDNDIIYKDIEDEVDRKLLKKALKKLSDREKQIMELRFGLNGGE  197 (234)
T ss_pred             HHHHHHHhccccccccccccccccCCCcccHHHhccCcccchHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHhccCCCC
Confidence            999997654211 0    0                 0  00    0   11223566666665442            25


Q ss_pred             CCCHHHHHHHhCCCHHHHHHHHHhhcc
Q 012638          398 YPEDIEIAKYTGLSLAEIRSASECLRI  424 (459)
Q Consensus       398 ~PT~eEIAe~LGIS~e~Vk~~l~~ar~  424 (459)
                      +.|++|||+.||||+++|+..+++++.
T Consensus       198 g~s~~EIA~~lgis~~tVk~~~~rA~~  224 (234)
T PRK08301        198 EKTQKEVADMLGISQSYISRLEKRIIK  224 (234)
T ss_pred             CCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            789999999999999999999888764

>TIGR02859 spore_sigH RNA polymerase sigma-H factor

Probab=99.74  E-value=4.6e-17  Score=151.65  Aligned_cols=144  Identities=18%  Similarity=0.200  Sum_probs=114.0

Q ss_pred             CCHHHHHHHHHhchH-HHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHH
Q 012638          281 VSERVLKQHLAFGWY-CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKS  359 (459)
Q Consensus       281 ~deeeL~~~l~~G~~-Are~LI~~nlrLV~sIAkry~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIrna  359 (459)
                      |++..|+..++.|+. |++.|+..|.+.|+++|++++++..+++|++||+++++|+++.+|++..+..|.||++.+|++.
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            567888999999987 9999999999999999999999999999999999999999999999987779999999999999


Q ss_pred             HHHHHHhhcccccc----------------------------ccch-------HHHHHHHHHHHHHHHHH--------cC
Q 012638          360 ISKMVARHARGIKI----------------------------PCKL-------NREISKIQKARKALTNS--------HG  396 (459)
Q Consensus       360 I~d~Lrk~sr~irl----------------------------P~~v-------~e~i~kI~ka~~~L~~~--------lg  396 (459)
                      +.+++++..+..+.                            +...       .+....+.++...|...        .-
T Consensus        84 ~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~e~~~~l~~~l~~Ll~~~~~~i~~~~~  163 (198)
T TIGR02859        84 IITAIKTATRQKHIPLNSYVSLNKPIYDEESDRTLLDVISGAKVTDPEELIISQEEYGDIESKMNELLSDLEWKVLQSYL  163 (198)
T ss_pred             HHHHHHHHHHhcccchhhhcCcccccccccccchHHHHhhccccCCHHHHHHHHHHHHHHHHHHHHhcCHHHHHHHHHHH
Confidence            98888743111100                            0000       11122344555553222        23


Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHHhhcc
Q 012638          397 KYPEDIEIAKYTGLSLAEIRSASECLRI  424 (459)
Q Consensus       397 r~PT~eEIAe~LGIS~e~Vk~~l~~ar~  424 (459)
                      .+.|++|||+.||+|+++|+.++++++.
T Consensus       164 ~~~s~~eIA~~l~~s~~tV~~~l~r~r~  191 (198)
T TIGR02859       164 DGKSYQEIACDLNRHVKSIDNALQRVKR  191 (198)
T ss_pred             cCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            6789999999999999999999998875

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.

>PRK08295 RNA polymerase factor sigma-70; Validated

Probab=99.74  E-value=6.4e-17  Score=152.04  Aligned_cols=145  Identities=21%  Similarity=0.254  Sum_probs=113.0

Q ss_pred             CCCHHHHHHHHHhchH-HHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHH
Q 012638          280 GVSERVLKQHLAFGWY-CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRK  358 (459)
Q Consensus       280 g~deeeL~~~l~~G~~-Are~LI~~nlrLV~sIAkry~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIrn  358 (459)
                      .++...|+..++.|+. |++.|+..|.++|+.+|++|.++..+++|++||+++++|+++.+||+.++.+|.||++.+++|
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            4567788888889987 999999999999999999999999999999999999999999999998777999999999999


Q ss_pred             HHHHHHHhhcccccccc-----------------------------chH------HHHHHH-HHHHHHHHHH-------c
Q 012638          359 SISKMVARHARGIKIPC-----------------------------KLN------REISKI-QKARKALTNS-------H  395 (459)
Q Consensus       359 aI~d~Lrk~sr~irlP~-----------------------------~v~------e~i~kI-~ka~~~L~~~-------l  395 (459)
                      .+.+++++..+..+.+.                             ...      +....+ ..+...|+..       .
T Consensus        88 ~~~d~~r~~~r~~~~~~~~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~L~~~~r~vl~l~  167 (208)
T PRK08295         88 QIITAIKTANRQKHIPLNSYVSLDKPIYDEESDRTLLDVISEAKVTDPEELIISKEELEDIEEKIEELLSELEKEVLELY  167 (208)
T ss_pred             HHHHHHHHhhhhccccccceeecCCcccCCccchhHHHHhcCcccCCHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHH
Confidence            99999985433211110                             000      011111 1122222211       3


Q ss_pred             CCCCCHHHHHHHhCCCHHHHHHHHHhhcc
Q 012638          396 GKYPEDIEIAKYTGLSLAEIRSASECLRI  424 (459)
Q Consensus       396 gr~PT~eEIAe~LGIS~e~Vk~~l~~ar~  424 (459)
                      -.+.+++|||+.||+|+++|+.++.+++.
T Consensus       168 ~e~~s~~EIA~~lgis~~tV~~~l~rar~  196 (208)
T PRK08295        168 LDGKSYQEIAEELNRHVKSIDNALQRVKR  196 (208)
T ss_pred             HccCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            46789999999999999999999998875

>PRK05602 RNA polymerase sigma factor; Reviewed

Probab=99.73  E-value=5.7e-17  Score=150.48  Aligned_cols=143  Identities=17%  Similarity=0.129  Sum_probs=117.1

Q ss_pred             CCHHHHHHHHHhchH-HHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHH
Q 012638          281 VSERVLKQHLAFGWY-CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKS  359 (459)
Q Consensus       281 ~deeeL~~~l~~G~~-Are~LI~~nlrLV~sIAkry~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIrna  359 (459)
                      ++++.|+..+..|+. |++.|+..|.++|+.+|++|.+++.+++|++||+|+++|+++.+|++. +.+|.||++.+++|.
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            567789999999987 999999999999999999999999999999999999999999999975 358999999999999


Q ss_pred             HHHHHHhhccccc--ccc---------c---hHHHHHHHHHHHHHHHHHc--------CCCCCHHHHHHHhCCCHHHHHH
Q 012638          360 ISKMVARHARGIK--IPC---------K---LNREISKIQKARKALTNSH--------GKYPEDIEIAKYTGLSLAEIRS  417 (459)
Q Consensus       360 I~d~Lrk~sr~ir--lP~---------~---v~e~i~kI~ka~~~L~~~l--------gr~PT~eEIAe~LGIS~e~Vk~  417 (459)
                      +.+++|++.....  ++.         .   ..+....+.++...|+.+.        -.+.+++|||+.||+|..+|+.
T Consensus        84 ~~d~~R~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~i~~l~~~~g~s~~EIA~~lgis~~tV~~  163 (186)
T PRK05602         84 CYDRLRRRREVPVEDAPDVPDPAPGPDAGLEARQRARRVEQALAALPERQREAIVLQYYQGLSNIEAAAVMDISVDALES  163 (186)
T ss_pred             HHHHHHhcCCCCcccccccCCCCCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHhhHHHhcCCCHHHHHHHhCcCHHHHHH
Confidence            9999997754211  110         0   0122334556666555432        3578999999999999999999


Q ss_pred             HHHhhcc
Q 012638          418 ASECLRI  424 (459)
Q Consensus       418 ~l~~ar~  424 (459)
                      .+++++.
T Consensus       164 ~l~Rar~  170 (186)
T PRK05602        164 LLARGRR  170 (186)
T ss_pred             HHHHHHH
Confidence            9998875

>TIGR02835 spore_sigmaE RNA polymerase sigma-E factor

Probab=99.73  E-value=6.7e-17  Score=156.58  Aligned_cols=142  Identities=24%  Similarity=0.385  Sum_probs=115.6

Q ss_pred             HHHHHHHHHhchH-HHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHH
Q 012638          283 ERVLKQHLAFGWY-CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSIS  361 (459)
Q Consensus       283 eeeL~~~l~~G~~-Are~LI~~nlrLV~sIAkry~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIrnaI~  361 (459)
                      +..|+..+..|+. |++.|+..|.+.|+++|++|.+++.+++|++||+++++|+++++|++..+++|.||++++++|.++
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            5678888888877 999999999999999999999999999999999999999999999988777899999999999999


Q ss_pred             HHHHhhccccc-cc----------------------c-----ch---HHHHHHHHHHHHHHHHHc------------CCC
Q 012638          362 KMVARHARGIK-IP----------------------C-----KL---NREISKIQKARKALTNSH------------GKY  398 (459)
Q Consensus       362 d~Lrk~sr~ir-lP----------------------~-----~v---~e~i~kI~ka~~~L~~~l------------gr~  398 (459)
                      +++|++.+... .+                      .     ..   ......+..++..|+...            ..+
T Consensus       119 d~~Rk~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~ai~~Lp~~~R~ii~L~~~l~~~eg  198 (234)
T TIGR02835       119 MYLRRNNKTRSEVSFDEPLNVDWDGNELLLSDVLGTDSDIVYKYLEEEVDRELLRKALAKLNDREKKIMELRFGLVGGTE  198 (234)
T ss_pred             HHHHHhccccCcccccccccCCCCCCcchHHHhcCCCCCcHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHccCCCCC
Confidence            99998654211 00                      0     00   011233666666665442            156


Q ss_pred             CCHHHHHHHhCCCHHHHHHHHHhhcc
Q 012638          399 PEDIEIAKYTGLSLAEIRSASECLRI  424 (459)
Q Consensus       399 PT~eEIAe~LGIS~e~Vk~~l~~ar~  424 (459)
                      .|++|||+.||+|+++|+..+++++.
T Consensus       199 ~s~~EIA~~Lgis~~tV~~~l~ra~~  224 (234)
T TIGR02835       199 KTQKEVADMLGISQSYISRLEKRILK  224 (234)
T ss_pred             CCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            89999999999999999999887764

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.

>PRK12513 RNA polymerase sigma factor; Provisional

Probab=99.72  E-value=1.3e-16  Score=149.13  Aligned_cols=142  Identities=18%  Similarity=0.143  Sum_probs=116.1

Q ss_pred             CCHHHHHHHHHhchH-HHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHH
Q 012638          281 VSERVLKQHLAFGWY-CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKS  359 (459)
Q Consensus       281 ~deeeL~~~l~~G~~-Are~LI~~nlrLV~sIAkry~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIrna  359 (459)
                      ++++.|+..++.|+. |++.|+..|.+.|+++|+++.++..+++|++||+|+++|+++++|++.  ..|.+|++++++|.
T Consensus        11 ~~~~~l~~~~~~gd~~a~~~l~~~y~~~l~~~~~~~~~~~~daeDlvQe~fi~l~~~~~~~~~~--~~f~~wl~~i~~n~   88 (194)
T PRK12513         11 ASDEALMLRYRAGDAAAFEALYARHRTGLYRFLLRLARDRALAEDIFQETWLRVIRARAQYQPR--ARFRTWLYQIARNL   88 (194)
T ss_pred             CCHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHhcCCC--CchHHHHHHHHHHH
Confidence            457788999999977 999999999999999999999999999999999999999999999974  36999999999999


Q ss_pred             HHHHHHhhcccccccc------------c--------hHHHHHHHHHHHHHHHHHcC--------CCCCHHHHHHHhCCC
Q 012638          360 ISKMVARHARGIKIPC------------K--------LNREISKIQKARKALTNSHG--------KYPEDIEIAKYTGLS  411 (459)
Q Consensus       360 I~d~Lrk~sr~irlP~------------~--------v~e~i~kI~ka~~~L~~~lg--------r~PT~eEIAe~LGIS  411 (459)
                      +++++|++.+....+.            .        ..+....+..+...|+....        .+.|++|||+.||||
T Consensus        89 ~~~~~R~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~i~~l~~~~g~s~~EIA~~lgis  168 (194)
T PRK12513         89 LIDHWRRHGARQAPSLDADEQLHALADDGAAPEQQLSLFRDRRRLQAALETLPDEQREVFLLREHGDLELEEIAELTGVP  168 (194)
T ss_pred             HHHHHHHhccccccccccchhhhhcCCCCCCHHHHHHHHHHHHHHHHHHHhCCHhHhhheeeehccCCCHHHHHHHHCCC
Confidence            9999998765332210            0        01122345566666655432        568999999999999


Q ss_pred             HHHHHHHHHhhcc
Q 012638          412 LAEIRSASECLRI  424 (459)
Q Consensus       412 ~e~Vk~~l~~ar~  424 (459)
                      +++|+..+.+++.
T Consensus       169 ~~tV~~~l~ra~~  181 (194)
T PRK12513        169 EETVKSRLRYALQ  181 (194)
T ss_pred             HHHHHHHHHHHHH
Confidence            9999999888875

>PRK06811 RNA polymerase factor sigma-70; Validated

Probab=99.71  E-value=1.4e-16  Score=148.74  Aligned_cols=144  Identities=16%  Similarity=0.122  Sum_probs=115.1

Q ss_pred             CCCHHHHHHHHHhchH-HHHHHHHHhHHHHHHHHHHhhCCC---CCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHH
Q 012638          280 GVSERVLKQHLAFGWY-CREELIKSTRPLVLFLARNYRGLG---IPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYW  355 (459)
Q Consensus       280 g~deeeL~~~l~~G~~-Are~LI~~nlrLV~sIAkry~g~g---~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~w  355 (459)
                      .++++.|+..+..|+. |+++|+..|.++|+.+|.++.+++   .+++|++||+++++|+++++|++..+ +|.||++.+
T Consensus         2 ~~~~~~li~~~~~gd~~a~~~l~~~y~~~l~~~~~~~~~~~~~~~daeDi~Qe~~i~l~~~~~~~~~~~~-~~~~wl~~i   80 (189)
T PRK06811          2 KINEDNFIKELKKKNEKALEFIVDTYGNLVKKIVHKVLGTVNYSQLIEECVNDIFLSIWNNIDKFDEEKG-SFKKWIAAI   80 (189)
T ss_pred             CCcHHHHHHHHHccCHHHHHHHHHHHHHHHHHHHHHHHcccCchhHHHHHHHHHHHHHHHhHHHhccccc-cHHHHHHHH
Confidence            4678889999999987 999999999999999999998853   57999999999999999999997544 799999999


Q ss_pred             HHHHHHHHHHhhccccccc---c-------c------hHHHHHHHHHHHHHHHHHc--------CCCCCHHHHHHHhCCC
Q 012638          356 IRKSISKMVARHARGIKIP---C-------K------LNREISKIQKARKALTNSH--------GKYPEDIEIAKYTGLS  411 (459)
Q Consensus       356 IrnaI~d~Lrk~sr~irlP---~-------~------v~e~i~kI~ka~~~L~~~l--------gr~PT~eEIAe~LGIS  411 (459)
                      ++|.+++++|++.+.....   .       .      ..+....+.++...|+...        -.+.+++|||+.||+|
T Consensus        81 arn~~~d~~rk~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~l~~~l~~L~~~~r~i~~l~~~~g~s~~EIAe~lgis  160 (189)
T PRK06811         81 SKYKAIDYKRKLTKNNEIDSIDEFILISEESIENEIILKENKEEILKLINDLEKLDREIFIRRYLLGEKIEEIAKKLGLT  160 (189)
T ss_pred             HHHHHHHHHHHhccccccccchhhhhcccCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHccCCHHHHHHHHCCC
Confidence            9999999999866432211   0       0      0112233555555554432        2678999999999999


Q ss_pred             HHHHHHHHHhhcc
Q 012638          412 LAEIRSASECLRI  424 (459)
Q Consensus       412 ~e~Vk~~l~~ar~  424 (459)
                      ..+|+..+.+++.
T Consensus       161 ~~~V~~~l~Ra~~  173 (189)
T PRK06811        161 RSAIDNRLSRGRK  173 (189)
T ss_pred             HHHHHHHHHHHHH
Confidence            9999999998864

>PRK09646 RNA polymerase sigma factor SigK; Reviewed

Probab=99.71  E-value=1.4e-16  Score=149.41  Aligned_cols=142  Identities=18%  Similarity=0.098  Sum_probs=114.8

Q ss_pred             CHHHHHHHHHhchH-HHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHH
Q 012638          282 SERVLKQHLAFGWY-CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSI  360 (459)
Q Consensus       282 deeeL~~~l~~G~~-Are~LI~~nlrLV~sIAkry~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIrnaI  360 (459)
                      +...|+..+..|+. |+++|+..|.++|+++|.+|.++..+++|++||+++++|+++++||+.+| .|.+|++.+++|.+
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            45678888899977 99999999999999999999999999999999999999999999998665 79999999999999


Q ss_pred             HHHHHhhcccccc---------cc---ch------HHHHHHHHHHHHHHHHHc--------CCCCCHHHHHHHhCCCHHH
Q 012638          361 SKMVARHARGIKI---------PC---KL------NREISKIQKARKALTNSH--------GKYPEDIEIAKYTGLSLAE  414 (459)
Q Consensus       361 ~d~Lrk~sr~irl---------P~---~v------~e~i~kI~ka~~~L~~~l--------gr~PT~eEIAe~LGIS~e~  414 (459)
                      ++++|++.+..+.         +.   ..      .+....+..++..|+...        ..+.+++|||+.||+|+++
T Consensus        95 ~d~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~vl~l~~~~~~s~~EIA~~Lgis~~t  174 (194)
T PRK09646         95 VDRVRSEQAASQREVRYGARNVDPAFDQVAEEVEARLERERVRDCLDALTDTQRESVTLAYYGGLTYREVAERLAVPLGT  174 (194)
T ss_pred             HHHHHhhccccccccccccccccccccchHHHHHHHhHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHhCCChHh
Confidence            9999986532111         00   00      112233555555554432        3678999999999999999


Q ss_pred             HHHHHHhhcc
Q 012638          415 IRSASECLRI  424 (459)
Q Consensus       415 Vk~~l~~ar~  424 (459)
                      |+..+.+++.
T Consensus       175 Vk~~l~ra~~  184 (194)
T PRK09646        175 VKTRMRDGLI  184 (194)
T ss_pred             HHHHHHHHHH
Confidence            9999998875

>PRK09648 RNA polymerase sigma factor SigD; Reviewed

Probab=99.69  E-value=4.6e-16  Score=144.80  Aligned_cols=141  Identities=18%  Similarity=0.193  Sum_probs=112.1

Q ss_pred             HHHHHHHHHhchH-HHHHHHHHhHHHHHHHHHHhhCC----CCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHH
Q 012638          283 ERVLKQHLAFGWY-CREELIKSTRPLVLFLARNYRGL----GIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIR  357 (459)
Q Consensus       283 eeeL~~~l~~G~~-Are~LI~~nlrLV~sIAkry~g~----g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIr  357 (459)
                      ...|+..+..|+. |+++|+..|.+.|+.+|.++.++    ..+++|++||+++++|+++.+|+.. +..|.||++.+++
T Consensus        11 ~~~l~~~~~~gd~~a~~~l~~~~~~~l~~~~~~~~~~~~~~~~~aeDlvQe~fi~l~~~~~~~~~~-~~~~~~wl~~i~~   89 (189)
T PRK09648         11 LDALVAEAVAGDRRALREVLEIIRPLVVRYCRARLGGVERPGLSADDVAQEVCLAVITALPRYRDQ-GRPFLAFVYGIAA   89 (189)
T ss_pred             HHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHhcccccCCCCHHHHHHHHHHHHHHHHHHHhcc-CCcHHHHHHHHHH
Confidence            3567888899977 99999999999999999998765    4689999999999999999999864 4589999999999


Q ss_pred             HHHHHHHHhhcccccccc-----------ch------HHHHHHHHHHHHHHHHHc--------CCCCCHHHHHHHhCCCH
Q 012638          358 KSISKMVARHARGIKIPC-----------KL------NREISKIQKARKALTNSH--------GKYPEDIEIAKYTGLSL  412 (459)
Q Consensus       358 naI~d~Lrk~sr~irlP~-----------~v------~e~i~kI~ka~~~L~~~l--------gr~PT~eEIAe~LGIS~  412 (459)
                      |.+++++|++.+....+.           ..      .+....+.+++..|+...        ..+.+++|||+.||+|+
T Consensus        90 n~~~d~~r~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~l~~~l~~L~~~~r~i~~l~~~~g~s~~EIA~~lgis~  169 (189)
T PRK09648         90 HKVADAHRAAGRDKAVPTEEVPERPSDDAGPEERALRSESSNRMRELLDTLPEKQREILILRVVVGLSAEETAEAVGSTP  169 (189)
T ss_pred             HHHHHHHHHhCCCccccccccccccccCCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHHCCCH
Confidence            999999998765322110           00      112233555555555432        35789999999999999


Q ss_pred             HHHHHHHHhhcc
Q 012638          413 AEIRSASECLRI  424 (459)
Q Consensus       413 e~Vk~~l~~ar~  424 (459)
                      ++|+..+.+++.
T Consensus       170 ~tV~~~l~Ra~~  181 (189)
T PRK09648        170 GAVRVAQHRALA  181 (189)
T ss_pred             HHHHHHHHHHHH
Confidence            999999988764

>PRK13919 putative RNA polymerase sigma E protein; Provisional

Probab=99.69  E-value=3.6e-16  Score=144.72  Aligned_cols=143  Identities=21%  Similarity=0.188  Sum_probs=114.8

Q ss_pred             CCHHHHHHHHHhchH-HHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHH
Q 012638          281 VSERVLKQHLAFGWY-CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKS  359 (459)
Q Consensus       281 ~deeeL~~~l~~G~~-Are~LI~~nlrLV~sIAkry~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIrna  359 (459)
                      +++.+|+..++.|+. |++.|+..|.+.|+.+|++|.+++.+++|++||+++++|+++++|++.. ..|.+|++++++|.
T Consensus         8 ~~~~~l~~~~~~~d~~a~~~l~~~y~~~l~~~~~~~~~~~~~aeDlvQe~~i~l~~~~~~~~~~~-~~~~~wl~~ia~n~   86 (186)
T PRK13919          8 LSDEALLALVARGEEEALRALFRRYAGAFLALARRMGLDGAAAEDVVQEVFIRVWKKAKEFDPRR-GSARAWLLALAHHA   86 (186)
T ss_pred             cCHHHHHHHHHcCcHHHHHHHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHhhhccCccc-cchHHHHHHHHHHH
Confidence            457788888889987 9999999999999999999999999999999999999999999998754 36999999999999


Q ss_pred             HHHHHHhhccccc-c------c------cc--h---HHHHHHHHHHHHHHHHHc--------CCCCCHHHHHHHhCCCHH
Q 012638          360 ISKMVARHARGIK-I------P------CK--L---NREISKIQKARKALTNSH--------GKYPEDIEIAKYTGLSLA  413 (459)
Q Consensus       360 I~d~Lrk~sr~ir-l------P------~~--v---~e~i~kI~ka~~~L~~~l--------gr~PT~eEIAe~LGIS~e  413 (459)
                      +++++|++.+... +      +      ..  .   ......+.++...|+...        -.+.+++|||+.||||++
T Consensus        87 ~~d~~rk~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~vl~l~~~~~~s~~eIA~~lgis~~  166 (186)
T PRK13919         87 AVDHVRRRAARPQPLEPDEREPEAFDLPGPGLDEEGHLDRTRLGRALKALSPEERRVIEVLYYQGYTHREAAQLLGLPLG  166 (186)
T ss_pred             HHHHHHhhhcccccccccccccccccCCCccccHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHHCcCHH
Confidence            9999997653211 1      0      00  0   011223556666554443        367899999999999999


Q ss_pred             HHHHHHHhhcc
Q 012638          414 EIRSASECLRI  424 (459)
Q Consensus       414 ~Vk~~l~~ar~  424 (459)
                      +|+..+++++.
T Consensus       167 ~V~~~l~ra~~  177 (186)
T PRK13919        167 TLKTRARRALS  177 (186)
T ss_pred             HHHHHHHHHHH
Confidence            99999998875

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

Probab=99.69  E-value=4.2e-16  Score=142.38  Aligned_cols=142  Identities=14%  Similarity=0.069  Sum_probs=115.3

Q ss_pred             CCHHHHHHHHHhchH-HHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHH
Q 012638          281 VSERVLKQHLAFGWY-CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKS  359 (459)
Q Consensus       281 ~deeeL~~~l~~G~~-Are~LI~~nlrLV~sIAkry~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIrna  359 (459)
                      |+++.|+..+..|+. |++.++..|.+.|+++|.++.++..+++|++||+++.+|+..++|++.  .+|.||++.+++|.
T Consensus         1 ~~~~~l~~~~~~gd~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeD~~Qe~~l~~~~~~~~~~~~--~~~~~wl~~i~~n~   78 (169)
T TIGR02954         1 MNDEELVKKAKRGNKPAFESLIKKHKEKLYKTAFIYVKNEHDALDVIQETVYKAYLSIDKLKHP--KYFNTWLTRILINE   78 (169)
T ss_pred             CCHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHhccCc--cccHHHHHHHHHHH
Confidence            457788888999977 999999999999999999999999999999999999999999999974  36999999999999


Q ss_pred             HHHHHHhhccccccccc----------hHHHHHHHHHHHHHHHHHc--------CCCCCHHHHHHHhCCCHHHHHHHHHh
Q 012638          360 ISKMVARHARGIKIPCK----------LNREISKIQKARKALTNSH--------GKYPEDIEIAKYTGLSLAEIRSASEC  421 (459)
Q Consensus       360 I~d~Lrk~sr~irlP~~----------v~e~i~kI~ka~~~L~~~l--------gr~PT~eEIAe~LGIS~e~Vk~~l~~  421 (459)
                      +++++|+..+...++..          ..+....+..+...|+...        -.+.+++|||+.||||+++|+..+.+
T Consensus        79 ~~d~~R~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~i~~l~~~~g~s~~eiA~~lgis~~tv~~~l~R  158 (169)
T TIGR02954        79 CIDLLKKKKKVIPFDPNTSIEKGECETHADSRLDLYKAIDTLNDKYQTAIILRYYHDLTIKEIAEVMNKPEGTVKTYLHR  158 (169)
T ss_pred             HHHHHHhcCCcCccccccccccchhhhchHHHHHHHHHHHhCCHHHhHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHH
Confidence            99999987654322111          0111123555555554433        36789999999999999999999998


Q ss_pred             hcc
Q 012638          422 LRI  424 (459)
Q Consensus       422 ar~  424 (459)
                      ++.
T Consensus       159 a~~  161 (169)
T TIGR02954       159 ALK  161 (169)
T ss_pred             HHH
Confidence            875

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.

>PRK12514 RNA polymerase sigma factor; Provisional

Probab=99.69  E-value=3.7e-16  Score=144.01  Aligned_cols=142  Identities=15%  Similarity=0.060  Sum_probs=113.7

Q ss_pred             CHHHHHHHHHhchH-HHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHH
Q 012638          282 SERVLKQHLAFGWY-CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSI  360 (459)
Q Consensus       282 deeeL~~~l~~G~~-Are~LI~~nlrLV~sIAkry~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIrnaI  360 (459)
                      +...|+..+..|+. |+++|+..|.+.|+.+|.++.++..+++|++||+|+++|+++++|++.. ..|.||++.+++|.+
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            45677888888977 9999999999999999999999999999999999999999999998654 369999999999999


Q ss_pred             HHHHHhhcccc-cc------------ccch---HHHHHHHHHHHHHHHHHc--------CCCCCHHHHHHHhCCCHHHHH
Q 012638          361 SKMVARHARGI-KI------------PCKL---NREISKIQKARKALTNSH--------GKYPEDIEIAKYTGLSLAEIR  416 (459)
Q Consensus       361 ~d~Lrk~sr~i-rl------------P~~v---~e~i~kI~ka~~~L~~~l--------gr~PT~eEIAe~LGIS~e~Vk  416 (459)
                      ++++|++.+.. .+            |...   .+....+..+...|+...        -.+.|++|||+.||||+++|+
T Consensus        84 ~d~~R~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~l~~~l~~L~~~~r~i~~l~~~~g~s~~eIA~~lgis~~tV~  163 (179)
T PRK12514         84 IDRLRARKAVAVDIDEAHDLADPSPGPEAEVIAGDEGQRIDACLEELEKDRAAAVRRAYLEGLSYKELAERHDVPLNTMR  163 (179)
T ss_pred             HHHHHhcCCcccccccchhccccCCCHHHHHHhHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHHCCChHHHH
Confidence            99999765421 00            0000   111233555555555433        257899999999999999999


Q ss_pred             HHHHhhcc
Q 012638          417 SASECLRI  424 (459)
Q Consensus       417 ~~l~~ar~  424 (459)
                      ..+.+++.
T Consensus       164 ~~l~Rar~  171 (179)
T PRK12514        164 TWLRRSLL  171 (179)
T ss_pred             HHHHHHHH
Confidence            99998875

>PRK09640 RNA polymerase sigma factor SigX; Reviewed

Probab=99.69  E-value=6.7e-16  Score=143.97  Aligned_cols=143  Identities=15%  Similarity=0.111  Sum_probs=116.1

Q ss_pred             CCCHHHHHHHHHh---chH-HHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHH
Q 012638          280 GVSERVLKQHLAF---GWY-CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYW  355 (459)
Q Consensus       280 g~deeeL~~~l~~---G~~-Are~LI~~nlrLV~sIAkry~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~w  355 (459)
                      .++++.|+..++.   |+. |++.|+..|.+.|+.+|.+|.++..+++|++||+|+++|+++++|++.  .+|.||++++
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            4677888888885   466 999999999999999999999999999999999999999999999963  4799999999


Q ss_pred             HHHHHHHHHHhhccccccc---------c---c---hHHHHHHHHHHHHHHHHHcC--------CCCCHHHHHHHhCCCH
Q 012638          356 IRKSISKMVARHARGIKIP---------C---K---LNREISKIQKARKALTNSHG--------KYPEDIEIAKYTGLSL  412 (459)
Q Consensus       356 IrnaI~d~Lrk~sr~irlP---------~---~---v~e~i~kI~ka~~~L~~~lg--------r~PT~eEIAe~LGIS~  412 (459)
                      ++|.+++++|+..+.....         .   .   ..+....+.++...|+....        .+.+++|||+.||||.
T Consensus        85 a~n~~~d~~R~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~v~~l~~~~g~s~~EIA~~lgis~  164 (188)
T PRK09640         85 TYNECITQYRKERRKRRLMDALSLDPLEEASEEKAPKPEERGGLDRWLVHVNPIDREILVLRFVAELEFQEIADIMHMGL  164 (188)
T ss_pred             HHHHHHHHHHHhcccccCcchhhhcccccccccccccHHHHHHHHHHHHhcChhheeeeeeHHhcCCCHHHHHHHHCCCH
Confidence            9999999999754322111         0   0   11233456677777765532        4579999999999999


Q ss_pred             HHHHHHHHhhcc
Q 012638          413 AEIRSASECLRI  424 (459)
Q Consensus       413 e~Vk~~l~~ar~  424 (459)
                      ++|+..+.+++.
T Consensus       165 ~tV~~~l~Ra~~  176 (188)
T PRK09640        165 SATKMRYKRALD  176 (188)
T ss_pred             HHHHHHHHHHHH
Confidence            999999998875

>PRK12537 RNA polymerase sigma factor; Provisional

Probab=99.69  E-value=3.9e-16  Score=144.84  Aligned_cols=143  Identities=16%  Similarity=0.095  Sum_probs=115.7

Q ss_pred             CCHHHHHHHHHhchH-HHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHH
Q 012638          281 VSERVLKQHLAFGWY-CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKS  359 (459)
Q Consensus       281 ~deeeL~~~l~~G~~-Are~LI~~nlrLV~sIAkry~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIrna  359 (459)
                      ++..+|+..+..|+. |++.|+..|.+.|+.+|.++.++..+++|++||+|+.+|+.+++|++.. ..|.||++.+++|.
T Consensus         8 ~~~~~l~~~~~~~d~~a~~~l~~~~~~~l~~~~~~~~~~~~~AeDivQe~fl~l~~~~~~~~~~~-~~~~~wL~~iarn~   86 (182)
T PRK12537          8 FDYEACLLACARGDRRALQALYQQESARLLGVARRIVRDRALAEDIVHDAFIKIWTGAASFDPAR-GSARGWIYSVTRHL   86 (182)
T ss_pred             hhHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHhCCHhHHHHHHHHHHHHHHhccccCCccc-ccHHHHHHHHHHHH
Confidence            345678889999977 9999999999999999999999999999999999999999999998644 37999999999999


Q ss_pred             HHHHHHhhcccccccc-----------c-----hHHHHHHHHHHHHHHHHHc--------CCCCCHHHHHHHhCCCHHHH
Q 012638          360 ISKMVARHARGIKIPC-----------K-----LNREISKIQKARKALTNSH--------GKYPEDIEIAKYTGLSLAEI  415 (459)
Q Consensus       360 I~d~Lrk~sr~irlP~-----------~-----v~e~i~kI~ka~~~L~~~l--------gr~PT~eEIAe~LGIS~e~V  415 (459)
                      ++++++++.+......           .     ..+....+.++...|+...        -.+.+++|||+.||||+++|
T Consensus        87 ~~d~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~i~~l~~~~~~s~~eIA~~lgis~~tV  166 (182)
T PRK12537         87 ALNVLRDTRREVVLDDDAEETAQTLHEIIDDFDLWANSGKIHRCLEQLEPARRNCILHAYVDGCSHAEIAQRLGAPLGTV  166 (182)
T ss_pred             HHHHHHhccccCccccchhhhcccccchHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHHCCChhhH
Confidence            9999998864322110           0     0112234555555554433        36789999999999999999


Q ss_pred             HHHHHhhcc
Q 012638          416 RSASECLRI  424 (459)
Q Consensus       416 k~~l~~ar~  424 (459)
                      +..+.+++.
T Consensus       167 ~~~l~ra~~  175 (182)
T PRK12537        167 KAWIKRSLK  175 (182)
T ss_pred             HHHHHHHHH
Confidence            999998875

>PRK12524 RNA polymerase sigma factor; Provisional

Probab=99.68  E-value=3.8e-16  Score=146.72  Aligned_cols=145  Identities=17%  Similarity=0.148  Sum_probs=116.9

Q ss_pred             CCCHHHHHHHHHhchH-HHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHH
Q 012638          280 GVSERVLKQHLAFGWY-CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRK  358 (459)
Q Consensus       280 g~deeeL~~~l~~G~~-Are~LI~~nlrLV~sIAkry~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIrn  358 (459)
                      .+++..|+.++..|+. |++.|+..|.+.|+.+|.++.++..+++|++||+++++|+.+.+|++.. ..|.||++.+++|
T Consensus        10 ~~~~~~li~~~~~gd~~a~~~l~~~y~~~l~~~~~~~~~~~~~AeDlvQe~~l~l~~~~~~~~~~~-~~~~~wl~~ia~n   88 (196)
T PRK12524         10 DVSDEALLVLYANGDPAAARALTLRLAPRALAVATRVLGDRAEAEDVTQEAMLRLWRIAPDWRQGE-ARVSTWLYRVVCN   88 (196)
T ss_pred             CcCHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhhhcccccc-chHHHHHHHHHHH
Confidence            4567889999999977 9999999999999999999999999999999999999999999998533 4799999999999


Q ss_pred             HHHHHHHhhccc-ccc---c------c---c---hHHHHHHHHHHHHHHHHHc--------CCCCCHHHHHHHhCCCHHH
Q 012638          359 SISKMVARHARG-IKI---P------C---K---LNREISKIQKARKALTNSH--------GKYPEDIEIAKYTGLSLAE  414 (459)
Q Consensus       359 aI~d~Lrk~sr~-irl---P------~---~---v~e~i~kI~ka~~~L~~~l--------gr~PT~eEIAe~LGIS~e~  414 (459)
                      .+++++|++.+. ..+   +      .   .   ..+....+.++...|+...        -.+.+++|||+.||||+.+
T Consensus        89 ~~~d~~Rk~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~i~~L~~~~g~s~~eIA~~lgis~~t  168 (196)
T PRK12524         89 LCTDRLRRRRRASVDLDDAPEPADAAPGAEEALIEGDRMRALDAALAALPERQRQAVVLRHIEGLSNPEIAEVMEIGVEA  168 (196)
T ss_pred             HHHHHHHhhcCCCCCccccccccccCCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHHCcCHHH
Confidence            999999975432 111   0      0   0   0112234555666555432        3678999999999999999


Q ss_pred             HHHHHHhhccC
Q 012638          415 IRSASECLRIV  425 (459)
Q Consensus       415 Vk~~l~~ar~~  425 (459)
                      |+..+++++..
T Consensus       169 V~~~l~Ra~~~  179 (196)
T PRK12524        169 VESLTARGKRA  179 (196)
T ss_pred             HHHHHHHHHHH
Confidence            99999998753

>PRK06759 RNA polymerase factor sigma-70; Validated

Probab=99.68  E-value=4.9e-16  Score=139.26  Aligned_cols=128  Identities=16%  Similarity=0.144  Sum_probs=102.9

Q ss_pred             HHHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhhccc----
Q 012638          295 YCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARG----  370 (459)
Q Consensus       295 ~Are~LI~~nlrLV~sIAkry~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIrnaI~d~Lrk~sr~----  370 (459)
                      .|+++|+..|.++|+.+++++ +...+++|++|||++++|+++++|++..| .|.||++.+++|.+++++|++.+.    
T Consensus         4 ~af~~l~~~y~~~l~~~~~~~-~~~~~aeDi~Qe~~l~l~~~~~~~~~~~~-~f~~wl~~i~~n~~ld~~rk~~~~~~~~   81 (154)
T PRK06759          4 ATFTEAVVLYEGLIVNQIKKL-GIYQDYEEYYQCGLIGLWHAYERYDEKKG-SFPAYAVVTVRGYILERLKKEFAVQEKC   81 (154)
T ss_pred             ccHHHHHHHHHHHHHHHHHHh-CCcccHHHHHHHHHHHHHHHHHHhCccCC-chHHHHHHHHHHHHHHHHHHHHhhcccc
Confidence            489999999999999999986 56789999999999999999999998666 799999999999999999987421    


Q ss_pred             --cccccc---hHHHHHHHHHHHHHHHHH--------cCCCCCHHHHHHHhCCCHHHHHHHHHhhcc
Q 012638          371 --IKIPCK---LNREISKIQKARKALTNS--------HGKYPEDIEIAKYTGLSLAEIRSASECLRI  424 (459)
Q Consensus       371 --irlP~~---v~e~i~kI~ka~~~L~~~--------lgr~PT~eEIAe~LGIS~e~Vk~~l~~ar~  424 (459)
                        ...|..   ..+....+..+...|+..        +..+.|++|||+.||+|+++|+..+.+++.
T Consensus        82 ~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~ii~l~~~~~~s~~EIA~~l~is~~tV~~~~~ra~~  148 (154)
T PRK06759         82 VCVGEYEDHFHFEDVEMKVKDFMSVLDEKEKYIIFERFFVGKTMGEIALETEMTYYQVRWIYRQALE  148 (154)
T ss_pred             cccCCCcccccHHHHHHHHHHHHHhCCHHHHHHHHHHHhcCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence              111222   122334456666555443        246789999999999999999999988764

>TIGR02948 SigW_bacill RNA polymerase sigma-W factor

Probab=99.68  E-value=6.6e-16  Score=142.45  Aligned_cols=140  Identities=14%  Similarity=0.069  Sum_probs=111.8

Q ss_pred             HHHHHHHHHhchH-HHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHH
Q 012638          283 ERVLKQHLAFGWY-CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSIS  361 (459)
Q Consensus       283 eeeL~~~l~~G~~-Are~LI~~nlrLV~sIAkry~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIrnaI~  361 (459)
                      ++.|+..+..|+. |+++|+..|.+.|+.+|.+|.++..+++|++||+++++|+++.+|++..  .|.||++.+++|.+.
T Consensus         5 ~~~li~~~~~gd~~a~~~l~~~y~~~v~~~~~~~~~~~~~aeDlvQe~~l~l~~~~~~~~~~~--~~~~wl~~i~~n~~~   82 (187)
T TIGR02948         5 IKKRIKEVRKGDENAFADLVDLYKDKIYQLCYRMLGNVHEAEDVAQEAFIRAYTNIDTYDIQR--KFSTWLYRIATNLTI   82 (187)
T ss_pred             HHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhHHhcCCCC--chHHHHHHHHHHHHH
Confidence            4567888899977 9999999999999999999999999999999999999999999999865  699999999999999


Q ss_pred             HHHHhhcccccccc-------------------ch------HHHHHHHHHHHHHHHHHc--------CCCCCHHHHHHHh
Q 012638          362 KMVARHARGIKIPC-------------------KL------NREISKIQKARKALTNSH--------GKYPEDIEIAKYT  408 (459)
Q Consensus       362 d~Lrk~sr~irlP~-------------------~v------~e~i~kI~ka~~~L~~~l--------gr~PT~eEIAe~L  408 (459)
                      +++|+..+......                   ..      .+....+.++...|+...        ..+.+++|||+.|
T Consensus        83 ~~~rk~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~l~~~l~~L~~~~r~v~~l~~~~g~s~~eIA~~l  162 (187)
T TIGR02948        83 DRLRKRKPDFYLDDEVQGTDGLTMESQLAADEAPPEDQVISLELRDTIQQEIQALPPKYRMVIVLKYMEDLSLKEISEIL  162 (187)
T ss_pred             HHHHhhcccccccccccCccccccccccccCcCCHHHHHHHHHHHHHHHHHHHhCCHHHhHHhhhHHhcCCCHHHHHHHH
Confidence            99997654211000                   00      011223445555544332        3568999999999


Q ss_pred             CCCHHHHHHHHHhhcc
Q 012638          409 GLSLAEIRSASECLRI  424 (459)
Q Consensus       409 GIS~e~Vk~~l~~ar~  424 (459)
                      |+|+++|+..+++++.
T Consensus       163 gis~~~v~~~l~Rar~  178 (187)
T TIGR02948       163 DLPVGTVKTRIHRGRE  178 (187)
T ss_pred             CCCHHHHHHHHHHHHH
Confidence            9999999999998875

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

>PRK09638 RNA polymerase sigma factor SigY; Reviewed

Probab=99.68  E-value=8.3e-16  Score=140.90  Aligned_cols=143  Identities=16%  Similarity=0.048  Sum_probs=116.0

Q ss_pred             CCCHHHHHHHHHhchH-HHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHH
Q 012638          280 GVSERVLKQHLAFGWY-CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRK  358 (459)
Q Consensus       280 g~deeeL~~~l~~G~~-Are~LI~~nlrLV~sIAkry~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIrn  358 (459)
                      .|++..++..+..|+. |++.|+..|.+.|+.+|+++.++..+++|++||+++++|+++++|++.  .+|.+|++.+++|
T Consensus         2 ~~~~~~l~~~~~~~d~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeD~vQe~~l~l~~~~~~~~~~--~~~~~wl~~i~~n   79 (176)
T PRK09638          2 QMDEKELIQKAKKGDDAALTTLFQQHYSFLYKYLLKLTLDPDLAEDLVQETMLKAIENLSSFQGR--SKFSTWLISIASR   79 (176)
T ss_pred             CccHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHcCCHhHHHHHHHHHHHHHHHHHHhcCCc--ccHHHHHHHHHHH
Confidence            4567888888999987 999999999999999999999999999999999999999999999874  4799999999999


Q ss_pred             HHHHHHHhhcccccccc-------c-h-------HHHHHHHHHHHHHHHHHcC--------CCCCHHHHHHHhCCCHHHH
Q 012638          359 SISKMVARHARGIKIPC-------K-L-------NREISKIQKARKALTNSHG--------KYPEDIEIAKYTGLSLAEI  415 (459)
Q Consensus       359 aI~d~Lrk~sr~irlP~-------~-v-------~e~i~kI~ka~~~L~~~lg--------r~PT~eEIAe~LGIS~e~V  415 (459)
                      .+++++|+..+......       . .       ......+.++...|+....        .+.+++|||+.||+|+.+|
T Consensus        80 ~~~d~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~v~~l~~~~g~s~~eIA~~l~is~~~V  159 (176)
T PRK09638         80 LYKDHLRKQKREKLRLQRAKEETLRKEKWEAAIKGAEWSEMLDALSKLDPEFRAPVILKHYYGYTYEEIAKMLNIPEGTV  159 (176)
T ss_pred             HHHHHHHHhccccchhhhcccccCCccchHHHHHhhhHHHHHHHHHcCCHHHhheeeehhhcCCCHHHHHHHHCCChhHH
Confidence            99999998754322110       0 0       1122345555555555432        5679999999999999999


Q ss_pred             HHHHHhhcc
Q 012638          416 RSASECLRI  424 (459)
Q Consensus       416 k~~l~~ar~  424 (459)
                      +..+.+++.
T Consensus       160 ~~~l~ra~~  168 (176)
T PRK09638        160 KSRVHHGIK  168 (176)
T ss_pred             HHHHHHHHH
Confidence            999988875

>PRK09643 RNA polymerase sigma factor SigM; Reviewed

Probab=99.67  E-value=1e-15  Score=143.60  Aligned_cols=142  Identities=16%  Similarity=0.107  Sum_probs=116.9

Q ss_pred             CCHHHHHHHHHhchH-HHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHH
Q 012638          281 VSERVLKQHLAFGWY-CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKS  359 (459)
Q Consensus       281 ~deeeL~~~l~~G~~-Are~LI~~nlrLV~sIAkry~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIrna  359 (459)
                      +++..++..+..|+. +++.|+..|.+.|+++|.++.++..+++|++||+|+.+|+++++|++.  ..|.+|++.+++|.
T Consensus        12 ~~~~~l~~~~~~gd~~~~~~l~~~y~~~l~~~~~~~~~~~~~AeDlvQEvfl~l~~~~~~~~~~--~~f~~wL~~i~rn~   89 (192)
T PRK09643         12 RSDAELLAAHVAGDRYAFGELFRRHHRRLWAVARRTSGTREDAADALQDAMLSAHRAAGSFRGD--AAVSSWLHRIVVNA   89 (192)
T ss_pred             cCHHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHHcCCHhhHHHHHHHHHHHHHHHHHhcCCC--CccHHHHHHHHHHH
Confidence            457888899999987 999999999999999999999999999999999999999999999975  36999999999999


Q ss_pred             HHHHHHhhccccccc-----------cc---hHHHHHHHHHHHHHHHHHc--------CCCCCHHHHHHHhCCCHHHHHH
Q 012638          360 ISKMVARHARGIKIP-----------CK---LNREISKIQKARKALTNSH--------GKYPEDIEIAKYTGLSLAEIRS  417 (459)
Q Consensus       360 I~d~Lrk~sr~irlP-----------~~---v~e~i~kI~ka~~~L~~~l--------gr~PT~eEIAe~LGIS~e~Vk~  417 (459)
                      +++++|+..+....+           ..   ..+....+..+...|+...        -.+.+++|||+.||+|.++|+.
T Consensus        90 ~~d~~Rk~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~l~~~l~~Lp~~~r~i~~l~~~~g~s~~EIA~~lg~s~~tV~~  169 (192)
T PRK09643         90 CLDRLRRAKARPTVPLDDVYPVAQLERDPTARVETALAVQRALMRLPVEQRAALVAVDMQGYSVADAARMLGVAEGTVKS  169 (192)
T ss_pred             HHHHHHccccCCCCCccccccccCCcccHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHH
Confidence            999999765432211           01   1122345666666665543        2668999999999999999999


Q ss_pred             HHHhhcc
Q 012638          418 ASECLRI  424 (459)
Q Consensus       418 ~l~~ar~  424 (459)
                      .+.+++.
T Consensus       170 rl~rar~  176 (192)
T PRK09643        170 RCARGRA  176 (192)
T ss_pred             HHHHHHH
Confidence            9998875

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

Probab=99.67  E-value=9.3e-16  Score=139.14  Aligned_cols=137  Identities=15%  Similarity=0.067  Sum_probs=109.2

Q ss_pred             HHHHHhchH-HHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHH
Q 012638          287 KQHLAFGWY-CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVA  365 (459)
Q Consensus       287 ~~~l~~G~~-Are~LI~~nlrLV~sIAkry~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIrnaI~d~Lr  365 (459)
                      +..+.+|+. |++.|+..|.+.|++++.++.++..+++|++||+++++|+++++|+...+ .|.+|++.+++|.+++++|
T Consensus         2 i~~~~~~d~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeD~vQe~~l~l~~~~~~~~~~~~-~~~~wl~~i~~n~~~d~~R   80 (170)
T TIGR02952         2 LERAQDREEDAFARIYETYSDRVYRYIYYRVGCKYTAEDLTSEVFERVLRKIDSFKEQKN-SFEAWLFTIARNVVNDYFR   80 (170)
T ss_pred             hHHHHccCHHHHHHHHHHHHHHHHHHHHHHHCChhhHHHHHHHHHHHHHHhHHhcccccc-cHHHHHHHHHHHHHHHHHH
Confidence            456777876 99999999999999999999998899999999999999999999997544 8999999999999999999


Q ss_pred             hhcccccccc-----------ch------HHHHHHHHHHHHHHHHHc--------CCCCCHHHHHHHhCCCHHHHHHHHH
Q 012638          366 RHARGIKIPC-----------KL------NREISKIQKARKALTNSH--------GKYPEDIEIAKYTGLSLAEIRSASE  420 (459)
Q Consensus       366 k~sr~irlP~-----------~v------~e~i~kI~ka~~~L~~~l--------gr~PT~eEIAe~LGIS~e~Vk~~l~  420 (459)
                      ++.+....+.           ..      .+....+.++...|+...        -.+.+++|||+.||||+++|+..+.
T Consensus        81 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~vl~l~~~~g~s~~eIA~~l~is~~tv~~~l~  160 (170)
T TIGR02952        81 GSKRHPLFSLDVFKELLSNEPNPEEAILKEEANEKLLKALKILTPKQQHVIALRFGQNLPIAEVARILGKTEGAVKILQF  160 (170)
T ss_pred             hcCCCCCCcHHHHhhcCCCCCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHhcCCCHHHHHHHHCCCHHHHHHHHH
Confidence            7654322110           00      112233455555554432        3678999999999999999999999


Q ss_pred             hhcc
Q 012638          421 CLRI  424 (459)
Q Consensus       421 ~ar~  424 (459)
                      +++.
T Consensus       161 ra~~  164 (170)
T TIGR02952       161 RAIK  164 (170)
T ss_pred             HHHH
Confidence            8864

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

>PRK09641 RNA polymerase sigma factor SigW; Provisional

Probab=99.67  E-value=9.3e-16  Score=141.44  Aligned_cols=142  Identities=15%  Similarity=0.086  Sum_probs=113.6

Q ss_pred             CCHHHHHHHHHhchH-HHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHH
Q 012638          281 VSERVLKQHLAFGWY-CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKS  359 (459)
Q Consensus       281 ~deeeL~~~l~~G~~-Are~LI~~nlrLV~sIAkry~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIrna  359 (459)
                      ...+.|+..++.|+. |++.++..|.++|+++|+++.++..+++|++||++++||+++.+|++..  +|.||++.+++|.
T Consensus         3 ~~~~~li~~~~~~d~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeDivQe~~l~l~~~~~~~~~~~--~~~~wl~~iarn~   80 (187)
T PRK09641          3 LLIKRLIKQVKKGDQNAFAELVDLYKDKIYQLCYRMLGNRHEAEDAAQEAFIRAYVNIDSYDINR--KFSTWLYRIATNL   80 (187)
T ss_pred             hHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHhhCCCc--chhHHHHHHHHHH
Confidence            345678888999987 9999999999999999999999999999999999999999999999853  7999999999999


Q ss_pred             HHHHHHhhcccccc----------------ccc---h------HHHHHHHHHHHHHHHHHc--------CCCCCHHHHHH
Q 012638          360 ISKMVARHARGIKI----------------PCK---L------NREISKIQKARKALTNSH--------GKYPEDIEIAK  406 (459)
Q Consensus       360 I~d~Lrk~sr~irl----------------P~~---v------~e~i~kI~ka~~~L~~~l--------gr~PT~eEIAe  406 (459)
                      +++++|++.+....                +..   .      .+....+.++...|+...        -.+.+++|||+
T Consensus        81 ~~d~~R~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~il~l~~~~~~s~~eIA~  160 (187)
T PRK09641         81 TIDRLRKRKPDYYLDAEVAGTEGLTMYSQLAADDALPEEQVVSLELQETIQEAILQLPEKYRTVIVLKYIEDLSLKEISE  160 (187)
T ss_pred             HHHHHHhcCccccccccccCCcchhhhcccccCcCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHhhhHHhhCCCHHHHHH
Confidence            99999987542211                000   0      111123555555554432        25689999999


Q ss_pred             HhCCCHHHHHHHHHhhcc
Q 012638          407 YTGLSLAEIRSASECLRI  424 (459)
Q Consensus       407 ~LGIS~e~Vk~~l~~ar~  424 (459)
                      .||||+++|+..+++++.
T Consensus       161 ~lgis~~~v~~~l~Rar~  178 (187)
T PRK09641        161 ILDLPVGTVKTRIHRGRE  178 (187)
T ss_pred             HHCCCHHHHHHHHHHHHH
Confidence            999999999999998875

>PRK12531 RNA polymerase sigma factor; Provisional

Probab=99.67  E-value=7.9e-16  Score=144.32  Aligned_cols=141  Identities=14%  Similarity=0.050  Sum_probs=112.3

Q ss_pred             HHHHHHHHHhchH-HHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHH
Q 012638          283 ERVLKQHLAFGWY-CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSIS  361 (459)
Q Consensus       283 eeeL~~~l~~G~~-Are~LI~~nlrLV~sIAkry~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIrnaI~  361 (459)
                      ...|+..+..|+. |++.|+..|.+.|+.+|.++.++..+++|++||+++.+|+...+|++.++ .|.||++.+++|.++
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            3467888899987 99999999999999999999999999999999999999999999997544 799999999999999


Q ss_pred             HHHHhhccccc-c------cc---------c-hH---HHHHHHHHHHHHHHHHc--------CCCCCHHHHHHHhCCCHH
Q 012638          362 KMVARHARGIK-I------PC---------K-LN---REISKIQKARKALTNSH--------GKYPEDIEIAKYTGLSLA  413 (459)
Q Consensus       362 d~Lrk~sr~ir-l------P~---------~-v~---e~i~kI~ka~~~L~~~l--------gr~PT~eEIAe~LGIS~e  413 (459)
                      +++|+..+... .      +.         . ..   .....+.++...|+...        -.+.+++|||+.||||++
T Consensus        93 d~~Rk~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~l~~~l~~Lp~~~r~v~~l~~~eg~s~~EIA~~lgis~~  172 (194)
T PRK12531         93 DLLRKQKGKDLHIHADDIWPSDYYPPDLVDHYSPEQDMLKEQVMKFLDRLPKAQRDVLQAVYLEELPHQQVAEMFDIPLG  172 (194)
T ss_pred             HHHHHhcccccccchhhcccccccccccccccCHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHhCcCHH
Confidence            99998653211 0      00         0 00   11133455555554432        257899999999999999


Q ss_pred             HHHHHHHhhcc
Q 012638          414 EIRSASECLRI  424 (459)
Q Consensus       414 ~Vk~~l~~ar~  424 (459)
                      +|+..+++++.
T Consensus       173 tVk~rl~ra~~  183 (194)
T PRK12531        173 TVKSRLRLAVE  183 (194)
T ss_pred             HHHHHHHHHHH
Confidence            99999998875

>PRK12534 RNA polymerase sigma factor; Provisional

Probab=99.66  E-value=9.7e-16  Score=142.17  Aligned_cols=141  Identities=16%  Similarity=0.041  Sum_probs=113.7

Q ss_pred             HHHHHHHHHhchH-HHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHH
Q 012638          283 ERVLKQHLAFGWY-CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSIS  361 (459)
Q Consensus       283 eeeL~~~l~~G~~-Are~LI~~nlrLV~sIAkry~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIrnaI~  361 (459)
                      ...+...+..|+. +++.|+..|.++|+.+|+++.++..+++|++||+|+++|+++++|++.++ .|.||++.+++|.++
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            4567777778876 99999999999999999999999999999999999999999999998654 689999999999999


Q ss_pred             HHHHhhccccc------cc---------cc---hHHHHHHHHHHHHHHHHHc--------CCCCCHHHHHHHhCCCHHHH
Q 012638          362 KMVARHARGIK------IP---------CK---LNREISKIQKARKALTNSH--------GKYPEDIEIAKYTGLSLAEI  415 (459)
Q Consensus       362 d~Lrk~sr~ir------lP---------~~---v~e~i~kI~ka~~~L~~~l--------gr~PT~eEIAe~LGIS~e~V  415 (459)
                      +++|++.+...      .+         ..   ..+....+..+...|+...        -.+.+++|||+.||||+++|
T Consensus        91 d~~R~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~l~~~l~~L~~~~r~i~~l~~~~g~s~~eIA~~lgis~~~v  170 (187)
T PRK12534         91 DHLRANAPQRRNVALDDAGELRAADASPLERTERASTRRRIDHCLAELEPPRSELIRTAFFEGITYEELAARTDTPIGTV  170 (187)
T ss_pred             HHHHhcccccccccccchhhhccccCChhhHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHhCCChhHH
Confidence            99997643210      11         00   1122345666666664432        36789999999999999999


Q ss_pred             HHHHHhhcc
Q 012638          416 RSASECLRI  424 (459)
Q Consensus       416 k~~l~~ar~  424 (459)
                      +..+++++.
T Consensus       171 ~~~l~Rar~  179 (187)
T PRK12534        171 KSWIRRGLA  179 (187)
T ss_pred             HHHHHHHHH
Confidence            999998875

>PRK12538 RNA polymerase sigma factor; Provisional

Probab=99.66  E-value=1.5e-15  Score=147.87  Aligned_cols=143  Identities=18%  Similarity=0.129  Sum_probs=115.2

Q ss_pred             CCHHHHHHHHHhchH-HHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHH
Q 012638          281 VSERVLKQHLAFGWY-CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKS  359 (459)
Q Consensus       281 ~deeeL~~~l~~G~~-Are~LI~~nlrLV~sIAkry~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIrna  359 (459)
                      .++..|+..++.|+. |++.|+..|.+.|+.+++++.++..+++|++||+|+++|+++++|++..+ .|.+|++.+++|.
T Consensus        48 ~~d~~Li~~~~~gd~~af~~L~~~y~~~l~~~~~~~~~d~~dAEDivQEvfl~l~~~~~~~~~~~~-~f~~WL~~IarN~  126 (233)
T PRK12538         48 DEDEELLDRLATDDEAAFRLLVERHIDRAYAIALRIVGNRADAEDVVQDTMLKVWTHRGRWQHGRA-KFSTWLYRVVSNR  126 (233)
T ss_pred             ccHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHcccccc-cHHHHHHHHHHHH
Confidence            356778888899987 99999999999999999999999999999999999999999999986544 7999999999999


Q ss_pred             HHHHHHhhccccc--c-------ccc-----hHHHHHHHHHHHHHHHHHc--------CCCCCHHHHHHHhCCCHHHHHH
Q 012638          360 ISKMVARHARGIK--I-------PCK-----LNREISKIQKARKALTNSH--------GKYPEDIEIAKYTGLSLAEIRS  417 (459)
Q Consensus       360 I~d~Lrk~sr~ir--l-------P~~-----v~e~i~kI~ka~~~L~~~l--------gr~PT~eEIAe~LGIS~e~Vk~  417 (459)
                      +++++|++.+...  .       |..     ..+....+..+...|+...        -.+.+++|||+.||+|+++|+.
T Consensus       127 ~id~~Rk~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~l~~~L~~Lp~~~R~v~~L~~~eg~s~~EIA~~Lgis~~tVk~  206 (233)
T PRK12538        127 CIDLRRKPRTENVDAVPEVADGKPDAVSVIERNELSDLLEAAMQRLPEQQRIAVILSYHENMSNGEIAEVMDTTVAAVES  206 (233)
T ss_pred             HHHHHHhhcccccccccccccCCCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHhhhHHhcCCCHHHHHHHHCcCHHHHHH
Confidence            9999997642211  1       110     0112234566666665543        2668999999999999999999


Q ss_pred             HHHhhcc
Q 012638          418 ASECLRI  424 (459)
Q Consensus       418 ~l~~ar~  424 (459)
                      .+++++.
T Consensus       207 ~l~RAr~  213 (233)
T PRK12538        207 LLKRGRQ  213 (233)
T ss_pred             HHHHHHH
Confidence            9998875

>TIGR02939 RpoE_Sigma70 RNA polymerase sigma factor RpoE

Probab=99.65  E-value=2.7e-15  Score=138.66  Aligned_cols=142  Identities=15%  Similarity=0.080  Sum_probs=113.4

Q ss_pred             CCHHHHHHHHHhchH-HHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHH
Q 012638          281 VSERVLKQHLAFGWY-CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKS  359 (459)
Q Consensus       281 ~deeeL~~~l~~G~~-Are~LI~~nlrLV~sIAkry~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIrna  359 (459)
                      .++..|+..+..|+. |++.|+..|.+.|+.+|+++.++..+++|++||+++++|+++.+|++.  .+|.+|++.+++|.
T Consensus         5 ~~d~~l~~~~~~gd~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeDlvQe~fi~l~~~~~~~~~~--~~~~~wl~~iarn~   82 (190)
T TIGR02939         5 ELDLELVERVQRGEKQAFDLLVRKYQHKVVALVGRYVRDSSEVEDVAQEAFVKAYRALSSFRGD--SAFYTWLYRIAVNT   82 (190)
T ss_pred             ccHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHhCCHhhHHHHHHHHHHHHHHhHHhcCCC--CccHhHHHHHHHHH
Confidence            346678888999987 999999999999999999999999999999999999999999999975  36999999999999


Q ss_pred             HHHHHHhhccccccc----------------------cc---hHHHHHHHHHHHHHHHHHc--------CCCCCHHHHHH
Q 012638          360 ISKMVARHARGIKIP----------------------CK---LNREISKIQKARKALTNSH--------GKYPEDIEIAK  406 (459)
Q Consensus       360 I~d~Lrk~sr~irlP----------------------~~---v~e~i~kI~ka~~~L~~~l--------gr~PT~eEIAe  406 (459)
                      ++++++++.+.....                      ..   ..+....+..+...|+...        -.+.+++|||+
T Consensus        83 ~~~~~r~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~l~~~l~~L~~~~r~v~~l~~~~~~s~~EIA~  162 (190)
T TIGR02939        83 AKNHLVAQGRRPPTSDVEIEDAEHFEGADRLREIDTPERLLLSRELEQTVMRAVEALPEDLRTAITLRELEGLSYEDIAR  162 (190)
T ss_pred             HHHHHHHhccCCCcccccccchhhhcccccccccCChHHHHHHHHHHHHHHHHHHcCCHHHhhhhhhhhhcCCCHHHHHH
Confidence            999998655422110                      00   0011123555555554433        25679999999


Q ss_pred             HhCCCHHHHHHHHHhhcc
Q 012638          407 YTGLSLAEIRSASECLRI  424 (459)
Q Consensus       407 ~LGIS~e~Vk~~l~~ar~  424 (459)
                      .|||++.+|+..+++++.
T Consensus       163 ~lgis~~tv~~~l~rar~  180 (190)
T TIGR02939       163 IMDCPVGTVRSRIFRARE  180 (190)
T ss_pred             HHCcCHHHHHHHHHHHHH
Confidence            999999999999998875

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

>PRK12519 RNA polymerase sigma factor; Provisional

Probab=99.65  E-value=1.9e-15  Score=140.98  Aligned_cols=141  Identities=21%  Similarity=0.192  Sum_probs=112.3

Q ss_pred             CHHHHHHHHHhchH-HHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHH
Q 012638          282 SERVLKQHLAFGWY-CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSI  360 (459)
Q Consensus       282 deeeL~~~l~~G~~-Are~LI~~nlrLV~sIAkry~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIrnaI  360 (459)
                      +..+|+..+..|+. |++.|+..|.+.|+.+|+++.++..+++|++||+++++|+. ..|++..+ .|.||++++++|.+
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            46778888899987 99999999999999999999999999999999999999976 67887554 79999999999999


Q ss_pred             HHHHHhhcccccc------------cc-c------hHHHHHHHHHHHHHHHHHc--------CCCCCHHHHHHHhCCCHH
Q 012638          361 SKMVARHARGIKI------------PC-K------LNREISKIQKARKALTNSH--------GKYPEDIEIAKYTGLSLA  413 (459)
Q Consensus       361 ~d~Lrk~sr~irl------------P~-~------v~e~i~kI~ka~~~L~~~l--------gr~PT~eEIAe~LGIS~e  413 (459)
                      ++++|++.+....            +. .      ..+....+..+...|+...        -.+.+++|||+.||+|+.
T Consensus        93 ~d~~Rk~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~~~v~~l~~~~g~s~~EIA~~lgis~~  172 (194)
T PRK12519         93 IDRLRSRRSRQRLLERWQQELLGEASEDTPLEQASLAERSQRVQTALAQLPESQRQVLELAYYEGLSQSEIAKRLGIPLG  172 (194)
T ss_pred             HHHHHhcccccchhhhhhhhhcccccCCCHHHHHHHHHHHHHHHHHHHhCCHHHhhhhhhhhhcCCCHHHHHHHhCCCHH
Confidence            9999976542111            00 0      0111234555555555443        256899999999999999


Q ss_pred             HHHHHHHhhcc
Q 012638          414 EIRSASECLRI  424 (459)
Q Consensus       414 ~Vk~~l~~ar~  424 (459)
                      +|+..+.+++.
T Consensus       173 tV~~~l~Ra~~  183 (194)
T PRK12519        173 TVKARARQGLL  183 (194)
T ss_pred             HHHHHHHHHHH
Confidence            99999888764

>PRK12536 RNA polymerase sigma factor; Provisional

Probab=99.64  E-value=3.4e-15  Score=138.39  Aligned_cols=140  Identities=15%  Similarity=0.067  Sum_probs=111.5

Q ss_pred             HHHHHHHHHhchH-HHHHHHHHhHHHHHHHHHHhhC-CCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHH
Q 012638          283 ERVLKQHLAFGWY-CREELIKSTRPLVLFLARNYRG-LGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSI  360 (459)
Q Consensus       283 eeeL~~~l~~G~~-Are~LI~~nlrLV~sIAkry~g-~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIrnaI  360 (459)
                      ...++..+..|+. |+++|+..|.+.|+.+|.++.+ ...+++|++||+++++|+.++.|++.  ..|.+|++.+++|.+
T Consensus         8 ~~~~~~~~~~~d~~a~~~l~~~~~~~l~~~~~~~~~~~~~~aeDlvQevfl~l~~~~~~~~~~--~~~~~wl~~iarN~~   85 (181)
T PRK12536          8 LRALLLRGLAGDAAAYRQFLSELAAHLRGFLRRRLPQLPDEVEDLVQEILLAVHNARHTYRAD--QPLTAWVHAIARYKL   85 (181)
T ss_pred             HHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHcCCChhhHHHHHHHHHHHHHHhHHhcCCC--CchHHHHHHHHHHHH
Confidence            4567788888877 9999999999999999988764 57899999999999999999999974  469999999999999


Q ss_pred             HHHHHhhccccccc--------------cchHHHHHHHHHHHHHHHHHc--------CCCCCHHHHHHHhCCCHHHHHHH
Q 012638          361 SKMVARHARGIKIP--------------CKLNREISKIQKARKALTNSH--------GKYPEDIEIAKYTGLSLAEIRSA  418 (459)
Q Consensus       361 ~d~Lrk~sr~irlP--------------~~v~e~i~kI~ka~~~L~~~l--------gr~PT~eEIAe~LGIS~e~Vk~~  418 (459)
                      ++++|++.+.....              ....+....+.++...|+...        -.+.+++|||+.||||+++|+..
T Consensus        86 ~d~~Rk~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~v~~l~~~~g~s~~EIA~~l~is~~tV~~~  165 (181)
T PRK12536         86 MDFLRSRARREALHDPLDDESELFATSDDEAAEARRDLGKLLEQLPDRQRLPIVHVKLEGLSVAETAQLTGLSESAVKVG  165 (181)
T ss_pred             HHHHHHHhccccccCCccchhhhcCCCCcchHHHHHHHHHHHHHCCHHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHH
Confidence            99999864422110              011223334566666554432        25689999999999999999999


Q ss_pred             HHhhcc
Q 012638          419 SECLRI  424 (459)
Q Consensus       419 l~~ar~  424 (459)
                      +++++.
T Consensus       166 l~rar~  171 (181)
T PRK12536        166 IHRGLK  171 (181)
T ss_pred             HHHHHH
Confidence            998875

>PRK12526 RNA polymerase sigma factor; Provisional

Probab=99.64  E-value=2.7e-15  Score=142.41  Aligned_cols=140  Identities=14%  Similarity=0.073  Sum_probs=110.7

Q ss_pred             HHHHHHHHhchH-HHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHH
Q 012638          284 RVLKQHLAFGWY-CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISK  362 (459)
Q Consensus       284 eeL~~~l~~G~~-Are~LI~~nlrLV~sIAkry~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIrnaI~d  362 (459)
                      ..|...+..|+. |+++|+..|.+.|+.++.++.++..+++|++||+|+++|+++.+|++.++ .|.||++++++|.+++
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            345666787877 99999999999999999999999999999999999999999999997665 6999999999999999


Q ss_pred             HHHhhcccccc-------cc-------c-h-HH-----HHHHHHHHHHHHHHHc--------CCCCCHHHHHHHhCCCHH
Q 012638          363 MVARHARGIKI-------PC-------K-L-NR-----EISKIQKARKALTNSH--------GKYPEDIEIAKYTGLSLA  413 (459)
Q Consensus       363 ~Lrk~sr~irl-------P~-------~-v-~e-----~i~kI~ka~~~L~~~l--------gr~PT~eEIAe~LGIS~e  413 (459)
                      ++|++.+....       |.       . . .+     ....+.++...|+.+.        ..+.|++|||+.||+|++
T Consensus       105 ~~Rk~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~vl~l~~~~g~s~~EIA~~lgis~~  184 (206)
T PRK12526        105 MLRKIKAKKEQNLGDDIWPIEQALAESQSESEEFSDHLMDKQILSYIEKLPEAQQTVVKGVYFQELSQEQLAQQLNVPLG  184 (206)
T ss_pred             HHHHhccccccccccccchhhhhcccccCchHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHHCCCHH
Confidence            99976532110       10       0 0 00     1123455555554432        367899999999999999


Q ss_pred             HHHHHHHhhcc
Q 012638          414 EIRSASECLRI  424 (459)
Q Consensus       414 ~Vk~~l~~ar~  424 (459)
                      +|+..+++++.
T Consensus       185 tV~~~l~Ra~~  195 (206)
T PRK12526        185 TVKSRLRLALA  195 (206)
T ss_pred             HHHHHHHHHHH
Confidence            99999998875

>PRK11922 RNA polymerase sigma factor; Provisional

Probab=99.64  E-value=4.1e-15  Score=143.69  Aligned_cols=142  Identities=16%  Similarity=0.130  Sum_probs=115.8

Q ss_pred             CCHHHHHHHHHhchH-HHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHH
Q 012638          281 VSERVLKQHLAFGWY-CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKS  359 (459)
Q Consensus       281 ~deeeL~~~l~~G~~-Are~LI~~nlrLV~sIAkry~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIrna  359 (459)
                      +++..|+..+..|+. |++.|+..|.+.|+.+|+++.+...+++|++||+|+++|+++++|++.  ..|.||++++++|.
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            456778888888977 999999999999999999999999999999999999999999999985  47999999999999


Q ss_pred             HHHHHHhhcccccccc------------------c--------hHHHHHHHHHHHHHHHHHcC--------CCCCHHHHH
Q 012638          360 ISKMVARHARGIKIPC------------------K--------LNREISKIQKARKALTNSHG--------KYPEDIEIA  405 (459)
Q Consensus       360 I~d~Lrk~sr~irlP~------------------~--------v~e~i~kI~ka~~~L~~~lg--------r~PT~eEIA  405 (459)
                      +++++|+..+...++.                  +        ..+....+.+++..|+....        .+.+++|||
T Consensus        93 ~~d~~Rk~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~e~~~~l~~~l~~L~~~~r~i~~l~~~~g~s~~EIA  172 (231)
T PRK11922         93 ALGRLRRRRRLVNLAEMVMASTIAGGERTPLADPAEDPERAAARREIRALLERAIDALPDAFRAVFVLRVVEELSVEETA  172 (231)
T ss_pred             HHHHHHhhcccccchhcccccccccccccccCcccCChHHHHHHHHHHHHHHHHHHhCCHHHhhhheeehhcCCCHHHHH
Confidence            9999997654322210                  0        01122345666666655432        568999999


Q ss_pred             HHhCCCHHHHHHHHHhhcc
Q 012638          406 KYTGLSLAEIRSASECLRI  424 (459)
Q Consensus       406 e~LGIS~e~Vk~~l~~ar~  424 (459)
                      +.||+|.++|+..+++++.
T Consensus       173 e~lgis~~tVk~~l~Rar~  191 (231)
T PRK11922        173 QALGLPEETVKTRLHRARR  191 (231)
T ss_pred             HHHCcCHHHHHHHHHHHHH
Confidence            9999999999999988864

>PRK11923 algU RNA polymerase sigma factor AlgU; Provisional

Probab=99.64  E-value=4.3e-15  Score=138.52  Aligned_cols=141  Identities=12%  Similarity=0.063  Sum_probs=111.8

Q ss_pred             CHHHHHHHHHhchH-HHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHH
Q 012638          282 SERVLKQHLAFGWY-CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSI  360 (459)
Q Consensus       282 deeeL~~~l~~G~~-Are~LI~~nlrLV~sIAkry~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIrnaI  360 (459)
                      +++.|+..++.|+. |++.|+..|.+.|+.+++++.++..+++|++||+++++|+++.+|++..  .|.+|++.+++|.+
T Consensus         6 ~~~~ll~~~~~gd~~a~~~l~~~y~~~l~~~~~~~~~~~~daeDlvQe~~i~l~~~~~~~~~~~--~~~~wl~~ia~n~~   83 (193)
T PRK11923          6 EDQQLVERVQRGDKRAFDLLVLKYQHKILGLIVRFVHDTAEAQDVAQEAFIKAYRALGNFRGDS--AFYTWLYRIAINTA   83 (193)
T ss_pred             cHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHhCCHhhHHHHHHHHHHHHHHhHhCcCCCC--ccHhHHHHHHHHHH
Confidence            35677888899977 9999999999999999999999999999999999999999999999864  59999999999999


Q ss_pred             HHHHHhhccccc---ccc-------------c---------hHHHHHHHHHHHHHHHHHc--------CCCCCHHHHHHH
Q 012638          361 SKMVARHARGIK---IPC-------------K---------LNREISKIQKARKALTNSH--------GKYPEDIEIAKY  407 (459)
Q Consensus       361 ~d~Lrk~sr~ir---lP~-------------~---------v~e~i~kI~ka~~~L~~~l--------gr~PT~eEIAe~  407 (459)
                      +++++++.+...   .+.             .         ..+....+.++...|+...        -.+.+++|||+.
T Consensus        84 ~d~~rk~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~l~~~l~~L~~~~r~v~~l~~~~g~s~~eIA~~  163 (193)
T PRK11923         84 KNHLVSRGRRPPDSDVSSEDAEFYDGDHALKDIESPERALLRDEIEGTVHRTIQQLPEDLRTALTLREFDGLSYEDIASV  163 (193)
T ss_pred             HHHHHHhcCCCccccccccchhhhcccccccCcCCHHHHHHHHHHHHHHHHHHHhCCHHHhHHHhhHHhcCCCHHHHHHH
Confidence            999987544321   000             0         0011123444555444432        256799999999


Q ss_pred             hCCCHHHHHHHHHhhcc
Q 012638          408 TGLSLAEIRSASECLRI  424 (459)
Q Consensus       408 LGIS~e~Vk~~l~~ar~  424 (459)
                      ||+|+.+|+..+.+++.
T Consensus       164 lgis~~tv~~~l~Rar~  180 (193)
T PRK11923        164 MQCPVGTVRSRIFRARE  180 (193)
T ss_pred             HCCCHHHHHHHHHHHHH
Confidence            99999999999988875

>PRK09652 RNA polymerase sigma factor RpoE; Provisional

Probab=99.64  E-value=2e-15  Score=137.43  Aligned_cols=134  Identities=17%  Similarity=0.118  Sum_probs=106.1

Q ss_pred             HHHhchH-HHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhh
Q 012638          289 HLAFGWY-CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARH  367 (459)
Q Consensus       289 ~l~~G~~-Are~LI~~nlrLV~sIAkry~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIrnaI~d~Lrk~  367 (459)
                      +++.|+. |+++|+..|.++|+.++++|.+++.+.+|++||++++||+++++|+  .+.+|.||++.++++.+.+++++.
T Consensus         3 ~~~~gd~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeDl~Qe~~l~l~~~~~~~~--~~~~~~~~l~~~~~~~~~~~~r~~   80 (182)
T PRK09652          3 RVQRGDRAAFALLVRRYQPRVKRLLSRLTRDPADAEDLVQETFIKAYRALHSFR--GGAAFYTWLYRIARNTAINYLRKQ   80 (182)
T ss_pred             hhhcCCHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHhcC--CCcchHHHHHHHHHHHHHHHHHcc
Confidence            4677876 9999999999999999999999999999999999999999999999  345899999999999999999976


Q ss_pred             ccccccc-------c---------c---h------HHHHHHHHHHHHHHHHHc--------CCCCCHHHHHHHhCCCHHH
Q 012638          368 ARGIKIP-------C---------K---L------NREISKIQKARKALTNSH--------GKYPEDIEIAKYTGLSLAE  414 (459)
Q Consensus       368 sr~irlP-------~---------~---v------~e~i~kI~ka~~~L~~~l--------gr~PT~eEIAe~LGIS~e~  414 (459)
                      .+....+       .         .   .      .+....+..+...|+...        ..+.+++|||+.||||+.+
T Consensus        81 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~vl~l~~~~~~s~~eIA~~lgis~~t  160 (182)
T PRK09652         81 GRRPPASDVDAEEAEDFDLADALRDISTPENELLSAELEQRVRAAIESLPEELRTAITLREIEGLSYEEIAEIMGCPIGT  160 (182)
T ss_pred             cCCCCccccccccccccccccccccccChHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHHCCCHHH
Confidence            5433211       0         0   0      012233444444443332        3678999999999999999


Q ss_pred             HHHHHHhhcc
Q 012638          415 IRSASECLRI  424 (459)
Q Consensus       415 Vk~~l~~ar~  424 (459)
                      |+..+.+++.
T Consensus       161 V~~~l~ra~~  170 (182)
T PRK09652        161 VRSRIFRARE  170 (182)
T ss_pred             HHHHHHHHHH
Confidence            9999887764

>PRK12539 RNA polymerase sigma factor; Provisional

Probab=99.64  E-value=4.3e-15  Score=138.08  Aligned_cols=140  Identities=11%  Similarity=0.051  Sum_probs=112.3

Q ss_pred             HHHHHHHHHhchH-HHHHHHHHhHHHHHHHHH----HhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHH
Q 012638          283 ERVLKQHLAFGWY-CREELIKSTRPLVLFLAR----NYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIR  357 (459)
Q Consensus       283 eeeL~~~l~~G~~-Are~LI~~nlrLV~sIAk----ry~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIr  357 (459)
                      ...|+..+..|+. |+++|+..|.+.|+.+|+    ++.++..+++|++||+++.+|++++.|++..  .|.+|++.+++
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            5677888889976 999999999999999987    4557889999999999999999999999753  69999999999


Q ss_pred             HHHHHHHHhhccc-cccc---------c---chHHHHHHHHHHHHHHHHHc--------CCCCCHHHHHHHhCCCHHHHH
Q 012638          358 KSISKMVARHARG-IKIP---------C---KLNREISKIQKARKALTNSH--------GKYPEDIEIAKYTGLSLAEIR  416 (459)
Q Consensus       358 naI~d~Lrk~sr~-irlP---------~---~v~e~i~kI~ka~~~L~~~l--------gr~PT~eEIAe~LGIS~e~Vk  416 (459)
                      |.+++++|+..+. ...+         .   ...+....+..+...|+...        -.+.+++|||+.||||+++|+
T Consensus        86 n~~~d~~R~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~l~~~l~~L~~~~r~v~~l~~~~g~s~~eIA~~lgis~~tV~  165 (184)
T PRK12539         86 YKLIDHLRRTRASLADVPIDDADELVAHDDHAAVESTLDLGRLLARLPEKMRLAIQAVKLEGLSVAEAATRSGMSESAVK  165 (184)
T ss_pred             HHHHHHHHHHhccccccChhhhccccCCcHHhhHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCcHHHHHHHHCcCHHHHH
Confidence            9999999986542 1111         0   01223345666666665543        257899999999999999999


Q ss_pred             HHHHhhcc
Q 012638          417 SASECLRI  424 (459)
Q Consensus       417 ~~l~~ar~  424 (459)
                      ..+.+++.
T Consensus       166 ~~l~ra~~  173 (184)
T PRK12539        166 VSVHRGLK  173 (184)
T ss_pred             HHHHHHHH
Confidence            99998875

>PRK12542 RNA polymerase sigma factor; Provisional

Probab=99.63  E-value=1.7e-15  Score=140.74  Aligned_cols=134  Identities=16%  Similarity=0.108  Sum_probs=107.2

Q ss_pred             HhchH-HHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhhcc
Q 012638          291 AFGWY-CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHAR  369 (459)
Q Consensus       291 ~~G~~-Are~LI~~nlrLV~sIAkry~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIrnaI~d~Lrk~sr  369 (459)
                      ..|+. |+++|+..|.+.|+.+|.+++++..+++|++||+|+.+|+++++|+...+..|.||++.+++|.+++++|++.+
T Consensus         4 ~~gd~~a~~~l~~~y~~~l~~~~~~~~~~~~~AeDlvQe~fl~~~~~~~~~~~~~~~~~~~wL~~Iarn~~~d~~Rk~~~   83 (185)
T PRK12542          4 TNNDYEKMEELYELYEQKVYYVAYSILNNIQQAEDAVQETFITLYKNLEKLHSLNTQELKRYILRVAKNKAIDSYRKNKR   83 (185)
T ss_pred             cccCHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHhcccccHHHHHHHHHHHHHHHHHHHHHHhhh
Confidence            45665 99999999999999999999999999999999999999999999986544579999999999999999998754


Q ss_pred             ccccc------------cch------HHHHHHHHHHHHHHHHHc--------CCCCCHHHHHHHhCCCHHHHHHHHHhhc
Q 012638          370 GIKIP------------CKL------NREISKIQKARKALTNSH--------GKYPEDIEIAKYTGLSLAEIRSASECLR  423 (459)
Q Consensus       370 ~irlP------------~~v------~e~i~kI~ka~~~L~~~l--------gr~PT~eEIAe~LGIS~e~Vk~~l~~ar  423 (459)
                      .....            ...      .+....|.++...|+...        -.+.+++|||+.||+|+++|+..+.+++
T Consensus        84 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~i~~l~~~~g~s~~EIA~~lgis~~tVk~~l~Rar  163 (185)
T PRK12542         84 HETFLEEYERESIEAVDENIEEWEKRKMSEVQIDTLLKELNESNRQVFKYKVFYNLTYQEISSVMGITEANVRKQFERAR  163 (185)
T ss_pred             hhhhhhhccccchhhhhccHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence            32210            000      011233555555555443        3568999999999999999999999887


Q ss_pred             c
Q 012638          424 I  424 (459)
Q Consensus       424 ~  424 (459)
                      .
T Consensus       164 ~  164 (185)
T PRK12542        164 K  164 (185)
T ss_pred             H
Confidence            6

>PRK12515 RNA polymerase sigma factor; Provisional

Probab=99.63  E-value=5.1e-15  Score=137.93  Aligned_cols=143  Identities=13%  Similarity=0.076  Sum_probs=115.0

Q ss_pred             CCCHHHHHHHHHhchH-HHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHH
Q 012638          280 GVSERVLKQHLAFGWY-CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRK  358 (459)
Q Consensus       280 g~deeeL~~~l~~G~~-Are~LI~~nlrLV~sIAkry~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIrn  358 (459)
                      .+++..|+..+..|+. |++.|+..|.+.|+.++.++.++..+++|++||+|+.+|++.++|++.  ..|.||++.+++|
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            4577889999999987 999999999999999999999999999999999999999999999974  4799999999999


Q ss_pred             HHHHHHHhhcccccc-------cc---ch------HHHHHHHHHHHHHHHHHc--------CCCCCHHHHHHHhCCCHHH
Q 012638          359 SISKMVARHARGIKI-------PC---KL------NREISKIQKARKALTNSH--------GKYPEDIEIAKYTGLSLAE  414 (459)
Q Consensus       359 aI~d~Lrk~sr~irl-------P~---~v------~e~i~kI~ka~~~L~~~l--------gr~PT~eEIAe~LGIS~e~  414 (459)
                      .+++++++..+....       +.   ..      .+....+.++...|+...        -.+.+++|||+.||+|+++
T Consensus        84 ~~~d~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~vl~l~~~~~~s~~eIA~~lgis~~t  163 (189)
T PRK12515         84 KALSALRRRKHEEIDDEAAAAIEDGADTPEVALQKSDTSAALRACLAKLSPAHREIIDLVYYHEKSVEEVGEIVGIPEST  163 (189)
T ss_pred             HHHHHHHccCCCCCccccccccCCCCCCHHHHHHhHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHHCcCHHH
Confidence            999999976432111       00   00      011223445555444432        3678999999999999999


Q ss_pred             HHHHHHhhcc
Q 012638          415 IRSASECLRI  424 (459)
Q Consensus       415 Vk~~l~~ar~  424 (459)
                      |+..+.+++.
T Consensus       164 V~~~l~Rar~  173 (189)
T PRK12515        164 VKTRMFYARK  173 (189)
T ss_pred             HHHHHHHHHH
Confidence            9999998875

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

Probab=99.62  E-value=5.8e-15  Score=136.14  Aligned_cols=140  Identities=16%  Similarity=0.145  Sum_probs=108.9

Q ss_pred             HHHHHHHHHhchH-HHHHHHHHhHHHHHHHHHHhhCCCC-----CHHHHHHHHHHHHHH-hhhhcCCCCCCchhhHHHHH
Q 012638          283 ERVLKQHLAFGWY-CREELIKSTRPLVLFLARNYRGLGI-----PFSDLLQAGNVGVLQ-GAERFDHTRGYKFSTYVQYW  355 (459)
Q Consensus       283 eeeL~~~l~~G~~-Are~LI~~nlrLV~sIAkry~g~g~-----d~EDLIQEG~IGLir-AieKFDp~kG~rFSTYa~~w  355 (459)
                      ...|+..+..|+. |+++|+..|.+.|+.+|++|.++..     +++|++||+|+.+|+ ...+|++.  ..|.||++.+
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            4567888899987 9999999999999999999999877     899999999999998 78889764  3699999999


Q ss_pred             HHHHHHHHHHhhccccc------c------cc---chHHHHHHHHHHHHH---HHHHc--------CCCCCHHHHHHHhC
Q 012638          356 IRKSISKMVARHARGIK------I------PC---KLNREISKIQKARKA---LTNSH--------GKYPEDIEIAKYTG  409 (459)
Q Consensus       356 IrnaI~d~Lrk~sr~ir------l------P~---~v~e~i~kI~ka~~~---L~~~l--------gr~PT~eEIAe~LG  409 (459)
                      ++|.+++++|++.+..+      .      |.   ...+....+..+...   |+...        ..+.|++|||+.||
T Consensus        82 ~~n~~~d~~R~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~l~~Lp~~~r~v~~l~~~~g~s~~EIA~~lg  161 (183)
T TIGR02999        82 MRRILVDHARRRRAQKRGGGAVRVPLDEVLPDAEADLDEELLDLDDALDKLAQVDPRQAEVVELRFFAGLTVEEIAELLG  161 (183)
T ss_pred             HHHHHHHHHHHHHHHhccCCccccccccccCCCCccHHHHHHHHHHHHHHhhcCCHHHHHHHHHHHHcCCCHHHHHHHhC
Confidence            99999999987543211      0      11   111222223333333   44332        36789999999999


Q ss_pred             CCHHHHHHHHHhhcc
Q 012638          410 LSLAEIRSASECLRI  424 (459)
Q Consensus       410 IS~e~Vk~~l~~ar~  424 (459)
                      ||+++|+..+++++.
T Consensus       162 is~~tVk~~l~Rar~  176 (183)
T TIGR02999       162 VSVRTVERDWRFARA  176 (183)
T ss_pred             CCHHHHHHHHHHHHH
Confidence            999999999998875

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.

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

Probab=99.62  E-value=9.8e-15  Score=135.62  Aligned_cols=135  Identities=20%  Similarity=0.188  Sum_probs=110.9

Q ss_pred             HHHHhch-HHHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHh
Q 012638          288 QHLAFGW-YCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVAR  366 (459)
Q Consensus       288 ~~l~~G~-~Are~LI~~nlrLV~sIAkry~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIrnaI~d~Lrk  366 (459)
                      .....|+ .+++.++..|.+.++.+|++++++..+++||+||+|+.+|+++..| .. +..|.||++.+++|.++|++|+
T Consensus         7 ~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~dAeDlvQE~~lr~~~~~~~~-~~-~~~~~~wl~~Ia~n~~iD~~R~   84 (182)
T COG1595           7 AEALRGDRAAFEELLERLRPRLRRLARRLLGDRADAEDLVQETFLRAWRAIDSF-RG-RSSFKAWLYRIARNLAIDRLRK   84 (182)
T ss_pred             HHHHhcchHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHhhc-CC-CCchHHHHHHHHHHHHHHHHHH
Confidence            3344454 4999999999999999999999998899999999999999999999 33 3479999999999999999997


Q ss_pred             hcccccc-c-------------cch-----HHHHHHHHHHHHHHHHHcC--------CCCCHHHHHHHhCCCHHHHHHHH
Q 012638          367 HARGIKI-P-------------CKL-----NREISKIQKARKALTNSHG--------KYPEDIEIAKYTGLSLAEIRSAS  419 (459)
Q Consensus       367 ~sr~irl-P-------------~~v-----~e~i~kI~ka~~~L~~~lg--------r~PT~eEIAe~LGIS~e~Vk~~l  419 (459)
                      ..+.... +             ...     .+....+.++...|+....        .+.|++|||+.||||+++|+..+
T Consensus        85 ~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~al~~Lp~~~R~~~~l~~~~gls~~EIA~~l~i~~~tVks~l  164 (182)
T COG1595          85 RKRRRARVEEADLLPEEADPAPDLAELLLAEEELERLRRALARLPPRQREAFLLRYLEGLSYEEIAEILGISVGTVKSRL  164 (182)
T ss_pred             hcccccccccccccccccCcccccchHHHHHHHHHHHHHHHHhCCHHHhHHhhhHhhcCCCHHHHHHHHCCCHHHHHHHH
Confidence            7654321 0             111     2444567788887777653        67899999999999999999999


Q ss_pred             Hhhcc
Q 012638          420 ECLRI  424 (459)
Q Consensus       420 ~~ar~  424 (459)
                      ++++.
T Consensus       165 ~ra~~  169 (182)
T COG1595         165 HRARK  169 (182)
T ss_pred             HHHHH
Confidence            98875

>PRK09649 RNA polymerase sigma factor SigC; Reviewed

Probab=99.61  E-value=7.4e-15  Score=137.11  Aligned_cols=141  Identities=18%  Similarity=0.090  Sum_probs=113.1

Q ss_pred             HHHHHHHHHhchH-HHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHH
Q 012638          283 ERVLKQHLAFGWY-CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSIS  361 (459)
Q Consensus       283 eeeL~~~l~~G~~-Are~LI~~nlrLV~sIAkry~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIrnaI~  361 (459)
                      ...|+.++..|+. |+++|+..|.+.|+.++. +.++..+++|++||+|+.+|+..++|++.  ..|.+|++.+++|.++
T Consensus        11 ~~~l~~~~~~gd~~af~~l~~~~~~~l~~~~~-~~~~~~~AeDivQe~flkl~~~~~~~~~~--~~~~~Wl~~Iarn~~~   87 (185)
T PRK09649         11 VTALALSAAKGNGRALEAFIKATQQDVWRFVA-YLSDVGSADDLTQETFLRAIGAIPRFSAR--SSARTWLLAIARHVVA   87 (185)
T ss_pred             HHHHHHHHHccCHHHHHHHHHHHHHHHHHHHH-HhCCHHHHHHHHHHHHHHHHHhccccCcc--chHHHHHHHHHHHHHH
Confidence            3567888889987 999999999999999995 67888999999999999999999999964  3799999999999999


Q ss_pred             HHHHhhcccccc-----ccc---------hHHHHHHHHHHHHHHHHHcC--------CCCCHHHHHHHhCCCHHHHHHHH
Q 012638          362 KMVARHARGIKI-----PCK---------LNREISKIQKARKALTNSHG--------KYPEDIEIAKYTGLSLAEIRSAS  419 (459)
Q Consensus       362 d~Lrk~sr~irl-----P~~---------v~e~i~kI~ka~~~L~~~lg--------r~PT~eEIAe~LGIS~e~Vk~~l  419 (459)
                      +++|++.+....     +..         ..+....+.++...|+....        .+.|++|||+.||+|+++|+..+
T Consensus        88 d~~Rk~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~l~~~l~~Lp~~~r~v~~L~~~~g~s~~EIA~~lgis~~tVk~~l  167 (185)
T PRK09649         88 DHIRHVRSRPRTTRGARPEHLIDGDRHARGFEDLVEVTTMIADLTTDQREALLLTQLLGLSYADAAAVCGCPVGTIRSRV  167 (185)
T ss_pred             HHHHHhccccccccccchhhccChhhhhhhHHHHHHHHHHHHhCCHHHhHHhhhHHHcCCCHHHHHHHHCCCHHHHHHHH
Confidence            999975432211     110         01223446666666655542        66899999999999999999999


Q ss_pred             HhhccCC
Q 012638          420 ECLRIVG  426 (459)
Q Consensus       420 ~~ar~~~  426 (459)
                      .+++..+
T Consensus       168 ~Rar~~L  174 (185)
T PRK09649        168 ARARDAL  174 (185)
T ss_pred             HHHHHHH
Confidence            9988643

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

Probab=99.61  E-value=9.1e-15  Score=143.46  Aligned_cols=144  Identities=12%  Similarity=-0.020  Sum_probs=115.9

Q ss_pred             cCCCHHHHHHHHHhchH-HHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHH-------hhhhcCCCCCCchhh
Q 012638          279 AGVSERVLKQHLAFGWY-CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQ-------GAERFDHTRGYKFST  350 (459)
Q Consensus       279 ~g~deeeL~~~l~~G~~-Are~LI~~nlrLV~sIAkry~g~g~d~EDLIQEG~IGLir-------AieKFDp~kG~rFST  350 (459)
                      ++.++..|+..++.|+. |++.|+..|.+.|+.++.++.++..+++|++||+|+.+|.       .+.+|++.  ..|.|
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            45567889999999987 9999999999999999999999999999999999999994       78889864  37999


Q ss_pred             HHHHHHHHHHHHHHHhhcccccccc---------c---hH----------HHHHHHHHHHHHHHHHc--------CCCCC
Q 012638          351 YVQYWIRKSISKMVARHARGIKIPC---------K---LN----------REISKIQKARKALTNSH--------GKYPE  400 (459)
Q Consensus       351 Ya~~wIrnaI~d~Lrk~sr~irlP~---------~---v~----------e~i~kI~ka~~~L~~~l--------gr~PT  400 (459)
                      |++.+++|.+++++|++.+...+..         .   ..          +....|.+++.+|+...        -.+.|
T Consensus       100 WL~~Ia~N~~id~lRk~~r~~~~~~~~~~~~~~~~~~~~e~~~~~~e~~~e~~~~l~~aL~~Lp~~~R~v~~L~~~eg~S  179 (244)
T TIGR03001       100 WVRIVATRIALELQAQERRHSPVEEPTELAALPAPGSDPELDLLRERYRQDFRQALREALAALSERERHLLRLHFVDGLS  179 (244)
T ss_pred             HHHHHHHHHHHHHHHHhcccCccccccccccccCCCCCHHHHHHHHhhHHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCC
Confidence            9999999999999997654222110         0   00          12234666666666543        26789


Q ss_pred             HHHHHHHhCCCHHHHHHHHHhhcc
Q 012638          401 DIEIAKYTGLSLAEIRSASECLRI  424 (459)
Q Consensus       401 ~eEIAe~LGIS~e~Vk~~l~~ar~  424 (459)
                      ++|||+.||||+++|+..+.+++.
T Consensus       180 ~~EIA~~Lgis~~TVk~rl~RAr~  203 (244)
T TIGR03001       180 MDRIGAMYQVHRSTVSRWVAQARE  203 (244)
T ss_pred             HHHHHHHHCcCHHHHHHHHHHHHH
Confidence            999999999999999999888764

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.

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

Probab=99.60  E-value=8.9e-15  Score=131.55  Aligned_cols=128  Identities=14%  Similarity=0.130  Sum_probs=103.1

Q ss_pred             HHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhhcccccccc
Q 012638          296 CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIPC  375 (459)
Q Consensus       296 Are~LI~~nlrLV~sIAkry~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIrnaI~d~Lrk~sr~irlP~  375 (459)
                      |++.++..|.+.|+.+|+++.++..++||++||+++.+|+++++|++..  .|.||++.+++|.++++++++.+......
T Consensus         2 ~~~~~~~~~~~~l~~~~~~~~~~~~~aEDivQe~~l~l~~~~~~~~~~~--~~~~wl~~i~~n~~~d~~r~~~~~~~~~~   79 (159)
T TIGR02989         2 AFAALLQRHQRSLRAFVRSLVPDRDDADDVLQETFVTAWRKFDEFDPGT--DFGAWARGIARNKVLNHRRKLGRDRLVFD   79 (159)
T ss_pred             HHHHHHHHhHHHHHHHHHHHcCChhhHHHHHHHHHHHHHHHHHhCCCCC--chHHHHHHHHHHHHHHHHHHhcccccccC
Confidence            7899999999999999999999999999999999999999999999753  69999999999999999998755322100


Q ss_pred             c-----------------hHHHHHHHHHHHHHHHHHc--------CCCCCHHHHHHHhCCCHHHHHHHHHhhccC
Q 012638          376 K-----------------LNREISKIQKARKALTNSH--------GKYPEDIEIAKYTGLSLAEIRSASECLRIV  425 (459)
Q Consensus       376 ~-----------------v~e~i~kI~ka~~~L~~~l--------gr~PT~eEIAe~LGIS~e~Vk~~l~~ar~~  425 (459)
                      .                 ..+....+.+++..|+...        -.+.+++|||+.||||+++|+..+++++..
T Consensus        80 ~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~L~~~~r~v~~l~~~~g~~~~eIA~~l~is~~tv~~~l~Rar~~  154 (159)
T TIGR02989        80 DELLEALAAEAEATEADRSEDELQALEGCLEKLPERQRELLQLRYQRGVSLTALAEQLGRTVNAVYKALSRLRVR  154 (159)
T ss_pred             HHHHHHHHhhcccchHhhHHHHHHHHHHHHHHCCHHHHHHHHHHHhcCCCHHHHHHHhCCCHHHHHHHHHHHHHH
Confidence            0                 0111223455555554432        367899999999999999999999988753

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).

>PRK12512 RNA polymerase sigma factor; Provisional

Probab=99.60  E-value=2.4e-14  Score=132.52  Aligned_cols=138  Identities=15%  Similarity=0.090  Sum_probs=109.7

Q ss_pred             HHHHHHHhchH-HHHHHHHHhHHHHHHHHHHhhCC----CCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHH
Q 012638          285 VLKQHLAFGWY-CREELIKSTRPLVLFLARNYRGL----GIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKS  359 (459)
Q Consensus       285 eL~~~l~~G~~-Are~LI~~nlrLV~sIAkry~g~----g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIrna  359 (459)
                      .|+..+..|+. |+++|+..|.+.|+.+|.+++++    ..+++|++||+++.+|...++|+..  ..|.+|++.+++|.
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            46677788876 99999999999999999998762    4689999999999999999999873  47999999999999


Q ss_pred             HHHHHHhhccccccc---------cc---hHHHHHHHHHHHHHHHHHc--------CCCCCHHHHHHHhCCCHHHHHHHH
Q 012638          360 ISKMVARHARGIKIP---------CK---LNREISKIQKARKALTNSH--------GKYPEDIEIAKYTGLSLAEIRSAS  419 (459)
Q Consensus       360 I~d~Lrk~sr~irlP---------~~---v~e~i~kI~ka~~~L~~~l--------gr~PT~eEIAe~LGIS~e~Vk~~l  419 (459)
                      +.+++|++.+....+         ..   .......+.++...|+...        -.+.+++|||+.||+|+.+|+..+
T Consensus        89 ~~d~~Rr~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~v~~l~~~~g~s~~eIA~~l~is~~tV~~~l  168 (184)
T PRK12512         89 LIDALRRRGRRVFVDIDDFAETLPAEPATETLPAGDVGRHLETLPPRQRDVVQSISVEGASIKETAAKLSMSEGAVRVAL  168 (184)
T ss_pred             HHHHHHhhcccccCCchhccccccccchhhHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHH
Confidence            999999876532221         10   1122344555666555543        257899999999999999999999


Q ss_pred             Hhhcc
Q 012638          420 ECLRI  424 (459)
Q Consensus       420 ~~ar~  424 (459)
                      .+++.
T Consensus       169 ~ra~~  173 (184)
T PRK12512        169 HRGLA  173 (184)
T ss_pred             HHHHH
Confidence            98875

>PRK11924 RNA polymerase sigma factor; Provisional

Probab=99.58  E-value=3.8e-14  Score=128.70  Aligned_cols=137  Identities=20%  Similarity=0.167  Sum_probs=108.6

Q ss_pred             HHHHHHhchH-HHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHH
Q 012638          286 LKQHLAFGWY-CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMV  364 (459)
Q Consensus       286 L~~~l~~G~~-Are~LI~~nlrLV~sIAkry~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIrnaI~d~L  364 (459)
                      |...+..|+. |++.++..|.+.|+++|+++.++..+++|++||++++||.++++|+  .+.+|.+|++.++++.+++++
T Consensus         3 ~~~~~~~~~~~a~~~l~~~y~~~l~~~~~~~~~~~~~aeDl~qe~~~~l~~~~~~~~--~~~~~~~~l~~i~~~~~~d~~   80 (179)
T PRK11924          3 LMPVDATGDKEAFSELFRPHAPDLLRYARRQLGDRALAEDAVQEAFLRAWRKADLFN--GKGSARTWLLTIARNVCYDLL   80 (179)
T ss_pred             HHHHHHccCHHHHHHHHHHHHHHHHHHHHHHhCCHhhHHHHHHHHHHHHHHHHhhcC--CcchHHHHHHHHHHHHHHHHH
Confidence            5667788876 9999999999999999999999999999999999999999999998  345899999999999999999


Q ss_pred             Hhhcccccccc-------------c------hHHHHHHHHHHHHHHHHHc--------CCCCCHHHHHHHhCCCHHHHHH
Q 012638          365 ARHARGIKIPC-------------K------LNREISKIQKARKALTNSH--------GKYPEDIEIAKYTGLSLAEIRS  417 (459)
Q Consensus       365 rk~sr~irlP~-------------~------v~e~i~kI~ka~~~L~~~l--------gr~PT~eEIAe~LGIS~e~Vk~  417 (459)
                      ++..+......             .      ..+....+.++...|+...        ..+.+++|||+.||||..+|+.
T Consensus        81 r~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~e~~~~l~~~l~~L~~~~r~i~~l~~~~~~~~~eIA~~lgis~~tv~~  160 (179)
T PRK11924         81 RRRRREKAVLSDDALEPEFAETAETPEAALLAKDDLARIDRCLDALPVKQREVFLLRYVEGLSYREIAEILGVPVGTVKS  160 (179)
T ss_pred             HhcccccccCcccccccccCCccCCHHHHHhhHHHHHHHHHHHHhCCHHHHHHhhHHHHcCCCHHHHHHHHCCCHHHHHH
Confidence            97654332110             0      0112233444444443332        3578999999999999999999


Q ss_pred             HHHhhcc
Q 012638          418 ASECLRI  424 (459)
Q Consensus       418 ~l~~ar~  424 (459)
                      .+.+++.
T Consensus       161 ~~~ra~~  167 (179)
T PRK11924        161 RLRRARQ  167 (179)
T ss_pred             HHHHHHH
Confidence            9888764

>PRK12522 RNA polymerase sigma factor; Provisional

Probab=99.58  E-value=2.6e-14  Score=131.22  Aligned_cols=127  Identities=10%  Similarity=0.101  Sum_probs=102.9

Q ss_pred             HHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhhccccccc-
Q 012638          296 CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIP-  374 (459)
Q Consensus       296 Are~LI~~nlrLV~sIAkry~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIrnaI~d~Lrk~sr~irlP-  374 (459)
                      .+++|+..|.++|+.+|++|.++..+++|++||+++.+|+++++|++..  +|.+|++.+++|.+++++|++.+....+ 
T Consensus         4 ~~~~l~~~y~~~i~~~~~~~~~~~~daeDvvQe~~i~l~~~~~~~~~~~--~~~~wl~~i~~n~~~d~~Rk~~~~~~~~~   81 (173)
T PRK12522          4 KVEELIDIYKQQIYSLCYKLAKTKEDAEDIFQETWIKVFSSRHQLSYVE--NYKKWITTICVRTFYDFYRKKKRWKDRIL   81 (173)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHcCCcc--chHHHHHHHHHHHHHHHHHHhcccccccc
Confidence            6899999999999999999999999999999999999999999999753  7999999999999999999765432110 


Q ss_pred             --------------c--ch------HHHHHHHHHHHHHHHHHc--------CCCCCHHHHHHHhCCCHHHHHHHHHhhcc
Q 012638          375 --------------C--KL------NREISKIQKARKALTNSH--------GKYPEDIEIAKYTGLSLAEIRSASECLRI  424 (459)
Q Consensus       375 --------------~--~v------~e~i~kI~ka~~~L~~~l--------gr~PT~eEIAe~LGIS~e~Vk~~l~~ar~  424 (459)
                                    .  ..      .+....+.++...|+...        -.+.+++|||+.||||+++|+..+.+++.
T Consensus        82 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~i~~l~~~~~~s~~EIA~~lgis~~tV~~~l~Ra~~  161 (173)
T PRK12522         82 DLFHKEDGGEIEFADDVNISEEFIQKVEAEMIREVIQLLNEKYKTVLVLYYYEQYSYKEMSEILNIPIGTVKYRLNYAKK  161 (173)
T ss_pred             cccchhhhhhhccccCCCChHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence                          0  00      112234555555555533        36789999999999999999999998875

>PRK12520 RNA polymerase sigma factor; Provisional

Probab=99.57  E-value=1.8e-14  Score=134.41  Aligned_cols=127  Identities=17%  Similarity=0.128  Sum_probs=103.2

Q ss_pred             HHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhhcccccccc
Q 012638          296 CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIPC  375 (459)
Q Consensus       296 Are~LI~~nlrLV~sIAkry~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIrnaI~d~Lrk~sr~irlP~  375 (459)
                      +|+.|+..|.+.|+.+|.+++++..+++|++||.|+.+|+.+++|++.  .+|.||++.+++|.+++++|++.+....+.
T Consensus         3 ~~~~l~~~~~~~l~~~a~~~~~~~~~AeDivQevfl~~~~~~~~~~~~--~~~~~WL~~ia~n~~~d~~Rk~~r~~~~~~   80 (191)
T PRK12520          3 IAPAQLEALRPHLLRFARLQLRDPALAEDAVSETLLAVLEHPERFAGQ--SSLKTYLVGILKHKIIDAIRSGRREVRLSL   80 (191)
T ss_pred             chHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhhhhhccc--ccHHHHHHHHHHHHHHHHHHhhcCcCcccc
Confidence            689999999999999999999999999999999999999999999864  369999999999999999998754322111


Q ss_pred             ------------------------------ch------HHHHHHHHHHHHHHHHHc--------CCCCCHHHHHHHhCCC
Q 012638          376 ------------------------------KL------NREISKIQKARKALTNSH--------GKYPEDIEIAKYTGLS  411 (459)
Q Consensus       376 ------------------------------~v------~e~i~kI~ka~~~L~~~l--------gr~PT~eEIAe~LGIS  411 (459)
                                                    ..      .+....|..++..|+...        -.+.|++|||+.||||
T Consensus        81 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~Lp~~~r~v~~l~~~~g~s~~EIA~~lgis  160 (191)
T PRK12520         81 DDADEQSDDDLFDALFAADGHYREPPSDWGDPDAALSRREFFEVLQACVDRLPPRTGRVFMMREWLELETEEICQELQIT  160 (191)
T ss_pred             cccccchhhhhhhhhcccccccccCccccCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHHCCC
Confidence                                          00      011233556666665543        2568999999999999


Q ss_pred             HHHHHHHHHhhcc
Q 012638          412 LAEIRSASECLRI  424 (459)
Q Consensus       412 ~e~Vk~~l~~ar~  424 (459)
                      +++|+..+.+++.
T Consensus       161 ~~tV~~~l~Rar~  173 (191)
T PRK12520        161 ATNAWVLLYRARM  173 (191)
T ss_pred             HHHHHHHHHHHHH
Confidence            9999999998875

>PRK12543 RNA polymerase sigma factor; Provisional

Probab=99.57  E-value=2.4e-14  Score=132.51  Aligned_cols=131  Identities=12%  Similarity=0.075  Sum_probs=104.4

Q ss_pred             hchH-HHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhhccc
Q 012638          292 FGWY-CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARG  370 (459)
Q Consensus       292 ~G~~-Are~LI~~nlrLV~sIAkry~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIrnaI~d~Lrk~sr~  370 (459)
                      .|+. |++.|+..|.+.|+.++++|.++..+++|++||+++.+|+++.+|++..  .|.+|++.+++|.+.+++++..+.
T Consensus         3 ~~d~~af~~l~~~~~~~l~~~~~~~~~~~~daeDl~Qevfl~l~~~~~~~~~~~--~f~~wl~~iarn~~~~~~r~~~~~   80 (179)
T PRK12543          3 SGDQEAFSEIYDVTIQEVYKTVHFLVEDKQDVDDVVNEIYIQLWESLRKYDSNR--PFRFWLIGLVIKQIHSWRRKRWRR   80 (179)
T ss_pred             CchHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhHHHcCCCC--ChHHHHHHHHHHHHHHHHHhhccc
Confidence            4555 9999999999999999999999999999999999999999999999864  699999999999999999865421


Q ss_pred             cc---------------cccch--HHHHHHHHHHHHHHHHHc--------CCCCCHHHHHHHhCCCHHHHHHHHHhhcc
Q 012638          371 IK---------------IPCKL--NREISKIQKARKALTNSH--------GKYPEDIEIAKYTGLSLAEIRSASECLRI  424 (459)
Q Consensus       371 ir---------------lP~~v--~e~i~kI~ka~~~L~~~l--------gr~PT~eEIAe~LGIS~e~Vk~~l~~ar~  424 (459)
                      .+               .|.++  .+....+.++...|+...        -.+.+++|||+.||||+++|+..+.+++.
T Consensus        81 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~Lp~~~r~i~~l~~~e~~s~~EIA~~lgis~~tV~~~l~ra~~  159 (179)
T PRK12543         81 FRIFEKAEEQRKPVSIDFSEDVLSKESNQELIELIHKLPYKLRQVIILRYLHDYSQEEIAQLLQIPIGTVKSRIHAALK  159 (179)
T ss_pred             cccccccccccccccccChHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHccCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            11               11110  122344555555555443        26689999999999999999999888765

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

Probab=99.56  E-value=3.4e-14  Score=132.84  Aligned_cols=131  Identities=12%  Similarity=-0.002  Sum_probs=105.7

Q ss_pred             hchH-HHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhhccc
Q 012638          292 FGWY-CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARG  370 (459)
Q Consensus       292 ~G~~-Are~LI~~nlrLV~sIAkry~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIrnaI~d~Lrk~sr~  370 (459)
                      .|+. +|++|+..|.+.|+.+|.+++++..+++|++||+|+.+|+++.+|++.  .+|.||++.+++|.+++++|++.+.
T Consensus         7 ~~~~~~f~~l~~~~~~~l~~~~~~~~~~~~~AEDlvQevfl~~~~~~~~~~~~--~~~~~wL~~iarN~~~d~~Rk~~~~   84 (193)
T TIGR02947         7 TQRAQRFERDALEYLDQLYGAALRMTRNPADAEDLVQEAYAKAFSSFHQFKPG--TNLKAWLYRILTNTYINSYRKAQRR   84 (193)
T ss_pred             hhhHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhhcccCCC--CcchHHHHHHHHHHHHHHHHHhcCC
Confidence            3444 999999999999999999999999999999999999999999999864  4699999999999999999976543


Q ss_pred             cccc--------------cc------hH-------HHHHHHHHHHHHHHHHcC--------CCCCHHHHHHHhCCCHHHH
Q 012638          371 IKIP--------------CK------LN-------REISKIQKARKALTNSHG--------KYPEDIEIAKYTGLSLAEI  415 (459)
Q Consensus       371 irlP--------------~~------v~-------e~i~kI~ka~~~L~~~lg--------r~PT~eEIAe~LGIS~e~V  415 (459)
                      ....              .+      ..       +....+..+...|+....        .+.+++|||+.||||+++|
T Consensus        85 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~l~~~l~~Lp~~~r~i~~L~~~~g~s~~EIA~~lgis~~tV  164 (193)
T TIGR02947        85 PQQSDDDDIEDWQLAKAASHTSNGLRSAELEALDGLPDQDIKDALQGLPEEFRQAVYLADVEGFAYKEIAEIMGTPIGTV  164 (193)
T ss_pred             cccccchhhhhhhhccccccccccccchhHHHHhhhhHHHHHHHHHhCCHHHhhheeehhhcCCCHHHHHHHHCCCHHHH
Confidence            2110              00      00       112446666766666543        5689999999999999999


Q ss_pred             HHHHHhhcc
Q 012638          416 RSASECLRI  424 (459)
Q Consensus       416 k~~l~~ar~  424 (459)
                      +..+.+++.
T Consensus       165 k~~l~Rar~  173 (193)
T TIGR02947       165 MSRLHRGRK  173 (193)
T ss_pred             HHHHHHHHH
Confidence            999998875

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.

>PRK12518 RNA polymerase sigma factor; Provisional

Probab=99.56  E-value=5.6e-14  Score=128.66  Aligned_cols=135  Identities=16%  Similarity=0.093  Sum_probs=104.6

Q ss_pred             HHHHHhchH-HHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHH
Q 012638          287 KQHLAFGWY-CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVA  365 (459)
Q Consensus       287 ~~~l~~G~~-Are~LI~~nlrLV~sIAkry~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIrnaI~d~Lr  365 (459)
                      +..++.|+. |++.|+..|.+.|+.+|+++.+ ..+++|++||+|+.+|+.+++|++.  ..|.+|++.+++|.+++++|
T Consensus         2 ~~~~~~gd~~a~~~l~~~~~~~l~~~~~~~~~-~~~aeDivQe~~l~l~~~~~~~~~~--~~~~~wl~~ia~n~~~d~~R   78 (175)
T PRK12518          2 ILRCQRGDRQSFRQLYRRYQQKVRSTLYQLCG-RELLDDLVQEVFLRVWKGLPKLRNP--AYFSTWLYRITWNVATDARR   78 (175)
T ss_pred             hhHHHcCCHHHHHHHHHHHHHHHHHHHHHHcC-HhHHHHHHHHHHHHHHHhHHhhCCc--ccHHHHHHHHHHHHHHHHHH
Confidence            456678876 9999999999999999999875 4789999999999999999999974  47999999999999999999


Q ss_pred             hhcccc----ccc--------cc---h--HHHHHHHHHHHHHHHHHcC--------CCCCHHHHHHHhCCCHHHHHHHHH
Q 012638          366 RHARGI----KIP--------CK---L--NREISKIQKARKALTNSHG--------KYPEDIEIAKYTGLSLAEIRSASE  420 (459)
Q Consensus       366 k~sr~i----rlP--------~~---v--~e~i~kI~ka~~~L~~~lg--------r~PT~eEIAe~LGIS~e~Vk~~l~  420 (459)
                      +..+..    ..+        ..   .  .+....+.++...|+....        .+.+++|||+.||+|+++|+..+.
T Consensus        79 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~vl~l~~~~g~s~~eIA~~lg~s~~tv~~~l~  158 (175)
T PRK12518         79 QFAQRPSRIQDDSLNDQPSRPSDTPDLMQLHYQDLVQQGLQTLSLEHRAVLVLHDLEDLPQKEIAEILNIPVGTVKSRLF  158 (175)
T ss_pred             HhhccccchhcccccccccCCCCcHHHHHHHHHHHHHHHHHhCCHHHeeeeeehHhcCCCHHHHHHHHCCCHHHHHHHHH
Confidence            764311    110        00   0  0111224455555554432        567999999999999999999999


Q ss_pred             hhcc
Q 012638          421 CLRI  424 (459)
Q Consensus       421 ~ar~  424 (459)
                      +++.
T Consensus       159 Rar~  162 (175)
T PRK12518        159 YARR  162 (175)
T ss_pred             HHHH
Confidence            8875

>PRK09415 RNA polymerase factor sigma C; Reviewed

Probab=99.56  E-value=5.6e-14  Score=130.24  Aligned_cols=128  Identities=16%  Similarity=0.057  Sum_probs=103.0

Q ss_pred             HHHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhhccccccc
Q 012638          295 YCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIP  374 (459)
Q Consensus       295 ~Are~LI~~nlrLV~sIAkry~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIrnaI~d~Lrk~sr~irlP  374 (459)
                      .|+++|+..|.+.|+++|.+++++..+++|++||+++.+|+++.+|++.  ..|.||++.+++|.+++++|+..+....+
T Consensus        16 ~a~~~l~~~~~~~l~~~~~~~~~~~~~AeDlvQd~fl~l~~~~~~~~~~--~~~~awl~~ia~n~~~d~~Rk~~~~~~~~   93 (179)
T PRK09415         16 DLIDEIMNEYGQEVLQLVYSYVKNKEVAEDLTQEIFVKCYKSLHTYKGK--SSLKTWLYRIAINHCKDYLKSWHNKKVIV   93 (179)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHhcCCC--cccHHHHHHHHHHHHHHHHHhhccccccc
Confidence            4999999999999999999999999999999999999999999999874  36999999999999999999753221110


Q ss_pred             ---------------cc---hHHHHHHHHHHHHHHHHHc--------CCCCCHHHHHHHhCCCHHHHHHHHHhhcc
Q 012638          375 ---------------CK---LNREISKIQKARKALTNSH--------GKYPEDIEIAKYTGLSLAEIRSASECLRI  424 (459)
Q Consensus       375 ---------------~~---v~e~i~kI~ka~~~L~~~l--------gr~PT~eEIAe~LGIS~e~Vk~~l~~ar~  424 (459)
                                     ..   ..+....+.++...|+...        -.+.|++|||+.||||+++|+..+.+++.
T Consensus        94 ~~~~~~~~~~~~~~~e~~~~~~e~~~~l~~~l~~L~~~~r~v~~l~~~~g~s~~EIA~~l~is~~tv~~~l~Ra~~  169 (179)
T PRK09415         94 TEDIFTYMESQKESVEEEVIQNAEDERLASAVMSLPIKYREVIYLFYYEELSIKEIAEVTGVNENTVKTRLKKAKE  169 (179)
T ss_pred             cccccccccccccCcHHHHHHHHHHHHHHHHHHhCCHHHhhHhHhHHhcCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence                           00   1122334555555555543        25679999999999999999999998875

>PRK12516 RNA polymerase sigma factor; Provisional

Probab=99.55  E-value=5.4e-14  Score=131.92  Aligned_cols=128  Identities=13%  Similarity=0.108  Sum_probs=104.7

Q ss_pred             HHHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhhccccccc
Q 012638          295 YCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIP  374 (459)
Q Consensus       295 ~Are~LI~~nlrLV~sIAkry~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIrnaI~d~Lrk~sr~irlP  374 (459)
                      .++++|+..|.+.|+.+|.+++++..+++|++||.|+.+|+..++|+..  ..|.+|++++++|.+++++|++.+.....
T Consensus        10 ~~f~~l~~~~~~~L~~~a~~~~~~~~~AEDivQevfl~~~~~~~~~~~~--~~~~awL~~Ia~n~~~d~~R~~~~~~~~~   87 (187)
T PRK12516         10 PPFKRELLAALPSLRAFAVSLIGRHDRADDLVQDTIMKAWAKQDHFEVG--TNMKAWLFTILRNEFYSQMRKRGREVQDT   87 (187)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHcCCHhHHHHHHHHHHHHHHHhhhccCCc--ccHHHHHHHHHHHHHHHHHHhhcCCcccc
Confidence            4999999999999999999999999999999999999999999999864  36999999999999999999876432111


Q ss_pred             c---------c----hHHHHHHHHHHHHHHHHHc--------CCCCCHHHHHHHhCCCHHHHHHHHHhhcc
Q 012638          375 C---------K----LNREISKIQKARKALTNSH--------GKYPEDIEIAKYTGLSLAEIRSASECLRI  424 (459)
Q Consensus       375 ~---------~----v~e~i~kI~ka~~~L~~~l--------gr~PT~eEIAe~LGIS~e~Vk~~l~~ar~  424 (459)
                      .         .    .......+..++..|+...        ..+.+++|||+.||||+++|+..+.+++.
T Consensus        88 ~~~~~~~~~~~~~~~~~~~~~~l~~~L~~Lp~~~r~i~~L~~~~g~s~~EIA~~Lgis~~tVk~~l~Rar~  158 (187)
T PRK12516         88 DGMFTEQLAVHPSQYGTLDLQDFRAALDQLPDDQREAIILVGASGFAYEEAAEICGCAVGTIKSRVNRARQ  158 (187)
T ss_pred             ccccccccCCCcchhhHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            0         0    1112344666666665543        36789999999999999999999998875

>PRK09645 RNA polymerase sigma factor SigL; Provisional

Probab=99.55  E-value=5.3e-14  Score=128.82  Aligned_cols=130  Identities=13%  Similarity=0.007  Sum_probs=103.2

Q ss_pred             hHHHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhhcccccc
Q 012638          294 WYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKI  373 (459)
Q Consensus       294 ~~Are~LI~~nlrLV~sIAkry~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIrnaI~d~Lrk~sr~irl  373 (459)
                      ..+++.|+..|.+.|+++|.++.++..+++|++||.|+.+|+..++|++.. ..|.+|++.+++|.+++++|++.+....
T Consensus         8 ~~~~~~l~~~~~~~l~~~~~~~~~~~~~AeD~vQevfl~~~~~~~~~~~~~-~~~~~wL~~iarn~~~d~~Rk~~~~~~~   86 (173)
T PRK09645          8 AALMRALYDEHAAPLWRYALRLTGDRARAEDVVQETLLRAWQHPEVLADTG-RSARAWLFTVARNLVIDERRSARARPVE   86 (173)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhHHhcCccc-ccHHHHHHHHHHHHHHHHHHhhcccccc
Confidence            349999999999999999999999999999999999999999999997532 4799999999999999999976432111


Q ss_pred             --------cc-----ch--HHHHHHHHHHHHHHHHHc--------CCCCCHHHHHHHhCCCHHHHHHHHHhhcc
Q 012638          374 --------PC-----KL--NREISKIQKARKALTNSH--------GKYPEDIEIAKYTGLSLAEIRSASECLRI  424 (459)
Q Consensus       374 --------P~-----~v--~e~i~kI~ka~~~L~~~l--------gr~PT~eEIAe~LGIS~e~Vk~~l~~ar~  424 (459)
                              |.     .+  ......+..+...|+...        -.+.+++|||+.||||+++|+..+++++.
T Consensus        87 ~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~vl~L~~~~g~s~~EIA~~lgis~~tV~~~l~ra~~  160 (173)
T PRK09645         87 GGDDVLGVPEQSAPDEVDRALDRLLVADALAQLSPEHRAVLVRSYYRGWSTAQIAADLGIPEGTVKSRLHYALR  160 (173)
T ss_pred             cccccccCCCCCCchHHHHHhHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence                    10     01  011123556666555543        36789999999999999999999998875

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

Probab=99.55  E-value=5.5e-14  Score=122.22  Aligned_cols=126  Identities=25%  Similarity=0.300  Sum_probs=101.0

Q ss_pred             HHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhhcccccc--
Q 012638          296 CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKI--  373 (459)
Q Consensus       296 Are~LI~~nlrLV~sIAkry~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIrnaI~d~Lrk~sr~irl--  373 (459)
                      |++.++..|.++|+++++++.+++.+.+|++|||+++++++++.|++.  .+|.||+++++++.+.++++++.+ .+.  
T Consensus         2 a~~~l~~~~~~~v~~~~~~~~~~~~~~~D~~qe~~~~l~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~rk~~~-~~~~~   78 (158)
T TIGR02937         2 AFEELYERYLPLLYRYARRYLGDDADAEDLVQEAFLKLLEALDRFDPE--GSFKAWLFRIARNLILDYLRRKRR-LRREL   78 (158)
T ss_pred             HHHHHHHHHHHHHHHHHHHHhCCHhHHHHHHHHHHHHHHHhHHhcCCc--chHHHHHHHHHHHHHHHHHHHhcc-CCcch
Confidence            789999999999999999999999999999999999999999999997  689999999999999999998764 110  


Q ss_pred             ------------ccc---hHHHHHHHHHHHHHHHHH--------cCCCCCHHHHHHHhCCCHHHHHHHHHhhcc
Q 012638          374 ------------PCK---LNREISKIQKARKALTNS--------HGKYPEDIEIAKYTGLSLAEIRSASECLRI  424 (459)
Q Consensus       374 ------------P~~---v~e~i~kI~ka~~~L~~~--------lgr~PT~eEIAe~LGIS~e~Vk~~l~~ar~  424 (459)
                                  |..   .......+.++...|+..        +..+.+.+|||+.+|+|+.+|...+..++.
T Consensus        79 ~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~~~ii~~~~~~g~s~~eIA~~l~~s~~~v~~~~~~~~~  152 (158)
T TIGR02937        79 DLLEELLDSDPSPEEELEQEEEREALREALEKLPEREREVLVLRYLEGLSYKEIAEILGISVGTVKRRLKRARK  152 (158)
T ss_pred             hhhhhcccccCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHhhHHhcCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence                        000   112223344444444322        246789999999999999999999887754

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.

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

Probab=99.55  E-value=5.6e-14  Score=127.16  Aligned_cols=131  Identities=15%  Similarity=0.023  Sum_probs=104.1

Q ss_pred             hchH-HHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhhccc
Q 012638          292 FGWY-CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARG  370 (459)
Q Consensus       292 ~G~~-Are~LI~~nlrLV~sIAkry~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIrnaI~d~Lrk~sr~  370 (459)
                      .|+. +++.|+..|.+.|+.+|.++.++..+++|++||+|+.+|++.++|+.  ...|.+|++.+++|.+++++|++.+.
T Consensus         2 ~~~~~~~~~l~~~~~~~l~~~~~~~~~~~~~aeDivQe~f~~~~~~~~~~~~--~~~~~~wl~~i~~n~~~d~~rk~~~~   79 (162)
T TIGR02983         2 SATEEEFTAFVAARYPRLLRTAYLLTGDPHEAEDLVQEALVRTYVRWDRIRD--PDAPDAYVRRVLVNLARSRWRRRRLL   79 (162)
T ss_pred             CCcHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHhhcCC--cccHHHHHHHHHHHHHHHHHHhhccc
Confidence            3554 99999999999999999999999999999999999999999999964  34799999999999999999976541


Q ss_pred             ccc----cc----c---hHHHHHHHHHHHHHHHHHc--------CCCCCHHHHHHHhCCCHHHHHHHHHhhcc
Q 012638          371 IKI----PC----K---LNREISKIQKARKALTNSH--------GKYPEDIEIAKYTGLSLAEIRSASECLRI  424 (459)
Q Consensus       371 irl----P~----~---v~e~i~kI~ka~~~L~~~l--------gr~PT~eEIAe~LGIS~e~Vk~~l~~ar~  424 (459)
                      ...    |.    .   .......|..+...|+...        -.+.+++|||+.||+|+++|+..+.+++.
T Consensus        80 ~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~i~~l~~~~g~s~~eIA~~lgis~~tV~~~l~ra~~  152 (162)
T TIGR02983        80 ELPTRELPDAAAPDPAPDVALRAALARALRRLPARQRAVVVLRYYEDLSEAQVAEALGISVGTVKSRLSRALA  152 (162)
T ss_pred             cccccccCcccCCccchhHHHHHHHHHHHHhCCHHHHHHhhhHHHhcCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence            100    10    0   1123334555555554433        25689999999999999999999998875

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

>PRK08241 RNA polymerase factor sigma-70; Validated

Probab=99.54  E-value=7.6e-14  Score=141.56  Aligned_cols=139  Identities=18%  Similarity=0.104  Sum_probs=111.6

Q ss_pred             HHHHHHHHhchH-HHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHH
Q 012638          284 RVLKQHLAFGWY-CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISK  362 (459)
Q Consensus       284 eeL~~~l~~G~~-Are~LI~~nlrLV~sIAkry~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIrnaI~d  362 (459)
                      .+|+..++.|+. |+++|+..|.+.|+.+|++++++..+++|++||.|+.+|+.+++|++.  ..|.+|++.+++|.+++
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            478889999987 999999999999999999999999999999999999999999999853  47999999999999999


Q ss_pred             HHHhhccccc---c-----------------------cc-----------ch---HHH-HHHHHHHHHHHHHHcC-----
Q 012638          363 MVARHARGIK---I-----------------------PC-----------KL---NRE-ISKIQKARKALTNSHG-----  396 (459)
Q Consensus       363 ~Lrk~sr~ir---l-----------------------P~-----------~v---~e~-i~kI~ka~~~L~~~lg-----  396 (459)
                      ++|++.+...   .                       +.           ..   .+. ...+..++..|+....     
T Consensus        85 ~~Rk~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~e~~~~~l~~~l~~Lp~~~R~v~~L  164 (339)
T PRK08241         85 ALEGRARRPLPTDLGAPAADPVDELVERPEVPWLEPYPDALLDPAAADPAARVVARESVRLAFVAALQHLPPRQRAVLIL  164 (339)
T ss_pred             HHHhhccccCccccCCCcCcccccccccccccccCCCCcccccccCCChHHHHHHHHHHHHHHHHHHHhCCHHHhhhhhh
Confidence            9997643210   0                       00           00   011 1235556666655432     


Q ss_pred             ---CCCCHHHHHHHhCCCHHHHHHHHHhhcc
Q 012638          397 ---KYPEDIEIAKYTGLSLAEIRSASECLRI  424 (459)
Q Consensus       397 ---r~PT~eEIAe~LGIS~e~Vk~~l~~ar~  424 (459)
                         .+.+++|||+.||+|+++|+..+.+++.
T Consensus       165 ~~~~g~s~~EIA~~lgis~~tVk~~l~RAr~  195 (339)
T PRK08241        165 RDVLGWSAAEVAELLDTSVAAVNSALQRARA  195 (339)
T ss_pred             HHhhCCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence               5679999999999999999999888764

>PRK12529 RNA polymerase sigma factor; Provisional

Probab=99.54  E-value=6e-14  Score=130.07  Aligned_cols=135  Identities=9%  Similarity=-0.018  Sum_probs=104.8

Q ss_pred             HHhchH-HHHHHHHHhHHHHHHHHHHhhC--CCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHh
Q 012638          290 LAFGWY-CREELIKSTRPLVLFLARNYRG--LGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVAR  366 (459)
Q Consensus       290 l~~G~~-Are~LI~~nlrLV~sIAkry~g--~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIrnaI~d~Lrk  366 (459)
                      +..|+. ||+.|+..|.+.|+.++.++++  +..+++|++||.|+.+|+..++|+......|.||++.+++|.+++++|+
T Consensus         7 ~~~~d~~af~~ly~~~~~~l~~~~~~~~~~~~~~~AeDivQevFl~~~~~~~~~~~~~~~~~~~wL~~ia~n~~~d~~Rk   86 (178)
T PRK12529          7 CLSADRDKVATLYRENHAWLRNWLAYRLRSWGRGVADDLAHDIFLRILASRDGGQREAIRQPRAYLARIANCVLVSWRRR   86 (178)
T ss_pred             CCCCCHHHHHHHHHHHHHHHHHHHHHHhCCCChHHHHHHHHHHHHHHHhcccccccccccCHHHHHHHHHHHHHHHHHHH
Confidence            345655 9999999999999998766665  4678999999999999999999975434579999999999999999997


Q ss_pred             hccccc-------c-------ccc---hHHHHHHHHHHHHHHHHHcC--------CCCCHHHHHHHhCCCHHHHHHHHHh
Q 012638          367 HARGIK-------I-------PCK---LNREISKIQKARKALTNSHG--------KYPEDIEIAKYTGLSLAEIRSASEC  421 (459)
Q Consensus       367 ~sr~ir-------l-------P~~---v~e~i~kI~ka~~~L~~~lg--------r~PT~eEIAe~LGIS~e~Vk~~l~~  421 (459)
                      +.+...       .       |..   ..+....|.+++.+|+.+..        .+.|++|||+.||||+++|+..+++
T Consensus        87 ~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~l~~~l~~Lp~~~R~v~~L~~~~g~s~~EIA~~lgis~~tVk~~l~r  166 (178)
T PRK12529         87 QSLELAWLEALATLPEPLHPSPEQQSVILETLHEIDALLDTLRPRVKQAFLMATLDGMKQKDIAQALDIALPTVKKYIHQ  166 (178)
T ss_pred             HHHHhhhhhHhhhccCcCCCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHH
Confidence            643110       1       111   11233456677777766543        5689999999999999999999888


Q ss_pred             hcc
Q 012638          422 LRI  424 (459)
Q Consensus       422 ar~  424 (459)
                      +..
T Consensus       167 Al~  169 (178)
T PRK12529        167 AYV  169 (178)
T ss_pred             HHH
Confidence            764

>PRK12547 RNA polymerase sigma factor; Provisional

Probab=99.53  E-value=1.1e-13  Score=126.32  Aligned_cols=128  Identities=13%  Similarity=0.107  Sum_probs=103.4

Q ss_pred             HHHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhhccccccc
Q 012638          295 YCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIP  374 (459)
Q Consensus       295 ~Are~LI~~nlrLV~sIAkry~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIrnaI~d~Lrk~sr~irlP  374 (459)
                      ..|.+++..|.+.|+.+|+++.++..+++|++||+++.+|+..++|+..  ..|.+|++.+++|.+++++|++++.....
T Consensus         6 ~~f~~~~~~~~~~l~~~a~~~~~~~~~AeDivQe~fl~l~~~~~~~~~~--~~~~~wl~~i~~n~~~d~~R~~~~~~~~~   83 (164)
T PRK12547          6 KNFKQELLLALPALRAFAVSLSSKHDKAEDLVQDTLMKAWAKQDSFEMG--TNLKAWLFTILRNEFYSQMRKRGREVQDS   83 (164)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHcCCHhhHHHHHHHHHHHHHHhhhhcCCc--ccHHHHHHHHHHHHHHHHHHhhccccccc
Confidence            4789999999999999999999999999999999999999999999864  36999999999999999999765432110


Q ss_pred             ---------cc----hHHHHHHHHHHHHHHHHHc--------CCCCCHHHHHHHhCCCHHHHHHHHHhhcc
Q 012638          375 ---------CK----LNREISKIQKARKALTNSH--------GKYPEDIEIAKYTGLSLAEIRSASECLRI  424 (459)
Q Consensus       375 ---------~~----v~e~i~kI~ka~~~L~~~l--------gr~PT~eEIAe~LGIS~e~Vk~~l~~ar~  424 (459)
                               .+    .......+..+...|+...        -.+.+++|||+.||||+++|+..+.+++.
T Consensus        84 ~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~v~~l~~~~g~s~~eIA~~lgis~~tV~~~l~Rar~  154 (164)
T PRK12547         84 DGVFTARVAVHPAQYGSLDLQDFKKALNLLSADQREAIILIGASGFSYEDAAAICGCAVGTIKSRVSRARN  154 (164)
T ss_pred             cccccccCCCCchhhhHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence                     00    0112234556666655543        26789999999999999999999998875

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

Probab=99.53  E-value=1.1e-13  Score=127.53  Aligned_cols=133  Identities=17%  Similarity=0.098  Sum_probs=102.0

Q ss_pred             hchH-HHHHHHHHhHHHHHHHHHHhh----CCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHh
Q 012638          292 FGWY-CREELIKSTRPLVLFLARNYR----GLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVAR  366 (459)
Q Consensus       292 ~G~~-Are~LI~~nlrLV~sIAkry~----g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIrnaI~d~Lrk  366 (459)
                      .|+. |++.|+..|.+.|+.+|++|.    ++..+++|++||+++.+|+++.+|+...+.+|.+|++.+++|.+++++++
T Consensus         3 ~~~~~a~~~l~~~y~~~l~~~~~~~l~~~~~~~~~aeD~vQe~~l~l~~~~~~~~~~~~~~~~~wl~~i~~n~~~d~~r~   82 (189)
T TIGR02984         3 GGDQEALGELLDRYRNYLRLLARVQLDPRLRRRVDPSDLVQETLLEAHRRFDQFRGKTEGEFAGWLRGILSNVLADALRR   82 (189)
T ss_pred             CCCHHHHHHHHHHHHHHHHHHHHHHhhhhcCCccCHHHHHHHHHHHHHHHHHhccCcccchHHHHHHHHHHHHHHHHHHH
Confidence            4665 999999999999999999875    35679999999999999999999987655689999999999999999986


Q ss_pred             hc----ccc--ccc-------------------------cc---hHHHHHHHHHHHHHHHHHc--------CCCCCHHHH
Q 012638          367 HA----RGI--KIP-------------------------CK---LNREISKIQKARKALTNSH--------GKYPEDIEI  404 (459)
Q Consensus       367 ~s----r~i--rlP-------------------------~~---v~e~i~kI~ka~~~L~~~l--------gr~PT~eEI  404 (459)
                      +.    +..  ..+                         ..   ..+....+.++...|+...        ..+.+++||
T Consensus        83 ~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~l~~~l~~L~~~~r~vi~l~~~~g~s~~eI  162 (189)
T TIGR02984        83 HLGAQKRDIRREQSLDAGGRLDESSVRLAAQLAADGPSPSQVAARREAAVRLAQALAKLPEDYREVILLRHLEGLSFAEV  162 (189)
T ss_pred             HHHHHhhhcccccCCCcccccCCcchhHHHHccCCCCCHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHhcCCCHHHH
Confidence            51    110  000                         00   0112233444555444332        367899999


Q ss_pred             HHHhCCCHHHHHHHHHhhcc
Q 012638          405 AKYTGLSLAEIRSASECLRI  424 (459)
Q Consensus       405 Ae~LGIS~e~Vk~~l~~ar~  424 (459)
                      |+.||||+++|+..+++++.
T Consensus       163 A~~lgis~~~v~~~l~Ra~~  182 (189)
T TIGR02984       163 AERMDRSEGAVSMLWVRGLA  182 (189)
T ss_pred             HHHHCcCHHHHHHHHHHHHH
Confidence            99999999999999988764

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

>PRK12541 RNA polymerase sigma factor; Provisional

Probab=99.53  E-value=1.3e-13  Score=125.06  Aligned_cols=127  Identities=17%  Similarity=0.101  Sum_probs=100.7

Q ss_pred             HHHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhhcccccc-
Q 012638          295 YCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKI-  373 (459)
Q Consensus       295 ~Are~LI~~nlrLV~sIAkry~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIrnaI~d~Lrk~sr~irl-  373 (459)
                      .|+++++..|.+.|+.+|.+++++..+++|++||+++.+|+..++|++.   .|.||++.+++|.+++++|++.+.... 
T Consensus         5 ~a~~~l~~~~~~~l~~~~~~~~~~~~~AeDv~Qe~f~~~~~~~~~~~~~---~~~~wl~~i~~n~~~d~~R~~~~~~~~~   81 (161)
T PRK12541          5 QSLEEIYSEHMQDLFRYLLSLTGDSHFAEDLMQETFYRMLVHIDYYKGE---EIRPWLFTIAYNAFIDWYRKEKKYKTTT   81 (161)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHhHHHccCC---ChHHHHHHHHHHHHHHHHHhcccccccc
Confidence            3899999999999999999999999999999999999999999999863   599999999999999999976532211 


Q ss_pred             ---------ccc-----hHHHHHHHHHHHHHHHHHc--------CCCCCHHHHHHHhCCCHHHHHHHHHhhcc
Q 012638          374 ---------PCK-----LNREISKIQKARKALTNSH--------GKYPEDIEIAKYTGLSLAEIRSASECLRI  424 (459)
Q Consensus       374 ---------P~~-----v~e~i~kI~ka~~~L~~~l--------gr~PT~eEIAe~LGIS~e~Vk~~l~~ar~  424 (459)
                               |..     ..+....+..+...|+...        -.+.+++|||+.||+|+++|+..+.+++.
T Consensus        82 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~L~~~~r~v~~l~~~~~~s~~eIA~~lgis~~tv~~~l~Rar~  154 (161)
T PRK12541         82 IEEFHLPNVPSTEHEYFIKHEIASWLDSLSSLPLERRNVLLLRDYYGFSYKEIAEMTGLSLAKVKIELHRGRK  154 (161)
T ss_pred             hhhhhccCCCCcHHHHHHHhHHHHHHHHHHHCCHHHHHHhhhHHhcCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence                     000     0111222334444444432        36789999999999999999999998875

>PRK12535 RNA polymerase sigma factor; Provisional

Probab=99.52  E-value=1.7e-13  Score=129.67  Aligned_cols=138  Identities=19%  Similarity=0.049  Sum_probs=109.4

Q ss_pred             HHHHHHHHhchH-HHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHH
Q 012638          284 RVLKQHLAFGWY-CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISK  362 (459)
Q Consensus       284 eeL~~~l~~G~~-Are~LI~~nlrLV~sIAkry~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIrnaI~d  362 (459)
                      .+|+..+..|+. |++.|+..|.+.++.+++ +.++..+++|++||.|+.+|+..++|++.  ..|.+|++.+++|.+++
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            567778888877 999999999999999975 57888899999999999999999999863  37999999999999999


Q ss_pred             HHHhhcccccc--------------cc--chHHHHHHHHHHHHHHHHHc--------CCCCCHHHHHHHhCCCHHHHHHH
Q 012638          363 MVARHARGIKI--------------PC--KLNREISKIQKARKALTNSH--------GKYPEDIEIAKYTGLSLAEIRSA  418 (459)
Q Consensus       363 ~Lrk~sr~irl--------------P~--~v~e~i~kI~ka~~~L~~~l--------gr~PT~eEIAe~LGIS~e~Vk~~  418 (459)
                      ++|++.+..+.              |.  ...+....+.+++..|+...        -.+.+++|||+.||+|+++|+..
T Consensus        90 ~~Rk~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~Lp~~~r~v~~l~~~~g~s~~EIAe~lgis~~tV~~~  169 (196)
T PRK12535         90 NIRHDMARPRKSATEYEDAAATTASNETTGSWSEWIDVRTLIDALPPERREALILTQVLGYTYEEAAKIADVRVGTIRSR  169 (196)
T ss_pred             HHHhhccCCCcccccccccccccCCcchhHHHHHHHHHHHHHHcCCHHHHHHhhhHHHhCCCHHHHHHHhCCCHHHHHHH
Confidence            99976432211              00  01122234566666665543        25679999999999999999999


Q ss_pred             HHhhcc
Q 012638          419 SECLRI  424 (459)
Q Consensus       419 l~~ar~  424 (459)
                      +.+++.
T Consensus       170 l~Rar~  175 (196)
T PRK12535        170 VARARA  175 (196)
T ss_pred             HHHHHH
Confidence            998875

>PRK12523 RNA polymerase sigma factor; Reviewed

Probab=99.51  E-value=6.7e-14  Score=128.56  Aligned_cols=132  Identities=15%  Similarity=0.066  Sum_probs=102.5

Q ss_pred             HhchH-HHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhhcc
Q 012638          291 AFGWY-CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHAR  369 (459)
Q Consensus       291 ~~G~~-Are~LI~~nlrLV~sIAkry~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIrnaI~d~Lrk~sr  369 (459)
                      +.|+. |+.+|+..|.+.|+.+|.+++++..+++|++||+|+.+|+. ..|+..  ..|.||++.+++|.+++++|++.+
T Consensus         5 ~~~~~~a~~~l~~~~~~~l~~~~~~~~~~~~~AeDlvQevflk~~~~-~~~~~~--~~~~~wL~~Iarn~~~d~~Rk~~~   81 (172)
T PRK12523          5 QSPHSELVGALYRDHRGWLLAWLRRNVACRQRAEDLSQDTFVRLLGR-PELPTP--REPRAFLAAVAKGLMFDHFRRAAL   81 (172)
T ss_pred             CCCCcHHHHHHHHHHHHHHHHHHHHHcCCHhhHHHHHHHHHHHHHcc-cccCcc--hhHHHHHHHHHHHHHHHHHHHHHH
Confidence            56765 99999999999999999999999999999999999999986 446543  369999999999999999997643


Q ss_pred             ccc-------cc-------cc---hHHHHHHHHHHHHHHHHHc--------CCCCCHHHHHHHhCCCHHHHHHHHHhhcc
Q 012638          370 GIK-------IP-------CK---LNREISKIQKARKALTNSH--------GKYPEDIEIAKYTGLSLAEIRSASECLRI  424 (459)
Q Consensus       370 ~ir-------lP-------~~---v~e~i~kI~ka~~~L~~~l--------gr~PT~eEIAe~LGIS~e~Vk~~l~~ar~  424 (459)
                      ...       .+       ..   ..+....+..++..|+...        -.+.+++|||+.||||+++|+..+.+++.
T Consensus        82 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~Lp~~~r~v~~L~~~~g~s~~EIA~~lgis~~tV~~~l~ra~~  161 (172)
T PRK12523         82 EQAYLAELALVPEAEQPSPEEQHLILEDLKAIDRLLGKLSSKARAAFLYNRLDGMGHAEIAERLGVSVSRVRQYLAQGLR  161 (172)
T ss_pred             HHHHHHHHhhcccccCCChHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            210       00       00   0122234556666555443        36789999999999999999999988765


Q ss_pred             C
Q 012638          425 V  425 (459)
Q Consensus       425 ~  425 (459)
                      .
T Consensus       162 ~  162 (172)
T PRK12523        162 Q  162 (172)
T ss_pred             H
Confidence            3

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

Probab=99.51  E-value=1.2e-13  Score=123.13  Aligned_cols=127  Identities=17%  Similarity=0.087  Sum_probs=99.7

Q ss_pred             HHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhhcccccc--
Q 012638          296 CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKI--  373 (459)
Q Consensus       296 Are~LI~~nlrLV~sIAkry~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIrnaI~d~Lrk~sr~irl--  373 (459)
                      |+++|+..|.+.|+.+++++.++..+.+|++||+++++|+++.+|++.  .+|.+|++.++++.+.+++++..+....  
T Consensus         2 a~~~l~~~~~~~l~~~~~~~~~~~~~aeD~~Qe~~~~~~~~~~~~~~~--~~~~~wl~~i~r~~~~d~~r~~~~~~~~~~   79 (161)
T TIGR02985         2 AFEQLYRRYYPKLCAFAYRYVKDEEEAEDIVQDVFVKLWENRETLEEV--ESFKAYLFTIVKNRSLNYLRHKQVEEKYQE   79 (161)
T ss_pred             hHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhHHhcccc--ccHHHHHHHHHHHHHHHHHHHHHhHhHHHH
Confidence            789999999999999999999999999999999999999999999874  4799999999999999999876532111  


Q ss_pred             ------c--------cc---hHHHHHHHHHHHHHHHHH--------cCCCCCHHHHHHHhCCCHHHHHHHHHhhcc
Q 012638          374 ------P--------CK---LNREISKIQKARKALTNS--------HGKYPEDIEIAKYTGLSLAEIRSASECLRI  424 (459)
Q Consensus       374 ------P--------~~---v~e~i~kI~ka~~~L~~~--------lgr~PT~eEIAe~LGIS~e~Vk~~l~~ar~  424 (459)
                            +        ..   ..+....+..+...|+..        ...+.+.+|||+.||+|..+|+..+++++.
T Consensus        80 ~~~~~~~~~~~~~~~~~~~~~~e~~~~l~~~l~~L~~~~r~il~l~~~~~~~~~eIA~~lgis~~tv~~~~~ra~~  155 (161)
T TIGR02985        80 EILEIEVDELSENDPEEELEAKELQLIIYKAIEKLPEQCRKIFILSRFEGKSYKEIAEELGISVKTVEYHISKALK  155 (161)
T ss_pred             HHHhhcccccCCCCcHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence                  0        00   011222344444433222        235789999999999999999999988764

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.

>PRK09644 RNA polymerase sigma factor SigM; Provisional

Probab=99.50  E-value=1.5e-13  Score=125.20  Aligned_cols=125  Identities=16%  Similarity=0.004  Sum_probs=100.1

Q ss_pred             HHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhhccccccc--
Q 012638          297 REELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIP--  374 (459)
Q Consensus       297 re~LI~~nlrLV~sIAkry~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIrnaI~d~Lrk~sr~irlP--  374 (459)
                      ++.|+..|.+.|+.+|+++.++..+++|++||+++.+|+++++|++.   +|.+|++.+++|.+++++|+.++.....  
T Consensus         3 ~~~l~~~y~~~l~~~~~~~~~~~~~AeDlvQe~fl~~~~~~~~~~~~---~~~~wL~~i~~n~~~d~~R~~~~~~~~~~~   79 (165)
T PRK09644          3 IEEIYKMYINDVYRYLFSLTKSHHAAEDLLQETFYRAYIYLEDYDNQ---KVKPWLFKVAYHTFIDFVRKEKKVSFVGTD   79 (165)
T ss_pred             HHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhHHhcccc---chHHHHHHHHHHHHHHHHHhhhhccccchh
Confidence            67899999999999999999999999999999999999999999863   5999999999999999999876432211  


Q ss_pred             ----------cc---hHHHHHHHHHHHHHHHHHc--------CCCCCHHHHHHHhCCCHHHHHHHHHhhcc
Q 012638          375 ----------CK---LNREISKIQKARKALTNSH--------GKYPEDIEIAKYTGLSLAEIRSASECLRI  424 (459)
Q Consensus       375 ----------~~---v~e~i~kI~ka~~~L~~~l--------gr~PT~eEIAe~LGIS~e~Vk~~l~~ar~  424 (459)
                                ..   ..+....+.++...|+...        -.+.+++|||+.||+|+++|+..+++++.
T Consensus        80 ~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~v~~l~~~~g~s~~eIA~~lgis~~tv~~~l~Rar~  150 (165)
T PRK09644         80 EIEAIQAESTEEYVVAKNSYEKLIQIIHTLPVIEAQAILLCDVHELTYEEAASVLDLKLNTYKSHLFRGRK  150 (165)
T ss_pred             HHhhhcccChHHHHHHHHHHHHHHHHHHhCCHHHHHHHHhHHHhcCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence                      01   0112234445555444432        25679999999999999999999998875

>PRK12533 RNA polymerase sigma factor; Provisional

Probab=99.50  E-value=2e-13  Score=131.62  Aligned_cols=131  Identities=15%  Similarity=0.053  Sum_probs=104.9

Q ss_pred             HhchHHHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhhccc
Q 012638          291 AFGWYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARG  370 (459)
Q Consensus       291 ~~G~~Are~LI~~nlrLV~sIAkry~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIrnaI~d~Lrk~sr~  370 (459)
                      .....+++.|+..|.+.|+.+++++.++..+++|++||+|+.+|+.+++|++  + .|.+|++++++|.++++++++++.
T Consensus        14 ~~~~~~f~~l~~~~~~~l~~~~~~~~~d~~dAEDlvQEvflkl~~~~~~~~~--~-~~~aWL~~IarN~~~d~~Rk~~~~   90 (216)
T PRK12533         14 AARGERFRQLVLPHLDAAYNLARWLCGNASDADDVVQEACMRALRFFDSFRG--D-NARPWLLAIVRHTWYSEWRRRANA   90 (216)
T ss_pred             hhhHHHHHHHHHHHHHHHHHHHHHHhCCHhhHHHHHHHHHHHHHHhHHhcCc--c-chHhHHHHHHHHHHHHHHHhhccc
Confidence            3345599999999999999999999999999999999999999999999985  2 599999999999999999976532


Q ss_pred             ccc------cc------------c------hHHHHHHHHHHHHHHHHHc--------CCCCCHHHHHHHhCCCHHHHHHH
Q 012638          371 IKI------PC------------K------LNREISKIQKARKALTNSH--------GKYPEDIEIAKYTGLSLAEIRSA  418 (459)
Q Consensus       371 irl------P~------------~------v~e~i~kI~ka~~~L~~~l--------gr~PT~eEIAe~LGIS~e~Vk~~  418 (459)
                      ...      +.            .      ..+....+.+++..|+...        -.+.+++|||+.||||+++|+..
T Consensus        91 ~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~e~~~~l~~al~~Lp~~~R~v~~L~y~eg~s~~EIAe~LgiS~~tVk~~  170 (216)
T PRK12533         91 HEVAAPDTLDDADSLDDWQPAGEDPLALLLRAEDVRLVNAALAKLPVEYREVLVLRELEDMSYREIAAIADVPVGTVMSR  170 (216)
T ss_pred             ccccccccccccccccccccCCCCHHHHHHHHHHHHHHHHHHHcCCHHHHhHhhhHHhcCCCHHHHHHHHCCCHHHHHHH
Confidence            110      00            0      0123344666666665543        25689999999999999999999


Q ss_pred             HHhhcc
Q 012638          419 SECLRI  424 (459)
Q Consensus       419 l~~ar~  424 (459)
                      +++++.
T Consensus       171 L~RAr~  176 (216)
T PRK12533        171 LARARR  176 (216)
T ss_pred             HHHHHH
Confidence            998875

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

Probab=99.49  E-value=2.1e-13  Score=137.04  Aligned_cols=130  Identities=17%  Similarity=0.070  Sum_probs=103.1

Q ss_pred             chH-HHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhhcccc
Q 012638          293 GWY-CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGI  371 (459)
Q Consensus       293 G~~-Are~LI~~nlrLV~sIAkry~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIrnaI~d~Lrk~sr~i  371 (459)
                      |+. |+++|+..|.+.|+++|++++++..+++|++||.|+.+|+.+++|+..  ..|.||++++++|.+++++|++.+..
T Consensus         2 gd~~af~~l~~~~~~~l~~~a~~~~~~~~~AEDivQe~fl~~~~~~~~~~~~--~~~~~WL~~Ia~n~~~d~~Rk~~~~~   79 (324)
T TIGR02960         2 VDGAAFTALAEPHRRELLAHCYRMLGSLHEAEDLVQETLLRAWRARDRFEGR--SSVRTWLYRIATNACLDALEARQRRP   79 (324)
T ss_pred             CcHHHHHHHHHHHHHHHHHHHHHhcCChhhHHHHHHHHHHHHHhhhhccCcc--cchHHHHHHHHHHHHHHHHHhccCCc
Confidence            554 999999999999999999999999999999999999999999999864  36999999999999999999764321


Q ss_pred             c--------------------------ccc-----------c---h---HHH-HHHHHHHHHHHHHHc--------CCCC
Q 012638          372 K--------------------------IPC-----------K---L---NRE-ISKIQKARKALTNSH--------GKYP  399 (459)
Q Consensus       372 r--------------------------lP~-----------~---v---~e~-i~kI~ka~~~L~~~l--------gr~P  399 (459)
                      .                          ++.           .   .   .+. ...+..++..|+...        -.+.
T Consensus        80 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~l~~~l~~Lp~~~R~v~~L~~~~g~  159 (324)
T TIGR02960        80 RPVGLGAPSADGTAAASEAAEVTWLEPLPDLTLDLDDPAAADPSVAAGSRESVRLAFVAAIQYLPPRQRAVLLLRDVLGW  159 (324)
T ss_pred             CccccCCCCCcccccccccccccccCCCCccccccccCCCCCHHHHHHHHHHHHHHHHHHHHhCCHHHhhHhhhHHHhCC
Confidence            1                          000           0   0   011 123455555555543        2568


Q ss_pred             CHHHHHHHhCCCHHHHHHHHHhhcc
Q 012638          400 EDIEIAKYTGLSLAEIRSASECLRI  424 (459)
Q Consensus       400 T~eEIAe~LGIS~e~Vk~~l~~ar~  424 (459)
                      +++|||+.||||+++|+..+.+++.
T Consensus       160 s~~EIA~~lgis~~tV~~~l~Rar~  184 (324)
T TIGR02960       160 RAAETAELLGTSTASVNSALQRARA  184 (324)
T ss_pred             CHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            9999999999999999999998875

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.

>PRK08311 putative RNA polymerase sigma factor SigI; Reviewed

Probab=99.49  E-value=4.8e-13  Score=131.14  Aligned_cols=91  Identities=19%  Similarity=0.293  Sum_probs=82.1

Q ss_pred             CHHHHHHHHHhchH-HHHHHHHHhHHHHHHHHHHhhCCCC--CHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHH
Q 012638          282 SERVLKQHLAFGWY-CREELIKSTRPLVLFLARNYRGLGI--PFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRK  358 (459)
Q Consensus       282 deeeL~~~l~~G~~-Are~LI~~nlrLV~sIAkry~g~g~--d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIrn  358 (459)
                      +.+.|+..++.|+. |++.|+..|.++|+++|.+++++..  +.+|++|||++++|+++++||+.+|.+|.||++++|+|
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            45677888899977 9999999999999999999998875  59999999999999999999999888899999999999


Q ss_pred             HHHHHHHhhccccc
Q 012638          359 SISKMVARHARGIK  372 (459)
Q Consensus       359 aI~d~Lrk~sr~ir  372 (459)
                      .+++++|++.+...
T Consensus        84 ~~iDylRk~~~~~~   97 (237)
T PRK08311         84 RLIDYFRKESKHNL   97 (237)
T ss_pred             HHHHHHHHhhcccc
Confidence            99999998766433

>PRK12528 RNA polymerase sigma factor; Provisional

Probab=99.48  E-value=3e-13  Score=122.63  Aligned_cols=127  Identities=17%  Similarity=0.096  Sum_probs=100.5

Q ss_pred             HHHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhhcccc---
Q 012638          295 YCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGI---  371 (459)
Q Consensus       295 ~Are~LI~~nlrLV~sIAkry~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIrnaI~d~Lrk~sr~i---  371 (459)
                      .|+++|+..|.+.|+.+|.+++++..+++|++||+|+.+|+..+.|++   ..|.+|++++++|.+++++|++.+..   
T Consensus         4 ~a~~~l~~~~~~~l~~~~~~~~~~~~~AeDivQe~flk~~~~~~~~~~---~~~~~wl~~i~~n~~~d~~R~~~~~~~~~   80 (161)
T PRK12528          4 ATVEGLYSAHHHWLTGWLRRRLGCPQSAADLAQDTFVKVLVARETAQI---IEPRAFLTTIAKRVLCNHYRRQDLERAYL   80 (161)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHcCCcccHHHHHHHHHHHHHhccccccc---cCHHHHHHHHHHHHHHHHHHHHHHHHhhH
Confidence            489999999999999999999999999999999999999999988864   26999999999999999999754211   


Q ss_pred             ----cccc----c------hHHHHHHHHHHHHHHHHHc--------CCCCCHHHHHHHhCCCHHHHHHHHHhhcc
Q 012638          372 ----KIPC----K------LNREISKIQKARKALTNSH--------GKYPEDIEIAKYTGLSLAEIRSASECLRI  424 (459)
Q Consensus       372 ----rlP~----~------v~e~i~kI~ka~~~L~~~l--------gr~PT~eEIAe~LGIS~e~Vk~~l~~ar~  424 (459)
                          ..|.    .      ..+....+.++...|+...        -.+.+++|||+.||+|+++|+..+.+++.
T Consensus        81 ~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~v~~L~~~~g~s~~EIA~~l~is~~tV~~~l~ra~~  155 (161)
T PRK12528         81 EALAQLPERVAPSEEERAIILETLVELDQLLDGLPPLVKRAFLLAQVDGLGYGEIATELGISLATVKRYLNKAAM  155 (161)
T ss_pred             HHhhccccccCCCHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence                0110    0      0122234555555555433        36789999999999999999999888754

>PRK09642 RNA polymerase sigma factor SigW; Reviewed

Probab=99.48  E-value=2e-13  Score=123.43  Aligned_cols=121  Identities=11%  Similarity=0.060  Sum_probs=95.7

Q ss_pred             HHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhhccccc-cc-----
Q 012638          301 IKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIK-IP-----  374 (459)
Q Consensus       301 I~~nlrLV~sIAkry~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIrnaI~d~Lrk~sr~ir-lP-----  374 (459)
                      +..|.+.|+.+|.+++++..+++|++||+|+.+|+++++|++.   .|.||++.+++|.+++++|++.+... ..     
T Consensus         1 ~~~y~~~l~~~~~~~~~~~~~AeDlvQe~fl~~~~~~~~~~~~---~~~~wl~~ia~n~~~d~~Rk~~~~~~~~~~~~~~   77 (160)
T PRK09642          1 MQTYRHYIFQVIFSILRHEEDAKDVTQEVFVKIHASLPNYQFR---GLKTWMARIATNHAIDYKRKKARENEELSLCKET   77 (160)
T ss_pred             CchHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHhcccccccc---hhHHHHHHHHHHHHHHHHHHhcccccccccchhh
Confidence            3578999999999999999999999999999999999999863   49999999999999999997654211 00     


Q ss_pred             -----c--ch------HHHHHHHHHHHHHHHHHc--------CCCCCHHHHHHHhCCCHHHHHHHHHhhcc
Q 012638          375 -----C--KL------NREISKIQKARKALTNSH--------GKYPEDIEIAKYTGLSLAEIRSASECLRI  424 (459)
Q Consensus       375 -----~--~v------~e~i~kI~ka~~~L~~~l--------gr~PT~eEIAe~LGIS~e~Vk~~l~~ar~  424 (459)
                           .  ..      .+....+.++...|+...        -.+.|++|||+.||+|+++|+..+.+++.
T Consensus        78 ~~~~~~~~~~~~~~~~~e~~~~l~~~l~~Lp~~~r~v~~l~~~~g~s~~EIA~~lgis~~tV~~~l~Rar~  148 (160)
T PRK09642         78 EENIKSSHNIEDLLLTKEQKLLIAQKLRELPENYRDVVLAHYLEEKSYQEIALQEKIEVKTVEMKLYRARK  148 (160)
T ss_pred             hhhccCCCChHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHhCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence                 0  00      011233555566555543        36789999999999999999999998875

>PRK12540 RNA polymerase sigma factor; Provisional

Probab=99.47  E-value=6.5e-13  Score=124.14  Aligned_cols=127  Identities=16%  Similarity=0.156  Sum_probs=103.1

Q ss_pred             HHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhhcccccc--
Q 012638          296 CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKI--  373 (459)
Q Consensus       296 Are~LI~~nlrLV~sIAkry~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIrnaI~d~Lrk~sr~irl--  373 (459)
                      ++..++..|.+.|+.+|.+++++..+++|++||+|+.+|+..++|++..  .|.+|++.+++|.++++++++.+....  
T Consensus         6 ~~~~~~~~~~~~l~~~~~~~~~~~~~AEDivQevflkl~~~~~~~~~~~--~~~~WL~~Ia~n~~~d~~Rk~~~~~~~~~   83 (182)
T PRK12540          6 SLRDDILAAVPSLRAFAISLSGNGDRADDLVQETLLRALANIDSFQPGS--NLPAWLFTILRNLFRSDYRKRRREVEDAD   83 (182)
T ss_pred             HHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhHHhcCCCc--hHHHHHHHHHHHHHHHHHHhccccccccc
Confidence            6789999999999999999999999999999999999999999998753  699999999999999999986543211  


Q ss_pred             --------ccc---hHHHHHHHHHHHHHHHHHc--------CCCCCHHHHHHHhCCCHHHHHHHHHhhcc
Q 012638          374 --------PCK---LNREISKIQKARKALTNSH--------GKYPEDIEIAKYTGLSLAEIRSASECLRI  424 (459)
Q Consensus       374 --------P~~---v~e~i~kI~ka~~~L~~~l--------gr~PT~eEIAe~LGIS~e~Vk~~l~~ar~  424 (459)
                              +..   .......+..++..|+...        -.+.+++|||+.||||+++|+..+.+++.
T Consensus        84 ~~~~~~~~~~~~~~~~~~~~~l~~~l~~Lp~~~R~v~~L~~~~g~s~~EIA~~Lgis~~tV~~~l~RAr~  153 (182)
T PRK12540         84 GSYAKTLKSQPGQNAHLEFEEFRAALDKLPQDQREALILVGASGFSYEDAAAICGCAVGTIKSRVNRARS  153 (182)
T ss_pred             ccccccccCCCchHHHHHHHHHHHHHHhCCHHHHHHhhHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence                    000   1112234566666665543        36789999999999999999999998875

>PRK09639 RNA polymerase sigma factor SigX; Provisional

Probab=99.46  E-value=6.4e-13  Score=120.51  Aligned_cols=125  Identities=15%  Similarity=0.050  Sum_probs=99.2

Q ss_pred             HHHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhhccccccc
Q 012638          295 YCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIP  374 (459)
Q Consensus       295 ~Are~LI~~nlrLV~sIAkry~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIrnaI~d~Lrk~sr~irlP  374 (459)
                      .++++|+..|.+.|+.+|.++.++..+++|++||+|+.+|++  .|+.  +..|.||++.+++|.+++++|+..+.....
T Consensus         3 ~~f~~l~~~y~~~l~~~~~~~~~~~~~aeDlvQe~fi~~~~~--~~~~--~~~~~~wl~~i~rn~~~d~~rk~~~~~~~~   78 (166)
T PRK09639          3 ETFEDLFEQYYPDVVQQIFYIVKDRTQAEDLAQEVFLRLYRS--DFKG--IENEKGWLIKSARNVAYNYLRSEKRRRARI   78 (166)
T ss_pred             hHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHH--hccc--ccchHHHHHHHHHHHHHHHHHHhccccccc
Confidence            489999999999999999999999999999999999999999  6764  347999999999999999999865432111


Q ss_pred             ---------------cch---HHHHHHHHHHHHHHHH--------HcCCCCCHHHHHHHhCCCHHHHHHHHHhhcc
Q 012638          375 ---------------CKL---NREISKIQKARKALTN--------SHGKYPEDIEIAKYTGLSLAEIRSASECLRI  424 (459)
Q Consensus       375 ---------------~~v---~e~i~kI~ka~~~L~~--------~lgr~PT~eEIAe~LGIS~e~Vk~~l~~ar~  424 (459)
                                     ...   .+....+.++...|+.        .+ .+.+++|||+.||+|+.+|+..+.+++.
T Consensus        79 ~~~~~~~~~~~~~~~e~~~~~~~~~~~l~~~l~~L~~~~r~il~l~~-~g~s~~eIA~~lgis~~tV~~~i~ra~~  153 (166)
T PRK09639         79 LGEFQWQEVDNEPSPEEIWIRKEEITKVQEVLAKMTERDRTVLLLRF-SGYSYKEIAEALGIKESSVGTTLARAKK  153 (166)
T ss_pred             cchhhhhhccCCCChHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHH-cCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence                           000   1222334455544433        24 7789999999999999999999988875

>PRK09647 RNA polymerase sigma factor SigE; Reviewed

Probab=99.45  E-value=9.2e-13  Score=125.49  Aligned_cols=130  Identities=24%  Similarity=0.201  Sum_probs=103.3

Q ss_pred             hchH-HHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhhccc
Q 012638          292 FGWY-CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARG  370 (459)
Q Consensus       292 ~G~~-Are~LI~~nlrLV~sIAkry~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIrnaI~d~Lrk~sr~  370 (459)
                      .|+. ++++|+..|.+.|+.++.++.++..+++|++||+++.+|+...+|++  + +|.+|++.+++|.+++++|+..+.
T Consensus        24 ~~d~~a~~~l~~~~~~~L~~~~~~~~~~~~~AEDivQEvflkl~~~~~~~~~--~-~~~~wL~~iarn~~~d~~Rk~~~~  100 (203)
T PRK09647         24 KATMPSWEELVRQHADRVYRLAYRLSGNQHDAEDLTQETFIRVFRSLQNYQP--G-TFEGWLHRITTNLFLDMVRRRARI  100 (203)
T ss_pred             CCCHHHHHHHHHHHHHHHHHHHHHHhCCHhHHHHHHHHHHHHHHHhHHhcCC--c-ccHHHHHHHHHHHHHHHHHhcccC
Confidence            3454 99999999999999999999999999999999999999999999985  3 699999999999999999987431


Q ss_pred             --cccc-------c------c---hHHHHHHHHHHHHHHHHHc--------CCCCCHHHHHHHhCCCHHHHHHHHHhhcc
Q 012638          371 --IKIP-------C------K---LNREISKIQKARKALTNSH--------GKYPEDIEIAKYTGLSLAEIRSASECLRI  424 (459)
Q Consensus       371 --irlP-------~------~---v~e~i~kI~ka~~~L~~~l--------gr~PT~eEIAe~LGIS~e~Vk~~l~~ar~  424 (459)
                        ..++       .      .   ..+....+..++..|+...        ..+.+++|||+.||||+++|+..+.+++.
T Consensus       101 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~L~~L~~~~r~v~~L~~~~g~s~~EIA~~Lgis~~tV~~~l~RArk  180 (203)
T PRK09647        101 RMEALPEDYDRVPGDEPNPEQIYHDARLDPDLQAALDSLPPEFRAAVVLCDIEGLSYEEIAATLGVKLGTVRSRIHRGRQ  180 (203)
T ss_pred             ccccccccccccCCCCCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence              1010       0      0   0112233455555554432        36789999999999999999999998875

>PRK12532 RNA polymerase sigma factor; Provisional

Probab=99.45  E-value=7.3e-13  Score=124.06  Aligned_cols=125  Identities=16%  Similarity=0.102  Sum_probs=98.4

Q ss_pred             HHHHHHhHHHHHHHHHHhhCCCCC-HHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhhccccccc--
Q 012638          298 EELIKSTRPLVLFLARNYRGLGIP-FSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIP--  374 (459)
Q Consensus       298 e~LI~~nlrLV~sIAkry~g~g~d-~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIrnaI~d~Lrk~sr~irlP--  374 (459)
                      +..+..|.+.|+.+|++++++..+ ++|++||+|+.+|+++++|++.  .+|.||++.+++|.+++++|++++.....  
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            466788999999999999999888 9999999999999999999864  37999999999999999999875432110  


Q ss_pred             ----------------------c----c---------hHHHHHHHHHHHHHHHHHc--------CCCCCHHHHHHHhCCC
Q 012638          375 ----------------------C----K---------LNREISKIQKARKALTNSH--------GKYPEDIEIAKYTGLS  411 (459)
Q Consensus       375 ----------------------~----~---------v~e~i~kI~ka~~~L~~~l--------gr~PT~eEIAe~LGIS  411 (459)
                                            .    .         ..+....+.++...|+...        -.+.+++|||+.||||
T Consensus        86 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~e~~~~l~~~l~~L~~~~r~i~~L~~~~g~s~~EIA~~lgis  165 (195)
T PRK12532         86 LDDELLDEAFESHFSQNGHWTPEGQPQHWNTPEKSLNNNEFQKILQSCLYNLPENTARVFTLKEILGFSSDEIQQMCGIS  165 (195)
T ss_pred             ccccccchhhhhhhccccccccccCccccCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHhhhHHHhCCCHHHHHHHHCCC
Confidence                                  0    0         0112233555555555432        2568999999999999


Q ss_pred             HHHHHHHHHhhcc
Q 012638          412 LAEIRSASECLRI  424 (459)
Q Consensus       412 ~e~Vk~~l~~ar~  424 (459)
                      +++|+..+.+++.
T Consensus       166 ~~tVk~~l~Rar~  178 (195)
T PRK12532        166 TSNYHTIMHRARE  178 (195)
T ss_pred             HHHHHHHHHHHHH
Confidence            9999999998875

>PRK12545 RNA polymerase sigma factor; Provisional

Probab=99.45  E-value=5.5e-13  Score=126.23  Aligned_cols=124  Identities=15%  Similarity=0.042  Sum_probs=98.1

Q ss_pred             HHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhhccccccc---c
Q 012638          299 ELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIP---C  375 (459)
Q Consensus       299 ~LI~~nlrLV~sIAkry~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIrnaI~d~Lrk~sr~irlP---~  375 (459)
                      .++..|.+.|+.+|++++++..+++|++||+|+.+|+.+++|++.  ..|.||++.+++|.+++++|++.+...++   .
T Consensus        12 ~~~~~~~~~l~~~~~~~~~d~~~AEDivQe~fl~~~~~~~~~~~~--~~~~~WL~~IarN~~~d~~Rk~~r~~~~~~~~~   89 (201)
T PRK12545         12 AYLAQLRHDLLRFARLQLRDADAAEDAVQEALAAAWSQAGRFAGQ--SAHKTWVFGILRNKLIDTLRARQRTVNLSALDA   89 (201)
T ss_pred             HHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhhhhcccc--chHHHHHHHHHHHHHHHHHHhhccccccccccc
Confidence            458899999999999999999999999999999999999999975  36999999999999999999876432211   0


Q ss_pred             -----------------------------chH------HHHHHHHHHHHHHHHHc--------CCCCCHHHHHHHhCCCH
Q 012638          376 -----------------------------KLN------REISKIQKARKALTNSH--------GKYPEDIEIAKYTGLSL  412 (459)
Q Consensus       376 -----------------------------~v~------e~i~kI~ka~~~L~~~l--------gr~PT~eEIAe~LGIS~  412 (459)
                                                   ...      +....+.++...|+...        ..+.+++|||+.||+|+
T Consensus        90 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~L~~Lp~~~r~v~~L~~~eg~s~~EIA~~lgis~  169 (201)
T PRK12545         90 ELDGEALLDRELFKDNGHWAAHAKPRPWPKPETILQQQQFWTLFETCLDHLPEQIGRVFMMREFLDFEIDDICTELTLTA  169 (201)
T ss_pred             ccchhhhhhhhhhcccccccccccCcCCCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHHCcCH
Confidence                                         000      11123455555554432        36789999999999999


Q ss_pred             HHHHHHHHhhcc
Q 012638          413 AEIRSASECLRI  424 (459)
Q Consensus       413 e~Vk~~l~~ar~  424 (459)
                      ++|+..+.+++.
T Consensus       170 ~tVk~~l~RAr~  181 (201)
T PRK12545        170 NHCSVLLYRART  181 (201)
T ss_pred             HHHHHHHHHHHH
Confidence            999999998875

>PRK09637 RNA polymerase sigma factor SigZ; Provisional

Probab=99.44  E-value=1.4e-12  Score=121.71  Aligned_cols=126  Identities=15%  Similarity=0.115  Sum_probs=99.8

Q ss_pred             HHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhhccccccccc
Q 012638          297 REELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIPCK  376 (459)
Q Consensus       297 re~LI~~nlrLV~sIAkry~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIrnaI~d~Lrk~sr~irlP~~  376 (459)
                      ++.|+..|.+.|+.+|.++.++..+++|++||.++.+|+.+..|++.  .+|.||++.+++|.+++++|++.+...++..
T Consensus         3 ~~~l~~~y~~~l~~~~~~~~~~~~~aeDi~QEvflkl~~~~~~~~~~--~~~~~wL~~i~~n~~~d~~Rk~~~~~~~~~~   80 (181)
T PRK09637          3 LESIWSEYKAQLKAFLHSRVSNEADVDDLLQEVLIKTHSNLHSLKDG--SSIKSWLYQIANNTIIDFYRKKNRSEELPDD   80 (181)
T ss_pred             HHHHHHHHHHHHHHHHHHHhCChhhHHHHHHHHHHHHHHhHHHhccc--cchHHHHHHHHHHHHHHHHHhccccCCcchh
Confidence            67899999999999999999999999999999999999999999853  4799999999999999999977544332210


Q ss_pred             ------------hHHHHHHHHHHHHHHHHHc--------CCCCCHHHHHHHhCCCHHHHHHHHHhhcc
Q 012638          377 ------------LNREISKIQKARKALTNSH--------GKYPEDIEIAKYTGLSLAEIRSASECLRI  424 (459)
Q Consensus       377 ------------v~e~i~kI~ka~~~L~~~l--------gr~PT~eEIAe~LGIS~e~Vk~~l~~ar~  424 (459)
                                  ..+....+..+...|+...        -.+.+.+|||+.||+|+++|+..+.+++.
T Consensus        81 ~~~~~~~~~~~~~~e~~~~l~~~l~~L~~~~r~i~~l~~~~g~~~~EIA~~lgis~~tV~~~l~Rar~  148 (181)
T PRK09637         81 LLFEDEEREENAKKELAPCLRPFIDALPEKYAEALRLTELEGLSQKEIAEKLGLSLSGAKSRVQRGRV  148 (181)
T ss_pred             hhccCCChhHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHhcCCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence                        0111223334444443322        36789999999999999999999888864

>PRK12530 RNA polymerase sigma factor; Provisional

Probab=99.44  E-value=9.2e-13  Score=123.42  Aligned_cols=125  Identities=13%  Similarity=0.062  Sum_probs=98.8

Q ss_pred             HHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhhccccccc---
Q 012638          298 EELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIP---  374 (459)
Q Consensus       298 e~LI~~nlrLV~sIAkry~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIrnaI~d~Lrk~sr~irlP---  374 (459)
                      +..|..|.+.|+.+|.+++++..+++|++||+|+.+|+..++|++.  .+|.||++++++|.+++++|++.+.....   
T Consensus        10 ~~~~~~~~~~l~~~~~~~~~d~~~AeDivQe~flk~~~~~~~~~~~--~~~~~wL~~Ia~n~~~d~~Rk~~~~~~~~~~~   87 (189)
T PRK12530         10 SLEIEEIRLQMLKFATLQLKDADLAEDVVQEALVSAYKNADSFKGQ--SALKTWIFAILKNKIIDLIRYRKRFVNESELI   87 (189)
T ss_pred             HHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHhchhccCC--ccHHHHHHHHHHHHHHHHHHhhccCCCccccc
Confidence            4567888999999999999999999999999999999999999875  36999999999999999999775432110   


Q ss_pred             ----------------------cc--h-------HHHHHHHHHHHHHHHHHc--------CCCCCHHHHHHHhCCCHHHH
Q 012638          375 ----------------------CK--L-------NREISKIQKARKALTNSH--------GKYPEDIEIAKYTGLSLAEI  415 (459)
Q Consensus       375 ----------------------~~--v-------~e~i~kI~ka~~~L~~~l--------gr~PT~eEIAe~LGIS~e~V  415 (459)
                                            ..  .       .+....+..++.+|+...        -.+.|++|||+.||+|+++|
T Consensus        88 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~Lp~~~R~v~~L~~~~g~s~~EIA~~lgis~~tV  167 (189)
T PRK12530         88 EEDSPNSFFDEKGHWKPEYYEPSEWQEVENTVYKEEFWLIFEACLNHLPAQQARVFMMREYLELSSEQICQECDISTSNL  167 (189)
T ss_pred             ccccchhhhcccccccccccCCccccCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHhHHHHcCCCHHHHHHHHCCCHHHH
Confidence                                  00  0       011123555666665543        25789999999999999999


Q ss_pred             HHHHHhhcc
Q 012638          416 RSASECLRI  424 (459)
Q Consensus       416 k~~l~~ar~  424 (459)
                      +..+.+++.
T Consensus       168 k~~l~RAr~  176 (189)
T PRK12530        168 HVLLYRARL  176 (189)
T ss_pred             HHHHHHHHH
Confidence            999998875

>TIGR02950 SigM_subfam RNA polymerase sigma factor, SigM family

Probab=99.44  E-value=7.7e-13  Score=118.36  Aligned_cols=121  Identities=17%  Similarity=0.038  Sum_probs=96.5

Q ss_pred             HHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhhcccccc-----c-
Q 012638          301 IKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKI-----P-  374 (459)
Q Consensus       301 I~~nlrLV~sIAkry~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIrnaI~d~Lrk~sr~irl-----P-  374 (459)
                      +..|.+.|+.+|.++.++..+++|++||+++.+|+.+++|++   .+|.||++.++++.++++++++.+....     + 
T Consensus         1 y~~~~~~l~~~~~~~~~~~~~aeD~~Qe~~~~l~~~~~~~~~---~~f~~wl~~i~~~~~~d~~r~~~~~~~~~~~~~~~   77 (154)
T TIGR02950         1 YREYMHDVFRYLYRLTKDKHLAEDLLQETFLKAYIHLHSFKD---SSIKPWLFRIARNAFIDWYRKDKKIQTIDDDAIGD   77 (154)
T ss_pred             CchHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhHHHhcC---CchHHHHHHHHHHHHHHHHHHhhhhccccHhhhhh
Confidence            357899999999999999999999999999999999999997   3799999999999999999976432211     0 


Q ss_pred             ---------cch---HHHHHHHHHHHHHHHHHc--------CCCCCHHHHHHHhCCCHHHHHHHHHhhcc
Q 012638          375 ---------CKL---NREISKIQKARKALTNSH--------GKYPEDIEIAKYTGLSLAEIRSASECLRI  424 (459)
Q Consensus       375 ---------~~v---~e~i~kI~ka~~~L~~~l--------gr~PT~eEIAe~LGIS~e~Vk~~l~~ar~  424 (459)
                               ...   .+....+.++...|+...        ..+.+++|||+.||+|+++|+..+.+++.
T Consensus        78 ~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~i~~l~~~~g~s~~eIA~~lgis~~tv~~~l~Ra~~  147 (154)
T TIGR02950        78 LEQHPVESPEHHLLIKIEQEEITHHLSRLPENYRTVLILREFKEFSYKEIAELLNLSLAKVKSNLFRARK  147 (154)
T ss_pred             ccccccCChhHHHHHHHHHHHHHHHHHhCCHhheeeeeehhhccCcHHHHHHHHCCCHHHHHHHHHHHHH
Confidence                     000   112234666666665543        25679999999999999999999998875

This family of RNA polymerase sigma factors is a member of the Sigma-70 subfamily (TIGR02937) and is restricted to certain lineages of the order Bacillales. This family encompasses at least two distinct sigma factors as two proteins are found in each of B. anthracis, B. subtilis subsp. subtilis str. 168, and B. lichiniformis (although these are not apparently the same two in each). One of these is designated as SigM in B. subtilis (Swiss_Prot: SIGM_BACSU) and is activated by various stressors.

>PRK12544 RNA polymerase sigma factor; Provisional

Probab=99.43  E-value=1.2e-12  Score=125.01  Aligned_cols=126  Identities=16%  Similarity=0.137  Sum_probs=99.6

Q ss_pred             HHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhhcccccccc-
Q 012638          297 REELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIPC-  375 (459)
Q Consensus       297 re~LI~~nlrLV~sIAkry~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIrnaI~d~Lrk~sr~irlP~-  375 (459)
                      -..++..|.+.|+.+|++++++..+++|++||+|+.+|+.+.+|+..  .+|.+|++++++|.+++++|++.+....+. 
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            46889999999999999999999999999999999999999999864  369999999999999999997654322110 


Q ss_pred             ---------------------------------ch---HHHHHHHHHHHHHHHHHc--------CCCCCHHHHHHHhCCC
Q 012638          376 ---------------------------------KL---NREISKIQKARKALTNSH--------GKYPEDIEIAKYTGLS  411 (459)
Q Consensus       376 ---------------------------------~v---~e~i~kI~ka~~~L~~~l--------gr~PT~eEIAe~LGIS  411 (459)
                                                       ..   .+....+..++..|+...        -.+.+++|||+.||+|
T Consensus        98 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~e~~~~l~~~L~~L~~~~r~v~~L~~~~g~s~~EIAe~lgis  177 (206)
T PRK12544         98 LRDEEEEEDFEELFDESGHWQKDERPQAWGNPEESLEQEQFWRIFEACLDGLPAKYARVFMMREFIELETNEICHAVDLS  177 (206)
T ss_pred             ccccchhhHHHHhhcccccccccccccccCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHHCcC
Confidence                                             00   011123444555554432        2578999999999999


Q ss_pred             HHHHHHHHHhhcc
Q 012638          412 LAEIRSASECLRI  424 (459)
Q Consensus       412 ~e~Vk~~l~~ar~  424 (459)
                      +++|+..+++++.
T Consensus       178 ~~tV~~~l~RAr~  190 (206)
T PRK12544        178 VSNLNVLLYRARL  190 (206)
T ss_pred             HHHHHHHHHHHHH
Confidence            9999999998875

>PRK12517 RNA polymerase sigma factor; Provisional

Probab=99.43  E-value=2e-12  Score=121.29  Aligned_cols=130  Identities=13%  Similarity=-0.003  Sum_probs=103.3

Q ss_pred             chHHHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhhccccc
Q 012638          293 GWYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIK  372 (459)
Q Consensus       293 G~~Are~LI~~nlrLV~sIAkry~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIrnaI~d~Lrk~sr~ir  372 (459)
                      ...+++.++..|.+.|+.+|.++.++..+++|++||+|+.+|+.+..|++.  ..|.+|++.+++|.+++..+++.+...
T Consensus        21 ~~~~f~~l~~~y~~~l~~~~~~~~~~~~~AeDlvQdvflkl~~~~~~~~~~--~~~~~wL~~Iarn~~~~~~r~~~~~~~   98 (188)
T PRK12517         21 KQRRYEALVKALHADIYRYAYWLCKDKHIAEDLVQETFLRAWRSLDSLKDE--KAAKAWLITILRRENARRFERKQFDLV   98 (188)
T ss_pred             cHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhHHhhcCc--cchHHHHHHHHHHHHHHHHHHhccCcc
Confidence            345999999999999999999999999999999999999999999999864  369999999999999888776432211


Q ss_pred             ------ccc---c---hHHHHHHHHHHHHHHHHHc--------CCCCCHHHHHHHhCCCHHHHHHHHHhhcc
Q 012638          373 ------IPC---K---LNREISKIQKARKALTNSH--------GKYPEDIEIAKYTGLSLAEIRSASECLRI  424 (459)
Q Consensus       373 ------lP~---~---v~e~i~kI~ka~~~L~~~l--------gr~PT~eEIAe~LGIS~e~Vk~~l~~ar~  424 (459)
                            .+.   .   .......+..++..|+...        ..+.+++|||+.||||+++|+..+.+++.
T Consensus        99 ~~~~~~~~~~~~~~~e~~~~~~~l~~~l~~Lp~~~r~v~~l~~~~g~s~~EIA~~lgis~~tV~~~l~Rar~  170 (188)
T PRK12517         99 DIEDDSIEDDASHSSEEEMEQEWLRRQIAKLDPEYREPLLLQVIGGFSGEEIAEILDLNKNTVMTRLFRARN  170 (188)
T ss_pred             CcccccccCccccChhHHHHHHHHHHHHHhCCHHHHHHHHHHHHhCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence                  010   0   0111234666666665543        25689999999999999999999998875

>TIGR02959 SigZ RNA polymerase sigma factor, SigZ family

Probab=99.42  E-value=1.3e-12  Score=120.20  Aligned_cols=121  Identities=19%  Similarity=0.168  Sum_probs=96.0

Q ss_pred             HHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhhccccccccch----
Q 012638          302 KSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIPCKL----  377 (459)
Q Consensus       302 ~~nlrLV~sIAkry~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIrnaI~d~Lrk~sr~irlP~~v----  377 (459)
                      ..|.+.|+.+++++.++..+++|++||+++.+|+++++|+..  .+|.+|++.+++|.+++++|+..+...++...    
T Consensus         2 ~~~~~~l~~~~~~~~~~~~~AeDlvQe~fl~l~~~~~~~~~~--~~f~~wl~~iarn~~~d~~Rk~~~~~~~~~~~~~~~   79 (170)
T TIGR02959         2 DEFRSELKAFIKSRVSDASDVEDLLQEVFIKIHRNLPSLKDG--QKIQSWLYQIARNTIIDFYRSKSRSVELPESLLAAD   79 (170)
T ss_pred             chHHHHHHHHHHHHcCCHhhHHHHHHHHHHHHHHHHHhcCCc--ccHHHHHHHHHHHHHHHHHHhccCccccchhhcccC
Confidence            468899999999999999999999999999999999999963  48999999999999999999876544332111    


Q ss_pred             --------HHHHHHHHHHHHHHHHHc--------CCCCCHHHHHHHhCCCHHHHHHHHHhhcc
Q 012638          378 --------NREISKIQKARKALTNSH--------GKYPEDIEIAKYTGLSLAEIRSASECLRI  424 (459)
Q Consensus       378 --------~e~i~kI~ka~~~L~~~l--------gr~PT~eEIAe~LGIS~e~Vk~~l~~ar~  424 (459)
                              .+....+.++...|+...        -.+.+++|||+.||||+.+|+..+.+++.
T Consensus        80 ~~~~~~~~~e~~~~l~~~l~~L~~~~r~v~~l~~~~g~s~~eIA~~lgis~~tV~~~l~Rar~  142 (170)
T TIGR02959        80 SAREETFVKELSQCIPPMIKELPDEYREAIRLTELEGLSQQEIAEKLGLSLSGAKSRVQRGRK  142 (170)
T ss_pred             CccHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence                    111223444444443332        36789999999999999999999998875

This family of RNA polymerase sigma factors is a member of the Sigma-70 subfamily (TIGR02937). One of these is designated as SigZ in B. subtilis (Swiss_Prot: SIGZ_BACSU). Interestingly, this group has a very sporatic distribution, B. subtilis, for instance, being the only sequenced strain of Bacilli with a member. Dechloromonas aromatica RCB appears to have two of these sigma factors. A member appears on a plasmid found in Photobacterium profundum SS9 and Vibrio fischeri ES114 (where a second one is chromosomally encoded).

>PF04542 Sigma70_r2: Sigma-70 region 2 ; InterPro: IPR007627 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription

Probab=99.42  E-value=6.4e-13  Score=103.84  Aligned_cols=70  Identities=24%  Similarity=0.375  Sum_probs=67.1

Q ss_pred             HHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhhcc
Q 012638          300 LIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHAR  369 (459)
Q Consensus       300 LI~~nlrLV~sIAkry~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIrnaI~d~Lrk~sr  369 (459)
                      |++.|.++|+++|.+|.+++.+.+|++||++++||+++++||+.++..|.+|++.+++|.++++++++.+
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            7899999999999999999999999999999999999999999999899999999999999999998764

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 ....

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

Probab=99.41  E-value=1.5e-12  Score=122.04  Aligned_cols=125  Identities=14%  Similarity=0.051  Sum_probs=98.8

Q ss_pred             HHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhhcccccccc--
Q 012638          298 EELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIPC--  375 (459)
Q Consensus       298 e~LI~~nlrLV~sIAkry~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIrnaI~d~Lrk~sr~irlP~--  375 (459)
                      .+.+..|.+.|+.+|++++++..+++|++||+|+++|+..++|++.  .+|.||++.+++|.+++++|++.+....+.  
T Consensus         5 ~~~~~~~~~~l~~~~~~~~~~~~dAeDivQevfl~l~~~~~~~~~~--~~~~~wL~~iarn~~~d~~R~~~r~~~~~~~~   82 (188)
T TIGR02943         5 PQELEQLRRDLLRFARLQLRDRDLAEDAVQETLLAALSHRDSFAGR--SALKTWLFAILKNKIIDALRAKGREVKVSDLD   82 (188)
T ss_pred             HHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhhhhhccc--cHHHHHHHHHHHHHHHHHHHhhcccCCccccc
Confidence            3678899999999999999999999999999999999999999964  479999999999999999997654322110  


Q ss_pred             -------------------------c---------hHHHHHHHHHHHHHHHHHc--------CCCCCHHHHHHHhCCCHH
Q 012638          376 -------------------------K---------LNREISKIQKARKALTNSH--------GKYPEDIEIAKYTGLSLA  413 (459)
Q Consensus       376 -------------------------~---------v~e~i~kI~ka~~~L~~~l--------gr~PT~eEIAe~LGIS~e  413 (459)
                                               .         ..+....+.+++..|+...        -.+.+++|||+.||+|++
T Consensus        83 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~e~~~~l~~~l~~L~~~~r~v~~l~~~~g~s~~EIA~~lgis~~  162 (188)
T TIGR02943        83 DELDDEAFNALFTQNGHWAQHGQPQHWNTPEKQLENKEFWEVFEACLYHLPEQTARVFMMREVLGFESDEICQELEISTS  162 (188)
T ss_pred             cccccchhhhhhccccchhccccccccCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHhCCCHHHHHHHhCCCHH
Confidence                                     0         0011133455555554432        367899999999999999


Q ss_pred             HHHHHHHhhcc
Q 012638          414 EIRSASECLRI  424 (459)
Q Consensus       414 ~Vk~~l~~ar~  424 (459)
                      +|+..+.+++.
T Consensus       163 tvk~rl~Rar~  173 (188)
T TIGR02943       163 NCHVLLYRARL  173 (188)
T ss_pred             HHHHHHHHHHH
Confidence            99999998875

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.

>PRK12546 RNA polymerase sigma factor; Provisional

Probab=99.41  E-value=2.9e-12  Score=120.62  Aligned_cols=126  Identities=17%  Similarity=0.202  Sum_probs=99.7

Q ss_pred             HHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhhccccccc-
Q 012638          296 CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIP-  374 (459)
Q Consensus       296 Are~LI~~nlrLV~sIAkry~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIrnaI~d~Lrk~sr~irlP-  374 (459)
                      +++.|+. |.+.|+++|++++++..+++|++||.|+.+|+.+..|+..  ..|.+|++.+++|.+++++|++.+..... 
T Consensus         9 ~~~~l~~-~~~~l~~~a~~~l~~~~~AEDivQevfl~l~~~~~~~~~~--~~~~awL~~ia~n~~~d~~Rk~~r~~~~~~   85 (188)
T PRK12546          9 PRDELVE-HLPALRAFAISLTRNVAVADDLVQDTIVKAWTNFDKFQEG--TNLRAWLFTILRNTFYSDRRKHKREVPDPE   85 (188)
T ss_pred             HHHHHHH-HHHHHHHHHHHHcCChhhHHHHHHHHHHHHHHHHhccCCC--cchHHHHHHHHHHHHHHHHHHhcccccCcc
Confidence            5666655 7799999999999999999999999999999999999863  36999999999999999999876432110 


Q ss_pred             -----------cc-hHHHHHHHHHHHHHHHHHc--------CCCCCHHHHHHHhCCCHHHHHHHHHhhcc
Q 012638          375 -----------CK-LNREISKIQKARKALTNSH--------GKYPEDIEIAKYTGLSLAEIRSASECLRI  424 (459)
Q Consensus       375 -----------~~-v~e~i~kI~ka~~~L~~~l--------gr~PT~eEIAe~LGIS~e~Vk~~l~~ar~  424 (459)
                                 .. .......+..+...|+...        -.+.+++|||+.||||+.+|+..+.+++.
T Consensus        86 ~~~~~~~~~~~~~~~~~~~~~l~~~L~~Lp~~~r~v~~L~~~~g~s~~EIA~~LgiS~~tVk~~l~Rar~  155 (188)
T PRK12546         86 GVHAASLAVKPAHDGRLAMSDFRAAFAQLPDEQREALILVGASGFSYEEAAEMCGVAVGTVKSRANRARA  155 (188)
T ss_pred             cccccccccCCcchhHHHHHHHHHHHHhCCHHHhHHhhhHHhcCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence                       00 0111234566666665543        25689999999999999999999998875

>PRK09651 RNA polymerase sigma factor FecI; Provisional

Probab=99.38  E-value=4.5e-12  Score=116.75  Aligned_cols=127  Identities=13%  Similarity=0.082  Sum_probs=99.2

Q ss_pred             HHHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhhcccc---
Q 012638          295 YCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGI---  371 (459)
Q Consensus       295 ~Are~LI~~nlrLV~sIAkry~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIrnaI~d~Lrk~sr~i---  371 (459)
                      .|++.++..|.+.|+.++.++.++..+++|++||.|+.+|+. ..|++..  +|.+|++.+++|.+++++|++.+..   
T Consensus        10 ~af~~l~~~~~~~l~~~~~~~~~~~~~AEDlvQe~flkl~~~-~~~~~~~--~~~~wL~~iarn~~~d~~R~~~~~~~~~   86 (172)
T PRK09651         10 LTFESLYGTHHGWLKSWLTRKLQSAFDADDIAQDTFLRVMVS-ETLSTIR--DPRSFLCTIAKRVMVDLFRRNALEKAYL   86 (172)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHcCCHhHHHHHHHHHHHHHHhh-ccccccc--CHHHHHHHHHHHHHHHHHHHHHHHhhhh
Confidence            489999999999999999999999999999999999999998 3565432  5999999999999999999754211   


Q ss_pred             ----cc-----ccc--h---HHHHHHHHHHHHHHHHHc--------CCCCCHHHHHHHhCCCHHHHHHHHHhhcc
Q 012638          372 ----KI-----PCK--L---NREISKIQKARKALTNSH--------GKYPEDIEIAKYTGLSLAEIRSASECLRI  424 (459)
Q Consensus       372 ----rl-----P~~--v---~e~i~kI~ka~~~L~~~l--------gr~PT~eEIAe~LGIS~e~Vk~~l~~ar~  424 (459)
                          .+     |..  .   .+....+..+...|+.+.        ..+.+++|||+.||+|+++|+..+.+++.
T Consensus        87 ~~~~~~~~~~~~~~~~~~~~~e~~~~l~~~l~~L~~~~r~i~~l~~~~g~s~~EIA~~lgis~~tV~~~l~Ra~~  161 (172)
T PRK09651         87 EMLALMPEGGAPSPEERESQLETLQLLDSMLDGLNGKTREAFLLSQLDGLTYSEIAHKLGVSVSSVKKYVAKATE  161 (172)
T ss_pred             hHHhhccccCCCChHHHHHHHHHHHHHHHHHHhCCHHHhHHhhhhhccCCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence                01     110  0   122334566666665543        36689999999999999999999988764

>PRK12511 RNA polymerase sigma factor; Provisional

Probab=99.38  E-value=4.5e-12  Score=118.60  Aligned_cols=127  Identities=13%  Similarity=0.074  Sum_probs=100.1

Q ss_pred             HHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhhccccccc-
Q 012638          296 CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIP-  374 (459)
Q Consensus       296 Are~LI~~nlrLV~sIAkry~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIrnaI~d~Lrk~sr~irlP-  374 (459)
                      ..+..+..+++.|+.+|.++.++..+++|++||.|+.+|+....|+..  .+|.||++.+++|.+++++|++.+..... 
T Consensus         5 ~~~~~~~~~~~~l~~~~~~~~~~~~dAEDivQe~flkl~~~~~~~~~~--~~~~~WL~~Iarn~~id~~Rk~~~~~~~~~   82 (182)
T PRK12511          5 SKRFDVLDQLVPLRRYARSLTRDSAEAEDLVHDALVRALERRASFRSG--GNLRTWLMSILHNAFIDELRRRRVEARRAD   82 (182)
T ss_pred             chhhhHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhHHhcCCc--cchHHHHHHHHHHHHHHHHHhhcccccccc
Confidence            345568899999999999999999999999999999999999999864  37999999999999999999865421110 


Q ss_pred             -----------cc--hHHHHHHHHHHHHHHHHHc--------CCCCCHHHHHHHhCCCHHHHHHHHHhhcc
Q 012638          375 -----------CK--LNREISKIQKARKALTNSH--------GKYPEDIEIAKYTGLSLAEIRSASECLRI  424 (459)
Q Consensus       375 -----------~~--v~e~i~kI~ka~~~L~~~l--------gr~PT~eEIAe~LGIS~e~Vk~~l~~ar~  424 (459)
                                 ..  .......+.++...|+...        -.+.+++|||+.||||+++|+..+.+++.
T Consensus        83 ~~~~~~~~~~~~~~~~~~~~~~l~~~l~~Lp~~~R~v~~L~~~eg~s~~EIA~~lgis~~tV~~~l~Rar~  153 (182)
T PRK12511         83 ELAVLADASLPAAQEHAVRLAQIRDAFFDLPEEQRAALHLVAIEGLSYQEAAAVLGIPIGTLMSRIGRARA  153 (182)
T ss_pred             chhhccccCCCcchHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHhCcCHHHHHHHHHHHHH
Confidence                       00  1112234555666555543        26789999999999999999999988875

>PRK06704 RNA polymerase factor sigma-70; Validated

Probab=99.33  E-value=1.1e-11  Score=120.96  Aligned_cols=133  Identities=15%  Similarity=-0.055  Sum_probs=100.4

Q ss_pred             HHHHHhchH-HHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHH
Q 012638          287 KQHLAFGWY-CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVA  365 (459)
Q Consensus       287 ~~~l~~G~~-Are~LI~~nlrLV~sIAkry~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIrnaI~d~Lr  365 (459)
                      .+....|+. +++.+++.| +.|+.+|.++.++..+++||+||.|+.+|+.   |+..  ..|.||++.+++|.+++++|
T Consensus         9 ~~~~~~~~~~~~~~l~~~y-~~L~r~~~~~~~d~~dAEDlvQE~flk~~~~---~~~~--~~~~~WL~~IarN~~id~~R   82 (228)
T PRK06704          9 LKNHIDMNHSNINFLIEQY-GELKRYCTFLTKNKWDGEDLAQETVCKVLQK---YSNK--DICMTLVYKIARNRWLDQIK   82 (228)
T ss_pred             HhcccCCCHHHHHHHHHHH-HHHHHHHHHHhCCHHHHHHHHHHHHHHHHHH---cCcc--ccHHHHHHHHHHHHHHHHHh
Confidence            444555655 888877777 7899999999999999999999999999986   5543  25999999999999999999


Q ss_pred             hhcccccccc--------c-hHHHHHHHHHHHHHHHHHc--------CCCCCHHHHHHHhCCCHHHHHHHHHhhccC
Q 012638          366 RHARGIKIPC--------K-LNREISKIQKARKALTNSH--------GKYPEDIEIAKYTGLSLAEIRSASECLRIV  425 (459)
Q Consensus       366 k~sr~irlP~--------~-v~e~i~kI~ka~~~L~~~l--------gr~PT~eEIAe~LGIS~e~Vk~~l~~ar~~  425 (459)
                      ++.+...+..        . ..+....+..+...|+...        ..+.|++|||+.||||+++|+..+.+++..
T Consensus        83 k~k~~~~~~~~~~~~~~~~~~~~~~~~l~~~L~~Lp~~~R~v~lL~~~eg~S~~EIAe~LgiS~~tVksrL~Rark~  159 (228)
T PRK06704         83 SKSVHEKIRDQITFEEPHEKIADLHEMVGKVLSSLNVQQSAILLLKDVFQYSIADIAKVCSVSEGAVKASLFRSRNR  159 (228)
T ss_pred             ccccccccccccccCChHHHHHHHHHHHHHHHHhCCHHHhhHhhhHHhhCCCHHHHHHHHCcCHHHHHHHHHHHHHH
Confidence            7654322111        0 1122233455555555543        256799999999999999999999998864

>PRK07037 extracytoplasmic-function sigma-70 factor; Validated

Probab=99.33  E-value=1.2e-11  Score=111.91  Aligned_cols=123  Identities=15%  Similarity=0.142  Sum_probs=94.5

Q ss_pred             HHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhhccccc------
Q 012638          299 ELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIK------  372 (459)
Q Consensus       299 ~LI~~nlrLV~sIAkry~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIrnaI~d~Lrk~sr~ir------  372 (459)
                      +++..|.+.|+.+|.++.++..+++|++||+++++|+....|++.   .|.+|++.+++|.+++++|++++...      
T Consensus         2 ~~~~~~~~~l~~~~~~~~~~~~~aeDivQe~~l~l~~~~~~~~~~---~~~~wl~~iarn~~~d~~R~~~~~~~~~~~~~   78 (163)
T PRK07037          2 DVFVDNRSMLVKIAARIVGCRSRAEDVVQDAFVKLVEAPNQDAVK---QPVAYLFRIVRNLAIDHYRRQALENKYHGDEE   78 (163)
T ss_pred             hHHHHHHHHHHHHHHHHcCCHhHHHHHHHHHHHHHHhccccCCcc---cHHHHHHHHHHHHHHHHHHhhccccccccccc
Confidence            467889999999999999999999999999999999998888753   48899999999999999997653211      


Q ss_pred             ----ccc---c------hHHHHHHHHHHHHHHHHHc--------CCCCCHHHHHHHhCCCHHHHHHHHHhhcc
Q 012638          373 ----IPC---K------LNREISKIQKARKALTNSH--------GKYPEDIEIAKYTGLSLAEIRSASECLRI  424 (459)
Q Consensus       373 ----lP~---~------v~e~i~kI~ka~~~L~~~l--------gr~PT~eEIAe~LGIS~e~Vk~~l~~ar~  424 (459)
                          .+.   .      ..+....+.++...|+...        -.+.+++|||+.||+|+++|+..+.+++.
T Consensus        79 ~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~v~~l~~~~~~s~~EIA~~lgis~~tV~~~l~ra~~  151 (163)
T PRK07037         79 DGLDVPSPEASPEAALINRDTLRHVADALSELPARTRYAFEMYRLHGETQKDIARELGVSPTLVNFMIRDALV  151 (163)
T ss_pred             cccccCCCCCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence                110   0      0112233444555444332        36789999999999999999999887764

>PRK12527 RNA polymerase sigma factor; Reviewed

Probab=99.32  E-value=1.2e-11  Score=112.03  Aligned_cols=121  Identities=12%  Similarity=0.030  Sum_probs=94.2

Q ss_pred             HHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhhcccccc-------
Q 012638          301 IKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKI-------  373 (459)
Q Consensus       301 I~~nlrLV~sIAkry~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIrnaI~d~Lrk~sr~irl-------  373 (459)
                      +..|.+.++.++.+++++..+++|++||+++.+|+..+.|++  + +|.||++.+++|.+++++|++.+....       
T Consensus         1 ~~~~~~~l~~~~~~~~~~~~~aeDi~Qevf~~l~~~~~~~~~--~-~~~~wL~~ia~n~~~d~~R~~~~~~~~~~~~~~~   77 (159)
T PRK12527          1 MENYYRELVRFLSARLGNRQAAEDVAHDAYLRVLERSSSAQI--E-HPRAFLYRTALNLVVDRHRRHRVRQAEPLEVLDE   77 (159)
T ss_pred             ChhHHHHHHHHHHHHcCCHhhHHHHHHHHHHHHHhccccccc--c-chHHHHHHHHHHHHHHHHHHHhcccccchhhhhc
Confidence            357889999999999999999999999999999999999875  2 799999999999999999975321110       


Q ss_pred             ------c--cch---HHHHHHHHHHHHHHHHHc--------CCCCCHHHHHHHhCCCHHHHHHHHHhhcc
Q 012638          374 ------P--CKL---NREISKIQKARKALTNSH--------GKYPEDIEIAKYTGLSLAEIRSASECLRI  424 (459)
Q Consensus       374 ------P--~~v---~e~i~kI~ka~~~L~~~l--------gr~PT~eEIAe~LGIS~e~Vk~~l~~ar~  424 (459)
                            |  ...   .+....+..+...|+...        ..+.+++|||+.||+|+++|+..+.+++.
T Consensus        78 ~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~v~~l~~~~~~s~~eIA~~lgis~~tv~~~l~ra~~  147 (159)
T PRK12527         78 EERLHSPSPQTRLDLGQRLALLQRALAELPPACRDSFLLRKLEGLSHQQIAEHLGISRSLVEKHIVNAMK  147 (159)
T ss_pred             cccccCCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence                  0  000   112234556666555543        36789999999999999999999988865

>PRK12525 RNA polymerase sigma factor; Provisional

Probab=99.31  E-value=2.3e-11  Score=111.51  Aligned_cols=127  Identities=12%  Similarity=0.010  Sum_probs=97.7

Q ss_pred             HHHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhhcccc---
Q 012638          295 YCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGI---  371 (459)
Q Consensus       295 ~Are~LI~~nlrLV~sIAkry~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIrnaI~d~Lrk~sr~i---  371 (459)
                      .++.+++..|.+.++.+|.+++++..+++|++||.|+.+|+..+.++.   ..|.+|++++++|.+++++|+.....   
T Consensus         9 ~~~~~~~~~~~~~l~~~~~~~~~~~~~aeDlvQevf~~l~~~~~~~~~---~~~~~wl~~Iarn~~~d~~Rr~~~~~~~~   85 (168)
T PRK12525          9 TLIGQMFQQDYDWLCKKLSRQLGCPHSAEDIASETFLQVLALPDPASI---REPRALLTTIARRLMYEGWRRQDLERAYL   85 (168)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHcCCcCcHHHHHHHHHHHHHhCCCcccc---cCHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            489999999999999999999999999999999999999986665542   36999999999999999998653210   


Q ss_pred             ----cccc----c------hHHHHHHHHHHHHHHHHHc--------CCCCCHHHHHHHhCCCHHHHHHHHHhhcc
Q 012638          372 ----KIPC----K------LNREISKIQKARKALTNSH--------GKYPEDIEIAKYTGLSLAEIRSASECLRI  424 (459)
Q Consensus       372 ----rlP~----~------v~e~i~kI~ka~~~L~~~l--------gr~PT~eEIAe~LGIS~e~Vk~~l~~ar~  424 (459)
                          ..|.    .      ..+....+.+++..|+...        -.+.+++|||+.||+|+++|+..+.++..
T Consensus        86 ~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~v~~L~~~eg~s~~EIA~~l~is~~tV~~~l~ra~~  160 (168)
T PRK12525         86 QSLAEAPEAVQPSPEEQWMVIETLLAIDRLLDGLSGKARAAFLMSQLEGLTYVEIGERLGVSLSRIHQYMVEAFK  160 (168)
T ss_pred             HHHhcccccccCChHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence                0110    0      1112233455555554443        36789999999999999999999887754

>PRK09636 RNA polymerase sigma factor SigJ; Provisional

Probab=99.25  E-value=5.1e-11  Score=119.11  Aligned_cols=125  Identities=16%  Similarity=0.054  Sum_probs=95.6

Q ss_pred             HHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhhccc--c--
Q 012638          296 CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARG--I--  371 (459)
Q Consensus       296 Are~LI~~nlrLV~sIAkry~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIrnaI~d~Lrk~sr~--i--  371 (459)
                      ...+++..|.+.++.+|++++++..++||++||.++. |.....|+.   ..|.||++++++|.+++++|++.+.  .  
T Consensus         5 ~~~~l~~~~~~~l~~~a~~~~~~~~dAEDlvQe~fl~-~~~~~~~~~---~~~~~WL~~Ia~n~~~d~lR~~~~~~~~~~   80 (293)
T PRK09636          5 DAAAEFEPLRPHLLSVAYRMLGSVADAEDIVQEAWLR-WNNADRAQI---RDPRAWLTRVVTRLCLDRLRSARHRRETYV   80 (293)
T ss_pred             HHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHH-HHhcccccc---cCHHHHHHHHHHHHHHHHHHhhhccccccc
Confidence            4678999999999999999999999999999999999 556677762   4799999999999999999975421  1  


Q ss_pred             --ccccch-------------HHH-HHHHHHHHHHHHHHc--------CCCCCHHHHHHHhCCCHHHHHHHHHhhcc
Q 012638          372 --KIPCKL-------------NRE-ISKIQKARKALTNSH--------GKYPEDIEIAKYTGLSLAEIRSASECLRI  424 (459)
Q Consensus       372 --rlP~~v-------------~e~-i~kI~ka~~~L~~~l--------gr~PT~eEIAe~LGIS~e~Vk~~l~~ar~  424 (459)
                        .+|...             .+. ...+..+...|+...        -.+.+++|||+.||+|+++|+..+++++.
T Consensus        81 ~~~~~e~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~R~v~~L~~~~g~s~~EIA~~lg~s~~tVk~~l~RAr~  157 (293)
T PRK09636         81 GPWLPEPVVEELDDPLEAVVAAEDLSLALMLALERLSPLERAAFLLHDVFGVPFDEIASTLGRSPAACRQLASRARK  157 (293)
T ss_pred             CCcCCcCCCCCCCChHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHhCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence              111110             111 122445555554443        25689999999999999999999998865

>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=99.20  E-value=3.5e-11  Score=97.47  Aligned_cols=74  Identities=30%  Similarity=0.359  Sum_probs=64.0

Q ss_pred             HHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHhhccCCccccccCCCCCCccccCCCCC-CCCcc
Q 012638          379 REISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCLNAKYLNIPPFF-FPSFA  452 (459)
Q Consensus       379 e~i~kI~ka~~~L~~~lgr~PT~eEIAe~LGIS~e~Vk~~l~~ar~~~SLD~~v~~d~~~~l~e~i~D~-~~~~~  452 (459)
                      +.+++|.++..+|.+++||.||.+|||+.|||++++|..++.+++.++|||.+++.+++.++.++|+|+ .++|+
T Consensus         1 E~l~~i~~a~~~L~~~lgr~Pt~eEiA~~lgis~~~v~~~l~~~~~~~Sl~~~~~~~~~~~l~~~i~d~~~~~P~   75 (78)
T PF04539_consen    1 EKLRKIERARRELEQELGREPTDEEIAEELGISVEEVRELLQASRRPVSLDLPVGDEDDSTLGDFIEDDDAPSPE   75 (78)
T ss_dssp             HHHHHHHHHHHHHHHHHSS--BHHHHHHHHTS-HHHHHHHHHHHSCCEESSHCCSSSSSEEGGGSSB-SSS--HH
T ss_pred             ChHHHHHHHHHHHHHHhCCCCCHHHHHHHHcccHHHHHHHHHhCCCCeEEeeeecCCCCCchhheecCCCCCChh
Confidence            467899999999999999999999999999999999999999999999999999999899999999998 56654

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 ....

>PRK09191 two-component response regulator; Provisional

Probab=99.18  E-value=9.7e-11  Score=112.58  Aligned_cols=121  Identities=16%  Similarity=0.034  Sum_probs=94.7

Q ss_pred             HHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhhcccccccc
Q 012638          296 CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIPC  375 (459)
Q Consensus       296 Are~LI~~nlrLV~sIAkry~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIrnaI~d~Lrk~sr~irlP~  375 (459)
                      |+.+|+..|.+.|+++|.++.++..+++|++||+|+.+|+...+|++.  ..|.||+++++++...+...... ....|.
T Consensus         2 ~~~~l~~~~~~~l~~~~~~~~~~~~~aeDi~qd~~~~~~~~~~~~~~~--~~~~~wl~~~~~~~~~~~~~~~~-~~~~~~   78 (261)
T PRK09191          2 SLSQRIAPHLPYLRRYARALTGSQSSGDAYVAATLEALLADPSIFPEA--SSPRVGLYRLFHRLWSSAGANDP-EPGSPF   78 (261)
T ss_pred             chHHHHHHHhHHHHHHHHHhcCChhhHHHHHHHHHHHHHHhHHhcCCC--cchhhHHHHHHHHHhccccccCC-CCCCCc
Confidence            578999999999999999999999999999999999999999999874  46999999999887644322110 001111


Q ss_pred             chHHHHHHHHHHHHHHHHHc--------CCCCCHHHHHHHhCCCHHHHHHHHHhhcc
Q 012638          376 KLNREISKIQKARKALTNSH--------GKYPEDIEIAKYTGLSLAEIRSASECLRI  424 (459)
Q Consensus       376 ~v~e~i~kI~ka~~~L~~~l--------gr~PT~eEIAe~LGIS~e~Vk~~l~~ar~  424 (459)
                           ...+.+++..|+...        -.+.|++|||+.||+|+++|+..+.+++.
T Consensus        79 -----~~~l~~~l~~L~~~~r~v~~l~~~~~~s~~eIA~~l~~s~~tV~~~l~ra~~  130 (261)
T PRK09191         79 -----EARAERRLAGLTPLPRQAFLLTALEGFSVEEAAEILGVDPAEAEALLDDARA  130 (261)
T ss_pred             -----hHHHHHHHHhCCHHHhHHHHHHHHhcCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence                 115666666665543        25689999999999999999999887764

>TIGR02957 SigX4 RNA polymerase sigma-70 factor, TIGR02957 family

Probab=99.18  E-value=1.7e-10  Score=115.00  Aligned_cols=122  Identities=17%  Similarity=0.046  Sum_probs=90.6

Q ss_pred             HHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhhcccc------c
Q 012638          299 ELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGI------K  372 (459)
Q Consensus       299 ~LI~~nlrLV~sIAkry~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIrnaI~d~Lrk~sr~i------r  372 (459)
                      +++..|.+.++.+|++++++..++||++||+++.+++.  .|+.  ...|.+|++++++|.++|++|++.+..      .
T Consensus         1 ~l~~~~~~~l~~~a~r~lg~~~dAEDvvQE~flk~~~~--~~~~--~~~~~awL~~Ia~n~~ld~lR~~~~~~~~~~~~~   76 (281)
T TIGR02957         1 EEFEALRPLLFSLAYRMLGSVADAEDIVQETFLRWQEA--DRAQ--IENPKAYLTKVVTRRCIDVLRSARARREVYVGPW   76 (281)
T ss_pred             ChHHHHHHHHHHHHHHHhCCHhHHHHHHHHHHHHHHhC--Cccc--ccCHHHHHHHHHHHHHHHHHHHhhhcccccCCCC
Confidence            47899999999999999999999999999999998775  5543  236999999999999999999764211      1


Q ss_pred             cccch----------HHHHH----HHHHHHHHHHHHc--------CCCCCHHHHHHHhCCCHHHHHHHHHhhcc
Q 012638          373 IPCKL----------NREIS----KIQKARKALTNSH--------GKYPEDIEIAKYTGLSLAEIRSASECLRI  424 (459)
Q Consensus       373 lP~~v----------~e~i~----kI~ka~~~L~~~l--------gr~PT~eEIAe~LGIS~e~Vk~~l~~ar~  424 (459)
                      +|...          .....    .+..+...|+...        -.+.+++|||+.||+|+.+|+..+++++.
T Consensus        77 ~~e~~~~~~~~~~~~~~~~e~~~~~l~~~l~~L~~~~R~v~~L~~~~g~s~~EIA~~lg~s~~tVr~~l~RAr~  150 (281)
T TIGR02957        77 LPEPLLTTSADPAESVELAESLSMAYLLLLERLSPLERAVFVLREVFDYPYEEIASIVGKSEANCRQLVSRARR  150 (281)
T ss_pred             CCcccCCCCCChHHHHHHHHHHHHHHHHHHhhCCHHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            22110          01111    1233333333322        25689999999999999999999998875

This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building and bidirectional best hits, to represent a conserved family. This family is found in a limited number of bacterial lineages. This family includes apparent paralogous expansion in Streptomyces coelicolor A3(2), and multiple copies in Mycobacterium smegmatis MC2, Streptomyces avermitilis MA-4680 and Nocardia farcinica IFM10152.

>TIGR03209 P21_Cbot clostridium toxin-associated regulator BotR

Probab=99.17  E-value=1.3e-10  Score=103.34  Aligned_cols=113  Identities=16%  Similarity=0.140  Sum_probs=83.8

Q ss_pred             HHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhh-----cCCCCCCchhhHHHHHHHHHHHHHHHhhcccc
Q 012638          297 REELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAER-----FDHTRGYKFSTYVQYWIRKSISKMVARHARGI  371 (459)
Q Consensus       297 re~LI~~nlrLV~sIAkry~g~g~d~EDLIQEG~IGLirAieK-----FDp~kG~rFSTYa~~wIrnaI~d~Lrk~sr~i  371 (459)
                      ++.++..|.++|+.+|++|...    +| +||.++.+|....+     |++.  ..|.||++.+++|.+++++|++.+..
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     5542  47999999999999999999765421


Q ss_pred             ccc-------------cc--hHHHHHHHHHHHHHHHHHc--------CCCCCHHHHHHHhCCCHHHHH
Q 012638          372 KIP-------------CK--LNREISKIQKARKALTNSH--------GKYPEDIEIAKYTGLSLAEIR  416 (459)
Q Consensus       372 rlP-------------~~--v~e~i~kI~ka~~~L~~~l--------gr~PT~eEIAe~LGIS~e~Vk  416 (459)
                      ...             ..  ..+....+.++...|+...        -.+.|++|||+.||||+++|+
T Consensus        74 ~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~Lp~~~r~v~~l~~~~~~s~~EIA~~l~is~~tV~  141 (142)
T TIGR03209        74 KIIYNSEITDIKLSLINVYSSNDLEFEFNDLISILPNKQKKIIYMKFFEDMKEIDIAKKLHISRQSVY  141 (142)
T ss_pred             hhhhhhhhhccccchhHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHHCcCHHhhc
Confidence            110             00  0112234566666666543        266899999999999999986

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.

>PRK09635 sigI RNA polymerase sigma factor SigI; Provisional

Probab=99.17  E-value=2.6e-10  Score=114.72  Aligned_cols=127  Identities=10%  Similarity=-0.110  Sum_probs=96.1

Q ss_pred             HHHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhhccc-c--
Q 012638          295 YCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARG-I--  371 (459)
Q Consensus       295 ~Are~LI~~nlrLV~sIAkry~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIrnaI~d~Lrk~sr~-i--  371 (459)
                      ..+..++..|.+.++.+|+++.++..++||++||.|+.+|++...+    ...|.+|++.+++|.|+|++|+..+. .  
T Consensus         5 ~~~~~l~~~~~~~L~~~a~r~lgs~~dAEDvvQE~flr~~~~~~~~----~~~~~aWL~~Ia~n~~id~lRk~~~rr~~~   80 (290)
T PRK09635          5 DPVSAAWRAHRAYLVDLAFRMVGDIGVAEDMVQEAFSRLLRAPVGD----IDDERGWLIVVTSRLCLDHIKSASTRRERP   80 (290)
T ss_pred             cHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHhcCccc----cccHHHHHHHHHHHHHHHHHhhhhccCcCc
Confidence            3688999999999999999999999999999999999999987543    13699999999999999999974321 1  


Q ss_pred             -----ccccc-------h------H-HHHHHHHHHHHHHHHHc--------CCCCCHHHHHHHhCCCHHHHHHHHHhhcc
Q 012638          372 -----KIPCK-------L------N-REISKIQKARKALTNSH--------GKYPEDIEIAKYTGLSLAEIRSASECLRI  424 (459)
Q Consensus       372 -----rlP~~-------v------~-e~i~kI~ka~~~L~~~l--------gr~PT~eEIAe~LGIS~e~Vk~~l~~ar~  424 (459)
                           ..|..       -      . +....+..+...|+...        ..+.+++|||+.||+|+.+|+..+++++.
T Consensus        81 ~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~al~~~L~~L~p~~R~vf~L~~~~g~s~~EIA~~Lgis~~tVr~~l~RAr~  160 (290)
T PRK09635         81 QDIAAWHDGDASVSSVDPADRVTLDDEVRLALLIMLERLGPAERVVFVLHEIFGLPYQQIATTIGSQASTCRQLAHRARR  160 (290)
T ss_pred             ccccccCccccCCCCCCcHHHHHHHHHHHHHHHHHHHhCCHHHHHHhhHHHHhCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence                 11100       0      0 01123444444444332        25689999999999999999999998875


Q ss_pred             C
Q 012638          425 V  425 (459)
Q Consensus       425 ~  425 (459)
                      .
T Consensus       161 ~  161 (290)
T PRK09635        161 K  161 (290)
T ss_pred             H
Confidence            3

>PRK09047 RNA polymerase factor sigma-70; Validated

Probab=99.07  E-value=6.8e-10  Score=100.00  Aligned_cols=105  Identities=11%  Similarity=0.024  Sum_probs=77.6

Q ss_pred             CCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhhccccccc----------------------
Q 012638          317 GLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIP----------------------  374 (459)
Q Consensus       317 g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIrnaI~d~Lrk~sr~irlP----------------------  374 (459)
                      ++..+++|++||+|+.+|+....+ +  +..|.+|++.+++|.+++++|++.+.....                      
T Consensus         2 ~~~~~AeDivQe~fl~~~~~~~~~-~--~~~~~~wl~~ia~n~~~d~~Rk~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   78 (161)
T PRK09047          2 RDDDAALDIVQDAMIKLAEKYGDR-P--AAEWPPLFQRILQNRIHDWFRRQKVRNTWVSLFSSFSDDDDDDDFDPLETLD   78 (161)
T ss_pred             CCHHHHHHHHHHHHHHHHHHHhhc-c--cCchHHHHHHHHHHHHHHHHHhhcccccccccccccccccccccccHHHHhc
Confidence            445679999999999999998863 3  357999999999999999999765321110                      


Q ss_pred             ------cch------HHHHHHHHHHHHHHHHHc--------CCCCCHHHHHHHhCCCHHHHHHHHHhhcc
Q 012638          375 ------CKL------NREISKIQKARKALTNSH--------GKYPEDIEIAKYTGLSLAEIRSASECLRI  424 (459)
Q Consensus       375 ------~~v------~e~i~kI~ka~~~L~~~l--------gr~PT~eEIAe~LGIS~e~Vk~~l~~ar~  424 (459)
                            ...      .+....+.++...|+...        ..+.+++|||+.||||+++|+..+.+++.
T Consensus        79 ~~~~~~~~~~~~~~~~~~~~~l~~~l~~Lp~~~r~v~~l~~~~g~s~~EIA~~lgis~~tV~~~l~ra~~  148 (161)
T PRK09047         79 SADEGAESPADKLERAQVLQLIEEAIQKLPARQREAFLLRYWEDMDVAETAAAMGCSEGSVKTHCSRATH  148 (161)
T ss_pred             cccccCCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHhcCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence                  000      112234555666555543        36789999999999999999999998875

>PF07638 Sigma70_ECF: ECF sigma factor

Probab=98.85  E-value=7.3e-08  Score=90.55  Aligned_cols=141  Identities=16%  Similarity=0.112  Sum_probs=100.8

Q ss_pred             HHHHHHHHhchH-HHHHHHHHhHHHHHHHHHHhhCC---CCCHHH--HHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHH
Q 012638          284 RVLKQHLAFGWY-CREELIKSTRPLVLFLARNYRGL---GIPFSD--LLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIR  357 (459)
Q Consensus       284 eeL~~~l~~G~~-Are~LI~~nlrLV~sIAkry~g~---g~d~ED--LIQEG~IGLirAieKFDp~kG~rFSTYa~~wIr  357 (459)
                      .+|+.+++.|+. |.++|+..|.+.++.+|+++...   +.+.+|  |++|.|+.+++.-...+...-..|..|+...++
T Consensus         5 t~ll~~~~~GD~~A~~~L~~~~y~~L~~~a~~~l~~~~~~~~~~~~~lv~ea~lrl~~~~~~~~~~~~~~f~~~~~~~~r   84 (185)
T PF07638_consen    5 TELLDRWRQGDEAALDQLFERYYPELRRLARRRLRRERRGHDLQDTALVHEAFLRLARRGRFVQFSDRRHFWALLARIMR   84 (185)
T ss_pred             HHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHhccccCCchhHHHHHHHHHHHHhccccccCCCCHHHHHHHHHHHHH
Confidence            578899999988 99999999999999999987633   345555  577888877773333233323469999999999


Q ss_pred             HHHHHHHHhhcccccc------c---------cchHHHHHHHHHHHHHHHH-----------HcCCCCCHHHHHHHhCCC
Q 012638          358 KSISKMVARHARGIKI------P---------CKLNREISKIQKARKALTN-----------SHGKYPEDIEIAKYTGLS  411 (459)
Q Consensus       358 naI~d~Lrk~sr~irl------P---------~~v~e~i~kI~ka~~~L~~-----------~lgr~PT~eEIAe~LGIS  411 (459)
                      +.++|++|++....|-      +         ....+..-.+.++...|..           ..-.+.|.+|||+.||||
T Consensus        85 r~lid~~R~~~a~KRg~~~~~~~l~~~~~~~~~~~~~~~~~l~e~l~~L~~l~~~~~~~v~l~~~~Gls~~EIA~~lgiS  164 (185)
T PF07638_consen   85 RKLIDHARRRQAQKRGGDQVRVELDERADSGDEPSPEELLELEEALERLLALDPRQRRVVELRFFEGLSVEEIAERLGIS  164 (185)
T ss_pred             HHHHHHHHHHHHHhcCCCCcccchhhhhccccCCCHHHHHHHHHHHHHHHccCHHHHHHHHHHHHCCCCHHHHHHHHCcC
Confidence            9999999976554331      1         1122233334444443322           123568999999999999


Q ss_pred             HHHHHHHHHhhcc
Q 012638          412 LAEIRSASECLRI  424 (459)
Q Consensus       412 ~e~Vk~~l~~ar~  424 (459)
                      +.+|+..++.++.
T Consensus       165 ~~tV~r~l~~aR~  177 (185)
T PF07638_consen  165 ERTVRRRLRRARA  177 (185)
T ss_pred             HHHHHHHHHHHHH
Confidence            9999999988763

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

Probab=96.46  E-value=0.062  Score=52.37  Aligned_cols=35  Identities=17%  Similarity=0.311  Sum_probs=29.0

Q ss_pred             HHHHHHHHHHHHhCCCCchHHHHHHcCCCHHHHHH
Q 012638          254 NLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQ  288 (459)
Q Consensus       254 ~le~~~~~l~~~~gr~pt~~ewa~a~g~deeeL~~  288 (459)
                      ++.+....+...+|++||.++.|+.+|++.+.+..
T Consensus        88 ~~~~~~~~l~~~~g~~pt~~eia~~l~~~~~~v~~  122 (238)
T TIGR02393        88 KLIKAERQLTQELGREPTDEELAERMGMPAEKVRE  122 (238)
T ss_pred             HHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHH
Confidence            44556677888899999999999999999887654

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.

>PF00140 Sigma70_r1_2: Sigma-70 factor, region 1

Probab=96.29  E-value=0.0011  Score=47.14  Aligned_cols=34  Identities=12%  Similarity=0.049  Sum_probs=24.9

Q ss_pred             ChhHHHHHHhccCCCCCCChHHHHHHHHHhHHHHHHH
Q 012638          220 PTIFSAERALNSRGRRLTIARNEAEMSKGVQVVANLE  256 (459)
Q Consensus       220 p~~~~~~~~~~~~~~~lLt~~eE~eL~~~i~~~~~le  256 (459)
                      |...|+   ....+.||||++||++|+++|+.+...+
T Consensus         3 ~l~~Yl---~ei~~~~LLt~eeE~~LA~~i~~g~~~a   36 (37)
T PF00140_consen    3 SLRLYL---KEIGRYPLLTAEEEIELARRIRKGDEAA   36 (37)
T ss_dssp             HHHHHH---HHHHHS-EETTHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHH---HHHcCCCCCCHHHHHHHHHHHHHhHHhc
Confidence            444555   3345679999999999999999987653

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 ....

>PRK07670 RNA polymerase sigma factor SigD; Validated

Probab=96.08  E-value=0.088  Score=51.73  Aligned_cols=36  Identities=17%  Similarity=0.178  Sum_probs=28.9

Q ss_pred             HHHHHHHHHHHHhCCCCchHHHHHHcCCCHHHHHHH
Q 012638          254 NLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQH  289 (459)
Q Consensus       254 ~le~~~~~l~~~~gr~pt~~ewa~a~g~deeeL~~~  289 (459)
                      .+.+....+...+|+.|+..++|+..|++.+++...
T Consensus       110 ~~~~~~~~~~~~~~~~~~~~eia~~l~~~~~~v~~~  145 (251)
T PRK07670        110 KVEAAIEKLEQRYMRNVTPKEVAAELGMTEEEVEAT  145 (251)
T ss_pred             HHHHHHHHHHHHHCCCCCHHHHHHHhCcCHHHHHHH
Confidence            345556667778899999999999999998886653

>PRK09210 RNA polymerase sigma factor RpoD; Validated

Probab=95.95  E-value=0.12  Score=54.20  Aligned_cols=128  Identities=13%  Similarity=0.166  Sum_probs=72.3

Q ss_pred             HHHHHHHHHHHHhCCCCchHHHHHHcCCCHHHHHHHHHhchHHHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHH-HHH
Q 012638          254 NLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQHLAFGWYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAG-NVG  332 (459)
Q Consensus       254 ~le~~~~~l~~~~gr~pt~~ewa~a~g~deeeL~~~l~~G~~Are~LI~~nlrLV~sIAkry~g~g~d~EDLIQEG-~IG  332 (459)
                      ++.+....|...+|+.||.++.|..+|++.+.+...+..                   +..    ...+++.+.++ -..
T Consensus       217 ~~~~~~~~l~~~lgr~pt~~EiA~~l~~~~~~v~~~~~~-------------------~~~----~~SLd~~~~~~~~~~  273 (367)
T PRK09210        217 KLIRVQRQLLQELGREPTPEEIAEEMDMPPEKVREILKI-------------------AQE----PVSLETPIGEEDDSH  273 (367)
T ss_pred             HHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHH-------------------hcC----CCCcCCCCCCCCcch
Confidence            455667788888999999999999999999886543221                   111    11111111110 011


Q ss_pred             HHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhhccccccccchHHHHHHHHHHHHHHHHHcC----CCCCHHHHHHHh
Q 012638          333 VLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIPCKLNREISKIQKARKALTNSHG----KYPEDIEIAKYT  408 (459)
Q Consensus       333 LirAieKFDp~kG~rFSTYa~~wIrnaI~d~Lrk~sr~irlP~~v~e~i~kI~ka~~~L~~~lg----r~PT~eEIAe~L  408 (459)
                      +...+.  |..............++..+.++|.      .+|..-.          .-|...+|    ...|.+|||+.|
T Consensus       274 l~d~i~--d~~~~~p~~~~~~~~~~~~l~~~l~------~L~~rEr----------~Vl~lrygl~~~~~~tl~EIa~~l  335 (367)
T PRK09210        274 LGDFIE--DQDATSPADHAAYELLKEQLEDVLD------TLTDREE----------NVLRLRFGLDDGRTRTLEEVGKVF  335 (367)
T ss_pred             hhhhcc--CCCCCCHHHHHHHHHHHHHHHHHHH------hCCHHHH----------HHHHHHhccCCCCCccHHHHHHHH
Confidence            111111  1111223444455556666666664      2332211          11222233    678999999999


Q ss_pred             CCCHHHHHHHHHhh
Q 012638          409 GLSLAEIRSASECL  422 (459)
Q Consensus       409 GIS~e~Vk~~l~~a  422 (459)
                      |||.++|+.+...+
T Consensus       336 gvs~erVrQi~~~A  349 (367)
T PRK09210        336 GVTRERIRQIEAKA  349 (367)
T ss_pred             CCCHHHHHHHHHHH
Confidence            99999999886654

>PRK07408 RNA polymerase sigma factor SigF; Reviewed

Probab=95.82  E-value=0.047  Score=54.06  Aligned_cols=35  Identities=20%  Similarity=0.280  Sum_probs=29.7

Q ss_pred             HHHHHHHHHHHHhCCCCchHHHHHHcCCCHHHHHH
Q 012638          254 NLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQ  288 (459)
Q Consensus       254 ~le~~~~~l~~~~gr~pt~~ewa~a~g~deeeL~~  288 (459)
                      ++.+.+..|...+|++|+.++.|+.+|++.+++..
T Consensus       114 ~~~~~~~~l~~~lgr~pt~~elA~~lgi~~~~v~~  148 (256)
T PRK07408        114 QAKKVRQELRQELGRQPTDQEIAQALDISLEEWQE  148 (256)
T ss_pred             HHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHH
Confidence            45567778888999999999999999999887654

>PF12645 HTH_16: Helix-turn-helix domain; InterPro: IPR024760 This domain appears to be a helix-turn-helix domain, suggesting a transcriptional regulatory protein

Probab=95.82  E-value=0.035  Score=44.37  Aligned_cols=57  Identities=21%  Similarity=0.243  Sum_probs=47.8

Q ss_pred             HHHHHHHhchH-HHHHHHHHhHHHHHHHHHHhh----C--CCCCHHHHHHHHHHHHHHhhhhcC
Q 012638          285 VLKQHLAFGWY-CREELIKSTRPLVLFLARNYR----G--LGIPFSDLLQAGNVGVLQGAERFD  341 (459)
Q Consensus       285 eL~~~l~~G~~-Are~LI~~nlrLV~sIAkry~----g--~g~d~EDLIQEG~IGLirAieKFD  341 (459)
                      +++.++.+|+. |.+++++.|.|++.+.+.|-.    |  .+.--+|+-|+--..|+.++-+|+
T Consensus         2 ~vI~~A~~GD~~A~~~IL~~y~~yI~kls~r~~~d~~g~~~~~vDedl~q~l~~kLi~~I~~F~   65 (65)
T PF12645_consen    2 EVIKAAKQGDPEAMEEILKHYEPYISKLSTRTLYDEYGNVYGYVDEDLKQRLEIKLIEAILKFE   65 (65)
T ss_pred             HHHHHHHcCCHHHHHHHHHHHHHHHHHHHHhhcccccCCcCceeCHHHHHHHHHHHHHHHHccC
Confidence            35677889987 999999999999999997722    2  244559999999999999999996

Some proteins with this domain are annotated as conjugative transposon proteins.

>PRK06288 RNA polymerase sigma factor WhiG; Reviewed

Probab=95.76  E-value=0.26  Score=48.95  Aligned_cols=35  Identities=26%  Similarity=0.284  Sum_probs=29.2

Q ss_pred             HHHHHHHHHHHHhCCCCchHHHHHHcCCCHHHHHH
Q 012638          254 NLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQ  288 (459)
Q Consensus       254 ~le~~~~~l~~~~gr~pt~~ewa~a~g~deeeL~~  288 (459)
                      .+.+.+..|+..+|++||.++.|...|++.+.+..
T Consensus       119 ~i~~~~~~l~~~~~~~pt~~eia~~lg~~~~~v~~  153 (268)
T PRK06288        119 QIERAIAMLEARLGRTPSDEEIADELGISLEEYNS  153 (268)
T ss_pred             HHHHHHHHHHHHHCCCCCHHHHHHHcCCCHHHHHH
Confidence            45566778888899999999999999999877654

>PRK05949 RNA polymerase sigma factor; Validated

Probab=95.70  E-value=0.14  Score=52.86  Aligned_cols=35  Identities=11%  Similarity=0.275  Sum_probs=28.5

Q ss_pred             HHHHHHHHHHHHhCCCCchHHHHHHcCCCHHHHHH
Q 012638          254 NLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQ  288 (459)
Q Consensus       254 ~le~~~~~l~~~~gr~pt~~ewa~a~g~deeeL~~  288 (459)
                      ++.+.+..+...+|++|+.++.|+.+|++.+.+..
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            45556667778889999999999999999877654

>PRK07122 RNA polymerase sigma factor SigF; Reviewed

Probab=95.38  E-value=0.27  Score=49.05  Aligned_cols=35  Identities=20%  Similarity=0.305  Sum_probs=28.8

Q ss_pred             HHHHHHHHHHHHhCCCCchHHHHHHcCCCHHHHHH
Q 012638          254 NLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQ  288 (459)
Q Consensus       254 ~le~~~~~l~~~~gr~pt~~ewa~a~g~deeeL~~  288 (459)
                      ++.+....|...+|+.||.++.|+..|++.+++..
T Consensus       128 ~i~~~~~~l~~~lg~~pt~~eiA~~lg~~~~~v~~  162 (264)
T PRK07122        128 RLGRATAELSQRLGRAPTASELAAELGMDREEVVE  162 (264)
T ss_pred             HHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHH
Confidence            34456667777889999999999999999988754

>PRK05911 RNA polymerase sigma factor sigma-28; Reviewed

Probab=95.37  E-value=0.23  Score=49.31  Aligned_cols=29  Identities=17%  Similarity=0.022  Sum_probs=25.5

Q ss_pred             CCCCCHHHHHHHhCCCHHHHHHHHHhhcc
Q 012638          396 GKYPEDIEIAKYTGLSLAEIRSASECLRI  424 (459)
Q Consensus       396 gr~PT~eEIAe~LGIS~e~Vk~~l~~ar~  424 (459)
                      ..+.|.+|||+.||+|.++|+.+..++..
T Consensus       219 ~e~~t~~EIA~~lgis~~~V~~~~~ral~  247 (257)
T PRK05911        219 YEELVLKEIGKILGVSESRVSQIHSKALL  247 (257)
T ss_pred             hcCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence            46789999999999999999999887653

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

Probab=95.30  E-value=0.36  Score=48.25  Aligned_cols=126  Identities=14%  Similarity=0.073  Sum_probs=73.7

Q ss_pred             HHHHHHHHHHHHhCCCCchHHHHHHcCCCHHHHHHHHHhchHHHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHH
Q 012638          254 NLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQHLAFGWYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGV  333 (459)
Q Consensus       254 ~le~~~~~l~~~~gr~pt~~ewa~a~g~deeeL~~~l~~G~~Are~LI~~nlrLV~sIAkry~g~g~d~EDLIQEG~IGL  333 (459)
                      +++.+..+|+.++||+||.++.|+..|++.++....+..+.          -..+.++--.....+..  +         
T Consensus       111 ~i~~~~~~l~~el~r~pt~~EIA~~L~i~~ee~~~~~~~~~----------~~~~~sld~~~~~~~d~--~---------  169 (247)
T COG1191         111 RIEEAIDELEQELGREPTDEEIAEELGIDKEEYIEALLAIN----------GSQLLSLDEDVLKDDDD--D---------  169 (247)
T ss_pred             HHHHHHHHHHHHhCCCCcHHHHHHHhCCCHHHHHHHHHHhc----------cccccchhhhhcccccc--c---------
Confidence            45667888999999999999999999999988765433322          11111111111111110  0         


Q ss_pred             HHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhhccccccccchHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHH
Q 012638          334 LQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLA  413 (459)
Q Consensus       334 irAieKFDp~kG~rFSTYa~~wIrnaI~d~Lrk~sr~irlP~~v~e~i~kI~ka~~~L~~~lgr~PT~eEIAe~LGIS~e  413 (459)
                         +.   ..-+..+..+-.+...+.+..++.      .+|..    -.      .-+.-.+..+.|..|||+.||||+.
T Consensus       170 ---~~---~~~~~~~~~~~~~~~~~~l~~ai~------~L~ER----Ek------~Vl~l~y~eelt~kEI~~~LgISes  227 (247)
T COG1191         170 ---VD---DQIENPDDGVEKEELLEILKEAIE------PLPER----EK------LVLVLRYKEELTQKEIAEVLGISES  227 (247)
T ss_pred             ---hh---hccccchhHHHHHHHHHHHHHHHH------ccCHH----HH------HHHHHHHHhccCHHHHHHHhCccHH
Confidence               11   112234555556666666666664      12211    11      1111223457899999999999999


Q ss_pred             HHHHHHHhh
Q 012638          414 EIRSASECL  422 (459)
Q Consensus       414 ~Vk~~l~~a  422 (459)
                      .|-.+...+
T Consensus       228 ~VSql~kka  236 (247)
T COG1191         228 RVSRLHKKA  236 (247)
T ss_pred             HHHHHHHHH
Confidence            998776544

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

Probab=95.16  E-value=0.41  Score=46.05  Aligned_cols=35  Identities=26%  Similarity=0.333  Sum_probs=28.7

Q ss_pred             HHHHHHHHHHHHhCCCCchHHHHHHcCCCHHHHHH
Q 012638          254 NLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQ  288 (459)
Q Consensus       254 ~le~~~~~l~~~~gr~pt~~ewa~a~g~deeeL~~  288 (459)
                      ++.+...+|...+|+.|+.++.|+.+|++.+.+..
T Consensus        84 ~l~~~~~~l~~~~~~~~~~~ela~~l~~~~~~v~~  118 (224)
T TIGR02479        84 KLERAIRELEARLGREPTEEEIAEELGMDLKEYRQ  118 (224)
T ss_pred             HHHHHHHHHHHHHCcCCCHHHHHHHhCCCHHHHHH
Confidence            45566777888899999999999999999877654

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.

>TIGR02394 rpoS_proteo RNA polymerase sigma factor RpoS

Probab=95.11  E-value=0.32  Score=48.84  Aligned_cols=28  Identities=18%  Similarity=0.061  Sum_probs=25.5

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHHhhcc
Q 012638          397 KYPEDIEIAKYTGLSLAEIRSASECLRI  424 (459)
Q Consensus       397 r~PT~eEIAe~LGIS~e~Vk~~l~~ar~  424 (459)
                      .+.|++|||+.||||+++|+.++++++.
T Consensus       241 e~~s~~EIA~~Lgis~~tVk~~l~rAlk  268 (285)
T TIGR02394       241 EPATLEEVAAEVGLTRERVRQIQVEALK  268 (285)
T ss_pred             CCccHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            5679999999999999999999988864

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).

>PRK05901 RNA polymerase sigma factor; Provisional

Probab=95.04  E-value=0.43  Score=52.30  Aligned_cols=128  Identities=15%  Similarity=0.177  Sum_probs=70.4

Q ss_pred             HHHHHHHHHHHHhCCCCchHHHHHHcCCCHHHHHHHHHhchHHHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHH-HHHH
Q 012638          254 NLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQHLAFGWYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQA-GNVG  332 (459)
Q Consensus       254 ~le~~~~~l~~~~gr~pt~~ewa~a~g~deeeL~~~l~~G~~Are~LI~~nlrLV~sIAkry~g~g~d~EDLIQE-G~IG  332 (459)
                      ++.++...|...+|+.||.++.|+.+|++.+.+....+                       +....+.+++.+.+ +-..
T Consensus       359 kl~~~~~~L~~~lgr~PT~eELAe~Lgis~e~V~~~~~-----------------------~~~~~~SLD~~i~~d~~~~  415 (509)
T PRK05901        359 KLGRIERELLQELGREPTPEELAKEMGFTPEKVREIQK-----------------------YNREPISLDKTIGKEGDSQ  415 (509)
T ss_pred             HHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHH-----------------------hcCCCcccccccccCCccc
Confidence            45567778888899999999999999999887654221                       11122223332211 1111


Q ss_pred             HHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhhccccccccchHHHHHHHHHHHHHHHHHc----CCCCCHHHHHHHh
Q 012638          333 VLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIPCKLNREISKIQKARKALTNSH----GKYPEDIEIAKYT  408 (459)
Q Consensus       333 LirAieKFDp~kG~rFSTYa~~wIrnaI~d~Lrk~sr~irlP~~v~e~i~kI~ka~~~L~~~l----gr~PT~eEIAe~L  408 (459)
                      +...+.  |...............+..+..+|.      .+|..    -..      -|...+    +...|.+|||+.|
T Consensus       416 l~d~l~--D~~~~~p~~~~~~~~l~~~L~~aL~------~L~eR----Er~------VI~lRyGL~~~e~~TL~EIa~~l  477 (509)
T PRK05901        416 FGDFIE--DSEAVSPVDAVSFTLLQDQLQEVLE------TLSER----EAG------VIRMRFGLTDGQPKTLDEIGQVY  477 (509)
T ss_pred             HHHhcc--CCCCCCHHHHHHHHHHHHHHHHHHh------hCCHH----HHH------HHHHHhhccCCCCCCHHHHHHHH
Confidence            222111  1111112333334444444444443      12211    111      122223    4678999999999


Q ss_pred             CCCHHHHHHHHHhh
Q 012638          409 GLSLAEIRSASECL  422 (459)
Q Consensus       409 GIS~e~Vk~~l~~a  422 (459)
                      |||.++|+.+...+
T Consensus       478 GVSrERVRQIe~kA  491 (509)
T PRK05901        478 GVTRERIRQIESKT  491 (509)
T ss_pred             CCCHHHHHHHHHHH
Confidence            99999999876554

>PRK07598 RNA polymerase sigma factor SigC; Validated

Probab=95.02  E-value=0.41  Score=51.24  Aligned_cols=37  Identities=11%  Similarity=0.313  Sum_probs=31.1

Q ss_pred             HHHHHHHHHHHHHhCCCCchHHHHHHcCCCHHHHHHH
Q 012638          253 ANLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQH  289 (459)
Q Consensus       253 ~~le~~~~~l~~~~gr~pt~~ewa~a~g~deeeL~~~  289 (459)
                      -++.+.+..|...+|+.|+.++.|+++|++.+.+...
T Consensus       262 ~~lrk~~r~L~~~lgR~pt~~EiA~~l~is~~~vr~~  298 (415)
T PRK07598        262 NKIKKAQRKISQEKGRTPTIEDIAQELEMTPTQVREV  298 (415)
T ss_pred             HHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHH
Confidence            3566777788888999999999999999999887653

>PRK07921 RNA polymerase sigma factor SigB; Reviewed

Probab=94.88  E-value=0.49  Score=48.88  Aligned_cols=35  Identities=29%  Similarity=0.470  Sum_probs=29.6

Q ss_pred             HHHHHHHHHHHHhCCCCchHHHHHHcCCCHHHHHH
Q 012638          254 NLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQ  288 (459)
Q Consensus       254 ~le~~~~~l~~~~gr~pt~~ewa~a~g~deeeL~~  288 (459)
                      ++.+++..|...+|+.||.++.|..+|++.+.+..
T Consensus       174 ~l~~~~~~l~~~lgr~pt~~EiA~~lgi~~~~v~~  208 (324)
T PRK07921        174 KLARIKRELHQQLGREATDEELAEESGIPEEKIAD  208 (324)
T ss_pred             HHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHH
Confidence            45667778888899999999999999999887654

>TIGR02885 spore_sigF RNA polymerase sigma-F factor

Probab=94.67  E-value=0.23  Score=47.94  Aligned_cols=34  Identities=32%  Similarity=0.446  Sum_probs=27.2

Q ss_pred             HHHHHHHHHHHhCCCCchHHHHHHcCCCHHHHHH
Q 012638          255 LERIKTTLEKESGKAASLNCWAQAAGVSERVLKQ  288 (459)
Q Consensus       255 le~~~~~l~~~~gr~pt~~ewa~a~g~deeeL~~  288 (459)
                      +.+....+...+|+.||.++.|+..|++.+++..
T Consensus        99 ~~~~~~~l~~~~~r~pt~~ela~~l~~~~~~v~~  132 (231)
T TIGR02885        99 IRYMKEELSKELGREPTINELAEALGVSPEEIVM  132 (231)
T ss_pred             HHHHHHHHHHHHCcCCCHHHHHHHHCcCHHHHHH
Confidence            3445567777889999999999999999877654

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.

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

Probab=94.65  E-value=0.54  Score=47.61  Aligned_cols=35  Identities=14%  Similarity=0.308  Sum_probs=28.5

Q ss_pred             HHHHHHHHHHHHhCCCCchHHHHHHcCCCHHHHHH
Q 012638          254 NLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQ  288 (459)
Q Consensus       254 ~le~~~~~l~~~~gr~pt~~ewa~a~g~deeeL~~  288 (459)
                      ++.+.+..+...+|+.|+.++.|..+|++.+.+..
T Consensus       162 ~~rk~~~~l~~~~~~~pt~~eia~~l~~~~~~v~~  196 (298)
T TIGR02997       162 KIKKVQRELSQKLGRTPSEAEIAEALELEPEQVRE  196 (298)
T ss_pred             HHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHH
Confidence            44555667777889999999999999999887654

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).

>TIGR02850 spore_sigG RNA polymerase sigma-G factor

Probab=94.25  E-value=0.43  Score=47.06  Aligned_cols=36  Identities=14%  Similarity=0.147  Sum_probs=29.1

Q ss_pred             HHHHHHHHHHHHhCCCCchHHHHHHcCCCHHHHHHH
Q 012638          254 NLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQH  289 (459)
Q Consensus       254 ~le~~~~~l~~~~gr~pt~~ewa~a~g~deeeL~~~  289 (459)
                      ++.+....+..++|++||.++.|+..|++.+.+...
T Consensus       121 ~~~~~~~~l~~~l~~~pt~~elA~~l~~~~e~v~~~  156 (254)
T TIGR02850       121 KALQVRDKLISENSKEPTVSEIAKELKVPQEEVVFA  156 (254)
T ss_pred             HHHHHHHHHHHHhCCCCCHHHHHHHHCcCHHHHHHH
Confidence            344556677788899999999999999998887653

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.

>PF04539 Sigma70_r3: Sigma-70 region 3; InterPro: IPR007624 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription

Probab=94.05  E-value=0.14  Score=41.06  Aligned_cols=38  Identities=26%  Similarity=0.408  Sum_probs=30.1

Q ss_pred             HHHHHHHHHHHHHhCCCCchHHHHHHcCCCHHHHHHHH
Q 012638          253 ANLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQHL  290 (459)
Q Consensus       253 ~~le~~~~~l~~~~gr~pt~~ewa~a~g~deeeL~~~l  290 (459)
                      .++.+++.+|+.++||.||.++.|+.+|++.+++...+
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            46778889999999999999999999999998876543

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 ....

>PRK07500 rpoH2 RNA polymerase factor sigma-32; Reviewed

Probab=93.89  E-value=0.62  Score=47.11  Aligned_cols=28  Identities=11%  Similarity=-0.003  Sum_probs=25.2

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHHhhcc
Q 012638          397 KYPEDIEIAKYTGLSLAEIRSASECLRI  424 (459)
Q Consensus       397 r~PT~eEIAe~LGIS~e~Vk~~l~~ar~  424 (459)
                      .+.|.+|||+.||||.++|+.+.+.+..
T Consensus       244 ~~~t~~EIa~~lgvs~~~V~q~~~~Al~  271 (289)
T PRK07500        244 DGATLEALGEELGISKERVRQIEARALE  271 (289)
T ss_pred             CCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            6789999999999999999999887754

>PRK07405 RNA polymerase sigma factor SigD; Validated

Probab=93.88  E-value=0.74  Score=47.29  Aligned_cols=36  Identities=14%  Similarity=0.375  Sum_probs=29.2

Q ss_pred             HHHHHHHHHHHHHhCCCCchHHHHHHcCCCHHHHHH
Q 012638          253 ANLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQ  288 (459)
Q Consensus       253 ~~le~~~~~l~~~~gr~pt~~ewa~a~g~deeeL~~  288 (459)
                      .++.+.+..+...+|+.||.++.|.++|++.+.+..
T Consensus       168 ~~l~~~~~~l~~~~gr~pt~~eiA~~~~~~~~~v~~  203 (317)
T PRK07405        168 NKIKKAQRQLSQQLGRAATIGELAEELELTPKQVRE  203 (317)
T ss_pred             HHHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHH
Confidence            345666777788889999999999999998877654

>PRK06986 fliA flagellar biosynthesis sigma factor; Validated

Probab=93.87  E-value=1.1  Score=43.36  Aligned_cols=29  Identities=14%  Similarity=-0.011  Sum_probs=25.7

Q ss_pred             CCCCCHHHHHHHhCCCHHHHHHHHHhhcc
Q 012638          396 GKYPEDIEIAKYTGLSLAEIRSASECLRI  424 (459)
Q Consensus       396 gr~PT~eEIAe~LGIS~e~Vk~~l~~ar~  424 (459)
                      ..+.|++|||+.||||+++|+..+.+++.
T Consensus       198 ~~g~s~~EIA~~lgis~~tV~~~~~ra~~  226 (236)
T PRK06986        198 QEELNLKEIGAVLGVSESRVSQIHSQAIK  226 (236)
T ss_pred             ccCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            46789999999999999999999887764

>PRK07406 RNA polymerase sigma factor RpoD; Validated

Probab=93.60  E-value=1.1  Score=47.17  Aligned_cols=35  Identities=14%  Similarity=0.230  Sum_probs=29.0

Q ss_pred             HHHHHHHHHHHHhCCCCchHHHHHHcCCCHHHHHH
Q 012638          254 NLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQ  288 (459)
Q Consensus       254 ~le~~~~~l~~~~gr~pt~~ewa~a~g~deeeL~~  288 (459)
                      ++.+....|...+|+.||.++.|+.+|++.+.+..
T Consensus       224 ~i~~a~~~l~~~lgr~Pt~~EIA~~lg~~~e~v~~  258 (373)
T PRK07406        224 RIKKTTKVLSQEFGRKPTEEEIAESMEMTIEKLRF  258 (373)
T ss_pred             HHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHH
Confidence            45566777888889999999999999999887643

>TIGR02941 Sigma_B RNA polymerase sigma-B factor

Probab=93.37  E-value=0.51  Score=46.37  Aligned_cols=30  Identities=10%  Similarity=0.016  Sum_probs=25.7

Q ss_pred             cCCCCCHHHHHHHhCCCHHHHHHHHHhhcc
Q 012638          395 HGKYPEDIEIAKYTGLSLAEIRSASECLRI  424 (459)
Q Consensus       395 lgr~PT~eEIAe~LGIS~e~Vk~~l~~ar~  424 (459)
                      +..+.|++|||+.||+|+++|+..++.+..
T Consensus       218 ~~~g~s~~eIA~~lgis~~~V~~~~~ra~~  247 (255)
T TIGR02941       218 FEENLSQKETGERLGISQMHVSRLQRQAIS  247 (255)
T ss_pred             HcCCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence            356789999999999999999998877653

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

>PF08281 Sigma70_r4_2: Sigma-70, region 4; InterPro: IPR013249 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription

Probab=92.80  E-value=0.11  Score=38.95  Aligned_cols=31  Identities=19%  Similarity=0.062  Sum_probs=23.4

Q ss_pred             HcCCCCCHHHHHHHhCCCHHHHHHHHHhhcc
Q 012638          394 SHGKYPEDIEIAKYTGLSLAEIRSASECLRI  424 (459)
Q Consensus       394 ~lgr~PT~eEIAe~LGIS~e~Vk~~l~~ar~  424 (459)
                      .+..+.|++|||+.+|+|+.+|+..+.+++.
T Consensus        22 ~~~~g~s~~eIa~~l~~s~~~v~~~l~ra~~   52 (54)
T PF08281_consen   22 RYFQGMSYAEIAEILGISESTVKRRLRRARK   52 (54)
T ss_dssp             HHTS---HHHHHHHCTS-HHHHHHHHHHHHH
T ss_pred             HHHHCcCHHHHHHHHCcCHHHHHHHHHHHHh
Confidence            3467889999999999999999999988763

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.

>PRK05572 sporulation sigma factor SigF; Validated

Probab=92.79  E-value=1.7  Score=42.71  Aligned_cols=34  Identities=24%  Similarity=0.357  Sum_probs=26.8

Q ss_pred             HHHHHHHHHHHHhCCCCchHHHHHHcCCCHHHHH
Q 012638          254 NLERIKTTLEKESGKAASLNCWAQAAGVSERVLK  287 (459)
Q Consensus       254 ~le~~~~~l~~~~gr~pt~~ewa~a~g~deeeL~  287 (459)
                      ++.+....+..+.|+.|+..+.|++.|++.+.+.
T Consensus       119 ~~~~~~~~l~~~~~r~p~~~eia~~l~~~~~~v~  152 (252)
T PRK05572        119 KIRKDKDELSKELGREPTIEELAEYLGVTPEEVV  152 (252)
T ss_pred             HHHHHHHHHHHHHCcCCCHHHHHHHhCcCHHHHH
Confidence            3455566777778999999999999999887653

>PRK08215 sporulation sigma factor SigG; Reviewed

Probab=92.69  E-value=1.8  Score=42.72  Aligned_cols=34  Identities=15%  Similarity=0.152  Sum_probs=27.8

Q ss_pred             HHHHHHHHHHHhCCCCchHHHHHHcCCCHHHHHH
Q 012638          255 LERIKTTLEKESGKAASLNCWAQAAGVSERVLKQ  288 (459)
Q Consensus       255 le~~~~~l~~~~gr~pt~~ewa~a~g~deeeL~~  288 (459)
                      +.+....+...+|+.|+..+.|..+|++.+.+..
T Consensus       125 ~~~~~~~l~~~~~r~p~~~eia~~l~v~~~~v~~  158 (258)
T PRK08215        125 ALQVREKLINENSKEPTVEEIAKELEVPREEVVF  158 (258)
T ss_pred             HHHHHHHHHHHhCCCCCHHHHHHHHCcCHHHHHH
Confidence            3445667777889999999999999999888654

>PRK12427 flagellar biosynthesis sigma factor; Provisional

Probab=91.90  E-value=2.7  Score=41.02  Aligned_cols=34  Identities=6%  Similarity=0.120  Sum_probs=28.2

Q ss_pred             HHHHHHHHHHHhCCCCchHHHHHHcCCCHHHHHH
Q 012638          255 LERIKTTLEKESGKAASLNCWAQAAGVSERVLKQ  288 (459)
Q Consensus       255 le~~~~~l~~~~gr~pt~~ewa~a~g~deeeL~~  288 (459)
                      +.+....+...+|+.|+.++.|+.+|++.+++..
T Consensus       103 i~~~~~~l~~~~g~~pt~~eiA~~lg~~~~~v~~  136 (231)
T PRK12427        103 TNDAIREIAKRLGHEPNFEEISAELNLTAEEYQE  136 (231)
T ss_pred             HHHHHHHHHHHHCCCCCHHHHHHHhCCCHHHHHH
Confidence            4455677778889999999999999999887654

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

Probab=91.64  E-value=0.79  Score=44.02  Aligned_cols=29  Identities=17%  Similarity=0.020  Sum_probs=25.5

Q ss_pred             CCCCCHHHHHHHhCCCHHHHHHHHHhhcc
Q 012638          396 GKYPEDIEIAKYTGLSLAEIRSASECLRI  424 (459)
Q Consensus       396 gr~PT~eEIAe~LGIS~e~Vk~~l~~ar~  424 (459)
                      ..+.|++|||+.||+|..+|...+.++..
T Consensus       192 ~~~~s~~eIA~~lgis~~~v~~~~~ra~~  220 (227)
T TIGR02980       192 FEDKTQSEIAERLGISQMHVSRLLRRALK  220 (227)
T ss_pred             hcCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence            45789999999999999999999887754

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.

>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=91.62  E-value=0.59  Score=37.30  Aligned_cols=44  Identities=18%  Similarity=0.240  Sum_probs=33.5

Q ss_pred             HHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCC-HHHHHHHHHhh
Q 012638          379 REISKIQKARKALTNSHGKYPEDIEIAKYTGLS-LAEIRSASECL  422 (459)
Q Consensus       379 e~i~kI~ka~~~L~~~lgr~PT~eEIAe~LGIS-~e~Vk~~l~~a  422 (459)
                      +...+|-.++.+...+.|..||..|||+.+|++ ..+|...+...
T Consensus         6 ~rQ~~vL~~I~~~~~~~G~~Pt~rEIa~~~g~~S~~tv~~~L~~L   50 (65)
T PF01726_consen    6 ERQKEVLEFIREYIEENGYPPTVREIAEALGLKSTSTVQRHLKAL   50 (65)
T ss_dssp             HHHHHHHHHHHHHHHHHSS---HHHHHHHHTSSSHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCChHHHHHHHHHH
Confidence            344566677777788889999999999999997 99999887754

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.

>PHA02547 55 RNA polymerase sigma factor; Provisional

Probab=91.06  E-value=0.66  Score=43.91  Aligned_cols=64  Identities=16%  Similarity=0.185  Sum_probs=51.2

Q ss_pred             HHHHHHHHHHhhCCCCC---HHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhhc
Q 012638          305 RPLVLFLARNYRGLGIP---FSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHA  368 (459)
Q Consensus       305 lrLV~sIAkry~g~g~d---~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIrnaI~d~Lrk~s  368 (459)
                      +..+-.+.++|--++-.   -+|.|.+|.-.+++.+..||+.+...+.+|++.++-++..+.|.+..
T Consensus        47 mkIa~glS~r~nF~~Yt~~wKedMI~DgIe~~i~ylhNFD~~k~~Np~aYiT~~~~~AF~~RI~kEk  113 (179)
T PHA02547         47 MKIAEGLSRRPNFSGYTQTWKEDMIADGIEACIKGLHNFDETKYKNPHAYITQACFNAFVQRIKKEK  113 (179)
T ss_pred             HHHHhccccCCccccchHHHHHHHHHHHHHHHHHHhhcCCcccccChHHHHHHHHHHHHHHHHHHHH
Confidence            44445555555333433   59999999999999999999999999999999999999999887653

>PRK05658 RNA polymerase sigma factor RpoD; Validated

Probab=90.83  E-value=2.1  Score=47.90  Aligned_cols=35  Identities=23%  Similarity=0.402  Sum_probs=29.4

Q ss_pred             HHHHHHHHHHHHhCCCCchHHHHHHcCCCHHHHHH
Q 012638          254 NLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQ  288 (459)
Q Consensus       254 ~le~~~~~l~~~~gr~pt~~ewa~a~g~deeeL~~  288 (459)
                      ++.++...+...+|++||.++.|..+|++.+.+..
T Consensus       468 k~~~~~~~~~~~~gr~pt~~eiA~~l~~~~~~v~~  502 (619)
T PRK05658        468 KLNRISRQMLQEIGREPTPEELAERLGMPEDKVRK  502 (619)
T ss_pred             HHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHH
Confidence            45566777888899999999999999999887654

>PF04545 Sigma70_r4: Sigma-70, region 4; InterPro: IPR007630 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription

Probab=90.75  E-value=0.68  Score=34.22  Aligned_cols=31  Identities=19%  Similarity=-0.037  Sum_probs=25.7

Q ss_pred             HHcCCCCCHHHHHHHhCCCHHHHHHHHHhhc
Q 012638          393 NSHGKYPEDIEIAKYTGLSLAEIRSASECLR  423 (459)
Q Consensus       393 ~~lgr~PT~eEIAe~LGIS~e~Vk~~l~~ar  423 (459)
                      ..+..+.|.+|||+.||+|.++|+.+...+.
T Consensus        15 ~~y~~~~t~~eIa~~lg~s~~~V~~~~~~al   45 (50)
T PF04545_consen   15 LRYFEGLTLEEIAERLGISRSTVRRILKRAL   45 (50)
T ss_dssp             HHHTST-SHHHHHHHHTSCHHHHHHHHHHHH
T ss_pred             HHhcCCCCHHHHHHHHCCcHHHHHHHHHHHH
Confidence            3457788999999999999999999887664

Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 4 of sigma-70 like sigma-factors is involved in binding to the -35 promoter element via a helix-turn-helix motif []. Due to the way Pfam works, the threshold has been set artificially high to prevent overlaps with other helix-turn-helix families. Therefore there are many false negatives.; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 2P7V_B 3IYD_F 1TLH_B 1KU7_A 1RIO_H 3N97_A 1KU3_A 1RP3_C 1SC5_A 1NR3_A ....

>PRK05657 RNA polymerase sigma factor RpoS; Validated

Probab=89.22  E-value=4.5  Score=41.73  Aligned_cols=29  Identities=14%  Similarity=0.038  Sum_probs=26.0

Q ss_pred             CCCCCHHHHHHHhCCCHHHHHHHHHhhcc
Q 012638          396 GKYPEDIEIAKYTGLSLAEIRSASECLRI  424 (459)
Q Consensus       396 gr~PT~eEIAe~LGIS~e~Vk~~l~~ar~  424 (459)
                      ..+.|++|||+.||||+++|+.++++++.
T Consensus       280 ~e~~s~~EIA~~Lgis~~tV~~~~~rAl~  308 (325)
T PRK05657        280 YEAATLEDVAREIGLTRERVRQIQVEALR  308 (325)
T ss_pred             CCCcCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence            45789999999999999999999888865

>PRK08583 RNA polymerase sigma factor SigB; Validated

Probab=88.54  E-value=2.9  Score=41.10  Aligned_cols=30  Identities=10%  Similarity=-0.028  Sum_probs=26.0

Q ss_pred             cCCCCCHHHHHHHhCCCHHHHHHHHHhhcc
Q 012638          395 HGKYPEDIEIAKYTGLSLAEIRSASECLRI  424 (459)
Q Consensus       395 lgr~PT~eEIAe~LGIS~e~Vk~~l~~ar~  424 (459)
                      +..+.|++|||+.||||+++|+..+++++.
T Consensus       218 ~~~g~s~~eIA~~l~is~~tV~~~~~ra~~  247 (257)
T PRK08583        218 FIENLSQKETGERLGISQMHVSRLQRQAIK  247 (257)
T ss_pred             HhCCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            356889999999999999999999887654

>PRK06596 RNA polymerase factor sigma-32; Reviewed

Probab=86.30  E-value=10  Score=38.18  Aligned_cols=27  Identities=19%  Similarity=0.129  Sum_probs=23.9

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHHhhc
Q 012638          397 KYPEDIEIAKYTGLSLAEIRSASECLR  423 (459)
Q Consensus       397 r~PT~eEIAe~LGIS~e~Vk~~l~~ar  423 (459)
                      .+.|.+|||+.||||.++|+.+.+.+.
T Consensus       247 ~~~Tl~EIA~~lgvS~~rVrqi~~~Al  273 (284)
T PRK06596        247 DKSTLQELAAEYGVSAERVRQIEKNAM  273 (284)
T ss_pred             CCcCHHHHHHHHCCCHHHHHHHHHHHH
Confidence            578999999999999999999877653

>COG4941 Predicted RNA polymerase sigma factor containing a TPR repeat domain [Transcription]

Probab=83.02  E-value=6.1  Score=41.54  Aligned_cols=125  Identities=20%  Similarity=0.062  Sum_probs=81.2

Q ss_pred             HHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhhccccccccch
Q 012638          298 EELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIPCKL  377 (459)
Q Consensus       298 e~LI~~nlrLV~sIAkry~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIrnaI~d~Lrk~sr~irlP~~v  377 (459)
                      +..+..-.+.++.---+|.++-.-.|+.+||+|+...+..-+=-+-+  .-..|++-..||.-+|.+|++.+....|.+.
T Consensus         8 e~~~r~~~~r~~a~L~r~~rd~dlAEEa~~dA~~~Ale~WPr~G~P~--~PaAWL~~v~R~~aiD~~Rr~~~~~~~~~el   85 (415)
T COG4941           8 EAAARIERPRAMAALARYLRDLDLAEEALQDAFAAALERWPRAGPPR--NPAAWLIAVGRNRAIDRVRRRARRDAAPPEL   85 (415)
T ss_pred             HHHHHHhhhHHHHHHHHHhcccchHHHHHHHHHHHHHHhCcccCCCC--ChHHHHHHHHhhhHHHHHHHHHHhccCChhh
Confidence            34445555666666666777767789999999876554443333322  4689999999999999999987766555443


Q ss_pred             HHHH--HHHHHH----------------------------HHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHhhcc
Q 012638          378 NREI--SKIQKA----------------------------RKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRI  424 (459)
Q Consensus       378 ~e~i--~kI~ka----------------------------~~~L~~~lgr~PT~eEIAe~LGIS~e~Vk~~l~~ar~  424 (459)
                      ....  ..+..+                            .-.|.-.+--+.|.+|||...=+++.++...+.+++.
T Consensus        86 ~~~~e~~e~~~a~~~~d~~i~Dd~LRLiFvccHPal~~~~riALtLR~v~GLs~~eIArAFLv~e~am~QRivRAK~  162 (415)
T COG4941          86 LLSDEDEEMEEAEALDDEHIRDDRLRLIFVCCHPALPPEQRIALTLRLVGGLSTAEIARAFLVPEAAMAQRIVRAKA  162 (415)
T ss_pred             cccccchhhhccccccccccchhhHHhhhhhcCCCCChhhHHHHHHHHHcCCcHHHHHHHHcCCcHHHHHHHHHHHH
Confidence            2221  111111                            0011111123569999999999999999888877764

>TIGR03879 near_KaiC_dom probable regulatory domain

Probab=80.79  E-value=2  Score=35.38  Aligned_cols=25  Identities=20%  Similarity=0.106  Sum_probs=22.8

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHHh
Q 012638          397 KYPEDIEIAKYTGLSLAEIRSASEC  421 (459)
Q Consensus       397 r~PT~eEIAe~LGIS~e~Vk~~l~~  421 (459)
                      .+.|+.|||+.||+|+.+|+..+..
T Consensus        31 eGlS~kEIAe~LGIS~~TVk~~l~~   55 (73)
T TIGR03879        31 AGKTASEIAEELGRTEQTVRNHLKG   55 (73)
T ss_pred             cCCCHHHHHHHHCcCHHHHHHHHhc
Confidence            5789999999999999999998774

This model describes a common domain shared by two different families of proteins, each of which occurs regularly next to its corresponding partner family, a probable regulatory with homology to KaiC. By implication, this protein family likely is also involved in sensory transduction and/or regulation.

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	459
3dxj_F	423	Crystal Structure Of Thermus Thermophilus Rna Polym		3e-21
1iw7_F	423	Crystal Structure Of The Rna Polymerase Holoenzyme		3e-21
1l9u_H	332	Thermus Aquaticus Rna Polymerase Holoenzyme At 4 A		4e-21
4g7h_F	443	Crystal Structure Of Thermus Thermophilus Transcrip		4e-21
3iyd_F	613	Three-Dimensional Em Structure Of An Intact Activat		4e-21
4igc_X	613	X-ray Crystal Structure Of Escherichia Coli Sigma70		4e-21
1l9z_H	438	Thermus Aquaticus Rna Polymerase HoloenzymeFORK-Jun		6e-21
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-11

>pdb|3DXJ|F Chain F, Crystal Structure Of Thermus Thermophilus Rna Polymerase Holoenzyme In Complex With The Antibiotic Myxopyronin Length = 423

Iteration: 1
 Score = 99.8 bits (247), Expect = 3e-21,   Method: Compositional matrix adjust.
 Identities = 58/167 (34%), Positives = 96/167 (57%), Gaps = 6/167 (3%)
Query: 289 HLAF-GWYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYK 347
           H+A  G   R+ LI++   LV+ +A+ Y G G+ F DL+Q GN G+++  E+F++ R +K
Sbjct: 175 HIAREGEAARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQEGNQGLIRAVEKFEYKRRFK 234
Query: 348 FSTYVQYWIRKSISKMVARHARGIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKY 407
           FSTY  +WIR++I++ +A  AR I+IP  +   I+K+ +  + L    G+ P   EIA+ 
Sbjct: 235 FSTYATWWIRQAINRAIADQARTIRIPVHMVETINKLSRTARQLQQELGREPTYEEIAEA 294
Query: 408 TGLSLAEIRSASECLRIVG---SIDQKIGDCLNAKYLN-IPPFFFPS 450
            G    + +   E L+I     S++  IGD  ++ Y + IP    PS
Sbjct: 295 MGPGW-DAKRVEETLKIAQEPVSLETPIGDEKDSFYGDFIPDEHLPS 340

>pdb|1IW7|F Chain F, Crystal Structure Of The Rna Polymerase Holoenzyme From Thermus Thermophilus At 2.6a Resolution Length = 423

Iteration: 1
 Score = 99.8 bits (247), Expect = 3e-21,   Method: Compositional matrix adjust.
 Identities = 58/167 (34%), Positives = 96/167 (57%), Gaps = 6/167 (3%)
Query: 289 HLAF-GWYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYK 347
           H+A  G   R+ LI++   LV+ +A+ Y G G+ F DL+Q GN G+++  E+F++ R +K
Sbjct: 175 HIAREGEAARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQEGNQGLIRAVEKFEYKRRFK 234
Query: 348 FSTYVQYWIRKSISKMVARHARGIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKY 407
           FSTY  +WIR++I++ +A  AR I+IP  +   I+K+ +  + L    G+ P   EIA+ 
Sbjct: 235 FSTYATWWIRQAINRAIADQARTIRIPVHMVETINKLSRTARQLQQELGREPTYEEIAEA 294
Query: 408 TGLSLAEIRSASECLRIVG---SIDQKIGDCLNAKYLN-IPPFFFPS 450
            G    + +   E L+I     S++  IGD  ++ Y + IP    PS
Sbjct: 295 MGPGW-DAKRVEETLKIAQEPVSLETPIGDEKDSFYGDFIPDEHLPS 340

>pdb|1L9U|H Chain H, Thermus Aquaticus Rna Polymerase Holoenzyme At 4 A Resolution Length = 332

Iteration: 1
 Score = 99.4 bits (246), Expect = 4e-21,   Method: Compositional matrix adjust.
 Identities = 59/172 (34%), Positives = 98/172 (56%), Gaps = 8/172 (4%)
Query: 286 LKQHLAF---GWYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDH 342
           LK++L     G   R+ LI++   LV+ +A+ Y G G+ F DL+Q GN G+++  E+F++
Sbjct: 79  LKRYLHIAREGEAARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQEGNQGLIRAVEKFEY 138
Query: 343 TRGYKFSTYVQYWIRKSISKMVARHARGIKIPCKLNREISKIQKARKALTNSHGKYPEDI 402
            R +KFSTY  +WIR++I++ +A  AR I+IP  +   I+K+ +  + L    G+ P   
Sbjct: 139 KRRFKFSTYATWWIRQAINRAIADQARTIRIPVHMVETINKLSRTARQLQQELGREPSYE 198
Query: 403 EIAKYTGLSLAEIRSASECLRIVG---SIDQKIGDCLNAKYLN-IPPFFFPS 450
           EIA+  G    + +   E L+I     S++  IGD  ++ Y + IP    PS
Sbjct: 199 EIAEAMGPGW-DAKRVEETLKIAQEPVSLETPIGDEKDSFYGDFIPDENLPS 249

>pdb|4G7H|F Chain F, Crystal Structure Of Thermus Thermophilus Transcription Initiation Complex Length = 443

Iteration: 1
 Score = 99.4 bits (246), Expect = 4e-21,   Method: Compositional matrix adjust.
 Identities = 58/167 (34%), Positives = 96/167 (57%), Gaps = 6/167 (3%)
Query: 289 HLAF-GWYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYK 347
           H+A  G   R+ LI++   LV+ +A+ Y G G+ F DL+Q GN G+++  E+F++ R +K
Sbjct: 195 HIAREGEAARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQEGNQGLIRAVEKFEYKRRFK 254
Query: 348 FSTYVQYWIRKSISKMVARHARGIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKY 407
           FSTY  +WIR++I++ +A  AR I+IP  +   I+K+ +  + L    G+ P   EIA+ 
Sbjct: 255 FSTYATWWIRQAINRAIADQARTIRIPVHMVETINKLSRTARQLQQELGREPTYEEIAEA 314
Query: 408 TGLSLAEIRSASECLRIVG---SIDQKIGDCLNAKYLN-IPPFFFPS 450
            G    + +   E L+I     S++  IGD  ++ Y + IP    PS
Sbjct: 315 MGPGW-DAKRVEETLKIAQEPVSLETPIGDEKDSFYGDFIPDEHLPS 360

>pdb|3IYD|F Chain F, Three-Dimensional Em Structure Of An Intact Activator-Dependent Transcription Initiation Complex Length = 613

Iteration: 1
 Score = 99.4 bits (246), Expect = 4e-21,   Method: Compositional matrix adjust.
 Identities = 44/139 (31%), Positives = 85/139 (61%)
Query: 296 CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYW 355
            ++E++++   LV+ +A+ Y   G+ F DL+Q GN+G+++  ++F++ RGYKFSTY  +W
Sbjct: 375 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 434
Query: 356 IRKSISKMVARHARGIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEI 415
           IR++I++ +A  AR I+IP  +   I+K+ +  + +    G+ P   E+A+   +   +I
Sbjct: 435 IRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELAERMLMPEDKI 494
Query: 416 RSASECLRIVGSIDQKIGD 434
           R   +  +   S++  IGD
Sbjct: 495 RKVLKIAKEPISMETPIGD 513

>pdb|4IGC|X Chain X, X-ray Crystal Structure Of Escherichia Coli Sigma70 Holoenzyme Length = 613

Iteration: 1
 Score = 99.4 bits (246), Expect = 4e-21,   Method: Compositional matrix adjust.
 Identities = 44/139 (31%), Positives = 85/139 (61%)
Query: 296 CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYW 355
            ++E++++   LV+ +A+ Y   G+ F DL+Q GN+G+++  ++F++ RGYKFSTY  +W
Sbjct: 375 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 434
Query: 356 IRKSISKMVARHARGIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEI 415
           IR++I++ +A  AR I+IP  +   I+K+ +  + +    G+ P   E+A+   +   +I
Sbjct: 435 IRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELAERMLMPEDKI 494
Query: 416 RSASECLRIVGSIDQKIGD 434
           R   +  +   S++  IGD
Sbjct: 495 RKVLKIAKEPISMETPIGD 513

>pdb|1L9Z|H Chain H, Thermus Aquaticus Rna Polymerase HoloenzymeFORK-Junction Promoter Dna Complex At 6.5 A Resolution Length = 438

Iteration: 1
 Score = 99.0 bits (245), Expect = 6e-21,   Method: Compositional matrix adjust.
 Identities = 65/197 (32%), Positives = 107/197 (54%), Gaps = 18/197 (9%)
Query: 261 TLEKESGKAASLNCWAQAAGVSERVLKQHLAF---GWYCREELIKSTRPLVLFLARNYRG 317
           T+E+  GK  SL           + LK++L     G   R+ LI++   LV+ +A+ Y G
Sbjct: 170 TVEEVDGKLKSLP----------KELKRYLHIAREGEAARQHLIEANLRLVVSIAKKYTG 219
Query: 318 LGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIPCKL 377
            G+ F DL+Q GN G+++  E+F++ R +KFSTY  +WIR++I++ +A  AR I+IP  +
Sbjct: 220 RGLSFLDLIQEGNQGLIRAVEKFEYKRRFKFSTYATWWIRQAINRAIADQARTIRIPVHM 279
Query: 378 NREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVG---SIDQKIGD 434
              I+K+ +  + L    G+ P   EIA+  G    + +   E L+I     S++  IGD
Sbjct: 280 VETINKLSRTARQLQQELGREPSYEEIAEAMGPGW-DAKRVEETLKIAQEPVSLETPIGD 338
Query: 435 CLNAKYLN-IPPFFFPS 450
             ++ Y + IP    PS
Sbjct: 339 EKDSFYGDFIPDENLPS 355

>pdb|1KU2|A Chain A, Crystal Structure Of Thermus Aquaticus Rna Polymerase Sigma Subunit Fragment Containing Regions 1.2 To 3.1 Length = 241

Iteration: 1
 Score = 94.4 bits (233), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 53/152 (34%), Positives = 87/152 (57%), Gaps = 13/152 (8%)
Query: 261 TLEKESGKAASLNCWAQAAGVSERVLKQHLAF---GWYCREELIKSTRPLVLFLARNYRG 317
           T+E+  GK  SL           + LK++L     G   R+ LI++   LV+ +A+ Y G
Sbjct: 79  TVEEVDGKLKSLP----------KELKRYLHIAREGEAARQHLIEANLRLVVSIAKKYTG 128
Query: 318 LGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIPCKL 377
            G+ F DL+Q GN G+++  E+F++ R +KFSTY  +WIR++I++ +A  AR I+IP  +
Sbjct: 129 RGLSFLDLIQEGNQGLIRAVEKFEYKRRFKFSTYATWWIRQAINRAIADQARTIRIPVHM 188
Query: 378 NREISKIQKARKALTNSHGKYPEDIEIAKYTG 409
              I+K+ +  + L    G+ P   EIA+  G
Sbjct: 189 VETINKLSRTARQLQQELGREPSYEEIAEAMG 220

>pdb|3UGO|A Chain A, Crystal Structure Of Rna-Polymerase Sigma Subunit Domain 2 Complexed With -10 Promoter Element Ssdna Oligo (Tacaat) Length = 245

Iteration: 1
 Score = 94.4 bits (233), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 53/152 (34%), Positives = 87/152 (57%), Gaps = 13/152 (8%)
Query: 261 TLEKESGKAASLNCWAQAAGVSERVLKQHLAF---GWYCREELIKSTRPLVLFLARNYRG 317
           T+E+  GK  SL           + LK++L     G   R+ LI++   LV+ +A+ Y G
Sbjct: 83  TVEEVDGKLKSLP----------KELKRYLHIAREGEAARQHLIEANLRLVVSIAKKYTG 132
Query: 318 LGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIPCKL 377
            G+ F DL+Q GN G+++  E+F++ R +KFSTY  +WIR++I++ +A  AR I+IP  +
Sbjct: 133 RGLSFLDLIQEGNQGLIRAVEKFEYKRRFKFSTYATWWIRQAINRAIADQARTIRIPVHM 192
Query: 378 NREISKIQKARKALTNSHGKYPEDIEIAKYTG 409
              I+K+ +  + L    G+ P   EIA+  G
Sbjct: 193 VETINKLSRTARQLQQELGREPSYEEIAEAMG 224

>pdb|1SIG|A Chain A, Crystal Structure Of A Sigma70 Subunit Fragment From Escherichia Coli Rna Polymerase Length = 339

Iteration: 1
 Score = 77.8 bits (190), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 29/74 (39%), Positives = 54/74 (72%)
Query: 296 CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYW 355
            ++E++++   LV+ +A+ Y   G+ F DL+Q GN+G+++  ++F++ RGYKFSTY  +W
Sbjct: 266 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 325
Query: 356 IRKSISKMVARHAR 369
           IR++I++ +A  AR
Sbjct: 326 IRQAITRSIADQAR 339

>pdb|3LES|A Chain A, 2f5 Epitope Scaffold Es2 Length = 179

Iteration: 1
 Score = 76.3 bits (186), Expect = 4e-14,   Method: Compositional matrix adjust.
 Identities = 41/112 (36%), Positives = 67/112 (59%), Gaps = 13/112 (11%)
Query: 261 TLEKESGKAASLNCWAQAAGVSERVLKQHLAF---GWYCREELIKSTRPLVLFLARNYRG 317
           T+E+  GK  SL           + LK++L     G   R+ LI++   LV+ +A+ Y G
Sbjct: 78  TVEEVDGKLKSLP----------KELKRYLHIAREGEAARQHLIEANLRLVVSIAKKYTG 127
Query: 318 LGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHAR 369
            G+ F DL+Q GN G+++  E+F++ RG+ FSTY  +WIR++I++ +A  AR
Sbjct: 128 RGLSFLDLIQEGNQGLIRAVEKFEYKRGFAFSTYATWWIRQAINRAIADQAR 179

>pdb|1L0O|C Chain C, Crystal Structure Of The Bacillus Stearothermophilus Anti- Sigma Factor Spoiiab With The Sporulation Sigma Factor Sigmaf Length = 243

Iteration: 1
 Score = 66.2 bits (160), Expect = 4e-11,   Method: Compositional matrix adjust.
 Identities = 41/137 (29%), Positives = 71/137 (51%), Gaps = 1/137 (0%)
Query: 296 CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYW 355
            R+E+I+    LV  + + +   G    DL Q G +G+L+  ++FD +   KFSTY    
Sbjct: 29  ARDEIIEKNMRLVWSVVQRFLNRGYEADDLFQIGCIGLLKSVDKFDLSYDVKFSTYAVPM 88
Query: 356 IRKSISKMVARHARGIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEI 415
           I   I + + R    +K+   L    +KI+KA+  L+ + G+ P   EIA + G+S  ++
Sbjct: 89  IIGEIQRFL-RDDGTVKVSRSLKEMGNKIRKAKDELSKTRGRAPTVTEIADHLGISPEDV 147
Query: 416 RSASECLRIVGSIDQKI 432
             A E +R+  SI + +
Sbjct: 148 VLAQEAVRLPTSIHETV 164

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	459
1l0o_C	243	Sigma factor; bergerat fold, helix-turn-helix, pro	2e-27
1rp3_A	239	RNA polymerase sigma factor sigma-28 (FLIA); trans	9e-26
3iyd_F	613	RNA polymerase sigma factor RPOD; transcription, i	2e-25
3ugo_A	245	RNA polymerase sigma factor; protein-DNA complex,	2e-23
2a6h_F	423	RNA polymerase sigma factor RPOD; RNA polymerase h	6e-23
1l9z_H	438	Sigma factor SIGA; helix-turn-helix, coiled-coil,	1e-22
1sig_A	339	Sigma70, RNA polymerase primary sigma factor; RNA	2e-15
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	8e-06
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	3e-05

>1l0o_C Sigma factor; bergerat fold, helix-turn-helix, protein binding; HET: ADP; 2.90A {Geobacillus stearothermophilus} SCOP: a.4.13.2 Length = 243

 Score =  108 bits (273), Expect = 2e-27
 Identities = 42/141 (29%), Positives = 71/141 (50%), Gaps = 7/141 (4%)

Query: 297 REELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWI 356
           R+E+I+    LV  + + +   G    DL Q G +G+L+  ++FD +   KFSTY    I
Sbjct: 30  RDEIIEKNMRLVWSVVQRFLNRGYEADDLFQIGCIGLLKSVDKFDLSYDVKFSTYAVPMI 89

Query: 357 RKSISKMVARHAR---GIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLA 413
              I     R  R    +K+   L    +KI+KA+  L+ + G+ P   EIA + G+S  
Sbjct: 90  IGEIQ----RFLRDDGTVKVSRSLKEMGNKIRKAKDELSKTRGRAPTVTEIADHLGISPE 145

Query: 414 EIRSASECLRIVGSIDQKIGD 434
           ++  A E +R+  SI + + +
Sbjct: 146 DVVLAQEAVRLPTSIHETVYE 166

>1rp3_A RNA polymerase sigma factor sigma-28 (FLIA); transcription; 2.30A {Aquifex aeolicus} SCOP: a.4.13.1 a.4.13.2 a.177.1.1 PDB: 1sc5_A Length = 239

 Score =  104 bits (261), Expect = 9e-26
 Identities = 33/144 (22%), Positives = 64/144 (44%), Gaps = 10/144 (6%)

Query: 297 REELIKSTRPLVLFLARNYR---GLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQ 353
           REELI    PLV  +A N +      +   DL+  G +G+++  +        +   Y++
Sbjct: 14  REELILKYLPLVKAIATNIKKHLPEDVDIRDLISYGVIGLIKAVDNLSTENPKRAEAYIK 73

Query: 354 YWIRKSISKMVARHARGIKIPCKLNREIS-KIQKARKALTNSHGKYPEDIEIAKYTGLSL 412
             I+ +I      + R +    +  RE   +I++  + L    G+ P D E+AK  G+S 
Sbjct: 74  LRIKGAI----YDYLRSLDFGSRQVREKERRIKEVVEKLKEKLGREPTDEEVAKELGIST 129

Query: 413 AEIRSASECLRI--VGSIDQKIGD 434
            E+    + +    + S+++   D
Sbjct: 130 EELFKTLDKINFSYILSLEEVFRD 153

>3iyd_F RNA polymerase sigma factor RPOD; transcription, initiation, class I, activator, RNA polymeras holoenzyme, sigma70, open complex, CAP, CRP; HET: DNA CMP; 19.80A {Escherichia coli k-12} Length = 613

 Score =  108 bits (271), Expect = 2e-25
 Identities = 44/138 (31%), Positives = 85/138 (61%)

Query: 297 REELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWI 356
           ++E++++   LV+ +A+ Y   G+ F DL+Q GN+G+++  ++F++ RGYKFSTY  +WI
Sbjct: 376 KKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWI 435

Query: 357 RKSISKMVARHARGIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIR 416
           R++I++ +A  AR I+IP  +   I+K+ +  + +    G+ P   E+A+   +   +IR
Sbjct: 436 RQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELAERMLMPEDKIR 495

Query: 417 SASECLRIVGSIDQKIGD 434
              +  +   S++  IGD
Sbjct: 496 KVLKIAKEPISMETPIGD 513

>3ugo_A RNA polymerase sigma factor; protein-DNA complex, bacterial promoter opening, G-quartet, quadruplex, DNA binding; 2.10A {Thermus aquaticus} PDB: 3ugp_A 1ku2_A 3lev_A* 3les_A* Length = 245

 Score = 98.0 bits (244), Expect = 2e-23
 Identities = 43/122 (35%), Positives = 73/122 (59%), Gaps = 2/122 (1%)

Query: 297 REELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWI 356
           R+ LI++   LV+ +A+ Y G G+ F DL+Q GN G+++  E+F++ R +KFSTY  +WI
Sbjct: 112 RQHLIEANLRLVVSIAKKYTGRGLSFLDLIQEGNQGLIRAVEKFEYKRRFKFSTYATWWI 171

Query: 357 RKSISKMVARHARGIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAK--YTGLSLAE 414
           R++I++ +A  AR I+IP  +   I+K+ +  + L    G+ P   EIA+    G     
Sbjct: 172 RQAINRAIADQARTIRIPVHMVETINKLSRTARQLQQELGREPSYEEIAEAMGPGWDAKR 231

Query: 415 IR 416
           + 
Sbjct: 232 VE 233

>2a6h_F RNA polymerase sigma factor RPOD; RNA polymerase holoenzyme, streptolydigin, antibiotic, transcription regulation; HET: STD; 2.40A {Thermus thermophilus} SCOP: a.4.13.1 a.4.13.2 a.177.1.1 PDB: 1smy_F* 1zyr_F* 1iw7_F* 2a69_F* 2a6e_F 2a68_F* 2be5_F* 2cw0_F 3eql_F* 3dxj_F* 1l9u_H Length = 423

 Score = 99.6 bits (248), Expect = 6e-23
 Identities = 63/288 (21%), Positives = 125/288 (43%), Gaps = 40/288 (13%)

Query: 157 DLSDVHTEEQKMNDS-RDY--HMGKILVPSKRKGKRKLKTARVSEESIETSLLSLPSEA- 212
           +  D+   +   +D  R Y   +G++ + +  +     +      E+I+        +  
Sbjct: 66  EEEDLPIPKISTSDPVRQYLHEIGQVPLLTLEEEVELARKVEEGMEAIKKLSEITGLDPD 125

Query: 213 -LQEGLKQPTIFSAERALNSRGRRLTIARNEAEMSKGVQVVANLERIKTTLEKESGKAAS 271
            ++E ++   + SA        +     +   E+ + ++ +    +    + +E   A  
Sbjct: 126 LIREVVRAKILGSARVRHIPGLKETLDPKTVEEIDQKLKSLPKEHKRYLHIAREGEAA-- 183

Query: 272 LNCWAQAAGVSERVLKQHLAFGWYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNV 331
                                    R+ LI++   LV+ +A+ Y G G+ F DL+Q GN 
Sbjct: 184 -------------------------RQHLIEANLRLVVSIAKKYTGRGLSFLDLIQEGNQ 218

Query: 332 GVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIPCKLNREISKIQKARKAL 391
           G+++  E+F++ R +KFSTY  +WIR++I++ +A  AR I+IP  +   I+K+ +  + L
Sbjct: 219 GLIRAVEKFEYKRRFKFSTYATWWIRQAINRAIADQARTIRIPVHMVETINKLSRTARQL 278

Query: 392 TNSHGKYPEDIEIAK--YTGLSLAEIRSASECLRIVG---SIDQKIGD 434
               G+ P   EIA+    G     +    E L+I     S++  IGD
Sbjct: 279 QQELGREPTYEEIAEAMGPGWDAKRVE---ETLKIAQEPVSLETPIGD 323

>1l9z_H Sigma factor SIGA; helix-turn-helix, coiled-coil, transcription/DNA complex; 6.50A {Thermus aquaticus} SCOP: i.8.1.1 Length = 438

 Score = 98.9 bits (246), Expect = 1e-22
 Identities = 50/143 (34%), Positives = 83/143 (58%), Gaps = 8/143 (5%)

Query: 297 REELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWI 356
           R+ LI++   LV+ +A+ Y G G+ F DL+Q GN G+++  E+F++ R +KFSTY  +WI
Sbjct: 199 RQHLIEANLRLVVSIAKKYTGRGLSFLDLIQEGNQGLIRAVEKFEYKRRFKFSTYATWWI 258

Query: 357 RKSISKMVARHARGIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAK--YTGLSLAE 414
           R++I++ +A  AR I+IP  +   I+K+ +  + L    G+ P   EIA+    G     
Sbjct: 259 RQAINRAIADQARTIRIPVHMVETINKLSRTARQLQQELGREPSYEEIAEAMGPGWDAKR 318

Query: 415 IRSASECLRIVG---SIDQKIGD 434
           +    E L+I     S++  IGD
Sbjct: 319 VE---ETLKIAQEPVSLETPIGD 338

>1sig_A Sigma70, RNA polymerase primary sigma factor; RNA polymerase sigma factor, transcription regulation; 2.60A {Escherichia coli} SCOP: a.177.1.1 Length = 339

 Score = 76.5 bits (188), Expect = 2e-15
 Identities = 29/71 (40%), Positives = 52/71 (73%)

Query: 299 ELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRK 358
           E++++   LV+ +A+ Y   G+ F DL+Q GN+G+++  ++F++ RGYKFSTY  +WIR+
Sbjct: 269 EMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQ 328

Query: 359 SISKMVARHAR 369
           +I++ +A  AR
Sbjct: 329 AITRSIADQAR 339

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221

 Score = 47.5 bits (112), Expect = 8e-06
 Identities = 47/379 (12%), Positives = 96/379 (25%), Gaps = 118/379 (31%)

Query: 160 DVHTEEQKMNDSRDYHMGKILVPSKRKGKRKLKTARVSEESIETSLLSLPSEALQEGLKQ 219
           D  T E        Y    IL   +           V +     S+LS   E +   +  
Sbjct: 8   DFETGEH------QYQYKDILSVFEDAFVDNFDCKDVQDM--PKSILS--KEEIDHIIMS 57

Query: 220 PTIFSAERALNSRGRRLTIARNEAEMSKGVQ--VVANLER----IKTTLEKESGKAASLN 273
               S    L           ++ E  + VQ  V   L      + + ++ E  +  S+ 
Sbjct: 58  KDAVSGTLRL------FWTLLSKQE--EMVQKFVEEVLRINYKFLMSPIKTEQ-RQPSMM 108

Query: 274 ------CWAQAAGVSERVLKQHLAFGWYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQ 327
                    +    ++   K ++      R +     R   L   R  + + I       
Sbjct: 109 TRMYIEQRDRLYNDNQVFAKYNV-----SRLQPYLKLR-QALLELRPAKNVLI------- 155

Query: 328 AGNVG----VLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIPCKLNREISK 383
            G +G     +       +    K    + +W+       +        +   L + + +
Sbjct: 156 DGVLGSGKTWVALDVCLSYKVQCKMDFKI-FWLN------LKNCNSPETVLEMLQKLLYQ 208

Query: 384 IQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECL-------------------RI 424
           I     + ++        I   +     L + +    CL                   +I
Sbjct: 209 IDPNWTSRSDHSSNIKLRIHSIQAELRRLLKSKPYENCLLVLLNVQNAKAWNAFNLSCKI 268

Query: 425 -VGSIDQKIGDCLN-------------------------AKYLNIPPFFFPSFA------ 452
            + +  +++ D L+                          KYL+  P   P         
Sbjct: 269 LLTTRFKQVTDFLSAATTTHISLDHHSMTLTPDEVKSLLLKYLDCRPQDLPREVLTTNPR 328

Query: 453 ----IWE--------WEEY 459
               I E        W+ +
Sbjct: 329 RLSIIAESIRDGLATWDNW 347

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221

 Score = 45.6 bits (107), Expect = 3e-05
 Identities = 58/436 (13%), Positives = 131/436 (30%), Gaps = 96/436 (22%)

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 MSKGVQVVANLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQH--------------- 289
                + V N +++ T +E      +SLN       +     ++                
Sbjct: 343 TWDNWKHV-NCDKLTTIIE------SSLNV------LEPAEYRKMFDRLSVFPPSAHIPT 389

Query: 290 --LAFGW-----YCREELIKSTRPLVLFLARN-----YRGLGIPFSDLLQAGNVGVLQGA 337
             L+  W          ++       L + +           I     ++  N   L  +
Sbjct: 390 ILLSLIWFDVIKSDVMVVVNKLHKYSL-VEKQPKESTISIPSIYLELKVKLENEYALHRS 448

Query: 338 --ERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIPCKLN--REI--------SKIQ 385
             + ++  + +     +  ++ +     +  H + I+ P ++   R +         KI+
Sbjct: 449 IVDHYNIPKTFDSDDLIPPYLDQYFYSHIGHHLKNIEHPERMTLFRMVFLDFRFLEQKIR 508

Query: 386 KARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSID---QKIG-DCLNAKYL 441
               A   S        ++  Y    + +     E  R+V +I     KI  + + +KY 
Sbjct: 509 HDSTAWNASGSILNTLQQLKFYKPY-ICDNDPKYE--RLVNAILDFLPKIEENLICSKYT 565

Query: 442 NI--PPFFFPSFAIWE 455
           ++          AI+E
Sbjct: 566 DLLRIALMAEDEAIFE 581

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	459
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
3ugo_A	245	RNA polymerase sigma factor; protein-DNA complex,	100.0
3iyd_F	613	RNA polymerase sigma factor RPOD; transcription, i	99.94
1l0o_C	243	Sigma factor; bergerat fold, helix-turn-helix, pro	99.82
1rp3_A	239	RNA polymerase sigma factor sigma-28 (FLIA); trans	99.81
1sig_A	339	Sigma70, RNA polymerase primary sigma factor; RNA	99.72
1or7_A	194	Sigma-24, RNA polymerase sigma-E factor; regulatio	99.72
2q1z_A	184	RPOE, ECF SIGE; ECF sigma factor, cupin fold, zinc	99.69
3mzy_A	164	RNA polymerase sigma-H factor; PSI, MCSG, structur	99.47
2lfw_A	157	PHYR sigma-like domain; signal transduction, respo	99.41
3n0r_A	286	Response regulator; sigma factor, receiver, two-co	99.39
2o7g_A	112	Probable RNA polymerase sigma-C factor; sigma fact	99.28
1h3l_A	87	RNA polymerase sigma factor; transcription, DNA-bi	99.19
3clo_A	258	Transcriptional regulator; NP_811094.1, bacterial	97.72
1rp3_A	239	RNA polymerase sigma factor sigma-28 (FLIA); trans	93.14
3hug_A	92	RNA polymerase sigma factor; ECF sigma factor, zin	92.04
1l9z_H	438	Sigma factor SIGA; helix-turn-helix, coiled-coil,	91.91
1x3u_A	79	Transcriptional regulatory protein FIXJ; helix-tur	90.91
2p7v_B	68	Sigma-70, RNA polymerase sigma factor RPOD; RSD, r	90.74
3t72_q	99	RNA polymerase sigma factor RPOD, DNA-directed RN	89.76
1tty_A	87	Sigma-A, RNA polymerase sigma factor RPOD; helix-t	89.21
1ku3_A	73	Sigma factor SIGA; helix-turn-helix, transcription	89.15
1je8_A	82	Nitrate/nitrite response regulator protein NARL; p	89.04
2o8x_A	70	Probable RNA polymerase sigma-C factor; promoter r	88.77
3c57_A	95	Two component transcriptional regulatory protein;	87.06
1tc3_C	51	Protein (TC3 transposase); DNA binding, helix-turn	86.3
2jpc_A	61	SSRB; DNA binding protein, structural genomics, PS	86.16
2jt1_A	77	PEFI protein; solution structure, winged helix-tur	85.0
1xsv_A	113	Hypothetical UPF0122 protein SAV1236; helix-turn-h	84.4
2x48_A	55	CAG38821; archeal virus, viral protein; 2.60A {Sul	83.41
1fse_A	74	GERE; helix-turn-helix DNA-binding protein transcr	82.87
3ulq_B	90	Transcriptional regulatory protein COMA; tetratric	81.87
2rnj_A	91	Response regulator protein VRAR; HTH LUXR-type dom	81.6
2a6h_F	423	RNA polymerase sigma factor RPOD; RNA polymerase h	80.98

>1l9z_H Sigma factor SIGA; helix-turn-helix, coiled-coil, transcription/DNA complex; 6.50A {Thermus aquaticus} SCOP: i.8.1.1

Probab=100.00  E-value=1.1e-36  Score=318.52  Aligned_cols=227  Identities=25%  Similarity=0.360  Sum_probs=199.3

Q ss_pred             CChhHHHHHHhccCCCCCCChHHHHHHHHHhHHHHHHHHHHHH------------------HHHHhCCCCchHHHHHH--
Q 012638          219 QPTIFSAERALNSRGRRLTIARNEAEMSKGVQVVANLERIKTT------------------LEKESGKAASLNCWAQA--  278 (459)
Q Consensus       219 ~p~~~~~~~~~~~~~~~lLt~~eE~eL~~~i~~~~~le~~~~~------------------l~~~~gr~pt~~ewa~a--  278 (459)
                      +|...|+   ......||||++||++|+++|+.++.++.....                  ....+++.|+..+|+..  
T Consensus        94 d~~~~Yl---~ei~~~pLLt~eEE~~La~~i~~g~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  170 (438)
T 1l9z_H           94 DPVRQYL---HEIGQVPLLTLEEEIDLARKVEEGMEAIKKLSEATGLDQELIREVVRAKILGTARIQKIPGLKEKPDPKT  170 (438)
T ss_pred             ChHHHHH---HHhccCCCCCHHHHHHHHHHHHHhhhHHHHHHhhhccchhhhhhhhhhhhhhcccccccccccccccchh
Confidence            5565666   345668999999999999999998765543221                  12335678888887432  


Q ss_pred             ----------cCCCHHHHHHHHHhchHHHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCch
Q 012638          279 ----------AGVSERVLKQHLAFGWYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKF  348 (459)
Q Consensus       279 ----------~g~deeeL~~~l~~G~~Are~LI~~nlrLV~sIAkry~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rF  348 (459)
                                .+++..+|+..++.|..|+++||.+|+++|+++|++|.++|.+++|||||||||||+|+++|||.+|++|
T Consensus       171 ~~~~~~~~~~~~~~~~eLi~~~~~d~~A~~~Li~~nlrlVv~iA~ry~~~g~~aeDLIQEg~IgL~kAvekFDp~kG~rF  250 (438)
T 1l9z_H          171 VEEVDGKLKSLPKELKRYLHIAREGEAARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQEGNQGLIRAVEKFEYKRRFKF  250 (438)
T ss_pred             hhhhhhhhhcccchHHHHHHHHhcCHHHHHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHhcCcccCCCh
Confidence                      3456678888888777799999999999999999999999999999999999999999999999999999


Q ss_pred             hhHHHHHHHHHHHHHHHhhccccccccchHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhC--CCHHHHHHHHHhhccCC
Q 012638          349 STYVQYWIRKSISKMVARHARGIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTG--LSLAEIRSASECLRIVG  426 (459)
Q Consensus       349 STYa~~wIrnaI~d~Lrk~sr~irlP~~v~e~i~kI~ka~~~L~~~lgr~PT~eEIAe~LG--IS~e~Vk~~l~~ar~~~  426 (459)
                      +|||+|||+|.|.++|+++.+.+++|.|+.+.+++++++.+.+.+.+|+.|+.+|||+.+|  +++++|..++..+..++
T Consensus       251 sTYA~~wIR~~I~~~i~~~~R~irlp~~~~~~l~~lrr~~r~l~~~lgr~pt~eeiA~~l~~~v~~e~V~~~~~~~~~~~  330 (438)
T 1l9z_H          251 STYATWWIRQAINRAIADQARTIRIPVHMVETINKLSRTARQLQQELGREPSYEEIAEAMGPGWDAKRVEETLKIAQEPV  330 (438)
T ss_pred             HHHHHHHHHHHHHHHHHHhcchhccchHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCCCHHHHHHHHHhccccc
Confidence            9999999999999999999999999999999999999999999999999999999999999  99999999999888999


Q ss_pred             ccccccCCCCCCccccCCCCCC
Q 012638          427 SIDQKIGDCLNAKYLNIPPFFF  448 (459)
Q Consensus       427 SLD~~v~~d~~~~l~e~i~D~~  448 (459)
                      |||.+++++++..+.|+++|..
T Consensus       331 SLd~~~~~d~d~~l~d~l~d~~  352 (438)
T 1l9z_H          331 SLETPIGDEKDSFYGDFIPDEN  352 (438)
T ss_pred             ccccccccccchhhhhhhcccc
Confidence            9999998877778889888763

>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=8.9e-37  Score=318.01  Aligned_cols=231  Identities=26%  Similarity=0.386  Sum_probs=197.9

Q ss_pred             CChhHHHHHHhccCCCCCCChHHHHHHHHHhHHHHHHHHHHHHH------------------HHHhCCCCchHHHH----
Q 012638          219 QPTIFSAERALNSRGRRLTIARNEAEMSKGVQVVANLERIKTTL------------------EKESGKAASLNCWA----  276 (459)
Q Consensus       219 ~p~~~~~~~~~~~~~~~lLt~~eE~eL~~~i~~~~~le~~~~~l------------------~~~~gr~pt~~ewa----  276 (459)
                      +|...|++   .....||||++||++|+++|+.+..+.......                  ....++.|+..+|+    
T Consensus        79 d~~~~Yl~---ei~~~plLt~eEE~~La~ri~~g~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  155 (423)
T 2a6h_F           79 DPVRQYLH---EIGQVPLLTLEEEVELARKVEEGMEAIKKLSEITGLDPDLIREVVRAKILGSARVRHIPGLKETLDPKT  155 (423)
T ss_dssp             HHHHHHHH---HHHHCCCCTTHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHCCHHHHHTTSCSSSCTTHH
T ss_pred             cHHHHHHH---HhcccCCCCHHHHHHHHHHHHhchhHHHHHHHhhccchhhhhhhHhhhhhhhhhcccccchhhhhhhhh
Confidence            44555552   345589999999999999999986554432211                  11234566654432    


Q ss_pred             -----H---HcCCCHHHHHHHHHhchHHHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCch
Q 012638          277 -----Q---AAGVSERVLKQHLAFGWYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKF  348 (459)
Q Consensus       277 -----~---a~g~deeeL~~~l~~G~~Are~LI~~nlrLV~sIAkry~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rF  348 (459)
                           .   +.++++.+|+..++.|..|+++||.+|+++|+++|++|.++|.+++|||||||||||+|+++|||.+|++|
T Consensus       156 ~~~~~~~~~~~~~~~~~L~~~~~~d~~A~~~Li~~~lrlV~~iA~~y~~~~~~~eDLiQEg~igL~kav~kFd~~~g~~F  235 (423)
T 2a6h_F          156 VEEIDQKLKSLPKEHKRYLHIAREGEAARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQEGNQGLIRAVEKFEYKRRFKF  235 (423)
T ss_dssp             HHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHHHTHHHHHHHHTTTCTTTSCHHHHHHHHHHHHHHHHHHCCTTSCCCH
T ss_pred             hhhhhhhhhcccccHHHHHHHHhcCHHHHHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHhcCcccCCCH
Confidence                 2   34667788999998887799999999999999999999999999999999999999999999999999999


Q ss_pred             hhHHHHHHHHHHHHHHHhhccccccccchHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhC--CCHHHHHHHHHhhccCC
Q 012638          349 STYVQYWIRKSISKMVARHARGIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTG--LSLAEIRSASECLRIVG  426 (459)
Q Consensus       349 STYa~~wIrnaI~d~Lrk~sr~irlP~~v~e~i~kI~ka~~~L~~~lgr~PT~eEIAe~LG--IS~e~Vk~~l~~ar~~~  426 (459)
                      +|||+|||+|+|.++|+++.+.+++|.|+.+.+++++++.+.+.+.+|+.|+.+|||+.||  +++++|..++..+..++
T Consensus       236 stYa~~wIr~~i~~~i~~~~r~ir~p~~~~~~~~~lrr~~~~l~~~~~r~p~~~eiA~~l~~~~~~~~v~~~~~~~~~~~  315 (423)
T 2a6h_F          236 STYATWWIRQAINRAIADQARTIRIPVHMVETINKLSRTARQLQQELGREPTYEEIAEAMGPGWDAKRVEETLKIAQEPV  315 (423)
T ss_dssp             HHHHHHHHHHHHHHHHHHHSSSSCCCHHHHHHHHHHHHHHHHHHHHHSSCCCHHHHHHHHCTTCCHHHHHHHHHHHSCCE
T ss_pred             HHHHHHHHHHHHHHHHHHccceeeccHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCCCHHHHHHHHHhccCCc
Confidence            9999999999999999999999999999999999999999999999999999999999999  99999999999999999


Q ss_pred             ccccccCCCCCCccccCCCCCC-CCcc
Q 012638          427 SIDQKIGDCLNAKYLNIPPFFF-PSFA  452 (459)
Q Consensus       427 SLD~~v~~d~~~~l~e~i~D~~-~~~~  452 (459)
                      |||.|++++++.++.|+++|+. ++|+
T Consensus       316 Sld~~~~~~~~~~l~d~l~d~~~~~pe  342 (423)
T 2a6h_F          316 SLETPIGDEKDSFYGDFIPDEHLPSPV  342 (423)
T ss_dssp             ESSCBCSSSSSCBGGGSSCCSSSCCHH
T ss_pred             ccccccCCCCccchhhhhccccCCCHH
Confidence            9999998888888999998864 4443

>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=7.3e-37  Score=297.70  Aligned_cols=207  Identities=25%  Similarity=0.384  Sum_probs=124.3

Q ss_pred             CChhHHHHHHhccCCCCCCChHHHHHHHHHhHHHHHHH-HHHHHH--HHH-----------------------hCCCCch
Q 012638          219 QPTIFSAERALNSRGRRLTIARNEAEMSKGVQVVANLE-RIKTTL--EKE-----------------------SGKAASL  272 (459)
Q Consensus       219 ~p~~~~~~~~~~~~~~~lLt~~eE~eL~~~i~~~~~le-~~~~~l--~~~-----------------------~gr~pt~  272 (459)
                      ||...++   ..++..||||++||++|+++|+.++.+. .+....  ...                       .+.+|+.
T Consensus         7 d~~~~yl---~~i~~~~llt~~~e~~la~~i~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~~~~~g~~~~~~~~~   83 (245)
T 3ugo_A            7 DPVRQYL---HEIGQVPLLTLEEEIDLARKVEEGMEAIKKLSEATGLDQELIREVVRAKILGTARIQKIPGLKEKPDPKT   83 (245)
T ss_dssp             HHHHHHH---HHHTTSCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHTTGGGCSCCCCTTCCCCCCHHH
T ss_pred             CcHHHHH---HHcccccCCCHHHHHHHHHHHHHHHHHHHHHHhccCCcHHHHHHhhhhhhhccchhcccccccccccchh
Confidence            5555555   3456689999999999999999987743 332210  000                       1468889


Q ss_pred             HHHHHHcCCC----HHHHHHHHHhchHHHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCch
Q 012638          273 NCWAQAAGVS----ERVLKQHLAFGWYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKF  348 (459)
Q Consensus       273 ~ewa~a~g~d----eeeL~~~l~~G~~Are~LI~~nlrLV~sIAkry~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rF  348 (459)
                      .+||.+.+++    ...|+..++.|..|+++||..|.++|+++|++|.+++.+++||+||||+|||+++++||+.+|++|
T Consensus        84 ~~~~~~~~~~~~~~~~~L~~~~~~d~~A~~~L~~~y~~lV~~ia~r~~~~~~~aeDLvQegfi~L~~a~~~fd~~~g~~F  163 (245)
T 3ugo_A           84 VEEVDGKLKSLPKELKRYLHIAREGEAARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQEGNQGLIRAVEKFEYKRRFKF  163 (245)
T ss_dssp             HHHHHHHHHTSCHHHHHHHHHHHHHHHHHHHHHHTTHHHHHHHHGGGTTSSSCHHHHHHHHHHHHHHHHHHCCGGGCCCH
T ss_pred             HHHHHHhhccchHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHcCCCCcHHHHHHHHHHHHHHHHHHcCcccCCcH
Confidence            9999998775    345666667777799999999999999999999999999999999999999999999999999999


Q ss_pred             hhHHHHHHHHHHHHHHHhhccccccccchHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhC--CCHHHHHHHHHhhccCC
Q 012638          349 STYVQYWIRKSISKMVARHARGIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTG--LSLAEIRSASECLRIVG  426 (459)
Q Consensus       349 STYa~~wIrnaI~d~Lrk~sr~irlP~~v~e~i~kI~ka~~~L~~~lgr~PT~eEIAe~LG--IS~e~Vk~~l~~ar~~~  426 (459)
                      +||++||||++|.++++++.+.+++|.++.+.++++.++.+.|...+++.||++|||+.||  ||+++|+.++.+++.++
T Consensus       164 ~tya~~~ir~~i~~~ir~~~r~~r~p~~l~e~i~~l~~~~~~L~~~~~~~ps~~EIAe~Lg~~is~~tVk~~l~~ar~~l  243 (245)
T 3ugo_A          164 STYATWWIRQAINRAIADQARTIRIPVHMVETINKLSRTARQLQQELGREPSYEEIAEAMGPGWDAKRVEETLKIAQEPV  243 (245)
T ss_dssp             HHHHHHHHHHHHHHHHHHHTC-----------------------------------------------------------
T ss_pred             HHHHHHHHHHHHHHHHHHhcccccccHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHCCCCCHHHHHHHHHHHhhcc
Confidence            9999999999999999999999999999999999999999999999999999999999999  99999999999999998


Q ss_pred             cc
Q 012638          427 SI  428 (459)
Q Consensus       427 SL  428 (459)
                      ||
T Consensus       244 sl  245 (245)
T 3ugo_A          244 SL  245 (245)
T ss_dssp             --
T ss_pred             CC
Confidence            86

>3iyd_F RNA polymerase sigma factor RPOD; transcription, initiation, class I, activator, RNA polymeras holoenzyme, sigma70, open complex, CAP, CRP; HET: DNA CMP; 19.80A {Escherichia coli k-12}

Probab=99.94  E-value=2.5e-28  Score=264.82  Aligned_cols=186  Identities=26%  Similarity=0.485  Sum_probs=168.2

Q ss_pred             HHHHHHHHHHHHHhCCCCchHHHHHHcCCCHHHHHHHHHhchH-H---HHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHH
Q 012638          253 ANLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQHLAFGWY-C---REELIKSTRPLVLFLARNYRGLGIPFSDLLQA  328 (459)
Q Consensus       253 ~~le~~~~~l~~~~gr~pt~~ewa~a~g~deeeL~~~l~~G~~-A---re~LI~~nlrLV~sIAkry~g~g~d~EDLIQE  328 (459)
                      ..+++....++...|-.+.          +...|+.+++.|+. |   |+.||..|.++|+++|++|++++.+++||+||
T Consensus       338 ~~~q~kL~~ie~~~~~~~~----------~~~~Li~~~~~Gd~~A~~A~~~L~~~y~~~v~~ia~r~~~~~~~aeDlvQE  407 (613)
T 3iyd_F          338 HRALQKLQQIEEETGLTIE----------QVKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQE  407 (613)
T ss_dssp             HHHHHHHHHHHHHHTSCTT----------THHHHHHTHHHHHHHHHHHHTTTTTTTTHHHHHGGGSSSTTSSCSTTTTHH
T ss_pred             HHHHHHHHHHHHHhCCChH----------HHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHhcCCCCHHHHHHH
Confidence            3344444455555554331          35678899999976 6   99999999999999999999999999999999


Q ss_pred             HHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhhccccccccchHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHh
Q 012638          329 GNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYT  408 (459)
Q Consensus       329 G~IGLirAieKFDp~kG~rFSTYa~~wIrnaI~d~Lrk~sr~irlP~~v~e~i~kI~ka~~~L~~~lgr~PT~eEIAe~L  408 (459)
                      ||||||+++++||+.+|++|+||++|||+|+|+++++++.+++++|.|+.+.+++++++...+.+++|+.||.+|||+.|
T Consensus       408 ~fi~l~~a~~~fd~~~g~~Fstyl~~~irn~i~~~lr~~~r~~rip~~~~~~~~k~~r~~~~l~~~~gr~pt~eela~~l  487 (613)
T 3iyd_F          408 GNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELAERM  487 (613)
T ss_dssp             HHHHHHHHTTSCCTTSSSCSTTTHHHHHHHHHHHHTTTSCSSSCCCSHHHHTTTTTTTTTTTTTTTTCSCCCTTTTTTTS
T ss_pred             HHHHHHHHHHHcCccccCcHHHHHHHHHHHHHHHHHHhcCcceeCcHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHh
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCHHHHHHHHHhhccCCccccccCCCCCCccccCCCCCC
Q 012638          409 GLSLAEIRSASECLRIVGSIDQKIGDCLNAKYLNIPPFFF  448 (459)
Q Consensus       409 GIS~e~Vk~~l~~ar~~~SLD~~v~~d~~~~l~e~i~D~~  448 (459)
                      |+++++|+.++..++.++||+.+++++++..+.++++|..
T Consensus       488 ~~~~~~v~~~~~~~~~~~sld~~~~~~~~~~l~d~i~d~~  527 (613)
T 3iyd_F          488 LMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTT  527 (613)
T ss_dssp             SCCSSHHHHHHHHSCCCCCSSCCCSSSSSCCGGGSCCCSS
T ss_pred             CCCHHHHHHHHHhccCCcccCCCCCCCCCccHHHHhcCCC
Confidence            9999999999999999999999999888889999998864

>1l0o_C Sigma factor; bergerat fold, helix-turn-helix, protein binding; HET: ADP; 2.90A {Geobacillus stearothermophilus} SCOP: a.4.13.2

Probab=99.82  E-value=4.4e-21  Score=178.93  Aligned_cols=165  Identities=26%  Similarity=0.356  Sum_probs=53.3

Q ss_pred             CHHHHHHHHHhchH-HHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHH
Q 012638          282 SERVLKQHLAFGWY-CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSI  360 (459)
Q Consensus       282 deeeL~~~l~~G~~-Are~LI~~nlrLV~sIAkry~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIrnaI  360 (459)
                      +..+|+..++.|+. |++.|+..|.++|+++|++|.++..+++||+|||++++|+++++||+.+|.+|.||+++|++|.+
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            45678888999977 99999999999999999999999999999999999999999999999988899999999999999


Q ss_pred             HHHHHhhccccccccchHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHhhccCCccccccCCCC--CC
Q 012638          361 SKMVARHARGIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIVGSIDQKIGDCL--NA  438 (459)
Q Consensus       361 ~d~Lrk~sr~irlP~~v~e~i~kI~ka~~~L~~~lgr~PT~eEIAe~LGIS~e~Vk~~l~~ar~~~SLD~~v~~d~--~~  438 (459)
                      .+++|++. .+++|.++.....+++++...+....++.|+.++|+..+|++.+.+...+.....+.|++.|+.+++  ..
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            99999886 7899999999999999999999999999999999999999999999998888777889998865433  24


Q ss_pred             ccccCCCCC
Q 012638          439 KYLNIPPFF  447 (459)
Q Consensus       439 ~l~e~i~D~  447 (459)
                      ++.+.++++
T Consensus       173 ~~~~~~~~~  181 (243)
T 1l0o_C          173 TLLDQIADA  181 (243)
T ss_dssp             ---------
T ss_pred             chhhccCcc
Confidence            455555543

>1rp3_A RNA polymerase sigma factor sigma-28 (FLIA); transcription; 2.30A {Aquifex aeolicus} SCOP: a.4.13.1 a.4.13.2 a.177.1.1 PDB: 1sc5_A

Probab=99.81  E-value=4.2e-20  Score=172.59  Aligned_cols=145  Identities=21%  Similarity=0.309  Sum_probs=127.3

Q ss_pred             HHHHHHHHHhHHHHHHHHHHhh---CCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhhcccc
Q 012638          295 YCREELIKSTRPLVLFLARNYR---GLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGI  371 (459)
Q Consensus       295 ~Are~LI~~nlrLV~sIAkry~---g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIrnaI~d~Lrk~sr~i  371 (459)
                      .|+++||..|.++|+.+|++|.   +++.+++||+|||+++||+++++||+.+|.+|.||+++||+|.++++++++.   
T Consensus        12 ~a~~~l~~~~~~~v~~~a~~~~~~~~~~~~aeDl~Qe~~l~l~~~~~~~~~~~~~~f~~~l~~~~~~~~~d~~r~~~---   88 (239)
T 1rp3_A           12 IEREELILKYLPLVKAIATNIKKHLPEDVDIRDLISYGVIGLIKAVDNLSTENPKRAEAYIKLRIKGAIYDYLRSLD---   88 (239)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHTTSCTTSCHHHHHHHHHHHHHHHHHTCCCCCTHHHHHHHHHHHHHHHHHHHHTSS---
T ss_pred             hHHHHHHHHhHHHHHHHHHHHHHhccCCCCHHHHHHHHHHHHHHHHHHcCcccCCCHHHHHHHHHHHHHHHHHHhcC---
Confidence            4899999999999999999998   6789999999999999999999999999889999999999999999999874   


Q ss_pred             ccccchHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHhhc--cCCccccccCCCCCCccccC
Q 012638          372 KIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLR--IVGSIDQKIGDCLNAKYLNI  443 (459)
Q Consensus       372 rlP~~v~e~i~kI~ka~~~L~~~lgr~PT~eEIAe~LGIS~e~Vk~~l~~ar--~~~SLD~~v~~d~~~~l~e~  443 (459)
                      +.|........++.++...+....++.|+.+|||+.+|++++.+..++....  ..+|+|.++.++++.+ .++
T Consensus        89 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~sl~~~~~~~~~~~-~~~  161 (239)
T 1rp3_A           89 FGSRQVREKERRIKEVVEKLKEKLGREPTDEEVAKELGISTEELFKTLDKINFSYILSLEEVFRDFARDY-SEL  161 (239)
T ss_dssp             TTCHHHHHHHHHHHHHHHHHHHHHSSCCCHHHHHHHHTSCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-TTT
T ss_pred             ccchHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHHhccCCCccccccccCCCccc-ccc
Confidence            5677778888999999999999999999999999999999999998876543  4568887764433333 444

>1sig_A Sigma70, RNA polymerase primary sigma factor; RNA polymerase sigma factor, transcription regulation; 2.60A {Escherichia coli} SCOP: a.177.1.1

Probab=99.72  E-value=1.6e-17  Score=167.36  Aligned_cols=85  Identities=34%  Similarity=0.789  Sum_probs=79.9

Q ss_pred             HHHHHHHHhch----HHHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHH
Q 012638          284 RVLKQHLAFGW----YCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKS  359 (459)
Q Consensus       284 eeL~~~l~~G~----~Are~LI~~nlrLV~sIAkry~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIrna  359 (459)
                      ..|+.+++.|+    .|++.||..|+++|+++|++|++++.+++||+||||+|||+++++||+.+|++|+||++|||+|.
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            56788888886    59999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHhhc
Q 012638          360 ISKMVARHA  368 (459)
Q Consensus       360 I~d~Lrk~s  368 (459)
                      |++++|++.
T Consensus       330 ~~~~lr~~~  338 (339)
T 1sig_A          330 ITRSIADQA  338 (339)
T ss_dssp             HHHHHHHC-
T ss_pred             HHHHHHHhc
Confidence            999999865

>1or7_A Sigma-24, RNA polymerase sigma-E factor; regulation, DNA-binding, transmembrane, transcription; 2.00A {Escherichia coli} SCOP: a.4.13.2 a.177.1.1 PDB: 2h27_A

Probab=99.72  E-value=3.6e-17  Score=148.78  Aligned_cols=139  Identities=15%  Similarity=0.103  Sum_probs=113.9

Q ss_pred             HHHHHHHHHhchH-HHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHH
Q 012638          283 ERVLKQHLAFGWY-CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSIS  361 (459)
Q Consensus       283 eeeL~~~l~~G~~-Are~LI~~nlrLV~sIAkry~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIrnaI~  361 (459)
                      +.+|+..++.|+. |++.|+..|.+.|+++|+++.+ ..+++|++||+++++|+++++|++..  .|.||++.+++|.++
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            5678999999987 9999999999999999999999 99999999999999999999999864  599999999999999


Q ss_pred             HHHHhhcccccc----------------------ccc---hHHHHHHHHHHHHHHHHH--------cCCCCCHHHHHHHh
Q 012638          362 KMVARHARGIKI----------------------PCK---LNREISKIQKARKALTNS--------HGKYPEDIEIAKYT  408 (459)
Q Consensus       362 d~Lrk~sr~irl----------------------P~~---v~e~i~kI~ka~~~L~~~--------lgr~PT~eEIAe~L  408 (459)
                      +++|++.+....                      |..   ..+....+..+...|+..        +..+.|++|||+.|
T Consensus        87 d~~R~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~l~~~l~~L~~~~r~vl~l~~~~g~s~~EIA~~l  166 (194)
T 1or7_A           87 NYLVAQGRRPPSSDVDAIEAENFESGGALKEISNPENLMLSEELRQIVFRTIESLPEDLRMAITLRELDGLSYEEIAAIM  166 (194)
T ss_dssp             HHHHHHTTCCTHHHHHHHHHHSCCSSCC--------CEEEHHHHHHHHHHHHHHSCHHHHHHHHHHHTTCCCHHHHHHHT
T ss_pred             HHHHHHhccCccccccccccccccccccccCCCChHHHHHHHHHHHHHHHHHHhCCHHHHHHhHHHHHcCCCHHHHHHHH
Confidence            999987653221                      111   012333455555555433        34789999999999


Q ss_pred             CCCHHHHHHHHHhhcc
Q 012638          409 GLSLAEIRSASECLRI  424 (459)
Q Consensus       409 GIS~e~Vk~~l~~ar~  424 (459)
                      |||+++|+..+.+++.
T Consensus       167 gis~~tV~~~l~ra~~  182 (194)
T 1or7_A          167 DCPVGTVRSRIFRARE  182 (194)
T ss_dssp             TSCHHHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHHH
Confidence            9999999999988865

>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=99.47  E-value=1.2e-13  Score=121.29  Aligned_cols=105  Identities=22%  Similarity=0.302  Sum_probs=76.8

Q ss_pred             CCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhhccccccc------------------------
Q 012638          319 GIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIP------------------------  374 (459)
Q Consensus       319 g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIrnaI~d~Lrk~sr~irlP------------------------  374 (459)
                      |.+++|++|||++++|+++++||+.+ .+|.||++++++|.+++++|++.+..+.+                        
T Consensus         1 g~daeDl~Qe~~~~l~~~~~~~~~~~-~~f~~~l~~i~~n~~~d~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   79 (164)
T 3mzy_A            1 GAEKEDLVQEGILGLLKAIKFYDETK-SSFSSFAFLCIRREMISAIRKANTQKHMVLNEALKTNAILEDSAYFDDEGHNI   79 (164)
T ss_dssp             ----CTTHHHHHHHHHHHHHHCCTTT-SCHHHHHHHHHHHHHHHHHHHHHHCC---------------------------
T ss_pred             CCcHHHHHHHHHHHHHHHHHHhCccC-CChHHHhHHHHHHHHHHHHHHhhcccchhhHHHhhhhhhhccCCCCCcccchh
Confidence            57899999999999999999999987 68999999999999999999865432211                        


Q ss_pred             ----------cc---hHHHHHHHHHHHH-HHHH-------HcCCCCCHHHHHHHhCCCHHHHHHHHHhhcc
Q 012638          375 ----------CK---LNREISKIQKARK-ALTN-------SHGKYPEDIEIAKYTGLSLAEIRSASECLRI  424 (459)
Q Consensus       375 ----------~~---v~e~i~kI~ka~~-~L~~-------~lgr~PT~eEIAe~LGIS~e~Vk~~l~~ar~  424 (459)
                                ..   ..+....+..+.. .|+.       ....+.|++|||+.||||+.+|+..+.+++.
T Consensus        80 ~~~~~~~~~~~~~~~~~e~~~~l~~~l~~~L~~~~r~v~~~~~~g~s~~EIA~~lgis~~tV~~~~~ra~~  150 (164)
T 3mzy_A           80 NNYKSSESNPEEAYLLKEEIEEFKKFSENNFSKFEKEVLTYLIRGYSYREIATILSKNLKSIDNTIQRIRK  150 (164)
T ss_dssp             ----------CHHHHHHHHHHHHHHHHHHHSCHHHHHHHHHHTTTCCHHHHHHHHTCCHHHHHHHHHHHHH
T ss_pred             hhhcccCCCHHHHHHHHHHHHHHHHHHHhhCCHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence                      00   1122233444444 3322       3457889999999999999999999988764

>2lfw_A PHYR sigma-like domain; signal transduction, response regulator, sigma factor mimicr sigma factor, general stress response, signaling protein; NMR {Sphingomonas SP}

Probab=99.41  E-value=2.2e-15  Score=135.09  Aligned_cols=126  Identities=6%  Similarity=-0.026  Sum_probs=97.0

Q ss_pred             HHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhhcccccccc-
Q 012638          297 REELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARGIKIPC-  375 (459)
Q Consensus       297 re~LI~~nlrLV~sIAkry~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIrnaI~d~Lrk~sr~irlP~-  375 (459)
                      |+.|+..|.+.|+.+|++++++..+++|++||+|+++|+++++|++.  ..|.+|++.+++|.+++++|+.......|. 
T Consensus         3 f~~l~~~~~~~l~~~~~~~~~~~~~AeDlvQe~fl~~~~~~~~~~~~--~~~~~wl~~ia~n~~~d~~R~~~~~~~~~e~   80 (157)
T 2lfw_A            3 LGQQLAPHLPFLRRYGRALTGSQNQGDKYVRATLEAIVAAPDQFPRD--VDPRLGLYRMFQGIWASANADGEAQTSQSDA   80 (157)
T ss_dssp             GGGGTGGGGGGGTTTGGGTTSCHHHHHHHHHHHHHTTTTCGGGCCCS--SCTTHHHHHHHHHHHHHHTTTTSCCCCCCSC
T ss_pred             HHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhHHHcCCC--CcHHHHHHHHHHHHHHHHhhccCcccCCcch
Confidence            67889999999999999999999999999999999999999999975  369999999999999999987532111010 


Q ss_pred             -----chHHHHHHHHHHHHHHHH-HcCCCCCHHHHHHHhCCCHHHHHHHHHhhcc
Q 012638          376 -----KLNREISKIQKARKALTN-SHGKYPEDIEIAKYTGLSLAEIRSASECLRI  424 (459)
Q Consensus       376 -----~v~e~i~kI~ka~~~L~~-~lgr~PT~eEIAe~LGIS~e~Vk~~l~~ar~  424 (459)
                           .+...+..+....+++.. ....+.|++|||+.||||+++|+..+.+++.
T Consensus        81 ~~~~~~l~~~l~~Lp~~~r~vl~L~~~~g~s~~EIA~~lgis~~tV~~~l~rar~  135 (157)
T 2lfw_A           81 EGTEAVARARLARMTPLSRQALLLTAMEGFSPEDAAYLIEVDTSEVETLVTEALA  135 (157)
T ss_dssp             SSSSSTTTTTTTTSCTTHHHHHTTTSSSCCCHHHHHHTTTSCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence                 111122222222222221 2346789999999999999999999998875

>3n0r_A Response regulator; sigma factor, receiver, two-component SI transduction, signaling protein; HET: MSE GOL; 1.25A {Caulobacter vibrioides} PDB: 3t0y_A

Probab=99.39  E-value=1.5e-13  Score=135.17  Aligned_cols=128  Identities=9%  Similarity=-0.065  Sum_probs=98.6

Q ss_pred             hchH-HHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhhccc
Q 012638          292 FGWY-CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHARG  370 (459)
Q Consensus       292 ~G~~-Are~LI~~nlrLV~sIAkry~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIrnaI~d~Lrk~sr~  370 (459)
                      .|+. +|++|+..|.+.|+.+|++|+++..+++|++||.|+.+|+...+|++.  ..|.||++++++|.+++++|+....
T Consensus        17 ~g~~~~f~~l~~~~~~~l~~~a~~~~~~~~~AeD~vQe~fl~~~~~~~~~~~~--~~~~~wL~~ia~n~~~d~~r~~~~~   94 (286)
T 3n0r_A           17 RGSEMHLLARLAPHLPYIRRYARALTGDQATGDHYVRVALEALAAGELVLDAN--LSPRVALYRVFHAIWLSSGAQLEVG   94 (286)
T ss_dssp             ---CCCHHHHHGGGHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHTTSSCCCSS--SCHHHHHHHHHHHHHSCTTC----C
T ss_pred             CCCcCCHHHHHHHHHHHHHHHHHHHhCCHhhHHHHHHHHHHHHHhCchhcCCC--cChHHHHHHHHHHHHHhhccccccC
Confidence            4555 999999999999999999999999999999999999999999999974  4699999999999999999864321


Q ss_pred             cccccchHHHHHHHHHHHHHHHHH--------cCCCCCHHHHHHHhCCCHHHHHHHHHhhcc
Q 012638          371 IKIPCKLNREISKIQKARKALTNS--------HGKYPEDIEIAKYTGLSLAEIRSASECLRI  424 (459)
Q Consensus       371 irlP~~v~e~i~kI~ka~~~L~~~--------lgr~PT~eEIAe~LGIS~e~Vk~~l~~ar~  424 (459)
                      .....   +....+.++...|+..        .-.+.+++|||+.+|+|+++|+..+..++.
T Consensus        95 ~~~~~---~~~~~l~~al~~Lp~~~R~v~~L~~~eg~s~~EIA~~lgis~~tVks~l~rA~~  153 (286)
T 3n0r_A           95 HDQGL---HAGDDAAQRLMRIAPRSRQAFLLTALEGFTPTEAAQILDCDFGEVERLIGDAQA  153 (286)
T ss_dssp             CCCCC---CTTSHHHHHHHHHSCHHHHHHHHHHTTCCCHHHHHHHHTCCHHHHHHHHHHHHH
T ss_pred             CCccc---chHHHHHHHHHhCCHHHeeEEEEEeeCCCCHHHHHHHhCcCHHHHHHHHHHHHh
Confidence            11111   1112344444444433        347889999999999999999998887654

>2o7g_A Probable RNA polymerase sigma-C factor; sigma factor, transcription regulation, -10 element recognit domain, transcription; 2.70A {Mycobacterium tuberculosis}

Probab=99.28  E-value=8.6e-12  Score=105.14  Aligned_cols=85  Identities=18%  Similarity=0.086  Sum_probs=73.2

Q ss_pred             HHHHHHHhchH-HHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHH
Q 012638          285 VLKQHLAFGWY-CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKM  363 (459)
Q Consensus       285 eL~~~l~~G~~-Are~LI~~nlrLV~sIAkry~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIrnaI~d~  363 (459)
                      .|+..++.|+. |++.|+..|.+.|+.+|.++ ++..+++|++||+++.+|+.+.+|++.  ..|.+|++.+++|.++++
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            67888889976 99999999999999999999 888999999999999999999999974  379999999999999999


Q ss_pred             HHhhccccc
Q 012638          364 VARHARGIK  372 (459)
Q Consensus       364 Lrk~sr~ir  372 (459)
                      +|++.+...
T Consensus        90 ~R~~~~~~~   98 (112)
T 2o7g_A           90 IRHVRSRPR   98 (112)
T ss_dssp             TC-------
T ss_pred             HHHhhcccc
Confidence            998765433

>1h3l_A RNA polymerase sigma factor; transcription, DNA-binding, transcription regulation; 2.37A {Streptomyces coelicolor A3} SCOP: a.177.1.1

Probab=99.19  E-value=1.8e-11  Score=98.64  Aligned_cols=77  Identities=8%  Similarity=-0.048  Sum_probs=68.6

Q ss_pred             HHhchH-HHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhhc
Q 012638          290 LAFGWY-CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHA  368 (459)
Q Consensus       290 l~~G~~-Are~LI~~nlrLV~sIAkry~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIrnaI~d~Lrk~s  368 (459)
                      +..|+. |++.|+..|.+.|+.+|.++.++..+++|++||+++.+|+.+++|++.  ..|.+|++.+++|.+++++|++.
T Consensus         6 ~~~g~~~af~~l~~~~~~~l~~~~~~~~~~~~~aeD~vQe~fl~~~~~~~~~~~~--~~~~~wl~~i~~n~~~d~~R~~~   83 (87)
T 1h3l_A            6 STAERSARFERDALEFLDQMYSAALRMTRNPADAEDLVQETYAKAYASFHQFREG--TNLKAWLYRILTNTFINSYRKKQ   83 (87)
T ss_dssp             CHHHHHHHHHHHHHHTHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHGGGCCSS--SCHHHHHHHHHHHHHHHTCC---
T ss_pred             cCcccHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHhcCCC--ccHHHHHHHHHHHHHHHHHHHhc
Confidence            345655 999999999999999999999999999999999999999999999974  47999999999999999998764

>3clo_A Transcriptional regulator; NP_811094.1, bacterial regulatory proteins, LUXR family, structural genomics; 2.04A {Bacteroides thetaiotaomicron vpi-5482}

Probab=97.72  E-value=9.5e-09  Score=99.19  Aligned_cols=140  Identities=7%  Similarity=-0.089  Sum_probs=101.7

Q ss_pred             HHHHHHHHhchH-HHHHHHHHhHHHHHHHHHHhhCCCCCHHHHH----HHHHHHHHHhhhhcCCCCCCchhhHHHHHHHH
Q 012638          284 RVLKQHLAFGWY-CREELIKSTRPLVLFLARNYRGLGIPFSDLL----QAGNVGVLQGAERFDHTRGYKFSTYVQYWIRK  358 (459)
Q Consensus       284 eeL~~~l~~G~~-Are~LI~~nlrLV~sIAkry~g~g~d~EDLI----QEG~IGLirAieKFDp~kG~rFSTYa~~wIrn  358 (459)
                      +.|..++..++. +.+.+...|.++|+.+............|+.    ||.++.+|+.+..|++..  +|.+|++.+++|
T Consensus        85 ~~ll~~i~p~D~~~~~~~~~~~~~fi~~l~~~~~~~~~~~~dl~~~~~qe~fl~~~~~~~~~~~~~--~~~~WL~~ia~n  162 (258)
T 3clo_A           85 DCIYRRIHPEDLVEKRLMEYKFFQKTFSMSPGERLKYRGRCRLRMMNEKGVYQYIDNLVQIMQNTP--AGNVWLIFCLYS  162 (258)
T ss_dssp             HHHHTTBCHHHHHHHHHHHHHHHHHHTTSCHHHHTTEEEEEEEEEECTTSCEEEEEEEEEEEEECT--TSCEEEEEEEEE
T ss_pred             HHHHHhCChHHHHHHHHHHHHHHHHHHhcCHHhccCCeeeEEeecCCcCHHHHHHHHhHHhcCCCC--chHHHHHHHHHH
Confidence            356667766665 8999999999999999988877777888986    999999999999998643  699999999999


Q ss_pred             HHHHHHHhhcccccc----------ccchHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHhhccC
Q 012638          359 SISKMVARHARGIKI----------PCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIV  425 (459)
Q Consensus       359 aI~d~Lrk~sr~irl----------P~~v~e~i~kI~ka~~~L~~~lgr~PT~eEIAe~LGIS~e~Vk~~l~~ar~~  425 (459)
                      .+.++.++......+          +..+......+..-.+++......+.|++|||+.||||+++|+..+++++..
T Consensus       163 ~~~d~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~~erevl~L~~~G~s~~EIA~~L~iS~~TVk~~l~ra~~k  239 (258)
T 3clo_A          163 LSADQRPEQGIYATITQMERGEVETLSLSEEHRNILSEREKEILRCIRKGLSSKEIAATLYISVNTVNRHRQNILEK  239 (258)
T ss_dssp             ECSCCCCCSSCCCEEEETTTTEEEECCCHHHHTTSSCHHHHHHHHHHHTTCCHHHHHHHHTCCHHHHHHHHHHHHHH
T ss_pred             HHcchhhhhHHHHHHHhhcccccccchhhHHHHccCCHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHHHHHHH
Confidence            888876542111100          1111222222322233322222468899999999999999999999988753

>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=93.14  E-value=3.2  Score=37.46  Aligned_cols=30  Identities=13%  Similarity=-0.042  Sum_probs=26.6

Q ss_pred             cCCCCCHHHHHHHhCCCHHHHHHHHHhhcc
Q 012638          395 HGKYPEDIEIAKYTGLSLAEIRSASECLRI  424 (459)
Q Consensus       395 lgr~PT~eEIAe~LGIS~e~Vk~~l~~ar~  424 (459)
                      +..+.|.+|||+.||||+++|+..+.+++.
T Consensus       200 ~~~g~s~~EIA~~lgis~~~V~~~~~ra~~  229 (239)
T 1rp3_A          200 FYEELPAKEVAKILETSVSRVSQLKAKALE  229 (239)
T ss_dssp             HTSCCCHHHHHHHTTSCHHHHHHHHHHHHH
T ss_pred             HhcCCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence            356899999999999999999999887764

>3hug_A RNA polymerase sigma factor; ECF sigma factor, zinc binding anti-sigma factor, oxidative transcription regulation; 2.35A {Mycobacterium tuberculosis}

Probab=92.04  E-value=0.15  Score=40.92  Aligned_cols=30  Identities=13%  Similarity=-0.012  Sum_probs=26.9

Q ss_pred             cCCCCCHHHHHHHhCCCHHHHHHHHHhhcc
Q 012638          395 HGKYPEDIEIAKYTGLSLAEIRSASECLRI  424 (459)
Q Consensus       395 lgr~PT~eEIAe~LGIS~e~Vk~~l~~ar~  424 (459)
                      +..+.|++|||+.|||++.+|+..+.+++.
T Consensus        50 ~~~g~s~~eIA~~lgis~~tV~~~l~ra~~   79 (92)
T 3hug_A           50 YYRGWSTAQIATDLGIAEGTVKSRLHYAVR   79 (92)
T ss_dssp             HTSCCCHHHHHHHHTSCHHHHHHHHHHHHH
T ss_pred             HHcCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence            467889999999999999999999988764

>1l9z_H Sigma factor SIGA; helix-turn-helix, coiled-coil, transcription/DNA complex; 6.50A {Thermus aquaticus} SCOP: i.8.1.1

Probab=91.91  E-value=1.9  Score=44.95  Aligned_cols=28  Identities=18%  Similarity=0.159  Sum_probs=25.3

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHHhhcc
Q 012638          397 KYPEDIEIAKYTGLSLAEIRSASECLRI  424 (459)
Q Consensus       397 r~PT~eEIAe~LGIS~e~Vk~~l~~ar~  424 (459)
                      .+.|.+|||+.||||.++|+.++.++..
T Consensus       394 e~~TleEIAe~LgIS~erVRqi~~RAlk  421 (438)
T 1l9z_H          394 REHTLEEVGAYFGVTRERIRQIENKALR  421 (438)
T ss_pred             CCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence            6889999999999999999999887754

>1x3u_A Transcriptional regulatory protein FIXJ; helix-turn-helix; NMR {Sinorhizobium meliloti}

Probab=90.91  E-value=0.42  Score=36.69  Aligned_cols=44  Identities=7%  Similarity=-0.022  Sum_probs=32.5

Q ss_pred             HHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHhhccC
Q 012638          382 SKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRIV  425 (459)
Q Consensus       382 ~kI~ka~~~L~~~lgr~PT~eEIAe~LGIS~e~Vk~~l~~ar~~  425 (459)
                      ..+.....++...+..+.+++|||+.|||+..+|+..+..++..
T Consensus        15 ~~L~~~e~~vl~l~~~g~s~~eIA~~l~is~~tV~~~~~r~~~k   58 (79)
T 1x3u_A           15 QTLSERERQVLSAVVAGLPNKSIAYDLDISPRTVEVHRANVMAK   58 (79)
T ss_dssp             HHHCHHHHHHHHHHTTTCCHHHHHHHTTSCHHHHHHHHHHHHHH
T ss_pred             HhCCHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHHHHHHH
Confidence            33434444444445678999999999999999999998877653

>2p7v_B Sigma-70, RNA polymerase sigma factor RPOD; RSD, regulator of sigma 70, sigma 70 domain 4, transcription, regulation, helix-turn-helix; 2.60A {Escherichia coli} SCOP: a.4.13.2

Probab=90.74  E-value=0.36  Score=36.47  Aligned_cols=29  Identities=14%  Similarity=-0.048  Sum_probs=26.1

Q ss_pred             CCCCCHHHHHHHhCCCHHHHHHHHHhhcc
Q 012638          396 GKYPEDIEIAKYTGLSLAEIRSASECLRI  424 (459)
Q Consensus       396 gr~PT~eEIAe~LGIS~e~Vk~~l~~ar~  424 (459)
                      ..+.|++|||+.||+|..+|+..+.++..
T Consensus        23 ~~g~s~~eIA~~lgis~~tV~~~~~ra~~   51 (68)
T 2p7v_B           23 NTDYTLEEVGKQFDVTRERIRQIEAKALR   51 (68)
T ss_dssp             SSCCCHHHHHHHHTCCHHHHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence            36899999999999999999999888765

>3t72_q RNA polymerase sigma factor RPOD, DNA-directed RN polymerase subunit beta; winged-helix motif, transcription activation, DNA-binding; 4.33A {Escherichia coli} PDB: 1tlh_B

Probab=89.76  E-value=0.38  Score=40.07  Aligned_cols=28  Identities=14%  Similarity=-0.054  Sum_probs=25.0

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHHhhcc
Q 012638          397 KYPEDIEIAKYTGLSLAEIRSASECLRI  424 (459)
Q Consensus       397 r~PT~eEIAe~LGIS~e~Vk~~l~~ar~  424 (459)
                      .+.|++|||+.||||.++|+..+..+..
T Consensus        38 e~~s~~EIA~~lgiS~~tVr~~~~rAlk   65 (99)
T 3t72_q           38 TDYTLEEVGKQFDVTRERIRQIEAKALR   65 (99)
T ss_pred             CCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence            5789999999999999999998887653

>1tty_A Sigma-A, RNA polymerase sigma factor RPOD; helix-turn-helix, transcription; NMR {Thermotoga maritima} SCOP: a.4.13.2

Probab=89.21  E-value=0.56  Score=37.38  Aligned_cols=28  Identities=18%  Similarity=0.082  Sum_probs=25.7

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHHhhcc
Q 012638          397 KYPEDIEIAKYTGLSLAEIRSASECLRI  424 (459)
Q Consensus       397 r~PT~eEIAe~LGIS~e~Vk~~l~~ar~  424 (459)
                      .+.|++|||+.||||+++|+..+.++..
T Consensus        37 ~~~s~~EIA~~lgis~~tV~~~~~ra~~   64 (87)
T 1tty_A           37 KPKTLEEVGQYFNVTRERIRQIEVKALR   64 (87)
T ss_dssp             SCCCHHHHHHHHTCCHHHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            7899999999999999999999888764

>1ku3_A Sigma factor SIGA; helix-turn-helix, transcription; 1.80A {Thermus aquaticus} SCOP: a.4.13.2 PDB: 1ku7_A 1rio_H 3n97_A*

Probab=89.15  E-value=0.67  Score=35.43  Aligned_cols=28  Identities=18%  Similarity=0.159  Sum_probs=25.2

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHHhhcc
Q 012638          397 KYPEDIEIAKYTGLSLAEIRSASECLRI  424 (459)
Q Consensus       397 r~PT~eEIAe~LGIS~e~Vk~~l~~ar~  424 (459)
                      .+.|.+|||+.||+|.++|+..+..+..
T Consensus        29 ~~~s~~eIA~~l~is~~tV~~~~~ra~~   56 (73)
T 1ku3_A           29 REHTLEEVGAYFGVTRERIRQIENKALR   56 (73)
T ss_dssp             SCCCHHHHHHHHTCCHHHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            7899999999999999999998877654

>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=89.04  E-value=0.14  Score=40.68  Aligned_cols=30  Identities=7%  Similarity=0.015  Sum_probs=26.4

Q ss_pred             cCCCCCHHHHHHHhCCCHHHHHHHHHhhcc
Q 012638          395 HGKYPEDIEIAKYTGLSLAEIRSASECLRI  424 (459)
Q Consensus       395 lgr~PT~eEIAe~LGIS~e~Vk~~l~~ar~  424 (459)
                      +..+.+++|||+.|||+..+|+..+.+++.
T Consensus        33 ~~~g~s~~eIA~~l~is~~tV~~~l~r~~~   62 (82)
T 1je8_A           33 IAQGLPNKMIARRLDITESTVKVHVKHMLK   62 (82)
T ss_dssp             HTTTCCHHHHHHHHTSCHHHHHHHHHHHHH
T ss_pred             HHcCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence            356789999999999999999999887764

>2o8x_A Probable RNA polymerase sigma-C factor; promoter recognition, transcription regulation, helix-turn-H motif, transcription; 3.00A {Mycobacterium tuberculosis}

Probab=88.77  E-value=0.68  Score=34.44  Aligned_cols=30  Identities=20%  Similarity=0.023  Sum_probs=26.7

Q ss_pred             cCCCCCHHHHHHHhCCCHHHHHHHHHhhcc
Q 012638          395 HGKYPEDIEIAKYTGLSLAEIRSASECLRI  424 (459)
Q Consensus       395 lgr~PT~eEIAe~LGIS~e~Vk~~l~~ar~  424 (459)
                      +..+.|++|||+.+|+|..+|+..+++++.
T Consensus        28 ~~~g~s~~eIA~~lgis~~tv~~~~~ra~~   57 (70)
T 2o8x_A           28 QLLGLSYADAAAVCGCPVGTIRSRVARARD   57 (70)
T ss_dssp             HTSCCCHHHHHHHHTSCHHHHHHHHHHHHH
T ss_pred             HHcCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence            356789999999999999999999888765

>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=87.06  E-value=0.32  Score=39.56  Aligned_cols=29  Identities=14%  Similarity=0.009  Sum_probs=25.8

Q ss_pred             CCCCCHHHHHHHhCCCHHHHHHHHHhhcc
Q 012638          396 GKYPEDIEIAKYTGLSLAEIRSASECLRI  424 (459)
Q Consensus       396 gr~PT~eEIAe~LGIS~e~Vk~~l~~ar~  424 (459)
                      ..+.|++|||+.|||++.+|+..+.+++.
T Consensus        40 ~~g~s~~eIA~~l~is~~tV~~~l~r~~~   68 (95)
T 3c57_A           40 SEGLTNKQIADRMFLAEKTVKNYVSRLLA   68 (95)
T ss_dssp             HTTCCHHHHHHHHTCCHHHHHHHHHHHHH
T ss_pred             HcCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence            45789999999999999999999887764

>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=86.30  E-value=1.1  Score=30.30  Aligned_cols=27  Identities=15%  Similarity=-0.152  Sum_probs=23.3

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHHhhc
Q 012638          397 KYPEDIEIAKYTGLSLAEIRSASECLR  423 (459)
Q Consensus       397 r~PT~eEIAe~LGIS~e~Vk~~l~~ar  423 (459)
                      .+.+..|||+.+||+..+|...+...+
T Consensus        20 ~g~s~~~IA~~lgis~~Tv~~~~~~~~   46 (51)
T 1tc3_C           20 LNVSLHEMSRKISRSRHCIRVYLKDPV   46 (51)
T ss_dssp             TTCCHHHHHHHHTCCHHHHHHHHHCST
T ss_pred             cCCCHHHHHHHHCcCHHHHHHHHhhHH
Confidence            357999999999999999999887554

>2jpc_A SSRB; DNA binding protein, structural genomics, PSI-2, protein structure initiative; NMR {Salmonella typhimurium}

Probab=86.16  E-value=0.57  Score=34.18  Aligned_cols=29  Identities=7%  Similarity=0.014  Sum_probs=25.4

Q ss_pred             CCCCCHHHHHHHhCCCHHHHHHHHHhhcc
Q 012638          396 GKYPEDIEIAKYTGLSLAEIRSASECLRI  424 (459)
Q Consensus       396 gr~PT~eEIAe~LGIS~e~Vk~~l~~ar~  424 (459)
                      ..+.|.+|||+.||+|+.+|+..+..+..
T Consensus        11 ~~g~s~~eIA~~l~is~~tV~~~~~~~~~   39 (61)
T 2jpc_A           11 DEGYTNHGISEKLHISIKTVETHRMNMMR   39 (61)
T ss_dssp             HTSCCSHHHHHHTCSCHHHHHHHHHHHHH
T ss_pred             HcCCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence            45789999999999999999998887764

>2jt1_A PEFI protein; solution structure, winged helix-turn-helix, transcripti regulatory protein, structural genomics, PSI-2; NMR {Salmonella typhimurium LT2}

Probab=85.00  E-value=1.3  Score=35.22  Aligned_cols=27  Identities=33%  Similarity=0.369  Sum_probs=24.4

Q ss_pred             CCCCCHHHHHHHhCCCHHHHHHHHHhh
Q 012638          396 GKYPEDIEIAKYTGLSLAEIRSASECL  422 (459)
Q Consensus       396 gr~PT~eEIAe~LGIS~e~Vk~~l~~a  422 (459)
                      |..||..|||+.+|+|..+|+..+...
T Consensus        22 g~~psv~EIa~~lgvS~~TVrr~L~~L   48 (77)
T 2jt1_A           22 GAPVKTRDIADAAGLSIYQVRLYLEQL   48 (77)
T ss_dssp             TSCEEHHHHHHHHTCCHHHHHHHHHHH
T ss_pred             CCCcCHHHHHHHHCCCHHHHHHHHHHH
Confidence            778999999999999999999887754

>1xsv_A Hypothetical UPF0122 protein SAV1236; helix-turn-helix, putative DNA-binding protein, signal recognition particle, unknown function; 1.70A {Staphylococcus aureus subsp} SCOP: a.4.13.3

Probab=84.40  E-value=1.4  Score=37.18  Aligned_cols=30  Identities=13%  Similarity=-0.182  Sum_probs=26.5

Q ss_pred             cCCCCCHHHHHHHhCCCHHHHHHHHHhhcc
Q 012638          395 HGKYPEDIEIAKYTGLSLAEIRSASECLRI  424 (459)
Q Consensus       395 lgr~PT~eEIAe~LGIS~e~Vk~~l~~ar~  424 (459)
                      +..+.|+.|||+.||+|+.+|+..+++++.
T Consensus        38 ~~~g~s~~EIA~~lgiS~~tV~~~l~ra~~   67 (113)
T 1xsv_A           38 YLEDYSLSEIADTFNVSRQAVYDNIRRTGD   67 (113)
T ss_dssp             HTSCCCHHHHHHHTTCCHHHHHHHHHHHHH
T ss_pred             HHcCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence            356889999999999999999999888764

>2x48_A CAG38821; archeal virus, viral protein; 2.60A {Sulfolobus islandicus rod-shaped virusorganism_taxid}

Probab=83.41  E-value=1.4  Score=31.49  Aligned_cols=25  Identities=24%  Similarity=0.101  Sum_probs=21.7

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHHh
Q 012638          397 KYPEDIEIAKYTGLSLAEIRSASEC  421 (459)
Q Consensus       397 r~PT~eEIAe~LGIS~e~Vk~~l~~  421 (459)
                      .+.|..|||+.+|++..+|...+..
T Consensus        30 ~g~s~~eIA~~lgis~~TV~~~l~~   54 (55)
T 2x48_A           30 MGYTVQQIANALGVSERKVRRYLES   54 (55)
T ss_dssp             TTCCHHHHHHHHTSCHHHHHHHHTC
T ss_pred             cCCCHHHHHHHHCcCHHHHHHHHHh
Confidence            4569999999999999999987753

>1fse_A GERE; helix-turn-helix DNA-binding protein transcriptional regulat transcription; 2.05A {Bacillus subtilis} SCOP: a.4.6.2

Probab=82.87  E-value=1.9  Score=32.31  Aligned_cols=29  Identities=17%  Similarity=-0.056  Sum_probs=25.4

Q ss_pred             CCCCCHHHHHHHhCCCHHHHHHHHHhhcc
Q 012638          396 GKYPEDIEIAKYTGLSLAEIRSASECLRI  424 (459)
Q Consensus       396 gr~PT~eEIAe~LGIS~e~Vk~~l~~ar~  424 (459)
                      ..+.+..|||+.+|+|..+|+..+..+..
T Consensus        24 ~~g~s~~eIA~~l~is~~tV~~~~~~~~~   52 (74)
T 1fse_A           24 VQDKTTKEIASELFISEKTVRNHISNAMQ   52 (74)
T ss_dssp             TTTCCHHHHHHHHTSCHHHHHHHHHHHHH
T ss_pred             HcCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            45779999999999999999998887654

>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=81.87  E-value=1.4  Score=35.62  Aligned_cols=30  Identities=23%  Similarity=0.010  Sum_probs=26.0

Q ss_pred             CCCCCHHHHHHHhCCCHHHHHHHHHhhccC
Q 012638          396 GKYPEDIEIAKYTGLSLAEIRSASECLRIV  425 (459)
Q Consensus       396 gr~PT~eEIAe~LGIS~e~Vk~~l~~ar~~  425 (459)
                      ..+.+++|||+.|||++.+|+..+..+...
T Consensus        42 ~~G~s~~eIA~~L~iS~~TV~~~~~~i~~K   71 (90)
T 3ulq_B           42 EKGFTNQEIADALHLSKRSIEYSLTSIFNK   71 (90)
T ss_dssp             HTTCCHHHHHHHHTCCHHHHHHHHHHHHHH
T ss_pred             HcCCCHHHHHHHHCcCHHHHHHHHHHHHHH
Confidence            367899999999999999999998876543

>2rnj_A Response regulator protein VRAR; HTH LUXR-type domain, DNA binding domain, activator, antibiotic resistance, cytoplasm, DNA-binding; NMR {Staphylococcus aureus}

Probab=81.60  E-value=0.77  Score=36.71  Aligned_cols=30  Identities=13%  Similarity=0.143  Sum_probs=26.1

Q ss_pred             CCCCCHHHHHHHhCCCHHHHHHHHHhhccC
Q 012638          396 GKYPEDIEIAKYTGLSLAEIRSASECLRIV  425 (459)
Q Consensus       396 gr~PT~eEIAe~LGIS~e~Vk~~l~~ar~~  425 (459)
                      ..+.|++|||+.|||+..+|+..+.+++..
T Consensus        42 ~~g~s~~eIA~~l~is~~tV~~~l~r~~~k   71 (91)
T 2rnj_A           42 AKGYSNQEIASASHITIKTVKTHVSNILSK   71 (91)
T ss_dssp             HTTCCTTHHHHHHTCCHHHHHHHHHHHHHH
T ss_pred             HcCCCHHHHHHHHCcCHHHHHHHHHHHHHH
Confidence            357899999999999999999998887653

>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=80.98  E-value=8.4  Score=39.62  Aligned_cols=28  Identities=14%  Similarity=0.127  Sum_probs=20.8

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHHhhcc
Q 012638          397 KYPEDIEIAKYTGLSLAEIRSASECLRI  424 (459)
Q Consensus       397 r~PT~eEIAe~LGIS~e~Vk~~l~~ar~  424 (459)
                      .+.|.+|||+.||||.++|+.+..++..
T Consensus       379 e~~Tl~EIA~~lgiS~erVrqi~~rAl~  406 (423)
T 2a6h_F          379 REHTLEEVGAFFGVTRERIRQIENKALR  406 (423)
T ss_dssp             -----CHHHHSSSSCHHHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence            6789999999999999999998877754

---

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	459
d1siga_	334	a.177.1.1 (A:) Sigma70 {Escherichia coli [TaxId: 5	9e-20
d1ku2a2	180	a.177.1.1 (A:93-272) Sigma factor SigA {Thermus aq	4e-16
d1rp3a3	87	a.177.1.1 (A:0-86) Sigma factor sigma-28 (FliA) {A	3e-14
d1l0oc_	57	a.4.13.2 (C:) SigmaF {Bacillus stearothermophilus	1e-06
d1rp3a1	77	a.4.13.1 (A:87-163) Sigma factor sigma-28 (FliA) {	8e-06
d1ku2a1	60	a.4.13.1 (A:273-332) Sigma factor SigA {Thermus aq	5e-04

>d1siga_ a.177.1.1 (A:) Sigma70 {Escherichia coli [TaxId: 562]} Length = 334

class: All alpha proteins
fold: Sigma2 domain of RNA polymerase sigma factors
superfamily: Sigma2 domain of RNA polymerase sigma factors
family: Sigma2 domain of RNA polymerase sigma factors
domain: Sigma70
species: Escherichia coli [TaxId: 562]

 Score = 87.6 bits (216), Expect = 9e-20
 Identities = 27/71 (38%), Positives = 52/71 (73%)

Query: 295 YCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQY 354
             ++E++++   LV+ +A+ Y   G+ F DL+Q GN+G+++  ++F++ RGYKFSTY  +
Sbjct: 262 RAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATW 321

Query: 355 WIRKSISKMVA 365
           WIR++I++ +A
Sbjct: 322 WIRQAITRSIA 332

>d1ku2a2 a.177.1.1 (A:93-272) Sigma factor SigA {Thermus aquaticus [TaxId: 271]} Length = 180

class: All alpha proteins
fold: Sigma2 domain of RNA polymerase sigma factors
superfamily: Sigma2 domain of RNA polymerase sigma factors
family: Sigma2 domain of RNA polymerase sigma factors
domain: Sigma factor SigA
species: Thermus aquaticus [TaxId: 271]

 Score = 73.7 bits (180), Expect = 4e-16
 Identities = 35/110 (31%), Positives = 60/110 (54%), Gaps = 3/110 (2%)

Query: 263 EKESGKAASLNCWAQAAGVSERVLKQHLAFGWYCRE---ELIKSTRPLVLFLARNYRGLG 319
            KE     ++           + LK++L            LI++   LV+ +A+ Y G G
Sbjct: 70  LKEKPDPKTVEEVDGKLKSLPKELKRYLHIAREGEAARQHLIEANLRLVVSIAKKYTGRG 129

Query: 320 IPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARHAR 369
           + F DL+Q GN G+++  E+F++ R +KFSTY  +WIR++I++ +A  AR
Sbjct: 130 LSFLDLIQEGNQGLIRAVEKFEYKRRFKFSTYATWWIRQAINRAIADQAR 179

>d1rp3a3 a.177.1.1 (A:0-86) Sigma factor sigma-28 (FliA) {Aquifex aeolicus [TaxId: 63363]} Length = 87

class: All alpha proteins
fold: Sigma2 domain of RNA polymerase sigma factors
superfamily: Sigma2 domain of RNA polymerase sigma factors
family: Sigma2 domain of RNA polymerase sigma factors
domain: Sigma factor sigma-28 (FliA)
species: Aquifex aeolicus [TaxId: 63363]

 Score = 65.7 bits (160), Expect = 3e-14
 Identities = 17/67 (25%), Positives = 31/67 (46%), Gaps = 3/67 (4%)

Query: 297 REELIKSTRPLVLFLARNYRG---LGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQ 353
           REELI    PLV  +A N +      +   DL+  G +G+++  +        +   Y++
Sbjct: 12  REELILKYLPLVKAIATNIKKHLPEDVDIRDLISYGVIGLIKAVDNLSTENPKRAEAYIK 71

Query: 354 YWIRKSI 360
             I+ +I
Sbjct: 72  LRIKGAI 78

>d1l0oc_ a.4.13.2 (C:) SigmaF {Bacillus stearothermophilus [TaxId: 1422]} Length = 57

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Sigma3 and sigma4 domains of RNA polymerase sigma factors
family: Sigma4 domain
domain: SigmaF
species: Bacillus stearothermophilus [TaxId: 1422]

 Score = 43.5 bits (103), Expect = 1e-06
 Identities = 17/54 (31%), Positives = 31/54 (57%)

Query: 371 IKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRI 424
           +K+   L    +KI+KA+  L+ + G+ P   EIA + G+S  ++  A E +R+
Sbjct: 4   VKVSRSLKEMGNKIRKAKDELSKTRGRAPTVTEIADHLGISPEDVVLAQEAVRL 57

>d1rp3a1 a.4.13.1 (A:87-163) Sigma factor sigma-28 (FliA) {Aquifex aeolicus [TaxId: 63363]} Length = 77

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Sigma3 and sigma4 domains of RNA polymerase sigma factors
family: Sigma3 domain
domain: Sigma factor sigma-28 (FliA)
species: Aquifex aeolicus [TaxId: 63363]

 Score = 41.7 bits (98), Expect = 8e-06
 Identities = 14/57 (24%), Positives = 26/57 (45%), Gaps = 4/57 (7%)

Query: 381 ISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIR---SASECLRIVGSIDQKIGD 434
             +I++  + L    G+ P D E+AK  G+S  E+           I+ S+++   D
Sbjct: 9   ERRIKEVVEKLKEKLGREPTDEEVAKELGISTEELFKTLDKINFSYIL-SLEEVFRD 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 = 36.2 bits (84), Expect = 5e-04
 Identities = 13/46 (28%), Positives = 21/46 (45%)

Query: 371 IKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIR 416
           I+IP  +   I+K+ +  + L    G+ P   EIA+  G      R
Sbjct: 1   IRIPVHMVETINKLSRTARQLQQELGREPSYEEIAEAMGPGWDAKR 46

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	459
d1ku2a2	180	Sigma factor SigA {Thermus aquaticus [TaxId: 271]}	99.97
d1siga_	334	Sigma70 {Escherichia coli [TaxId: 562]}	99.85
d1rp3a3	87	Sigma factor sigma-28 (FliA) {Aquifex aeolicus [Ta	99.78
d1or7a2	113	SigmaE factor (RpoE) {Escherichia coli [TaxId: 562	99.47
d1ku2a1	60	Sigma factor SigA {Thermus aquaticus [TaxId: 271]}	99.03
d1h3la_	75	Sigma factor SigR {Streptomyces coelicolor a3(2) [	98.97
d1l0oc_	57	SigmaF {Bacillus stearothermophilus [TaxId: 1422]}	98.83
d1rp3a1	77	Sigma factor sigma-28 (FliA) {Aquifex aeolicus [Ta	98.78
d1l0oc_	57	SigmaF {Bacillus stearothermophilus [TaxId: 1422]}	95.87
d1rp3a1	77	Sigma factor sigma-28 (FliA) {Aquifex aeolicus [Ta	95.03
d1or7a1	68	SigmaE factor (RpoE) {Escherichia coli [TaxId: 562	94.78
d1rp3a2	71	Sigma factor sigma-28 (FliA) {Aquifex aeolicus [Ta	93.89
d1ku2a1	60	Sigma factor SigA {Thermus aquaticus [TaxId: 271]}	92.45
d1jhfa1	71	LexA repressor, N-terminal DNA-binding domain {Esc	92.24
d1s7oa_	106	Hypothetical protein SPy1201 {Streptococcus pyogen	88.71
d1xsva_	106	Hypothetical protein SAV1236 {Staphylococcus aureu	88.62
d1l3la1	65	Quorum-sensing transcription factor TraR, C-termin	84.46
d1yioa1	70	Response regulatory protein StyR, C-terminal domai	83.63
d1fsea_	67	Germination protein GerE {Bacillus subtilis [TaxId	83.28
d1a04a1	67	Nitrate/nitrite response regulator (NarL) {Escheri	80.68

>d1ku2a2 a.177.1.1 (A:93-272) Sigma factor SigA {Thermus aquaticus [TaxId: 271]}

class: All alpha proteins
fold: Sigma2 domain of RNA polymerase sigma factors
superfamily: Sigma2 domain of RNA polymerase sigma factors
family: Sigma2 domain of RNA polymerase sigma factors
domain: Sigma factor SigA
species: Thermus aquaticus [TaxId: 271]

Probab=99.97  E-value=1.2e-31  Score=246.04  Aligned_cols=149  Identities=26%  Similarity=0.403  Sum_probs=120.2

Q ss_pred             CChhHHHHHHhccCCCCCCChHHHHHHHHHhHHHHHHHHHHHHHH------------------HHhCCCCchHHHHHHcC
Q 012638          219 QPTIFSAERALNSRGRRLTIARNEAEMSKGVQVVANLERIKTTLE------------------KESGKAASLNCWAQAAG  280 (459)
Q Consensus       219 ~p~~~~~~~~~~~~~~~lLt~~eE~eL~~~i~~~~~le~~~~~l~------------------~~~gr~pt~~ewa~a~g  280 (459)
                      ||...|+   ..++..||||++||++|+++|+.++.+.+......                  ...+..|...+|.....
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            6777787   46788999999999999999999876554432221                  11233344333332211


Q ss_pred             C------------CHHHHHHHHHhchHHHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCch
Q 012638          281 V------------SERVLKQHLAFGWYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKF  348 (459)
Q Consensus       281 ~------------deeeL~~~l~~G~~Are~LI~~nlrLV~sIAkry~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rF  348 (459)
                      .            ....+......|..|+++||.+|++||+++|++|.+.|.+++||||||+|||++|+++|||++|++|
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            1245667778888999999999999999999999999999999999999999999999999999999


Q ss_pred             hhHHHHHHHHHHHHHHHhhccc
Q 012638          349 STYVQYWIRKSISKMVARHARG  370 (459)
Q Consensus       349 STYa~~wIrnaI~d~Lrk~sr~  370 (459)
                      +|||+|||+++|.++|++++|+
T Consensus       159 ~tya~~~i~~~i~~~~~~~~rt  180 (180)
T d1ku2a2         159 STYATWWIRQAINRAIADQART  180 (180)
T ss_dssp             HHHHHHHHHHHHHHHHTTSCCC
T ss_pred             HHHHHHHHHHHHHHHHHHhCCC
Confidence            9999999999999999998874

>d1siga_ a.177.1.1 (A:) Sigma70 {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: Sigma2 domain of RNA polymerase sigma factors
superfamily: Sigma2 domain of RNA polymerase sigma factors
family: Sigma2 domain of RNA polymerase sigma factors
domain: Sigma70
species: Escherichia coli [TaxId: 562]

Probab=99.85  E-value=2e-21  Score=191.44  Aligned_cols=83  Identities=34%  Similarity=0.799  Sum_probs=76.4

Q ss_pred             HHHHHHHhc----hHHHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHH
Q 012638          285 VLKQHLAFG----WYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSI  360 (459)
Q Consensus       285 eL~~~l~~G----~~Are~LI~~nlrLV~sIAkry~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIrnaI  360 (459)
                      .+.+.+..|    .+|+++||++|++||++||++|.++|++++||||+|++||++|++||||.+|++|+|||+||||++|
T Consensus       248 ~i~~~i~~ge~~~~~ak~~~~~~~~~lv~~~~~~~~~~~~~~~dl~~~~~~~l~~~~~~~~~~~~~~f~~~~~~~~~~~~  327 (334)
T d1siga_         248 DINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAI  327 (334)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHTHHHHHHHHTTSTTSSSCHHHHHHHHHHHHHHHHHHCCGGGCCCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhhccchHHHHHHhHHHHHHHHHHhccCCCCCHHHHHHhhHHHHHHHHHhcCCCCCCchHhhhHHHHHHHH
Confidence            344555556    3499999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHhh
Q 012638          361 SKMVARH  367 (459)
Q Consensus       361 ~d~Lrk~  367 (459)
                      .++|++|
T Consensus       328 ~~~~~~~  334 (334)
T d1siga_         328 TRSIADQ  334 (334)
T ss_dssp             HHHHHHC
T ss_pred             HHHHhCC
Confidence            9999875

>d1rp3a3 a.177.1.1 (A:0-86) Sigma factor sigma-28 (FliA) {Aquifex aeolicus [TaxId: 63363]}

class: All alpha proteins
fold: Sigma2 domain of RNA polymerase sigma factors
superfamily: Sigma2 domain of RNA polymerase sigma factors
family: Sigma2 domain of RNA polymerase sigma factors
domain: Sigma factor sigma-28 (FliA)
species: Aquifex aeolicus [TaxId: 63363]

Probab=99.78  E-value=1.9e-19  Score=147.48  Aligned_cols=72  Identities=24%  Similarity=0.393  Sum_probs=68.6

Q ss_pred             HHHHHHHHhHHHHHHHHHHhhCC---CCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhh
Q 012638          296 CREELIKSTRPLVLFLARNYRGL---GIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVARH  367 (459)
Q Consensus       296 Are~LI~~nlrLV~sIAkry~g~---g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIrnaI~d~Lrk~  367 (459)
                      .+++||..|++||.++|.+|.++   +++.+||+|+|++||++|+++|||++|.+|+|||.+|||++|++++|+.
T Consensus        11 ~re~li~~~~~LV~~ia~~~~~~~~~~~e~eDL~q~G~igL~~A~~~yd~~~g~~F~tYA~~~Irgai~d~lRk~   85 (87)
T d1rp3a3          11 EREELILKYLPLVKAIATNIKKHLPEDVDIRDLISYGVIGLIKAVDNLSTENPKRAEAYIKLRIKGAIYDYLRSL   85 (87)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHTTSCTTSCHHHHHHHHHHHHHHHHHTCCCCCTHHHHHHHHHHHHHHHHHHHHTS
T ss_pred             HHHHHHHHhHHHHHHHHHHHhccCCCCCCHHHHHHHHHHHHHHHHHhhCCCCCCCHHHHHHHHHHHHHHHHHHhC
Confidence            68999999999999999999764   7899999999999999999999999999999999999999999999975

>d1ku2a1 a.4.13.1 (A:273-332) Sigma factor SigA {Thermus aquaticus [TaxId: 271]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Sigma3 and sigma4 domains of RNA polymerase sigma factors
family: Sigma3 domain
domain: Sigma factor SigA
species: Thermus aquaticus [TaxId: 271]

Probab=99.03  E-value=1.6e-10  Score=87.70  Aligned_cols=58  Identities=22%  Similarity=0.345  Sum_probs=55.3

Q ss_pred             cccccchHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCC--CHHHHHHHHHhhccCCcc
Q 012638          371 IKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGL--SLAEIRSASECLRIVGSI  428 (459)
Q Consensus       371 irlP~~v~e~i~kI~ka~~~L~~~lgr~PT~eEIAe~LGI--S~e~Vk~~l~~ar~~~SL  428 (459)
                      ||+|.|+.+.++++.++.++|.+++||.||.+|||+.||+  ++++|+.++..++.++||
T Consensus         1 IRlPvH~~e~i~rv~r~~~~l~qe~gRePt~eEiA~~l~~~l~~ekV~~~l~~~~~p~SL   60 (60)
T d1ku2a1           1 IRIPVHMVETINKLSRTARQLQQELGREPSYEEIAEAMGPGWDAKRVEETLKIAQEPVSL   60 (60)
T ss_dssp             CCCCHHHHHHHHHHHHHHHHHHHHHTSCCCHHHHHHHHCSSCCHHHHHHHGGGSSSCCCC
T ss_pred             CccchhHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHCCCCCHHHHHHHHHHccCCCCC
Confidence            6899999999999999999999999999999999999985  588999999999999997

>d1h3la_ a.177.1.1 (A:) Sigma factor SigR {Streptomyces coelicolor a3(2) [TaxId: 100226]}

class: All alpha proteins
fold: Sigma2 domain of RNA polymerase sigma factors
superfamily: Sigma2 domain of RNA polymerase sigma factors
family: Sigma2 domain of RNA polymerase sigma factors
domain: Sigma factor SigR
species: Streptomyces coelicolor a3(2) [TaxId: 100226]

Probab=98.97  E-value=3.6e-10  Score=87.98  Aligned_cols=68  Identities=9%  Similarity=-0.030  Sum_probs=64.1

Q ss_pred             HHHHHHHHhHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHH
Q 012638          296 CREELIKSTRPLVLFLARNYRGLGIPFSDLLQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSISKMVA  365 (459)
Q Consensus       296 Are~LI~~nlrLV~sIAkry~g~g~d~EDLIQEG~IGLirAieKFDp~kG~rFSTYa~~wIrnaI~d~Lr  365 (459)
                      +|++++..|.+.|+.+|.+++++..+++|++||.++.+|+..++|++.  .+|.+|++++++|.+++++|
T Consensus         8 ~f~~~~~~y~~~l~~~~~~~~~d~~~aeDivQd~f~~~~~~~~~~~~~--~~~~~wl~~i~~n~~~d~~R   75 (75)
T d1h3la_           8 RFERDALEFLDQMYSAALRMTRNPADAEDLVQETYAKAYASFHQFREG--TNLKAWLYRILTNTFINSYR   75 (75)
T ss_dssp             HHHHHHHHTHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHGGGCCSS--SCHHHHHHHHHHHHHHHTCC
T ss_pred             HHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhhhhcCCC--CCHHHHHHHHHHHHHHHHhC
Confidence            799999999999999999999999999999999999999999999874  47999999999999998764

>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=98.83  E-value=1.9e-09  Score=80.71  Aligned_cols=55  Identities=31%  Similarity=0.446  Sum_probs=52.3

Q ss_pred             cccccccchHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHhhc
Q 012638          369 RGIKIPCKLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLR  423 (459)
Q Consensus       369 r~irlP~~v~e~i~kI~ka~~~L~~~lgr~PT~eEIAe~LGIS~e~Vk~~l~~ar  423 (459)
                      .+|++|+++.+.+++|.++..+|.+++||.||.+|||+.||+|+++|..++..++
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            4789999999999999999999999999999999999999999999999988765

>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=98.78  E-value=5.5e-10  Score=88.01  Aligned_cols=71  Identities=20%  Similarity=0.310  Sum_probs=61.5

Q ss_pred             chHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHhh--ccCCccccccCCCCCCccccCCCCC
Q 012638          376 KLNREISKIQKARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECL--RIVGSIDQKIGDCLNAKYLNIPPFF  447 (459)
Q Consensus       376 ~v~e~i~kI~ka~~~L~~~lgr~PT~eEIAe~LGIS~e~Vk~~l~~a--r~~~SLD~~v~~d~~~~l~e~i~D~  447 (459)
                      .+.+..++|+++...|.+++||.||.+|||+.|||++++|..++...  ..++|||.+++ +++.++.|++|+.
T Consensus         4 s~r~~~~ki~~a~~~L~~~lGR~Pt~~EiA~~lg~s~~e~~~~l~~~~~~~~~SLD~~~~-d~~~~~~e~lpss   76 (77)
T d1rp3a1           4 QVREKERRIKEVVEKLKEKLGREPTDEEVAKELGISTEELFKTLDKINFSYILSLEEVFR-DFARDYSELIPSS   76 (77)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHSSCCCHHHHHHHHTSCHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHTTTGGGS
T ss_pred             HHHHHHHHHHHHHHHHHHHHCcCCCHHHHHHHHCcCHHHHHHHHHHHhcCCceecccCcc-CCCCchhccCCCC
Confidence            34578899999999999999999999999999999999999998754  46799999876 4556788998874

>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=95.87  E-value=0.0084  Score=43.61  Aligned_cols=41  Identities=20%  Similarity=0.225  Sum_probs=35.4

Q ss_pred             HHHHHHHHHHHHHhCCCCchHHHHHHcCCCHHHHHHHHHhc
Q 012638          253 ANLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQHLAFG  293 (459)
Q Consensus       253 ~~le~~~~~l~~~~gr~pt~~ewa~a~g~deeeL~~~l~~G  293 (459)
                      .++.++..+|..++||+||.+|.|+++|++.+++...+..+
T Consensus        15 ~ki~~~~~~l~q~lgRePT~~EiA~~l~~~~e~V~~~l~a~   55 (57)
T d1l0oc_          15 NKIRKAKDELSKTRGRAPTVTEIADHLGISPEDVVLAQEAV   55 (57)
T ss_dssp             HHHHHHHHHHHHHHTSCCBHHHHHHHHTSCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCCCCCHHHHHHHHCcCHHHHHHHHHHh
Confidence            45677888999999999999999999999999988766543

>d1rp3a1 a.4.13.1 (A:87-163) Sigma factor sigma-28 (FliA) {Aquifex aeolicus [TaxId: 63363]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Sigma3 and sigma4 domains of RNA polymerase sigma factors
family: Sigma3 domain
domain: Sigma factor sigma-28 (FliA)
species: Aquifex aeolicus [TaxId: 63363]

Probab=95.03  E-value=0.021  Score=43.33  Aligned_cols=39  Identities=18%  Similarity=0.262  Sum_probs=34.3

Q ss_pred             HHHHHHHHHHHHHHhCCCCchHHHHHHcCCCHHHHHHHH
Q 012638          252 VANLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQHL  290 (459)
Q Consensus       252 ~~~le~~~~~l~~~~gr~pt~~ewa~a~g~deeeL~~~l  290 (459)
                      ..+++++...|..++||+||.+|.|..+||+.+++...+
T Consensus         9 ~~ki~~a~~~L~~~lGR~Pt~~EiA~~lg~s~~e~~~~l   47 (77)
T d1rp3a1           9 ERRIKEVVEKLKEKLGREPTDEEVAKELGISTEELFKTL   47 (77)
T ss_dssp             HHHHHHHHHHHHHHHSSCCCHHHHHHHHTSCHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHCcCCCHHHHHHHHCcCHHHHHHHH
Confidence            346888999999999999999999999999998877644

>d1or7a1 a.4.13.2 (A:120-187) SigmaE factor (RpoE) {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Sigma3 and sigma4 domains of RNA polymerase sigma factors
family: Sigma4 domain
domain: SigmaE factor (RpoE)
species: Escherichia coli [TaxId: 562]

Probab=94.78  E-value=0.013  Score=43.37  Aligned_cols=30  Identities=20%  Similarity=-0.034  Sum_probs=27.0

Q ss_pred             cCCCCCHHHHHHHhCCCHHHHHHHHHhhcc
Q 012638          395 HGKYPEDIEIAKYTGLSLAEIRSASECLRI  424 (459)
Q Consensus       395 lgr~PT~eEIAe~LGIS~e~Vk~~l~~ar~  424 (459)
                      +-.+.|++|||+.||+|+++|+..+++++.
T Consensus        31 ~~~~~s~~eIA~~lgis~~tv~~~l~ra~~   60 (68)
T d1or7a1          31 ELDGLSYEEIAAIMDCPVGTVRSRIFRARE   60 (68)
T ss_dssp             HTTCCCHHHHHHHTTSCHHHHHHHHHHHHH
T ss_pred             HHhCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence            457889999999999999999999998874

>d1rp3a2 a.4.13.2 (A:164-234) Sigma factor sigma-28 (FliA) {Aquifex aeolicus [TaxId: 63363]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Sigma3 and sigma4 domains of RNA polymerase sigma factors
family: Sigma4 domain
domain: Sigma factor sigma-28 (FliA)
species: Aquifex aeolicus [TaxId: 63363]

Probab=93.89  E-value=0.018  Score=42.47  Aligned_cols=30  Identities=13%  Similarity=-0.042  Sum_probs=26.8

Q ss_pred             cCCCCCHHHHHHHhCCCHHHHHHHHHhhcc
Q 012638          395 HGKYPEDIEIAKYTGLSLAEIRSASECLRI  424 (459)
Q Consensus       395 lgr~PT~eEIAe~LGIS~e~Vk~~l~~ar~  424 (459)
                      +..+.|++|||+.||+|+.+|+..+.+++.
T Consensus        34 ~~~~~s~~eIA~~lgis~~tv~~~~~ra~~   63 (71)
T d1rp3a2          34 FYEELPAKEVAKILETSVSRVSQLKAKALE   63 (71)
T ss_dssp             HTSCCCHHHHHHHTTSCHHHHHHHHHHHHH
T ss_pred             HhHhCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            457899999999999999999999988764

>d1ku2a1 a.4.13.1 (A:273-332) Sigma factor SigA {Thermus aquaticus [TaxId: 271]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Sigma3 and sigma4 domains of RNA polymerase sigma factors
family: Sigma3 domain
domain: Sigma factor SigA
species: Thermus aquaticus [TaxId: 271]

Probab=92.45  E-value=0.12  Score=37.70  Aligned_cols=39  Identities=23%  Similarity=0.371  Sum_probs=30.4

Q ss_pred             HHHHHHHHHHHHHHHhCCCCchHHHHHHcC--CCHHHHHHH
Q 012638          251 VVANLERIKTTLEKESGKAASLNCWAQAAG--VSERVLKQH  289 (459)
Q Consensus       251 ~~~~le~~~~~l~~~~gr~pt~~ewa~a~g--~deeeL~~~  289 (459)
                      .+-++.++..+|..++||+||.+|.|+++|  ++.+.+...
T Consensus        10 ~i~rv~r~~~~l~qe~gRePt~eEiA~~l~~~l~~ekV~~~   50 (60)
T d1ku2a1          10 TINKLSRTARQLQQELGREPSYEEIAEAMGPGWDAKRVEET   50 (60)
T ss_dssp             HHHHHHHHHHHHHHHHTSCCCHHHHHHHHCSSCCHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHhCCCCCHHHHHHHHCCCCCHHHHHHH
Confidence            344667788899999999999999999997  456555443

>d1jhfa1 a.4.5.2 (A:2-72) LexA repressor, N-terminal DNA-binding domain {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: LexA repressor, N-terminal DNA-binding domain
domain: LexA repressor, N-terminal DNA-binding domain
species: Escherichia coli [TaxId: 562]

Probab=92.24  E-value=0.14  Score=38.35  Aligned_cols=45  Identities=18%  Similarity=0.183  Sum_probs=37.3

Q ss_pred             HHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCC-CHHHHHHHHHhhc
Q 012638          379 REISKIQKARKALTNSHGKYPEDIEIAKYTGL-SLAEIRSASECLR  423 (459)
Q Consensus       379 e~i~kI~ka~~~L~~~lgr~PT~eEIAe~LGI-S~e~Vk~~l~~ar  423 (459)
                      ....+|-.++.....+.|..||.+|||+.+|+ |..+|...+.+..
T Consensus         5 ~rQ~~vL~~I~~~~~~~G~~Ps~rei~~~~g~~S~stv~~~l~~Le   50 (71)
T d1jhfa1           5 ARQQEVFDLIRDHISQTGMPPTRAEIAQRLGFRSPNAAEEHLKALA   50 (71)
T ss_dssp             HHHHHHHHHHHHHHHHHSSCCCHHHHHHHTTCSSHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCCHHHHHHHHHHHH
Confidence            34456677777888888999999999999999 8999999887653

>d1s7oa_ a.4.13.3 (A:) Hypothetical protein SPy1201 {Streptococcus pyogenes [TaxId: 1314]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Sigma3 and sigma4 domains of RNA polymerase sigma factors
family: YlxM/p13-like
domain: Hypothetical protein SPy1201
species: Streptococcus pyogenes [TaxId: 1314]

Probab=88.71  E-value=0.21  Score=40.33  Aligned_cols=31  Identities=16%  Similarity=-0.041  Sum_probs=27.4

Q ss_pred             HcCCCCCHHHHHHHhCCCHHHHHHHHHhhcc
Q 012638          394 SHGKYPEDIEIAKYTGLSLAEIRSASECLRI  424 (459)
Q Consensus       394 ~lgr~PT~eEIAe~LGIS~e~Vk~~l~~ar~  424 (459)
                      .+..+.|++|||+.||||+++|+..+++++.
T Consensus        28 ~y~~~ls~~EIA~~lgiS~~aV~~~l~RA~~   58 (106)
T d1s7oa_          28 YYADDYSLAEIADEFGVSRQAVYDNIKRTEK   58 (106)
T ss_dssp             HHHTCCCHHHHHHHHTCCHHHHHHHHHHHHH
T ss_pred             HHHcCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence            3456899999999999999999999998875

>d1xsva_ a.4.13.3 (A:) Hypothetical protein SAV1236 {Staphylococcus aureus, strain Mu50 / ATCC 700699 [TaxId: 1280]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Sigma3 and sigma4 domains of RNA polymerase sigma factors
family: YlxM/p13-like
domain: Hypothetical protein SAV1236
species: Staphylococcus aureus, strain Mu50 / ATCC 700699 [TaxId: 1280]

Probab=88.62  E-value=0.28  Score=39.58  Aligned_cols=31  Identities=13%  Similarity=-0.206  Sum_probs=27.9

Q ss_pred             HcCCCCCHHHHHHHhCCCHHHHHHHHHhhcc
Q 012638          394 SHGKYPEDIEIAKYTGLSLAEIRSASECLRI  424 (459)
Q Consensus       394 ~lgr~PT~eEIAe~LGIS~e~Vk~~l~~ar~  424 (459)
                      .+-.+.|+.|||+.||||.++|+..+++++.
T Consensus        30 ~~~e~ls~~EIA~~lgiS~~aV~~~l~Ra~~   60 (106)
T d1xsva_          30 FYLEDYSLSEIADTFNVSRQAVYDNIRRTGD   60 (106)
T ss_dssp             HHTSCCCHHHHHHHTTCCHHHHHHHHHHHHH
T ss_pred             HHHhCCcHHHHHHHHCcCHHHHHHHHHHHHH
Confidence            4567899999999999999999999998875

>d1l3la1 a.4.6.2 (A:170-234) Quorum-sensing transcription factor TraR, C-terminal domain {Agrobacterium tumefaciens [TaxId: 358]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: C-terminal effector domain of the bipartite response regulators
family: GerE-like (LuxR/UhpA family of transcriptional regulators)
domain: Quorum-sensing transcription factor TraR, C-terminal domain
species: Agrobacterium tumefaciens [TaxId: 358]

Probab=84.46  E-value=0.79  Score=33.09  Aligned_cols=35  Identities=14%  Similarity=-0.027  Sum_probs=28.4

Q ss_pred             HHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHhhcc
Q 012638          390 ALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRI  424 (459)
Q Consensus       390 ~L~~~lgr~PT~eEIAe~LGIS~e~Vk~~l~~ar~  424 (459)
                      ++......+.|.+|||+.||||+.+|+..+.....
T Consensus        11 ~vl~l~~~G~s~~eIA~~l~iS~~TV~~~~~~i~~   45 (65)
T d1l3la1          11 TYLRWIAVGKTMEEIADVEGVKYNSVRVKLREAMK   45 (65)
T ss_dssp             HHHHHHTTTCCHHHHHHHHTCCHHHHHHHHHHHHH
T ss_pred             HHHHHHHhcCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            33445577899999999999999999998876543

>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=83.63  E-value=0.58  Score=34.48  Aligned_cols=39  Identities=8%  Similarity=0.012  Sum_probs=30.5

Q ss_pred             HHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHhhcc
Q 012638          386 KARKALTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRI  424 (459)
Q Consensus       386 ka~~~L~~~lgr~PT~eEIAe~LGIS~e~Vk~~l~~ar~  424 (459)
                      ....++...+..+.+..|||..||||+.+|+..+.....
T Consensus        15 ~rE~~vl~~l~~G~s~~eIA~~l~iS~~TV~~~~~~i~~   53 (70)
T d1yioa1          15 GREQQVLQLTIRGLMNKQIAGELGIAEVTVKVHRHNIMQ   53 (70)
T ss_dssp             HHHHHHHHHHTTTCCHHHHHHHHTCCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            334444455677899999999999999999998876654

>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=83.28  E-value=0.92  Score=32.82  Aligned_cols=34  Identities=15%  Similarity=-0.081  Sum_probs=27.8

Q ss_pred             HHHHcCCCCCHHHHHHHhCCCHHHHHHHHHhhcc
Q 012638          391 LTNSHGKYPEDIEIAKYTGLSLAEIRSASECLRI  424 (459)
Q Consensus       391 L~~~lgr~PT~eEIAe~LGIS~e~Vk~~l~~ar~  424 (459)
                      +..-+..+.+..|||+.||+++.+|+..+.....
T Consensus        12 vl~l~~~G~s~~eIA~~L~is~~TV~~~~~~i~~   45 (67)
T d1fsea_          12 VFELLVQDKTTKEIASELFISEKTVRNHISNAMQ   45 (67)
T ss_dssp             HHHHHTTTCCHHHHHHHHTSCHHHHHHHHHHHHH
T ss_pred             HHHHHHccCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            3344567899999999999999999998876543

>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=80.68  E-value=1  Score=32.70  Aligned_cols=32  Identities=6%  Similarity=0.000  Sum_probs=26.2

Q ss_pred             HHcCCCCCHHHHHHHhCCCHHHHHHHHHhhcc
Q 012638          393 NSHGKYPEDIEIAKYTGLSLAEIRSASECLRI  424 (459)
Q Consensus       393 ~~lgr~PT~eEIAe~LGIS~e~Vk~~l~~ar~  424 (459)
                      .-+..+.+..|||+.|||++.+|+..+.....
T Consensus        16 ~ll~~G~s~~eIA~~l~iS~~TV~~~~~~i~~   47 (67)
T d1a04a1          16 KLIAQGLPNKMIARRLDITESTVKVHVKHMLK   47 (67)
T ss_dssp             HHHHTTCCHHHHHHHHTCCHHHHHHHHHHHHH
T ss_pred             HHHHhCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            33456889999999999999999998776543