Citrus Sinensis ID: 046578

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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-------38
Protein Sequence
MAVTSIWSSSPTHSTLPSLKTLHPLPPPSLSSSPSSCSNKYNININLVTNEALALHPVIESATDAAALASAAVRTAKDAVSFANGAEEVCFDDGECESVLKMMRRRSRRKKRTKESDFLDKENGELDYNLVKYKILCKERESQERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYWWIKQAIIRAIANKSRTIRLPGSMAGMVAKIAEANNVLSRRLRRMPTDSEIAEMLNIHVSTVRLAIERTRHPISLDGAVTDRGCMTMQDIIPGPDETMPERMVQKQLMKQELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQTNILNNLKVYMV
Secondary Structure (PSIPRED)
ccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHcccHHHHHHHHHHHHHHHHcHHHHHHHHHccccccccHHHHHHHHHHHHHHHHHHHHHHcccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHccEEEEEEcccccccccHHHHHHHcccHHHHHHHccccccccccHHHHHHHHHHHHHHHHHHccccccccHHHHHHHHHHHHHHHHHHHHHcccccHHHHHHHccccHHHHHHHHHHHccccccccccccccccccccccccccccccHHHHHHHHHHHHHHHHHHHccHHHHHHHHHHccccccccccHHHHHccccccHHHHHHHHHHHHHHHcccccccccccccc
Secondary Structure Prediction (SSPRO)
ccEEEEEcccccccccccHccccccccccccccccccccccEEcHHHHHHHHHHHHHHHHcccccccccccccccccccccccccHHHHHHHHcHHHcccccccccHHHHHHHHHHcccccccHHHHHHHHHHHHHcccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccHHHHHHHHHccccccccHHHHHHHHHHHHHHHHHHHHHcHccccHHHHHHHHHHHHHHHHHHHHHcccccHHHHHHHccccHHHHHHHHHHHccccEEccccccccccccccccccccccccHHHHHHHHHHccccHHHHcccHHHHHHHHHHHcccccccccHHHHHHHHcccHHHHHHHHHHHHHHHHcccHHHHHHHHcc
Coil and Loop (DISEMBL)
mavtsiwssspthstlpslktlhplpppslssspsscsnkyninINLVtnealalhpvieSATDAAALASAAVRTAKDAvsfangaeevcfddgeCESVLKMMRRRSrrkkrtkesdfldkengeldYNLVKYKILCKERESQERIIRSYRSLVVSIAtgyqgkglslkDLIQEGSIGllrgakrfnpergykLSTYVYWWIKQAIIRAIANKsrtirlpgsmAGMVAKIAEANNVLSRRLRRMPTDSEIAEMLNIHVSTVRLAIErtrhpisldgavtdrgcmtmqdiipgpdetmpERMVQKQLMKQELKELLQTLSEREADILRLHfgldgqtpvscKEIGRLLSLSRERIRQIRGIALTKLQQTNILNNLKVYMV
Flexible Loop (DISEMBL)
mavtsiwssspthstLPSLKTLHPLPPPSLSSSPSSCSNKYNININLVTNEALALHPVIESATDAAALASAAVRTAKDAVSfangaeevcfddgecesvlkmmrrrsrrkkrtkesdfldkengeldynlVKYKILCKERESQERIIRSYRSLVVSIATgyqgkglslkdLIQEGSIGLlrgakrfnpergYKLSTYVYWWIKQAIIRAIANKSRTIRLPGSMAGMVAKIAEANNVLSRRLRRMPTDSEIAEMLNIHVSTVRLAIERTRhpisldgavtdrgcMTMQDIIPGPDETMPERMVQKQLMKQELKELLQTLSEREADILRLhfgldgqtpvsCKEIGRLLSLSRERIRQIRGialtklqqtnilnnlkvymv
Low Complexity Region (SEG)
MAVTSIWssspthstlpslktlhplpppslssspsscsNKYNININLVTNEALALHPVIESatdaaalasaavrtaKDAVSFANGAEEVCFDDGECESVLkmmrrrsrrkkrtkESDFLDKENGELDYNLVKYKILCKERESQERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYWWIKQAIIRAIANKSRTIRLPGSMAGMVAKIAEANNVLSRRLRRMPTDSEIAEMLNIHVSTVRLAIERTRHPISLDGAVTDRGCMTMQDIIPGPDETMPERMVqkqlmkqelkellqTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQTNILNNLKVYMV
Disordered region (IsUnstruct)
***************************************KYNININLVTNEALALHPVIESATDAAALASAAVRTAKDAVSFANGAEEVCFDDGECES**************************ELDYNLVKYKILCKERESQERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYWWIKQAIIRAIANKSRTIRLPGSMAGMVAKIAEANNVLSRRLR*****SEIAEMLNIHVSTVRLAIERTRHPISLDGAVTDRGCMTMQDII**************************TLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQTNILNNLKVY**
Disordered Region (DISOPRED)
****S****************************************NLVTNEALALHPVIESATDAAALASAAVRTAKDAVSFANGAEEVCFDDGEC***********************DKENGELDYNL***************IIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYWWIKQAIIRAIANKSRTIRLPGSMAGMVAKIAEANNVLS*****MPTDSEIAEMLNIHVSTVRLAIERTRHPISLDGAVTDRGCMTMQDIIPGPDETMPERMVQKQLMKQELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQTNILNNLKVYMV
Disordered Region (DISEMBL)
***************LPSLKTLHPL***********CSNKYNININLVTNEALALHPVIESATDAAALASAAVRTAKDAVSFANGAEEVCFDDGECESVLKMMR************DFLDKENGELDYNLVKYKILCKERESQERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYWWIKQAIIRAIANKSRTIRLPGSMAGMVAKIAEANNVLSRRLRRMPTDSEIAEMLNIHVSTVRLAIERTRHPISLDGAVTDRGCMTMQDIIPGPDETMPERMVQKQLMKQELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQTNILNNLKVYMV
Disordered Region (DISPRO)
***************LPSLKTLHPLP**SL**S*SSCSNKYNININLVTNEALALHPVIES**********************NGAEEVCFDDGECESVLKMMRRRSRRKKRTKESDFLDKENGELDYNLVKYKILCKERESQERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYWWIKQAIIRAIANKSRTIRLPGSMAGMVAKIAEANNVLSRRLRRMPTDSEIAEMLNIHVSTVRLAIERTRHPISLDGAVTDRGCMTMQDIIPGPDETMPERMVQKQLMKQELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQTNILNNLK**MV
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
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Transmembrane Helix (MEMSAT)
ooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
SSSSSSSSSSSSSSSSSSSSSSSSSiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MAVTSIWSSSPTHSTLPSLKTLHPLPPPSLSSSPSSCSNKYNININLVTNEALALHPVIESATDAAALASAAVRTAKDAVSFANGAEEVCFDDGECESVLKMMRRRSRRKKRTKESDFLDKENGELDYNLVKYKILCKERESQERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYWWIKQAIIRAIANKSRTIRLPGSMAGMVAKIAEANNVLSRRLRRMPTDSEIAEMLNIHVSTVRLAIERTRHPISLDGAVTDRGCMTMQDIIPGPDETMPERxxxxxxxxxxxxxxxxxxxxxxxxILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQTNILNNLKVYMV
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	379	2.2.26 [Sep-21-2011]
Q9ZSL6	419	RNA polymerase sigma fact	yes	no	0.643	0.582	0.635	4e-90
P52322	416	RNA polymerase sigma fact	yes	no	0.627	0.572	0.439	2e-51
P74565	425	RNA polymerase sigma fact	N/A	no	0.622	0.555	0.438	2e-51
P26683	390	RNA polymerase sigma fact	yes	no	0.627	0.610	0.426	9e-50
P38023	399	RNA polymerase sigma fact	yes	no	0.622	0.591	0.434	1e-49
P06224	371	RNA polymerase sigma fact	yes	no	0.646	0.660	0.383	3e-44
P52329	368	RNA polymerase sigma fact	yes	no	0.646	0.665	0.371	3e-44
O83506	611	RNA polymerase sigma fact	yes	no	0.712	0.441	0.351	5e-44
Q31QR8	311	RNA polymerase sigma fact	no	no	0.643	0.784	0.387	7e-44
P52328	377	RNA polymerase sigma fact	N/A	no	0.646	0.649	0.371	1e-43

>sp|Q9ZSL6|SIGD_ARATH RNA polymerase sigma factor sigD, chloroplastic OS=Arabidopsis thaliana GN=SIGD PE=2 SV=1

 Score =  332 bits (850), Expect = 4e-90,   Method: Compositional matrix adjust.
 Identities = 155/244 (63%), Positives = 207/244 (84%)

Query: 134 KILCKERESQERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYK 193
           +ILC+ +E++E+I R YR LVVSIATGYQGKGL+L+DLIQEGSIGLLRGA+RF+P+RGYK
Sbjct: 171 EILCRRKEAREKITRCYRRLVVSIATGYQGKGLNLQDLIQEGSIGLLRGAERFDPDRGYK 230

Query: 194 LSTYVYWWIKQAIIRAIANKSRTIRLPGSMAGMVAKIAEANNVLSRRLRRMPTDSEIAEM 253
           LSTYVYWWIKQAI+RAIA+KSR ++LPGSM  + AK+AEA+NVL+R+LRR P+  EIAE 
Sbjct: 231 LSTYVYWWIKQAILRAIAHKSRLVKLPGSMWELTAKVAEASNVLTRKLRRQPSCEEIAEH 290

Query: 254 LNIHVSTVRLAIERTRHPISLDGAVTDRGCMTMQDIIPGPDETMPERMVQKQLMKQELKE 313
           LN++VS VRLA+ER+R P+SLD   +  G MT+Q+I+ GPDET PE MV+++ MK E+++
Sbjct: 291 LNLNVSAVRLAVERSRSPVSLDRVASQNGRMTLQEIVRGPDETRPEEMVKREHMKHEIEQ 350

Query: 314 LLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQTNILNN 373
           LL +L+ RE+ +L L+FGL+G+TP+S +EIG+ L LSRER+RQI GIAL KL+  + +N+
Sbjct: 351 LLGSLTARESRVLGLYFGLNGETPMSFEEIGKSLKLSRERVRQINGIALKKLRNVHNVND 410

Query: 374 LKVY 377
           LK+Y
Sbjct: 411 LKIY 414

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 of the ndhF gene which codes for a subunit of the plastid NDH [NAD(P)H dehydrogenase] complex.
Arabidopsis thaliana (taxid: 3702)

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

 Score =  203 bits (517), Expect = 2e-51,   Method: Compositional matrix adjust.
 Identities = 105/239 (43%), Positives = 158/239 (66%), Gaps = 1/239 (0%)

Query: 140 RESQERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVY 199
           R ++E++++S   LVVSIA  Y  +GLS +DLIQEGS+GL+R A++F+ E+GYK STY  
Sbjct: 178 RRAKEKMVQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYAT 237

Query: 200 WWIKQAIIRAIANKSRTIRLPGSMAGMVAKIAEANNVLSRRLRRMPTDSEIAEMLNIHVS 259
           WWI+QAI RAIA++SRTIRLP  +   +++I +   +LS+ +RR PT+ EIA  + + + 
Sbjct: 238 WWIRQAITRAIADQSRTIRLPVHLYETISRIKKTTKILSQEMRRKPTEEEIATKMEMTIE 297

Query: 260 TVRLAIERTRHPISLDGAVTDRGCMTMQDIIPGPDETMPERMVQKQLMKQELKELLQTLS 319
            +R   +  + PISL+  +       + D I    ET PE  V K L++++L+ +L TLS
Sbjct: 298 KLRFIAKSAQLPISLETPIGKEEDSRLGDFIEADGET-PEDEVSKNLLREDLENVLDTLS 356

Query: 320 EREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQTNILNNLKVYM 378
            RE D+LRL +GLD     + +EIG++ +++RERIRQI   AL KL+  N  + LK Y+
Sbjct: 357 PRERDVLRLRYGLDDGRMKTLEEIGQIFNVTRERIRQIEAKALRKLRHPNRNSILKEYI 415

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

 Score =  203 bits (517), Expect = 2e-51,   Method: Compositional matrix adjust.
 Identities = 104/237 (43%), Positives = 158/237 (66%), Gaps = 1/237 (0%)

Query: 142 SQERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYWW 201
           +++++++S   LVVSIA  Y  +GLS +DLIQEGS+GL+R A++F+ E+GYK STY  WW
Sbjct: 189 AKDKMVQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYATWW 248

Query: 202 IKQAIIRAIANKSRTIRLPGSMAGMVAKIAEANNVLSRRLRRMPTDSEIAEMLNIHVSTV 261
           I+QAI RAIA++SRTIRLP  +   +++I +   +LS+ +RR PT+ EIAE + + +  +
Sbjct: 249 IRQAITRAIADQSRTIRLPVHLYETISRIKKTTKLLSQEMRRKPTEEEIAEKMEMTIEKL 308

Query: 262 RLAIERTRHPISLDGAVTDRGCMTMQDIIPGPDETMPERMVQKQLMKQELKELLQTLSER 321
           R   +  + PISL+  +       + D I    ET PE  V K L++++L+ +L TLS R
Sbjct: 309 RFIAKSAQLPISLETPIGKEEDSRLGDFIEADGET-PEDEVSKNLLREDLENVLDTLSPR 367

Query: 322 EADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQTNILNNLKVYM 378
           E D+LRL +GLD     + +EIG++ +++RERIRQI   AL KL+  N  + LK Y+
Sbjct: 368 ERDVLRLRYGLDDGRMKTLEEIGQIFNVTRERIRQIEAKALRKLRHPNRNSILKEYI 424

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

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

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

 Score =  197 bits (502), Expect = 9e-50,   Method: Compositional matrix adjust.
 Identities = 102/239 (42%), Positives = 158/239 (66%), Gaps = 1/239 (0%)

Query: 140 RESQERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVY 199
           R +++++++S   LVVSIA  Y  +GLS +DLIQEGS+GL+R A++F+ E+GYK STY  
Sbjct: 152 RRAKDKMVQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYAT 211

Query: 200 WWIKQAIIRAIANKSRTIRLPGSMAGMVAKIAEANNVLSRRLRRMPTDSEIAEMLNIHVS 259
           WWI+QAI RAIA++SRTIRLP  +   +++I +   +LS+ + R PT+ EIA  + + + 
Sbjct: 212 WWIRQAITRAIADQSRTIRLPVHLYETISRIKKTTKLLSQEMGRKPTEEEIATRMEMTIE 271

Query: 260 TVRLAIERTRHPISLDGAVTDRGCMTMQDIIPGPDETMPERMVQKQLMKQELKELLQTLS 319
            +R   +  + PISL+  +       + D I    ET PE  V K L++++L+++L +LS
Sbjct: 272 KLRFIAKSAQLPISLETPIGKEEDSRLGDFIESDGET-PEDQVSKNLLREDLEKVLDSLS 330

Query: 320 EREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQTNILNNLKVYM 378
            RE D+LRL +GLD     + +EIG++ +++RERIRQI   AL KL+  N  + LK Y+
Sbjct: 331 PRERDVLRLRYGLDDGRMKTLEEIGQIFNVTRERIRQIEAKALRKLRHPNRNSVLKEYI 389

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

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

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

 Score =  197 bits (501), Expect = 1e-49,   Method: Compositional matrix adjust.
 Identities = 103/237 (43%), Positives = 156/237 (65%), Gaps = 1/237 (0%)

Query: 142 SQERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYWW 201
           +++++++S   LVVSIA  Y  +GLS +DLIQEGS+GL+R A++F+ E+GYK STY  WW
Sbjct: 163 AKDKMVQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYATWW 222

Query: 202 IKQAIIRAIANKSRTIRLPGSMAGMVAKIAEANNVLSRRLRRMPTDSEIAEMLNIHVSTV 261
           I+QAI RAIA++SRTIRLP  +   +++I +   +LS+ + R PT+ EIA  + + +  +
Sbjct: 223 IRQAITRAIADQSRTIRLPVHLYETISRIKKTTKLLSQEMGRKPTEEEIATRMEMTIEKL 282

Query: 262 RLAIERTRHPISLDGAVTDRGCMTMQDIIPGPDETMPERMVQKQLMKQELKELLQTLSER 321
           R   +  + PISL+  +       + D I    ET PE  V K L++++L+ +L TLS R
Sbjct: 283 RFIAKSAQLPISLETPIGKEEDSRLGDFIEADGET-PEDEVAKNLLREDLEGVLSTLSPR 341

Query: 322 EADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQTNILNNLKVYM 378
           E D+LRL +GLD     + +EIG+L +++RERIRQI   AL KL+  N  + LK Y+
Sbjct: 342 ERDVLRLRYGLDDGRMKTLEEIGQLFNVTRERIRQIEAKALRKLRHPNRNSILKEYI 398

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|P06224|RPOD_BACSU RNA polymerase sigma factor RpoD OS=Bacillus subtilis (strain 168) GN=sigA PE=1 SV=2

 Score =  179 bits (455), Expect = 3e-44,   Method: Compositional matrix adjust.
 Identities = 94/245 (38%), Positives = 150/245 (61%)

Query: 134 KILCKERESQERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYK 193
           KI   + ES+ R+  +   LVVSIA  Y G+G+   DLIQEG++GL++  ++F+  +GYK
Sbjct: 126 KIEEGDEESKRRLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNMGLMKAVEKFDYRKGYK 185

Query: 194 LSTYVYWWIKQAIIRAIANKSRTIRLPGSMAGMVAKIAEANNVLSRRLRRMPTDSEIAEM 253
            STY  WWI+QAI RAIA+++RTIR+P  M   + K+      L + L R PT  EIAE 
Sbjct: 186 FSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLIRVQRQLLQDLGREPTPEEIAED 245

Query: 254 LNIHVSTVRLAIERTRHPISLDGAVTDRGCMTMQDIIPGPDETMPERMVQKQLMKQELKE 313
           +++    VR  ++  + P+SL+  + +     + D I   + T P      +L+K++L++
Sbjct: 246 MDLTPEKVREILKIAQEPVSLETPIGEEDDSHLGDFIEDQEATSPSDHAAYELLKEQLED 305

Query: 314 LLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQTNILNN 373
           +L TL++RE ++LRL FGLD     + +E+G++  ++RERIRQI   AL KL+  +    
Sbjct: 306 VLDTLTDREENVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRSKR 365

Query: 374 LKVYM 378
           LK ++
Sbjct: 366 LKDFL 370

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.

Bacillus subtilis (strain 168) (taxid: 224308)

>sp|P52329|RPOD_ENTFA RNA polymerase sigma factor RpoD OS=Enterococcus faecalis (strain ATCC 700802 / V583) GN=rpoD PE=3 SV=2

 Score =  179 bits (454), Expect = 3e-44,   Method: Compositional matrix adjust.
 Identities = 91/245 (37%), Positives = 150/245 (61%)

Query: 134 KILCKERESQERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYK 193
           KI   ++E+++R+  +   LVVSIA  Y G+G+   DLIQEG++GL++  ++F+  +G+K
Sbjct: 123 KIEEGDQEAKQRLAEANLRLVVSIAKRYVGRGMQFLDLIQEGNMGLMKAVEKFDYRKGFK 182

Query: 194 LSTYVYWWIKQAIIRAIANKSRTIRLPGSMAGMVAKIAEANNVLSRRLRRMPTDSEIAEM 253
            STY  WWI+QAI RAIA+++RTIR+P  M   + K+      L + L R PT  EI   
Sbjct: 183 FSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLIRIQRQLLQDLGREPTPEEIGAE 242

Query: 254 LNIHVSTVRLAIERTRHPISLDGAVTDRGCMTMQDIIPGPDETMPERMVQKQLMKQELKE 313
           +++    VR  ++  + P+SL+  + +     + D I   D T P      +L+K++L++
Sbjct: 243 MDLPTEKVREILKIAQEPVSLETPIGEEDDSHLGDFIEDQDATSPAEHAAYELLKEQLED 302

Query: 314 LLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQTNILNN 373
           +L TL++RE ++LRL FGLD     + +E+G++  ++RERIRQI   AL KL+  +    
Sbjct: 303 VLDTLTDREENVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRSKQ 362

Query: 374 LKVYM 378
           LK ++
Sbjct: 363 LKDFL 367

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.

Enterococcus faecalis (strain ATCC 700802 / V583) (taxid: 226185)

>sp|O83506|RPOD_TREPA RNA polymerase sigma factor RpoD OS=Treponema pallidum (strain Nichols) GN=rpoD PE=3 SV=1

 Score =  178 bits (452), Expect = 5e-44,   Method: Compositional matrix adjust.
 Identities = 95/270 (35%), Positives = 157/270 (58%)

Query: 109 RKKRTKESDFLDKENGELDYNLVKYKILCKERESQERIIRSYRSLVVSIATGYQGKGLSL 168
           R+ R  E DF +  +G L      ++     +++++++I +   LVVSIA  Y  +GL  
Sbjct: 340 RRLRRIEYDFENTIDGILSMARAIHRGHVMLKKAKDKLINANLRLVVSIAKKYTNRGLLF 399

Query: 169 KDLIQEGSIGLLRGAKRFNPERGYKLSTYVYWWIKQAIIRAIANKSRTIRLPGSMAGMVA 228
            DL+QEG+IGL++  ++F   +GYK STY  WWI+QAI R+I++++RTIR+P  M   + 
Sbjct: 400 FDLVQEGNIGLIKAVEKFEYRKGYKFSTYATWWIRQAITRSISDQARTIRVPVHMIEQIN 459

Query: 229 KIAEANNVLSRRLRRMPTDSEIAEMLNIHVSTVRLAIERTRHPISLDGAVTDRGCMTMQD 288
           K+   +  L ++  R P+D EIA+ L   V  V+      R PISL+  + +    ++ D
Sbjct: 460 KVTRESRQLLQKFGREPSDEEIAQQLCWTVEKVKQVKSVAREPISLETPIGEEEDSSLGD 519

Query: 289 IIPGPDETMPERMVQKQLMKQELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLS 348
            +P  D   P R+ ++ L+K+E++ +L  L  RE ++LR+ FGLDG    + +E+G    
Sbjct: 520 FVPDADVENPSRVTERVLLKEEVRSILSALPAREHEVLRMRFGLDGDYSQTLEEVGLYFD 579

Query: 349 LSRERIRQIRGIALTKLQQTNILNNLKVYM 378
           ++RERIRQI   AL +L+       LK ++
Sbjct: 580 VTRERIRQIEAKALKRLRHPRHSRRLKDFL 609

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.

Treponema pallidum (strain Nichols) (taxid: 243276)

>sp|Q31QR8|RPOD4_SYNE7 RNA polymerase sigma factor rpoD4 OS=Synechococcus elongatus (strain PCC 7942) GN=rpoD4 PE=3 SV=1

 Score =  178 bits (451), Expect = 7e-44,   Method: Compositional matrix adjust.
 Identities = 95/245 (38%), Positives = 149/245 (60%), Gaps = 1/245 (0%)

Query: 122 ENGELDYNLVKYKILCKERESQERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLR 181
           EN + + N     +L   + ++ +++++   LVVS+A  YQ +GL L DLIQEGS+GL R
Sbjct: 54  ENPDAESNSENQAVLQAGQRAKTKMLKANLRLVVSVAKKYQNQGLELLDLIQEGSLGLER 113

Query: 182 GAKRFNPERGYKLSTYVYWWIKQAIIRAIANKSRTIRLPGSMAGMVAKIAEANNVLSRRL 241
             ++F+P  GYK STY YWWI+Q++ RAI N +RTIRLP  ++  +++I +    L+ +L
Sbjct: 114 AVEKFDPALGYKFSTYAYWWIRQSMTRAIDNHARTIRLPIHVSEKISRIKKMTRELTHQL 173

Query: 242 RRMPTDSEIAEMLNIHVSTVRLAIERTRHPISLDG-AVTDRGCMTMQDIIPGPDETMPER 300
           +R+P+ +EIAE L + +  V + + ++    SLD  A  D G   + D+IP P    P  
Sbjct: 174 KRLPSRAEIAEALKLPLQDVEMLLSQSTPCTSLDAQARGDDGRSFLGDLIPDPKSLEPMD 233

Query: 301 MVQKQLMKQELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGI 360
            + + +  +++   L  L+ERE  +L+L FGL      +  EIGR L++SRERIRQ+   
Sbjct: 234 AMDRHIQHEQISTWLAHLTEREQQVLQLRFGLHDGEQHTLAEIGRRLNVSRERIRQVEAR 293

Query: 361 ALTKL 365
           AL KL
Sbjct: 294 ALQKL 298

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|P52328|RPSD2_BACSP RNA polymerase sigma factor RpoD OS=Bacillus sp. GN=sigA PE=3 SV=1

 Score =  177 bits (449), Expect = 1e-43,   Method: Compositional matrix adjust.
 Identities = 91/245 (37%), Positives = 150/245 (61%)

Query: 134 KILCKERESQERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYK 193
           +I+  + E++ R+  +   LVVSIA  Y G+G+   DLIQEG++GL++  ++F+  +G+K
Sbjct: 132 RIMNGDEEAKRRLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNMGLIKAVEKFDHNKGFK 191

Query: 194 LSTYVYWWIKQAIIRAIANKSRTIRLPGSMAGMVAKIAEANNVLSRRLRRMPTDSEIAEM 253
            STY  WWI+QAI RAIA+++RTIR+P  M   + K+   +  L + L R PT  EIA  
Sbjct: 192 FSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLIRVSRQLLQELGREPTPEEIAAE 251

Query: 254 LNIHVSTVRLAIERTRHPISLDGAVTDRGCMTMQDIIPGPDETMPERMVQKQLMKQELKE 313
           + + V  VR  ++  + P+SL+  + +     + D I   +   P      +L+K++L++
Sbjct: 252 MELSVEKVREIMKIAQEPVSLETPIGEEDDSHLGDFIEDQEALTPADAAAYELLKEQLED 311

Query: 314 LLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQTNILNN 373
           +L TL+ERE ++LRL FGLD     + +E+G++  ++RERIRQI   AL KL+  +    
Sbjct: 312 VLDTLTEREENVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRSKR 371

Query: 374 LKVYM 378
           LK ++
Sbjct: 372 LKDFL 376

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.

Bacillus sp (taxid: 1409)

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	379
225450015	426	PREDICTED: RNA polymerase sigma factor r	0.649	0.577	0.707	1e-98
297736323	319	unnamed protein product [Vitis vinifera]	0.649	0.771	0.707	2e-98
15240693	419	sigma factor 4 [Arabidopsis thaliana] gi	0.643	0.582	0.635	3e-88
357458317	403	RNA polymerase sigma factor [Medicago tr	0.649	0.610	0.642	7e-85
357458321	267	RNA polymerase sigma factor [Medicago tr	0.649	0.921	0.642	1e-84
449464016	436	PREDICTED: RNA polymerase sigma factor s	0.649	0.564	0.601	2e-82
449525642	341	PREDICTED: RNA polymerase sigma factor s	0.649	0.721	0.601	5e-82
297811483	273	hypothetical protein ARALYDRAFT_909325 [	0.572	0.794	0.645	6e-79
255553456	389	RNA polymerase sigma factor rpoD, putati	0.580	0.565	0.65	2e-75
407327703	615	sigma factor 2 [Marchantia polymorpha]	0.622	0.383	0.436	4e-52

>gi|225450015|ref|XP_002272444.1| PREDICTED: RNA polymerase sigma factor rpoD-like [Vitis vinifera]

 Score =  366 bits (939), Expect = 1e-98,   Method: Compositional matrix adjust.
 Identities = 174/246 (70%), Positives = 216/246 (87%)

Query: 134 KILCKERESQERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYK 193
           K+LC  RES+ERI +SYR LVVSIA  YQGKGLSL+DLIQEGSIGLLRGA+RF+P+RGYK
Sbjct: 181 KMLCNGRESRERINQSYRRLVVSIAARYQGKGLSLQDLIQEGSIGLLRGAERFDPDRGYK 240

Query: 194 LSTYVYWWIKQAIIRAIANKSRTIRLPGSMAGMVAKIAEANNVLSRRLRRMPTDSEIAEM 253
           LSTYVYWWI+QAI+RAIANKSR IRLPGS+  MVAKIAEA  VLSRRLRR+PT  EIAE 
Sbjct: 241 LSTYVYWWIRQAIVRAIANKSRIIRLPGSICEMVAKIAEARTVLSRRLRRLPTYDEIAEF 300

Query: 254 LNIHVSTVRLAIERTRHPISLDGAVTDRGCMTMQDIIPGPDETMPERMVQKQLMKQELKE 313
           ++++VSTVRL  ER+R PIS+D AVT +GCMT+Q+IIPGPDET P++MV++QLMKQE++ 
Sbjct: 301 IDVNVSTVRLVSERSRTPISVDQAVTSQGCMTLQEIIPGPDETTPQKMVKRQLMKQEVER 360

Query: 314 LLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQTNILNN 373
            L TL EREA ILRL+FG++G+TP+S +EIGRL+ LSRER+RQI  IAL+KL+QT++++ 
Sbjct: 361 ALNTLCEREAYILRLYFGINGETPLSFEEIGRLMKLSRERVRQINSIALSKLRQTSVVDY 420

Query: 374 LKVYMV 379
           LK+YM+
Sbjct: 421 LKLYMM 426

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297736323|emb|CBI24961.3| unnamed protein product [Vitis vinifera]

 Score =  365 bits (936), Expect = 2e-98,   Method: Compositional matrix adjust.
 Identities = 174/246 (70%), Positives = 216/246 (87%)

Query: 134 KILCKERESQERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYK 193
           K+LC  RES+ERI +SYR LVVSIA  YQGKGLSL+DLIQEGSIGLLRGA+RF+P+RGYK
Sbjct: 74  KMLCNGRESRERINQSYRRLVVSIAARYQGKGLSLQDLIQEGSIGLLRGAERFDPDRGYK 133

Query: 194 LSTYVYWWIKQAIIRAIANKSRTIRLPGSMAGMVAKIAEANNVLSRRLRRMPTDSEIAEM 253
           LSTYVYWWI+QAI+RAIANKSR IRLPGS+  MVAKIAEA  VLSRRLRR+PT  EIAE 
Sbjct: 134 LSTYVYWWIRQAIVRAIANKSRIIRLPGSICEMVAKIAEARTVLSRRLRRLPTYDEIAEF 193

Query: 254 LNIHVSTVRLAIERTRHPISLDGAVTDRGCMTMQDIIPGPDETMPERMVQKQLMKQELKE 313
           ++++VSTVRL  ER+R PIS+D AVT +GCMT+Q+IIPGPDET P++MV++QLMKQE++ 
Sbjct: 194 IDVNVSTVRLVSERSRTPISVDQAVTSQGCMTLQEIIPGPDETTPQKMVKRQLMKQEVER 253

Query: 314 LLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQTNILNN 373
            L TL EREA ILRL+FG++G+TP+S +EIGRL+ LSRER+RQI  IAL+KL+QT++++ 
Sbjct: 254 ALNTLCEREAYILRLYFGINGETPLSFEEIGRLMKLSRERVRQINSIALSKLRQTSVVDY 313

Query: 374 LKVYMV 379
           LK+YM+
Sbjct: 314 LKLYMM 319

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|15240693|ref|NP_196877.1| sigma factor 4 [Arabidopsis thaliana] gi|75216509|sp|Q9ZSL6.1|SIGD_ARATH RecName: Full=RNA polymerase sigma factor sigD, chloroplastic; Short=Sigma factor D; Short=Sigma-D; AltName: Full=RNA polymerase sigma factor sig4; Short=Atsig4; Short=Sigma factor 4; Flags: Precursor gi|3983260|gb|AAC97954.1| sigma-like factor [Arabidopsis thaliana] gi|4972296|dbj|BAA78110.1| RNA polymerase sigma subunit SigD [Arabidopsis thaliana] gi|9758039|dbj|BAB08700.1| sigma-like factor [Arabidopsis thaliana] gi|332004550|gb|AED91933.1| sigma factor 4 [Arabidopsis thaliana]

 Score =  332 bits (850), Expect = 3e-88,   Method: Compositional matrix adjust.
 Identities = 155/244 (63%), Positives = 207/244 (84%)

Query: 134 KILCKERESQERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYK 193
           +ILC+ +E++E+I R YR LVVSIATGYQGKGL+L+DLIQEGSIGLLRGA+RF+P+RGYK
Sbjct: 171 EILCRRKEAREKITRCYRRLVVSIATGYQGKGLNLQDLIQEGSIGLLRGAERFDPDRGYK 230

Query: 194 LSTYVYWWIKQAIIRAIANKSRTIRLPGSMAGMVAKIAEANNVLSRRLRRMPTDSEIAEM 253
           LSTYVYWWIKQAI+RAIA+KSR ++LPGSM  + AK+AEA+NVL+R+LRR P+  EIAE 
Sbjct: 231 LSTYVYWWIKQAILRAIAHKSRLVKLPGSMWELTAKVAEASNVLTRKLRRQPSCEEIAEH 290

Query: 254 LNIHVSTVRLAIERTRHPISLDGAVTDRGCMTMQDIIPGPDETMPERMVQKQLMKQELKE 313
           LN++VS VRLA+ER+R P+SLD   +  G MT+Q+I+ GPDET PE MV+++ MK E+++
Sbjct: 291 LNLNVSAVRLAVERSRSPVSLDRVASQNGRMTLQEIVRGPDETRPEEMVKREHMKHEIEQ 350

Query: 314 LLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQTNILNN 373
           LL +L+ RE+ +L L+FGL+G+TP+S +EIG+ L LSRER+RQI GIAL KL+  + +N+
Sbjct: 351 LLGSLTARESRVLGLYFGLNGETPMSFEEIGKSLKLSRERVRQINGIALKKLRNVHNVND 410

Query: 374 LKVY 377
           LK+Y
Sbjct: 411 LKIY 414

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357458317|ref|XP_003599439.1| RNA polymerase sigma factor [Medicago truncatula] gi|355488487|gb|AES69690.1| RNA polymerase sigma factor [Medicago truncatula]

 Score =  320 bits (820), Expect = 7e-85,   Method: Compositional matrix adjust.
 Identities = 158/246 (64%), Positives = 205/246 (83%)

Query: 134 KILCKERESQERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYK 193
           K+L   R+S+ER+ R YR LV SIA  YQGKGLS++DLIQEG+IGLL GA++F+P RG K
Sbjct: 158 KVLINTRKSKERLARDYRGLVASIAAHYQGKGLSIQDLIQEGTIGLLHGAEKFDPNRGCK 217

Query: 194 LSTYVYWWIKQAIIRAIANKSRTIRLPGSMAGMVAKIAEANNVLSRRLRRMPTDSEIAEM 253
           LSTYVYWWIKQ II+A+A KSR IRLPG   GMVAKIAEANNVL RRLRR PT +EIAE+
Sbjct: 218 LSTYVYWWIKQGIIKALAKKSRLIRLPGEKYGMVAKIAEANNVLRRRLRRKPTYNEIAEV 277

Query: 254 LNIHVSTVRLAIERTRHPISLDGAVTDRGCMTMQDIIPGPDETMPERMVQKQLMKQELKE 313
           LN++VSTV+L  ER+R PISLD ++TD+  + +++IIPGP E +PE+MV++QLMKQ + +
Sbjct: 278 LNVNVSTVKLVSERSRQPISLDRSITDQSNLILKEIIPGPVEMIPEKMVERQLMKQGVVK 337

Query: 314 LLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQTNILNN 373
           LL TL +RE +I+RL+FGL+G+TP+S +EIG+LL LSRERIRQI GIAL+KL+Q  ++++
Sbjct: 338 LLNTLDKREEEIVRLYFGLNGETPLSFEEIGKLLKLSRERIRQIHGIALSKLEQNTLVDS 397

Query: 374 LKVYMV 379
           LK Y+V
Sbjct: 398 LKFYVV 403

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357458321|ref|XP_003599441.1| RNA polymerase sigma factor [Medicago truncatula] gi|355488489|gb|AES69692.1| RNA polymerase sigma factor [Medicago truncatula]

 Score =  319 bits (818), Expect = 1e-84,   Method: Compositional matrix adjust.
 Identities = 158/246 (64%), Positives = 205/246 (83%)

Query: 134 KILCKERESQERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYK 193
           K+L   R+S+ER+ R YR LV SIA  YQGKGLS++DLIQEG+IGLL GA++F+P RG K
Sbjct: 22  KVLINTRKSKERLARDYRGLVASIAAHYQGKGLSIQDLIQEGTIGLLHGAEKFDPNRGCK 81

Query: 194 LSTYVYWWIKQAIIRAIANKSRTIRLPGSMAGMVAKIAEANNVLSRRLRRMPTDSEIAEM 253
           LSTYVYWWIKQ II+A+A KSR IRLPG   GMVAKIAEANNVL RRLRR PT +EIAE+
Sbjct: 82  LSTYVYWWIKQGIIKALAKKSRLIRLPGEKYGMVAKIAEANNVLRRRLRRKPTYNEIAEV 141

Query: 254 LNIHVSTVRLAIERTRHPISLDGAVTDRGCMTMQDIIPGPDETMPERMVQKQLMKQELKE 313
           LN++VSTV+L  ER+R PISLD ++TD+  + +++IIPGP E +PE+MV++QLMKQ + +
Sbjct: 142 LNVNVSTVKLVSERSRQPISLDRSITDQSNLILKEIIPGPVEMIPEKMVERQLMKQGVVK 201

Query: 314 LLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQTNILNN 373
           LL TL +RE +I+RL+FGL+G+TP+S +EIG+LL LSRERIRQI GIAL+KL+Q  ++++
Sbjct: 202 LLNTLDKREEEIVRLYFGLNGETPLSFEEIGKLLKLSRERIRQIHGIALSKLEQNTLVDS 261

Query: 374 LKVYMV 379
           LK Y+V
Sbjct: 262 LKFYVV 267

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449464016|ref|XP_004149725.1| PREDICTED: RNA polymerase sigma factor sigD, chloroplastic-like [Cucumis sativus]

 Score =  312 bits (800), Expect = 2e-82,   Method: Compositional matrix adjust.
 Identities = 148/246 (60%), Positives = 194/246 (78%)

Query: 134 KILCKERESQERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYK 193
           +ILC+ RES++R+IR Y  LV+SIA  YQGKGLSL+DL QEG+IGLL+GA+RF P RG+K
Sbjct: 191 RILCRARESRDRLIRCYSKLVISIAAPYQGKGLSLQDLTQEGNIGLLKGAERFEPNRGHK 250

Query: 194 LSTYVYWWIKQAIIRAIANKSRTIRLPGSMAGMVAKIAEANNVLSRRLRRMPTDSEIAEM 253
           LSTY YWWI+QAIIRA+  KSR +RLPG M  MVA+IAE NN L  +L R PT+ E+AE 
Sbjct: 251 LSTYAYWWIRQAIIRALDKKSRLVRLPGHMGQMVARIAEENNHLGIKLSRPPTNKEVAES 310

Query: 254 LNIHVSTVRLAIERTRHPISLDGAVTDRGCMTMQDIIPGPDETMPERMVQKQLMKQELKE 313
           L +H+ST+RL +ER++ PIS++  V DR C+T+Q+I+PGPD   PE MV ++LMKQELK 
Sbjct: 311 LKVHLSTIRLVMERSKRPISINQPVNDRSCLTLQEIMPGPDNLTPENMVMRKLMKQELKR 370

Query: 314 LLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQTNILNN 373
           LL TLS+REA IL L+FGL+G+ P S +EIG+ L+LSRE IRQ     L+KL++T++L+ 
Sbjct: 371 LLNTLSKREARILSLYFGLNGEIPQSFEEIGKSLNLSRETIRQTNIATLSKLKKTDVLDY 430

Query: 374 LKVYMV 379
           LK Y+V
Sbjct: 431 LKDYLV 436

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449525642|ref|XP_004169825.1| PREDICTED: RNA polymerase sigma factor sigD, chloroplastic-like [Cucumis sativus]

 Score =  311 bits (796), Expect = 5e-82,   Method: Compositional matrix adjust.
 Identities = 148/246 (60%), Positives = 194/246 (78%)

Query: 134 KILCKERESQERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYK 193
           +ILC+ RES++R+IR Y  LV+SIA  YQGKGLSL+DL QEG+IGLL+GA+RF P RG+K
Sbjct: 96  RILCRARESRDRLIRCYSKLVISIAAPYQGKGLSLQDLTQEGNIGLLKGAERFEPNRGHK 155

Query: 194 LSTYVYWWIKQAIIRAIANKSRTIRLPGSMAGMVAKIAEANNVLSRRLRRMPTDSEIAEM 253
           LSTY YWWI+QAIIRA+  KSR +RLPG M  MVA+IAE NN L  +L R PT+ E+AE 
Sbjct: 156 LSTYAYWWIRQAIIRALDKKSRLVRLPGHMGQMVARIAEENNHLGIKLSRPPTNKEVAES 215

Query: 254 LNIHVSTVRLAIERTRHPISLDGAVTDRGCMTMQDIIPGPDETMPERMVQKQLMKQELKE 313
           L +H+ST+RL +ER++ PIS++  V DR C+T+Q+I+PGPD   PE MV ++LMKQELK 
Sbjct: 216 LKVHLSTIRLVMERSKRPISINQPVNDRSCLTLQEIMPGPDNLTPENMVMRKLMKQELKR 275

Query: 314 LLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQTNILNN 373
           LL TLS+REA IL L+FGL+G+ P S +EIG+ L+LSRE IRQ     L+KL++T++L+ 
Sbjct: 276 LLNTLSKREARILSLYFGLNGEIPQSFEEIGKSLNLSRETIRQTNIATLSKLKKTDVLDY 335

Query: 374 LKVYMV 379
           LK Y+V
Sbjct: 336 LKDYLV 341

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297811483|ref|XP_002873625.1| hypothetical protein ARALYDRAFT_909325 [Arabidopsis lyrata subsp. lyrata] gi|297319462|gb|EFH49884.1| hypothetical protein ARALYDRAFT_909325 [Arabidopsis lyrata subsp. lyrata]

 Score =  300 bits (769), Expect = 6e-79,   Method: Compositional matrix adjust.
 Identities = 140/217 (64%), Positives = 185/217 (85%)

Query: 161 YQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYWWIKQAIIRAIANKSRTIRLP 220
           YQGKGL+L+DLIQEGSIGLLRGA+RF+P+RGYKLSTYVYWWIKQAI+RAIA+KSR ++LP
Sbjct: 52  YQGKGLNLQDLIQEGSIGLLRGAERFDPDRGYKLSTYVYWWIKQAILRAIAHKSRLVKLP 111

Query: 221 GSMAGMVAKIAEANNVLSRRLRRMPTDSEIAEMLNIHVSTVRLAIERTRHPISLDGAVTD 280
           GSM  + AK+AEA+NVL+R+LRR P+  EIAE LN+HVS VRLA+ER+R P+SLD  V+ 
Sbjct: 112 GSMWELTAKVAEASNVLTRKLRRQPSCEEIAEHLNLHVSAVRLAVERSRSPVSLDRVVSQ 171

Query: 281 RGCMTMQDIIPGPDETMPERMVQKQLMKQELKELLQTLSEREADILRLHFGLDGQTPVSC 340
            G MT+Q+I+ GPDET PE MV+++ MK E+++LL +L+ RE+ +L L+FGL+G+TP+S 
Sbjct: 172 NGRMTLQEIVRGPDETRPEEMVKREHMKHEIEQLLGSLTARESRVLGLYFGLNGETPMSF 231

Query: 341 KEIGRLLSLSRERIRQIRGIALTKLQQTNILNNLKVY 377
           +EIG+ L LSRER+RQI GIAL KL+  + +N+LK+Y
Sbjct: 232 EEIGKSLKLSRERVRQINGIALKKLRNVHNVNDLKIY 268

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255553456|ref|XP_002517769.1| RNA polymerase sigma factor rpoD, putative [Ricinus communis] gi|223543041|gb|EEF44576.1| RNA polymerase sigma factor rpoD, putative [Ricinus communis]

 Score =  288 bits (738), Expect = 2e-75,   Method: Compositional matrix adjust.
 Identities = 143/220 (65%), Positives = 176/220 (80%)

Query: 134 KILCKERESQERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYK 193
           KILCK R+S+ERI  +YR LV+SIA  Y+GKGLSL+DLIQEGSIGLLRGA+RF+P+RG K
Sbjct: 168 KILCKGRQSRERITGNYRRLVLSIANRYRGKGLSLQDLIQEGSIGLLRGAERFDPKRGNK 227

Query: 194 LSTYVYWWIKQAIIRAIANKSRTIRLPGSMAGMVAKIAEANNVLSRRLRRMPTDSEIAEM 253
           LSTYVYWWIK+AII +I+  SR +R P S+     KIAEA   L+ RL R+P+  EIA+ 
Sbjct: 228 LSTYVYWWIKEAIITSISINSRIVRQPRSLWDRTTKIAEAKISLTERLGRLPSYREIAKE 287

Query: 254 LNIHVSTVRLAIERTRHPISLDGAVTDRGCMTMQDIIPGPDETMPERMVQKQLMKQELKE 313
           LN+HVSTVRL   R+R  +SLD AV+D+G MT+Q+IIPGP+E MPE MV+KQL+K+EL+E
Sbjct: 288 LNVHVSTVRLVFSRSRSTVSLDQAVSDQGGMTLQEIIPGPEEMMPENMVKKQLLKKELEE 347

Query: 314 LLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRER 353
           L+QTL +REA  LRL FGL+GQTP SC EIGR L L RER
Sbjct: 348 LIQTLGKREAHTLRLIFGLNGQTPQSCDEIGRSLKLCRER 387

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|407327703|dbj|BAM45409.1| sigma factor 2 [Marchantia polymorpha]

 Score =  211 bits (538), Expect = 4e-52,   Method: Compositional matrix adjust.
 Identities = 103/236 (43%), Positives = 161/236 (68%)

Query: 143 QERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYWWI 202
           ++R++ S   LVVSIA  YQG+G++++DLIQEGS+GL+RGA++F+  RG+K STY +WWI
Sbjct: 378 KDRMVNSNLRLVVSIAKRYQGRGMTIQDLIQEGSMGLIRGAEKFDHTRGFKFSTYAHWWI 437

Query: 203 KQAIIRAIANKSRTIRLPGSMAGMVAKIAEANNVLSRRLRRMPTDSEIAEMLNIHVSTVR 262
           +QAI RAIA++SRTIRLP  +  ++++I +A ++L+    R P D E+AE++ + +  ++
Sbjct: 438 RQAITRAIADQSRTIRLPVHVYELLSRITKAKSMLAAEHGRAPRDEEVAELVGLSIEKLK 497

Query: 263 LAIERTRHPISLDGAVTDRGCMTMQDIIPGPDETMPERMVQKQLMKQELKELLQTLSERE 322
           + I+  R P S++  V      T+ ++IP  D   PE  + K+L+KQ+L  +L TLS RE
Sbjct: 498 MVIKSARSPKSMEFPVGKNNDTTLGEVIPDKDIDSPEEAISKRLLKQDLDVVLHTLSPRE 557

Query: 323 ADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQTNILNNLKVYM 378
            D+LRL +GLD     + +EIG +  ++RERIRQI   AL KL+Q +    L+ Y+
Sbjct: 558 RDVLRLRYGLDDGRMRTLEEIGNVFKVTRERIRQIEAKALRKLRQPSRNTALREYL 613

Source: Marchantia polymorpha

Species: Marchantia polymorpha

Genus: Marchantia

Family: Marchantiaceae

Order: Marchantiales

Class: Marchantiopsida

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	379
TAIR|locus:2173249	419	SIG4 "AT5G13730" [Arabidopsis	0.643	0.582	0.614	3.4e-77
UNIPROTKB|P0A602	528	rpoD "RNA polymerase sigma fac	0.635	0.456	0.378	1.6e-38
TIGR_CMR|CHY_0455	370	CHY_0455 "RNA polymerase sigma	0.633	0.648	0.366	2.1e-38
UNIPROTKB|Q59563	323	mysB "RNA polymerase sigma fac	0.633	0.743	0.369	8.9e-38
TIGR_CMR|ECH_0760	622	ECH_0760 "RNA polymerase sigma	0.678	0.413	0.356	1.5e-37
TIGR_CMR|BA_4515	373	BA_4515 "RNA polymerase sigma-	0.633	0.643	0.35	1.7e-36
TIGR_CMR|APH_0576	627	APH_0576 "RNA polymerase sigma	0.617	0.373	0.382	2.2e-36
TIGR_CMR|GSU_3089	577	GSU_3089 "RNA polymerase sigma	0.635	0.417	0.348	2.2e-36
TIGR_CMR|DET_0551	520	DET_0551 "RNA polymerase sigma	0.680	0.496	0.35	2.7e-36
TIGR_CMR|SPO_1750	660	SPO_1750 "RNA polymerase sigma	0.635	0.365	0.347	1.1e-35

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

 Score = 777 (278.6 bits), Expect = 3.4e-77, P = 3.4e-77
 Identities = 150/244 (61%), Positives = 196/244 (80%)

Query:   134 KILCKERESQERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYK 193
             +ILC+ +E++E+I R YR LVVSIATGYQGKGL+L+DLIQEGSIGLLRGA+RF+P+RGYK
Sbjct:   171 EILCRRKEAREKITRCYRRLVVSIATGYQGKGLNLQDLIQEGSIGLLRGAERFDPDRGYK 230

Query:   194 LSTYVYWWIKQAIIRAIANKSRTIRLPGSMAGMVAKIAEANNVLSRRLRRMPTDSEIAEM 253
             LSTYVYWWIKQAI+RAIA+KSR ++LPGSM  + AK+AEA+NVL+R+LRR P+  EIAE 
Sbjct:   231 LSTYVYWWIKQAILRAIAHKSRLVKLPGSMWELTAKVAEASNVLTRKLRRQPSCEEIAEH 290

Query:   254 LNIHVSTVRLAIERTRHPISLDGAVTDRGCMTMQDIIPGPDETMPERMVXXXXXXXXXXX 313
             LN++VS VRLA+ER+R P+SLD   +  G MT+Q+I+ GPDET PE MV           
Sbjct:   291 LNLNVSAVRLAVERSRSPVSLDRVASQNGRMTLQEIVRGPDETRPEEMVKREHMKHEIEQ 350

Query:   314 XXXTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQTNILNN 373
                +L+ RE+ +L L+FGL+G+TP+S +EIG+ L LSRER+RQI GIAL KL+  + +N+
Sbjct:   351 LLGSLTARESRVLGLYFGLNGETPMSFEEIGKSLKLSRERVRQINGIALKKLRNVHNVND 410

Query:   374 LKVY 377
             LK+Y
Sbjct:   411 LKIY 414

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 = 412 (150.1 bits), Expect = 1.6e-38, P = 1.6e-38
 Identities = 93/246 (37%), Positives = 146/246 (59%)

Query:   136 LCKERE-SQERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYKL 194
             +C++ + ++  ++ +   LVVS+A  Y G+G++  DLIQEG++GL+R  ++F+  +GYK 
Sbjct:   284 ICRDGDRAKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLGLIRAVEKFDYTKGYKF 343

Query:   195 STYVYWWIKQAIIRAIANKSRTIRLPGSMAGMVAKIAEANNVLSRRLRRMPTDSEIAEML 254
             STY  WWI+QAI RA+A+++RTIR+P  M  ++ K+      L + L R PT  E+A+ +
Sbjct:   344 STYATWWIRQAITRAMADQARTIRIPVHMVEVINKLGRIQRELLQDLGREPTPEELAKEM 403

Query:   255 NIHVSTVRLAIER-TRHPISLDGAVTDRGCMTMQDIIPGPDETMPERMVXXXXXXXXXXX 313
             +I    V L I++  R PISLD  + D G   + D I   +  +    V           
Sbjct:   404 DITPEKV-LEIQQYAREPISLDQTIGDEGDSQLGDFIEDSEAVVAVDAVSFTLLQDQLQS 462

Query:   314 XXXTLSEREADILRLHFGL-DGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQTNILN 372
                TLSEREA ++RL FGL DGQ P +  EIG++  ++RERIRQI    ++KL+  +   
Sbjct:   463 VLDTLSEREAGVVRLRFGLTDGQ-PRTLDEIGQVYGVTRERIRQIESKTMSKLRHPSRSQ 521

Query:   373 NLKVYM 378
              L+ Y+
Sbjct:   522 VLRDYL 527

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

 Score = 411 (149.7 bits), Expect = 2.1e-38, P = 2.1e-38
 Identities = 88/240 (36%), Positives = 136/240 (56%)

Query:   139 ERESQERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYV 198
             + E++ ++  +   LVVSIA  Y G+G+   DLIQEG++GLL+  ++F+  +GYK STY 
Sbjct:   130 DEEAKRKLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNLGLLKAVEKFDYRKGYKFSTYA 189

Query:   199 YWWIKQAIIRAIANKSRTIRLPGSMAGMVAKIAEANNVLSRRLRRMPTDSEIAEMLNIHV 258
              WWI+QAI RAIA+++RTIR+P  M   + K+   +  L + L R PT  EIA+ + I  
Sbjct:   190 TWWIRQAITRAIADQARTIRIPVHMVETINKLIRVSRNLLQELGREPTPEEIAKEMGISE 249

Query:   259 STVRLAIERTRHPISLDGAVTDRGCMTMQDIIPGPDETMPERMVXXXXXXXXXXXXXXTL 318
               VR  ++  + P+SL+  + +     + D +  PD   P                  TL
Sbjct:   250 DKVREIMKIAQEPVSLETPIGEEEDSHLGDFVEDPDAKAPVEEASYTLLREQLDEVLKTL 309

Query:   319 SEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQTNILNNLKVYM 378
             +ERE  +LRL FGLD     + +E+G++  ++RERIRQI   AL KL+  +    LK ++
Sbjct:   310 TEREQKVLRLRFGLDDGRARTLEEVGQIFGVTRERIRQIEAKALRKLRHPSRSKKLKDFL 369

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

GO:0016987 "sigma factor activity" evidence=ISS

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

 Score = 405 (147.6 bits), Expect = 8.9e-38, P = 8.9e-38
 Identities = 89/241 (36%), Positives = 133/241 (55%)

Query:   138 KERESQER-IIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLST 196
             ++ E+  R ++ +   LVVS+A  Y G+G+ L DLIQEG++GL+R  ++F+  +G+K ST
Sbjct:    81 RDGEAARRHLLEANLRLVVSLAKRYTGRGMPLLDLIQEGNLGLIRAMEKFDYTKGFKFST 140

Query:   197 YVYWWIKQAIIRAIANKSRTIRLPGSMAGMVAKIAEANNVLSRRLRRMPTDSEIAEMLNI 256
             Y  WWI+QAI R +A++SRTIRLP  +   V K+A     + + L R  TD E+A    I
Sbjct:   141 YATWWIRQAITRGMADQSRTIRLPVHLVEQVNKLARIKREMHQHLGREATDEELAAESGI 200

Query:   257 HVSTVRLAIERTRHPISLDGAVTDRGCMTMQDIIPGPDETMPERMVXXXXXXXXXXXXXX 316
              +  +   +E +R P+SLD  V       + D I   +    E  V              
Sbjct:   201 PIDKINDLLEHSRDPVSLDMPVGSEEEAPLGDFIEDAEAMSAENAVIAELLHTDIRSVLA 260

Query:   317 TLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQTNILNNLKV 376
             TL ERE  ++RL FGLD   P +  +IG+L  LSRER+RQI    ++KL+     + L+ 
Sbjct:   261 TLDEREHQVIRLRFGLDDGQPRTLDQIGKLFGLSRERVRQIERDVMSKLRHGERADRLRS 320

Query:   377 Y 377
             Y
Sbjct:   321 Y 321

GO:0001666 "response to hypoxia" evidence=IEP

GO:0005829 "cytosol" evidence=IDA

GO:0005886 "plasma membrane" evidence=IDA

GO:0009408 "response to heat" evidence=IEP

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

GO:0016987 "sigma factor activity" evidence=IGI

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

GO:0040007 "growth" evidence=IMP

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

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

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

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

 Score = 406 (148.0 bits), Expect = 1.5e-37, P = 1.5e-37
 Identities = 93/261 (35%), Positives = 143/261 (54%)

Query:   119 LDKENGELDYNLVKYKILCKER---ESQERIIRSYRSLVVSIATGYQGKGLSLKDLIQEG 175
             L  EN   ++  +  KI   ER   ++++ +I++   LVVSIA  Y  +GL   DL+QEG
Sbjct:   359 LSGENNLTEFKALVTKIQKHERAANQAKQEMIKANLRLVVSIAKKYSNRGLQFLDLVQEG 418

Query:   176 SIGLLRGAKRFNPERGYKLSTYVYWWIKQAIIRAIANKSRTIRLPGSMAGMVAKIAEANN 235
             +IGL++   +F+ +RGYK STY  WW++QAI RAIA+++RTIR+P  M   V KI     
Sbjct:   419 NIGLMKAVDKFDYKRGYKFSTYATWWVRQAITRAIADQARTIRIPVHMIETVNKINRTLR 478

Query:   236 VLSRRLRRMPTDSEIAEMLNIHVSTVRLAIERTRHPISLDGAVTDRGCMTMQDIIPGPDE 295
              +   + R PT  E++  LNI+V  +R  ++  + P+SL+  + D    T  D I     
Sbjct:   479 QMLHEMGREPTLEELSARLNINVDKIRKVMKIVKDPVSLESPIGDDDSSTFGDCIEDKRA 538

Query:   296 TMPERMVXXXXXXXXXXXXXXTLSEREADILRLHFGLD-GQTPVSCKEIGRLLSLSRERI 354
               PE                 TL+ +E  ILR+ FG+  G    + +E+G+L +++RERI
Sbjct:   539 VKPEDAAVLADLREITTKVLSTLTPKEERILRMRFGIGKGGKDHTLEEVGKLFNVTRERI 598

Query:   355 RQIRGIALTKLQQTNILNNLK 375
             RQI   AL KL+  +    L+
Sbjct:   599 RQIEAKALRKLRHPSRARKLR 619

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

GO:0016987 "sigma factor activity" evidence=ISS

TIGR_CMR|BA_4515 BA_4515 "RNA polymerase sigma-43 factor" [Bacillus anthracis str. Ames (taxid:198094)]

 Score = 393 (143.4 bits), Expect = 1.7e-36, P = 1.7e-36
 Identities = 84/240 (35%), Positives = 136/240 (56%)

Query:   139 ERESQERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYV 198
             + E++ R+  +   LVVSIA  Y G+G+   DLIQEG++GL++  ++F+  +G+K STY 
Sbjct:   133 DEEAKRRLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNMGLIKAVEKFDYRKGFKFSTYA 192

Query:   199 YWWIKQAIIRAIANKSRTIRLPGSMAGMVAKIAEANNVLSRRLRRMPTDSEIAEMLNIHV 258
              WWI+QAI RAIA+++RTIR+P  M   + K+      L + L R P+  EI E +++  
Sbjct:   193 TWWIRQAITRAIADQARTIRIPVHMVETINKLIRVQRQLLQDLGREPSPEEIGEEMDLAP 252

Query:   259 STVRLAIERTRHPISLDGAVTDRGCMTMQDIIPGPDETMPERMVXXXXXXXXXXXXXXTL 318
               VR  ++  + P+SL+  + +     + D I   + T P                  TL
Sbjct:   253 EKVREILKIAQEPVSLETPIGEEDDSHLGDFIEDQEATSPADHAAYELLKEQLEDVLDTL 312

Query:   319 SEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQTNILNNLKVYM 378
             ++RE ++LRL FGLD     + +E+G++  ++RERIRQI   AL KL+  +    LK ++
Sbjct:   313 TDREENVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRSKRLKDFL 372

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

GO:0016987 "sigma factor activity" evidence=ISS

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

 Score = 396 (144.5 bits), Expect = 2.2e-36, P = 2.2e-36
 Identities = 91/238 (38%), Positives = 133/238 (55%)

Query:   140 RESQERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVY 199
             R  QE I  + R LVVSIA  Y  +GL   DL+QEG+IGL++   +F+ +RGYK STY  
Sbjct:   389 RAKQEMIKANLR-LVVSIAKKYSNRGLQFLDLVQEGNIGLMKAVDKFDYKRGYKFSTYAT 447

Query:   200 WWIKQAIIRAIANKSRTIRLPGSMAGMVAKIAEANNVLSRRLRRMPTDSEIAEMLNIHVS 259
             WW++QAI RAIA+++RTIR+P  M   V KI      +   + R PT  E++  LNI+V 
Sbjct:   448 WWVRQAITRAIADQARTIRIPVHMIETVNKINRTLRQMLHEIGREPTLEELSARLNINVE 507

Query:   260 TVRLAIERTRHPISLDGAVTDRGCMTMQDIIPGPDETMPERMVXXXXXXXXXXXXXXTLS 319
              +R  ++  + P+SL+  + D    T  D I       PE                 TL+
Sbjct:   508 KIRKVMKIVKDPVSLESPIGDDDSSTFGDCIEDKRAVKPENAAVLADLREITTKVLSTLT 567

Query:   320 EREADILRLHFGLDGQTPV--SCKEIGRLLSLSRERIRQIRGIALTKLQQTNILNNLK 375
              +E  ILR+ FG+ G++    + +E+GRL +++RERIRQI   AL KL+  +    L+
Sbjct:   568 PKEERILRMRFGI-GKSGKDHTLEEVGRLFNVTRERIRQIEAKALRKLRHPSRARKLR 624

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

GO:0016987 "sigma factor activity" evidence=ISS

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

 Score = 393 (143.4 bits), Expect = 2.2e-36, P = 2.2e-36
 Identities = 84/241 (34%), Positives = 134/241 (55%)

Query:   138 KERESQERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTY 197
             K + ++  ++ +   LVVSIA  Y  +GL   DLIQEG+IGL++   +F  +RGYK STY
Sbjct:   336 KSKLAKSELVEANLRLVVSIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYQRGYKFSTY 395

Query:   198 VYWWIKQAIIRAIANKSRTIRLPGSMAGMVAKIAEANNVLSRRLRRMPTDSEIAEMLNIH 257
               WWI+QAI RAIA+++RTIR+P  M   + K+   +  L + + R P+  EIAE +N+ 
Sbjct:   396 ATWWIRQAITRAIADQARTIRIPVHMIETINKLIRTSRQLVQEIGREPSPEEIAERMNLP 455

Query:   258 VSTVRLAIERTRHPISLDGAVTDRGCMTMQDIIPGPDETMPERMVXXXXXXXXXXXXXXT 317
             +  VR  ++  + PISL+  + +     + D I       P   V              T
Sbjct:   456 LDKVRKVLKIAKEPISLETPIGEEEDSHLGDFIEDKGVVSPLEAVIKANLSEQTARVLAT 515

Query:   318 LSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQTNILNNLKVY 377
             L+ RE  +LR+ FG+  ++  + +E+G+   ++RERIRQI   AL KL+  +    L+ +
Sbjct:   516 LTPREEKVLRMRFGIGEKSDHTLEEVGQDFEVTRERIRQIEAKALRKLRHPSRAKKLRSF 575

Query:   378 M 378
             +
Sbjct:   576 V 576

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

GO:0016987 "sigma factor activity" evidence=ISS

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

 Score = 391 (142.7 bits), Expect = 2.7e-36, P = 2.7e-36
 Identities = 91/260 (35%), Positives = 144/260 (55%)

Query:   119 LDKENGELDYNLVKYKILCKERESQERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIG 178
             L++    L Y L   +I  K  E    +I++   LVVS+A  + G+G+ L DLIQEG+IG
Sbjct:   262 LERHEASLKYYLDNLEIDAKRAE--RHLIQANLRLVVSVAKKHIGRGMPLLDLIQEGNIG 319

Query:   179 LLRGAKRFNPERGYKLSTYVYWWIKQAIIRAIANKSRTIRLPGSMAGMVAKIAEANNVLS 238
             L+R  ++F+  RG+K STY  WWI+QAI RAIA+++RTIR+P  M   + K+   +  LS
Sbjct:   320 LIRAVEKFDFHRGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLLSISRQLS 379

Query:   239 RRLRRMPTDSEIAEMLNIHVSTVRLAIERTRHPISLDGAVTDRGCMTMQDIIPGPDETMP 298
             ++L R PT  EIA  +++    VR   + ++ P+SL+  + +     + D I   +   P
Sbjct:   380 QKLGREPTPDEIAVEMDLPPEKVREIAKVSQLPVSLESPIGEEEDSHLGDFIEDQNALAP 439

Query:   299 ERMVXXXXXXXXXXXXXXTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIR 358
                               +L+ RE  +L+L FGL+     + +E+G+  +++RERIRQI 
Sbjct:   440 PDAASRQLLKEQIDTVLGSLTPRERRVLQLRFGLEDGRSRTLEEVGKEFNVTRERIRQIE 499

Query:   359 GIALTKLQQTNILNNLKVYM 378
               AL KL+  +    LK Y+
Sbjct:   500 AKALRKLRHPSRSRKLKDYL 519

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

GO:0016987 "sigma factor activity" evidence=ISS

TIGR_CMR|SPO_1750 SPO_1750 "RNA polymerase sigma-70 factor RpoD" [Ruegeria pomeroyi DSS-3 (taxid:246200)]

 Score = 391 (142.7 bits), Expect = 1.1e-35, P = 1.1e-35
 Identities = 84/242 (34%), Positives = 134/242 (55%)

Query:   138 KE-RESQERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLST 196
             KE R++++ ++ +   LV+SIA  Y  +GL   DLIQEG+IGL++   +F   RGYK ST
Sbjct:   417 KEARQAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFST 476

Query:   197 YVYWWIKQAIIRAIANKSRTIRLPGSMAGMVAKIAEANNVLSRRLRRMPTDSEIAEMLNI 256
             Y  WWI+QAI R+IA+++RTIR+P  M   + K+      +   + R PT  E+AE L +
Sbjct:   477 YATWWIRQAITRSIADQARTIRIPVHMIETINKLVRTGRQMLHEIGREPTPEELAEKLQM 536

Query:   257 HVSTVRLAIERTRHPISLDGAVTDRGCMTMQDIIPGPDETMPERMVXXXXXXXXXXXXXX 316
              +  VR  ++  + PISL+  + D     + D I   +  +P                  
Sbjct:   537 PLEKVRKVMKIAKEPISLETPIGDEEDSQLGDFIEDKNAVLPLDSAIQENLKETTTRVLA 596

Query:   317 TLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQTNILNNLKV 376
             +L+ RE  +LR+ FG+   T  + +E+G+  S++RERIRQI   AL KL+  +    L+ 
Sbjct:   597 SLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLKHPSRSRKLRS 656

Query:   377 YM 378
             ++
Sbjct:   657 FL 658

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

GO:0016987 "sigma factor activity" evidence=ISS

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Fail to connect to STRING server

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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	379
TIGR02997	298	TIGR02997, Sig70-cyanoRpoD, RNA polymerase sigma f	1e-85
COG0568	342	COG0568, RpoD, DNA-directed RNA polymerase, sigma	5e-68
TIGR02393	238	TIGR02393, RpoD_Cterm, RNA polymerase sigma factor	2e-66
PRK07406	373	PRK07406, PRK07406, RNA polymerase sigma factor Rp	5e-65
PRK07921	324	PRK07921, PRK07921, RNA polymerase sigma factor Si	5e-58
PRK05949	327	PRK05949, PRK05949, RNA polymerase sigma factor; V	3e-56
PRK07405	317	PRK07405, PRK07405, RNA polymerase sigma factor Si	1e-55
PRK07598	415	PRK07598, PRK07598, RNA polymerase sigma factor Si	5e-55
TIGR02394	285	TIGR02394, rpoS_proteo, RNA polymerase sigma facto	3e-52
PRK05901	509	PRK05901, PRK05901, RNA polymerase sigma factor; P	2e-51
PRK09210	367	PRK09210, PRK09210, RNA polymerase sigma factor Rp	7e-51
PRK05657	325	PRK05657, PRK05657, RNA polymerase sigma factor Rp	5e-46
PRK05658	619	PRK05658, PRK05658, RNA polymerase sigma factor Rp	3e-37
TIGR02392	270	TIGR02392, rpoH_proteo, alternative sigma factor R	4e-28
TIGR02980	227	TIGR02980, SigBFG, RNA polymerase sigma-70 factor,	2e-27
COG1191	247	COG1191, FliA, DNA-directed RNA polymerase special	3e-26
TIGR02479	224	TIGR02479, FliA_WhiG, RNA polymerase sigma factor,	1e-25
PRK07500	289	PRK07500, rpoH2, RNA polymerase factor sigma-32; R	3e-25
PRK06596	284	PRK06596, PRK06596, RNA polymerase factor sigma-32	7e-25
PRK07670	251	PRK07670, PRK07670, RNA polymerase sigma factor Si	5e-21
pfam04542	71	pfam04542, Sigma70_r2, Sigma-70 region 2	6e-20
TIGR02941	255	TIGR02941, Sigma_B, RNA polymerase sigma-B factor	8e-19
PRK08583	257	PRK08583, PRK08583, RNA polymerase sigma factor Si	2e-18
PRK06288	268	PRK06288, PRK06288, RNA polymerase sigma factor Wh	1e-17
PRK07408	256	PRK07408, PRK07408, RNA polymerase sigma factor Si	7e-17
PRK05911	257	PRK05911, PRK05911, RNA polymerase sigma factor si	4e-16
PRK06986	236	PRK06986, fliA, flagellar biosynthesis sigma facto	8e-16
TIGR02850	254	TIGR02850, spore_sigG, RNA polymerase sigma-G fact	3e-14
PRK05572	252	PRK05572, PRK05572, sporulation sigma factor SigF;	7e-14
TIGR02885	231	TIGR02885, spore_sigF, RNA polymerase sigma-F fact	4e-13
TIGR02937	158	TIGR02937, sigma70-ECF, RNA polymerase sigma facto	7e-13
PRK08215	258	PRK08215, PRK08215, sporulation sigma factor SigG;	3e-12
PRK07122	264	PRK07122, PRK07122, RNA polymerase sigma factor Si	4e-12
TIGR02846	227	TIGR02846, spore_sigmaK, RNA polymerase sigma-K fa	4e-11
pfam04539	78	pfam04539, Sigma70_r3, Sigma-70 region 3	4e-10
TIGR02835	234	TIGR02835, spore_sigmaE, RNA polymerase sigma-E fa	5e-10
pfam04545	50	pfam04545, Sigma70_r4, Sigma-70, region 4	4e-08
PRK05803	233	PRK05803, PRK05803, sporulation sigma factor SigK;	4e-07
cd06171	55	cd06171, Sigma70_r4, Sigma70, region (SR) 4 refers	5e-07
PRK08295	208	PRK08295, PRK08295, RNA polymerase factor sigma-70	7e-07
PRK08301	234	PRK08301, PRK08301, sporulation sigma factor SigE;	2e-05
PRK12427	231	PRK12427, PRK12427, flagellar biosynthesis sigma f	7e-05
PRK05803	233	PRK05803, PRK05803, sporulation sigma factor SigK;	1e-04
TIGR02859	198	TIGR02859, spore_sigH, RNA polymerase sigma-H fact	2e-04

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

 Score =  261 bits (669), Expect = 1e-85
 Identities = 109/226 (48%), Positives = 153/226 (67%), Gaps = 1/226 (0%)

Query: 140 RESQERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVY 199
           + ++E++I++   LVVS+A  YQ +GL L DLIQEGS+GL R  ++F+P RGYK STY Y
Sbjct: 73  QRAKEKMIKANLRLVVSVAKKYQNRGLELLDLIQEGSLGLERAVEKFDPTRGYKFSTYAY 132

Query: 200 WWIKQAIIRAIANKSRTIRLPGSMAGMVAKIAEANNVLSRRLRRMPTDSEIAEMLNIHVS 259
           WWI+Q I RAIAN+SRTIRLP  +   + KI +    LS++L R P+++EIAE L +   
Sbjct: 133 WWIRQGITRAIANQSRTIRLPIHITEKLNKIKKVQRELSQKLGRTPSEAEIAEALELEPE 192

Query: 260 TVRLAIERTRHPISLDGAVTDRGCMTMQDIIPGPDETMPERMVQKQLMKQELKELLQTLS 319
            VR  ++R R P+SLD  V D     + D++    E+ PE  V+++ ++Q+L+ LL  L+
Sbjct: 193 QVRELLQRARQPVSLDAPVGDEEDTELGDLLEDDGES-PEEQVERESLRQDLESLLAELT 251

Query: 320 EREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKL 365
            RE  +LRL FGLDG  P++  EIGR L+LSRER+RQI   AL KL
Sbjct: 252 PRERQVLRLRFGLDGGEPLTLAEIGRRLNLSRERVRQIEAKALRKL 297

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

 Score =  217 bits (555), Expect = 5e-68
 Identities = 101/266 (37%), Positives = 151/266 (56%), Gaps = 2/266 (0%)

Query: 102 MMRRRSRRKKRTKESDFLDKENGELDYNLVKYKILCKERESQERIIRSYRSLVVSIATGY 161
               R     R  E+  L     E        K   ++ +++++++ S   LVVSIA  Y
Sbjct: 64  RPAGRLSFYIRAIEAAPLLTPEEEKALARR-LKRGERDLDAKKKLVESNLRLVVSIAKKY 122

Query: 162 QGKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYWWIKQAIIRAIANKSRTIRLPG 221
            G+GL   DLIQEG+IGL++  ++F+PE+G+K STY  WWI+QAI RAIA+++RTIR+P 
Sbjct: 123 TGRGLPFLDLIQEGNIGLMKAVEKFDPEKGFKFSTYATWWIRQAITRAIADQARTIRIPV 182

Query: 222 SMAGMVAKIAEANNVLSRRLRRMPTDSEIAEMLNIHVSTVRLAIERTRHPISLDGAVTDR 281
               ++ K+      L + L R PT  EIAE L +    VR  ++R   PISLD  + D 
Sbjct: 183 HQVELINKLRRVKRELLQELGREPTPEEIAEELGVSPDKVREMLKRASEPISLDTPIGDD 242

Query: 282 GCMTMQDIIPGPDETMPERMVQKQLMKQELKELLQT-LSEREADILRLHFGLDGQTPVSC 340
               + D +       PE  V+++ +K++L E+L   L+ERE  ++RL FGLD   P + 
Sbjct: 243 EDSELGDFLEDDKSVSPEDAVERESLKEDLNEVLAEALTERERRVIRLRFGLDDGEPKTL 302

Query: 341 KEIGRLLSLSRERIRQIRGIALTKLQ 366
           +E+G    +SRER+RQI   AL KL+
Sbjct: 303 EELGEEFGISRERVRQIEAKALRKLR 328

Length = 342

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

 Score =  209 bits (535), Expect = 2e-66
 Identities = 93/236 (39%), Positives = 147/236 (62%)

Query: 144 ERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYWWIK 203
           ++++ S   LVVSIA  Y  +GLS  DLIQEG+IGL++  ++F+  +GYK STY  WWI+
Sbjct: 3   KQLVESNLRLVVSIAKKYTNRGLSFLDLIQEGNIGLMKAVEKFDYRKGYKFSTYATWWIR 62

Query: 204 QAIIRAIANKSRTIRLPGSMAGMVAKIAEANNVLSRRLRRMPTDSEIAEMLNIHVSTVRL 263
           QAI RAIA+++RTIR+P  M   + K+ +A   L++ L R PTD E+AE + +    VR 
Sbjct: 63  QAITRAIADQARTIRIPVHMVETINKLIKAERQLTQELGREPTDEELAERMGMPAEKVRE 122

Query: 264 AIERTRHPISLDGAVTDRGCMTMQDIIPGPDETMPERMVQKQLMKQELKELLQTLSEREA 323
             +  + PISL+  + +     + D I       P+    K+L++++L E+L+TL+ERE 
Sbjct: 123 IKKIAQEPISLETPIGEEEDSFLGDFIEDTSIESPDDYAAKELLREQLDEVLETLTEREE 182

Query: 324 DILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQTNILNNLKVYMV 379
            +LR+ +GL    P + +E+G+  +++RERIRQI   AL KL+  +    LK ++ 
Sbjct: 183 KVLRMRYGLLDGQPHTLEEVGKEFNVTRERIRQIESKALRKLRHPSRSKKLKSFLD 238

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

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

 Score =  210 bits (537), Expect = 5e-65
 Identities = 115/261 (44%), Positives = 168/261 (64%), Gaps = 3/261 (1%)

Query: 120 DKENGEL-DYNLVKYK-ILCKERESQERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSI 177
           DKE  EL D  L K++  L   R ++E++++S   LVVSIA  Y  +GLS +DLIQEGS+
Sbjct: 113 DKEWAELVDMPLPKFRRRLMLGRRAKEKMVQSNLRLVVSIAKKYMNRGLSFQDLIQEGSL 172

Query: 178 GLLRGAKRFNPERGYKLSTYVYWWIKQAIIRAIANKSRTIRLPGSMAGMVAKIAEANNVL 237
           GL+R A++F+ E+GYK STY  WWI+QAI RAIA++SRTIRLP  +   +++I +   VL
Sbjct: 173 GLIRAAEKFDHEKGYKFSTYATWWIRQAITRAIADQSRTIRLPVHLYETISRIKKTTKVL 232

Query: 238 SRRLRRMPTDSEIAEMLNIHVSTVRLAIERTRHPISLDGAVTDRGCMTMQDIIPGPDETM 297
           S+   R PT+ EIAE + + +  +R   +  + PISL+  +       + D I    ET 
Sbjct: 233 SQEFGRKPTEEEIAESMEMTIEKLRFIAKSAQLPISLETPIGKEEDSRLGDFIEADGET- 291

Query: 298 PERMVQKQLMKQELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQI 357
           PE  V K L++++L+ +L TLS RE D+LRL +GLD     + +EIG++ +++RERIRQI
Sbjct: 292 PEDDVAKNLLREDLEGVLATLSPRERDVLRLRYGLDDGRMKTLEEIGQIFNVTRERIRQI 351

Query: 358 RGIALTKLQQTNILNNLKVYM 378
              AL KL+  N  + LK Y+
Sbjct: 352 EAKALRKLRHPNRNSVLKEYI 372

Length = 373

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

 Score =  191 bits (487), Expect = 5e-58
 Identities = 92/225 (40%), Positives = 134/225 (59%)

Query: 153 LVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYWWIKQAIIRAIAN 212
           LVVS+A  Y G+G+ L DLIQEG++GL+R  ++F+  +G+K STY  WWI+QAI R +A+
Sbjct: 98  LVVSLAKRYTGRGMPLLDLIQEGNLGLIRAMEKFDYTKGFKFSTYATWWIRQAITRGMAD 157

Query: 213 KSRTIRLPGSMAGMVAKIAEANNVLSRRLRRMPTDSEIAEMLNIHVSTVRLAIERTRHPI 272
           +SRTIRLP  +   V K+A     L ++L R  TD E+AE   I    +   +E +R P+
Sbjct: 158 QSRTIRLPVHLVEQVNKLARIKRELHQQLGREATDEELAEESGIPEEKIADLLEHSRDPV 217

Query: 273 SLDGAVTDRGCMTMQDIIPGPDETMPERMVQKQLMKQELKELLQTLSEREADILRLHFGL 332
           SLD  V       + D I   + T  E  V   L+  +++ +L TL ERE  ++RL FGL
Sbjct: 218 SLDMPVGSDEEAPLGDFIEDSEATSAENAVIAGLLHTDIRSVLATLDEREQQVIRLRFGL 277

Query: 333 DGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQTNILNNLKVY 377
           D   P +  +IG+L  LSRER+RQI    ++KL+     + L+ Y
Sbjct: 278 DDGQPRTLDQIGKLFGLSRERVRQIEREVMSKLRNGERADRLRSY 322

Length = 324

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

 Score =  186 bits (475), Expect = 3e-56
 Identities = 98/276 (35%), Positives = 159/276 (57%), Gaps = 11/276 (3%)

Query: 99  VLKMMRRRSRRKKRTKESDFLDKENGELDYN---LVKYKILCKERESQER----IIRSYR 151
           V +MM     ++   K+   L +E    ++     +    L +  +  +R    +I +  
Sbjct: 45  VQQMMSLLEAKEALAKK---LGREPSLPEWAEAVNLSETELKQTLKQGKRAKQKMIEANL 101

Query: 152 SLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYWWIKQAIIRAIA 211
            LVV+IA  YQ + +   DLIQEG++GL RG ++F+P RGYK STY YWWI+QAI RAIA
Sbjct: 102 RLVVAIAKKYQKRNMEFLDLIQEGTLGLERGVEKFDPTRGYKFSTYAYWWIRQAITRAIA 161

Query: 212 NKSRTIRLPGSMAGMVAKIAEANNVLSRRLRRMPTDSEIAEMLNIHVSTVRLAIERTRHP 271
            ++RTIRLP  +   + KI +    LS++L R  T +EIA+ L +  S +R  +   R P
Sbjct: 162 QQARTIRLPIHITEKLNKIKKTQRELSQKLGRSATPAEIAKELELEPSQIREYLSMARQP 221

Query: 272 ISLDGAVTDRGCMTMQDIIPGPDETMPERMVQKQLMKQELKELLQTLSEREADILRLHFG 331
           ISLD  V D     + +++   +   P++ + ++L++Q+L  LL  L+ ++ ++L L FG
Sbjct: 222 ISLDVRVGDNQDTELSELLED-EGPSPDQYITQELLRQDLNNLLAELTPQQREVLTLRFG 280

Query: 332 LDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQ 367
           L+    +S  ++G  L+LSRER+RQ+   AL  L++
Sbjct: 281 LEDGKELSLAKVGERLNLSRERVRQLEHQALAHLRR 316

Length = 327

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

 Score =  184 bits (469), Expect = 1e-55
 Identities = 90/215 (41%), Positives = 138/215 (64%), Gaps = 1/215 (0%)

Query: 153 LVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYWWIKQAIIRAIAN 212
           LVVS+A  Y  + + L DLIQEG+IG+ RG ++F+P +GY+ STY YWWI+QAI RAIA 
Sbjct: 93  LVVSVAKKYLKRNVDLLDLIQEGTIGMQRGVEKFDPTKGYRFSTYAYWWIRQAITRAIAE 152

Query: 213 KSRTIRLPGSMAGMVAKIAEANNVLSRRLRRMPTDSEIAEMLNIHVSTVRLAIERTRHPI 272
           KSRTIRLP  +   + KI +A   LS++L R  T  E+AE L +    VR  +ER R P+
Sbjct: 153 KSRTIRLPIHITEKLNKIKKAQRQLSQQLGRAATIGELAEELELTPKQVREYLERARQPL 212

Query: 273 SLDGAVTDRGCMTMQDIIPGPDETMPERMVQKQLMKQELKELLQTLSEREADILRLHFGL 332
           SLD  V D     + +++     + PE    +  ++ +L+ L++ L+ ++ +++ L FGL
Sbjct: 213 SLDLRVGDNQDTELGELLEDTGAS-PEDFATQSSLQLDLERLMEDLTPQQKEVIALRFGL 271

Query: 333 DGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQ 367
           +   P++  +IG  L++SRER+RQI   AL+KL++
Sbjct: 272 EDGQPLTLAKIGERLNISRERVRQIEREALSKLRK 306

Length = 317

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

 Score =  186 bits (473), Expect = 5e-55
 Identities = 97/237 (40%), Positives = 147/237 (62%), Gaps = 1/237 (0%)

Query: 142 SQERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYWW 201
           ++E +I++   LVVS+A  YQ +GL L DL+QEG++GL R  ++F+P +GY+ STY YWW
Sbjct: 176 AKEHMIKANLRLVVSVAKKYQNRGLELLDLVQEGTLGLERAVEKFDPTKGYRFSTYAYWW 235

Query: 202 IKQAIIRAIANKSRTIRLPGSMAGMVAKIAEANNVLSRRLRRMPTDSEIAEMLNIHVSTV 261
           I+Q I RAIA +SRTIRLP  +   + KI +A   +S+   R PT  +IA+ L +  + V
Sbjct: 236 IRQGITRAIATQSRTIRLPVHITEKLNKIKKAQRKISQEKGRTPTIEDIAQELEMTPTQV 295

Query: 262 RLAIERTRHPISLDGAVTDRGCMTMQDIIPGPDETMPERMVQKQLMKQELKELLQTLSER 321
           R  + R    +SL+  V       + D++   D+  PE M+ ++ ++++L+ LL  L+ R
Sbjct: 296 REVLLRVPRSVSLETKVGKDKDTELGDLLE-TDDISPEEMLMRESLQRDLQHLLADLTSR 354

Query: 322 EADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQTNILNNLKVYM 378
           E D++R+ FGL      S  EIGR L LSRER+RQI   AL KL+Q    N ++ Y+
Sbjct: 355 ERDVIRMRFGLADGHTYSLAEIGRALDLSRERVRQIESKALQKLRQPKRRNRIRDYL 411

Length = 415

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

 Score =  175 bits (445), Expect = 3e-52
 Identities = 89/230 (38%), Positives = 135/230 (58%)

Query: 139 ERESQERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYV 198
           + E+++ +I S   LVVSIA  Y  +GL L DLI+EG++GL+   ++F+PERG++ STY 
Sbjct: 44  DFEARKVMIESNLRLVVSIAKHYVNRGLPLLDLIEEGNLGLMHAVEKFDPERGFRFSTYA 103

Query: 199 YWWIKQAIIRAIANKSRTIRLPGSMAGMVAKIAEANNVLSRRLRRMPTDSEIAEMLNIHV 258
            WWI+Q I RAI N++RTIRLP  +   +     A   L ++L R P+  EIAE+L+  V
Sbjct: 104 TWWIRQTIERAIMNQARTIRLPVHVIKELNVYLRAARQLEKKLGREPSVEEIAELLDKPV 163

Query: 259 STVRLAIERTRHPISLDGAVTDRGCMTMQDIIPGPDETMPERMVQKQLMKQELKELLQTL 318
             V   +       SLD  + D    ++ D I       PE +VQ   +KQ ++  L  L
Sbjct: 164 EDVSRVLALNERITSLDAPLDDDSSKSLLDTIADEQSIDPESLVQNDDLKQLIEAWLAEL 223

Query: 319 SEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQT 368
           +ER+ ++L   FGL G  P + +E+   + L+RER+RQI+  AL KL++ 
Sbjct: 224 NERQREVLARRFGLLGYEPATLEEVAAEVGLTRERVRQIQVEALKKLRRI 273

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|235640 PRK05901, PRK05901, RNA polymerase sigma factor; Provisional

 Score =  178 bits (454), Expect = 2e-51
 Identities = 92/218 (42%), Positives = 130/218 (59%), Gaps = 10/218 (4%)

Query: 153 LVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYWWIKQAIIRAIAN 212
           LVVS+A  Y  +GLS  DLIQEG++GL++  ++F+  +GYK STY  WWI+QAI RA+A+
Sbjct: 283 LVVSLAKRYTNRGLSFLDLIQEGNLGLIKAVEKFDYTKGYKFSTYATWWIRQAITRAMAD 342

Query: 213 KSRTIRLPGSMAGMVAKIAEANNVLSRRLRRMPTDSEIAEMLNIHVSTVR----LAIERT 268
           ++RTIR+P  M   + K+      L + L R PT  E+A+ +      VR       E  
Sbjct: 343 QARTIRIPVHMVETINKLGRIERELLQELGREPTPEELAKEMGFTPEKVREIQKYNRE-- 400

Query: 269 RHPISLDGAVTDRGCMTMQDIIPGPDETMPERMVQKQLMKQELKELLQTLSEREADILRL 328
             PISLD  +   G     D I   +   P   V   L++ +L+E+L+TLSEREA ++R+
Sbjct: 401 --PISLDKTIGKEGDSQFGDFIEDSEAVSPVDAVSFTLLQDQLQEVLETLSEREAGVIRM 458

Query: 329 HFGL-DGQTPVSCKEIGRLLSLSRERIRQIRGIALTKL 365
            FGL DGQ P +  EIG++  ++RERIRQI    L KL
Sbjct: 459 RFGLTDGQ-PKTLDEIGQVYGVTRERIRQIESKTLRKL 495

Length = 509

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

 Score =  174 bits (442), Expect = 7e-51
 Identities = 91/240 (37%), Positives = 149/240 (62%)

Query: 139 ERESQERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYV 198
           + E+++R+  +   LVVSIA  Y G+G+   DLIQEG++GL++  ++F+  +G+K STY 
Sbjct: 127 DEEAKQRLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNMGLMKAVEKFDYRKGFKFSTYA 186

Query: 199 YWWIKQAIIRAIANKSRTIRLPGSMAGMVAKIAEANNVLSRRLRRMPTDSEIAEMLNIHV 258
            WWI+QAI RAIA+++RTIR+P  M   + K+      L + L R PT  EIAE +++  
Sbjct: 187 TWWIRQAITRAIADQARTIRIPVHMVETINKLIRVQRQLLQELGREPTPEEIAEEMDMPP 246

Query: 259 STVRLAIERTRHPISLDGAVTDRGCMTMQDIIPGPDETMPERMVQKQLMKQELKELLQTL 318
             VR  ++  + P+SL+  + +     + D I   D T P      +L+K++L+++L TL
Sbjct: 247 EKVREILKIAQEPVSLETPIGEEDDSHLGDFIEDQDATSPADHAAYELLKEQLEDVLDTL 306

Query: 319 SEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQTNILNNLKVYM 378
           ++RE ++LRL FGLD     + +E+G++  ++RERIRQI   AL KL+  +    LK ++
Sbjct: 307 TDREENVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRSKQLKDFL 366

Length = 367

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

 Score =  159 bits (405), Expect = 5e-46
 Identities = 86/233 (36%), Positives = 133/233 (57%), Gaps = 12/233 (5%)

Query: 141 ESQERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYW 200
            +++R+I S   LVV IA  Y  +GL+L DLI+EG++GL+R  ++F+PERG++ STY  W
Sbjct: 86  AARQRMIESNLRLVVKIAKRYLNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATW 145

Query: 201 WIKQAIIRAIANKSRTIRLPGSMAGMVAKIAEANNVL------SRRLRRMPTDSEIAEML 254
           WI+Q I RAI N++RTIRLP      V  + E N  L        +L   P+  EIAE+L
Sbjct: 146 WIRQTIERAIMNQTRTIRLP------VHVVKELNVYLRAARELEHKLDHEPSAEEIAELL 199

Query: 255 NIHVSTVRLAIERTRHPISLDGAVTDRGCMTMQDIIPGPDETMPERMVQKQLMKQELKEL 314
           +  V  V   +       SLD  +      ++ DI+    E  PE   Q   MKQ + + 
Sbjct: 200 DKPVDDVSRMLALNERITSLDTPLGGDPEKSLLDILADEQENGPEDTTQDDDMKQSIVKW 259

Query: 315 LQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQ 367
           L  L++++ ++L   FGL G    + +++ R + L+RER+RQI+  AL +L++
Sbjct: 260 LFELNDKQREVLARRFGLLGYEAATLEDVAREIGLTRERVRQIQVEALRRLRE 312

Length = 325

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

 Score =  141 bits (358), Expect = 3e-37
 Identities = 89/228 (39%), Positives = 130/228 (57%), Gaps = 28/228 (12%)

Query: 153 LVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYWWIKQAIIRAIAN 212
           LV+SIA  Y  +GL   DLIQEG+IGL++   +F   RGYK STY  WWI+QAI R+IA+
Sbjct: 392 LVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIAD 451

Query: 213 KSRTIRLPGSMAGMVAKIAEANNVLSRRLRRM-------PTDSEIAEMLNIHVSTVRLAI 265
           ++RTIR+P  M      I E  N L+R  R+M       PT  E+AE L +    VR  +
Sbjct: 452 QARTIRIPVHM------I-ETINKLNRISRQMLQEIGREPTPEELAERLGMPEDKVRKVL 504

Query: 266 ERTRHPISLDGAVTDR-----GCMTMQDIIPGPDETM--PERMVQKQLMKQELKELLQTL 318
           +  + PISL+  + D      G     D I   D+    P     ++ +++   ++L +L
Sbjct: 505 KIAKEPISLETPIGDDEDSHLG-----DFI--EDKNAELPIDAAIQESLREATTDVLASL 557

Query: 319 SEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQ 366
           + REA +LR+ FG+D  T  + +E+G+   ++RERIRQI   AL KL+
Sbjct: 558 TPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 605

Length = 619

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

 Score =  110 bits (278), Expect = 4e-28
 Identities = 76/249 (30%), Positives = 114/249 (45%), Gaps = 33/249 (13%)

Query: 138 KERESQERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTY 197
            + ++ ++++ S+   VV IA GY+G GL   DLIQEG+IGL++  KRF+PERG +L ++
Sbjct: 32  GDLDAAKKLVLSHLRFVVKIARGYRGYGLPQADLIQEGNIGLMKAVKRFDPERGVRLVSF 91

Query: 198 VYWWIKQAIIRAIANKSRTIRLPGSMAGMVAKIA--EANNVLSRRLRRMP-------TDS 248
              WIK  I   I    R  RL         K+A  +A   L   LR+M           
Sbjct: 92  AVHWIKAEIHEYIL---RNWRL--------VKVATTKAQRKLFFNLRKMKKRLQGWLNPE 140

Query: 249 E---IAEMLNIHVSTVRLAIERTRHP-ISLDGAVTDRG------CMTMQDIIPGPDETMP 298
           E   IAE L +    VR    R     +SL+ ++ D           + D    P E   
Sbjct: 141 EVEAIAEELGVSEREVREMESRLSGQDMSLNASIDDDEDDGGAPIAYLVDKRSDP-EDTL 199

Query: 299 ERMVQKQLMKQELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIR 358
           E    ++L +Q L   L +L  R   I+   +  D    ++ +E+     +S ERIRQI 
Sbjct: 200 EEEQWEELQRQALANALGSLDARSRRIIEARWLDD--DKLTLQELAAEYGVSAERIRQIE 257

Query: 359 GIALTKLQQ 367
             A+ KL+ 
Sbjct: 258 KNAMKKLKA 266

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

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

 Score =  107 bits (270), Expect = 2e-27
 Identities = 74/236 (31%), Positives = 121/236 (51%), Gaps = 19/236 (8%)

Query: 139 ERESQERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYV 198
           ++E++E+++     LV SIA  ++ +G   +DL+Q G+IGL++   RF+P  G K ST+ 
Sbjct: 1   DKEAREKLVELNLPLVRSIARRFRNRGEPHEDLVQVGTIGLVKAIDRFDPSYGVKFSTFA 60

Query: 199 YWWIKQAIIRAIANKSRTIRLPGSMAGMVAKIAEANNVLSRRLRRMPTDSEIAEMLNIHV 258
              I   I R   + +  +R+P  +  +  KI +A   L++RL R PT +EIAE L +  
Sbjct: 61  VPTIMGEIKRFFRDDTWAVRVPRRLKELGVKINKATEELTQRLGRSPTIAEIAERLGVSE 120

Query: 259 STVRLAIE--RTRHPISLDGAV--TDRGCMTMQDIIPGPD---ETMPERMVQKQLMKQEL 311
             V  A+E       +SLD ++   D   + + D +   D   ET+ +R+         L
Sbjct: 121 EEVVEALEAGNAYQALSLDASIEDDDGDPIALLDTLGDEDDALETVEDRLA--------L 172

Query: 312 KELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQ 367
           K LL  L ERE  IL L F  + +T     EI   L +S+  + ++   AL KL++
Sbjct: 173 KPLLAALPERERRILLLRF-FEDKTQ---SEIAERLGISQMHVSRLLRRALKKLRE 224

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

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

 Score =  105 bits (263), Expect = 3e-26
 Identities = 74/229 (32%), Positives = 118/229 (51%), Gaps = 13/229 (5%)

Query: 141 ESQERIIRSYRSLVVSIATGYQGKGLSLK-DLIQEGSIGLLRGAKRFNPERGYKLSTYVY 199
           E   R+I  Y  LV SIA  ++ +G S   DLIQ G IGL++  +R++P +G K STY  
Sbjct: 23  EEARRLIERYLPLVKSIARKFENRGPSEYDDLIQIGMIGLIKAIERYDPSKGTKFSTYAV 82

Query: 200 WWIKQAIIRAIANKSRTIRLPGSMAGMVAKIAEANNVLSRRLRRMPTDSEIAEMLNIHVS 259
             I+  I+  +     ++++P S+  +  +I EA + L + L R PTD EIAE L I   
Sbjct: 83  RRIRGEILDYLRKND-SVKVPRSLRELGRRIEEAIDELEQELGREPTDEEIAEELGIDKE 141

Query: 260 TVRLAIERT--RHPISLDGAVTDRGCMTMQDIIPGPDETMPERMVQKQLMKQELKELLQT 317
               A+        +SLD  V       + D I  PD+      V+K+ + + LKE ++ 
Sbjct: 142 EYIEALLAINGSQLLSLDEDVLKDDDDDVDDQIENPDDG-----VEKEELLEILKEAIEP 196

Query: 318 LSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQ 366
           L ERE  +L L +  +    ++ KEI  +L +S  R+ ++   A+ KL+
Sbjct: 197 LPEREKLVLVLRYKEE----LTQKEIAEVLGISESRVSRLHKKAIKKLR 241

Length = 247

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

 Score =  102 bits (257), Expect = 1e-25
 Identities = 72/231 (31%), Positives = 112/231 (48%), Gaps = 19/231 (8%)

Query: 146 IIRSYRSLVVSIA---TGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYWWI 202
           +IR Y  LV  IA   +      + L DLIQ G  GLL   +R++P RG K  TY    I
Sbjct: 1   LIRRYLPLVKRIAGRLSVGLPSSVELDDLIQAGMFGLLDAIERYDPSRGAKFETYAVQRI 60

Query: 203 KQAII---RAIANKSRTIRLPGSMAGMVAKIAEANNVLSRRLRRMPTDSEIAEMLNIHVS 259
           + A++   R +    R++R          K+  A   L  RL R PT+ EIAE L + + 
Sbjct: 61  RGAMLDELRRLDWVPRSLR------QKARKLERAIRELEARLGREPTEEEIAEELGMDLK 114

Query: 260 TVRLAIERTRHP--ISLDGAVTDRG-CMTMQDIIPGPDETMPERMVQKQLMKQELKELLQ 316
             R A+        +SLD  +       ++ D I       PE  ++++ +++ L E ++
Sbjct: 115 EYRQALNEINALSLVSLDELLESGDDGGSLIDRIEDDKSEDPEEELEREELREALAEAIE 174

Query: 317 TLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQ 367
           +LSERE  +L L++       ++ KEIG +L L+  R+ QI   AL KL+ 
Sbjct: 175 SLSEREQLVLSLYY----YEELNLKEIGEVLGLTESRVSQIHSQALKKLRA 221

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

 Score =  103 bits (259), Expect = 3e-25
 Identities = 74/245 (30%), Positives = 121/245 (49%), Gaps = 25/245 (10%)

Query: 138 KERESQERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTY 197
           ++ ++  RII ++  LV+S+A  ++  GL + DLIQEG +GLL  A RF P+R  + STY
Sbjct: 37  RDEDALHRIISAHMRLVISMAGKFRRFGLPMNDLIQEGYVGLLEAAARFEPDREVRFSTY 96

Query: 198 VYWWIKQAIIRAIANKSRTIR---------LPGSMAGMVAKIAEANNVLSR-RLRRMPTD 247
             WWI+ +I   I      +R         L  ++  + A++A+A+  L++  + R    
Sbjct: 97  ATWWIRASIQDYILRNWSIVRGGTSSAQKALFFNLRRLRARLAQADEELTKQEIHRE--- 153

Query: 248 SEIAEMLNIHVSTVRLAIER-------TRHPISLDGAVTDRGCMTMQDIIPGPDETMPER 300
             IA  L + +S V +   R          P S +          + D  P PDE + E 
Sbjct: 154 --IATALGVSLSDVEMMDARLSGPDASLNAPQSEEDEGRSERMDFLVDDSPLPDEQV-ES 210

Query: 301 MVQKQLMKQELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGI 360
            +  +  ++ L + LQTL+ERE  I+R     +     + + +G  L +S+ER+RQI   
Sbjct: 211 SIDGERRRRWLTQALQTLNERELRIIRERRLRE--DGATLEALGEELGISKERVRQIEAR 268

Query: 361 ALTKL 365
           AL KL
Sbjct: 269 ALEKL 273

Length = 289

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

 Score =  102 bits (256), Expect = 7e-25
 Identities = 71/249 (28%), Positives = 113/249 (45%), Gaps = 38/249 (15%)

Query: 140 RESQERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVY 199
            E+ ++++ S+   VV IA GY+G GL   DLIQEG+IGL++  KRF+PE G +L ++  
Sbjct: 47  LEAAKQLVLSHLRFVVHIARGYRGYGLPQADLIQEGNIGLMKAVKRFDPEVGVRLVSFAV 106

Query: 200 WWIKQAIIRAIANKSRTIRLPGSMAGMVAKIA--EANNVLSRRLRRM--------PTD-S 248
            WIK  I   I    R          +V K+A  +A   L   LR+         P +  
Sbjct: 107 HWIKAEIHEYILRNWR----------IV-KVATTKAQRKLFFNLRKAKKRLGWLNPEEVE 155

Query: 249 EIAEMLNIHVSTVRLAIER--TRHPISLDGAVTDRGCMTMQDIIPGPDETM-PERMVQKQ 305
            +AE L +    VR  +E   +    SLD  + D    +        D++  P  ++++ 
Sbjct: 156 MVAEELGVSEEEVR-EMESRLSGQDASLDAPIDDDDEESGAPQDYLEDKSSDPADVLEED 214

Query: 306 ----LMKQELKELLQTLSEREADIL---RLHFGLDGQTPVSCKEIGRLLSLSRERIRQIR 358
                 +  L + L+ L ER  DI+    L          + +E+     +S ER+RQI 
Sbjct: 215 NWEDQRRALLADALEGLDERSRDIIEARWLD-----DDKSTLQELAAEYGVSAERVRQIE 269

Query: 359 GIALTKLQQ 367
             A+ KL+ 
Sbjct: 270 KNAMKKLKA 278

Length = 284

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

 Score = 90.9 bits (226), Expect = 5e-21
 Identities = 69/239 (28%), Positives = 110/239 (46%), Gaps = 17/239 (7%)

Query: 138 KERESQERIIRSYRSLVV----SIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYK 193
           ++ ++ + +IR Y  LV      I+ G   K +S  DL   G +GL    ++F+P R  K
Sbjct: 19  RDPDAADELIRRYMPLVHYHVQRISVGLP-KSVSKDDLKSLGMLGLYDALEKFDPSRDLK 77

Query: 194 LSTYVYWWIKQAIIRAIANKSRTIRLPGSMAGMVAKIAEANNVLSRRLRRMPTDSEIAEM 253
             TY  + I+ AII  +  +     LP SM     K+  A   L +R  R  T  E+A  
Sbjct: 78  FDTYASFRIRGAIIDGLRKED---WLPRSMREKTKKVEAAIEKLEQRYMRNVTPKEVAAE 134

Query: 254 LNIHVSTVRLAIERT--RHPISLDGAVT--DRGCMTMQDIIPGPDETMPERMVQKQLMKQ 309
           L +    V   +      + +S+D      D G   +   I       PE  + K+ + +
Sbjct: 135 LGMTEEEVEATMNEGFFANLLSIDEKTHDQDDG-ENVSVTIRDDKTPTPEEKLLKEELIE 193

Query: 310 ELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQT 368
           EL E ++ LSE+E    +L   L  +  ++  EIG++L+LS  RI QI   AL KL++ 
Sbjct: 194 ELAEKIKQLSEKE----QLVISLFYKEELTLTEIGQVLNLSTSRISQIHSKALFKLKKL 248

Length = 251

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

 Score = 82.6 bits (205), Expect = 6e-20
 Identities = 33/71 (46%), Positives = 46/71 (64%)

Query: 146 IIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYWWIKQA 205
           ++  Y  LV S+A  Y G G   +DL+QEG +GLLR  +RF+PERG   ST++Y  I+ A
Sbjct: 1   LVERYLPLVYSLARRYLGDGADAEDLVQEGFLGLLRAVERFDPERGVSFSTWLYTIIRNA 60

Query: 206 IIRAIANKSRT 216
           II A+  + RT
Sbjct: 61  IIDALRKQRRT 71

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

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

 Score = 84.6 bits (209), Expect = 8e-19
 Identities = 61/249 (24%), Positives = 122/249 (48%), Gaps = 14/249 (5%)

Query: 124 GELDYNLVKYKILCKERESQERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGA 183
            E     +      +  E+QE+++  Y++LV SIA  Y   G   +DL+Q G +GLL   
Sbjct: 12  KEDVIQWIAEFQQNQNGEAQEKLVDHYQNLVYSIAYKYSKGGPMHEDLVQVGMLGLLGAI 71

Query: 184 KRFNPERGYKLSTYVYWWIKQAIIRAIANKSRTIRLPGSMAGMVAKIAEANNVLSRRLRR 243
           +R++   G     +    I   I R + +K+ ++ +P  +  +  KI +A + L+  L+R
Sbjct: 72  RRYDYSIGNAFEPFAIPTIIGEIKRYLRDKTWSVHVPRRIKELGPKIKKAIDELTDHLQR 131

Query: 244 MPTDSEIAEMLNIHVSTVRLAIE--RTRHPISLDGAV---TDRGCMTMQDIIPGPDETMP 298
            P   EIA+ L +    V   +E  ++   +S+D  +   +D   +   D +   ++   
Sbjct: 132 SPKIIEIADHLGLSEEEVLEIMEMGQSYRALSVDDVIEADSDGSTVARLDSVGEVEDGY- 190

Query: 299 ERMVQKQLMKQELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIR 358
               +++++   L+++L  LSERE  I+   F    +  +S KE G  L +S+  + +++
Sbjct: 191 -DQTERRMV---LEKILPILSEREKSIIHCTF----EENLSQKETGERLGISQMHVSRLQ 242

Query: 359 GIALTKLQQ 367
             A++KL++
Sbjct: 243 RQAISKLKE 251

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

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

 Score = 83.6 bits (207), Expect = 2e-18
 Identities = 73/260 (28%), Positives = 139/260 (53%), Gaps = 16/260 (6%)

Query: 114 KESDFLDKENGELDYNLVKYKILCKERESQERIIRSYRSLVVSIATGYQGKGLSL-KDLI 172
           KES    K   E     +      ++ E+QE++++ Y++LV S+A  Y  KG S  +DL+
Sbjct: 2   KESSQPTKLTKEEVNKWIAEYQENQDEEAQEKLVKHYKNLVESLAYKYS-KGQSHHEDLV 60

Query: 173 QEGSIGLLRGAKRFNPERGYKLSTYVYWWIKQAIIRAIANKSRTIRLPGSMAGMVAKIAE 232
           Q G +GLL   +R++P  G     +    I   I R + +K+ ++ +P  +  +  KI +
Sbjct: 61  QVGMVGLLGAIRRYDPSFGRSFEAFAVPTIIGEIKRYLRDKTWSVHVPRRIKELGPKIKK 120

Query: 233 ANNVLSRRLRRMPTDSEIAEMLNIHVSTVRLAIE--RTRHPISLDGAV---TDRGCMTMQ 287
           A + L+  L+R P  SEIA+ L +    V  A+E  ++   +S+D ++   +D   +T+ 
Sbjct: 121 AVDELTTELQRSPKISEIADRLGVSEEEVLEAMEMGKSYQALSVDHSIEADSDGSTVTLL 180

Query: 288 DIIPGPDETMPERMVQKQLMKQELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLL 347
           DI+ G  E   E   +++++   L+++L  LS+RE  I++  F ++    +S KE G  L
Sbjct: 181 DIV-GQQEDGYEL-TEQRMI---LEKILPVLSDREKSIIQCTF-IEN---LSQKETGERL 231

Query: 348 SLSRERIRQIRGIALTKLQQ 367
            +S+  + +++  A+ KL++
Sbjct: 232 GISQMHVSRLQRQAIKKLRE 251

Length = 257

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

 Score = 82.0 bits (203), Expect = 1e-17
 Identities = 66/235 (28%), Positives = 114/235 (48%), Gaps = 25/235 (10%)

Query: 144 ERIIRSYRSLVVSIATGYQGKGL----SLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVY 199
           E +I  Y  LV  +A G    G+       DL+  G  GL+   ++F+PER  K  TY  
Sbjct: 34  EYLILKYSPLVKYVA-GRIAVGMPQNVEFDDLVSYGVFGLIDAIEKFDPEREIKFKTYAV 92

Query: 200 WWIKQAII---RAIANKSRTIRLPGSMAGMVAK-IAEANNVLSRRLRRMPTDSEIAEMLN 255
             I+ AI    R+I    R++R         A+ I  A  +L  RL R P+D EIA+ L 
Sbjct: 93  TRIRGAIFDELRSIDWIPRSVR-------QKARQIERAIAMLEARLGRTPSDEEIADELG 145

Query: 256 IHVSTVRLAIERTR--HPISLDGAVT---DRGCMTMQDIIPGPDETMPERMVQKQLMKQE 310
           I +      + +      +SL+       +   +++ D +  P    P+ + +++ +K+ 
Sbjct: 146 ISLEEYNSLLSKLSGTSVVSLNDLWFGGDEGDEVSLMDTLESPAALNPDEIAEREEIKRV 205

Query: 311 LKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKL 365
           + E ++TL ERE  +L L++  D    ++ KEIG++L ++  RI Q+   A+ +L
Sbjct: 206 IVEAIKTLPEREKKVLILYYYED----LTLKEIGKVLGVTESRISQLHTKAVLQL 256

Length = 268

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

 Score = 79.2 bits (196), Expect = 7e-17
 Identities = 52/170 (30%), Positives = 89/170 (52%), Gaps = 11/170 (6%)

Query: 167 SLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYWWIKQAIIRAIANKSRTIRLPGSMAGM 226
             +DL+Q GS+GL+R  +RF+P +G+  S++   +I+  I   + +KS T+R+P     +
Sbjct: 52  PYEDLVQVGSLGLIRAIERFDPSKGHAFSSFAIPYIRGEIQHYLRDKSPTVRIPRRWQEL 111

Query: 227 VAKIAEANNVLSRRLRRMPTDSEIAEMLNIHVS---TVRLAIERTRHPISLDGAVTD--R 281
             +  +    L + L R PTD EIA+ L+I +     ++LA+ + R P+SLD  V     
Sbjct: 112 QRQAKKVRQELRQELGRQPTDQEIAQALDISLEEWQEIKLAL-QNRTPLSLDAPVNQDED 170

Query: 282 GCMTMQDIIPGPDETMPERMVQKQLMKQ-ELKELLQTLSEREADILRLHF 330
           G  ++ D++P P      R  Q     +  L++ L  L ER  ++L   F
Sbjct: 171 GSTSLGDLLPDPR----YRSFQLAQEDRIRLQQALAQLEERTREVLEFVF 216

Length = 256

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

 Score = 77.0 bits (189), Expect = 4e-16
 Identities = 66/244 (27%), Positives = 115/244 (47%), Gaps = 24/244 (9%)

Query: 138 KERESQERIIRSYRSLVVSIA----TGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYK 193
           +E E ++ +I  Y  LV ++A    +G     +  +DL   G  GL+R  +RF+PE+  +
Sbjct: 20  QEIEYRDVLIEFYLPLVKNVAHRLISGMPSH-VKTEDLYASGVEGLVRAVERFDPEKSRR 78

Query: 194 LSTYVYWWIKQAIIRAIANKSRTIRLPGSMAGMVAKIAEANNVLSRRLRRMPTDSEIAEM 253
              Y  + IK AII  +  +     +P S+     K+A+A + L + L + PTD E+ E 
Sbjct: 79  FEGYALFLIKAAIIDDLRKQD---WVPRSVHQKANKLADAMDSLRQSLGKEPTDGELCEY 135

Query: 254 LNIHVSTVR--LAIERTRHPISLDGAVTDRGC-------MTMQDIIPGPDETMPERMVQK 304
           LNI    +    +  R    +SL+    +  C       + +++ I          +V K
Sbjct: 136 LNISQQELSGWFSSARPALILSLN---EEFPCQSDDEAGLALEERIADERAETGYDVVDK 192

Query: 305 QLMKQELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTK 364
           +     L E +  L E+E  ++ L++  +    +  KEIG++L +S  R+ QI   AL K
Sbjct: 193 KEFSSILAEAILALEEKERKVMALYYYEE----LVLKEIGKILGVSESRVSQIHSKALLK 248

Query: 365 LQQT 368
           L+ T
Sbjct: 249 LRAT 252

Length = 257

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

 Score = 75.7 bits (187), Expect = 8e-16
 Identities = 66/246 (26%), Positives = 117/246 (47%), Gaps = 34/246 (13%)

Query: 137 CKERESQERIIRSYRSLVVSIATGYQGKG-----LSLKDLIQEGSIGLLRGAKRFNPERG 191
            + +  Q+ ++  Y  LV  IA   + K      + L DLIQ G IGLL  A+R++ E+G
Sbjct: 4   AEGKMDQDELVEQYAPLVKRIA--LRLKARLPASVDLDDLIQAGMIGLLEAARRYDGEQG 61

Query: 192 YKLSTYVYWWIKQAI---IRAIANKSRTIRLPGSMAGMVAKIAEANNVLSRRLRRMPTDS 248
               TY    I+ A+   +R++    R++R           +A+A   L + L R PTD+
Sbjct: 62  ASFETYAGQRIRGAMLDELRSLDWVPRSVRRNARE------VAQAIRQLEQELGREPTDT 115

Query: 249 EIAEMLNIHVSTVRLA-----IERTRHPISLD--GAVTDRGCMTMQDIIPGPDETMPERM 301
           E+AE L + +   R       I +     S+D          +  +D      +  P + 
Sbjct: 116 EVAEKLGLSLEEYREMLLDTNISQL---FSIDELRGEHGDSILVTEDH----QDEDPLQQ 168

Query: 302 VQKQLMKQELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIA 361
           ++ + +++ L E +++L ERE  +L L++    Q  ++ KEIG +L +S  R+ QI   A
Sbjct: 169 LEDEELREALVEAIESLPEREQLVLSLYY----QEELNLKEIGAVLGVSESRVSQIHSQA 224

Query: 362 LTKLQQ 367
           + +L+ 
Sbjct: 225 IKRLRA 230

Length = 236

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

 Score = 71.4 bits (175), Expect = 3e-14
 Identities = 63/232 (27%), Positives = 113/232 (48%), Gaps = 12/232 (5%)

Query: 139 ERESQERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYV 198
           +  ++E++I     LV+S+   +  +G  + DL Q G IGL++    F+  +  K STY 
Sbjct: 32  DTTAREKLINGNLRLVLSVIQRFNNRGEYVDDLFQVGCIGLMKSIDNFDLSQNVKFSTYA 91

Query: 199 YWWIKQAIIRAIANKSRTIRLPGSMAGMVAKIAEANNVLSRRLRRMPTDSEIAEMLNIHV 258
              I   I R + + +  IR+  S+  +  K  +  + L     + PT SEIA+ L +  
Sbjct: 92  VPMIIGEIRRYLRDNN-PIRVSRSLRDIAYKALQVRDKLISENSKEPTVSEIAKELKVPQ 150

Query: 259 STVRLAIERTRHPISLDGAVTDRGCMTMQDIIPGPDETMPERMVQKQ-LMKQELKELLQT 317
             V  A++  + P+SL   + + G     D I   D+   E+    Q L    LKE ++ 
Sbjct: 151 EEVVFALDAIQDPVSLFEPIYNDG----GDPIYVMDQISDEKNKDSQWLEGIALKEAMKR 206

Query: 318 LSEREADILRLHFGLDGQTPVS-CKEIGRLLSLSRERIRQIRGIALTKLQQT 368
           L+ERE  IL + F  +G+T +   +EIG    +S+ ++ ++   AL  +++ 
Sbjct: 207 LNEREKMILNMRF-FEGKTQMEVAEEIG----ISQAQVSRLEKAALKHMRKY 253

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

 Score = 70.4 bits (173), Expect = 7e-14
 Identities = 67/223 (30%), Positives = 104/223 (46%), Gaps = 15/223 (6%)

Query: 110 KKRTKESDFLDKENGELDYNLVKYKILCKERESQERIIRSYRSLVVSIATGYQGKGLSLK 169
           K + K+    D+EN EL   + K +    ++E+++ ++     LV S+   +  +G    
Sbjct: 6   KNKKKKPQLKDEENKEL---IKKSQ--DGDQEARDTLVEKNLRLVWSVVQRFLNRGYEPD 60

Query: 170 DLIQEGSIGLLRGAKRFNPERGYKLSTYVYWWIKQAIIRAIANKSRTIRLPGSMAGMVAK 229
           DL Q G IGLL+   +F+     K STY    I   I R + +   T+++  S+     K
Sbjct: 61  DLFQIGCIGLLKAVDKFDLSYDVKFSTYAVPMIIGEIQRFLRDDG-TVKVSRSLKETANK 119

Query: 230 IAEANNVLSRRLRRMPTDSEIAEMLNIHVSTVRLAIERTRHPISLDGAV--TDRGCMTMQ 287
           I +  + LS+ L R PT  E+AE L +    V LA E +R P S+   V   D   +T+ 
Sbjct: 120 IRKDKDELSKELGREPTIEELAEYLGVTPEEVVLAQEASRSPQSIHETVHENDGDPITLL 179

Query: 288 DIIPGPDETMPERMVQKQLMKQELKELLQTLSEREADILRLHF 330
           D I    E   E        K  LKE ++ L ERE  I+ L +
Sbjct: 180 DQIADQSE---EDWFD----KIALKEAIRELDERERLIVYLRY 215

Length = 252

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

 Score = 67.8 bits (166), Expect = 4e-13
 Identities = 66/234 (28%), Positives = 111/234 (47%), Gaps = 18/234 (7%)

Query: 139 ERESQERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYV 198
           ++E+++++I     LV SI   +  +G   +DL Q G IGL++   +F+     K STY 
Sbjct: 9   DKEARDKLIECNLRLVWSIVKRFLNRGYEPEDLFQIGCIGLVKAIDKFDLSYDVKFSTYA 68

Query: 199 YWWIKQAIIRAIANKSRTIRLPGSMAGMVAKIAEANNVLSRRLRRMPTDSEIAEMLNIHV 258
              I   I R + +    I++  S+  +  KI      LS+ L R PT +E+AE L +  
Sbjct: 69  VPMIMGEIKRFLRDDG-IIKVSRSLKELARKIRYMKEELSKELGREPTINELAEALGVSP 127

Query: 259 STVRLAIERTRHPISLDGAV--TDRGCMTMQDII--PGPDETMPERMVQKQLMKQELKEL 314
             + +A+E  R P SL   V   D   + + D I   G ++          L K  LKE 
Sbjct: 128 EEIVMALESARSPQSLYDTVHQDDGDPIYLLDQIADKGSED-------SDWLEKIALKEA 180

Query: 315 LQTLSEREADILRLHFGLD-GQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQ 367
           +  L ERE  I+ L +  D  QT     E+  +L +S+ ++ ++    L K+++
Sbjct: 181 ISKLDERERQIIMLRYFKDKTQT-----EVANMLGISQVQVSRLEKKVLKKMKE 229

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

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

 Score = 65.4 bits (160), Expect = 7e-13
 Identities = 46/227 (20%), Positives = 82/227 (36%), Gaps = 71/227 (31%)

Query: 141 ESQERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYW 200
           E+ E +   Y  LV   A  Y G     +DL+QE  + LL    RF+PE       +++ 
Sbjct: 1   EAFEELYERYLPLVYRYARRYLGDDADAEDLVQEAFLKLLEALDRFDPE--GSFKAWLFR 58

Query: 201 WIKQAIIRAIANKSRTIRLPGSMAGMVAKIAEANNVLSRRLRRMPTDSEIAEMLNIHVST 260
             +                               N++   LRR        ++L      
Sbjct: 59  IAR-------------------------------NLILDYLRRKRRLRRELDLL------ 81

Query: 261 VRLAIERTRHPISLDGAVTDRGCMTMQDIIPGPDETMPERMVQKQLMKQELKELLQTLSE 320
                                    + D  P P+E      ++++  ++ L+E L+ L E
Sbjct: 82  -----------------------EELLDSDPSPEEE-----LEQEEEREALREALEKLPE 113

Query: 321 READILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQ 367
           RE ++L L + L+G +    KEI  +L +S   +++    A  KL++
Sbjct: 114 REREVLVLRY-LEGLSY---KEIAEILGISVGTVKRRLKRARKKLRE 156

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

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

 Score = 65.7 bits (161), Expect = 3e-12
 Identities = 59/209 (28%), Positives = 103/209 (49%), Gaps = 10/209 (4%)

Query: 139 ERESQERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYV 198
           ++E++E++I     LV+S+   +  +G ++ DL Q G IGL++    F+  +  K STY 
Sbjct: 35  DKEAREKLINGNLRLVLSVIQRFNNRGENVDDLFQVGCIGLMKAIDNFDLSQNVKFSTYA 94

Query: 199 YWWIKQAIIRAIANKSRTIRLPGSMAGMVAKIAEANNVLSRRLRRMPTDSEIAEMLNIHV 258
              I   I R + + +  IR+  S+  +  K  +    L     + PT  EIA+ L +  
Sbjct: 95  VPMIIGEIRRYLRDNN-PIRVSRSLRDIAYKALQVREKLINENSKEPTVEEIAKELEVPR 153

Query: 259 STVRLAIERTRHPISL-DGAVTDRGCMTMQDIIPGPDETMPERMVQKQLMKQ-ELKELLQ 316
             V  A++  + P+SL +    D G     D I   D+   E+   +  +++  LKE ++
Sbjct: 154 EEVVFALDAIQDPVSLFEPIYHDGG-----DPIYVMDQISDEKNKDENWLEEIALKEAMK 208

Query: 317 TLSEREADILRLHFGLDGQTPVS-CKEIG 344
            L++RE  IL L F   G+T +   +EIG
Sbjct: 209 KLNDREKLILNLRF-FQGKTQMEVAEEIG 236

Length = 258

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

 Score = 65.2 bits (159), Expect = 4e-12
 Identities = 59/226 (26%), Positives = 99/226 (43%), Gaps = 20/226 (8%)

Query: 143 QERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYWWI 202
           ++RI+     L   IA  + G+G    DL+Q   +GL+    RF+ E G    ++    I
Sbjct: 42  RDRIVTRCLPLADHIARRFDGRGEPRDDLVQVARVGLVNAVNRFDVETGSDFVSFAVPTI 101

Query: 203 KQAIIRAIANKSRTIRLPGSMAGMVAKIAEANNVLSRRLRRMPTDSEIAEMLNIHVSTV- 261
              + R   + S ++++P  +  +  ++  A   LS+RL R PT SE+A  L +    V 
Sbjct: 102 MGEVRRHFRDNSWSVKVPRRLKELHLRLGRATAELSQRLGRAPTASELAAELGMDREEVV 161

Query: 262 -RLAIERTRHPISLD--GAVTDRGCMTMQDIIPGPDETMPERMVQKQLMKQE-LKELLQT 317
             L      + +S+D  G   D     + D +   D  +       Q+  +E L+ LL  
Sbjct: 162 EGLVAGSAYNTLSIDSGGGSGDDDARAIADTLGDVDAGL------DQIENREALRPLLAA 215

Query: 318 LSEREADILRLHFGLDGQTP--------VSCKEIGRLLSLSRERIR 355
           L ERE  +L L F  +  T         +S   + RLL+ +  R+R
Sbjct: 216 LPERERTVLVLRF-FESMTQTQIAERVGISQMHVSRLLAKTLARLR 260

Length = 264

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

 Score = 62.0 bits (151), Expect = 4e-11
 Identities = 48/227 (21%), Positives = 95/227 (41%), Gaps = 50/227 (22%)

Query: 139 ERESQERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYV 198
           + E++  +I     LV  I   +   G  + DLI  G+IGL++    F+P++G +L+TY 
Sbjct: 46  DEEARNVLIERNLRLVAHIVKKFSNTGEDVDDLISIGTIGLIKAIDSFDPDKGTRLATYA 105

Query: 199 YWWIKQAIIRAIANKSRTIRLPGSMAGMVAKIAEANNVLSRRLRRMPTDSEIAEMLNIHV 258
              I+  I+  +                            R L++   +  + +      
Sbjct: 106 ARCIENEILMHL----------------------------RALKKTKGEVSLQD------ 131

Query: 259 STVRLAIERTRHPISLDGAVTDRGCMTMQDIIPGPDETMPERMVQKQLMKQELKELLQTL 318
                       PI +D    +   +++ DI+    +++ E  V+  L  ++L + L  L
Sbjct: 132 ------------PIGVDKEGNE---ISLIDILGSDGDSVIE-QVELNLEIKKLYKKLSVL 175

Query: 319 SEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKL 365
             RE +++ + +GL      + +EI ++L +SR  + +I   AL KL
Sbjct: 176 DGREREVIEMRYGLGDGRRKTQREIAKILGISRSYVSRIEKRALMKL 222

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

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

 Score = 55.3 bits (134), Expect = 4e-10
 Identities = 28/74 (37%), Positives = 35/74 (47%)

Query: 229 KIAEANNVLSRRLRRMPTDSEIAEMLNIHVSTVRLAIERTRHPISLDGAVTDRGCMTMQD 288
           KI  A   L + L R PT  EIAE L I    VR  +E  R P+SLD  V +     + D
Sbjct: 5   KIKRAQRELEQELGREPTPEEIAEELGISEEKVREVLEAAREPVSLDLPVGEEEDGELGD 64

Query: 289 IIPGPDETMPERMV 302
           ++   D   PE  V
Sbjct: 65  LLEDDDAESPEDAV 78

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

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

 Score = 58.7 bits (142), Expect = 5e-10
 Identities = 57/224 (25%), Positives = 101/224 (45%), Gaps = 55/224 (24%)

Query: 146 IIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYWWIKQA 205
           I R+ R LVV IA  ++  G+ ++DL+  G+IGL++    FNP +  KL+TY        
Sbjct: 58  IERNLR-LVVYIARKFENTGIGIEDLVSIGTIGLIKAVNTFNPSKKIKLATYA------- 109

Query: 206 IIRAIANKSRTIRLPGSMAGMVAKIAEANNVLSRRLRRMPTDSEIA--EMLNIHVSTVRL 263
                   SR I                N +L    R   T SE++  E LN+       
Sbjct: 110 --------SRCIE---------------NEILMYLRRNNKTRSEVSFDEPLNVD------ 140

Query: 264 AIERTRHPISLDGAVTDRGCMTMQDIIPGPDETMPERMVQKQLMKQELKELLQTLSEREA 323
                           D   + + D++ G D  +  + +++++ ++ L++ L  L++RE 
Sbjct: 141 ---------------WDGNELLLSDVL-GTDSDIVYKYLEEEVDRELLRKALAKLNDREK 184

Query: 324 DILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQ 367
            I+ L FGL G T  + KE+  +L +S+  I ++    L +L++
Sbjct: 185 KIMELRFGLVGGTEKTQKEVADMLGISQSYISRLEKRILKRLKK 228

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

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

 Score = 48.6 bits (117), Expect = 4e-08
 Identities = 23/54 (42%), Positives = 33/54 (61%), Gaps = 4/54 (7%)

Query: 314 LLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQ 367
            L +L  RE ++L L FG      ++ +EIG  L +SRER+RQI   AL KL++
Sbjct: 1   ALASLPPREREVLVLRFG----EGLTLEEIGERLGISRERVRQIEKRALRKLRK 50

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

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

 Score = 50.3 bits (121), Expect = 4e-07
 Identities = 21/81 (25%), Positives = 45/81 (55%), Gaps = 1/81 (1%)

Query: 285 TMQDIIPGPDETMPERMVQKQLMKQELKELLQTLSEREADILRLHFGLDGQTPVSCKEIG 344
           ++ DI+   ++ + E  V+ ++  ++L + +  L ERE +++ + +GL      + +EI 
Sbjct: 144 SLIDILGSEEDDVIE-QVELKMEVEKLYKKIDILDEREKEVIEMRYGLGNGKEKTQREIA 202

Query: 345 RLLSLSRERIRQIRGIALTKL 365
           + L +SR  + +I   AL KL
Sbjct: 203 KALGISRSYVSRIEKRALKKL 223

Length = 233

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

 Score = 45.9 bits (110), Expect = 5e-07
 Identities = 22/59 (37%), Positives = 33/59 (55%), Gaps = 4/59 (6%)

Query: 308 KQELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQ 366
           ++ L+E L  L ERE +++ L FG       S +EI  +L +SR  +RQ    AL KL+
Sbjct: 1   RERLEEALDKLPEREREVILLRFGEGL----SYEEIAEILGISRSTVRQRLHRALKKLR 55

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

>gnl|CDD|181361 PRK08295, PRK08295, RNA polymerase factor sigma-70; Validated

 Score = 49.1 bits (118), Expect = 7e-07
 Identities = 50/208 (24%), Positives = 90/208 (43%), Gaps = 56/208 (26%)

Query: 140 RESQERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVY 199
           +E+ E +I  Y++ V + A  Y   G   +D++QEG IGL +  + ++ ++     ++  
Sbjct: 23  KEALEYLIEKYKNFVRAKARSYFLIGADREDIVQEGMIGLYKAIRDYDKDKLSSFKSFAE 82

Query: 200 WWIKQAIIRAI--ANKSRTIRLPGSMAGMVAKIAEANNVLSRRLRRMPTDSEIAEMLNIH 257
             I + II AI  AN+ + I                                    LN +
Sbjct: 83  LCITRQIITAIKTANRQKHI-----------------------------------PLNSY 107

Query: 258 VSTVRLAIERTRHPISLDGAVTDRGCMTMQDIIPGPDETMPERMV-QKQLMKQELKELLQ 316
           VS  +        PI  +   +DR   T+ D+I     T PE ++  K+ ++   +++ +
Sbjct: 108 VSLDK--------PIYDEE--SDR---TLLDVISEAKVTDPEELIISKEELEDIEEKIEE 154

Query: 317 TLSEREADILRLHFGLDGQTPVSCKEIG 344
            LSE E ++L L+  LDG+   S +EI 
Sbjct: 155 LLSELEKEVLELY--LDGK---SYQEIA 177

Length = 208

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

 Score = 44.8 bits (107), Expect = 2e-05
 Identities = 24/54 (44%), Positives = 36/54 (66%), Gaps = 4/54 (7%)

Query: 144 ERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTY 197
           ER +R    LVV IA  ++  G++++DLI  G+IGL++    FNPE+  KL+TY
Sbjct: 59  ERNLR----LVVYIARKFENTGINIEDLISIGTIGLIKAVNTFNPEKKIKLATY 108

Length = 234

>gnl|CDD|183523 PRK12427, PRK12427, flagellar biosynthesis sigma factor; Provisional

 Score = 43.3 bits (102), Expect = 7e-05
 Identities = 49/205 (23%), Positives = 95/205 (46%), Gaps = 29/205 (14%)

Query: 169 KDLIQEGSIGLLRGAKRFN-PERGYKLSTYVYWWIKQAII---RAIANKSRTIRLPGSMA 224
           +D+ Q   +GLL   +R+  P+  +  + Y    I+ AI+   R +  + R +R      
Sbjct: 46  EDMEQIALMGLLEALRRYGHPDEQF--AAYAVHRIRGAILDELRELDWRPRRLR------ 97

Query: 225 GMVAKIAEANNVLSRRLRRMPTDSEIAEMLNIHVSTVRLAIERTRHPISLDGAVTDRGCM 284
               K  +A   +++RL   P   EI+  LN+         E  +  + L+ A T     
Sbjct: 98  QKTHKTNDAIREIAKRLGHEPNFEEISAELNL-------TAEEYQEYLLLENAGT---LE 147

Query: 285 TMQDII--PGPDETMPERMVQKQLMKQE-LKELLQTLSEREADILRLHFGLDGQTPVSCK 341
           ++ +++     ++ +  R +++ ++ ++ LK+ L  L ERE  IL L++    Q  +S K
Sbjct: 148 SLDELLALEAHNDILQSRDLEENIIIEDNLKQALSQLDEREQLILHLYY----QHEMSLK 203

Query: 342 EIGRLLSLSRERIRQIRGIALTKLQ 366
           EI  +L L+  RI Q+      K++
Sbjct: 204 EIALVLDLTEARICQLNKKIAQKIK 228

Length = 231

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

 Score = 43.0 bits (102), Expect = 1e-04
 Identities = 17/45 (37%), Positives = 27/45 (60%)

Query: 153 LVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTY 197
           LV  I   ++  G  + DLI  G+IGL++  + F+  +G KL+TY
Sbjct: 61  LVAHIVKKFENTGEDVDDLISIGTIGLIKAIESFDAGKGTKLATY 105

Length = 233

>gnl|CDD|131906 TIGR02859, spore_sigH, RNA polymerase sigma-H factor

 Score = 41.7 bits (98), Expect = 2e-04
 Identities = 23/79 (29%), Positives = 39/79 (49%)

Query: 142 SQERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYWW 201
           + E +I  Y++ V + A  Y   G   +D+IQEG IGL +  + F P++      +    
Sbjct: 20  ALEYLINKYKNFVRAKARSYFLIGADKEDIIQEGMIGLYKAIRDFRPDKLSSFKAFAELC 79

Query: 202 IKQAIIRAIANKSRTIRLP 220
           + + II AI   +R   +P
Sbjct: 80  VTRQIITAIKTATRQKHIP 98

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 in Listeria score above the noise cutoff to This model, Listeria does not form spores and the role of the related sigma factor in that genus is in doubt [Transcription, Transcription factors, Cellular processes, Sporulation and germination]. Length = 198

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	379
PRK09210	367	RNA polymerase sigma factor RpoD; Validated	100.0
PRK07921	324	RNA polymerase sigma factor SigB; Reviewed	100.0
PRK05658	619	RNA polymerase sigma factor RpoD; Validated	100.0
PRK05901	509	RNA polymerase sigma factor; Provisional	100.0
COG0568	342	RpoD DNA-directed RNA polymerase, sigma subunit (s	100.0
PRK07598	415	RNA polymerase sigma factor SigC; Validated	100.0
PRK05949	327	RNA polymerase sigma factor; Validated	100.0
PRK07406	373	RNA polymerase sigma factor RpoD; Validated	100.0
TIGR02393	238	RpoD_Cterm RNA polymerase sigma factor RpoD, C-ter	100.0
PRK07405	317	RNA polymerase sigma factor SigD; Validated	100.0
TIGR02997	298	Sig70-cyanoRpoD RNA polymerase sigma factor, cyano	100.0
PRK07408	256	RNA polymerase sigma factor SigF; Reviewed	100.0
PRK05657	325	RNA polymerase sigma factor RpoS; Validated	100.0
PRK07122	264	RNA polymerase sigma factor SigF; Reviewed	100.0
COG1191	247	FliA DNA-directed RNA polymerase specialized sigma	100.0
PRK05911	257	RNA polymerase sigma factor sigma-28; Reviewed	100.0
PRK07500	289	rpoH2 RNA polymerase factor sigma-32; Reviewed	100.0
PRK06596	284	RNA polymerase factor sigma-32; Reviewed	100.0
TIGR02850	254	spore_sigG RNA polymerase sigma-G factor. Members	100.0
TIGR02394	285	rpoS_proteo RNA polymerase sigma factor RpoS. A si	100.0
TIGR02392	270	rpoH_proteo alternative sigma factor RpoH. A sigma	100.0
PRK08215	258	sporulation sigma factor SigG; Reviewed	100.0
TIGR02885	231	spore_sigF RNA polymerase sigma-F factor. Members	100.0
TIGR02941	255	Sigma_B RNA polymerase sigma-B factor. This sigma	100.0
PRK07670	251	RNA polymerase sigma factor SigD; Validated	100.0
TIGR02980	227	SigBFG RNA polymerase sigma-70 factor, sigma-B/F/G	100.0
PRK06288	268	RNA polymerase sigma factor WhiG; Reviewed	100.0
PRK05572	252	sporulation sigma factor SigF; Validated	100.0
PRK08583	257	RNA polymerase sigma factor SigB; Validated	100.0
TIGR02479	224	FliA_WhiG RNA polymerase sigma factor, FliA/WhiG f	100.0
PRK06986	236	fliA flagellar biosynthesis sigma factor; Validate	100.0
PRK12427	231	flagellar biosynthesis sigma factor; Provisional	100.0
PRK05803	233	sporulation sigma factor SigK; Reviewed	99.96
PRK08301	234	sporulation sigma factor SigE; Reviewed	99.96
TIGR02846	227	spore_sigmaK RNA polymerase sigma-K factor. The sp	99.95
PRK08295	208	RNA polymerase factor sigma-70; Validated	99.95
TIGR02835	234	spore_sigmaE RNA polymerase sigma-E factor. Member	99.95
PRK05602	186	RNA polymerase sigma factor; Reviewed	99.95
PRK09646	194	RNA polymerase sigma factor SigK; Reviewed	99.95
TIGR02948	187	SigW_bacill RNA polymerase sigma-W factor. This si	99.94
PRK12513	194	RNA polymerase sigma factor; Provisional	99.94
PRK09648	189	RNA polymerase sigma factor SigD; Reviewed	99.94
PRK09641	187	RNA polymerase sigma factor SigW; Provisional	99.94
TIGR02859	198	spore_sigH RNA polymerase sigma-H factor. Members	99.94
TIGR02952	170	Sig70_famx2 RNA polymerase sigma-70 factor, TIGR02	99.94
PRK12537	182	RNA polymerase sigma factor; Provisional	99.94
PRK12524	196	RNA polymerase sigma factor; Provisional	99.94
TIGR02939	190	RpoE_Sigma70 RNA polymerase sigma factor RpoE. A s	99.93
PRK12514	179	RNA polymerase sigma factor; Provisional	99.93
PRK12538	233	RNA polymerase sigma factor; Provisional	99.93
PRK11923	193	algU RNA polymerase sigma factor AlgU; Provisional	99.93
PRK12519	194	RNA polymerase sigma factor; Provisional	99.93
PRK09652	182	RNA polymerase sigma factor RpoE; Provisional	99.93
PRK13919	186	putative RNA polymerase sigma E protein; Provision	99.93
PRK06811	189	RNA polymerase factor sigma-70; Validated	99.93
PRK12531	194	RNA polymerase sigma factor; Provisional	99.93
PRK12542	185	RNA polymerase sigma factor; Provisional	99.93
PRK09643	192	RNA polymerase sigma factor SigM; Reviewed	99.93
PRK12515	189	RNA polymerase sigma factor; Provisional	99.93
PRK12534	187	RNA polymerase sigma factor; Provisional	99.93
PRK11922	231	RNA polymerase sigma factor; Provisional	99.93
PRK06759	154	RNA polymerase factor sigma-70; Validated	99.92
TIGR02954	169	Sig70_famx3 RNA polymerase sigma-70 factor, TIGR02	99.92
TIGR02984	189	Sig-70_plancto1 RNA polymerase sigma-70 factor, Pl	99.92
PRK12526	206	RNA polymerase sigma factor; Provisional	99.92
PRK11924	179	RNA polymerase sigma factor; Provisional	99.92
TIGR03001	244	Sig-70_gmx1 RNA polymerase sigma-70 factor, Myxoco	99.92
PRK09640	188	RNA polymerase sigma factor SigX; Reviewed	99.92
PRK09649	185	RNA polymerase sigma factor SigC; Reviewed	99.92
PRK12543	179	RNA polymerase sigma factor; Provisional	99.92
PRK12536	181	RNA polymerase sigma factor; Provisional	99.92
PRK12539	184	RNA polymerase sigma factor; Provisional	99.92
PRK09638	176	RNA polymerase sigma factor SigY; Reviewed	99.92
PRK09645	173	RNA polymerase sigma factor SigL; Provisional	99.92
TIGR02999	183	Sig-70_X6 RNA polymerase sigma factor, TIGR02999 f	99.91
PRK12518	175	RNA polymerase sigma factor; Provisional	99.91
PRK12529	178	RNA polymerase sigma factor; Provisional	99.91
PRK12512	184	RNA polymerase sigma factor; Provisional	99.91
PRK12520	191	RNA polymerase sigma factor; Provisional	99.91
PRK12535	196	RNA polymerase sigma factor; Provisional	99.91
PRK09415	179	RNA polymerase factor sigma C; Reviewed	99.91
COG1595	182	RpoE DNA-directed RNA polymerase specialized sigma	99.9
PRK12522	173	RNA polymerase sigma factor; Provisional	99.9
TIGR02947	193	SigH_actino RNA polymerase sigma-70 factor, TIGR02	99.9
PRK12523	172	RNA polymerase sigma factor; Reviewed	99.9
PRK12516	187	RNA polymerase sigma factor; Provisional	99.9
TIGR02983	162	SigE-fam_strep RNA polymerase sigma-70 factor, sig	99.9
PRK12533	216	RNA polymerase sigma factor; Provisional	99.9
PRK08241	339	RNA polymerase factor sigma-70; Validated	99.9
PRK09647	203	RNA polymerase sigma factor SigE; Reviewed	99.9
TIGR02989	159	Sig-70_gvs1 RNA polymerase sigma-70 factor, Rhodop	99.9
TIGR02985	161	Sig70_bacteroi1 RNA polymerase sigma-70 factor, Ba	99.89
PRK09642	160	RNA polymerase sigma factor SigW; Reviewed	99.89
TIGR02960	324	SigX5 RNA polymerase sigma-70 factor, TIGR02960 fa	99.89
PRK09644	165	RNA polymerase sigma factor SigM; Provisional	99.89
PRK12541	161	RNA polymerase sigma factor; Provisional	99.89
TIGR02943	188	Sig70_famx1 RNA polymerase sigma-70 factor, TIGR02	99.88
PRK12545	201	RNA polymerase sigma factor; Provisional	99.88
PRK12530	189	RNA polymerase sigma factor; Provisional	99.88
PRK12547	164	RNA polymerase sigma factor; Provisional	99.88
PRK12532	195	RNA polymerase sigma factor; Provisional	99.88
PRK12528	161	RNA polymerase sigma factor; Provisional	99.88
PRK12544	206	RNA polymerase sigma factor; Provisional	99.88
PRK09639	166	RNA polymerase sigma factor SigX; Provisional	99.88
PRK12517	188	RNA polymerase sigma factor; Provisional	99.87
TIGR02937	158	sigma70-ECF RNA polymerase sigma factor, sigma-70	99.87
PRK09651	172	RNA polymerase sigma factor FecI; Provisional	99.87
PRK09637	181	RNA polymerase sigma factor SigZ; Provisional	99.87
PRK12540	182	RNA polymerase sigma factor; Provisional	99.87
PRK12527	159	RNA polymerase sigma factor; Reviewed	99.86
TIGR02950	154	SigM_subfam RNA polymerase sigma factor, SigM fami	99.86
PRK07037	163	extracytoplasmic-function sigma-70 factor; Validat	99.86
PRK12511	182	RNA polymerase sigma factor; Provisional	99.86
PRK12546	188	RNA polymerase sigma factor; Provisional	99.85
TIGR02959	170	SigZ RNA polymerase sigma factor, SigZ family. Thi	99.85
PRK12525	168	RNA polymerase sigma factor; Provisional	99.84
TIGR02895	218	spore_sigI RNA polymerase sigma-I factor. Members	99.84
PRK06704	228	RNA polymerase factor sigma-70; Validated	99.84
PRK09636	293	RNA polymerase sigma factor SigJ; Provisional	99.83
PRK09047	161	RNA polymerase factor sigma-70; Validated	99.82
PRK09635	290	sigI RNA polymerase sigma factor SigI; Provisional	99.8
TIGR02957	281	SigX4 RNA polymerase sigma-70 factor, TIGR02957 fa	99.79
PF07638	185	Sigma70_ECF: ECF sigma factor	99.73
TIGR03209	142	P21_Cbot clostridium toxin-associated regulator Bo	99.71
PRK08311	237	putative RNA polymerase sigma factor SigI; Reviewe	99.7
PRK09191	261	two-component response regulator; Provisional	99.69
PF04542	71	Sigma70_r2: Sigma-70 region 2 ; InterPro: IPR00762	99.43
PF04545	50	Sigma70_r4: Sigma-70, region 4; InterPro: IPR00763	99.28
PF08281	54	Sigma70_r4_2: Sigma-70, region 4; InterPro: IPR013	99.08
PF04539	78	Sigma70_r3: Sigma-70 region 3; InterPro: IPR007624	98.97
PRK06930	170	positive control sigma-like factor; Validated	98.87
PRK00118	104	putative DNA-binding protein; Validated	98.72
cd06171	55	Sigma70_r4 Sigma70, region (SR) 4 refers to the mo	98.55
TIGR00721	137	tfx DNA-binding protein, Tfx family. Tfx from Meth	98.42
PRK03975	141	tfx putative transcriptional regulator; Provisiona	98.38
PRK04217	110	hypothetical protein; Provisional	98.36
PF04297	101	UPF0122: Putative helix-turn-helix protein, YlxM /	98.22
smart00421	58	HTH_LUXR helix_turn_helix, Lux Regulon. lux regulo	98.12
COG4941	415	Predicted RNA polymerase sigma factor containing a	98.11
TIGR01636	134	phage_rinA phage transcriptional activator, RinA f	98.08
PF00196	58	GerE: Bacterial regulatory proteins, luxR family;	98.06
cd06170	57	LuxR_C_like C-terminal DNA-binding domain of LuxR-	97.98
TIGR03879	73	near_KaiC_dom probable regulatory domain. This mod	97.96
PF07374	100	DUF1492: Protein of unknown function (DUF1492); In	97.94
PF12645	65	HTH_16: Helix-turn-helix domain; InterPro: IPR0247	97.89
PF04967	53	HTH_10: HTH DNA binding domain; InterPro: IPR00705	97.87
PRK15201	198	fimbriae regulatory protein FimW; Provisional	97.81
PRK15411	207	rcsA colanic acid capsular biosynthesis activation	97.8
PRK13719	217	conjugal transfer transcriptional regulator TraJ;	97.78
COG4566	202	TtrR Response regulator [Signal transduction mecha	97.76
TIGR01321	94	TrpR trp operon repressor, proteobacterial. This m	97.73
PRK11475	207	DNA-binding transcriptional activator BglJ; Provis	97.73
PF02001	106	DUF134: Protein of unknown function DUF134; InterP	97.68
PRK10840	216	transcriptional regulator RcsB; Provisional	97.65
COG2197	211	CitB Response regulator containing a CheY-like rec	97.64
PRK10100	216	DNA-binding transcriptional regulator CsgD; Provis	97.63
TIGR03020	247	EpsA transcriptional regulator EpsA. Proteins in t	97.62
PF13936	44	HTH_38: Helix-turn-helix domain; PDB: 2W48_A.	97.61
TIGR03541	232	reg_near_HchA LuxR family transcriptional regulato	97.59
PRK10188	240	DNA-binding transcriptional activator SdiA; Provis	97.49
PRK13870	234	transcriptional regulator TraR; Provisional	97.48
TIGR01637	132	phage_arpU phage transcriptional regulator, ArpU f	97.48
COG2771	65	CsgD DNA-binding HTH domain-containing proteins [T	97.39
PRK09483	217	response regulator; Provisional	97.33
PRK01381	99	Trp operon repressor; Provisional	97.17
PRK15369	211	two component system sensor kinase SsrB; Provision	97.16
COG2739	105	Uncharacterized protein conserved in bacteria [Fun	97.14
PRK15320	251	transcriptional activator SprB; Provisional	97.11
COG1342	99	Predicted DNA-binding proteins [General function p	97.06
PRK10651	216	transcriptional regulator NarL; Provisional	97.05
COG1356	143	tfx Transcriptional regulator [DNA replication, re	97.0
PRK09390	202	fixJ response regulator FixJ; Provisional	96.95
COG3413	215	Predicted DNA binding protein [General function pr	96.94
PF13613	53	HTH_Tnp_4: Helix-turn-helix of DDE superfamily end	96.74
PRK10403	215	transcriptional regulator NarP; Provisional	96.63
PRK10360	196	DNA-binding transcriptional activator UhpA; Provis	96.47
PRK09935	210	transcriptional regulator FimZ; Provisional	96.41
PRK09958	204	DNA-binding transcriptional activator EvgA; Provis	96.38
TIGR02531	88	yecD_yerC TrpR-related protein YerC/YecD. This mod	96.32
PF13412	48	HTH_24: Winged helix-turn-helix DNA-binding; PDB:	96.3
PF13384	50	HTH_23: Homeodomain-like domain; PDB: 2X48_C.	96.29
PRK04841	903	transcriptional regulator MalT; Provisional	96.27
PRK13558	665	bacterio-opsin activator; Provisional	96.2
PF02796	45	HTH_7: Helix-turn-helix domain of resolvase; Inter	96.15
PRK15418	318	transcriptional regulator LsrR; Provisional	96.0
PF05263	130	DUF722: Protein of unknown function (DUF722); Inte	95.8
PF06056	58	Terminase_5: Putative ATPase subunit of terminase	95.69
PF09862	113	DUF2089: Protein of unknown function (DUF2089); In	95.54
PF00325	32	Crp: Bacterial regulatory proteins, crp family; In	95.3
PF13404	42	HTH_AsnC-type: AsnC-type helix-turn-helix domain;	95.29
PF01726	65	LexA_DNA_bind: LexA DNA binding domain; InterPro:	95.22
PF06530	125	Phage_antitermQ: Phage antitermination protein Q;	94.97
PF10668	60	Phage_terminase: Phage terminase small subunit; In	94.95
cd00569	42	HTH_Hin_like Helix-turn-helix domain of Hin and re	94.86
COG2390	321	DeoR Transcriptional regulator, contains sigma fac	94.74
PF13518	52	HTH_28: Helix-turn-helix domain	94.65
PHA00675	78	hypothetical protein	94.55
PF04218	53	CENP-B_N: CENP-B N-terminal DNA-binding domain; In	94.52
PF12802	62	MarR_2: MarR family; PDB: 3ECO_B 2QWW_B 3KP6_B 3KP	94.46
PF13730	55	HTH_36: Helix-turn-helix domain	94.4
COG2909	894	MalT ATP-dependent transcriptional regulator [Tran	94.3
smart00351	125	PAX Paired Box domain.	94.11
PF02650	85	HTH_WhiA: WhiA C-terminal HTH domain; InterPro: IP	93.71
PRK10430	239	DNA-binding transcriptional activator DcuR; Provis	93.52
PF08279	55	HTH_11: HTH domain; InterPro: IPR013196 Winged hel	93.47
PF01371	87	Trp_repressor: Trp repressor protein; InterPro: IP	93.29
PHA02547	179	55 RNA polymerase sigma factor; Provisional	93.05
PF01047	59	MarR: MarR family; InterPro: IPR000835 The MarR-ty	92.84
cd00131	128	PAX Paired Box domain	92.83
PHA02591	83	hypothetical protein; Provisional	92.73
PRK14082	65	hypothetical protein; Provisional	92.56
smart00550	68	Zalpha Z-DNA-binding domain in adenosine deaminase	92.54
PF01022	47	HTH_5: Bacterial regulatory protein, arsR family;	92.45
COG3415	138	Transposase and inactivated derivatives [DNA repli	92.09
PF13022	142	HTH_Tnp_1_2: Helix-turn-helix of insertion element	91.84
PF01418	77	HTH_6: Helix-turn-helix domain, rpiR family; Inter	91.68
PF13542	52	HTH_Tnp_ISL3: Helix-turn-helix domain of transposa	91.67
PF00356	46	LacI: Bacterial regulatory proteins, lacI family;	91.64
smart00344	108	HTH_ASNC helix_turn_helix ASNC type. AsnC: an auto	91.58
PF03444	78	HrcA_DNA-bdg: Winged helix-turn-helix transcriptio	91.58
PF12840	61	HTH_20: Helix-turn-helix domain; PDB: 1ULY_A 2CWE_	91.54
PF13011	85	LZ_Tnp_IS481: leucine-zipper of insertion element	91.52
PF01710	119	HTH_Tnp_IS630: Transposase; InterPro: IPR002622 Tr	91.51
PF01325	60	Fe_dep_repress: Iron dependent repressor, N-termin	91.31
PRK11083	228	DNA-binding response regulator CreB; Provisional	91.26
PF13463	68	HTH_27: Winged helix DNA-binding domain; PDB: 3GFL	91.2
PRK11179	153	DNA-binding transcriptional regulator AsnC; Provis	90.85
PRK10336	219	DNA-binding transcriptional regulator QseB; Provis	90.62
PRK10046	225	dpiA two-component response regulator DpiA; Provis	90.53
PF08822	165	DUF1804: Protein of unknown function (DUF1804); In	90.5
PF01978	68	TrmB: Sugar-specific transcriptional regulator Trm	90.28
TIGR01610	95	phage_O_Nterm phage replication protein O, N-termi	90.01
PF02954	42	HTH_8: Bacterial regulatory protein, Fis family; I	90.01
PF09339	52	HTH_IclR: IclR helix-turn-helix domain; InterPro:	90.0
PRK13413	200	mpi multiple promoter invertase; Provisional	90.0
PF12728	51	HTH_17: Helix-turn-helix domain	89.59
PRK00423	310	tfb transcription initiation factor IIB; Reviewed	89.43
PRK11169	164	leucine-responsive transcriptional regulator; Prov	89.13
PF13744	80	HTH_37: Helix-turn-helix domain; PDB: 2A6C_B 2O38_	89.12
PRK10710	240	DNA-binding transcriptional regulator BaeR; Provis	89.1
PF11427	50	HTH_Tnp_Tc3_1: Tc3 transposase; PDB: 1U78_A 1TC3_C	89.03
PRK12423	202	LexA repressor; Provisional	88.84
PRK15479	221	transcriptional regulatory protein TctD; Provision	88.74
cd04762	49	HTH_MerR-trunc Helix-Turn-Helix DNA binding domain	88.48
PF13551	112	HTH_29: Winged helix-turn helix	88.45
COG3355	126	Predicted transcriptional regulator [Transcription	88.45
TIGR01764	49	excise DNA binding domain, excisionase family. An	88.15
TIGR02337	118	HpaR homoprotocatechuate degradation operon regula	88.12
COG2522	119	Predicted transcriptional regulator [General funct	87.94
TIGR02154	226	PhoB phosphate regulon transcriptional regulatory	87.78
COG1522	154	Lrp Transcriptional regulators [Transcription]	87.71
COG2973	103	TrpR Trp operon repressor [Transcription]	87.69
PF01381	55	HTH_3: Helix-turn-helix; InterPro: IPR001387 This	87.06
PF01726	65	LexA_DNA_bind: LexA DNA binding domain; InterPro:	86.83
PF08220	57	HTH_DeoR: DeoR-like helix-turn-helix domain; Inter	86.79
CHL00148	240	orf27 Ycf27; Reviewed	86.65
PF08280	59	HTH_Mga: M protein trans-acting positive regulator	86.53
TIGR00498	199	lexA SOS regulatory protein LexA. LexA acts as a h	86.53
TIGR03787	227	marine_sort_RR proteobacterial dedicated sortase s	86.49
PF00046	57	Homeobox: Homeobox domain not present here.; Inter	86.43
PRK11512	144	DNA-binding transcriptional repressor MarR; Provis	86.26
PRK07598	415	RNA polymerase sigma factor SigC; Validated	86.17
cd04761	49	HTH_MerR-SF Helix-Turn-Helix DNA binding domain of	86.09
smart00420	53	HTH_DEOR helix_turn_helix, Deoxyribose operon repr	86.09
PRK00215	205	LexA repressor; Validated	85.91
COG5484	279	Uncharacterized conserved protein [Function unknow	85.22
COG0856	203	Orotate phosphoribosyltransferase homologs [Nucleo	84.86
PRK10870	176	transcriptional repressor MprA; Provisional	84.67
smart00345	60	HTH_GNTR helix_turn_helix gluconate operon transcr	83.88
cd06571	90	Bac_DnaA_C C-terminal domain of bacterial DnaA pro	83.87
smart00419	48	HTH_CRP helix_turn_helix, cAMP Regulatory protein.	83.84
PRK09413	121	IS2 repressor TnpA; Reviewed	83.66
PRK11337	292	DNA-binding transcriptional repressor RpiR; Provis	83.32
PF01527	76	HTH_Tnp_1: Transposase; InterPro: IPR002514 Transp	83.32
PRK03573	144	transcriptional regulator SlyA; Provisional	83.26
TIGR02844	80	spore_III_D sporulation transcriptional regulator	83.23
PRK11302	284	DNA-binding transcriptional regulator HexR; Provis	83.12
PF08535	93	KorB: KorB domain; InterPro: IPR013741 This entry	83.08
PF08765	108	Mor: Mor transcription activator family; InterPro:	83.06
PF07750	162	GcrA: GcrA cell cycle regulator; InterPro: IPR0116	82.9
TIGR03830	127	CxxCG_CxxCG_HTH putative zinc finger/helix-turn-he	82.74
TIGR01884	203	cas_HTH CRISPR locus-related DNA-binding protein.	82.72
PHA00542	82	putative Cro-like protein	82.7
KOG0484	125	consensus Transcription factor PHOX2/ARIX, contain	82.68
smart00347	101	HTH_MARR helix_turn_helix multiple antibiotic resi	82.68
cd00092	67	HTH_CRP helix_turn_helix, cAMP Regulatory protein	82.3
PF05043	87	Mga: Mga helix-turn-helix domain; InterPro: IPR007	82.22
PF13560	64	HTH_31: Helix-turn-helix domain; PDB: 3F51_C 3F52_	82.15
PF14493	91	HTH_40: Helix-turn-helix domain	82.03
smart00342	84	HTH_ARAC helix_turn_helix, arabinose operon contro	81.96
TIGR00122	69	birA_repr_reg BirA biotin operon repressor domain.	81.95
COG1318	182	Predicted transcriptional regulators [Transcriptio	81.91
PF13411	69	MerR_1: MerR HTH family regulatory protein; PDB: 2	81.86
TIGR01889	109	Staph_reg_Sar staphylococcal accessory regulator f	81.61
TIGR03070	58	couple_hipB transcriptional regulator, y4mF family	81.59
PRK11564	426	stationary phase inducible protein CsiE; Provision	81.45
COG3877	122	Uncharacterized protein conserved in bacteria [Fun	81.3
PHA01976	67	helix-turn-helix protein	81.21
PRK15482	285	transcriptional regulator MurR; Provisional	81.02
PRK10072	96	putative transcriptional regulator; Provisional	81.0
PF13545	76	HTH_Crp_2: Crp-like helix-turn-helix domain; PDB:	80.89
TIGR00647	279	MG103 conserved hypothetical protein.	80.71
PF12116	82	SpoIIID: Stage III sporulation protein D; InterPro	80.49
smart00354	70	HTH_LACI helix_turn _helix lactose operon represso	80.46
cd00090	78	HTH_ARSR Arsenical Resistance Operon Repressor and	80.42

>PRK09210 RNA polymerase sigma factor RpoD; Validated

Probab=100.00  E-value=2.1e-45  Score=363.96  Aligned_cols=250  Identities=37%  Similarity=0.642  Sum_probs=240.0

Q ss_pred             HHHHHHHhcccHHHHHHHHHHhHHHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHhccCCCCCCCchhHHHHHHHHHHHH
Q 046578          129 NLVKYKILCKERESQERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYWWIKQAIIR  208 (379)
Q Consensus       129 ~eLi~~~~~Gd~~A~e~Li~~y~~lV~~ia~r~~~~~~d~eDLvQEg~i~L~~ai~~fD~~~g~~FsTYa~~~Ir~~i~~  208 (379)
                      .+|+.+++.||..|++.|+..|.++|+++|++|.+++.+++||+|||++|||+++++|||.+|++|+|||+|||++.|.+
T Consensus       117 ~~L~~~~~~Gd~~A~~~Li~~~~~lV~~iA~~~~~~~~~~eDLiQEg~igL~~a~~~fd~~~g~~FsTyA~~wIr~aI~~  196 (367)
T PRK09210        117 IELAKRIEEGDEEAKQRLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNMGLMKAVEKFDYRKGFKFSTYATWWIRQAITR  196 (367)
T ss_pred             HHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHhcCCCCCCchHHHHHHHHHHHHHH
Confidence            57899999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHhhcCcccCCcchHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCccccCCCCcccc
Q 046578          209 AIANKSRTIRLPGSMAGMVAKIAEANNVLSRRLRRMPTDSEIAEMLNIHVSTVRLAIERTRHPISLDGAVTDRGCMTMQD  288 (379)
Q Consensus       209 ~lr~~~r~irip~~~~~~~~ki~~a~~~l~~~lgr~pt~~eia~~Lgis~~~~~~~l~~~~~~iSLd~~~~~~~~~~l~d  288 (379)
                      +++++.+.+|+|+|+...++++.++.+.+...+|++||.+|||+.+|++.+++..++.....++|||.+++++++..+.+
T Consensus       197 ~i~~~~r~irip~~~~~~~~~~~~~~~~l~~~lgr~pt~~EiA~~l~~~~~~v~~~~~~~~~~~SLd~~~~~~~~~~l~d  276 (367)
T PRK09210        197 AIADQARTIRIPVHMVETINKLIRVQRQLLQELGREPTPEEIAEEMDMPPEKVREILKIAQEPVSLETPIGEEDDSHLGD  276 (367)
T ss_pred             HHHHcCCceeccHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHHhcCCCCcCCCCCCCCcchhhh
Confidence            99999999999999999999999999999999999999999999999999999999988888999999998777777889


Q ss_pred             cCCCCCCCChHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhH
Q 046578          289 IIPGPDETMPERMVQKQLMKQELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQT  368 (379)
Q Consensus       289 ~i~~~~~~~pe~~~~~~e~~~~L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~~  368 (379)
                      ++++....+|++.+....+...|..+|..||++||.||.++||++|++++|++|||+.||||+++|+|+..+|++|||..
T Consensus       277 ~i~d~~~~~p~~~~~~~~~~~~l~~~l~~L~~rEr~Vl~lrygl~~~~~~tl~EIa~~lgvs~erVrQi~~~Al~kLr~~  356 (367)
T PRK09210        277 FIEDQDATSPADHAAYELLKEQLEDVLDTLTDREENVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRHP  356 (367)
T ss_pred             hccCCCCCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHhccCCCCCccHHHHHHHHCCCHHHHHHHHHHHHHHHhCh
Confidence            98888778899999888888999999999999999999999999877999999999999999999999999999999999


Q ss_pred             Hhhchhhhhc
Q 046578          369 NILNNLKVYM  378 (379)
Q Consensus       369 l~~~~L~~y~  378 (379)
                      .....|++|+
T Consensus       357 ~~~~~l~~~~  366 (367)
T PRK09210        357 SRSKQLKDFL  366 (367)
T ss_pred             HHHhHHHHhh
Confidence            9999999986

>PRK07921 RNA polymerase sigma factor SigB; Reviewed

Probab=100.00  E-value=2.9e-45  Score=356.27  Aligned_cols=249  Identities=37%  Similarity=0.626  Sum_probs=233.1

Q ss_pred             HHHHHHHhcccHHHHHHHHHHhHHHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHhccCCCCCCCchhHHHHHHHHHHHH
Q 046578          129 NLVKYKILCKERESQERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYWWIKQAIIR  208 (379)
Q Consensus       129 ~eLi~~~~~Gd~~A~e~Li~~y~~lV~~ia~r~~~~~~d~eDLvQEg~i~L~~ai~~fD~~~g~~FsTYa~~~Ir~~i~~  208 (379)
                      .++...+. .+..|++.||..|.++|+++|++|.+++.+++||+|||++|||+++++|||++|++|+|||+|||++.|.+
T Consensus        75 ~~l~~~~~-~~~~A~~~Lv~~~~~lV~~iA~r~~~~~~~~eDLvQEg~igL~~a~~~fdp~~G~rFsTYA~~wIr~aI~~  153 (324)
T PRK07921         75 RDLAAVVR-DGEAARRHLLEANLRLVVSLAKRYTGRGMPLLDLIQEGNLGLIRAMEKFDYTKGFKFSTYATWWIRQAITR  153 (324)
T ss_pred             HHHHHHHh-cCHHHHHHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHcCCccCCCHHHHHHHHHHHHHHH
Confidence            34555555 45789999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHhhcCcccCCcchHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCccccCCCCcccc
Q 046578          209 AIANKSRTIRLPGSMAGMVAKIAEANNVLSRRLRRMPTDSEIAEMLNIHVSTVRLAIERTRHPISLDGAVTDRGCMTMQD  288 (379)
Q Consensus       209 ~lr~~~r~irip~~~~~~~~ki~~a~~~l~~~lgr~pt~~eia~~Lgis~~~~~~~l~~~~~~iSLd~~~~~~~~~~l~d  288 (379)
                      +++++.+.+++|.++....+++.++...+.+.+|+.|+.+|||+.+|++.+++..++......+|||.+++++++..+.+
T Consensus       154 ~i~~~~r~vrlP~~~~~~~~~l~~~~~~l~~~lgr~pt~~EiA~~lgi~~~~v~~~~~~~~~~~SLd~~~~~~~~~~l~d  233 (324)
T PRK07921        154 GMADQSRTIRLPVHLVEQVNKLARIKRELHQQLGREATDEELAEESGIPEEKIADLLEHSRDPVSLDMPVGSDEEAPLGD  233 (324)
T ss_pred             HHHHcCCCccCCHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHHcCCCceecCCCCCCCCchHHH
Confidence            99999999999999999999999999999999999999999999999999999999888889999999987776667888


Q ss_pred             cCCCCCCCChHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhH
Q 046578          289 IIPGPDETMPERMVQKQLMKQELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQT  368 (379)
Q Consensus       289 ~i~~~~~~~pe~~~~~~e~~~~L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~~  368 (379)
                      ++++....+|++.+...++...|..+|..|+++|+.||.++||++|++++|++|||+.||||+++|+|+..+|++|||..
T Consensus       234 ~l~d~~~~~pe~~~~~~~~~~~l~~~L~~L~eREr~Vl~~rygl~~~~~~Tl~eIa~~lgvS~eRVrQIe~~Al~KLr~~  313 (324)
T PRK07921        234 FIEDSEATSAENAVIAGLLHTDIRSVLATLDEREQQVIRLRFGLDDGQPRTLDQIGKLFGLSRERVRQIEREVMSKLRNG  313 (324)
T ss_pred             HhcCCCCCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHhcCCCCCcCHHHHHHHHCCCHHHHHHHHHHHHHHHHhH
Confidence            88887777888888888888899999999999999999999999877899999999999999999999999999999999


Q ss_pred             Hhhchhhhhc
Q 046578          369 NILNNLKVYM  378 (379)
Q Consensus       369 l~~~~L~~y~  378 (379)
                      .....|+.|+
T Consensus       314 ~~~~~l~~~~  323 (324)
T PRK07921        314 ERADRLRSYA  323 (324)
T ss_pred             HHHHHHHHhh
Confidence            9999999886

>PRK05658 RNA polymerase sigma factor RpoD; Validated

Probab=100.00  E-value=2.4e-45  Score=385.81  Aligned_cols=299  Identities=31%  Similarity=0.508  Sum_probs=269.5

Q ss_pred             hhhhcCCcccccchhHHHHHHHHHHHHHhhhcccccccchhh----------------hcCcC---cHHHHHHHHhcccH
Q 046578           80 VSFANGAEEVCFDDGECESVLKMMRRRSRRKKRTKESDFLDK----------------ENGEL---DYNLVKYKILCKER  140 (379)
Q Consensus        80 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----------------~~~~~---~~~eLi~~~~~Gd~  140 (379)
                      ++..+|+++-+|...+.+.+.+..|..+..+.++.+......                ....+   +..+++.+++.||.
T Consensus       297 ~~~~~~m~R~~Fi~~f~gnEt~~~w~~~~~~~~~~~a~~l~~~~~~I~~lq~~L~~ie~~~~Ls~eElk~l~~~i~~g~~  376 (619)
T PRK05658        297 LVERLKMPRKDFLKLFQGNELDITWLEKEIASGKPWSEFLVRVYDEIKKLQQELEAIEEETGLTIEELKEINRQISKGEA  376 (619)
T ss_pred             HHHHcCCCHHHHHHHccCCcCCHHHHHHHHhccCchHHHHHHHHHHHHHHHHHHHHHHHHhCCCHHHHHHHHHHHhccch
Confidence            457899999999999988888887766555544433332211                01112   24678888999965


Q ss_pred             ---HHHHHHHHHhHHHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHhccCCCCCCCchhHHHHHHHHHHHHHHHhhcCcc
Q 046578          141 ---ESQERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYWWIKQAIIRAIANKSRTI  217 (379)
Q Consensus       141 ---~A~e~Li~~y~~lV~~ia~r~~~~~~d~eDLvQEg~i~L~~ai~~fD~~~g~~FsTYa~~~Ir~~i~~~lr~~~r~i  217 (379)
                         .|+++|+..|.++|.++|++|.++|.+++||+|||++||++|+++|||++|++|+|||+|||+++|.++++++.+++
T Consensus       377 ~~~~a~~~Li~~nlrlV~~iA~ky~~~gl~~~DLiQeG~iGL~~Av~kfd~~~G~~FstYA~~wIr~aI~~~i~~~~r~i  456 (619)
T PRK05658        377 KARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTI  456 (619)
T ss_pred             hhhHHHHHHHHHHHHHHHHHHHHHhhCCCCHHHHHHHHHHHHHHHHHhcCccCCCchHHHhHHHHHHHHHHHHHHcCCce
Confidence               78899999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cCCcchHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCccccCCCCcccccCCCCCCCC
Q 046578          218 RLPGSMAGMVAKIAEANNVLSRRLRRMPTDSEIAEMLNIHVSTVRLAIERTRHPISLDGAVTDRGCMTMQDIIPGPDETM  297 (379)
Q Consensus       218 rip~~~~~~~~ki~~a~~~l~~~lgr~pt~~eia~~Lgis~~~~~~~l~~~~~~iSLd~~~~~~~~~~l~d~i~~~~~~~  297 (379)
                      |+|+|+....+++.++...+.+.+|++|+++|||+.+|++.+++..++.....++|||.+++++++..+.+++++....+
T Consensus       457 rip~~~~~~~~k~~~~~~~~~~~~gr~pt~~eiA~~l~~~~~~v~~~~~~~~~~~Sld~~i~~~~~~~l~d~i~d~~~~~  536 (619)
T PRK05658        457 RIPVHMIETINKLNRISRQMLQEIGREPTPEELAERLGMPEDKVRKVLKIAKEPISLETPIGDDEDSHLGDFIEDKNAEL  536 (619)
T ss_pred             ecCHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCCcCCCCCCCCCCCchhhhcCCCCCCC
Confidence            99999999999999999999999999999999999999999999999988889999999998887778889999887788


Q ss_pred             hHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHHhhchhhhh
Q 046578          298 PERMVQKQLMKQELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQTNILNNLKVY  377 (379)
Q Consensus       298 pe~~~~~~e~~~~L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~~l~~~~L~~y  377 (379)
                      |++.+....+...+..+|..||++|+.||.+|||+++.+++|++|||+.||||+++|+|+..+|++|||.......|+.|
T Consensus       537 p~~~~~~~~~~~~l~~~l~~L~~rE~~Vl~~r~g~~~~~~~tl~ei~~~lgvs~eRVrQie~~al~kLr~~~~~~~l~~~  616 (619)
T PRK05658        537 PIDAAIQESLREATTDVLASLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSRKLRSF  616 (619)
T ss_pred             hHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHhcCCCCCCCccHHHHHHHhCCCHHHHHHHHHHHHHHHhchHHHHHHHHH
Confidence            99988888888999999999999999999999999877899999999999999999999999999999999999999998


Q ss_pred             c
Q 046578          378 M  378 (379)
Q Consensus       378 ~  378 (379)
                      +
T Consensus       617 ~  617 (619)
T PRK05658        617 L  617 (619)
T ss_pred             h
Confidence            6

>PRK05901 RNA polymerase sigma factor; Provisional

Probab=100.00  E-value=3e-45  Score=371.51  Aligned_cols=240  Identities=38%  Similarity=0.652  Sum_probs=230.2

Q ss_pred             HHHHHHHHHHhHHHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHhccCCCCCCCchhHHHHHHHHHHHHHHHhhcCcccC
Q 046578          140 RESQERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYWWIKQAIIRAIANKSRTIRL  219 (379)
Q Consensus       140 ~~A~e~Li~~y~~lV~~ia~r~~~~~~d~eDLvQEg~i~L~~ai~~fD~~~g~~FsTYa~~~Ir~~i~~~lr~~~r~iri  219 (379)
                      ..|++.|+..|+++|+++|++|.++|.+++||+|||++||++|+++|||++|++|+|||+||||+.|.++++++.+.+|+
T Consensus       270 ~~Ar~~LI~sNLrLVvsIAkrY~~~Gl~~eDLIQEGnIGLikAvekFDp~rG~rFSTYA~wWIRqaI~raI~d~~r~IRv  349 (509)
T PRK05901        270 KRAKNHLLEANLRLVVSLAKRYTNRGLSFLDLIQEGNLGLIKAVEKFDYTKGYKFSTYATWWIRQAITRAMADQARTIRI  349 (509)
T ss_pred             HHHHHHHHHHhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHhCcccCCCchhhhHHHHHHHHHHHHHHcCCceec
Confidence            68999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CcchHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCccccCCCCcccccCCCCCCCChH
Q 046578          220 PGSMAGMVAKIAEANNVLSRRLRRMPTDSEIAEMLNIHVSTVRLAIERTRHPISLDGAVTDRGCMTMQDIIPGPDETMPE  299 (379)
Q Consensus       220 p~~~~~~~~ki~~a~~~l~~~lgr~pt~~eia~~Lgis~~~~~~~l~~~~~~iSLd~~~~~~~~~~l~d~i~~~~~~~pe  299 (379)
                      |+++...++++.++...+.+.+|++|+.+|||+.+|++++++..++.....++|||.+++++++..+.+++.+.....|+
T Consensus       350 P~~~~e~i~kl~~~~~~L~~~lgr~PT~eELAe~Lgis~e~V~~~~~~~~~~~SLD~~i~~d~~~~l~d~l~D~~~~~p~  429 (509)
T PRK05901        350 PVHMVETINKLGRIERELLQELGREPTPEELAKEMGFTPEKVREIQKYNREPISLDKTIGKEGDSQFGDFIEDSEAVSPV  429 (509)
T ss_pred             CHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccccccccCCcccHHHhccCCCCCCHH
Confidence            99999999999999999999999999999999999999999999988888999999999877777788889888777899


Q ss_pred             HHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHHhhchhhhhcC
Q 046578          300 RMVQKQLMKQELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQTNILNNLKVYMV  379 (379)
Q Consensus       300 ~~~~~~e~~~~L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~~l~~~~L~~y~~  379 (379)
                      +.+....+...|..+|..|+++||.||.+||||+|++++|++|||+.||||+++|+|+..+|++|||.......|++|+.
T Consensus       430 ~~~~~~~l~~~L~~aL~~L~eREr~VI~lRyGL~~~e~~TL~EIa~~lGVSrERVRQIe~kAL~KLR~~~~~~~l~~~l~  509 (509)
T PRK05901        430 DAVSFTLLQDQLQEVLETLSEREAGVIRMRFGLTDGQPKTLDEIGQVYGVTRERIRQIESKTLRKLRHPSRSQVLRDFLD  509 (509)
T ss_pred             HHHHHHHHHHHHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhC
Confidence            98888888899999999999999999999999987799999999999999999999999999999999999999999973

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

Probab=100.00  E-value=4.4e-45  Score=351.19  Aligned_cols=250  Identities=39%  Similarity=0.677  Sum_probs=238.7

Q ss_pred             HHHHHHHhcc--cHHHHHHHHHHhHHHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHhccCCCCCCCchhHHHHHHHHHH
Q 046578          129 NLVKYKILCK--ERESQERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYWWIKQAI  206 (379)
Q Consensus       129 ~eLi~~~~~G--d~~A~e~Li~~y~~lV~~ia~r~~~~~~d~eDLvQEg~i~L~~ai~~fD~~~g~~FsTYa~~~Ir~~i  206 (379)
                      .++..++..|  |..|...++..|+++|.++|++|.++|..+.||+|||.+||++|+++|||++|++|+|||+||||..|
T Consensus        88 ~~la~~~~~g~~~~~Ak~klv~snLRlVvsIAk~Y~~rGL~~~DLIQEGniGLmkAVekFdp~rG~kFsTYA~wWIrqaI  167 (342)
T COG0568          88 KALARRLKRGERDLDAKKKLVESNLRLVVSIAKKYTGRGLPFLDLIQEGNIGLMKAVEKFDPEKGFKFSTYATWWIRQAI  167 (342)
T ss_pred             HHHHHHHHcCCccHHHHHHHHHHHHHHHHHHHHHhhcCCCcHHHHHhcccHHHHHHHHhcCcccCCcchhHHHHHHHHHH
Confidence            5688899999  89999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHhhcCcccCCcchHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCccccCCCCcc
Q 046578          207 IRAIANKSRTIRLPGSMAGMVAKIAEANNVLSRRLRRMPTDSEIAEMLNIHVSTVRLAIERTRHPISLDGAVTDRGCMTM  286 (379)
Q Consensus       207 ~~~lr~~~r~irip~~~~~~~~ki~~a~~~l~~~lgr~pt~~eia~~Lgis~~~~~~~l~~~~~~iSLd~~~~~~~~~~l  286 (379)
                      .+++.++.|++|+|.|+.+..+++.+..+++.+.+|++|+.+|||+.+|++++++..++.....++|||.+++++++..+
T Consensus       168 ~raI~~q~rtIRipvh~~e~~nkl~r~~r~l~q~~~r~p~~eeia~~l~~~~~~V~~m~~~~~~~~SLd~~ig~ded~~l  247 (342)
T COG0568         168 TRAIADQARTIRIPVHQVELINKLRRVKRELLQELGREPTPEEIAEELGVSPDKVREMLKRASEPISLDTPIGDDEDSEL  247 (342)
T ss_pred             HHHHHHhcchhhHhHHHHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHhCCCHHHHHHHHHhcccCcccCCcCCCCcccHH
Confidence            99999999999999999999999999999999999999999999999999999999999998889999999999888889


Q ss_pred             cccCCCCCCCChHHHHHHHHHHHHHHHHHhc-CCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Q 046578          287 QDIIPGPDETMPERMVQKQLMKQELKELLQT-LSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKL  365 (379)
Q Consensus       287 ~d~i~~~~~~~pe~~~~~~e~~~~L~~~L~~-L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kL  365 (379)
                      .|++++....+|++.+........+...|.. |+|+|+.||.+|||++|.++.|+.|||+.+|||+.+|+|+..+|++||
T Consensus       248 ~d~leD~~~~~p~~~~~~~~~~~~~~~~L~~~Lt~rE~~Vi~~R~gl~~~~~~TLeevg~~~~isrERvRQIE~kAl~KL  327 (342)
T COG0568         248 GDFLEDDKSVSPEDAVERESLKEDLNEVLAEALTERERRVIRLRFGLDDGEPKTLEELGEEFGISRERVRQIEAKALRKL  327 (342)
T ss_pred             HHHhhcCCcCCHHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhccCCCCcchHHHHHHHhCCcHHHHHHHHHHHHHHH
Confidence            9999998888999999999999999999999 999999999999999977999999999999999999999999999999


Q ss_pred             HhHH-hhchhhhhc
Q 046578          366 QQTN-ILNNLKVYM  378 (379)
Q Consensus       366 R~~l-~~~~L~~y~  378 (379)
                      |.+. ....+++|+
T Consensus       328 r~~~~~~~~~~~~l  341 (342)
T COG0568         328 RRHPERSALLRSYL  341 (342)
T ss_pred             HHhhhhhhHHHHhh
Confidence            9544 455568876

>PRK07598 RNA polymerase sigma factor SigC; Validated

Probab=100.00  E-value=1.1e-44  Score=359.31  Aligned_cols=253  Identities=39%  Similarity=0.644  Sum_probs=239.6

Q ss_pred             CcCcHHHHHHHHhcccHHHHHHHHHHhHHHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHhccCCCCCCCchhHHHHHHH
Q 046578          124 GELDYNLVKYKILCKERESQERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYWWIK  203 (379)
Q Consensus       124 ~~~~~~eLi~~~~~Gd~~A~e~Li~~y~~lV~~ia~r~~~~~~d~eDLvQEg~i~L~~ai~~fD~~~g~~FsTYa~~~Ir  203 (379)
                      -.++..+|+..++.| ..|++.||..|.++|+++|++|.+++.+++||+|||++|||+++++|||++|++|+||++||||
T Consensus       159 ~~l~~~eL~~~l~~G-~~A~e~LI~~nlrLVvsiAkky~~~g~~~eDLiQEG~iGL~ravekFDp~rG~rFSTYa~wwIR  237 (415)
T PRK07598        159 AKLTVEELEQIQKQG-LRAKEHMIKANLRLVVSVAKKYQNRGLELLDLVQEGTLGLERAVEKFDPTKGYRFSTYAYWWIR  237 (415)
T ss_pred             ccCCHHHHHHHHHCC-HHHHHHHHHHHHHHHHHHHHHHccCCCCHHHHHHHHHHHHHHHHHHcCcccCCCHHHHHHHHHH
Confidence            346778999999999 6899999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHhhcCcccCCcchHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCccccCCC
Q 046578          204 QAIIRAIANKSRTIRLPGSMAGMVAKIAEANNVLSRRLRRMPTDSEIAEMLNIHVSTVRLAIERTRHPISLDGAVTDRGC  283 (379)
Q Consensus       204 ~~i~~~lr~~~r~irip~~~~~~~~ki~~a~~~l~~~lgr~pt~~eia~~Lgis~~~~~~~l~~~~~~iSLd~~~~~~~~  283 (379)
                      +.|.+++.++.+++++|.|+...+++++++.+.+.+.+|+.|+.+|||+.+|+++++++.++.....++|||.+++++++
T Consensus       238 qaI~r~i~~~srtIrlP~~i~e~l~~lrk~~r~L~~~lgR~pt~~EiA~~l~is~~~vr~~l~~~~~~~SLd~~vg~~~d  317 (415)
T PRK07598        238 QGITRAIATQSRTIRLPVHITEKLNKIKKAQRKISQEKGRTPTIEDIAQELEMTPTQVREVLLRVPRSVSLETKVGKDKD  317 (415)
T ss_pred             HHHHHHHHHcCCceehhHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHHccCCcccccccCCCcc
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999988877


Q ss_pred             CcccccCCCCCCCChHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 046578          284 MTMQDIIPGPDETMPERMVQKQLMKQELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALT  363 (379)
Q Consensus       284 ~~l~d~i~~~~~~~pe~~~~~~e~~~~L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~  363 (379)
                      ..+.+.+.+ ...+|++.+...+....|..+|..|||+||.||.++|||+|++++|++|||+.||+|+++|++++++|++
T Consensus       318 ~~l~d~l~~-~~~~pee~~~~~~l~~~L~~~L~~L~~reR~VI~LRygl~d~~~~Tl~EIA~~LGvS~erVRqie~rAl~  396 (415)
T PRK07598        318 TELGDLLET-DDISPEEMLMRESLQRDLQHLLADLTSRERDVIRMRFGLADGHTYSLAEIGRALDLSRERVRQIESKALQ  396 (415)
T ss_pred             ccHHHhccC-CCCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence            777777764 3457888888888889999999999999999999999988778999999999999999999999999999


Q ss_pred             HHHhHHhhchhhhhc
Q 046578          364 KLQQTNILNNLKVYM  378 (379)
Q Consensus       364 kLR~~l~~~~L~~y~  378 (379)
                      |||+.-....|++|+
T Consensus       397 KLR~~~~~~~l~~y~  411 (415)
T PRK07598        397 KLRQPKRRNRIRDYL  411 (415)
T ss_pred             HHhchhHHHHHHHHH
Confidence            999999999999996

>PRK05949 RNA polymerase sigma factor; Validated

Probab=100.00  E-value=8.9e-44  Score=346.70  Aligned_cols=250  Identities=38%  Similarity=0.660  Sum_probs=234.0

Q ss_pred             cCcHHHHHHHHhcccHHHHHHHHHHhHHHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHhccCCCCCCCchhHHHHHHHH
Q 046578          125 ELDYNLVKYKILCKERESQERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYWWIKQ  204 (379)
Q Consensus       125 ~~~~~eLi~~~~~Gd~~A~e~Li~~y~~lV~~ia~r~~~~~~d~eDLvQEg~i~L~~ai~~fD~~~g~~FsTYa~~~Ir~  204 (379)
                      .++..+|+.+++.|+ .|++.||..|.++|+++|++|.+++.+++||+||||+|||+++++||+++|++|+||++||||+
T Consensus        76 ~~~~~eL~~~~~~g~-~A~~~Li~~~~~~V~~iA~~y~~~~~~~eDLvQEg~igL~~a~~kfd~~~G~rFsTYa~wwIrq  154 (327)
T PRK05949         76 NLSETELKQTLKQGK-RAKQKMIEANLRLVVAIAKKYQKRNMEFLDLIQEGTLGLERGVEKFDPTRGYKFSTYAYWWIRQ  154 (327)
T ss_pred             cCCHHHHHHHHHccH-HHHHHHHHHHHHHHHHHHHHHccCCCCHHHHHHHHHHHHHHHHHhcCCcCCCChhhhhHHHHHH
Confidence            356788999999996 5999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHhhcCcccCCcchHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCccccCCCC
Q 046578          205 AIIRAIANKSRTIRLPGSMAGMVAKIAEANNVLSRRLRRMPTDSEIAEMLNIHVSTVRLAIERTRHPISLDGAVTDRGCM  284 (379)
Q Consensus       205 ~i~~~lr~~~r~irip~~~~~~~~ki~~a~~~l~~~lgr~pt~~eia~~Lgis~~~~~~~l~~~~~~iSLd~~~~~~~~~  284 (379)
                      .|.+++.++.+++|+|.|+...++++.++...+...+|++|+.+|||+.+|++++++..++.....++|||.+++++++.
T Consensus       155 ~I~r~i~~~~r~iRlP~~~~~~~~~l~k~~~~l~~~lgr~pt~~eiA~~l~i~~~~v~~~~~~~~~~~SLd~~~~~~~~~  234 (327)
T PRK05949        155 AITRAIAQQARTIRLPIHITEKLNKIKKTQRELSQKLGRSATPAEIAKELELEPSQIREYLSMARQPISLDVRVGDNQDT  234 (327)
T ss_pred             HHHHHHHHcCCceeCCHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHHhccccccCCCcCCCCCc
Confidence            99999999999999999999999999999999999999999999999999999999999998888999999999877666


Q ss_pred             cccccCCCCCCCChHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHH
Q 046578          285 TMQDIIPGPDETMPERMVQKQLMKQELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTK  364 (379)
Q Consensus       285 ~l~d~i~~~~~~~pe~~~~~~e~~~~L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~k  364 (379)
                      .+.+.+++.. .+|++.+...+....|..+|+.||++||.||.++|||+|++++|++|||+.||+|+++|++++++|+++
T Consensus       235 ~l~~~l~d~~-~~pe~~~~~~~~~~~L~~~L~~L~~rer~Vi~lr~gl~~~e~~Tl~EIa~~lgiS~erVrq~~~rAl~k  313 (327)
T PRK05949        235 ELSELLEDEG-PSPDQYITQELLRQDLNNLLAELTPQQREVLTLRFGLEDGKELSLAKVGERLNLSRERVRQLEHQALAH  313 (327)
T ss_pred             cHHhhcCCCC-CCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHhccCCCCCCCHHHHHHHHCcCHHHHHHHHHHHHHH
Confidence            7777777654 678988888888899999999999999999999999988899999999999999999999999999999


Q ss_pred             HHhHHhhchhhhhc
Q 046578          365 LQQTNILNNLKVYM  378 (379)
Q Consensus       365 LR~~l~~~~L~~y~  378 (379)
                      ||+.  ...|++|+
T Consensus       314 Lr~~--~~~l~~~~  325 (327)
T PRK05949        314 LRRR--RANVKEYL  325 (327)
T ss_pred             HHHH--HHHHHHHH
Confidence            9994  45677775

>PRK07406 RNA polymerase sigma factor RpoD; Validated

Probab=100.00  E-value=2.2e-44  Score=354.89  Aligned_cols=252  Identities=41%  Similarity=0.696  Sum_probs=236.6

Q ss_pred             CcHHHHHHHHhcccHHHHHHHHHHhHHHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHhccCCCCCCCchhHHHHHHHHH
Q 046578          126 LDYNLVKYKILCKERESQERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYWWIKQA  205 (379)
Q Consensus       126 ~~~~eLi~~~~~Gd~~A~e~Li~~y~~lV~~ia~r~~~~~~d~eDLvQEg~i~L~~ai~~fD~~~g~~FsTYa~~~Ir~~  205 (379)
                      ++..+|..++..| ..|++.||..|.++|+++|++|.+++.+++||+|||++|||+++++||+.+|.+|+|||+||||+.
T Consensus       122 ~~~~~l~~~~~~g-~~A~~~Li~~~l~lV~~iA~ry~~~~~~~eDLiQEG~igL~~Ai~kFd~~kg~~FsTYA~wWIRqa  200 (373)
T PRK07406        122 MPLPKFRRRLMLG-RRAKEKMVQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYATWWIRQA  200 (373)
T ss_pred             ccHHHHHHHHhcC-HHHHHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHhcCCccCCCHHHHHHHHHHHH
Confidence            4567788887777 999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHhhcCcccCCcchHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCccccCCCCc
Q 046578          206 IIRAIANKSRTIRLPGSMAGMVAKIAEANNVLSRRLRRMPTDSEIAEMLNIHVSTVRLAIERTRHPISLDGAVTDRGCMT  285 (379)
Q Consensus       206 i~~~lr~~~r~irip~~~~~~~~ki~~a~~~l~~~lgr~pt~~eia~~Lgis~~~~~~~l~~~~~~iSLd~~~~~~~~~~  285 (379)
                      |.++++++.+.+|+|+++....+++.++...+.+.+|+.|+.+|||+.+|++.+++..++.....++|||.+++++++..
T Consensus       201 I~~~I~~~~r~IRlP~~~~~~~~~i~~a~~~l~~~lgr~Pt~~EIA~~lg~~~e~v~~~~~~~~~~~SLd~~i~~~~~~~  280 (373)
T PRK07406        201 ITRAIADQSRTIRLPVHLYETISRIKKTTKVLSQEFGRKPTEEEIAESMEMTIEKLRFIAKSAQLPISLETPIGKEEDSR  280 (373)
T ss_pred             HHHHHHhcCCceeCCHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCccc
Confidence            99999999999999999999999999999999999999999999999999999999999888889999999988776667


Q ss_pred             ccccCCCCCCCChHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Q 046578          286 MQDIIPGPDETMPERMVQKQLMKQELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKL  365 (379)
Q Consensus       286 l~d~i~~~~~~~pe~~~~~~e~~~~L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kL  365 (379)
                      +.+++++. ..+|++.+........|..+|..||++||.||.++||++|.+++|++|||+.||||+++|+|+..+|++||
T Consensus       281 l~d~l~d~-~~~pee~~~~~~~~~~L~~aL~~L~~rEr~IL~lrygl~~~~~~Tl~EIA~~lgiS~eRVRQie~rAL~KL  359 (373)
T PRK07406        281 LGDFIEAD-GETPEDDVAKNLLREDLEGVLATLSPRERDVLRLRYGLDDGRMKTLEEIGQIFNVTRERIRQIEAKALRKL  359 (373)
T ss_pred             HHHhcCCC-CCCHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCcCHHHHHHHHHHHHHHH
Confidence            88888765 45788888888888999999999999999999999998877889999999999999999999999999999


Q ss_pred             HhHHhhchhhhhcC
Q 046578          366 QQTNILNNLKVYMV  379 (379)
Q Consensus       366 R~~l~~~~L~~y~~  379 (379)
                      |+......|++|++
T Consensus       360 R~~~~~~~l~~~~~  373 (373)
T PRK07406        360 RHPNRNSVLKEYIR  373 (373)
T ss_pred             hchhHHHHHHHHhC
Confidence            99999999999974

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

Probab=100.00  E-value=2.2e-43  Score=330.57  Aligned_cols=237  Identities=39%  Similarity=0.681  Sum_probs=224.0

Q ss_pred             HHHHHHHHhHHHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHhccCCCCCCCchhHHHHHHHHHHHHHHHhhcCcccCCc
Q 046578          142 SQERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYWWIKQAIIRAIANKSRTIRLPG  221 (379)
Q Consensus       142 A~e~Li~~y~~lV~~ia~r~~~~~~d~eDLvQEg~i~L~~ai~~fD~~~g~~FsTYa~~~Ir~~i~~~lr~~~r~irip~  221 (379)
                      |+++|+..|.++|+++|++|.+++.+.+||+|||++||++|+++|||++|.+|+|||+|||++.|.++++++.+.+++|+
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            56889999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             chHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCccccCCCCcccccCCCCCCCChHHH
Q 046578          222 SMAGMVAKIAEANNVLSRRLRRMPTDSEIAEMLNIHVSTVRLAIERTRHPISLDGAVTDRGCMTMQDIIPGPDETMPERM  301 (379)
Q Consensus       222 ~~~~~~~ki~~a~~~l~~~lgr~pt~~eia~~Lgis~~~~~~~l~~~~~~iSLd~~~~~~~~~~l~d~i~~~~~~~pe~~  301 (379)
                      ++...++++.++...+.+.+|++||.+|||+.+|++.+++..++......+|||.++.+++...+.+.++++...+|++.
T Consensus        81 ~~~~~~~~~~~~~~~l~~~~g~~pt~~eia~~l~~~~~~v~~~~~~~~~~~SLd~~~~~~~~~~l~d~l~d~~~~~p~~~  160 (238)
T TIGR02393        81 HMVETINKLIKAERQLTQELGREPTDEELAERMGMPAEKVREIKKIAQEPISLETPIGEEEDSFLGDFIEDTSIESPDDY  160 (238)
T ss_pred             HHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHHhccCCCcCCCCCCCCcccHHHHhcCCCCCChHHH
Confidence            99999999999999999999999999999999999999999998877789999999877666577788888777788888


Q ss_pred             HHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHHhhchhhhhc
Q 046578          302 VQKQLMKQELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQTNILNNLKVYM  378 (379)
Q Consensus       302 ~~~~e~~~~L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~~l~~~~L~~y~  378 (379)
                      +...+....|..+|..||++||.||.++||+++.+++|++|||+.||+|+++|++++.+|++|||+.+....|+.|+
T Consensus       161 ~~~~~~~~~l~~~l~~L~~~er~vl~l~ygl~~~~~~t~~EIA~~lgis~~~V~q~~~~al~kLr~~~~~~~~~~~~  237 (238)
T TIGR02393       161 AAKELLREQLDEVLETLTERERKVLRMRYGLLDGRPHTLEEVGKEFNVTRERIRQIESKALRKLRHPSRSKKLKSFL  237 (238)
T ss_pred             HHHHHHHHHHHHHHHhCCHHHHHHHHHHhCCCCCCCccHHHHHHHHCCCHHHHHHHHHHHHHHHhhhHHHhHHHHhh
Confidence            88888889999999999999999999999888779999999999999999999999999999999999998888886

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.

>PRK07405 RNA polymerase sigma factor SigD; Validated

Probab=100.00  E-value=1.1e-42  Score=338.34  Aligned_cols=250  Identities=38%  Similarity=0.657  Sum_probs=233.3

Q ss_pred             cCcHHHHHHHHhcccHHHHHHHHHHhHHHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHhccCCCCCCCchhHHHHHHHH
Q 046578          125 ELDYNLVKYKILCKERESQERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYWWIKQ  204 (379)
Q Consensus       125 ~~~~~eLi~~~~~Gd~~A~e~Li~~y~~lV~~ia~r~~~~~~d~eDLvQEg~i~L~~ai~~fD~~~g~~FsTYa~~~Ir~  204 (379)
                      .++..+|+.++..|+ .|++.||..|.++|+++|++|.+++.+++||+||||+|||+++++|||++|++|+||++||||+
T Consensus        66 ~~~~~~L~~~~~~g~-~A~~~L~~~~~~~V~~~a~~~~~~~~~~eDLvQEg~i~L~~a~~~fd~~~g~rf~tYa~~wIR~  144 (317)
T PRK07405         66 KLSEEELRSAIAEGE-AAKRKMVEANLRLVVSVAKKYLKRNVDLLDLIQEGTIGMQRGVEKFDPTKGYRFSTYAYWWIRQ  144 (317)
T ss_pred             cCCHHHHHHHHhccH-HHHHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHhCcCCCCChHHHHHHHHHH
Confidence            356788999999996 8999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHhhcCcccCCcchHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCccccCCCC
Q 046578          205 AIIRAIANKSRTIRLPGSMAGMVAKIAEANNVLSRRLRRMPTDSEIAEMLNIHVSTVRLAIERTRHPISLDGAVTDRGCM  284 (379)
Q Consensus       205 ~i~~~lr~~~r~irip~~~~~~~~ki~~a~~~l~~~lgr~pt~~eia~~Lgis~~~~~~~l~~~~~~iSLd~~~~~~~~~  284 (379)
                      .|.+++.++.+++|+|.++...++++.++...+...+|+.|+.+|||+.+|++.+++..++......+|||.+++++++.
T Consensus       145 ~I~~~i~~~~~~ir~p~~~~~~~~~l~~~~~~l~~~~gr~pt~~eiA~~~~~~~~~v~~~~~~~~~~~SLd~~~~~~~~~  224 (317)
T PRK07405        145 AITRAIAEKSRTIRLPIHITEKLNKIKKAQRQLSQQLGRAATIGELAEELELTPKQVREYLERARQPLSLDLRVGDNQDT  224 (317)
T ss_pred             HHHHHHHhcCCCccCChHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHHcCCCeeecCCCCCCCCc
Confidence            99999999999999999999999999999999999999999999999999999999999998888999999998777666


Q ss_pred             cccccCCCCCCCChHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHH
Q 046578          285 TMQDIIPGPDETMPERMVQKQLMKQELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTK  364 (379)
Q Consensus       285 ~l~d~i~~~~~~~pe~~~~~~e~~~~L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~k  364 (379)
                      .+.+.+++. ..+|++.+...+....|..+|+.||++||.||.++|||+|.+++|++|||+.||||+++|+++..+|++|
T Consensus       225 ~l~~~~~d~-~~~pe~~~~~~~~~~~l~~al~~L~~rer~Vi~lr~gl~~~~~~Tl~EIa~~lgiS~erVRqi~~rAl~k  303 (317)
T PRK07405        225 ELGELLEDT-GASPEDFATQSSLQLDLERLMEDLTPQQKEVIALRFGLEDGQPLTLAKIGERLNISRERVRQIEREALSK  303 (317)
T ss_pred             cHHHhhcCC-CCCHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHhhcCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHH
Confidence            777777765 3678988888888899999999999999999999999988899999999999999999999999999999


Q ss_pred             HHhHHhhchhhhhc
Q 046578          365 LQQTNILNNLKVYM  378 (379)
Q Consensus       365 LR~~l~~~~L~~y~  378 (379)
                      ||+.  ...|++|+
T Consensus       304 Lr~~--~~~l~~~~  315 (317)
T PRK07405        304 LRKR--KANIQEYL  315 (317)
T ss_pred             HHHH--HHHHHHHH
Confidence            9996  45667765

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

Probab=100.00  E-value=2.1e-42  Score=334.05  Aligned_cols=239  Identities=46%  Similarity=0.771  Sum_probs=224.5

Q ss_pred             CcHHHHHHHHhcccHHHHHHHHHHhHHHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHhccCCCCCCCchhHHHHHHHHH
Q 046578          126 LDYNLVKYKILCKERESQERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYWWIKQA  205 (379)
Q Consensus       126 ~~~~eLi~~~~~Gd~~A~e~Li~~y~~lV~~ia~r~~~~~~d~eDLvQEg~i~L~~ai~~fD~~~g~~FsTYa~~~Ir~~  205 (379)
                      ++..+|+.+++.| ..|++.||..|.++|+++|++|.+++.+++||+|||++|||+|+++|||.+|++|+||++|||++.
T Consensus        60 ~~~~~l~~~~~~g-~~A~~~Lv~~~lrlV~~iA~~y~~~~~~~eDLiQEg~igL~~a~~kfd~~~g~rFsTya~~wIr~~  138 (298)
T TIGR02997        60 LSEAELRQRLRQG-QRAKEKMIKANLRLVVSVAKKYQNRGLELLDLIQEGSLGLERAVEKFDPTRGYKFSTYAYWWIRQG  138 (298)
T ss_pred             CCHHHHHHHHhcc-HHHHHHHHHHhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHhCccCCCChHHHHHHHHHHH
Confidence            5667899999989 689999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHhhcCcccCCcchHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCccccCCCCc
Q 046578          206 IIRAIANKSRTIRLPGSMAGMVAKIAEANNVLSRRLRRMPTDSEIAEMLNIHVSTVRLAIERTRHPISLDGAVTDRGCMT  285 (379)
Q Consensus       206 i~~~lr~~~r~irip~~~~~~~~ki~~a~~~l~~~lgr~pt~~eia~~Lgis~~~~~~~l~~~~~~iSLd~~~~~~~~~~  285 (379)
                      |.+++..+.+.+|+|.++....+++.++...+...+|+.|+.+|+|+.+|++.+++..++......+|||.+++++++..
T Consensus       139 I~r~i~~~~r~vr~p~~~~~~~~~~rk~~~~l~~~~~~~pt~~eia~~l~~~~~~v~~~~~~~~~~~SLd~~~~~~~~~~  218 (298)
T TIGR02997       139 ITRAIANQSRTIRLPIHITEKLNKIKKVQRELSQKLGRTPSEAEIAEALELEPEQVRELLQRARQPVSLDAPVGDEEDTE  218 (298)
T ss_pred             HHHHHHhcCCCeeCcHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHHcccCcccCCCcCCCCcch
Confidence            99999999999999999999999999999999999999999999999999999999999988889999999987665556


Q ss_pred             ccccCCCCCCCChHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Q 046578          286 MQDIIPGPDETMPERMVQKQLMKQELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKL  365 (379)
Q Consensus       286 l~d~i~~~~~~~pe~~~~~~e~~~~L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kL  365 (379)
                      +.+.+++ ...+|++.+...+....|..+|+.||++||.||.++|||+|.+++|++|||+.||||+++|++++++|++||
T Consensus       219 ~~~~~~~-~~~~pe~~~~~~~~~~~L~~~L~~L~~rer~Vi~lr~gl~~~~~~Tl~EIa~~lgiS~erVrq~~~rAl~kL  297 (298)
T TIGR02997       219 LGDLLED-DGESPEEQVERESLRQDLESLLAELTPRERQVLRLRFGLDGGEPLTLAEIGRRLNLSRERVRQIEAKALRKL  297 (298)
T ss_pred             HHHhccC-CCCCHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHhccCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHHc
Confidence            6666666 356788888888888899999999999999999999999888999999999999999999999999999999


Q ss_pred             H
Q 046578          366 Q  366 (379)
Q Consensus       366 R  366 (379)
                      |
T Consensus       298 r  298 (298)
T TIGR02997       298 R  298 (298)
T ss_pred             C
Confidence            7

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).

>PRK07408 RNA polymerase sigma factor SigF; Reviewed

Probab=100.00  E-value=1.2e-39  Score=308.39  Aligned_cols=238  Identities=24%  Similarity=0.348  Sum_probs=207.6

Q ss_pred             HHHHHHHH-hcccHHHHHHHHHHhHHHHHHHHHhccCC-CCCHHHHHHHHHHHHHHHHhccCCCCCCCchhHHHHHHHHH
Q 046578          128 YNLVKYKI-LCKERESQERIIRSYRSLVVSIATGYQGK-GLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYWWIKQA  205 (379)
Q Consensus       128 ~~eLi~~~-~~Gd~~A~e~Li~~y~~lV~~ia~r~~~~-~~d~eDLvQEg~i~L~~ai~~fD~~~g~~FsTYa~~~Ir~~  205 (379)
                      ..+++.+. .+||..|+++||..|.|+|+++|++|.+. +.+++||+|||++|||+|+++|||++|++|+||+++||+|.
T Consensus        11 ~~~~~~~~~~~gd~~a~~~Lv~~~~~lV~~ia~~~~~~~~~~~eDL~Qeg~igL~~a~~~fd~~~g~~F~tya~~~Ir~~   90 (256)
T PRK07408         11 TMELLRAYQQNPSIALRNQLVELNLGLVRKEAHRWSNQCSEPYEDLVQVGSLGLIRAIERFDPSKGHAFSSFAIPYIRGE   90 (256)
T ss_pred             HHHHHHHHHHCCCHHHHHHHHHHhHHHHHHHHHHHhccCCCCHHHHHHHHHHHHHHHHHhcCCCCCCCcHHHHHHHHHHH
Confidence            34555555 47899999999999999999999999875 66799999999999999999999999999999999999999


Q ss_pred             HHHHHHhhcCcccCCcchHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHH--hcCCccccCCccccCCC
Q 046578          206 IIRAIANKSRTIRLPGSMAGMVAKIAEANNVLSRRLRRMPTDSEIAEMLNIHVSTVRLAIE--RTRHPISLDGAVTDRGC  283 (379)
Q Consensus       206 i~~~lr~~~r~irip~~~~~~~~ki~~a~~~l~~~lgr~pt~~eia~~Lgis~~~~~~~l~--~~~~~iSLd~~~~~~~~  283 (379)
                      |.+++|++.+.+|+|+++....+++.++...+.+.+|++|+.+|||+.+|++++++..++.  .....+|||.++.++++
T Consensus        91 i~~~lr~~~~~vr~pr~~~~~~~~~~~~~~~l~~~lgr~pt~~elA~~lgi~~~~v~~~~~~~~~~~~~SLd~~~~~~~~  170 (256)
T PRK07408         91 IQHYLRDKSPTVRIPRRWQELQRQAKKVRQELRQELGRQPTDQEIAQALDISLEEWQEIKLALQNRTPLSLDAPVNQDED  170 (256)
T ss_pred             HHHHHHHcCCeeeeCHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHhhccCCccccccCCCCCC
Confidence            9999999999999999999999999999999999999999999999999999999998864  35678999998754433


Q ss_pred             --CcccccCCCCCCCChHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 046578          284 --MTMQDIIPGPDETMPERMVQKQLMKQELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIA  361 (379)
Q Consensus       284 --~~l~d~i~~~~~~~pe~~~~~~e~~~~L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rA  361 (379)
                        ..+.+.++++... +..  ...+....|..++..||+++|.||.++|+    +++|++|||+.||+|+++|+++++||
T Consensus       171 ~~~~l~d~~~d~~~~-~~~--~~~~~~~~l~~~l~~L~~~~r~vl~l~y~----~~~s~~eIA~~lgvs~~~V~~~~~ra  243 (256)
T PRK07408        171 GSTSLGDLLPDPRYR-SFQ--LAQEDRIRLQQALAQLEERTREVLEFVFL----HDLTQKEAAERLGISPVTVSRRVKKG  243 (256)
T ss_pred             CccccccccCCcccc-hhh--hhHHHHHHHHHHHHcCCHHHHHHHHHHHH----CCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence              2455666654432 111  23344567999999999999999999995    77999999999999999999999999


Q ss_pred             HHHHHhHHhhc
Q 046578          362 LTKLQQTNILN  372 (379)
Q Consensus       362 l~kLR~~l~~~  372 (379)
                      +++||+.+..+
T Consensus       244 ~~kLr~~l~~~  254 (256)
T PRK07408        244 LDQLKKLLQPE  254 (256)
T ss_pred             HHHHHHHhhcc
Confidence            99999998754

>PRK05657 RNA polymerase sigma factor RpoS; Validated

Probab=100.00  E-value=2.2e-39  Score=315.89  Aligned_cols=247  Identities=35%  Similarity=0.556  Sum_probs=231.6

Q ss_pred             HHHHHHHhcccHHHHHHHHHHhHHHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHhccCCCCCCCchhHHHHHHHHHHHH
Q 046578          129 NLVKYKILCKERESQERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYWWIKQAIIR  208 (379)
Q Consensus       129 ~eLi~~~~~Gd~~A~e~Li~~y~~lV~~ia~r~~~~~~d~eDLvQEg~i~L~~ai~~fD~~~g~~FsTYa~~~Ir~~i~~  208 (379)
                      .+++.++++||..|++.||..|.++|+++|++|.+++.+++||+||||+++|+++++||+.+|.+|+||++|||+..+.+
T Consensus        74 ~~li~~~~~Gd~~A~~~Li~~y~~~V~~~a~~~~~~~~~aeDLvQE~fi~l~~ai~~fd~~rg~~Fstyatw~iR~ai~~  153 (325)
T PRK05657         74 VYFARRALRGDFAARQRMIESNLRLVVKIAKRYLNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIER  153 (325)
T ss_pred             HHHHHHHHcCCHHHHHHHHHHhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHhCCccCCCHHHHHHHHHHHHHHH
Confidence            67899999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHhhcCcccCCcchHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCccccCCCCcccc
Q 046578          209 AIANKSRTIRLPGSMAGMVAKIAEANNVLSRRLRRMPTDSEIAEMLNIHVSTVRLAIERTRHPISLDGAVTDRGCMTMQD  288 (379)
Q Consensus       209 ~lr~~~r~irip~~~~~~~~ki~~a~~~l~~~lgr~pt~~eia~~Lgis~~~~~~~l~~~~~~iSLd~~~~~~~~~~l~d  288 (379)
                      +++++.+.+++|+++...++.+.++...+...+|+.|+.++||+.+|++++++..++.......|+|.+..++...++.+
T Consensus       154 ~i~~~~r~ir~p~~~~~~l~~~~R~~~~l~~~l~r~~t~~eiA~~l~~~~~~v~~~l~~~~~~~sld~~~~~~~~~~l~d  233 (325)
T PRK05657        154 AIMNQTRTIRLPVHVVKELNVYLRAARELEHKLDHEPSAEEIAELLDKPVDDVSRMLALNERITSLDTPLGGDPEKSLLD  233 (325)
T ss_pred             HHHHcCCccccCHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHhccCCcccCCCCCCCCCcchhh
Confidence            99999999999999998888899999999999999999999999999999999999988778899999887776667777


Q ss_pred             cCCCCCCCChHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhH
Q 046578          289 IIPGPDETMPERMVQKQLMKQELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQT  368 (379)
Q Consensus       289 ~i~~~~~~~pe~~~~~~e~~~~L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~~  368 (379)
                      .+.+....+|++.+...+....|..+|..||+++|.||.++|||.+.+++|++|||+.||+|+++|+++++||+++||+.
T Consensus       234 ~l~d~~~~~pe~~~~~~e~~~~L~~aL~~L~~~~R~vl~lrygL~~~e~~s~~EIA~~Lgis~~tV~~~~~rAl~kLr~~  313 (325)
T PRK05657        234 ILADEQENGPEDTTQDDDMKQSIVKWLFELNDKQREVLARRFGLLGYEAATLEDVAREIGLTRERVRQIQVEALRRLREI  313 (325)
T ss_pred             hccCCCCCCHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHhccCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence            78776667888888888888899999999999999999999988877999999999999999999999999999999999


Q ss_pred             Hhhchhh
Q 046578          369 NILNNLK  375 (379)
Q Consensus       369 l~~~~L~  375 (379)
                      +...++.
T Consensus       314 l~~~~~~  320 (325)
T PRK05657        314 LQTQGLS  320 (325)
T ss_pred             HHhCccc
Confidence            9887764

>PRK07122 RNA polymerase sigma factor SigF; Reviewed

Probab=100.00  E-value=4.7e-39  Score=305.52  Aligned_cols=224  Identities=23%  Similarity=0.362  Sum_probs=200.9

Q ss_pred             cccHH---HHHHHHHHhHHHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHhccCCCCCCCchhHHHHHHHHHHHHHHHhh
Q 046578          137 CKERE---SQERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYWWIKQAIIRAIANK  213 (379)
Q Consensus       137 ~Gd~~---A~e~Li~~y~~lV~~ia~r~~~~~~d~eDLvQEg~i~L~~ai~~fD~~~g~~FsTYa~~~Ir~~i~~~lr~~  213 (379)
                      .|+..   ++++|+..|.|+|.++|++|.+++.+.+||+|+|++||++|+++|||++|++|+|||++||++.|.++++++
T Consensus        33 ~~~~~~~~~r~~Lv~~~l~LV~~iA~~y~~~g~~~~DLiQeG~iGLi~AierFDp~~G~~FsTYA~~~Irg~I~~~lr~~  112 (264)
T PRK07122         33 AGSPEFQRQRDRIVTRCLPLADHIARRFDGRGEPRDDLVQVARVGLVNAVNRFDVETGSDFVSFAVPTIMGEVRRHFRDN  112 (264)
T ss_pred             CCCHHHHHHHHHHHHHhHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHHHHHHcCCCCCCChHHHHHHHHHHHHHHHHHHc
Confidence            34554   889999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cCcccCCcchHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHh--cCCccccCCccccCCC--Cccccc
Q 046578          214 SRTIRLPGSMAGMVAKIAEANNVLSRRLRRMPTDSEIAEMLNIHVSTVRLAIER--TRHPISLDGAVTDRGC--MTMQDI  289 (379)
Q Consensus       214 ~r~irip~~~~~~~~ki~~a~~~l~~~lgr~pt~~eia~~Lgis~~~~~~~l~~--~~~~iSLd~~~~~~~~--~~l~d~  289 (379)
                      .+.+++|+++....+++.++...+.+.+|+.|+.+|||+.||++.+++..++..  ...++|||.++.++++  ..+.+.
T Consensus       113 ~~~ir~Pr~~~~~~~~i~~~~~~l~~~lg~~pt~~eiA~~lg~~~~~v~~~~~~~~~~~~~SLd~~~~~~~~~~~~~~d~  192 (264)
T PRK07122        113 SWSVKVPRRLKELHLRLGRATAELSQRLGRAPTASELAAELGMDREEVVEGLVAGSAYNTLSIDSGGGSGDDDARAIADT  192 (264)
T ss_pred             CCccccCHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHHhhcCCCCcccccccCCCCCcccchhc
Confidence            999999999999999999999999999999999999999999999999998764  4578999998764332  123333


Q ss_pred             CCCCCCCChHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHH
Q 046578          290 IPGPDETMPERMVQKQLMKQELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQTN  369 (379)
Q Consensus       290 i~~~~~~~pe~~~~~~e~~~~L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~~l  369 (379)
                      ++     +++..++..+....+..++..||+++|.||.++|+    +++|++|||+.||+|.++|++++++|+++||+.+
T Consensus       193 ~~-----~~~~~~e~~~~~~~l~~~l~~L~~rer~vl~l~y~----~~~t~~EIA~~lgis~~~V~~~~~ral~kLr~~l  263 (264)
T PRK07122        193 LG-----DVDAGLDQIENREALRPLLAALPERERTVLVLRFF----ESMTQTQIAERVGISQMHVSRLLAKTLARLRDQL  263 (264)
T ss_pred             cC-----CcHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHhc----CCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHc
Confidence            32     34555666677788999999999999999999995    7799999999999999999999999999999975

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

Probab=100.00  E-value=1.3e-38  Score=295.93  Aligned_cols=234  Identities=30%  Similarity=0.429  Sum_probs=211.3

Q ss_pred             cHHHHHHHHhcccHHHHHHHHHHhHHHHHHHHHhccCCCC-CHHHHHHHHHHHHHHHHhccCCCCCCCchhHHHHHHHHH
Q 046578          127 DYNLVKYKILCKERESQERIIRSYRSLVVSIATGYQGKGL-SLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYWWIKQA  205 (379)
Q Consensus       127 ~~~eLi~~~~~Gd~~A~e~Li~~y~~lV~~ia~r~~~~~~-d~eDLvQEg~i~L~~ai~~fD~~~g~~FsTYa~~~Ir~~  205 (379)
                      +...++...++||+.+. .|++.|.|+|.++|++|.+++. +.|||+|-|++||++|+++|||++|.+|+|||..+|+++
T Consensus        10 e~~~~~~~~~~g~~~~~-~Li~~ylpLV~~ia~k~~~r~~~~~dDLiqiG~iGLi~Aieryd~~kg~kF~tyA~~~I~Ge   88 (247)
T COG1191          10 EEEKLLEYYAEGDEEAR-RLIERYLPLVKSIARKFENRGPSEYDDLIQIGMIGLIKAIERYDPSKGTKFSTYAVRRIRGE   88 (247)
T ss_pred             HHHHHHHHHHhcCHHHH-HHHHHHHHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHHHHHcCcccCcchHHHHHHHHHHH
Confidence            34678889999999999 9999999999999999998766 999999999999999999999999999999999999999


Q ss_pred             HHHHHHhhcCcccCCcchHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhc--CCccccCCccccCCC
Q 046578          206 IIRAIANKSRTIRLPGSMAGMVAKIAEANNVLSRRLRRMPTDSEIAEMLNIHVSTVRLAIERT--RHPISLDGAVTDRGC  283 (379)
Q Consensus       206 i~~~lr~~~r~irip~~~~~~~~ki~~a~~~l~~~lgr~pt~~eia~~Lgis~~~~~~~l~~~--~~~iSLd~~~~~~~~  283 (379)
                      |++++|++. .+++|+..++..+++..+.+++..++||+||+.|||+.||++.+++...+...  ...+|+|.....+++
T Consensus        89 i~d~LR~~~-~v~vpR~~~~~~~~i~~~~~~l~~el~r~pt~~EIA~~L~i~~ee~~~~~~~~~~~~~~sld~~~~~~~d  167 (247)
T COG1191          89 ILDYLRKND-SVKVPRSLRELGRRIEEAIDELEQELGREPTDEEIAEELGIDKEEYIEALLAINGSQLLSLDEDVLKDDD  167 (247)
T ss_pred             HHHHHHhCC-CccCcHHHHHHHHHHHHHHHHHHHHhCCCCcHHHHHHHhCCCHHHHHHHHHHhccccccchhhhhccccc
Confidence            999999999 99999999999999999999999999999999999999999999999998775  478888876654433


Q ss_pred             CcccccCCCCCCCChHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 046578          284 MTMQDIIPGPDETMPERMVQKQLMKQELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALT  363 (379)
Q Consensus       284 ~~l~d~i~~~~~~~pe~~~~~~e~~~~L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~  363 (379)
                      ..     ..+...+|.+.++..+....+.+++..|+++||.|+.++|+    +++|++|||+.||||+++|+|++++|++
T Consensus       168 ~~-----~~~~~~~~~~~~~~~~~~~~l~~ai~~L~EREk~Vl~l~y~----eelt~kEI~~~LgISes~VSql~kkai~  238 (247)
T COG1191         168 DD-----VDDQIENPDDGVEKEELLEILKEAIEPLPEREKLVLVLRYK----EELTQKEIAEVLGISESRVSRLHKKAIK  238 (247)
T ss_pred             cc-----hhhccccchhHHHHHHHHHHHHHHHHccCHHHHHHHHHHHH----hccCHHHHHHHhCccHHHHHHHHHHHHH
Confidence            22     22233456777888888888999999999999999999995    8899999999999999999999999999


Q ss_pred             HHHhHHhh
Q 046578          364 KLQQTNIL  371 (379)
Q Consensus       364 kLR~~l~~  371 (379)
                      +||+.+..
T Consensus       239 kLr~~l~~  246 (247)
T COG1191         239 KLRKELNK  246 (247)
T ss_pred             HHHHHhcc
Confidence            99998753

>PRK05911 RNA polymerase sigma factor sigma-28; Reviewed

Probab=100.00  E-value=5.6e-38  Score=297.14  Aligned_cols=236  Identities=27%  Similarity=0.370  Sum_probs=208.9

Q ss_pred             HHHHHHH-hcccHHHHHHHHHHhHHHHHHHHHhcc---CCCCCHHHHHHHHHHHHHHHHhccCCCCCCCchhHHHHHHHH
Q 046578          129 NLVKYKI-LCKERESQERIIRSYRSLVVSIATGYQ---GKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYWWIKQ  204 (379)
Q Consensus       129 ~eLi~~~-~~Gd~~A~e~Li~~y~~lV~~ia~r~~---~~~~d~eDLvQEg~i~L~~ai~~fD~~~g~~FsTYa~~~Ir~  204 (379)
                      ++++... ..||..|+++|+..|.|+|+++|++|.   ..+.+.+||+|+|++|||+|+++|||++|++|+||+.+||++
T Consensus        10 ~~~~~~~~~~~~~~ar~~Li~~~~~lV~~ia~~~~~~~~~~~~~eDL~QeG~igL~~ai~~fd~~~g~~F~tya~~~Ir~   89 (257)
T PRK05911         10 AETWQLYWSTQEIEYRDVLIEFYLPLVKNVAHRLISGMPSHVKTEDLYASGVEGLVRAVERFDPEKSRRFEGYALFLIKA   89 (257)
T ss_pred             HHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHHHHHhcCCccCCCHHHHHHHHHHH
Confidence            4555555 469999999999999999999999985   235689999999999999999999999999999999999999


Q ss_pred             HHHHHHHhhcCcccCCcchHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhc--CCccccCCcccc--
Q 046578          205 AIIRAIANKSRTIRLPGSMAGMVAKIAEANNVLSRRLRRMPTDSEIAEMLNIHVSTVRLAIERT--RHPISLDGAVTD--  280 (379)
Q Consensus       205 ~i~~~lr~~~r~irip~~~~~~~~ki~~a~~~l~~~lgr~pt~~eia~~Lgis~~~~~~~l~~~--~~~iSLd~~~~~--  280 (379)
                      +|.+++|+..   ++|+++....+++..+...+.+.+|++|+.+|||+.+|++.+++...+...  ...+|+|.++.+  
T Consensus        90 ~i~~~lr~~~---~~pr~~~~~~~~l~~~~~~l~~~~gr~pt~~eiA~~l~i~~~~v~~~~~~~~~~~~~Sld~~~~~~~  166 (257)
T PRK05911         90 AIIDDLRKQD---WVPRSVHQKANKLADAMDSLRQSLGKEPTDGELCEYLNISQQELSGWFSSARPALILSLNEEFPCQS  166 (257)
T ss_pred             HHHHHHHhcC---CCCHHHHHHHHHHHHHHHHHHHHHCcCCCHHHHHHHhCcCHHHHHHHHHHhhccceeeccccCCCCC
Confidence            9999999876   489999999999999999999999999999999999999999999887653  356899987643  


Q ss_pred             C--CCCcccccCCCCCCCChHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHH
Q 046578          281 R--GCMTMQDIIPGPDETMPERMVQKQLMKQELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIR  358 (379)
Q Consensus       281 ~--~~~~l~d~i~~~~~~~pe~~~~~~e~~~~L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~  358 (379)
                      +  +...+.+.+++.....|++.+...+....|..+|..||+++|.||.++|+    +++|++|||+.||+|.++|++++
T Consensus       167 ~~~~~~~l~~~l~d~~~~~~~~~~~~~~~~~~l~~al~~L~~~er~vi~l~y~----e~~t~~EIA~~lgis~~~V~~~~  242 (257)
T PRK05911        167 DDEAGLALEERIADERAETGYDVVDKKEFSSILAEAILALEEKERKVMALYYY----EELVLKEIGKILGVSESRVSQIH  242 (257)
T ss_pred             CCccccchhhhccCCCCCCHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHh----cCCCHHHHHHHHCcCHHHHHHHH
Confidence            1  22346677777766678888888888889999999999999999999995    78999999999999999999999


Q ss_pred             HHHHHHHHhHHhh
Q 046578          359 GIALTKLQQTNIL  371 (379)
Q Consensus       359 ~rAl~kLR~~l~~  371 (379)
                      ++|+++||+.+..
T Consensus       243 ~ral~kLr~~l~~  255 (257)
T PRK05911        243 SKALLKLRATLSA  255 (257)
T ss_pred             HHHHHHHHHHHHh
Confidence            9999999999754

>PRK07500 rpoH2 RNA polymerase factor sigma-32; Reviewed

Probab=100.00  E-value=8.2e-38  Score=300.58  Aligned_cols=243  Identities=29%  Similarity=0.450  Sum_probs=206.0

Q ss_pred             HHHHHHHH-hcccHHHHHHHHHHhHHHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHhccCCCCCCCchhHHHHHHHHHH
Q 046578          128 YNLVKYKI-LCKERESQERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYWWIKQAI  206 (379)
Q Consensus       128 ~~eLi~~~-~~Gd~~A~e~Li~~y~~lV~~ia~r~~~~~~d~eDLvQEg~i~L~~ai~~fD~~~g~~FsTYa~~~Ir~~i  206 (379)
                      ..+|+.+. ..||..|+++||..|.|+|+++|++|.+++.+++||+||||+|||+++++||+.+|.+|+||+++||++.|
T Consensus        26 e~~L~~~~~~~gd~~A~~~Lv~~~~~lV~~~a~~~~~~~~~~eDLvQeg~i~L~~a~~~fd~~~~~~f~tya~~~Ir~~I  105 (289)
T PRK07500         26 EHALAYRWKDHRDEDALHRIISAHMRLVISMAGKFRRFGLPMNDLIQEGYVGLLEAAARFEPDREVRFSTYATWWIRASI  105 (289)
T ss_pred             HHHHHHHHHHCCCHHHHHHHHHHhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHcCCCCCCChHHHHHHHHHHHH
Confidence            46788886 48999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHhhcCcccCCcchHH--HHHHHHHHHHHHHH---HhCCCCCHHHHHHHhCCCHHHHHHHHHh-cCCccccCCcccc
Q 046578          207 IRAIANKSRTIRLPGSMAG--MVAKIAEANNVLSR---RLRRMPTDSEIAEMLNIHVSTVRLAIER-TRHPISLDGAVTD  280 (379)
Q Consensus       207 ~~~lr~~~r~irip~~~~~--~~~ki~~a~~~l~~---~lgr~pt~~eia~~Lgis~~~~~~~l~~-~~~~iSLd~~~~~  280 (379)
                      .+++++..+.+|+|.+...  ...++.+....+..   .+|+.|+.+|||+.||++.+++...... ....+|||.++++
T Consensus       106 ~~~lr~~~~~iR~p~~~~~~~~~~~~~~~~~~~~~~~~~l~~~pt~~eiA~~l~~~~~~v~~~~~~~~~~~~SLd~~~~~  185 (289)
T PRK07500        106 QDYILRNWSIVRGGTSSAQKALFFNLRRLRARLAQADEELTKQEIHREIATALGVSLSDVEMMDARLSGPDASLNAPQSE  185 (289)
T ss_pred             HHHHHHCCCceecCccHHHHHHHHHHHHHHHHHHhhhcccCCCCCHHHHHHHhCcCHHHHHHHHHHhcCCCccccCCCCC
Confidence            9999999999999988654  33444444444444   6899999999999999999999877543 5579999999875


Q ss_pred             CCCC--cccccCCCCCCCChHHHHHH----HHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHH
Q 046578          281 RGCM--TMQDIIPGPDETMPERMVQK----QLMKQELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERI  354 (379)
Q Consensus       281 ~~~~--~l~d~i~~~~~~~pe~~~~~----~e~~~~L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~V  354 (379)
                      +++.  .+.+.+.+.. .+|++.+..    .+....|..+|+.||++||.||.++|+ . .+++|++|||+.||+|+++|
T Consensus       186 ~~~~~~~l~d~i~d~~-~~pe~~~~~~~~~~~~~~~l~~al~~L~~rer~vl~lr~~-~-~~~~t~~EIa~~lgvs~~~V  262 (289)
T PRK07500        186 EDEGRSERMDFLVDDS-PLPDEQVESSIDGERRRRWLTQALQTLNERELRIIRERRL-R-EDGATLEALGEELGISKERV  262 (289)
T ss_pred             CCCCcccHHHhccCCC-CCchHHHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhc-C-CCCCCHHHHHHHHCCCHHHH
Confidence            5432  4667777653 356655432    345677999999999999999999984 2 27799999999999999999


Q ss_pred             HHHHHHHHHHHHhHHhhch
Q 046578          355 RQIRGIALTKLQQTNILNN  373 (379)
Q Consensus       355 r~~~~rAl~kLR~~l~~~~  373 (379)
                      ++++++|+++||..+....
T Consensus       263 ~q~~~~Al~kLr~~l~~~~  281 (289)
T PRK07500        263 RQIEARALEKLRRALLSQS  281 (289)
T ss_pred             HHHHHHHHHHHHHHHHhcC
Confidence            9999999999999987543

>PRK06596 RNA polymerase factor sigma-32; Reviewed

Probab=100.00  E-value=1.2e-37  Score=298.73  Aligned_cols=238  Identities=29%  Similarity=0.409  Sum_probs=200.9

Q ss_pred             HHHHHH-HhcccHHHHHHHHHHhHHHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHhccCCCCCCCchhHHHHHHHHHHH
Q 046578          129 NLVKYK-ILCKERESQERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYWWIKQAII  207 (379)
Q Consensus       129 ~eLi~~-~~~Gd~~A~e~Li~~y~~lV~~ia~r~~~~~~d~eDLvQEg~i~L~~ai~~fD~~~g~~FsTYa~~~Ir~~i~  207 (379)
                      .+|+.+ ...||..|++.||..|.|+|+++|++|.+.+.+.+||+|||++||++|+++|||++|.+|+|||++||++.|.
T Consensus        35 ~~l~~~~~~~Gd~~a~~~Lv~~~~~lV~~ia~~~~~~~~~~eDLvQeg~igL~~a~~~fd~~~~~~FstYA~~~Ir~~i~  114 (284)
T PRK06596         35 YMLAKRLREHGDLEAAKQLVLSHLRFVVHIARGYRGYGLPQADLIQEGNIGLMKAVKRFDPEVGVRLVSFAVHWIKAEIH  114 (284)
T ss_pred             HHHHHHHHHcCCHHHHHHHHHHhHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHHHhCcccCCCHHHHHHHHHHHHHH
Confidence            567888 4689999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHhhcCcccCCcchHHHHHHHHHHHHHHHHHh--CCCCCHHHHHHHhCCCHHHHHHHHHh-cCCccccCCccccCC--
Q 046578          208 RAIANKSRTIRLPGSMAGMVAKIAEANNVLSRRL--RRMPTDSEIAEMLNIHVSTVRLAIER-TRHPISLDGAVTDRG--  282 (379)
Q Consensus       208 ~~lr~~~r~irip~~~~~~~~ki~~a~~~l~~~l--gr~pt~~eia~~Lgis~~~~~~~l~~-~~~~iSLd~~~~~~~--  282 (379)
                      +++++..+.+++|.+...  +++......+...+  +++|+.+|||+.||++.+++..++.. ....+|||.++++++  
T Consensus       115 ~~l~~~~~~vr~p~~~~~--~~~~~~~~~~~~~l~~~~~~t~~eiA~~l~~~~~~v~~~~~~~~~~~~SLd~~~~~~~~~  192 (284)
T PRK06596        115 EYILRNWRIVKVATTKAQ--RKLFFNLRKAKKRLGWLNPEEVEMVAEELGVSEEEVREMESRLSGQDASLDAPIDDDDEE  192 (284)
T ss_pred             HHHHHcCCeeeccchHHH--HHHHHHHHHHHHHhccCCCCCHHHHHHHhCcCHHHHHHHHHHhcCCCcCcCCCCCCCCCC
Confidence            999998778899987532  23333333444444  48999999999999999999998753 458999999886442  


Q ss_pred             CCcccccCCCCCCCChHHHHHHH----HHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHH
Q 046578          283 CMTMQDIIPGPDETMPERMVQKQ----LMKQELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIR  358 (379)
Q Consensus       283 ~~~l~d~i~~~~~~~pe~~~~~~----e~~~~L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~  358 (379)
                      ...+.+.+++. ..+|++.+...    +....|..+++.||++||.||.++|| .+ +++|++|||+.||||+++|+|++
T Consensus       193 ~~~l~~~l~d~-~~~p~~~~~~~~~~~~~~~~L~~al~~L~~rEr~VL~lry~-~~-~~~Tl~EIA~~lgvS~~rVrqi~  269 (284)
T PRK06596        193 SGAPQDYLEDK-SSDPADVLEEDNWEDQRRALLADALEGLDERSRDIIEARWL-DD-DKSTLQELAAEYGVSAERVRQIE  269 (284)
T ss_pred             cchHHHHcCCC-CCCchHHHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhc-CC-CCcCHHHHHHHHCCCHHHHHHHH
Confidence            23466777765 34677666543    35678999999999999999999995 32 68999999999999999999999


Q ss_pred             HHHHHHHHhHHhh
Q 046578          359 GIALTKLQQTNIL  371 (379)
Q Consensus       359 ~rAl~kLR~~l~~  371 (379)
                      ++|++|||+.+..
T Consensus       270 ~~Al~kLR~~l~~  282 (284)
T PRK06596        270 KNAMKKLKAAIEA  282 (284)
T ss_pred             HHHHHHHHHHHHh
Confidence            9999999998764

>TIGR02850 spore_sigG RNA polymerase sigma-G factor

Probab=100.00  E-value=2.2e-37  Score=292.71  Aligned_cols=231  Identities=24%  Similarity=0.363  Sum_probs=205.4

Q ss_pred             HHHHHHHhcccHHHHHHHHHHhHHHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHhccCCCCCCCchhHHHHHHHHHHHH
Q 046578          129 NLVKYKILCKERESQERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYWWIKQAIIR  208 (379)
Q Consensus       129 ~eLi~~~~~Gd~~A~e~Li~~y~~lV~~ia~r~~~~~~d~eDLvQEg~i~L~~ai~~fD~~~g~~FsTYa~~~Ir~~i~~  208 (379)
                      .+++.+++.||..|++.||..|.|+|+++|++|.+++.+++||+||||++||+++++||+.+|.+|+||+++||+|.+.+
T Consensus        22 ~~li~~~~~gd~~a~~~L~~~~~~~v~~~a~~~~~~~~~aeDlvQe~~i~l~~a~~~fd~~~~~~f~tyl~~~irn~~~~  101 (254)
T TIGR02850        22 RELFIRMQSGDTTAREKLINGNLRLVLSVIQRFNNRGEYVDDLFQVGCIGLMKSIDNFDLSQNVKFSTYAVPMIIGEIRR  101 (254)
T ss_pred             HHHHHHHHcCCHHHHHHHHHHhHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCChHHHHHHHHHHHHHH
Confidence            67888999999999999999999999999999999999999999999999999999999999899999999999999999


Q ss_pred             HHHhhcCcccCCcchHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCccccCCC--Ccc
Q 046578          209 AIANKSRTIRLPGSMAGMVAKIAEANNVLSRRLRRMPTDSEIAEMLNIHVSTVRLAIERTRHPISLDGAVTDRGC--MTM  286 (379)
Q Consensus       209 ~lr~~~r~irip~~~~~~~~ki~~a~~~l~~~lgr~pt~~eia~~Lgis~~~~~~~l~~~~~~iSLd~~~~~~~~--~~l  286 (379)
                      ++|+.. .+++|+++.....++.++..++...+|++|+.+|||+.+|++++++..++.....++|||.++.++++  ..+
T Consensus       102 ~lr~~~-~ir~p~~~~~~~~~~~~~~~~l~~~l~~~pt~~elA~~l~~~~e~v~~~~~~~~~~~Sld~~~~~~~~~~~~~  180 (254)
T TIGR02850       102 YLRDNN-PIRVSRSLRDIAYKALQVRDKLISENSKEPTVSEIAKELKVPQEEVVFALDAIQDPVSLFEPIYNDGGDPIYV  180 (254)
T ss_pred             HHHhCC-CccCchHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHCcCHHHHHHHHHhcCCCCcccCCCCCCCCCcchh
Confidence            999975 78999999999999999999999999999999999999999999999999888888999988754433  234


Q ss_pred             cccCCCCCCCChHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 046578          287 QDIIPGPDETMPERMVQKQLMKQELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQ  366 (379)
Q Consensus       287 ~d~i~~~~~~~pe~~~~~~e~~~~L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR  366 (379)
                      .+.+.+... .++    .......+..++..|++++|.||.++|+    +++|++|||+.||+|+++|++++++|+++||
T Consensus       181 ~~~~~d~~~-~~~----~~~~~~~l~~~l~~L~~rer~vi~~~~~----~~~t~~eIA~~lgis~~~V~~~~~ral~kLr  251 (254)
T TIGR02850       181 MDQISDEKN-KDS----QWLEGIALKEAMKRLNEREKMILNMRFF----EGKTQMEVAEEIGISQAQVSRLEKAALKHMR  251 (254)
T ss_pred             hhhcCCccc-cHH----HHHhHHHHHHHHHcCCHHHHHHHHHHHc----CCCCHHHHHHHHCcCHHHHHHHHHHHHHHHH
Confidence            555555422 122    1223456889999999999999999994    6799999999999999999999999999999


Q ss_pred             hHH
Q 046578          367 QTN  369 (379)
Q Consensus       367 ~~l  369 (379)
                      +.+
T Consensus       252 ~~~  254 (254)
T TIGR02850       252 KYV  254 (254)
T ss_pred             hhC
Confidence            863

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

>TIGR02394 rpoS_proteo RNA polymerase sigma factor RpoS

Probab=100.00  E-value=4.6e-37  Score=295.14  Aligned_cols=247  Identities=36%  Similarity=0.566  Sum_probs=227.2

Q ss_pred             HHHHHHHHhcccHHHHHHHHHHhHHHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHhccCCCCCCCchhHHHHHHHHHHH
Q 046578          128 YNLVKYKILCKERESQERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYWWIKQAII  207 (379)
Q Consensus       128 ~~eLi~~~~~Gd~~A~e~Li~~y~~lV~~ia~r~~~~~~d~eDLvQEg~i~L~~ai~~fD~~~g~~FsTYa~~~Ir~~i~  207 (379)
                      ..+|+.++++||..|++.||..|.++|+++|++|.+++.+++||+||||+|+|+++++||+..|.+|+||+.|+++..+.
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            47899999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHhhcCcccCCcchHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCccccCCCCccc
Q 046578          208 RAIANKSRTIRLPGSMAGMVAKIAEANNVLSRRLRRMPTDSEIAEMLNIHVSTVRLAIERTRHPISLDGAVTDRGCMTMQ  287 (379)
Q Consensus       208 ~~lr~~~r~irip~~~~~~~~ki~~a~~~l~~~lgr~pt~~eia~~Lgis~~~~~~~l~~~~~~iSLd~~~~~~~~~~l~  287 (379)
                      ++++++.+.+++|+++...++.+.+..+.+...+|+.|+..++|+.+|++.+.+..++....+..|+|.+..+++...+.
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            99999999999999999999999888888889999999999999999999999999998888899999877665544555


Q ss_pred             ccCCCCCCCChHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHh
Q 046578          288 DIIPGPDETMPERMVQKQLMKQELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQ  367 (379)
Q Consensus       288 d~i~~~~~~~pe~~~~~~e~~~~L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~  367 (379)
                      +.+.++...+|++.+...+....|..+|.+||+++|.||.++|||.+.+++|++|||+.||+|.++|++++++|+++||+
T Consensus       193 ~~~~~~~~~~pe~~~~~~e~~~~L~~al~~Lp~~~R~Vl~l~ygL~~~e~~s~~EIA~~Lgis~~tVk~~l~rAlkkLr~  272 (285)
T TIGR02394       193 DTIADEQSIDPESLVQNDDLKQLIEAWLAELNERQREVLARRFGLLGYEPATLEEVAAEVGLTRERVRQIQVEALKKLRR  272 (285)
T ss_pred             hhhcCCCCCCHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHhCCCCCCCccHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence            56665555678888888888899999999999999999999997766788999999999999999999999999999999


Q ss_pred             HHhhchh
Q 046578          368 TNILNNL  374 (379)
Q Consensus       368 ~l~~~~L  374 (379)
                      .+...++
T Consensus       273 ~l~~~~~  279 (285)
T TIGR02394       273 ILERDGV  279 (285)
T ss_pred             HHHHhhh
Confidence            9987655

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).

>TIGR02392 rpoH_proteo alternative sigma factor RpoH

Probab=100.00  E-value=4.8e-37  Score=292.82  Aligned_cols=238  Identities=28%  Similarity=0.415  Sum_probs=196.5

Q ss_pred             HHHHHHH-HhcccHHHHHHHHHHhHHHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHhccCCCCCCCchhHHHHHHHHHH
Q 046578          128 YNLVKYK-ILCKERESQERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYWWIKQAI  206 (379)
Q Consensus       128 ~~eLi~~-~~~Gd~~A~e~Li~~y~~lV~~ia~r~~~~~~d~eDLvQEg~i~L~~ai~~fD~~~g~~FsTYa~~~Ir~~i  206 (379)
                      ..+|+.+ .+.||..|++.|+..|.|+|+++|++|.+++.+++||+|||++||++++++|||++|.+|+|||.+||+++|
T Consensus        21 e~~l~~~~~~~gd~~a~~~Lv~~~~~lV~~~a~~~~~~~~~~eDLvQeg~igl~~a~~~fd~~~~~~FsTYA~~~Ir~~i  100 (270)
T TIGR02392        21 EYQLAKRLREHGDLDAAKKLVLSHLRFVVKIARGYRGYGLPQADLIQEGNIGLMKAVKRFDPERGVRLVSFAVHWIKAEI  100 (270)
T ss_pred             HHHHHHHHHHCCCHHHHHHHHHHhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHhCcccCCChHHhhHHHHHHHH
Confidence            3567887 578999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHhhcCcccCCcchH--HHHHHHHHHHHHHHHHhCCCC-CHHHHHHHhCCCHHHHHHHHHh-cCCccccCCccccCC
Q 046578          207 IRAIANKSRTIRLPGSMA--GMVAKIAEANNVLSRRLRRMP-TDSEIAEMLNIHVSTVRLAIER-TRHPISLDGAVTDRG  282 (379)
Q Consensus       207 ~~~lr~~~r~irip~~~~--~~~~ki~~a~~~l~~~lgr~p-t~~eia~~Lgis~~~~~~~l~~-~~~~iSLd~~~~~~~  282 (379)
                      .+++++..+.+|+|.+..  ....++.+....+.  .++.| +.+|||+.||++.+++.+++.. ....+|||.++++++
T Consensus       101 ~~~l~~~~~~ir~p~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~eiA~~l~~~~~~v~~~~~~~~~~~~Sld~~~~~~~  178 (270)
T TIGR02392       101 HEYILRNWRLVKVATTKAQRKLFFNLRKMKKRLQ--GWLNPEEVEAIAEELGVSEREVREMESRLSGQDMSLNASIDDDE  178 (270)
T ss_pred             HHHHHHcCCceecCchHHHHHHHHHHHHHHHHHh--cCCCCCCHHHHHHHhCCCHHHHHHHHHHccCCCccCCCCCCCCC
Confidence            999999877789897654  23334443333332  12555 5899999999999999998654 335899999886644


Q ss_pred             C--CcccccCCCCCCCChHHHHHHH----HHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHH
Q 046578          283 C--MTMQDIIPGPDETMPERMVQKQ----LMKQELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQ  356 (379)
Q Consensus       283 ~--~~l~d~i~~~~~~~pe~~~~~~----e~~~~L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~  356 (379)
                      +  ..+.+.+.+.. .+|++.+...    +....|..+|..||++||.||.++|+ . .+++|++|||+.||||+++|++
T Consensus       179 ~~~~~~~~~l~d~~-~~pe~~~~~~~~~~~~~~~L~~al~~L~~rer~vl~l~y~-~-~~~~t~~eIA~~lgvS~~~V~q  255 (270)
T TIGR02392       179 DDGGAPIAYLVDKT-SDPEDTLEEEQWEELQRQALANALGSLDARSRRIIEARWL-D-DDKLTLQELAAEYGVSAERIRQ  255 (270)
T ss_pred             CccccHHHHhcCCC-CChHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHhc-C-CCCcCHHHHHHHHCCCHHHHHH
Confidence            3  24556666654 4567666543    35577999999999999999999995 2 2579999999999999999999


Q ss_pred             HHHHHHHHHHhHHh
Q 046578          357 IRGIALTKLQQTNI  370 (379)
Q Consensus       357 ~~~rAl~kLR~~l~  370 (379)
                      ++.+|++|||+.+.
T Consensus       256 ~~~~Al~kLr~~l~  269 (270)
T TIGR02392       256 IEKNAMKKLKAALA  269 (270)
T ss_pred             HHHHHHHHHHHHhc
Confidence            99999999999864

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=100.00  E-value=1.5e-36  Score=287.70  Aligned_cols=232  Identities=25%  Similarity=0.360  Sum_probs=205.9

Q ss_pred             HHHHHHHHhcccHHHHHHHHHHhHHHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHhccCCCCCCCchhHHHHHHHHHHH
Q 046578          128 YNLVKYKILCKERESQERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYWWIKQAII  207 (379)
Q Consensus       128 ~~eLi~~~~~Gd~~A~e~Li~~y~~lV~~ia~r~~~~~~d~eDLvQEg~i~L~~ai~~fD~~~g~~FsTYa~~~Ir~~i~  207 (379)
                      ..+|+.+++.||..+++.||..|.|+|+++|++|.+++.+++||+|||++++|+++++||+.+|.+|.||+++||+|.|.
T Consensus        24 ~~~l~~~~~~gd~~a~~~l~~~~~~~v~~~a~~~~~~~~~aeDlvQe~~i~l~~a~~~fd~~~~~~f~t~l~~~ir~~i~  103 (258)
T PRK08215         24 MRELFERMQNGDKEAREKLINGNLRLVLSVIQRFNNRGENVDDLFQVGCIGLMKAIDNFDLSQNVKFSTYAVPMIIGEIR  103 (258)
T ss_pred             HHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCCcHHHHHHHHHHHHH
Confidence            36688899999999999999999999999999999999999999999999999999999999998999999999999999


Q ss_pred             HHHHhhcCcccCCcchHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCccccCCCC--c
Q 046578          208 RAIANKSRTIRLPGSMAGMVAKIAEANNVLSRRLRRMPTDSEIAEMLNIHVSTVRLAIERTRHPISLDGAVTDRGCM--T  285 (379)
Q Consensus       208 ~~lr~~~r~irip~~~~~~~~ki~~a~~~l~~~lgr~pt~~eia~~Lgis~~~~~~~l~~~~~~iSLd~~~~~~~~~--~  285 (379)
                      +++|+.. .+++|++......++.++..++...+|+.|+..|+|+.+|++++++...+.....+.|++.++.++++.  .
T Consensus       104 ~~lr~~~-~vrip~~~~~~~~~~~~~~~~l~~~~~r~p~~~eia~~l~v~~~~v~~~~~~~~~~~sl~~~~~~~~~~~~~  182 (258)
T PRK08215        104 RYLRDNN-PIRVSRSLRDIAYKALQVREKLINENSKEPTVEEIAKELEVPREEVVFALDAIQDPVSLFEPIYHDGGDPIY  182 (258)
T ss_pred             HHHHhCC-ceEecHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHCcCHHHHHHHHHhcCCCccccCCCCCCCCcchh
Confidence            9999985 789999999999999999999999999999999999999999999999888777888999887654432  2


Q ss_pred             ccccCCCCCCCChHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Q 046578          286 MQDIIPGPDETMPERMVQKQLMKQELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKL  365 (379)
Q Consensus       286 l~d~i~~~~~~~pe~~~~~~e~~~~L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kL  365 (379)
                      +.+.++++.. .++.    ......+..++..||++++.||.++|+    +++|++|||+.||+|+++|++++++|+++|
T Consensus       183 ~~~~~~~~~~-~~~~----~~~~~~l~~~l~~L~~~er~vi~~~~~----~~~t~~eIA~~lgis~~~V~~~~~~al~kL  253 (258)
T PRK08215        183 VMDQISDEKN-KDEN----WLEEIALKEAMKKLNDREKLILNLRFF----QGKTQMEVAEEIGISQAQVSRLEKAALKHM  253 (258)
T ss_pred             hhhhccCccc-cHHH----HHhHHHHHHHHHcCCHHHHHHHHHHHh----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHH
Confidence            3455554322 2222    223356889999999999999999994    679999999999999999999999999999


Q ss_pred             HhHH
Q 046578          366 QQTN  369 (379)
Q Consensus       366 R~~l  369 (379)
                      |+.+
T Consensus       254 r~~l  257 (258)
T PRK08215        254 RKYI  257 (258)
T ss_pred             HHHh
Confidence            9876

>TIGR02885 spore_sigF RNA polymerase sigma-F factor

Probab=100.00  E-value=1.7e-36  Score=282.51  Aligned_cols=229  Identities=27%  Similarity=0.373  Sum_probs=202.2

Q ss_pred             HHHHHhcccHHHHHHHHHHhHHHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHhccCCCCCCCchhHHHHHHHHHHHHHH
Q 046578          131 VKYKILCKERESQERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYWWIKQAIIRAI  210 (379)
Q Consensus       131 Li~~~~~Gd~~A~e~Li~~y~~lV~~ia~r~~~~~~d~eDLvQEg~i~L~~ai~~fD~~~g~~FsTYa~~~Ir~~i~~~l  210 (379)
                      |+.+++.||..|++.||..|.|+|+++|++|.+++.+++||+||||+++|+++++||+..|.+|.||+++||+|.|.+++
T Consensus         1 li~~~~~gd~~a~~~l~~~y~~~v~~~a~~~~~~~~~aeDl~Qe~~i~l~~a~~~f~~~~~~~f~tyl~~~i~~~i~~~l   80 (231)
T TIGR02885         1 LIKLAQNGDKEARDKLIECNLRLVWSIVKRFLNRGYEPEDLFQIGCIGLVKAIDKFDLSYDVKFSTYAVPMIMGEIKRFL   80 (231)
T ss_pred             ChHHHHcCCHHHHHHHHHHhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHhcCCCCCCCcHHHHHHHHHHHHHHHH
Confidence            35677899999999999999999999999999999999999999999999999999998888999999999999999999


Q ss_pred             HhhcCcccCCcchHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCccccCCCC--cccc
Q 046578          211 ANKSRTIRLPGSMAGMVAKIAEANNVLSRRLRRMPTDSEIAEMLNIHVSTVRLAIERTRHPISLDGAVTDRGCM--TMQD  288 (379)
Q Consensus       211 r~~~r~irip~~~~~~~~ki~~a~~~l~~~lgr~pt~~eia~~Lgis~~~~~~~l~~~~~~iSLd~~~~~~~~~--~l~d  288 (379)
                      |++. .+++|+++.....++.++...+...+|+.|+.+|||+.+|++.+++..++.......|||.++.++++.  .+.+
T Consensus        81 r~~~-~i~~p~~~~~~~~~~~~~~~~l~~~~~r~pt~~ela~~l~~~~~~v~~~~~~~~~~~sl~~~~~~~~~~~~~~~d  159 (231)
T TIGR02885        81 RDDG-IIKVSRSLKELARKIRYMKEELSKELGREPTINELAEALGVSPEEIVMALESARSPQSLYDTVHQDDGDPIYLLD  159 (231)
T ss_pred             HhCC-CeECCHHHHHHHHHHHHHHHHHHHHHCcCCCHHHHHHHHCcCHHHHHHHHHHccCCcCcccCCCCCCCCcchhhh
Confidence            9986 789999999999999999999999999999999999999999999999988877889999887654332  3345


Q ss_pred             cCCCCCCCChHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhH
Q 046578          289 IIPGPDETMPERMVQKQLMKQELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQT  368 (379)
Q Consensus       289 ~i~~~~~~~pe~~~~~~e~~~~L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~~  368 (379)
                      .+.++.. .++.    ......+..+++.||++++.||.++|+    +++|++|||+.||+|+++|++++++|+++||+.
T Consensus       160 ~~~~~~~-~~~~----~~~~~~l~~~l~~L~~~e~~i~~~~~~----~~~t~~eIA~~lgis~~~V~~~~~~al~~Lr~~  230 (231)
T TIGR02885       160 QIADKGS-EDSD----WLEKIALKEAISKLDERERQIIMLRYF----KDKTQTEVANMLGISQVQVSRLEKKVLKKMKEK  230 (231)
T ss_pred             hcCCCCc-cHHh----HHHHHHHHHHHHcCCHHHHHHHHHHHH----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHh
Confidence            5554422 1222    123457889999999999999999995    679999999999999999999999999999986


Q ss_pred             H
Q 046578          369 N  369 (379)
Q Consensus       369 l  369 (379)
                      |
T Consensus       231 l  231 (231)
T TIGR02885       231 L  231 (231)
T ss_pred             C
Confidence            4

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.

>TIGR02941 Sigma_B RNA polymerase sigma-B factor

Probab=100.00  E-value=4.5e-36  Score=283.83  Aligned_cols=237  Identities=25%  Similarity=0.342  Sum_probs=210.3

Q ss_pred             cHHHHHHHHhc-ccHHHHHHHHHHhHHHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHhccCCCCCCCchhHHHHHHHHH
Q 046578          127 DYNLVKYKILC-KERESQERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYWWIKQA  205 (379)
Q Consensus       127 ~~~eLi~~~~~-Gd~~A~e~Li~~y~~lV~~ia~r~~~~~~d~eDLvQEg~i~L~~ai~~fD~~~g~~FsTYa~~~Ir~~  205 (379)
                      +..+|+.+++. ||..|+++||..|.|+|+++|++|.+++.++|||+||||+++|+++++|+++.|.+|.||+++|++|.
T Consensus        14 ~~~~li~~~~~~gd~~a~~~l~~~y~~~v~~~a~~~~~~~~~aeDlvQe~~i~l~~a~~~~~~~~~~~f~tyl~~~i~n~   93 (255)
T TIGR02941        14 DVIQWIAEFQQNQNGEAQEKLVDHYQNLVYSIAYKYSKGGPMHEDLVQVGMLGLLGAIRRYDYSIGNAFEPFAIPTIIGE   93 (255)
T ss_pred             HHHHHHHHHHHCCCHHHHHHHHHHhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHcCCcCCCCcHhHHHHHHHHH
Confidence            34678999988 79999999999999999999999999999999999999999999999999998889999999999999


Q ss_pred             HHHHHHhhcCcccCCcchHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHh--cCCccccCCccccCCC
Q 046578          206 IIRAIANKSRTIRLPGSMAGMVAKIAEANNVLSRRLRRMPTDSEIAEMLNIHVSTVRLAIER--TRHPISLDGAVTDRGC  283 (379)
Q Consensus       206 i~~~lr~~~r~irip~~~~~~~~ki~~a~~~l~~~lgr~pt~~eia~~Lgis~~~~~~~l~~--~~~~iSLd~~~~~~~~  283 (379)
                      |.+++|+..+.+++|++.....+++.++.+.+...+|+.|+.+|+|+.+|++.+++..++..  .....|||.++.++++
T Consensus        94 ~~~~lr~~~~~iri~~~~~~~~~~~~~~~~~l~~~~~r~p~~~eia~~l~i~~~~~~~~~~~~~~~~~~sl~~~~~~~~~  173 (255)
T TIGR02941        94 IKRYLRDKTWSVHVPRRIKELGPKIKKAIDELTDHLQRSPKIIEIADHLGLSEEEVLEIMEMGQSYRALSVDDVIEADSD  173 (255)
T ss_pred             HHHHHHHcCCCcCCCHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHHHhccCCccccccccCCCC
Confidence            99999999889999999999999999999999999999999999999999999999887765  4577899988765544


Q ss_pred             CcccccCCCCCCCChHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 046578          284 MTMQDIIPGPDETMPERMVQKQLMKQELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALT  363 (379)
Q Consensus       284 ~~l~d~i~~~~~~~pe~~~~~~e~~~~L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~  363 (379)
                      ......+.  ...+|++.+...+....+..+++.||+++|.||.++|+    +|+|++|||+.||+|.++|++++++|++
T Consensus       174 ~~~~~~~~--~~~~~~~~~~~~e~~~~l~~~l~~L~~~~r~ii~l~~~----~g~s~~eIA~~lgis~~~V~~~~~ra~~  247 (255)
T TIGR02941       174 GSTVARLD--SVGEVEDGYDQTERRMVLEKILPILSEREKSIIHCTFE----ENLSQKETGERLGISQMHVSRLQRQAIS  247 (255)
T ss_pred             Cccccccc--ccCCcchHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHc----CCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence            32222111  11235666667777788999999999999999999994    7799999999999999999999999999


Q ss_pred             HHHhHH
Q 046578          364 KLQQTN  369 (379)
Q Consensus       364 kLR~~l  369 (379)
                      +||+.+
T Consensus       248 ~Lr~~~  253 (255)
T TIGR02941       248 KLKEAA  253 (255)
T ss_pred             HHHHHh
Confidence            999875

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=100.00  E-value=1.4e-35  Score=279.86  Aligned_cols=236  Identities=28%  Similarity=0.372  Sum_probs=208.2

Q ss_pred             HHHHHHH-HhcccHHHHHHHHHHhHHHHHHHHHhccC---CCCCHHHHHHHHHHHHHHHHhccCCCCCCCchhHHHHHHH
Q 046578          128 YNLVKYK-ILCKERESQERIIRSYRSLVVSIATGYQG---KGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYWWIK  203 (379)
Q Consensus       128 ~~eLi~~-~~~Gd~~A~e~Li~~y~~lV~~ia~r~~~---~~~d~eDLvQEg~i~L~~ai~~fD~~~g~~FsTYa~~~Ir  203 (379)
                      ..+|+.+ ...||..|++.||..|.|+|+++|++|.+   ++.+++|++||||++||+++++||+.+|.+|.||+++|++
T Consensus         8 e~~l~~~~~~~~d~~a~~~L~~~y~~~v~~~~~~~~~~~~~~~~~eDl~Qe~~i~l~~~~~~f~~~~~~~f~tyl~~~ir   87 (251)
T PRK07670          8 EQKLWDRWKEERDPDAADELIRRYMPLVHYHVQRISVGLPKSVSKDDLKSLGMLGLYDALEKFDPSRDLKFDTYASFRIR   87 (251)
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHHHHHHHHHcCcccCCCHHHHHHHHHH
Confidence            3678888 45579999999999999999999999965   6789999999999999999999999998999999999999


Q ss_pred             HHHHHHHHhhcCcccCCcchHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHh--cCCccccCCccccC
Q 046578          204 QAIIRAIANKSRTIRLPGSMAGMVAKIAEANNVLSRRLRRMPTDSEIAEMLNIHVSTVRLAIER--TRHPISLDGAVTDR  281 (379)
Q Consensus       204 ~~i~~~lr~~~r~irip~~~~~~~~ki~~a~~~l~~~lgr~pt~~eia~~Lgis~~~~~~~l~~--~~~~iSLd~~~~~~  281 (379)
                      |.+.+++|++.   ++|+++...++++.++.+.+.+.+|+.|+.+|+|+.+|++.+++..++..  .....|+|.++.++
T Consensus        88 n~~~d~lR~~~---~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~eia~~l~~~~~~v~~~~~~~~~~~~~sld~~~~~~  164 (251)
T PRK07670         88 GAIIDGLRKED---WLPRSMREKTKKVEAAIEKLEQRYMRNVTPKEVAAELGMTEEEVEATMNEGFFANLLSIDEKTHDQ  164 (251)
T ss_pred             HHHHHHHHhcC---CCCHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHhCcCHHHHHHHHHHHhccCccccCccccCC
Confidence            99999999865   68999999999999999999999999999999999999999999998764  56889999987654


Q ss_pred             CCC-cccccCCCCCCCChHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 046578          282 GCM-TMQDIIPGPDETMPERMVQKQLMKQELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGI  360 (379)
Q Consensus       282 ~~~-~l~d~i~~~~~~~pe~~~~~~e~~~~L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~r  360 (379)
                      ++. .+.+.+.+....++++.+...+....|..+|..||+++|.||.++|+    +|+|++|||+.||+|.++|+++++|
T Consensus       165 ~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~l~~~l~~L~~~~r~vl~l~~~----~~~s~~EIA~~lgis~~tV~~~~~r  240 (251)
T PRK07670        165 DDGENVSVTIRDDKTPTPEEKLLKEELIEELAEKIKQLSEKEQLVISLFYK----EELTLTEIGQVLNLSTSRISQIHSK  240 (251)
T ss_pred             CCcchhhhhhcCcCCCCHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHh----cCCCHHHHHHHHCcCHHHHHHHHHH
Confidence            332 22233344455677877777788888999999999999999999994    7799999999999999999999999


Q ss_pred             HHHHHHhHHh
Q 046578          361 ALTKLQQTNI  370 (379)
Q Consensus       361 Al~kLR~~l~  370 (379)
                      |+++||+++.
T Consensus       241 a~~~Lr~~l~  250 (251)
T PRK07670        241 ALFKLKKLLE  250 (251)
T ss_pred             HHHHHHHHhh
Confidence            9999999864

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

Probab=100.00  E-value=2.9e-35  Score=273.42  Aligned_cols=222  Identities=31%  Similarity=0.445  Sum_probs=197.1

Q ss_pred             cHHHHHHHHHHhHHHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHhccCCCCCCCchhHHHHHHHHHHHHHHHhhcCccc
Q 046578          139 ERESQERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYWWIKQAIIRAIANKSRTIR  218 (379)
Q Consensus       139 d~~A~e~Li~~y~~lV~~ia~r~~~~~~d~eDLvQEg~i~L~~ai~~fD~~~g~~FsTYa~~~Ir~~i~~~lr~~~r~ir  218 (379)
                      |..|+++|+..|.|+|+++|++|.+++.++|||+|||++++|+++++||+.+|.+|+||+++||+|.|.++++++.+.++
T Consensus         1 ~~~a~~~lv~~y~~~v~~~a~~~~~~~~~~eDl~Qe~~i~l~~a~~~f~~~~~~~F~ty~~~~i~~~~~~~~r~~~~~~r   80 (227)
T TIGR02980         1 DKEAREKLVELNLPLVRSIARRFRNRGEPHEDLVQVGTIGLVKAIDRFDPSYGVKFSTFAVPTIMGEIKRFFRDDTWAVR   80 (227)
T ss_pred             CHHHHHHHHHHhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHhcCcccCCCcHHHHHHHHHHHHHHHHHHcCCcee
Confidence            56799999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCcchHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcC--CccccCCccccCCC--CcccccCCCCC
Q 046578          219 LPGSMAGMVAKIAEANNVLSRRLRRMPTDSEIAEMLNIHVSTVRLAIERTR--HPISLDGAVTDRGC--MTMQDIIPGPD  294 (379)
Q Consensus       219 ip~~~~~~~~ki~~a~~~l~~~lgr~pt~~eia~~Lgis~~~~~~~l~~~~--~~iSLd~~~~~~~~--~~l~d~i~~~~  294 (379)
                      +|+++....+++.++...+...+|+.|+.+|+|+.+|++.+++..++....  ...|+|.++.++++  ..+.+.+.   
T Consensus        81 i~~~~~~~~~~~~~~~~~l~~~~~~~p~~~ela~~l~~~~~~v~~~~~~~~~~~~~sld~~~~~~~~~~~~~~d~~~---  157 (227)
T TIGR02980        81 VPRRLKELGLKINKATEELTQRLGRSPTIAEIAEELGVSEEEVVEALEAGNSYSALSLDAPIEDDDGDPIALLDTLG---  157 (227)
T ss_pred             cCHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHhCCCHHHHHHHHHhhccCCCeeccccCCCCCCCCcccccccC---
Confidence            999999999999999999999999999999999999999999998877644  48999988763222  12233332   


Q ss_pred             CCChHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHH
Q 046578          295 ETMPERMVQKQLMKQELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQTN  369 (379)
Q Consensus       295 ~~~pe~~~~~~e~~~~L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~~l  369 (379)
                        ++++.+...+....+..++..||++++.||.++|+    +|+|++|||+.||+|+++|++++++|+++||+.+
T Consensus       158 --~~~~~~~~~~~~~~l~~~l~~L~~~~r~vl~l~y~----~~~s~~eIA~~lgis~~~v~~~~~ra~~~Lr~~l  226 (227)
T TIGR02980       158 --DEDDALETVEDRLALKPLLAALPERERRILLLRFF----EDKTQSEIAERLGISQMHVSRLLRRALKKLREQL  226 (227)
T ss_pred             --CcchHHHhHHHHHHHHHHHHcCCHHHHHHHHHHHh----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHh
Confidence              23444555566678999999999999999999995    6799999999999999999999999999999875

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=100.00  E-value=7e-35  Score=277.66  Aligned_cols=237  Identities=26%  Similarity=0.401  Sum_probs=210.2

Q ss_pred             HHHHHHHHh-cccHHHHHHHHHHhHHHHHHHHHhcc-C--CCCCHHHHHHHHHHHHHHHHhccCCCCCCCchhHHHHHHH
Q 046578          128 YNLVKYKIL-CKERESQERIIRSYRSLVVSIATGYQ-G--KGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYWWIK  203 (379)
Q Consensus       128 ~~eLi~~~~-~Gd~~A~e~Li~~y~~lV~~ia~r~~-~--~~~d~eDLvQEg~i~L~~ai~~fD~~~g~~FsTYa~~~Ir  203 (379)
                      ..+|+.+++ .||.++++.++..|.|+|+.+|+++. +  .+.+++||+||||+|||+++++||+.+|.+|+||+++||+
T Consensus        17 e~~l~~~~~~~~d~~a~~~l~~~y~~lv~~~a~~~~~~~~~~~~~eDl~Qeg~l~L~~a~~~fd~~~~~~f~ty~~~~ir   96 (268)
T PRK06288         17 ETELWREYKKTGDPKIREYLILKYSPLVKYVAGRIAVGMPQNVEFDDLVSYGVFGLIDAIEKFDPEREIKFKTYAVTRIR   96 (268)
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHHHHHHcCcccCCCHHHHHHHHHH
Confidence            467888855 58999999999999999999999986 2  4678999999999999999999999888899999999999


Q ss_pred             HHHHHHHHhhcCcccCCcchHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHh--cCCccccCCcccc-
Q 046578          204 QAIIRAIANKSRTIRLPGSMAGMVAKIAEANNVLSRRLRRMPTDSEIAEMLNIHVSTVRLAIER--TRHPISLDGAVTD-  280 (379)
Q Consensus       204 ~~i~~~lr~~~r~irip~~~~~~~~ki~~a~~~l~~~lgr~pt~~eia~~Lgis~~~~~~~l~~--~~~~iSLd~~~~~-  280 (379)
                      |.+.+++|+.   .++|+++....+++.++...+.+.+|++|+.+|||+.+|++.+.+..++..  ....+|+|..+.. 
T Consensus        97 ~~i~d~~R~~---~~~p~~~~~~~~~i~~~~~~l~~~~~~~pt~~eia~~lg~~~~~v~~~~~~~~~~~~~sld~~~~~~  173 (268)
T PRK06288         97 GAIFDELRSI---DWIPRSVRQKARQIERAIAMLEARLGRTPSDEEIADELGISLEEYNSLLSKLSGTSVVSLNDLWFGG  173 (268)
T ss_pred             HHHHHHHHhc---CccCHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHcCCCHHHHHHHHHHHhcccccchhhhhccC
Confidence            9999999965   468999999999999999999999999999999999999999999988765  3567899887632 


Q ss_pred             C--CCCcccccCCCCCCCChHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHH
Q 046578          281 R--GCMTMQDIIPGPDETMPERMVQKQLMKQELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIR  358 (379)
Q Consensus       281 ~--~~~~l~d~i~~~~~~~pe~~~~~~e~~~~L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~  358 (379)
                      +  +...+.+.++++...+|++.+...+....|..+|..||+++|.||.++|+    +++|++|||+.||+|.++|++++
T Consensus       174 ~~~~~~~l~~~~~~~~~~~pe~~~~~~e~~~~l~~~l~~L~~~~r~vl~l~~~----~~~s~~eIA~~lgis~~tV~~~~  249 (268)
T PRK06288        174 DEGDEVSLMDTLESPAALNPDEIAEREEIKRVIVEAIKTLPEREKKVLILYYY----EDLTLKEIGKVLGVTESRISQLH  249 (268)
T ss_pred             CCcccchhhhhccCCCCCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHHCcCHHHHHHHH
Confidence            2  12345566777667788988888888899999999999999999999995    77999999999999999999999


Q ss_pred             HHHHHHHHhHHhh
Q 046578          359 GIALTKLQQTNIL  371 (379)
Q Consensus       359 ~rAl~kLR~~l~~  371 (379)
                      +||+++||+++..
T Consensus       250 ~ra~~~Lr~~l~~  262 (268)
T PRK06288        250 TKAVLQLRAKLAE  262 (268)
T ss_pred             HHHHHHHHHHHHH
Confidence            9999999999864

>PRK05572 sporulation sigma factor SigF; Validated

Probab=100.00  E-value=3.6e-34  Score=270.39  Aligned_cols=232  Identities=27%  Similarity=0.370  Sum_probs=203.6

Q ss_pred             cHHHHHHHHhcccHHHHHHHHHHhHHHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHhccCCCCCCCchhHHHHHHHHHH
Q 046578          127 DYNLVKYKILCKERESQERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYWWIKQAI  206 (379)
Q Consensus       127 ~~~eLi~~~~~Gd~~A~e~Li~~y~~lV~~ia~r~~~~~~d~eDLvQEg~i~L~~ai~~fD~~~g~~FsTYa~~~Ir~~i  206 (379)
                      +..+++.+++.||..|++.||..|.++|+++|++|.+++.+++|++||||+++|+++++|++..+.+|.||+++||+|.|
T Consensus        18 ~~~~li~~~~~gd~~a~~~L~~~y~~~v~~~a~~~~~~~~~aeDl~Qe~~l~l~~~~~~f~~~~~~~f~twl~~~i~~~i   97 (252)
T PRK05572         18 ENKELIKKSQDGDQEARDTLVEKNLRLVWSVVQRFLNRGYEPDDLFQIGCIGLLKAVDKFDLSYDVKFSTYAVPMIIGEI   97 (252)
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHhHHHHHHHHHHHccCCCCHHHHHHHHHHHHHHHHHHcCCCCCCChHHHHHHHHHHHH
Confidence            34678899999999999999999999999999999999999999999999999999999999888899999999999999


Q ss_pred             HHHHHhhcCcccCCcchHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCccccCCCC--
Q 046578          207 IRAIANKSRTIRLPGSMAGMVAKIAEANNVLSRRLRRMPTDSEIAEMLNIHVSTVRLAIERTRHPISLDGAVTDRGCM--  284 (379)
Q Consensus       207 ~~~lr~~~r~irip~~~~~~~~ki~~a~~~l~~~lgr~pt~~eia~~Lgis~~~~~~~l~~~~~~iSLd~~~~~~~~~--  284 (379)
                      .+++|+.. .+++|+++....+++.++...+...+|+.|+..|+|+.+|++.+.+..+........|++.++.+++..  
T Consensus        98 ~~~lr~~~-~~r~~~~~~~~~~~~~~~~~~l~~~~~r~p~~~eia~~l~~~~~~v~~~~~~~~~~~sl~~~~~~~~~~~~  176 (252)
T PRK05572         98 QRFLRDDG-TVKVSRSLKETANKIRKDKDELSKELGREPTIEELAEYLGVTPEEVVLAQEASRSPQSIHETVHENDGDPI  176 (252)
T ss_pred             HHHHHhCC-CCCCCHHHHHHHHHHHHHHHHHHHHHCcCCCHHHHHHHhCcCHHHHHHHHHhcCCCcCcccCcccCCCCcc
Confidence            99999885 789999999999999999999999999999999999999999999998887777888998877554322  


Q ss_pred             cccccCCCCCCCChHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHH
Q 046578          285 TMQDIIPGPDETMPERMVQKQLMKQELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTK  364 (379)
Q Consensus       285 ~l~d~i~~~~~~~pe~~~~~~e~~~~L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~k  364 (379)
                      .+.+.+.++..   +.    ......+..++..||++++.||.++|+    +++|++|||+.+|+|.++|++++++|+++
T Consensus       177 ~~~d~~~~~~~---~~----~~~~~~l~~~l~~L~~~~~~v~~l~~~----~~~s~~eIA~~lgis~~~V~~~~~ral~k  245 (252)
T PRK05572        177 TLLDQIADQSE---ED----WFDKIALKEAIRELDERERLIVYLRYF----KDKTQSEVAKRLGISQVQVSRLEKKILKQ  245 (252)
T ss_pred             hhhhhcCCCch---hh----HHHHHHHHHHHHcCCHHHHHHHHHHHh----CCCCHHHHHHHHCcCHHHHHHHHHHHHHH
Confidence            22333333211   11    223456889999999999999999994    67999999999999999999999999999


Q ss_pred             HHhHHh
Q 046578          365 LQQTNI  370 (379)
Q Consensus       365 LR~~l~  370 (379)
                      ||+.+.
T Consensus       246 Lr~~l~  251 (252)
T PRK05572        246 MKEKLD  251 (252)
T ss_pred             HHHHhc
Confidence            998864

>PRK08583 RNA polymerase sigma factor SigB; Validated

Probab=100.00  E-value=4.2e-34  Score=270.65  Aligned_cols=236  Identities=27%  Similarity=0.394  Sum_probs=208.1

Q ss_pred             HHHHHHHHhc-ccHHHHHHHHHHhHHHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHhccCCCCCCCchhHHHHHHHHHH
Q 046578          128 YNLVKYKILC-KERESQERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYWWIKQAI  206 (379)
Q Consensus       128 ~~eLi~~~~~-Gd~~A~e~Li~~y~~lV~~ia~r~~~~~~d~eDLvQEg~i~L~~ai~~fD~~~g~~FsTYa~~~Ir~~i  206 (379)
                      ..+|+.+++. ||..|++.||..|.|+|+++|++|.++..+++|++||||+++|+++++||+..|.+|.||+++||+|.|
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            4678898875 899999999999999999999999999999999999999999999999999888899999999999999


Q ss_pred             HHHHHhhcCcccCCcchHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHh--cCCccccCCccccCCCC
Q 046578          207 IRAIANKSRTIRLPGSMAGMVAKIAEANNVLSRRLRRMPTDSEIAEMLNIHVSTVRLAIER--TRHPISLDGAVTDRGCM  284 (379)
Q Consensus       207 ~~~lr~~~r~irip~~~~~~~~ki~~a~~~l~~~lgr~pt~~eia~~Lgis~~~~~~~l~~--~~~~iSLd~~~~~~~~~  284 (379)
                      .+++|++.+.+++|++.....+++.++...+...+++.|+.+++++.+|++.+.+..+...  .....|+|.+++++++.
T Consensus        95 ~~~lr~~~~~~~i~r~~~~~~~~~~~~~~~~~~~~~r~~~~~e~a~~~~~~~~~~~~~~~~~~~~~~~sld~~~~~~~~~  174 (257)
T PRK08583         95 KRYLRDKTWSVHVPRRIKELGPKIKKAVDELTTELQRSPKISEIADRLGVSEEEVLEAMEMGKSYQALSVDHSIEADSDG  174 (257)
T ss_pred             HHHHHhcCCCcCCCHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHHhccCCceecCccccCCCCC
Confidence            9999999999999999999999999999999999999999999999999999999887654  34677888877544322


Q ss_pred             c---ccccCCCCCCCChHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 046578          285 T---MQDIIPGPDETMPERMVQKQLMKQELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIA  361 (379)
Q Consensus       285 ~---l~d~i~~~~~~~pe~~~~~~e~~~~L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rA  361 (379)
                      .   +.+..     .+|++.+...+....+..++..||+++|+||.++|+    +|+|++|||+.||||+++|++++++|
T Consensus       175 ~~~~~~~~~-----~~~e~~~~~~~~~~~l~~~l~~L~~~~r~vl~l~~~----~g~s~~eIA~~l~is~~tV~~~~~ra  245 (257)
T PRK08583        175 STVTLLDIV-----GQQEDGYELTEQRMILEKILPVLSDREKSIIQCTFI----ENLSQKETGERLGISQMHVSRLQRQA  245 (257)
T ss_pred             ccchHhhhc-----CCcchhHHHHHHHHHHHHHHHhCCHHHHHHHHHHHh----CCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence            1   11222     245555666677778999999999999999999995    77999999999999999999999999


Q ss_pred             HHHHHhHHhhc
Q 046578          362 LTKLQQTNILN  372 (379)
Q Consensus       362 l~kLR~~l~~~  372 (379)
                      +++||+.+...
T Consensus       246 ~~kLr~~l~~~  256 (257)
T PRK08583        246 IKKLREAAFLD  256 (257)
T ss_pred             HHHHHHHhccC
Confidence            99999998653

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

Probab=100.00  E-value=3.1e-34  Score=266.19  Aligned_cols=217  Identities=33%  Similarity=0.481  Sum_probs=194.2

Q ss_pred             HHHHhHHHHHHHHHhccC---CCCCHHHHHHHHHHHHHHHHhccCCCCCCCchhHHHHHHHHHHHHHHHhhcCcccCCcc
Q 046578          146 IIRSYRSLVVSIATGYQG---KGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYWWIKQAIIRAIANKSRTIRLPGS  222 (379)
Q Consensus       146 Li~~y~~lV~~ia~r~~~---~~~d~eDLvQEg~i~L~~ai~~fD~~~g~~FsTYa~~~Ir~~i~~~lr~~~r~irip~~  222 (379)
                      |+..|.|+|+++|++|.+   ++.+++||+|||++|+|+++++||+++|.+|+||+++||+|.+.+++|+..   ++|++
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            578999999999999985   689999999999999999999999999999999999999999999999764   68999


Q ss_pred             hHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHh--cCCccccCCccccC-CCCcccccCCCCCCCChH
Q 046578          223 MAGMVAKIAEANNVLSRRLRRMPTDSEIAEMLNIHVSTVRLAIER--TRHPISLDGAVTDR-GCMTMQDIIPGPDETMPE  299 (379)
Q Consensus       223 ~~~~~~ki~~a~~~l~~~lgr~pt~~eia~~Lgis~~~~~~~l~~--~~~~iSLd~~~~~~-~~~~l~d~i~~~~~~~pe  299 (379)
                      ....++++.++..++.+.+|++|+.+|+|+.+|++.+++..++..  ....+|+|....++ +...+.+.++++...+|+
T Consensus        78 ~~~~~~~l~~~~~~l~~~~~~~~~~~ela~~l~~~~~~v~~~~~~~~~~~~~sl~~~~~~~~~~~~~~~~~~~~~~~~~~  157 (224)
T TIGR02479        78 LRQKARKLERAIRELEARLGREPTEEEIAEELGMDLKEYRQALNEINALSLVSLDELLESGDDGGSLIDRIEDDKSEDPE  157 (224)
T ss_pred             HHHHHHHHHHHHHHHHHHHCcCCCHHHHHHHhCCCHHHHHHHHHHHhcCCccccCCcccCCCccchhhhhccccccCCHH
Confidence            999999999999999999999999999999999999999999864  45677888765432 233455556655666888


Q ss_pred             HHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHH
Q 046578          300 RMVQKQLMKQELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQTN  369 (379)
Q Consensus       300 ~~~~~~e~~~~L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~~l  369 (379)
                      +.+...+....+..+|+.||+++|+||.++|+    +++|++|||+.||+|.++|++++++|+++||+.+
T Consensus       158 ~~~~~~~~~~~l~~~l~~L~~~~r~il~l~y~----~~~s~~eIA~~lgis~~tV~~~~~ra~~~Lr~~l  223 (224)
T TIGR02479       158 EELEREELREALAEAIESLSEREQLVLSLYYY----EELNLKEIGEVLGLTESRVSQIHSQALKKLRAKL  223 (224)
T ss_pred             HHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHh----CCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHc
Confidence            88888888899999999999999999999994    7799999999999999999999999999999875

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

>PRK06986 fliA flagellar biosynthesis sigma factor; Validated

Probab=100.00  E-value=6e-33  Score=259.60  Aligned_cols=223  Identities=28%  Similarity=0.425  Sum_probs=194.3

Q ss_pred             HHHHHHHHHHhHHHHHHHHHhcc---CCCCCHHHHHHHHHHHHHHHHhccCCCCCCCchhHHHHHHHHHHHHHHHhhcCc
Q 046578          140 RESQERIIRSYRSLVVSIATGYQ---GKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYWWIKQAIIRAIANKSRT  216 (379)
Q Consensus       140 ~~A~e~Li~~y~~lV~~ia~r~~---~~~~d~eDLvQEg~i~L~~ai~~fD~~~g~~FsTYa~~~Ir~~i~~~lr~~~r~  216 (379)
                      .-+.++||..|.|+|+++|++|.   +++.+++||+||||++||+++++|+++.|.+|+||+++|++|.+.+++|++.  
T Consensus         7 ~~~~~~L~~~~~~~v~~~a~~~~~~~~~~~~aeDlvQe~~i~l~~~~~~f~~~~~~~f~tyl~~~irn~~~~~lR~~~--   84 (236)
T PRK06986          7 KMDQDELVEQYAPLVKRIALRLKARLPASVDLDDLIQAGMIGLLEAARRYDGEQGASFETYAGQRIRGAMLDELRSLD--   84 (236)
T ss_pred             cccHHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHHHHHhcCcccCCChHHHHHHHHHHHHHHHHHHcC--
Confidence            45789999999999999999997   6789999999999999999999999988889999999999999999999875  


Q ss_pred             ccCCcchHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHh--cCCccccCCccccCCCCcccccCCCCC
Q 046578          217 IRLPGSMAGMVAKIAEANNVLSRRLRRMPTDSEIAEMLNIHVSTVRLAIER--TRHPISLDGAVTDRGCMTMQDIIPGPD  294 (379)
Q Consensus       217 irip~~~~~~~~ki~~a~~~l~~~lgr~pt~~eia~~Lgis~~~~~~~l~~--~~~~iSLd~~~~~~~~~~l~d~i~~~~  294 (379)
                       ++|.+......++.++...+.+.+|++|+.+|||+.+|++.+++..++..  ....+|++..++++++. +.. .....
T Consensus        85 -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ela~~l~i~~~~v~~~~~~~~~~~~~sl~~~~~~~~~~-~~~-~~~~~  161 (236)
T PRK06986         85 -WVPRSVRRNAREVAQAIRQLEQELGREPTDTEVAEKLGLSLEEYREMLLDTNISQLFSIDELRGEHGDS-ILV-TEDHQ  161 (236)
T ss_pred             -CCCHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHcCCCHHHHHHHHHHHhccCCccccccccCCCcc-ccc-ccCCC
Confidence             36777777778888899999999999999999999999999999988875  44667888876554432 222 22233


Q ss_pred             CCChHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHHhh
Q 046578          295 ETMPERMVQKQLMKQELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQTNIL  371 (379)
Q Consensus       295 ~~~pe~~~~~~e~~~~L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~~l~~  371 (379)
                      ..+|++.+...+....|..+|+.||+++|.||.++|+    +|+|++|||+.||+|.++|+++++||+++||+.+..
T Consensus       162 ~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~vl~l~~~----~g~s~~EIA~~lgis~~tV~~~~~ra~~~Lr~~l~~  234 (236)
T PRK06986        162 DEDPLQQLEDEELREALVEAIESLPEREQLVLSLYYQ----EELNLKEIGAVLGVSESRVSQIHSQAIKRLRARLGE  234 (236)
T ss_pred             CCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHhHhc----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHhc
Confidence            4567888888888889999999999999999999994    779999999999999999999999999999998754

>PRK12427 flagellar biosynthesis sigma factor; Provisional

Probab=100.00  E-value=3.4e-32  Score=253.69  Aligned_cols=209  Identities=23%  Similarity=0.304  Sum_probs=179.4

Q ss_pred             HHHHHHHhHHHHHHHHHhccC---CCCCHHHHHHHHHHHHHHHHhccCCCCCCCchhHHHHHHHHHHHHHHHhhcCcccC
Q 046578          143 QERIIRSYRSLVVSIATGYQG---KGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYWWIKQAIIRAIANKSRTIRL  219 (379)
Q Consensus       143 ~e~Li~~y~~lV~~ia~r~~~---~~~d~eDLvQEg~i~L~~ai~~fD~~~g~~FsTYa~~~Ir~~i~~~lr~~~r~iri  219 (379)
                      ..+++..|.|+|..++++|..   .+.+.+||+|||++|||+++++||+..+ +|+||+++||+|.|.+++|+..   +.
T Consensus        17 ~~~lv~~y~~lV~~la~~~~~~~~~~~~~eDLvQeg~igL~~a~~~fd~~~~-~F~tYa~~~Ir~~il~~lr~~~---~~   92 (231)
T PRK12427         17 EGKYLNAYLPLVKKVVRQLAFQADSVIDREDMEQIALMGLLEALRRYGHPDE-QFAAYAVHRIRGAILDELRELD---WR   92 (231)
T ss_pred             HHHHHHHHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHHHHHHHHhcCCCCC-ChHHHHHHHHHHHHHHHHHhcC---CC
Confidence            357899999999999999874   4679999999999999999999997655 8999999999999999999854   47


Q ss_pred             CcchHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHh--cCCccccCCccccCCCCcccccCCCCCCCC
Q 046578          220 PGSMAGMVAKIAEANNVLSRRLRRMPTDSEIAEMLNIHVSTVRLAIER--TRHPISLDGAVTDRGCMTMQDIIPGPDETM  297 (379)
Q Consensus       220 p~~~~~~~~ki~~a~~~l~~~lgr~pt~~eia~~Lgis~~~~~~~l~~--~~~~iSLd~~~~~~~~~~l~d~i~~~~~~~  297 (379)
                      |+++....+++.++...+.+.+|++|+.+|||+.||++.+++.+++..  .....|||.++.+++...   .+++   ..
T Consensus        93 ~r~vr~~~~~i~~~~~~l~~~~g~~pt~~eiA~~lg~~~~~v~~~~~~~~~~~~~SLd~~~~~~~~~~---~~~~---~~  166 (231)
T PRK12427         93 PRRLRQKTHKTNDAIREIAKRLGHEPNFEEISAELNLTAEEYQEYLLLENAGTLESLDELLALEAHND---ILQS---RD  166 (231)
T ss_pred             CHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHhCCCHHHHHHHHHHhccCCceeccCcccCCCccc---ccCC---CC
Confidence            899999999999999999999999999999999999999999988753  467899999876654321   2211   22


Q ss_pred             hHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhH
Q 046578          298 PERMVQKQLMKQELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQT  368 (379)
Q Consensus       298 pe~~~~~~e~~~~L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~~  368 (379)
                      +++..   .....+..++..||+++|.||.++|+    +++|++|||+.||+|+++|+++..+++++||..
T Consensus       167 ~~~~~---~~~~~l~~~l~~L~~~er~vi~l~~~----~~~t~~EIA~~lgis~~~V~q~~~~~~~kLr~~  230 (231)
T PRK12427        167 LEENI---IIEDNLKQALSQLDEREQLILHLYYQ----HEMSLKEIALVLDLTEARICQLNKKIAQKIKSF  230 (231)
T ss_pred             HHHHH---HHHHHHHHHHHcCCHHHHHHHHHHHH----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHhh
Confidence            33322   23456889999999999999999995    779999999999999999999999999999964

>PRK05803 sporulation sigma factor SigK; Reviewed

Probab=99.96  E-value=2.4e-27  Score=221.39  Aligned_cols=192  Identities=24%  Similarity=0.385  Sum_probs=155.9

Q ss_pred             HHHHHHHHhcccHHHHHHHHHHhHHHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHhccCCCCCCCchhHHHHHHHHHHH
Q 046578          128 YNLVKYKILCKERESQERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYWWIKQAII  207 (379)
Q Consensus       128 ~~eLi~~~~~Gd~~A~e~Li~~y~~lV~~ia~r~~~~~~d~eDLvQEg~i~L~~ai~~fD~~~g~~FsTYa~~~Ir~~i~  207 (379)
                      ...++..+..||..|++.++..|.|+|+++|.++.+++.++||++||+|+++|+++.+|+++++.+|.+|++++++|.++
T Consensus        36 e~~l~~~~~~gd~~a~~~l~~~y~~~l~~~a~~~~~~~~daeDlvQE~fi~l~~~~~~f~~~~~~~f~~wl~~i~rn~~i  115 (233)
T PRK05803         36 ERKYLELMKEGDEEARNILIERNLRLVAHIVKKFENTGEDVDDLISIGTIGLIKAIESFDAGKGTKLATYAARCIENEIL  115 (233)
T ss_pred             HHHHHHHHHcCCHHHHHHHHHHhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHhcCcccCCChHHHHHHHHHHHHH
Confidence            35789999999999999999999999999999999999999999999999999999999998888999999999999999


Q ss_pred             HHHHhhcCcccCCcchHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCccc-cC--CCC
Q 046578          208 RAIANKSRTIRLPGSMAGMVAKIAEANNVLSRRLRRMPTDSEIAEMLNIHVSTVRLAIERTRHPISLDGAVT-DR--GCM  284 (379)
Q Consensus       208 ~~lr~~~r~irip~~~~~~~~ki~~a~~~l~~~lgr~pt~~eia~~Lgis~~~~~~~l~~~~~~iSLd~~~~-~~--~~~  284 (379)
                      +++|+..+..                                                    ...+++.... ++  ...
T Consensus       116 d~~Rk~~~~~----------------------------------------------------~~~~~~~~~~~~~~~~~~  143 (233)
T PRK05803        116 MHLRNLKKTK----------------------------------------------------KEVSLQDPIGVDKEGNEI  143 (233)
T ss_pred             HHHHHHhccc----------------------------------------------------cCCCccccccCCCCcCcc
Confidence            9999765310                                                    1112221111 10  111


Q ss_pred             cccccCCCCCCCChHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHH
Q 046578          285 TMQDIIPGPDETMPERMVQKQLMKQELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTK  364 (379)
Q Consensus       285 ~l~d~i~~~~~~~pe~~~~~~e~~~~L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~k  364 (379)
                      .+.+..++. ...+++.+...+....+..++..||+++|+||.++|++.+.+|+|++|||+.||+|.++|+++++||+++
T Consensus       144 ~~~~~~~~~-~~~~~~~~~~~~~~~~l~~~l~~Lp~~~R~i~~l~y~~~~~e~~S~~EIA~~lgis~~tV~~~~~rA~~k  222 (233)
T PRK05803        144 SLIDILGSE-EDDVIEQVELKMEVEKLYKKIDILDEREKEVIEMRYGLGNGKEKTQREIAKALGISRSYVSRIEKRALKK  222 (233)
T ss_pred             cHHHHccCC-CCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHhCCCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHH
Confidence            222222222 2346676777777778999999999999999999996554588999999999999999999999999999


Q ss_pred             HHhHHhhc
Q 046578          365 LQQTNILN  372 (379)
Q Consensus       365 LR~~l~~~  372 (379)
                      ||+.+...
T Consensus       223 Lr~~l~~~  230 (233)
T PRK05803        223 LFKELYRA  230 (233)
T ss_pred             HHHHHHHh
Confidence            99998653

>PRK08301 sporulation sigma factor SigE; Reviewed

Probab=99.96  E-value=3.2e-27  Score=220.51  Aligned_cols=192  Identities=26%  Similarity=0.452  Sum_probs=150.2

Q ss_pred             cHHHHHHHHhcccHHHHHHHHHHhHHHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHhccCCCCCCCchhHHHHHHHHHH
Q 046578          127 DYNLVKYKILCKERESQERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYWWIKQAI  206 (379)
Q Consensus       127 ~~~eLi~~~~~Gd~~A~e~Li~~y~~lV~~ia~r~~~~~~d~eDLvQEg~i~L~~ai~~fD~~~g~~FsTYa~~~Ir~~i  206 (379)
                      ...+++.++++||..|++.++..|.++|+.+|+++.+++.++||++||+|+++|+++++|++..+.+|.||++++++|.+
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            45789999999999999999999999999999999999999999999999999999999998777789999999999999


Q ss_pred             HHHHHhhcCcccCCcchHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCccccC--C-C
Q 046578          207 IRAIANKSRTIRLPGSMAGMVAKIAEANNVLSRRLRRMPTDSEIAEMLNIHVSTVRLAIERTRHPISLDGAVTDR--G-C  283 (379)
Q Consensus       207 ~~~lr~~~r~irip~~~~~~~~ki~~a~~~l~~~lgr~pt~~eia~~Lgis~~~~~~~l~~~~~~iSLd~~~~~~--~-~  283 (379)
                      ++++|++.+..                                                    ...+++.+..++  + .
T Consensus       118 ~d~lRk~~~~~----------------------------------------------------~~~~~~~~~~~~~~~~~  145 (234)
T PRK08301        118 LMYLRRNNKVK----------------------------------------------------AEVSFDEPLNIDWDGNE  145 (234)
T ss_pred             HHHHHHHhccc----------------------------------------------------cccccccccccccCCCc
Confidence            99999865310                                                    111222211100  0 0


Q ss_pred             CcccccCCCCCCCChHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 046578          284 MTMQDIIPGPDETMPERMVQKQLMKQELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALT  363 (379)
Q Consensus       284 ~~l~d~i~~~~~~~pe~~~~~~e~~~~L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~  363 (379)
                      ....+.... ....+...+........+..++++||+++|.||.++|++...+|+|++|||+.||+|.+||+++++||++
T Consensus       146 ~~~~~~~~~-~~~~~~~~~~~~~~~~~l~~al~~Lp~~~R~v~~L~y~l~~~eg~s~~EIA~~lgis~~tVk~~~~rA~~  224 (234)
T PRK08301        146 LLLSDVLGT-DNDIIYKDIEDEVDRKLLKKALKKLSDREKQIMELRFGLNGGEEKTQKEVADMLGISQSYISRLEKRIIK  224 (234)
T ss_pred             ccHHHhccC-cccchHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHhccCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            011111111 1123334444445556799999999999999999998543347799999999999999999999999999


Q ss_pred             HHHhHHhh
Q 046578          364 KLQQTNIL  371 (379)
Q Consensus       364 kLR~~l~~  371 (379)
                      +||+.+..
T Consensus       225 ~Lr~~l~~  232 (234)
T PRK08301        225 RLKKEINK  232 (234)
T ss_pred             HHHHHHHh
Confidence            99998753

>TIGR02846 spore_sigmaK RNA polymerase sigma-K factor

Probab=99.95  E-value=5.4e-27  Score=218.18  Aligned_cols=191  Identities=24%  Similarity=0.392  Sum_probs=151.6

Q ss_pred             CcHHHHHHHHhcccHHHHHHHHHHhHHHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHhccCCCCCCCchhHHHHHHHHH
Q 046578          126 LDYNLVKYKILCKERESQERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYWWIKQA  205 (379)
Q Consensus       126 ~~~~eLi~~~~~Gd~~A~e~Li~~y~~lV~~ia~r~~~~~~d~eDLvQEg~i~L~~ai~~fD~~~g~~FsTYa~~~Ir~~  205 (379)
                      .+..+++.++++||..|++.+|+.|.|.|+++|.++.++..++||++||+|+++|+++++|+++.+.+|.||++++++|.
T Consensus        33 ~~~~~li~~~~~gd~~af~~l~~~y~~~v~~~~~~~~~~~~dAEDlvQevfi~l~~~~~~~~~~~~~~f~twl~~i~rN~  112 (227)
T TIGR02846        33 EEEKKYLDRLKEGDEEARNVLIERNLRLVAHIVKKFSNTGEDVDDLISIGTIGLIKAIDSFDPDKGTRLATYAARCIENE  112 (227)
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHhHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHHhCCcccCCChHHHHHHHHHHH
Confidence            34578999999999999999999999999999999999999999999999999999999999887778999999999999


Q ss_pred             HHHHHHhhcCcccCCcchHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCcccc--C-C
Q 046578          206 IIRAIANKSRTIRLPGSMAGMVAKIAEANNVLSRRLRRMPTDSEIAEMLNIHVSTVRLAIERTRHPISLDGAVTD--R-G  282 (379)
Q Consensus       206 i~~~lr~~~r~irip~~~~~~~~ki~~a~~~l~~~lgr~pt~~eia~~Lgis~~~~~~~l~~~~~~iSLd~~~~~--~-~  282 (379)
                      +.+++|+..+..                                                    ...+++.....  + .
T Consensus       113 ~~d~~Rk~~r~~----------------------------------------------------~~~~~~~~~~~~~~~~  140 (227)
T TIGR02846       113 ILMHLRALKKTK----------------------------------------------------GEVSLQDPIGVDKEGN  140 (227)
T ss_pred             HHHHHHHHhccc----------------------------------------------------cceeccccccCCcccC
Confidence            999999865310                                                    01111111100  0 0


Q ss_pred             CCcccccCCCCCCCChHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHH
Q 046578          283 CMTMQDIIPGPDETMPERMVQKQLMKQELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIAL  362 (379)
Q Consensus       283 ~~~l~d~i~~~~~~~pe~~~~~~e~~~~L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl  362 (379)
                      ...+.+...+ ....+++.....+....|..+++.||+++|+||.++|+++..+++|++|||+.||+|+++|+++++||+
T Consensus       141 ~~~~~~~~~~-~~~~~~~~~~~~~~~~~l~~~i~~L~~~~r~il~l~y~~~~~e~~S~~EIAe~lgis~~tV~~~~~rAl  219 (227)
T TIGR02846       141 EISLIDILGS-DGDSVIEQVELNLEIKKLYKKLSVLDGREREVIEMRYGLGDGRRKTQREIAKILGISRSYVSRIEKRAL  219 (227)
T ss_pred             cccHHHHhcC-CCCChHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHcCCCCCCcCHHHHHHHHCCCHHHHHHHHHHHH
Confidence            0011121111 223456666666666789999999999999999999853323679999999999999999999999999


Q ss_pred             HHHHhHH
Q 046578          363 TKLQQTN  369 (379)
Q Consensus       363 ~kLR~~l  369 (379)
                      ++||+.+
T Consensus       220 ~~Lr~~~  226 (227)
T TIGR02846       220 MKLYKEL  226 (227)
T ss_pred             HHHHHHh
Confidence            9999875

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

>PRK08295 RNA polymerase factor sigma-70; Validated

Probab=99.95  E-value=1.7e-26  Score=211.09  Aligned_cols=197  Identities=24%  Similarity=0.323  Sum_probs=153.2

Q ss_pred             CcCcHHHHHHHHhcccHHHHHHHHHHhHHHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHhccCCCCCCCchhHHHHHHH
Q 046578          124 GELDYNLVKYKILCKERESQERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYWWIK  203 (379)
Q Consensus       124 ~~~~~~eLi~~~~~Gd~~A~e~Li~~y~~lV~~ia~r~~~~~~d~eDLvQEg~i~L~~ai~~fD~~~g~~FsTYa~~~Ir  203 (379)
                      ..+....++.++++||..|++.||+.|.|.|+++|.++.++..++||++||+|+++|+++.+|++.++.+|.||++.+++
T Consensus         7 ~~~~~~~l~~~~~~~d~~a~~~l~~~y~~~v~~~~~~~~~~~~~aeDlvQe~~l~l~~~~~~~~~~~~~~f~twl~~i~~   86 (208)
T PRK08295          7 DELEDEELVELARSGDKEALEYLIEKYKNFVRAKARSYFLIGADREDIVQEGMIGLYKAIRDYDKDKLSSFKSFAELCIT   86 (208)
T ss_pred             cCCChHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHhCcccCCCHHHHHHHHHH
Confidence            34566789999999999999999999999999999999999999999999999999999999998876799999999999


Q ss_pred             HHHHHHHHhhcCcccCCcchHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCcccc-CC
Q 046578          204 QAIIRAIANKSRTIRLPGSMAGMVAKIAEANNVLSRRLRRMPTDSEIAEMLNIHVSTVRLAIERTRHPISLDGAVTD-RG  282 (379)
Q Consensus       204 ~~i~~~lr~~~r~irip~~~~~~~~ki~~a~~~l~~~lgr~pt~~eia~~Lgis~~~~~~~l~~~~~~iSLd~~~~~-~~  282 (379)
                      |.+.+++++..+..+.+.                                               ....+.+....+ +.
T Consensus        87 n~~~d~~r~~~r~~~~~~-----------------------------------------------~~~~s~~~~~~~~~~  119 (208)
T PRK08295         87 RQIITAIKTANRQKHIPL-----------------------------------------------NSYVSLDKPIYDEES  119 (208)
T ss_pred             HHHHHHHHHhhhhccccc-----------------------------------------------cceeecCCcccCCcc
Confidence            999999997553111110                                               011223322211 11


Q ss_pred             CCcccccCCCCCCCChHHHHHHHHHHHHH-HHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 046578          283 CMTMQDIIPGPDETMPERMVQKQLMKQEL-KELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIA  361 (379)
Q Consensus       283 ~~~l~d~i~~~~~~~pe~~~~~~e~~~~L-~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rA  361 (379)
                      ...+.+.+.++...+|++.+...+....+ ..++..||+.+|.||.+ |+    +|+|++|||+.||+|.++|++.++||
T Consensus       120 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~L~~~~r~vl~l-~~----e~~s~~EIA~~lgis~~tV~~~l~ra  194 (208)
T PRK08295        120 DRTLLDVISEAKVTDPEELIISKEELEDIEEKIEELLSELEKEVLEL-YL----DGKSYQEIAEELNRHVKSIDNALQRV  194 (208)
T ss_pred             chhHHHHhcCcccCCHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHH-HH----ccCCHHHHHHHHCCCHHHHHHHHHHH
Confidence            11223333333334667666555555555 45678999999999999 74    77999999999999999999999999


Q ss_pred             HHHHHhHHhhc
Q 046578          362 LTKLQQTNILN  372 (379)
Q Consensus       362 l~kLR~~l~~~  372 (379)
                      +++||+++...
T Consensus       195 r~~Lr~~l~~~  205 (208)
T PRK08295        195 KRKLEKYLENR  205 (208)
T ss_pred             HHHHHHHHHhh
Confidence            99999998654

>TIGR02835 spore_sigmaE RNA polymerase sigma-E factor

Probab=99.95  E-value=2.6e-26  Score=214.58  Aligned_cols=192  Identities=26%  Similarity=0.462  Sum_probs=150.5

Q ss_pred             cHHHHHHHHhcccHHHHHHHHHHhHHHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHhccCCCCCCCchhHHHHHHHHHH
Q 046578          127 DYNLVKYKILCKERESQERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYWWIKQAI  206 (379)
Q Consensus       127 ~~~eLi~~~~~Gd~~A~e~Li~~y~~lV~~ia~r~~~~~~d~eDLvQEg~i~L~~ai~~fD~~~g~~FsTYa~~~Ir~~i  206 (379)
                      ...+++.++..||..|++.++..|.+.|+++|+++.+++.++||++||+|+++|+++++|++..+.+|.||++++++|.+
T Consensus        38 ~~~~l~~~~~~~d~~a~~~l~~~y~~~l~~~~~~~~~~~~~AEDlvQE~fl~l~~~~~~f~~~~~~~f~~wl~~iarN~~  117 (234)
T TIGR02835        38 EEEALLQKLTQGDESAKSTLIERNLRLVVYIARKFENTGIGIEDLVSIGTIGLIKAVNTFNPSKKIKLATYASRCIENEI  117 (234)
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHhHHHHHHHHHHhccCCCCHHHHHHHHHHHHHHHHHHhCcccCCCHHHHHHHHHHHHH
Confidence            34778999999999999999999999999999999999999999999999999999999998777789999999999999


Q ss_pred             HHHHHhhcCcccCCcchHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCccccC--CC-
Q 046578          207 IRAIANKSRTIRLPGSMAGMVAKIAEANNVLSRRLRRMPTDSEIAEMLNIHVSTVRLAIERTRHPISLDGAVTDR--GC-  283 (379)
Q Consensus       207 ~~~lr~~~r~irip~~~~~~~~ki~~a~~~l~~~lgr~pt~~eia~~Lgis~~~~~~~l~~~~~~iSLd~~~~~~--~~-  283 (379)
                      .+++|++.+..                                                    ...+++.....+  +. 
T Consensus       118 ~d~~Rk~~r~~----------------------------------------------------~~~~~~~~~~~~~~~~~  145 (234)
T TIGR02835       118 LMYLRRNNKTR----------------------------------------------------SEVSFDEPLNVDWDGNE  145 (234)
T ss_pred             HHHHHHhcccc----------------------------------------------------CcccccccccCCCCCCc
Confidence            99999865310                                                    011112111100  00 


Q ss_pred             CcccccCCCCCCCChHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 046578          284 MTMQDIIPGPDETMPERMVQKQLMKQELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALT  363 (379)
Q Consensus       284 ~~l~d~i~~~~~~~pe~~~~~~e~~~~L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~  363 (379)
                      ....+. .++....+++.+........+..+|+.||+++|.|+.++|++.+.+|+|++|||+.||+|.+||+++++||++
T Consensus       146 ~~~~~~-~~~~~~~~~~~~~~~~~~~~l~~ai~~Lp~~~R~ii~L~~~l~~~eg~s~~EIA~~Lgis~~tV~~~l~ra~~  224 (234)
T TIGR02835       146 LLLSDV-LGTDSDIVYKYLEEEVDRELLRKALAKLNDREKKIMELRFGLVGGTEKTQKEVADMLGISQSYISRLEKRILK  224 (234)
T ss_pred             chHHHh-cCCCCCcHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHccCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            001111 1112222334445555567799999999999999999998544337799999999999999999999999999


Q ss_pred             HHHhHHhh
Q 046578          364 KLQQTNIL  371 (379)
Q Consensus       364 kLR~~l~~  371 (379)
                      +||+.+..
T Consensus       225 ~LR~~l~~  232 (234)
T TIGR02835       225 RLKKEINR  232 (234)
T ss_pred             HHHHHhhc
Confidence            99998764

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.

>PRK05602 RNA polymerase sigma factor; Reviewed

Probab=99.95  E-value=4.9e-26  Score=204.93  Aligned_cols=178  Identities=12%  Similarity=0.176  Sum_probs=149.9

Q ss_pred             cCcHHHHHHHHhcccHHHHHHHHHHhHHHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHhccCCCCCCCchhHHHHHHHH
Q 046578          125 ELDYNLVKYKILCKERESQERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYWWIKQ  204 (379)
Q Consensus       125 ~~~~~eLi~~~~~Gd~~A~e~Li~~y~~lV~~ia~r~~~~~~d~eDLvQEg~i~L~~ai~~fD~~~g~~FsTYa~~~Ir~  204 (379)
                      ..+..+++.+++.||..|++.||..|.++|+.+|++++++..+++|++||+|+++|+++.+|+++ +.+|.+|++.+++|
T Consensus         4 ~~~~~~l~~~~~~~d~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeDlvQe~fi~l~~~~~~~~~~-~~~f~~wl~~ia~n   82 (186)
T PRK05602          4 ADPDEELLARVAAGDPAAFRVLVARKLPRLLALATRMLGDPAEAEDVAQETFLRIWKQAPSWRPG-EARFDTWLHRVVLN   82 (186)
T ss_pred             cccHHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHhhhcCCC-CCcHHHHHHHHHHH
Confidence            35668899999999999999999999999999999999999999999999999999999999975 34899999999999


Q ss_pred             HHHHHHHhhcCcccCCcchHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCccccCCCC
Q 046578          205 AIIRAIANKSRTIRLPGSMAGMVAKIAEANNVLSRRLRRMPTDSEIAEMLNIHVSTVRLAIERTRHPISLDGAVTDRGCM  284 (379)
Q Consensus       205 ~i~~~lr~~~r~irip~~~~~~~~ki~~a~~~l~~~lgr~pt~~eia~~Lgis~~~~~~~l~~~~~~iSLd~~~~~~~~~  284 (379)
                      .+.+++|++...                                                        ..+.        
T Consensus        83 ~~~d~~R~~~~~--------------------------------------------------------~~~~--------   98 (186)
T PRK05602         83 LCYDRLRRRREV--------------------------------------------------------PVED--------   98 (186)
T ss_pred             HHHHHHHhcCCC--------------------------------------------------------Cccc--------
Confidence            999999975420                                                        0000        


Q ss_pred             cccccCCCCCCCChHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHH
Q 046578          285 TMQDIIPGPDETMPERMVQKQLMKQELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTK  364 (379)
Q Consensus       285 ~l~d~i~~~~~~~pe~~~~~~e~~~~L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~k  364 (379)
                       ..+ ..+ ....++..+...+....+..+|..||+++|+||.++|+    +|+|++|||+.||+|.++|+++++||+++
T Consensus        99 -~~~-~~~-~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~i~~l~~~----~g~s~~EIA~~lgis~~tV~~~l~Rar~~  171 (186)
T PRK05602         99 -APD-VPD-PAPGPDAGLEARQRARRVEQALAALPERQREAIVLQYY----QGLSNIEAAAVMDISVDALESLLARGRRA  171 (186)
T ss_pred             -ccc-cCC-CCCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHhhHHHh----cCCCHHHHHHHhCcCHHHHHHHHHHHHHH
Confidence             000 001 12235555666666778999999999999999999985    77999999999999999999999999999


Q ss_pred             HHhHHhhchh
Q 046578          365 LQQTNILNNL  374 (379)
Q Consensus       365 LR~~l~~~~L  374 (379)
                      ||+.+...+.
T Consensus       172 Lr~~l~~~~~  181 (186)
T PRK05602        172 LRAQLADLPG  181 (186)
T ss_pred             HHHHHHhccc
Confidence            9999987654

>PRK09646 RNA polymerase sigma factor SigK; Reviewed

Probab=99.95  E-value=4.2e-26  Score=207.01  Aligned_cols=186  Identities=12%  Similarity=0.197  Sum_probs=150.2

Q ss_pred             chhhhcCcCcHHHHHHHHhcccHHHHHHHHHHhHHHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHhccCCCCCCCchhH
Q 046578          118 FLDKENGELDYNLVKYKILCKERESQERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTY  197 (379)
Q Consensus       118 ~~~~~~~~~~~~eLi~~~~~Gd~~A~e~Li~~y~~lV~~ia~r~~~~~~d~eDLvQEg~i~L~~ai~~fD~~~g~~FsTY  197 (379)
                      +...+.+.-+..+|+..+.+||..+++.||+.|.+.|+++|.+++++..++||++||+|+++|+++++|++.+| .|.+|
T Consensus         7 ~~~~~~~~~~~~~li~~~~~g~~~a~~~l~~~y~~~l~~~~~~~~~~~~dAeDivQe~fi~l~~~~~~~~~~~~-~~~~w   85 (194)
T PRK09646          7 MTGPPAESPDLDALLRRVARGDQDAFAELYDRTSSRVYGLVRRVLRDPGYSEETTQEVYLEVWRTASRFDPARG-SALAW   85 (194)
T ss_pred             ccCCCCCcccHHHHHHHHHccCHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhhhhcCcccc-cHHHH
Confidence            33344556778999999999999999999999999999999999999999999999999999999999997655 79999


Q ss_pred             HHHHHHHHHHHHHHhhcCcccCCcchHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCc
Q 046578          198 VYWWIKQAIIRAIANKSRTIRLPGSMAGMVAKIAEANNVLSRRLRRMPTDSEIAEMLNIHVSTVRLAIERTRHPISLDGA  277 (379)
Q Consensus       198 a~~~Ir~~i~~~lr~~~r~irip~~~~~~~~ki~~a~~~l~~~lgr~pt~~eia~~Lgis~~~~~~~l~~~~~~iSLd~~  277 (379)
                      ++.+++|.+++++|++.+..+.                                                   ....   
T Consensus        86 l~~ia~n~~~d~~r~~~~~~~~---------------------------------------------------~~~~---  111 (194)
T PRK09646         86 LLTLAHRRAVDRVRSEQAASQR---------------------------------------------------EVRY---  111 (194)
T ss_pred             HHHHHHHHHHHHHHhhcccccc---------------------------------------------------cccc---
Confidence            9999999999999986531000                                                   0000   


Q ss_pred             cccCCCCcccccCCCCCCCChHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHH
Q 046578          278 VTDRGCMTMQDIIPGPDETMPERMVQKQLMKQELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQI  357 (379)
Q Consensus       278 ~~~~~~~~l~d~i~~~~~~~pe~~~~~~e~~~~L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~  357 (379)
                       ..      .+.  ......+.+.+...+....+..+|..||+++|.||.++|+    +|+|++|||+.||+|.++|+++
T Consensus       112 -~~------~~~--~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~vl~l~~~----~~~s~~EIA~~Lgis~~tVk~~  178 (194)
T PRK09646        112 -GA------RNV--DPAFDQVAEEVEARLERERVRDCLDALTDTQRESVTLAYY----GGLTYREVAERLAVPLGTVKTR  178 (194)
T ss_pred             -cc------ccc--cccccchHHHHHHHhHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHhCCChHhHHHH
Confidence             00      000  0011123444444555678999999999999999999984    6799999999999999999999


Q ss_pred             HHHHHHHHHhHHhh
Q 046578          358 RGIALTKLQQTNIL  371 (379)
Q Consensus       358 ~~rAl~kLR~~l~~  371 (379)
                      ++||+++||+.+..
T Consensus       179 l~ra~~~Lr~~l~~  192 (194)
T PRK09646        179 MRDGLIRLRDCLGV  192 (194)
T ss_pred             HHHHHHHHHHHhcc
Confidence            99999999999854

>TIGR02948 SigW_bacill RNA polymerase sigma-W factor

Probab=99.94  E-value=1.7e-25  Score=200.88  Aligned_cols=182  Identities=18%  Similarity=0.250  Sum_probs=146.5

Q ss_pred             HHHHHHHHhcccHHHHHHHHHHhHHHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHhccCCCCCCCchhHHHHHHHHHHH
Q 046578          128 YNLVKYKILCKERESQERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYWWIKQAII  207 (379)
Q Consensus       128 ~~eLi~~~~~Gd~~A~e~Li~~y~~lV~~ia~r~~~~~~d~eDLvQEg~i~L~~ai~~fD~~~g~~FsTYa~~~Ir~~i~  207 (379)
                      .++++..+.+||..++++||..|.|.|+.+|.++.++..+++|++||+|+++|+++.+|++..  +|.+|++++++|.+.
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            356899999999999999999999999999999999999999999999999999999999764  699999999999999


Q ss_pred             HHHHhhcCcccCCcchHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCccccCCCCccc
Q 046578          208 RAIANKSRTIRLPGSMAGMVAKIAEANNVLSRRLRRMPTDSEIAEMLNIHVSTVRLAIERTRHPISLDGAVTDRGCMTMQ  287 (379)
Q Consensus       208 ~~lr~~~r~irip~~~~~~~~ki~~a~~~l~~~lgr~pt~~eia~~Lgis~~~~~~~l~~~~~~iSLd~~~~~~~~~~l~  287 (379)
                      +++|+..+..                                                       .++......+...+.
T Consensus        83 ~~~rk~~~~~-------------------------------------------------------~~~~~~~~~~~~~~~  107 (187)
T TIGR02948        83 DRLRKRKPDF-------------------------------------------------------YLDDEVQGTDGLTME  107 (187)
T ss_pred             HHHHhhcccc-------------------------------------------------------cccccccCccccccc
Confidence            9999754210                                                       000000000000111


Q ss_pred             ccCCCCCCCChHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHh
Q 046578          288 DIIPGPDETMPERMVQKQLMKQELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQ  367 (379)
Q Consensus       288 d~i~~~~~~~pe~~~~~~e~~~~L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~  367 (379)
                      +...+ ..+.|++.+...+....+..++.+|||++|.||.++|+    +|+|++|||+.||+|.++|++.++||+++||+
T Consensus       108 ~~~~~-~~~~~~~~~~~~e~~~~l~~~l~~L~~~~r~v~~l~~~----~g~s~~eIA~~lgis~~~v~~~l~Rar~~Lr~  182 (187)
T TIGR02948       108 SQLAA-DEAPPEDQVISLELRDTIQQEIQALPPKYRMVIVLKYM----EDLSLKEISEILDLPVGTVKTRIHRGREALRK  182 (187)
T ss_pred             ccccc-CcCCHHHHHHHHHHHHHHHHHHHhCCHHHhHHhhhHHh----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence            11111 12356666666666778999999999999999999884    67999999999999999999999999999999


Q ss_pred             HHhh
Q 046578          368 TNIL  371 (379)
Q Consensus       368 ~l~~  371 (379)
                      .+..
T Consensus       183 ~l~~  186 (187)
T TIGR02948       183 QLRH  186 (187)
T ss_pred             Hhhc
Confidence            8754

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

>PRK12513 RNA polymerase sigma factor; Provisional

Probab=99.94  E-value=1.2e-25  Score=203.62  Aligned_cols=182  Identities=15%  Similarity=0.220  Sum_probs=151.0

Q ss_pred             CcHHHHHHHHhcccHHHHHHHHHHhHHHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHhccCCCCCCCchhHHHHHHHHH
Q 046578          126 LDYNLVKYKILCKERESQERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYWWIKQA  205 (379)
Q Consensus       126 ~~~~eLi~~~~~Gd~~A~e~Li~~y~~lV~~ia~r~~~~~~d~eDLvQEg~i~L~~ai~~fD~~~g~~FsTYa~~~Ir~~  205 (379)
                      .+..+++.+++.||..|++.|+..|.+.|+++|.++.++..++||++||+|+++|+++.+|++.  .+|.+|++++++|.
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            4568899999999999999999999999999999999999999999999999999999999864  37999999999999


Q ss_pred             HHHHHHhhcCcccCCcchHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCccccCCCCc
Q 046578          206 IIRAIANKSRTIRLPGSMAGMVAKIAEANNVLSRRLRRMPTDSEIAEMLNIHVSTVRLAIERTRHPISLDGAVTDRGCMT  285 (379)
Q Consensus       206 i~~~lr~~~r~irip~~~~~~~~ki~~a~~~l~~~lgr~pt~~eia~~Lgis~~~~~~~l~~~~~~iSLd~~~~~~~~~~  285 (379)
                      +++++|+..+....+                                                     .+.    +.  .
T Consensus        89 ~~~~~R~~~~~~~~~-----------------------------------------------------~~~----~~--~  109 (194)
T PRK12513         89 LIDHWRRHGARQAPS-----------------------------------------------------LDA----DE--Q  109 (194)
T ss_pred             HHHHHHHhccccccc-----------------------------------------------------ccc----ch--h
Confidence            999999876421110                                                     000    00  0


Q ss_pred             ccccCCCCCCCChHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Q 046578          286 MQDIIPGPDETMPERMVQKQLMKQELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKL  365 (379)
Q Consensus       286 l~d~i~~~~~~~pe~~~~~~e~~~~L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kL  365 (379)
                      . ... ......|+..+...+....+..+|+.||+++|.||.++|+    +|+|++|||+.||+|+++|+++++||+++|
T Consensus       110 ~-~~~-~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~i~~l~~~----~g~s~~EIA~~lgis~~tV~~~l~ra~~~L  183 (194)
T PRK12513        110 L-HAL-ADDGAAPEQQLSLFRDRRRLQAALETLPDEQREVFLLREH----GDLELEEIAELTGVPEETVKSRLRYALQKL  183 (194)
T ss_pred             h-hhc-CCCCCCHHHHHHHHHHHHHHHHHHHhCCHhHhhheeeehc----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence            0 000 1122356666677777788999999999999999999984    779999999999999999999999999999


Q ss_pred             HhHHhhchh
Q 046578          366 QQTNILNNL  374 (379)
Q Consensus       366 R~~l~~~~L  374 (379)
                      |+.+...++
T Consensus       184 r~~l~~~~~  192 (194)
T PRK12513        184 RELLAEEVA  192 (194)
T ss_pred             HHHHHHhhc
Confidence            999887654

>PRK09648 RNA polymerase sigma factor SigD; Reviewed

Probab=99.94  E-value=2.8e-25  Score=200.53  Aligned_cols=177  Identities=21%  Similarity=0.320  Sum_probs=146.3

Q ss_pred             cCcHHHHHHHHhcccHHHHHHHHHHhHHHHHHHHHhccCC----CCCHHHHHHHHHHHHHHHHhccCCCCCCCchhHHHH
Q 046578          125 ELDYNLVKYKILCKERESQERIIRSYRSLVVSIATGYQGK----GLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYW  200 (379)
Q Consensus       125 ~~~~~eLi~~~~~Gd~~A~e~Li~~y~~lV~~ia~r~~~~----~~d~eDLvQEg~i~L~~ai~~fD~~~g~~FsTYa~~  200 (379)
                      ..+..+++..+.+||..|++.||..|.+.|+++|.++.++    ..++||++||+|+++|+++.+|++. +.+|.+|++.
T Consensus         8 ~~~~~~l~~~~~~gd~~a~~~l~~~~~~~l~~~~~~~~~~~~~~~~~aeDlvQe~fi~l~~~~~~~~~~-~~~~~~wl~~   86 (189)
T PRK09648          8 GEELDALVAEAVAGDRRALREVLEIIRPLVVRYCRARLGGVERPGLSADDVAQEVCLAVITALPRYRDQ-GRPFLAFVYG   86 (189)
T ss_pred             chHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHhcccccCCCCHHHHHHHHHHHHHHHHHHHhcc-CCcHHHHHHH
Confidence            3456889999999999999999999999999999998765    3689999999999999999999864 4589999999


Q ss_pred             HHHHHHHHHHHhhcCcccCCcchHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCcccc
Q 046578          201 WIKQAIIRAIANKSRTIRLPGSMAGMVAKIAEANNVLSRRLRRMPTDSEIAEMLNIHVSTVRLAIERTRHPISLDGAVTD  280 (379)
Q Consensus       201 ~Ir~~i~~~lr~~~r~irip~~~~~~~~ki~~a~~~l~~~lgr~pt~~eia~~Lgis~~~~~~~l~~~~~~iSLd~~~~~  280 (379)
                      +++|.+.+++|++.+....+                                                     .+.    
T Consensus        87 i~~n~~~d~~r~~~r~~~~~-----------------------------------------------------~~~----  109 (189)
T PRK09648         87 IAAHKVADAHRAAGRDKAVP-----------------------------------------------------TEE----  109 (189)
T ss_pred             HHHHHHHHHHHHhCCCcccc-----------------------------------------------------ccc----
Confidence            99999999999866311000                                                     000    


Q ss_pred             CCCCcccccCCCCCCCChHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 046578          281 RGCMTMQDIIPGPDETMPERMVQKQLMKQELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGI  360 (379)
Q Consensus       281 ~~~~~l~d~i~~~~~~~pe~~~~~~e~~~~L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~r  360 (379)
                           ..+...  ...+|++.+...+....+..+|..||+++|+||.++|+    +|+|++|||+.||+|.++|+++++|
T Consensus       110 -----~~~~~~--~~~~~~~~~~~~e~~~~l~~~l~~L~~~~r~i~~l~~~----~g~s~~EIA~~lgis~~tV~~~l~R  178 (189)
T PRK09648        110 -----VPERPS--DDAGPEERALRSESSNRMRELLDTLPEKQREILILRVV----VGLSAEETAEAVGSTPGAVRVAQHR  178 (189)
T ss_pred             -----cccccc--cCCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHHCCCHHHHHHHHHH
Confidence                 000011  12356776667777788999999999999999999995    6799999999999999999999999


Q ss_pred             HHHHHHhHHh
Q 046578          361 ALTKLQQTNI  370 (379)
Q Consensus       361 Al~kLR~~l~  370 (379)
                      |+++||+.+.
T Consensus       179 a~~~Lr~~l~  188 (189)
T PRK09648        179 ALARLRAEIE  188 (189)
T ss_pred             HHHHHHHHhc
Confidence            9999999864

>PRK09641 RNA polymerase sigma factor SigW; Provisional

Probab=99.94  E-value=2.2e-25  Score=200.19  Aligned_cols=184  Identities=18%  Similarity=0.261  Sum_probs=148.8

Q ss_pred             CcHHHHHHHHhcccHHHHHHHHHHhHHHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHhccCCCCCCCchhHHHHHHHHH
Q 046578          126 LDYNLVKYKILCKERESQERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYWWIKQA  205 (379)
Q Consensus       126 ~~~~eLi~~~~~Gd~~A~e~Li~~y~~lV~~ia~r~~~~~~d~eDLvQEg~i~L~~ai~~fD~~~g~~FsTYa~~~Ir~~  205 (379)
                      ++...++.++.+||..+++.+|..|.|.|+++|+++.++..+++|++||+|+++|+++++|++..  +|.+|++++++|.
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            34578999999999999999999999999999999999999999999999999999999998753  7999999999999


Q ss_pred             HHHHHHhhcCcccCCcchHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCccccCCCCc
Q 046578          206 IIRAIANKSRTIRLPGSMAGMVAKIAEANNVLSRRLRRMPTDSEIAEMLNIHVSTVRLAIERTRHPISLDGAVTDRGCMT  285 (379)
Q Consensus       206 i~~~lr~~~r~irip~~~~~~~~ki~~a~~~l~~~lgr~pt~~eia~~Lgis~~~~~~~l~~~~~~iSLd~~~~~~~~~~  285 (379)
                      +.+++|+..+..                                                       +++....+++...
T Consensus        81 ~~d~~R~~~~~~-------------------------------------------------------~~~~~~~~~~~~~  105 (187)
T PRK09641         81 TIDRLRKRKPDY-------------------------------------------------------YLDAEVAGTEGLT  105 (187)
T ss_pred             HHHHHHhcCccc-------------------------------------------------------cccccccCCcchh
Confidence            999999865210                                                       0111111111111


Q ss_pred             ccccCCCCCCCChHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Q 046578          286 MQDIIPGPDETMPERMVQKQLMKQELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKL  365 (379)
Q Consensus       286 l~d~i~~~~~~~pe~~~~~~e~~~~L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kL  365 (379)
                      ..+.+.+ ...+|++.+...+....+..++..||+++++||.++|+    +|+|++|||+.||+|.++|++.++||+++|
T Consensus       106 ~~~~~~~-~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~il~l~~~----~~~s~~eIA~~lgis~~~v~~~l~Rar~~L  180 (187)
T PRK09641        106 MYSQLAA-DDALPEEQVVSLELQETIQEAILQLPEKYRTVIVLKYI----EDLSLKEISEILDLPVGTVKTRIHRGREAL  180 (187)
T ss_pred             hhccccc-CcCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHhhhHHh----hCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence            1111111 22356666667777778999999999999999999984    679999999999999999999999999999


Q ss_pred             HhHHhh
Q 046578          366 QQTNIL  371 (379)
Q Consensus       366 R~~l~~  371 (379)
                      |+.+..
T Consensus       181 r~~l~~  186 (187)
T PRK09641        181 RKQLRH  186 (187)
T ss_pred             HHHHhc
Confidence            998753

>TIGR02859 spore_sigH RNA polymerase sigma-H factor

Probab=99.94  E-value=2e-25  Score=202.38  Aligned_cols=192  Identities=24%  Similarity=0.321  Sum_probs=147.6

Q ss_pred             CcHHHHHHHHhcccHHHHHHHHHHhHHHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHhccCCCCCCCchhHHHHHHHHH
Q 046578          126 LDYNLVKYKILCKERESQERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYWWIKQA  205 (379)
Q Consensus       126 ~~~~eLi~~~~~Gd~~A~e~Li~~y~~lV~~ia~r~~~~~~d~eDLvQEg~i~L~~ai~~fD~~~g~~FsTYa~~~Ir~~  205 (379)
                      ++..+++..+++||..|++.||+.|.|.|+++|+++.++..+++|++||+|+++|+++.+|++..+.+|.||++.++++.
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            45678999999999999999999999999999999999999999999999999999999999877679999999999999


Q ss_pred             HHHHHHhhcCcccCCcchHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCcccc-CCCC
Q 046578          206 IIRAIANKSRTIRLPGSMAGMVAKIAEANNVLSRRLRRMPTDSEIAEMLNIHVSTVRLAIERTRHPISLDGAVTD-RGCM  284 (379)
Q Consensus       206 i~~~lr~~~r~irip~~~~~~~~ki~~a~~~l~~~lgr~pt~~eia~~Lgis~~~~~~~l~~~~~~iSLd~~~~~-~~~~  284 (379)
                      +.+++|+..+..+.+                                               .....|++.+..+ +++.
T Consensus        84 ~~~~~r~~~~~~~~~-----------------------------------------------~~~~~~~~~~~~~~~~~~  116 (198)
T TIGR02859        84 IITAIKTATRQKHIP-----------------------------------------------LNSYVSLNKPIYDEESDR  116 (198)
T ss_pred             HHHHHHHHHHhcccc-----------------------------------------------hhhhcCcccccccccccc
Confidence            999988653211100                                               0011222322111 1111


Q ss_pred             cccccCCCCCCCChHHHHHHHHHHHHHHHHHhcC-CHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 046578          285 TMQDIIPGPDETMPERMVQKQLMKQELKELLQTL-SEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALT  363 (379)
Q Consensus       285 ~l~d~i~~~~~~~pe~~~~~~e~~~~L~~~L~~L-~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~  363 (379)
                      .+.+.+.+....+|++.+...+....+.++|..| ++.++.|+. .|+    +|+|++|||+.||+|.++|++.++||++
T Consensus       117 ~~~~~~~~~~~~~~e~~~~~~e~~~~l~~~l~~Ll~~~~~~i~~-~~~----~~~s~~eIA~~l~~s~~tV~~~l~r~r~  191 (198)
T TIGR02859       117 TLLDVISGAKVTDPEELIISQEEYGDIESKMNELLSDLEWKVLQ-SYL----DGKSYQEIACDLNRHVKSIDNALQRVKR  191 (198)
T ss_pred             hHHHHhhccccCCHHHHHHHHHHHHHHHHHHHHhcCHHHHHHHH-HHH----cCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            2222222222346777777777778899999985 566666665 463    6799999999999999999999999999


Q ss_pred             HHHhHH
Q 046578          364 KLQQTN  369 (379)
Q Consensus       364 kLR~~l  369 (379)
                      +||+.+
T Consensus       192 ~L~~~l  197 (198)
T TIGR02859       192 KLEKYL  197 (198)
T ss_pred             HHHHhc
Confidence            999875

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

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

Probab=99.94  E-value=1.7e-25  Score=197.81  Aligned_cols=170  Identities=19%  Similarity=0.310  Sum_probs=141.9

Q ss_pred             HHHHHhcccHHHHHHHHHHhHHHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHhccCCCCCCCchhHHHHHHHHHHHHHH
Q 046578          131 VKYKILCKERESQERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYWWIKQAIIRAI  210 (379)
Q Consensus       131 Li~~~~~Gd~~A~e~Li~~y~~lV~~ia~r~~~~~~d~eDLvQEg~i~L~~ai~~fD~~~g~~FsTYa~~~Ir~~i~~~l  210 (379)
                      |+.++++||..|++.||..|.+.+++++.++.++..++||++||+|+.+|+++++|+...+ +|.+|++.+++|.+++++
T Consensus         1 li~~~~~~d~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeD~vQe~~l~l~~~~~~~~~~~~-~~~~wl~~i~~n~~~d~~   79 (170)
T TIGR02952         1 LLERAQDREEDAFARIYETYSDRVYRYIYYRVGCKYTAEDLTSEVFERVLRKIDSFKEQKN-SFEAWLFTIARNVVNDYF   79 (170)
T ss_pred             ChHHHHccCHHHHHHHHHHHHHHHHHHHHHHHCChhhHHHHHHHHHHHHHHhHHhcccccc-cHHHHHHHHHHHHHHHHH
Confidence            4778999999999999999999999999999988899999999999999999999986544 899999999999999999


Q ss_pred             HhhcCcccCCcchHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCccccCCCCcccccC
Q 046578          211 ANKSRTIRLPGSMAGMVAKIAEANNVLSRRLRRMPTDSEIAEMLNIHVSTVRLAIERTRHPISLDGAVTDRGCMTMQDII  290 (379)
Q Consensus       211 r~~~r~irip~~~~~~~~ki~~a~~~l~~~lgr~pt~~eia~~Lgis~~~~~~~l~~~~~~iSLd~~~~~~~~~~l~d~i  290 (379)
                      |++.+...                                                     .+.+.         ..+..
T Consensus        80 R~~~~~~~-----------------------------------------------------~~~~~---------~~~~~   97 (170)
T TIGR02952        80 RGSKRHPL-----------------------------------------------------FSLDV---------FKELL   97 (170)
T ss_pred             HhcCCCCC-----------------------------------------------------CcHHH---------HhhcC
Confidence            98653110                                                     00000         00000


Q ss_pred             CCCCCCChHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHH
Q 046578          291 PGPDETMPERMVQKQLMKQELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQTN  369 (379)
Q Consensus       291 ~~~~~~~pe~~~~~~e~~~~L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~~l  369 (379)
                      .  ...+|++.+...+....+..++..|||++|+||.++|+    +|+|++|||+.||+|.++|++.++||+++||+.+
T Consensus        98 ~--~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~vl~l~~~----~g~s~~eIA~~l~is~~tv~~~l~ra~~~Lr~~l  170 (170)
T TIGR02952        98 S--NEPNPEEAILKEEANEKLLKALKILTPKQQHVIALRFG----QNLPIAEVARILGKTEGAVKILQFRAIKKLARQM  170 (170)
T ss_pred             C--CCCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHh----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHhC
Confidence            1  12246666666677788999999999999999999984    7799999999999999999999999999999864

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.

>PRK12537 RNA polymerase sigma factor; Provisional

Probab=99.94  E-value=1.9e-25  Score=200.59  Aligned_cols=175  Identities=13%  Similarity=0.183  Sum_probs=144.3

Q ss_pred             cCcHHHHHHHHhcccHHHHHHHHHHhHHHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHhccCCCCCCCchhHHHHHHHH
Q 046578          125 ELDYNLVKYKILCKERESQERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYWWIKQ  204 (379)
Q Consensus       125 ~~~~~eLi~~~~~Gd~~A~e~Li~~y~~lV~~ia~r~~~~~~d~eDLvQEg~i~L~~ai~~fD~~~g~~FsTYa~~~Ir~  204 (379)
                      .+++.+|+..+..||..+++.||..|.+.++.++.++.++..+++|++||+|+.+|+.+++|++.. ..|.+|++++++|
T Consensus         7 ~~~~~~l~~~~~~~d~~a~~~l~~~~~~~l~~~~~~~~~~~~~AeDivQe~fl~l~~~~~~~~~~~-~~~~~wL~~iarn   85 (182)
T PRK12537          7 PFDYEACLLACARGDRRALQALYQQESARLLGVARRIVRDRALAEDIVHDAFIKIWTGAASFDPAR-GSARGWIYSVTRH   85 (182)
T ss_pred             hhhHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHhCCHhHHHHHHHHHHHHHHhccccCCccc-ccHHHHHHHHHHH
Confidence            477889999999999999999999999999999999999999999999999999999999998643 3799999999999


Q ss_pred             HHHHHHHhhcCcccCCcchHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCccccCCCC
Q 046578          205 AIIRAIANKSRTIRLPGSMAGMVAKIAEANNVLSRRLRRMPTDSEIAEMLNIHVSTVRLAIERTRHPISLDGAVTDRGCM  284 (379)
Q Consensus       205 ~i~~~lr~~~r~irip~~~~~~~~ki~~a~~~l~~~lgr~pt~~eia~~Lgis~~~~~~~l~~~~~~iSLd~~~~~~~~~  284 (379)
                      .+++++|+..+...                                                       .+.    .   
T Consensus        86 ~~~d~~r~~~~~~~-------------------------------------------------------~~~----~---  103 (182)
T PRK12537         86 LALNVLRDTRREVV-------------------------------------------------------LDD----D---  103 (182)
T ss_pred             HHHHHHHhccccCc-------------------------------------------------------ccc----c---
Confidence            99999998653100                                                       000    0   


Q ss_pred             cccccCCCCCCCChHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHH
Q 046578          285 TMQDIIPGPDETMPERMVQKQLMKQELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTK  364 (379)
Q Consensus       285 ~l~d~i~~~~~~~pe~~~~~~e~~~~L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~k  364 (379)
                       ..+...  ....+++.....+....+..+|+.||+++|+||.++|+    +|+|++|||+.||+|.++|+++++||+++
T Consensus       104 -~~~~~~--~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~i~~l~~~----~~~s~~eIA~~lgis~~tV~~~l~ra~~~  176 (182)
T PRK12537        104 -AEETAQ--TLHEIIDDFDLWANSGKIHRCLEQLEPARRNCILHAYV----DGCSHAEIAQRLGAPLGTVKAWIKRSLKA  176 (182)
T ss_pred             -hhhhcc--cccchHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHHCCChhhHHHHHHHHHHH
Confidence             000000  01123334444455667999999999999999999985    77999999999999999999999999999


Q ss_pred             HHhHH
Q 046578          365 LQQTN  369 (379)
Q Consensus       365 LR~~l  369 (379)
                      ||+++
T Consensus       177 Lr~~l  181 (182)
T PRK12537        177 LRECM  181 (182)
T ss_pred             HHHHh
Confidence            99986

>PRK12524 RNA polymerase sigma factor; Provisional

Probab=99.94  E-value=5e-25  Score=200.22  Aligned_cols=178  Identities=16%  Similarity=0.174  Sum_probs=148.5

Q ss_pred             CcHHHHHHHHhcccHHHHHHHHHHhHHHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHhccCCCCCCCchhHHHHHHHHH
Q 046578          126 LDYNLVKYKILCKERESQERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYWWIKQA  205 (379)
Q Consensus       126 ~~~~eLi~~~~~Gd~~A~e~Li~~y~~lV~~ia~r~~~~~~d~eDLvQEg~i~L~~ai~~fD~~~g~~FsTYa~~~Ir~~  205 (379)
                      ++...|+.++..||..|++.||..|.|.|+.+|.++.++..+++|++||+|+++|+.+.+|++.. .+|.+|++.+++|.
T Consensus        11 ~~~~~li~~~~~gd~~a~~~l~~~y~~~l~~~~~~~~~~~~~AeDlvQe~~l~l~~~~~~~~~~~-~~~~~wl~~ia~n~   89 (196)
T PRK12524         11 VSDEALLVLYANGDPAAARALTLRLAPRALAVATRVLGDRAEAEDVTQEAMLRLWRIAPDWRQGE-ARVSTWLYRVVCNL   89 (196)
T ss_pred             cCHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhhhcccccc-chHHHHHHHHHHHH
Confidence            45689999999999999999999999999999999999999999999999999999999997533 47999999999999


Q ss_pred             HHHHHHhhcCcccCCcchHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCccccCCCCc
Q 046578          206 IIRAIANKSRTIRLPGSMAGMVAKIAEANNVLSRRLRRMPTDSEIAEMLNIHVSTVRLAIERTRHPISLDGAVTDRGCMT  285 (379)
Q Consensus       206 i~~~lr~~~r~irip~~~~~~~~ki~~a~~~l~~~lgr~pt~~eia~~Lgis~~~~~~~l~~~~~~iSLd~~~~~~~~~~  285 (379)
                      +++++|++.+.                                                      ...++..     .  
T Consensus        90 ~~d~~Rk~~~~------------------------------------------------------~~~~~~~-----~--  108 (196)
T PRK12524         90 CTDRLRRRRRA------------------------------------------------------SVDLDDA-----P--  108 (196)
T ss_pred             HHHHHHhhcCC------------------------------------------------------CCCcccc-----c--
Confidence            99999976520                                                      0001100     0  


Q ss_pred             ccccCCCCCCCChHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Q 046578          286 MQDIIPGPDETMPERMVQKQLMKQELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKL  365 (379)
Q Consensus       286 l~d~i~~~~~~~pe~~~~~~e~~~~L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kL  365 (379)
                        +. .+ ....+++.+...+....+..+++.||+++|.||.|+|+    +|++++|||+.||+|.+||+++++||+++|
T Consensus       109 --~~-~~-~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~i~~L~~~----~g~s~~eIA~~lgis~~tV~~~l~Ra~~~L  180 (196)
T PRK12524        109 --EP-AD-AAPGAEEALIEGDRMRALDAALAALPERQRQAVVLRHI----EGLSNPEIAEVMEIGVEAVESLTARGKRAL  180 (196)
T ss_pred             --cc-cc-cCCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHH
Confidence              00 01 11245566666677788999999999999999999985    779999999999999999999999999999


Q ss_pred             HhHHhhch
Q 046578          366 QQTNILNN  373 (379)
Q Consensus       366 R~~l~~~~  373 (379)
                      |+++...+
T Consensus       181 r~~l~~~~  188 (196)
T PRK12524        181 AALLAGQR  188 (196)
T ss_pred             HHHHHhcc
Confidence            99987644

>TIGR02939 RpoE_Sigma70 RNA polymerase sigma factor RpoE

Probab=99.93  E-value=9e-25  Score=196.74  Aligned_cols=183  Identities=15%  Similarity=0.192  Sum_probs=146.6

Q ss_pred             CcHHHHHHHHhcccHHHHHHHHHHhHHHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHhccCCCCCCCchhHHHHHHHHH
Q 046578          126 LDYNLVKYKILCKERESQERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYWWIKQA  205 (379)
Q Consensus       126 ~~~~eLi~~~~~Gd~~A~e~Li~~y~~lV~~ia~r~~~~~~d~eDLvQEg~i~L~~ai~~fD~~~g~~FsTYa~~~Ir~~  205 (379)
                      .+...++..+.+||+.+++.||..|.+.|+.+|+++.++..+++|++||+|+++|+++++|++.  .+|.+|++.+++|.
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            3457899999999999999999999999999999999999999999999999999999999864  37999999999999


Q ss_pred             HHHHHHhhcCcccCCcchHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCccccCCCCc
Q 046578          206 IIRAIANKSRTIRLPGSMAGMVAKIAEANNVLSRRLRRMPTDSEIAEMLNIHVSTVRLAIERTRHPISLDGAVTDRGCMT  285 (379)
Q Consensus       206 i~~~lr~~~r~irip~~~~~~~~ki~~a~~~l~~~lgr~pt~~eia~~Lgis~~~~~~~l~~~~~~iSLd~~~~~~~~~~  285 (379)
                      +.+++++..+.....                                                  ..+.+..    +...
T Consensus        83 ~~~~~r~~~r~~~~~--------------------------------------------------~~~~~~~----~~~~  108 (190)
T TIGR02939        83 AKNHLVAQGRRPPTS--------------------------------------------------DVEIEDA----EHFE  108 (190)
T ss_pred             HHHHHHHhccCCCcc--------------------------------------------------cccccch----hhhc
Confidence            999998755311000                                                  0000000    0000


Q ss_pred             ccccCCCCCCCChHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Q 046578          286 MQDIIPGPDETMPERMVQKQLMKQELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKL  365 (379)
Q Consensus       286 l~d~i~~~~~~~pe~~~~~~e~~~~L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kL  365 (379)
                      ..+.+  ....+|++.+...+....+..++..||+++|.||.++|+    +|+|++|||+.||+|.++|++.++||+++|
T Consensus       109 ~~~~~--~~~~~~e~~~~~~~~~~~l~~~l~~L~~~~r~v~~l~~~----~~~s~~EIA~~lgis~~tv~~~l~rar~~L  182 (190)
T TIGR02939       109 GADRL--REIDTPERLLLSRELEQTVMRAVEALPEDLRTAITLREL----EGLSYEDIARIMDCPVGTVRSRIFRAREAI  182 (190)
T ss_pred             ccccc--cccCChHHHHHHHHHHHHHHHHHHcCCHHHhhhhhhhhh----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHH
Confidence            00000  012346666666777788999999999999999999984    779999999999999999999999999999


Q ss_pred             HhHHh
Q 046578          366 QQTNI  370 (379)
Q Consensus       366 R~~l~  370 (379)
                      |+++.
T Consensus       183 r~~l~  187 (190)
T TIGR02939       183 AIRLR  187 (190)
T ss_pred             HHHhh
Confidence            99975

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.

>PRK12514 RNA polymerase sigma factor; Provisional

Probab=99.93  E-value=6.7e-25  Score=196.21  Aligned_cols=175  Identities=15%  Similarity=0.167  Sum_probs=143.9

Q ss_pred             CcHHHHHHHHhcccHHHHHHHHHHhHHHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHhccCCCCCCCchhHHHHHHHHH
Q 046578          126 LDYNLVKYKILCKERESQERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYWWIKQA  205 (379)
Q Consensus       126 ~~~~eLi~~~~~Gd~~A~e~Li~~y~~lV~~ia~r~~~~~~d~eDLvQEg~i~L~~ai~~fD~~~g~~FsTYa~~~Ir~~  205 (379)
                      .+..+|+..+..||..+++.|+..|.+.++.+|.++.++..++||++||+|+++|+++++|++.. ..|.||++.+++|.
T Consensus         4 ~~~~~li~~~~~g~~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeD~~Qe~fl~~~~~~~~~~~~~-~~~~~wl~~ia~n~   82 (179)
T PRK12514          4 DDIEKLIVRVSLGDRDAFSSLYDATSAKLFGICLRVLKDRSEAEEALQDVYVKIWTKADRFAVSG-LSPMTWLITIARNH   82 (179)
T ss_pred             hHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHHcCHHHHHHHHHHHHHHHHHhHHhcCccc-ccHHHHHHHHHHHH
Confidence            34678999999999999999999999999999999999999999999999999999999998643 37999999999999


Q ss_pred             HHHHHHhhcCcccCCcchHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCccccCCCCc
Q 046578          206 IIRAIANKSRTIRLPGSMAGMVAKIAEANNVLSRRLRRMPTDSEIAEMLNIHVSTVRLAIERTRHPISLDGAVTDRGCMT  285 (379)
Q Consensus       206 i~~~lr~~~r~irip~~~~~~~~ki~~a~~~l~~~lgr~pt~~eia~~Lgis~~~~~~~l~~~~~~iSLd~~~~~~~~~~  285 (379)
                      +++++|++.+. .                                                     ...+.         
T Consensus        83 ~~d~~R~~~~~-~-----------------------------------------------------~~~~~---------   99 (179)
T PRK12514         83 AIDRLRARKAV-A-----------------------------------------------------VDIDE---------   99 (179)
T ss_pred             HHHHHHhcCCc-c-----------------------------------------------------ccccc---------
Confidence            99999975420 0                                                     00000         


Q ss_pred             ccccCCCCCCCChHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Q 046578          286 MQDIIPGPDETMPERMVQKQLMKQELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKL  365 (379)
Q Consensus       286 l~d~i~~~~~~~pe~~~~~~e~~~~L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kL  365 (379)
                      ..+ ..+ ....|++.+...+....+..+|..||+++++||.++|+    +|+|++|||+.||+|.++|++.++||+++|
T Consensus       100 ~~~-~~~-~~~~~e~~~~~~~~~~~l~~~l~~L~~~~r~i~~l~~~----~g~s~~eIA~~lgis~~tV~~~l~Rar~~L  173 (179)
T PRK12514        100 AHD-LAD-PSPGPEAEVIAGDEGQRIDACLEELEKDRAAAVRRAYL----EGLSYKELAERHDVPLNTMRTWLRRSLLKL  173 (179)
T ss_pred             chh-ccc-cCCCHHHHHHhHHHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHHCCChHHHHHHHHHHHHHH
Confidence            000 001 11245555555555567899999999999999999995    679999999999999999999999999999


Q ss_pred             HhHHh
Q 046578          366 QQTNI  370 (379)
Q Consensus       366 R~~l~  370 (379)
                      |+++.
T Consensus       174 r~~l~  178 (179)
T PRK12514        174 RECLS  178 (179)
T ss_pred             HHHhc
Confidence            99874

>PRK12538 RNA polymerase sigma factor; Provisional

Probab=99.93  E-value=6.7e-25  Score=204.90  Aligned_cols=176  Identities=13%  Similarity=0.195  Sum_probs=145.9

Q ss_pred             CcHHHHHHHHhcccHHHHHHHHHHhHHHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHhccCCCCCCCchhHHHHHHHHH
Q 046578          126 LDYNLVKYKILCKERESQERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYWWIKQA  205 (379)
Q Consensus       126 ~~~~eLi~~~~~Gd~~A~e~Li~~y~~lV~~ia~r~~~~~~d~eDLvQEg~i~L~~ai~~fD~~~g~~FsTYa~~~Ir~~  205 (379)
                      .+..+|+.++++||..+++.||..|.+.|++++.++.++..++||++||+|+.+|+++++|++..+ +|.+|++.+++|.
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            355789999999999999999999999999999999999999999999999999999999986444 7999999999999


Q ss_pred             HHHHHHhhcCcccCCcchHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCccccCCCCc
Q 046578          206 IIRAIANKSRTIRLPGSMAGMVAKIAEANNVLSRRLRRMPTDSEIAEMLNIHVSTVRLAIERTRHPISLDGAVTDRGCMT  285 (379)
Q Consensus       206 i~~~lr~~~r~irip~~~~~~~~ki~~a~~~l~~~lgr~pt~~eia~~Lgis~~~~~~~l~~~~~~iSLd~~~~~~~~~~  285 (379)
                      +++++|++.+.                                                     .   ++. .       
T Consensus       127 ~id~~Rk~~~~-----------------------------------------------------~---~~~-~-------  142 (233)
T PRK12538        127 CIDLRRKPRTE-----------------------------------------------------N---VDA-V-------  142 (233)
T ss_pred             HHHHHHhhccc-----------------------------------------------------c---ccc-c-------
Confidence            99999874310                                                     0   000 0       


Q ss_pred             ccccCCCCCCCChHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Q 046578          286 MQDIIPGPDETMPERMVQKQLMKQELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKL  365 (379)
Q Consensus       286 l~d~i~~~~~~~pe~~~~~~e~~~~L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kL  365 (379)
                       .+.. + ....+++.+...+....+..+|..||+++|+||.|+|+    +|+|++|||+.||+|.++|+++++||+++|
T Consensus       143 -~~~~-~-~~~~~~~~~~~~e~~~~l~~~L~~Lp~~~R~v~~L~~~----eg~s~~EIA~~Lgis~~tVk~~l~RAr~kL  215 (233)
T PRK12538        143 -PEVA-D-GKPDAVSVIERNELSDLLEAAMQRLPEQQRIAVILSYH----ENMSNGEIAEVMDTTVAAVESLLKRGRQQL  215 (233)
T ss_pred             -cccc-c-CCCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHhhhHHh----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHH
Confidence             0000 0 11234455555666678999999999999999999994    779999999999999999999999999999


Q ss_pred             HhHHhhch
Q 046578          366 QQTNILNN  373 (379)
Q Consensus       366 R~~l~~~~  373 (379)
                      |+.+....
T Consensus       216 r~~l~~~~  223 (233)
T PRK12538        216 RDLLRRHE  223 (233)
T ss_pred             HHHHHHhh
Confidence            99987544

>PRK11923 algU RNA polymerase sigma factor AlgU; Provisional

Probab=99.93  E-value=1.3e-24  Score=196.57  Aligned_cols=185  Identities=14%  Similarity=0.176  Sum_probs=147.8

Q ss_pred             cCcHHHHHHHHhcccHHHHHHHHHHhHHHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHhccCCCCCCCchhHHHHHHHH
Q 046578          125 ELDYNLVKYKILCKERESQERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYWWIKQ  204 (379)
Q Consensus       125 ~~~~~eLi~~~~~Gd~~A~e~Li~~y~~lV~~ia~r~~~~~~d~eDLvQEg~i~L~~ai~~fD~~~g~~FsTYa~~~Ir~  204 (379)
                      ..+...++..++.||..+++.||..|.|.|+++++++.++..++||++||+|+++|+++.+|++..  .|.+|++++++|
T Consensus         4 ~~~~~~ll~~~~~gd~~a~~~l~~~y~~~l~~~~~~~~~~~~daeDlvQe~~i~l~~~~~~~~~~~--~~~~wl~~ia~n   81 (193)
T PRK11923          4 QEEDQQLVERVQRGDKRAFDLLVLKYQHKILGLIVRFVHDTAEAQDVAQEAFIKAYRALGNFRGDS--AFYTWLYRIAIN   81 (193)
T ss_pred             cccHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHhCCHhhHHHHHHHHHHHHHHhHhCcCCCC--ccHhHHHHHHHH
Confidence            345578999999999999999999999999999999999999999999999999999999998764  699999999999


Q ss_pred             HHHHHHHhhcCcccCCcchHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCccccCCCC
Q 046578          205 AIIRAIANKSRTIRLPGSMAGMVAKIAEANNVLSRRLRRMPTDSEIAEMLNIHVSTVRLAIERTRHPISLDGAVTDRGCM  284 (379)
Q Consensus       205 ~i~~~lr~~~r~irip~~~~~~~~ki~~a~~~l~~~lgr~pt~~eia~~Lgis~~~~~~~l~~~~~~iSLd~~~~~~~~~  284 (379)
                      .+.+++|++.+....                                                  ....++......+  
T Consensus        82 ~~~d~~rk~~~~~~~--------------------------------------------------~~~~~~~~~~~~~--  109 (193)
T PRK11923         82 TAKNHLVSRGRRPPD--------------------------------------------------SDVSSEDAEFYDG--  109 (193)
T ss_pred             HHHHHHHHhcCCCcc--------------------------------------------------ccccccchhhhcc--
Confidence            999999976531000                                                  0000110000000  


Q ss_pred             cccccCCCCCCCChHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHH
Q 046578          285 TMQDIIPGPDETMPERMVQKQLMKQELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTK  364 (379)
Q Consensus       285 ~l~d~i~~~~~~~pe~~~~~~e~~~~L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~k  364 (379)
                        ...+.  ....|++.+...+....+..++..||+++|.||.++|+    +|+|++|||+.||+|.++|+++++||+++
T Consensus       110 --~~~~~--~~~~~e~~~~~~~~~~~l~~~l~~L~~~~r~v~~l~~~----~g~s~~eIA~~lgis~~tv~~~l~Rar~~  181 (193)
T PRK11923        110 --DHALK--DIESPERALLRDEIEGTVHRTIQQLPEDLRTALTLREF----DGLSYEDIASVMQCPVGTVRSRIFRAREA  181 (193)
T ss_pred             --ccccc--CcCCHHHHHHHHHHHHHHHHHHHhCCHHHhHHHhhHHh----cCCCHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence              00011  12356666666777788999999999999999999984    67999999999999999999999999999


Q ss_pred             HHhHHhh
Q 046578          365 LQQTNIL  371 (379)
Q Consensus       365 LR~~l~~  371 (379)
                      ||++++.
T Consensus       182 Lr~~l~~  188 (193)
T PRK11923        182 IDKALQP  188 (193)
T ss_pred             HHHHHHH
Confidence            9999763

>PRK12519 RNA polymerase sigma factor; Provisional

Probab=99.93  E-value=7e-25  Score=198.60  Aligned_cols=178  Identities=19%  Similarity=0.238  Sum_probs=143.9

Q ss_pred             cCcHHHHHHHHhcccHHHHHHHHHHhHHHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHhccCCCCCCCchhHHHHHHHH
Q 046578          125 ELDYNLVKYKILCKERESQERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYWWIKQ  204 (379)
Q Consensus       125 ~~~~~eLi~~~~~Gd~~A~e~Li~~y~~lV~~ia~r~~~~~~d~eDLvQEg~i~L~~ai~~fD~~~g~~FsTYa~~~Ir~  204 (379)
                      ..+..+++.+++.||..+++.|+..|.+.|+++++++.++..++||++||+|+++|+. ..|++..+ +|.||++++++|
T Consensus        13 ~~~~~~l~~~~~~gd~~a~~~L~~~y~~~l~~~~~~~~~~~~~aeDlvQe~fl~l~~~-~~~~~~~~-~f~~wl~~iarn   90 (194)
T PRK12519         13 SRSDAELFSALKAGQSAALGVLYDRHAGLVYGLALKILGNSQEAEDLTQEIFLSLWRK-SSYDPKRG-SLSSYLLTLTRS   90 (194)
T ss_pred             cccHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHh-cCCCcccc-cHHHHHHHHHHH
Confidence            4556889999999999999999999999999999999999899999999999999976 67876544 799999999999


Q ss_pred             HHHHHHHhhcCcccCCcchHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCccccCCCC
Q 046578          205 AIIRAIANKSRTIRLPGSMAGMVAKIAEANNVLSRRLRRMPTDSEIAEMLNIHVSTVRLAIERTRHPISLDGAVTDRGCM  284 (379)
Q Consensus       205 ~i~~~lr~~~r~irip~~~~~~~~ki~~a~~~l~~~lgr~pt~~eia~~Lgis~~~~~~~l~~~~~~iSLd~~~~~~~~~  284 (379)
                      .+++++|++.+.....                                                 .  ..+.        
T Consensus        91 ~~~d~~Rk~~~~~~~~-------------------------------------------------~--~~~~--------  111 (194)
T PRK12519         91 RAIDRLRSRRSRQRLL-------------------------------------------------E--RWQQ--------  111 (194)
T ss_pred             HHHHHHHhcccccchh-------------------------------------------------h--hhhh--------
Confidence            9999999865310000                                                 0  0000        


Q ss_pred             cccccCCCCCCCChHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHH
Q 046578          285 TMQDIIPGPDETMPERMVQKQLMKQELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTK  364 (379)
Q Consensus       285 ~l~d~i~~~~~~~pe~~~~~~e~~~~L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~k  364 (379)
                      ..   ..+.....+++.+...+....+..++..||+++++||.++|+    +|+|++|||+.||+|.++|+++++||+++
T Consensus       112 ~~---~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~~~v~~l~~~----~g~s~~EIA~~lgis~~tV~~~l~Ra~~~  184 (194)
T PRK12519        112 EL---LGEASEDTPLEQASLAERSQRVQTALAQLPESQRQVLELAYY----EGLSQSEIAKRLGIPLGTVKARARQGLLK  184 (194)
T ss_pred             hh---cccccCCCHHHHHHHHHHHHHHHHHHHhCCHHHhhhhhhhhh----cCCCHHHHHHHhCCCHHHHHHHHHHHHHH
Confidence            00   000112245555666666677999999999999999999984    67999999999999999999999999999


Q ss_pred             HHhHHh
Q 046578          365 LQQTNI  370 (379)
Q Consensus       365 LR~~l~  370 (379)
                      ||+.+.
T Consensus       185 Lr~~l~  190 (194)
T PRK12519        185 LRELLQ  190 (194)
T ss_pred             HHHHHH
Confidence            999865

>PRK09652 RNA polymerase sigma factor RpoE; Provisional

Probab=99.93  E-value=9.8e-25  Score=194.32  Aligned_cols=177  Identities=18%  Similarity=0.237  Sum_probs=142.5

Q ss_pred             HHHHhcccHHHHHHHHHHhHHHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHhccCCCCCCCchhHHHHHHHHHHHHHHH
Q 046578          132 KYKILCKERESQERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYWWIKQAIIRAIA  211 (379)
Q Consensus       132 i~~~~~Gd~~A~e~Li~~y~~lV~~ia~r~~~~~~d~eDLvQEg~i~L~~ai~~fD~~~g~~FsTYa~~~Ir~~i~~~lr  211 (379)
                      |.++++||..|++.|+..|.+.|+++++++.+++.+++|++||+|+++|+++++|+  .+.+|.+|++.+++|.+.+++|
T Consensus         1 v~~~~~gd~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeDl~Qe~~l~l~~~~~~~~--~~~~~~~~l~~~~~~~~~~~~r   78 (182)
T PRK09652          1 VERVQRGDRAAFALLVRRYQPRVKRLLSRLTRDPADAEDLVQETFIKAYRALHSFR--GGAAFYTWLYRIARNTAINYLR   78 (182)
T ss_pred             CchhhcCCHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHhcC--CCcchHHHHHHHHHHHHHHHHH
Confidence            35788999999999999999999999999999989999999999999999999998  3458999999999999999999


Q ss_pred             hhcCcccCCcchHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCccccCCCCcccccCC
Q 046578          212 NKSRTIRLPGSMAGMVAKIAEANNVLSRRLRRMPTDSEIAEMLNIHVSTVRLAIERTRHPISLDGAVTDRGCMTMQDIIP  291 (379)
Q Consensus       212 ~~~r~irip~~~~~~~~ki~~a~~~l~~~lgr~pt~~eia~~Lgis~~~~~~~l~~~~~~iSLd~~~~~~~~~~l~d~i~  291 (379)
                      +..+....+                                                    +++  ..+.+.....+...
T Consensus        79 ~~~~~~~~~----------------------------------------------------~~~--~~~~~~~~~~~~~~  104 (182)
T PRK09652         79 KQGRRPPAS----------------------------------------------------DVD--AEEAEDFDLADALR  104 (182)
T ss_pred             cccCCCCcc----------------------------------------------------ccc--cccccccccccccc
Confidence            865311100                                                    000  00000001111111


Q ss_pred             CCCCCChHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHHh
Q 046578          292 GPDETMPERMVQKQLMKQELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQTNI  370 (379)
Q Consensus       292 ~~~~~~pe~~~~~~e~~~~L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~~l~  370 (379)
                        ...+|++.+...+....+..++..|||+++.||.++|+    +|+|++|||+.||+|+++|++.++||+++||+.+.
T Consensus       105 --~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~vl~l~~~----~~~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~l~  177 (182)
T PRK09652        105 --DISTPENELLSAELEQRVRAAIESLPEELRTAITLREI----EGLSYEEIAEIMGCPIGTVRSRIFRAREALRAKLQ  177 (182)
T ss_pred             --cccChHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence              12356777777777788999999999999999999984    67999999999999999999999999999999875

>PRK13919 putative RNA polymerase sigma E protein; Provisional

Probab=99.93  E-value=1e-24  Score=196.15  Aligned_cols=179  Identities=21%  Similarity=0.300  Sum_probs=141.0

Q ss_pred             CcCcHHHHHHHHhcccHHHHHHHHHHhHHHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHhccCCCCCCCchhHHHHHHH
Q 046578          124 GELDYNLVKYKILCKERESQERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYWWIK  203 (379)
Q Consensus       124 ~~~~~~eLi~~~~~Gd~~A~e~Li~~y~~lV~~ia~r~~~~~~d~eDLvQEg~i~L~~ai~~fD~~~g~~FsTYa~~~Ir  203 (379)
                      ..++..+++.++++||..+++.+|..|.|.|+.+++++.+++.+++|++||+|+++|+++.+|++.. ..|.+|++++++
T Consensus         6 ~~~~~~~l~~~~~~~d~~a~~~l~~~y~~~l~~~~~~~~~~~~~aeDlvQe~~i~l~~~~~~~~~~~-~~~~~wl~~ia~   84 (186)
T PRK13919          6 ESLSDEALLALVARGEEEALRALFRRYAGAFLALARRMGLDGAAAEDVVQEVFIRVWKKAKEFDPRR-GSARAWLLALAH   84 (186)
T ss_pred             cccCHHHHHHHHHcCcHHHHHHHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHhhhccCccc-cchHHHHHHHHH
Confidence            3456789999999999999999999999999999999998889999999999999999999998654 369999999999


Q ss_pred             HHHHHHHHhhcCcccCCcchHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCccccCCC
Q 046578          204 QAIIRAIANKSRTIRLPGSMAGMVAKIAEANNVLSRRLRRMPTDSEIAEMLNIHVSTVRLAIERTRHPISLDGAVTDRGC  283 (379)
Q Consensus       204 ~~i~~~lr~~~r~irip~~~~~~~~ki~~a~~~l~~~lgr~pt~~eia~~Lgis~~~~~~~l~~~~~~iSLd~~~~~~~~  283 (379)
                      |.+.+++|+..+...                                                    .  ++.   +...
T Consensus        85 n~~~d~~rk~~~~~~----------------------------------------------------~--~~~---~~~~  107 (186)
T PRK13919         85 HAAVDHVRRRAARPQ----------------------------------------------------P--LEP---DERE  107 (186)
T ss_pred             HHHHHHHHhhhcccc----------------------------------------------------c--ccc---cccc
Confidence            999999998652100                                                    0  000   0000


Q ss_pred             CcccccCCCCCCCChHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 046578          284 MTMQDIIPGPDETMPERMVQKQLMKQELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALT  363 (379)
Q Consensus       284 ~~l~d~i~~~~~~~pe~~~~~~e~~~~L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~  363 (379)
                      ....+ .+++     .......+....+..++..||+++++||.++|+    +|+|++|||+.||+|.++|+++++||++
T Consensus       108 ~~~~~-~~~~-----~~~~~~~~~~~~l~~~l~~L~~~~r~vl~l~~~----~~~s~~eIA~~lgis~~~V~~~l~ra~~  177 (186)
T PRK13919        108 PEAFD-LPGP-----GLDEEGHLDRTRLGRALKALSPEERRVIEVLYY----QGYTHREAAQLLGLPLGTLKTRARRALS  177 (186)
T ss_pred             ccccc-CCCc-----cccHHHHHHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence            00000 0111     111112223456889999999999999999984    7799999999999999999999999999


Q ss_pred             HHHhHHh
Q 046578          364 KLQQTNI  370 (379)
Q Consensus       364 kLR~~l~  370 (379)
                      +||+.+.
T Consensus       178 ~Lr~~l~  184 (186)
T PRK13919        178 RLKEVLR  184 (186)
T ss_pred             HHHHHhc
Confidence            9999875

>PRK06811 RNA polymerase factor sigma-70; Validated

Probab=99.93  E-value=1.2e-24  Score=196.63  Aligned_cols=180  Identities=18%  Similarity=0.231  Sum_probs=147.5

Q ss_pred             CcHHHHHHHHhcccHHHHHHHHHHhHHHHHHHHHhccCC---CCCHHHHHHHHHHHHHHHHhccCCCCCCCchhHHHHHH
Q 046578          126 LDYNLVKYKILCKERESQERIIRSYRSLVVSIATGYQGK---GLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYWWI  202 (379)
Q Consensus       126 ~~~~eLi~~~~~Gd~~A~e~Li~~y~~lV~~ia~r~~~~---~~d~eDLvQEg~i~L~~ai~~fD~~~g~~FsTYa~~~I  202 (379)
                      ++..+|+.++++||..|++++++.|.|.|++++.++.++   ..++||++||+|+++|+++++|+++.+ +|.+|++.++
T Consensus         3 ~~~~~li~~~~~gd~~a~~~l~~~y~~~l~~~~~~~~~~~~~~~daeDi~Qe~~i~l~~~~~~~~~~~~-~~~~wl~~ia   81 (189)
T PRK06811          3 INEDNFIKELKKKNEKALEFIVDTYGNLVKKIVHKVLGTVNYSQLIEECVNDIFLSIWNNIDKFDEEKG-SFKKWIAAIS   81 (189)
T ss_pred             CcHHHHHHHHHccCHHHHHHHHHHHHHHHHHHHHHHHcccCchhHHHHHHHHHHHHHHHhHHHhccccc-cHHHHHHHHH
Confidence            455789999999999999999999999999999999875   357999999999999999999986544 7999999999


Q ss_pred             HHHHHHHHHhhcCcccCCcchHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCccccCC
Q 046578          203 KQAIIRAIANKSRTIRLPGSMAGMVAKIAEANNVLSRRLRRMPTDSEIAEMLNIHVSTVRLAIERTRHPISLDGAVTDRG  282 (379)
Q Consensus       203 r~~i~~~lr~~~r~irip~~~~~~~~ki~~a~~~l~~~lgr~pt~~eia~~Lgis~~~~~~~l~~~~~~iSLd~~~~~~~  282 (379)
                      +|.+.+++|++.+....                                                    .+.+.      
T Consensus        82 rn~~~d~~rk~~~~~~~----------------------------------------------------~~~~~------  103 (189)
T PRK06811         82 KYKAIDYKRKLTKNNEI----------------------------------------------------DSIDE------  103 (189)
T ss_pred             HHHHHHHHHHhcccccc----------------------------------------------------ccchh------
Confidence            99999999986631000                                                    00000      


Q ss_pred             CCcccccCCCCCCCChHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHH
Q 046578          283 CMTMQDIIPGPDETMPERMVQKQLMKQELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIAL  362 (379)
Q Consensus       283 ~~~l~d~i~~~~~~~pe~~~~~~e~~~~L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl  362 (379)
                           ...  ....+|++.+...+....+..++..|||++|.||.++|+    +|+|++|||+.||+|.++|+++++||+
T Consensus       104 -----~~~--~~~~~~~~~~~~~e~~~~l~~~l~~L~~~~r~i~~l~~~----~g~s~~EIAe~lgis~~~V~~~l~Ra~  172 (189)
T PRK06811        104 -----FIL--ISEESIENEIILKENKEEILKLINDLEKLDREIFIRRYL----LGEKIEEIAKKLGLTRSAIDNRLSRGR  172 (189)
T ss_pred             -----hhh--cccCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHH----ccCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence                 000  012345666666777788999999999999999999984    679999999999999999999999999


Q ss_pred             HHHHhHHhhchhh
Q 046578          363 TKLQQTNILNNLK  375 (379)
Q Consensus       363 ~kLR~~l~~~~L~  375 (379)
                      ++||+..-...++
T Consensus       173 ~~Lr~~~~~~~~~  185 (189)
T PRK06811        173 KKLQKNKLNISLG  185 (189)
T ss_pred             HHHHHcccCcccC
Confidence            9999986655443

>PRK12531 RNA polymerase sigma factor; Provisional

Probab=99.93  E-value=8.1e-25  Score=198.54  Aligned_cols=188  Identities=15%  Similarity=0.245  Sum_probs=146.7

Q ss_pred             hhcCcCcHHHHHHHHhcccHHHHHHHHHHhHHHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHhccCCCCCCCchhHHHH
Q 046578          121 KENGELDYNLVKYKILCKERESQERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYW  200 (379)
Q Consensus       121 ~~~~~~~~~eLi~~~~~Gd~~A~e~Li~~y~~lV~~ia~r~~~~~~d~eDLvQEg~i~L~~ai~~fD~~~g~~FsTYa~~  200 (379)
                      ...+..++.+++.++..||..+++.||+.|.|.|+.+|.++.++..+++|++||+|+.+|+.+++|++..+ +|.+|+++
T Consensus         7 ~~~~~~~~~~li~~~~~~d~~af~~l~~~y~~~l~~~~~~~~~~~~~AeDlvQev~l~l~~~~~~~~~~~~-~~~~wL~~   85 (194)
T PRK12531          7 HTFGRQEWLECMEKVKSRDKQAFALVFSYYAPKLKQFAMKHVGNEQVAMEMVQETMSTVWQKAHLFDGQKS-ALSTWIYT   85 (194)
T ss_pred             cccccHhHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhHHhcCcccc-hHHHHHHH
Confidence            34556788999999999999999999999999999999999999889999999999999999999986444 79999999


Q ss_pred             HHHHHHHHHHHhhcCcccCCcchHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCcccc
Q 046578          201 WIKQAIIRAIANKSRTIRLPGSMAGMVAKIAEANNVLSRRLRRMPTDSEIAEMLNIHVSTVRLAIERTRHPISLDGAVTD  280 (379)
Q Consensus       201 ~Ir~~i~~~lr~~~r~irip~~~~~~~~ki~~a~~~l~~~lgr~pt~~eia~~Lgis~~~~~~~l~~~~~~iSLd~~~~~  280 (379)
                      +++|.+++++|+..+....                                                    ...+....+
T Consensus        86 iarn~~ld~~Rk~~~~~~~----------------------------------------------------~~~~~~~~~  113 (194)
T PRK12531         86 IIRNLCFDLLRKQKGKDLH----------------------------------------------------IHADDIWPS  113 (194)
T ss_pred             HHHHHHHHHHHHhcccccc----------------------------------------------------cchhhcccc
Confidence            9999999999986521000                                                    000000000


Q ss_pred             CCCCcccccCCCCCCCChHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 046578          281 RGCMTMQDIIPGPDETMPERMVQKQLMKQELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGI  360 (379)
Q Consensus       281 ~~~~~l~d~i~~~~~~~pe~~~~~~e~~~~L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~r  360 (379)
                      +   .....+.  ....++..    .....+..++.+||+++|+||.++|+    +|+|++|||+.||+|.++|+.+++|
T Consensus       114 ~---~~~~~~~--~~~~~e~~----~~~~~l~~~l~~Lp~~~r~v~~l~~~----eg~s~~EIA~~lgis~~tVk~rl~r  180 (194)
T PRK12531        114 D---YYPPDLV--DHYSPEQD----MLKEQVMKFLDRLPKAQRDVLQAVYL----EELPHQQVAEMFDIPLGTVKSRLRL  180 (194)
T ss_pred             c---ccccccc--cccCHHHH----HHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHhCcCHHHHHHHHHH
Confidence            0   0000000  01122222    22356889999999999999999985    7799999999999999999999999


Q ss_pred             HHHHHHhHHhhchh
Q 046578          361 ALTKLQQTNILNNL  374 (379)
Q Consensus       361 Al~kLR~~l~~~~L  374 (379)
                      |+++||+.+..+.|
T Consensus       181 a~~~Lr~~l~~~~~  194 (194)
T PRK12531        181 AVEKLRHSMDAESL  194 (194)
T ss_pred             HHHHHHHHhhhccC
Confidence            99999999887653

>PRK12542 RNA polymerase sigma factor; Provisional

Probab=99.93  E-value=4.6e-25  Score=198.54  Aligned_cols=176  Identities=15%  Similarity=0.210  Sum_probs=140.0

Q ss_pred             HhcccHHHHHHHHHHhHHHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHhccCCCCCCCchhHHHHHHHHHHHHHHHhhc
Q 046578          135 ILCKERESQERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYWWIKQAIIRAIANKS  214 (379)
Q Consensus       135 ~~~Gd~~A~e~Li~~y~~lV~~ia~r~~~~~~d~eDLvQEg~i~L~~ai~~fD~~~g~~FsTYa~~~Ir~~i~~~lr~~~  214 (379)
                      +.+||..+++.||..|.+.|+.+|.+++++..++||++||+|+.+|+++.+|+...+..|.||++++++|.+++++|++.
T Consensus         3 ~~~gd~~a~~~l~~~y~~~l~~~~~~~~~~~~~AeDlvQe~fl~~~~~~~~~~~~~~~~~~~wL~~Iarn~~~d~~Rk~~   82 (185)
T PRK12542          3 VTNNDYEKMEELYELYEQKVYYVAYSILNNIQQAEDAVQETFITLYKNLEKLHSLNTQELKRYILRVAKNKAIDSYRKNK   82 (185)
T ss_pred             ccccCHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHhcccccHHHHHHHHHHHHHHHHHHHHHHhh
Confidence            56799999999999999999999999999999999999999999999999998644457999999999999999999865


Q ss_pred             CcccCCcchHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCccccCCCCcccccCCCCC
Q 046578          215 RTIRLPGSMAGMVAKIAEANNVLSRRLRRMPTDSEIAEMLNIHVSTVRLAIERTRHPISLDGAVTDRGCMTMQDIIPGPD  294 (379)
Q Consensus       215 r~irip~~~~~~~~ki~~a~~~l~~~lgr~pt~~eia~~Lgis~~~~~~~l~~~~~~iSLd~~~~~~~~~~l~d~i~~~~  294 (379)
                      +....                                                      .+. ...       +.... .
T Consensus        83 ~~~~~------------------------------------------------------~~~-~~~-------~~~~~-~   99 (185)
T PRK12542         83 RHETF------------------------------------------------------LEE-YER-------ESIEA-V   99 (185)
T ss_pred             hhhhh------------------------------------------------------hhh-ccc-------cchhh-h
Confidence            20000                                                      000 000       00000 0


Q ss_pred             CCChHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHHhhchh
Q 046578          295 ETMPERMVQKQLMKQELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQTNILNNL  374 (379)
Q Consensus       295 ~~~pe~~~~~~e~~~~L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~~l~~~~L  374 (379)
                      ...+++.....+....|..+|..|||++|+||.|+|+    +|+|++|||+.||+|.++|+++++||+++||+.+.....
T Consensus       100 ~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~i~~l~~~----~g~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~l~~~~~  175 (185)
T PRK12542        100 DENIEEWEKRKMSEVQIDTLLKELNESNRQVFKYKVF----YNLTYQEISSVMGITEANVRKQFERARKRVQNMIGGIQH  175 (185)
T ss_pred             hccHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHcccch
Confidence            1123333333444567999999999999999999985    779999999999999999999999999999999877665


Q ss_pred             hhh
Q 046578          375 KVY  377 (379)
Q Consensus       375 ~~y  377 (379)
                      ..|
T Consensus       176 ~~~  178 (185)
T PRK12542        176 DEF  178 (185)
T ss_pred             HHH
Confidence            554

>PRK09643 RNA polymerase sigma factor SigM; Reviewed

Probab=99.93  E-value=3.9e-24  Score=193.93  Aligned_cols=174  Identities=12%  Similarity=0.115  Sum_probs=143.8

Q ss_pred             cCcHHHHHHHHhcccHHHHHHHHHHhHHHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHhccCCCCCCCchhHHHHHHHH
Q 046578          125 ELDYNLVKYKILCKERESQERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYWWIKQ  204 (379)
Q Consensus       125 ~~~~~eLi~~~~~Gd~~A~e~Li~~y~~lV~~ia~r~~~~~~d~eDLvQEg~i~L~~ai~~fD~~~g~~FsTYa~~~Ir~  204 (379)
                      ..+..+++..+.+||..+++.+|+.|.+.|++++.++.++..++||++||+|+.+|+++++|++..  +|.+|++++++|
T Consensus        11 ~~~~~~l~~~~~~gd~~~~~~l~~~y~~~l~~~~~~~~~~~~~AeDlvQEvfl~l~~~~~~~~~~~--~f~~wL~~i~rn   88 (192)
T PRK09643         11 ERSDAELLAAHVAGDRYAFGELFRRHHRRLWAVARRTSGTREDAADALQDAMLSAHRAAGSFRGDA--AVSSWLHRIVVN   88 (192)
T ss_pred             CcCHHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHHcCCHhhHHHHHHHHHHHHHHHHHhcCCCC--ccHHHHHHHHHH
Confidence            355688999999999999999999999999999999999999999999999999999999998643  699999999999


Q ss_pred             HHHHHHHhhcCcccCCcchHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCccccCCCC
Q 046578          205 AIIRAIANKSRTIRLPGSMAGMVAKIAEANNVLSRRLRRMPTDSEIAEMLNIHVSTVRLAIERTRHPISLDGAVTDRGCM  284 (379)
Q Consensus       205 ~i~~~lr~~~r~irip~~~~~~~~ki~~a~~~l~~~lgr~pt~~eia~~Lgis~~~~~~~l~~~~~~iSLd~~~~~~~~~  284 (379)
                      .+++++|+..+...                                                     .+++.    . . 
T Consensus        89 ~~~d~~Rk~~~~~~-----------------------------------------------------~~~~~----~-~-  109 (192)
T PRK09643         89 ACLDRLRRAKARPT-----------------------------------------------------VPLDD----V-Y-  109 (192)
T ss_pred             HHHHHHHccccCCC-----------------------------------------------------CCccc----c-c-
Confidence            99999997653100                                                     00100    0 0 


Q ss_pred             cccccCCCCCCCChHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHH
Q 046578          285 TMQDIIPGPDETMPERMVQKQLMKQELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTK  364 (379)
Q Consensus       285 ~l~d~i~~~~~~~pe~~~~~~e~~~~L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~k  364 (379)
                         + ..    ..+++.+...+....+..+|+.||+++|+||.|+|+    +|+|++|||+.||+|.++|+++++||+++
T Consensus       110 ---~-~~----~~~~~~~~~~e~~~~l~~~l~~Lp~~~r~i~~l~~~----~g~s~~EIA~~lg~s~~tV~~rl~rar~~  177 (192)
T PRK09643        110 ---P-VA----QLERDPTARVETALAVQRALMRLPVEQRAALVAVDM----QGYSVADAARMLGVAEGTVKSRCARGRAR  177 (192)
T ss_pred             ---c-cc----CCcccHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHHCcCHHHHHHHHHHHHHH
Confidence               0 00    012233444455667999999999999999999984    77999999999999999999999999999


Q ss_pred             HHhHHhh
Q 046578          365 LQQTNIL  371 (379)
Q Consensus       365 LR~~l~~  371 (379)
                      ||+.+..
T Consensus       178 Lr~~l~~  184 (192)
T PRK09643        178 LAELLGY  184 (192)
T ss_pred             HHHHHHH
Confidence            9999864

>PRK12515 RNA polymerase sigma factor; Provisional

Probab=99.93  E-value=5e-24  Score=192.44  Aligned_cols=180  Identities=17%  Similarity=0.221  Sum_probs=149.6

Q ss_pred             CcCcHHHHHHHHhcccHHHHHHHHHHhHHHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHhccCCCCCCCchhHHHHHHH
Q 046578          124 GELDYNLVKYKILCKERESQERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYWWIK  203 (379)
Q Consensus       124 ~~~~~~eLi~~~~~Gd~~A~e~Li~~y~~lV~~ia~r~~~~~~d~eDLvQEg~i~L~~ai~~fD~~~g~~FsTYa~~~Ir  203 (379)
                      +..+..+++..+++||..|++.||..|.+.++.++.++.++..++||++||+|+.+|++.++|++.  ..|.+|++.+++
T Consensus         5 ~~~~~~~l~~~~~~gd~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeDivQe~f~~l~~~~~~~~~~--~~~~~wl~~i~~   82 (189)
T PRK12515          5 QATTDEMLLARIAQGDRTAMQTLYGRHHVRVYRFGLRLVRDEQTAEDLVSEVFLDVWRQAGQFEGR--SQVSTWLLSIAR   82 (189)
T ss_pred             cccCHHHHHHHHHccCHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHhcCCC--CChHHHHHHHHH
Confidence            345668899999999999999999999999999999999999999999999999999999999864  379999999999


Q ss_pred             HHHHHHHHhhcCcccCCcchHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCccccCCC
Q 046578          204 QAIIRAIANKSRTIRLPGSMAGMVAKIAEANNVLSRRLRRMPTDSEIAEMLNIHVSTVRLAIERTRHPISLDGAVTDRGC  283 (379)
Q Consensus       204 ~~i~~~lr~~~r~irip~~~~~~~~ki~~a~~~l~~~lgr~pt~~eia~~Lgis~~~~~~~l~~~~~~iSLd~~~~~~~~  283 (379)
                      |.+.+++|+..+.                                                      .  +.    ++  
T Consensus        83 n~~~d~~r~~~~~------------------------------------------------------~--~~----~~--  100 (189)
T PRK12515         83 FKALSALRRRKHE------------------------------------------------------E--ID----DE--  100 (189)
T ss_pred             HHHHHHHHccCCC------------------------------------------------------C--Cc----cc--
Confidence            9999999975420                                                      0  00    00  


Q ss_pred             CcccccCCCCCCCChHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 046578          284 MTMQDIIPGPDETMPERMVQKQLMKQELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALT  363 (379)
Q Consensus       284 ~~l~d~i~~~~~~~pe~~~~~~e~~~~L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~  363 (379)
                       .. ....+ ...+|+......+....+..++..||+++|+||.++|+    +|+|++|||+.||+|.++|+++++||++
T Consensus       101 -~~-~~~~~-~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~vl~l~~~----~~~s~~eIA~~lgis~~tV~~~l~Rar~  173 (189)
T PRK12515        101 -AA-AAIED-GADTPEVALQKSDTSAALRACLAKLSPAHREIIDLVYY----HEKSVEEVGEIVGIPESTVKTRMFYARK  173 (189)
T ss_pred             -cc-cccCC-CCCCHHHHHHhHHHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence             00 00111 12345665666666778999999999999999999995    7799999999999999999999999999


Q ss_pred             HHHhHHhhchh
Q 046578          364 KLQQTNILNNL  374 (379)
Q Consensus       364 kLR~~l~~~~L  374 (379)
                      +||+.+...++
T Consensus       174 ~Lr~~l~~~~~  184 (189)
T PRK12515        174 KLAELLKAAGV  184 (189)
T ss_pred             HHHHHHHHhcc
Confidence            99999887654

>PRK12534 RNA polymerase sigma factor; Provisional

Probab=99.93  E-value=2e-24  Score=194.45  Aligned_cols=177  Identities=12%  Similarity=0.169  Sum_probs=144.3

Q ss_pred             CcHHHHHHHHhcccHHHHHHHHHHhHHHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHhccCCCCCCCchhHHHHHHHHH
Q 046578          126 LDYNLVKYKILCKERESQERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYWWIKQA  205 (379)
Q Consensus       126 ~~~~eLi~~~~~Gd~~A~e~Li~~y~~lV~~ia~r~~~~~~d~eDLvQEg~i~L~~ai~~fD~~~g~~FsTYa~~~Ir~~  205 (379)
                      .+..+++.+...||..+++++|..|.+.|+++|.++.++..++||++||+|+++|+++++|++..+ +|.+|++.+++|.
T Consensus        10 ~~~~~l~~~~~~~~~~~~~~l~~~y~~~l~~~~~~~~~~~~~aeDlvQe~fl~~~~~~~~~~~~~~-~~~~wl~~I~~n~   88 (187)
T PRK12534         10 DETGRLLTATAGGDRHAFEALYRQTSPKLFGVCLRMIPQRAEAEEVLQDVFTLIWHKAGQFDPSRA-RGLTWLAMIARNK   88 (187)
T ss_pred             chHHHHHHHHHcCCHHHHHHHHHHhhHHHHHHHHHHhcCHHHHHHHHHHHHHHHHhccccCCcccc-cHHHHHHHHHHHH
Confidence            345788999999999999999999999999999999999999999999999999999999987544 6899999999999


Q ss_pred             HHHHHHhhcCcccCCcchHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCccccCCCCc
Q 046578          206 IIRAIANKSRTIRLPGSMAGMVAKIAEANNVLSRRLRRMPTDSEIAEMLNIHVSTVRLAIERTRHPISLDGAVTDRGCMT  285 (379)
Q Consensus       206 i~~~lr~~~r~irip~~~~~~~~ki~~a~~~l~~~lgr~pt~~eia~~Lgis~~~~~~~l~~~~~~iSLd~~~~~~~~~~  285 (379)
                      +++++|+..+..                                                    ...+.+.         
T Consensus        89 ~~d~~R~~~~~~----------------------------------------------------~~~~~~~---------  107 (187)
T PRK12534         89 AIDHLRANAPQR----------------------------------------------------RNVALDD---------  107 (187)
T ss_pred             HHHHHHhccccc----------------------------------------------------ccccccc---------
Confidence            999999754200                                                    0000110         


Q ss_pred             ccccCCCCCCCChHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Q 046578          286 MQDIIPGPDETMPERMVQKQLMKQELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKL  365 (379)
Q Consensus       286 l~d~i~~~~~~~pe~~~~~~e~~~~L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kL  365 (379)
                      ......  ...++++.....+....+..+|..||++++.|+.++|+    +|+|++|||+.||+|.++|+++++||+++|
T Consensus       108 ~~~~~~--~~~~~~~~~~~~e~~~~l~~~l~~L~~~~r~i~~l~~~----~g~s~~eIA~~lgis~~~v~~~l~Rar~~L  181 (187)
T PRK12534        108 AGELRA--ADASPLERTERASTRRRIDHCLAELEPPRSELIRTAFF----EGITYEELAARTDTPIGTVKSWIRRGLAKL  181 (187)
T ss_pred             hhhhcc--ccCChhhHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHhCCChhHHHHHHHHHHHHH
Confidence            000000  01133444455566778999999999999999999984    779999999999999999999999999999


Q ss_pred             HhHHh
Q 046578          366 QQTNI  370 (379)
Q Consensus       366 R~~l~  370 (379)
                      |+.+.
T Consensus       182 r~~l~  186 (187)
T PRK12534        182 KACLE  186 (187)
T ss_pred             HHHHc
Confidence            99874

>PRK11922 RNA polymerase sigma factor; Provisional

Probab=99.93  E-value=3.8e-24  Score=199.50  Aligned_cols=187  Identities=14%  Similarity=0.191  Sum_probs=151.0

Q ss_pred             CcCcHHHHHHHHhcccHHHHHHHHHHhHHHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHhccCCCCCCCchhHHHHHHH
Q 046578          124 GELDYNLVKYKILCKERESQERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYWWIK  203 (379)
Q Consensus       124 ~~~~~~eLi~~~~~Gd~~A~e~Li~~y~~lV~~ia~r~~~~~~d~eDLvQEg~i~L~~ai~~fD~~~g~~FsTYa~~~Ir  203 (379)
                      +..+..+|+.++.+||..+++.+|..|.+.|++++.++.++..++||++||+|+++|+++++|++.  ..|.+|++++++
T Consensus        13 ~~~~~~~l~~~~~~gd~~a~~~l~~~y~~~l~~~a~~~~~~~~~AEDlvQE~fi~l~~~~~~~~~~--~~~~~wL~~iar   90 (231)
T PRK11922         13 SAASDRELVARVLAGDEAAFEALMRRHNRRLYRTARAILRNDAEAEDVVQEAYLRAFRALGTFRGD--ASLSTWLSRIVL   90 (231)
T ss_pred             CcccHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHhCChhhHHHHHHHHHHHHHHHHHhcCCC--chhHHHHHHHHH
Confidence            345568899999999999999999999999999999999999999999999999999999999875  379999999999


Q ss_pred             HHHHHHHHhhcCcccCCcchHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCccccCCC
Q 046578          204 QAIIRAIANKSRTIRLPGSMAGMVAKIAEANNVLSRRLRRMPTDSEIAEMLNIHVSTVRLAIERTRHPISLDGAVTDRGC  283 (379)
Q Consensus       204 ~~i~~~lr~~~r~irip~~~~~~~~ki~~a~~~l~~~lgr~pt~~eia~~Lgis~~~~~~~l~~~~~~iSLd~~~~~~~~  283 (379)
                      |.+++++|+..+....+.                                                  . .+.....+ +
T Consensus        91 n~~~d~~Rk~~r~~~~~~--------------------------------------------------~-~~~~~~~~-~  118 (231)
T PRK11922         91 NEALGRLRRRRRLVNLAE--------------------------------------------------M-VMASTIAG-G  118 (231)
T ss_pred             HHHHHHHHhhcccccchh--------------------------------------------------c-cccccccc-c
Confidence            999999998664211100                                                  0 00000000 0


Q ss_pred             CcccccCCCCCCCChHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 046578          284 MTMQDIIPGPDETMPERMVQKQLMKQELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALT  363 (379)
Q Consensus       284 ~~l~d~i~~~~~~~pe~~~~~~e~~~~L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~  363 (379)
                        ... .......+|++.+...+..+.+..+|..||+++|+||.++|+    +|+|++|||+.||+|.++|+++++||++
T Consensus       119 --~~~-~~~~~~~~~e~~~~~~e~~~~l~~~l~~L~~~~r~i~~l~~~----~g~s~~EIAe~lgis~~tVk~~l~Rar~  191 (231)
T PRK11922        119 --ERT-PLADPAEDPERAAARREIRALLERAIDALPDAFRAVFVLRVV----EELSVEETAQALGLPEETVKTRLHRARR  191 (231)
T ss_pred             --ccc-ccCcccCChHHHHHHHHHHHHHHHHHHhCCHHHhhhheeehh----cCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence              000 001123356777777788888999999999999999999884    6799999999999999999999999999


Q ss_pred             HHHhHHhh
Q 046578          364 KLQQTNIL  371 (379)
Q Consensus       364 kLR~~l~~  371 (379)
                      +||+.+..
T Consensus       192 kLr~~l~~  199 (231)
T PRK11922        192 LLRESLAR  199 (231)
T ss_pred             HHHHHHHH
Confidence            99999875

>PRK06759 RNA polymerase factor sigma-70; Validated

Probab=99.92  E-value=1.8e-24  Score=188.37  Aligned_cols=153  Identities=18%  Similarity=0.257  Sum_probs=124.9

Q ss_pred             ccHHHHHHHHHHhHHHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHhccCCCCCCCchhHHHHHHHHHHHHHHHhhcCcc
Q 046578          138 KERESQERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYWWIKQAIIRAIANKSRTI  217 (379)
Q Consensus       138 Gd~~A~e~Li~~y~~lV~~ia~r~~~~~~d~eDLvQEg~i~L~~ai~~fD~~~g~~FsTYa~~~Ir~~i~~~lr~~~r~i  217 (379)
                      +|..||++|++.|.|+|+++++++ ++..++||++||+|+++|+++++|++..+ +|.+|++.+++|.+++++|++.+..
T Consensus         1 ~~~~af~~l~~~y~~~l~~~~~~~-~~~~~aeDi~Qe~~l~l~~~~~~~~~~~~-~f~~wl~~i~~n~~ld~~rk~~~~~   78 (154)
T PRK06759          1 MKPATFTEAVVLYEGLIVNQIKKL-GIYQDYEEYYQCGLIGLWHAYERYDEKKG-SFPAYAVVTVRGYILERLKKEFAVQ   78 (154)
T ss_pred             CCcccHHHHHHHHHHHHHHHHHHh-CCcccHHHHHHHHHHHHHHHHHHhCccCC-chHHHHHHHHHHHHHHHHHHHHhhc
Confidence            366899999999999999999986 56689999999999999999999997665 7999999999999999999864200


Q ss_pred             cCCcchHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCccccCCCCcccccCCCCCCCC
Q 046578          218 RLPGSMAGMVAKIAEANNVLSRRLRRMPTDSEIAEMLNIHVSTVRLAIERTRHPISLDGAVTDRGCMTMQDIIPGPDETM  297 (379)
Q Consensus       218 rip~~~~~~~~ki~~a~~~l~~~lgr~pt~~eia~~Lgis~~~~~~~l~~~~~~iSLd~~~~~~~~~~l~d~i~~~~~~~  297 (379)
                                                                               +....          .     +.
T Consensus        79 ---------------------------------------------------------~~~~~----------~-----~~   86 (154)
T PRK06759         79 ---------------------------------------------------------EKCVC----------V-----GE   86 (154)
T ss_pred             ---------------------------------------------------------ccccc----------c-----CC
Confidence                                                                     00000          0     01


Q ss_pred             hHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhH
Q 046578          298 PERMVQKQLMKQELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQT  368 (379)
Q Consensus       298 pe~~~~~~e~~~~L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~~  368 (379)
                      |++.....+....+..++.+||+++|.||.++|+    +|+|++|||+.||+|.++|+++++||+++||+.
T Consensus        87 ~~~~~~~~~~~~~l~~~l~~L~~~~r~ii~l~~~----~~~s~~EIA~~l~is~~tV~~~~~ra~~~Lr~~  153 (154)
T PRK06759         87 YEDHFHFEDVEMKVKDFMSVLDEKEKYIIFERFF----VGKTMGEIALETEMTYYQVRWIYRQALEKMRNS  153 (154)
T ss_pred             CcccccHHHHHHHHHHHHHhCCHHHHHHHHHHHh----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHhhc
Confidence            1112223334567899999999999999999994    779999999999999999999999999999974

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

Probab=99.92  E-value=4.2e-24  Score=189.33  Aligned_cols=167  Identities=16%  Similarity=0.179  Sum_probs=136.4

Q ss_pred             cHHHHHHHHhcccHHHHHHHHHHhHHHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHhccCCCCCCCchhHHHHHHHHHH
Q 046578          127 DYNLVKYKILCKERESQERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYWWIKQAI  206 (379)
Q Consensus       127 ~~~eLi~~~~~Gd~~A~e~Li~~y~~lV~~ia~r~~~~~~d~eDLvQEg~i~L~~ai~~fD~~~g~~FsTYa~~~Ir~~i  206 (379)
                      +..+++..+.+||..|++.+|..|.+.|++++.++.++..++||++||+|+.+|+++.+|++.  .+|.+|++.+++|.+
T Consensus         2 ~~~~l~~~~~~gd~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeD~~Qe~~l~~~~~~~~~~~~--~~~~~wl~~i~~n~~   79 (169)
T TIGR02954         2 NDEELVKKAKRGNKPAFESLIKKHKEKLYKTAFIYVKNEHDALDVIQETVYKAYLSIDKLKHP--KYFNTWLTRILINEC   79 (169)
T ss_pred             CHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHhccCc--cccHHHHHHHHHHHH
Confidence            356889999999999999999999999999999999999999999999999999999999864  379999999999999


Q ss_pred             HHHHHhhcCcccCCcchHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCccccCCCCcc
Q 046578          207 IRAIANKSRTIRLPGSMAGMVAKIAEANNVLSRRLRRMPTDSEIAEMLNIHVSTVRLAIERTRHPISLDGAVTDRGCMTM  286 (379)
Q Consensus       207 ~~~lr~~~r~irip~~~~~~~~ki~~a~~~l~~~lgr~pt~~eia~~Lgis~~~~~~~l~~~~~~iSLd~~~~~~~~~~l  286 (379)
                      ++++|+..+.  .                                                     .++....       
T Consensus        80 ~d~~R~~~~~--~-----------------------------------------------------~~~~~~~-------   97 (169)
T TIGR02954        80 IDLLKKKKKV--I-----------------------------------------------------PFDPNTS-------   97 (169)
T ss_pred             HHHHHhcCCc--C-----------------------------------------------------ccccccc-------
Confidence            9999976521  0                                                     0000000       


Q ss_pred             cccCCCCCCCChHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 046578          287 QDIIPGPDETMPERMVQKQLMKQELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQ  366 (379)
Q Consensus       287 ~d~i~~~~~~~pe~~~~~~e~~~~L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR  366 (379)
                         ..+   ..++  ....+ ...+..+|+.||+++|+||.++|+    +|+|++|||+.||+|.++|+++++||+++||
T Consensus        98 ---~~~---~~~~--~~~~~-~~~l~~~l~~L~~~~r~i~~l~~~----~g~s~~eiA~~lgis~~tv~~~l~Ra~~~Lr  164 (169)
T TIGR02954        98 ---IEK---GECE--THADS-RLDLYKAIDTLNDKYQTAIILRYY----HDLTIKEIAEVMNKPEGTVKTYLHRALKKLK  164 (169)
T ss_pred             ---ccc---chhh--hchHH-HHHHHHHHHhCCHHHhHHHHHHHH----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence               000   0011  11111 226889999999999999999995    7799999999999999999999999999999


Q ss_pred             hHHh
Q 046578          367 QTNI  370 (379)
Q Consensus       367 ~~l~  370 (379)
                      +.+.
T Consensus       165 ~~l~  168 (169)
T TIGR02954       165 KRLE  168 (169)
T ss_pred             HHhc
Confidence            9864

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.

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

Probab=99.92  E-value=8.8e-24  Score=189.98  Aligned_cols=181  Identities=17%  Similarity=0.209  Sum_probs=140.1

Q ss_pred             hcccHHHHHHHHHHhHHHHHHHHHhcc----CCCCCHHHHHHHHHHHHHHHHhccCCCCCCCchhHHHHHHHHHHHHHHH
Q 046578          136 LCKERESQERIIRSYRSLVVSIATGYQ----GKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYWWIKQAIIRAIA  211 (379)
Q Consensus       136 ~~Gd~~A~e~Li~~y~~lV~~ia~r~~----~~~~d~eDLvQEg~i~L~~ai~~fD~~~g~~FsTYa~~~Ir~~i~~~lr  211 (379)
                      +.||..|+++|+..|.+.|+.+|+++.    ++..++||++||+|+.+|+++.+|+...+.+|.+|++++++|.+.+++|
T Consensus         2 ~~~~~~a~~~l~~~y~~~l~~~~~~~l~~~~~~~~~aeD~vQe~~l~l~~~~~~~~~~~~~~~~~wl~~i~~n~~~d~~r   81 (189)
T TIGR02984         2 RGGDQEALGELLDRYRNYLRLLARVQLDPRLRRRVDPSDLVQETLLEAHRRFDQFRGKTEGEFAGWLRGILSNVLADALR   81 (189)
T ss_pred             CCCCHHHHHHHHHHHHHHHHHHHHHHhhhhcCCccCHHHHHHHHHHHHHHHHHhccCcccchHHHHHHHHHHHHHHHHHH
Confidence            579999999999999999999999874    3567999999999999999999998765568999999999999999999


Q ss_pred             hhcC-cccCCcchHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCcc-ccCCCCccccc
Q 046578          212 NKSR-TIRLPGSMAGMVAKIAEANNVLSRRLRRMPTDSEIAEMLNIHVSTVRLAIERTRHPISLDGAV-TDRGCMTMQDI  289 (379)
Q Consensus       212 ~~~r-~irip~~~~~~~~ki~~a~~~l~~~lgr~pt~~eia~~Lgis~~~~~~~l~~~~~~iSLd~~~-~~~~~~~l~d~  289 (379)
                      +..+ ..+.+                                                ....+++... .++....+.+.
T Consensus        82 ~~~~~~~r~~------------------------------------------------~~~~~~~~~~~~~~~~~~~~~~  113 (189)
T TIGR02984        82 RHLGAQKRDI------------------------------------------------RREQSLDAGGRLDESSVRLAAQ  113 (189)
T ss_pred             HHHHHHhhhc------------------------------------------------ccccCCCcccccCCcchhHHHH
Confidence            7521 00000                                                0111222211 01111122222


Q ss_pred             CCCCCCCChHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHH
Q 046578          290 IPGPDETMPERMVQKQLMKQELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQTN  369 (379)
Q Consensus       290 i~~~~~~~pe~~~~~~e~~~~L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~~l  369 (379)
                      +.+ ...+|++.+...+....|..+|..|||++|.||.++|+    +|+|++|||+.||+|+++|++.++||+++||+.+
T Consensus       114 ~~~-~~~~~~~~~~~~e~~~~l~~~l~~L~~~~r~vi~l~~~----~g~s~~eIA~~lgis~~~v~~~l~Ra~~~Lr~~l  188 (189)
T TIGR02984       114 LAA-DGPSPSQVAARREAAVRLAQALAKLPEDYREVILLRHL----EGLSFAEVAERMDRSEGAVSMLWVRGLARLRQIL  188 (189)
T ss_pred             ccC-CCCCHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHh----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHh
Confidence            222 23456777777777788999999999999999999985    6799999999999999999999999999999876

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).

>PRK12526 RNA polymerase sigma factor; Provisional

Probab=99.92  E-value=9.2e-24  Score=193.58  Aligned_cols=179  Identities=13%  Similarity=0.245  Sum_probs=139.7

Q ss_pred             HHHHHHHhcccHHHHHHHHHHhHHHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHhccCCCCCCCchhHHHHHHHHHHHH
Q 046578          129 NLVKYKILCKERESQERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYWWIKQAIIR  208 (379)
Q Consensus       129 ~eLi~~~~~Gd~~A~e~Li~~y~~lV~~ia~r~~~~~~d~eDLvQEg~i~L~~ai~~fD~~~g~~FsTYa~~~Ir~~i~~  208 (379)
                      ..++..+.+||..++++||..|.+.|++++.++.++..+++|++||+|+.+|++++.|++.++ .|.+|++.+++|.+++
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            445667889999999999999999999999999999899999999999999999999987654 6999999999999999


Q ss_pred             HHHhhcCcccCCcchHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCccccCCCCcccc
Q 046578          209 AIANKSRTIRLPGSMAGMVAKIAEANNVLSRRLRRMPTDSEIAEMLNIHVSTVRLAIERTRHPISLDGAVTDRGCMTMQD  288 (379)
Q Consensus       209 ~lr~~~r~irip~~~~~~~~ki~~a~~~l~~~lgr~pt~~eia~~Lgis~~~~~~~l~~~~~~iSLd~~~~~~~~~~l~d  288 (379)
                      ++|+..+.....                                                     ...    + .....+
T Consensus       105 ~~Rk~~~~~~~~-----------------------------------------------------~~~----~-~~~~~~  126 (206)
T PRK12526        105 MLRKIKAKKEQN-----------------------------------------------------LGD----D-IWPIEQ  126 (206)
T ss_pred             HHHHhccccccc-----------------------------------------------------ccc----c-cchhhh
Confidence            999865311000                                                     000    0 000001


Q ss_pred             cCCCCCCCChHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhH
Q 046578          289 IIPGPDETMPERMVQKQLMKQELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQT  368 (379)
Q Consensus       289 ~i~~~~~~~pe~~~~~~e~~~~L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~~  368 (379)
                      .+.+. ...+. ..........|..+|..||+++|.||.++|+    +|+|++|||+.||+|.++|+.+++||+++||+.
T Consensus       127 ~~~~~-~~~~~-~~~~~~~~~~l~~~l~~L~~~~r~vl~l~~~----~g~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~  200 (206)
T PRK12526        127 ALAES-QSESE-EFSDHLMDKQILSYIEKLPEAQQTVVKGVYF----QELSQEQLAQQLNVPLGTVKSRLRLALAKLKVQ  200 (206)
T ss_pred             hcccc-cCchH-HHHHHHHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence            11111 11122 2223333457899999999999999999995    779999999999999999999999999999999


Q ss_pred             Hhhc
Q 046578          369 NILN  372 (379)
Q Consensus       369 l~~~  372 (379)
                      +...
T Consensus       201 l~~~  204 (206)
T PRK12526        201 MGEQ  204 (206)
T ss_pred             Hhhc
Confidence            8653

>PRK11924 RNA polymerase sigma factor; Provisional

Probab=99.92  E-value=1.6e-23  Score=186.04  Aligned_cols=175  Identities=14%  Similarity=0.128  Sum_probs=146.2

Q ss_pred             HHHHHHhcccHHHHHHHHHHhHHHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHhccCCCCCCCchhHHHHHHHHHHHHH
Q 046578          130 LVKYKILCKERESQERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYWWIKQAIIRA  209 (379)
Q Consensus       130 eLi~~~~~Gd~~A~e~Li~~y~~lV~~ia~r~~~~~~d~eDLvQEg~i~L~~ai~~fD~~~g~~FsTYa~~~Ir~~i~~~  209 (379)
                      .|+..+..||..|++.||+.|.+.|+++++++.++..+++|++||+|+++|+++++|+  .+.+|.+|++.++++.+.++
T Consensus         2 ~~~~~~~~~~~~a~~~l~~~y~~~l~~~~~~~~~~~~~aeDl~qe~~~~l~~~~~~~~--~~~~~~~~l~~i~~~~~~d~   79 (179)
T PRK11924          2 QLMPVDATGDKEAFSELFRPHAPDLLRYARRQLGDRALAEDAVQEAFLRAWRKADLFN--GKGSARTWLLTIARNVCYDL   79 (179)
T ss_pred             hHHHHHHccCHHHHHHHHHHHHHHHHHHHHHHhCCHhhHHHHHHHHHHHHHHHHhhcC--CcchHHHHHHHHHHHHHHHH
Confidence            4678899999999999999999999999999999999999999999999999999998  34489999999999999999


Q ss_pred             HHhhcCcccCCcchHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCccccCCCCccccc
Q 046578          210 IANKSRTIRLPGSMAGMVAKIAEANNVLSRRLRRMPTDSEIAEMLNIHVSTVRLAIERTRHPISLDGAVTDRGCMTMQDI  289 (379)
Q Consensus       210 lr~~~r~irip~~~~~~~~ki~~a~~~l~~~lgr~pt~~eia~~Lgis~~~~~~~l~~~~~~iSLd~~~~~~~~~~l~d~  289 (379)
                      +++..+....                                                     ..+.         ..+.
T Consensus        80 ~r~~~~~~~~-----------------------------------------------------~~~~---------~~~~   97 (179)
T PRK11924         80 LRRRRREKAV-----------------------------------------------------LSDD---------ALEP   97 (179)
T ss_pred             HHhccccccc-----------------------------------------------------Cccc---------cccc
Confidence            9976531100                                                     0000         0000


Q ss_pred             CCCCCCCChHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHH
Q 046578          290 IPGPDETMPERMVQKQLMKQELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQTN  369 (379)
Q Consensus       290 i~~~~~~~pe~~~~~~e~~~~L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~~l  369 (379)
                      ..+....+|++.+...+....+..++..||++++.||.++|+    +|+|++|||+.||+|+++|++.++||+++||+.+
T Consensus        98 ~~~~~~~~~e~~~~~~e~~~~l~~~l~~L~~~~r~i~~l~~~----~~~~~~eIA~~lgis~~tv~~~~~ra~~~lr~~l  173 (179)
T PRK11924         98 EFAETAETPEAALLAKDDLARIDRCLDALPVKQREVFLLRYV----EGLSYREIAEILGVPVGTVKSRLRRARQLLRECL  173 (179)
T ss_pred             ccCCccCCHHHHHhhHHHHHHHHHHHHhCCHHHHHHhhHHHH----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence            000023467788888888889999999999999999999984    6799999999999999999999999999999998


Q ss_pred             hhc
Q 046578          370 ILN  372 (379)
Q Consensus       370 ~~~  372 (379)
                      ...
T Consensus       174 ~~~  176 (179)
T PRK11924        174 EAQ  176 (179)
T ss_pred             HHH
Confidence            754

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

Probab=99.92  E-value=1.5e-23  Score=196.98  Aligned_cols=183  Identities=20%  Similarity=0.206  Sum_probs=145.9

Q ss_pred             CcHHHHHHHHhcccHHHHHHHHHHhHHHHHHHHHhccCCCCCHHHHHHHHHHHHHH-------HHhccCCCCCCCchhHH
Q 046578          126 LDYNLVKYKILCKERESQERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLR-------GAKRFNPERGYKLSTYV  198 (379)
Q Consensus       126 ~~~~eLi~~~~~Gd~~A~e~Li~~y~~lV~~ia~r~~~~~~d~eDLvQEg~i~L~~-------ai~~fD~~~g~~FsTYa  198 (379)
                      .+...|+.++++||..||+.|++.|.+.++.++.++.++..++||++||+|+.+|.       .+++|++.  ..|.||+
T Consensus        24 ~~d~~Li~~~~~gd~~Af~~L~~~y~~~l~~~~~~~~~~~~dAEDivQEvFlkl~~~~~~~~~~~~~~~~~--~~~~tWL  101 (244)
T TIGR03001        24 AADLYLACACAQGEPAALAALERHVLSKVPARLAGLRPPTAFVDEVLQRLRQRLLVPRAERPPRIAEYSGR--GPLLSWV  101 (244)
T ss_pred             ccHHHHHHHHHcCcHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhccchhhhhhccCCC--CchHhHH
Confidence            34577999999999999999999999999999999999999999999999999994       78889863  3799999


Q ss_pred             HHHHHHHHHHHHHhhcCcccCCcchHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCcc
Q 046578          199 YWWIKQAIIRAIANKSRTIRLPGSMAGMVAKIAEANNVLSRRLRRMPTDSEIAEMLNIHVSTVRLAIERTRHPISLDGAV  278 (379)
Q Consensus       199 ~~~Ir~~i~~~lr~~~r~irip~~~~~~~~ki~~a~~~l~~~lgr~pt~~eia~~Lgis~~~~~~~l~~~~~~iSLd~~~  278 (379)
                      +++++|.+++++|++.+...                                                       ++.  
T Consensus       102 ~~Ia~N~~id~lRk~~r~~~-------------------------------------------------------~~~--  124 (244)
T TIGR03001       102 RIVATRIALELQAQERRHSP-------------------------------------------------------VEE--  124 (244)
T ss_pred             HHHHHHHHHHHHHHhcccCc-------------------------------------------------------ccc--
Confidence            99999999999997653100                                                       000  


Q ss_pred             ccCCCCcccccCCCCCCCChHHHHHH----HHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHH
Q 046578          279 TDRGCMTMQDIIPGPDETMPERMVQK----QLMKQELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERI  354 (379)
Q Consensus       279 ~~~~~~~l~d~i~~~~~~~pe~~~~~----~e~~~~L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~V  354 (379)
                        +.  ...+ ..+ ...+|++....    .+....|..+|++||+++|+||.|+|+    +|+|++|||+.||||.+||
T Consensus       125 --~~--~~~~-~~~-~~~~~e~~~~~~e~~~e~~~~l~~aL~~Lp~~~R~v~~L~~~----eg~S~~EIA~~Lgis~~TV  194 (244)
T TIGR03001       125 --PT--ELAA-LPA-PGSDPELDLLRERYRQDFRQALREALAALSERERHLLRLHFV----DGLSMDRIGAMYQVHRSTV  194 (244)
T ss_pred             --cc--cccc-ccC-CCCCHHHHHHHHhhHHHHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHHCcCHHHH
Confidence              00  0000 001 11234444332    235567999999999999999999995    7799999999999999999


Q ss_pred             HHHHHHHHHHHHhHHhhchhhhh
Q 046578          355 RQIRGIALTKLQQTNILNNLKVY  377 (379)
Q Consensus       355 r~~~~rAl~kLR~~l~~~~L~~y  377 (379)
                      +.+++||+++||+.+.......|
T Consensus       195 k~rl~RAr~~Lr~~l~~~~~~~~  217 (244)
T TIGR03001       195 SRWVAQARERLLERTRRRLAERL  217 (244)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHhc
Confidence            99999999999999987765443

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.

>PRK09640 RNA polymerase sigma factor SigX; Reviewed

Probab=99.92  E-value=3e-24  Score=193.78  Aligned_cols=175  Identities=20%  Similarity=0.273  Sum_probs=138.8

Q ss_pred             cCcHHHHHHHHhc---ccHHHHHHHHHHhHHHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHhccCCCCCCCchhHHHHH
Q 046578          125 ELDYNLVKYKILC---KERESQERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYWW  201 (379)
Q Consensus       125 ~~~~~eLi~~~~~---Gd~~A~e~Li~~y~~lV~~ia~r~~~~~~d~eDLvQEg~i~L~~ai~~fD~~~g~~FsTYa~~~  201 (379)
                      .++..+++..+++   ||..|++.||..|.|.|+++|.++.++..+++|++||+|+.+|+++++|++.  .+|.+|++++
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            4566788888885   6999999999999999999999999999999999999999999999999853  4799999999


Q ss_pred             HHHHHHHHHHhhcCcccCCcchHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCccccC
Q 046578          202 IKQAIIRAIANKSRTIRLPGSMAGMVAKIAEANNVLSRRLRRMPTDSEIAEMLNIHVSTVRLAIERTRHPISLDGAVTDR  281 (379)
Q Consensus       202 Ir~~i~~~lr~~~r~irip~~~~~~~~ki~~a~~~l~~~lgr~pt~~eia~~Lgis~~~~~~~l~~~~~~iSLd~~~~~~  281 (379)
                      ++|.+++++|+..+...                                                     ...+..    
T Consensus        85 a~n~~~d~~R~~~~~~~-----------------------------------------------------~~~~~~----  107 (188)
T PRK09640         85 TYNECITQYRKERRKRR-----------------------------------------------------LMDALS----  107 (188)
T ss_pred             HHHHHHHHHHHhccccc-----------------------------------------------------Ccchhh----
Confidence            99999999997542100                                                     000000    


Q ss_pred             CCCcccccCCCCCCCChHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 046578          282 GCMTMQDIIPGPDETMPERMVQKQLMKQELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIA  361 (379)
Q Consensus       282 ~~~~l~d~i~~~~~~~pe~~~~~~e~~~~L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rA  361 (379)
                          . +...++.    ++.....+....|..+++.||+++|+||.++|+    +|+|++|||+.||+|.++|+.+++||
T Consensus       108 ----~-~~~~~~~----~~~~~~~~~~~~l~~~l~~L~~~~r~v~~l~~~----~g~s~~EIA~~lgis~~tV~~~l~Ra  174 (188)
T PRK09640        108 ----L-DPLEEAS----EEKAPKPEERGGLDRWLVHVNPIDREILVLRFV----AELEFQEIADIMHMGLSATKMRYKRA  174 (188)
T ss_pred             ----h-ccccccc----ccccccHHHHHHHHHHHHhcChhheeeeeeHHh----cCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence                0 0000000    000112233456899999999999999999984    77999999999999999999999999


Q ss_pred             HHHHHhHHhh
Q 046578          362 LTKLQQTNIL  371 (379)
Q Consensus       362 l~kLR~~l~~  371 (379)
                      +++||+.+..
T Consensus       175 ~~~Lr~~l~~  184 (188)
T PRK09640        175 LDKLREKFAG  184 (188)
T ss_pred             HHHHHHHHHH
Confidence            9999998753

>PRK09649 RNA polymerase sigma factor SigC; Reviewed

Probab=99.92  E-value=5.7e-24  Score=191.72  Aligned_cols=175  Identities=15%  Similarity=0.108  Sum_probs=137.7

Q ss_pred             CcHHHHHHHHhcccHHHHHHHHHHhHHHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHhccCCCCCCCchhHHHHHHHHH
Q 046578          126 LDYNLVKYKILCKERESQERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYWWIKQA  205 (379)
Q Consensus       126 ~~~~eLi~~~~~Gd~~A~e~Li~~y~~lV~~ia~r~~~~~~d~eDLvQEg~i~L~~ai~~fD~~~g~~FsTYa~~~Ir~~  205 (379)
                      .....|+.++.+||..|+++||..|.+.++.++. +.++..++||++||+|+.+|+.+++|++.  .+|.+|++.+++|.
T Consensus         9 ~~~~~l~~~~~~gd~~af~~l~~~~~~~l~~~~~-~~~~~~~AeDivQe~flkl~~~~~~~~~~--~~~~~Wl~~Iarn~   85 (185)
T PRK09649          9 EAVTALALSAAKGNGRALEAFIKATQQDVWRFVA-YLSDVGSADDLTQETFLRAIGAIPRFSAR--SSARTWLLAIARHV   85 (185)
T ss_pred             HHHHHHHHHHHccCHHHHHHHHHHHHHHHHHHHH-HhCCHHHHHHHHHHHHHHHHHhccccCcc--chHHHHHHHHHHHH
Confidence            3457899999999999999999999999999995 57788899999999999999999999864  37999999999999


Q ss_pred             HHHHHHhhcCcccCCcchHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCccccCCCCc
Q 046578          206 IIRAIANKSRTIRLPGSMAGMVAKIAEANNVLSRRLRRMPTDSEIAEMLNIHVSTVRLAIERTRHPISLDGAVTDRGCMT  285 (379)
Q Consensus       206 i~~~lr~~~r~irip~~~~~~~~ki~~a~~~l~~~lgr~pt~~eia~~Lgis~~~~~~~l~~~~~~iSLd~~~~~~~~~~  285 (379)
                      +++++|+..+....                                                     +.+.    .    
T Consensus        86 ~~d~~Rk~~~~~~~-----------------------------------------------------~~~~----~----  104 (185)
T PRK09649         86 VADHIRHVRSRPRT-----------------------------------------------------TRGA----R----  104 (185)
T ss_pred             HHHHHHHhcccccc-----------------------------------------------------cccc----c----
Confidence            99999985421000                                                     0000    0    


Q ss_pred             ccccCCCCCCCChHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Q 046578          286 MQDIIPGPDETMPERMVQKQLMKQELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKL  365 (379)
Q Consensus       286 l~d~i~~~~~~~pe~~~~~~e~~~~L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kL  365 (379)
                       .+...+.     +......+....+..+|.+||+++|+||.|+|+    +|+|++|||+.||+|.++|+++++||+++|
T Consensus       105 -~~~~~~~-----~~~~~~~e~~~~l~~~l~~Lp~~~r~v~~L~~~----~g~s~~EIA~~lgis~~tVk~~l~Rar~~L  174 (185)
T PRK09649        105 -PEHLIDG-----DRHARGFEDLVEVTTMIADLTTDQREALLLTQL----LGLSYADAAAVCGCPVGTIRSRVARARDAL  174 (185)
T ss_pred             -hhhccCh-----hhhhhhHHHHHHHHHHHHhCCHHHhHHhhhHHH----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence             0000000     000111122245888999999999999999995    779999999999999999999999999999


Q ss_pred             HhHHhhchh
Q 046578          366 QQTNILNNL  374 (379)
Q Consensus       366 R~~l~~~~L  374 (379)
                      |+.+....|
T Consensus       175 r~~~~~~~~  183 (185)
T PRK09649        175 LADAEPDDL  183 (185)
T ss_pred             HhhCCcccc
Confidence            998766554

>PRK12543 RNA polymerase sigma factor; Provisional

Probab=99.92  E-value=7.9e-24  Score=189.57  Aligned_cols=168  Identities=18%  Similarity=0.222  Sum_probs=137.1

Q ss_pred             hcccHHHHHHHHHHhHHHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHhccCCCCCCCchhHHHHHHHHHHHHHHHhhcC
Q 046578          136 LCKERESQERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYWWIKQAIIRAIANKSR  215 (379)
Q Consensus       136 ~~Gd~~A~e~Li~~y~~lV~~ia~r~~~~~~d~eDLvQEg~i~L~~ai~~fD~~~g~~FsTYa~~~Ir~~i~~~lr~~~r  215 (379)
                      ++||..|++.+|..|.|.|+.++.++.++..++||++||+|+.+|+++.+|++..  +|.+|++.+++|.+.+++|+..+
T Consensus         2 ~~~d~~af~~l~~~~~~~l~~~~~~~~~~~~daeDl~Qevfl~l~~~~~~~~~~~--~f~~wl~~iarn~~~~~~r~~~~   79 (179)
T PRK12543          2 LSGDQEAFSEIYDVTIQEVYKTVHFLVEDKQDVDDVVNEIYIQLWESLRKYDSNR--PFRFWLIGLVIKQIHSWRRKRWR   79 (179)
T ss_pred             cCchHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhHHHcCCCC--ChHHHHHHHHHHHHHHHHHhhcc
Confidence            5799999999999999999999999999999999999999999999999998764  79999999999999999876542


Q ss_pred             cccCCcchHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCccccCCCCcccccCCCCCC
Q 046578          216 TIRLPGSMAGMVAKIAEANNVLSRRLRRMPTDSEIAEMLNIHVSTVRLAIERTRHPISLDGAVTDRGCMTMQDIIPGPDE  295 (379)
Q Consensus       216 ~irip~~~~~~~~ki~~a~~~l~~~lgr~pt~~eia~~Lgis~~~~~~~l~~~~~~iSLd~~~~~~~~~~l~d~i~~~~~  295 (379)
                      ..+                                                      .++. ..+     ..+.   ...
T Consensus        80 ~~~------------------------------------------------------~~~~-~~~-----~~~~---~~~   96 (179)
T PRK12543         80 RFR------------------------------------------------------IFEK-AEE-----QRKP---VSI   96 (179)
T ss_pred             ccc------------------------------------------------------cccc-ccc-----cccc---ccc
Confidence            100                                                      0000 000     0000   011


Q ss_pred             CChHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHHhhch
Q 046578          296 TMPERMVQKQLMKQELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQTNILNN  373 (379)
Q Consensus       296 ~~pe~~~~~~e~~~~L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~~l~~~~  373 (379)
                      ..|+. +...+....+..++..|||++|+||.++|+    +|+|++|||+.||+|.++|+..++||+++||+.+....
T Consensus        97 ~~~~~-~~~~~~~~~l~~~l~~Lp~~~r~i~~l~~~----e~~s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~l~~~~  169 (179)
T PRK12543         97 DFSED-VLSKESNQELIELIHKLPYKLRQVIILRYL----HDYSQEEIAQLLQIPIGTVKSRIHAALKKLRQKEQIEE  169 (179)
T ss_pred             cChHH-HHHHHHHHHHHHHHHhCCHHHHHHHHHHHH----ccCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHH
Confidence            13444 555666678999999999999999999985    77999999999999999999999999999999997654

>PRK12536 RNA polymerase sigma factor; Provisional

Probab=99.92  E-value=7.5e-24  Score=190.05  Aligned_cols=173  Identities=13%  Similarity=0.144  Sum_probs=137.5

Q ss_pred             cHHHHHHHHhcccHHHHHHHHHHhHHHHHHHHHhccC-CCCCHHHHHHHHHHHHHHHHhccCCCCCCCchhHHHHHHHHH
Q 046578          127 DYNLVKYKILCKERESQERIIRSYRSLVVSIATGYQG-KGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYWWIKQA  205 (379)
Q Consensus       127 ~~~eLi~~~~~Gd~~A~e~Li~~y~~lV~~ia~r~~~-~~~d~eDLvQEg~i~L~~ai~~fD~~~g~~FsTYa~~~Ir~~  205 (379)
                      ....++.++.+||..|++.+|..|.+.|+.++.++.+ +..++||++||+|+.+|+.++.|++.  .+|.+|++.+++|.
T Consensus         7 ~~~~~~~~~~~~d~~a~~~l~~~~~~~l~~~~~~~~~~~~~~aeDlvQevfl~l~~~~~~~~~~--~~~~~wl~~iarN~   84 (181)
T PRK12536          7 RLRALLLRGLAGDAAAYRQFLSELAAHLRGFLRRRLPQLPDEVEDLVQEILLAVHNARHTYRAD--QPLTAWVHAIARYK   84 (181)
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHcCCChhhHHHHHHHHHHHHHHhHHhcCCC--CchHHHHHHHHHHH
Confidence            4577999999999999999999999999999988764 57899999999999999999999974  37999999999999


Q ss_pred             HHHHHHhhcCcccCCcchHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCccccCCCCc
Q 046578          206 IIRAIANKSRTIRLPGSMAGMVAKIAEANNVLSRRLRRMPTDSEIAEMLNIHVSTVRLAIERTRHPISLDGAVTDRGCMT  285 (379)
Q Consensus       206 i~~~lr~~~r~irip~~~~~~~~ki~~a~~~l~~~lgr~pt~~eia~~Lgis~~~~~~~l~~~~~~iSLd~~~~~~~~~~  285 (379)
                      ++|++|+..+...                                                       .+....+.    
T Consensus        85 ~~d~~Rk~~~~~~-------------------------------------------------------~~~~~~~~----  105 (181)
T PRK12536         85 LMDFLRSRARREA-------------------------------------------------------LHDPLDDE----  105 (181)
T ss_pred             HHHHHHHHhcccc-------------------------------------------------------ccCCccch----
Confidence            9999998653100                                                       00000000    


Q ss_pred             ccccCCCCCCCChHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Q 046578          286 MQDIIPGPDETMPERMVQKQLMKQELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKL  365 (379)
Q Consensus       286 l~d~i~~~~~~~pe~~~~~~e~~~~L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kL  365 (379)
                       .+...+. ...+      .+....+..++..||++++.||.++|.    +|+|++|||+.||+|+++|+++++||+++|
T Consensus       106 -~~~~~~~-~~~~------~~~~~~l~~~l~~L~~~~r~v~~l~~~----~g~s~~EIA~~l~is~~tV~~~l~rar~~L  173 (181)
T PRK12536        106 -SELFATS-DDEA------AEARRDLGKLLEQLPDRQRLPIVHVKL----EGLSVAETAQLTGLSESAVKVGIHRGLKAL  173 (181)
T ss_pred             -hhhcCCC-Ccch------HHHHHHHHHHHHHCCHHHHHHHHHHHH----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence             0000011 0111      123346889999999999999999984    779999999999999999999999999999


Q ss_pred             HhHHhhc
Q 046578          366 QQTNILN  372 (379)
Q Consensus       366 R~~l~~~  372 (379)
                      |+.+..+
T Consensus       174 r~~l~~~  180 (181)
T PRK12536        174 AAKIRGE  180 (181)
T ss_pred             HHHhcCC
Confidence            9998754

>PRK12539 RNA polymerase sigma factor; Provisional

Probab=99.92  E-value=1.6e-23  Score=188.35  Aligned_cols=173  Identities=13%  Similarity=0.145  Sum_probs=138.3

Q ss_pred             CcHHHHHHHHhcccHHHHHHHHHHhHHHHHHHHH----hccCCCCCHHHHHHHHHHHHHHHHhccCCCCCCCchhHHHHH
Q 046578          126 LDYNLVKYKILCKERESQERIIRSYRSLVVSIAT----GYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYWW  201 (379)
Q Consensus       126 ~~~~eLi~~~~~Gd~~A~e~Li~~y~~lV~~ia~----r~~~~~~d~eDLvQEg~i~L~~ai~~fD~~~g~~FsTYa~~~  201 (379)
                      .+..+++.+++.||..|++++|..|.+.++.+++    ++.++..+++|++||+|+.+|++++.|++..  .|.+|++.+
T Consensus         6 ~~~~~l~~~~~~gd~~af~~l~~~~~~~l~~~~~~~~~~~~~~~~~AeDlvQe~~l~l~~~~~~~~~~~--~f~~wl~~i   83 (184)
T PRK12539          6 NELKALMLASLDGDAAAHRALLERLSGHLRAYYKGKLARIGRGAEEAEDLVQEALMAIHTRRHTYDPEQ--PLTPWVYAI   83 (184)
T ss_pred             hHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHHHhccCCcchHHHHHHHHHHHHHHHHhhcCCCC--ChHHHHHHH
Confidence            3468899999999999999999999999999976    4557889999999999999999999998743  699999999


Q ss_pred             HHHHHHHHHHhhcCcccCCcchHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCccccC
Q 046578          202 IKQAIIRAIANKSRTIRLPGSMAGMVAKIAEANNVLSRRLRRMPTDSEIAEMLNIHVSTVRLAIERTRHPISLDGAVTDR  281 (379)
Q Consensus       202 Ir~~i~~~lr~~~r~irip~~~~~~~~ki~~a~~~l~~~lgr~pt~~eia~~Lgis~~~~~~~l~~~~~~iSLd~~~~~~  281 (379)
                      ++|.++|++|+..+. .                                                   .....+.    .
T Consensus        84 ~~n~~~d~~R~~~~~-~---------------------------------------------------~~~~~~~----~  107 (184)
T PRK12539         84 ARYKLIDHLRRTRAS-L---------------------------------------------------ADVPIDD----A  107 (184)
T ss_pred             HHHHHHHHHHHHhcc-c---------------------------------------------------cccChhh----h
Confidence            999999999985420 0                                                   0000000    0


Q ss_pred             CCCcccccCCCCCCCChHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 046578          282 GCMTMQDIIPGPDETMPERMVQKQLMKQELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIA  361 (379)
Q Consensus       282 ~~~~l~d~i~~~~~~~pe~~~~~~e~~~~L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rA  361 (379)
                           .....       .+.....+....+..++..||+++|+|+.++|+    +|+|++|||+.||+|.++|+++++||
T Consensus       108 -----~~~~~-------~~~~~~~e~~~~l~~~l~~L~~~~r~v~~l~~~----~g~s~~eIA~~lgis~~tV~~~l~ra  171 (184)
T PRK12539        108 -----DELVA-------HDDHAAVESTLDLGRLLARLPEKMRLAIQAVKL----EGLSVAEAATRSGMSESAVKVSVHRG  171 (184)
T ss_pred             -----ccccC-------CcHHhhHHHHHHHHHHHHhCCHHHHHHHHHHHH----cCCcHHHHHHHHCcCHHHHHHHHHHH
Confidence                 00000       001122233456899999999999999999984    67999999999999999999999999


Q ss_pred             HHHHHhHHhhc
Q 046578          362 LTKLQQTNILN  372 (379)
Q Consensus       362 l~kLR~~l~~~  372 (379)
                      +++||+.+...
T Consensus       172 ~~~Lr~~l~~~  182 (184)
T PRK12539        172 LKALAALIGRE  182 (184)
T ss_pred             HHHHHHHHhhc
Confidence            99999998654

>PRK09638 RNA polymerase sigma factor SigY; Reviewed

Probab=99.92  E-value=1.1e-23  Score=187.71  Aligned_cols=172  Identities=12%  Similarity=0.068  Sum_probs=138.4

Q ss_pred             cHHHHHHHHhcccHHHHHHHHHHhHHHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHhccCCCCCCCchhHHHHHHHHHH
Q 046578          127 DYNLVKYKILCKERESQERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYWWIKQAI  206 (379)
Q Consensus       127 ~~~eLi~~~~~Gd~~A~e~Li~~y~~lV~~ia~r~~~~~~d~eDLvQEg~i~L~~ai~~fD~~~g~~FsTYa~~~Ir~~i  206 (379)
                      +..+++..+.+||..+++.||..|.|.|+++|+++.++..+++|++||+|+++|+++++|++.  .+|.+|++.+++|.+
T Consensus         4 ~~~~l~~~~~~~d~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeD~vQe~~l~l~~~~~~~~~~--~~~~~wl~~i~~n~~   81 (176)
T PRK09638          4 DEKELIQKAKKGDDAALTTLFQQHYSFLYKYLLKLTLDPDLAEDLVQETMLKAIENLSSFQGR--SKFSTWLISIASRLY   81 (176)
T ss_pred             cHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHcCCHhHHHHHHHHHHHHHHHHHHhcCCc--ccHHHHHHHHHHHHH
Confidence            456789999999999999999999999999999999999999999999999999999999864  489999999999999


Q ss_pred             HHHHHhhcCcccCCcchHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCccccCCCCcc
Q 046578          207 IRAIANKSRTIRLPGSMAGMVAKIAEANNVLSRRLRRMPTDSEIAEMLNIHVSTVRLAIERTRHPISLDGAVTDRGCMTM  286 (379)
Q Consensus       207 ~~~lr~~~r~irip~~~~~~~~ki~~a~~~l~~~lgr~pt~~eia~~Lgis~~~~~~~l~~~~~~iSLd~~~~~~~~~~l  286 (379)
                      ++++|+..+.....                                                      +. ..+      
T Consensus        82 ~d~~r~~~~~~~~~------------------------------------------------------~~-~~~------  100 (176)
T PRK09638         82 KDHLRKQKREKLRL------------------------------------------------------QR-AKE------  100 (176)
T ss_pred             HHHHHHhccccchh------------------------------------------------------hh-ccc------
Confidence            99999865310000                                                      00 000      


Q ss_pred             cccCCCCCCCChHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 046578          287 QDIIPGPDETMPERMVQKQLMKQELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQ  366 (379)
Q Consensus       287 ~d~i~~~~~~~pe~~~~~~e~~~~L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR  366 (379)
                       + ..+..  .. +.....+....+..+|..||+++|+||.++|+    +|+|++|||+.||+|.++|++.++||+++||
T Consensus       101 -~-~~~~~--~~-~~~~~~~~~~~l~~~l~~L~~~~r~v~~l~~~----~g~s~~eIA~~l~is~~~V~~~l~ra~~~l~  171 (176)
T PRK09638        101 -E-TLRKE--KW-EAAIKGAEWSEMLDALSKLDPEFRAPVILKHY----YGYTYEEIAKMLNIPEGTVKSRVHHGIKQLR  171 (176)
T ss_pred             -c-cCCcc--ch-HHHHHhhhHHHHHHHHHcCCHHHhheeeehhh----cCCCHHHHHHHHCCChhHHHHHHHHHHHHHH
Confidence             0 00000  00 11222334456889999999999999999884    6799999999999999999999999999999


Q ss_pred             hHHh
Q 046578          367 QTNI  370 (379)
Q Consensus       367 ~~l~  370 (379)
                      +.+.
T Consensus       172 ~~l~  175 (176)
T PRK09638        172 KEWG  175 (176)
T ss_pred             HHhc
Confidence            9863

>PRK09645 RNA polymerase sigma factor SigL; Provisional

Probab=99.92  E-value=1.4e-23  Score=186.47  Aligned_cols=167  Identities=13%  Similarity=0.094  Sum_probs=133.1

Q ss_pred             hcccHHHHHHHHHHhHHHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHhccCCCCCCCchhHHHHHHHHHHHHHHHhhcC
Q 046578          136 LCKERESQERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYWWIKQAIIRAIANKSR  215 (379)
Q Consensus       136 ~~Gd~~A~e~Li~~y~~lV~~ia~r~~~~~~d~eDLvQEg~i~L~~ai~~fD~~~g~~FsTYa~~~Ir~~i~~~lr~~~r  215 (379)
                      ..+|+.+++.||..|.+.++++|.++.++..++||++||+|+.+|+..++|++.. ..|.+|++++++|.+++++|++.+
T Consensus         4 ~~~~~~~~~~l~~~~~~~l~~~~~~~~~~~~~AeD~vQevfl~~~~~~~~~~~~~-~~~~~wL~~iarn~~~d~~Rk~~~   82 (173)
T PRK09645          4 ATAEAALMRALYDEHAAPLWRYALRLTGDRARAEDVVQETLLRAWQHPEVLADTG-RSARAWLFTVARNLVIDERRSARA   82 (173)
T ss_pred             CcchHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhHHhcCccc-ccHHHHHHHHHHHHHHHHHHhhcc
Confidence            4579999999999999999999999999989999999999999999999997432 479999999999999999997652


Q ss_pred             cccCCcchHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCccccCCCCcccccCCCCCC
Q 046578          216 TIRLPGSMAGMVAKIAEANNVLSRRLRRMPTDSEIAEMLNIHVSTVRLAIERTRHPISLDGAVTDRGCMTMQDIIPGPDE  295 (379)
Q Consensus       216 ~irip~~~~~~~~ki~~a~~~l~~~lgr~pt~~eia~~Lgis~~~~~~~l~~~~~~iSLd~~~~~~~~~~l~d~i~~~~~  295 (379)
                      ...                                                     ...+.      .   .+ .++   
T Consensus        83 ~~~-----------------------------------------------------~~~~~------~---~~-~~~---   96 (173)
T PRK09645         83 RPV-----------------------------------------------------EGGDD------V---LG-VPE---   96 (173)
T ss_pred             ccc-----------------------------------------------------ccccc------c---cc-CCC---
Confidence            100                                                     00000      0   00 000   


Q ss_pred             CChHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHHhhch
Q 046578          296 TMPERMVQKQLMKQELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQTNILNN  373 (379)
Q Consensus       296 ~~pe~~~~~~e~~~~L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~~l~~~~  373 (379)
                      ..+.+.+...+....|..+|+.||+++|+||.|+|+    +|+|++|||+.||+|.++|+++++||+++||+.+...+
T Consensus        97 ~~~~~~~~~~~~~~~l~~~l~~L~~~~r~vl~L~~~----~g~s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~l~~~~  170 (173)
T PRK09645         97 QSAPDEVDRALDRLLVADALAQLSPEHRAVLVRSYY----RGWSTAQIAADLGIPEGTVKSRLHYALRALRLALQERG  170 (173)
T ss_pred             CCCchHHHHHhHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHhhccc
Confidence            111222333334457889999999999999999995    77999999999999999999999999999999987543

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

Probab=99.91  E-value=2.3e-23  Score=186.70  Aligned_cols=174  Identities=11%  Similarity=0.153  Sum_probs=132.1

Q ss_pred             cHHHHHHHHhcccHHHHHHHHHHhHHHHHHHHHhccCCCC-----CHHHHHHHHHHHHHH-HHhccCCCCCCCchhHHHH
Q 046578          127 DYNLVKYKILCKERESQERIIRSYRSLVVSIATGYQGKGL-----SLKDLIQEGSIGLLR-GAKRFNPERGYKLSTYVYW  200 (379)
Q Consensus       127 ~~~eLi~~~~~Gd~~A~e~Li~~y~~lV~~ia~r~~~~~~-----d~eDLvQEg~i~L~~-ai~~fD~~~g~~FsTYa~~  200 (379)
                      ...+++..++.||..|++.||..|.+.++.+|.++.++..     +++|++||+|+.+|+ ..++|++.  ..|.+|++.
T Consensus         3 ~~~~li~~~~~gd~~a~~~l~~~~~~~l~~~~~~~~~~~~~~~~~~AeDlvQevfl~~~~~~~~~~~~~--~~~~~wl~~   80 (183)
T TIGR02999         3 PVTELLQQWQNGDAAARDQLFPQLYQELRRIARRQLRRERSGQTLQTTALVHEAYLRLSDQDEQKWDDR--AHFFAAAAK   80 (183)
T ss_pred             cHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHhhcccccccchHHHHHHHHHHHHhhcccCCCCch--HHHHHHHHH
Confidence            3578899999999999999999999999999999998877     899999999999998 77888754  379999999


Q ss_pred             HHHHHHHHHHHhhcCcccCCcchHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCcccc
Q 046578          201 WIKQAIIRAIANKSRTIRLPGSMAGMVAKIAEANNVLSRRLRRMPTDSEIAEMLNIHVSTVRLAIERTRHPISLDGAVTD  280 (379)
Q Consensus       201 ~Ir~~i~~~lr~~~r~irip~~~~~~~~ki~~a~~~l~~~lgr~pt~~eia~~Lgis~~~~~~~l~~~~~~iSLd~~~~~  280 (379)
                      +++|.+++++|+..+..+..                                                 .  ..+.    
T Consensus        81 i~~n~~~d~~R~~~~~~~~~-------------------------------------------------~--~~~~----  105 (183)
T TIGR02999        81 AMRRILVDHARRRRAQKRGG-------------------------------------------------G--AVRV----  105 (183)
T ss_pred             HHHHHHHHHHHHHHHHhccC-------------------------------------------------C--cccc----
Confidence            99999999999754210000                                                 0  0000    


Q ss_pred             CCCCcccccCCCCCCCChHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 046578          281 RGCMTMQDIIPGPDETMPERMVQKQLMKQELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGI  360 (379)
Q Consensus       281 ~~~~~l~d~i~~~~~~~pe~~~~~~e~~~~L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~r  360 (379)
                          .+.+..+. .  .++.. ........+...|++||+++|+||.|+|+    +|+|++|||+.||+|.+||+.+++|
T Consensus       106 ----~~~~~~~~-~--~~~~~-~~~~~l~~~~~~l~~Lp~~~r~v~~l~~~----~g~s~~EIA~~lgis~~tVk~~l~R  173 (183)
T TIGR02999       106 ----PLDEVLPD-A--EADLD-EELLDLDDALDKLAQVDPRQAEVVELRFF----AGLTVEEIAELLGVSVRTVERDWRF  173 (183)
T ss_pred             ----ccccccCC-C--CccHH-HHHHHHHHHHHHhhcCCHHHHHHHHHHHH----cCCCHHHHHHHhCCCHHHHHHHHHH
Confidence                00000000 0  11111 11111223445567799999999999995    7799999999999999999999999


Q ss_pred             HHHHHHhHH
Q 046578          361 ALTKLQQTN  369 (379)
Q Consensus       361 Al~kLR~~l  369 (379)
                      |+++||+.+
T Consensus       174 ar~~Lr~~l  182 (183)
T TIGR02999       174 ARAWLADEL  182 (183)
T ss_pred             HHHHHHHHh
Confidence            999999986

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.

>PRK12518 RNA polymerase sigma factor; Provisional

Probab=99.91  E-value=1.3e-23  Score=186.91  Aligned_cols=172  Identities=19%  Similarity=0.194  Sum_probs=134.8

Q ss_pred             HHHHHhcccHHHHHHHHHHhHHHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHhccCCCCCCCchhHHHHHHHHHHHHHH
Q 046578          131 VKYKILCKERESQERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYWWIKQAIIRAI  210 (379)
Q Consensus       131 Li~~~~~Gd~~A~e~Li~~y~~lV~~ia~r~~~~~~d~eDLvQEg~i~L~~ai~~fD~~~g~~FsTYa~~~Ir~~i~~~l  210 (379)
                      ++.+++.||..+++.+|..|.|.|+.+++++.+ ..++||++||+|+.+|+.++.|++.  .+|.+|++++++|.++|++
T Consensus         1 l~~~~~~gd~~a~~~l~~~~~~~l~~~~~~~~~-~~~aeDivQe~~l~l~~~~~~~~~~--~~~~~wl~~ia~n~~~d~~   77 (175)
T PRK12518          1 LILRCQRGDRQSFRQLYRRYQQKVRSTLYQLCG-RELLDDLVQEVFLRVWKGLPKLRNP--AYFSTWLYRITWNVATDAR   77 (175)
T ss_pred             ChhHHHcCCHHHHHHHHHHHHHHHHHHHHHHcC-HhHHHHHHHHHHHHHHHhHHhhCCc--ccHHHHHHHHHHHHHHHHH
Confidence            467889999999999999999999999999874 4789999999999999999999864  3799999999999999999


Q ss_pred             HhhcCcccCCcchHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCccccCCCCcccccC
Q 046578          211 ANKSRTIRLPGSMAGMVAKIAEANNVLSRRLRRMPTDSEIAEMLNIHVSTVRLAIERTRHPISLDGAVTDRGCMTMQDII  290 (379)
Q Consensus       211 r~~~r~irip~~~~~~~~ki~~a~~~l~~~lgr~pt~~eia~~Lgis~~~~~~~l~~~~~~iSLd~~~~~~~~~~l~d~i  290 (379)
                      |+..+...                                                    .  .+... .  .   ..  
T Consensus        78 R~~~~~~~----------------------------------------------------~--~~~~~-~--~---~~--   95 (175)
T PRK12518         78 RQFAQRPS----------------------------------------------------R--IQDDS-L--N---DQ--   95 (175)
T ss_pred             HHhhcccc----------------------------------------------------c--hhccc-c--c---cc--
Confidence            97542000                                                    0  00000 0  0   00  


Q ss_pred             CCCCCCChHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHHh
Q 046578          291 PGPDETMPERMVQKQLMKQELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQTNI  370 (379)
Q Consensus       291 ~~~~~~~pe~~~~~~e~~~~L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~~l~  370 (379)
                      +......++  ....+....+..+++.||+++|.||.++|+    +|+|++|||+.||+|.++|++.++||+++||+.+.
T Consensus        96 ~~~~~~~~~--~~~~~~~~~l~~~l~~L~~~~r~vl~l~~~----~g~s~~eIA~~lg~s~~tv~~~l~Rar~~L~~~l~  169 (175)
T PRK12518         96 PSRPSDTPD--LMQLHYQDLVQQGLQTLSLEHRAVLVLHDL----EDLPQKEIAEILNIPVGTVKSRLFYARRQLRKFLQ  169 (175)
T ss_pred             ccCCCCcHH--HHHHHHHHHHHHHHHhCCHHHeeeeeehHh----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence            000111222  222233456889999999999999999984    77999999999999999999999999999999987


Q ss_pred             hch
Q 046578          371 LNN  373 (379)
Q Consensus       371 ~~~  373 (379)
                      ..+
T Consensus       170 ~~~  172 (175)
T PRK12518        170 QQG  172 (175)
T ss_pred             hcc
Confidence            644

>PRK12529 RNA polymerase sigma factor; Provisional

Probab=99.91  E-value=1.3e-23  Score=188.07  Aligned_cols=168  Identities=14%  Similarity=0.105  Sum_probs=133.9

Q ss_pred             HHhcccHHHHHHHHHHhHHHHHHHHHhccC--CCCCHHHHHHHHHHHHHHHHhccCCCCCCCchhHHHHHHHHHHHHHHH
Q 046578          134 KILCKERESQERIIRSYRSLVVSIATGYQG--KGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYWWIKQAIIRAIA  211 (379)
Q Consensus       134 ~~~~Gd~~A~e~Li~~y~~lV~~ia~r~~~--~~~d~eDLvQEg~i~L~~ai~~fD~~~g~~FsTYa~~~Ir~~i~~~lr  211 (379)
                      .+..||..+++.||..|.+.|+.++.+.++  +..++||++||+|+.+|+..+.|+......|.||++++++|.+++++|
T Consensus         6 ~~~~~d~~af~~ly~~~~~~l~~~~~~~~~~~~~~~AeDivQevFl~~~~~~~~~~~~~~~~~~~wL~~ia~n~~~d~~R   85 (178)
T PRK12529          6 SCLSADRDKVATLYRENHAWLRNWLAYRLRSWGRGVADDLAHDIFLRILASRDGGQREAIRQPRAYLARIANCVLVSWRR   85 (178)
T ss_pred             cCCCCCHHHHHHHHHHHHHHHHHHHHHHhCCCChHHHHHHHHHHHHHHHhcccccccccccCHHHHHHHHHHHHHHHHHH
Confidence            467899999999999999999998666555  467899999999999999999997544457999999999999999998


Q ss_pred             hhcCcccCCcchHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCccccCCCCcccccCC
Q 046578          212 NKSRTIRLPGSMAGMVAKIAEANNVLSRRLRRMPTDSEIAEMLNIHVSTVRLAIERTRHPISLDGAVTDRGCMTMQDIIP  291 (379)
Q Consensus       212 ~~~r~irip~~~~~~~~ki~~a~~~l~~~lgr~pt~~eia~~Lgis~~~~~~~l~~~~~~iSLd~~~~~~~~~~l~d~i~  291 (379)
                      +..+.   .                                                 .  ..+.         ..+ ..
T Consensus        86 k~~~~---~-------------------------------------------------~--~~~~---------~~~-~~  101 (178)
T PRK12529         86 RQSLE---L-------------------------------------------------A--WLEA---------LAT-LP  101 (178)
T ss_pred             HHHHH---h-------------------------------------------------h--hhhH---------hhh-cc
Confidence            75310   0                                                 0  0000         000 00


Q ss_pred             CCCCCChHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHH
Q 046578          292 GPDETMPERMVQKQLMKQELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQTN  369 (379)
Q Consensus       292 ~~~~~~pe~~~~~~e~~~~L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~~l  369 (379)
                      ....++|++.+...+....|..+|.+||+++|.||.|+|+    +|+|++|||+.||+|.+||+.+++||+.+|++.+
T Consensus       102 ~~~~~~~e~~~~~~~~~~~l~~~l~~Lp~~~R~v~~L~~~----~g~s~~EIA~~lgis~~tVk~~l~rAl~~~~~~~  175 (178)
T PRK12529        102 EPLHPSPEQQSVILETLHEIDALLDTLRPRVKQAFLMATL----DGMKQKDIAQALDIALPTVKKYIHQAYVTCLSLM  175 (178)
T ss_pred             CcCCCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHhC
Confidence            1112355666666666678999999999999999999985    7799999999999999999999999999999875

>PRK12512 RNA polymerase sigma factor; Provisional

Probab=99.91  E-value=3.8e-23  Score=185.68  Aligned_cols=170  Identities=15%  Similarity=0.226  Sum_probs=136.2

Q ss_pred             HHHHHHHHhcccHHHHHHHHHHhHHHHHHHHHhccC----CCCCHHHHHHHHHHHHHHHHhccCCCCCCCchhHHHHHHH
Q 046578          128 YNLVKYKILCKERESQERIIRSYRSLVVSIATGYQG----KGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYWWIK  203 (379)
Q Consensus       128 ~~eLi~~~~~Gd~~A~e~Li~~y~~lV~~ia~r~~~----~~~d~eDLvQEg~i~L~~ai~~fD~~~g~~FsTYa~~~Ir  203 (379)
                      +..++..+..||..|+++||..|.+.|+.+|.++++    +..+++|++||+|+.+|...++|+..  .+|.+|++.+++
T Consensus         9 ~~~l~~~~~~gd~~a~~~l~~~y~~~l~~~~~~~l~~~~~~~~~aeDlvQe~fl~l~~~~~~~~~~--~~~~~wl~~i~r   86 (184)
T PRK12512          9 WTDLMRSANAGDAAAYRRLLKAVTPVLRAAARRGLARAGQPADQAEDIVQEILLAVHLKRHTWDPG--APFAPWLFAIAR   86 (184)
T ss_pred             HHHHHHHHHccCHHHHHHHHHHHHHHHHHHHHHHHHhccCCcccHHHHHHHHHHHHHHhHHhcCcc--ccHHHHHHHHHH
Confidence            567899999999999999999999999999998875    35699999999999999999999863  379999999999


Q ss_pred             HHHHHHHHhhcCcccCCcchHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCccccCCC
Q 046578          204 QAIIRAIANKSRTIRLPGSMAGMVAKIAEANNVLSRRLRRMPTDSEIAEMLNIHVSTVRLAIERTRHPISLDGAVTDRGC  283 (379)
Q Consensus       204 ~~i~~~lr~~~r~irip~~~~~~~~ki~~a~~~l~~~lgr~pt~~eia~~Lgis~~~~~~~l~~~~~~iSLd~~~~~~~~  283 (379)
                      |.+.+++|++.+...                                                     ..++.       
T Consensus        87 n~~~d~~Rr~~~~~~-----------------------------------------------------~~~~~-------  106 (184)
T PRK12512         87 NKLIDALRRRGRRVF-----------------------------------------------------VDIDD-------  106 (184)
T ss_pred             HHHHHHHHhhccccc-----------------------------------------------------CCchh-------
Confidence            999999997653100                                                     00110       


Q ss_pred             CcccccCCCCCCCChHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 046578          284 MTMQDIIPGPDETMPERMVQKQLMKQELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALT  363 (379)
Q Consensus       284 ~~l~d~i~~~~~~~pe~~~~~~e~~~~L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~  363 (379)
                        ..+.+++..   +.+    ......+..+|+.||+++++||.++|+    +|+|++|||+.||+|.++|+..++||++
T Consensus       107 --~~~~~~~~~---~~~----~~~~~~l~~~l~~L~~~~r~v~~l~~~----~g~s~~eIA~~l~is~~tV~~~l~ra~~  173 (184)
T PRK12512        107 --FAETLPAEP---ATE----TLPAGDVGRHLETLPPRQRDVVQSISV----EGASIKETAAKLSMSEGAVRVALHRGLA  173 (184)
T ss_pred             --ccccccccc---hhh----HHHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence              001111110   011    122345788999999999999999984    6799999999999999999999999999


Q ss_pred             HHHhHHhhc
Q 046578          364 KLQQTNILN  372 (379)
Q Consensus       364 kLR~~l~~~  372 (379)
                      +||+.+..+
T Consensus       174 ~Lr~~l~~~  182 (184)
T PRK12512        174 ALAAKFRSE  182 (184)
T ss_pred             HHHHHhhcC
Confidence            999998764

>PRK12520 RNA polymerase sigma factor; Provisional

Probab=99.91  E-value=3.2e-23  Score=187.42  Aligned_cols=181  Identities=18%  Similarity=0.193  Sum_probs=136.4

Q ss_pred             HHHHHHHHhHHHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHhccCCCCCCCchhHHHHHHHHHHHHHHHhhcCcccCCc
Q 046578          142 SQERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYWWIKQAIIRAIANKSRTIRLPG  221 (379)
Q Consensus       142 A~e~Li~~y~~lV~~ia~r~~~~~~d~eDLvQEg~i~L~~ai~~fD~~~g~~FsTYa~~~Ir~~i~~~lr~~~r~irip~  221 (379)
                      ++++||..|.+.|+.+|.+++++..++||++||+|+.+|+.+++|+..  .+|.+|++++++|.+++++|++.+......
T Consensus         3 ~~~~l~~~~~~~l~~~a~~~~~~~~~AeDivQevfl~~~~~~~~~~~~--~~~~~WL~~ia~n~~~d~~Rk~~r~~~~~~   80 (191)
T PRK12520          3 IAPAQLEALRPHLLRFARLQLRDPALAEDAVSETLLAVLEHPERFAGQ--SSLKTYLVGILKHKIIDAIRSGRREVRLSL   80 (191)
T ss_pred             chHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhhhhhccc--ccHHHHHHHHHHHHHHHHHHhhcCcCcccc
Confidence            689999999999999999999999999999999999999999999854  379999999999999999998764211110


Q ss_pred             chHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCccccCCCCcccccCCCCCCCChHHH
Q 046578          222 SMAGMVAKIAEANNVLSRRLRRMPTDSEIAEMLNIHVSTVRLAIERTRHPISLDGAVTDRGCMTMQDIIPGPDETMPERM  301 (379)
Q Consensus       222 ~~~~~~~ki~~a~~~l~~~lgr~pt~~eia~~Lgis~~~~~~~l~~~~~~iSLd~~~~~~~~~~l~d~i~~~~~~~pe~~  301 (379)
                      ...                  ......++                       ++.....  . ......++ ...+|++.
T Consensus        81 ~~~------------------~~~~~~~~-----------------------~~~~~~~--~-~~~~~~~~-~~~~~~~~  115 (191)
T PRK12520         81 DDA------------------DEQSDDDL-----------------------FDALFAA--D-GHYREPPS-DWGDPDAA  115 (191)
T ss_pred             ccc------------------ccchhhhh-----------------------hhhhccc--c-cccccCcc-ccCCHHHH
Confidence            000                  00000000                       0000000  0 00000111 12356777


Q ss_pred             HHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHHhhch
Q 046578          302 VQKQLMKQELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQTNILNN  373 (379)
Q Consensus       302 ~~~~e~~~~L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~~l~~~~  373 (379)
                      +...+....|..+|.+||+++|.||.|+|+    +|+|++|||+.||+|.++|+++++||+++||+++...+
T Consensus       116 ~~~~~~~~~l~~~l~~Lp~~~r~v~~l~~~----~g~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~~~~  183 (191)
T PRK12520        116 LSRREFFEVLQACVDRLPPRTGRVFMMREW----LELETEEICQELQITATNAWVLLYRARMRLRECLDLHW  183 (191)
T ss_pred             HHHHHHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHH
Confidence            777777788999999999999999999995    77999999999999999999999999999999998765

>PRK12535 RNA polymerase sigma factor; Provisional

Probab=99.91  E-value=5.6e-23  Score=187.07  Aligned_cols=179  Identities=15%  Similarity=0.101  Sum_probs=140.4

Q ss_pred             hcCcCcHHHHHHHHhcccHHHHHHHHHHhHHHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHhccCCCCCCCchhHHHHH
Q 046578          122 ENGELDYNLVKYKILCKERESQERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYWW  201 (379)
Q Consensus       122 ~~~~~~~~eLi~~~~~Gd~~A~e~Li~~y~~lV~~ia~r~~~~~~d~eDLvQEg~i~L~~ai~~fD~~~g~~FsTYa~~~  201 (379)
                      ..++..+.+|+.++..||..+++.+|..|.+.++.+++ +.++..++||++||+|+.+|+...+|++.  .+|.+|++.+
T Consensus         6 ~~~~~~~~~l~~~~~~~d~~a~~~l~~~y~~~l~~~~~-~~~~~~~AEDivQevflkl~~~~~~~~~~--~~~~~WL~~I   82 (196)
T PRK12535          6 ERDDAHVTDLALAAGRGDRAALTEFIRETQDDVWRLLA-HLGGHDIADDLTQETYLRVMSALPRFAAR--SSARTWLLSL   82 (196)
T ss_pred             ccccHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHH-HhCCHHHHHHHHHHHHHHHHHHhhhcCCc--ccHHHHHHHH
Confidence            34566778999999999999999999999999999975 56788899999999999999999999863  3799999999


Q ss_pred             HHHHHHHHHHhhcCcccCCcchHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCccccC
Q 046578          202 IKQAIIRAIANKSRTIRLPGSMAGMVAKIAEANNVLSRRLRRMPTDSEIAEMLNIHVSTVRLAIERTRHPISLDGAVTDR  281 (379)
Q Consensus       202 Ir~~i~~~lr~~~r~irip~~~~~~~~ki~~a~~~l~~~lgr~pt~~eia~~Lgis~~~~~~~l~~~~~~iSLd~~~~~~  281 (379)
                      ++|.+++++|+..+..+                                                     ...+. ..  
T Consensus        83 arn~~id~~Rk~~~~~~-----------------------------------------------------~~~~~-~~--  106 (196)
T PRK12535         83 ARRVWVDNIRHDMARPR-----------------------------------------------------KSATE-YE--  106 (196)
T ss_pred             HHHHHHHHHHhhccCCC-----------------------------------------------------ccccc-cc--
Confidence            99999999998653100                                                     00000 00  


Q ss_pred             CCCcccccCCCCCCCChHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 046578          282 GCMTMQDIIPGPDETMPERMVQKQLMKQELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIA  361 (379)
Q Consensus       282 ~~~~l~d~i~~~~~~~pe~~~~~~e~~~~L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rA  361 (379)
                         ...+   .  ...++..... +....+..+|+.||+++|+||.|+|+    +|+|++|||+.||+|.++|+++++||
T Consensus       107 ---~~~~---~--~~~~~~~~~~-~~~~~l~~~l~~Lp~~~r~v~~l~~~----~g~s~~EIAe~lgis~~tV~~~l~Ra  173 (196)
T PRK12535        107 ---DAAA---T--TASNETTGSW-SEWIDVRTLIDALPPERREALILTQV----LGYTYEEAAKIADVRVGTIRSRVARA  173 (196)
T ss_pred             ---cccc---c--cCCcchhHHH-HHHHHHHHHHHcCCHHHHHHhhhHHH----hCCCHHHHHHHhCCCHHHHHHHHHHH
Confidence               0000   0  0111111111 12346889999999999999999995    77999999999999999999999999


Q ss_pred             HHHHHhHHhhc
Q 046578          362 LTKLQQTNILN  372 (379)
Q Consensus       362 l~kLR~~l~~~  372 (379)
                      +++||+.+...
T Consensus       174 r~~Lr~~l~~~  184 (196)
T PRK12535        174 RADLIAATATG  184 (196)
T ss_pred             HHHHHHHhccc
Confidence            99999997643

>PRK09415 RNA polymerase factor sigma C; Reviewed

Probab=99.91  E-value=6.1e-23  Score=183.89  Aligned_cols=165  Identities=14%  Similarity=0.159  Sum_probs=135.5

Q ss_pred             ccHHHHHHHHHHhHHHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHhccCCCCCCCchhHHHHHHHHHHHHHHHhhcCcc
Q 046578          138 KERESQERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYWWIKQAIIRAIANKSRTI  217 (379)
Q Consensus       138 Gd~~A~e~Li~~y~~lV~~ia~r~~~~~~d~eDLvQEg~i~L~~ai~~fD~~~g~~FsTYa~~~Ir~~i~~~lr~~~r~i  217 (379)
                      .|+.|++++|..|.|.|+++|.++.++..+++|++||+|+.+|+++++|++.  .+|.+|++.+++|.+.+++|+..+..
T Consensus        13 ~~~~a~~~l~~~~~~~l~~~~~~~~~~~~~AeDlvQd~fl~l~~~~~~~~~~--~~~~awl~~ia~n~~~d~~Rk~~~~~   90 (179)
T PRK09415         13 DKEDLIDEIMNEYGQEVLQLVYSYVKNKEVAEDLTQEIFVKCYKSLHTYKGK--SSLKTWLYRIAINHCKDYLKSWHNKK   90 (179)
T ss_pred             ccHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHhcCCC--cccHHHHHHHHHHHHHHHHHhhcccc
Confidence            5788999999999999999999999999999999999999999999999864  37999999999999999999854210


Q ss_pred             cCCcchHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCccccCCCCcccccCCCCCCCC
Q 046578          218 RLPGSMAGMVAKIAEANNVLSRRLRRMPTDSEIAEMLNIHVSTVRLAIERTRHPISLDGAVTDRGCMTMQDIIPGPDETM  297 (379)
Q Consensus       218 rip~~~~~~~~ki~~a~~~l~~~lgr~pt~~eia~~Lgis~~~~~~~l~~~~~~iSLd~~~~~~~~~~l~d~i~~~~~~~  297 (379)
                      .                                                     ...+.        ......  ....+
T Consensus        91 ~-----------------------------------------------------~~~~~--------~~~~~~--~~~~~  107 (179)
T PRK09415         91 V-----------------------------------------------------IVTED--------IFTYME--SQKES  107 (179)
T ss_pred             c-----------------------------------------------------ccccc--------cccccc--ccccC
Confidence            0                                                     00000        000000  11234


Q ss_pred             hHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHHhh
Q 046578          298 PERMVQKQLMKQELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQTNIL  371 (379)
Q Consensus       298 pe~~~~~~e~~~~L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~~l~~  371 (379)
                      |++.+...+....+..+|.+||+++|+||.++|+    +|+|++|||+.||+|.++|+++++||+++||+.+..
T Consensus       108 ~e~~~~~~e~~~~l~~~l~~L~~~~r~v~~l~~~----~g~s~~EIA~~l~is~~tv~~~l~Ra~~~Lr~~l~~  177 (179)
T PRK09415        108 VEEEVIQNAEDERLASAVMSLPIKYREVIYLFYY----EELSIKEIAEVTGVNENTVKTRLKKAKELLKKGLEE  177 (179)
T ss_pred             cHHHHHHHHHHHHHHHHHHhCCHHHhhHhHhHHh----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHhc
Confidence            5666666677778999999999999999999984    779999999999999999999999999999998754

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

Probab=99.90  E-value=1.1e-22  Score=182.71  Aligned_cols=175  Identities=17%  Similarity=0.235  Sum_probs=140.6

Q ss_pred             HHHHHHhcccHHHHHHHHHHhHHHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHhccCCCCCCCchhHHHHHHHHHHHHH
Q 046578          130 LVKYKILCKERESQERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYWWIKQAIIRA  209 (379)
Q Consensus       130 eLi~~~~~Gd~~A~e~Li~~y~~lV~~ia~r~~~~~~d~eDLvQEg~i~L~~ai~~fD~~~g~~FsTYa~~~Ir~~i~~~  209 (379)
                      .+......|+..++.+++..|.+.++.+++++.++..++|||+||+|+.+|+++..| .. +.+|.||++++++|.++|+
T Consensus         4 ~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~dAeDlvQE~~lr~~~~~~~~-~~-~~~~~~wl~~Ia~n~~iD~   81 (182)
T COG1595           4 LLLAEALRGDRAAFEELLERLRPRLRRLARRLLGDRADAEDLVQETFLRAWRAIDSF-RG-RSSFKAWLYRIARNLAIDR   81 (182)
T ss_pred             HHHHHHHhcchHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHhhc-CC-CCchHHHHHHHHHHHHHHH
Confidence            456778899999999999999999999999999998899999999999999999999 33 3489999999999999999


Q ss_pred             HHhhcCcccCCcchHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCccccCCCCccccc
Q 046578          210 IANKSRTIRLPGSMAGMVAKIAEANNVLSRRLRRMPTDSEIAEMLNIHVSTVRLAIERTRHPISLDGAVTDRGCMTMQDI  289 (379)
Q Consensus       210 lr~~~r~irip~~~~~~~~ki~~a~~~l~~~lgr~pt~~eia~~Lgis~~~~~~~l~~~~~~iSLd~~~~~~~~~~l~d~  289 (379)
                      +|+.++....                                                      .+.    .+.   .+.
T Consensus        82 ~R~~~r~~~~------------------------------------------------------~~~----~~~---~~~  100 (182)
T COG1595          82 LRKRKRRRAR------------------------------------------------------VEE----ADL---LPE  100 (182)
T ss_pred             HHHhcccccc------------------------------------------------------ccc----ccc---ccc
Confidence            9987642110                                                      000    000   000


Q ss_pred             CCCCCCCChHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHH
Q 046578          290 IPGPDETMPERMVQKQLMKQELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQTN  369 (379)
Q Consensus       290 i~~~~~~~pe~~~~~~e~~~~L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~~l  369 (379)
                      ......... +.+...+....+..+|..||+++|++|.|+|+    +|+|++|||+.||||.+||+++++||+++||+.+
T Consensus       101 ~~~~~~~~~-~~~~~~~~~~~l~~al~~Lp~~~R~~~~l~~~----~gls~~EIA~~l~i~~~tVks~l~ra~~~l~~~l  175 (182)
T COG1595         101 EADPAPDLA-ELLLAEEELERLRRALARLPPRQREAFLLRYL----EGLSYEEIAEILGISVGTVKSRLHRARKKLREQL  175 (182)
T ss_pred             ccCcccccc-hHHHHHHHHHHHHHHHHhCCHHHhHHhhhHhh----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence            000000000 24555666788999999999999999999994    7799999999999999999999999999999998


Q ss_pred             hhc
Q 046578          370 ILN  372 (379)
Q Consensus       370 ~~~  372 (379)
                      ...
T Consensus       176 ~~~  178 (182)
T COG1595         176 EEA  178 (182)
T ss_pred             hhc
Confidence            754

>PRK12522 RNA polymerase sigma factor; Provisional

Probab=99.90  E-value=1e-22  Score=181.28  Aligned_cols=167  Identities=15%  Similarity=0.160  Sum_probs=130.8

Q ss_pred             HHHHHHHHHhHHHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHhccCCCCCCCchhHHHHHHHHHHHHHHHhhcCcccCC
Q 046578          141 ESQERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYWWIKQAIIRAIANKSRTIRLP  220 (379)
Q Consensus       141 ~A~e~Li~~y~~lV~~ia~r~~~~~~d~eDLvQEg~i~L~~ai~~fD~~~g~~FsTYa~~~Ir~~i~~~lr~~~r~irip  220 (379)
                      ..+++++..|.++|+.+|+++.++..++||++||+|+.+|+++++|++..  +|.+|++.+++|.+.+++|++.+....+
T Consensus         3 ~~~~~l~~~y~~~i~~~~~~~~~~~~daeDvvQe~~i~l~~~~~~~~~~~--~~~~wl~~i~~n~~~d~~Rk~~~~~~~~   80 (173)
T PRK12522          3 EKVEELIDIYKQQIYSLCYKLAKTKEDAEDIFQETWIKVFSSRHQLSYVE--NYKKWITTICVRTFYDFYRKKKRWKDRI   80 (173)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHcCCcc--chHHHHHHHHHHHHHHHHHHhccccccc
Confidence            46899999999999999999999999999999999999999999998753  7999999999999999999866310000


Q ss_pred             cchHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCccccCCCCcccccCCCCCCCChHH
Q 046578          221 GSMAGMVAKIAEANNVLSRRLRRMPTDSEIAEMLNIHVSTVRLAIERTRHPISLDGAVTDRGCMTMQDIIPGPDETMPER  300 (379)
Q Consensus       221 ~~~~~~~~ki~~a~~~l~~~lgr~pt~~eia~~Lgis~~~~~~~l~~~~~~iSLd~~~~~~~~~~l~d~i~~~~~~~pe~  300 (379)
                      ..                                                  ..+.    +.   ..+.........++.
T Consensus        81 ~~--------------------------------------------------~~~~----~~---~~~~~~~~~~~~~~~  103 (173)
T PRK12522         81 LD--------------------------------------------------LFHK----ED---GGEIEFADDVNISEE  103 (173)
T ss_pred             cc--------------------------------------------------ccch----hh---hhhhccccCCCChHH
Confidence            00                                                  0000    00   000000011112333


Q ss_pred             HHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHHhh
Q 046578          301 MVQKQLMKQELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQTNIL  371 (379)
Q Consensus       301 ~~~~~e~~~~L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~~l~~  371 (379)
                       ....+..+.+..++..||+++++||.++|.    +|+|++|||+.||+|.++|+.+++||+++||+.+..
T Consensus       104 -~~~~~~~~~l~~~l~~L~~~~r~i~~l~~~----~~~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~l~~  169 (173)
T PRK12522        104 -FIQKVEAEMIREVIQLLNEKYKTVLVLYYY----EQYSYKEMSEILNIPIGTVKYRLNYAKKQMREHLEG  169 (173)
T ss_pred             -HHHHHHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHHH
Confidence             444556678999999999999999999984    779999999999999999999999999999999754

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

Probab=99.90  E-value=4.4e-23  Score=186.86  Aligned_cols=177  Identities=16%  Similarity=0.149  Sum_probs=134.0

Q ss_pred             HhcccHHHHHHHHHHhHHHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHhccCCCCCCCchhHHHHHHHHHHHHHHHhhc
Q 046578          135 ILCKERESQERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYWWIKQAIIRAIANKS  214 (379)
Q Consensus       135 ~~~Gd~~A~e~Li~~y~~lV~~ia~r~~~~~~d~eDLvQEg~i~L~~ai~~fD~~~g~~FsTYa~~~Ir~~i~~~lr~~~  214 (379)
                      ...++..+|+.|+..|.+.|+.+|.+++++..++||++||+|+.+|+.+.+|++.  .+|.+|++++++|.+++++|++.
T Consensus         5 ~~~~~~~~f~~l~~~~~~~l~~~~~~~~~~~~~AEDlvQevfl~~~~~~~~~~~~--~~~~~wL~~iarN~~~d~~Rk~~   82 (193)
T TIGR02947         5 TKTQRAQRFERDALEYLDQLYGAALRMTRNPADAEDLVQEAYAKAFSSFHQFKPG--TNLKAWLYRILTNTYINSYRKAQ   82 (193)
T ss_pred             hhhhhHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhhcccCCC--CcchHHHHHHHHHHHHHHHHHhc
Confidence            4457789999999999999999999999999999999999999999999999864  37999999999999999999865


Q ss_pred             CcccCCcchHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCccccCCCCcccccCCCCC
Q 046578          215 RTIRLPGSMAGMVAKIAEANNVLSRRLRRMPTDSEIAEMLNIHVSTVRLAIERTRHPISLDGAVTDRGCMTMQDIIPGPD  294 (379)
Q Consensus       215 r~irip~~~~~~~~ki~~a~~~l~~~lgr~pt~~eia~~Lgis~~~~~~~l~~~~~~iSLd~~~~~~~~~~l~d~i~~~~  294 (379)
                      +.....                                                     ......+.......+ .....
T Consensus        83 ~~~~~~-----------------------------------------------------~~~~~~~~~~~~~~~-~~~~~  108 (193)
T TIGR02947        83 RRPQQS-----------------------------------------------------DDDDIEDWQLAKAAS-HTSNG  108 (193)
T ss_pred             CCcccc-----------------------------------------------------cchhhhhhhhccccc-ccccc
Confidence            311000                                                     000000000000000 00001


Q ss_pred             CCChHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHHhh
Q 046578          295 ETMPERMVQKQLMKQELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQTNIL  371 (379)
Q Consensus       295 ~~~pe~~~~~~e~~~~L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~~l~~  371 (379)
                      ...++......+....|..+|.+||+++|+||.|+|+    +|+|++|||+.||+|.++|+++++||+++||+.+..
T Consensus       109 ~~~~e~~~~~~~~~~~l~~~l~~Lp~~~r~i~~L~~~----~g~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~l~~  181 (193)
T TIGR02947       109 LRSAELEALDGLPDQDIKDALQGLPEEFRQAVYLADV----EGFAYKEIAEIMGTPIGTVMSRLHRGRKQLRKQLVD  181 (193)
T ss_pred             ccchhHHHHhhhhHHHHHHHHHhCCHHHhhheeehhh----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH
Confidence            1123333333344567899999999999999999984    779999999999999999999999999999999864

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.

>PRK12523 RNA polymerase sigma factor; Reviewed

Probab=99.90  E-value=4.3e-23  Score=183.53  Aligned_cols=167  Identities=15%  Similarity=0.093  Sum_probs=132.4

Q ss_pred             HhcccHHHHHHHHHHhHHHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHhccCCCCCCCchhHHHHHHHHHHHHHHHhhc
Q 046578          135 ILCKERESQERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYWWIKQAIIRAIANKS  214 (379)
Q Consensus       135 ~~~Gd~~A~e~Li~~y~~lV~~ia~r~~~~~~d~eDLvQEg~i~L~~ai~~fD~~~g~~FsTYa~~~Ir~~i~~~lr~~~  214 (379)
                      .++||..++..+|..|.+.|+.+|.+++++..++||++||+|+.+|+. ..|...  ..|.+|++++++|.+++++|++.
T Consensus         4 ~~~~~~~a~~~l~~~~~~~l~~~~~~~~~~~~~AeDlvQevflk~~~~-~~~~~~--~~~~~wL~~Iarn~~~d~~Rk~~   80 (172)
T PRK12523          4 AQSPHSELVGALYRDHRGWLLAWLRRNVACRQRAEDLSQDTFVRLLGR-PELPTP--REPRAFLAAVAKGLMFDHFRRAA   80 (172)
T ss_pred             CCCCCcHHHHHHHHHHHHHHHHHHHHHcCCHhhHHHHHHHHHHHHHcc-cccCcc--hhHHHHHHHHHHHHHHHHHHHHH
Confidence            478999999999999999999999999999999999999999999986 456543  37999999999999999999854


Q ss_pred             CcccCCcchHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCccccCCCCcccccCCCCC
Q 046578          215 RTIRLPGSMAGMVAKIAEANNVLSRRLRRMPTDSEIAEMLNIHVSTVRLAIERTRHPISLDGAVTDRGCMTMQDIIPGPD  294 (379)
Q Consensus       215 r~irip~~~~~~~~ki~~a~~~l~~~lgr~pt~~eia~~Lgis~~~~~~~l~~~~~~iSLd~~~~~~~~~~l~d~i~~~~  294 (379)
                      +..           .       ....                                 +..             .....
T Consensus        81 ~~~-----------~-------~~~~---------------------------------~~~-------------~~~~~   96 (172)
T PRK12523         81 LEQ-----------A-------YLAE---------------------------------LAL-------------VPEAE   96 (172)
T ss_pred             HHH-----------H-------HHHH---------------------------------Hhh-------------ccccc
Confidence            200           0       0000                                 000             00001


Q ss_pred             CCChHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHHhhc
Q 046578          295 ETMPERMVQKQLMKQELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQTNILN  372 (379)
Q Consensus       295 ~~~pe~~~~~~e~~~~L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~~l~~~  372 (379)
                      ...|+......+....+..+|..||+++|.||.|+|+    +|+|++|||+.||+|.++|+++++||+++||..+..+
T Consensus        97 ~~~~~~~~~~~~~~~~l~~~l~~Lp~~~r~v~~L~~~----~g~s~~EIA~~lgis~~tV~~~l~ra~~~~~~~l~~~  170 (172)
T PRK12523         97 QPSPEEQHLILEDLKAIDRLLGKLSSKARAAFLYNRL----DGMGHAEIAERLGVSVSRVRQYLAQGLRQCYIALYGE  170 (172)
T ss_pred             CCChHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHhcCC
Confidence            1234444444444567999999999999999999995    7799999999999999999999999999999988654

>PRK12516 RNA polymerase sigma factor; Provisional

Probab=99.90  E-value=1.6e-22  Score=182.76  Aligned_cols=163  Identities=12%  Similarity=0.181  Sum_probs=130.3

Q ss_pred             cccHHHHHHHHHHhHHHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHhccCCCCCCCchhHHHHHHHHHHHHHHHhhcCc
Q 046578          137 CKERESQERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYWWIKQAIIRAIANKSRT  216 (379)
Q Consensus       137 ~Gd~~A~e~Li~~y~~lV~~ia~r~~~~~~d~eDLvQEg~i~L~~ai~~fD~~~g~~FsTYa~~~Ir~~i~~~lr~~~r~  216 (379)
                      -||..+++++|..|.+.++.+|.+++++..++||++||+|+.+|+..++|+..  ..|.+|++++++|.+++++|++.+.
T Consensus         6 ~~~~~~f~~l~~~~~~~L~~~a~~~~~~~~~AEDivQevfl~~~~~~~~~~~~--~~~~awL~~Ia~n~~~d~~R~~~~~   83 (187)
T PRK12516          6 VEGTPPFKRELLAALPSLRAFAVSLIGRHDRADDLVQDTIMKAWAKQDHFEVG--TNMKAWLFTILRNEFYSQMRKRGRE   83 (187)
T ss_pred             cccHHHHHHHHHHHHHHHHHHHHHHcCCHhHHHHHHHHHHHHHHHhhhccCCc--ccHHHHHHHHHHHHHHHHHHhhcCC
Confidence            36889999999999999999999999999999999999999999999999854  3699999999999999999986531


Q ss_pred             ccCCcchHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCccccCCCCcccccCCCCCCC
Q 046578          217 IRLPGSMAGMVAKIAEANNVLSRRLRRMPTDSEIAEMLNIHVSTVRLAIERTRHPISLDGAVTDRGCMTMQDIIPGPDET  296 (379)
Q Consensus       217 irip~~~~~~~~ki~~a~~~l~~~lgr~pt~~eia~~Lgis~~~~~~~l~~~~~~iSLd~~~~~~~~~~l~d~i~~~~~~  296 (379)
                      .                                                      ...+..        ..+....  .+
T Consensus        84 ~------------------------------------------------------~~~~~~--------~~~~~~~--~~   99 (187)
T PRK12516         84 V------------------------------------------------------QDTDGM--------FTEQLAV--HP   99 (187)
T ss_pred             c------------------------------------------------------cccccc--------cccccCC--Cc
Confidence            0                                                      000000        0000000  00


Q ss_pred             ChHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHHhhch
Q 046578          297 MPERMVQKQLMKQELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQTNILNN  373 (379)
Q Consensus       297 ~pe~~~~~~e~~~~L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~~l~~~~  373 (379)
                      ...    .......+..+|..||+++|+||.|+|+    +|+|++|||+.||+|.++|+++++||+++||+.+...+
T Consensus       100 ~~~----~~~~~~~l~~~L~~Lp~~~r~i~~L~~~----~g~s~~EIA~~Lgis~~tVk~~l~Rar~~Lr~~l~~~~  168 (187)
T PRK12516        100 SQY----GTLDLQDFRAALDQLPDDQREAIILVGA----SGFAYEEAAEICGCAVGTIKSRVNRARQRLQEILQIEG  168 (187)
T ss_pred             chh----hHHHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHhhc
Confidence            111    1112346889999999999999999984    77999999999999999999999999999999997654

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

Probab=99.90  E-value=1.1e-22  Score=178.77  Aligned_cols=160  Identities=14%  Similarity=0.131  Sum_probs=130.1

Q ss_pred             hcccHHHHHHHHHHhHHHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHhccCCCCCCCchhHHHHHHHHHHHHHHHhhcC
Q 046578          136 LCKERESQERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYWWIKQAIIRAIANKSR  215 (379)
Q Consensus       136 ~~Gd~~A~e~Li~~y~~lV~~ia~r~~~~~~d~eDLvQEg~i~L~~ai~~fD~~~g~~FsTYa~~~Ir~~i~~~lr~~~r  215 (379)
                      ++||..+++.+|..|.+.|+.++.++.++..+++|++||+|+.+|+.+++|+.  ...|.+|++.+++|.+++++|+..+
T Consensus         1 ~~~~~~~~~~l~~~~~~~l~~~~~~~~~~~~~aeDivQe~f~~~~~~~~~~~~--~~~~~~wl~~i~~n~~~d~~rk~~~   78 (162)
T TIGR02983         1 RSATEEEFTAFVAARYPRLLRTAYLLTGDPHEAEDLVQEALVRTYVRWDRIRD--PDAPDAYVRRVLVNLARSRWRRRRL   78 (162)
T ss_pred             CCCcHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHhhcCC--cccHHHHHHHHHHHHHHHHHHhhcc
Confidence            37999999999999999999999999999999999999999999999999964  3489999999999999999997652


Q ss_pred             cccCCcchHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCccccCCCCcccccCCCCCC
Q 046578          216 TIRLPGSMAGMVAKIAEANNVLSRRLRRMPTDSEIAEMLNIHVSTVRLAIERTRHPISLDGAVTDRGCMTMQDIIPGPDE  295 (379)
Q Consensus       216 ~irip~~~~~~~~ki~~a~~~l~~~lgr~pt~~eia~~Lgis~~~~~~~l~~~~~~iSLd~~~~~~~~~~l~d~i~~~~~  295 (379)
                      . .                                                     ...+.         ..+   . ..
T Consensus        79 ~-~-----------------------------------------------------~~~~~---------~~~---~-~~   91 (162)
T TIGR02983        79 L-E-----------------------------------------------------LPTRE---------LPD---A-AA   91 (162)
T ss_pred             c-c-----------------------------------------------------ccccc---------cCc---c-cC
Confidence            0 0                                                     00000         000   0 00


Q ss_pred             CChHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHHhh
Q 046578          296 TMPERMVQKQLMKQELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQTNIL  371 (379)
Q Consensus       296 ~~pe~~~~~~e~~~~L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~~l~~  371 (379)
                         .+.....+....|..++..||+++|+||.++|+    +|+|++|||+.||+|.++|+++++||+++||+.+..
T Consensus        92 ---~~~~~~~~~~~~l~~~l~~L~~~~r~i~~l~~~----~g~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~l~~  160 (162)
T TIGR02983        92 ---PDPAPDVALRAALARALRRLPARQRAVVVLRYY----EDLSEAQVAEALGISVGTVKSRLSRALARLRELLEE  160 (162)
T ss_pred             ---CccchhHHHHHHHHHHHHhCCHHHHHHhhhHHH----hcCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhcC
Confidence               001122334466889999999999999999984    679999999999999999999999999999998754

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.

>PRK12533 RNA polymerase sigma factor; Provisional

Probab=99.90  E-value=2.6e-22  Score=185.33  Aligned_cols=173  Identities=13%  Similarity=0.133  Sum_probs=137.9

Q ss_pred             cccHHHHHHHHHHhHHHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHhccCCCCCCCchhHHHHHHHHHHHHHHHhhcCc
Q 046578          137 CKERESQERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYWWIKQAIIRAIANKSRT  216 (379)
Q Consensus       137 ~Gd~~A~e~Li~~y~~lV~~ia~r~~~~~~d~eDLvQEg~i~L~~ai~~fD~~~g~~FsTYa~~~Ir~~i~~~lr~~~r~  216 (379)
                      .....+++.||..|.+.+++++.++.++..++||++||+|+.+|+.+++|++  + .|.+|++++++|.+++++|++.+.
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            3567899999999999999999999999999999999999999999999975  2 599999999999999999986531


Q ss_pred             ccCCcchHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCccccCCCCcccccCCCCCCC
Q 046578          217 IRLPGSMAGMVAKIAEANNVLSRRLRRMPTDSEIAEMLNIHVSTVRLAIERTRHPISLDGAVTDRGCMTMQDIIPGPDET  296 (379)
Q Consensus       217 irip~~~~~~~~ki~~a~~~l~~~lgr~pt~~eia~~Lgis~~~~~~~l~~~~~~iSLd~~~~~~~~~~l~d~i~~~~~~  296 (379)
                      ...                                                    ...+. ..+..  .... . .+...
T Consensus        91 ~~~----------------------------------------------------~~~~~-~~~~~--~~~~-~-~~~~~  113 (216)
T PRK12533         91 HEV----------------------------------------------------AAPDT-LDDAD--SLDD-W-QPAGE  113 (216)
T ss_pred             ccc----------------------------------------------------ccccc-ccccc--cccc-c-ccCCC
Confidence            000                                                    00000 00000  0000 0 11123


Q ss_pred             ChHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHHhhch
Q 046578          297 MPERMVQKQLMKQELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQTNILNN  373 (379)
Q Consensus       297 ~pe~~~~~~e~~~~L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~~l~~~~  373 (379)
                      +|++.+...+....|..+|..||+++|+||.|+|+    +++|++|||+.||||.++|+++++||+++||+.+....
T Consensus       114 ~~e~~~~~~e~~~~l~~al~~Lp~~~R~v~~L~y~----eg~s~~EIAe~LgiS~~tVk~~L~RAr~~Lr~~l~~~~  186 (216)
T PRK12533        114 DPLALLLRAEDVRLVNAALAKLPVEYREVLVLREL----EDMSYREIAAIADVPVGTVMSRLARARRRLAALLGGAS  186 (216)
T ss_pred             CHHHHHHHHHHHHHHHHHHHcCCHHHHhHhhhHHh----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHcccc
Confidence            56777777777888999999999999999999984    77999999999999999999999999999999986543

>PRK08241 RNA polymerase factor sigma-70; Validated

Probab=99.90  E-value=2.9e-22  Score=196.88  Aligned_cols=183  Identities=19%  Similarity=0.236  Sum_probs=142.2

Q ss_pred             HHHHHHHHhcccHHHHHHHHHHhHHHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHhccCCCCCCCchhHHHHHHHHHHH
Q 046578          128 YNLVKYKILCKERESQERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYWWIKQAII  207 (379)
Q Consensus       128 ~~eLi~~~~~Gd~~A~e~Li~~y~~lV~~ia~r~~~~~~d~eDLvQEg~i~L~~ai~~fD~~~g~~FsTYa~~~Ir~~i~  207 (379)
                      ..+|+.++++||..++++||+.|.+.|+++|.+++++..++||++||+|+.+|+.+++|++.  .+|.+|++++++|.++
T Consensus         6 ~~~l~~~~~~gd~~af~~l~~~y~~~l~~~~~~~~~~~~dAEDivQevfl~~~~~~~~~~~~--~~~~~wL~~Ia~n~~~   83 (339)
T PRK08241          6 AAALLARAAAGDRDAFAALVEPHRRELLAHCYRMLGSVHDAEDAVQETLLRAWRGYDRFEGR--SSLRTWLYRIATNVCL   83 (339)
T ss_pred             HHHHHHHhhcCCHHHHHHHHHHHHHHHHHHHHHHhCChhhHHHHHHHHHHHHHhhhhccccc--cchHHHHHHHHHHHHH
Confidence            36899999999999999999999999999999999999999999999999999999999853  3799999999999999


Q ss_pred             HHHHhhcCcccCCcchHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCccccC-C----
Q 046578          208 RAIANKSRTIRLPGSMAGMVAKIAEANNVLSRRLRRMPTDSEIAEMLNIHVSTVRLAIERTRHPISLDGAVTDR-G----  282 (379)
Q Consensus       208 ~~lr~~~r~irip~~~~~~~~ki~~a~~~l~~~lgr~pt~~eia~~Lgis~~~~~~~l~~~~~~iSLd~~~~~~-~----  282 (379)
                      +++|++.+... +                                                   ...+.+..+. +    
T Consensus        84 d~~Rk~~~~~~-~---------------------------------------------------~~~~~~~~~~~~~~~~  111 (339)
T PRK08241         84 DALEGRARRPL-P---------------------------------------------------TDLGAPAADPVDELVE  111 (339)
T ss_pred             HHHHhhccccC-c---------------------------------------------------cccCCCcCcccccccc
Confidence            99998653100 0                                                   0000000000 0    


Q ss_pred             --CCcccccCCC----CCCCChHHHHHHHH-HHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHH
Q 046578          283 --CMTMQDIIPG----PDETMPERMVQKQL-MKQELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIR  355 (379)
Q Consensus       283 --~~~l~d~i~~----~~~~~pe~~~~~~e-~~~~L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr  355 (379)
                        ...+.+.+.+    ....+|++.+...+ ....+..+|.+||+++|+||.|+|+    +|+|++|||+.||+|.++|+
T Consensus       112 ~~~~~~~~~~~~~~~~~~~~~~e~~~~~~e~~~~~l~~~l~~Lp~~~R~v~~L~~~----~g~s~~EIA~~lgis~~tVk  187 (339)
T PRK08241        112 RPEVPWLEPYPDALLDPAAADPAARVVARESVRLAFVAALQHLPPRQRAVLILRDV----LGWSAAEVAELLDTSVAAVN  187 (339)
T ss_pred             cccccccCCCCcccccccCCChHHHHHHHHHHHHHHHHHHHhCCHHHhhhhhhHHh----hCCCHHHHHHHhCCCHHHHH
Confidence              0001111111    01235666555444 3456889999999999999999994    77999999999999999999


Q ss_pred             HHHHHHHHHHHhH
Q 046578          356 QIRGIALTKLQQT  368 (379)
Q Consensus       356 ~~~~rAl~kLR~~  368 (379)
                      ++++||+++||+.
T Consensus       188 ~~l~RAr~~Lr~~  200 (339)
T PRK08241        188 SALQRARATLAER  200 (339)
T ss_pred             HHHHHHHHHHhhc
Confidence            9999999999993

>PRK09647 RNA polymerase sigma factor SigE; Reviewed

Probab=99.90  E-value=4.4e-22  Score=182.17  Aligned_cols=167  Identities=20%  Similarity=0.267  Sum_probs=137.8

Q ss_pred             hcccHHHHHHHHHHhHHHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHhccCCCCCCCchhHHHHHHHHHHHHHHHhhcC
Q 046578          136 LCKERESQERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYWWIKQAIIRAIANKSR  215 (379)
Q Consensus       136 ~~Gd~~A~e~Li~~y~~lV~~ia~r~~~~~~d~eDLvQEg~i~L~~ai~~fD~~~g~~FsTYa~~~Ir~~i~~~lr~~~r  215 (379)
                      ..||..+++++|..|.+.|+.++.++.++..++||++||+|+.+|+...+|++  + +|.+|++++++|.+++++|+..+
T Consensus        23 ~~~d~~a~~~l~~~~~~~L~~~~~~~~~~~~~AEDivQEvflkl~~~~~~~~~--~-~~~~wL~~iarn~~~d~~Rk~~~   99 (203)
T PRK09647         23 DKATMPSWEELVRQHADRVYRLAYRLSGNQHDAEDLTQETFIRVFRSLQNYQP--G-TFEGWLHRITTNLFLDMVRRRAR   99 (203)
T ss_pred             CCCCHHHHHHHHHHHHHHHHHHHHHHhCCHhHHHHHHHHHHHHHHHhHHhcCC--c-ccHHHHHHHHHHHHHHHHHhccc
Confidence            45899999999999999999999999999999999999999999999999974  3 69999999999999999998642


Q ss_pred             cccCCcchHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCccccCCCCcccccCCCCCC
Q 046578          216 TIRLPGSMAGMVAKIAEANNVLSRRLRRMPTDSEIAEMLNIHVSTVRLAIERTRHPISLDGAVTDRGCMTMQDIIPGPDE  295 (379)
Q Consensus       216 ~irip~~~~~~~~ki~~a~~~l~~~lgr~pt~~eia~~Lgis~~~~~~~l~~~~~~iSLd~~~~~~~~~~l~d~i~~~~~  295 (379)
                       .+.                                                    ..++.     +   . +... ...
T Consensus       100 -~~~----------------------------------------------------~~~~~-----~---~-~~~~-~~~  116 (203)
T PRK09647        100 -IRM----------------------------------------------------EALPE-----D---Y-DRVP-GDE  116 (203)
T ss_pred             -Ccc----------------------------------------------------ccccc-----c---c-cccC-CCC
Confidence             000                                                    00000     0   0 0011 122


Q ss_pred             CChHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHHhhc
Q 046578          296 TMPERMVQKQLMKQELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQTNILN  372 (379)
Q Consensus       296 ~~pe~~~~~~e~~~~L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~~l~~~  372 (379)
                      .+|+..+...+....|..+|..||++++.||.|+|+    +|++++|||+.||+|.++|++.++||+++||+.+...
T Consensus       117 ~~~~~~~~~~~~~~~l~~~L~~L~~~~r~v~~L~~~----~g~s~~EIA~~Lgis~~tV~~~l~RArk~Lr~~l~~~  189 (203)
T PRK09647        117 PNPEQIYHDARLDPDLQAALDSLPPEFRAAVVLCDI----EGLSYEEIAATLGVKLGTVRSRIHRGRQQLRAALAAH  189 (203)
T ss_pred             CCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHh
Confidence            355666667777778999999999999999999985    7799999999999999999999999999999998653

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

Probab=99.90  E-value=1.3e-22  Score=177.56  Aligned_cols=159  Identities=13%  Similarity=0.184  Sum_probs=125.6

Q ss_pred             HHHHHHHHHhHHHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHhccCCCCCCCchhHHHHHHHHHHHHHHHhhcCcccCC
Q 046578          141 ESQERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYWWIKQAIIRAIANKSRTIRLP  220 (379)
Q Consensus       141 ~A~e~Li~~y~~lV~~ia~r~~~~~~d~eDLvQEg~i~L~~ai~~fD~~~g~~FsTYa~~~Ir~~i~~~lr~~~r~irip  220 (379)
                      ++++.++..|.|.|+++++++.++..++||++||+|+.+|+++++|++..  .|.+|++++++|.+++++|++.+... +
T Consensus         1 ~~~~~~~~~~~~~l~~~~~~~~~~~~~aEDivQe~~l~l~~~~~~~~~~~--~~~~wl~~i~~n~~~d~~r~~~~~~~-~   77 (159)
T TIGR02989         1 EAFAALLQRHQRSLRAFVRSLVPDRDDADDVLQETFVTAWRKFDEFDPGT--DFGAWARGIARNKVLNHRRKLGRDRL-V   77 (159)
T ss_pred             CHHHHHHHHhHHHHHHHHHHHcCChhhHHHHHHHHHHHHHHHHHhCCCCC--chHHHHHHHHHHHHHHHHHHhccccc-c
Confidence            37899999999999999999999999999999999999999999998653  69999999999999999998763110 0


Q ss_pred             cchHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCccccCCCCcccccCCCCCCCChHH
Q 046578          221 GSMAGMVAKIAEANNVLSRRLRRMPTDSEIAEMLNIHVSTVRLAIERTRHPISLDGAVTDRGCMTMQDIIPGPDETMPER  300 (379)
Q Consensus       221 ~~~~~~~~ki~~a~~~l~~~lgr~pt~~eia~~Lgis~~~~~~~l~~~~~~iSLd~~~~~~~~~~l~d~i~~~~~~~pe~  300 (379)
                                                                           ++..        ..+.+.+..  ++.+
T Consensus        78 -----------------------------------------------------~~~~--------~~~~~~~~~--~~~~   94 (159)
T TIGR02989        78 -----------------------------------------------------FDDE--------LLEALAAEA--EATE   94 (159)
T ss_pred             -----------------------------------------------------cCHH--------HHHHHHhhc--ccch
Confidence                                                                 0000        000000000  1111


Q ss_pred             HHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHH
Q 046578          301 MVQKQLMKQELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQTN  369 (379)
Q Consensus       301 ~~~~~e~~~~L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~~l  369 (379)
                      .....+....+..+++.||++++.||.++|+    +|+|++|||+.||+|.++|++.++||+++||+++
T Consensus        95 ~~~~~~~~~~l~~~i~~L~~~~r~v~~l~~~----~g~~~~eIA~~l~is~~tv~~~l~Rar~~Lr~~~  159 (159)
T TIGR02989        95 ADRSEDELQALEGCLEKLPERQRELLQLRYQ----RGVSLTALAEQLGRTVNAVYKALSRLRVRLRDCV  159 (159)
T ss_pred             HhhHHHHHHHHHHHHHHCCHHHHHHHHHHHh----cCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhcC
Confidence            1223334467889999999999999999884    6799999999999999999999999999999864

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).

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

Probab=99.89  E-value=1.7e-22  Score=176.15  Aligned_cols=161  Identities=17%  Similarity=0.214  Sum_probs=129.7

Q ss_pred             HHHHHHHHHhHHHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHhccCCCCCCCchhHHHHHHHHHHHHHHHhhcCcccCC
Q 046578          141 ESQERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYWWIKQAIIRAIANKSRTIRLP  220 (379)
Q Consensus       141 ~A~e~Li~~y~~lV~~ia~r~~~~~~d~eDLvQEg~i~L~~ai~~fD~~~g~~FsTYa~~~Ir~~i~~~lr~~~r~irip  220 (379)
                      .|+++|+..|.|.|+++++++.++..++||++||+|+++|+++++|++.  .+|.+|++.++++.+.+++++..+...  
T Consensus         1 ~a~~~l~~~~~~~l~~~~~~~~~~~~~aeD~~Qe~~~~~~~~~~~~~~~--~~~~~wl~~i~r~~~~d~~r~~~~~~~--   76 (161)
T TIGR02985         1 KAFEQLYRRYYPKLCAFAYRYVKDEEEAEDIVQDVFVKLWENRETLEEV--ESFKAYLFTIVKNRSLNYLRHKQVEEK--   76 (161)
T ss_pred             ChHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhHHhcccc--ccHHHHHHHHHHHHHHHHHHHHHhHhH--
Confidence            3789999999999999999999998999999999999999999999864  379999999999999999997652000  


Q ss_pred             cchHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCccccCCCCcccccCCCCCCCChHH
Q 046578          221 GSMAGMVAKIAEANNVLSRRLRRMPTDSEIAEMLNIHVSTVRLAIERTRHPISLDGAVTDRGCMTMQDIIPGPDETMPER  300 (379)
Q Consensus       221 ~~~~~~~~ki~~a~~~l~~~lgr~pt~~eia~~Lgis~~~~~~~l~~~~~~iSLd~~~~~~~~~~l~d~i~~~~~~~pe~  300 (379)
                                      ....                                 +    .+...       ......++++
T Consensus        77 ----------------~~~~---------------------------------~----~~~~~-------~~~~~~~~~~   96 (161)
T TIGR02985        77 ----------------YQEE---------------------------------I----LEIEV-------DELSENDPEE   96 (161)
T ss_pred             ----------------HHHH---------------------------------H----Hhhcc-------cccCCCCcHH
Confidence                            0000                                 0    00000       0001124555


Q ss_pred             HHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHH
Q 046578          301 MVQKQLMKQELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQTN  369 (379)
Q Consensus       301 ~~~~~e~~~~L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~~l  369 (379)
                      .+...+....+..++..||+++++||.++|.    +|+|.+|||+.||+|+++|+++++||+++||+.|
T Consensus        97 ~~~~~e~~~~l~~~l~~L~~~~r~il~l~~~----~~~~~~eIA~~lgis~~tv~~~~~ra~~~Lr~~l  161 (161)
T TIGR02985        97 ELEAKELQLIIYKAIEKLPEQCRKIFILSRF----EGKSYKEIAEELGISVKTVEYHISKALKELRKEL  161 (161)
T ss_pred             HHHHHHHHHHHHHHHHHCCHHHHHHHHHHHH----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhhC
Confidence            6666677778999999999999999999884    6799999999999999999999999999999864

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.

>PRK09642 RNA polymerase sigma factor SigW; Reviewed

Probab=99.89  E-value=2.1e-22  Score=176.68  Aligned_cols=156  Identities=16%  Similarity=0.128  Sum_probs=125.8

Q ss_pred             HHhHHHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHhccCCCCCCCchhHHHHHHHHHHHHHHHhhcCcccCCcchHHHH
Q 046578          148 RSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYWWIKQAIIRAIANKSRTIRLPGSMAGMV  227 (379)
Q Consensus       148 ~~y~~lV~~ia~r~~~~~~d~eDLvQEg~i~L~~ai~~fD~~~g~~FsTYa~~~Ir~~i~~~lr~~~r~irip~~~~~~~  227 (379)
                      +.|.+.|+.+|.+++++..++||++||+|+.+|+++++|++.   .|.+|++++++|.++|++|+..+...         
T Consensus         2 ~~y~~~l~~~~~~~~~~~~~AeDlvQe~fl~~~~~~~~~~~~---~~~~wl~~ia~n~~~d~~Rk~~~~~~---------   69 (160)
T PRK09642          2 QTYRHYIFQVIFSILRHEEDAKDVTQEVFVKIHASLPNYQFR---GLKTWMARIATNHAIDYKRKKARENE---------   69 (160)
T ss_pred             chHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHhcccccccc---hhHHHHHHHHHHHHHHHHHHhccccc---------
Confidence            579999999999999999999999999999999999999852   59999999999999999998653100         


Q ss_pred             HHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCccccCCCCcccccCCCCCCCChHHHHHHHHH
Q 046578          228 AKIAEANNVLSRRLRRMPTDSEIAEMLNIHVSTVRLAIERTRHPISLDGAVTDRGCMTMQDIIPGPDETMPERMVQKQLM  307 (379)
Q Consensus       228 ~ki~~a~~~l~~~lgr~pt~~eia~~Lgis~~~~~~~l~~~~~~iSLd~~~~~~~~~~l~d~i~~~~~~~pe~~~~~~e~  307 (379)
                                                                 ......    +    ..+...  ....+++.+...+.
T Consensus        70 -------------------------------------------~~~~~~----~----~~~~~~--~~~~~~~~~~~~e~   96 (160)
T PRK09642         70 -------------------------------------------ELSLCK----E----TEENIK--SSHNIEDLLLTKEQ   96 (160)
T ss_pred             -------------------------------------------ccccch----h----hhhhcc--CCCChHHHHHHHHH
Confidence                                                       000000    0    000000  12245566666677


Q ss_pred             HHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHHhhc
Q 046578          308 KQELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQTNILN  372 (379)
Q Consensus       308 ~~~L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~~l~~~  372 (379)
                      ...+..+|+.||+.+|.||.++|+    +|+|++|||+.||+|.++|+++++||+++||+.+...
T Consensus        97 ~~~l~~~l~~Lp~~~r~v~~l~~~----~g~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~~~  157 (160)
T PRK09642         97 KLLIAQKLRELPENYRDVVLAHYL----EEKSYQEIALQEKIEVKTVEMKLYRARKWIKKHWKEE  157 (160)
T ss_pred             HHHHHHHHHhCCHHHHHHHHHHHH----hCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHhhh
Confidence            778999999999999999999994    7799999999999999999999999999999998654

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

Probab=99.89  E-value=5.9e-22  Score=193.37  Aligned_cols=184  Identities=17%  Similarity=0.181  Sum_probs=136.3

Q ss_pred             cccHHHHHHHHHHhHHHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHhccCCCCCCCchhHHHHHHHHHHHHHHHhhcCc
Q 046578          137 CKERESQERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYWWIKQAIIRAIANKSRT  216 (379)
Q Consensus       137 ~Gd~~A~e~Li~~y~~lV~~ia~r~~~~~~d~eDLvQEg~i~L~~ai~~fD~~~g~~FsTYa~~~Ir~~i~~~lr~~~r~  216 (379)
                      .||..++++||..|.+.|+++|.+++++..++||++||+|+.+|+.+++|+..  .+|.+|++++++|.++|++|++.+.
T Consensus         1 ~gd~~af~~l~~~~~~~l~~~a~~~~~~~~~AEDivQe~fl~~~~~~~~~~~~--~~~~~WL~~Ia~n~~~d~~Rk~~~~   78 (324)
T TIGR02960         1 SVDGAAFTALAEPHRRELLAHCYRMLGSLHEAEDLVQETLLRAWRARDRFEGR--SSVRTWLYRIATNACLDALEARQRR   78 (324)
T ss_pred             CCcHHHHHHHHHHHHHHHHHHHHHhcCChhhHHHHHHHHHHHHHhhhhccCcc--cchHHHHHHHHHHHHHHHHHhccCC
Confidence            48999999999999999999999999999999999999999999999999864  3799999999999999999986531


Q ss_pred             ccCCcchHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCccccCCCCcccccCC-----
Q 046578          217 IRLPGSMAGMVAKIAEANNVLSRRLRRMPTDSEIAEMLNIHVSTVRLAIERTRHPISLDGAVTDRGCMTMQDIIP-----  291 (379)
Q Consensus       217 irip~~~~~~~~ki~~a~~~l~~~lgr~pt~~eia~~Lgis~~~~~~~l~~~~~~iSLd~~~~~~~~~~l~d~i~-----  291 (379)
                      .......                                            ......... ..++......+.++     
T Consensus        79 ~~~~~~~--------------------------------------------~~~~~~~~~-~~~~~~~~~~~~~~~~~~~  113 (324)
T TIGR02960        79 PRPVGLG--------------------------------------------APSADGTAA-ASEAAEVTWLEPLPDLTLD  113 (324)
T ss_pred             cCccccC--------------------------------------------CCCCccccc-ccccccccccCCCCccccc
Confidence            1000000                                            000000000 00000000000000     


Q ss_pred             --CCCCCChHHHHHHHH-HHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhH
Q 046578          292 --GPDETMPERMVQKQL-MKQELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQT  368 (379)
Q Consensus       292 --~~~~~~pe~~~~~~e-~~~~L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~~  368 (379)
                        .....+|++.+...+ ....+..+|.+||+++|.||.|+|+    +++|++|||+.||+|.++|+++++||+++||++
T Consensus       114 ~~~~~~~~~~~~~~~~e~~~~~l~~~l~~Lp~~~R~v~~L~~~----~g~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~  189 (324)
T TIGR02960       114 LDDPAAADPSVAAGSRESVRLAFVAAIQYLPPRQRAVLLLRDV----LGWRAAETAELLGTSTASVNSALQRARATLDEV  189 (324)
T ss_pred             cccCCCCCHHHHHHHHHHHHHHHHHHHHhCCHHHhhHhhhHHH----hCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHh
Confidence              111235666555444 4456889999999999999999995    779999999999999999999999999999999


Q ss_pred             Hhh
Q 046578          369 NIL  371 (379)
Q Consensus       369 l~~  371 (379)
                      +..
T Consensus       190 l~~  192 (324)
T TIGR02960       190 GPS  192 (324)
T ss_pred             ccc
Confidence            874

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

>PRK09644 RNA polymerase sigma factor SigM; Provisional

Probab=99.89  E-value=6.2e-22  Score=174.83  Aligned_cols=158  Identities=15%  Similarity=0.127  Sum_probs=130.7

Q ss_pred             HHHHHHHhHHHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHhccCCCCCCCchhHHHHHHHHHHHHHHHhhcCcccCCcc
Q 046578          143 QERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYWWIKQAIIRAIANKSRTIRLPGS  222 (379)
Q Consensus       143 ~e~Li~~y~~lV~~ia~r~~~~~~d~eDLvQEg~i~L~~ai~~fD~~~g~~FsTYa~~~Ir~~i~~~lr~~~r~irip~~  222 (379)
                      ++.||+.|.|.|+++|+++.++..++||++||+|+.+|+++++|++.   .|.+|++++++|.+.+++|+..+.....  
T Consensus         3 ~~~l~~~y~~~l~~~~~~~~~~~~~AeDlvQe~fl~~~~~~~~~~~~---~~~~wL~~i~~n~~~d~~R~~~~~~~~~--   77 (165)
T PRK09644          3 IEEIYKMYINDVYRYLFSLTKSHHAAEDLLQETFYRAYIYLEDYDNQ---KVKPWLFKVAYHTFIDFVRKEKKVSFVG--   77 (165)
T ss_pred             HHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhHHhcccc---chHHHHHHHHHHHHHHHHHhhhhccccc--
Confidence            68899999999999999999999999999999999999999999852   6999999999999999999865310000  


Q ss_pred             hHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCccccCCCCcccccCCCCCCCChHHHH
Q 046578          223 MAGMVAKIAEANNVLSRRLRRMPTDSEIAEMLNIHVSTVRLAIERTRHPISLDGAVTDRGCMTMQDIIPGPDETMPERMV  302 (379)
Q Consensus       223 ~~~~~~ki~~a~~~l~~~lgr~pt~~eia~~Lgis~~~~~~~l~~~~~~iSLd~~~~~~~~~~l~d~i~~~~~~~pe~~~  302 (379)
                                                                               .+   .+ +.+.   ..+|++.+
T Consensus        78 ---------------------------------------------------------~~---~~-~~~~---~~~~~~~~   93 (165)
T PRK09644         78 ---------------------------------------------------------TD---EI-EAIQ---AESTEEYV   93 (165)
T ss_pred             ---------------------------------------------------------hh---HH-hhhc---ccChHHHH
Confidence                                                                     00   00 0000   12355555


Q ss_pred             HHHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHHhhch
Q 046578          303 QKQLMKQELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQTNILNN  373 (379)
Q Consensus       303 ~~~e~~~~L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~~l~~~~  373 (379)
                      ...+....+..++..||+++|++|.++|+    +|+|++|||+.||+|.++|+++++||+++||+.+....
T Consensus        94 ~~~~~~~~l~~~l~~L~~~~r~v~~l~~~----~g~s~~eIA~~lgis~~tv~~~l~Rar~~Lr~~l~~~~  160 (165)
T PRK09644         94 VAKNSYEKLIQIIHTLPVIEAQAILLCDV----HELTYEEAASVLDLKLNTYKSHLFRGRKRLKALLKEEK  160 (165)
T ss_pred             HHHHHHHHHHHHHHhCCHHHHHHHHhHHH----hcCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHhhh
Confidence            66666778999999999999999999984    77999999999999999999999999999999987554

>PRK12541 RNA polymerase sigma factor; Provisional

Probab=99.89  E-value=9.2e-22  Score=172.95  Aligned_cols=158  Identities=15%  Similarity=0.140  Sum_probs=125.8

Q ss_pred             ccHHHHHHHHHHhHHHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHhccCCCCCCCchhHHHHHHHHHHHHHHHhhcCcc
Q 046578          138 KERESQERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYWWIKQAIIRAIANKSRTI  217 (379)
Q Consensus       138 Gd~~A~e~Li~~y~~lV~~ia~r~~~~~~d~eDLvQEg~i~L~~ai~~fD~~~g~~FsTYa~~~Ir~~i~~~lr~~~r~i  217 (379)
                      |+..+++++|..|.+.|+.+|.++.++..++||++||+|+.+|+.+++|++.   +|.||++++++|.+++++|+..+..
T Consensus         2 ~~~~a~~~l~~~~~~~l~~~~~~~~~~~~~AeDv~Qe~f~~~~~~~~~~~~~---~~~~wl~~i~~n~~~d~~R~~~~~~   78 (161)
T PRK12541          2 KRKQSLEEIYSEHMQDLFRYLLSLTGDSHFAEDLMQETFYRMLVHIDYYKGE---EIRPWLFTIAYNAFIDWYRKEKKYK   78 (161)
T ss_pred             chHHHHHHHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHhHHHccCC---ChHHHHHHHHHHHHHHHHHhccccc
Confidence            6788999999999999999999999999999999999999999999999853   5999999999999999999865310


Q ss_pred             cCCcchHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCccccCCCCcccccCCCCCCCC
Q 046578          218 RLPGSMAGMVAKIAEANNVLSRRLRRMPTDSEIAEMLNIHVSTVRLAIERTRHPISLDGAVTDRGCMTMQDIIPGPDETM  297 (379)
Q Consensus       218 rip~~~~~~~~ki~~a~~~l~~~lgr~pt~~eia~~Lgis~~~~~~~l~~~~~~iSLd~~~~~~~~~~l~d~i~~~~~~~  297 (379)
                      .                                                     ...+.         . .  .......
T Consensus        79 ~-----------------------------------------------------~~~~~---------~-~--~~~~~~~   93 (161)
T PRK12541         79 T-----------------------------------------------------TTIEE---------F-H--LPNVPST   93 (161)
T ss_pred             c-----------------------------------------------------cchhh---------h-h--ccCCCCc
Confidence            0                                                     00000         0 0  0000111


Q ss_pred             hHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhH
Q 046578          298 PERMVQKQLMKQELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQT  368 (379)
Q Consensus       298 pe~~~~~~e~~~~L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~~  368 (379)
                      +++.....+. ..+..++..||+++|.||.|+|+    +|+|++|||+.||+|.++|++.++||+++||+.
T Consensus        94 ~~~~~~~~~~-~~~~~~l~~L~~~~r~v~~l~~~----~~~s~~eIA~~lgis~~tv~~~l~Rar~~L~~~  159 (161)
T PRK12541         94 EHEYFIKHEI-ASWLDSLSSLPLERRNVLLLRDY----YGFSYKEIAEMTGLSLAKVKIELHRGRKETKSI  159 (161)
T ss_pred             HHHHHHHhHH-HHHHHHHHHCCHHHHHHhhhHHh----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhh
Confidence            2222333333 34568899999999999999984    679999999999999999999999999999975

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

Probab=99.88  E-value=1.3e-21  Score=176.78  Aligned_cols=172  Identities=19%  Similarity=0.201  Sum_probs=134.2

Q ss_pred             HHHHHhHHHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHhccCCCCCCCchhHHHHHHHHHHHHHHHhhcCcccCCcchH
Q 046578          145 RIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYWWIKQAIIRAIANKSRTIRLPGSMA  224 (379)
Q Consensus       145 ~Li~~y~~lV~~ia~r~~~~~~d~eDLvQEg~i~L~~ai~~fD~~~g~~FsTYa~~~Ir~~i~~~lr~~~r~irip~~~~  224 (379)
                      +.+..|.+.|+.+|++++++..++||++||+|+.+|+...+|++.  .+|.+|++++++|.+++++|++.+....+    
T Consensus         6 ~~~~~~~~~l~~~~~~~~~~~~dAeDivQevfl~l~~~~~~~~~~--~~~~~wL~~iarn~~~d~~R~~~r~~~~~----   79 (188)
T TIGR02943         6 QELEQLRRDLLRFARLQLRDRDLAEDAVQETLLAALSHRDSFAGR--SALKTWLFAILKNKIIDALRAKGREVKVS----   79 (188)
T ss_pred             HHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhhhhhccc--cHHHHHHHHHHHHHHHHHHHhhcccCCcc----
Confidence            578899999999999999999999999999999999999999864  38999999999999999999866311110    


Q ss_pred             HHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCcccc--------CCCCcccccCCCCCCC
Q 046578          225 GMVAKIAEANNVLSRRLRRMPTDSEIAEMLNIHVSTVRLAIERTRHPISLDGAVTD--------RGCMTMQDIIPGPDET  296 (379)
Q Consensus       225 ~~~~ki~~a~~~l~~~lgr~pt~~eia~~Lgis~~~~~~~l~~~~~~iSLd~~~~~--------~~~~~l~d~i~~~~~~  296 (379)
                                                                      +++....+        +.+....+..++ ..+
T Consensus        80 ------------------------------------------------~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~  110 (188)
T TIGR02943        80 ------------------------------------------------DLDDELDDEAFNALFTQNGHWAQHGQPQ-HWN  110 (188)
T ss_pred             ------------------------------------------------ccccccccchhhhhhccccchhcccccc-ccC
Confidence                                                            00000000        000000011111 223


Q ss_pred             ChHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHHhhchhh
Q 046578          297 MPERMVQKQLMKQELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQTNILNNLK  375 (379)
Q Consensus       297 ~pe~~~~~~e~~~~L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~~l~~~~L~  375 (379)
                      .|+..+...+....+..+|.+||+++|+||.++|+    +|+|++|||+.||+|.++|+++++||+++||+++....+.
T Consensus       111 ~~e~~~~~~e~~~~l~~~l~~L~~~~r~v~~l~~~----~g~s~~EIA~~lgis~~tvk~rl~Rar~~Lr~~l~~~~~~  185 (188)
T TIGR02943       111 TPEKQLENKEFWEVFEACLYHLPEQTARVFMMREV----LGFESDEICQELEISTSNCHVLLYRARLSLRACLSINWFG  185 (188)
T ss_pred             CHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHH----hCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHHHHhhh
Confidence            56677777777788999999999999999999985    7799999999999999999999999999999999876553

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.

>PRK12545 RNA polymerase sigma factor; Provisional

Probab=99.88  E-value=1.5e-21  Score=178.34  Aligned_cols=182  Identities=18%  Similarity=0.168  Sum_probs=131.5

Q ss_pred             HHHHHHhHHHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHhccCCCCCCCchhHHHHHHHHHHHHHHHhhcCcccCCcch
Q 046578          144 ERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYWWIKQAIIRAIANKSRTIRLPGSM  223 (379)
Q Consensus       144 e~Li~~y~~lV~~ia~r~~~~~~d~eDLvQEg~i~L~~ai~~fD~~~g~~FsTYa~~~Ir~~i~~~lr~~~r~irip~~~  223 (379)
                      +.++..|.+.++.+|.+++++..++||++||+|+.+|+.+++|++..  +|.+|++++++|.+++++|++.+....+...
T Consensus        11 ~~~~~~~~~~l~~~~~~~~~d~~~AEDivQe~fl~~~~~~~~~~~~~--~~~~WL~~IarN~~~d~~Rk~~r~~~~~~~~   88 (201)
T PRK12545         11 PAYLAQLRHDLLRFARLQLRDADAAEDAVQEALAAAWSQAGRFAGQS--AHKTWVFGILRNKLIDTLRARQRTVNLSALD   88 (201)
T ss_pred             HHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhhhhccccc--hHHHHHHHHHHHHHHHHHHhhcccccccccc
Confidence            34589999999999999999999999999999999999999998653  6999999999999999999876311110000


Q ss_pred             HHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCccccCCCCcccccCCCCCCCChHHHHH
Q 046578          224 AGMVAKIAEANNVLSRRLRRMPTDSEIAEMLNIHVSTVRLAIERTRHPISLDGAVTDRGCMTMQDIIPGPDETMPERMVQ  303 (379)
Q Consensus       224 ~~~~~ki~~a~~~l~~~lgr~pt~~eia~~Lgis~~~~~~~l~~~~~~iSLd~~~~~~~~~~l~d~i~~~~~~~pe~~~~  303 (379)
                                              .+..                  ....++............+..++ ....+++...
T Consensus        89 ------------------------~~~~------------------~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~  125 (201)
T PRK12545         89 ------------------------AELD------------------GEALLDRELFKDNGHWAAHAKPR-PWPKPETILQ  125 (201)
T ss_pred             ------------------------cccc------------------hhhhhhhhhhcccccccccccCc-CCCCHHHHHH
Confidence                                    0000                  00000000000000000000111 1224555565


Q ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHHhhchh
Q 046578          304 KQLMKQELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQTNILNNL  374 (379)
Q Consensus       304 ~~e~~~~L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~~l~~~~L  374 (379)
                      ..+....+..+|..||+++|.||.|+|+    +|+|++|||+.||+|.++|+++++||+++||+++...++
T Consensus       126 ~~~~~~~l~~~L~~Lp~~~r~v~~L~~~----eg~s~~EIA~~lgis~~tVk~~l~RAr~~Lr~~l~~~~~  192 (201)
T PRK12545        126 QQQFWTLFETCLDHLPEQIGRVFMMREF----LDFEIDDICTELTLTANHCSVLLYRARTRLRTCLSEKGL  192 (201)
T ss_pred             HHHHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHHhc
Confidence            6666677999999999999999999995    779999999999999999999999999999999975543

>PRK12530 RNA polymerase sigma factor; Provisional

Probab=99.88  E-value=1.9e-21  Score=175.83  Aligned_cols=175  Identities=18%  Similarity=0.142  Sum_probs=130.1

Q ss_pred             HHHHHhHHHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHhccCCCCCCCchhHHHHHHHHHHHHHHHhhcCcccCCcchH
Q 046578          145 RIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYWWIKQAIIRAIANKSRTIRLPGSMA  224 (379)
Q Consensus       145 ~Li~~y~~lV~~ia~r~~~~~~d~eDLvQEg~i~L~~ai~~fD~~~g~~FsTYa~~~Ir~~i~~~lr~~~r~irip~~~~  224 (379)
                      +-+..|.+.++.+|.+++++..++||++||+|+.+|+.+++|++..  +|.+|++++++|.+++++|++.+..... ...
T Consensus        11 ~~~~~~~~~l~~~~~~~~~d~~~AeDivQe~flk~~~~~~~~~~~~--~~~~wL~~Ia~n~~~d~~Rk~~~~~~~~-~~~   87 (189)
T PRK12530         11 LEIEEIRLQMLKFATLQLKDADLAEDVVQEALVSAYKNADSFKGQS--ALKTWIFAILKNKIIDLIRYRKRFVNES-ELI   87 (189)
T ss_pred             HHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHhchhccCCc--cHHHHHHHHHHHHHHHHHHhhccCCCcc-ccc
Confidence            4578899999999999999989999999999999999999998643  6999999999999999999865311100 000


Q ss_pred             HHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCccccCCCCcccccCCCCCCCChHHHHHH
Q 046578          225 GMVAKIAEANNVLSRRLRRMPTDSEIAEMLNIHVSTVRLAIERTRHPISLDGAVTDRGCMTMQDIIPGPDETMPERMVQK  304 (379)
Q Consensus       225 ~~~~ki~~a~~~l~~~lgr~pt~~eia~~Lgis~~~~~~~l~~~~~~iSLd~~~~~~~~~~l~d~i~~~~~~~pe~~~~~  304 (379)
                                                                   ....... ..+.......+.........|+..+..
T Consensus        88 ---------------------------------------------~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~  121 (189)
T PRK12530         88 ---------------------------------------------EEDSPNS-FFDEKGHWKPEYYEPSEWQEVENTVYK  121 (189)
T ss_pred             ---------------------------------------------ccccchh-hhcccccccccccCCccccCHHHHHHH
Confidence                                                         0000000 000000000000001112345666666


Q ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHHhhc
Q 046578          305 QLMKQELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQTNILN  372 (379)
Q Consensus       305 ~e~~~~L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~~l~~~  372 (379)
                      .+....+..+|++||+++|+||.|+|+    +|+|++|||+.||+|.+||+++++||+++||+++...
T Consensus       122 ~~~~~~l~~~l~~Lp~~~R~v~~L~~~----~g~s~~EIA~~lgis~~tVk~~l~RAr~~Lr~~l~~~  185 (189)
T PRK12530        122 EEFWLIFEACLNHLPAQQARVFMMREY----LELSSEQICQECDISTSNLHVLLYRARLQLQACLSKN  185 (189)
T ss_pred             HHHHHHHHHHHHhCCHHHHHHHhHHHH----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHH
Confidence            777788999999999999999999995    6799999999999999999999999999999998654

>PRK12547 RNA polymerase sigma factor; Provisional

Probab=99.88  E-value=2.6e-21  Score=170.83  Aligned_cols=159  Identities=14%  Similarity=0.186  Sum_probs=126.1

Q ss_pred             HHHHHHHHHHhHHHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHhccCCCCCCCchhHHHHHHHHHHHHHHHhhcCcccC
Q 046578          140 RESQERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYWWIKQAIIRAIANKSRTIRL  219 (379)
Q Consensus       140 ~~A~e~Li~~y~~lV~~ia~r~~~~~~d~eDLvQEg~i~L~~ai~~fD~~~g~~FsTYa~~~Ir~~i~~~lr~~~r~iri  219 (379)
                      ...|.++|..|.+.++.+|+++.++..++||++||+|+.+|+..++|+...  .|.+|++++++|.+++++|+..+... 
T Consensus         5 ~~~f~~~~~~~~~~l~~~a~~~~~~~~~AeDivQe~fl~l~~~~~~~~~~~--~~~~wl~~i~~n~~~d~~R~~~~~~~-   81 (164)
T PRK12547          5 SKNFKQELLLALPALRAFAVSLSSKHDKAEDLVQDTLMKAWAKQDSFEMGT--NLKAWLFTILRNEFYSQMRKRGREVQ-   81 (164)
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHcCCHhhHHHHHHHHHHHHHHhhhhcCCcc--cHHHHHHHHHHHHHHHHHHhhccccc-
Confidence            468899999999999999999999999999999999999999999997533  69999999999999999998653100 


Q ss_pred             CcchHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCccccCCCCcccccCCCCCCCChH
Q 046578          220 PGSMAGMVAKIAEANNVLSRRLRRMPTDSEIAEMLNIHVSTVRLAIERTRHPISLDGAVTDRGCMTMQDIIPGPDETMPE  299 (379)
Q Consensus       220 p~~~~~~~~ki~~a~~~l~~~lgr~pt~~eia~~Lgis~~~~~~~l~~~~~~iSLd~~~~~~~~~~l~d~i~~~~~~~pe  299 (379)
                                                                         .  .+.        .... ...   ..++
T Consensus        82 ---------------------------------------------------~--~~~--------~~~~-~~~---~~~~   96 (164)
T PRK12547         82 ---------------------------------------------------D--SDG--------VFTA-RVA---VHPA   96 (164)
T ss_pred             ---------------------------------------------------c--ccc--------cccc-cCC---CCch
Confidence                                                               0  000        0000 000   0111


Q ss_pred             HHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHHhhc
Q 046578          300 RMVQKQLMKQELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQTNILN  372 (379)
Q Consensus       300 ~~~~~~e~~~~L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~~l~~~  372 (379)
                      .  ........+..+|..||+.+|+||.++|+    +|+|++|||+.||+|.++|+++++||+++||+.+...
T Consensus        97 ~--~~~~~~~~l~~~l~~L~~~~r~v~~l~~~----~g~s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~l~~~  163 (164)
T PRK12547         97 Q--YGSLDLQDFKKALNLLSADQREAIILIGA----SGFSYEDAAAICGCAVGTIKSRVSRARNRLQELLKVD  163 (164)
T ss_pred             h--hhHHHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHhcc
Confidence            1  11122356889999999999999999984    7799999999999999999999999999999998643

>PRK12532 RNA polymerase sigma factor; Provisional

Probab=99.88  E-value=2.1e-21  Score=176.18  Aligned_cols=178  Identities=18%  Similarity=0.179  Sum_probs=133.1

Q ss_pred             HHHHHHhHHHHHHHHHhccCCCCC-HHHHHHHHHHHHHHHHhccCCCCCCCchhHHHHHHHHHHHHHHHhhcCcccCCcc
Q 046578          144 ERIIRSYRSLVVSIATGYQGKGLS-LKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYWWIKQAIIRAIANKSRTIRLPGS  222 (379)
Q Consensus       144 e~Li~~y~~lV~~ia~r~~~~~~d-~eDLvQEg~i~L~~ai~~fD~~~g~~FsTYa~~~Ir~~i~~~lr~~~r~irip~~  222 (379)
                      ++.+..|.+.|+++|.++.++..+ +||++||+|+.+|+++++|++.  .+|.+|++++++|.+++++|++.+.......
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            467889999999999999998888 9999999999999999999864  3799999999999999999986531110000


Q ss_pred             hHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCccc---cCCCCcccccCCCCCCCChH
Q 046578          223 MAGMVAKIAEANNVLSRRLRRMPTDSEIAEMLNIHVSTVRLAIERTRHPISLDGAVT---DRGCMTMQDIIPGPDETMPE  299 (379)
Q Consensus       223 ~~~~~~ki~~a~~~l~~~lgr~pt~~eia~~Lgis~~~~~~~l~~~~~~iSLd~~~~---~~~~~~l~d~i~~~~~~~pe  299 (379)
                      .                                              .....+....   ..+.....+.. .....+|+
T Consensus        86 ~----------------------------------------------~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~e  118 (195)
T PRK12532         86 L----------------------------------------------DDELLDEAFESHFSQNGHWTPEGQ-PQHWNTPE  118 (195)
T ss_pred             c----------------------------------------------cccccchhhhhhhccccccccccC-ccccCCHH
Confidence            0                                              0000000000   00000000000 11223677


Q ss_pred             HHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHHhhchh
Q 046578          300 RMVQKQLMKQELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQTNILNNL  374 (379)
Q Consensus       300 ~~~~~~e~~~~L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~~l~~~~L  374 (379)
                      ..+...+....+..++..||+++|+||.|+|+    +|+|++|||+.||+|.++|+++++||+++||+++....+
T Consensus       119 ~~~~~~e~~~~l~~~l~~L~~~~r~i~~L~~~----~g~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~l~~~~~  189 (195)
T PRK12532        119 KSLNNNEFQKILQSCLYNLPENTARVFTLKEI----LGFSSDEIQQMCGISTSNYHTIMHRARESLRQCLQIKWF  189 (195)
T ss_pred             HHHHHHHHHHHHHHHHHhCCHHHHHHhhhHHH----hCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHhhc
Confidence            77777777788999999999999999999984    779999999999999999999999999999999976654

>PRK12528 RNA polymerase sigma factor; Provisional

Probab=99.88  E-value=1.8e-21  Score=171.02  Aligned_cols=158  Identities=14%  Similarity=0.059  Sum_probs=124.8

Q ss_pred             HHHHHHHHHHhHHHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHhccCCCCCCCchhHHHHHHHHHHHHHHHhhcCcccC
Q 046578          140 RESQERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYWWIKQAIIRAIANKSRTIRL  219 (379)
Q Consensus       140 ~~A~e~Li~~y~~lV~~ia~r~~~~~~d~eDLvQEg~i~L~~ai~~fD~~~g~~FsTYa~~~Ir~~i~~~lr~~~r~iri  219 (379)
                      ..++++||+.|.+.+++++.++.++..++||++||+|+.+|+..+.|++   ..|.+|++++++|.+++++|+..+... 
T Consensus         3 ~~a~~~l~~~~~~~l~~~~~~~~~~~~~AeDivQe~flk~~~~~~~~~~---~~~~~wl~~i~~n~~~d~~R~~~~~~~-   78 (161)
T PRK12528          3 SATVEGLYSAHHHWLTGWLRRRLGCPQSAADLAQDTFVKVLVARETAQI---IEPRAFLTTIAKRVLCNHYRRQDLERA-   78 (161)
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHcCCcccHHHHHHHHHHHHHhccccccc---cCHHHHHHHHHHHHHHHHHHHHHHHHh-
Confidence            3689999999999999999999999999999999999999999887764   269999999999999999997541000 


Q ss_pred             CcchHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCccccCCCCcccccCCCCCCCChH
Q 046578          220 PGSMAGMVAKIAEANNVLSRRLRRMPTDSEIAEMLNIHVSTVRLAIERTRHPISLDGAVTDRGCMTMQDIIPGPDETMPE  299 (379)
Q Consensus       220 p~~~~~~~~ki~~a~~~l~~~lgr~pt~~eia~~Lgis~~~~~~~l~~~~~~iSLd~~~~~~~~~~l~d~i~~~~~~~pe  299 (379)
                                                                        ....++            + .+......++
T Consensus        79 --------------------------------------------------~~~~~~------------~-~~~~~~~~~~   95 (161)
T PRK12528         79 --------------------------------------------------YLEALA------------Q-LPERVAPSEE   95 (161)
T ss_pred             --------------------------------------------------hHHHhh------------c-cccccCCCHH
Confidence                                                              000000            0 0001112333


Q ss_pred             HHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhH
Q 046578          300 RMVQKQLMKQELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQT  368 (379)
Q Consensus       300 ~~~~~~e~~~~L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~~  368 (379)
                      ......+....+..+|.+||+++|+||.|+|+    +|+|++|||+.||+|.+||+++++||+++||..
T Consensus        96 ~~~~~~~~~~~l~~~l~~L~~~~r~v~~L~~~----~g~s~~EIA~~l~is~~tV~~~l~ra~~~~~~~  160 (161)
T PRK12528         96 ERAIILETLVELDQLLDGLPPLVKRAFLLAQV----DGLGYGEIATELGISLATVKRYLNKAAMRCYFA  160 (161)
T ss_pred             HHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHH----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhc
Confidence            33333344567899999999999999999995    779999999999999999999999999999975

>PRK12544 RNA polymerase sigma factor; Provisional

Probab=99.88  E-value=3.1e-21  Score=176.98  Aligned_cols=182  Identities=18%  Similarity=0.185  Sum_probs=134.5

Q ss_pred             HHHHHHHhHHHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHhccCCCCCCCchhHHHHHHHHHHHHHHHhhcCcccCCcc
Q 046578          143 QERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYWWIKQAIIRAIANKSRTIRLPGS  222 (379)
Q Consensus       143 ~e~Li~~y~~lV~~ia~r~~~~~~d~eDLvQEg~i~L~~ai~~fD~~~g~~FsTYa~~~Ir~~i~~~lr~~~r~irip~~  222 (379)
                      -..+++.|.+.|+.+|++++++..++||++||+|+.+|+.+.+|+..  .+|.+|++++++|.+++++|+..+....+..
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            36799999999999999999999999999999999999999999854  3799999999999999999986531111000


Q ss_pred             hHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCccccCCCCcccccCCCCCCCChHHHH
Q 046578          223 MAGMVAKIAEANNVLSRRLRRMPTDSEIAEMLNIHVSTVRLAIERTRHPISLDGAVTDRGCMTMQDIIPGPDETMPERMV  302 (379)
Q Consensus       223 ~~~~~~ki~~a~~~l~~~lgr~pt~~eia~~Lgis~~~~~~~l~~~~~~iSLd~~~~~~~~~~l~d~i~~~~~~~pe~~~  302 (379)
                      .                  +.......                        ++... +. ...............|+..+
T Consensus        98 ~------------------~~~~~~~~------------------------~~~~~-~~-~~~~~~~~~~~~~~~~e~~~  133 (206)
T PRK12544         98 L------------------RDEEEEED------------------------FEELF-DE-SGHWQKDERPQAWGNPEESL  133 (206)
T ss_pred             c------------------cccchhhH------------------------HHHhh-cc-cccccccccccccCCHHHHH
Confidence            0                  00000000                        00000 00 00000000011223567777


Q ss_pred             HHHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHHhhchh
Q 046578          303 QKQLMKQELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQTNILNNL  374 (379)
Q Consensus       303 ~~~e~~~~L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~~l~~~~L  374 (379)
                      ...+....+..+|..||+++|+||.|+|+    +|+|++|||+.||+|.++|+++++||+++||+.+....+
T Consensus       134 ~~~e~~~~l~~~L~~L~~~~r~v~~L~~~----~g~s~~EIAe~lgis~~tV~~~l~RAr~~Lr~~l~~~~~  201 (206)
T PRK12544        134 EQEQFWRIFEACLDGLPAKYARVFMMREF----IELETNEICHAVDLSVSNLNVLLYRARLRLRECLENKWF  201 (206)
T ss_pred             HHHHHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHHhh
Confidence            77777778999999999999999999995    779999999999999999999999999999999876443

>PRK09639 RNA polymerase sigma factor SigX; Provisional

Probab=99.88  E-value=2.7e-21  Score=170.43  Aligned_cols=161  Identities=20%  Similarity=0.211  Sum_probs=130.7

Q ss_pred             HHHHHHHHHHhHHHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHhccCCCCCCCchhHHHHHHHHHHHHHHHhhcCcccC
Q 046578          140 RESQERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYWWIKQAIIRAIANKSRTIRL  219 (379)
Q Consensus       140 ~~A~e~Li~~y~~lV~~ia~r~~~~~~d~eDLvQEg~i~L~~ai~~fD~~~g~~FsTYa~~~Ir~~i~~~lr~~~r~iri  219 (379)
                      +.+++.+|+.|.+.++.+|.++.++..++||++||+|+.+|++  .|+.  +..|.+|++.+++|.+.+++|+..+....
T Consensus         2 ~~~f~~l~~~y~~~l~~~~~~~~~~~~~aeDlvQe~fi~~~~~--~~~~--~~~~~~wl~~i~rn~~~d~~rk~~~~~~~   77 (166)
T PRK09639          2 DETFEDLFEQYYPDVVQQIFYIVKDRTQAEDLAQEVFLRLYRS--DFKG--IENEKGWLIKSARNVAYNYLRSEKRRRAR   77 (166)
T ss_pred             chHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHH--hccc--ccchHHHHHHHHHHHHHHHHHHhcccccc
Confidence            4689999999999999999999999999999999999999999  6763  34799999999999999999986531110


Q ss_pred             CcchHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCccccCCCCcccccCCCCCCCChH
Q 046578          220 PGSMAGMVAKIAEANNVLSRRLRRMPTDSEIAEMLNIHVSTVRLAIERTRHPISLDGAVTDRGCMTMQDIIPGPDETMPE  299 (379)
Q Consensus       220 p~~~~~~~~ki~~a~~~l~~~lgr~pt~~eia~~Lgis~~~~~~~l~~~~~~iSLd~~~~~~~~~~l~d~i~~~~~~~pe  299 (379)
                      .                                                      +...      ...+.   .....|+
T Consensus        78 ~------------------------------------------------------~~~~------~~~~~---~~~~~~e   94 (166)
T PRK09639         78 I------------------------------------------------------LGEF------QWQEV---DNEPSPE   94 (166)
T ss_pred             c------------------------------------------------------cchh------hhhhc---cCCCChH
Confidence            0                                                      0000      00000   1123566


Q ss_pred             HHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHHhhc
Q 046578          300 RMVQKQLMKQELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQTNILN  372 (379)
Q Consensus       300 ~~~~~~e~~~~L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~~l~~~  372 (379)
                      +.....+....+..+|..||+++|.||.++|     +|+|++|||+.||+|.++|++.++||+++||+.+...
T Consensus        95 ~~~~~~~~~~~l~~~l~~L~~~~r~il~l~~-----~g~s~~eIA~~lgis~~tV~~~i~ra~~~Lr~~l~~~  162 (166)
T PRK09639         95 EIWIRKEEITKVQEVLAKMTERDRTVLLLRF-----SGYSYKEIAEALGIKESSVGTTLARAKKKFRKIYEQM  162 (166)
T ss_pred             HHHHHHHHHHHHHHHHHcCCHHHHHHHHHHH-----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHh
Confidence            6666667777899999999999999999998     4599999999999999999999999999999998643

>PRK12517 RNA polymerase sigma factor; Provisional

Probab=99.87  E-value=2.6e-21  Score=174.86  Aligned_cols=164  Identities=15%  Similarity=0.137  Sum_probs=130.0

Q ss_pred             HHhcccHHHHHHHHHHhHHHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHhccCCCCCCCchhHHHHHHHHHHHHHHHhh
Q 046578          134 KILCKERESQERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYWWIKQAIIRAIANK  213 (379)
Q Consensus       134 ~~~~Gd~~A~e~Li~~y~~lV~~ia~r~~~~~~d~eDLvQEg~i~L~~ai~~fD~~~g~~FsTYa~~~Ir~~i~~~lr~~  213 (379)
                      .=..++..+++.+|..|.+.|+.+|.++.++..++||++||+|+.+|+.++.|++.  ..|.+|++++++|.+.+..++.
T Consensus        16 ~~~~~~~~~f~~l~~~y~~~l~~~~~~~~~~~~~AeDlvQdvflkl~~~~~~~~~~--~~~~~wL~~Iarn~~~~~~r~~   93 (188)
T PRK12517         16 SDMLSKQRRYEALVKALHADIYRYAYWLCKDKHIAEDLVQETFLRAWRSLDSLKDE--KAAKAWLITILRRENARRFERK   93 (188)
T ss_pred             HhhhccHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhHHhhcCc--cchHHHHHHHHHHHHHHHHHHh
Confidence            33456899999999999999999999999999999999999999999999999864  3799999999999988776653


Q ss_pred             cCcccCCcchHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCccccCCCCcccccCCCC
Q 046578          214 SRTIRLPGSMAGMVAKIAEANNVLSRRLRRMPTDSEIAEMLNIHVSTVRLAIERTRHPISLDGAVTDRGCMTMQDIIPGP  293 (379)
Q Consensus       214 ~r~irip~~~~~~~~ki~~a~~~l~~~lgr~pt~~eia~~Lgis~~~~~~~l~~~~~~iSLd~~~~~~~~~~l~d~i~~~  293 (379)
                      .+                                                      .....+.           +...+.
T Consensus        94 ~~------------------------------------------------------~~~~~~~-----------~~~~~~  108 (188)
T PRK12517         94 QF------------------------------------------------------DLVDIED-----------DSIEDD  108 (188)
T ss_pred             cc------------------------------------------------------CccCccc-----------ccccCc
Confidence            31                                                      0000000           000111


Q ss_pred             CCCChHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHHhhc
Q 046578          294 DETMPERMVQKQLMKQELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQTNILN  372 (379)
Q Consensus       294 ~~~~pe~~~~~~e~~~~L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~~l~~~  372 (379)
                      ....++...    ....|..+|..||+++|.||.++|+    +|++++|||+.||+|.++|+.+++||+++||+.+...
T Consensus       109 ~~~~~e~~~----~~~~l~~~l~~Lp~~~r~v~~l~~~----~g~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~~~  179 (188)
T PRK12517        109 ASHSSEEEM----EQEWLRRQIAKLDPEYREPLLLQVI----GGFSGEEIAEILDLNKNTVMTRLFRARNQLKEALEKP  179 (188)
T ss_pred             cccChhHHH----HHHHHHHHHHhCCHHHHHHHHHHHH----hCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHH
Confidence            112233222    2246889999999999999999995    7799999999999999999999999999999998754

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

Probab=99.87  E-value=4e-21  Score=164.87  Aligned_cols=158  Identities=27%  Similarity=0.412  Sum_probs=131.3

Q ss_pred             HHHHHHHHHhHHHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHhccCCCCCCCchhHHHHHHHHHHHHHHHhhcCcccCC
Q 046578          141 ESQERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYWWIKQAIIRAIANKSRTIRLP  220 (379)
Q Consensus       141 ~A~e~Li~~y~~lV~~ia~r~~~~~~d~eDLvQEg~i~L~~ai~~fD~~~g~~FsTYa~~~Ir~~i~~~lr~~~r~irip  220 (379)
                      +|++.++..|.|+|+++++++..+..+++|++||+++++|++++.|++.  .+|.+|+..++++.+.+++++..+   .+
T Consensus         1 ~a~~~l~~~~~~~v~~~~~~~~~~~~~~~D~~qe~~~~l~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~rk~~~---~~   75 (158)
T TIGR02937         1 EAFEELYERYLPLLYRYARRYLGDDADAEDLVQEAFLKLLEALDRFDPE--GSFKAWLFRIARNLILDYLRRKRR---LR   75 (158)
T ss_pred             CHHHHHHHHHHHHHHHHHHHHhCCHhHHHHHHHHHHHHHHHhHHhcCCc--chHHHHHHHHHHHHHHHHHHHhcc---CC
Confidence            3789999999999999999999998999999999999999999999987  589999999999999999998763   11


Q ss_pred             cchHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCccccCCCCcccccCCCCCCCChHH
Q 046578          221 GSMAGMVAKIAEANNVLSRRLRRMPTDSEIAEMLNIHVSTVRLAIERTRHPISLDGAVTDRGCMTMQDIIPGPDETMPER  300 (379)
Q Consensus       221 ~~~~~~~~ki~~a~~~l~~~lgr~pt~~eia~~Lgis~~~~~~~l~~~~~~iSLd~~~~~~~~~~l~d~i~~~~~~~pe~  300 (379)
                      ...                                                   ....      .    . ......+++
T Consensus        76 ~~~---------------------------------------------------~~~~------~----~-~~~~~~~~~   93 (158)
T TIGR02937        76 REL---------------------------------------------------DLLE------E----L-LDSDPSPEE   93 (158)
T ss_pred             cch---------------------------------------------------hhhh------h----c-ccccCCHHH
Confidence            000                                                   0000      0    0 011224566


Q ss_pred             HHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHH
Q 046578          301 MVQKQLMKQELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQTN  369 (379)
Q Consensus       301 ~~~~~e~~~~L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~~l  369 (379)
                      .....+....+..++..||+.++.||.++|+    .|+|.+|||+.+|+|+++|++++++++++||+.+
T Consensus        94 ~~~~~~~~~~l~~~l~~L~~~~~~ii~~~~~----~g~s~~eIA~~l~~s~~~v~~~~~~~~~kl~~~l  158 (158)
T TIGR02937        94 ELEQEEEREALREALEKLPEREREVLVLRYL----EGLSYKEIAEILGISVGTVKRRLKRARKKLRELL  158 (158)
T ss_pred             HHHHHHHHHHHHHHHHhCCHHHHHHHhhHHh----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhhC
Confidence            6667777788999999999999999999884    6699999999999999999999999999999864

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.

>PRK09651 RNA polymerase sigma factor FecI; Provisional

Probab=99.87  E-value=6.2e-21  Score=169.79  Aligned_cols=165  Identities=13%  Similarity=0.127  Sum_probs=128.7

Q ss_pred             cccHHHHHHHHHHhHHHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHhccCCCCCCCchhHHHHHHHHHHHHHHHhhcCc
Q 046578          137 CKERESQERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYWWIKQAIIRAIANKSRT  216 (379)
Q Consensus       137 ~Gd~~A~e~Li~~y~~lV~~ia~r~~~~~~d~eDLvQEg~i~L~~ai~~fD~~~g~~FsTYa~~~Ir~~i~~~lr~~~r~  216 (379)
                      .-+..|++.+|+.|.+.|+.++.++.++..++||++||+|+.+|+. ..|++..  +|.+|++++++|.+++++|+..+.
T Consensus         6 ~~~~~af~~l~~~~~~~l~~~~~~~~~~~~~AEDlvQe~flkl~~~-~~~~~~~--~~~~wL~~iarn~~~d~~R~~~~~   82 (172)
T PRK09651          6 TTASLTFESLYGTHHGWLKSWLTRKLQSAFDADDIAQDTFLRVMVS-ETLSTIR--DPRSFLCTIAKRVMVDLFRRNALE   82 (172)
T ss_pred             hhHHHHHHHHHHHHHHHHHHHHHHHcCCHhHHHHHHHHHHHHHHhh-ccccccc--CHHHHHHHHHHHHHHHHHHHHHHH
Confidence            4567899999999999999999999999999999999999999998 3554332  689999999999999999975410


Q ss_pred             ccCCcchHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCccccCCCCcccccCCCCCCC
Q 046578          217 IRLPGSMAGMVAKIAEANNVLSRRLRRMPTDSEIAEMLNIHVSTVRLAIERTRHPISLDGAVTDRGCMTMQDIIPGPDET  296 (379)
Q Consensus       217 irip~~~~~~~~ki~~a~~~l~~~lgr~pt~~eia~~Lgis~~~~~~~l~~~~~~iSLd~~~~~~~~~~l~d~i~~~~~~  296 (379)
                      .                                                    ..  .+. ..     .+    ......
T Consensus        83 ~----------------------------------------------------~~--~~~-~~-----~~----~~~~~~   98 (172)
T PRK09651         83 K----------------------------------------------------AY--LEM-LA-----LM----PEGGAP   98 (172)
T ss_pred             h----------------------------------------------------hh--hhH-Hh-----hc----cccCCC
Confidence            0                                                    00  000 00     00    001112


Q ss_pred             ChHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHHhhc
Q 046578          297 MPERMVQKQLMKQELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQTNILN  372 (379)
Q Consensus       297 ~pe~~~~~~e~~~~L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~~l~~~  372 (379)
                      +|+......+....+..+|..||+++|+||.++|+    +|+|++|||+.||+|.++|+++++||+++|+......
T Consensus        99 ~~~~~~~~~e~~~~l~~~l~~L~~~~r~i~~l~~~----~g~s~~EIA~~lgis~~tV~~~l~Ra~~~~~~~~~~~  170 (172)
T PRK09651         99 SPEERESQLETLQLLDSMLDGLNGKTREAFLLSQL----DGLTYSEIAHKLGVSVSSVKKYVAKATEHCLLFRLEY  170 (172)
T ss_pred             ChHHHHHHHHHHHHHHHHHHhCCHHHhHHhhhhhc----cCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHHHc
Confidence            33444444455567999999999999999999995    7799999999999999999999999999999875543

>PRK09637 RNA polymerase sigma factor SigZ; Provisional

Probab=99.87  E-value=8.1e-21  Score=170.66  Aligned_cols=154  Identities=21%  Similarity=0.220  Sum_probs=126.4

Q ss_pred             HHHHHHHhHHHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHhccCCCCCCCchhHHHHHHHHHHHHHHHhhcCcccCCcc
Q 046578          143 QERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYWWIKQAIIRAIANKSRTIRLPGS  222 (379)
Q Consensus       143 ~e~Li~~y~~lV~~ia~r~~~~~~d~eDLvQEg~i~L~~ai~~fD~~~g~~FsTYa~~~Ir~~i~~~lr~~~r~irip~~  222 (379)
                      ++.+|+.|.+.|+.++.++.++..++||++||+|+.+|+.+..|+..  .+|.+|++++++|.++|++|++.+....+  
T Consensus         3 ~~~l~~~y~~~l~~~~~~~~~~~~~aeDi~QEvflkl~~~~~~~~~~--~~~~~wL~~i~~n~~~d~~Rk~~~~~~~~--   78 (181)
T PRK09637          3 LESIWSEYKAQLKAFLHSRVSNEADVDDLLQEVLIKTHSNLHSLKDG--SSIKSWLYQIANNTIIDFYRKKNRSEELP--   78 (181)
T ss_pred             HHHHHHHHHHHHHHHHHHHhCChhhHHHHHHHHHHHHHHhHHHhccc--cchHHHHHHHHHHHHHHHHHhccccCCcc--
Confidence            68899999999999999999999999999999999999999999853  37999999999999999999765310000  


Q ss_pred             hHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCccccCCCCcccccCCCCCCCChHHHH
Q 046578          223 MAGMVAKIAEANNVLSRRLRRMPTDSEIAEMLNIHVSTVRLAIERTRHPISLDGAVTDRGCMTMQDIIPGPDETMPERMV  302 (379)
Q Consensus       223 ~~~~~~ki~~a~~~l~~~lgr~pt~~eia~~Lgis~~~~~~~l~~~~~~iSLd~~~~~~~~~~l~d~i~~~~~~~pe~~~  302 (379)
                                                                               ++      +...+    .+++..
T Consensus        79 ---------------------------------------------------------~~------~~~~~----~~~~~~   91 (181)
T PRK09637         79 ---------------------------------------------------------DD------LLFED----EEREEN   91 (181)
T ss_pred             ---------------------------------------------------------hh------hhccC----CChhHH
Confidence                                                                     00      00000    112223


Q ss_pred             HHHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHHhh
Q 046578          303 QKQLMKQELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQTNIL  371 (379)
Q Consensus       303 ~~~e~~~~L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~~l~~  371 (379)
                      ...+....+..++..||+++|.||.++|+    +|++++|||+.||+|.++|++++.||+++||+.+..
T Consensus        92 ~~~e~~~~l~~~l~~L~~~~r~i~~l~~~----~g~~~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~~  156 (181)
T PRK09637         92 AKKELAPCLRPFIDALPEKYAEALRLTEL----EGLSQKEIAEKLGLSLSGAKSRVQRGRVKLKELLEG  156 (181)
T ss_pred             HHHHHHHHHHHHHHhCCHHHHHHHHHHHh----cCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHHH
Confidence            34455677999999999999999999984    779999999999999999999999999999999864

>PRK12540 RNA polymerase sigma factor; Provisional

Probab=99.87  E-value=8e-21  Score=170.90  Aligned_cols=160  Identities=17%  Similarity=0.227  Sum_probs=126.6

Q ss_pred             HHHHHHHHHhHHHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHhccCCCCCCCchhHHHHHHHHHHHHHHHhhcCcccCC
Q 046578          141 ESQERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYWWIKQAIIRAIANKSRTIRLP  220 (379)
Q Consensus       141 ~A~e~Li~~y~~lV~~ia~r~~~~~~d~eDLvQEg~i~L~~ai~~fD~~~g~~FsTYa~~~Ir~~i~~~lr~~~r~irip  220 (379)
                      .++..+|..|.+.|+++|.+++++..++||++||+|+.+|+..++|++..  +|.+|++++++|.+++++|++.+...  
T Consensus         5 ~~~~~~~~~~~~~l~~~~~~~~~~~~~AEDivQevflkl~~~~~~~~~~~--~~~~WL~~Ia~n~~~d~~Rk~~~~~~--   80 (182)
T PRK12540          5 DSLRDDILAAVPSLRAFAISLSGNGDRADDLVQETLLRALANIDSFQPGS--NLPAWLFTILRNLFRSDYRKRRREVE--   80 (182)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhHHhcCCCc--hHHHHHHHHHHHHHHHHHHhcccccc--
Confidence            46788999999999999999999999999999999999999999998653  69999999999999999997653100  


Q ss_pred             cchHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCccccCCCCcccccCCCCCCCChHH
Q 046578          221 GSMAGMVAKIAEANNVLSRRLRRMPTDSEIAEMLNIHVSTVRLAIERTRHPISLDGAVTDRGCMTMQDIIPGPDETMPER  300 (379)
Q Consensus       221 ~~~~~~~~ki~~a~~~l~~~lgr~pt~~eia~~Lgis~~~~~~~l~~~~~~iSLd~~~~~~~~~~l~d~i~~~~~~~pe~  300 (379)
                                                                         . .+.        ...+... . ....+.
T Consensus        81 ---------------------------------------------------~-~~~--------~~~~~~~-~-~~~~~~   98 (182)
T PRK12540         81 ---------------------------------------------------D-ADG--------SYAKTLK-S-QPGQNA   98 (182)
T ss_pred             ---------------------------------------------------c-ccc--------ccccccc-C-CCchHH
Confidence                                                               0 000        0000000 0 011111


Q ss_pred             HHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHHhhchh
Q 046578          301 MVQKQLMKQELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQTNILNNL  374 (379)
Q Consensus       301 ~~~~~e~~~~L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~~l~~~~L  374 (379)
                          ......+..+|++||+++|+||.|+|+    +|+|++|||+.||+|.++|+++++||+++||+.+.....
T Consensus        99 ----~~~~~~l~~~l~~Lp~~~R~v~~L~~~----~g~s~~EIA~~Lgis~~tV~~~l~RAr~~Lr~~l~~~~~  164 (182)
T PRK12540         99 ----HLEFEEFRAALDKLPQDQREALILVGA----SGFSYEDAAAICGCAVGTIKSRVNRARSKLSALLYVDGA  164 (182)
T ss_pred             ----HHHHHHHHHHHHhCCHHHHHHhhHHHH----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHhccc
Confidence                112245889999999999999999984    779999999999999999999999999999999986553

>PRK12527 RNA polymerase sigma factor; Reviewed

Probab=99.86  E-value=9.9e-21  Score=166.04  Aligned_cols=156  Identities=12%  Similarity=0.104  Sum_probs=125.6

Q ss_pred             HHHhHHHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHhccCCCCCCCchhHHHHHHHHHHHHHHHhhcCcccCCcchHHH
Q 046578          147 IRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYWWIKQAIIRAIANKSRTIRLPGSMAGM  226 (379)
Q Consensus       147 i~~y~~lV~~ia~r~~~~~~d~eDLvQEg~i~L~~ai~~fD~~~g~~FsTYa~~~Ir~~i~~~lr~~~r~irip~~~~~~  226 (379)
                      +..|.+.++.++.+++++..++||++||+|+.+|+..+.|++   .+|.+|++.+++|.++|++|++.+.          
T Consensus         1 ~~~~~~~l~~~~~~~~~~~~~aeDi~Qevf~~l~~~~~~~~~---~~~~~wL~~ia~n~~~d~~R~~~~~----------   67 (159)
T PRK12527          1 MENYYRELVRFLSARLGNRQAAEDVAHDAYLRVLERSSSAQI---EHPRAFLYRTALNLVVDRHRRHRVR----------   67 (159)
T ss_pred             ChhHHHHHHHHHHHHcCCHhhHHHHHHHHHHHHHhccccccc---cchHHHHHHHHHHHHHHHHHHHhcc----------
Confidence            357899999999999999899999999999999999998864   2799999999999999999975420          


Q ss_pred             HHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCccccCCCCcccccCCCCCCCChHHHHHHHH
Q 046578          227 VAKIAEANNVLSRRLRRMPTDSEIAEMLNIHVSTVRLAIERTRHPISLDGAVTDRGCMTMQDIIPGPDETMPERMVQKQL  306 (379)
Q Consensus       227 ~~ki~~a~~~l~~~lgr~pt~~eia~~Lgis~~~~~~~l~~~~~~iSLd~~~~~~~~~~l~d~i~~~~~~~pe~~~~~~e  306 (379)
                                                                 ....++.         +.+. .....++|++.+..++
T Consensus        68 -------------------------------------------~~~~~~~---------~~~~-~~~~~~~~~~~~~~~~   94 (159)
T PRK12527         68 -------------------------------------------QAEPLEV---------LDEE-ERLHSPSPQTRLDLGQ   94 (159)
T ss_pred             -------------------------------------------cccchhh---------hhcc-ccccCCCHHHHHHHHH
Confidence                                                       0000000         0000 0011235677776777


Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHHhhc
Q 046578          307 MKQELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQTNILN  372 (379)
Q Consensus       307 ~~~~L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~~l~~~  372 (379)
                      ....+..+|.+||+++++||.|+|+    +|+|++|||+.||+|.++|++.+.||+++||+.+...
T Consensus        95 ~~~~l~~~l~~L~~~~r~v~~l~~~----~~~s~~eIA~~lgis~~tv~~~l~ra~~~Lr~~l~~~  156 (159)
T PRK12527         95 RLALLQRALAELPPACRDSFLLRKL----EGLSHQQIAEHLGISRSLVEKHIVNAMKHCRVRMRQW  156 (159)
T ss_pred             HHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHHhc
Confidence            7778999999999999999999995    7799999999999999999999999999999998754

>TIGR02950 SigM_subfam RNA polymerase sigma factor, SigM family

Probab=99.86  E-value=2.6e-21  Score=168.41  Aligned_cols=153  Identities=20%  Similarity=0.206  Sum_probs=123.6

Q ss_pred             HHHhHHHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHhccCCCCCCCchhHHHHHHHHHHHHHHHhhcCcccCCcchHHH
Q 046578          147 IRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYWWIKQAIIRAIANKSRTIRLPGSMAGM  226 (379)
Q Consensus       147 i~~y~~lV~~ia~r~~~~~~d~eDLvQEg~i~L~~ai~~fD~~~g~~FsTYa~~~Ir~~i~~~lr~~~r~irip~~~~~~  226 (379)
                      |+.|.|.|++++.++.++..+++|++||+|+.+|+++++|++   .+|.+|++.+++|.+.+++|++.+.....      
T Consensus         1 y~~~~~~l~~~~~~~~~~~~~aeD~~Qe~~~~l~~~~~~~~~---~~f~~wl~~i~~~~~~d~~r~~~~~~~~~------   71 (154)
T TIGR02950         1 YREYMHDVFRYLYRLTKDKHLAEDLLQETFLKAYIHLHSFKD---SSIKPWLFRIARNAFIDWYRKDKKIQTID------   71 (154)
T ss_pred             CchHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhHHHhcC---CchHHHHHHHHHHHHHHHHHHhhhhcccc------
Confidence            467999999999999999899999999999999999999986   37999999999999999999765310000      


Q ss_pred             HHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCccccCCCCcccccCCCCCCCChHHHHHHHH
Q 046578          227 VAKIAEANNVLSRRLRRMPTDSEIAEMLNIHVSTVRLAIERTRHPISLDGAVTDRGCMTMQDIIPGPDETMPERMVQKQL  306 (379)
Q Consensus       227 ~~ki~~a~~~l~~~lgr~pt~~eia~~Lgis~~~~~~~l~~~~~~iSLd~~~~~~~~~~l~d~i~~~~~~~pe~~~~~~e  306 (379)
                                                                      +.        .+.+... .....|++.+...+
T Consensus        72 ------------------------------------------------~~--------~~~~~~~-~~~~~~~~~~~~~~   94 (154)
T TIGR02950        72 ------------------------------------------------DD--------AIGDLEQ-HPVESPEHHLLIKI   94 (154)
T ss_pred             ------------------------------------------------Hh--------hhhhccc-cccCChhHHHHHHH
Confidence                                                            00        0000000 11224555566666


Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHH
Q 046578          307 MKQELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQTN  369 (379)
Q Consensus       307 ~~~~L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~~l  369 (379)
                      ....+..+|..||+.+++||.+.|+    +|+|++|||+.||+|.++|++.++||+++||+.+
T Consensus        95 ~~~~l~~~l~~L~~~~r~i~~l~~~----~g~s~~eIA~~lgis~~tv~~~l~Ra~~~Lr~~l  153 (154)
T TIGR02950        95 EQEEITHHLSRLPENYRTVLILREF----KEFSYKEIAELLNLSLAKVKSNLFRARKELKKLL  153 (154)
T ss_pred             HHHHHHHHHHhCCHhheeeeeehhh----ccCcHHHHHHHHCCCHHHHHHHHHHHHHHHHHHh
Confidence            6678999999999999999999984    6799999999999999999999999999999875

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.

>PRK07037 extracytoplasmic-function sigma-70 factor; Validated

Probab=99.86  E-value=2.6e-20  Score=163.80  Aligned_cols=159  Identities=17%  Similarity=0.208  Sum_probs=125.8

Q ss_pred             HHHHHhHHHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHhccCCCCCCCchhHHHHHHHHHHHHHHHhhcCcccCCcchH
Q 046578          145 RIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYWWIKQAIIRAIANKSRTIRLPGSMA  224 (379)
Q Consensus       145 ~Li~~y~~lV~~ia~r~~~~~~d~eDLvQEg~i~L~~ai~~fD~~~g~~FsTYa~~~Ir~~i~~~lr~~~r~irip~~~~  224 (379)
                      .++..|.+.++++|.++.++..++||++||+|+.+|+....|++.   +|.+|++.+++|.+++++|+..+...      
T Consensus         2 ~~~~~~~~~l~~~~~~~~~~~~~aeDivQe~~l~l~~~~~~~~~~---~~~~wl~~iarn~~~d~~R~~~~~~~------   72 (163)
T PRK07037          2 DVFVDNRSMLVKIAARIVGCRSRAEDVVQDAFVKLVEAPNQDAVK---QPVAYLFRIVRNLAIDHYRRQALENK------   72 (163)
T ss_pred             hHHHHHHHHHHHHHHHHcCCHhHHHHHHHHHHHHHHhccccCCcc---cHHHHHHHHHHHHHHHHHHhhccccc------
Confidence            367889999999999999999999999999999999988777642   58899999999999999997652100      


Q ss_pred             HHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCccccCCCCcccccCCCCCCCChHHHHHH
Q 046578          225 GMVAKIAEANNVLSRRLRRMPTDSEIAEMLNIHVSTVRLAIERTRHPISLDGAVTDRGCMTMQDIIPGPDETMPERMVQK  304 (379)
Q Consensus       225 ~~~~ki~~a~~~l~~~lgr~pt~~eia~~Lgis~~~~~~~l~~~~~~iSLd~~~~~~~~~~l~d~i~~~~~~~pe~~~~~  304 (379)
                                                                     ....    ++..  . + ... ...+|+..+..
T Consensus        73 -----------------------------------------------~~~~----~~~~--~-~-~~~-~~~~~~~~~~~   96 (163)
T PRK07037         73 -----------------------------------------------YHGD----EEDG--L-D-VPS-PEASPEAALIN   96 (163)
T ss_pred             -----------------------------------------------cccc----cccc--c-c-cCC-CCCCHHHHHHH
Confidence                                                           0000    0000  0 0 011 12345666666


Q ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHHhhc
Q 046578          305 QLMKQELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQTNILN  372 (379)
Q Consensus       305 ~e~~~~L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~~l~~~  372 (379)
                      .+..+.+..+|+.|||++|.||.++|+    +|+|++|||+.||+|.++|++.++||+++||+.+...
T Consensus        97 ~~~~~~l~~~l~~L~~~~r~v~~l~~~----~~~s~~EIA~~lgis~~tV~~~l~ra~~~lr~~l~~~  160 (163)
T PRK07037         97 RDTLRHVADALSELPARTRYAFEMYRL----HGETQKDIARELGVSPTLVNFMIRDALVHCRKCLDAC  160 (163)
T ss_pred             HHHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHhcc
Confidence            666778999999999999999999985    7799999999999999999999999999999998653

>PRK12511 RNA polymerase sigma factor; Provisional

Probab=99.86  E-value=1.3e-20  Score=169.65  Aligned_cols=157  Identities=13%  Similarity=0.136  Sum_probs=122.7

Q ss_pred             HHHHHHHhHHHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHhccCCCCCCCchhHHHHHHHHHHHHHHHhhcCcccCCcc
Q 046578          143 QERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYWWIKQAIIRAIANKSRTIRLPGS  222 (379)
Q Consensus       143 ~e~Li~~y~~lV~~ia~r~~~~~~d~eDLvQEg~i~L~~ai~~fD~~~g~~FsTYa~~~Ir~~i~~~lr~~~r~irip~~  222 (379)
                      .+..+..|++.|+.+|.++.++..++||++||+|+.+|+.+..|+..  .+|.+|++.+++|.+++++|++.+....   
T Consensus         6 ~~~~~~~~~~~l~~~~~~~~~~~~dAEDivQe~flkl~~~~~~~~~~--~~~~~WL~~Iarn~~id~~Rk~~~~~~~---   80 (182)
T PRK12511          6 KRFDVLDQLVPLRRYARSLTRDSAEAEDLVHDALVRALERRASFRSG--GNLRTWLMSILHNAFIDELRRRRVEARR---   80 (182)
T ss_pred             hhhhHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhHHhcCCc--cchHHHHHHHHHHHHHHHHHhhcccccc---
Confidence            45568899999999999999999999999999999999999999863  3799999999999999999986531000   


Q ss_pred             hHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCccccCCCCcccccCCCCCCCChHHHH
Q 046578          223 MAGMVAKIAEANNVLSRRLRRMPTDSEIAEMLNIHVSTVRLAIERTRHPISLDGAVTDRGCMTMQDIIPGPDETMPERMV  302 (379)
Q Consensus       223 ~~~~~~ki~~a~~~l~~~lgr~pt~~eia~~Lgis~~~~~~~l~~~~~~iSLd~~~~~~~~~~l~d~i~~~~~~~pe~~~  302 (379)
                                                                         .+. ..        +. .+.....+..  
T Consensus        81 ---------------------------------------------------~~~-~~--------~~-~~~~~~~~~~--   97 (182)
T PRK12511         81 ---------------------------------------------------ADE-LA--------VL-ADASLPAAQE--   97 (182)
T ss_pred             ---------------------------------------------------ccc-hh--------hc-cccCCCcchH--
Confidence                                                               000 00        00 0000001111  


Q ss_pred             HHHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHHhhc
Q 046578          303 QKQLMKQELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQTNILN  372 (379)
Q Consensus       303 ~~~e~~~~L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~~l~~~  372 (379)
                       .......+..+|..||+++|+||.|+|+    +|+|++|||+.||+|.++|+++++||+++||+.+...
T Consensus        98 -~~~~~~~l~~~l~~Lp~~~R~v~~L~~~----eg~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~~~~~  162 (182)
T PRK12511         98 -HAVRLAQIRDAFFDLPEEQRAALHLVAI----EGLSYQEAAAVLGIPIGTLMSRIGRARAALRAFEEGT  162 (182)
T ss_pred             -HHHHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHhCcCHHHHHHHHHHHHHHHHHHHHhc
Confidence             1223356889999999999999999984    7799999999999999999999999999999998754

>PRK12546 RNA polymerase sigma factor; Provisional

Probab=99.85  E-value=3.8e-20  Score=167.38  Aligned_cols=158  Identities=11%  Similarity=0.191  Sum_probs=122.2

Q ss_pred             cHHHHHHHHHHhHHHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHhccCCCCCCCchhHHHHHHHHHHHHHHHhhcCccc
Q 046578          139 ERESQERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYWWIKQAIIRAIANKSRTIR  218 (379)
Q Consensus       139 d~~A~e~Li~~y~~lV~~ia~r~~~~~~d~eDLvQEg~i~L~~ai~~fD~~~g~~FsTYa~~~Ir~~i~~~lr~~~r~ir  218 (379)
                      +...++.|+. |.+.++++|.++.++..++||++||+|+.+|+.+..|+..  ..|.+|++.+++|.+++++|+..+.  
T Consensus         6 ~~~~~~~l~~-~~~~l~~~a~~~l~~~~~AEDivQevfl~l~~~~~~~~~~--~~~~awL~~ia~n~~~d~~Rk~~r~--   80 (188)
T PRK12546          6 HRDPRDELVE-HLPALRAFAISLTRNVAVADDLVQDTIVKAWTNFDKFQEG--TNLRAWLFTILRNTFYSDRRKHKRE--   80 (188)
T ss_pred             hhhHHHHHHH-HHHHHHHHHHHHcCChhhHHHHHHHHHHHHHHHHhccCCC--cchHHHHHHHHHHHHHHHHHHhccc--
Confidence            3455566655 7799999999999999999999999999999999999863  3799999999999999999986531  


Q ss_pred             CCcchHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCccccCCCCcccccCCCCCCCCh
Q 046578          219 LPGSMAGMVAKIAEANNVLSRRLRRMPTDSEIAEMLNIHVSTVRLAIERTRHPISLDGAVTDRGCMTMQDIIPGPDETMP  298 (379)
Q Consensus       219 ip~~~~~~~~ki~~a~~~l~~~lgr~pt~~eia~~Lgis~~~~~~~l~~~~~~iSLd~~~~~~~~~~l~d~i~~~~~~~p  298 (379)
                       +                                                   ...+.        ...+....  ....
T Consensus        81 -~---------------------------------------------------~~~~~--------~~~~~~~~--~~~~   98 (188)
T PRK12546         81 -V---------------------------------------------------PDPEG--------VHAASLAV--KPAH   98 (188)
T ss_pred             -c---------------------------------------------------cCccc--------cccccccc--CCcc
Confidence             0                                                   00000        00000000  0011


Q ss_pred             HHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHHhh
Q 046578          299 ERMVQKQLMKQELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQTNIL  371 (379)
Q Consensus       299 e~~~~~~e~~~~L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~~l~~  371 (379)
                      +    .......+..+|..||+++|+||.|+|+    +|+|++|||+.||+|.++|+++++||+++||+.+..
T Consensus        99 ~----~~~~~~~l~~~L~~Lp~~~r~v~~L~~~----~g~s~~EIA~~LgiS~~tVk~~l~Rar~~Lr~~l~~  163 (188)
T PRK12546         99 D----GRLAMSDFRAAFAQLPDEQREALILVGA----SGFSYEEAAEMCGVAVGTVKSRANRARARLAELLQL  163 (188)
T ss_pred             h----hHHHHHHHHHHHHhCCHHHhHHhhhHHh----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHhc
Confidence            1    1122245889999999999999999984    779999999999999999999999999999999865

>TIGR02959 SigZ RNA polymerase sigma factor, SigZ family

Probab=99.85  E-value=3.5e-20  Score=164.72  Aligned_cols=149  Identities=20%  Similarity=0.264  Sum_probs=121.3

Q ss_pred             HHhHHHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHhccCCCCCCCchhHHHHHHHHHHHHHHHhhcCcccCCcchHHHH
Q 046578          148 RSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYWWIKQAIIRAIANKSRTIRLPGSMAGMV  227 (379)
Q Consensus       148 ~~y~~lV~~ia~r~~~~~~d~eDLvQEg~i~L~~ai~~fD~~~g~~FsTYa~~~Ir~~i~~~lr~~~r~irip~~~~~~~  227 (379)
                      ..|.+.++.++.++.++..++||++||+|+.+|+++++|+..  .+|.+|++.+++|.+++++|+..+...++       
T Consensus         2 ~~~~~~l~~~~~~~~~~~~~AeDlvQe~fl~l~~~~~~~~~~--~~f~~wl~~iarn~~~d~~Rk~~~~~~~~-------   72 (170)
T TIGR02959         2 DEFRSELKAFIKSRVSDASDVEDLLQEVFIKIHRNLPSLKDG--QKIQSWLYQIARNTIIDFYRSKSRSVELP-------   72 (170)
T ss_pred             chHHHHHHHHHHHHcCCHhhHHHHHHHHHHHHHHHHHhcCCc--ccHHHHHHHHHHHHHHHHHHhccCccccc-------
Confidence            578999999999999999999999999999999999999863  48999999999999999999865311000       


Q ss_pred             HHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCccccCCCCcccccCCCCCCCChHHHHHHHHH
Q 046578          228 AKIAEANNVLSRRLRRMPTDSEIAEMLNIHVSTVRLAIERTRHPISLDGAVTDRGCMTMQDIIPGPDETMPERMVQKQLM  307 (379)
Q Consensus       228 ~ki~~a~~~l~~~lgr~pt~~eia~~Lgis~~~~~~~l~~~~~~iSLd~~~~~~~~~~l~d~i~~~~~~~pe~~~~~~e~  307 (379)
                                                                     +.            .... .  .+++.....+.
T Consensus        73 -----------------------------------------------~~------------~~~~-~--~~~~~~~~~e~   90 (170)
T TIGR02959        73 -----------------------------------------------ES------------LLAA-D--SAREETFVKEL   90 (170)
T ss_pred             -----------------------------------------------hh------------hccc-C--CccHHHHHHHH
Confidence                                                           00            0000 0  11222334445


Q ss_pred             HHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHHhh
Q 046578          308 KQELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQTNIL  371 (379)
Q Consensus       308 ~~~L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~~l~~  371 (379)
                      ...+..+|..||+++|.||.++|+    +|+|++|||+.||+|.++|++.++||+++||+.+..
T Consensus        91 ~~~l~~~l~~L~~~~r~v~~l~~~----~g~s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~l~~  150 (170)
T TIGR02959        91 SQCIPPMIKELPDEYREAIRLTEL----EGLSQQEIAEKLGLSLSGAKSRVQRGRKKLKELLET  150 (170)
T ss_pred             HHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH
Confidence            567899999999999999999984    679999999999999999999999999999999863

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).

>PRK12525 RNA polymerase sigma factor; Provisional

Probab=99.84  E-value=7.1e-20  Score=162.29  Aligned_cols=160  Identities=15%  Similarity=0.087  Sum_probs=126.7

Q ss_pred             HHHHHHHHHHhHHHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHhccCCCCCCCchhHHHHHHHHHHHHHHHhhcCcccC
Q 046578          140 RESQERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYWWIKQAIIRAIANKSRTIRL  219 (379)
Q Consensus       140 ~~A~e~Li~~y~~lV~~ia~r~~~~~~d~eDLvQEg~i~L~~ai~~fD~~~g~~FsTYa~~~Ir~~i~~~lr~~~r~iri  219 (379)
                      ..++.++|..|.+.++.+|.+++++..++||++||+|+.+|+....++.   ..|.+|++++++|.+.+++|+.... + 
T Consensus         8 ~~~~~~~~~~~~~~l~~~~~~~~~~~~~aeDlvQevf~~l~~~~~~~~~---~~~~~wl~~Iarn~~~d~~Rr~~~~-~-   82 (168)
T PRK12525          8 NTLIGQMFQQDYDWLCKKLSRQLGCPHSAEDIASETFLQVLALPDPASI---REPRALLTTIARRLMYEGWRRQDLE-R-   82 (168)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHcCCcCcHHHHHHHHHHHHHhCCCcccc---cCHHHHHHHHHHHHHHHHHHHHHHH-H-
Confidence            4688999999999999999999999899999999999999986554432   3799999999999999999874310 0 


Q ss_pred             CcchHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCccccCCCCcccccCCCCCCCChH
Q 046578          220 PGSMAGMVAKIAEANNVLSRRLRRMPTDSEIAEMLNIHVSTVRLAIERTRHPISLDGAVTDRGCMTMQDIIPGPDETMPE  299 (379)
Q Consensus       220 p~~~~~~~~ki~~a~~~l~~~lgr~pt~~eia~~Lgis~~~~~~~l~~~~~~iSLd~~~~~~~~~~l~d~i~~~~~~~pe  299 (379)
                               .       .                                    .+.         ..+ .+.....+|+
T Consensus        83 ---------~-------~------------------------------------~~~---------~~~-~~~~~~~~~~  100 (168)
T PRK12525         83 ---------A-------Y------------------------------------LQS---------LAE-APEAVQPSPE  100 (168)
T ss_pred             ---------H-------H------------------------------------HHH---------Hhc-ccccccCChH
Confidence                     0       0                                    000         000 0001123455


Q ss_pred             HHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHHh
Q 046578          300 RMVQKQLMKQELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQTNI  370 (379)
Q Consensus       300 ~~~~~~e~~~~L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~~l~  370 (379)
                      +.+...+....+..++..||+++|.||.|+|+    +|+|++|||+.||+|.+||++.+.||+++||..+.
T Consensus       101 ~~~~~~~~~~~l~~~l~~L~~~~r~v~~L~~~----eg~s~~EIA~~l~is~~tV~~~l~ra~~~~~~~~~  167 (168)
T PRK12525        101 EQWMVIETLLAIDRLLDGLSGKARAAFLMSQL----EGLTYVEIGERLGVSLSRIHQYMVEAFKCCYQGFQ  167 (168)
T ss_pred             HHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHhhc
Confidence            55556666688999999999999999999984    77999999999999999999999999999998763

>TIGR02895 spore_sigI RNA polymerase sigma-I factor

Probab=99.84  E-value=2.8e-19  Score=164.62  Aligned_cols=186  Identities=17%  Similarity=0.248  Sum_probs=138.6

Q ss_pred             HHHhcccHHHHHHHHHHhHHHHHHHHHhccCCC--CCHHHHHHHHHHHHHHHHhccCCCCCCCchhHHHHHHHHHHHHHH
Q 046578          133 YKILCKERESQERIIRSYRSLVVSIATGYQGKG--LSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYWWIKQAIIRAI  210 (379)
Q Consensus       133 ~~~~~Gd~~A~e~Li~~y~~lV~~ia~r~~~~~--~d~eDLvQEg~i~L~~ai~~fD~~~g~~FsTYa~~~Ir~~i~~~l  210 (379)
                      ..+++||.. +++|+..|.|+|.++|.+|.++.  .+.||++|+|++|+|+|+++||+++|.+|.+|+.++|++.+.+++
T Consensus         2 ~~~~~gd~~-~e~LI~~Y~plI~~~a~~~~~~~~~~e~dDlvQ~glial~eAi~~yd~~kg~~F~sya~~~Ir~~i~dyl   80 (218)
T TIGR02895         2 QPIQPGNEE-REELIRQYKPFIAKIVSSVCGRYIDTKSDDELSIGLIAFNEAIESYDSNKGKSFLSFAKLIIKRRLIDYI   80 (218)
T ss_pred             chhhcCChH-HHHHHHHhHHHHHHHHHHHHccCCCCChhHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHH
Confidence            568899999 99999999999999999997664  589999999999999999999999999999999999999999999


Q ss_pred             Hhhc---CcccCCcchHHHHHHHHHHHHHHHHHhCCCCCHHHHHHH------hCCCHHHHHHHHHhcCCccccCCccccC
Q 046578          211 ANKS---RTIRLPGSMAGMVAKIAEANNVLSRRLRRMPTDSEIAEM------LNIHVSTVRLAIERTRHPISLDGAVTDR  281 (379)
Q Consensus       211 r~~~---r~irip~~~~~~~~ki~~a~~~l~~~lgr~pt~~eia~~------Lgis~~~~~~~l~~~~~~iSLd~~~~~~  281 (379)
                      |+..   ..+++|+........+..+..++...+++.|+.+||+..      .|++.+.+-.                  
T Consensus        81 Rk~~k~~~~v~~~~~~~e~~~~~~~~~~~~~~~~~~~~~~eEI~~~~~~L~~~gi~~~dLv~------------------  142 (218)
T TIGR02895        81 RKNQKYQNLLYLDEDYDENPLEFNKSMEEYRNEIENENRRLEILEYKKLLKQFGIEFVELVK------------------  142 (218)
T ss_pred             HhcccccCeeeCCchHHHHHHHHHHHHHHHHHHHccccHHHHHHHHHHHHHHcCCcHHHHhh------------------
Confidence            9987   456888766666667777888899999999999998743      2444332221                  


Q ss_pred             CCCcccccCCCCCCCChHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 046578          282 GCMTMQDIIPGPDETMPERMVQKQLMKQELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRG  359 (379)
Q Consensus       282 ~~~~l~d~i~~~~~~~pe~~~~~~e~~~~L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~  359 (379)
                                .    +|-.. +..+....+...+..=+.--..+..       ...++.+|++..+|||+.|+.+...
T Consensus       143 ----------~----sPkh~-d~r~~~i~ia~~~~~~~~l~~~l~~-------kk~LP~k~l~~~~~v~rktier~rk  198 (218)
T TIGR02895       143 ----------V----SPKHR-DTRKKAIKIAKVIVENEELLEYLIR-------KKKLPIKEIEERVRISRKTIERYRK  198 (218)
T ss_pred             ----------c----CCCCH-HHHHHHHHHHHHHhcCHHHHHHHHH-------hCCCCHHHHHHHcCCCHHHHHHhhH
Confidence                      1    11111 1112222233333322222222222       2569999999999999999876544

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).

>PRK06704 RNA polymerase factor sigma-70; Validated

Probab=99.84  E-value=1.3e-19  Score=168.33  Aligned_cols=161  Identities=17%  Similarity=0.155  Sum_probs=128.6

Q ss_pred             HHHHHHHhcccHHHHHHHHHHhHHHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHhccCCCCCCCchhHHHHHHHHHHHH
Q 046578          129 NLVKYKILCKERESQERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYWWIKQAIIR  208 (379)
Q Consensus       129 ~eLi~~~~~Gd~~A~e~Li~~y~~lV~~ia~r~~~~~~d~eDLvQEg~i~L~~ai~~fD~~~g~~FsTYa~~~Ir~~i~~  208 (379)
                      ..++++..+||..+++.+++.| +.++++|.++.++..++||++||+|+.+|+.   |+..  ..|.+|++++++|.++|
T Consensus         6 ~~~~~~~~~~~~~~~~~l~~~y-~~L~r~~~~~~~d~~dAEDlvQE~flk~~~~---~~~~--~~~~~WL~~IarN~~id   79 (228)
T PRK06704          6 THILKNHIDMNHSNINFLIEQY-GELKRYCTFLTKNKWDGEDLAQETVCKVLQK---YSNK--DICMTLVYKIARNRWLD   79 (228)
T ss_pred             HHHHhcccCCCHHHHHHHHHHH-HHHHHHHHHHhCCHHHHHHHHHHHHHHHHHH---cCcc--ccHHHHHHHHHHHHHHH
Confidence            4568889999999999888888 7899999999999999999999999999986   5432  25999999999999999


Q ss_pred             HHHhhcCcccCCcchHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCccccCCCCcccc
Q 046578          209 AIANKSRTIRLPGSMAGMVAKIAEANNVLSRRLRRMPTDSEIAEMLNIHVSTVRLAIERTRHPISLDGAVTDRGCMTMQD  288 (379)
Q Consensus       209 ~lr~~~r~irip~~~~~~~~ki~~a~~~l~~~lgr~pt~~eia~~Lgis~~~~~~~l~~~~~~iSLd~~~~~~~~~~l~d  288 (379)
                      ++|++.+...                                                       +.    ++       
T Consensus        80 ~~Rk~k~~~~-------------------------------------------------------~~----~~-------   93 (228)
T PRK06704         80 QIKSKSVHEK-------------------------------------------------------IR----DQ-------   93 (228)
T ss_pred             HHhccccccc-------------------------------------------------------cc----cc-------
Confidence            9997652000                                                       00    00       


Q ss_pred             cCCCCCCCChHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhH
Q 046578          289 IIPGPDETMPERMVQKQLMKQELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQT  368 (379)
Q Consensus       289 ~i~~~~~~~pe~~~~~~e~~~~L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~~  368 (379)
                       ...   ..+....  .+..+.+..+++.||+++|.||.|+|+    +++|++|||+.||+|.++|+++++||+++||+.
T Consensus        94 -~~~---~~~~~~~--~~~~~~l~~~L~~Lp~~~R~v~lL~~~----eg~S~~EIAe~LgiS~~tVksrL~Rark~Lr~~  163 (228)
T PRK06704         94 -ITF---EEPHEKI--ADLHEMVGKVLSSLNVQQSAILLLKDV----FQYSIADIAKVCSVSEGAVKASLFRSRNRLKTV  163 (228)
T ss_pred             -ccc---CChHHHH--HHHHHHHHHHHHhCCHHHhhHhhhHHh----hCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence             000   0111111  223356889999999999999999984    779999999999999999999999999999998


Q ss_pred             Hhh
Q 046578          369 NIL  371 (379)
Q Consensus       369 l~~  371 (379)
                      +..
T Consensus       164 l~~  166 (228)
T PRK06704        164 SEE  166 (228)
T ss_pred             HHh
Confidence            854

>PRK09636 RNA polymerase sigma factor SigJ; Provisional

Probab=99.83  E-value=1.9e-19  Score=173.60  Aligned_cols=161  Identities=16%  Similarity=0.116  Sum_probs=124.3

Q ss_pred             HHHHHHHHHHhHHHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHhccCCCCCCCchhHHHHHHHHHHHHHHHhhcCcccC
Q 046578          140 RESQERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYWWIKQAIIRAIANKSRTIRL  219 (379)
Q Consensus       140 ~~A~e~Li~~y~~lV~~ia~r~~~~~~d~eDLvQEg~i~L~~ai~~fD~~~g~~FsTYa~~~Ir~~i~~~lr~~~r~iri  219 (379)
                      ...++++|+.|.+.++.+|++++++..++||++||+|+. |.....|+   ...|.+|++++++|.++|++|+..+..  
T Consensus         3 ~~~~~~l~~~~~~~l~~~a~~~~~~~~dAEDlvQe~fl~-~~~~~~~~---~~~~~~WL~~Ia~n~~~d~lR~~~~~~--   76 (293)
T PRK09636          3 MADAAAEFEPLRPHLLSVAYRMLGSVADAEDIVQEAWLR-WNNADRAQ---IRDPRAWLTRVVTRLCLDRLRSARHRR--   76 (293)
T ss_pred             ccHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHH-HHhccccc---ccCHHHHHHHHHHHHHHHHHHhhhccc--
Confidence            456789999999999999999999999999999999999 66667775   247999999999999999999764200  


Q ss_pred             CcchHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCccccCCCCcccccCCCCCCCChH
Q 046578          220 PGSMAGMVAKIAEANNVLSRRLRRMPTDSEIAEMLNIHVSTVRLAIERTRHPISLDGAVTDRGCMTMQDIIPGPDETMPE  299 (379)
Q Consensus       220 p~~~~~~~~ki~~a~~~l~~~lgr~pt~~eia~~Lgis~~~~~~~l~~~~~~iSLd~~~~~~~~~~l~d~i~~~~~~~pe  299 (379)
                                                                         ......        .+.+...+. ..+|+
T Consensus        77 ---------------------------------------------------~~~~~~--------~~~e~~~~~-~~~~~   96 (293)
T PRK09636         77 ---------------------------------------------------ETYVGP--------WLPEPVVEE-LDDPL   96 (293)
T ss_pred             ---------------------------------------------------ccccCC--------cCCcCCCCC-CCChH
Confidence                                                               000000        000001111 11234


Q ss_pred             HHH-HHHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHHh
Q 046578          300 RMV-QKQLMKQELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQTNI  370 (379)
Q Consensus       300 ~~~-~~~e~~~~L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~~l~  370 (379)
                      +.. ...+....+..+|++|||++|.||.|+|+    +++|++|||+.||+|.++|+++++||+++||+.+.
T Consensus        97 ~~~~~~~~~~~~l~~~l~~L~~~~R~v~~L~~~----~g~s~~EIA~~lg~s~~tVk~~l~RAr~~Lr~~~~  164 (293)
T PRK09636         97 EAVVAAEDLSLALMLALERLSPLERAAFLLHDV----FGVPFDEIASTLGRSPAACRQLASRARKHVRAARP  164 (293)
T ss_pred             HHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHH----hCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhhCC
Confidence            333 34444567899999999999999999994    67999999999999999999999999999999764

>PRK09047 RNA polymerase factor sigma-70; Validated

Probab=99.82  E-value=3.2e-19  Score=156.34  Aligned_cols=156  Identities=13%  Similarity=0.121  Sum_probs=113.3

Q ss_pred             CCCCCHHHHHHHHHHHHHHHHhccCCCCCCCchhHHHHHHHHHHHHHHHhhcCcccCCcchHHHHHHHHHHHHHHHHHhC
Q 046578          163 GKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYWWIKQAIIRAIANKSRTIRLPGSMAGMVAKIAEANNVLSRRLR  242 (379)
Q Consensus       163 ~~~~d~eDLvQEg~i~L~~ai~~fD~~~g~~FsTYa~~~Ir~~i~~~lr~~~r~irip~~~~~~~~ki~~a~~~l~~~lg  242 (379)
                      ++..++||++||+|+.+|+.++.+ +  +..|.+|++++++|.+++++|++.+......                     
T Consensus         2 ~~~~~AeDivQe~fl~~~~~~~~~-~--~~~~~~wl~~ia~n~~~d~~Rk~~~~~~~~~---------------------   57 (161)
T PRK09047          2 RDDDAALDIVQDAMIKLAEKYGDR-P--AAEWPPLFQRILQNRIHDWFRRQKVRNTWVS---------------------   57 (161)
T ss_pred             CCHHHHHHHHHHHHHHHHHHHhhc-c--cCchHHHHHHHHHHHHHHHHHhhcccccccc---------------------
Confidence            445689999999999999998863 2  3479999999999999999998653110000                     


Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCccccCCCCcccccCCCCC--CCChHHHHHHHHHHHHHHHHHhcCCH
Q 046578          243 RMPTDSEIAEMLNIHVSTVRLAIERTRHPISLDGAVTDRGCMTMQDIIPGPD--ETMPERMVQKQLMKQELKELLQTLSE  320 (379)
Q Consensus       243 r~pt~~eia~~Lgis~~~~~~~l~~~~~~iSLd~~~~~~~~~~l~d~i~~~~--~~~pe~~~~~~e~~~~L~~~L~~L~~  320 (379)
                                                 ...++.....+++. ...+.+.+..  ..+|++.+...+....+..+|..||+
T Consensus        58 ---------------------------~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~Lp~  109 (161)
T PRK09047         58 ---------------------------LFSSFSDDDDDDDF-DPLETLDSADEGAESPADKLERAQVLQLIEEAIQKLPA  109 (161)
T ss_pred             ---------------------------cccccccccccccc-cHHHHhccccccCCCHHHHHHHHHHHHHHHHHHHhCCH
Confidence                                       00000000000000 1111111111  24677777777788889999999999


Q ss_pred             HHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHHhhchh
Q 046578          321 READILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQTNILNNL  374 (379)
Q Consensus       321 rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~~l~~~~L  374 (379)
                      ++|+||.|+|+    +|+|++|||+.||+|.++|+++++||+++||+.+...++
T Consensus       110 ~~r~v~~l~~~----~g~s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~l~~~~~  159 (161)
T PRK09047        110 RQREAFLLRYW----EDMDVAETAAAMGCSEGSVKTHCSRATHALAKALEAKGI  159 (161)
T ss_pred             HHHHHHHHHHH----hcCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHhcCc
Confidence            99999999995    779999999999999999999999999999999876554

>PRK09635 sigI RNA polymerase sigma factor SigI; Provisional

Probab=99.80  E-value=1.3e-18  Score=167.58  Aligned_cols=162  Identities=17%  Similarity=0.152  Sum_probs=124.2

Q ss_pred             HHHHHHHHHHhHHHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHhccCCCCCCCchhHHHHHHHHHHHHHHHhhcCcccC
Q 046578          140 RESQERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYWWIKQAIIRAIANKSRTIRL  219 (379)
Q Consensus       140 ~~A~e~Li~~y~~lV~~ia~r~~~~~~d~eDLvQEg~i~L~~ai~~fD~~~g~~FsTYa~~~Ir~~i~~~lr~~~r~iri  219 (379)
                      ...+..+|+.|.+.++++|++++++..++||++||+|+.+|++...+    ...|.+|++++++|.++|++|+..+... 
T Consensus         4 ~~~~~~l~~~~~~~L~~~a~r~lgs~~dAEDvvQE~flr~~~~~~~~----~~~~~aWL~~Ia~n~~id~lRk~~~rr~-   78 (290)
T PRK09635          4 HDPVSAAWRAHRAYLVDLAFRMVGDIGVAEDMVQEAFSRLLRAPVGD----IDDERGWLIVVTSRLCLDHIKSASTRRE-   78 (290)
T ss_pred             ccHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHhcCccc----cccHHHHHHHHHHHHHHHHHhhhhccCc-
Confidence            35678999999999999999999999999999999999999986542    2369999999999999999997542000 


Q ss_pred             CcchHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCccccCCCCcccccCCCCCCCChH
Q 046578          220 PGSMAGMVAKIAEANNVLSRRLRRMPTDSEIAEMLNIHVSTVRLAIERTRHPISLDGAVTDRGCMTMQDIIPGPDETMPE  299 (379)
Q Consensus       220 p~~~~~~~~ki~~a~~~l~~~lgr~pt~~eia~~Lgis~~~~~~~l~~~~~~iSLd~~~~~~~~~~l~d~i~~~~~~~pe  299 (379)
                                                                        .....+... .      .+..+  ...+|+
T Consensus        79 --------------------------------------------------~~~~~~~~~-~------~~~~~--~~~~~~   99 (290)
T PRK09635         79 --------------------------------------------------RPQDIAAWH-D------GDASV--SSVDPA   99 (290)
T ss_pred             --------------------------------------------------CcccccccC-c------cccCC--CCCCcH
Confidence                                                              000000000 0      00011  112333


Q ss_pred             H-HHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHH
Q 046578          300 R-MVQKQLMKQELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQTN  369 (379)
Q Consensus       300 ~-~~~~~e~~~~L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~~l  369 (379)
                      + ....++....+..+|..|||+||.||.|+|+    .++|++|||+.||+|.++|+++++||+++||+..
T Consensus       100 ~~~~~~~e~~~al~~~L~~L~p~~R~vf~L~~~----~g~s~~EIA~~Lgis~~tVr~~l~RAr~~Lr~~~  166 (290)
T PRK09635        100 DRVTLDDEVRLALLIMLERLGPAERVVFVLHEI----FGLPYQQIATTIGSQASTCRQLAHRARRKINESR  166 (290)
T ss_pred             HHHHHHHHHHHHHHHHHHhCCHHHHHHhhHHHH----hCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHhhC
Confidence            3 3445556678999999999999999999995    6799999999999999999999999999999864

>TIGR02957 SigX4 RNA polymerase sigma-70 factor, TIGR02957 family

Probab=99.79  E-value=2.9e-18  Score=164.58  Aligned_cols=156  Identities=17%  Similarity=0.143  Sum_probs=119.5

Q ss_pred             HHHHHhHHHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHhccCCCCCCCchhHHHHHHHHHHHHHHHhhcCcccCCcchH
Q 046578          145 RIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYWWIKQAIIRAIANKSRTIRLPGSMA  224 (379)
Q Consensus       145 ~Li~~y~~lV~~ia~r~~~~~~d~eDLvQEg~i~L~~ai~~fD~~~g~~FsTYa~~~Ir~~i~~~lr~~~r~irip~~~~  224 (379)
                      ++|+.|.+.++.+|++++++..++||++||+|+.+++.  .|+.  ...|.+|++++++|.++|++|+..+..       
T Consensus         1 ~l~~~~~~~l~~~a~r~lg~~~dAEDvvQE~flk~~~~--~~~~--~~~~~awL~~Ia~n~~ld~lR~~~~~~-------   69 (281)
T TIGR02957         1 EEFEALRPLLFSLAYRMLGSVADAEDIVQETFLRWQEA--DRAQ--IENPKAYLTKVVTRRCIDVLRSARARR-------   69 (281)
T ss_pred             ChHHHHHHHHHHHHHHHhCCHhHHHHHHHHHHHHHHhC--Cccc--ccCHHHHHHHHHHHHHHHHHHHhhhcc-------
Confidence            37899999999999999999999999999999997764  4543  237999999999999999999764200       


Q ss_pred             HHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCccccCCCCcccccCCCCCCCChHHHHHH
Q 046578          225 GMVAKIAEANNVLSRRLRRMPTDSEIAEMLNIHVSTVRLAIERTRHPISLDGAVTDRGCMTMQDIIPGPDETMPERMVQK  304 (379)
Q Consensus       225 ~~~~ki~~a~~~l~~~lgr~pt~~eia~~Lgis~~~~~~~l~~~~~~iSLd~~~~~~~~~~l~d~i~~~~~~~pe~~~~~  304 (379)
                                                                   ..  ...+       .+.+.... ...+|++....
T Consensus        70 ---------------------------------------------~~--~~~~-------~~~e~~~~-~~~~~~~~~~~   94 (281)
T TIGR02957        70 ---------------------------------------------EV--YVGP-------WLPEPLLT-TSADPAESVEL   94 (281)
T ss_pred             ---------------------------------------------cc--cCCC-------CCCcccCC-CCCChHHHHHH
Confidence                                                         00  0000       00000111 11245554443


Q ss_pred             -HHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHHh
Q 046578          305 -QLMKQELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQTNI  370 (379)
Q Consensus       305 -~e~~~~L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~~l~  370 (379)
                       +++...+..+|++|||+||.||.|+|+    +++|++|||+.||+|.++|+++++||+++||+...
T Consensus        95 ~e~~~~~l~~~l~~L~~~~R~v~~L~~~----~g~s~~EIA~~lg~s~~tVr~~l~RAr~~Lr~~~~  157 (281)
T TIGR02957        95 AESLSMAYLLLLERLSPLERAVFVLREV----FDYPYEEIASIVGKSEANCRQLVSRARRHLDARRP  157 (281)
T ss_pred             HHHHHHHHHHHHhhCCHHHHHHHHHHHH----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhhCC
Confidence             344567889999999999999999984    67999999999999999999999999999998754

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.

>PF07638 Sigma70_ECF: ECF sigma factor

Probab=99.73  E-value=2.1e-16  Score=142.54  Aligned_cols=177  Identities=18%  Similarity=0.250  Sum_probs=127.6

Q ss_pred             cHHHHHHHHhcccHHHHHHHHHHhHHHHHHHHHhccCC---CCCHHH--HHHHHHHHHHHHHhccCCCCCCCchhHHHHH
Q 046578          127 DYNLVKYKILCKERESQERIIRSYRSLVVSIATGYQGK---GLSLKD--LIQEGSIGLLRGAKRFNPERGYKLSTYVYWW  201 (379)
Q Consensus       127 ~~~eLi~~~~~Gd~~A~e~Li~~y~~lV~~ia~r~~~~---~~d~eD--LvQEg~i~L~~ai~~fD~~~g~~FsTYa~~~  201 (379)
                      ++.+||.++++||+.|+++|+..|++.+..+|+++...   +.+.+|  +++|+|+.++......+.+....|..|+..+
T Consensus         3 ~it~ll~~~~~GD~~A~~~L~~~~y~~L~~~a~~~l~~~~~~~~~~~~~lv~ea~lrl~~~~~~~~~~~~~~f~~~~~~~   82 (185)
T PF07638_consen    3 EITELLDRWRQGDEAALDQLFERYYPELRRLARRRLRRERRGHDLQDTALVHEAFLRLARRGRFVQFSDRRHFWALLARI   82 (185)
T ss_pred             hHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHhccccCCchhHHHHHHHHHHHHhccccccCCCCHHHHHHHHHHH
Confidence            46789999999999999999999999999999987533   334444  4778888777643332333334799999999


Q ss_pred             HHHHHHHHHHhhcCcccCCcchHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCccccC
Q 046578          202 IKQAIIRAIANKSRTIRLPGSMAGMVAKIAEANNVLSRRLRRMPTDSEIAEMLNIHVSTVRLAIERTRHPISLDGAVTDR  281 (379)
Q Consensus       202 Ir~~i~~~lr~~~r~irip~~~~~~~~ki~~a~~~l~~~lgr~pt~~eia~~Lgis~~~~~~~l~~~~~~iSLd~~~~~~  281 (379)
                      +++.++|+.|++.+..|-...                                               ...+++..    
T Consensus        83 ~rr~lid~~R~~~a~KRg~~~-----------------------------------------------~~~~l~~~----  111 (185)
T PF07638_consen   83 MRRKLIDHARRRQAQKRGGDQ-----------------------------------------------VRVELDER----  111 (185)
T ss_pred             HHHHHHHHHHHHHHHhcCCCC-----------------------------------------------cccchhhh----
Confidence            999999999986642221100                                               01112211    


Q ss_pred             CCCcccccCCCCCCCChHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 046578          282 GCMTMQDIIPGPDETMPERMVQKQLMKQELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIA  361 (379)
Q Consensus       282 ~~~~l~d~i~~~~~~~pe~~~~~~e~~~~L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rA  361 (379)
                              ..+...+.|+..+.   +.+.+..+.. |+|+++++|.++|+    +|+|.+|||+.||||+.||++.+..|
T Consensus       112 --------~~~~~~~~~~~~~~---l~e~l~~L~~-l~~~~~~~v~l~~~----~Gls~~EIA~~lgiS~~tV~r~l~~a  175 (185)
T PF07638_consen  112 --------ADSGDEPSPEELLE---LEEALERLLA-LDPRQRRVVELRFF----EGLSVEEIAERLGISERTVRRRLRRA  175 (185)
T ss_pred             --------hccccCCCHHHHHH---HHHHHHHHHc-cCHHHHHHHHHHHH----CCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence                    11111234555443   3344555555 99999999999985    67999999999999999999999999


Q ss_pred             HHHHHhHHh
Q 046578          362 LTKLQQTNI  370 (379)
Q Consensus       362 l~kLR~~l~  370 (379)
                      +.+|++.+.
T Consensus       176 R~~l~~~l~  184 (185)
T PF07638_consen  176 RAWLRRELR  184 (185)
T ss_pred             HHHHHHHhc
Confidence            999998864

>TIGR03209 P21_Cbot clostridium toxin-associated regulator BotR

Probab=99.71  E-value=1.5e-16  Score=136.86  Aligned_cols=136  Identities=18%  Similarity=0.265  Sum_probs=99.8

Q ss_pred             HHHHHHHhHHHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHhc-----cCCCCCCCchhHHHHHHHHHHHHHHHhhcCcc
Q 046578          143 QERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKR-----FNPERGYKLSTYVYWWIKQAIIRAIANKSRTI  217 (379)
Q Consensus       143 ~e~Li~~y~~lV~~ia~r~~~~~~d~eDLvQEg~i~L~~ai~~-----fD~~~g~~FsTYa~~~Ir~~i~~~lr~~~r~i  217 (379)
                      ++.+|..|.++++.+|+++..    .+|+ ||+|+.+|....+     |++.  .+|.||++++++|.++|++|++.+..
T Consensus         1 f~~~~~~y~~~l~~~~~~~~~----~~~~-qdvf~~~w~~~~~~~~~~~~~~--~~~~~wL~~iarN~~id~~Rk~~~~~   73 (142)
T TIGR03209         1 FEEIYMNFKNTIDIFTRKYNL----YYDY-NDILYHLWIILKKIDLNKFNTE--NDLEKYISTSLKRYCLDICNKKNRDK   73 (142)
T ss_pred             ChHHHHHHHHHHHHHHHHhcc----hhhH-HHHHHHHHHHHHHhhhhhcCch--hHHHHHHHHHHHHHHHHHHHHHhhhh
Confidence            467999999999999999964    3344 9999999999865     5532  47999999999999999999765200


Q ss_pred             cCCcchHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCccccCCCCcccccCCCCCCCC
Q 046578          218 RLPGSMAGMVAKIAEANNVLSRRLRRMPTDSEIAEMLNIHVSTVRLAIERTRHPISLDGAVTDRGCMTMQDIIPGPDETM  297 (379)
Q Consensus       218 rip~~~~~~~~ki~~a~~~l~~~lgr~pt~~eia~~Lgis~~~~~~~l~~~~~~iSLd~~~~~~~~~~l~d~i~~~~~~~  297 (379)
                      ..                                                    .. +.        ...+    . ...
T Consensus        74 ~~----------------------------------------------------~~-~~--------~~~~----~-~~~   87 (142)
T TIGR03209        74 KI----------------------------------------------------IY-NS--------EITD----I-KLS   87 (142)
T ss_pred             hh----------------------------------------------------hh-hh--------hhhc----c-ccc
Confidence            00                                                    00 00        0000    0 001


Q ss_pred             hHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHH
Q 046578          298 PERMVQKQLMKQELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIR  355 (379)
Q Consensus       298 pe~~~~~~e~~~~L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr  355 (379)
                      +.+.....+....+..+++.||+.+|+||.|+|+    +|+|++|||+.||+|.+||+
T Consensus        88 ~~~~~~~~~~~~~l~~~l~~Lp~~~r~v~~l~~~----~~~s~~EIA~~l~is~~tV~  141 (142)
T TIGR03209        88 LINVYSSNDLEFEFNDLISILPNKQKKIIYMKFF----EDMKEIDIAKKLHISRQSVY  141 (142)
T ss_pred             hhHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHHCcCHHhhc
Confidence            1222333444566889999999999999999985    77999999999999999996

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.

>PRK08311 putative RNA polymerase sigma factor SigI; Reviewed

Probab=99.70  E-value=1.8e-15  Score=141.38  Aligned_cols=92  Identities=17%  Similarity=0.300  Sum_probs=84.7

Q ss_pred             cHHHHHHHHhcccHHHHHHHHHHhHHHHHHHHHhccCCCC--CHHHHHHHHHHHHHHHHhccCCCCCCCchhHHHHHHHH
Q 046578          127 DYNLVKYKILCKERESQERIIRSYRSLVVSIATGYQGKGL--SLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYWWIKQ  204 (379)
Q Consensus       127 ~~~eLi~~~~~Gd~~A~e~Li~~y~~lV~~ia~r~~~~~~--d~eDLvQEg~i~L~~ai~~fD~~~g~~FsTYa~~~Ir~  204 (379)
                      +..+++.++++||..|++.|++.|.|+|+++|.+++++..  ++||++|+||+++|+++++|++++|.+|.+|+.++++|
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            5788999999999999999999999999999999988765  59999999999999999999998887999999999999


Q ss_pred             HHHHHHHhhcCccc
Q 046578          205 AIIRAIANKSRTIR  218 (379)
Q Consensus       205 ~i~~~lr~~~r~ir  218 (379)
                      .++|++|+..+...
T Consensus        84 ~~iDylRk~~~~~~   97 (237)
T PRK08311         84 RLIDYFRKESKHNL   97 (237)
T ss_pred             HHHHHHHHhhcccc
Confidence            99999998765433

>PRK09191 two-component response regulator; Provisional

Probab=99.69  E-value=3.2e-16  Score=147.29  Aligned_cols=137  Identities=15%  Similarity=0.091  Sum_probs=111.9

Q ss_pred             HHHHHHHHhHHHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHhccCCCCCCCchhHHHHHHHHHHHHHHHhhcCcccCCc
Q 046578          142 SQERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYWWIKQAIIRAIANKSRTIRLPG  221 (379)
Q Consensus       142 A~e~Li~~y~~lV~~ia~r~~~~~~d~eDLvQEg~i~L~~ai~~fD~~~g~~FsTYa~~~Ir~~i~~~lr~~~r~irip~  221 (379)
                      ++.++|..|.+.++++|.++.++..++||++||+|+.+|+...+|++.  ..|.+|+++++++...+.    ..      
T Consensus         2 ~~~~l~~~~~~~l~~~~~~~~~~~~~aeDi~qd~~~~~~~~~~~~~~~--~~~~~wl~~~~~~~~~~~----~~------   69 (261)
T PRK09191          2 SLSQRIAPHLPYLRRYARALTGSQSSGDAYVAATLEALLADPSIFPEA--SSPRVGLYRLFHRLWSSA----GA------   69 (261)
T ss_pred             chHHHHHHHhHHHHHHHHHhcCChhhHHHHHHHHHHHHHHhHHhcCCC--cchhhHHHHHHHHHhccc----cc------
Confidence            578999999999999999999999999999999999999999999864  369999999876542110    00      


Q ss_pred             chHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCccccCCCCcccccCCCCCCCChHHH
Q 046578          222 SMAGMVAKIAEANNVLSRRLRRMPTDSEIAEMLNIHVSTVRLAIERTRHPISLDGAVTDRGCMTMQDIIPGPDETMPERM  301 (379)
Q Consensus       222 ~~~~~~~ki~~a~~~l~~~lgr~pt~~eia~~Lgis~~~~~~~l~~~~~~iSLd~~~~~~~~~~l~d~i~~~~~~~pe~~  301 (379)
                                                                           +    .  .        ...  .+.. 
T Consensus        70 -----------------------------------------------------~----~--~--------~~~--~~~~-   79 (261)
T PRK09191         70 -----------------------------------------------------N----D--P--------EPG--SPFE-   79 (261)
T ss_pred             -----------------------------------------------------c----C--C--------CCC--CCch-
Confidence                                                                 0    0  0        000  1111 


Q ss_pred             HHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHHhh
Q 046578          302 VQKQLMKQELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQTNIL  371 (379)
Q Consensus       302 ~~~~e~~~~L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~~l~~  371 (379)
                             ..+..+|++||+++|+|+.|+|+    +|+|++|||+.||+|.++|+.+++||+++||+.+..
T Consensus        80 -------~~l~~~l~~L~~~~r~v~~l~~~----~~~s~~eIA~~l~~s~~tV~~~l~ra~~~l~~~~~~  138 (261)
T PRK09191         80 -------ARAERRLAGLTPLPRQAFLLTAL----EGFSVEEAAEILGVDPAEAEALLDDARAEIARQVAT  138 (261)
T ss_pred             -------HHHHHHHHhCCHHHhHHHHHHHH----hcCCHHHHHHHHCCCHHHHHHHHHHHHHHHhccCCC
Confidence                   15889999999999999999984    779999999999999999999999999999987753

>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=99.43  E-value=5e-13  Score=100.66  Aligned_cols=70  Identities=24%  Similarity=0.497  Sum_probs=66.8

Q ss_pred             HHHHhHHHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHhccCCCCCCCchhHHHHHHHHHHHHHHHhhcC
Q 046578          146 IIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYWWIKQAIIRAIANKSR  215 (379)
Q Consensus       146 Li~~y~~lV~~ia~r~~~~~~d~eDLvQEg~i~L~~ai~~fD~~~g~~FsTYa~~~Ir~~i~~~lr~~~r  215 (379)
                      ||+.|.|.|++++.++.++..++||++||+++++|+++++|+++.+.+|.+|++.+++|.+.+++|++.+
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            6899999999999999999999999999999999999999999888889999999999999999998764

Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 2 of sigma-70 is the most conserved region of the entire protein. All members of this class of sigma-factor contain region 2. The high conservation is due to region 2 containing both the -10 promoter recognition helix and the primary core RNA polymerase binding determinant. The core-binding helix, interacts with the clamp domain of the largest polymerase subunit, beta prime [, ]. The aromatic residues of the recognition helix, found at the C terminus of this domain are thought to mediate strand separation, thereby allowing transcription initiation [, ].; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 1OR7_B 1H3L_B 2Z2S_C 2Q1Z_C 2O7G_B 1SMY_F 1IW7_P 2BE5_F 2A6E_F 2CW0_F ....

>PF04545 Sigma70_r4: Sigma-70, region 4; InterPro: IPR007630 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription

Probab=99.28  E-value=1.1e-11  Score=87.60  Aligned_cols=50  Identities=34%  Similarity=0.528  Sum_probs=45.7

Q ss_pred             HHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHh
Q 046578          314 LLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQ  367 (379)
Q Consensus       314 ~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~  367 (379)
                      +|+.||++|++||.++|+    +++|+.|||+.||+|+++|+++..+|+++||+
T Consensus         1 Al~~L~~~er~vi~~~y~----~~~t~~eIa~~lg~s~~~V~~~~~~al~kLR~   50 (50)
T PF04545_consen    1 ALDQLPPREREVIRLRYF----EGLTLEEIAERLGISRSTVRRILKRALKKLRK   50 (50)
T ss_dssp             HHCTS-HHHHHHHHHHHT----ST-SHHHHHHHHTSCHHHHHHHHHHHHHHHHH
T ss_pred             ChhhCCHHHHHHHHHHhc----CCCCHHHHHHHHCCcHHHHHHHHHHHHHHhcC
Confidence            588999999999999995    78999999999999999999999999999995

Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 4 of sigma-70 like sigma-factors is involved in binding to the -35 promoter element via a helix-turn-helix motif []. Due to the way Pfam works, the threshold has been set artificially high to prevent overlaps with other helix-turn-helix families. Therefore there are many false negatives.; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 2P7V_B 3IYD_F 1TLH_B 1KU7_A 1RIO_H 3N97_A 1KU3_A 1RP3_C 1SC5_A 1NR3_A ....

>PF08281 Sigma70_r4_2: Sigma-70, region 4; InterPro: IPR013249 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription

Probab=99.08  E-value=4.4e-10  Score=80.62  Aligned_cols=53  Identities=28%  Similarity=0.413  Sum_probs=45.1

Q ss_pred             HHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Q 046578          309 QELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKL  365 (379)
Q Consensus       309 ~~L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kL  365 (379)
                      +.|..++..||+++|.||.++|+    +|+|++|||+.+|+|.++|++.++||+++|
T Consensus         2 ~~l~~~l~~L~~~~r~i~~l~~~----~g~s~~eIa~~l~~s~~~v~~~l~ra~~~L   54 (54)
T PF08281_consen    2 EALQQALAQLPERQREIFLLRYF----QGMSYAEIAEILGISESTVKRRLRRARKKL   54 (54)
T ss_dssp             HHHHHHHHCS-HHHHHHHHHHHT----S---HHHHHHHCTS-HHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHCCCHHHHHHHHHHHH----HCcCHHHHHHHHCcCHHHHHHHHHHHHhhC
Confidence            46889999999999999999994    779999999999999999999999999987

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.

>PF04539 Sigma70_r3: Sigma-70 region 3; InterPro: IPR007624 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription

Probab=98.97  E-value=2.2e-09  Score=82.96  Aligned_cols=76  Identities=41%  Similarity=0.526  Sum_probs=65.1

Q ss_pred             HHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCccccCCCCcccccCCCCCCCChHHH
Q 046578          226 MVAKIAEANNVLSRRLRRMPTDSEIAEMLNIHVSTVRLAIERTRHPISLDGAVTDRGCMTMQDIIPGPDETMPERM  301 (379)
Q Consensus       226 ~~~ki~~a~~~l~~~lgr~pt~~eia~~Lgis~~~~~~~l~~~~~~iSLd~~~~~~~~~~l~d~i~~~~~~~pe~~  301 (379)
                      .++++.++...|.+.+||.||.+|||+.||++.+++..++......+||+.+...+++..+.+++.++...+|++.
T Consensus         2 ~l~~i~~a~~~L~~~lgr~Pt~eEiA~~lgis~~~v~~~l~~~~~~~Sl~~~~~~~~~~~l~~~i~d~~~~~P~e~   77 (78)
T PF04539_consen    2 KLRKIERARRELEQELGREPTDEEIAEELGISVEEVRELLQASRRPVSLDLPVGDEDDSTLGDFIEDDDAPSPEEE   77 (78)
T ss_dssp             HHHHHHHHHHHHHHHHSS--BHHHHHHHHTS-HHHHHHHHHHHSCCEESSHCCSSSSSEEGGGSSB-SSS--HHHH
T ss_pred             hHHHHHHHHHHHHHHhCCCCCHHHHHHHHcccHHHHHHHHHhCCCCeEEeeeecCCCCCchhheecCCCCCChhhc
Confidence            5789999999999999999999999999999999999999999999999999988888899999999888888765

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 ....

>PRK06930 positive control sigma-like factor; Validated

Probab=98.87  E-value=1.3e-08  Score=90.52  Aligned_cols=70  Identities=21%  Similarity=0.296  Sum_probs=61.0

Q ss_pred             HHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHHhhc
Q 046578          299 ERMVQKQLMKQELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQTNILN  372 (379)
Q Consensus       299 e~~~~~~e~~~~L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~~l~~~  372 (379)
                      .+.....+....+..++..||+++|.||.++|+    +|+|++|||+.||+|.++|+++++||+++|++.+...
T Consensus        96 ~~~~~~~e~~~~l~~al~~L~~rer~V~~L~~~----eg~s~~EIA~~lgiS~~tVk~~l~Ra~~kLr~~l~~~  165 (170)
T PRK06930         96 PESVISEWDKIRIEDALSVLTEREKEVYLMHRG----YGLSYSEIADYLNIKKSTVQSMIERAEKKIARQINES  165 (170)
T ss_pred             hhHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHh
Confidence            333444555678999999999999999999884    7799999999999999999999999999999987653

>PRK00118 putative DNA-binding protein; Validated

Probab=98.72  E-value=7.5e-08  Score=78.33  Aligned_cols=62  Identities=16%  Similarity=0.095  Sum_probs=55.5

Q ss_pred             HHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHHhhchh
Q 046578          309 QELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQTNILNNL  374 (379)
Q Consensus       309 ~~L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~~l~~~~L  374 (379)
                      ..+.-....||+++++++.++|+    +++|++|||+.+|+|++||++++.||+++||+++...++
T Consensus         9 ~l~d~~~~~L~ekqRevl~L~y~----eg~S~~EIAe~lGIS~~TV~r~L~RArkkLr~~~~~~~~   70 (104)
T PRK00118          9 LLFDFYGSLLTEKQRNYMELYYL----DDYSLGEIAEEFNVSRQAVYDNIKRTEKLLEDYEEKLHL   70 (104)
T ss_pred             HHHHHHhccCCHHHHHHHHHHHH----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHHCh
Confidence            44555778999999999999985    789999999999999999999999999999999987654

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

Probab=98.55  E-value=2.9e-07  Score=64.59  Aligned_cols=54  Identities=41%  Similarity=0.622  Sum_probs=49.0

Q ss_pred             HHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 046578          309 QELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQ  366 (379)
Q Consensus       309 ~~L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR  366 (379)
                      ..+..++..|++.++.++.++|+    +++|.++||+.+|+|.++|++++++++.+||
T Consensus         2 ~~~~~~~~~l~~~~~~~~~~~~~----~~~~~~~ia~~~~~s~~~i~~~~~~~~~~l~   55 (55)
T cd06171           2 ERLEEALDKLPEREREVILLRFG----EGLSYEEIAEILGISRSTVRQRLHRALKKLR   55 (55)
T ss_pred             HHHHHHHHhCCHHHHHHHHHHHh----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHcC
Confidence            35778899999999999999984    6699999999999999999999999998875

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

>TIGR00721 tfx DNA-binding protein, Tfx family

Probab=98.42  E-value=6.5e-07  Score=76.47  Aligned_cols=55  Identities=24%  Similarity=0.316  Sum_probs=48.7

Q ss_pred             cCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHHhhchhhh
Q 046578          317 TLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQTNILNNLKV  376 (379)
Q Consensus       317 ~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~~l~~~~L~~  376 (379)
                      .|+++|++|+.+++     +|+|++|||+.||+|+++|++++++|+++|++......+-.
T Consensus         6 ~Lte~qr~VL~Lr~-----~GlTq~EIAe~LgiS~stV~~~e~ra~kkLr~a~~~~~l~~   60 (137)
T TIGR00721         6 FLTERQIKVLELRE-----KGLSQKEIAKELKTTRANVSAIEKRAMENIEKARNTLDFVK   60 (137)
T ss_pred             CCCHHHHHHHHHHH-----cCCCHHHHHHHHCcCHHHHHHHHHhHHHHHHHHhhHHHHHH
Confidence            59999999999975     77999999999999999999999999999998766554433

Tfx from Methanobacterium thermoautotrophicum is associated with the operon for molybdenum formyl-methanofuran dehydrogenase and binds a DNA sequence near its promoter.

>PRK03975 tfx putative transcriptional regulator; Provisional

Probab=98.38  E-value=8.9e-07  Score=75.98  Aligned_cols=52  Identities=25%  Similarity=0.349  Sum_probs=47.6

Q ss_pred             hcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHHhhc
Q 046578          316 QTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQTNILN  372 (379)
Q Consensus       316 ~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~~l~~~  372 (379)
                      ..|+|+|++||.+++     +|+|++|||+.||+|+++|++++++++++||+.....
T Consensus         5 ~~Lt~rqreVL~lr~-----~GlTq~EIAe~LGiS~~tVs~ie~ra~kkLr~~~~tl   56 (141)
T PRK03975          5 SFLTERQIEVLRLRE-----RGLTQQEIADILGTSRANVSSIEKRARENIEKARETL   56 (141)
T ss_pred             cCCCHHHHHHHHHHH-----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHH
Confidence            469999999999965     7899999999999999999999999999999987653

>PRK04217 hypothetical protein; Provisional

Probab=98.36  E-value=1.1e-06  Score=72.23  Aligned_cols=55  Identities=20%  Similarity=0.148  Sum_probs=50.0

Q ss_pred             hcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHHhhchh
Q 046578          316 QTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQTNILNNL  374 (379)
Q Consensus       316 ~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~~l~~~~L  374 (379)
                      ..|++.|++++.++|+    +++|++|||+.||||++||++++++|+++|++++.....
T Consensus        41 ~~Lt~eereai~l~~~----eGlS~~EIAk~LGIS~sTV~r~L~RArkkLre~L~~~~~   95 (110)
T PRK04217         41 IFMTYEEFEALRLVDY----EGLTQEEAGKRMGVSRGTVWRALTSARKKVAQMLVEGRE   95 (110)
T ss_pred             ccCCHHHHHHHHHHHH----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHhccc
Confidence            4699999999999984    779999999999999999999999999999999876544

>PF04297 UPF0122: Putative helix-turn-helix protein, YlxM / p13 like; InterPro: IPR007394 Members of this family are predicted to contain a helix-turn-helix motif, for example residues 37-55 in Mycoplasma mycoides p13 (O05290 from SWISSPROT)

Probab=98.22  E-value=7.8e-06  Score=66.00  Aligned_cols=60  Identities=27%  Similarity=0.314  Sum_probs=45.7

Q ss_pred             HHHHHh-cCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHHhhchh
Q 046578          311 LKELLQ-TLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQTNILNNL  374 (379)
Q Consensus       311 L~~~L~-~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~~l~~~~L  374 (379)
                      +..... -|+++|+.++.++|.    +++|+.|||+.+|||+.+|+-.++||.++|...-...+|
T Consensus        10 L~d~Yg~LLT~kQ~~~l~lyy~----eDlSlsEIAe~~~iSRqaV~d~ikr~~~~L~~yE~kL~l   70 (101)
T PF04297_consen   10 LFDFYGELLTEKQREILELYYE----EDLSLSEIAEELGISRQAVYDSIKRAEKKLEEYEEKLGL   70 (101)
T ss_dssp             HHHHHGGGS-HHHHHHHHHHCT----S---HHHHHHHCTS-HHHHHHHHHHHHHHHHHHHHHH-H
T ss_pred             HHHHHHHHCCHHHHHHHHHHHc----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHhh
Confidence            444444 599999999999994    779999999999999999999999999999877655444

Genes encoding family members are often part of operons that encode components of the SRP pathway, and this protein may regulate the expression of an operon related to the SRP pathway [].; PDB: 1S7O_A 1XSV_B.

>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon

Probab=98.12  E-value=6.7e-06  Score=58.52  Aligned_cols=48  Identities=27%  Similarity=0.374  Sum_probs=42.2

Q ss_pred             hcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhH
Q 046578          316 QTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQT  368 (379)
Q Consensus       316 ~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~~  368 (379)
                      ..|++.|+.++.+.+     .|+|.+|||+.+|+|+++|++++.+++++|+-.
T Consensus         2 ~~l~~~e~~i~~~~~-----~g~s~~eia~~l~is~~tv~~~~~~~~~kl~~~   49 (58)
T smart00421        2 ASLTPREREVLRLLA-----EGLTNKEIAERLGISEKTVKTHLSNIMRKLGVR   49 (58)
T ss_pred             CCCCHHHHHHHHHHH-----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCC
Confidence            468999999987743     669999999999999999999999999988744

lux regulon (activates the bioluminescence operon

>COG4941 Predicted RNA polymerase sigma factor containing a TPR repeat domain [Transcription]

Probab=98.11  E-value=0.00011  Score=70.76  Aligned_cols=161  Identities=14%  Similarity=0.109  Sum_probs=108.5

Q ss_pred             HHHHHHHHhHHHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHhccCCCCCCCchhHHHHHHHHHHHHHHHhhcCcccCCc
Q 046578          142 SQERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYWWIKQAIIRAIANKSRTIRLPG  221 (379)
Q Consensus       142 A~e~Li~~y~~lV~~ia~r~~~~~~d~eDLvQEg~i~L~~ai~~fD~~~g~~FsTYa~~~Ir~~i~~~lr~~~r~irip~  221 (379)
                      ..+..+..-.|.+..---+|+++-.-+||.+||+|+..++...+=-+-.  .-.+|++..-||..+|.+|++.+.-..|.
T Consensus         6 ~ie~~~r~~~~r~~a~L~r~~rd~dlAEEa~~dA~~~Ale~WPr~G~P~--~PaAWL~~v~R~~aiD~~Rr~~~~~~~~~   83 (415)
T COG4941           6 WIEAAARIERPRAMAALARYLRDLDLAEEALQDAFAAALERWPRAGPPR--NPAAWLIAVGRNRAIDRVRRRARRDAAPP   83 (415)
T ss_pred             HHHHHHHHhhhHHHHHHHHHhcccchHHHHHHHHHHHHHHhCcccCCCC--ChHHHHHHHHhhhHHHHHHHHHHhccCCh
Confidence            4466677777777776667777777899999999987766554333322  46899999999999999998764222221


Q ss_pred             chHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCccccCCCCcccccCCCCCCCChHHH
Q 046578          222 SMAGMVAKIAEANNVLSRRLRRMPTDSEIAEMLNIHVSTVRLAIERTRHPISLDGAVTDRGCMTMQDIIPGPDETMPERM  301 (379)
Q Consensus       222 ~~~~~~~ki~~a~~~l~~~lgr~pt~~eia~~Lgis~~~~~~~l~~~~~~iSLd~~~~~~~~~~l~d~i~~~~~~~pe~~  301 (379)
                      +.                                               .++.     ++.+....+..        ++.
T Consensus        84 el-----------------------------------------------~~~~-----e~~e~~~a~~~--------~d~  103 (415)
T COG4941          84 EL-----------------------------------------------LLSD-----EDEEMEEAEAL--------DDE  103 (415)
T ss_pred             hh-----------------------------------------------cccc-----cchhhhccccc--------ccc
Confidence            10                                               0000     01110100000        111


Q ss_pred             HHHHHHHHHHHHHHh-cCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhH
Q 046578          302 VQKQLMKQELKELLQ-TLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQT  368 (379)
Q Consensus       302 ~~~~e~~~~L~~~L~-~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~~  368 (379)
                      ...++....|.-|.. -|++.+|-.+.|+. +   .|+|..|||..|=+++.++-|++-||.++++..
T Consensus       104 ~i~Dd~LRLiFvccHPal~~~~riALtLR~-v---~GLs~~eIArAFLv~e~am~QRivRAK~ri~~a  167 (415)
T COG4941         104 HIRDDRLRLIFVCCHPALPPEQRIALTLRL-V---GGLSTAEIARAFLVPEAAMAQRIVRAKARIREA  167 (415)
T ss_pred             ccchhhHHhhhhhcCCCCChhhHHHHHHHH-H---cCCcHHHHHHHHcCCcHHHHHHHHHHHHHHHhc
Confidence            112223344555555 79999999999998 3   559999999999999999999999999999975

>TIGR01636 phage_rinA phage transcriptional activator, RinA family

Probab=98.08  E-value=1.8e-05  Score=67.71  Aligned_cols=62  Identities=11%  Similarity=0.205  Sum_probs=54.7

Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHH
Q 046578          306 LMKQELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQTN  369 (379)
Q Consensus       306 e~~~~L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~~l  369 (379)
                      .....|..+++.|++.++.||.++|+ .+ ..+|..+||..||+|+.+|+++..+++.+|++.+
T Consensus        71 ~~~~~I~~~l~~Ld~~er~II~~rY~-~~-~~~t~~~Ia~~l~iS~~t~~r~r~~~l~kla~~l  132 (134)
T TIGR01636        71 RNRDAIENCLNEADEQTRVIIQELYM-KK-RPLTLVGLAQQLFISKSTAYRLRNHIIEAVAEEL  132 (134)
T ss_pred             HHHHHHHHHHHhCCHHHHHHHHHHHc-cC-CCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHh
Confidence            34567999999999999999999994 33 3469999999999999999999999999999874

This model represents a family of phage proteins, including RinA, a transcriptional activator in staphylococcal phage phi 11. This family shows similarity to ArpU, a phage-related putative autolysin regulator, and to some sporulation-specific sigma factors.

>PF00196 GerE: Bacterial regulatory proteins, luxR family; InterPro: IPR000792 This domain is a DNA-binding, helix-turn-helix (HTH) domain of about 65 amino acids, present in transcription regulators of the LuxR/FixJ family of response regulators

Probab=98.06  E-value=9.9e-06  Score=58.84  Aligned_cols=48  Identities=33%  Similarity=0.445  Sum_probs=41.3

Q ss_pred             hcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhH
Q 046578          316 QTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQT  368 (379)
Q Consensus       316 ~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~~  368 (379)
                      ..|+++|.+|+.+..     .|++.+|||+.+|+|..||+.++.++++||.-.
T Consensus         2 ~~LT~~E~~vl~~l~-----~G~~~~eIA~~l~is~~tV~~~~~~i~~Kl~~~   49 (58)
T PF00196_consen    2 PSLTERELEVLRLLA-----QGMSNKEIAEELGISEKTVKSHRRRIMKKLGVK   49 (58)
T ss_dssp             GSS-HHHHHHHHHHH-----TTS-HHHHHHHHTSHHHHHHHHHHHHHHHHT-S
T ss_pred             CccCHHHHHHHHHHH-----hcCCcchhHHhcCcchhhHHHHHHHHHHHhCCC
Confidence            479999999999876     779999999999999999999999999998643

The domain is named after Vibrio fischeri luxR, a transcriptional activator for quorum-sensing control of luminescence. LuxR-type HTH domain proteins occur in a variety of organisms. The DNA-binding HTH domain is usually located in the C-terminal region; the N-terminal region often containing an autoinducer-binding domain or a response regulatory domain. Most luxR-type regulators act as transcription activators, but some can be repressors or have a dual role for different sites. LuxR-type HTH regulators control a wide variety of activities in various biological processes. The luxR-type, DNA-binding HTH domain forms a four-helical bundle structure. The HTH motif comprises the second and third helices, known as the scaffold and recognition helix, respectively. The HTH binds DNA in the major groove, where the N-terminal part of the recognition helix makes most of the DNA contacts. The fourth helix is involved in dimerisation of gerE and traR. Signalling events by one of the four activation mechanisms described below lead to multimerisation of the regulator. The regulators bind DNA as multimers [, , ]. LuxR-type HTH proteins can be activated by one of four different mechanisms: 1) Regulators which belong to a two-component sensory transduction system where the protein is activated by its phosphorylation, generally on an aspartate residue, by a transmembrane kinase [, ]. Some proteins that belong to this category are: Rhizobiaceae fixJ (global regulator inducing expression of nitrogen-fixation genes in microaerobiosis) Escherichia coli and Salmonella typhimurium uhpA (activates hexose phosphate transport gene uhpT) E. coli narL and narP (activate nitrate reductase operon) Enterobacteria rcsB (regulation of exopolysaccharide biosynthesis in enteric and plant pathogenesis) Bordetella pertussis bvgA (virulence factor) Bacillus subtilis coma (involved in expression of late-expressing competence genes) 2) Regulators which are activated, or in very rare cases repressed, when bound to N-acyl homoserine lactones, which are used as quorum sensing molecules in a variety of Gram-negative bacteria []: V. fischeri luxR (activates bioluminescence operon) Agrobacterium tumefaciens traR (regulation of Ti plasmid transfer) Erwinia carotovora carR (control of carbapenem antibiotics biosynthesis) E. carotovora expR (virulence factor for soft rot disease; activates plant tissue macerating enzyme genes) Pseudomonas aeruginosa lasR (activates elastase gene lasB) Erwinia chrysanthemi echR and Erwinia stewartii esaR Pseudomonas chlororaphis phzR (positive regulator of phenazine antibiotic production) Pseudomonas aeruginosa rhlR (activates rhlAB operon and lasB gene) 3) Autonomous effector domain regulators, without a regulatory domain, represented by gerE []. B. subtilis gerE (transcription activator and repressor for the regulation of spore formation) 4) Multiple ligand-binding regulators, exemplified by malT []. E. coli malT (activates maltose operon; MalT binds ATP and maltotriose); GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3SZT_A 3CLO_A 1H0M_A 1L3L_A 3C57_B 1ZLK_B 1ZLJ_H 3C3W_B 1RNL_A 1ZG1_A ....

>cd06170 LuxR_C_like C-terminal DNA-binding domain of LuxR-like proteins

Probab=97.98  E-value=2.1e-05  Score=55.98  Aligned_cols=46  Identities=28%  Similarity=0.379  Sum_probs=41.0

Q ss_pred             CCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhH
Q 046578          318 LSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQT  368 (379)
Q Consensus       318 L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~~  368 (379)
                      |+++|+.++.+.+     .++|.+|||+.+|+|+++|++++++++++|+..
T Consensus         1 l~~~e~~i~~~~~-----~~~s~~eia~~l~~s~~tv~~~~~~~~~~l~~~   46 (57)
T cd06170           1 LTPREREVLRLLA-----EGKTNKEIADILGISEKTVKTHLRNIMRKLGVK   46 (57)
T ss_pred             CCHHHHHHHHHHH-----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHhCCC
Confidence            6889999998754     669999999999999999999999999988764

This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many are active as homodimers. Many are two domain proteins in which the DNA binding property of the C-terminal DNA binding domain is modulated by modifications of the N-terminal domain. For example in the case of Lux R which participates in the regulation of gene expression in response to fluctuations in cell-population density (quorum-sensing), a signaling molecule, the pheromone Acyl HSL (N-acyl derivatives of homoserine lactone), binds to the N-terminal domain and leads to LuxR dimerization. For others phophorylation of the N-terminal domain leads to multimerization, for example Escherichia coli NarL and Sinorhizobium melilot FixJ. NarL controls gene expression of many respiratory-related operons when environmental

>TIGR03879 near_KaiC_dom probable regulatory domain

Probab=97.96  E-value=2.2e-05  Score=59.58  Aligned_cols=48  Identities=17%  Similarity=0.070  Sum_probs=41.6

Q ss_pred             HHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 046578          310 ELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGI  360 (379)
Q Consensus       310 ~L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~r  360 (379)
                      .+.+-++.||++.+.++.|.+.+   +++|++|||+.||+|.++|++++++
T Consensus         8 ~~~~~l~~l~~~~r~af~L~R~~---eGlS~kEIAe~LGIS~~TVk~~l~~   55 (73)
T TIGR03879         8 KLAERLTWVDSLAEAAAALAREE---AGKTASEIAEELGRTEQTVRNHLKG   55 (73)
T ss_pred             hHHHHHhcCCHHHHHHHHHHHHH---cCCCHHHHHHHHCcCHHHHHHHHhc
Confidence            46677899999999999996432   6699999999999999999998875

This model describes a common domain shared by two different families of proteins, each of which occurs regularly next to its corresponding partner family, a probable regulatory with homology to KaiC. By implication, this protein family likely is also involved in sensory transduction and/or regulation.

>PF07374 DUF1492: Protein of unknown function (DUF1492); InterPro: IPR010861 This entry is represented by Streptococcus phage 7201, Orf19

Probab=97.94  E-value=5.9e-05  Score=61.22  Aligned_cols=54  Identities=28%  Similarity=0.413  Sum_probs=47.9

Q ss_pred             HHHHHHHHhcCC-HHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Q 046578          308 KQELKELLQTLS-EREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKL  365 (379)
Q Consensus       308 ~~~L~~~L~~L~-~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kL  365 (379)
                      ...+..++++|+ +.+|.||.++|.    .+++..+||+.||+|+.++.+++.+|++.|
T Consensus        45 k~ei~~~I~~l~d~~~r~iL~~~Yi----~~~~~~~I~~~l~~S~~t~yr~~~~Al~~L   99 (100)
T PF07374_consen   45 KLEIRRAINKLEDPDERLILRMRYI----NKLTWEQIAEELNISRRTYYRIHKKALKEL   99 (100)
T ss_pred             HHHHHHHHHHccChhHHHHHHHHHH----cCCCHHHHHHHHCCCHHHHHHHHHHHHHhc
Confidence            345788889886 789999999994    559999999999999999999999999876

The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This entry consists of several hypothetical, highly conserved Streptococcal and related phage proteins. The function of this family is unknown.

>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=97.89  E-value=5e-05  Score=56.63  Aligned_cols=58  Identities=22%  Similarity=0.256  Sum_probs=50.6

Q ss_pred             HHHHHHhcccHHHHHHHHHHhHHHHHHHHHhccCC------CCCHHHHHHHHHHHHHHHHhccC
Q 046578          130 LVKYKILCKERESQERIIRSYRSLVVSIATGYQGK------GLSLKDLIQEGSIGLLRGAKRFN  187 (379)
Q Consensus       130 eLi~~~~~Gd~~A~e~Li~~y~~lV~~ia~r~~~~------~~d~eDLvQEg~i~L~~ai~~fD  187 (379)
                      ++|.++++||+.|.++++..|.|+|.+++.+-..+      +.--+|+-|+--..|++++.+|+
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            57899999999999999999999999999884322      34459999999999999999985

Some proteins with this domain are annotated as conjugative transposon proteins.

>PF04967 HTH_10: HTH DNA binding domain; InterPro: IPR007050 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif

Probab=97.87  E-value=6.2e-05  Score=53.64  Aligned_cols=48  Identities=23%  Similarity=0.373  Sum_probs=41.1

Q ss_pred             CCHHHHHHHHHHhhcC---CCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Q 046578          318 LSEREADILRLHFGLD---GQTPVSCKEIGRLLSLSRERIRQIRGIALTKL  365 (379)
Q Consensus       318 L~~rer~Vl~l~ygL~---g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kL  365 (379)
                      |+++|++++...|-.+   -..+.|..|||+.||||.+++..++++|.+||
T Consensus         1 LT~~Q~e~L~~A~~~GYfd~PR~~tl~elA~~lgis~st~~~~LRrae~kl   51 (53)
T PF04967_consen    1 LTDRQREILKAAYELGYFDVPRRITLEELAEELGISKSTVSEHLRRAERKL   51 (53)
T ss_pred             CCHHHHHHHHHHHHcCCCCCCCcCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Confidence            7899999999875322   23578999999999999999999999999987

This entry represents the HTH DNA binding domain found in Halobacterium salinarium (Halobacterium halobium) and described as a putative bacterio-opsin activator.

>PRK15201 fimbriae regulatory protein FimW; Provisional

Probab=97.81  E-value=4.5e-05  Score=67.28  Aligned_cols=47  Identities=30%  Similarity=0.370  Sum_probs=43.7

Q ss_pred             cCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhH
Q 046578          317 TLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQT  368 (379)
Q Consensus       317 ~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~~  368 (379)
                      .|+++|++|+.+.-     +|+|.+|||+.|++|.+||+....++++||.-.
T Consensus       133 ~LSpRErEVLrLLA-----qGkTnKEIAe~L~IS~rTVkth~srImkKLgV~  179 (198)
T PRK15201        133 HFSVTERHLLKLIA-----SGYHLSETAALLSLSEEQTKSLRRSIMRKLHVK  179 (198)
T ss_pred             CCCHHHHHHHHHHH-----CCCCHHHHHHHhCCCHHHHHHHHHHHHHHhCCC
Confidence            58999999999886     889999999999999999999999999999754

>PRK15411 rcsA colanic acid capsular biosynthesis activation protein A; Provisional

Probab=97.80  E-value=4e-05  Score=70.35  Aligned_cols=47  Identities=17%  Similarity=0.327  Sum_probs=43.8

Q ss_pred             cCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhH
Q 046578          317 TLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQT  368 (379)
Q Consensus       317 ~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~~  368 (379)
                      .|+|+|++|+.+.-     +|+|.+|||+.||+|..||+.+.++.++||.-.
T Consensus       137 ~LT~RE~eVL~lla-----~G~snkeIA~~L~iS~~TVk~h~~~I~~KL~v~  183 (207)
T PRK15411        137 SLSRTESSMLRMWM-----AGQGTIQISDQMNIKAKTVSSHKGNIKRKIKTH  183 (207)
T ss_pred             cCCHHHHHHHHHHH-----cCCCHHHHHHHcCCCHHHHHHHHHHHHHHhCCC
Confidence            49999999999986     889999999999999999999999999999753

>PRK13719 conjugal transfer transcriptional regulator TraJ; Provisional

Probab=97.78  E-value=4.5e-05  Score=69.83  Aligned_cols=52  Identities=15%  Similarity=0.110  Sum_probs=47.4

Q ss_pred             HHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhH
Q 046578          312 KELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQT  368 (379)
Q Consensus       312 ~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~~  368 (379)
                      .++...|+|+|++|+.+.-     +|+|.+|||+.|++|.+||+..+.+.++||.-.
T Consensus       138 ~~~~~~LS~RE~eVL~Lia-----~G~SnkEIA~~L~IS~~TVk~hvs~I~~KLgv~  189 (217)
T PRK13719        138 LEAKNKVTKYQNDVFILYS-----FGFSHEYIAQLLNITVGSSKNKISEILKFFGIS  189 (217)
T ss_pred             hhccCCCCHHHHHHHHHHH-----CCCCHHHHHHHhCCCHHHHHHHHHHHHHHhCCC
Confidence            5667899999999999986     789999999999999999999999999998643

>COG4566 TtrR Response regulator [Signal transduction mechanisms]

Probab=97.76  E-value=0.00013  Score=65.27  Aligned_cols=63  Identities=22%  Similarity=0.268  Sum_probs=54.7

Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHHhhch
Q 046578          306 LMKQELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQTNILNN  373 (379)
Q Consensus       306 e~~~~L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~~l~~~~  373 (379)
                      +....+...+.+|+|+||+|+...-     .|+..++||..||||+.||..+..+..+||+..-....
T Consensus       131 ~~~~~~~~~l~tLT~RERqVl~~vV-----~G~~NKqIA~dLgiS~rTVe~HRanvM~Km~a~SlaeL  193 (202)
T COG4566         131 DRQAAIRARLATLTPRERQVLDLVV-----RGLMNKQIAFDLGISERTVELHRANVMEKMQARSLAEL  193 (202)
T ss_pred             HHHHHHHHHHHhcCHHHHHHHHHHH-----cCcccHHHHHHcCCchhhHHHHHHHHHHHHhhccHHHH
Confidence            3456788999999999999999875     77999999999999999999999999999987654433

>TIGR01321 TrpR trp operon repressor, proteobacterial

Probab=97.73  E-value=6e-05  Score=59.99  Aligned_cols=54  Identities=22%  Similarity=0.238  Sum_probs=44.3

Q ss_pred             HHHHHHHh-cCCHHHHHHHHHHhhcCC---CCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 046578          309 QELKELLQ-TLSEREADILRLHFGLDG---QTPVSCKEIGRLLSLSRERIRQIRGIALT  363 (379)
Q Consensus       309 ~~L~~~L~-~L~~rer~Vl~l~ygL~g---~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~  363 (379)
                      +.+..++. -|+|+|+.++..||++.+   ..++|++|||+.+|||..+|.+. .++++
T Consensus        23 ~~l~~~l~~lLTp~E~~~l~~R~~i~~~Ll~~~~tQrEIa~~lGiS~atIsR~-sn~lk   80 (94)
T TIGR01321        23 DDMQLLLELILTRSEREDLGDRIRIVNELLNGNMSQREIASKLGVSIATITRG-SNNLK   80 (94)
T ss_pred             HHHHHHHHHhCCHHHHHHHHHHHHHHHHHHhCCCCHHHHHHHhCCChhhhhHH-Hhhcc
Confidence            34566664 599999999999999986   57899999999999999999764 44444

This model represents TrpR, the repressor of the trp operon. It is found so far only in the gamma subdivision of the proteobacteria and in Chlamydia trachomatis. All members belong to species capable of tryptophan biosynthesis.

>PRK11475 DNA-binding transcriptional activator BglJ; Provisional

Probab=97.73  E-value=6.2e-05  Score=69.15  Aligned_cols=47  Identities=28%  Similarity=0.265  Sum_probs=43.6

Q ss_pred             hcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHh
Q 046578          316 QTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQ  367 (379)
Q Consensus       316 ~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~  367 (379)
                      ..|+++|++|+.+..     +|+|.+|||+.|++|..||+.++.+.++||.-
T Consensus       133 ~~LT~RE~eVL~ll~-----~G~snkeIA~~L~iS~~TV~~h~~~I~~KLgv  179 (207)
T PRK11475        133 RMLSPTEREILRFMS-----RGYSMPQIAEQLERNIKTIRAHKFNVMSKLGV  179 (207)
T ss_pred             CCCCHHHHHHHHHHH-----CCCCHHHHHHHHCCCHHHHHHHHHHHHHHcCC
Confidence            469999999999986     78999999999999999999999999999953

>PF02001 DUF134: Protein of unknown function DUF134; InterPro: IPR002852 The bacterial and archaeal proteins in this family have no known function

Probab=97.68  E-value=0.00012  Score=59.79  Aligned_cols=53  Identities=21%  Similarity=0.201  Sum_probs=48.5

Q ss_pred             cCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHHhhch
Q 046578          317 TLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQTNILNN  373 (379)
Q Consensus       317 ~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~~l~~~~  373 (379)
                      .|+..|-+.|+|.++    +++|++|-|+.||||+.|+.+++..|++|+-++|-...
T Consensus        41 ~L~~dElEAiRL~D~----egl~QeeaA~~MgVSR~T~~ril~~ARkKiA~ALv~Gk   93 (106)
T PF02001_consen   41 VLTVDELEAIRLVDY----EGLSQEEAAERMGVSRPTFQRILESARKKIADALVEGK   93 (106)
T ss_pred             EeeHHHHHHHHHHHH----cCCCHHHHHHHcCCcHHHHHHHHHHHHHHHHHHHHCCC
Confidence            488899999999984    77999999999999999999999999999999987654

>PRK10840 transcriptional regulator RcsB; Provisional

Probab=97.65  E-value=8.8e-05  Score=67.78  Aligned_cols=46  Identities=30%  Similarity=0.377  Sum_probs=43.0

Q ss_pred             hcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 046578          316 QTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQ  366 (379)
Q Consensus       316 ~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR  366 (379)
                      ..|+++|++|+.+.-     +|+|.+|||+.|++|..||+.++.+.++||-
T Consensus       149 ~~Lt~rE~evl~~~~-----~G~s~~eIA~~l~iS~~TV~~h~~~i~~Kl~  194 (216)
T PRK10840        149 KRLSPKESEVLRLFA-----EGFLVTEIAKKLNRSIKTISSQKKSAMMKLG  194 (216)
T ss_pred             ccCCHHHHHHHHHHH-----CCCCHHHHHHHHCCCHHHHHHHHHHHHHHcC
Confidence            359999999999886     7899999999999999999999999999995

>COG2197 CitB Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]

Probab=97.64  E-value=8.5e-05  Score=68.43  Aligned_cols=48  Identities=33%  Similarity=0.386  Sum_probs=44.0

Q ss_pred             hcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhH
Q 046578          316 QTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQT  368 (379)
Q Consensus       316 ~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~~  368 (379)
                      ..|++||++|+.+.-     +|+|.+|||+.|++|.+||+.++++.++||.-.
T Consensus       147 ~~LT~RE~eVL~lla-----~G~snkeIA~~L~iS~~TVk~h~~~i~~KL~v~  194 (211)
T COG2197         147 ELLTPRELEVLRLLA-----EGLSNKEIAEELNLSEKTVKTHVSNILRKLGVR  194 (211)
T ss_pred             CCCCHHHHHHHHHHH-----CCCCHHHHHHHHCCCHhHHHHHHHHHHHHcCCC
Confidence            469999999999875     789999999999999999999999999998643

>PRK10100 DNA-binding transcriptional regulator CsgD; Provisional

Probab=97.63  E-value=9.7e-05  Score=68.33  Aligned_cols=48  Identities=25%  Similarity=0.232  Sum_probs=44.3

Q ss_pred             hcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhH
Q 046578          316 QTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQT  368 (379)
Q Consensus       316 ~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~~  368 (379)
                      ..|+++|++|+.+.+     +|+|.+|||+.|++|..||+.++.++++||.-.
T Consensus       154 ~~Lt~rE~~Vl~l~~-----~G~s~~eIA~~L~iS~~TVk~~~~~i~~Kl~v~  201 (216)
T PRK10100        154 ALLTHREKEILNKLR-----IGASNNEIARSLFISENTVKTHLYNLFKKIAVK  201 (216)
T ss_pred             CCCCHHHHHHHHHHH-----cCCCHHHHHHHhCCCHHHHHHHHHHHHHHhCCC
Confidence            359999999999987     689999999999999999999999999999754

>TIGR03020 EpsA transcriptional regulator EpsA

Probab=97.62  E-value=0.0001  Score=69.53  Aligned_cols=50  Identities=24%  Similarity=0.270  Sum_probs=45.2

Q ss_pred             HhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHH
Q 046578          315 LQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQTN  369 (379)
Q Consensus       315 L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~~l  369 (379)
                      +..|+++|++|+.+..     +|+|.+|||+.||||+.||+.+++++++||.-.-
T Consensus       188 ~~~LT~RE~evl~l~a-----~G~s~~eIA~~L~IS~~TVk~hl~~i~~KL~v~n  237 (247)
T TIGR03020       188 AGLITAREAEILAWVR-----DGKTNEEIAAILGISSLTVKNHLQHIFKKLDVRN  237 (247)
T ss_pred             ccCCCHHHHHHHHHHH-----CCCCHHHHHHHHCcCHHHHHHHHHHHHHHhCCCC
Confidence            4579999999999875     7899999999999999999999999999997543

Proteins in this family include a C-terminal LuxR transcriptional regulator domain (pfam00196). These proteins are positioned proximal to either EpsH-containing exopolysaccharide biosynthesis operons of the Methylobacillus type, or the associated PEP-CTERM-containing genes.

>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A

Probab=97.61  E-value=9.9e-05  Score=50.60  Aligned_cols=41  Identities=20%  Similarity=0.255  Sum_probs=24.2

Q ss_pred             hcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 046578          316 QTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGI  360 (379)
Q Consensus       316 ~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~r  360 (379)
                      ..|++.||..|...+    .+|+|..+||+.||++++||++.+.|
T Consensus         3 ~~Lt~~eR~~I~~l~----~~G~s~~~IA~~lg~s~sTV~relkR   43 (44)
T PF13936_consen    3 KHLTPEERNQIEALL----EQGMSIREIAKRLGRSRSTVSRELKR   43 (44)
T ss_dssp             ---------HHHHHH----CS---HHHHHHHTT--HHHHHHHHHH
T ss_pred             cchhhhHHHHHHHHH----HcCCCHHHHHHHHCcCcHHHHHHHhc
Confidence            468999999998776    48899999999999999999998876

>TIGR03541 reg_near_HchA LuxR family transcriptional regulatory, chaperone HchA-associated

Probab=97.59  E-value=0.00013  Score=68.22  Aligned_cols=51  Identities=24%  Similarity=0.230  Sum_probs=45.6

Q ss_pred             HhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHHh
Q 046578          315 LQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQTNI  370 (379)
Q Consensus       315 L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~~l~  370 (379)
                      ...|+++|++|+.+..     +|+|.+|||+.||+|..||+.++.++++||+..-+
T Consensus       169 ~~~Lt~re~evl~~~a-----~G~t~~eIa~~l~is~~Tv~~~l~~~~~kl~~~~~  219 (232)
T TIGR03541       169 AGVLSEREREVLAWTA-----LGRRQADIAAILGISERTVENHLRSARRKLGVATT  219 (232)
T ss_pred             hccCCHHHHHHHHHHH-----CCCCHHHHHHHHCcCHHHHHHHHHHHHHHHCCCCH
Confidence            3479999999999965     77999999999999999999999999999985543

Members of this protein family belong to the LuxR transcriptional regulator family, and contain both autoinducer binding (pfam03472) and transcriptional regulator (pfam00196) domains. Members, however, occur only in a few members of the Gammaproteobacteria that have the chaperone/aminopeptidase HchA, and are always encoded by the adjacent gene.

>PRK10188 DNA-binding transcriptional activator SdiA; Provisional

Probab=97.49  E-value=0.00021  Score=67.12  Aligned_cols=47  Identities=23%  Similarity=0.306  Sum_probs=43.6

Q ss_pred             cCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhH
Q 046578          317 TLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQT  368 (379)
Q Consensus       317 ~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~~  368 (379)
                      .|+++|++||.+..     +|+|.+|||+.||||..||+.++.++++||--.
T Consensus       179 ~LT~rE~evl~~~a-----~G~t~~eIa~~l~is~~TV~~h~~~~~~KL~~~  225 (240)
T PRK10188        179 NFSKREKEILKWTA-----EGKTSAEIAMILSISENTVNFHQKNMQKKFNAP  225 (240)
T ss_pred             CCCHHHHHHHHHHH-----cCCCHHHHHHHhCCCHHHHHHHHHHHHHHhCCC
Confidence            69999999999886     789999999999999999999999999999644

>PRK13870 transcriptional regulator TraR; Provisional

Probab=97.48  E-value=0.0002  Score=67.02  Aligned_cols=47  Identities=19%  Similarity=0.186  Sum_probs=43.2

Q ss_pred             cCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhH
Q 046578          317 TLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQT  368 (379)
Q Consensus       317 ~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~~  368 (379)
                      .|++||+++|...-     +|.|..|||.+||||+.||..+++.|++||--.
T Consensus       173 ~LT~RE~E~L~W~A-----~GKT~~EIa~ILgISe~TV~~Hl~na~~KLga~  219 (234)
T PRK13870        173 WLDPKEATYLRWIA-----VGKTMEEIADVEGVKYNSVRVKLREAMKRFDVR  219 (234)
T ss_pred             CCCHHHHHHHHHHH-----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHcCCC
Confidence            59999999999875     889999999999999999999999999999543

>TIGR01637 phage_arpU phage transcriptional regulator, ArpU family

Probab=97.48  E-value=0.0028  Score=53.85  Aligned_cols=61  Identities=18%  Similarity=0.149  Sum_probs=53.3

Q ss_pred             HHHHHHHH-hcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHHh
Q 046578          308 KQELKELL-QTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQTNI  370 (379)
Q Consensus       308 ~~~L~~~L-~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~~l~  370 (379)
                      ...+..++ +.|++.+|.||..+| +.+ ++++..+|+..+|+|+.+.+++..+|+.++-..+.
T Consensus        69 ~~~i~~ai~~~l~~~~r~Il~~~Y-l~~-~~~~~~~I~~~l~~s~~~~y~~k~~Al~~fA~~l~  130 (132)
T TIGR01637        69 ARAIVNAIVNQLDEISRQILYDKY-LEP-DQKYDYQIMMELGYSHRQYYRIKKRALLRFATLYG  130 (132)
T ss_pred             HHHHHHHHHHhCCHHHHHHHHHHH-cCc-cccchHHHHHHhCCcHHHHHHHHHHHHHHHHHHhC
Confidence            45677777 899999999999999 442 46899999999999999999999999999988764

This model represents a family of phage proteins, including ArpU, called a putative autolysin regulatory protein. ArpU was described as a regulator of cellular muramidase-2 of Enterococcus hirae but appears to have been cloned from a prophage. This family appears related to the RinA family of bacteriophage transcriptional activators and to some sporulation-specific sigma factors. We propose that this is a phage transcriptional activator family.

>COG2771 CsgD DNA-binding HTH domain-containing proteins [Transcription]

Probab=97.39  E-value=0.00057  Score=50.00  Aligned_cols=50  Identities=36%  Similarity=0.398  Sum_probs=44.1

Q ss_pred             hcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHHh
Q 046578          316 QTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQTNI  370 (379)
Q Consensus       316 ~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~~l~  370 (379)
                      ..|+++|.+++.+.-     .|.+.+|||..+|+|..||+..+.++.+||.-.-+
T Consensus         3 ~~Lt~rE~~v~~l~~-----~G~s~~eia~~l~is~~tV~~h~~~i~~Kl~~~~r   52 (65)
T COG2771           3 ADLTPREREILRLVA-----QGKSNKEIARILGISEETVKTHLRNIYRKLGVKNR   52 (65)
T ss_pred             ccCCHHHHHHHHHHH-----CCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCCCH
Confidence            368999999998875     67999999999999999999999999999875543

>PRK09483 response regulator; Provisional

Probab=97.33  E-value=0.0004  Score=62.60  Aligned_cols=46  Identities=30%  Similarity=0.363  Sum_probs=42.2

Q ss_pred             hcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 046578          316 QTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQ  366 (379)
Q Consensus       316 ~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR  366 (379)
                      ..|+++|++|+.+..     +|+|.+|||+.|++|..||+.++++.++||-
T Consensus       147 ~~Lt~rE~~vl~~~~-----~G~~~~~Ia~~l~is~~TV~~~~~~i~~Kl~  192 (217)
T PRK09483        147 ASLSERELQIMLMIT-----KGQKVNEISEQLNLSPKTVNSYRYRMFSKLN  192 (217)
T ss_pred             cccCHHHHHHHHHHH-----CCCCHHHHHHHhCCCHHHHHHHHHHHHHHcC
Confidence            459999999998764     7799999999999999999999999999984

>PRK01381 Trp operon repressor; Provisional

Probab=97.17  E-value=0.00048  Score=55.25  Aligned_cols=55  Identities=20%  Similarity=0.196  Sum_probs=42.5

Q ss_pred             HHHHHHHHhc-CCHHHHHHHHHHhhcCC---CCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 046578          308 KQELKELLQT-LSEREADILRLHFGLDG---QTPVSCKEIGRLLSLSRERIRQIRGIALT  363 (379)
Q Consensus       308 ~~~L~~~L~~-L~~rer~Vl~l~ygL~g---~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~  363 (379)
                      .+.+..++.. |+|.|+..|..|+++..   ..++|++|||+.+|+|..||.+ -+++|+
T Consensus        22 ~~~~~~~l~~llTp~Er~al~~R~~I~~~L~~g~~sQREIa~~lGvSiaTITR-gsn~Lk   80 (99)
T PRK01381         22 EDLHLPLLTLLLTPDEREALGTRVRIVEELLRGELSQREIKQELGVGIATITR-GSNSLK   80 (99)
T ss_pred             HHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHcCCcCHHHHHHHhCCceeeehh-hHHHhc
Confidence            3456666664 99999999999988763   2469999999999999998865 344444

>PRK15369 two component system sensor kinase SsrB; Provisional

Probab=97.16  E-value=0.00092  Score=58.97  Aligned_cols=47  Identities=28%  Similarity=0.321  Sum_probs=42.7

Q ss_pred             hcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHh
Q 046578          316 QTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQ  367 (379)
Q Consensus       316 ~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~  367 (379)
                      ..|+++|++|+.+..     +|++.+|||+.+++|..||+.++.++++||.-
T Consensus       148 ~~lt~~e~~vl~l~~-----~g~~~~~Ia~~l~~s~~tv~~~~~~~~~kl~~  194 (211)
T PRK15369        148 PLLTPRERQILKLIT-----EGYTNRDIAEQLSISIKTVETHRLNMMRKLDV  194 (211)
T ss_pred             cCCCHHHHHHHHHHH-----CCCCHHHHHHHhCCCHHHHHHHHHHHHHHhCC
Confidence            359999999999853     77999999999999999999999999999964

>COG2739 Uncharacterized protein conserved in bacteria [Function unknown]

Probab=97.14  E-value=0.00098  Score=53.26  Aligned_cols=49  Identities=20%  Similarity=0.232  Sum_probs=43.2

Q ss_pred             cCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHH
Q 046578          317 TLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQTN  369 (379)
Q Consensus       317 ~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~~l  369 (379)
                      -|+.+|+..+.++|.    +++|+.|||+.++||+++|...++|+-+.|-+.-
T Consensus        17 LLT~KQ~~Y~~lyy~----dDlSl~EIAee~~VSRqAIyDnIKr~~~~L~~YE   65 (105)
T COG2739          17 LLTKKQKNYLELYYL----DDLSLSEIAEEFNVSRQAIYDNIKRTEKILEDYE   65 (105)
T ss_pred             HHhHHHHHHHHHHHH----hhccHHHHHHHhCccHHHHHHHHHHHHHHHHHHH
Confidence            589999999999994    5699999999999999999999999877765543

>PRK15320 transcriptional activator SprB; Provisional

Probab=97.11  E-value=0.00097  Score=59.96  Aligned_cols=50  Identities=14%  Similarity=0.185  Sum_probs=44.1

Q ss_pred             HHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHh
Q 046578          313 ELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQ  367 (379)
Q Consensus       313 ~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~  367 (379)
                      .+--.|+++|.+|+.+--     +|+|.+|||+.|++|.+||+..+++.+.||.-
T Consensus       160 ~~~~~LSdREIEVL~LLA-----kG~SNKEIAekL~LS~KTVSTYKnRLLeKLgA  209 (251)
T PRK15320        160 NLPPGVTQAKYALLILLS-----SGHPAIELAKKFGLGTKTVSIYRKKVMYRLGM  209 (251)
T ss_pred             cCCCCCCHHHHHHHHHHH-----cCCCHHHHHHHhccchhhHHHHHHHHHHHcCC
Confidence            344578999999999875     78999999999999999999999999999864

>COG1342 Predicted DNA-binding proteins [General function prediction only]

Probab=97.06  E-value=0.0017  Score=51.43  Aligned_cols=52  Identities=19%  Similarity=0.176  Sum_probs=46.6

Q ss_pred             CCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHHhhch
Q 046578          318 LSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQTNILNN  373 (379)
Q Consensus       318 L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~~l~~~~  373 (379)
                      |+..|-+.|+|...    ++++++|-|..||||+.|+.+.+..|++|+-.+|-...
T Consensus        34 lt~eElEAlRLvD~----~~l~QeeAA~rMgISr~Tfwr~l~sAR~KvA~aLveGk   85 (99)
T COG1342          34 LTIEELEALRLVDY----EGLTQEEAALRMGISRQTFWRLLTSARKKVADALVEGK   85 (99)
T ss_pred             ecHHHHHHHHHHhH----hhccHHHHHHHhcccHHHHHHHHHHHHHHHHHHHhcCC
Confidence            77788899999874    77999999999999999999999999999999986543

>PRK10651 transcriptional regulator NarL; Provisional

Probab=97.05  E-value=0.0011  Score=59.20  Aligned_cols=48  Identities=27%  Similarity=0.353  Sum_probs=43.2

Q ss_pred             hcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhH
Q 046578          316 QTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQT  368 (379)
Q Consensus       316 ~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~~  368 (379)
                      ..|+++|++|+.+..     +|++.++||+.+++|..||+.++++.++||.-.
T Consensus       154 ~~Lt~rE~~vl~~l~-----~g~~~~~ia~~l~is~~tV~~~~~~l~~Kl~~~  201 (216)
T PRK10651        154 NQLTPRERDILKLIA-----QGLPNKMIARRLDITESTVKVHVKHMLKKMKLK  201 (216)
T ss_pred             ccCCHHHHHHHHHHH-----cCCCHHHHHHHcCCCHHHHHHHHHHHHHHcCCC
Confidence            359999999999865     779999999999999999999999999998643

>COG1356 tfx Transcriptional regulator [DNA replication, recombination and repair]

Probab=97.00  E-value=0.00058  Score=56.64  Aligned_cols=51  Identities=24%  Similarity=0.331  Sum_probs=46.3

Q ss_pred             cCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHHhhc
Q 046578          317 TLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQTNILN  372 (379)
Q Consensus       317 ~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~~l~~~  372 (379)
                      -|+++|-+|+.||-     .|.|++|||++||.|+.+|+-+.++|+..+.++-+-.
T Consensus         8 flte~qikvl~lRe-----kG~tQ~eIA~~L~TTraNvSaIEkrA~enIekarnTL   58 (143)
T COG1356           8 FLTEQQIKVLVLRE-----KGLTQSEIARILKTTRANVSAIEKRALENIEKARNTL   58 (143)
T ss_pred             eeehhheeeeehhh-----ccccHHHHHHHHccchhhHHHHHHHHHHHHHHHHHHH
Confidence            48999999999996     8899999999999999999999999999998875543

>PRK09390 fixJ response regulator FixJ; Provisional

Probab=96.95  E-value=0.0026  Score=55.75  Aligned_cols=55  Identities=27%  Similarity=0.376  Sum_probs=47.7

Q ss_pred             HHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHHh
Q 046578          311 LKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQTNI  370 (379)
Q Consensus       311 L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~~l~  370 (379)
                      +...+..|++++++|+.+.+     .+++.++||+.+|+|..+|+....++++||+..-.
T Consensus       135 ~~~~~~~l~~~e~~vl~~~~-----~~~~~~~ia~~l~~s~~tv~~~~~~~~~kl~~~~~  189 (202)
T PRK09390        135 IRARIASLSERERQVMDGLV-----AGLSNKVIARDLDISPRTVEVYRANVMTKMQAGSL  189 (202)
T ss_pred             HHHHHHhhhhhHHHHHHHHH-----ccCchHHHHHHcCCCHHHHHHHHHHHHHHHccccH
Confidence            45667789999999999754     56999999999999999999999999999976543

>COG3413 Predicted DNA binding protein [General function prediction only]

Probab=96.94  E-value=0.0022  Score=59.20  Aligned_cols=53  Identities=25%  Similarity=0.379  Sum_probs=45.1

Q ss_pred             cCCHHHHHHHHHHhhcC---CCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHH
Q 046578          317 TLSEREADILRLHFGLD---GQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQTN  369 (379)
Q Consensus       317 ~L~~rer~Vl~l~ygL~---g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~~l  369 (379)
                      .|+++|+++|...|-.+   -....+.+|||+.||||.+|+.++++||.+||=..+
T Consensus       155 ~LTdrQ~~vL~~A~~~GYFd~PR~~~l~dLA~~lGISkst~~ehLRrAe~Kl~~~~  210 (215)
T COG3413         155 DLTDRQLEVLRLAYKMGYFDYPRRVSLKDLAKELGISKSTLSEHLRRAERKLIEAY  210 (215)
T ss_pred             cCCHHHHHHHHHHHHcCCCCCCccCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHh
Confidence            59999999999876322   225679999999999999999999999999997664

>PF13613 HTH_Tnp_4: Helix-turn-helix of DDE superfamily endonuclease

Probab=96.74  E-value=0.0042  Score=44.24  Aligned_cols=50  Identities=16%  Similarity=0.181  Sum_probs=43.7

Q ss_pred             cCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHH
Q 046578          317 TLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQTN  369 (379)
Q Consensus       317 ~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~~l  369 (379)
                      +|+..++-++.+.|.   ..+.+++++|..+|||++||+++.+..+.-|...+
T Consensus         2 kLs~~d~lll~L~~L---R~~~~~~~La~~FgIs~stvsri~~~~~~~L~~~l   51 (53)
T PF13613_consen    2 KLSLEDQLLLTLMYL---RLNLTFQDLAYRFGISQSTVSRIFHEWIPLLYQVL   51 (53)
T ss_pred             CCCHHHHHHHHHHHH---HcCCcHhHHhhheeecHHHHHHHHHHHHHHHHHhc
Confidence            688899999998874   37799999999999999999999999988877653

>PRK10403 transcriptional regulator NarP; Provisional

Probab=96.63  E-value=0.0038  Score=55.46  Aligned_cols=49  Identities=29%  Similarity=0.329  Sum_probs=43.5

Q ss_pred             cCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHHh
Q 046578          317 TLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQTNI  370 (379)
Q Consensus       317 ~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~~l~  370 (379)
                      .|+++|.+|+.+..     +|+|.+|||+.+|+|..||+.++.+.++||.-.-+
T Consensus       153 ~Lt~~e~~vl~~~~-----~g~s~~~ia~~l~~s~~tv~~~~~~i~~kl~~~~~  201 (215)
T PRK10403        153 VLTERELDVLHELA-----QGLSNKQIASVLNISEQTVKVHIRNLLRKLNVRSR  201 (215)
T ss_pred             cCCHHHHHHHHHHH-----CCCCHHHHHHHcCCCHHHHHHHHHHHHHHcCCCCH
Confidence            59999999998765     67999999999999999999999999999865433

>PRK10360 DNA-binding transcriptional activator UhpA; Provisional

Probab=96.47  E-value=0.007  Score=53.45  Aligned_cols=48  Identities=25%  Similarity=0.294  Sum_probs=43.1

Q ss_pred             hcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhH
Q 046578          316 QTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQT  368 (379)
Q Consensus       316 ~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~~  368 (379)
                      ..|+++|.+|+.+..     +|++.++||+.+++|..||+.++++.++||.-.
T Consensus       136 ~~Lt~~E~~il~~l~-----~g~~~~~Ia~~l~~s~~tv~~~~~~l~~Kl~~~  183 (196)
T PRK10360        136 DPLTKRERQVAEKLA-----QGMAVKEIAAELGLSPKTVHVHRANLMEKLGVS  183 (196)
T ss_pred             cCCCHHHHHHHHHHH-----CCCCHHHHHHHhCCCHHHHHHHHHHHHHHhCCC
Confidence            369999999999865     679999999999999999999999999998643

>PRK09935 transcriptional regulator FimZ; Provisional

Probab=96.41  E-value=0.0069  Score=53.86  Aligned_cols=47  Identities=34%  Similarity=0.359  Sum_probs=41.1

Q ss_pred             cCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhH
Q 046578          317 TLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQT  368 (379)
Q Consensus       317 ~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~~  368 (379)
                      .|+++|..++.+..     +|+|.+|||+.+++|..||+.++.++++||.-.
T Consensus       149 ~lt~re~~vl~~l~-----~g~s~~eIa~~l~~s~~tv~~~~~~~~~kl~~~  195 (210)
T PRK09935        149 VLSNREVTILRYLV-----SGLSNKEIADQLLLSNKTVSAHKSNIYGKLGLH  195 (210)
T ss_pred             cCCHHHHHHHHHHH-----cCCCHHHHHHHhCCCHHHHHHHHHHHHHHcCCC
Confidence            38889998887643     669999999999999999999999999998643

>PRK09958 DNA-binding transcriptional activator EvgA; Provisional

Probab=96.38  E-value=0.0073  Score=53.70  Aligned_cols=46  Identities=17%  Similarity=0.337  Sum_probs=42.0

Q ss_pred             hcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 046578          316 QTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQ  366 (379)
Q Consensus       316 ~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR  366 (379)
                      ..|+++|.+|+.+..     .|.+.+|||+.+++|.+||+..+++.++||.
T Consensus       142 ~~lt~~E~~vl~~l~-----~g~~~~~I~~~l~~s~~tv~~~~~~l~~Kl~  187 (204)
T PRK09958        142 DSLSKQEISVMRYIL-----DGKDNNDIAEKMFISNKTVSTYKSRLMEKLE  187 (204)
T ss_pred             ccCCHHHHHHHHHHH-----cCCCHHHHHHHhCCCHHHHHHHHHHHHHHcC
Confidence            469999999999876     6789999999999999999999999999984

>TIGR02531 yecD_yerC TrpR-related protein YerC/YecD

Probab=96.32  E-value=0.0087  Score=47.34  Aligned_cols=39  Identities=15%  Similarity=0.155  Sum_probs=31.6

Q ss_pred             hcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 046578          316 QTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIA  361 (379)
Q Consensus       316 ~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rA  361 (379)
                      +.|+++ ..|+.+.-     .|+|.+|||+.+|+|++||++ +.|+
T Consensus        35 ~~Ls~R-~~I~~ll~-----~G~S~~eIA~~LgISrsTIyR-i~R~   73 (88)
T TIGR02531        35 QSLAQR-LQVAKMLK-----QGKTYSDIEAETGASTATISR-VKRC   73 (88)
T ss_pred             HhhhHH-HHHHHHHH-----CCCCHHHHHHHHCcCHHHHHH-HHHh
Confidence            358888 77777653     679999999999999999998 4454

This model represents a protein subfamily found mostly in the Firmicutes (Bacillus and allies). This family is similar in sequence to the trp operon repressor TrpR described by TIGR01321, and represents a distinct clade within the broader family described by pfam01371. At least one species, Xylella fastidiosa, in the Proteobacteria, has a member of both this family and TIGR01321. Several genomes with a member of this family do not synthesize tryptophan, and members of this family should not be considered trp operon repressors without new evidence.

>PF13412 HTH_24: Winged helix-turn-helix DNA-binding; PDB: 1I1G_B 2IA0_B 3I4P_A 2GQQ_A 2L4A_A 2CFX_B 2DBB_B 2EFO_A 2EFQ_A 2PN6_A

Probab=96.30  E-value=0.013  Score=40.49  Aligned_cols=41  Identities=22%  Similarity=0.279  Sum_probs=30.3

Q ss_pred             CCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 046578          318 LSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIA  361 (379)
Q Consensus       318 L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rA  361 (379)
                      |++.++.|+....-   ..+.|..|||+.+|+|.++|++++++-
T Consensus         1 l~~~~~~Il~~l~~---~~~~t~~ela~~~~is~~tv~~~l~~L   41 (48)
T PF13412_consen    1 LDETQRKILNYLRE---NPRITQKELAEKLGISRSTVNRYLKKL   41 (48)
T ss_dssp             --HHHHHHHHHHHH---CTTS-HHHHHHHHTS-HHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHH---cCCCCHHHHHHHhCCCHHHHHHHHHHH
Confidence            56788889876652   366999999999999999998886654

...

>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C

Probab=96.29  E-value=0.0041  Score=43.34  Aligned_cols=33  Identities=27%  Similarity=0.258  Sum_probs=22.5

Q ss_pred             HHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 046578          324 DILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIA  361 (379)
Q Consensus       324 ~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rA  361 (379)
                      .++.++.     +|+|.++||+.+|||++||++++++-
T Consensus         9 ~ii~l~~-----~G~s~~~ia~~lgvs~~Tv~~w~kr~   41 (50)
T PF13384_consen    9 QIIRLLR-----EGWSIREIAKRLGVSRSTVYRWIKRY   41 (50)
T ss_dssp             -HHHHHH-----HT--HHHHHHHHTS-HHHHHHHHT--
T ss_pred             HHHHHHH-----CCCCHHHHHHHHCcCHHHHHHHHHHc
Confidence            3555554     57999999999999999999987663

>PRK04841 transcriptional regulator MalT; Provisional

Probab=96.27  E-value=0.007  Score=66.95  Aligned_cols=48  Identities=23%  Similarity=0.261  Sum_probs=43.9

Q ss_pred             hcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhH
Q 046578          316 QTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQT  368 (379)
Q Consensus       316 ~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~~  368 (379)
                      ..|+++|++|+.+..     +|+|++|||+.|+||.+||+.++++..+||.-.
T Consensus       837 ~~lt~~e~~v~~~~~-----~g~~~~~ia~~l~~s~~tv~~h~~~~~~kl~v~  884 (903)
T PRK04841        837 SPLTQREWQVLGLIY-----SGYSNEQIAGELDVAATTIKTHIRNLYQKLGIA  884 (903)
T ss_pred             CCCCHHHHHHHHHHH-----cCCCHHHHHHHhCCCHHHHHHHHHHHHHHhCCC
Confidence            359999999999976     889999999999999999999999999999643

>PRK13558 bacterio-opsin activator; Provisional

Probab=96.20  E-value=0.0098  Score=63.68  Aligned_cols=51  Identities=20%  Similarity=0.204  Sum_probs=45.3

Q ss_pred             HhcCCHHHHHHHHHHhhcCCCCCC-------CHHHHHHHhCCCHHHHHHHHHHHHHHHHhHH
Q 046578          315 LQTLSEREADILRLHFGLDGQTPV-------SCKEIGRLLSLSRERIRQIRGIALTKLQQTN  369 (379)
Q Consensus       315 L~~L~~rer~Vl~l~ygL~g~e~~-------S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~~l  369 (379)
                      ...|+++|+++|...|.    .||       |..|||+.||||++|+++++++|.+||=..+
T Consensus       605 ~~~lt~~q~e~l~~a~~----~gyf~~pr~~~~~e~a~~l~is~~t~~~~lr~a~~~l~~~~  662 (665)
T PRK13558        605 ENDLTDRQLTALQKAYV----SGYFEWPRRVEGEELAESMGISRSTFHQHLRAAERKLVGAF  662 (665)
T ss_pred             hhhCCHHHHHHHHHHHH----cCCCCCCccCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHH
Confidence            45899999999999883    446       9999999999999999999999999986654

>PF02796 HTH_7: Helix-turn-helix domain of resolvase; InterPro: IPR006120 Site-specific recombination plays an important role in DNA rearrangement in prokaryotic organisms

Probab=96.15  E-value=0.0098  Score=40.80  Aligned_cols=33  Identities=21%  Similarity=0.234  Sum_probs=24.3

Q ss_pred             HHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 046578          322 EADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRG  359 (379)
Q Consensus       322 er~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~  359 (379)
                      ..+|+.|+-     +|+|..+||+.+|||++||++.+.
T Consensus        11 ~~~i~~l~~-----~G~si~~IA~~~gvsr~TvyR~l~   43 (45)
T PF02796_consen   11 IEEIKELYA-----EGMSIAEIAKQFGVSRSTVYRYLN   43 (45)
T ss_dssp             HHHHHHHHH-----TT--HHHHHHHTTS-HHHHHHHHC
T ss_pred             HHHHHHHHH-----CCCCHHHHHHHHCcCHHHHHHHHh
Confidence            455666664     779999999999999999998763

Two types of site-specific recombination are known to occur: Recombination between inverted repeats resulting in the reversal of a DNA segment. Recombination between repeat sequences on two DNA molecules resulting in their cointegration, or between repeats on one DNA molecule resulting in the excision of a DNA fragment. Site-specific recombination is characterised by a strand exchange mechanism that requires no DNA synthesis or high energy cofactor; the phosphodiester bond energy is conserved in a phospho-protein linkage during strand cleavage and re-ligation. Two unrelated families of recombinases are currently known []. The first, called the 'phage integrase' family, groups a number of bacterial phage and yeast plasmid enzymes. The second [], called the 'resolvase' family, groups enzymes which share the following structural characteristics: an N-terminal catalytic and dimerization domain that contains a conserved serine residue involved in the transient covalent attachment to DNA IPR006119 from INTERPRO, and a C-terminal helix-turn-helix DNA-binding domain. ; GO: 0000150 recombinase activity, 0003677 DNA binding, 0006310 DNA recombination; PDB: 1ZR2_A 2GM4_B 1RES_A 1ZR4_A 1RET_A 1GDT_B 2R0Q_C 1JKP_C 1IJW_C 1JJ6_C ....

>PRK15418 transcriptional regulator LsrR; Provisional

Probab=96.00  E-value=0.0092  Score=58.45  Aligned_cols=36  Identities=19%  Similarity=0.314  Sum_probs=31.7

Q ss_pred             HHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 046578          324 DILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALT  363 (379)
Q Consensus       324 ~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~  363 (379)
                      +|-.|||    .+++|++|||++||+|+.+|++++.+|++
T Consensus        20 ~vA~lYY----~~g~tQ~eIA~~lgiSR~~VsRlL~~Ar~   55 (318)
T PRK15418         20 RIAWFYY----HDGLTQSEIGERLGLTRLKVSRLLEKGRQ   55 (318)
T ss_pred             HHHHHHH----hcCCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence            4566788    37799999999999999999999999976

>PF05263 DUF722: Protein of unknown function (DUF722); InterPro: IPR007927 This entry is represented by Bacteriophage bIL285, Orf38

Probab=95.80  E-value=0.039  Score=46.82  Aligned_cols=56  Identities=21%  Similarity=0.367  Sum_probs=46.7

Q ss_pred             HHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Q 046578          308 KQELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKL  365 (379)
Q Consensus       308 ~~~L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kL  365 (379)
                      .+.+...++.|.+.++.||.++|+  +..++|..+||..|++++.++++....-...+
T Consensus        72 k~~id~~~~~l~de~k~Ii~lry~--~r~~~TW~~IA~~l~i~erta~r~~~~fK~~i  127 (130)
T PF05263_consen   72 KEAIDRWLETLIDEEKRIIKLRYD--RRSRRTWYQIAQKLHISERTARRWRDRFKNDI  127 (130)
T ss_pred             HHHHHHHHHhhCHHHHHHHHHHHc--ccccchHHHHHHHhCccHHHHHHHHHHHHHHh
Confidence            456788889999999999999995  22569999999999999999998876655444

The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.

>PF06056 Terminase_5: Putative ATPase subunit of terminase (gpP-like); InterPro: IPR010332 This family of proteins are annotated as ATPase subunits of phage terminase after []

Probab=95.69  E-value=0.023  Score=41.32  Aligned_cols=26  Identities=23%  Similarity=0.194  Sum_probs=24.0

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHHHH
Q 046578          336 TPVSCKEIGRLLSLSRERIRQIRGIA  361 (379)
Q Consensus       336 e~~S~~EIAe~LgiS~~~Vr~~~~rA  361 (379)
                      +|++.+|||+.||+++.||++...+-
T Consensus        12 ~G~~~~eIA~~Lg~~~~TV~~W~~r~   37 (58)
T PF06056_consen   12 QGWSIKEIAEELGVPRSTVYSWKDRY   37 (58)
T ss_pred             cCCCHHHHHHHHCCChHHHHHHHHhh
Confidence            67999999999999999999998774

Terminases are viral proteins that are involved in packaging viral DNA into the capsid.; GO: 0005524 ATP binding, 0019069 viral capsid assembly

>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins

Probab=95.54  E-value=0.041  Score=45.45  Aligned_cols=50  Identities=20%  Similarity=0.272  Sum_probs=43.0

Q ss_pred             HHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHh
Q 046578          314 LLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQ  367 (379)
Q Consensus       314 ~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~  367 (379)
                      .+..|++.|...+.... ..   .=+++|+++.||||..|||.++.+.+++|..
T Consensus        30 ~~~~L~~E~~~Fi~~Fi-~~---rGnlKe~e~~lgiSYPTvR~rLd~ii~~lg~   79 (113)
T PF09862_consen   30 WFARLSPEQLEFIKLFI-KN---RGNLKEMEKELGISYPTVRNRLDKIIEKLGY   79 (113)
T ss_pred             hhhcCCHHHHHHHHHHH-Hh---cCCHHHHHHHHCCCcHHHHHHHHHHHHHhCC
Confidence            46789999999888765 22   3499999999999999999999999999976

>PF00325 Crp: Bacterial regulatory proteins, crp family; InterPro: IPR001808 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif

Probab=95.30  E-value=0.023  Score=36.15  Aligned_cols=23  Identities=26%  Similarity=0.440  Sum_probs=17.3

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHHH
Q 046578          338 VSCKEIGRLLSLSRERIRQIRGI  360 (379)
Q Consensus       338 ~S~~EIAe~LgiS~~~Vr~~~~r  360 (379)
                      +|.+|||+.+|+|+++|++.+.+
T Consensus         3 mtr~diA~~lG~t~ETVSR~l~~   25 (32)
T PF00325_consen    3 MTRQDIADYLGLTRETVSRILKK   25 (32)
T ss_dssp             --HHHHHHHHTS-HHHHHHHHHH
T ss_pred             cCHHHHHHHhCCcHHHHHHHHHH
Confidence            78999999999999999866544

These proteins are very diverse, but for convenience may be grouped into subfamilies on the basis of sequence similarity. This family groups together a range of proteins, including anr, crp, clp, cysR, fixK, flp, fnr, fnrN, hlyX and ntcA [, ]. Within this family, the HTH motif is situated towards the C terminus.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 2OZ6_A 1CGP_B 2GZW_C 1O3T_B 3ROU_A 2CGP_A 3RDI_A 1I5Z_A 3IYD_H 3FWE_B ....

>PF13404 HTH_AsnC-type: AsnC-type helix-turn-helix domain; PDB: 2ZNY_E 2ZNZ_G 1RI7_A 2CYY_A 2E1C_A 2VC1_B 2QZ8_A 2W29_C 2IVM_B 2VBX_B

Probab=95.29  E-value=0.059  Score=36.44  Aligned_cols=40  Identities=33%  Similarity=0.306  Sum_probs=27.9

Q ss_pred             CCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 046578          318 LSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGI  360 (379)
Q Consensus       318 L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~r  360 (379)
                      |++.++.||...- -+  ...|+.+||+.+|+|.++|.+++.+
T Consensus         1 lD~~D~~Il~~Lq-~d--~r~s~~~la~~lglS~~~v~~Ri~r   40 (42)
T PF13404_consen    1 LDELDRKILRLLQ-ED--GRRSYAELAEELGLSESTVRRRIRR   40 (42)
T ss_dssp             --HHHHHHHHHHH-H---TTS-HHHHHHHHTS-HHHHHHHHHH
T ss_pred             CCHHHHHHHHHHH-Hc--CCccHHHHHHHHCcCHHHHHHHHHH
Confidence            4556777777654 22  5699999999999999999988665

...

>PF01726 LexA_DNA_bind: LexA DNA binding domain; InterPro: IPR006199 This is the DNA binding domain of the LexA SOS regulon repressor which prevents expression of DNA repair proteins in bacteria

Probab=95.22  E-value=0.034  Score=41.38  Aligned_cols=45  Identities=22%  Similarity=0.441  Sum_probs=28.5

Q ss_pred             HhcCCHHHHHHHHHH--hhc-CCCCCCCHHHHHHHhCCC-HHHHHHHHHH
Q 046578          315 LQTLSEREADILRLH--FGL-DGQTPVSCKEIGRLLSLS-RERIRQIRGI  360 (379)
Q Consensus       315 L~~L~~rer~Vl~l~--ygL-~g~e~~S~~EIAe~LgiS-~~~Vr~~~~r  360 (379)
                      +..|+++|++|+...  |.- .| -.-|.+|||+.||++ .++|.+.+..
T Consensus         1 M~~LT~rQ~~vL~~I~~~~~~~G-~~Pt~rEIa~~~g~~S~~tv~~~L~~   49 (65)
T PF01726_consen    1 MKELTERQKEVLEFIREYIEENG-YPPTVREIAEALGLKSTSTVQRHLKA   49 (65)
T ss_dssp             -----HHHHHHHHHHHHHHHHHS-S---HHHHHHHHTSSSHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHHHHHHHcC-CCCCHHHHHHHhCCCChHHHHHHHHH
Confidence            457999999999863  211 14 556999999999997 9999877543

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.

>PF06530 Phage_antitermQ: Phage antitermination protein Q; InterPro: IPR010534 This entry is represented by Bacteriophage 933W, GpQ

Probab=94.97  E-value=0.16  Score=42.76  Aligned_cols=55  Identities=24%  Similarity=0.153  Sum_probs=48.0

Q ss_pred             HhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHHhhch
Q 046578          315 LQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQTNILNN  373 (379)
Q Consensus       315 L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~~l~~~~  373 (379)
                      |.+-.|.+-.+|.++|.    .+.|...||..+++|..+|++.+.+|-.-+..++...+
T Consensus        60 L~~~~~~~~~ll~~~Yv----~g~s~r~IA~~~~~s~~~ir~~l~~ae~~i~g~l~~~~  114 (125)
T PF06530_consen   60 LKKRDPEEYDLLILYYV----YGWSKRQIARKLKCSEGKIRKRLQRAEGFIDGCLSMLT  114 (125)
T ss_pred             HHccCHHHHHHHHHHHH----cCCCHHHHHHHHCCCHHHHHHHHHHhhhhHhhhhHHhh
Confidence            44578899999999994    67999999999999999999999999999998875444

The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This family consists of several phage antitermination protein Q and related bacterial sequences. Phage 993W gene Q encodes a phage-specific positive regulator of late gene expression, thought, by analogy to the corresponding gene of phage lambda, to be a transcription antiterminator. GpQ positively regulates expression of the phage late gene operons. Bacterial host RNA polymerase modified by antitermination proteins transcribes through termination sites that otherwise prevent expression of the regulated genes [, ].; GO: 0003677 DNA binding, 0060567 negative regulation of transcription termination, DNA-dependent

>PF10668 Phage_terminase: Phage terminase small subunit; InterPro: IPR018925 This entry describes the terminase small subunit from Enterococcus phage phiFL1A, related proteins in other bacteriophage, and prophage regions of bacterial genomes

Probab=94.95  E-value=0.048  Score=39.82  Aligned_cols=36  Identities=17%  Similarity=0.233  Sum_probs=27.4

Q ss_pred             HHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 046578          323 ADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGI  360 (379)
Q Consensus       323 r~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~r  360 (379)
                      -..+.++.-.+  ..+++++||+.||||.+||+....+
T Consensus        10 dkA~e~y~~~~--g~i~lkdIA~~Lgvs~~tIr~WK~~   45 (60)
T PF10668_consen   10 DKAFEIYKESN--GKIKLKDIAEKLGVSESTIRKWKSR   45 (60)
T ss_pred             HHHHHHHHHhC--CCccHHHHHHHHCCCHHHHHHHhhh
Confidence            34555554222  5699999999999999999998765

Packaging of double-stranded viral DNA concatemers requires interaction of the prohead with virus DNA. This process is mediated by a phage-encoded DNA recognition and terminase protein. The terminase enzymes described so far, which are hetero-oligomers composed of a small and a large subunit, do not have a significant level of sequence homology. The small terminase subunit is thought to form a nucleoprotein structure that helps to position the terminase large subunit at the packaging initiation site [].

>cd00569 HTH_Hin_like Helix-turn-helix domain of Hin and related proteins, a family of DNA-binding domains unique to bacteria and represented by the Hin protein of Salmonella

Probab=94.86  E-value=0.068  Score=33.24  Aligned_cols=36  Identities=25%  Similarity=0.303  Sum_probs=27.5

Q ss_pred             CCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHH
Q 046578          318 LSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQI  357 (379)
Q Consensus       318 L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~  357 (379)
                      +++.++..+...+.    .+.+..+||+.+|++..+|+++
T Consensus         6 ~~~~~~~~i~~~~~----~~~s~~~ia~~~~is~~tv~~~   41 (42)
T cd00569           6 LTPEQIEEARRLLA----AGESVAEIARRLGVSRSTLYRY   41 (42)
T ss_pred             CCHHHHHHHHHHHH----cCCCHHHHHHHHCCCHHHHHHh
Confidence            45556655555552    5589999999999999999875

The basic HTH domain is a simple fold comprised of three core helices that form a right-handed helical bundle. The principal DNA-protein interface is formed by the third helix, the recognition helix, inserting itself into the major groove of the DNA. A diverse array of HTH domains participate in a variety of functions that depend on their DNA-binding properties. HTH_Hin represents one of the simplest versions of the HTH domains; the characterization of homologous relationships between various sequence-diverse HTH domain families remains difficult. The Hin recombinase induces the site-specific inversion of a chromosomal DNA segment containing a promoter, which controls the alternate expression of two genes by reversibly switching orientation. The Hin recombinase consists of a single polypeptide chain containing a D

>COG2390 DeoR Transcriptional regulator, contains sigma factor-related N-terminal domain [Transcription]

Probab=94.74  E-value=0.041  Score=53.87  Aligned_cols=35  Identities=20%  Similarity=0.238  Sum_probs=30.4

Q ss_pred             HHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 046578          325 ILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALT  363 (379)
Q Consensus       325 Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~  363 (379)
                      +-.+||    .+++|+.|||++||||+.+|++.+.+|++
T Consensus        18 ~A~lYY----~~gltQ~eIA~~LgiSR~~v~rlL~~Ar~   52 (321)
T COG2390          18 AAWLYY----VEGLTQSEIAERLGISRATVSRLLAKARE   52 (321)
T ss_pred             HHHHHH----hcCCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence            445677    48899999999999999999999999875

>PF13518 HTH_28: Helix-turn-helix domain

Probab=94.65  E-value=0.077  Score=36.89  Aligned_cols=27  Identities=22%  Similarity=0.176  Sum_probs=23.3

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHHHHH
Q 046578          336 TPVSCKEIGRLLSLSRERIRQIRGIAL  362 (379)
Q Consensus       336 e~~S~~EIAe~LgiS~~~Vr~~~~rAl  362 (379)
                      ++.|..+||+.+|||+++|++++.+-.
T Consensus        11 ~g~s~~~~a~~~gis~~tv~~w~~~y~   37 (52)
T PF13518_consen   11 EGESVREIAREFGISRSTVYRWIKRYR   37 (52)
T ss_pred             cCCCHHHHHHHHCCCHhHHHHHHHHHH
Confidence            457999999999999999998877654

>PHA00675 hypothetical protein

Probab=94.55  E-value=0.085  Score=40.21  Aligned_cols=41  Identities=17%  Similarity=0.186  Sum_probs=30.8

Q ss_pred             hcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 046578          316 QTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRG  359 (379)
Q Consensus       316 ~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~  359 (379)
                      ++|++.|-+.|+..+-   .+|.|+.+||+.||+|+++|.++.+
T Consensus        21 AKLt~~qV~~IR~l~~---r~G~s~~~IA~~fGVsrstV~~I~~   61 (78)
T PHA00675         21 AKLTDAEVERIRELHE---VEGMSYAVLAEKFEQSKGAIAKICR   61 (78)
T ss_pred             cccCHHHHHHHHHHHH---hcCccHHHHHHHhCCCHHHHHHHHc
Confidence            3566666555554441   1668999999999999999999865

>PF04218 CENP-B_N: CENP-B N-terminal DNA-binding domain; InterPro: IPR006695 Centromere Protein B (CENP-B) is a DNA-binding protein localized to the centromere

Probab=94.52  E-value=0.036  Score=39.44  Aligned_cols=46  Identities=20%  Similarity=0.199  Sum_probs=29.5

Q ss_pred             cCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHh
Q 046578          317 TLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQ  367 (379)
Q Consensus       317 ~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~  367 (379)
                      .|+..|+.=+.-.+    ..|.+..+||..|||+.+||+.++.. .+++++
T Consensus         6 ~LTl~eK~~iI~~~----e~g~s~~~ia~~fgv~~sTv~~I~K~-k~~i~~   51 (53)
T PF04218_consen    6 SLTLEEKLEIIKRL----EEGESKRDIAREFGVSRSTVSTILKN-KDKILE   51 (53)
T ss_dssp             S--HHHHHHHHHHH----HCTT-HHHHHHHHT--CCHHHHHHHC-HHHHCC
T ss_pred             cCCHHHHHHHHHHH----HcCCCHHHHHHHhCCCHHHHHHHHHh-HHHHHh
Confidence            46666655554455    26689999999999999999998876 444443

Within the N-terminal 125 residues, there is a DNA-binding region, which binds to a corresponding 17bp CENP-B box sequence. CENP-B dimers either bind two separate DNA molecules or alternatively, they may bind two CENP-B boxes on one DNA molecule, with the intervening stretch of DNA forming a loop structure. The CENP-B DNA-binding domain consists of two repeating domains, RP1 and RP2. This family corresponds to RP1 has been shown to consist of four helices in a helix-turn-helix structure [].; GO: 0003677 DNA binding, 0000775 chromosome, centromeric region; PDB: 1BW6_A 1HLV_A 2ELH_A.

>PF12802 MarR_2: MarR family; PDB: 3ECO_B 2QWW_B 3KP6_B 3KP4_B 3KP2_A 3KP5_A 3KP3_B 3KP7_A 3NQO_B 3K0L_B

Probab=94.46  E-value=0.1  Score=37.68  Aligned_cols=44  Identities=14%  Similarity=0.135  Sum_probs=33.1

Q ss_pred             cCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 046578          317 TLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIA  361 (379)
Q Consensus       317 ~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rA  361 (379)
                      .|++.|..||...+.-+ ..++|..|||+.+++++++|++.+.+-
T Consensus         2 glt~~q~~vL~~l~~~~-~~~~t~~~la~~l~~~~~~vs~~v~~L   45 (62)
T PF12802_consen    2 GLTPSQFRVLMALARHP-GEELTQSELAERLGISKSTVSRIVKRL   45 (62)
T ss_dssp             TSTHHHHHHHHHHHHST-TSGEEHHHHHHHHTS-HHHHHHHHHHH
T ss_pred             ccCHHHHHHHHHHHHCC-CCCcCHHHHHHHHCcCHHHHHHHHHHH
Confidence            37888888888766422 234899999999999999998876653

...

>PF13730 HTH_36: Helix-turn-helix domain

Probab=94.40  E-value=0.16  Score=35.86  Aligned_cols=44  Identities=14%  Similarity=0.098  Sum_probs=30.9

Q ss_pred             cCCHHHHHHHHHHhhcCCCCC---CCHHHHHHHhCCCHHHHHHHHHH
Q 046578          317 TLSEREADILRLHFGLDGQTP---VSCKEIGRLLSLSRERIRQIRGI  360 (379)
Q Consensus       317 ~L~~rer~Vl~l~ygL~g~e~---~S~~EIAe~LgiS~~~Vr~~~~r  360 (379)
                      .|++.++.|+.......+..+   .|++.||+.+|+|+.||++.+..
T Consensus         2 ~Ls~~~~~v~~~l~~~~~~~~~~~pS~~~la~~~g~s~~Tv~~~i~~   48 (55)
T PF13730_consen    2 NLSPTAKLVYLYLASYANKNGGCFPSQETLAKDLGVSRRTVQRAIKE   48 (55)
T ss_pred             CCCHHHHHHHHHHHHhcCCCCCCCcCHHHHHHHHCcCHHHHHHHHHH
Confidence            588888888775432322222   38999999999999999765443

>COG2909 MalT ATP-dependent transcriptional regulator [Transcription]

Probab=94.30  E-value=0.052  Score=58.71  Aligned_cols=47  Identities=28%  Similarity=0.268  Sum_probs=43.3

Q ss_pred             cCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhH
Q 046578          317 TLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQT  368 (379)
Q Consensus       317 ~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~~  368 (379)
                      -|+.+|++|+.+.|     .|+|.+|||+.+.||..||+.++++.-.||.-.
T Consensus       831 ~Ls~RE~eVL~Lia-----~G~SN~eIa~~L~isl~TVKtH~rniy~KLgV~  877 (894)
T COG2909         831 PLSQRELEVLGLIA-----QGLSNEEIAQELFISLTTVKTHIRNIYQKLGVA  877 (894)
T ss_pred             CccHHHHHHHHHHH-----ccCCHHHHHHHHHHHHHHHHHHHHHHHHHhCcc
Confidence            38999999999998     889999999999999999999999998888544

>smart00351 PAX Paired Box domain

Probab=94.11  E-value=0.13  Score=43.32  Aligned_cols=42  Identities=21%  Similarity=0.177  Sum_probs=32.7

Q ss_pred             CCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 046578          318 LSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALT  363 (379)
Q Consensus       318 L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~  363 (379)
                      ++..+|.-|...|-    +|.|..+||+.||||++||++++.+..+
T Consensus        18 ~s~~~R~riv~~~~----~G~s~~~iA~~~gvs~~tV~kwi~r~~~   59 (125)
T smart00351       18 LPDEERQRIVELAQ----NGVRPCDISRQLCVSHGCVSKILGRYYE   59 (125)
T ss_pred             CCHHHHHHHHHHHH----cCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence            55555555555552    6699999999999999999999988643

>PF02650 HTH_WhiA: WhiA C-terminal HTH domain; InterPro: IPR023054 This domain is found at the C terminus of the sporulation regulator WhiA

Probab=93.71  E-value=0.17  Score=39.80  Aligned_cols=44  Identities=25%  Similarity=0.376  Sum_probs=34.1

Q ss_pred             HhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHh--CCCHHHHHHHHHHH
Q 046578          315 LQTLSEREADILRLHFGLDGQTPVSCKEIGRLL--SLSRERIRQIRGIA  361 (379)
Q Consensus       315 L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~L--giS~~~Vr~~~~rA  361 (379)
                      ++.||+..+++..+|.-   ..+.|+.|+|+.|  .||.++|..++.+.
T Consensus        35 ~~~l~~~l~~~a~lRl~---~Pd~SL~EL~~~~~~~iSKSgvnhrlrKl   80 (85)
T PF02650_consen   35 LDKLPEKLREFAELRLE---NPDASLKELGELLEPPISKSGVNHRLRKL   80 (85)
T ss_dssp             GGGS-HHHHHHHHHHHH----TTS-HHHHHHTT--T--HHHHHHHHHHH
T ss_pred             cccCCHHHHHHHHHHHH---CccccHHHHHHHHcCcCcHHHHHHHHHHH
Confidence            56899999999999863   4789999999999  99999999887664

It is predicted to form a DNA binding helix-turn-helix structure []. ; PDB: 3HYI_A.

>PRK10430 DNA-binding transcriptional activator DcuR; Provisional

Probab=93.52  E-value=0.16  Score=46.97  Aligned_cols=46  Identities=15%  Similarity=0.127  Sum_probs=35.3

Q ss_pred             cCCHHHHHHHHHHh-hcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 046578          317 TLSEREADILRLHF-GLDGQTPVSCKEIGRLLSLSRERIRQIRGIALT  363 (379)
Q Consensus       317 ~L~~rer~Vl~l~y-gL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~  363 (379)
                      .|++++.+++.... +.. .+|+|.+|||+.||+|..||+..+.++..
T Consensus       158 ~Lt~re~~~l~~~i~~~~-~~g~s~~eIA~~l~iS~~Tv~~~~~~~~~  204 (239)
T PRK10430        158 GLTPQTLRTLCQWIDAHQ-DYEFSTDELANAVNISRVSCRKYLIWLVN  204 (239)
T ss_pred             CCCHHHHHHHHHHHHhCC-CCCcCHHHHHHHhCchHHHHHHHHHHHHh
Confidence            48888877765432 111 27899999999999999999999887743

>PF08279 HTH_11: HTH domain; InterPro: IPR013196 Winged helix DNA-binding proteins share a related winged helix-turn-helix DNA-binding motif, where the "wings", or loops, are small beta-sheets

Probab=93.47  E-value=0.21  Score=35.27  Aligned_cols=39  Identities=31%  Similarity=0.504  Sum_probs=27.5

Q ss_pred             HHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 046578          321 READILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIA  361 (379)
Q Consensus       321 rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rA  361 (379)
                      +++.|+.+..  ...+..|.+|||+.||||+.||++.+...
T Consensus         1 R~~~il~~L~--~~~~~it~~eLa~~l~vS~rTi~~~i~~L   39 (55)
T PF08279_consen    1 RQKQILKLLL--ESKEPITAKELAEELGVSRRTIRRDIKEL   39 (55)
T ss_dssp             HHHHHHHHHH--HTTTSBEHHHHHHHCTS-HHHHHHHHHHH
T ss_pred             CHHHHHHHHH--HcCCCcCHHHHHHHhCCCHHHHHHHHHHH
Confidence            4556666543  22245999999999999999998876553

The winged helix motif consists of two wings (W1, W2), three alpha helices (H1, H2, H3) and three beta-sheets (S1, S2, S3) arranged in the order H1-S1-H2-H3-S2-W1-S3-W2 []. The DNA-recognition helix makes sequence-specific DNA contacts with the major groove of DNA, while the wings make different DNA contacts, often with the minor groove or the backbone of DNA. Several winged-helix proteins display an exposed patch of hydrophobic residues thought to mediate protein-protein interactions. This entry represents a subset of the winged helix domain superfamily which is predominantly found in bacterial proteins, though there are also some archaeal and eukaryotic examples. This domain is commonly found in the biotin (vitamin H) repressor protein BirA which regulates transcription of the biotin operon []. It is also found in other proteins including regulators of amino acid biosynthsis such as LysM [], and regulators of carbohydrate metabolisms such as LicR and FrvR [, ].; PDB: 1HXD_B 2EWN_B 1BIA_A 1BIB_A 1J5Y_A 3V7S_A 3V7C_A 3RKW_A 3RIR_A 3RKX_A ....

>PF01371 Trp_repressor: Trp repressor protein; InterPro: IPR000831 The Trp repressor (TrpR) binds to at least five operators in the Escherichia coli genome, repressing gene expression

Probab=93.29  E-value=0.25  Score=38.95  Aligned_cols=47  Identities=17%  Similarity=0.140  Sum_probs=32.4

Q ss_pred             cCCHHHHHHHHHHhhcCC---CCCCCHHHHHHHhCCCHHHHHHHHHHHHHH
Q 046578          317 TLSEREADILRLHFGLDG---QTPVSCKEIGRLLSLSRERIRQIRGIALTK  364 (379)
Q Consensus       317 ~L~~rer~Vl~l~ygL~g---~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~k  364 (379)
                      -++|.|+.-+..|+-+-.   .+|+|++|||+.+|+|..||.+ .+|+++.
T Consensus        26 L~T~~E~~~l~~R~~va~~lL~~g~syreIa~~tgvS~aTItR-vsr~Lk~   75 (87)
T PF01371_consen   26 LCTPDELEALAQRWQVAKELLDEGKSYREIAEETGVSIATITR-VSRCLKY   75 (87)
T ss_dssp             HSSHHHHHHHHHHHHHHHHHHHTTSSHHHHHHHHTSTHHHHHH-HHHHHHH
T ss_pred             hCCHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHhCCCHHHHHH-HHHHHHc
Confidence            377777666554432210   1679999999999999999975 3555554

The operators at which it binds vary considerably in DNA sequence and location within the promoter; when bound to the Trp operon it recognises the sequence 5'-ACTAGT-3' and acts to prevent the initiation of transcription. The TrpR controls the trpEDCBA (trpO) operon and the genes for trpR, aroH, mtr and aroL, which are involved in the biosynthesis and uptake of the amino acid tryptophan []. The repressor binds to the operators only in the presence of L-tryptophan, thereby controlling the intracellular level of its effector; the complex also regulates Trp repressor biosynthesis by binding to its own regulatory region. TrpR acts as a dimer that is composed of identical 6-helical subunits, where four of the helices form the core of the protein and intertwine with the corresponding helices from the other subunit.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3FRW_H 3KOR_A 3SSW_N 1P6Z_N 1CO0_B 1JHG_A 1WRT_S 1WRS_R 1WRP_R 1RCS_B ....

>PHA02547 55 RNA polymerase sigma factor; Provisional

Probab=93.05  E-value=0.44  Score=41.92  Aligned_cols=67  Identities=13%  Similarity=0.218  Sum_probs=54.8

Q ss_pred             HHhHHHHHHHHHhccCCCCC---HHHHHHHHHHHHHHHHhccCCCCCCCchhHHHHHHHHHHHHHHHhhc
Q 046578          148 RSYRSLVVSIATGYQGKGLS---LKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYWWIKQAIIRAIANKS  214 (379)
Q Consensus       148 ~~y~~lV~~ia~r~~~~~~d---~eDLvQEg~i~L~~ai~~fD~~~g~~FsTYa~~~Ir~~i~~~lr~~~  214 (379)
                      ...+..+.++.++|.-.+..   .||.+.+|.-..++.+++||+++...+-+|++.++.++..+.++...
T Consensus        44 ~~imkIa~glS~r~nF~~Yt~~wKedMI~DgIe~~i~ylhNFD~~k~~Np~aYiT~~~~~AF~~RI~kEk  113 (179)
T PHA02547         44 LAIMKIAEGLSRRPNFSGYTQTWKEDMIADGIEACIKGLHNFDETKYKNPHAYITQACFNAFVQRIKKEK  113 (179)
T ss_pred             HHHHHHHhccccCCccccchHHHHHHHHHHHHHHHHHHhhcCCcccccChHHHHHHHHHHHHHHHHHHHH
Confidence            34455555666666544554   79999999999999999999999888999999999999999888765

>PF01047 MarR: MarR family; InterPro: IPR000835 The MarR-type HTH domain is a DNA-binding, winged helix-turn-helix (wHTH) domain of about 135 amino acids present in transcription regulators of the MarR/SlyA family, involved in the development of antibiotic resistance

Probab=92.84  E-value=0.23  Score=35.49  Aligned_cols=41  Identities=22%  Similarity=0.349  Sum_probs=31.4

Q ss_pred             CCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 046578          318 LSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIA  361 (379)
Q Consensus       318 L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rA  361 (379)
                      |++.|-.+|...+-   ..+.+..|||+.+++++++|.+.+.+-
T Consensus         1 lt~~q~~iL~~l~~---~~~~~~~~la~~~~~~~~~~t~~i~~L   41 (59)
T PF01047_consen    1 LTPSQFRILRILYE---NGGITQSELAEKLGISRSTVTRIIKRL   41 (59)
T ss_dssp             STHHHHHHHHHHHH---HSSEEHHHHHHHHTS-HHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHH---cCCCCHHHHHHHHCCChhHHHHHHHHH
Confidence            56677777776654   355999999999999999998876654

This family of transcription regulators is named after Escherichia coli MarR, a repressor of genes which activate the multiple antibiotic resistance and oxidative stress regulons, and after slyA from Salmonella typhimurium and E. coli, a transcription regulator that is required for virulence and survival in the macrophage environment. Regulators with the MarR-type HTH domain are present in bacteria and archaea and control a variety of biological functions, including resistance to multiple antibiotics, household disinfectants, organic solvents, oxidative stress agents and regulation of the virulence factor synthesis in pathogens of humans and plants. Many of the MarR-like regulators respond to aromatic compounds [, , ]. The crystal structures of MarR, MexR and SlyA have been determined and show a winged HTH DNA-binding core flanked by helices involved in dimerisation. The DNA-binding domains are ascribed to the superfamily of winged helix proteins, containing a three (four)-helix (H) bundle and a three-stranded antiparallel beta-sheet (B) in the topology: H1-(H1')-H2-B1-H3-H4-B2-B3-H5-H6. Helices 3 and 4 comprise the helix-turn-helix motif and the beta-sheet is called the wing. Helix 4 is termed the recognition helix, like in other HTHs where it binds the DNA major groove. The helices 1, 5 and 6 are involved in dimerisation, as most MarR-like transcription regulators form dimers [, ]. ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 1JGS_A 2NYX_D 2PEX_B 2PFB_A 3BPX_A 3BPV_A 2BV6_A 3BJA_A 3E6M_B 2ETH_A ....

>cd00131 PAX Paired Box domain

Probab=92.83  E-value=0.28  Score=41.52  Aligned_cols=41  Identities=15%  Similarity=0.079  Sum_probs=31.3

Q ss_pred             CCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHH
Q 046578          318 LSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIAL  362 (379)
Q Consensus       318 L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl  362 (379)
                      |+...|.-|.+.|-    +|+|..+||+.||||+++|.+++.+-.
T Consensus        18 lS~d~R~rIv~~~~----~G~s~~~iA~~~~Vs~~tV~r~i~r~~   58 (128)
T cd00131          18 LPDSIRQRIVELAQ----SGIRPCDISRQLRVSHGCVSKILNRYY   58 (128)
T ss_pred             CCHHHHHHHHHHHH----cCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence            45544444444452    679999999999999999999988754

>PHA02591 hypothetical protein; Provisional

Probab=92.73  E-value=0.14  Score=39.07  Aligned_cols=24  Identities=21%  Similarity=0.361  Sum_probs=22.0

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHH
Q 046578          336 TPVSCKEIGRLLSLSRERIRQIRG  359 (379)
Q Consensus       336 e~~S~~EIAe~LgiS~~~Vr~~~~  359 (379)
                      .|+|.++||+.||+|+.+|++.+.
T Consensus        58 qGlSqeqIA~~LGVsqetVrKYL~   81 (83)
T PHA02591         58 KGFTVEKIASLLGVSVRKVRRYLE   81 (83)
T ss_pred             cCCCHHHHHHHhCCCHHHHHHHHh
Confidence            669999999999999999998765

>PRK14082 hypothetical protein; Provisional

Probab=92.56  E-value=0.46  Score=34.94  Aligned_cols=58  Identities=16%  Similarity=0.166  Sum_probs=45.6

Q ss_pred             ccHHHHHHHHHHhHHHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHhccCCCCCCCchhH
Q 046578          138 KERESQERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTY  197 (379)
Q Consensus       138 Gd~~A~e~Li~~y~~lV~~ia~r~~~~~~d~eDLvQEg~i~L~~ai~~fD~~~g~~FsTY  197 (379)
                      .+....+.++..+.|.|.+-...-.  -...|||.||--+.+++.++.++...+.-|.-|
T Consensus         6 ~~~~e~e~ii~~FepkIkKsL~~T~--yqeREDLeQElk~Ki~eK~~~~~~~e~PGF~ef   63 (65)
T PRK14082          6 DDTEEIEHLIENFSPMIKKKLSNTS--YQEREDLEQELKIKIIEKADMLLCQEVPGFWEF   63 (65)
T ss_pred             hhHHHHHHHHHHccHHHHHHHhcCC--hhhHHHHHHHHHHHHHHHHHHhhcccCCcHHHh
Confidence            3456778899999999998665542  257899999999999999999987666556544

>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases

Probab=92.54  E-value=0.35  Score=36.17  Aligned_cols=39  Identities=15%  Similarity=0.243  Sum_probs=27.3

Q ss_pred             HHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 046578          321 READILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGI  360 (379)
Q Consensus       321 rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~r  360 (379)
                      .+..|+.+.. -.|.+++|..|||+.+|++..+|++++++
T Consensus         7 ~~~~IL~~L~-~~g~~~~ta~eLa~~lgl~~~~v~r~L~~   45 (68)
T smart00550        7 LEEKILEFLE-NSGDETSTALQLAKNLGLPKKEVNRVLYS   45 (68)
T ss_pred             HHHHHHHHHH-HCCCCCcCHHHHHHHHCCCHHHHHHHHHH
Confidence            3445555443 22323699999999999999999877654

Helix-turn-helix-containing domain. Also known as Zab.

>PF01022 HTH_5: Bacterial regulatory protein, arsR family; InterPro: IPR001845 Bacterial transcription regulatory proteins that bind DNA via a helix-turn-helix (HTH) motif can be grouped into families on the basis of sequence similarities

Probab=92.45  E-value=0.42  Score=32.83  Aligned_cols=37  Identities=22%  Similarity=0.298  Sum_probs=27.1

Q ss_pred             HHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 046578          320 EREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGI  360 (379)
Q Consensus       320 ~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~r  360 (379)
                      |.-..|+.+-.    ..+++..||++.+|+|+++|++.+..
T Consensus         2 ~~R~~Il~~L~----~~~~~~~el~~~l~~s~~~vs~hL~~   38 (47)
T PF01022_consen    2 PTRLRILKLLS----EGPLTVSELAEELGLSQSTVSHHLKK   38 (47)
T ss_dssp             HHHHHHHHHHT----TSSEEHHHHHHHHTS-HHHHHHHHHH
T ss_pred             HHHHHHHHHHH----hCCCchhhHHHhccccchHHHHHHHH
Confidence            34455655544    26799999999999999999988654

One such group, termed arsR, includes several proteins that appear to dissociate from DNA in the presence of metal ions: arsR, which functions as a transcriptional repressor of an arsenic resistance operon; smtB from Synechococcus sp. (strain PCC 7942), which acts as a transcriptional repressor of the smtA gene that codes for a metallothionein; cadC, a protein required for cadmium-resistance; and hypothetical protein yqcJ from Bacillus subtilis. The HTH motif is thought to be located in the central part of these proteins []. The motif is characterised by a number of well-conserved residues: at its N-terminal extremity is a cysteine residue; a second Cys is found in arsR and cadC, but not in smtA; and at the C terminus lie one or two histidines. These residues may be involved in metal-binding (Zn in smtB; metal-oxyanions such as arsenite, antimonite and arsenate for arsR; and cadmium for cadC) []. It is believed that binding of a metal ion could induce a conformational change that would prevent the protein from binding DNA []. The crystal structure of the cyanobacterial smtB shows a fold of five alpha-helices (H) and a pair of antiparallel beta-strands (B) in the topology H1-H2-H3-H4-B1-B2-H5. Helices 3 and 4 comprise the helix-turn-helix motif and the beta-sheet is called the wing as in other wHTH, such as the dtxR-type or the merR-type. Helix 4 is termed the recognition helix, like in other HTHs where it binds the DNA major groove. Most arsR/smtB-like metalloregulators form homodimers []. The dimer interface is formed by helix 5 and an N-terminal part []. Two distinct metal-binding sites have been identified. The first site comprises cysteine thiolates located in the HTH in helix 3 and for some cases in the N terminus, called the alpha3(N) site []. The second metal-binding site is located in helix 5 (and C terminus) and is called the alpha5(C) site. The alpha3N site binds large thiophilic, toxic metals including Cd, Pb, and Bi, as in S. aureus cadC. ArsR lacks the N-terminal arm and its alpha3 site coordinates smaller thiophilic ions like As and Sb. The alpha5 site contains carboxylate and imidazole ligands and interacts preferentially with biologically required metal ions including Zn, Co, and Ni. ArsR-type metalloregulators contain one of these sites, both, or other potential metal-binding sites [, ]. Binding of metal ions to these sites leads to allosteric changes that can derepress the operator/promotor DNA. The metal-inducible operons contain one or two imperfect 12-2-12 inverted repeats, which can be recognised by multimeric arsR-type metalloregulators. ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3CUO_A 1U2W_C 3F72_C 3F6V_A 3JTH_B 2P4W_B 1KU9_B 2LKP_B 1SMT_A 1R22_B ....

>COG3415 Transposase and inactivated derivatives [DNA replication, recombination, and repair]

Probab=92.09  E-value=0.28  Score=42.08  Aligned_cols=27  Identities=15%  Similarity=0.193  Sum_probs=24.9

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHHHHH
Q 046578          336 TPVSCKEIGRLLSLSRERIRQIRGIAL  362 (379)
Q Consensus       336 e~~S~~EIAe~LgiS~~~Vr~~~~rAl  362 (379)
                      +|+|.+|||+++|+|.+||..+++|-.
T Consensus        20 ~G~S~re~Ak~~gvs~sTvy~wv~r~~   46 (138)
T COG3415          20 EGLSCREAAKRFGVSISTVYRWVRRYR   46 (138)
T ss_pred             cCccHHHHHHHhCccHHHHHHHHHHhc
Confidence            779999999999999999999988754

>PF13022 HTH_Tnp_1_2: Helix-turn-helix of insertion element transposase; PDB: 2AO9_I

Probab=91.84  E-value=0.85  Score=39.04  Aligned_cols=50  Identities=22%  Similarity=0.224  Sum_probs=31.8

Q ss_pred             HHHHHhcCCHHHHHHHHHH----hhcCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 046578          311 LKELLQTLSEREADILRLH----FGLDGQTPVSCKEIGRLLSLSRERIRQIRGI  360 (379)
Q Consensus       311 L~~~L~~L~~rer~Vl~l~----ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~r  360 (379)
                      +.++-.+|++.|+....+.    +...+.+..|+.|||+.+||+++|..++.+.
T Consensus         4 ~~~le~~L~~~Q~kAa~ll~~ne~~~~~~~r~T~~eiAee~Gis~~tLYrWr~~   57 (142)
T PF13022_consen    4 LKELEAKLTLQQRKAAQLLVENELMPENGERRTQAEIAEEVGISRSTLYRWRQQ   57 (142)
T ss_dssp             HHHHHTTS-HHHHHHHHHHHHHHHS------S-HHHHHHHHTS-HHHHHHHHHH
T ss_pred             HHHHHHHcCHHHHHHHHHHHHHHHhhhccccchHHHHHHHhCCCHHHHHHHHhc
Confidence            4555678999998854432    1112236799999999999999999999853

>PF01418 HTH_6: Helix-turn-helix domain, rpiR family; InterPro: IPR000281 This domain contains a helix-turn-helix motif []

Probab=91.68  E-value=0.45  Score=36.40  Aligned_cols=53  Identities=17%  Similarity=0.151  Sum_probs=36.4

Q ss_pred             HHHHHHHHhcCCHHHHHHHHHHhh-cCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 046578          308 KQELKELLQTLSEREADILRLHFG-LDGQTPVSCKEIGRLLSLSRERIRQIRGI  360 (379)
Q Consensus       308 ~~~L~~~L~~L~~rer~Vl~l~yg-L~g~e~~S~~EIAe~LgiS~~~Vr~~~~r  360 (379)
                      ...|......|++.|+.|.....- ......+|..|||+..|+|.++|.+..++
T Consensus         4 ~~~i~~~~~~ls~~e~~Ia~yil~~~~~~~~~si~elA~~~~vS~sti~Rf~kk   57 (77)
T PF01418_consen    4 LEKIRSQYNSLSPTEKKIADYILENPDEIAFMSISELAEKAGVSPSTIVRFCKK   57 (77)
T ss_dssp             HHHHHHHGGGS-HHHHHHHHHHHH-HHHHCT--HHHHHHHCTS-HHHHHHHHHH
T ss_pred             HHHHHHHHhhCCHHHHHHHHHHHhCHHHHHHccHHHHHHHcCCCHHHHHHHHHH
Confidence            356777788999999998875421 01224699999999999999999877654

Every member of this family is N-terminal to a SIS domain IPR001347 from INTERPRO. Members of this family are probably regulators of genes involved in phosphosugar metobolism.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 2O3F_B 3IWF_B.

>PF13542 HTH_Tnp_ISL3: Helix-turn-helix domain of transposase family ISL3

Probab=91.67  E-value=0.46  Score=33.07  Aligned_cols=34  Identities=29%  Similarity=0.297  Sum_probs=26.5

Q ss_pred             HHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 046578          323 ADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIA  361 (379)
Q Consensus       323 r~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rA  361 (379)
                      +.|+.+..     +..|.++||+.+|+|..||.+++.+.
T Consensus        18 ~~i~~~~~-----~~~s~~~vA~~~~vs~~TV~ri~~~~   51 (52)
T PF13542_consen   18 QYILKLLR-----ESRSFKDVARELGVSWSTVRRIFDRY   51 (52)
T ss_pred             HHHHHHHh-----hcCCHHHHHHHHCCCHHHHHHHHHhh
Confidence            34555543     33699999999999999999998764

>PF00356 LacI: Bacterial regulatory proteins, lacI family; InterPro: IPR000843 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif

Probab=91.64  E-value=0.18  Score=34.80  Aligned_cols=22  Identities=18%  Similarity=0.302  Sum_probs=20.1

Q ss_pred             CHHHHHHHhCCCHHHHHHHHHH
Q 046578          339 SCKEIGRLLSLSRERIRQIRGI  360 (379)
Q Consensus       339 S~~EIAe~LgiS~~~Vr~~~~r  360 (379)
                      |++|||+..|+|..||++.++.
T Consensus         1 Ti~dIA~~agvS~~TVSr~ln~   22 (46)
T PF00356_consen    1 TIKDIAREAGVSKSTVSRVLNG   22 (46)
T ss_dssp             CHHHHHHHHTSSHHHHHHHHTT
T ss_pred             CHHHHHHHHCcCHHHHHHHHhC
Confidence            6899999999999999998864

These proteins are very diverse, but for convenience may be grouped into subfamilies on the basis of sequence similarity. One such family groups together a range of proteins, including ascG, ccpA, cytR, ebgR, fruR, galR, galS, lacI, malI, opnR, purF, rafR, rbtR and scrR [, ]. Within this family, the HTH motif is situated towards the N terminus.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3KJX_C 1ZAY_A 1VPW_A 2PUA_A 1QQA_A 1PNR_A 1JFT_A 1QP4_A 2PUD_A 1JH9_A ....

>smart00344 HTH_ASNC helix_turn_helix ASNC type

Probab=91.58  E-value=0.48  Score=38.30  Aligned_cols=42  Identities=21%  Similarity=0.189  Sum_probs=32.7

Q ss_pred             CCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHH
Q 046578          318 LSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIAL  362 (379)
Q Consensus       318 L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl  362 (379)
                      |++.++.|+....- +  ...|+.+||+.+|+|+.+|++++.+-.
T Consensus         1 ld~~D~~il~~L~~-~--~~~~~~~la~~l~~s~~tv~~~l~~L~   42 (108)
T smart00344        1 LDEIDRKILEELQK-D--ARISLAELAKKVGLSPSTVHNRVKRLE   42 (108)
T ss_pred             CCHHHHHHHHHHHH-h--CCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence            46778888876542 2  469999999999999999988766543

AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli

>PF03444 HrcA_DNA-bdg: Winged helix-turn-helix transcription repressor, HrcA DNA-binding; InterPro: IPR005104 Prokaryotic cells have a defence mechanism against a sudden heat-shock stress

Probab=91.58  E-value=0.51  Score=36.32  Aligned_cols=42  Identities=31%  Similarity=0.465  Sum_probs=34.2

Q ss_pred             cCCHHHHHHHHHH---hhcCCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 046578          317 TLSEREADILRLH---FGLDGQTPVSCKEIGRLLSLSRERIRQIRG  359 (379)
Q Consensus       317 ~L~~rer~Vl~l~---ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~  359 (379)
                      .|+++|++||...   | ....+...-++||+.+++|..|||+...
T Consensus         1 ~Lt~rq~~IL~alV~~Y-~~~~~PVgSk~ia~~l~~s~aTIRN~M~   45 (78)
T PF03444_consen    1 MLTERQREILKALVELY-IETGEPVGSKTIAEELGRSPATIRNEMA   45 (78)
T ss_pred             CCCHHHHHHHHHHHHHH-HhcCCCcCHHHHHHHHCCChHHHHHHHH
Confidence            3889999988753   3 3445889999999999999999998754

Commonly, they induce a set of proteins that protect cellular proteins from being denatured by heat. Among such proteins are the GroE and DnaK chaperones whose transcription is regulated by a heat-shock repressor protein HrcA. HrcA is a winged helix-turn-helix repressor that negatively regulates the transcription of dnaK and groE operons by binding the upstream CIRCE (controlling inverted repeat of chaperone expression) element. In Bacillus subtilis this element is a perfect 9 base pair inverted repeat separated by a 9 base pair spacer. The crystal structure of a heat-inducible transcriptional repressor, HrcA, from Thermotoga maritima has been reported at 2.2A resolution. HrcA is composed of three domains: an N-terminal winged helix-turn-helix domain (WHTH), a GAF-like domain, and an inserted dimerizing domain (IDD). The IDD shows a unique structural fold with an anti-parallel beta-sheet composed of three beta-strands sided by four alpha-helices. HrcA crystallises as a dimer, which is formed through hydrophobic contact between the IDDs and a limited contact that involves conserved residues between the GAF-like domains []. The structural studies suggest that the inactive form of HrcA is the dimer and this is converted to its DNA-binding form by interaction with GroEL, which binds to a conserved C-terminal sequence region [, ]. Comparison of the HrcA-CIRCE complexes from B. subtilis and Bacillus thermoglucosidasius (Geobacillus thermoglucosidasius), which grow at vastly different ranges of temperature shows that the thermostability profiles were consistent with the difference in the growth temperatures suggesting that HrcA can function as a thermosensor to detect temperature changes in cells []. Any increase in temperature causes the dissociation of the HrcA from the CIRCE complex with the concomitant activation of transcription of the groE and dnaK operons. This domain represents the winged helix-turn-helix DNA-binding domain which is located close to the N terminus of HrcA. This domain is also found at the N terminus of a set of uncharacterised proteins that have two C-terminal CBS domains. ; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent

>PF12840 HTH_20: Helix-turn-helix domain; PDB: 1ULY_A 2CWE_A 1Y0U_B 2QUF_B 2QLZ_C 2OQG_B 2ZKZ_C 3PQK_A 3PQJ_D 3F6O_B

Probab=91.54  E-value=1.1  Score=32.50  Aligned_cols=38  Identities=21%  Similarity=0.269  Sum_probs=28.5

Q ss_pred             HHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 046578          320 EREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGI  360 (379)
Q Consensus       320 ~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~r  360 (379)
                      |.-+.|+.+...   ..++|..|||+.+|++.++|++.+..
T Consensus        10 p~R~~Il~~L~~---~~~~t~~ela~~l~~~~~t~s~hL~~   47 (61)
T PF12840_consen   10 PTRLRILRLLAS---NGPMTVSELAEELGISQSTVSYHLKK   47 (61)
T ss_dssp             HHHHHHHHHHHH---CSTBEHHHHHHHHTS-HHHHHHHHHH
T ss_pred             HHHHHHHHHHhc---CCCCCHHHHHHHHCCCHHHHHHHHHH
Confidence            666667665521   37899999999999999999887543

...

>PF13011 LZ_Tnp_IS481: leucine-zipper of insertion element IS481

Probab=91.52  E-value=0.51  Score=36.99  Aligned_cols=43  Identities=12%  Similarity=-0.004  Sum_probs=36.7

Q ss_pred             cCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHH
Q 046578          317 TLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIAL  362 (379)
Q Consensus       317 ~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl  362 (379)
                      .|+|.-|..|..+. ++  ++.+..++|+.+|||..|+++++.|=+
T Consensus         8 ~Lt~~gR~~lv~~v-v~--~g~~~a~aA~~~gVS~~Ta~kW~~Ryr   50 (85)
T PF13011_consen    8 RLTPRGRLRLVRRV-VE--QGWPVAHAAAEFGVSRRTAYKWLARYR   50 (85)
T ss_pred             CCCHHHHHHHHHHH-HH--cCCcHHHHHHHhCCCHHHHHHHHHHHH
Confidence            68999998888876 33  569999999999999999999987744

>PF01710 HTH_Tnp_IS630: Transposase; InterPro: IPR002622 Transposase proteins are necessary for efficient DNA transposition

Probab=91.51  E-value=2.7  Score=34.93  Aligned_cols=25  Identities=16%  Similarity=0.165  Sum_probs=21.4

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHHH
Q 046578          336 TPVSCKEIGRLLSLSRERIRQIRGI  360 (379)
Q Consensus       336 e~~S~~EIAe~LgiS~~~Vr~~~~r  360 (379)
                      .+.|+.|||+.||||.++|...+.+
T Consensus        70 pd~tl~Ela~~l~Vs~~ti~~~Lkr   94 (119)
T PF01710_consen   70 PDATLRELAERLGVSPSTIWRALKR   94 (119)
T ss_pred             CCcCHHHHHHHcCCCHHHHHHHHHH
Confidence            6799999999999999999765544

This entry includes insertion sequences from Synechocystis sp. (strain PCC 6803) three of which are characterised as homologous to bacterial IS5- and IS4- and to several members of the IS630-Tc1-mariner superfamily []. More information about these proteins can be found at Protein of the Month: Transposase [].

>PF01325 Fe_dep_repress: Iron dependent repressor, N-terminal DNA binding domain; InterPro: IPR022687 The DtxR-type HTH domain is a DNA-binding, winged helix-turn-helix (wHTH) domain of about 65 residues present in metalloregulators of the DtxR/MntR family

Probab=91.31  E-value=0.43  Score=34.84  Aligned_cols=43  Identities=28%  Similarity=0.410  Sum_probs=28.0

Q ss_pred             CCHHHHHHHHHHhhcC-CCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 046578          318 LSEREADILRLHFGLD-GQTPVSCKEIGRLLSLSRERIRQIRGI  360 (379)
Q Consensus       318 L~~rer~Vl~l~ygL~-g~e~~S~~EIAe~LgiS~~~Vr~~~~r  360 (379)
                      |++....-|...|-+. +....+..+||+.||+|+++|...+++
T Consensus         2 Lt~~~e~YL~~Iy~l~~~~~~v~~~~iA~~L~vs~~tvt~ml~~   45 (60)
T PF01325_consen    2 LTESEEDYLKAIYELSEEGGPVRTKDIAERLGVSPPTVTEMLKR   45 (60)
T ss_dssp             CSCHHHHHHHHHHHHHHCTSSBBHHHHHHHHTS-HHHHHHHHHH
T ss_pred             CCcHHHHHHHHHHHHHcCCCCccHHHHHHHHCCChHHHHHHHHH
Confidence            3444444444443333 347799999999999999999766544

The family is named after Corynebacterium diphtheriae DtxR, an iron-specific diphtheria toxin repressor, and Bacillus subtilis MntR, a manganese transport regulator. Iron-responsive metalloregulators such as DtxR and IdeR occur in Gram-positive bacteria of the high GC branch, while manganese-responsive metalloregulators like MntR are described in diverse genera of Gram-positive and Gram-negative bacteria and also in Archaea [].The metalloregulators like DtxR/MntR contain the DNA-binding DtxR-type HTH domain usually in the N-terminal part. The C-terminal part contains a dimerisation domain with two metal-binding sites, although the primary metal-binding site is less conserved in the Mn(II)-regulators. Fe(II)-regulated proteins contain an SH3-like domain as a C-terminal extension, which is absent in Mn(II)-regulated MntR [, ]. Metal-ion dependent regulators orchestrate the virulence of several important human pathogens. The DtxR protein regulates the expression of diphtheria toxinin response to environmental iron concentrations. Furthermore, DtxR and IdeR control iron uptake []. Homeostasis of manganese, which is an essential nutrient, is regulated by MntR. A typical DtxR-type metalloregulator binds two divalent metal effectors per monomer, upon which allosteric changes occur that moderate binding to the cognate DNA operators. Iron-bound DtxR homodimers bind to an interrupted palindrome of 19 bp, protecting a sequence of ~30 bp. The crystal structures of iron-regulated and manganese-regulated repressors show that the DNA binding domain contains three alpha-helices and a pair of antiparallel beta-strands. Helices 2 and 3 comprise the helix-turn-helix motif and the beta-strands are called the wing []. This wHTH topology is similar to the lysR-type HTH (see PDOC00043 from PROSITEDOC). Most DtxR-type metalloregulators bind as dimers to the DNA major groove. Several proteins are known to contain a DtxR-type HTH domain. These include- Corynebacterium diphtheriae DtxR, a diphtheria toxin repressor [], which regulates the expression of the high-affinity iron uptake system, other iron-sensitive genes, and the bacteriophage tox gene. Metal-bound DtxR represses transcription by binding the tox operator; if iron is limiting, conformational changes of the wHTH disrupt DNA-binding and the diphtheria toxin is produced. Mycobacterium tuberculosis IdeR, an iron-dependent regulator that is essential for this pathogen. The regulator represses genes for iron acquisition and activates iron storage genes, and is a positive regulator of oxidative stress responses []. Bacillus subtilis MntR, a manganese transport regulator, binds Mn2+ as an effector and is a transcriptional repressor of transporters for the import of manganese. Treponema pallidum troR, a metal-dependent transcriptional repressor. Archaeoglobus fulgidus MDR1 (troR), a metal-dependent transcriptional repressor, which negatively regulates its own transcription. This entry covers the entire DtxR-type HTH domain.; GO: 0005506 iron ion binding; PDB: 3HRT_B 3HRS_A 3HRU_B 2X4H_D 1ON1_B 2HYF_C 2F5E_A 3R60_B 1ON2_B 2F5F_A ....

>PRK11083 DNA-binding response regulator CreB; Provisional

Probab=91.26  E-value=0.32  Score=43.58  Aligned_cols=51  Identities=16%  Similarity=0.099  Sum_probs=42.7

Q ss_pred             cCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCC-----HHHHHHHHHHHHHHHHhH
Q 046578          317 TLSEREADILRLHFGLDGQTPVSCKEIGRLLSLS-----RERIRQIRGIALTKLQQT  368 (379)
Q Consensus       317 ~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS-----~~~Vr~~~~rAl~kLR~~  368 (379)
                      .|+++|.+|+.+.. -+.+.++|.+||++.++.+     ..||+.++++.++||...
T Consensus       154 ~Lt~~E~~il~~l~-~~~~~~~s~~~i~~~l~~~~~~~~~~tv~~~i~~l~~Kl~~~  209 (228)
T PRK11083        154 TLTRYEFLLLKTLL-LSPGRVFSRQQLMDIVWEDAQDSYDRTVDTHIKTLRAKLRAI  209 (228)
T ss_pred             ecCHHHHHHHHHHH-hCCCceECHHHHHHHhcCCCCCCCccCHHHHHHHHHHHhccC
Confidence            59999999999876 2222569999999999986     789999999999999743

>PF13463 HTH_27: Winged helix DNA-binding domain; PDB: 3GFL_A 2YR2_B 3GFM_A 3GFJ_A 3GF2_A 3GEZ_A 2GXG_A 3GFI_A 2EB7_A

Probab=91.20  E-value=0.49  Score=34.63  Aligned_cols=43  Identities=16%  Similarity=0.269  Sum_probs=27.8

Q ss_pred             CCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHH
Q 046578          318 LSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIAL  362 (379)
Q Consensus       318 L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl  362 (379)
                      |++.|..||....  ....+++..+||+.++++..+|++.+++..
T Consensus         1 lt~~q~~vL~~l~--~~~~~~t~~~l~~~~~~~~~~vs~~i~~L~   43 (68)
T PF13463_consen    1 LTRPQWQVLRALA--HSDGPMTQSDLAERLGISKSTVSRIIKKLE   43 (68)
T ss_dssp             --HHHHHHHHHHT----TS-BEHHHHHHHTT--HHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHH--ccCCCcCHHHHHHHHCcCHHHHHHHHHHHH
Confidence            4667777776544  124789999999999999999986655543

>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional

Probab=90.85  E-value=0.66  Score=40.30  Aligned_cols=42  Identities=12%  Similarity=0.139  Sum_probs=33.8

Q ss_pred             cCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 046578          317 TLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIA  361 (379)
Q Consensus       317 ~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rA  361 (379)
                      .|++.++.||..-- -+  ...|+.|||+.+|+|+++|++++.+-
T Consensus         6 ~lD~~D~~Il~~Lq-~d--~R~s~~eiA~~lglS~~tV~~Ri~rL   47 (153)
T PRK11179          6 QIDNLDRGILEALM-EN--ARTPYAELAKQFGVSPGTIHVRVEKM   47 (153)
T ss_pred             ccCHHHHHHHHHHH-Hc--CCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence            47888999988654 23  46999999999999999998876553

>PRK10336 DNA-binding transcriptional regulator QseB; Provisional

Probab=90.62  E-value=0.34  Score=43.14  Aligned_cols=50  Identities=20%  Similarity=0.153  Sum_probs=41.6

Q ss_pred             cCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhC-----CCHHHHHHHHHHHHHHHHh
Q 046578          317 TLSEREADILRLHFGLDGQTPVSCKEIGRLLS-----LSRERIRQIRGIALTKLQQ  367 (379)
Q Consensus       317 ~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~Lg-----iS~~~Vr~~~~rAl~kLR~  367 (379)
                      .|+++|.+++.+.. -+.+..+|.++|++.+.     ++..+|+..+++.++||..
T Consensus       149 ~Lt~~E~~il~~l~-~~~~~~~s~~~i~~~l~~~~~~~~~~tv~~~i~~lr~Kl~~  203 (219)
T PRK10336        149 TLKPKEFALLELLM-RNAGRVLPRKLIEEKLYTWDEEVTSNAVEVHVHHLRRKLGS  203 (219)
T ss_pred             ecCHHHHHHHHHHH-hCCCccCcHHHHHHHhcCCCCCCCccCHHHHHHHHHHhcCC
Confidence            49999999999765 22224589999999996     9999999999999999863

>PRK10046 dpiA two-component response regulator DpiA; Provisional

Probab=90.53  E-value=0.26  Score=45.26  Aligned_cols=39  Identities=15%  Similarity=0.238  Sum_probs=29.2

Q ss_pred             CCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 046578          318 LSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGI  360 (379)
Q Consensus       318 L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~r  360 (379)
                      |+++  +|+.+.-  .|..|+|.+|||+.||+|+.||++.+..
T Consensus       162 Lt~r--~Vl~~~~--~g~~g~s~~eIa~~l~iS~~Tv~~~~~~  200 (225)
T PRK10046        162 LTLN--AVRKLFK--EPGVQHTAETVAQALTISRTTARRYLEY  200 (225)
T ss_pred             HHHH--HHHHHHH--cCCCCcCHHHHHHHhCccHHHHHHHHHH
Confidence            5554  5666543  2334699999999999999999998753

>PF08822 DUF1804: Protein of unknown function (DUF1804); InterPro: IPR014926 This entry is represented by Bacteriophage D3112, Orf24

Probab=90.50  E-value=0.64  Score=40.99  Aligned_cols=42  Identities=14%  Similarity=0.152  Sum_probs=34.5

Q ss_pred             CHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 046578          319 SEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALT  363 (379)
Q Consensus       319 ~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~  363 (379)
                      |+.-|.-++..|.+   +++|+..+|..+|||.+|+++++.+|..
T Consensus         4 ~~e~R~~~R~~YV~---~~~sLe~aA~~~gVs~~TarrWK~~Ak~   45 (165)
T PF08822_consen    4 PQETRDAVRRAYVF---DRLSLEQAAAKCGVSYATARRWKREAKA   45 (165)
T ss_pred             cHHHHHHHHHHHHh---CCCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence            45567777777742   5599999999999999999999998864

The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.

>PF01978 TrmB: Sugar-specific transcriptional regulator TrmB; InterPro: IPR002831 TrmB, is a protein of 38,800 apparent molecular weight, that is involved in the maltose-specific regulation of the trehalose/maltose ABC transport operon in Thermococcus litoralis

Probab=90.28  E-value=0.27  Score=36.45  Aligned_cols=41  Identities=27%  Similarity=0.351  Sum_probs=30.9

Q ss_pred             cCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 046578          317 TLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGI  360 (379)
Q Consensus       317 ~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~r  360 (379)
                      .|++.|.+|+..-.  . ..+.|..|||+.+|+++++|+..+.+
T Consensus         5 gLs~~E~~vy~~Ll--~-~~~~t~~eIa~~l~i~~~~v~~~L~~   45 (68)
T PF01978_consen    5 GLSENEAKVYLALL--K-NGPATAEEIAEELGISRSTVYRALKS   45 (68)
T ss_dssp             CHHHHHHHHHHHHH--H-HCHEEHHHHHHHHTSSHHHHHHHHHH
T ss_pred             CcCHHHHHHHHHHH--H-cCCCCHHHHHHHHCcCHHHHHHHHHH
Confidence            46677777776432  1 25699999999999999999766544

TrmB has been shown to be a maltose-specific repressor, and this inhibition is counteracted by maltose and trehalose. TrmB binds maltose and trehalose half-maximally at 20 uM and 0.5 mM sugar concentration, respectively []. Other members of this family are annotated as either transcriptional regulators or hypothetical proteins. ; PDB: 2D1H_A 3QPH_A 1SFX_A.

>TIGR01610 phage_O_Nterm phage replication protein O, N-terminal domain

Probab=90.01  E-value=1.6  Score=34.75  Aligned_cols=46  Identities=28%  Similarity=0.281  Sum_probs=33.7

Q ss_pred             HhcCCHHHHHHHHHHh----hcC-CCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 046578          315 LQTLSEREADILRLHF----GLD-GQTPVSCKEIGRLLSLSRERIRQIRGI  360 (379)
Q Consensus       315 L~~L~~rer~Vl~l~y----gL~-g~e~~S~~EIAe~LgiS~~~Vr~~~~r  360 (379)
                      ...+++++..+|....    |.. ....+|..|||+.+|+++.+|++.+.+
T Consensus        20 ~~~l~~r~~~vLl~L~~~~~G~~~~~~~is~~eLa~~~g~sr~tVsr~L~~   70 (95)
T TIGR01610        20 GADLSGREFRVLLAIIRLTYGWNKKQDRVTATVIAELTGLSRTHVSDAIKS   70 (95)
T ss_pred             hCCCCHHHHHHHHHHHHHHhCccccCCccCHHHHHHHHCcCHHHHHHHHHH
Confidence            3478999998877432    211 236799999999999999998765443

This model represents the N-terminal region of the phage lambda replication protein O and homologous regions of other phage proteins.

>PF02954 HTH_8: Bacterial regulatory protein, Fis family; InterPro: IPR002197 The Factor for Inversion Stimulation (FIS) protein is a regulator of bacterial functions, and binds specifically to weakly related DNA sequences [,]

Probab=90.01  E-value=0.52  Score=31.65  Aligned_cols=39  Identities=21%  Similarity=0.256  Sum_probs=25.9

Q ss_pred             CHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 046578          319 SEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGI  360 (379)
Q Consensus       319 ~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~r  360 (379)
                      ..-|+.+|.-..-   ..+-+..+.|+.||||+.++++.+.+
T Consensus         3 ~~~E~~~i~~aL~---~~~gn~~~aA~~Lgisr~tL~~klkk   41 (42)
T PF02954_consen    3 EEFEKQLIRQALE---RCGGNVSKAARLLGISRRTLYRKLKK   41 (42)
T ss_dssp             HHHHHHHHHHHHH---HTTT-HHHHHHHHTS-HHHHHHHHHH
T ss_pred             HHHHHHHHHHHHH---HhCCCHHHHHHHHCCCHHHHHHHHHh
Confidence            3456666665432   13468999999999999999876653

It activates ribosomal RNA transcription, and is involved in upstream activation of rRNA promoters. The protein has been shown to play a role in the regulation of virulence factors in both Salmonella typhimurium and Escherichia coli []. Some of its functions include inhibition of the initiation of DNA replication from the OriC site, and promotion of Hin-mediated DNA inversion. In its C-terminal extremity, FIS encodes a helix-turn-helix (HTH) DNA- binding motif, which shares a high degree of similarity with other HTH motifs of more primitive bacterial transcriptional regulators, such as the nitrogen assimilation regulatory proteins (NtrC) from species like Azobacter, Rhodobacter and Rhizobium. This has led to speculation that both evolved from a single common ancestor []. The 3-dimensional structure of the E. coli FIS DNA-binding protein has been determined by means of X-ray diffraction to 2.0A resolution [,]. FIS is composed of four alpha-helices tightly intertwined to form a globular dimer with two protruding HTH motifs. The 24 N-terminal amino acids are poorly defined, indicating that they might act as `feelers' suitable for DNA or protein (invertase) recognition []. Other proteins belonging to this subfamily include: E. coli: atoC, hydG, ntrC, fhlA, tyrR, Rhizobium spp.: ntrC, nifA, dctD ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 1NTC_A 3JRH_A 3JRB_A 3IV5_A 3JRI_A 1ETQ_A 1ETW_B 1ETY_A 3JRF_A 3JRA_A ....

>PF09339 HTH_IclR: IclR helix-turn-helix domain; InterPro: IPR005471 The many bacterial transcription regulation proteins which bind DNA through a 'helix-turn-helix' motif can be classified into subfamilies on the basis of sequence similarities

Probab=90.00  E-value=0.55  Score=32.93  Aligned_cols=33  Identities=21%  Similarity=0.348  Sum_probs=23.7

Q ss_pred             HHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 046578          328 LHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGI  360 (379)
Q Consensus       328 l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~r  360 (379)
                      +.++-....++|..|||+.+|+++++|.+++..
T Consensus         9 L~~l~~~~~~~t~~eia~~~gl~~stv~r~L~t   41 (52)
T PF09339_consen    9 LEALAESGGPLTLSEIARALGLPKSTVHRLLQT   41 (52)
T ss_dssp             HHCHHCTBSCEEHHHHHHHHTS-HHHHHHHHHH
T ss_pred             HHHHHcCCCCCCHHHHHHHHCcCHHHHHHHHHH
Confidence            334333346689999999999999999877543

One of these subfamilies, called 'iclR', groups several proteins including: gylR, a possible activator protein for the gylABX glycerol operon in Streptomyces. iclR, the repressor of the acetate operon (also known as glyoxylate bypass operon) in Escherichia coli and Salmonella typhimurium. These proteins have a Helix-Turn-Helix motif at the N terminus that is similar to that of other DNA-binding proteins [].; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1MKM_A 3MQ0_A 3R4K_A 2G7U_C 2O0Y_C 2XRO_F 2XRN_B 2IA2_D.

>PRK13413 mpi multiple promoter invertase; Provisional

Probab=90.00  E-value=0.58  Score=42.45  Aligned_cols=34  Identities=29%  Similarity=0.282  Sum_probs=27.3

Q ss_pred             HHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 046578          322 EADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGI  360 (379)
Q Consensus       322 er~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~r  360 (379)
                      ++.|..++-     +|+|..+||+.||||++||+++++.
T Consensus       162 ~~~i~~~~~-----~g~s~~~iak~lgis~~Tv~r~~k~  195 (200)
T PRK13413        162 EEKIKKLLD-----KGTSKSEIARKLGVSRTTLARFLKT  195 (200)
T ss_pred             HHHHHHHHH-----CCCCHHHHHHHHCCCHHHHHHHHHh
Confidence            345666543     6799999999999999999998763

>PF12728 HTH_17: Helix-turn-helix domain

Probab=89.59  E-value=0.38  Score=33.40  Aligned_cols=24  Identities=25%  Similarity=0.342  Sum_probs=21.6

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHHHH
Q 046578          338 VSCKEIGRLLSLSRERIRQIRGIA  361 (379)
Q Consensus       338 ~S~~EIAe~LgiS~~~Vr~~~~rA  361 (379)
                      +|.+|+|+.||||+++|+++..+.
T Consensus         2 lt~~e~a~~l~is~~tv~~~~~~g   25 (51)
T PF12728_consen    2 LTVKEAAELLGISRSTVYRWIRQG   25 (51)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHcC
Confidence            789999999999999999988654

>PRK00423 tfb transcription initiation factor IIB; Reviewed

Probab=89.43  E-value=17  Score=35.46  Aligned_cols=180  Identities=17%  Similarity=0.070  Sum_probs=90.1

Q ss_pred             HHHHHHhHHHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHhccCCCCCCCchhHHHHHHHHHHHHHHHhhcCcccCCcch
Q 046578          144 ERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYWWIKQAIIRAIANKSRTIRLPGSM  223 (379)
Q Consensus       144 e~Li~~y~~lV~~ia~r~~~~~~d~eDLvQEg~i~L~~ai~~fD~~~g~~FsTYa~~~Ir~~i~~~lr~~~r~irip~~~  223 (379)
                      ++-+......|..++.++.-.     +-+.|....+++.+.....-+|.+..+.+..++.-++..    .          
T Consensus       119 er~l~~a~~~I~~~~~~L~Lp-----~~v~e~A~~iyk~~~~~~~~rgrs~~~i~AAclYiACR~----~----------  179 (310)
T PRK00423        119 ERNLAFALSELDRIASQLGLP-----RSVREEAAVIYRKAVEKGLIRGRSIEGVVAAALYAACRR----C----------  179 (310)
T ss_pred             hHHHHHHHHHHHHHHHHcCCC-----HHHHHHHHHHHHHHHhcCcccCCCHHHHHHHHHHHHHHH----c----------
Confidence            334455557778888777322     345555556666665555556767777766666654432    1          


Q ss_pred             HHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCccccCCCCcccccCCCCCCCChHHHHH
Q 046578          224 AGMVAKIAEANNVLSRRLRRMPTDSEIAEMLNIHVSTVRLAIERTRHPISLDGAVTDRGCMTMQDIIPGPDETMPERMVQ  303 (379)
Q Consensus       224 ~~~~~ki~~a~~~l~~~lgr~pt~~eia~~Lgis~~~~~~~l~~~~~~iSLd~~~~~~~~~~l~d~i~~~~~~~pe~~~~  303 (379)
                                        |-.-+..||++.++++..++........+.+.++.+..+  ...+..-+.+.-. -+.+.. 
T Consensus       180 ------------------~~prtl~eI~~~~~v~~k~i~~~~~~l~k~L~~~~~~~~--p~~~i~r~~~~L~-L~~~v~-  237 (310)
T PRK00423        180 ------------------KVPRTLDEIAEVSRVSRKEIGRCYRFLLRELNLKLPPTD--PIDYVPRFASELG-LSGEVQ-  237 (310)
T ss_pred             ------------------CCCcCHHHHHHHhCCCHHHHHHHHHHHHHHhCCCCCCCC--HHHHHHHHHHHcC-CCHHHH-
Confidence                              222356677777777777666554432222222221110  0000000000000 011111 


Q ss_pred             HHHHHHHHHHHHh-cC----CHH--HHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 046578          304 KQLMKQELKELLQ-TL----SER--EADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQ  366 (379)
Q Consensus       304 ~~e~~~~L~~~L~-~L----~~r--er~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR  366 (379)
                       +.....+..+.+ .|    .|.  -..+|.+..-+.| .+.|++|||+..|++..||++.++.-.+.|.
T Consensus       238 -~~A~~i~~~a~~~~l~~Gr~P~sIAAAaIYlA~~~~g-~~~t~keIa~v~~Vs~~tI~~~ykel~~~l~  305 (310)
T PRK00423        238 -KKAIEILQKAKEKGLTSGKGPTGLAAAAIYIASLLLG-ERRTQREVAEVAGVTEVTVRNRYKELAEKLD  305 (310)
T ss_pred             -HHHHHHHHHHHhcCcccCCCHHHHHHHHHHHHHHHhC-CCCCHHHHHHHcCCCHHHHHHHHHHHHHHhC
Confidence             111122222221 11    121  1223333322344 6799999999999999999988777666543

>PRK11169 leucine-responsive transcriptional regulator; Provisional

Probab=89.13  E-value=0.77  Score=40.41  Aligned_cols=41  Identities=20%  Similarity=0.121  Sum_probs=32.5

Q ss_pred             cCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 046578          317 TLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGI  360 (379)
Q Consensus       317 ~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~r  360 (379)
                      .|++.+++||..-- -+  ...|+.|||+.+|+|+++|++++.|
T Consensus        11 ~lD~~D~~IL~~Lq-~d--~R~s~~eiA~~lglS~~tv~~Ri~r   51 (164)
T PRK11169         11 DLDRIDRNILNELQ-KD--GRISNVELSKRVGLSPTPCLERVRR   51 (164)
T ss_pred             hHHHHHHHHHHHhc-cC--CCCCHHHHHHHHCcCHHHHHHHHHH
Confidence            36777888887543 23  5699999999999999999887655

>PF13744 HTH_37: Helix-turn-helix domain; PDB: 2A6C_B 2O38_A

Probab=89.12  E-value=0.9  Score=34.99  Aligned_cols=39  Identities=15%  Similarity=0.209  Sum_probs=27.1

Q ss_pred             CCCCCHHHHHHHhCCCHHHHHHHHH-H----HHHHHHhHHhhch
Q 046578          335 QTPVSCKEIGRLLSLSRERIRQIRG-I----ALTKLQQTNILNN  373 (379)
Q Consensus       335 ~e~~S~~EIAe~LgiS~~~Vr~~~~-r----Al~kLR~~l~~~~  373 (379)
                      ..++|++|+|+.+|+|+++|+++.+ +    .+.+|.+.+...+
T Consensus        29 ~~~ltQ~e~A~~lgisq~~vS~l~~g~~~~~sl~~L~~~l~aLG   72 (80)
T PF13744_consen   29 ERGLTQAELAERLGISQPRVSRLENGKIDDFSLDTLLRYLEALG   72 (80)
T ss_dssp             CCT--HHHHHHHHTS-HHHHHHHHTT-GCC--HHHHHHHHHHTT
T ss_pred             HcCCCHHHHHHHHCCChhHHHHHHcCcccCCCHHHHHHHHHHcC
Confidence            3679999999999999999999884 2    3666666665544

>PRK10710 DNA-binding transcriptional regulator BaeR; Provisional

Probab=89.10  E-value=0.61  Score=42.22  Aligned_cols=50  Identities=16%  Similarity=0.082  Sum_probs=43.0

Q ss_pred             cCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhC-----CCHHHHHHHHHHHHHHHHh
Q 046578          317 TLSEREADILRLHFGLDGQTPVSCKEIGRLLS-----LSRERIRQIRGIALTKLQQ  367 (379)
Q Consensus       317 ~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~Lg-----iS~~~Vr~~~~rAl~kLR~  367 (379)
                      .|+++|++|+.+... +.+++.|.++|++.+.     ++..||...+++.++||..
T Consensus       160 ~Lt~~e~~il~~l~~-~~~~~~s~~~i~~~~~~~~~~~~~~tv~~~i~~lr~kl~~  214 (240)
T PRK10710        160 DLTPAEFRLLKTLSH-EPGKVFSREQLLNHLYDDYRVVTDRTIDSHIKNLRRKLES  214 (240)
T ss_pred             ecCHHHHHHHHHHHh-CCCceEcHHHHHHHhcCcCcCCCccCHHHHHHHHHHHhhc
Confidence            499999999998762 3235799999999998     9999999999999999964

>PF11427 HTH_Tnp_Tc3_1: Tc3 transposase; PDB: 1U78_A 1TC3_C

Probab=89.03  E-value=0.93  Score=31.89  Aligned_cols=39  Identities=31%  Similarity=0.354  Sum_probs=24.3

Q ss_pred             cCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 046578          317 TLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRG  359 (379)
Q Consensus       317 ~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~  359 (379)
                      .|++.||--|....    ..|+++.|||..+|-|+..|++.++
T Consensus         4 ~Lt~~Eqaqid~m~----qlG~s~~~isr~i~RSr~~Ir~yl~   42 (50)
T PF11427_consen    4 TLTDAEQAQIDVMH----QLGMSLREISRRIGRSRTCIRRYLK   42 (50)
T ss_dssp             ---HHHHHHHHHHH----HTT--HHHHHHHHT--HHHHHHHHH
T ss_pred             cCCHHHHHHHHHHH----HhchhHHHHHHHhCccHHHHHHHhc
Confidence            46766666665554    2569999999999999999988754

>PRK12423 LexA repressor; Provisional

Probab=88.84  E-value=0.7  Score=42.15  Aligned_cols=48  Identities=27%  Similarity=0.364  Sum_probs=34.0

Q ss_pred             hcCCHHHHHHHHHHhh-c-CCCCCCCHHHHHHHhC-CCHHHHHHHHHHHHHHHHh
Q 046578          316 QTLSEREADILRLHFG-L-DGQTPVSCKEIGRLLS-LSRERIRQIRGIALTKLQQ  367 (379)
Q Consensus       316 ~~L~~rer~Vl~l~yg-L-~g~e~~S~~EIAe~Lg-iS~~~Vr~~~~rAl~kLR~  367 (379)
                      ..|++++++|+...-- + .++-..|.+|||+.|| .|+++|+.    ++++|++
T Consensus         2 ~~lt~~q~~il~~l~~~i~~~g~~Ps~~eia~~~g~~s~~~v~~----~l~~L~~   52 (202)
T PRK12423          2 DTLTPKRAAILAFIRERIAQAGQPPSLAEIAQAFGFASRSVARK----HVQALAE   52 (202)
T ss_pred             CcCCHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCChHHHHH----HHHHHHH
Confidence            3589999999985421 1 1223459999999999 59999985    4555555

>PRK15479 transcriptional regulatory protein TctD; Provisional

Probab=88.74  E-value=0.74  Score=40.93  Aligned_cols=50  Identities=26%  Similarity=0.252  Sum_probs=41.1

Q ss_pred             cCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhC-----CCHHHHHHHHHHHHHHHHh
Q 046578          317 TLSEREADILRLHFGLDGQTPVSCKEIGRLLS-----LSRERIRQIRGIALTKLQQ  367 (379)
Q Consensus       317 ~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~Lg-----iS~~~Vr~~~~rAl~kLR~  367 (379)
                      .|+++|.+|+.+.. -+-+...|.++|++.+.     +|..||..++++.++||..
T Consensus       148 ~Lt~~E~~il~~l~-~~~~~~~~~~~i~~~l~~~~~~~~~~tv~~~i~~ir~kl~~  202 (221)
T PRK15479        148 ALTPREQALLTVLM-YRRTRPVSRQQLFEQVFSLNDEVSPESIELYIHRLRKKLQG  202 (221)
T ss_pred             ecCHHHHHHHHHHH-hCCCCcCcHHHHHHHhcCCCCCCCcccHHHHHHHHHHhcCC
Confidence            59999999998765 22114579999999986     9999999999999999863

>cd04762 HTH_MerR-trunc Helix-Turn-Helix DNA binding domain of truncated MerR-like proteins

Probab=88.48  E-value=0.46  Score=31.92  Aligned_cols=25  Identities=24%  Similarity=0.282  Sum_probs=22.3

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHHHHH
Q 046578          338 VSCKEIGRLLSLSRERIRQIRGIAL  362 (379)
Q Consensus       338 ~S~~EIAe~LgiS~~~Vr~~~~rAl  362 (379)
                      +|..|+|+.+|||+++|+++...+.
T Consensus         1 ~s~~e~a~~lgvs~~tl~~~~~~g~   25 (49)
T cd04762           1 LTTKEAAELLGVSPSTLRRWVKEGK   25 (49)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHcCC
Confidence            5789999999999999999987764

Proteins in this family mostly have a truncated helix-turn-helix (HTH) MerR-like domain. They lack a portion of the C-terminal region, called Wing 2 and the long dimerization helix that is typically present in MerR-like proteins. These truncated domains are found in response regulator receiver (REC) domain proteins (i.e., CheY), cytosine-C5 specific DNA methylases, IS607 transposase-like proteins, and RacA, a bacterial protein that anchors chromosomes to cell poles.

>PF13551 HTH_29: Winged helix-turn helix

Probab=88.45  E-value=0.89  Score=36.53  Aligned_cols=26  Identities=27%  Similarity=0.254  Sum_probs=23.2

Q ss_pred             CCC-CHHHHHHHhCCCHHHHHHHHHHH
Q 046578          336 TPV-SCKEIGRLLSLSRERIRQIRGIA  361 (379)
Q Consensus       336 e~~-S~~EIAe~LgiS~~~Vr~~~~rA  361 (379)
                      +|. |..+||+.+|+|+.||++++++-
T Consensus        10 ~g~~~~~~ia~~lg~s~~Tv~r~~~~~   36 (112)
T PF13551_consen   10 EGVSTIAEIARRLGISRRTVYRWLKRY   36 (112)
T ss_pred             cCCCcHHHHHHHHCcCHHHHHHHHHHH
Confidence            668 59999999999999999998873

>COG3355 Predicted transcriptional regulator [Transcription]

Probab=88.45  E-value=2.2  Score=35.94  Aligned_cols=49  Identities=16%  Similarity=0.318  Sum_probs=38.0

Q ss_pred             HHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 046578          310 ELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGI  360 (379)
Q Consensus       310 ~L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~r  360 (379)
                      .+..++-.|++.+-+|+....- . ..+.|..|||+.+|++++||++.+++
T Consensus        17 dvl~c~~GLs~~Dv~v~~~LL~-~-~~~~tvdelae~lnr~rStv~rsl~~   65 (126)
T COG3355          17 DVLKCVYGLSELDVEVYKALLE-E-NGPLTVDELAEILNRSRSTVYRSLQN   65 (126)
T ss_pred             HHHHHHhCCcHHHHHHHHHHHh-h-cCCcCHHHHHHHHCccHHHHHHHHHH
Confidence            4667788999999999876531 1 26799999999999999999654443

>TIGR01764 excise DNA binding domain, excisionase family

Probab=88.15  E-value=0.49  Score=31.96  Aligned_cols=24  Identities=13%  Similarity=0.299  Sum_probs=21.9

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHHHH
Q 046578          338 VSCKEIGRLLSLSRERIRQIRGIA  361 (379)
Q Consensus       338 ~S~~EIAe~LgiS~~~Vr~~~~rA  361 (379)
                      +|.+|+|+.||||+++|+++.+.+
T Consensus         2 lt~~e~a~~lgis~~ti~~~~~~g   25 (49)
T TIGR01764         2 LTVEEAAEYLGVSKDTVYRLIHEG   25 (49)
T ss_pred             CCHHHHHHHHCCCHHHHHHHHHcC
Confidence            789999999999999999988665

An excisionase, or Xis protein, is a small protein that binds and promotes excisive recombination; it is not enzymatically active. This model represents a number of putative excisionases and related proteins from temperate phage, plasmids, and transposons, as well as DNA binding domains of other proteins, such as a DNA modification methylase. This model identifies mostly small proteins and N-terminal regions of large proteins, but some proteins appear to have two copies. This domain appears similar, in both sequence and predicted secondary structure (PSIPRED) to the MerR family of transcriptional regulators (pfam00376).

>TIGR02337 HpaR homoprotocatechuate degradation operon regulator, HpaR

Probab=88.12  E-value=2.6  Score=34.59  Aligned_cols=41  Identities=20%  Similarity=0.243  Sum_probs=33.3

Q ss_pred             cCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 046578          317 TLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGI  360 (379)
Q Consensus       317 ~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~r  360 (379)
                      .|++.|..||.....   ..+.|..|||+.+|++.++|.+.+.+
T Consensus        25 ~lt~~q~~iL~~l~~---~~~~t~~ela~~~~~~~~tvs~~l~~   65 (118)
T TIGR02337        25 GLTEQQWRILRILAE---QGSMEFTQLANQACILRPSLTGILAR   65 (118)
T ss_pred             CCCHHHHHHHHHHHH---cCCcCHHHHHHHhCCCchhHHHHHHH
Confidence            689999988876542   35799999999999999999766554

This Helix-Turn-Helix transcriptional regulator is a member of the MarR family (pfam01047) and is found in association with operons for the degradation of 4-hydroxyphenylacetic acid via homoprotocatechuate.

>COG2522 Predicted transcriptional regulator [General function prediction only]

Probab=87.94  E-value=0.95  Score=37.78  Aligned_cols=24  Identities=25%  Similarity=0.325  Sum_probs=22.4

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHH
Q 046578          336 TPVSCKEIGRLLSLSRERIRQIRG  359 (379)
Q Consensus       336 e~~S~~EIAe~LgiS~~~Vr~~~~  359 (379)
                      +|+|+.+||+.||+|+..|++.++
T Consensus        21 eG~Sq~~iA~LLGltqaAVS~Yls   44 (119)
T COG2522          21 EGLSQYRIAKLLGLTQAAVSQYLS   44 (119)
T ss_pred             cCCcHHHHHHHhCCCHHHHHHHHc
Confidence            579999999999999999999875

>TIGR02154 PhoB phosphate regulon transcriptional regulatory protein PhoB

Probab=87.78  E-value=0.45  Score=42.46  Aligned_cols=50  Identities=14%  Similarity=0.155  Sum_probs=41.1

Q ss_pred             cCCHHHHHHHHHHhhcCCCCCCCHHHH-----HHHhCCCHHHHHHHHHHHHHHHHh
Q 046578          317 TLSEREADILRLHFGLDGQTPVSCKEI-----GRLLSLSRERIRQIRGIALTKLQQ  367 (379)
Q Consensus       317 ~L~~rer~Vl~l~ygL~g~e~~S~~EI-----Ae~LgiS~~~Vr~~~~rAl~kLR~  367 (379)
                      .|+++|.+|+.+..- +-+.++|.++|     |+.++++..||+..+++.++||..
T Consensus       154 ~Lt~~E~~il~~l~~-~~~~~~s~~~i~~~~~~~~~~~~~~tv~~~i~~l~~Kl~~  208 (226)
T TIGR02154       154 SLGPTEFRLLHFFMT-HPERVYSREQLLDRVWGRDVYVEERTVDVHIRRLRKALNP  208 (226)
T ss_pred             EcCHHHHHHHHHHHh-CCCceEcHHHHHHHhcCCCCCCCCccHHHHHHHHHHhhcc
Confidence            599999999988752 21246788888     788999999999999999999963

PhoB is a DNA-binding response regulator protein acting with PhoR in a 2-component system responding to phosphate ion. PhoB acts as a positive regulator of gene expression for phosphate-related genes such as phoA, phoS, phoE and ugpAB as well as itself. It is often found proximal to genes for the high-affinity phosphate ABC transporter (pstSCAB; GenProp0190) and presumably regulates these as well.

>COG1522 Lrp Transcriptional regulators [Transcription]

Probab=87.71  E-value=1.4  Score=37.81  Aligned_cols=42  Identities=24%  Similarity=0.234  Sum_probs=33.7

Q ss_pred             hcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 046578          316 QTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGI  360 (379)
Q Consensus       316 ~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~r  360 (379)
                      ..|++.++.||...- -+  -..|+.|||+.+|+|+.+|+.++.+
T Consensus         4 ~~lD~~D~~IL~~L~-~d--~r~~~~eia~~lglS~~~v~~Ri~~   45 (154)
T COG1522           4 MKLDDIDRRILRLLQ-ED--ARISNAELAERVGLSPSTVLRRIKR   45 (154)
T ss_pred             ccccHHHHHHHHHHH-Hh--CCCCHHHHHHHHCCCHHHHHHHHHH
Confidence            468888999998653 22  4499999999999999999877554

>COG2973 TrpR Trp operon repressor [Transcription]

Probab=87.69  E-value=1.8  Score=34.67  Aligned_cols=40  Identities=23%  Similarity=0.235  Sum_probs=30.0

Q ss_pred             cCCHHHHHHHHHHhhcC---CCCCCCHHHHHHHhCCCHHHHHH
Q 046578          317 TLSEREADILRLHFGLD---GQTPVSCKEIGRLLSLSRERIRQ  356 (379)
Q Consensus       317 ~L~~rer~Vl~l~ygL~---g~e~~S~~EIAe~LgiS~~~Vr~  356 (379)
                      -|+|.||+-+-.|+-+-   =..++|++||+..||+|..+|-+
T Consensus        37 lLTpdEReal~~Rv~Iv~eLL~ge~sQREi~~~LgvsiAtITR   79 (103)
T COG2973          37 LLTPDEREALGTRVRIVEELLRGELSQREIAQKLGVSIATITR   79 (103)
T ss_pred             HcCHhHHHHHHHHHHHHHHHHhccccHHHHHHHhCcchhhhcc
Confidence            48888888877765432   01369999999999999988843

>PF01381 HTH_3: Helix-turn-helix; InterPro: IPR001387 This is large family of DNA binding helix-turn helix proteins that include a bacterial plasmid copy control protein, bacterial methylases, various bacteriophage transcription control proteins and a vegetative specific protein from Dictyostelium discoideum (Slime mould)

Probab=87.06  E-value=0.66  Score=32.49  Aligned_cols=25  Identities=32%  Similarity=0.377  Sum_probs=20.8

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHHH
Q 046578          336 TPVSCKEIGRLLSLSRERIRQIRGI  360 (379)
Q Consensus       336 e~~S~~EIAe~LgiS~~~Vr~~~~r  360 (379)
                      .++|++|+|+.+|+|+++|+++++.
T Consensus         8 ~gls~~~la~~~gis~~~i~~~~~g   32 (55)
T PF01381_consen    8 KGLSQKELAEKLGISRSTISRIENG   32 (55)
T ss_dssp             TTS-HHHHHHHHTS-HHHHHHHHTT
T ss_pred             cCCCHHHHHHHhCCCcchhHHHhcC
Confidence            5699999999999999999998765

; GO: 0043565 sequence-specific DNA binding; PDB: 2AXU_A 2AWI_D 2AXV_D 2AXZ_C 2AW6_A 3KXA_C 3BS3_A 2CRO_A 1ZUG_A 3CRO_R ....

>PF01726 LexA_DNA_bind: LexA DNA binding domain; InterPro: IPR006199 This is the DNA binding domain of the LexA SOS regulon repressor which prevents expression of DNA repair proteins in bacteria

Probab=86.83  E-value=2.8  Score=31.04  Aligned_cols=42  Identities=26%  Similarity=0.199  Sum_probs=31.4

Q ss_pred             HHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCC-HHHHHHHHHh
Q 046578          226 MVAKIAEANNVLSRRLRRMPTDSEIAEMLNIH-VSTVRLAIER  267 (379)
Q Consensus       226 ~~~ki~~a~~~l~~~lgr~pt~~eia~~Lgis-~~~~~~~l~~  267 (379)
                      .-.++..+......+.|..||..|||+.+|++ ...+...+..
T Consensus         7 rQ~~vL~~I~~~~~~~G~~Pt~rEIa~~~g~~S~~tv~~~L~~   49 (65)
T PF01726_consen    7 RQKEVLEFIREYIEENGYPPTVREIAEALGLKSTSTVQRHLKA   49 (65)
T ss_dssp             HHHHHHHHHHHHHHHHSS---HHHHHHHHTSSSHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCChHHHHHHHHH
Confidence            44566677777888999999999999999997 8888877654

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.

>PF08220 HTH_DeoR: DeoR-like helix-turn-helix domain; InterPro: IPR001034 The deoR-type HTH domain is a DNA-binding, helix-turn-helix (HTH) domain of about 50-60 amino acids present in transcription regulators of the deoR family, involved in sugar catabolism

Probab=86.79  E-value=1.2  Score=31.99  Aligned_cols=25  Identities=28%  Similarity=0.251  Sum_probs=21.8

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHHH
Q 046578          336 TPVSCKEIGRLLSLSRERIRQIRGI  360 (379)
Q Consensus       336 e~~S~~EIAe~LgiS~~~Vr~~~~r  360 (379)
                      ...|.+|+|+.||+|..||++-+..
T Consensus        13 ~~~s~~ela~~~~VS~~TiRRDl~~   37 (57)
T PF08220_consen   13 GKVSVKELAEEFGVSEMTIRRDLNK   37 (57)
T ss_pred             CCEEHHHHHHHHCcCHHHHHHHHHH
Confidence            5689999999999999999876543

This family of prokaryotic regulators is named after the Escherichia coli protein DeoR, a repressor of the deo operon, which encodes nucleotide and deoxyribonucleotide catabolic enzymes. DeoR also negatively regulates the expression of nupG and tsx, a nucleoside-specific transport protein and a channel-forming protein, respectively. DeoR-like transcription repressors occur in diverse bacteria as regulators of sugar and nucleoside metabolic systems. The effector molecules for deoR-like regulators are generally phosphorylated intermediates of the relevant metabolic pathway. The DNA-binding deoR-type HTH domain occurs usually in the N-terminal part. The C-terminal part can contain an effector-binding domain and/or an oligomerisation domain. DeoR occurs as an octamer, whilst glpR and agaR are tetramers. Several operators may be bound simultaneously, which could facilitate DNA looping [, ].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular

>CHL00148 orf27 Ycf27; Reviewed

Probab=86.65  E-value=0.96  Score=40.92  Aligned_cols=50  Identities=16%  Similarity=0.095  Sum_probs=41.9

Q ss_pred             cCCHHHHHHHHHHhhcCCCCCCCHHHHHHHh-------CCCHHHHHHHHHHHHHHHHh
Q 046578          317 TLSEREADILRLHFGLDGQTPVSCKEIGRLL-------SLSRERIRQIRGIALTKLQQ  367 (379)
Q Consensus       317 ~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~L-------giS~~~Vr~~~~rAl~kLR~  367 (379)
                      .|+++|.+|+.+.. -+.+.++|.+||++.+       +++..+|..++++.++||..
T Consensus       161 ~Lt~~E~~il~~l~-~~~~~~~s~~~i~~~l~~~~~~~~~~~~tv~~~i~~lr~KL~~  217 (240)
T CHL00148        161 RLTGMEFSLLELLI-SKSGEIFSRATILKEVWGYTPERHIDTRVVDVHISRLRAKLED  217 (240)
T ss_pred             EcCHHHHHHHHHHH-HCCCEEEcHHHHHHHhcCCCcccCCCcccHHHHHHHHHHHhcc
Confidence            49999999998765 2222679999999999       48999999999999999974

>PF08280 HTH_Mga: M protein trans-acting positive regulator (MGA) HTH domain; InterPro: IPR013199 Mga is a DNA-binding protein that activates the expression of several important virulence genes in group A streptococcus in response to changing environmental conditions []

Probab=86.53  E-value=1.5  Score=31.69  Aligned_cols=37  Identities=22%  Similarity=0.316  Sum_probs=27.2

Q ss_pred             HHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 046578          321 READILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGI  360 (379)
Q Consensus       321 rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~r  360 (379)
                      ++-.++.+-+.   ...+++.|+|+.+|+|..+|++.+..
T Consensus         6 rq~~Ll~~L~~---~~~~~~~ela~~l~~S~rti~~~i~~   42 (59)
T PF08280_consen    6 RQLKLLELLLK---NKWITLKELAKKLNISERTIKNDINE   42 (59)
T ss_dssp             HHHHHHHHHHH---HTSBBHHHHHHHCTS-HHHHHHHHHH
T ss_pred             HHHHHHHHHHc---CCCCcHHHHHHHHCCCHHHHHHHHHH
Confidence            45556665553   46799999999999999999877544

; PDB: 2WTE_A 3SQN_A.

>TIGR00498 lexA SOS regulatory protein LexA

Probab=86.53  E-value=0.91  Score=41.05  Aligned_cols=45  Identities=22%  Similarity=0.272  Sum_probs=34.0

Q ss_pred             hcCCHHHHHHHHHHhh--cCCCCCCCHHHHHHHhCCC-HHHHHHHHHH
Q 046578          316 QTLSEREADILRLHFG--LDGQTPVSCKEIGRLLSLS-RERIRQIRGI  360 (379)
Q Consensus       316 ~~L~~rer~Vl~l~yg--L~g~e~~S~~EIAe~LgiS-~~~Vr~~~~r  360 (379)
                      ..|+++|++|+....-  ..+..+.|.+|||+.+|++ ++||+.++.+
T Consensus         2 ~~lt~~q~~iL~~l~~~~~~~~~~~~~~ela~~~~~~s~~tv~~~l~~   49 (199)
T TIGR00498         2 KPLTARQQEVLDLIRAHIESTGYPPSIREIARAVGLRSPSAAEEHLKA   49 (199)
T ss_pred             CccCHHHHHHHHHHHHHHHhcCCCCcHHHHHHHhCCCChHHHHHHHHH
Confidence            3589999999987541  1123458899999999998 9999876544

LexA acts as a homodimer to repress a number of genes involved in the response to DNA damage (SOS response), including itself and RecA. RecA, in the presence of single-stranded DNA, acts as a co-protease to activate a latent autolytic protease activity (EC 3.4.21.88) of LexA, where the active site Ser is part of LexA. The autolytic cleavage site is an Ala-Gly bond in LexA (at position 84-85 in E. coli LexA; this sequence is replaced by Gly-Gly in Synechocystis). The cleavage leads to derepression of the SOS regulon and eventually to DNA repair. LexA in Bacillus subtilis is called DinR. LexA is much less broadly distributed than RecA.

>TIGR03787 marine_sort_RR proteobacterial dedicated sortase system response regulator

Probab=86.49  E-value=1.2  Score=40.12  Aligned_cols=50  Identities=12%  Similarity=-0.003  Sum_probs=41.0

Q ss_pred             cCCHHHHHHHHHHhhcCCCCCCCHHHH--HHHhCCCHHHHHHHHHHHHHHHHh
Q 046578          317 TLSEREADILRLHFGLDGQTPVSCKEI--GRLLSLSRERIRQIRGIALTKLQQ  367 (379)
Q Consensus       317 ~L~~rer~Vl~l~ygL~g~e~~S~~EI--Ae~LgiS~~~Vr~~~~rAl~kLR~  367 (379)
                      .|+++|.+|+.+.. -+.+.-+|.++|  |..++++..||+.++.|.++||..
T Consensus       156 ~Lt~~E~~il~~l~-~~~g~v~s~~~i~~~~~~~~~~~tv~~~v~rlr~Kl~~  207 (227)
T TIGR03787       156 DLTVTEFWMVHALA-KHPGHVKSRQQLMDAAKIVVDDSTITSHIKRIRKKFQA  207 (227)
T ss_pred             cCCHHHHHHHHHHH-hCCCccccHHHHHHHhhhcCCccCHHHHHHHHHHHhcc
Confidence            49999999999875 111133599999  888999999999999999999974

This model describes a family of DNA-binding response regulator proteins, associated with an adjacent histidine kinase (TIGR03785) to form a two-component system. This system co-occurs with, and often is adjacent to, a proteobacterial variant form of the protein sorting transpeptidase called sortase (TIGR03784), and a single target protein for the sortase. We give this protein the gene symbol pdsR, for Proteobacterial Dedicated Sortase system Response regulator.

>PF00046 Homeobox: Homeobox domain not present here

Probab=86.43  E-value=1.6  Score=30.83  Aligned_cols=51  Identities=12%  Similarity=0.171  Sum_probs=38.4

Q ss_pred             cCCHHHHHHHHHHhhcCCC-CCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHh
Q 046578          317 TLSEREADILRLHFGLDGQ-TPVSCKEIGRLLSLSRERIRQIRGIALTKLQQ  367 (379)
Q Consensus       317 ~L~~rer~Vl~l~ygL~g~-e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~  367 (379)
                      .+++.+..+|...|-.+.. ......+||..+|++...|..+...-+.+.|+
T Consensus         6 ~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk   57 (57)
T PF00046_consen    6 RFTKEQLKVLEEYFQENPYPSKEEREELAKELGLTERQVKNWFQNRRRKEKK   57 (57)
T ss_dssp             SSSHHHHHHHHHHHHHSSSCHHHHHHHHHHHHTSSHHHHHHHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHHHhccccccccccccccccccccccccCHHHhHHHhCc
Confidence            4678888888888753321 12345679999999999999999988777664

; InterPro: IPR001356 The homeobox domain was first identified in a number of drosophila homeotic and segmentation proteins, but is now known to be well-conserved in many other animals, including vertebrates [, , ]. Hox genes encode homeodomain-containing transcriptional regulators that operate differential genetic programs along the anterior-posterior axis of animal bodies []. The domain binds DNA through a helix-turn-helix (HTH) structure. The HTH motif is characterised by two alpha-helices, which make intimate contacts with the DNA and are joined by a short turn. The second helix binds to DNA via a number of hydrogen bonds and hydrophobic interactions, which occur between specific side chains and the exposed bases and thymine methyl groups within the major groove of the DNA []. The first helix helps to stabilise the structure. The motif is very similar in sequence and structure in a wide range of DNA-binding proteins (e.g., cro and repressor proteins, homeotic proteins, etc.). One of the principal differences between HTH motifs in these different proteins arises from the stereo-chemical requirement for glycine in the turn which is needed to avoid steric interference of the beta-carbon with the main chain: for cro and repressor proteins the glycine appears to be mandatory, while for many of the homeotic and other DNA-binding proteins the requirement is relaxed.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2DA3_A 1LFB_A 2LFB_A 2ECB_A 2DA5_A 3D1N_O 3A03_A 2XSD_C 3CMY_A 1AHD_P ....

>PRK11512 DNA-binding transcriptional repressor MarR; Provisional

Probab=86.26  E-value=3.8  Score=34.97  Aligned_cols=47  Identities=15%  Similarity=0.183  Sum_probs=36.6

Q ss_pred             HHHHHh--cCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 046578          311 LKELLQ--TLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGI  360 (379)
Q Consensus       311 L~~~L~--~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~r  360 (379)
                      +...+.  .|++.|..||...+.   .++.|..|||+.+|++.++|.+.+.+
T Consensus        29 ~~~~l~~~glt~~q~~vL~~l~~---~~~~t~~eLa~~l~i~~~tvsr~l~~   77 (144)
T PRK11512         29 LNEYLSPLDITAAQFKVLCSIRC---AACITPVELKKVLSVDLGALTRMLDR   77 (144)
T ss_pred             HHHHhcccCCCHHHHHHHHHHHH---cCCCCHHHHHHHHCCCHHHHHHHHHH
Confidence            444443  589999988886552   35699999999999999999877655

>PRK07598 RNA polymerase sigma factor SigC; Validated

Probab=86.17  E-value=8.3  Score=39.24  Aligned_cols=37  Identities=16%  Similarity=0.284  Sum_probs=28.2

Q ss_pred             HHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHH
Q 046578          228 AKIAEANNVLSRRLRRMPTDSEIAEMLNIHVSTVRLA  264 (379)
Q Consensus       228 ~ki~~a~~~l~~~lgr~pt~~eia~~Lgis~~~~~~~  264 (379)
                      ..+.+....+..++|++|+..|.|...|++...++..
T Consensus       111 ~~l~~~~~~l~~~~g~~pt~~ewa~~~~~~~~~l~~~  147 (415)
T PRK07598        111 LRLIEVRERLTSELGHRPSLERWAKTADISLADLKPT  147 (415)
T ss_pred             HHHHHHHHHHHHHhCCCCCHHHHHHHhCCcHHHHHHh
Confidence            3455666788999999999999997777765555544

>cd04761 HTH_MerR-SF Helix-Turn-Helix DNA binding domain of transcription regulators from the MerR superfamily

Probab=86.09  E-value=0.58  Score=31.87  Aligned_cols=25  Identities=24%  Similarity=0.361  Sum_probs=22.4

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHHHHH
Q 046578          338 VSCKEIGRLLSLSRERIRQIRGIAL  362 (379)
Q Consensus       338 ~S~~EIAe~LgiS~~~Vr~~~~rAl  362 (379)
                      +|..|+|+.+|||..+|+.+..+++
T Consensus         1 ~~~~e~a~~~gv~~~tlr~~~~~g~   25 (49)
T cd04761           1 YTIGELAKLTGVSPSTLRYYERIGL   25 (49)
T ss_pred             CcHHHHHHHHCcCHHHHHHHHHCCC
Confidence            5789999999999999999987765

Helix-turn-helix (HTH) transcription regulator MerR superfamily, N-terminal domain. The MerR family transcription regulators have been shown to mediate responses to stress including exposure to heavy metals, drugs, or oxygen radicals in eubacterial and some archaeal species. They regulate transcription of multidrug/metal ion transporter genes and oxidative stress regulons by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.

>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor

Probab=86.09  E-value=1.9  Score=29.36  Aligned_cols=25  Identities=32%  Similarity=0.341  Sum_probs=21.7

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHHH
Q 046578          336 TPVSCKEIGRLLSLSRERIRQIRGI  360 (379)
Q Consensus       336 e~~S~~EIAe~LgiS~~~Vr~~~~r  360 (379)
                      .+.+..+|++.+|+|+.+|++.+.+
T Consensus        13 ~~~s~~~l~~~l~~s~~tv~~~l~~   37 (53)
T smart00420       13 GKVSVEELAELLGVSEMTIRRDLNK   37 (53)
T ss_pred             CCcCHHHHHHHHCCCHHHHHHHHHH
Confidence            4599999999999999999877654

>PRK00215 LexA repressor; Validated

Probab=85.91  E-value=1.7  Score=39.48  Aligned_cols=45  Identities=24%  Similarity=0.230  Sum_probs=33.8

Q ss_pred             CCHHHHHHHHHHh--hcCCCCCCCHHHHHHHhCC-CHHHHHHHHHHHH
Q 046578          318 LSEREADILRLHF--GLDGQTPVSCKEIGRLLSL-SRERIRQIRGIAL  362 (379)
Q Consensus       318 L~~rer~Vl~l~y--gL~g~e~~S~~EIAe~Lgi-S~~~Vr~~~~rAl  362 (379)
                      |+++|++|+.+..  ...+..+.|++|||+.+|+ ++++|.+++.+-.
T Consensus         2 lt~~q~~il~~i~~~~~~~~~~~s~~ela~~~~~~~~~tv~~~l~~L~   49 (205)
T PRK00215          2 LTKRQQEILDFIRDHIEETGYPPSRREIADALGLRSPSAVHEHLKALE   49 (205)
T ss_pred             CCHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCChHHHHHHHHHHH
Confidence            7889999987543  1122256799999999999 9999988766543

>COG5484 Uncharacterized conserved protein [Function unknown]

Probab=85.22  E-value=0.91  Score=42.53  Aligned_cols=25  Identities=20%  Similarity=0.268  Sum_probs=23.3

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHHH
Q 046578          336 TPVSCKEIGRLLSLSRERIRQIRGI  360 (379)
Q Consensus       336 e~~S~~EIAe~LgiS~~~Vr~~~~r  360 (379)
                      ++|.+.+||+.||||+.||+.+++|
T Consensus        18 ~gmk~~dIAeklGvspntiksWKrr   42 (279)
T COG5484          18 KGMKLKDIAEKLGVSPNTIKSWKRR   42 (279)
T ss_pred             hhccHHHHHHHhCCChHHHHHHHHh
Confidence            5699999999999999999999876

>COG0856 Orotate phosphoribosyltransferase homologs [Nucleotide transport and metabolism]

Probab=84.86  E-value=1.3  Score=39.46  Aligned_cols=40  Identities=23%  Similarity=0.156  Sum_probs=32.8

Q ss_pred             HHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHh
Q 046578          323 ADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQ  367 (379)
Q Consensus       323 r~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~  367 (379)
                      +..+.|.-     .|+|..|||++||+|++|++.++.|+.++...
T Consensus         9 ~kA~eLk~-----~Glt~gEIAdELNvSreTa~WL~~r~~~~~~~   48 (203)
T COG0856           9 KKARELKS-----KGLTTGEIADELNVSRETATWLLTRAFKKESV   48 (203)
T ss_pred             HHHHHHHH-----CCCcHHHhhhhhhhhHHHHHHHHhhhhhccCC
Confidence            34556664     77999999999999999999999998766543

>PRK10870 transcriptional repressor MprA; Provisional

Probab=84.67  E-value=5.1  Score=35.63  Aligned_cols=51  Identities=16%  Similarity=0.101  Sum_probs=37.2

Q ss_pred             HHHHHHh--cCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 046578          310 ELKELLQ--TLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIA  361 (379)
Q Consensus       310 ~L~~~L~--~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rA  361 (379)
                      .+...+.  .|++.|..|+...+. .+..+.|..|||+.+|++.++|.+.+.+-
T Consensus        43 ~~~~~l~~~gLt~~q~~iL~~L~~-~~~~~it~~eLa~~l~l~~~tvsr~v~rL   95 (176)
T PRK10870         43 NRNKMLKAQGINETLFMALITLES-QENHSIQPSELSCALGSSRTNATRIADEL   95 (176)
T ss_pred             HHHHHHHHCCCCHHHHHHHHHHhc-CCCCCcCHHHHHHHHCCCHHHHHHHHHHH
Confidence            3455554  478888888876652 22256899999999999999998776553

>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor

Probab=83.88  E-value=1.9  Score=30.22  Aligned_cols=25  Identities=24%  Similarity=0.336  Sum_probs=20.3

Q ss_pred             CCC-CHHHHHHHhCCCHHHHHHHHHH
Q 046578          336 TPV-SCKEIGRLLSLSRERIRQIRGI  360 (379)
Q Consensus       336 e~~-S~~EIAe~LgiS~~~Vr~~~~r  360 (379)
                      +.+ |..|||+.+|+|+.+|++.+.+
T Consensus        18 ~~l~s~~~la~~~~vs~~tv~~~l~~   43 (60)
T smart00345       18 DKLPSERELAAQLGVSRTTVREALSR   43 (60)
T ss_pred             CcCcCHHHHHHHHCCCHHHHHHHHHH
Confidence            445 8999999999999999765443

>cd06571 Bac_DnaA_C C-terminal domain of bacterial DnaA proteins

Probab=83.87  E-value=3.9  Score=32.16  Aligned_cols=31  Identities=19%  Similarity=0.186  Sum_probs=26.9

Q ss_pred             CCCHHHHHHHhC-CCHHHHHHHHHHHHHHHHh
Q 046578          337 PVSCKEIGRLLS-LSRERIRQIRGIALTKLQQ  367 (379)
Q Consensus       337 ~~S~~EIAe~Lg-iS~~~Vr~~~~rAl~kLR~  367 (379)
                      ++|+.+||+.|| .+.+||.....+.-+++.+
T Consensus        44 ~~s~~~Ig~~fg~r~hStV~~a~~ri~~~~~~   75 (90)
T cd06571          44 GLSLPEIGRAFGGRDHSTVLHAVRKIEELLEE   75 (90)
T ss_pred             CCCHHHHHHHhCCCCHhHHHHHHHHHHHHHHh
Confidence            599999999999 9999999888777776664

The DNA-binding C-terminal domain of DnaA contains a helix-turn-helix motif that specifically interacts with the DnaA box, a 9-mer motif that occurs repetitively in the replication origin oriC. Multiple copies of DnaA, which is an ATPase, bind to 9-mers at the origin and form an initial complex in which the DNA strands are being separated in an ATP-dependent step.

>smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein

Probab=83.84  E-value=1.7  Score=29.24  Aligned_cols=24  Identities=33%  Similarity=0.540  Sum_probs=19.8

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHHHH
Q 046578          337 PVSCKEIGRLLSLSRERIRQIRGI  360 (379)
Q Consensus       337 ~~S~~EIAe~LgiS~~~Vr~~~~r  360 (379)
                      ..|..|||+.+|+|+++|++.+.+
T Consensus         8 ~~s~~~la~~l~~s~~tv~~~l~~   31 (48)
T smart00419        8 PLTRQEIAELLGLTRETVSRTLKR   31 (48)
T ss_pred             ccCHHHHHHHHCCCHHHHHHHHHH
Confidence            489999999999999999655433

>PRK09413 IS2 repressor TnpA; Reviewed

Probab=83.66  E-value=3.3  Score=34.46  Aligned_cols=27  Identities=7%  Similarity=0.030  Sum_probs=24.3

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHHHHH
Q 046578          336 TPVSCKEIGRLLSLSRERIRQIRGIAL  362 (379)
Q Consensus       336 e~~S~~EIAe~LgiS~~~Vr~~~~rAl  362 (379)
                      .|.|..+||+.+||+.++++++..+..
T Consensus        28 ~g~sv~evA~e~gIs~~tl~~W~r~y~   54 (121)
T PRK09413         28 PGMTVSLVARQHGVAASQLFLWRKQYQ   54 (121)
T ss_pred             CCCCHHHHHHHHCcCHHHHHHHHHHHh
Confidence            569999999999999999999988753

>PRK11337 DNA-binding transcriptional repressor RpiR; Provisional

Probab=83.32  E-value=2.3  Score=40.70  Aligned_cols=60  Identities=15%  Similarity=0.192  Sum_probs=45.8

Q ss_pred             HHHHHHHhcCCHHHHHHHHHHhhcCC---CCCCCHHHHHHHhCCCHHHHHHHHHH----HHHHHHhHHh
Q 046578          309 QELKELLQTLSEREADILRLHFGLDG---QTPVSCKEIGRLLSLSRERIRQIRGI----ALTKLQQTNI  370 (379)
Q Consensus       309 ~~L~~~L~~L~~rer~Vl~l~ygL~g---~e~~S~~EIAe~LgiS~~~Vr~~~~r----Al~kLR~~l~  370 (379)
                      ..|...+..|++.|+.|....  ++.   ...+|..+||+..|+|..||.+..++    +..-||..+.
T Consensus        17 ~~i~~~~~~Lt~~e~~Ia~yi--l~~~~~v~~~si~~lA~~~~vS~aTi~Rf~kkLGf~gf~efk~~l~   83 (292)
T PRK11337         17 PYIRMKQEGLTPLESRVVEWL--LKPGDLSEATALKDIAEALAVSEAMIVKVAKKLGFSGFRNLRSALE   83 (292)
T ss_pred             HHHHHHHhhcCHHHHHHHHHH--HhCHHHHHhcCHHHHHHHhCCChHHHHHHHHHcCCCCHHHHHHHHH
Confidence            468888999999999998854  321   23589999999999999999887665    4455555443

>PF01527 HTH_Tnp_1: Transposase; InterPro: IPR002514 Transposase proteins are necessary for efficient DNA transposition

Probab=83.32  E-value=1.6  Score=32.74  Aligned_cols=27  Identities=19%  Similarity=0.139  Sum_probs=23.9

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHHHHH
Q 046578          336 TPVSCKEIGRLLSLSRERIRQIRGIAL  362 (379)
Q Consensus       336 e~~S~~EIAe~LgiS~~~Vr~~~~rAl  362 (379)
                      .|.|..+||..+||+++++++++....
T Consensus        22 ~g~sv~~va~~~gi~~~~l~~W~~~~~   48 (76)
T PF01527_consen   22 SGESVSEVAREYGISPSTLYNWRKQYR   48 (76)
T ss_dssp             HHCHHHHHHHHHTS-HHHHHHHHHHHH
T ss_pred             CCCceEeeecccccccccccHHHHHHh
Confidence            569999999999999999999988876

This family consists of various Escherichia coli insertion elements and other bacterial transposases some of which are members of the IS3 family. This region includes a helix-turn-helix motif (HTH) at the N terminus followed by a leucine zipper (LZ) motif. The LZ motif has been shown to mediate oligomerisation of the transposase components in IS911 []. More information about these proteins can be found at Protein of the Month: Transposase [].; GO: 0003677 DNA binding, 0004803 transposase activity, 0006313 transposition, DNA-mediated; PDB: 2JN6_A 2RN7_A.

>PRK03573 transcriptional regulator SlyA; Provisional

Probab=83.26  E-value=6.2  Score=33.48  Aligned_cols=42  Identities=7%  Similarity=0.013  Sum_probs=33.0

Q ss_pred             cCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 046578          317 TLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGI  360 (379)
Q Consensus       317 ~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~r  360 (379)
                      .|++.|..||...+- . .++.|..|||+.+|++.++|.+.+.+
T Consensus        28 glt~~q~~vL~~l~~-~-~~~~t~~eLa~~l~~~~~tvt~~v~~   69 (144)
T PRK03573         28 ELTQTHWVTLHNIHQ-L-PPEQSQIQLAKAIGIEQPSLVRTLDQ   69 (144)
T ss_pred             CCCHHHHHHHHHHHH-c-CCCCCHHHHHHHhCCChhhHHHHHHH
Confidence            688999888876542 1 14689999999999999999876655

>TIGR02844 spore_III_D sporulation transcriptional regulator SpoIIID

Probab=83.23  E-value=1.9  Score=33.38  Aligned_cols=36  Identities=14%  Similarity=0.211  Sum_probs=27.2

Q ss_pred             HHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 046578          321 READILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGI  360 (379)
Q Consensus       321 rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~r  360 (379)
                      ++.+|+.+.-   . ...|.++||+.+|+|.+||++.+..
T Consensus         7 R~~~I~e~l~---~-~~~ti~dvA~~~gvS~~TVsr~L~~   42 (80)
T TIGR02844         7 RVLEIGKYIV---E-TKATVRETAKVFGVSKSTVHKDVTE   42 (80)
T ss_pred             HHHHHHHHHH---H-CCCCHHHHHHHhCCCHHHHHHHhcC
Confidence            5555555443   2 4589999999999999999997753

Members of this protein are the transcriptional regulator SpoIIID, or stage III sporulation protein D. It is present in genomes if and only if the species is capable of endospore formation as occurs in the model species Bacillus subtilis. SpoIIID is a DNA binding protein that, in B. subtilis, downregulates many genes but also turns on ten genes.

>PRK11302 DNA-binding transcriptional regulator HexR; Provisional

Probab=83.12  E-value=2.3  Score=40.45  Aligned_cols=60  Identities=12%  Similarity=0.218  Sum_probs=45.0

Q ss_pred             HHHHHHHhcCCHHHHHHHHHHhhcCC---CCCCCHHHHHHHhCCCHHHHHHHHHH----HHHHHHhHHh
Q 046578          309 QELKELLQTLSEREADILRLHFGLDG---QTPVSCKEIGRLLSLSRERIRQIRGI----ALTKLQQTNI  370 (379)
Q Consensus       309 ~~L~~~L~~L~~rer~Vl~l~ygL~g---~e~~S~~EIAe~LgiS~~~Vr~~~~r----Al~kLR~~l~  370 (379)
                      ..+...+..|+|.|+.|....  ++.   ...+|..|||+..|+|.+||.+..++    +..-||..+.
T Consensus         5 ~~i~~~~~~Lt~~e~~Ia~yi--l~n~~~v~~~si~~lA~~~~vS~aTv~Rf~kklG~~gf~e~k~~l~   71 (284)
T PRK11302          5 EKIQSRLEHLSKSERKVAEVI--LASPQTAIHSSIATLAKMANVSEPTVNRFCRSLDTKGFPDFKLHLA   71 (284)
T ss_pred             HHHHHHHhhCCHHHHHHHHHH--HhCHHHHHhcCHHHHHHHhCCCHHHHHHHHHHcCCCCHHHHHHHHH
Confidence            567888899999999998754  331   13489999999999999999887765    3444444443

>PF08535 KorB: KorB domain; InterPro: IPR013741 This entry contains several KorB transcriptional repressor proteins

Probab=83.08  E-value=1.1  Score=35.52  Aligned_cols=24  Identities=21%  Similarity=0.141  Sum_probs=17.7

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHH
Q 046578          336 TPVSCKEIGRLLSLSRERIRQIRG  359 (379)
Q Consensus       336 e~~S~~EIAe~LgiS~~~Vr~~~~  359 (379)
                      .|+|..|||+.+|.|++.|++++.
T Consensus         2 ~G~tq~eIA~~lGks~s~Vs~~l~   25 (93)
T PF08535_consen    2 FGWTQEEIAKRLGKSRSWVSNHLA   25 (93)
T ss_dssp             TT--HHHHHHHTT--HHHHHHHHG
T ss_pred             CCCCHHHHHHHHCCCHHHHHHHHH
Confidence            359999999999999999998765

The korB gene is a major regulatory element in the replication and maintenance of broad host-range plasmid RK2. It negatively controls the replication gene trfA, the host-lethal determinants kilA and kilB, and the korA-korB operon []. This domain includes the DNA-binding HTH motif []. ; PDB: 1R71_C.

>PF08765 Mor: Mor transcription activator family; InterPro: IPR014875 Mor (Middle operon regulator) is a sequence specific DNA binding protein

Probab=83.06  E-value=2.6  Score=34.38  Aligned_cols=42  Identities=21%  Similarity=0.287  Sum_probs=27.2

Q ss_pred             HHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhH
Q 046578          321 READILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQT  368 (379)
Q Consensus       321 rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~~  368 (379)
                      +.++|...+      .|.+..|+|..+|+|..+|++++++..++-++.
T Consensus        62 R~~~I~~~f------~G~n~~eLA~kyglS~r~I~~Ii~~~~~~~~~~  103 (108)
T PF08765_consen   62 RNREIRREF------NGMNVRELARKYGLSERQIYRIIKRVRRRERRR  103 (108)
T ss_dssp             HHHHHHHH--------SS-HHHHHHHHT--HHHHHHHHHHHHH-----
T ss_pred             HHHHHHHHh------CCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHh
Confidence            556666643      459999999999999999999999987766554

It mediates transcription activation through its interactions with the C-terminal domains of the alpha and sigma subunits of bacterial RNA polymerase. The N-terminal region of Mor is the dimerisation region, and the C-terminal contains a helix-turn-helix motif which binds DNA []. ; PDB: 1RR7_A.

>PF07750 GcrA: GcrA cell cycle regulator; InterPro: IPR011681 GcrA, together with CtrA (see IPR001789 from INTERPRO and IPR001867 from INTERPRO), form a master cell cycle regulator

Probab=82.90  E-value=1.7  Score=38.40  Aligned_cols=25  Identities=24%  Similarity=0.252  Sum_probs=22.8

Q ss_pred             CCCCHHHHHHHhC-CCHHHHHHHHHH
Q 046578          336 TPVSCKEIGRLLS-LSRERIRQIRGI  360 (379)
Q Consensus       336 e~~S~~EIAe~Lg-iS~~~Vr~~~~r  360 (379)
                      +|+|..|||+.|| +|++.|--..+|
T Consensus        17 ~G~SasqIA~~lg~vsRnAViGk~hR   42 (162)
T PF07750_consen   17 EGLSASQIARQLGGVSRNAVIGKAHR   42 (162)
T ss_pred             cCCCHHHHHHHhCCcchhhhhhhhhc
Confidence            7899999999999 999999877766

These bacterial regulators are involved in controlling the progression and asymmetric polar morphogenesis []. During this process, there are temporal and spatial variations in the concentrations of GcrA and CtrA. The variation in concentration produces time and space dependent transcriptional regulation of modular functions that implement cell-cycle processes []. More specifically, GcrA acts as an activator of components of the replisome and the segregation machinery [].

>TIGR03830 CxxCG_CxxCG_HTH putative zinc finger/helix-turn-helix protein, YgiT family

Probab=82.74  E-value=5  Score=33.22  Aligned_cols=45  Identities=16%  Similarity=0.101  Sum_probs=33.6

Q ss_pred             HHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 046578          310 ELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGI  360 (379)
Q Consensus       310 ~L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~r  360 (379)
                      .....-..+.+.+-.-++..+      ++|++++|+.+|+++++|+++.+.
T Consensus        57 ~~~~~~~~~~~~~i~~~r~~~------gltq~~lA~~lg~~~~tis~~e~g  101 (127)
T TIGR03830        57 FYRKVDGLLTPPEIRRIRKKL------GLSQREAAELLGGGVNAFSRYERG  101 (127)
T ss_pred             HHHHccCCcCHHHHHHHHHHc------CCCHHHHHHHhCCCHHHHHHHHCC
Confidence            334444567777665565555      399999999999999999998764

This model describes a family of predicted regulatory proteins with a conserved zinc finger/HTH architecture. The amino-terminal region contains a novel domain, featuring two CXXC motifs and occuring in a number of small bacterial proteins as well as in the present family. The carboxyl-terminal region consists of a helix-turn-helix domain, modeled by pfam01381. The predicted function is DNA binding and transcriptional regulation.

>TIGR01884 cas_HTH CRISPR locus-related DNA-binding protein

Probab=82.72  E-value=3.6  Score=37.43  Aligned_cols=45  Identities=27%  Similarity=0.224  Sum_probs=35.4

Q ss_pred             HHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 046578          313 ELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGI  360 (379)
Q Consensus       313 ~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~r  360 (379)
                      .....|++++..|+....-   ..+.+..|||+.+|+|+++|++.+.+
T Consensus       136 ~~~~~ls~~~~~IL~~l~~---~g~~s~~eia~~l~is~stv~r~L~~  180 (203)
T TIGR01884       136 PLLAGLSREELKVLEVLKA---EGEKSVKNIAKKLGKSLSTISRHLRE  180 (203)
T ss_pred             hhhcCCCHHHHHHHHHHHH---cCCcCHHHHHHHHCcCHHHHHHHHHH
Confidence            3455799999988876541   13579999999999999999877665

Most but not all examples of this family are associated with CRISPR loci, a combination of DNA repeats and characteristic proteins encoded near the repeat cluster. The C-terminal region of this protein is homologous to DNA-binding helix-turn-helix domains with predicted transcriptional regulatory activity.

>PHA00542 putative Cro-like protein

Probab=82.70  E-value=2.1  Score=33.15  Aligned_cols=25  Identities=20%  Similarity=0.102  Sum_probs=22.7

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHHH
Q 046578          336 TPVSCKEIGRLLSLSRERIRQIRGI  360 (379)
Q Consensus       336 e~~S~~EIAe~LgiS~~~Vr~~~~r  360 (379)
                      .++|..++|+.+|||+++|++++..
T Consensus        30 ~glTq~elA~~lgIs~~tIsr~e~g   54 (82)
T PHA00542         30 AGWSQEQIADATDVSQPTICRIYSG   54 (82)
T ss_pred             CCCCHHHHHHHHCcCHHHHHHHHcC
Confidence            5699999999999999999999854

>KOG0484 consensus Transcription factor PHOX2/ARIX, contains HOX domain [Transcription]

Probab=82.68  E-value=2.3  Score=34.46  Aligned_cols=52  Identities=17%  Similarity=0.177  Sum_probs=45.3

Q ss_pred             hcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHHhh
Q 046578          316 QTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQTNIL  371 (379)
Q Consensus       316 ~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~~l~~  371 (379)
                      .+|.+-||-...-+|    .+-+|-+|||-.+.+++.+|..+...-+.|.|+.-+.
T Consensus        27 ~QLkELErvF~ETHY----PDIYTREEiA~kidLTEARVQVWFQNRRAKfRKQEr~   78 (125)
T KOG0484|consen   27 AQLKELERVFAETHY----PDIYTREEIALKIDLTEARVQVWFQNRRAKFRKQERA   78 (125)
T ss_pred             HHHHHHHHHHHhhcC----CcchhHHHHHHhhhhhHHHHHHHHHhhHHHHHHHHHH
Confidence            378888888888888    4679999999999999999999999999999987553

>smart00347 HTH_MARR helix_turn_helix multiple antibiotic resistance protein

Probab=82.68  E-value=3.4  Score=32.09  Aligned_cols=41  Identities=20%  Similarity=0.378  Sum_probs=31.9

Q ss_pred             cCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 046578          317 TLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGI  360 (379)
Q Consensus       317 ~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~r  360 (379)
                      .|+..+..||.+.+.   ..+++..+||+.++++..+|++.+.+
T Consensus         7 ~l~~~~~~il~~l~~---~~~~~~~~la~~~~~s~~~i~~~l~~   47 (101)
T smart00347        7 GLTPTQFLVLRILYE---EGPLSVSELAKRLGVSPSTVTRVLDR   47 (101)
T ss_pred             CCCHHHHHHHHHHHH---cCCcCHHHHHHHHCCCchhHHHHHHH
Confidence            467778888877663   24589999999999999998765544

>cd00092 HTH_CRP helix_turn_helix, cAMP Regulatory protein C-terminus; DNA binding domain of prokaryotic regulatory proteins belonging to the catabolite activator protein family

Probab=82.30  E-value=2.1  Score=31.01  Aligned_cols=25  Identities=28%  Similarity=0.434  Sum_probs=21.1

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHHH
Q 046578          336 TPVSCKEIGRLLSLSRERIRQIRGI  360 (379)
Q Consensus       336 e~~S~~EIAe~LgiS~~~Vr~~~~r  360 (379)
                      ..+|..|||+.+|+|+++|++.+.+
T Consensus        24 ~~~s~~ela~~~g~s~~tv~r~l~~   48 (67)
T cd00092          24 LPLTRQEIADYLGLTRETVSRTLKE   48 (67)
T ss_pred             CCcCHHHHHHHHCCCHHHHHHHHHH
Confidence            4689999999999999999766544

>PF05043 Mga: Mga helix-turn-helix domain; InterPro: IPR007737 Mga is a DNA-binding protein that activates the expression of several important virulence genes in group A streptococcus in response to changing environmental conditions []

Probab=82.22  E-value=1.2  Score=34.53  Aligned_cols=32  Identities=22%  Similarity=0.128  Sum_probs=25.4

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHh
Q 046578          336 TPVSCKEIGRLLSLSRERIRQIRGIALTKLQQ  367 (379)
Q Consensus       336 e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~  367 (379)
                      +..|..++|+.+++|++++.+.+.+..+.|++
T Consensus        29 ~~~s~~~la~~~~iS~sti~~~i~~l~~~l~~   60 (87)
T PF05043_consen   29 EYVSIEDLAEELFISRSTIYRDIKKLNKYLKK   60 (87)
T ss_dssp             SEEEHHHHHHHHT--HHHHHHHHHHHHHHHHC
T ss_pred             CCcCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence            78999999999999999998887776666654

The family also contains VirR like proteins which match only at the C terminus of the alignment.; PDB: 3SQN_A.

>PF13560 HTH_31: Helix-turn-helix domain; PDB: 3F51_C 3F52_A 3PXP_A 2OFY_A

Probab=82.15  E-value=1.4  Score=32.16  Aligned_cols=24  Identities=17%  Similarity=0.285  Sum_probs=19.9

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHH
Q 046578          336 TPVSCKEIGRLLSLSRERIRQIRG  359 (379)
Q Consensus       336 e~~S~~EIAe~LgiS~~~Vr~~~~  359 (379)
                      .++|+.++|+.+|+|.++|+++.+
T Consensus        13 ~gls~~~lA~~~g~s~s~v~~iE~   36 (64)
T PF13560_consen   13 AGLSQAQLADRLGVSQSTVSRIER   36 (64)
T ss_dssp             HTS-HHHHHHHHTS-HHHHHHHHT
T ss_pred             cCCCHHHHHHHHCcCHHHHHHHHC
Confidence            569999999999999999999875

>PF14493 HTH_40: Helix-turn-helix domain

Probab=82.03  E-value=3.6  Score=32.36  Aligned_cols=29  Identities=17%  Similarity=0.176  Sum_probs=26.4

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHHHHHHH
Q 046578          336 TPVSCKEIGRLLSLSRERIRQIRGIALTK  364 (379)
Q Consensus       336 e~~S~~EIAe~LgiS~~~Vr~~~~rAl~k  364 (379)
                      +|+|..|||+.-|++.+||..++.++...
T Consensus        12 ~G~si~eIA~~R~L~~sTI~~HL~~~~~~   40 (91)
T PF14493_consen   12 KGLSIEEIAKIRGLKESTIYGHLAELIES   40 (91)
T ss_pred             cCCCHHHHHHHcCCCHHHHHHHHHHHHHh
Confidence            77999999999999999999999887654

>smart00342 HTH_ARAC helix_turn_helix, arabinose operon control protein

Probab=81.96  E-value=18  Score=26.59  Aligned_cols=25  Identities=16%  Similarity=0.099  Sum_probs=21.0

Q ss_pred             CCCHHHHHHHhCC-CHHHHHHHHHHH
Q 046578          337 PVSCKEIGRLLSL-SRERIRQIRGIA  361 (379)
Q Consensus       337 ~~S~~EIAe~Lgi-S~~~Vr~~~~rA  361 (379)
                      +.+..+||..+|+ +.+...+..++.
T Consensus        50 ~~~~~~ia~~~g~~s~~~f~r~Fk~~   75 (84)
T smart00342       50 DLSVTEIALRVGFSSQSYFSRAFKKL   75 (84)
T ss_pred             CCCHHHHHHHhCCCChHHHHHHHHHH
Confidence            5899999999999 988887766543

>TIGR00122 birA_repr_reg BirA biotin operon repressor domain

Probab=81.95  E-value=3.4  Score=30.53  Aligned_cols=25  Identities=24%  Similarity=0.421  Sum_probs=21.4

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHHH
Q 046578          336 TPVSCKEIGRLLSLSRERIRQIRGI  360 (379)
Q Consensus       336 e~~S~~EIAe~LgiS~~~Vr~~~~r  360 (379)
                      ...+..|||+.+|+|+.+|++.+.+
T Consensus        12 ~~~~~~eLa~~l~vS~~tv~~~l~~   36 (69)
T TIGR00122        12 NPFSGEKLGEALGMSRTAVNKHIQT   36 (69)
T ss_pred             CCcCHHHHHHHHCCCHHHHHHHHHH
Confidence            3478999999999999999877655

This model may recognize some other putative repressor proteins, such as DnrO of Streptomyces peucetius with scores below the noise cutoff but with significance shown by low E-value.

>COG1318 Predicted transcriptional regulators [Transcription]

Probab=81.91  E-value=1.4  Score=38.88  Aligned_cols=25  Identities=16%  Similarity=0.147  Sum_probs=22.6

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHHH
Q 046578          336 TPVSCKEIGRLLSLSRERIRQIRGI  360 (379)
Q Consensus       336 e~~S~~EIAe~LgiS~~~Vr~~~~r  360 (379)
                      -++|..|||+.+|.|+.||++++.-
T Consensus        60 ag~Ti~EIAeelG~TeqTir~hlkg   84 (182)
T COG1318          60 AGMTISEIAEELGRTEQTVRNHLKG   84 (182)
T ss_pred             ccCcHHHHHHHhCCCHHHHHHHHhc
Confidence            4599999999999999999998764

>PF13411 MerR_1: MerR HTH family regulatory protein; PDB: 2JML_A 3GP4_A 3GPV_B

Probab=81.86  E-value=0.79  Score=33.74  Aligned_cols=25  Identities=28%  Similarity=0.404  Sum_probs=22.5

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHHHHH
Q 046578          338 VSCKEIGRLLSLSRERIRQIRGIAL  362 (379)
Q Consensus       338 ~S~~EIAe~LgiS~~~Vr~~~~rAl  362 (379)
                      ||..|+|+.+|||.++|+.+..+.+
T Consensus         1 yti~eva~~~gvs~~tlr~y~~~gl   25 (69)
T PF13411_consen    1 YTIKEVAKLLGVSPSTLRYYEREGL   25 (69)
T ss_dssp             EEHHHHHHHTTTTHHHHHHHHHTTS
T ss_pred             CcHHHHHHHHCcCHHHHHHHHHhcC
Confidence            5789999999999999999988765

>TIGR01889 Staph_reg_Sar staphylococcal accessory regulator family

Probab=81.61  E-value=4.3  Score=32.99  Aligned_cols=45  Identities=22%  Similarity=0.150  Sum_probs=34.8

Q ss_pred             cCCHHHHHHHHHHhhcC-CCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 046578          317 TLSEREADILRLHFGLD-GQTPVSCKEIGRLLSLSRERIRQIRGIA  361 (379)
Q Consensus       317 ~L~~rer~Vl~l~ygL~-g~e~~S~~EIAe~LgiS~~~Vr~~~~rA  361 (379)
                      .|++.|..||...+.+. ...+.|..|||+.++++.++|.+.+.+-
T Consensus        22 ~ls~~q~~vL~~l~~~~~~~~~~t~~eL~~~l~~~~stvs~~i~~L   67 (109)
T TIGR01889        22 NLSLEELLILYYLGKLENNEGKLTLKEIIKEILIKQSALVKIIKKL   67 (109)
T ss_pred             CCCHHHHHHHHHHHhhhccCCcCcHHHHHHHHCCCHHHHHHHHHHH
Confidence            68999999987654111 1256999999999999999998876653

This model represents a family of transcriptional regulatory proteins in Staphylococcus aureus and Staphylococcus epidermidis. Some members contain two tandem copies of this region. This family is related to the MarR transcriptional regulator family described by pfam model pfam01047.

>TIGR03070 couple_hipB transcriptional regulator, y4mF family

Probab=81.59  E-value=1.6  Score=30.40  Aligned_cols=25  Identities=12%  Similarity=0.171  Sum_probs=22.3

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHHH
Q 046578          336 TPVSCKEIGRLLSLSRERIRQIRGI  360 (379)
Q Consensus       336 e~~S~~EIAe~LgiS~~~Vr~~~~r  360 (379)
                      .++|+.++|+.+|+|+++|+++.+.
T Consensus        14 ~gltq~~lA~~~gvs~~~vs~~e~g   38 (58)
T TIGR03070        14 LGLTQADLADLAGVGLRFIRDVENG   38 (58)
T ss_pred             cCCCHHHHHHHhCCCHHHHHHHHCC
Confidence            4599999999999999999998753

Members of this family belong to a clade of helix-turn-helix DNA-binding proteins, among the larger family pfam01381 (HTH_3; Helix-turn-helix). Members are similar in sequence to the HipB protein of E. coli. Genes for members of the seed alignment for this protein family were found to be closely linked to genes encoding proteins related to HipA. The HibBA operon appears to have some features in common with toxin-antitoxin post-segregational killing systems.

>PRK11564 stationary phase inducible protein CsiE; Provisional

Probab=81.45  E-value=4  Score=41.38  Aligned_cols=51  Identities=16%  Similarity=0.101  Sum_probs=39.8

Q ss_pred             cCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHh
Q 046578          317 TLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQ  367 (379)
Q Consensus       317 ~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~  367 (379)
                      .+++.||..+.+.+.|...+..|..++|+.|+||++|+.+-+.+..+.|.+
T Consensus        10 ~~s~~ER~~~il~~LL~~~~~v~l~~Lae~l~VSrsTi~~DLk~l~~~L~~   60 (426)
T PRK11564         10 VLSAPQRRCQILLMLFQPGLTVTLETFSQLNGVDDDTARQDIAETGREIQR   60 (426)
T ss_pred             CCCHHHHHHHHHHHHhcCCCCccHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence            367788777666554554578999999999999999999987777666655

>COG3877 Uncharacterized protein conserved in bacteria [Function unknown]

Probab=81.30  E-value=4  Score=33.14  Aligned_cols=48  Identities=19%  Similarity=0.258  Sum_probs=40.0

Q ss_pred             HhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 046578          315 LQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQ  366 (379)
Q Consensus       315 L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR  366 (379)
                      .+.|++.|-+.+.+++-..    =+++||-..+|+|..+|+..+...+++|-
T Consensus        39 F~~Lt~d~LeFv~lf~r~R----GnlKEvEr~lg~sYptvR~kld~vlramg   86 (122)
T COG3877          39 FEYLTSDQLEFVELFLRCR----GNLKEVERELGISYPTVRTKLDEVLRAMG   86 (122)
T ss_pred             ccccCHhHhHHHHHHHHHc----cCHHHHHHHHCCccHHHHHHHHHHHHHcC
Confidence            3568888888888877533    38999999999999999999988888764

>PHA01976 helix-turn-helix protein

Probab=81.21  E-value=1.8  Score=31.63  Aligned_cols=25  Identities=16%  Similarity=0.129  Sum_probs=22.6

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHHH
Q 046578          336 TPVSCKEIGRLLSLSRERIRQIRGI  360 (379)
Q Consensus       336 e~~S~~EIAe~LgiS~~~Vr~~~~r  360 (379)
                      .++|++|+|+.+|+|+++|+++.+.
T Consensus        14 ~glt~~~lA~~~gvs~~~v~~~e~g   38 (67)
T PHA01976         14 RAWSAPELSRRAGVRHSLIYDFEAD   38 (67)
T ss_pred             cCCCHHHHHHHhCCCHHHHHHHHcC
Confidence            5699999999999999999998764

>PRK15482 transcriptional regulator MurR; Provisional

Probab=81.02  E-value=2.9  Score=39.94  Aligned_cols=59  Identities=17%  Similarity=0.273  Sum_probs=44.5

Q ss_pred             HHHHHHHhcCCHHHHHHHHHHhhcCC---CCCCCHHHHHHHhCCCHHHHHHHHHH----HHHHHHhHH
Q 046578          309 QELKELLQTLSEREADILRLHFGLDG---QTPVSCKEIGRLLSLSRERIRQIRGI----ALTKLQQTN  369 (379)
Q Consensus       309 ~~L~~~L~~L~~rer~Vl~l~ygL~g---~e~~S~~EIAe~LgiS~~~Vr~~~~r----Al~kLR~~l  369 (379)
                      ..|......|++.|+.|....  ++.   ...+|..|||+..|+|.+||-+..++    +...||..+
T Consensus         5 ~~i~~~~~~Lt~~e~~Ia~yI--l~n~~~v~~~si~elA~~~~vS~aTv~Rf~kkLGf~Gf~efk~~l   70 (285)
T PRK15482          5 TKIRNAESEFTENEQKIADFL--RANVSELKSVSSRKMAKQLGISQSSIVKFAQKLGAQGFTELRMAL   70 (285)
T ss_pred             HHHHHHHhhcCHHHHHHHHHH--HhCHHHHHhcCHHHHHHHhCCCHHHHHHHHHHhCCCCHHHHHHHH
Confidence            457788889999999998754  331   23599999999999999999887665    344444444

>PRK10072 putative transcriptional regulator; Provisional

Probab=81.00  E-value=6.9  Score=31.40  Aligned_cols=24  Identities=17%  Similarity=0.336  Sum_probs=22.3

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHH
Q 046578          336 TPVSCKEIGRLLSLSRERIRQIRG  359 (379)
Q Consensus       336 e~~S~~EIAe~LgiS~~~Vr~~~~  359 (379)
                      .++|+.|+|+.+|+|.++|+++.+
T Consensus        45 ~glTQ~elA~~lGvS~~TVs~WE~   68 (96)
T PRK10072         45 TGLKIDDFARVLGVSVAMVKEWES   68 (96)
T ss_pred             cCCCHHHHHHHhCCCHHHHHHHHc
Confidence            569999999999999999999976

>PF13545 HTH_Crp_2: Crp-like helix-turn-helix domain; PDB: 3LA2_A 3LA3_B 3LA7_A 3B02_A 3E97_A 2H6C_B 1OMI_A 2BGC_H 2BEO_A 2GAU_A

Probab=80.89  E-value=2  Score=32.12  Aligned_cols=27  Identities=37%  Similarity=0.721  Sum_probs=21.6

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHHHHHHHHHHh
Q 046578          337 PVSCKEIGRLLSLSRERIRQIRGIALTKLQQ  367 (379)
Q Consensus       337 ~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~  367 (379)
                      .+|.++||+.+|+|+.+|.+.    +++|++
T Consensus        28 ~lt~~~iA~~~g~sr~tv~r~----l~~l~~   54 (76)
T PF13545_consen   28 PLTQEEIADMLGVSRETVSRI----LKRLKD   54 (76)
T ss_dssp             ESSHHHHHHHHTSCHHHHHHH----HHHHHH
T ss_pred             cCCHHHHHHHHCCCHHHHHHH----HHHHHH
Confidence            489999999999999998665    455544

...

>TIGR00647 MG103 conserved hypothetical protein

Probab=80.71  E-value=3.9  Score=39.31  Aligned_cols=44  Identities=18%  Similarity=0.196  Sum_probs=37.8

Q ss_pred             HhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhC------CCHHHHHHHHHHH
Q 046578          315 LQTLSEREADILRLHFGLDGQTPVSCKEIGRLLS------LSRERIRQIRGIA  361 (379)
Q Consensus       315 L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~Lg------iS~~~Vr~~~~rA  361 (379)
                      ++.||+.-+++..+|.-   .++.|++|+|+.|.      +|.+.|..+++|.
T Consensus       225 l~~Lp~~L~~~a~lRl~---~Pd~SL~ELgell~~~~~~~isKSgvnhRlrKl  274 (279)
T TIGR00647       225 FEKLPLNFQRICLLKID---HPDWSLEQIAEFFASKYKVKISRSGIQHRLRKL  274 (279)
T ss_pred             cccCCHHHHHHHHHHHh---CcccCHHHHHHHhccCCCCCcCHHHHHHHHHHH
Confidence            46899999999999863   48899999999994      9999999887664

>PF12116 SpoIIID: Stage III sporulation protein D; InterPro: IPR014208 Members of this entry represent the transcriptional regulator SpoIIID, or stage III sporulation protein D

Probab=80.49  E-value=2.9  Score=32.30  Aligned_cols=46  Identities=13%  Similarity=0.210  Sum_probs=28.3

Q ss_pred             HHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHH
Q 046578          322 EADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQTN  369 (379)
Q Consensus       322 er~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~~l  369 (379)
                      +|.+-...|.++  ...|.++.|..||||.+||.+-+..=|.++-..|
T Consensus         6 eR~i~i~~yIi~--~~aTVR~~Ak~FGvSKSTVHkDvteRL~~in~~L   51 (82)
T PF12116_consen    6 ERVIEIANYIIE--TKATVRQAAKVFGVSKSTVHKDVTERLPKINPEL   51 (82)
T ss_dssp             HHHHHHHHHHHH--H---HHHHHHHHTS-HHHHHHHHTTHHHHH-HHH
T ss_pred             HHHHHHHHHHHH--cccHHHHHHHHHCCcHHHHHHHHHHHHHhcCHHH
Confidence            344444455444  5689999999999999999987766555544433

It is present in genomes if, and only if, the species is capable of endospore formation. In Bacillus subtilis SpoIIID is a DNA binding protein that is involved in gene repression as well as activation [].; PDB: 2L0K_A.

>smart00354 HTH_LACI helix_turn _helix lactose operon repressor

Probab=80.46  E-value=1.7  Score=32.46  Aligned_cols=23  Identities=17%  Similarity=0.372  Sum_probs=20.1

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHHH
Q 046578          338 VSCKEIGRLLSLSRERIRQIRGI  360 (379)
Q Consensus       338 ~S~~EIAe~LgiS~~~Vr~~~~r  360 (379)
                      .|++|||+.+|+|.+||++.++.
T Consensus         1 ~t~~~iA~~~gvS~~TVSr~ln~   23 (70)
T smart00354        1 ATIKDVARLAGVSKATVSRVLNG   23 (70)
T ss_pred             CCHHHHHHHHCCCHHHHHHHHCC
Confidence            37899999999999999987754

>cd00090 HTH_ARSR Arsenical Resistance Operon Repressor and similar prokaryotic, metal regulated homodimeric repressors

Probab=80.42  E-value=4.6  Score=29.17  Aligned_cols=37  Identities=24%  Similarity=0.376  Sum_probs=26.4

Q ss_pred             HHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 046578          320 EREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGI  360 (379)
Q Consensus       320 ~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~r  360 (379)
                      ..+..|+...+  .  .+.+..||++.+|++..+|++.+.+
T Consensus         7 ~~~~~il~~l~--~--~~~~~~ei~~~~~i~~~~i~~~l~~   43 (78)
T cd00090           7 PTRLRILRLLL--E--GPLTVSELAERLGLSQSTVSRHLKK   43 (78)
T ss_pred             hHHHHHHHHHH--H--CCcCHHHHHHHHCcCHhHHHHHHHH
Confidence            34555555433  2  2399999999999999999776555

ARSR subfamily of helix-turn-helix bacterial transcription regulatory proteins (winged helix topology). Includes several proteins that appear to dissociate from DNA in the presence of metal ions.

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	379
4igc_X	613	X-ray Crystal Structure Of Escherichia Coli Sigma70		2e-37
3iyd_F	613	Three-Dimensional Em Structure Of An Intact Activat		3e-37
1l9u_H	332	Thermus Aquaticus Rna Polymerase Holoenzyme At 4 A		2e-34
1l9z_H	438	Thermus Aquaticus Rna Polymerase HoloenzymeFORK-Jun		3e-34
3dxj_F	423	Crystal Structure Of Thermus Thermophilus Rna Polym		4e-34
1iw7_F	423	Crystal Structure Of The Rna Polymerase Holoenzyme		4e-34
4g7h_F	443	Crystal Structure Of Thermus Thermophilus Transcrip		5e-34
1ku2_A	241	Crystal Structure Of Thermus Aquaticus Rna Polymera		1e-23
3ugo_A	245	Crystal Structure Of Rna-Polymerase Sigma Subunit D		1e-23
1sig_A	339	Crystal Structure Of A Sigma70 Subunit Fragment Fro		4e-17
3les_A	179	2f5 Epitope Scaffold Es2 Length = 179		1e-16
1l0o_C	243	Crystal Structure Of The Bacillus Stearothermophilu		6e-12
1rp3_A	239	Cocrystal Structure Of The Flagellar SigmaANTI-Sigm		1e-08
4g6d_A	73	G1 Orf67 / Staphyloccus Aureus Sigmaa Domain 4 Comp		6e-08
1tlh_B	81	T4 Asia Bound To Sigma70 Region 4 Length = 81		9e-07
2p7v_B	68	Crystal Structure Of The Escherichia Coli Regulator		1e-06
3t72_q	99	Phob(E)-Sigma70(4)-(Rnap-Betha-Flap-Tip-Helix)-Dna		2e-06
4g94_A	62	G1 Orf67 / Staphyloccus Aureus Sigmaa Domain 4 Comp		3e-06
1tty_A	87	Solution Structure Of Sigma A Region 4 From Thermot		1e-05

>pdb|4IGC|X Chain X, X-ray Crystal Structure Of Escherichia Coli Sigma70 Holoenzyme Length = 613

Iteration: 1
 Score =  153 bits (386), Expect = 2e-37,   Method: Compositional matrix adjust.
 Identities = 81/242 (33%), Positives = 132/242 (54%)
Query: 137 CKERESQERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLST 196
            K R +++ ++ +   LV+SIA  Y  +GL   DLIQEG+IGL++   +F   RGYK ST
Sbjct: 370 AKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFST 429
Query: 197 YVYWWIKQAIIRAIANKSRTIRLPGSMAGMVAKIAEANNVLSRRLRRMPTDSEIAEMLNI 256
           Y  WWI+QAI R+IA+++RTIR+P  M   + K+   +  + + + R PT  E+AE + +
Sbjct: 430 YATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELAERMLM 489
Query: 257 HVSTVRLAIERTRHPISLDGAVTDRGCMTMQDIIPGPDETMPERMVXXXXXXXXXXXXXX 316
               +R  ++  + PIS++  + D     + D I      +P                  
Sbjct: 490 PEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATTESLRAATHDVLA 549
Query: 317 TLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQTNILNNLKV 376
            L+ REA +LR+ FG+D  T  + +E+G+   ++RERIRQI   AL KL+  +    L+ 
Sbjct: 550 GLTAREAKVLRMRFGIDMNTDYTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRS 609
Query: 377 YM 378
           ++
Sbjct: 610 FL 611

>pdb|3IYD|F Chain F, Three-Dimensional Em Structure Of An Intact Activator-Dependent Transcription Initiation Complex Length = 613

Iteration: 1
 Score =  152 bits (384), Expect = 3e-37,   Method: Compositional matrix adjust.
 Identities = 81/242 (33%), Positives = 132/242 (54%)
Query: 137 CKERESQERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLST 196
            K R +++ ++ +   LV+SIA  Y  +GL   DLIQEG+IGL++   +F   RGYK ST
Sbjct: 370 AKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFST 429
Query: 197 YVYWWIKQAIIRAIANKSRTIRLPGSMAGMVAKIAEANNVLSRRLRRMPTDSEIAEMLNI 256
           Y  WWI+QAI R+IA+++RTIR+P  M   + K+   +  + + + R PT  E+AE + +
Sbjct: 430 YATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELAERMLM 489
Query: 257 HVSTVRLAIERTRHPISLDGAVTDRGCMTMQDIIPGPDETMPERMVXXXXXXXXXXXXXX 316
               +R  ++  + PIS++  + D     + D I      +P                  
Sbjct: 490 PEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATTESLRAATHDVLA 549
Query: 317 TLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQTNILNNLKV 376
            L+ REA +LR+ FG+D  T  + +E+G+   ++RERIRQI   AL KL+  +    L+ 
Sbjct: 550 GLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRS 609
Query: 377 YM 378
           ++
Sbjct: 610 FL 611

>pdb|1L9U|H Chain H, Thermus Aquaticus Rna Polymerase Holoenzyme At 4 A Resolution Length = 332

Iteration: 1
 Score =  143 bits (360), Expect = 2e-34,   Method: Compositional matrix adjust.
 Identities = 89/244 (36%), Positives = 131/244 (53%), Gaps = 3/244 (1%)
Query: 126 LDYNLVKYKILCKERES-QERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAK 184
           L   L +Y  + +E E+ ++ +I +   LVVSIA  Y G+GLS  DLIQEG+ GL+R  +
Sbjct: 75  LPKELKRYLHIAREGEAARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQEGNQGLIRAVE 134
Query: 185 RFNPERGYKLSTYVYWWIKQAIIRAIANKSRTIRLPGSMAGMVAKIAEANNVLSRRLRRM 244
           +F  +R +K STY  WWI+QAI RAIA+++RTIR+P  M   + K++     L + L R 
Sbjct: 135 KFEYKRRFKFSTYATWWIRQAINRAIADQARTIRIPVHMVETINKLSRTARQLQQELGRE 194
Query: 245 PTDSEIAEMLNIHVSTVRL--AIERTRHPISLDGAVTDRGCMTMQDIIPGPDETMPERMV 302
           P+  EIAE +       R+   ++  + P+SL+  + D       D IP  +   P    
Sbjct: 195 PSYEEIAEAMGPGWDAKRVEETLKIAQEPVSLETPIGDEKDSFYGDFIPDENLPSPVEAA 254
Query: 303 XXXXXXXXXXXXXXTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIAL 362
                          LSEREA +L+L  GL      + +E+G    ++RERIRQI   AL
Sbjct: 255 AQSLLSEELEKALSKLSEREAMVLKLRKGLIDGREHTLEEVGAYFGVTRERIRQIENKAL 314
Query: 363 TKLQ 366
            KL+
Sbjct: 315 RKLK 318

>pdb|1L9Z|H Chain H, Thermus Aquaticus Rna Polymerase HoloenzymeFORK-Junction Promoter Dna Complex At 6.5 A Resolution Length = 438

Iteration: 1
 Score =  142 bits (358), Expect = 3e-34,   Method: Compositional matrix adjust.
 Identities = 91/245 (37%), Positives = 134/245 (54%), Gaps = 5/245 (2%)
Query: 126 LDYNLVKYKILCKERES-QERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAK 184
           L   L +Y  + +E E+ ++ +I +   LVVSIA  Y G+GLS  DLIQEG+ GL+R  +
Sbjct: 181 LPKELKRYLHIAREGEAARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQEGNQGLIRAVE 240
Query: 185 RFNPERGYKLSTYVYWWIKQAIIRAIANKSRTIRLPGSMAGMVAKIAEANNVLSRRLRRM 244
           +F  +R +K STY  WWI+QAI RAIA+++RTIR+P  M   + K++     L + L R 
Sbjct: 241 KFEYKRRFKFSTYATWWIRQAINRAIADQARTIRIPVHMVETINKLSRTARQLQQELGRE 300
Query: 245 PTDSEIAEMLNIHVSTVRL--AIERTRHPISLDGAVTDRGCMTMQDIIPGPDETMPERMV 302
           P+  EIAE +       R+   ++  + P+SL+  + D       D IP  +   P    
Sbjct: 301 PSYEEIAEAMGPGWDAKRVEETLKIAQEPVSLETPIGDEKDSFYGDFIPDENLPSPVEAA 360
Query: 303 XXXXXXXXXXXXXXTLSEREADILRLHFGL-DGQTPVSCKEIGRLLSLSRERIRQIRGIA 361
                          LSEREA +L+L  GL DG+   + +E+G    ++RERIRQI   A
Sbjct: 361 AQSLLSEELEKALSKLSEREAMVLKLRKGLIDGRE-HTLEEVGAYFGVTRERIRQIENKA 419
Query: 362 LTKLQ 366
           L KL+
Sbjct: 420 LRKLK 424

>pdb|3DXJ|F Chain F, Crystal Structure Of Thermus Thermophilus Rna Polymerase Holoenzyme In Complex With The Antibiotic Myxopyronin Length = 423

Iteration: 1
 Score =  142 bits (357), Expect = 4e-34,   Method: Compositional matrix adjust.
 Identities = 92/253 (36%), Positives = 137/253 (54%), Gaps = 7/253 (2%)
Query: 119 LDKENGELDYNLVKYKILCKERES-QERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSI 177
           +D++   L     +Y  + +E E+ ++ +I +   LVVSIA  Y G+GLS  DLIQEG+ 
Sbjct: 159 IDQKLKSLPKEHKRYLHIAREGEAARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQEGNQ 218
Query: 178 GLLRGAKRFNPERGYKLSTYVYWWIKQAIIRAIANKSRTIRLPGSMAGMVAKIAEANNVL 237
           GL+R  ++F  +R +K STY  WWI+QAI RAIA+++RTIR+P  M   + K++     L
Sbjct: 219 GLIRAVEKFEYKRRFKFSTYATWWIRQAINRAIADQARTIRIPVHMVETINKLSRTARQL 278
Query: 238 SRRLRRMPTDSEIAEMLNIHVSTVRL--AIERTRHPISLDGAVTDRGCMTMQDIIPGPDE 295
            + L R PT  EIAE +       R+   ++  + P+SL+  + D       D I  PDE
Sbjct: 279 QQELGREPTYEEIAEAMGPGWDAKRVEETLKIAQEPVSLETPIGDEKDSFYGDFI--PDE 336
Query: 296 TMPERM--VXXXXXXXXXXXXXXTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRER 353
            +P  +                  LSEREA +L+L  GL      + +E+G    ++RER
Sbjct: 337 HLPSPVDAATQSLLSEELEKALSKLSEREAMVLKLRKGLIDGREHTLEEVGAFFGVTRER 396
Query: 354 IRQIRGIALTKLQ 366
           IRQI   AL KL+
Sbjct: 397 IRQIENKALRKLK 409

>pdb|1IW7|F Chain F, Crystal Structure Of The Rna Polymerase Holoenzyme From Thermus Thermophilus At 2.6a Resolution Length = 423

Iteration: 1
 Score =  142 bits (357), Expect = 4e-34,   Method: Compositional matrix adjust.
 Identities = 92/253 (36%), Positives = 137/253 (54%), Gaps = 7/253 (2%)
Query: 119 LDKENGELDYNLVKYKILCKERES-QERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSI 177
           +D++   L     +Y  + +E E+ ++ +I +   LVVSIA  Y G+GLS  DLIQEG+ 
Sbjct: 159 IDQKLKSLPKEHKRYLHIAREGEAARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQEGNQ 218
Query: 178 GLLRGAKRFNPERGYKLSTYVYWWIKQAIIRAIANKSRTIRLPGSMAGMVAKIAEANNVL 237
           GL+R  ++F  +R +K STY  WWI+QAI RAIA+++RTIR+P  M   + K++     L
Sbjct: 219 GLIRAVEKFEYKRRFKFSTYATWWIRQAINRAIADQARTIRIPVHMVETINKLSRTARQL 278
Query: 238 SRRLRRMPTDSEIAEMLNIHVSTVRL--AIERTRHPISLDGAVTDRGCMTMQDIIPGPDE 295
            + L R PT  EIAE +       R+   ++  + P+SL+  + D       D I  PDE
Sbjct: 279 QQELGREPTYEEIAEAMGPGWDAKRVEETLKIAQEPVSLETPIGDEKDSFYGDFI--PDE 336
Query: 296 TMPERM--VXXXXXXXXXXXXXXTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRER 353
            +P  +                  LSEREA +L+L  GL      + +E+G    ++RER
Sbjct: 337 HLPSPVDAATQSLLSEELEKALSKLSEREAMVLKLRKGLIDGREHTLEEVGAFFGVTRER 396
Query: 354 IRQIRGIALTKLQ 366
           IRQI   AL KL+
Sbjct: 397 IRQIENKALRKLK 409

>pdb|4G7H|F Chain F, Crystal Structure Of Thermus Thermophilus Transcription Initiation Complex Length = 443

Iteration: 1
 Score =  141 bits (356), Expect = 5e-34,   Method: Compositional matrix adjust.
 Identities = 92/253 (36%), Positives = 137/253 (54%), Gaps = 7/253 (2%)
Query: 119 LDKENGELDYNLVKYKILCKERES-QERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSI 177
           +D++   L     +Y  + +E E+ ++ +I +   LVVSIA  Y G+GLS  DLIQEG+ 
Sbjct: 179 IDQKLKSLPKEHKRYLHIAREGEAARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQEGNQ 238
Query: 178 GLLRGAKRFNPERGYKLSTYVYWWIKQAIIRAIANKSRTIRLPGSMAGMVAKIAEANNVL 237
           GL+R  ++F  +R +K STY  WWI+QAI RAIA+++RTIR+P  M   + K++     L
Sbjct: 239 GLIRAVEKFEYKRRFKFSTYATWWIRQAINRAIADQARTIRIPVHMVETINKLSRTARQL 298
Query: 238 SRRLRRMPTDSEIAEMLNIHVSTVRL--AIERTRHPISLDGAVTDRGCMTMQDIIPGPDE 295
            + L R PT  EIAE +       R+   ++  + P+SL+  + D       D I  PDE
Sbjct: 299 QQELGREPTYEEIAEAMGPGWDAKRVEETLKIAQEPVSLETPIGDEKDSFYGDFI--PDE 356
Query: 296 TMPERM--VXXXXXXXXXXXXXXTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRER 353
            +P  +                  LSEREA +L+L  GL      + +E+G    ++RER
Sbjct: 357 HLPSPVDAATQSLLSEELEKALSKLSEREAMVLKLRKGLIDGREHTLEEVGAFFGVTRER 416
Query: 354 IRQIRGIALTKLQ 366
           IRQI   AL KL+
Sbjct: 417 IRQIENKALRKLK 429

>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 =  107 bits (267), Expect = 1e-23,   Method: Compositional matrix adjust.
 Identities = 61/152 (40%), Positives = 92/152 (60%), Gaps = 3/152 (1%)
Query: 126 LDYNLVKYKILCKERES-QERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAK 184
           L   L +Y  + +E E+ ++ +I +   LVVSIA  Y G+GLS  DLIQEG+ GL+R  +
Sbjct: 90  LPKELKRYLHIAREGEAARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQEGNQGLIRAVE 149
Query: 185 RFNPERGYKLSTYVYWWIKQAIIRAIANKSRTIRLPGSMAGMVAKIAEANNVLSRRLRRM 244
           +F  +R +K STY  WWI+QAI RAIA+++RTIR+P  M   + K++     L + L R 
Sbjct: 150 KFEYKRRFKFSTYATWWIRQAINRAIADQARTIRIPVHMVETINKLSRTARQLQQELGRE 209
Query: 245 PTDSEIAEMLNIHVSTVRL--AIERTRHPISL 274
           P+  EIAE +       R+   ++  + P+SL
Sbjct: 210 PSYEEIAEAMGPGWDAKRVEETLKIAQEPVSL 241

>pdb|3UGO|A Chain A, Crystal Structure Of Rna-Polymerase Sigma Subunit Domain 2 Complexed With -10 Promoter Element Ssdna Oligo (Tacaat) Length = 245

Iteration: 1
 Score =  107 bits (267), Expect = 1e-23,   Method: Compositional matrix adjust.
 Identities = 61/152 (40%), Positives = 92/152 (60%), Gaps = 3/152 (1%)
Query: 126 LDYNLVKYKILCKERES-QERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAK 184
           L   L +Y  + +E E+ ++ +I +   LVVSIA  Y G+GLS  DLIQEG+ GL+R  +
Sbjct: 94  LPKELKRYLHIAREGEAARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQEGNQGLIRAVE 153
Query: 185 RFNPERGYKLSTYVYWWIKQAIIRAIANKSRTIRLPGSMAGMVAKIAEANNVLSRRLRRM 244
           +F  +R +K STY  WWI+QAI RAIA+++RTIR+P  M   + K++     L + L R 
Sbjct: 154 KFEYKRRFKFSTYATWWIRQAINRAIADQARTIRIPVHMVETINKLSRTARQLQQELGRE 213
Query: 245 PTDSEIAEMLNIHVSTVRL--AIERTRHPISL 274
           P+  EIAE +       R+   ++  + P+SL
Sbjct: 214 PSYEEIAEAMGPGWDAKRVEETLKIAQEPVSL 245

>pdb|1SIG|A Chain A, Crystal Structure Of A Sigma70 Subunit Fragment From Escherichia Coli Rna Polymerase Length = 339

Iteration: 1
 Score = 85.5 bits (210), Expect = 4e-17,   Method: Compositional matrix adjust.
 Identities = 37/79 (46%), Positives = 54/79 (68%)
Query: 137 CKERESQERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLST 196
            K R +++ ++ +   LV+SIA  Y  +GL   DLIQEG+IGL++   +F   RGYK ST
Sbjct: 261 AKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFST 320
Query: 197 YVYWWIKQAIIRAIANKSR 215
           Y  WWI+QAI R+IA+++R
Sbjct: 321 YATWWIRQAITRSIADQAR 339

>pdb|3LES|A Chain A, 2f5 Epitope Scaffold Es2 Length = 179

Iteration: 1
 Score = 84.3 bits (207), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 43/91 (47%), Positives = 62/91 (68%), Gaps = 1/91 (1%)
Query: 126 LDYNLVKYKILCKERES-QERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAK 184
           L   L +Y  + +E E+ ++ +I +   LVVSIA  Y G+GLS  DLIQEG+ GL+R  +
Sbjct: 89  LPKELKRYLHIAREGEAARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQEGNQGLIRAVE 148
Query: 185 RFNPERGYKLSTYVYWWIKQAIIRAIANKSR 215
           +F  +RG+  STY  WWI+QAI RAIA+++R
Sbjct: 149 KFEYKRGFAFSTYATWWIRQAINRAIADQAR 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 = 68.6 bits (166), Expect = 6e-12,   Method: Compositional matrix adjust.
 Identities = 53/160 (33%), Positives = 78/160 (48%), Gaps = 3/160 (1%)
Query: 139 ERESQERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYV 198
           ++E+++ II     LV S+   +  +G    DL Q G IGLL+   +F+     K STY 
Sbjct: 26  DQEARDEIIEKNMRLVWSVVQRFLNRGYEADDLFQIGCIGLLKSVDKFDLSYDVKFSTYA 85
Query: 199 YWWIKQAIIRAIANKSRTIRLPGSMAGMVAKIAEANNVLSRRLRRMPTDSEIAEMLNIHV 258
              I   I R + +   T+++  S+  M  KI +A + LS+   R PT +EIA+ L I  
Sbjct: 86  VPMIIGEIQRFLRDDG-TVKVSRSLKEMGNKIRKAKDELSKTRGRAPTVTEIADHLGISP 144
Query: 259 STVRLAIERTRHPISLDGAV--TDRGCMTMQDIIPGPDET 296
             V LA E  R P S+   V   D   +T+ D I   DE 
Sbjct: 145 EDVVLAQEAVRLPTSIHETVYENDGDPITLLDQIADADEA 184

>pdb|1RP3|A Chain A, Cocrystal Structure Of The Flagellar SigmaANTI-Sigma Complex, Sigma-28FLGM Length = 239

Iteration: 1
 Score = 57.4 bits (137), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 60/233 (25%), Positives = 104/233 (44%), Gaps = 21/233 (9%)
Query: 143 QERIIRSYRSLVVSIATGYQG---KGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVY 199
           +E +I  Y  LV +IAT  +    + + ++DLI  G IGL++     + E   +   Y+ 
Sbjct: 14  REELILKYLPLVKAIATNIKKHLPEDVDIRDLISYGVIGLIKAVDNLSTENPKRAEAYIK 73
Query: 200 WWIKQAI---IRAIANKSRTIRLPGSMAGMVAKIAEANNVLSRRLRRMPTDSEIAEMLNI 256
             IK AI   +R++   SR +R          +I E    L  +L R PTD E+A+ L I
Sbjct: 74  LRIKGAIYDYLRSLDFGSRQVR------EKERRIKEVVEKLKEKLGREPTDEEVAKELGI 127
Query: 257 HVSTVRLAIERTR--HPISLDGAVTDRGCMTMQDIIPGPDETMPERMVXXXXXXXXXXXX 314
               +   +++    + +SL+    D       ++IP    T  E  V            
Sbjct: 128 STEELFKTLDKINFSYILSLEEVFRD-FARDYSELIPSS--TNVEEEVIKRELTEKVKEA 184
Query: 315 XXTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQ 367
              L ERE  +++L F  +    +  KE+ ++L  S  R+ Q++  AL +L++
Sbjct: 185 VSKLPEREKLVIQLIFYEE----LPAKEVAKILETSVSRVSQLKAKALERLRE 233

>pdb|4G6D|A Chain A, G1 Orf67 / Staphyloccus Aureus Sigmaa Domain 4 Complex Length = 73

Iteration: 1
 Score = 55.1 bits (131), Expect = 6e-08,   Method: Compositional matrix adjust.
 Identities = 27/62 (43%), Positives = 41/62 (66%)
Query: 317 TLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQTNILNNLKV 376
           TL++RE ++LRL FGLD     + +E+G++  ++RERIRQI   AL KL+  +    LK 
Sbjct: 11  TLTDREENVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRSKRLKD 70
Query: 377 YM 378
           +M
Sbjct: 71  FM 72

>pdb|1TLH|B Chain B, T4 Asia Bound To Sigma70 Region 4 Length = 81

Iteration: 1
 Score = 51.2 bits (121), Expect = 9e-07,   Method: Compositional matrix adjust.
 Identities = 24/61 (39%), Positives = 39/61 (63%)
Query: 318 LSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQTNILNNLKVY 377
           L+ REA +LR+ FG+D  T  + +E+G+   ++RERIRQI   AL KL+  +    L+ +
Sbjct: 19  LTAREAKVLRMRFGIDMNTDYTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRSF 78
Query: 378 M 378
           +
Sbjct: 79  L 79

>pdb|2P7V|B Chain B, Crystal Structure Of The Escherichia Coli Regulator Of Sigma 70, Rsd, In Complex With Sigma 70 Domain 4 Length = 68

Iteration: 1
 Score = 50.4 bits (119), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 24/61 (39%), Positives = 39/61 (63%)
Query: 318 LSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQTNILNNLKVY 377
           L+ REA +LR+ FG+D  T  + +E+G+   ++RERIRQI   AL KL+  +    L+ +
Sbjct: 6   LTAREAKVLRMRFGIDMNTDYTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRSF 65
Query: 378 M 378
           +
Sbjct: 66  L 66

>pdb|3T72|QQ Chain q, Phob(E)-Sigma70(4)-(Rnap-Betha-Flap-Tip-Helix)-Dna Transcription Activation Sub-Complex Length = 99

Iteration: 1
 Score = 50.1 bits (118), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 23/50 (46%), Positives = 34/50 (68%)
Query: 318 LSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQ 367
           L+ REA +LR+ FG+D  T  + +E+G+   ++RERIRQI   AL KL+ 
Sbjct: 20  LTAREAKVLRMRFGIDMNTDYTLEEVGKQFDVTRERIRQIEAKALRKLRH 69

>pdb|4G94|A Chain A, G1 Orf67 / Staphyloccus Aureus Sigmaa Domain 4 Complex Length = 62

Iteration: 1
 Score = 49.3 bits (116), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 24/51 (47%), Positives = 36/51 (70%)
Query: 317 TLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQ 367
           TL++RE ++LRL FGLD     + +E+G++  ++RERIRQI   AL KL+ 
Sbjct: 11  TLTDREENVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRH 61

>pdb|1TTY|A Chain A, Solution Structure Of Sigma A Region 4 From Thermotoga Maritima Length = 87

Iteration: 1
 Score = 47.8 bits (112), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 26/59 (44%), Positives = 38/59 (64%)
Query: 317 TLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQTNILNNLK 375
           TLS REA +LR+ +GL    P + +E+G+  +++RERIRQI   AL KL+  +    LK
Sbjct: 18  TLSPREAMVLRMRYGLLDGKPKTLEEVGQYFNVTRERIRQIEVKALRKLRHPSRSKYLK 76

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	379
3iyd_F	613	RNA polymerase sigma factor RPOD; transcription, i	1e-58
1l9z_H	438	Sigma factor SIGA; helix-turn-helix, coiled-coil,	2e-57
2a6h_F	423	RNA polymerase sigma factor RPOD; RNA polymerase h	2e-57
1l0o_C	243	Sigma factor; bergerat fold, helix-turn-helix, pro	7e-53
1rp3_A	239	RNA polymerase sigma factor sigma-28 (FLIA); trans	3e-48
3ugo_A	245	RNA polymerase sigma factor; protein-DNA complex,	2e-35
1sig_A	339	Sigma70, RNA polymerase primary sigma factor; RNA	2e-21
3t72_q	99	RNA polymerase sigma factor RPOD, DNA-directed RN	3e-16
1tty_A	87	Sigma-A, RNA polymerase sigma factor RPOD; helix-t	6e-16
2p7v_B	68	Sigma-70, RNA polymerase sigma factor RPOD; RSD, r	1e-13
1ku3_A	73	Sigma factor SIGA; helix-turn-helix, transcription	3e-13
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	8e-13
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	2e-05
3mzy_A	164	RNA polymerase sigma-H factor; PSI, MCSG, structur	7e-10

>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 =  199 bits (508), Expect = 1e-58
 Identities = 82/241 (34%), Positives = 138/241 (57%)

Query: 138 KERESQERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTY 197
           K R +++ ++ +   LV+SIA  Y  +GL   DLIQEG+IGL++   +F   RGYK STY
Sbjct: 371 KARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTY 430

Query: 198 VYWWIKQAIIRAIANKSRTIRLPGSMAGMVAKIAEANNVLSRRLRRMPTDSEIAEMLNIH 257
             WWI+QAI R+IA+++RTIR+P  M   + K+   +  + + + R PT  E+AE + + 
Sbjct: 431 ATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELAERMLMP 490

Query: 258 VSTVRLAIERTRHPISLDGAVTDRGCMTMQDIIPGPDETMPERMVQKQLMKQELKELLQT 317
              +R  ++  + PIS++  + D     + D I      +P      + ++    ++L  
Sbjct: 491 EDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATTESLRAATHDVLAG 550

Query: 318 LSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQTNILNNLKVY 377
           L+ REA +LR+ FG+D  T  + +E+G+   ++RERIRQI   AL KL+  +    L+ +
Sbjct: 551 LTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRSF 610

Query: 378 M 378
           +
Sbjct: 611 L 611

>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 =  192 bits (489), Expect = 2e-57
 Identities = 92/276 (33%), Positives = 143/276 (51%), Gaps = 3/276 (1%)

Query: 92  DDGECESVLKMMRRRSRRKKRTKESDFLDKENGELDYNLVKYKILCKERESQERIIRSYR 151
                  + K+   + +   +T E      ++   +       I  +   +++ +I +  
Sbjct: 149 KILGTARIQKIPGLKEKPDPKTVEEVDGKLKSLPKELKRYL-HIAREGEAARQHLIEANL 207

Query: 152 SLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYWWIKQAIIRAIA 211
            LVVSIA  Y G+GLS  DLIQEG+ GL+R  ++F  +R +K STY  WWI+QAI RAIA
Sbjct: 208 RLVVSIAKKYTGRGLSFLDLIQEGNQGLIRAVEKFEYKRRFKFSTYATWWIRQAINRAIA 267

Query: 212 NKSRTIRLPGSMAGMVAKIAEANNVLSRRLRRMPTDSEIAEML--NIHVSTVRLAIERTR 269
           +++RTIR+P  M   + K++     L + L R P+  EIAE +        V   ++  +
Sbjct: 268 DQARTIRIPVHMVETINKLSRTARQLQQELGREPSYEEIAEAMGPGWDAKRVEETLKIAQ 327

Query: 270 HPISLDGAVTDRGCMTMQDIIPGPDETMPERMVQKQLMKQELKELLQTLSEREADILRLH 329
            P+SL+  + D       D IP  +   P     + L+ +EL++ L  LSEREA +L+L 
Sbjct: 328 EPVSLETPIGDEKDSFYGDFIPDENLPSPVEAAAQSLLSEELEKALSKLSEREAMVLKLR 387

Query: 330 FGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKL 365
            GL      + +E+G    ++RERIRQI   AL KL
Sbjct: 388 KGLIDGREHTLEEVGAYFGVTRERIRQIENKALRKL 423

>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 =  192 bits (488), Expect = 2e-57
 Identities = 90/234 (38%), Positives = 131/234 (55%), Gaps = 2/234 (0%)

Query: 134 KILCKERESQERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYK 193
            I  +   +++ +I +   LVVSIA  Y G+GLS  DLIQEG+ GL+R  ++F  +R +K
Sbjct: 175 HIAREGEAARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQEGNQGLIRAVEKFEYKRRFK 234

Query: 194 LSTYVYWWIKQAIIRAIANKSRTIRLPGSMAGMVAKIAEANNVLSRRLRRMPTDSEIAEM 253
            STY  WWI+QAI RAIA+++RTIR+P  M   + K++     L + L R PT  EIAE 
Sbjct: 235 FSTYATWWIRQAINRAIADQARTIRIPVHMVETINKLSRTARQLQQELGREPTYEEIAEA 294

Query: 254 L--NIHVSTVRLAIERTRHPISLDGAVTDRGCMTMQDIIPGPDETMPERMVQKQLMKQEL 311
           +        V   ++  + P+SL+  + D       D IP      P     + L+ +EL
Sbjct: 295 MGPGWDAKRVEETLKIAQEPVSLETPIGDEKDSFYGDFIPDEHLPSPVDAATQSLLSEEL 354

Query: 312 KELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKL 365
           ++ L  LSEREA +L+L  GL      + +E+G    ++RERIRQI   AL KL
Sbjct: 355 EKALSKLSEREAMVLKLRKGLIDGREHTLEEVGAFFGVTRERIRQIENKALRKL 408

>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 =  174 bits (444), Expect = 7e-53
 Identities = 68/229 (29%), Positives = 107/229 (46%), Gaps = 14/229 (6%)

Query: 139 ERESQERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYV 198
           ++E+++ II     LV S+   +  +G    DL Q G IGLL+   +F+     K STY 
Sbjct: 26  DQEARDEIIEKNMRLVWSVVQRFLNRGYEADDLFQIGCIGLLKSVDKFDLSYDVKFSTYA 85

Query: 199 YWWIKQAIIRAIANKSRTIRLPGSMAGMVAKIAEANNVLSRRLRRMPTDSEIAEMLNIHV 258
              I   I R + +   T+++  S+  M  KI +A + LS+   R PT +EIA+ L I  
Sbjct: 86  VPMIIGEIQRFLRDDG-TVKVSRSLKEMGNKIRKAKDELSKTRGRAPTVTEIADHLGISP 144

Query: 259 STVRLAIERTRHPISLDGAVTDRG--CMTMQDIIPGPDETMPERMVQKQLMKQELKELLQ 316
             V LA E  R P S+   V +     +T+ D I   DE            K  LK+ ++
Sbjct: 145 EDVVLAQEAVRLPTSIHETVYENDGDPITLLDQIADADEASWF-------DKIALKKAIE 197

Query: 317 TLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKL 365
            L ERE  I+ L +  D QT     E+   L +S+ ++ ++    L  +
Sbjct: 198 ELDERERLIVYLRYYKD-QTQS---EVASRLGISQVQMSRLEKKILQHI 242

>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 =  162 bits (413), Expect = 3e-48
 Identities = 60/236 (25%), Positives = 109/236 (46%), Gaps = 17/236 (7%)

Query: 138 KERESQERIIRSYRSLVVSIAT---GYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYKL 194
             +  +E +I  Y  LV +IAT    +  + + ++DLI  G IGL++     + E   + 
Sbjct: 9   SNQIEREELILKYLPLVKAIATNIKKHLPEDVDIRDLISYGVIGLIKAVDNLSTENPKRA 68

Query: 195 STYVYWWIKQAIIRAIANKSRTI-RLPGSMAGMVAKIAEANNVLSRRLRRMPTDSEIAEM 253
             Y+   IK AI   +    R++      +     +I E    L  +L R PTD E+A+ 
Sbjct: 69  EAYIKLRIKGAIYDYL----RSLDFGSRQVREKERRIKEVVEKLKEKLGREPTDEEVAKE 124

Query: 254 LNIHVSTVRLAIERTRHP--ISLDGAVTDRGCMTMQDIIPGPDETMPERMVQKQLMKQEL 311
           L I    +   +++      +SL+    D      + I   P  T  E  V K+ + +++
Sbjct: 125 LGISTEELFKTLDKINFSYILSLEEVFRDFARDYSELI---PSSTNVEEEVIKRELTEKV 181

Query: 312 KELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQ 367
           KE +  L ERE  +++L F  +    +  KE+ ++L  S  R+ Q++  AL +L++
Sbjct: 182 KEAVSKLPEREKLVIQLIFYEE----LPAKEVAKILETSVSRVSQLKAKALERLRE 233

>3ugo_A RNA polymerase sigma factor; protein-DNA complex, bacterial promoter opening, G-quartet, quadruplex, DNA binding; 2.10A {Thermus aquaticus} PDB: 3ugp_A 1ku2_A 3lev_A* 3les_A* Length = 245

 Score =  128 bits (324), Expect = 2e-35
 Identities = 60/180 (33%), Positives = 96/180 (53%), Gaps = 3/180 (1%)

Query: 97  ESVLKMMRRRSRRKKRTKESDFLDKENGELDYNLVKYKILCKERESQERIIRSYRSLVVS 156
             + K+   + +   +T E      ++   +       I  +   +++ +I +   LVVS
Sbjct: 67  ARIQKIPGLKEKPDPKTVEEVDGKLKSLPKELKRYL-HIAREGEAARQHLIEANLRLVVS 125

Query: 157 IATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYWWIKQAIIRAIANKSRT 216
           IA  Y G+GLS  DLIQEG+ GL+R  ++F  +R +K STY  WWI+QAI RAIA+++RT
Sbjct: 126 IAKKYTGRGLSFLDLIQEGNQGLIRAVEKFEYKRRFKFSTYATWWIRQAINRAIADQART 185

Query: 217 IRLPGSMAGMVAKIAEANNVLSRRLRRMPTDSEIAEML--NIHVSTVRLAIERTRHPISL 274
           IR+P  M   + K++     L + L R P+  EIAE +        V   ++  + P+SL
Sbjct: 186 IRIPVHMVETINKLSRTARQLQQELGREPSYEEIAEAMGPGWDAKRVEETLKIAQEPVSL 245

>1sig_A Sigma70, RNA polymerase primary sigma factor; RNA polymerase sigma factor, transcription regulation; 2.60A {Escherichia coli} SCOP: a.177.1.1 Length = 339

 Score = 93.0 bits (231), Expect = 2e-21
 Identities = 44/137 (32%), Positives = 65/137 (47%), Gaps = 13/137 (9%)

Query: 92  DDGECESVLKMMRRRSRRKKRTKE-----SDFLDKENGELDYNLVKYKILCKERESQERI 146
            D    + + M +  S +     E        L +   E    + + K + +     E  
Sbjct: 203 SDTWFNAAIAMNKPWSEKLHDVSEEVHRALQKLQQIEEETGLTIEQVKDINRRMSIGEAK 262

Query: 147 IRSYRS--------LVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYV 198
            R  +         LV+SIA  Y  +GL   DLIQEG+IGL++   +F   RGYK STY 
Sbjct: 263 ARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYA 322

Query: 199 YWWIKQAIIRAIANKSR 215
            WWI+QAI R+IA+++R
Sbjct: 323 TWWIRQAITRSIADQAR 339

>3t72_q RNA polymerase sigma factor RPOD, DNA-directed RN polymerase subunit beta; winged-helix motif, transcription activation, DNA-binding; 4.33A {Escherichia coli} PDB: 1tlh_B Length = 99

 Score = 72.5 bits (178), Expect = 3e-16
 Identities = 25/78 (32%), Positives = 43/78 (55%)

Query: 301 MVQKQLMKQELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGI 360
               + ++    ++L  L+ REA +LR+ FG+D  T  + +E+G+   ++RERIRQI   
Sbjct: 3   SATTESLRAATHDVLAGLTAREAKVLRMRFGIDMNTDYTLEEVGKQFDVTRERIRQIEAK 62

Query: 361 ALTKLQQTNILNNLKVYM 378
           AL KL+  +    L+   
Sbjct: 63  ALRKLRHPSRSEVLRSGS 80

>1tty_A Sigma-A, RNA polymerase sigma factor RPOD; helix-turn-helix, transcription; NMR {Thermotoga maritima} SCOP: a.4.13.2 Length = 87

 Score = 71.3 bits (175), Expect = 6e-16
 Identities = 31/77 (40%), Positives = 51/77 (66%)

Query: 302 VQKQLMKQELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIA 361
             + LM++EL+++L+TLS REA +LR+ +GL    P + +E+G+  +++RERIRQI   A
Sbjct: 3   AMRMLMREELEKVLKTLSPREAMVLRMRYGLLDGKPKTLEEVGQYFNVTRERIRQIEVKA 62

Query: 362 LTKLQQTNILNNLKVYM 378
           L KL+  +    LK  +
Sbjct: 63  LRKLRHPSRSKYLKSLL 79

>2p7v_B Sigma-70, RNA polymerase sigma factor RPOD; RSD, regulator of sigma 70, sigma 70 domain 4, transcription, regulation, helix-turn-helix; 2.60A {Escherichia coli} SCOP: a.4.13.2 Length = 68

 Score = 64.2 bits (157), Expect = 1e-13
 Identities = 25/66 (37%), Positives = 42/66 (63%)

Query: 313 ELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQTNILN 372
           ++L  L+ REA +LR+ FG+D  T  + +E+G+   ++RERIRQI   AL KL+  +   
Sbjct: 1   DVLAGLTAREAKVLRMRFGIDMNTDYTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSE 60

Query: 373 NLKVYM 378
            L+ ++
Sbjct: 61  VLRSFL 66

>1ku3_A Sigma factor SIGA; helix-turn-helix, transcription; 1.80A {Thermus aquaticus} SCOP: a.4.13.2 PDB: 1ku7_A 1rio_H 3n97_A* Length = 73

 Score = 63.5 bits (155), Expect = 3e-13
 Identities = 25/59 (42%), Positives = 37/59 (62%)

Query: 309 QELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQ 367
           +EL++ L  LSEREA +L++  GL      + +E+G    ++RERIRQI   AL KL+ 
Sbjct: 2   EELEKALSKLSEREAMVLKMRKGLIDGREHTLEEVGAYFGVTRERIRQIENKALRKLKY 60

>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 = 69.1 bits (168), Expect = 8e-13
 Identities = 52/363 (14%), Positives = 105/363 (28%), Gaps = 105/363 (28%)

Query: 92  DDGECESVLKMMRRRSRRKKRTKESDFLDKENGELDYNLVKYKILCKERESQ-ERIIRS- 149
           D+ +C+ V  M +         +E D +      +   L  +  L  ++E   ++ +   
Sbjct: 31  DNFDCKDVQDMPKS----ILSKEEIDHIIMSKDAVSGTLRLFWTLLSKQEEMVQKFVEEV 86

Query: 150 ----YRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNP---ERGYKLSTYVYWWI 202
               Y+ L+  I T  +   +  +  I++    L    + F      R        Y  +
Sbjct: 87  LRINYKFLMSPIKTEQRQPSMMTRMYIEQRDR-LYNDNQVFAKYNVSRLQP-----YLKL 140

Query: 203 KQAIIRAIANKSRTIRLPGSMAGMVAKIAEANNVLS--RRLRRMP------------TDS 248
           +QA++      ++ + + G + G   K   A +V    +   +M             +  
Sbjct: 141 RQALLEL--RPAKNVLIDG-VLGS-GKTWVALDVCLSYKVQCKMDFKIFWLNLKNCNSPE 196

Query: 249 EIAEMLNI--------------HVSTVRLAIE-----------RTRHPISL---DGAVTD 280
            + EML                H S ++L I               +   L      V +
Sbjct: 197 TVLEMLQKLLYQIDPNWTSRSDHSSNIKLRIHSIQAELRRLLKSKPYENCLLVLLN-VQN 255

Query: 281 R--------GC---MTMQDI----IPGPDETMPERMVQKQ--LMKQELKELL-------- 315
                     C   +T +            T    +      L   E+K LL        
Sbjct: 256 AKAWNAFNLSCKILLTTRFKQVTDFLSAATTTHISLDHHSMTLTPDEVKSLLLKYLDCRP 315

Query: 316 QTLSEREADILRLHFGLDGQTPVSCKEIGRLLS--LSR-ERIRQIRGIALTKLQQTNILN 372
           Q L             +          I   +   L+  +  + +    LT + ++  LN
Sbjct: 316 QDLPREVLTTNPRRLSI----------IAESIRDGLATWDNWKHVNCDKLTTIIES-SLN 364

Query: 373 NLK 375
            L+
Sbjct: 365 VLE 367

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221

 Score = 46.0 bits (108), Expect = 2e-05
 Identities = 47/343 (13%), Positives = 85/343 (24%), Gaps = 116/343 (33%)

Query: 14  STLPS-LKTLHPLPPPSLSSSPSSCSNKYNININLVTNEALALHPVIESATDAAALASAA 72
             LP  + T +P     LS    S  +      N        L  +IES+ +   L  A 
Sbjct: 316 QDLPREVLTTNPR---RLSIIAESIRDGLATWDNWKHVNCDKLTTIIESSLNV--LEPAE 370

Query: 73  VRTA-KDAVSFANGA---EEVC------FDDGECESVLKMMRRRSRRKKRTKESDFLDKE 122
            R        F   A     +           +   V+  + + S  +K+ KES      
Sbjct: 371 YRKMFDRLSVFPPSAHIPTILLSLIWFDVIKSDVMVVVNKLHKYSLVEKQPKES------ 424

Query: 123 NGELDYNLVKYKILCKERESQE---RIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGL 179
              +    +  ++  K          I+  Y      I   +    L             
Sbjct: 425 --TISIPSIYLELKVKLENEYALHRSIVDHYN-----IPKTFDSDDLIP----------- 466

Query: 180 LRGAKRFNPERGYKLSTYVYWWIKQAIIRAIANKSRTIRLPG---SMAGMVAKIAEANNV 236
                            Y Y  I                  G          ++     V
Sbjct: 467 -------PYLDQ-----YFYSHI------------------GHHLKNIEHPERMTLFRMV 496

Query: 237 LSRRLRRMPTDSEIAEMLNIHVSTVRLAIERTRHPISLDGAVTDRGCMTMQDI------I 290
                            L+     +   I       +  G++ +    T+Q +      I
Sbjct: 497 F----------------LDFRF--LEQKIRHDSTAWNASGSILN----TLQQLKFYKPYI 534

Query: 291 PGPDETMPERMVQKQLMKQELKELLQTLSE-----READILRL 328
              ++   ER+V        + + L  + E     +  D+LR+
Sbjct: 535 C-DNDPKYERLV------NAILDFLPKIEENLICSKYTDLLRI 570

>3mzy_A RNA polymerase sigma-H factor; PSI, MCSG, structural genomics, midwest center for structura genomics, protein structure initiative; 2.50A {Fusobacterium nucleatum subsp} Length = 164

 Score = 56.4 bits (136), Expect = 7e-10
 Identities = 29/191 (15%), Positives = 67/191 (35%), Gaps = 49/191 (25%)

Query: 165 GLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYWWIKQAIIRAIANKSRTIRLPGSMA 224
           G   +DL+QEG +GLL+  K ++  +    S++ +  I++ +I AI   +    +  + A
Sbjct: 1   GAEKEDLVQEGILGLLKAIKFYDETKS-SFSSFAFLCIRREMISAIRKANTQKHMVLNEA 59

Query: 225 GMVAKIAEANNVLSRRLRRMPTDSEIAEMLNIHVSTVRLAIERTRHPISLDGAVTDRGCM 284
                              + T++ + +          +                     
Sbjct: 60  -------------------LKTNAILEDSAYFDDEGHNI--------------------- 79

Query: 285 TMQDIIPGPDETMPERMVQKQLMKQELKELLQTLSEREADILRLHFGLDGQTPVSCKEIG 344
              +     +    E  + K+ +++  K      S+ E ++L     + G +    +EI 
Sbjct: 80  ---NNYKSSESNPEEAYLLKEEIEEFKKFSENNFSKFEKEVLTYL--IRGYSY---REIA 131

Query: 345 RLLSLSRERIR 355
            +LS + + I 
Sbjct: 132 TILSKNLKSID 142

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	379
2a6h_F	423	RNA polymerase sigma factor RPOD; RNA polymerase h	100.0
1l9z_H	438	Sigma factor SIGA; helix-turn-helix, coiled-coil,	100.0
3iyd_F	613	RNA polymerase sigma factor RPOD; transcription, i	100.0
1rp3_A	239	RNA polymerase sigma factor sigma-28 (FLIA); trans	100.0
1l0o_C	243	Sigma factor; bergerat fold, helix-turn-helix, pro	99.97
2q1z_A	184	RPOE, ECF SIGE; ECF sigma factor, cupin fold, zinc	99.94
1or7_A	194	Sigma-24, RNA polymerase sigma-E factor; regulatio	99.94
3ugo_A	245	RNA polymerase sigma factor; protein-DNA complex,	99.9
3mzy_A	164	RNA polymerase sigma-H factor; PSI, MCSG, structur	99.89
2lfw_A	157	PHYR sigma-like domain; signal transduction, respo	99.82
3n0r_A	286	Response regulator; sigma factor, receiver, two-co	99.75
1sig_A	339	Sigma70, RNA polymerase primary sigma factor; RNA	99.73
3t72_q	99	RNA polymerase sigma factor RPOD, DNA-directed RN	99.56
2o7g_A	112	Probable RNA polymerase sigma-C factor; sigma fact	99.42
3hug_A	92	RNA polymerase sigma factor; ECF sigma factor, zin	99.4
1tty_A	87	Sigma-A, RNA polymerase sigma factor RPOD; helix-t	99.37
2p7v_B	68	Sigma-70, RNA polymerase sigma factor RPOD; RSD, r	99.36
1h3l_A	87	RNA polymerase sigma factor; transcription, DNA-bi	99.34
1ku3_A	73	Sigma factor SIGA; helix-turn-helix, transcription	99.34
3clo_A	258	Transcriptional regulator; NP_811094.1, bacterial	99.15
2o8x_A	70	Probable RNA polymerase sigma-C factor; promoter r	99.12
1xsv_A	113	Hypothetical UPF0122 protein SAV1236; helix-turn-h	99.01
1s7o_A	113	Hypothetical UPF0122 protein SPY1201/SPYM3_0842/SP	98.89
2rnj_A	91	Response regulator protein VRAR; HTH LUXR-type dom	98.74
3c57_A	95	Two component transcriptional regulatory protein;	98.72
1x3u_A	79	Transcriptional regulatory protein FIXJ; helix-tur	98.68
1jhg_A	101	Trp operon repressor; complex (regulatory protein-	98.65
1je8_A	82	Nitrate/nitrite response regulator protein NARL; p	98.63
1fse_A	74	GERE; helix-turn-helix DNA-binding protein transcr	98.4
3ulq_B	90	Transcriptional regulatory protein COMA; tetratric	98.3
1p4w_A	99	RCSB; solution structure, DNA binding domain, DNA	98.22
2jpc_A	61	SSRB; DNA binding protein, structural genomics, PS	98.19
2q0o_A	236	Probable transcriptional activator protein TRAR; h	97.77
1l3l_A	234	Transcriptional activator protein TRAR; helix-turn	97.76
3szt_A	237	QCSR, quorum-sensing control repressor; quorum sen	97.65
3qp6_A	265	CVIR transcriptional regulator; quorum sensing, ag	97.54
2w7n_A	101	TRFB transcriptional repressor protein; INCP, plas	97.42
1tc3_C	51	Protein (TC3 transposase); DNA binding, helix-turn	97.35
2x48_A	55	CAG38821; archeal virus, viral protein; 2.60A {Sul	97.05
1yio_A	208	Response regulatory protein; transcription regulat	97.0
1a04_A	215	Nitrate/nitrite response regulator protein NARL; s	96.86
3c3w_A	225	Two component transcriptional regulatory protein;	96.69
3klo_A	225	Transcriptional regulator VPST; REC domain, HTH do	96.28
3p7n_A	258	Sensor histidine kinase; LOV domain, light-activat	95.83
3kor_A	119	Possible Trp repressor; putative DNA-binding Trp r	95.51
1p2f_A	220	Response regulator; DRRB, OMPR/PHOB, transcription	95.21
1jko_C	52	HIN recombinase, DNA-invertase HIN; water-mediated	95.15
2gwr_A	238	DNA-binding response regulator MTRA; two-component	95.07
2oqr_A	230	Sensory transduction protein REGX3; response regul	94.94
1kgs_A	225	DRRD, DNA binding response regulator D; DNA-bindin	94.65
1qgp_A	77	Protein (double stranded RNA adenosine deaminase);	94.54
1ys7_A	233	Transcriptional regulatory protein PRRA; response	94.33
1zx4_A	192	P1 PARB, plasmid partition PAR B protein, PARB; tr	93.74
3q9s_A	249	DNA-binding response regulator; DNA binding protei	93.55
1qbj_A	81	Protein (double-stranded RNA specific adenosine D	93.54
2hqr_A	223	Putative transcriptional regulator; phosporylation	93.49
1u78_A	141	TC3 transposase, transposable element TC3 transpos	93.43
3r0a_A	123	Putative transcriptional regulator; structural gen	93.37
3ugo_A	245	RNA polymerase sigma factor; protein-DNA complex,	93.27
1pdn_C	128	Protein (PRD paired); protein-DNA complex, double	93.2
3r0j_A	250	Possible two component system response transcript	92.85
2dbb_A	151	Putative HTH-type transcriptional regulator PH006;	92.5
1oyi_A	82	Double-stranded RNA-binding protein; (alpha+beta)	92.44
1k78_A	149	Paired box protein PAX5; paired domain, ETS domain	92.17
2elh_A	87	CG11849-PA, LD40883P; structural genomics, NPPSFA,	92.03
1sfx_A	109	Conserved hypothetical protein AF2008; structural	91.91
2cfx_A	144	HTH-type transcriptional regulator LRPC; transcrip	91.86
2o3f_A	111	Putative HTH-type transcriptional regulator YBBH;	91.7
2cyy_A	151	Putative HTH-type transcriptional regulator PH151;	91.61
2d1h_A	109	ST1889, 109AA long hypothetical transcriptional re	91.52
2cg4_A	152	Regulatory protein ASNC; DNA binding, FFRP, LRP fa	91.3
2jn6_A	97	Protein CGL2762, transposase; GFT PSI-2, protein s	91.29
3k2z_A	196	LEXA repressor; winged helix-turn-helix, SOS syste	91.17
3ech_A	142	MEXR, multidrug resistance operon repressor; winge	91.1
2w48_A	315	Sorbitol operon regulator; SORC, activator, repres	91.02
2heo_A	67	Z-DNA binding protein 1; protein DLM1-Z-DNA comple	90.95
2w25_A	150	Probable transcriptional regulatory protein; trans	90.95
2glo_A	59	Brinker CG9653-PA; protein-DNA complex, helix-turn	90.91
3eco_A	139	MEPR; mutlidrug efflux pump regulator winged helix	90.85
3bro_A	141	Transcriptional regulator; helix_TURN_helix, multi	90.79
2p5v_A	162	Transcriptional regulator, LRP/ASNC family; NMB057	90.75
1i1g_A	141	Transcriptional regulator LRPA; helix-turn-helix,	90.71
1ku9_A	152	Hypothetical protein MJ223; putative transcription	90.64
3nqo_A	189	MARR-family transcriptional regulator; structural	90.55
2pn6_A	150	ST1022, 150AA long hypothetical transcriptional re	90.39
3frw_A	107	Putative Trp repressor protein; structural genomic	90.38
4hbl_A	149	Transcriptional regulator, MARR family; HTH, trans	90.3
1y0u_A	96	Arsenical resistance operon repressor, putative; s	90.24
3bpv_A	138	Transcriptional regulator; MARR, DNA binding, tran	90.21
3i4p_A	162	Transcriptional regulator, ASNC family; PSI, struc	90.09
1r1u_A	106	CZRA, repressor protein; zinc, DNA binding, transc	90.05
3iwf_A	107	Transcription regulator RPIR family; transcription	89.96
2e1c_A	171	Putative HTH-type transcriptional regulator PH151;	89.92
3bdd_A	142	Regulatory protein MARR; putative multiple antibio	89.79
2nnn_A	140	Probable transcriptional regulator; structural gen	89.77
2dk5_A	91	DNA-directed RNA polymerase III 39 kDa polypeptide	89.72
3tgn_A	146	ADC operon repressor ADCR; helix-turn-helix, trans	89.57
3cdh_A	155	Transcriptional regulator, MARR family; helix-turn	89.49
4b8x_A	147	SCO5413, possible MARR-transcriptional regulator;	89.46
1uxc_A	65	FRUR (1-57), fructose repressor; DNA-binding prote	89.44
1jgs_A	138	Multiple antibiotic resistance protein MARR; trans	89.43
3hsr_A	140	HTH-type transcriptional regulator SARZ; helix-tur	89.4
2ia0_A	171	Putative HTH-type transcriptional regulator PF086;	89.26
2fa5_A	162	Transcriptional regulator MARR/EMRR family; multip	89.23
2rdp_A	150	Putative transcriptional regulator MARR; PFAM PF01	89.11
1p6r_A	82	Penicillinase repressor; transcription regulation,	89.06
3g3z_A	145	NMB1585, transcriptional regulator, MARR family; t	89.05
2qww_A	154	Transcriptional regulator, MARR family; YP_013417.	89.05
3bj6_A	152	Transcriptional regulator, MARR family; helix-turn	88.81
3nrv_A	148	Putative transcriptional regulator (MARR/EMRR FAM;	88.78
2p5k_A	64	Arginine repressor; DNA-binding domain, winged hel	88.75
2htj_A	81	P fimbrial regulatory protein KS71A; winged helix-	88.74
2gxg_A	146	146AA long hypothetical transcriptional regulator;	88.72
2x4h_A	139	Hypothetical protein SSO2273; transcription; 2.30A	88.7
1jhf_A	202	LEXA repressor; LEXA SOS repressor, hydrolase; 1.8	88.66
2k27_A	159	Paired box protein PAX-8; paired domain, solution	88.65
2pex_A	153	Transcriptional regulator OHRR; transcription regu	88.63
3oop_A	143	LIN2960 protein; protein structure initiative, PSI	88.52
2lkp_A	119	Transcriptional regulator, ARSR family; symmetric	88.51
3jth_A	98	Transcription activator HLYU; transcription factor	88.39
1sfu_A	75	34L protein; protein/Z-DNA complex, DNA binding pr	88.25
3k0l_A	162	Repressor protein; helix-turn-helix, structural ge	87.99
3s2w_A	159	Transcriptional regulator, MARR family; structural	87.96
2nyx_A	168	Probable transcriptional regulatory protein, RV14;	87.92
1s3j_A	155	YUSO protein; structural genomics, MARR transcript	87.76
3pqk_A	102	Biofilm growth-associated repressor; helix-turn-he	87.67
3cuo_A	99	Uncharacterized HTH-type transcriptional regulato;	87.66
3fm5_A	150	Transcriptional regulator; MCSG, PF04017, PSI, MAR	87.6
2fbh_A	146	Transcriptional regulator PA3341; MARR, transcript	87.44
1lj9_A	144	Transcriptional regulator SLYA; HTH DNA binding pr	87.42
3cjn_A	162	Transcriptional regulator, MARR family; silicibact	87.28
2a61_A	145	Transcriptional regulator TM0710; APC4350, MCSG, m	87.26
2zkz_A	99	Transcriptional repressor PAGR; protein-DNA, HTH m	87.14
2l0k_A	93	Stage III sporulation protein D; SPOIIID, solution	86.88
2fbi_A	142	Probable transcriptional regulator; MARR, APC5816,	86.73
3f3x_A	144	Transcriptional regulator, MARR family, putative;	86.59
3sqn_A	485	Conserved domain protein; structural genomics, PSI	86.54
3bja_A	139	Transcriptional regulator, MARR family, putative;	86.53
3kp7_A	151	Transcriptional regulator TCAR; multiple drug resi	86.48
3e6m_A	161	MARR family transcriptional regulator; APC88769, s	86.48
2eth_A	154	Transcriptional regulator, putative, MAR family; M	86.4
2oqg_A	114	Possible transcriptional regulator, ARSR family P;	86.35
2fu4_A	83	Ferric uptake regulation protein; DNA binding doma	85.97
3o9x_A	133	Uncharacterized HTH-type transcriptional regulato;	85.87
2qvo_A	95	Uncharacterized protein AF_1382; PSI, structural g	85.82
1q1h_A	110	TFE, transcription factor E, TFE; TFIIE, transcrip	85.63
1uly_A	192	Hypothetical protein PH1932; helix-turn-helix, str	85.36
3hyi_A	295	Protein DUF199/WHIA; laglidadg, homing endonucleas	85.24
2jt1_A	77	PEFI protein; solution structure, winged helix-tur	85.18
2kko_A	108	Possible transcriptional regulatory protein (possi	85.13
2bv6_A	142	MGRA, HTH-type transcriptional regulator MGRA; mul	85.11
1tbx_A	99	ORF F-93, hypothetical 11.0 kDa protein; sulfolobu	85.09
4aik_A	151	Transcriptional regulator SLYA; transcription, tra	85.07
2frh_A	127	SARA, staphylococcal accessory regulator A; winged	85.03
3deu_A	166	Transcriptional regulator SLYA; MARR, WING-helix,	84.93
4fx0_A	148	Probable transcriptional repressor protein; helix-	84.93
1u2w_A	122	CADC repressor, cadmium efflux system accessory pr	84.84
1xmk_A	79	Double-stranded RNA-specific adenosine deaminase;	84.77
2xi8_A	66	Putative transcription regulator; HTH DNA-binding	84.62
1okr_A	123	MECI, methicillin resistance regulatory protein ME	84.55
3u2r_A	168	Regulatory protein MARR; structural genomics, PSI-	84.54
3kz3_A	80	Repressor protein CI; five helix bundle, DNA-bindi	84.48
1ub9_A	100	Hypothetical protein PH1061; helix-turn-helix moti	84.32
1r1t_A	122	Transcriptional repressor SMTB; zinc, transcriptio	84.3
2fxa_A	207	Protease production regulatory protein HPR; protea	83.93
1z91_A	147	Organic hydroperoxide resistance transcriptional;	83.83
1u78_A	141	TC3 transposase, transposable element TC3 transpos	83.73
3omt_A	73	Uncharacterized protein; structural genomics, PSI-	83.58
2wte_A	244	CSA3; antiviral protein, viral resistance, winged	83.38
1r69_A	69	Repressor protein CI; gene regulating protein; 2.0	83.37
1hlv_A	131	CENP-B, major centromere autoantigen B; helix-turn	83.3
1zug_A	71	Phage 434 CRO protein; gene regulating protein, tr	83.09
3boq_A	160	Transcriptional regulator, MARR family; MARR famil	83.06
2r1j_L	68	Repressor protein C2; protein-DNA complex, helix-t	82.97
3fmy_A	73	HTH-type transcriptional regulator MQSA (YGIT/B302	82.89
1gdt_A	183	GD resolvase, protein (gamma delta resolvase); pro	82.83
2r0q_C	209	Putative transposon TN552 DNA-invertase BIN3; site	82.82
2a6c_A	83	Helix-turn-helix motif; putative transcriptional r	82.75
2k9q_A	77	Uncharacterized protein; all helix, helix-turn-hel	82.72
3qq6_A	78	HTH-type transcriptional regulator SINR; helix-tur	82.63
2g9w_A	138	Conserved hypothetical protein; DNA-binding domain	82.46
2o0m_A	345	Transcriptional regulator, SORC family; structural	82.26
2l8n_A	67	Transcriptional repressor CYTR; bacterial gene rep	82.15
1sd4_A	126	Penicillinase repressor; BLAI, MECI, methicillin,	82.04
2fbk_A	181	Transcriptional regulator, MARR family; winged-hel	82.02
3jw4_A	148	Transcriptional regulator, MARR/EMRR family; DNA-b	82.01
1on2_A	142	Transcriptional regulator MNTR; helix-turn-helix,	81.95
2hr3_A	147	Probable transcriptional regulator; MCSG, structur	81.35
3f6w_A	83	XRE-family like protein; helix-turn-helix, DNA bin	81.34
1neq_A	74	DNA-binding protein NER; NMR {Enterobacteria phage	81.3
3t76_A	88	VANU, transcriptional regulator vanug; structural	81.27
2hin_A	71	GP39, repressor protein; transcription factor, dim	81.21
1adr_A	76	P22 C2 repressor; transcription regulation; NMR {E	81.16
2b5a_A	77	C.BCLI; helix-turn-helix motif, gene regulation; 1	81.15
1y7y_A	74	C.AHDI; helix-turn-helix, DNA-binding protein, tra	81.12
2da4_A	80	Hypothetical protein DKFZP686K21156; homeobox doma	80.82
1z4h_A	66	TORI, TOR inhibition protein; winged helix, revers	80.75
2cw1_A	65	SN4M; lambda CRO fold, de novo protein; NMR {Synth	80.67
2wiu_B	88	HTH-type transcriptional regulator HIPB; transfera	80.6
3bs3_A	76	Putative DNA-binding protein; XRE-family, structur	80.5
3bd1_A	79	CRO protein; transcription factor, helix-turn-heli	80.46
3eus_A	86	DNA-binding protein; structural genomics, PSI2,MCS	80.37
2ao9_A	155	Phage protein; structural genomics, nine-fold NCS.	80.35
1r71_A	178	Transcriptional repressor protein KORB; INCP, plas	80.29
2jsc_A	118	Transcriptional regulator RV1994C/MT2050; cadmium,	80.26
3b7h_A	78	Prophage LP1 protein 11; structural genomics, PSI2	80.16

>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=8e-42  Score=343.14  Aligned_cols=251  Identities=36%  Similarity=0.558  Sum_probs=230.0

Q ss_pred             cHHHHHHHHhcccHHHHHHHHHHhHHHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHhccCCCCCCCchhHHHHHHHHHH
Q 046578          127 DYNLVKYKILCKERESQERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYWWIKQAI  206 (379)
Q Consensus       127 ~~~eLi~~~~~Gd~~A~e~Li~~y~~lV~~ia~r~~~~~~d~eDLvQEg~i~L~~ai~~fD~~~g~~FsTYa~~~Ir~~i  206 (379)
                      +..+|+.+++. |..|++.||..|.++|+++|++|.+++.+++||+||||+|||+++++|||.+|++|+||++|||++.|
T Consensus       169 ~~~~L~~~~~~-d~~A~~~Li~~~lrlV~~iA~~y~~~~~~~eDLiQEg~igL~kav~kFd~~~g~~FstYa~~wIr~~i  247 (423)
T 2a6h_F          169 EHKRYLHIARE-GEAARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQEGNQGLIRAVEKFEYKRRFKFSTYATWWIRQAI  247 (423)
T ss_dssp             HHHHHHHHHHH-HHHHHHHHHHHTHHHHHHHHTTTCTTTSCHHHHHHHHHHHHHHHHHHCCTTSCCCHHHHHHHHHHHHH
T ss_pred             cHHHHHHHHhc-CHHHHHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHhcCcccCCCHHHHHHHHHHHHH
Confidence            34677777775 59999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHhhcCcccCCcchHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhC--CCHHHHHHHHHhcCCccccCCccccCCCC
Q 046578          207 IRAIANKSRTIRLPGSMAGMVAKIAEANNVLSRRLRRMPTDSEIAEMLN--IHVSTVRLAIERTRHPISLDGAVTDRGCM  284 (379)
Q Consensus       207 ~~~lr~~~r~irip~~~~~~~~ki~~a~~~l~~~lgr~pt~~eia~~Lg--is~~~~~~~l~~~~~~iSLd~~~~~~~~~  284 (379)
                      .++++++.+.+++|.|+...++++.++.+.+.+.+|+.|+.++||+.+|  ++++++..++......+|++.+++++++.
T Consensus       248 ~~~i~~~~r~ir~p~~~~~~~~~lrr~~~~l~~~~~r~p~~~eiA~~l~~~~~~~~v~~~~~~~~~~~Sld~~~~~~~~~  327 (423)
T 2a6h_F          248 NRAIADQARTIRIPVHMVETINKLSRTARQLQQELGREPTYEEIAEAMGPGWDAKRVEETLKIAQEPVSLETPIGDEKDS  327 (423)
T ss_dssp             HHHHHHHSSSSCCCHHHHHHHHHHHHHHHHHHHHHSSCCCHHHHHHHHCTTCCHHHHHHHHHHHSCCEESSCBCSSSSSC
T ss_pred             HHHHHHccceeeccHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCCCHHHHHHHHHhccCCcccccccCCCCcc
Confidence            9999999999999999999999999999999999999999999999999  99999999998888999999998777666


Q ss_pred             cccccCCCCCCCChHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHH
Q 046578          285 TMQDIIPGPDETMPERMVQKQLMKQELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTK  364 (379)
Q Consensus       285 ~l~d~i~~~~~~~pe~~~~~~e~~~~L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~k  364 (379)
                      .+.+.+++....+|++.+...+....|..+|..||++||.||.++|||+|++++|++|||+.||||+++|+++++||++|
T Consensus       328 ~l~d~l~d~~~~~pe~~~~~~~~~~~L~~aL~~L~~rer~Vl~lr~~L~~~e~~Tl~EIA~~lgiS~erVrqi~~rAl~k  407 (423)
T 2a6h_F          328 FYGDFIPDEHLPSPVDAATQSLLSEELEKALSKLSEREAMVLKLRKGLIDGREHTLEEVGAFFGVTRERIRQIENKALRK  407 (423)
T ss_dssp             BGGGSSCCSSSCCHHHHHHHHHHHHHHHHHHHSSCHHHHHHHHHHHHTTCC-----CHHHHSSSSCHHHHHHHHHHHHHH
T ss_pred             chhhhhccccCCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHhccCCCCCCCHHHHHHHHCcCHHHHHHHHHHHHHH
Confidence            78888887666788988888888889999999999999999999999988789999999999999999999999999999


Q ss_pred             HH-hHHhhchhhhhc
Q 046578          365 LQ-QTNILNNLKVYM  378 (379)
Q Consensus       365 LR-~~l~~~~L~~y~  378 (379)
                      || ..+....|++|+
T Consensus       408 LR~~~~~~~~l~~~l  422 (423)
T 2a6h_F          408 LKYHESRTRKLRDFL  422 (423)
T ss_dssp             HHHHHHHTTSSSSCC
T ss_pred             HHhhhhhhHHHHHhh
Confidence            99 888888899987

>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=9.8e-42  Score=341.67  Aligned_cols=251  Identities=35%  Similarity=0.566  Sum_probs=232.5

Q ss_pred             cHHHHHHHHhcccHHHHHHHHHHhHHHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHhccCCCCCCCchhHHHHHHHHHH
Q 046578          127 DYNLVKYKILCKERESQERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYWWIKQAI  206 (379)
Q Consensus       127 ~~~eLi~~~~~Gd~~A~e~Li~~y~~lV~~ia~r~~~~~~d~eDLvQEg~i~L~~ai~~fD~~~g~~FsTYa~~~Ir~~i  206 (379)
                      +..+|+..+ .||..|++.||..|.++|+++|++|.+++.+++||+||||+|||+++++||+++|++|+||++|||++.|
T Consensus       184 ~~~eLi~~~-~~d~~A~~~Li~~nlrlVv~iA~ry~~~g~~aeDLIQEg~IgL~kAvekFDp~kG~rFsTYA~~wIR~~I  262 (438)
T 1l9z_H          184 ELKRYLHIA-REGEAARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQEGNQGLIRAVEKFEYKRRFKFSTYATWWIRQAI  262 (438)
T ss_pred             hHHHHHHHH-hcCHHHHHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHhcCcccCCChHHHHHHHHHHHH
Confidence            346667666 4679999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHhhcCcccCCcchHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhC--CCHHHHHHHHHhcCCccccCCccccCCCC
Q 046578          207 IRAIANKSRTIRLPGSMAGMVAKIAEANNVLSRRLRRMPTDSEIAEMLN--IHVSTVRLAIERTRHPISLDGAVTDRGCM  284 (379)
Q Consensus       207 ~~~lr~~~r~irip~~~~~~~~ki~~a~~~l~~~lgr~pt~~eia~~Lg--is~~~~~~~l~~~~~~iSLd~~~~~~~~~  284 (379)
                      .++++++.+.+++|.|+...++++.++.+.+.+.+|+.|+.++||+.+|  ++.+++..++......+|+|.+++++++.
T Consensus       263 ~~~i~~~~R~irlp~~~~~~l~~lrr~~r~l~~~lgr~pt~eeiA~~l~~~v~~e~V~~~~~~~~~~~SLd~~~~~d~d~  342 (438)
T 1l9z_H          263 NRAIADQARTIRIPVHMVETINKLSRTARQLQQELGREPSYEEIAEAMGPGWDAKRVEETLKIAQEPVSLETPIGDEKDS  342 (438)
T ss_pred             HHHHHHhcchhccchHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCCCHHHHHHHHHhcccccccccccccccch
Confidence            9999999999999999999999999999999999999999999999999  99999999988888899999988776665


Q ss_pred             cccccCCCCCCCChHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHH
Q 046578          285 TMQDIIPGPDETMPERMVQKQLMKQELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTK  364 (379)
Q Consensus       285 ~l~d~i~~~~~~~pe~~~~~~e~~~~L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~k  364 (379)
                      .+.+.+++....+|++.+...+....|..+|+.||++||.||.++|||+|++++|++|||+.||||+++|+++++||++|
T Consensus       343 ~l~d~l~d~~~~~pee~~~~~~~~~~L~~aL~~L~ereR~VI~LRygL~~~e~~TleEIAe~LgIS~erVRqi~~RAlkK  422 (438)
T 1l9z_H          343 FYGDFIPDENLPSPVEAAAQSLLSEELEKALSKLSEREAMVLKLRKGLIDGREHTLEEVGAYFGVTRERIRQIENKALRK  422 (438)
T ss_pred             hhhhhhcccccCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHhccCCCCCCHHHHHHHHCcCHHHHHHHHHHHHHH
Confidence            67777776655678888888888889999999999999999999999887789999999999999999999999999999


Q ss_pred             HH-hHHhhchhhhhc
Q 046578          365 LQ-QTNILNNLKVYM  378 (379)
Q Consensus       365 LR-~~l~~~~L~~y~  378 (379)
                      || ..+....|++|+
T Consensus       423 LR~~~~~~~~l~~yl  437 (438)
T 1l9z_H          423 LKYHESRTRKLRDFL  437 (438)
T ss_pred             HHHhHhhHHHHHHhh
Confidence            99 888888899997

>3iyd_F RNA polymerase sigma factor RPOD; transcription, initiation, class I, activator, RNA polymeras holoenzyme, sigma70, open complex, CAP, CRP; HET: DNA CMP; 19.80A {Escherichia coli k-12}

Probab=100.00  E-value=3.5e-43  Score=368.38  Aligned_cols=331  Identities=27%  Similarity=0.403  Sum_probs=282.3

Q ss_pred             hhhhhhhhhhhhhhhhhHHHhhHHH---HHHH---HHhhh-hhcCCcccccchhHHHHHHHHHHHHHhhhcccccccchh
Q 046578           48 VTNEALALHPVIESATDAAALASAA---VRTA---KDAVS-FANGAEEVCFDDGECESVLKMMRRRSRRKKRTKESDFLD  120 (379)
Q Consensus        48 ~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~---~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  120 (379)
                      +......|+++.+.-...|.--.+.   |...   -..++ ...|+|+-+|...+.+.+.+..|..+..+..+++.....
T Consensus       252 l~~~~~~lkL~~k~id~Lv~~lr~~~~~ir~~Er~i~~l~v~~~~mpr~~Fi~~f~g~e~~~~w~~~~~~~~~~~~~~l~  331 (613)
T 3iyd_F          252 LSEVFKQFRLVPKQFDYLVNSMRVMMDRVRTQERLIMKLCVEQCKMPKKNFITLFTGNETSDTWFNAAIAMNKPWSEKLH  331 (613)
T ss_dssp             HHHHHTTSCBCHHHHHHHTHHHHTTTHHHHHHHHHHHHTTTTTTTCCGGGTTTTTTTCCSSTTTTHHHHTTCCTTGGGGG
T ss_pred             HHHHHHHcCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCHHHHHHHcccccCCHHHHHHHHHhhccHHHHHH
Confidence            4445555666555544333332222   2222   22333 447999999999999998888886665555555543321


Q ss_pred             h-------------------hcCcCcHHHHHHHHhcccHHH---HHHHHHHhHHHHHHHHHhccCCCCCHHHHHHHHHHH
Q 046578          121 K-------------------ENGELDYNLVKYKILCKERES---QERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIG  178 (379)
Q Consensus       121 ~-------------------~~~~~~~~eLi~~~~~Gd~~A---~e~Li~~y~~lV~~ia~r~~~~~~d~eDLvQEg~i~  178 (379)
                      .                   .....+..+|+.++++||..|   ++.||+.|.++|+++|++|.+++.+++||+||||++
T Consensus       332 ~~~~~I~~~q~kL~~ie~~~~~~~~~~~~Li~~~~~Gd~~A~~A~~~L~~~y~~~v~~ia~r~~~~~~~aeDlvQE~fi~  411 (613)
T 3iyd_F          332 DVSEEVHRALQKLQQIEEETGLTIEQVKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIG  411 (613)
T ss_dssp             GTHHHHHHHHHHHHHHHHHHTSCTTTHHHHHHTHHHHHHHHHHHHTTTTTTTTHHHHHGGGSSSTTSSCSTTTTHHHHHH
T ss_pred             HhHHHHHHHHHHHHHHHHHhCCChHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHH
Confidence            1                   111224678999999999998   999999999999999999999999999999999999


Q ss_pred             HHHHHhccCCCCCCCchhHHHHHHHHHHHHHHHhhcCcccCCcchHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCH
Q 046578          179 LLRGAKRFNPERGYKLSTYVYWWIKQAIIRAIANKSRTIRLPGSMAGMVAKIAEANNVLSRRLRRMPTDSEIAEMLNIHV  258 (379)
Q Consensus       179 L~~ai~~fD~~~g~~FsTYa~~~Ir~~i~~~lr~~~r~irip~~~~~~~~ki~~a~~~l~~~lgr~pt~~eia~~Lgis~  258 (379)
                      ||+++++|++.+|.+|+||+++|++|.+.++++++.+.+++|.|+...++++.++...+.+.+|++|+++|||+.+|++.
T Consensus       412 l~~a~~~fd~~~g~~Fstyl~~~irn~i~~~lr~~~r~~rip~~~~~~~~k~~r~~~~l~~~~gr~pt~eela~~l~~~~  491 (613)
T 3iyd_F          412 LMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELAERMLMPE  491 (613)
T ss_dssp             HHHHTTSCCTTSSSCSTTTHHHHHHHHHHHHTTTSCSSSCCCSHHHHTTTTTTTTTTTTTTTTCSCCCTTTTTTTSSCCS
T ss_pred             HHHHHHHcCccccCcHHHHHHHHHHHHHHHHHHhcCcceeCcHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHhcCCccccCCccccCCCCcccccCCCCCCCChHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCC
Q 046578          259 STVRLAIERTRHPISLDGAVTDRGCMTMQDIIPGPDETMPERMVQKQLMKQELKELLQTLSEREADILRLHFGLDGQTPV  338 (379)
Q Consensus       259 ~~~~~~l~~~~~~iSLd~~~~~~~~~~l~d~i~~~~~~~pe~~~~~~e~~~~L~~~L~~L~~rer~Vl~l~ygL~g~e~~  338 (379)
                      ++++.++.....++|++.+++++++..+.+++.+....+|++.+...++...|..+|..||+++|.||.|+||+++.+++
T Consensus       492 ~~v~~~~~~~~~~~sld~~~~~~~~~~l~d~i~d~~~~~p~~~~~~~e~~~~l~~aL~~Lp~~er~Vl~Lr~~~~~~e~~  571 (613)
T 3iyd_F          492 DKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATTESLRAATHDVLAGLTAREAKVLRMRFGIDMNTDH  571 (613)
T ss_dssp             SHHHHHHHHSCCCCCSSCCCSSSSSCCGGGSCCCSSSCCHHHHHHHHTTSSSHHHHTTSSCHHHHHHHHHHHTSSSCCCC
T ss_pred             HHHHHHHHhccCCcccCCCCCCCCCccHHHHhcCCCCCCHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHhccCCCCCc
Confidence            99999999999999999999877777788888887777899988888888889999999999999999999988766899


Q ss_pred             CHHHHHHHhCCCHHHHHHHHHHHHHHHHhHHhhchhhhhc
Q 046578          339 SCKEIGRLLSLSRERIRQIRGIALTKLQQTNILNNLKVYM  378 (379)
Q Consensus       339 S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~~l~~~~L~~y~  378 (379)
                      |++|||+.||||++||+++++||+++||+++....|+.|+
T Consensus       572 s~~EIA~~lgis~~tVk~~~~rAl~kLR~~~~~~~l~~~l  611 (613)
T 3iyd_F          572 TLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRSFL  611 (613)
T ss_dssp             STTGGGTTTSSCSSHHHHHHHHHHTTTTSCSSSCSSTTCC
T ss_pred             CHHHHHHHhCCCHHHHHHHHHHHHHHhhCcchhhHHHHHh
Confidence            9999999999999999999999999999999999998886

>1rp3_A RNA polymerase sigma factor sigma-28 (FLIA); transcription; 2.30A {Aquifex aeolicus} SCOP: a.4.13.1 a.4.13.2 a.177.1.1 PDB: 1sc5_A

Probab=100.00  E-value=3.3e-32  Score=250.49  Aligned_cols=223  Identities=26%  Similarity=0.352  Sum_probs=190.6

Q ss_pred             cHHHHHHHHHHhHHHHHHHHHhcc---CCCCCHHHHHHHHHHHHHHHHhccCCCCCCCchhHHHHHHHHHHHHHHHhhcC
Q 046578          139 ERESQERIIRSYRSLVVSIATGYQ---GKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYWWIKQAIIRAIANKSR  215 (379)
Q Consensus       139 d~~A~e~Li~~y~~lV~~ia~r~~---~~~~d~eDLvQEg~i~L~~ai~~fD~~~g~~FsTYa~~~Ir~~i~~~lr~~~r  215 (379)
                      +..|++.||..|.++|+++|+++.   ++..++||++||||+++|+++++|++.+|.+|.||++++++|.+.+++|++. 
T Consensus        10 ~~~a~~~l~~~~~~~v~~~a~~~~~~~~~~~~aeDl~Qe~~l~l~~~~~~~~~~~~~~f~~~l~~~~~~~~~d~~r~~~-   88 (239)
T 1rp3_A           10 NQIEREELILKYLPLVKAIATNIKKHLPEDVDIRDLISYGVIGLIKAVDNLSTENPKRAEAYIKLRIKGAIYDYLRSLD-   88 (239)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHTTSCTTSCHHHHHHHHHHHHHHHHHTCCCCCTHHHHHHHHHHHHHHHHHHHHTSS-
T ss_pred             cchHHHHHHHHhHHHHHHHHHHHHHhccCCCCHHHHHHHHHHHHHHHHHHcCcccCCCHHHHHHHHHHHHHHHHHHhcC-
Confidence            445899999999999999999998   6789999999999999999999999998889999999999999999999865 


Q ss_pred             cccCCcchHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhc--CCccccCCccccCCCCcccccCCCC
Q 046578          216 TIRLPGSMAGMVAKIAEANNVLSRRLRRMPTDSEIAEMLNIHVSTVRLAIERT--RHPISLDGAVTDRGCMTMQDIIPGP  293 (379)
Q Consensus       216 ~irip~~~~~~~~ki~~a~~~l~~~lgr~pt~~eia~~Lgis~~~~~~~l~~~--~~~iSLd~~~~~~~~~~l~d~i~~~  293 (379)
                        +.|........++.++...+...+|+.|+.+++++.+|++.+.+..++...  ....+++.+..++++.. .+. ++.
T Consensus        89 --~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~sl~~~~~~~~~~~-~~~-~~~  164 (239)
T 1rp3_A           89 --FGSRQVREKERRIKEVVEKLKEKLGREPTDEEVAKELGISTEELFKTLDKINFSYILSLEEVFRDFARDY-SEL-IPS  164 (239)
T ss_dssp             --TTCHHHHHHHHHHHHHHHHHHHHHSSCCCHHHHHHHHTSCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-TTT-GGG
T ss_pred             --ccchHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHHhccCCCccccccccCCCccc-ccc-cCC
Confidence              577788888999999999999999999999999999999999998776542  23445655433222111 222 222


Q ss_pred             CCCChHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHHhh
Q 046578          294 DETMPERMVQKQLMKQELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQTNIL  371 (379)
Q Consensus       294 ~~~~pe~~~~~~e~~~~L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~~l~~  371 (379)
                       ..+|++.+...+....|..+|..||+++|.||.++|+    +|+|++|||+.||+|.++|+++++||+++||+.+..
T Consensus       165 -~~~~~~~~~~~e~~~~l~~~l~~L~~~~r~vl~l~~~----~g~s~~EIA~~lgis~~~V~~~~~ra~~~Lr~~l~~  237 (239)
T 1rp3_A          165 -STNVEEEVIKRELTEKVKEAVSKLPEREKLVIQLIFY----EELPAKEVAKILETSVSRVSQLKAKALERLREMLSN  237 (239)
T ss_dssp             -SCHHHHHHHHHHHHHHHHHHHTTSCHHHHHHHHHHHT----SCCCHHHHHHHTTSCHHHHHHHHHHHHHHHHHHHHC
T ss_pred             -CCCHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHh----cCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHhc
Confidence             3467777888888889999999999999999999994    779999999999999999999999999999998753

>1l0o_C Sigma factor; bergerat fold, helix-turn-helix, protein binding; HET: ADP; 2.90A {Geobacillus stearothermophilus} SCOP: a.4.13.2

Probab=99.97  E-value=1.2e-32  Score=253.43  Aligned_cols=229  Identities=28%  Similarity=0.370  Sum_probs=52.3

Q ss_pred             CcHHHHHHHHhcccHHHHHHHHHHhHHHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHhccCCCCCCCchhHHHHHHHHH
Q 046578          126 LDYNLVKYKILCKERESQERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYWWIKQA  205 (379)
Q Consensus       126 ~~~~eLi~~~~~Gd~~A~e~Li~~y~~lV~~ia~r~~~~~~d~eDLvQEg~i~L~~ai~~fD~~~g~~FsTYa~~~Ir~~  205 (379)
                      .+..+|+.++++||..|++.||..|.++|+++|+++.++..++||++||||+++|+++++|++.+|.+|.||++++++|.
T Consensus        13 ~~~~~l~~~~~~gd~~a~~~l~~~~~~~v~~~~~~~~~~~~~aeDl~Qe~~l~l~~~~~~~~~~~~~~f~~~l~~i~~~~   92 (243)
T 1l0o_C           13 QEMKELIRRSQEGDQEARDEIIEKNMRLVWSVVQRFLNRGYEADDLFQIGCIGLLKSVDKFDLSYDVKFSTYAVPMIIGE   92 (243)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHhHHHHHHHHHHHhccCCCHHHHHHHHHHHHHHHHHHcCcccCCCHHHHHHHHHHHH
Confidence            44578999999999999999999999999999999999989999999999999999999999988889999999999999


Q ss_pred             HHHHHHhhcCcccCCcchHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCccccCCC--
Q 046578          206 IIRAIANKSRTIRLPGSMAGMVAKIAEANNVLSRRLRRMPTDSEIAEMLNIHVSTVRLAIERTRHPISLDGAVTDRGC--  283 (379)
Q Consensus       206 i~~~lr~~~r~irip~~~~~~~~ki~~a~~~l~~~lgr~pt~~eia~~Lgis~~~~~~~l~~~~~~iSLd~~~~~~~~--  283 (379)
                      +.+++|++. .+++|++......++.++...+....|+.|+.+++++.+|++.+.+...+.......|++.+..++++  
T Consensus        93 ~~d~~r~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~~~~~~  171 (243)
T 1l0o_C           93 IQRFLRDDG-TVKVSRSLKEMGNKIRKAKDELSKTRGRAPTVTEIADHLGISPEDVVLAQEAVRLPTSIHETVYENDGDP  171 (243)
T ss_dssp             -------CC-CCTTHHHHHHHHHHHHHHHHHHHHHHTSCCBHHHHHHHHTSCHHHHHHHHHHHHC---------------
T ss_pred             HHHHHHhcC-CccCcHHHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHHCCCHHHHHHHHHHhccccCccccccccCCcc
Confidence            999999987 78999999999999999999999999999999999999999999988887766567778776543221  


Q ss_pred             CcccccCCCCCCCChHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 046578          284 MTMQDIIPGPDETMPERMVQKQLMKQELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALT  363 (379)
Q Consensus       284 ~~l~d~i~~~~~~~pe~~~~~~e~~~~L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~  363 (379)
                      .++.+.+       |++.+...+....|..+|..||+++|.||.++|+    +|+|++|||+.||+|.++|+++++||++
T Consensus       172 ~~~~~~~-------~~~~~~~~~~~~~l~~~l~~L~~~~r~vl~l~~~----~g~s~~EIA~~lgis~~tV~~~~~ra~~  240 (243)
T 1l0o_C          172 ITLLDQI-------ADADEASWFDKIALKKAIEELDERERLIVYLRYY----KDQTQSEVASRLGISQVQMSRLEKKILQ  240 (243)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             cchhhcc-------CcchhHHHHHHHHHHHHHHhCCHHHHHHHHHHHh----cCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence            1222222       2223334455567899999999999999999984    7799999999999999999999999999


Q ss_pred             HHH
Q 046578          364 KLQ  366 (379)
Q Consensus       364 kLR  366 (379)
                      +||
T Consensus       241 ~Lr  243 (243)
T 1l0o_C          241 HIK  243 (243)
T ss_dssp             ---
T ss_pred             HcC
Confidence            997

>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=99.94  E-value=8.2e-27  Score=208.33  Aligned_cols=181  Identities=13%  Similarity=0.176  Sum_probs=140.7

Q ss_pred             cHHHHHHHHhcccHHHHHHHHHHhHHHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHhccCCCCCCCchhHHHHHHHHHH
Q 046578          127 DYNLVKYKILCKERESQERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYWWIKQAI  206 (379)
Q Consensus       127 ~~~eLi~~~~~Gd~~A~e~Li~~y~~lV~~ia~r~~~~~~d~eDLvQEg~i~L~~ai~~fD~~~g~~FsTYa~~~Ir~~i  206 (379)
                      +..+|+.++++||..|++.||..|.+.|+++|+++.+ ..++||++||+|+++|+++++|++..  .|.+|++.+++|.+
T Consensus         9 ~~~~l~~~~~~gd~~a~~~l~~~~~~~l~~~~~~~~~-~~~aeDl~Qe~~l~~~~~~~~~~~~~--~~~~~l~~i~~n~~   85 (194)
T 1or7_A            9 TDQVLVERVQKGDQKAFNLLVVRYQHKVASLVSRYVP-SGDVPDVVQEAFIKAYRALDSFRGDS--AFYTWLYRIAVNTA   85 (194)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHHTTTSC-GGGHHHHHHHHHHHHHHHGGGCCSSS--CHHHHHHHHHHHHH
T ss_pred             ChHHHHHHHHccCHHHHHHHHHHHHHHHHHHHHHHcC-HHhHHHHHHHHHHHHHHhHHhcCCcc--chHHHHHHHHHHHH
Confidence            4578999999999999999999999999999999999 89999999999999999999999764  69999999999999


Q ss_pred             HHHHHhhcCcccCCcchHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCccccCCCCcc
Q 046578          207 IRAIANKSRTIRLPGSMAGMVAKIAEANNVLSRRLRRMPTDSEIAEMLNIHVSTVRLAIERTRHPISLDGAVTDRGCMTM  286 (379)
Q Consensus       207 ~~~lr~~~r~irip~~~~~~~~ki~~a~~~l~~~lgr~pt~~eia~~Lgis~~~~~~~l~~~~~~iSLd~~~~~~~~~~l  286 (379)
                      .+++|+..+.....                            ++..           .     ....++.      .   
T Consensus        86 ~d~~R~~~~~~~~~----------------------------~~~~-----------~-----~~~~~~~------~---  112 (194)
T 1or7_A           86 KNYLVAQGRRPPSS----------------------------DVDA-----------I-----EAENFES------G---  112 (194)
T ss_dssp             HHHHHHHTTCCTHH----------------------------HHHH-----------H-----HHHSCCS------S---
T ss_pred             HHHHHHHhccCccc----------------------------cccc-----------c-----ccccccc------c---
Confidence            99999876421100                            0000           0     0000000      0   


Q ss_pred             cccCCCCCCCChHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 046578          287 QDIIPGPDETMPERMVQKQLMKQELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQ  366 (379)
Q Consensus       287 ~d~i~~~~~~~pe~~~~~~e~~~~L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR  366 (379)
                       +.+++  ..+|++.+...+....+..++..||+++|.||.++|+    +|+|++|||+.||+|.++|+++++||+++||
T Consensus       113 -~~~~~--~~~~~~~~~~~e~~~~l~~~l~~L~~~~r~vl~l~~~----~g~s~~EIA~~lgis~~tV~~~l~ra~~~Lr  185 (194)
T 1or7_A          113 -GALKE--ISNPENLMLSEELRQIVFRTIESLPEDLRMAITLREL----DGLSYEEIAAIMDCPVGTVRSRIFRAREAID  185 (194)
T ss_dssp             -CC----------CEEEHHHHHHHHHHHHHHSCHHHHHHHHHHHT----TCCCHHHHHHHTTSCHHHHHHHHHHHHHHHH
T ss_pred             -ccccC--CCChHHHHHHHHHHHHHHHHHHhCCHHHHHHhHHHHH----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence             00001  0123333333455567889999999999999999984    7799999999999999999999999999999


Q ss_pred             hHHh
Q 046578          367 QTNI  370 (379)
Q Consensus       367 ~~l~  370 (379)
                      +.+.
T Consensus       186 ~~l~  189 (194)
T 1or7_A          186 NKVQ  189 (194)
T ss_dssp             HHHC
T ss_pred             HHHH
Confidence            9874

>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=99.90  E-value=2.6e-24  Score=201.02  Aligned_cols=144  Identities=40%  Similarity=0.657  Sum_probs=80.7

Q ss_pred             HHHHHhcccHHHHHHHHHHhHHHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHhccCCCCCCCchhHHHHHHHHHHHHHH
Q 046578          131 VKYKILCKERESQERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYWWIKQAIIRAI  210 (379)
Q Consensus       131 Li~~~~~Gd~~A~e~Li~~y~~lV~~ia~r~~~~~~d~eDLvQEg~i~L~~ai~~fD~~~g~~FsTYa~~~Ir~~i~~~l  210 (379)
                      .+.++.+||..|++.||+.|.++|+++|++|.+++.+++||+||||+++|+++++||+++|.+|+||++||+++.+.+++
T Consensus       100 ~L~~~~~~d~~A~~~L~~~y~~lV~~ia~r~~~~~~~aeDLvQegfi~L~~a~~~fd~~~g~~F~tya~~~ir~~i~~~i  179 (245)
T 3ugo_A          100 RYLHIAREGEAARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQEGNQGLIRAVEKFEYKRRFKFSTYATWWIRQAINRAI  179 (245)
T ss_dssp             HHHHHHHHHHHHHHHHHHTTHHHHHHHHGGGTTSSSCHHHHHHHHHHHHHHHHHHCCGGGCCCHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHcCCCCcHHHHHHHHHHHHHHHHHHcCcccCCcHHHHHHHHHHHHHHHHH
Confidence            34556678889999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HhhcCcccCCcchHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhC--CCHHHHHHHHHhcCCcccc
Q 046578          211 ANKSRTIRLPGSMAGMVAKIAEANNVLSRRLRRMPTDSEIAEMLN--IHVSTVRLAIERTRHPISL  274 (379)
Q Consensus       211 r~~~r~irip~~~~~~~~ki~~a~~~l~~~lgr~pt~~eia~~Lg--is~~~~~~~l~~~~~~iSL  274 (379)
                      +++.+.+++|.++...++++.++.+.+...+|+.|+.+|||+.||  ++.+++...+......+||
T Consensus       180 r~~~r~~r~p~~l~e~i~~l~~~~~~L~~~~~~~ps~~EIAe~Lg~~is~~tVk~~l~~ar~~lsl  245 (245)
T 3ugo_A          180 ADQARTIRIPVHMVETINKLSRTARQLQQELGREPSYEEIAEAMGPGWDAKRVEETLKIAQEPVSL  245 (245)
T ss_dssp             HHHTC-------------------------------------------------------------
T ss_pred             HHhcccccccHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHCCCCCHHHHHHHHHHHhhccCC
Confidence            999999999999999999999999999999999999999999999  9999999998887777664

>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=99.89  E-value=6.6e-23  Score=177.24  Aligned_cols=155  Identities=20%  Similarity=0.282  Sum_probs=107.0

Q ss_pred             CCCHHHHHHHHHHHHHHHHhccCCCCCCCchhHHHHHHHHHHHHHHHhhcCcccCCcchHHHHHHHHHHHHHHHHHhCCC
Q 046578          165 GLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYWWIKQAIIRAIANKSRTIRLPGSMAGMVAKIAEANNVLSRRLRRM  244 (379)
Q Consensus       165 ~~d~eDLvQEg~i~L~~ai~~fD~~~g~~FsTYa~~~Ir~~i~~~lr~~~r~irip~~~~~~~~ki~~a~~~l~~~lgr~  244 (379)
                      |.++||++||+|+++|+++.+|++.+ .+|.||++++++|.+.+++|+..+..+.+..                      
T Consensus         1 g~daeDl~Qe~~~~l~~~~~~~~~~~-~~f~~~l~~i~~n~~~d~~r~~~~~~~~~~~----------------------   57 (164)
T 3mzy_A            1 GAEKEDLVQEGILGLLKAIKFYDETK-SSFSSFAFLCIRREMISAIRKANTQKHMVLN----------------------   57 (164)
T ss_dssp             ----CTTHHHHHHHHHHHHHHCCTTT-SCHHHHHHHHHHHHHHHHHHHHHHCC---------------------------
T ss_pred             CCcHHHHHHHHHHHHHHHHHHhCccC-CChHHHhHHHHHHHHHHHHHHhhcccchhhH----------------------
Confidence            46899999999999999999999887 6899999999999999999987532222100                      


Q ss_pred             CCHHHHHHHhCCCHHHHHHHHHhcCCccccCCccccCCCCccc----ccCCCCCCCChHHHHHHHHHHHHHHHHHh-cCC
Q 046578          245 PTDSEIAEMLNIHVSTVRLAIERTRHPISLDGAVTDRGCMTMQ----DIIPGPDETMPERMVQKQLMKQELKELLQ-TLS  319 (379)
Q Consensus       245 pt~~eia~~Lgis~~~~~~~l~~~~~~iSLd~~~~~~~~~~l~----d~i~~~~~~~pe~~~~~~e~~~~L~~~L~-~L~  319 (379)
                                               ..++.+.+..++....+.    +.+. ....+|++.+...+....+..+|. .||
T Consensus        58 -------------------------~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~e~~~~l~~~l~~~L~  111 (164)
T 3mzy_A           58 -------------------------EALKTNAILEDSAYFDDEGHNINNYK-SSESNPEEAYLLKEEIEEFKKFSENNFS  111 (164)
T ss_dssp             ----------------------------------------------------------CHHHHHHHHHHHHHHHHHHHSC
T ss_pred             -------------------------HHhhhhhhhccCCCCCcccchhhhhc-ccCCCHHHHHHHHHHHHHHHHHHHhhCC
Confidence                                     111122111111111111    1111 223456777777788888999999 999


Q ss_pred             HHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHHhhch
Q 046578          320 EREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQTNILNN  373 (379)
Q Consensus       320 ~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~~l~~~~  373 (379)
                      +++|.||. +|+    +|+|++|||+.||+|.++|+++++||+++||+.+...+
T Consensus       112 ~~~r~v~~-~~~----~g~s~~EIA~~lgis~~tV~~~~~ra~~~Lr~~l~~~~  160 (164)
T 3mzy_A          112 KFEKEVLT-YLI----RGYSYREIATILSKNLKSIDNTIQRIRKKSEEWIKEEE  160 (164)
T ss_dssp             HHHHHHHH-HHT----TTCCHHHHHHHHTCCHHHHHHHHHHHHHHHHHHHHHHT
T ss_pred             HHHHHHHH-HHH----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHcC
Confidence            99999999 563    67999999999999999999999999999999987654

>2lfw_A PHYR sigma-like domain; signal transduction, response regulator, sigma factor mimicr sigma factor, general stress response, signaling protein; NMR {Sphingomonas SP}

Probab=99.82  E-value=1.2e-22  Score=176.87  Aligned_cols=143  Identities=9%  Similarity=0.075  Sum_probs=119.3

Q ss_pred             HHHHHHHhHHHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHhccCCCCCCCchhHHHHHHHHHHHHHHHhhcCcccCCcc
Q 046578          143 QERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYWWIKQAIIRAIANKSRTIRLPGS  222 (379)
Q Consensus       143 ~e~Li~~y~~lV~~ia~r~~~~~~d~eDLvQEg~i~L~~ai~~fD~~~g~~FsTYa~~~Ir~~i~~~lr~~~r~irip~~  222 (379)
                      |+.||..|.+.|+.+|.++.++..++||++||+|+++|+++++|++..  .|.+|++.+++|.+.+++|+...       
T Consensus         3 f~~l~~~~~~~l~~~~~~~~~~~~~AeDlvQe~fl~~~~~~~~~~~~~--~~~~wl~~ia~n~~~d~~R~~~~-------   73 (157)
T 2lfw_A            3 LGQQLAPHLPFLRRYGRALTGSQNQGDKYVRATLEAIVAAPDQFPRDV--DPRLGLYRMFQGIWASANADGEA-------   73 (157)
T ss_dssp             GGGGTGGGGGGGTTTGGGTTSCHHHHHHHHHHHHHTTTTCGGGCCCSS--CTTHHHHHHHHHHHHHHTTTTSC-------
T ss_pred             HHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhHHHcCCCC--cHHHHHHHHHHHHHHHHhhccCc-------
Confidence            577999999999999999999989999999999999999999998753  79999999999999999886320       


Q ss_pred             hHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCccccCCCCcccccCCCCCCCChHHHH
Q 046578          223 MAGMVAKIAEANNVLSRRLRRMPTDSEIAEMLNIHVSTVRLAIERTRHPISLDGAVTDRGCMTMQDIIPGPDETMPERMV  302 (379)
Q Consensus       223 ~~~~~~ki~~a~~~l~~~lgr~pt~~eia~~Lgis~~~~~~~l~~~~~~iSLd~~~~~~~~~~l~d~i~~~~~~~pe~~~  302 (379)
                                                                     .    +.      .  . +   . .        
T Consensus        74 -----------------------------------------------~----~~------~--~-e---~-~--------   81 (157)
T 2lfw_A           74 -----------------------------------------------Q----TS------Q--S-D---A-E--------   81 (157)
T ss_dssp             -----------------------------------------------C----CC------C--C-S---C-S--------
T ss_pred             -----------------------------------------------c----cC------C--c-c---h-H--------
Confidence                                                           0    00      0  0 0   0 0        


Q ss_pred             HHHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHHhhch
Q 046578          303 QKQLMKQELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQTNILNN  373 (379)
Q Consensus       303 ~~~e~~~~L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~~l~~~~  373 (379)
                         +....+..+|..||+++|+||.|+|+    +|+|++|||+.||+|.++|+++++||+++||+.+....
T Consensus        82 ---~~~~~l~~~l~~Lp~~~r~vl~L~~~----~g~s~~EIA~~lgis~~tV~~~l~rar~~Lr~~l~~~~  145 (157)
T 2lfw_A           82 ---GTEAVARARLARMTPLSRQALLLTAM----EGFSPEDAAYLIEVDTSEVETLVTEALAEIEKQTRALE  145 (157)
T ss_dssp             ---SSSSTTTTTTTTSCTTHHHHHTTTSS----SCCCHHHHHHTTTSCHHHHHHHHHHHHHHHHTTSSCCC
T ss_pred             ---HHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHhcc
Confidence               00123667889999999999999984    77999999999999999999999999999999986543

>3n0r_A Response regulator; sigma factor, receiver, two-component SI transduction, signaling protein; HET: MSE GOL; 1.25A {Caulobacter vibrioides} PDB: 3t0y_A

Probab=99.75  E-value=4.3e-19  Score=169.20  Aligned_cols=145  Identities=10%  Similarity=0.054  Sum_probs=119.5

Q ss_pred             hcccHHHHHHHHHHhHHHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHhccCCCCCCCchhHHHHHHHHHHHHHHHhhcC
Q 046578          136 LCKERESQERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYWWIKQAIIRAIANKSR  215 (379)
Q Consensus       136 ~~Gd~~A~e~Li~~y~~lV~~ia~r~~~~~~d~eDLvQEg~i~L~~ai~~fD~~~g~~FsTYa~~~Ir~~i~~~lr~~~r  215 (379)
                      .+||..+|++||..|.+.++.+|.+++++..++||++||+|+.+|+...+|++.  .+|.+|++++++|.+++++|+...
T Consensus        16 ~~g~~~~f~~l~~~~~~~l~~~a~~~~~~~~~AeD~vQe~fl~~~~~~~~~~~~--~~~~~wL~~ia~n~~~d~~r~~~~   93 (286)
T 3n0r_A           16 PRGSEMHLLARLAPHLPYIRRYARALTGDQATGDHYVRVALEALAAGELVLDAN--LSPRVALYRVFHAIWLSSGAQLEV   93 (286)
T ss_dssp             ----CCCHHHHHGGGHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHTTSSCCCSS--SCHHHHHHHHHHHHHSCTTC----
T ss_pred             CCCCcCCHHHHHHHHHHHHHHHHHHHhCCHhhHHHHHHHHHHHHHhCchhcCCC--cChHHHHHHHHHHHHHhhcccccc
Confidence            457888999999999999999999999999999999999999999999999864  379999999999999988774210


Q ss_pred             cccCCcchHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCccccCCCCcccccCCCCCC
Q 046578          216 TIRLPGSMAGMVAKIAEANNVLSRRLRRMPTDSEIAEMLNIHVSTVRLAIERTRHPISLDGAVTDRGCMTMQDIIPGPDE  295 (379)
Q Consensus       216 ~irip~~~~~~~~ki~~a~~~l~~~lgr~pt~~eia~~Lgis~~~~~~~l~~~~~~iSLd~~~~~~~~~~l~d~i~~~~~  295 (379)
                                                                             .        ..         .....
T Consensus        94 -------------------------------------------------------~--------~~---------~~~~~  101 (286)
T 3n0r_A           94 -------------------------------------------------------G--------HD---------QGLHA  101 (286)
T ss_dssp             -------------------------------------------------------C--------CC---------CCCCT
T ss_pred             -------------------------------------------------------C--------CC---------cccch
Confidence                                                                   0        00         00000


Q ss_pred             CChHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHHh
Q 046578          296 TMPERMVQKQLMKQELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQTNI  370 (379)
Q Consensus       296 ~~pe~~~~~~e~~~~L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~~l~  370 (379)
                                  ...+..+|++||+++|+||.|+|+    +|+|++|||+.+|+|.++|+..+.+|+++|+..+.
T Consensus       102 ------------~~~l~~al~~Lp~~~R~v~~L~~~----eg~s~~EIA~~lgis~~tVks~l~rA~~~Lr~~l~  160 (286)
T 3n0r_A          102 ------------GDDAAQRLMRIAPRSRQAFLLTAL----EGFTPTEAAQILDCDFGEVERLIGDAQAEIDAELA  160 (286)
T ss_dssp             ------------TSHHHHHHHHHSCHHHHHHHHHHT----TCCCHHHHHHHHTCCHHHHHHHHHHHHHHHHTSCC
T ss_pred             ------------HHHHHHHHHhCCHHHeeEEEEEee----CCCCHHHHHHHhCcCHHHHHHHHHHHHhhhhccCC
Confidence                        023778999999999999999994    77999999999999999999999999999998754

>1sig_A Sigma70, RNA polymerase primary sigma factor; RNA polymerase sigma factor, transcription regulation; 2.60A {Escherichia coli} SCOP: a.177.1.1

Probab=99.73  E-value=4.5e-18  Score=165.93  Aligned_cols=133  Identities=30%  Similarity=0.450  Sum_probs=109.9

Q ss_pred             hhcCCcccccchhHHHHHHHHHHHHHhhhcccccccchhh---------------h-cCcC---cHHHHHHHHhcccH--
Q 046578           82 FANGAEEVCFDDGECESVLKMMRRRSRRKKRTKESDFLDK---------------E-NGEL---DYNLVKYKILCKER--  140 (379)
Q Consensus        82 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---------------~-~~~~---~~~eLi~~~~~Gd~--  140 (379)
                      ...|+|+-+|...+.+.+.+..|-.+..+..+++......               . ...+   +..+|+.+++.||.  
T Consensus       184 ~~~~mpr~~fi~~f~g~e~~~~w~~~~~~~~~~~~~~l~~~~~~i~~~q~kl~~ie~~~~l~~~~~~~l~~~~~~gd~~~  263 (339)
T 1sig_A          184 EQCKMPKKNFITLFTGNETSDTWFNAAIAMNKPWSEKLHDVSEEVHRALQKLQQIEEETGLTIEQVKDINRRMSIGEAKA  263 (339)
T ss_dssp             TTSCCCHHHHHHHHTTTCSSGGGTHHHHTTCSHHHHHGGGTHHHHHHHHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHH
T ss_pred             HHcCCCHHHHHHHcccccCcHHHHHHHhhccchHHHHHHHhHHHHHHHHHHHHHHHHHcCCChHHHHHHHHHHHhccccc
Confidence            5579999999999888888777765555544433321110               0 1112   24678999999999  


Q ss_pred             -HHHHHHHHHhHHHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHhccCCCCCCCchhHHHHHHHHHHHHHHHhhc
Q 046578          141 -ESQERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYWWIKQAIIRAIANKS  214 (379)
Q Consensus       141 -~A~e~Li~~y~~lV~~ia~r~~~~~~d~eDLvQEg~i~L~~ai~~fD~~~g~~FsTYa~~~Ir~~i~~~lr~~~  214 (379)
                       .|++.||..|.++|+++|++|.+++.+++||+||||++||+++++|++.+|.+|+||+++|++|.|.+++|++.
T Consensus       264 ~~A~~~L~~~~~~~v~~~a~~~~~~~~~aeDlvQe~~i~l~~a~~~f~~~~g~~f~twl~~iirn~~~~~lr~~~  338 (339)
T 1sig_A          264 RRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQA  338 (339)
T ss_dssp             HHHHHHHHHHTHHHHHHHHTTSTTSSSCHHHHHHHHHHHHHHHHHHCCGGGCCCHHHHHHHHHHHHHHHHHHHC-
T ss_pred             hhhhHHHHHHHHHHHHHHHHHHhcCCCCHhHHHHHHHHHHHHHHHHhCCccCCCHHHHHHHHHHHHHHHHHHHhc
Confidence             99999999999999999999999999999999999999999999999988889999999999999999999864

>3t72_q RNA polymerase sigma factor RPOD, DNA-directed RN polymerase subunit beta; winged-helix motif, transcription activation, DNA-binding; 4.33A {Escherichia coli} PDB: 1tlh_B

Probab=99.56  E-value=1.6e-14  Score=115.93  Aligned_cols=77  Identities=32%  Similarity=0.532  Sum_probs=71.8

Q ss_pred             HHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHHhhchhhhhc
Q 046578          302 VQKQLMKQELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQTNILNNLKVYM  378 (379)
Q Consensus       302 ~~~~e~~~~L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~~l~~~~L~~y~  378 (379)
                      +...+....|..+++.|||+||.||.++||++|.+++|++|||+.||+|+++|++++++|+++||+.+....|++|+
T Consensus         4 ~~~~el~~~l~~aL~~Lp~reR~Vi~Lry~l~~~e~~s~~EIA~~lgiS~~tVr~~~~rAlkkLR~~~~~~~l~~~~   80 (99)
T 3t72_q            4 ATTESLRAATHDVLAGLTAREAKVLRMRFGIDMNTDYTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRSGS   80 (99)
T ss_pred             HHHHHHHHHHHHHHHcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            45667778899999999999999999999888778999999999999999999999999999999999999999986

>2o7g_A Probable RNA polymerase sigma-C factor; sigma factor, transcription regulation, -10 element recognit domain, transcription; 2.70A {Mycobacterium tuberculosis}

Probab=99.42  E-value=3.5e-13  Score=109.85  Aligned_cols=85  Identities=14%  Similarity=0.105  Sum_probs=76.2

Q ss_pred             HHHHHHHHhcccHHHHHHHHHHhHHHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHhccCCCCCCCchhHHHHHHHHHHH
Q 046578          128 YNLVKYKILCKERESQERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYWWIKQAII  207 (379)
Q Consensus       128 ~~eLi~~~~~Gd~~A~e~Li~~y~~lV~~ia~r~~~~~~d~eDLvQEg~i~L~~ai~~fD~~~g~~FsTYa~~~Ir~~i~  207 (379)
                      ..+|+.+++.||+.+++.||..|.+.++++|.++ ++..++||++||+|+.+|+.+.+|++.  .+|.+|++.+++|.++
T Consensus        11 ~~~l~~~~~~gd~~a~~~l~~~~~~~l~~~~~~~-~~~~~aeD~vQe~fl~~~~~~~~~~~~--~~~~~wl~~i~~n~~~   87 (112)
T 2o7g_A           11 VTALALSAAKGNGRALEAFIKATQQDVWRFVAYL-SDVGSADDLTQETFLRAIGAIPRFSAR--SSARTWLLAIARHVVA   87 (112)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHHHHHHHHHHHHH-SCHHHHHHHHHHHHHHHHHHGGGCCCS--SCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHh-CCHHHHHHHHHHHHHHHHHHHHhcCCC--CCHHHHHHHHHHHHHH
Confidence            3589999999999999999999999999999999 888899999999999999999999864  3799999999999999


Q ss_pred             HHHHhhcC
Q 046578          208 RAIANKSR  215 (379)
Q Consensus       208 ~~lr~~~r  215 (379)
                      +++|++.+
T Consensus        88 d~~R~~~~   95 (112)
T 2o7g_A           88 DHIRHVRS   95 (112)
T ss_dssp             HHTC----
T ss_pred             HHHHHhhc
Confidence            99998664

>3hug_A RNA polymerase sigma factor; ECF sigma factor, zinc binding anti-sigma factor, oxidative transcription regulation; 2.35A {Mycobacterium tuberculosis}

Probab=99.40  E-value=2e-12  Score=102.04  Aligned_cols=76  Identities=16%  Similarity=0.121  Sum_probs=69.6

Q ss_pred             CCCChHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHHhhch
Q 046578          294 DETMPERMVQKQLMKQELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQTNILNN  373 (379)
Q Consensus       294 ~~~~pe~~~~~~e~~~~L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~~l~~~~  373 (379)
                      ...+|++.+...+....|..+|..||+++|+||.++|+    +|+|++|||+.||+|.++|+++++||+++||+.+...+
T Consensus        14 ~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~vl~l~~~----~g~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~l~~~~   89 (92)
T 3hug_A           14 PEQSTPDEVNAALDRLLIADALAQLSAEHRAVIQRSYY----RGWSTAQIATDLGIAEGTVKSRLHYAVRALRLTLQELG   89 (92)
T ss_dssp             CCCCHHHHHHHHHHHHHHHHHHHTSCHHHHHHHHHHHT----SCCCHHHHHHHHTSCHHHHHHHHHHHHHHHHHHHHHHT
T ss_pred             CCCCchHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHH----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHhC
Confidence            34578888999999999999999999999999999984    77999999999999999999999999999999987654

>1tty_A Sigma-A, RNA polymerase sigma factor RPOD; helix-turn-helix, transcription; NMR {Thermotoga maritima} SCOP: a.4.13.2

Probab=99.37  E-value=1.1e-12  Score=102.62  Aligned_cols=69  Identities=42%  Similarity=0.637  Sum_probs=63.2

Q ss_pred             HHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHHhhchhhhhc
Q 046578          310 ELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQTNILNNLKVYM  378 (379)
Q Consensus       310 ~L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~~l~~~~L~~y~  378 (379)
                      .|..+|+.||+++|.||.++|+++|.+++|++|||+.||+|+++|+++++||+++||+.+....++.|+
T Consensus        11 ~l~~~l~~L~~~er~vl~l~~~l~~~~~~s~~EIA~~lgis~~tV~~~~~ra~~kLr~~l~~~~~~~~~   79 (87)
T 1tty_A           11 ELEKVLKTLSPREAMVLRMRYGLLDGKPKTLEEVGQYFNVTRERIRQIEVKALRKLRHPSRSKYLKSLL   79 (87)
T ss_dssp             HHHHHHTTSCHHHHHHHHHHHTTTTSSCCCHHHHHHHHTCCHHHHHHHHHHHHHHHBTTBSSHHHHHHH
T ss_pred             HHHHHHHhCCHHHHHHHHHHHccCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHhHHHHHH
Confidence            477899999999999999999877668899999999999999999999999999999999887777664

>2p7v_B Sigma-70, RNA polymerase sigma factor RPOD; RSD, regulator of sigma 70, sigma 70 domain 4, transcription, regulation, helix-turn-helix; 2.60A {Escherichia coli} SCOP: a.4.13.2

Probab=99.36  E-value=5.7e-13  Score=99.22  Aligned_cols=65  Identities=38%  Similarity=0.661  Sum_probs=60.5

Q ss_pred             HHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHHhhchhhhhc
Q 046578          314 LLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQTNILNNLKVYM  378 (379)
Q Consensus       314 ~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~~l~~~~L~~y~  378 (379)
                      +++.||++|++||.++||++|.+++|++|||+.||+|+++|++++++|+++||..+....++.|+
T Consensus         2 ~l~~L~~~er~il~l~~~l~~~~g~s~~eIA~~lgis~~tV~~~~~ra~~kLr~~~~~~~~~~~~   66 (68)
T 2p7v_B            2 VLAGLTAREAKVLRMRFGIDMNTDYTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRSFL   66 (68)
T ss_dssp             CSCCCCHHHHHHHHHHTTTTSSSCCCHHHHHHHHTCCHHHHHHHHHHHHHGGGSCCGGGGGSCTT
T ss_pred             HHHcCCHHHHHHHHHHHccCCCCCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            46789999999999999887678899999999999999999999999999999999999888875

>1h3l_A RNA polymerase sigma factor; transcription, DNA-binding, transcription regulation; 2.37A {Streptomyces coelicolor A3} SCOP: a.177.1.1

Probab=99.34  E-value=5.9e-13  Score=103.51  Aligned_cols=80  Identities=16%  Similarity=0.180  Sum_probs=71.2

Q ss_pred             HHHhcccHHHHHHHHHHhHHHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHhccCCCCCCCchhHHHHHHHHHHHHHHHh
Q 046578          133 YKILCKERESQERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYWWIKQAIIRAIAN  212 (379)
Q Consensus       133 ~~~~~Gd~~A~e~Li~~y~~lV~~ia~r~~~~~~d~eDLvQEg~i~L~~ai~~fD~~~g~~FsTYa~~~Ir~~i~~~lr~  212 (379)
                      .++..||..++++||..|.+.++.++.++.++..++||++||+|+.+|+.++.|++.  .+|.+|++.+++|.+++++|+
T Consensus         4 ~~~~~g~~~af~~l~~~~~~~l~~~~~~~~~~~~~aeD~vQe~fl~~~~~~~~~~~~--~~~~~wl~~i~~n~~~d~~R~   81 (87)
T 1h3l_A            4 AESTAERSARFERDALEFLDQMYSAALRMTRNPADAEDLVQETYAKAYASFHQFREG--TNLKAWLYRILTNTFINSYRK   81 (87)
T ss_dssp             --CHHHHHHHHHHHHHHTHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHGGGCCSS--SCHHHHHHHHHHHHHHHTCC-
T ss_pred             cccCcccHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHhcCCC--ccHHHHHHHHHHHHHHHHHHH
Confidence            356789999999999999999999999999998999999999999999999999864  379999999999999999987


Q ss_pred             hc
Q 046578          213 KS  214 (379)
Q Consensus       213 ~~  214 (379)
                      +.
T Consensus        82 ~~   83 (87)
T 1h3l_A           82 KQ   83 (87)
T ss_dssp             --
T ss_pred             hc
Confidence            54

>1ku3_A Sigma factor SIGA; helix-turn-helix, transcription; 1.80A {Thermus aquaticus} SCOP: a.4.13.2 PDB: 1ku7_A 1rio_H 3n97_A*

Probab=99.34  E-value=5.3e-13  Score=100.80  Aligned_cols=68  Identities=37%  Similarity=0.554  Sum_probs=54.8

Q ss_pred             HHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH-hHHhhchhhhhc
Q 046578          311 LKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQ-QTNILNNLKVYM  378 (379)
Q Consensus       311 L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR-~~l~~~~L~~y~  378 (379)
                      +..+++.||++|++||.++|+++|.+++|++|||+.||+|.++|++++++|+++|| +.+....+++|+
T Consensus         4 l~~~l~~L~~~er~il~l~~~l~~~~~~s~~eIA~~l~is~~tV~~~~~ra~~kLr~~~~~~~~~~~~~   72 (73)
T 1ku3_A            4 LEKALSKLSEREAMVLKMRKGLIDGREHTLEEVGAYFGVTRERIRQIENKALRKLKYHESRTRKLRDFL   72 (73)
T ss_dssp             CSSSTTTSCHHHHHHHHHHHTTTTSSCCCHHHHHHHHTCCHHHHHHHHHHHHHHHHHTTC---------
T ss_pred             HHHHHHhCCHHHHHHHHHHHhcccCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhhHhhHHHHHHhh
Confidence            45678899999999999999877668899999999999999999999999999999 888888888875

>3clo_A Transcriptional regulator; NP_811094.1, bacterial regulatory proteins, LUXR family, structural genomics; 2.04A {Bacteroides thetaiotaomicron vpi-5482}

Probab=99.15  E-value=1.5e-14  Score=135.54  Aligned_cols=159  Identities=16%  Similarity=0.095  Sum_probs=120.9

Q ss_pred             HHHHHHHhcccHHHHHHHHHHhHHHHHHHHHhccCCCCCHHHHH----HHHHHHHHHHHhccCCCCCCCchhHHHHHHHH
Q 046578          129 NLVKYKILCKERESQERIIRSYRSLVVSIATGYQGKGLSLKDLI----QEGSIGLLRGAKRFNPERGYKLSTYVYWWIKQ  204 (379)
Q Consensus       129 ~eLi~~~~~Gd~~A~e~Li~~y~~lV~~ia~r~~~~~~d~eDLv----QEg~i~L~~ai~~fD~~~g~~FsTYa~~~Ir~  204 (379)
                      ..++.++..+|..+++.+...|.++++.+...........+|+.    ||+|+.+|+.+..|++..  +|.+|++.+++|
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            46888887888999999999999999999888766667788886    999999999999997643  799999999888


Q ss_pred             HHHHHHHhhcCcccCCcchHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCccccCCCC
Q 046578          205 AIIRAIANKSRTIRLPGSMAGMVAKIAEANNVLSRRLRRMPTDSEIAEMLNIHVSTVRLAIERTRHPISLDGAVTDRGCM  284 (379)
Q Consensus       205 ~i~~~lr~~~r~irip~~~~~~~~ki~~a~~~l~~~lgr~pt~~eia~~Lgis~~~~~~~l~~~~~~iSLd~~~~~~~~~  284 (379)
                      .+.++.++..                                                           +...+..... 
T Consensus       163 ~~~d~~r~~~-----------------------------------------------------------~~~~~~~~~~-  182 (258)
T 3clo_A          163 LSADQRPEQG-----------------------------------------------------------IYATITQMER-  182 (258)
T ss_dssp             ECSCCCCCSS-----------------------------------------------------------CCCEEEETTT-
T ss_pred             HHcchhhhhH-----------------------------------------------------------HHHHHHhhcc-
Confidence            7766533211                                                           0000000000 


Q ss_pred             cccccCCCCCCCChHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHH
Q 046578          285 TMQDIIPGPDETMPERMVQKQLMKQELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTK  364 (379)
Q Consensus       285 ~l~d~i~~~~~~~pe~~~~~~e~~~~L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~k  364 (379)
                        .+....   .             .+..++..||+++|+||.+++     +|+|++|||+.||+|.+||+.+++||+++
T Consensus       183 --~~~~~~---~-------------~~~~~~~~L~~~erevl~L~~-----~G~s~~EIA~~L~iS~~TVk~~l~ra~~k  239 (258)
T 3clo_A          183 --GEVETL---S-------------LSEEHRNILSEREKEILRCIR-----KGLSSKEIAATLYISVNTVNRHRQNILEK  239 (258)
T ss_dssp             --TEEEEC---C-------------CHHHHTTSSCHHHHHHHHHHH-----TTCCHHHHHHHHTCCHHHHHHHHHHHHHH
T ss_pred             --cccccc---h-------------hhHHHHccCCHHHHHHHHHHH-----cCCCHHHHHHHHCcCHHHHHHHHHHHHHH
Confidence              000000   0             134567899999999999975     77999999999999999999999999999


Q ss_pred             HHhHHhhc
Q 046578          365 LQQTNILN  372 (379)
Q Consensus       365 LR~~l~~~  372 (379)
                      ||......
T Consensus       240 L~~~~~~~  247 (258)
T 3clo_A          240 LSVGNSIE  247 (258)
T ss_dssp             TTCSSHHH
T ss_pred             HcCCCHHH
Confidence            99875443

>2o8x_A Probable RNA polymerase sigma-C factor; promoter recognition, transcription regulation, helix-turn-H motif, transcription; 3.00A {Mycobacterium tuberculosis}

Probab=99.12  E-value=1.1e-10  Score=86.51  Aligned_cols=63  Identities=16%  Similarity=0.109  Sum_probs=52.4

Q ss_pred             HHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHHhhchh
Q 046578          308 KQELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQTNILNNL  374 (379)
Q Consensus       308 ~~~L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~~l~~~~L  374 (379)
                      ...+..+++.||++++.||.++|+    +|+|++|||+.||+|+++|++++++|+++||+.+....+
T Consensus         6 ~~~l~~~l~~L~~~~r~il~l~~~----~g~s~~eIA~~lgis~~tv~~~~~ra~~~l~~~l~~~~~   68 (70)
T 2o8x_A            6 LVEVTTMIADLTTDQREALLLTQL----LGLSYADAAAVCGCPVGTIRSRVARARDALLADAEPDDL   68 (70)
T ss_dssp             HHHHHTTTTSSCHHHHHHHHHHHT----SCCCHHHHHHHHTSCHHHHHHHHHHHHHHHHC-------
T ss_pred             HHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHhhcccC
Confidence            456888999999999999999984    679999999999999999999999999999999876544

>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=99.01  E-value=1.4e-09  Score=89.14  Aligned_cols=69  Identities=17%  Similarity=0.168  Sum_probs=60.2

Q ss_pred             HHHHHHHHHHHHHH-hcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHHhhchh
Q 046578          302 VQKQLMKQELKELL-QTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQTNILNNL  374 (379)
Q Consensus       302 ~~~~e~~~~L~~~L-~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~~l~~~~L  374 (379)
                      ++..+....+..++ ..||+++|.||.++|+    +|+|++|||+.||+|.++|+++++||+++||+.+....+
T Consensus         9 ~e~~~~~~~l~~~l~~~L~~~~r~vl~l~~~----~g~s~~EIA~~lgiS~~tV~~~l~ra~~kLr~~l~~~~~   78 (113)
T 1xsv_A            9 LVKTLRMNYLFDFYQSLLTNKQRNYLELFYL----EDYSLSEIADTFNVSRQAVYDNIRRTGDLVEDYEKKLEL   78 (113)
T ss_dssp             HHHHHHHHHHHHHHGGGSCHHHHHHHHHHHT----SCCCHHHHHHHTTCCHHHHHHHHHHHHHHHHHHHHHHCH
T ss_pred             HHHHHHHHHHHHHHHhcCCHHHHHHHHHHHH----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHHhH
Confidence            34445556788899 9999999999999984    779999999999999999999999999999999876544

>1s7o_A Hypothetical UPF0122 protein SPY1201/SPYM3_0842/SPS1042/SPYM18_1152; putative DNA binding protein, structural genomics; 2.31A {Streptococcus pyogenes serotype M3} SCOP: a.4.13.3

Probab=98.89  E-value=6.2e-09  Score=85.30  Aligned_cols=62  Identities=16%  Similarity=0.220  Sum_probs=56.0

Q ss_pred             HHHHHHH-hcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHHhhchh
Q 046578          309 QELKELL-QTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQTNILNNL  374 (379)
Q Consensus       309 ~~L~~~L-~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~~l~~~~L  374 (379)
                      ..+..++ ..|||+++.|+.++|+    +|+|++|||+.||+|++||+++++||+++||+.+...++
T Consensus        13 ~~l~~~l~~~L~~~~r~vl~l~y~----~g~s~~EIA~~lgiS~~tV~~~l~ra~~kLr~~l~~~~~   75 (113)
T 1s7o_A           13 NALFEFYAALLTDKQMNYIELYYA----DDYSLAEIADEFGVSRQAVYDNIKRTEKILETYEMKLHM   75 (113)
T ss_dssp             HHHHHHHGGGSCHHHHHHHHHHHH----TCCCHHHHHHHHTCCHHHHHHHHHHHHHHHHHHHHHHCH
T ss_pred             HHHHHHHHhcCCHHHHHHHHHHHH----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHhhH
Confidence            4577788 8999999999999985    779999999999999999999999999999999876554

>2rnj_A Response regulator protein VRAR; HTH LUXR-type domain, DNA binding domain, activator, antibiotic resistance, cytoplasm, DNA-binding; NMR {Staphylococcus aureus}

Probab=98.74  E-value=4.9e-09  Score=82.28  Aligned_cols=59  Identities=25%  Similarity=0.276  Sum_probs=48.8

Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHHh
Q 046578          307 MKQELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQTNI  370 (379)
Q Consensus       307 ~~~~L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~~l~  370 (379)
                      ....+..++..|+++|++||.+++     +|+|++|||+.||+|.+||+++++++++||+..-.
T Consensus        19 ~~~~l~~~l~~Lt~~e~~vl~l~~-----~g~s~~eIA~~l~is~~tV~~~l~r~~~kL~~~~~   77 (91)
T 2rnj_A           19 HMKKRAELYEMLTEREMEILLLIA-----KGYSNQEIASASHITIKTVKTHVSNILSKLEVQDR   77 (91)
T ss_dssp             ------CTGGGCCSHHHHHHHHHH-----TTCCTTHHHHHHTCCHHHHHHHHHHHHHHTTCCSS
T ss_pred             HHHHHHHHHhcCCHHHHHHHHHHH-----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHCCCCH
Confidence            345678899999999999999954     67999999999999999999999999999987544

>3c57_A Two component transcriptional regulatory protein; response regulator, two-component regulatory system, DNA-BIN protein; 1.70A {Mycobacterium tuberculosis} PDB: 1zlk_A 1zlj_A

Probab=98.72  E-value=1.9e-08  Score=79.61  Aligned_cols=58  Identities=19%  Similarity=0.268  Sum_probs=46.1

Q ss_pred             HHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHHhh
Q 046578          309 QELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQTNIL  371 (379)
Q Consensus       309 ~~L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~~l~~  371 (379)
                      ..+..++..|+++|++||.+++     +|+|++|||+.||+|.+||+++++++++||+..-+.
T Consensus        19 ~~l~~~l~~Lt~~e~~vl~l~~-----~g~s~~eIA~~l~is~~tV~~~l~r~~~kL~~~~~~   76 (95)
T 3c57_A           19 SHMQDPLSGLTDQERTLLGLLS-----EGLTNKQIADRMFLAEKTVKNYVSRLLAKLGMERRT   76 (95)
T ss_dssp             --------CCCHHHHHHHHHHH-----TTCCHHHHHHHHTCCHHHHHHHHHHHHHHHTCCCCC
T ss_pred             HHHHHHHhcCCHHHHHHHHHHH-----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHcCCCHH
Confidence            4578889999999999999974     779999999999999999999999999999976543

>1x3u_A Transcriptional regulatory protein FIXJ; helix-turn-helix; NMR {Sinorhizobium meliloti}

Probab=98.68  E-value=2.5e-08  Score=75.62  Aligned_cols=58  Identities=26%  Similarity=0.363  Sum_probs=51.2

Q ss_pred             HHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHHhh
Q 046578          309 QELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQTNIL  371 (379)
Q Consensus       309 ~~L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~~l~~  371 (379)
                      ..+..++..||++|++|+.+++     +|+|++|||+.||+|.++|++++.+++++|+..-..
T Consensus         8 ~~l~~~l~~L~~~e~~vl~l~~-----~g~s~~eIA~~l~is~~tV~~~~~r~~~kl~~~~~~   65 (79)
T 1x3u_A            8 NDIRARLQTLSERERQVLSAVV-----AGLPNKSIAYDLDISPRTVEVHRANVMAKMKAKSLP   65 (79)
T ss_dssp             HHHHHHHHHHCHHHHHHHHHHT-----TTCCHHHHHHHTTSCHHHHHHHHHHHHHHTTCCSHH
T ss_pred             HHHHHHHHhCCHHHHHHHHHHH-----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHcCCCHH
Confidence            3477888999999999999953     679999999999999999999999999999975443

>1jhg_A Trp operon repressor; complex (regulatory protein-peptide), DNA-binding regulatory complex (regulatory protein-peptide) complex; HET: TRP; 1.30A {Escherichia coli} SCOP: a.4.12.1 PDB: 1co0_A* 1mi7_R 1p6z_R 1wrp_R* 1zt9_A* 2oz9_R* 3ssw_R 3wrp_A 1rcs_A* 1wrs_R* 1wrt_R 2xdi_A 3ssx_R* 1trr_A* 1tro_A*

Probab=98.65  E-value=2.7e-08  Score=79.32  Aligned_cols=64  Identities=16%  Similarity=0.060  Sum_probs=54.0

Q ss_pred             HHHHHHHHHH-hcCCHHHHHHHHHHhhcCC---CCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHHh
Q 046578          306 LMKQELKELL-QTLSEREADILRLHFGLDG---QTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQTNI  370 (379)
Q Consensus       306 e~~~~L~~~L-~~L~~rer~Vl~l~ygL~g---~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~~l~  370 (379)
                      ...+.+..++ ..|+++|+.+|.+||++.+   ..++|++|||+.+|+|++||++. +|++++|...++
T Consensus        23 ~~~~~l~~~l~~lLT~~Er~~l~~R~~l~~~L~~ge~TQREIA~~lGiS~stISRi-~r~L~~l~~~~k   90 (101)
T 1jhg_A           23 YQNDLHLPLLNLMLTPDEREALGTRVRIIEELLRGEMSQRELKNELGAGIATITRG-SNSLKAAPVELR   90 (101)
T ss_dssp             HHTTCHHHHHHHHSCHHHHHHHHHHHHHHHHHHHCCSCHHHHHHHHCCCHHHHHHH-HHHHHHSCHHHH
T ss_pred             CCHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHcCCcCHHHHHHHHCCChhhhhHH-HHHHHHccHHHH
Confidence            3344566777 5799999999999999863   34599999999999999999999 899999988765

>1je8_A Nitrate/nitrite response regulator protein NARL; protein-DNA complex, two-component response regulator, helix-turn-helix, DNA bending; 2.12A {Escherichia coli} SCOP: a.4.6.2 PDB: 1zg1_A 1zg5_A

Probab=98.63  E-value=2.2e-08  Score=77.03  Aligned_cols=57  Identities=23%  Similarity=0.294  Sum_probs=49.7

Q ss_pred             HHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHHhhc
Q 046578          311 LKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQTNILN  372 (379)
Q Consensus       311 L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~~l~~~  372 (379)
                      +..++..|+++|++|+.+++     +|+|++|||+.||+|.+||+++++++++||+...+.+
T Consensus        15 ~~~~~~~Lt~~e~~vl~l~~-----~g~s~~eIA~~l~is~~tV~~~l~r~~~kL~~~~~~~   71 (82)
T 1je8_A           15 TERDVNQLTPRERDILKLIA-----QGLPNKMIARRLDITESTVKVHVKHMLKKMKLKSRVE   71 (82)
T ss_dssp             --CCGGGSCHHHHHHHHHHT-----TTCCHHHHHHHHTSCHHHHHHHHHHHHHHTTCSSHHH
T ss_pred             HHHHHccCCHHHHHHHHHHH-----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHcCCCHHH
Confidence            56778899999999999953     6799999999999999999999999999999875543

>1fse_A GERE; helix-turn-helix DNA-binding protein transcriptional regulat transcription; 2.05A {Bacillus subtilis} SCOP: a.4.6.2

Probab=98.40  E-value=2.8e-07  Score=68.64  Aligned_cols=57  Identities=23%  Similarity=0.220  Sum_probs=47.6

Q ss_pred             HHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHHhhc
Q 046578          311 LKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQTNILN  372 (379)
Q Consensus       311 L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~~l~~~  372 (379)
                      ....+..|+++|++|+.+++     +|+|.+|||+.||+|.++|++++.+++++|+..-...
T Consensus         5 ~~~~~~~L~~~e~~il~~~~-----~g~s~~eIA~~l~is~~tV~~~~~~~~~kl~~~~~~~   61 (74)
T 1fse_A            5 EFQSKPLLTKREREVFELLV-----QDKTTKEIASELFISEKTVRNHISNAMQKLGVKGRSQ   61 (74)
T ss_dssp             ---CCCCCCHHHHHHHHHHT-----TTCCHHHHHHHHTSCHHHHHHHHHHHHHHHTCSSHHH
T ss_pred             cCCCCCCCCHHHHHHHHHHH-----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCCCHHH
Confidence            34556789999999999953     6799999999999999999999999999998765433

>3ulq_B Transcriptional regulatory protein COMA; tetratricopeptide repeat, response regulator helix-turn-HELX binding, 3-helix bundle; 2.30A {Bacillus subtilis} PDB: 2krf_A

Probab=98.30  E-value=1e-06  Score=68.99  Aligned_cols=51  Identities=25%  Similarity=0.201  Sum_probs=43.9

Q ss_pred             HHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhH
Q 046578          313 ELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQT  368 (379)
Q Consensus       313 ~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~~  368 (379)
                      .....|+++|++|+.+.+     +|+|.+|||+.||+|..||+.++.++++||.-.
T Consensus        25 ~~~~~Lt~rE~~Vl~l~~-----~G~s~~eIA~~L~iS~~TV~~~~~~i~~Klgv~   75 (90)
T 3ulq_B           25 KEQDVLTPRECLILQEVE-----KGFTNQEIADALHLSKRSIEYSLTSIFNKLNVG   75 (90)
T ss_dssp             ----CCCHHHHHHHHHHH-----TTCCHHHHHHHHTCCHHHHHHHHHHHHHHTTCS
T ss_pred             ccccCCCHHHHHHHHHHH-----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHCCC
Confidence            446789999999999987     779999999999999999999999999998654

>1p4w_A RCSB; solution structure, DNA binding domain, DNA binding protein; NMR {Erwinia amylovora} SCOP: a.4.6.2

Probab=98.22  E-value=1.7e-06  Score=68.97  Aligned_cols=48  Identities=29%  Similarity=0.351  Sum_probs=44.0

Q ss_pred             hcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhH
Q 046578          316 QTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQT  368 (379)
Q Consensus       316 ~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~~  368 (379)
                      ..|+++|++||.+.+     +|+|.+|||+.||+|.+||+..+.++++||.-.
T Consensus        33 ~~Lt~re~~Vl~l~~-----~G~s~~EIA~~L~iS~~TV~~~l~ri~~KLgv~   80 (99)
T 1p4w_A           33 KRLSPKESEVLRLFA-----EGFLVTEIAKKLNRSIKTISSQKKSAMMKLGVD   80 (99)
T ss_dssp             SSCCHHHHHHHHHHH-----HTCCHHHHHHHHTSCHHHHHHHHHHHHHHHTCS
T ss_pred             CCCCHHHHHHHHHHH-----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHCCC
Confidence            579999999999865     679999999999999999999999999999754

>2jpc_A SSRB; DNA binding protein, structural genomics, PSI-2, protein structure initiative; NMR {Salmonella typhimurium}

Probab=98.19  E-value=1.6e-06  Score=62.09  Aligned_cols=46  Identities=24%  Similarity=0.299  Sum_probs=40.9

Q ss_pred             HHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHHh
Q 046578          320 EREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQTNI  370 (379)
Q Consensus       320 ~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~~l~  370 (379)
                      |+|++|+.+ +.    +|+|.+|||+.||+|.+||+..+.++++||+..-.
T Consensus         1 ~re~~vl~l-~~----~g~s~~eIA~~l~is~~tV~~~~~~~~~kl~~~~~   46 (61)
T 2jpc_A            1 LRERQVLKL-ID----EGYTNHGISEKLHISIKTVETHRMNMMRKLQVHKV   46 (61)
T ss_dssp             CHHHHHHHH-HH----TSCCSHHHHHHTCSCHHHHHHHHHHHHHHHTCSSH
T ss_pred             CHHHHHHHH-HH----cCCCHHHHHHHhCCCHHHHHHHHHHHHHHHCCCCH
Confidence            478999999 42    77999999999999999999999999999987544

>2q0o_A Probable transcriptional activator protein TRAR; helix-turn-helix, two-helix coiled coil; HET: LAE; 2.00A {Rhizobium SP}

Probab=97.77  E-value=3.6e-05  Score=70.34  Aligned_cols=47  Identities=19%  Similarity=0.133  Sum_probs=43.4

Q ss_pred             cCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhH
Q 046578          317 TLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQT  368 (379)
Q Consensus       317 ~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~~  368 (379)
                      .|+++|++|+.+..     +|+|.+|||+.||||.+||+.++.++++||.-.
T Consensus       175 ~Lt~~e~~vl~~~~-----~g~s~~eIa~~l~is~~tV~~~~~~~~~kl~~~  221 (236)
T 2q0o_A          175 MLSPREMLCLVWAS-----KGKTASVTANLTGINARTVQHYLDKARAKLDAE  221 (236)
T ss_dssp             SCCHHHHHHHHHHH-----TTCCHHHHHHHHCCCHHHHHHHHHHHHHHHTCS
T ss_pred             CCCHHHHHHHHHHH-----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHhCCC
Confidence            59999999999865     779999999999999999999999999999754

>1l3l_A Transcriptional activator protein TRAR; helix-turn-helix DNA binding motif, alpha/beta/alpha sandwich; HET: LAE; 1.66A {Agrobacterium tumefaciens} SCOP: a.4.6.2 d.110.5.1 PDB: 1h0m_A*

Probab=97.76  E-value=3.6e-05  Score=70.24  Aligned_cols=47  Identities=19%  Similarity=0.186  Sum_probs=43.0

Q ss_pred             cCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhH
Q 046578          317 TLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQT  368 (379)
Q Consensus       317 ~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~~  368 (379)
                      .|+++|++|+.+..     +|+|.+|||+.||+|.+||+.++.++++||.-.
T Consensus       173 ~Lt~~e~~vl~~~~-----~g~s~~eIa~~l~is~~tV~~~~~~~~~kl~~~  219 (234)
T 1l3l_A          173 WLDPKEATYLRWIA-----VGKTMEEIADVEGVKYNSVRVKLREAMKRFDVR  219 (234)
T ss_dssp             CCCHHHHHHHHHHT-----TTCCHHHHHHHHTCCHHHHHHHHHHHHHHHTCS
T ss_pred             CCCHHHHHHHHHHH-----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHhCCC
Confidence            59999999999864     779999999999999999999999999999654

>3szt_A QCSR, quorum-sensing control repressor; quorum sensing acyl-homoserine lactone, helix-turn-helix, transcription factor, 3-OXO-C12 HSL; HET: OHN; 2.55A {Pseudomonas aeruginosa}

Probab=97.65  E-value=5.5e-05  Score=69.36  Aligned_cols=48  Identities=25%  Similarity=0.356  Sum_probs=43.8

Q ss_pred             hcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhH
Q 046578          316 QTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQT  368 (379)
Q Consensus       316 ~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~~  368 (379)
                      ..|+++|++|+.+..     +|+|.+|||+.||||..||+..+.++++||.-.
T Consensus       174 ~~Lt~re~~vl~~~~-----~G~s~~eIa~~l~is~~tV~~~~~~~~~kl~~~  221 (237)
T 3szt_A          174 VRLTARETEMLKWTA-----VGKTYGEIGLILSIDQRTVKFHIVNAMRKLNSS  221 (237)
T ss_dssp             CCCCHHHHHHHHHHH-----TTCCHHHHHHHHTSCHHHHHHHHHHHHHHTTCS
T ss_pred             CCCCHHHHHHHHHHH-----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHhCCC
Confidence            469999999999975     779999999999999999999999999998643

>3qp6_A CVIR transcriptional regulator; quorum sensing, agonist, antagonist, LUXR, acylated homoseri lactone, transcription factor; HET: HL6; 2.00A {Chromobacterium violaceum} PDB: 3qp5_A*

Probab=97.54  E-value=9.6e-05  Score=69.02  Aligned_cols=47  Identities=26%  Similarity=0.300  Sum_probs=43.8

Q ss_pred             cCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhH
Q 046578          317 TLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQT  368 (379)
Q Consensus       317 ~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~~  368 (379)
                      .|+++|++|+.+..     +|+|.+|||+.||||..||+.++.++++||.-.
T Consensus       197 ~Lt~re~~vl~~~~-----~G~s~~eIA~~l~is~~TV~~~~~~~~~kl~~~  243 (265)
T 3qp6_A          197 PLSQREYDIFHWMS-----RGKTNWEIATILNISERTVKFHVANVIRKLNAN  243 (265)
T ss_dssp             CCCHHHHHHHHHHH-----TTCCHHHHHHHHTSCHHHHHHHHHHHHHHTTCS
T ss_pred             CCCHHHHHHHHHHH-----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHhCCC
Confidence            69999999999986     779999999999999999999999999998754

>2w7n_A TRFB transcriptional repressor protein; INCP, plasmid, repressor, DNA-binding, transcription/DNA; HET: BRU; 1.85A {Escherichia coli}

Probab=97.42  E-value=0.00034  Score=55.64  Aligned_cols=46  Identities=13%  Similarity=0.130  Sum_probs=41.4

Q ss_pred             cCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 046578          317 TLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQ  366 (379)
Q Consensus       317 ~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR  366 (379)
                      .+++.-..|-.++|    .+|+|+.|||+.||+|+.+|++.+.+|.+.+-
T Consensus        18 ~~~~~~~~~A~lyY----v~g~tQ~eIA~~lGiSR~~VsrlL~~Ar~~~~   63 (101)
T 2w7n_A           18 EVGQQTIEIARGVL----VDGKPQATFATSLGLTRGAVSQAVHRVWAAFE   63 (101)
T ss_dssp             CCCHHHHHHHHHHH----TTCCCHHHHHHHHTCCHHHHHHHHHHHHHHHH
T ss_pred             ChHHHHHHHHHHHH----HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHh
Confidence            67888889999999    47799999999999999999999999998764

>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=97.35  E-value=0.0003  Score=47.11  Aligned_cols=40  Identities=33%  Similarity=0.214  Sum_probs=32.3

Q ss_pred             cCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 046578          317 TLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGI  360 (379)
Q Consensus       317 ~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~r  360 (379)
                      .|++.++..+...+.    +++|..|||+.||||++||++++.+
T Consensus         5 ~l~~~~~~~i~~~~~----~g~s~~~IA~~lgis~~Tv~~~~~~   44 (51)
T 1tc3_C            5 ALSDTERAQLDVMKL----LNVSLHEMSRKISRSRHCIRVYLKD   44 (51)
T ss_dssp             CCCHHHHHHHHHHHH----TTCCHHHHHHHHTCCHHHHHHHHHC
T ss_pred             CCCHHHHHHHHHHHH----cCCCHHHHHHHHCcCHHHHHHHHhh
Confidence            578888865555552    6799999999999999999988754

>2x48_A CAG38821; archeal virus, viral protein; 2.60A {Sulfolobus islandicus rod-shaped virusorganism_taxid}

Probab=97.05  E-value=0.00035  Score=48.61  Aligned_cols=38  Identities=13%  Similarity=0.149  Sum_probs=29.1

Q ss_pred             CHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 046578          319 SEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIA  361 (379)
Q Consensus       319 ~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rA  361 (379)
                      ++..+.|+.+ +.    +|+|++|||+.||+|++||++++.+|
T Consensus        18 ~~~~~~i~~l-~~----~g~s~~eIA~~lgis~~TV~~~l~~a   55 (55)
T 2x48_A           18 DDLVSVAHEL-AK----MGYTVQQIANALGVSERKVRRYLESC   55 (55)
T ss_dssp             HHHHHHHHHH-HH----TTCCHHHHHHHHTSCHHHHHHHHTC-
T ss_pred             HHHHHHHHHH-HH----cCCCHHHHHHHHCcCHHHHHHHHHhC
Confidence            3445566666 42    66999999999999999999987654

>1yio_A Response regulatory protein; transcription regulation, DNA binding protein; 2.20A {Pseudomonas fluorescens} SCOP: a.4.6.2 c.23.1.1 PDB: 1zn2_A

Probab=97.00  E-value=0.0021  Score=56.33  Aligned_cols=53  Identities=25%  Similarity=0.387  Sum_probs=45.8

Q ss_pred             HHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhH
Q 046578          311 LKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQT  368 (379)
Q Consensus       311 L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~~  368 (379)
                      +...+..|+++|++|+.+..     +|+|.+|||+.+|+|..||+.+++++++||...
T Consensus       136 ~~~~~~~Lt~rE~~vl~~l~-----~g~s~~~Ia~~l~is~~TV~~~~~~i~~Kl~~~  188 (208)
T 1yio_A          136 LEQLFSSLTGREQQVLQLTI-----RGLMNKQIAGELGIAEVTVKVHRHNIMQKLNVR  188 (208)
T ss_dssp             HHHHHHTSCHHHHHHHHHHT-----TTCCHHHHHHHHTCCHHHHHHHHHHHHHHTTCS
T ss_pred             HHHHHHhcCHHHHHHHHHHH-----cCCcHHHHHHHcCCCHHHHHHHHHHHHHHhCCC
Confidence            34455689999999998764     679999999999999999999999999999643

>1a04_A Nitrate/nitrite response regulator protein NARL; signal transduction protein, response regulators, two- component systems; 2.20A {Escherichia coli} SCOP: a.4.6.2 c.23.1.1 PDB: 1rnl_A

Probab=96.86  E-value=0.0018  Score=57.09  Aligned_cols=48  Identities=27%  Similarity=0.353  Sum_probs=43.1

Q ss_pred             hcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhH
Q 046578          316 QTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQT  368 (379)
Q Consensus       316 ~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~~  368 (379)
                      ..|+++|++|+.+..     +|+|.+|||+.+++|..||+.++++.++||.-.
T Consensus       153 ~~Lt~rE~~vl~~l~-----~g~s~~~Ia~~l~is~~TV~~hi~~i~~Kl~~~  200 (215)
T 1a04_A          153 NQLTPRERDILKLIA-----QGLPNKMIARRLDITESTVKVHVKHMLKKMKLK  200 (215)
T ss_dssp             GGSCHHHHHHHHHHH-----TTCCHHHHHHHHTCCHHHHHHHHHHHHHHHTCC
T ss_pred             cCCCHHHHHHHHHHH-----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHcCCC
Confidence            359999999999875     679999999999999999999999999999643

>3c3w_A Two component transcriptional regulatory protein; response regulator, two-component regulatory system, DNA-BIN protein; 2.20A {Mycobacterium tuberculosis}

Probab=96.69  E-value=0.0023  Score=57.21  Aligned_cols=47  Identities=21%  Similarity=0.289  Sum_probs=42.4

Q ss_pred             hcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHh
Q 046578          316 QTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQ  367 (379)
Q Consensus       316 ~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~  367 (379)
                      ..|+++|++|+.+..     +|+|.+|||+.+++|..||+..+++.++||.-
T Consensus       148 ~~LT~rE~~vL~~l~-----~g~s~~eIa~~l~is~~TV~~hi~~l~~KL~~  194 (225)
T 3c3w_A          148 SGLTDQERTLLGLLS-----EGLTNKQIADRMFLAEKTVKNYVSRLLAKLGM  194 (225)
T ss_dssp             TTSCHHHHHHHHHHH-----TTCCHHHHHHHHTCCHHHHHHHHHHHHHHTTC
T ss_pred             CCCCHHHHHHHHHHH-----CCCCHHHHHHHhCCCHHHHHHHHHHHHHHhCC
Confidence            369999999998765     67999999999999999999999999999854

>3klo_A Transcriptional regulator VPST; REC domain, HTH domain, DNA-binding, transcription regulation; HET: C2E TAR; 2.80A {Vibrio cholerae} PDB: 3kln_A*

Probab=96.28  E-value=0.0037  Score=55.68  Aligned_cols=47  Identities=23%  Similarity=0.273  Sum_probs=41.8

Q ss_pred             hcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHh
Q 046578          316 QTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQ  367 (379)
Q Consensus       316 ~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~  367 (379)
                      ..|+++|++|+.+..     +|+|.+|||+.+++|..||+.++++.++||.-
T Consensus       158 ~~Lt~rE~~vL~~l~-----~g~s~~~Ia~~l~~s~~Tv~~~i~~l~~KL~~  204 (225)
T 3klo_A          158 AKLTKREQQIIKLLG-----SGASNIEIADKLFVSENTVKTHLHNVFKKINA  204 (225)
T ss_dssp             HTSCHHHHHHHHHHT-----TTCCHHHHHHHTTCCHHHHHHHHHHHTTTSCC
T ss_pred             ccCCHHHHHHHHHHH-----cCCCHHHHHHHhCCCHHHHHHHHHHHHHHhCC
Confidence            469999999999854     67999999999999999999999999888753

>3p7n_A Sensor histidine kinase; LOV domain, light-activated transcription factor, DNA bindin; HET: FMN; 2.10A {Erythrobacter litoralis}

Probab=95.83  E-value=0.024  Score=51.06  Aligned_cols=56  Identities=29%  Similarity=0.463  Sum_probs=49.6

Q ss_pred             HHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhH
Q 046578          308 KQELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQT  368 (379)
Q Consensus       308 ~~~L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~~  368 (379)
                      .......+..|+++++.++.+..     .+++.++||+.||+|..+|+..+.++++||.-.
T Consensus       189 ~~~~~~~l~~L~~r~~~i~~~~~-----~g~~~~eia~~l~~s~~tv~~~l~~i~~kl~~~  244 (258)
T 3p7n_A          189 RERAAEMLKTLSPRQLEVTTLVA-----SGLRNKEVAARLGLSEKTVKMHRGLVMEKLNLK  244 (258)
T ss_dssp             HHHHHHHHTTSCHHHHHHHHHHH-----TTCCHHHHHHHHTCCHHHHHHHHHHHHHHTTCS
T ss_pred             HHHHHHHHhhcCHHHHHHHHHHH-----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHCCC
Confidence            35577888999999999999876     679999999999999999999999999998644

>3kor_A Possible Trp repressor; putative DNA-binding Trp repressor, TRPR like protein, struc genomics, transcription; 1.60A {Staphylococcus aureus}

Probab=95.51  E-value=0.012  Score=47.81  Aligned_cols=39  Identities=18%  Similarity=0.166  Sum_probs=29.3

Q ss_pred             cCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHH
Q 046578          317 TLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIAL  362 (379)
Q Consensus       317 ~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl  362 (379)
                      .|+.| .+|+.+..     +|+|++|||+.+|+|..||.+ ..++|
T Consensus        61 aLs~R-~eV~klL~-----~G~syreIA~~~g~S~aTIsR-v~r~L   99 (119)
T 3kor_A           61 SLSQR-LQVAKMIK-----QGYTYATIEQESGASTATISR-VKRSL   99 (119)
T ss_dssp             HHHHH-HHHHHHHH-----HTCCHHHHHHHHCCCHHHHHH-HHHHH
T ss_pred             HHHHH-HHHHHHHH-----cCCCHHHHHHHHCCCHHHHHH-HHHHH
Confidence            34555 56777654     669999999999999999987 34444

>1p2f_A Response regulator; DRRB, OMPR/PHOB, transcription; HET: MSE; 1.80A {Thermotoga maritima} SCOP: a.4.6.1 c.23.1.1 PDB: 3nns_A*

Probab=95.21  E-value=0.019  Score=50.61  Aligned_cols=50  Identities=12%  Similarity=0.120  Sum_probs=42.2

Q ss_pred             cCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhC---CCHHHHHHHHHHHHHHHHh
Q 046578          317 TLSEREADILRLHFGLDGQTPVSCKEIGRLLS---LSRERIRQIRGIALTKLQQ  367 (379)
Q Consensus       317 ~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~Lg---iS~~~Vr~~~~rAl~kLR~  367 (379)
                      .|+++|++|+.+.. -+..+.+|.+|||+.++   +|..||+.++++.++||..
T Consensus       145 ~Lt~rE~~vl~~l~-~~~~~~~s~~~Ia~~l~~~~~s~~tv~~~i~~l~~Kl~~  197 (220)
T 1p2f_A          145 HLPKKEFEILLFLA-ENAGKVVTREKLLETFWEDPVSPRVVDTVIKRIRKAIED  197 (220)
T ss_dssp             CCCHHHHHHHHHHH-HTTTSCEEHHHHHHHHCSSCCCTHHHHHHHHHHHHHHCS
T ss_pred             ecCHHHHHHHHHHH-HCCCceEcHHHHHHHHhCCCCCcchHHHHHHHHHHHHhc
Confidence            59999999998765 11113499999999999   9999999999999999974

>1jko_C HIN recombinase, DNA-invertase HIN; water-mediated recognition, protein-DNA complex, A10G mutant, DNA binding protein/DNA complex; 2.24A {Synthetic} SCOP: a.4.1.2 PDB: 1ijw_C* 1jj6_C* 1jj8_C* 1hcr_A 1jkp_C 1jkq_C 1jkr_C

Probab=95.15  E-value=0.0099  Score=39.84  Aligned_cols=25  Identities=0%  Similarity=0.021  Sum_probs=22.1

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHHH
Q 046578          336 TPVSCKEIGRLLSLSRERIRQIRGI  360 (379)
Q Consensus       336 e~~S~~EIAe~LgiS~~~Vr~~~~r  360 (379)
                      ++.|..+||+.+|||++||++++.+
T Consensus        20 ~g~s~~~ia~~lgvs~~Tv~r~l~~   44 (52)
T 1jko_C           20 KGHPRQQLAIIFGIGVSTLYRYFPA   44 (52)
T ss_dssp             TTCCHHHHHHTTSCCHHHHHHHSCT
T ss_pred             cCCCHHHHHHHHCCCHHHHHHHHHH
Confidence            5699999999999999999987654

>2gwr_A DNA-binding response regulator MTRA; two-component regulatory system, transcription regulation, phosphorylation, OMPR family; 2.10A {Mycobacterium tuberculosis} PDB: 3nhz_A

Probab=95.07  E-value=0.026  Score=50.56  Aligned_cols=50  Identities=10%  Similarity=0.014  Sum_probs=41.2

Q ss_pred             cCCHHHHHHHHHHhhcCCCCCCCHHHHHHHh-----CCCHHHHHHHHHHHHHHHHh
Q 046578          317 TLSEREADILRLHFGLDGQTPVSCKEIGRLL-----SLSRERIRQIRGIALTKLQQ  367 (379)
Q Consensus       317 ~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~L-----giS~~~Vr~~~~rAl~kLR~  367 (379)
                      .|+++|.+|+.+..- +-...+|.+|||+.+     ++|..||+..+++.++||..
T Consensus       153 ~LT~rE~~vL~~l~~-~~~~~~s~~eIa~~lw~~~~~~s~~tV~~hi~~lr~KL~~  207 (238)
T 2gwr_A          153 SLTPLEFDLLVALAR-KPRQVFTRDVLLEQVWGYRHPADTRLVNVHVQRLRAKVEK  207 (238)
T ss_dssp             CCCHHHHHHHHHHHH-STTCCBCHHHHHHHHTCCC--CCTHHHHHHHHHHHHHHCS
T ss_pred             ccCHHHHHHHHHHHH-CCCceecHHHHHHHHcCCCCCCCcccHHHHHHHHHHHhcc
Confidence            599999999987651 111349999999999     99999999999999999964

>2oqr_A Sensory transduction protein REGX3; response regulator, winged-helix-turn-helix, DNA-binding, 3D swapping, two component system; 2.03A {Mycobacterium tuberculosis H37RV}

Probab=94.94  E-value=0.023  Score=50.37  Aligned_cols=50  Identities=12%  Similarity=0.077  Sum_probs=42.4

Q ss_pred             cCCHHHHHHHHHHhhcCCCCCCCHHHHHHHh-----CCCHHHHHHHHHHHHHHHHh
Q 046578          317 TLSEREADILRLHFGLDGQTPVSCKEIGRLL-----SLSRERIRQIRGIALTKLQQ  367 (379)
Q Consensus       317 ~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~L-----giS~~~Vr~~~~rAl~kLR~  367 (379)
                      .|+++|.+|+.+.. -+..+.+|.+|||+.+     ++|..||+.++++.++||..
T Consensus       156 ~Lt~rE~~vL~~l~-~~~~~~~s~~~Ia~~lw~~~~~~s~~tv~~hi~~i~~Kl~~  210 (230)
T 2oqr_A          156 TLPLKEFDLLEYLM-RNSGRVLTRGQLIDRVWGADYVGDTKTLDVHVKRLRSKIEA  210 (230)
T ss_dssp             CCCHHHHHHHHHHH-HTTTSCEEHHHHHHHHTSSCCTTHHHHHHHHHHHHHHHHCS
T ss_pred             ecCHHHHHHHHHHH-hCCCceEcHHHHHHHhcCCCCCCCCcCHHHHHHHHHHHHhh
Confidence            49999999999765 1212459999999999     99999999999999999964

>1kgs_A DRRD, DNA binding response regulator D; DNA-binding protein, ALPH-beta sandwich, winged-helix, helix helix, DNA binding protein; HET: DNA MSE; 1.50A {Thermotoga maritima} SCOP: a.4.6.1 c.23.1.1 PDB: 3nnn_A*

Probab=94.65  E-value=0.03  Score=49.27  Aligned_cols=50  Identities=18%  Similarity=0.171  Sum_probs=41.9

Q ss_pred             cCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhC-----CCHHHHHHHHHHHHHHHHh
Q 046578          317 TLSEREADILRLHFGLDGQTPVSCKEIGRLLS-----LSRERIRQIRGIALTKLQQ  367 (379)
Q Consensus       317 ~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~Lg-----iS~~~Vr~~~~rAl~kLR~  367 (379)
                      .|+++|.+|+.+..- +....+|.+|||+.++     +|..||+.++++.++||..
T Consensus       151 ~Lt~rE~~vL~~l~~-~~~~~~s~~eIa~~l~~~~~~~s~~tv~~hi~~l~~Kl~~  205 (225)
T 1kgs_A          151 DLTKKEYQILEYLVM-NKNRVVTKEELQEHLWSFDDEVFSDVLRSHIKNLRKKVDK  205 (225)
T ss_dssp             CCCHHHHHHHHHHHH-TTTSCEEHHHHHHHCC-----CHHHHHHHHHHHHHHHHHT
T ss_pred             ecCHHHHHHHHHHHh-CCCcccCHHHHHHHhcCCCCCCCcchHHHHHHHHHHHhhC
Confidence            599999999987651 1113399999999998     9999999999999999974

>1qgp_A Protein (double stranded RNA adenosine deaminase); Z-alpha-Z-DNA binding domain, RNA-editing, Z-DNA recognition, ADAR1, helix- turn-helix; NMR {Homo sapiens} SCOP: a.4.5.19

Probab=94.54  E-value=0.054  Score=40.49  Aligned_cols=41  Identities=15%  Similarity=0.247  Sum_probs=28.9

Q ss_pred             HHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 046578          320 EREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGI  360 (379)
Q Consensus       320 ~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~r  360 (379)
                      +.++.|+.+..-....++.|..|||+.||+|+.+|++++++
T Consensus        14 ~~~~~IL~~L~~~~~~~~~t~~eLA~~Lgvs~~tV~~~L~~   54 (77)
T 1qgp_A           14 DQEQRILKFLEELGEGKATTAHDLSGKLGTPKKEINRVLYS   54 (77)
T ss_dssp             HHHHHHHHHHHHHCSSSCEEHHHHHHHHCCCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCCCCcCHHHHHHHHCcCHHHHHHHHHH
Confidence            34566765443222124699999999999999999877555

>1ys7_A Transcriptional regulatory protein PRRA; response regulator, DNA binding domain, phosphorylation; 1.58A {Mycobacterium tuberculosis} SCOP: a.4.6.1 c.23.1.1 PDB: 1ys6_A

Probab=94.33  E-value=0.029  Score=49.66  Aligned_cols=51  Identities=20%  Similarity=0.202  Sum_probs=41.4

Q ss_pred             cCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhC-----CCHHHHHHHHHHHHHHHHhH
Q 046578          317 TLSEREADILRLHFGLDGQTPVSCKEIGRLLS-----LSRERIRQIRGIALTKLQQT  368 (379)
Q Consensus       317 ~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~Lg-----iS~~~Vr~~~~rAl~kLR~~  368 (379)
                      .|+++|.+|+.+..- +....+|.+|||+.++     +|..||+.++++.++||...
T Consensus       159 ~Lt~rE~~vL~~l~~-g~~~~~s~~~Ia~~l~~~~~~~s~~tv~~hi~~l~~Kl~~~  214 (233)
T 1ys7_A          159 DLTKREFDLLAVLAE-HKTAVLSRAQLLELVWGYDFAADTNVVDVFIGYLRRKLEAG  214 (233)
T ss_dssp             CCCHHHHHHHHHHHH-TTTCCBCHHHHHHHHHCCCCC-CCCHHHHHHHHHHHHHHCC
T ss_pred             ccCHHHHHHHHHHHh-CCCCeEcHHHHHHHhcCcccCCCccCHHHHHHHHHHHhccC
Confidence            499999999987651 1112399999999998     99999999999999999753

>1zx4_A P1 PARB, plasmid partition PAR B protein, PARB; translation; HET: CIT; 2.98A {Enterobacteria phage P1} PDB: 2ntz_A

Probab=93.74  E-value=0.087  Score=46.51  Aligned_cols=36  Identities=19%  Similarity=0.220  Sum_probs=29.1

Q ss_pred             HHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHH
Q 046578          322 EADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIAL  362 (379)
Q Consensus       322 er~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl  362 (379)
                      -..+..+ |    ..|+|+.|||+.||||+.+|++++..|.
T Consensus        14 G~ria~~-y----~~g~tQ~eIA~~lGiSr~~VSR~L~~A~   49 (192)
T 1zx4_A           14 GLRLMRM-K----NDGMSQKDIAAKEGLSQAKVTRALQAAS   49 (192)
T ss_dssp             HHHHHHH-H----HTTCCHHHHHHHHTCCHHHHHHHHHHHT
T ss_pred             HHHHHHH-H----HcCCCHHHHHHHhCcCHHHHHHHHHHhc
Confidence            3445555 5    2679999999999999999999988765

>3q9s_A DNA-binding response regulator; DNA binding protein; 2.40A {Deinococcus radiodurans}

Probab=93.55  E-value=0.048  Score=49.46  Aligned_cols=51  Identities=27%  Similarity=0.224  Sum_probs=42.5

Q ss_pred             cCCHHHHHHHHHHhhcCCCCCCCHHHHHH-----HhCCCHHHHHHHHHHHHHHHHhH
Q 046578          317 TLSEREADILRLHFGLDGQTPVSCKEIGR-----LLSLSRERIRQIRGIALTKLQQT  368 (379)
Q Consensus       317 ~L~~rer~Vl~l~ygL~g~e~~S~~EIAe-----~LgiS~~~Vr~~~~rAl~kLR~~  368 (379)
                      .|+++|++|+.+.. -+....+|.+|||+     .++++..||+..+++.++||...
T Consensus       182 ~LT~rE~evL~ll~-~g~~~~~s~~eIa~~l~~~~l~~s~~TV~~hi~~lr~KL~~~  237 (249)
T 3q9s_A          182 RLSPKEFDILALLI-RQPGRVYSRQEIGQEIWQGRLPEGSNVVDVHMANLRAKLRDL  237 (249)
T ss_dssp             CCCHHHHHHHHHHH-HSTTCCCCHHHHHHHHHTTCSCTTCSHHHHHHHHHHHHHCCC
T ss_pred             ecCHHHHHHHHHHH-HCCCceEcHHHHHHHhcCCCCCCCccCHHHHHHHHHHHhhcC
Confidence            59999999999876 12124599999999     58899999999999999999754

>1qbj_A Protein (double-stranded RNA specific adenosine D (ADAR1)); protein-Z-DNA complex, hydrolase-DNA complex; HET: DNA; 2.10A {Homo sapiens} SCOP: a.4.5.19 PDB: 3f21_A* 3f22_A* 3f23_A* 3irr_A* 3irq_D* 2gxb_A 2acj_A 2l54_A

Probab=93.54  E-value=0.17  Score=38.22  Aligned_cols=40  Identities=15%  Similarity=0.231  Sum_probs=27.8

Q ss_pred             HHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 046578          321 READILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGI  360 (379)
Q Consensus       321 rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~r  360 (379)
                      .++.|+.+..-...++..|..|||+.||+|+.+|++.+++
T Consensus        11 ~~~~IL~~L~~~~pg~~~t~~eLA~~Lgvsr~tV~~~L~~   50 (81)
T 1qbj_A           11 QEQRILKFLEELGEGKATTAHDLSGKLGTPKKEINRVLYS   50 (81)
T ss_dssp             HHHHHHHHHHHHCTTCCBCHHHHHHHHTCCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHcCCCCCcCHHHHHHHHCcCHHHHHHHHHH
Confidence            4556665443222124799999999999999998766544

>2hqr_A Putative transcriptional regulator; phosporylation-independent response regulator, H. pylori, SY dimer, signaling protein; NMR {Helicobacter pylori}

Probab=93.49  E-value=0.024  Score=49.96  Aligned_cols=51  Identities=10%  Similarity=0.056  Sum_probs=42.2

Q ss_pred             cCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhC-----CCHHHHHHHHHHHHHHHHhH
Q 046578          317 TLSEREADILRLHFGLDGQTPVSCKEIGRLLS-----LSRERIRQIRGIALTKLQQT  368 (379)
Q Consensus       317 ~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~Lg-----iS~~~Vr~~~~rAl~kLR~~  368 (379)
                      .|+++|++|+.+..- +....+|.+|||+.++     +|..||+.++++.++||...
T Consensus       143 ~Lt~rE~~vL~~l~~-~~~~~~s~~~Ia~~l~~~~~~~s~~tv~~~i~~lr~KL~~~  198 (223)
T 2hqr_A          143 EVKGKPFEVLTHLAR-HRDQIVSKEQLLDAIWEEPEMVTPNVIEVAINQIRQKMDKP  198 (223)
T ss_dssp             CCCSTTTHHHHHHHH-TCSEEEEHHHHHHHHCCSSCSCGGGTHHHHHHHHHHHHHTT
T ss_pred             ecCHHHHHHHHHHHh-CCCCcCCHHHHHHHhcCCccCCCCcCHHHHHHHHHHHHhcC
Confidence            499999999987651 1012299999999999     99999999999999999753

>1u78_A TC3 transposase, transposable element TC3 transposase; transposon DNA, bipartite DNA-binding, HTH- motif, DNA binding protein/DNA complex; 2.69A {Caenorhabditis elegans} SCOP: a.4.1.2 a.4.1.2

Probab=93.43  E-value=0.1  Score=42.65  Aligned_cols=40  Identities=33%  Similarity=0.214  Sum_probs=32.3

Q ss_pred             cCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 046578          317 TLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGI  360 (379)
Q Consensus       317 ~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~r  360 (379)
                      .|++.++..+...+-    .|+|..+||+.||+|++||++++.+
T Consensus         6 ~~s~~~r~~i~~~~~----~G~s~~~ia~~lgis~~Tv~r~~~~   45 (141)
T 1u78_A            6 ALSDTERAQLDVMKL----LNVSLHEMSRKISRSRHCIRVYLKD   45 (141)
T ss_dssp             CCCHHHHHHHHHHHH----TTCCHHHHHHHHTCCHHHHHHHHHS
T ss_pred             cCCHHHHHHHHHHHH----cCCCHHHHHHHHCcCHHHHHHHHHc
Confidence            467777766665552    6699999999999999999998765

>3r0a_A Putative transcriptional regulator; structural genomics, PSI-biology, midwest center for structu genomics, MCSG; 2.31A {Methanosarcina mazei}

Probab=93.37  E-value=0.2  Score=40.62  Aligned_cols=46  Identities=7%  Similarity=0.214  Sum_probs=35.5

Q ss_pred             HHHhcCCHHHHHHHHHHhhcCCCCC-CCHHHHHHHhCCCHHHHHHHHHH
Q 046578          313 ELLQTLSEREADILRLHFGLDGQTP-VSCKEIGRLLSLSRERIRQIRGI  360 (379)
Q Consensus       313 ~~L~~L~~rer~Vl~l~ygL~g~e~-~S~~EIAe~LgiS~~~Vr~~~~r  360 (379)
                      ...-.|++.+..|+..... .+ .+ +|..|||+.+|++++||++.+.+
T Consensus        19 ~~~~gLt~~e~~il~~L~~-~~-~~~~t~~eLa~~l~~s~sTV~r~L~~   65 (123)
T 3r0a_A           19 KCALNLTKADLNVMKSFLN-EP-DRWIDTDALSKSLKLDVSTVQRSVKK   65 (123)
T ss_dssp             HHHHTCCHHHHHHHHHHHH-ST-TCCEEHHHHHHHHTSCHHHHHHHHHH
T ss_pred             HHHcCCCHHHHHHHHHHHH-CC-CCCcCHHHHHHHHCcCHHHHHHHHHH
Confidence            4456799999999986552 11 23 89999999999999999776554

>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=93.27  E-value=0.015  Score=53.40  Aligned_cols=51  Identities=20%  Similarity=0.320  Sum_probs=0.0

Q ss_pred             HHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhC--CCHHHHHHHHHHHHHHHH
Q 046578          311 LKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLS--LSRERIRQIRGIALTKLQ  366 (379)
Q Consensus       311 L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~Lg--iS~~~Vr~~~~rAl~kLR  366 (379)
                      +.+.+..|++.++.+.. .++    .+.|++|||+.||  +|.++|+.++.+|++.|.
T Consensus       192 l~e~i~~l~~~~~~L~~-~~~----~~ps~~EIAe~Lg~~is~~tVk~~l~~ar~~ls  244 (245)
T 3ugo_A          192 MVETINKLSRTARQLQQ-ELG----REPSYEEIAEAMGPGWDAKRVEETLKIAQEPVS  244 (245)
T ss_dssp             ----------------------------------------------------------
T ss_pred             HHHHHHHHHHHHHHHHH-HhC----CCCCHHHHHHHHCCCCCHHHHHHHHHHHhhccC
Confidence            45566778877777544 443    6799999999999  999999999999987763

>1pdn_C Protein (PRD paired); protein-DNA complex, double helix, PAX, paired domain, DNA-binding protein, gene regulation/DNA complex; HET: DNA; 2.50A {Drosophila melanogaster} SCOP: a.4.1.5

Probab=93.20  E-value=0.15  Score=40.46  Aligned_cols=42  Identities=14%  Similarity=-0.013  Sum_probs=31.7

Q ss_pred             cCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHH
Q 046578          317 TLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIAL  362 (379)
Q Consensus       317 ~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl  362 (379)
                      .+++.++.-+...+-    +++|..+||+.||+|++||++++.+-.
T Consensus        17 ~~s~~~r~~i~~~~~----~g~s~~~ia~~lgis~~Tv~~w~~~~~   58 (128)
T 1pdn_C           17 PLPNNIRLKIVEMAA----DGIRPCVISRQLRVSHGCVSKILNRYQ   58 (128)
T ss_dssp             CCCHHHHHHHHHHHH----TTCCHHHHHHHHTCCHHHHHHHHHHHH
T ss_pred             cCCHHHHHHHHHHHH----cCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence            456665555444442    569999999999999999999987753

>3r0j_A Possible two component system response transcript positive regulator PHOP; beta-alpha fold, winged helix-turn-helix; 2.50A {Mycobacterium tuberculosis}

Probab=92.85  E-value=0.17  Score=45.54  Aligned_cols=50  Identities=18%  Similarity=0.158  Sum_probs=43.3

Q ss_pred             cCCHHHHHHHHHHhhcCCCCCCCHHHHHHHh-----CCCHHHHHHHHHHHHHHHHh
Q 046578          317 TLSEREADILRLHFGLDGQTPVSCKEIGRLL-----SLSRERIRQIRGIALTKLQQ  367 (379)
Q Consensus       317 ~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~L-----giS~~~Vr~~~~rAl~kLR~  367 (379)
                      .|+++|.+|+.+.. -+.+..+|.+||++.+     +++..||+.++++.++||..
T Consensus       176 ~LT~rE~~iL~~l~-~~~~~~~s~~~i~~~lw~~~~~~~~~tv~~~i~~lr~KL~~  230 (250)
T 3r0j_A          176 SLSPTEFTLLRYFV-INAGTVLSKPKILDHVWRYDFGGDVNVVESYVSYLRRKIDT  230 (250)
T ss_dssp             CCCHHHHHHHHHHH-HTTTCCBCHHHHHHHHTTTSCCSCTHHHHHHHHHHHHHHCC
T ss_pred             ecCHHHHHHHHHHH-HCCCceEcHHHHHHHHcCCCCCCCccCHHHHHHHHHHhhcC
Confidence            59999999999875 3323779999999999     78999999999999999975

>2dbb_A Putative HTH-type transcriptional regulator PH006; ASNC family, helix-turn-helix (HTH) domain, structural genom NPPSFA; 2.00A {Pyrococcus horikoshii}

Probab=92.50  E-value=0.27  Score=41.00  Aligned_cols=42  Identities=14%  Similarity=0.339  Sum_probs=33.3

Q ss_pred             hcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 046578          316 QTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGI  360 (379)
Q Consensus       316 ~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~r  360 (379)
                      ..|++.++.|+.+...   ....|..|||+.+|+|+++|++++.+
T Consensus         5 ~~ld~~d~~il~~L~~---~~~~s~~ela~~lg~s~~tv~~~l~~   46 (151)
T 2dbb_A            5 RKLDRVDMQLVKILSE---NSRLTYRELADILNTTRQRIARRIDK   46 (151)
T ss_dssp             -CCCHHHHHHHHHHHH---CTTCCHHHHHHHTTSCHHHHHHHHHH
T ss_pred             hhCCHHHHHHHHHHHH---cCCCCHHHHHHHHCcCHHHHHHHHHH
Confidence            3589999999875442   25699999999999999999877554

>1oyi_A Double-stranded RNA-binding protein; (alpha+beta) helix-turn-helix, viral protein; NMR {Vaccinia virus} SCOP: a.4.5.19

Probab=92.44  E-value=0.13  Score=39.03  Aligned_cols=26  Identities=8%  Similarity=0.141  Sum_probs=22.7

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHHHH
Q 046578          336 TPVSCKEIGRLLSLSRERIRQIRGIA  361 (379)
Q Consensus       336 e~~S~~EIAe~LgiS~~~Vr~~~~rA  361 (379)
                      .+.|..|||+.||+|+++|++++++-
T Consensus        29 ~g~sa~eLAk~LgiSk~aVr~~L~~L   54 (82)
T 1oyi_A           29 EGATAAQLTRQLNMEKREVNKALYDL   54 (82)
T ss_dssp             STEEHHHHHHHSSSCHHHHHHHHHHH
T ss_pred             cCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence            44999999999999999999887653

>1k78_A Paired box protein PAX5; paired domain, ETS domain, transcription factor, transcription/DNA complex; 2.25A {Homo sapiens} SCOP: a.4.1.5 a.4.1.5 PDB: 1mdm_A 6pax_A

Probab=92.17  E-value=0.29  Score=40.58  Aligned_cols=42  Identities=19%  Similarity=0.106  Sum_probs=32.2

Q ss_pred             cCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHH
Q 046578          317 TLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIAL  362 (379)
Q Consensus       317 ~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl  362 (379)
                      .+++.++.-+...+-    +|+|..+||+.+|||++||++++.+-.
T Consensus        32 ~~s~e~r~~iv~~~~----~G~s~~~iA~~lgis~~TV~rw~~~~~   73 (149)
T 1k78_A           32 PLPDVVRQRIVELAH----QGVRPCDISRQLRVSHGCVSKILGRYY   73 (149)
T ss_dssp             CCCHHHHHHHHHHHH----TTCCHHHHHHHHTCCHHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHH----cCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence            466666555554442    569999999999999999999988754

>2elh_A CG11849-PA, LD40883P; structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Drosophila melanogaster}

Probab=92.03  E-value=0.3  Score=36.95  Aligned_cols=27  Identities=11%  Similarity=0.008  Sum_probs=23.3

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHHHHH
Q 046578          336 TPVSCKEIGRLLSLSRERIRQIRGIAL  362 (379)
Q Consensus       336 e~~S~~EIAe~LgiS~~~Vr~~~~rAl  362 (379)
                      .+.|..+||+.+||++++|++++.+..
T Consensus        37 ~g~s~~~iA~~~gIs~sTl~rW~k~~~   63 (87)
T 2elh_A           37 DGESKASVARDIGVPESTLRGWCKNED   63 (87)
T ss_dssp             HTCCHHHHHHHHTCCHHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence            448999999999999999999876543

>1sfx_A Conserved hypothetical protein AF2008; structural genomics, HTH MOT protein structure initiative, midwest center for structural genomics; 1.55A {Archaeoglobus fulgidus} SCOP: a.4.5.50

Probab=91.91  E-value=0.49  Score=36.23  Aligned_cols=42  Identities=21%  Similarity=0.279  Sum_probs=33.5

Q ss_pred             cCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 046578          317 TLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIA  361 (379)
Q Consensus       317 ~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rA  361 (379)
                      .|++.+..|+.....   ..+.|..|||+.+|+++++|++.+.+-
T Consensus        17 ~l~~~~~~il~~l~~---~~~~s~~ela~~l~is~~tv~~~l~~L   58 (109)
T 1sfx_A           17 SFKPSDVRIYSLLLE---RGGMRVSEIARELDLSARFVRDRLKVL   58 (109)
T ss_dssp             CCCHHHHHHHHHHHH---HCCBCHHHHHHHHTCCHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHH---cCCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence            578888888876542   256999999999999999998776553

>2cfx_A HTH-type transcriptional regulator LRPC; transcriptional regulation, DNA binding, FFRP; 2.4A {Bacillus subtilis} SCOP: a.4.5.32 d.58.4.2

Probab=91.86  E-value=0.31  Score=40.38  Aligned_cols=41  Identities=20%  Similarity=0.273  Sum_probs=32.9

Q ss_pred             cCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 046578          317 TLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGI  360 (379)
Q Consensus       317 ~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~r  360 (379)
                      .|++.++.|+.+...   ....|..|||+.+|+|+++|++++.+
T Consensus         2 ~ld~~d~~il~~L~~---~~~~s~~ela~~lg~s~~tv~~~l~~   42 (144)
T 2cfx_A            2 KLDQIDLNIIEELKK---DSRLSMRELGRKIKLSPPSVTERVRQ   42 (144)
T ss_dssp             CCCHHHHHHHHHHHH---CSCCCHHHHHHHHTCCHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHH---cCCCCHHHHHHHHCcCHHHHHHHHHH
Confidence            478889998886542   25699999999999999999877554

>2o3f_A Putative HTH-type transcriptional regulator YBBH; APC85504, putative transcriptional regulator YBBH; HET: MLY; 1.75A {Bacillus subtilis} SCOP: a.4.1.20

Probab=91.70  E-value=0.42  Score=38.12  Aligned_cols=52  Identities=12%  Similarity=0.121  Sum_probs=39.7

Q ss_pred             HHHHHHHhcCCHHHHHHHHHHhhc-CCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 046578          309 QELKELLQTLSEREADILRLHFGL-DGQTPVSCKEIGRLLSLSRERIRQIRGI  360 (379)
Q Consensus       309 ~~L~~~L~~L~~rer~Vl~l~ygL-~g~e~~S~~EIAe~LgiS~~~Vr~~~~r  360 (379)
                      ..|......|++.|+.|.....-= .....+|..|||+..|+|.+||.+..++
T Consensus        10 ~~i~~~~~~ls~~e~~ia~yil~~~~~~~~~si~elA~~~~vS~aTv~Rf~kk   62 (111)
T 2o3f_A           10 AIIQSMXHXLPPSERKLADYILAHPHXAIESTVNEISALANSSDAAVIRLCXS   62 (111)
T ss_dssp             HHHHHHGGGSCHHHHHHHHHHHHCHHHHHTCCHHHHHHHTTCCHHHHHHHHHH
T ss_pred             HHHHHHhccCCHHHHHHHHHHHHChHHHHhcCHHHHHHHHCCCHHHHHHHHHH
Confidence            356677889999999998765310 0013599999999999999999887654

>2cyy_A Putative HTH-type transcriptional regulator PH151; structural genomics, pyrococcus horikosii OT3, NPPSFA; HET: MSE GLN; 1.80A {Pyrococcus horikoshii} SCOP: a.4.5.32 d.58.4.2

Probab=91.61  E-value=0.4  Score=39.99  Aligned_cols=42  Identities=19%  Similarity=0.294  Sum_probs=33.3

Q ss_pred             cCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 046578          317 TLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIA  361 (379)
Q Consensus       317 ~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rA  361 (379)
                      .|++.++.|+.+... +  ...|+.|||+.+|+|+++|++++.+-
T Consensus         4 ~ld~~~~~il~~L~~-~--~~~s~~ela~~lg~s~~tv~~~l~~L   45 (151)
T 2cyy_A            4 PLDEIDKKIIKILQN-D--GKAPLREISKITGLAESTIHERIRKL   45 (151)
T ss_dssp             CCCHHHHHHHHHHHH-C--TTCCHHHHHHHHCSCHHHHHHHHHHH
T ss_pred             CcCHHHHHHHHHHHH-c--CCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence            478888888875541 2  46999999999999999998775553

>2d1h_A ST1889, 109AA long hypothetical transcriptional regulator; helix-turn-helix, intermolecular and intramolecular S-S bond structural genomics; 2.05A {Sulfolobus tokodaii} SCOP: a.4.5.50

Probab=91.52  E-value=0.45  Score=36.49  Aligned_cols=45  Identities=11%  Similarity=0.310  Sum_probs=34.3

Q ss_pred             HHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 046578          314 LLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGI  360 (379)
Q Consensus       314 ~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~r  360 (379)
                      ....|++.+..+|...+.-+  .+.|..|||+.+|+|+++|++.+.+
T Consensus        15 ~~~~l~~~~~~~l~~l~~~~--~~~t~~ela~~l~is~~tv~~~l~~   59 (109)
T 2d1h_A           15 CCYKITDTDVAVLLKMVEIE--KPITSEELADIFKLSKTTVENSLKK   59 (109)
T ss_dssp             HHHTCCHHHHHHHHHHHHHC--SCEEHHHHHHHHTCCHHHHHHHHHH
T ss_pred             HhhcCCHHHHHHHHHHHHcC--CCCCHHHHHHHHCcCHHHHHHHHHH
Confidence            34578998888876544112  5699999999999999999876544

>2cg4_A Regulatory protein ASNC; DNA binding, FFRP, LRP family, transcription, DNA- binding, transcription regulation; 2.4A {Escherichia coli} SCOP: a.4.5.32 d.58.4.2

Probab=91.30  E-value=0.45  Score=39.68  Aligned_cols=42  Identities=17%  Similarity=0.232  Sum_probs=33.4

Q ss_pred             cCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 046578          317 TLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIA  361 (379)
Q Consensus       317 ~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rA  361 (379)
                      .|++.++.|+.+...   ....|+.|||+.+|+|+++|++++.+-
T Consensus         5 ~ld~~d~~il~~L~~---~~~~s~~ela~~lg~s~~tv~~~l~~L   46 (152)
T 2cg4_A            5 LIDNLDRGILEALMG---NARTAYAELAKQFGVSPETIHVRVEKM   46 (152)
T ss_dssp             CCCHHHHHHHHHHHH---CTTSCHHHHHHHHTSCHHHHHHHHHHH
T ss_pred             ccCHHHHHHHHHHHH---cCCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence            478888888876532   256999999999999999998876553

>2jn6_A Protein CGL2762, transposase; GFT PSI-2, protein structure, structural genomics, protein structure initiative; NMR {Corynebacterium glutamicum} SCOP: a.4.1.19

Probab=91.29  E-value=0.36  Score=37.04  Aligned_cols=43  Identities=16%  Similarity=0.049  Sum_probs=30.1

Q ss_pred             cCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 046578          317 TLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIA  361 (379)
Q Consensus       317 ~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rA  361 (379)
                      ..++..+.-+...| +.+ ++.|..+||+.+|||+++|++++.+.
T Consensus         5 ~ys~e~k~~~v~~~-~~~-~g~s~~~ia~~~gIs~~tl~rW~~~~   47 (97)
T 2jn6_A            5 TYSEEFKRDAVALY-ENS-DGASLQQIANDLGINRVTLKNWIIKY   47 (97)
T ss_dssp             CCCHHHHHHHHHHH-TTG-GGSCHHHHHHHHTSCHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHH-HHc-CCChHHHHHHHHCcCHHHHHHHHHHH
Confidence            35565554443333 221 26999999999999999999998653

>3k2z_A LEXA repressor; winged helix-turn-helix, SOS system, autoca cleavage, DNA damage, DNA repair, DNA replication, DNA-BIND hydrolase; 1.37A {Thermotoga maritima}

Probab=91.17  E-value=0.29  Score=42.89  Aligned_cols=43  Identities=21%  Similarity=0.240  Sum_probs=32.7

Q ss_pred             cCCHHHHHHHHHHhh-cC-CCCCCCHHHHHHHhCCCHHHHHHHHH
Q 046578          317 TLSEREADILRLHFG-LD-GQTPVSCKEIGRLLSLSRERIRQIRG  359 (379)
Q Consensus       317 ~L~~rer~Vl~l~yg-L~-g~e~~S~~EIAe~LgiS~~~Vr~~~~  359 (379)
                      .|+++|++|+....- +. .+.+.|.+|||+.||+|..+|++++.
T Consensus         2 ~lt~~q~~il~~I~~~~~~~g~~~s~~eia~~lgl~~~tv~~~l~   46 (196)
T 3k2z_A            2 DLTERQRKVLLFIEEFIEKNGYPPSVREIARRFRITPRGALLHLI   46 (196)
T ss_dssp             CCCHHHHHHHHHHHHHHHHHSSCCCHHHHHHHHTSCHHHHHHHHH
T ss_pred             CcCHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCcHHHHHHHH
Confidence            589999999987531 11 11468999999999999998876654

>3ech_A MEXR, multidrug resistance operon repressor; winged helix, helix-turn-helix, protein-peptide complex; 1.80A {Pseudomonas aeruginosa} SCOP: a.4.5.28 PDB: 1lnw_A 3mex_A

Probab=91.10  E-value=0.52  Score=38.29  Aligned_cols=51  Identities=16%  Similarity=0.258  Sum_probs=37.0

Q ss_pred             HHHHHHHHhc----CCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 046578          308 KQELKELLQT----LSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIA  361 (379)
Q Consensus       308 ~~~L~~~L~~----L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rA  361 (379)
                      ...+...+..    |++.|..||...+.   ..+.|..|||+.+|++.++|++.+.+-
T Consensus        21 ~~~~~~~l~~~~~~lt~~~~~vL~~l~~---~~~~t~~eLa~~l~~~~~tvs~~l~~L   75 (142)
T 3ech_A           21 RTRIQSELDCQRLDLTPPDVHVLKLIDE---QRGLNLQDLGRQMCRDKALITRKIREL   75 (142)
T ss_dssp             HHHHHHHHHHTTCCCCHHHHHHHHHHHH---TTTCCHHHHHHHHC---CHHHHHHHHH
T ss_pred             HHHHHHHHhhccCCCCHHHHHHHHHHHh---CCCcCHHHHHHHhCCCHHHHHHHHHHH
Confidence            3445566654    89999999987663   257999999999999999998876653

>2w48_A Sorbitol operon regulator; SORC, activator, repressor, DNA-binding, transcription, transcription regulator, transcription regulation; 3.20A {Klebsiella pneumoniae}

Probab=91.02  E-value=0.27  Score=46.40  Aligned_cols=36  Identities=19%  Similarity=0.292  Sum_probs=30.5

Q ss_pred             HHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 046578          324 DILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALT  363 (379)
Q Consensus       324 ~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~  363 (379)
                      .|..++|    .+++|.+|||+.||+|+.||++.+.++.+
T Consensus        12 ~ia~l~~----~~~~~~~ela~~l~vS~~tIrRdL~~l~~   47 (315)
T 2w48_A           12 KIAQLYY----EQDMTQAQIARELGIYRTTISRLLKRGRE   47 (315)
T ss_dssp             HHHHHHH----TSCCCHHHHHHHTTCCHHHHHHHHHHHHH
T ss_pred             HHHHHHH----cCCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence            4666776    36799999999999999999999988755

>2heo_A Z-DNA binding protein 1; protein DLM1-Z-DNA complex, immune system-DNA complex; 1.70A {Mus musculus} PDB: 1j75_A

Probab=90.95  E-value=0.37  Score=34.67  Aligned_cols=40  Identities=20%  Similarity=0.272  Sum_probs=27.3

Q ss_pred             CCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 046578          318 LSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRG  359 (379)
Q Consensus       318 L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~  359 (379)
                      +++..+.||.+.-- ++ ..+|..|||+.+|+|+++|.+++.
T Consensus         8 m~~~~~~IL~~L~~-~~-~~~s~~eLA~~lglsr~tv~~~l~   47 (67)
T 2heo_A            8 GDNLEQKILQVLSD-DG-GPVAIFQLVKKCQVPKKTLNQVLY   47 (67)
T ss_dssp             -CHHHHHHHHHHHH-HC-SCEEHHHHHHHHCSCHHHHHHHHH
T ss_pred             ccHHHHHHHHHHHH-cC-CCcCHHHHHHHHCcCHHHHHHHHH
Confidence            44455566664321 11 468999999999999999876643

>2w25_A Probable transcriptional regulatory protein; transcription regulation, mutant, RV3291C, Glu104Ala, DNA-binding; 2.15A {Mycobacterium tuberculosis} PDB: 2vbw_A* 2vbx_A* 2vby_A* 2vbz_A* 2vc0_A 2vc1_A 2w24_A 2ivm_A 2w29_A 2qz8_A

Probab=90.95  E-value=0.42  Score=39.77  Aligned_cols=41  Identities=15%  Similarity=0.115  Sum_probs=33.1

Q ss_pred             cCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 046578          317 TLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGI  360 (379)
Q Consensus       317 ~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~r  360 (379)
                      .|++.++.||.+... +  ...|..|||+.+|+|+++|++++.+
T Consensus         4 ~ld~~~~~iL~~L~~-~--~~~s~~ela~~lg~s~~tv~~~l~~   44 (150)
T 2w25_A            4 ALDDIDRILVRELAA-D--GRATLSELATRAGLSVSAVQSRVRR   44 (150)
T ss_dssp             CCCHHHHHHHHHHHH-C--TTCCHHHHHHHHTSCHHHHHHHHHH
T ss_pred             ccCHHHHHHHHHHHH-c--CCCCHHHHHHHHCcCHHHHHHHHHH
Confidence            488999999886531 2  4699999999999999999877554

>2glo_A Brinker CG9653-PA; protein-DNA complex, helix-turn-helix motif, transcription/DNA complex; NMR {Drosophila melanogaster}

Probab=90.91  E-value=0.36  Score=33.61  Aligned_cols=47  Identities=9%  Similarity=0.082  Sum_probs=32.0

Q ss_pred             CCHHHHHHHHHHhhcCCCCCCC----HHHHHHHhCCCHHHHHHHHHHHHHHHHhHH
Q 046578          318 LSEREADILRLHFGLDGQTPVS----CKEIGRLLSLSRERIRQIRGIALTKLQQTN  369 (379)
Q Consensus       318 L~~rer~Vl~l~ygL~g~e~~S----~~EIAe~LgiS~~~Vr~~~~rAl~kLR~~l  369 (379)
                      .++..+.-+...+  .  .+.|    ..+||..+||+.++|++++.+ .+.++..+
T Consensus         6 ys~efK~~~~~~~--~--~g~s~~~~~~~vA~~~gIs~~tl~~W~~~-~~~~~~~~   56 (59)
T 2glo_A            6 FTPHFKLQVLESY--R--NDNDCKGNQRATARKYNIHRRQIQKWLQC-ESNLRSSV   56 (59)
T ss_dssp             CCHHHHHHHHHHH--H--HCTTTTTCHHHHHHHTTSCHHHHHHHHTT-HHHHHHHH
T ss_pred             CCHHHHHHHHHHH--H--cCCCcchHHHHHHHHHCcCHHHHHHHHHH-HHHHHHHH
Confidence            4455444443333  1  3478    999999999999999999765 45565554

>3eco_A MEPR; mutlidrug efflux pump regulator winged helix-turn-helix motif, DNA-binding, transcription, transcription regulation; 2.40A {Staphylococcus aureus} SCOP: a.4.5.0

Probab=90.85  E-value=0.8  Score=36.87  Aligned_cols=53  Identities=13%  Similarity=0.240  Sum_probs=39.9

Q ss_pred             HHHHHHHHh--cCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 046578          308 KQELKELLQ--TLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIA  361 (379)
Q Consensus       308 ~~~L~~~L~--~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rA  361 (379)
                      ...+...+.  .|++.|..|+...+. .|.++.|..|||+.+|+++++|++.+.+-
T Consensus        17 ~~~~~~~~~~~~lt~~~~~vL~~l~~-~~~~~~t~~ela~~l~~~~~tvs~~l~~L   71 (139)
T 3eco_A           17 KQKADQKLEQFDITNEQGHTLGYLYA-HQQDGLTQNDIAKALQRTGPTVSNLLRNL   71 (139)
T ss_dssp             HHHHHHHHGGGTCCHHHHHHHHHHHH-STTTCEEHHHHHHHHTCCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHcCCCHHHHHHHHHHHh-cCCCCcCHHHHHHHhCCCcccHHHHHHHH
Confidence            344555554  589999999987663 22247999999999999999998776553

>3bro_A Transcriptional regulator; helix_TURN_helix, multiple antibiotic resistance protein (MA structural genomics, PSI-2, protein structure initiative; HET: MSE; 2.04A {Oenococcus oeni} SCOP: a.4.5.28

Probab=90.79  E-value=1.1  Score=36.05  Aligned_cols=52  Identities=8%  Similarity=0.095  Sum_probs=38.5

Q ss_pred             HHHHHHHh--cCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 046578          309 QELKELLQ--TLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIA  361 (379)
Q Consensus       309 ~~L~~~L~--~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rA  361 (379)
                      ..+...+.  .|++.|..|+...+. .+..+.|..|||+.+|+++++|++.+.+-
T Consensus        21 ~~~~~~~~~~~lt~~~~~iL~~l~~-~~~~~~~~~ela~~l~~~~~tvs~~l~~L   74 (141)
T 3bro_A           21 TRFDIFAKKYDLTGTQMTIIDYLSR-NKNKEVLQRDLESEFSIKSSTATVLLQRM   74 (141)
T ss_dssp             HHHHHHHHTTTCCHHHHHHHHHHHH-TTTSCCBHHHHHHHHTCCHHHHHHHHHHH
T ss_pred             HHHHHHHHHcCCCHHHHHHHHHHHH-CCCCCcCHHHHHHHHCCCcchHHHHHHHH
Confidence            34444454  589999999887663 22237999999999999999998766553

>2p5v_A Transcriptional regulator, LRP/ASNC family; NMB0573, structu genomics; 1.99A {Neisseria meningitidis} PDB: 2p6s_A 2p6t_A

Probab=90.75  E-value=0.43  Score=40.26  Aligned_cols=41  Identities=17%  Similarity=0.161  Sum_probs=33.2

Q ss_pred             cCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 046578          317 TLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGI  360 (379)
Q Consensus       317 ~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~r  360 (379)
                      .|++.++.|+.+... +  ...|..|||+.+|+|+++|++++.+
T Consensus         7 ~ld~~~~~il~~L~~-~--~~~s~~ela~~lg~s~~tv~~~l~~   47 (162)
T 2p5v_A            7 TLDKTDIKILQVLQE-N--GRLTNVELSERVALSPSPCLRRLKQ   47 (162)
T ss_dssp             CCCHHHHHHHHHHHH-C--TTCCHHHHHHHHTSCHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHH-c--CCCCHHHHHHHHCcCHHHHHHHHHH
Confidence            488889998886542 2  4589999999999999999887654

>1i1g_A Transcriptional regulator LRPA; helix-turn-helix, LRP/ASNC family; 2.90A {Pyrococcus furiosus} SCOP: a.4.5.32 d.58.4.2

Probab=90.71  E-value=0.43  Score=39.04  Aligned_cols=41  Identities=24%  Similarity=0.311  Sum_probs=31.6

Q ss_pred             CCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 046578          318 LSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIA  361 (379)
Q Consensus       318 L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rA  361 (379)
                      |++.++.|+..... +  ...|+.|||+.+|+|+++|++.+.+-
T Consensus         2 ld~~~~~il~~L~~-~--~~~~~~ela~~lg~s~~tv~~~l~~L   42 (141)
T 1i1g_A            2 IDERDKIILEILEK-D--ARTPFTEIAKKLGISETAVRKRVKAL   42 (141)
T ss_dssp             CCSHHHHHHHHHHH-C--TTCCHHHHHHHHTSCHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHH-c--CCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence            67778888875431 2  46899999999999999998775543

>1ku9_A Hypothetical protein MJ223; putative transcription factor, homodimeric winged-helix fold, structural genomics, PSI; 2.80A {Methanocaldococcus jannaschii} SCOP: a.4.5.36

Probab=90.64  E-value=0.76  Score=37.23  Aligned_cols=42  Identities=14%  Similarity=0.264  Sum_probs=34.3

Q ss_pred             cCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 046578          317 TLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGI  360 (379)
Q Consensus       317 ~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~r  360 (379)
                      .|++.+..++.+.+ +.+ .+.|..|||+.+|+++++|++.+.+
T Consensus        23 gl~~~~~~il~~L~-~~~-~~~t~~ela~~l~~~~stvs~~l~~   64 (152)
T 1ku9_A           23 GLNKSVGAVYAILY-LSD-KPLTISDIMEELKISKGNVSMSLKK   64 (152)
T ss_dssp             TCCHHHHHHHHHHH-HCS-SCEEHHHHHHHHTCCHHHHHHHHHH
T ss_pred             CCChhHHHHHHHHH-HcC-CCCCHHHHHHHHCcCHHHHHHHHHH
Confidence            58999999987764 332 5699999999999999999877654

>3nqo_A MARR-family transcriptional regulator; structural genomics, joint center for structural genomics, J protein structure initiative, PSI-2; HET: MSE PG4; 2.20A {Clostridium difficile}

Probab=90.55  E-value=0.72  Score=39.83  Aligned_cols=53  Identities=15%  Similarity=0.186  Sum_probs=40.4

Q ss_pred             HHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 046578          308 KQELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIA  361 (379)
Q Consensus       308 ~~~L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rA  361 (379)
                      ...+...+..|++.|..||...+... ..+.|..+||+.+|++.++|++.+.+-
T Consensus        29 ~~~~~~~~~~lt~~q~~vL~~L~~~~-~~~~t~~eLa~~l~is~~tvs~~l~~L   81 (189)
T 3nqo_A           29 QIEGDKYFGILTSRQYMTILSILHLP-EEETTLNNIARKMGTSKQNINRLVANL   81 (189)
T ss_dssp             HHHHHHHHCSSCHHHHHHHHHHHHSC-GGGCCHHHHHHHHTSCHHHHHHHHHHH
T ss_pred             HHHHHHHHccCCHHHHHHHHHHHhcc-CCCcCHHHHHHHHCCCHHHHHHHHHHH
Confidence            34455666679999999998765211 257999999999999999998776553

>2pn6_A ST1022, 150AA long hypothetical transcriptional regulator; LRP/ASNC family Gln binding, structural genomics, NPPSFA; HET: GLN; 1.44A {Sulfolobus tokodaii} PDB: 2efn_A* 2e7x_A* 2e7w_A* 2yx4_A* 2efq_A* 2pmh_A* 2yx7_A* 2efp_A* 2efo_A*

Probab=90.39  E-value=0.49  Score=39.25  Aligned_cols=40  Identities=18%  Similarity=0.201  Sum_probs=31.1

Q ss_pred             CCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 046578          318 LSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGI  360 (379)
Q Consensus       318 L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~r  360 (379)
                      |++.++.|+.+..  . ....|..|||+.+|+|+++|++++.+
T Consensus         1 ld~~~~~il~~L~--~-~~~~~~~ela~~lg~s~~tv~~~l~~   40 (150)
T 2pn6_A            1 MDEIDLRILKILQ--Y-NAKYSLDEIAREIRIPKATLSYRIKK   40 (150)
T ss_dssp             CCHHHHHHHHHHT--T-CTTSCHHHHHHHHTSCHHHHHHHHHH
T ss_pred             CChHHHHHHHHHH--H-cCCCCHHHHHHHHCcCHHHHHHHHHH
Confidence            5677888887543  1 24699999999999999999877554

>3frw_A Putative Trp repressor protein; structural genomics, APC21159, PSI-2, P structure initiative; 2.05A {Ruminococcus obeum atcc 29174} PDB: 3g1c_A

Probab=90.38  E-value=0.52  Score=37.40  Aligned_cols=40  Identities=15%  Similarity=0.086  Sum_probs=27.9

Q ss_pred             CCHHHHHHHHHHhhcC--CCCCCCHHHHHHHhCCCHHHHHHH
Q 046578          318 LSEREADILRLHFGLD--GQTPVSCKEIGRLLSLSRERIRQI  357 (379)
Q Consensus       318 L~~rer~Vl~l~ygL~--g~e~~S~~EIAe~LgiS~~~Vr~~  357 (379)
                      +++.|+.-+..|+-+.  =.+|+|+.||++.+|+|..||.+.
T Consensus        37 ~T~~E~~alaqR~~Ia~lL~~G~SyreIa~~tG~StaTIsRv   78 (107)
T 3frw_A           37 CTINELLSLSQRFEVAKMLTDKRTYLDISEKTGASTATISRV   78 (107)
T ss_dssp             SCHHHHHHHHHHHHHHHHHHTTCCHHHHHHHHCCCHHHHHHH
T ss_pred             CCHHHHHHHHHHHHHHHHHHcCCCHHHHHHHHCccHHHHHHH
Confidence            6777765554332111  015699999999999999999763

>4hbl_A Transcriptional regulator, MARR family; HTH, transcription factor, DNA binding; 2.50A {Staphylococcus epidermidis}

Probab=90.30  E-value=1.1  Score=36.74  Aligned_cols=42  Identities=17%  Similarity=0.248  Sum_probs=35.1

Q ss_pred             cCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 046578          317 TLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIA  361 (379)
Q Consensus       317 ~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rA  361 (379)
                      .|++.|..||...+.   ..+.|..|||+.+|+++++|++.+.+-
T Consensus        38 ~lt~~q~~iL~~l~~---~~~~~~~eLa~~l~~~~~~vs~~l~~L   79 (149)
T 4hbl_A           38 GITYSQYLVMLTLWE---ENPQTLNSIGRHLDLSSNTLTPMLKRL   79 (149)
T ss_dssp             TCCHHHHHHHHHHHH---SSSEEHHHHHHHHTCCHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHH---CCCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence            589999999887653   367999999999999999998876654

>1y0u_A Arsenical resistance operon repressor, putative; structural genomics, protein structure initiative, PSI; HET: MSE; 1.60A {Archaeoglobus fulgidus} SCOP: a.4.5.5

Probab=90.24  E-value=2.1  Score=32.52  Aligned_cols=37  Identities=30%  Similarity=0.311  Sum_probs=28.5

Q ss_pred             CHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 046578          319 SEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGI  360 (379)
Q Consensus       319 ~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~r  360 (379)
                      ++....|+.+.   +  .+++..|||+.+|+|+++|++.+..
T Consensus        30 ~~~r~~Il~~L---~--~~~~~~eLa~~l~is~~tv~~~L~~   66 (96)
T 1y0u_A           30 NPVRRKILRML---D--KGRSEEEIMQTLSLSKKQLDYHLKV   66 (96)
T ss_dssp             CHHHHHHHHHH---H--TTCCHHHHHHHHTCCHHHHHHHHHH
T ss_pred             CHHHHHHHHHH---c--CCCCHHHHHHHHCcCHHHHHHHHHH
Confidence            46666676654   2  4599999999999999999877544

>3bpv_A Transcriptional regulator; MARR, DNA binding, transcription factor, winged helix motif, DNA-binding; 1.40A {Methanobacterium thermoautotrophicum} PDB: 3bpx_A*

Probab=90.21  E-value=0.98  Score=36.16  Aligned_cols=49  Identities=10%  Similarity=0.116  Sum_probs=37.7

Q ss_pred             HHHHHHh--cCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 046578          310 ELKELLQ--TLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIA  361 (379)
Q Consensus       310 ~L~~~L~--~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rA  361 (379)
                      .+...+.  .|++.+..|+...+.   ..+.|..|||+.+|+++++|++.+.+-
T Consensus        17 ~~~~~~~~~~l~~~~~~iL~~l~~---~~~~~~~ela~~l~~s~~tvs~~l~~L   67 (138)
T 3bpv_A           17 FIGRELGHLNLTDAQVACLLRIHR---EPGIKQDELATFFHVDKGTIARTLRRL   67 (138)
T ss_dssp             HHHHHSGGGTCCHHHHHHHHHHHH---STTCBHHHHHHHHTCCHHHHHHHHHHH
T ss_pred             HHHHHHHhcCCCHHHHHHHHHHHH---cCCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence            3444444  589999999887653   256999999999999999998776553

>3i4p_A Transcriptional regulator, ASNC family; PSI, structural genom protein structure initiative, midwest center for structural genomics; 2.30A {Agrobacterium tumefaciens str}

Probab=90.09  E-value=0.53  Score=39.86  Aligned_cols=41  Identities=15%  Similarity=0.206  Sum_probs=32.4

Q ss_pred             CCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 046578          318 LSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIA  361 (379)
Q Consensus       318 L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rA  361 (379)
                      |++.++.|+.+.- -+  ...|+.|||+.+|+|+++|++++.+-
T Consensus         1 lD~~d~~il~~L~-~~--~~~s~~~la~~lg~s~~tv~~rl~~L   41 (162)
T 3i4p_A            1 MDRLDRKILRILQ-ED--STLAVADLAKKVGLSTTPCWRRIQKM   41 (162)
T ss_dssp             CCHHHHHHHHHHT-TC--SCSCHHHHHHHHTCCHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHH-HC--CCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence            5677888887653 12  46899999999999999999886653

>1r1u_A CZRA, repressor protein; zinc, DNA binding, transcriptional regulation, winged HTH protein, transcription repressor; 2.00A {Staphylococcus aureus} SCOP: a.4.5.5 PDB: 1r1v_A 2kjb_A 2kjc_A

Probab=90.05  E-value=1.1  Score=34.77  Aligned_cols=46  Identities=20%  Similarity=0.278  Sum_probs=33.1

Q ss_pred             HHHHHhcCC-HHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 046578          311 LKELLQTLS-EREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGI  360 (379)
Q Consensus       311 L~~~L~~L~-~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~r  360 (379)
                      +..++..|. +....|+.+..  +  .+++..|||+.+|+|+++|++++.+
T Consensus        16 ~~~~~~~l~~~~r~~IL~~L~--~--~~~~~~ela~~l~is~stvs~~L~~   62 (106)
T 1r1u_A           16 VTEIFKALGDYNRIRIMELLS--V--SEASVGHISHQLNLSQSNVSHQLKL   62 (106)
T ss_dssp             HHHHHHHTCSHHHHHHHHHHH--H--CCBCHHHHHHHHTCCHHHHHHHHHH
T ss_pred             HHHHHHHhCCHHHHHHHHHHH--h--CCCCHHHHHHHHCcCHHHHHHHHHH
Confidence            445555555 55566666543  2  4589999999999999999887554

>3iwf_A Transcription regulator RPIR family; transcriptional, N-terminal, PSI, MCSG, structural genomics, midwest center structural genomics; 1.40A {Staphylococcus epidermidis}

Probab=89.96  E-value=0.77  Score=36.38  Aligned_cols=62  Identities=13%  Similarity=0.180  Sum_probs=45.9

Q ss_pred             HHHHHHHhcCCHHHHHHHHHHhh-cCCCCCCCHHHHHHHhCCCHHHHHHHHHH----HHHHHHhHHh
Q 046578          309 QELKELLQTLSEREADILRLHFG-LDGQTPVSCKEIGRLLSLSRERIRQIRGI----ALTKLQQTNI  370 (379)
Q Consensus       309 ~~L~~~L~~L~~rer~Vl~l~yg-L~g~e~~S~~EIAe~LgiS~~~Vr~~~~r----Al~kLR~~l~  370 (379)
                      ..|......|++.|+.|.....- ......+|..|+|+..|+|.+||.+..++    +..-||..+.
T Consensus         6 ~~I~~~~~~lt~~e~~ia~yil~~~~~~~~~si~elA~~~~vS~aTv~Rf~kkLGf~gf~efk~~l~   72 (107)
T 3iwf_A            6 YKIDNQYPYFTKNEKKIAQFILNYPHKVVNMTSQEIANQLETSSTSIIRLSKKVTPGGFNELKTRLS   72 (107)
T ss_dssp             HHHHHHGGGSCHHHHHHHHHHHHCHHHHTTCCHHHHHHHHTSCHHHHHHHHHHHSTTHHHHHHHHHH
T ss_pred             HHHHHHHHhcCHHHHHHHHHHHhCHHHHHHCCHHHHHHHHCCCHHHHHHHHHHhCCCCHHHHHHHHH
Confidence            46778889999999999875431 00124699999999999999999887664    4555555554

>3bdd_A Regulatory protein MARR; putative multiple antibiotic-resistance repressor, structura genomics, joint center for structural genomics, JCSG; 2.20A {Streptococcus suis}

Probab=89.79  E-value=1.1  Score=36.08  Aligned_cols=42  Identities=14%  Similarity=0.201  Sum_probs=34.6

Q ss_pred             cCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 046578          317 TLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIA  361 (379)
Q Consensus       317 ~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rA  361 (379)
                      .|++.+..|+...+.   ..+.|..|||+.+|+|+++|++.+.+-
T Consensus        28 ~l~~~~~~iL~~l~~---~~~~~~~ela~~l~is~~~vs~~l~~L   69 (142)
T 3bdd_A           28 GISLTRYSILQTLLK---DAPLHQLALQERLQIDRAAVTRHLKLL   69 (142)
T ss_dssp             SSCHHHHHHHHHHHH---HCSBCHHHHHHHHTCCHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHh---CCCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence            699999999887652   246999999999999999998776553

>2nnn_A Probable transcriptional regulator; structural genomics, PSI-2, protein structure initiative, M center for structural genomics, MCSG; 2.40A {Pseudomonas aeruginosa}

Probab=89.77  E-value=0.81  Score=36.69  Aligned_cols=49  Identities=14%  Similarity=0.135  Sum_probs=37.1

Q ss_pred             HHHHHHh-cCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 046578          310 ELKELLQ-TLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIA  361 (379)
Q Consensus       310 ~L~~~L~-~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rA  361 (379)
                      .+...+. .|++.|..|+...+.   ..+.|..|||+.+|+++++|++.+.+-
T Consensus        27 ~~~~~~~~~l~~~~~~iL~~l~~---~~~~t~~ela~~l~~~~~tvs~~l~~L   76 (140)
T 2nnn_A           27 LFANGIGNGLTPTQWAALVRLGE---TGPCPQNQLGRLTAMDAATIKGVVERL   76 (140)
T ss_dssp             HHHHHCSSCCCHHHHHHHHHHHH---HSSBCHHHHHHHTTCCHHHHHHHHHHH
T ss_pred             HHHHHHHCCCCHHHHHHHHHHHH---cCCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence            3444443 699999999887652   246999999999999999998776553

>2dk5_A DNA-directed RNA polymerase III 39 kDa polypeptide; structural genomics, winged helix domain, NPPSFA; NMR {Homo sapiens} SCOP: a.4.5.85

Probab=89.72  E-value=0.26  Score=37.97  Aligned_cols=44  Identities=11%  Similarity=0.115  Sum_probs=34.7

Q ss_pred             hcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 046578          316 QTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGI  360 (379)
Q Consensus       316 ~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~r  360 (379)
                      ..|++.|..|+...+-. |.+|.+++|||+.+|++..+|.+++.+
T Consensus        16 ~~Lt~~q~~Vl~~I~~~-g~~gi~qkeLa~~~~l~~~tvt~iLk~   59 (91)
T 2dk5_A           16 KGSDNQEKLVYQIIEDA-GNKGIWSRDVRYKSNLPLTEINKILKN   59 (91)
T ss_dssp             CCSCSSHHHHHHHHHHH-CTTCEEHHHHHHHTTCCHHHHHHHHHH
T ss_pred             cCCCHHHHHHHHHHHHc-CCCCcCHHHHHHHHCCCHHHHHHHHHH
Confidence            45888888888877622 236899999999999999998766554

>3tgn_A ADC operon repressor ADCR; helix-turn-helix, transcriptional regulator, transcription; 2.00A {Streptococcus pneumoniae}

Probab=89.57  E-value=0.63  Score=37.80  Aligned_cols=41  Identities=20%  Similarity=0.261  Sum_probs=32.7

Q ss_pred             cCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 046578          317 TLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIA  361 (379)
Q Consensus       317 ~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rA  361 (379)
                      .|++.|..|+...+.    .+.|..|||+.+|+++++|++.+.+-
T Consensus        35 ~lt~~~~~iL~~l~~----~~~t~~eLa~~l~~s~~tvs~~l~~L   75 (146)
T 3tgn_A           35 ALTNTQEHILMLLSE----ESLTNSELARRLNVSQAAVTKAIKSL   75 (146)
T ss_dssp             CCCHHHHHHHHHHTT----CCCCHHHHHHHHTCCHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHh----CCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence            378888888876552    23999999999999999998776553

>3cdh_A Transcriptional regulator, MARR family; helix-turn-hleix, structura genomics, PSI-2, protein structure initiative; 2.69A {Silicibacter pomeroyi dss-3}

Probab=89.49  E-value=1.3  Score=36.45  Aligned_cols=50  Identities=12%  Similarity=0.210  Sum_probs=37.9

Q ss_pred             HHHHHHHh--cCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 046578          309 QELKELLQ--TLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIA  361 (379)
Q Consensus       309 ~~L~~~L~--~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rA  361 (379)
                      ..+...+.  .|++.|..||...+.   ..+.|..|||+.+|++.++|++.+.+-
T Consensus        30 ~~~~~~l~~~~lt~~~~~iL~~l~~---~~~~t~~ela~~l~i~~~tvs~~l~~L   81 (155)
T 3cdh_A           30 AQFHDHIRAQGLRVPEWRVLACLVD---NDAMMITRLAKLSLMEQSRMTRIVDQM   81 (155)
T ss_dssp             HHHHHHHHHTTCCHHHHHHHHHHSS---CSCBCHHHHHHHTTCCHHHHHHHHHHH
T ss_pred             HHHHHHHHHcCCCHHHHHHHHHHHH---CCCcCHHHHHHHHCCCHHHHHHHHHHH
Confidence            33444443  689999998876652   256999999999999999998876553

>4b8x_A SCO5413, possible MARR-transcriptional regulator; winged helix motif; HET: CME; 1.25A {Streptomyces coelicolor}

Probab=89.46  E-value=0.88  Score=37.59  Aligned_cols=53  Identities=13%  Similarity=0.093  Sum_probs=39.6

Q ss_pred             HHHHHHHHh--cCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 046578          308 KQELKELLQ--TLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIA  361 (379)
Q Consensus       308 ~~~L~~~L~--~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rA  361 (379)
                      ...+...+.  .|+..|..|+.+.+. ....++|..|||+.+|++.++|.+.+.+-
T Consensus        21 ~~~~~~~l~~~gLt~~q~~vL~~L~~-~~~~~~t~~eLa~~l~~~~~tvs~~v~~L   75 (147)
T 4b8x_A           21 LGEVDAVVKPYGLTFARYEALVLLTF-SKSGELPMSKIGERLMVHPTSVTNTVDRL   75 (147)
T ss_dssp             HHHHHHHHGGGTCCHHHHHHHHHHHT-SGGGEEEHHHHHHHHTCCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHcCCCHHHHHHHHHHHH-CCCCCcCHHHHHHHHCCCHHHHHHHHHHH
Confidence            344556665  589999999887652 21245899999999999999998876553

>1uxc_A FRUR (1-57), fructose repressor; DNA-binding protein, LACI family, transc regulation; NMR {Escherichia coli} SCOP: a.35.1.5 PDB: 1uxd_A

Probab=89.44  E-value=0.29  Score=35.23  Aligned_cols=23  Identities=26%  Similarity=0.277  Sum_probs=20.9

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHHH
Q 046578          338 VSCKEIGRLLSLSRERIRQIRGI  360 (379)
Q Consensus       338 ~S~~EIAe~LgiS~~~Vr~~~~r  360 (379)
                      +|++|||+.+|+|++||++.++.
T Consensus         1 ~T~~diA~~aGVS~sTVSrvLng   23 (65)
T 1uxc_A            1 MKLDEIARLAGVSRTTASYVING   23 (65)
T ss_dssp             CCHHHHHHHHTSCHHHHHHHHHT
T ss_pred             CCHHHHHHHHCcCHHHHHHHHcC
Confidence            47899999999999999999874

>1jgs_A Multiple antibiotic resistance protein MARR; transcription regulation, DNA-binding, repressor, transcription; HET: SAL; 2.30A {Escherichia coli} SCOP: a.4.5.28

Probab=89.43  E-value=1.2  Score=35.61  Aligned_cols=52  Identities=13%  Similarity=0.164  Sum_probs=39.4

Q ss_pred             HHHHHHHHh--cCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHH
Q 046578          308 KQELKELLQ--TLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIAL  362 (379)
Q Consensus       308 ~~~L~~~L~--~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl  362 (379)
                      ...+...+.  .|++.|..|+...+.   ..+.|..+||+.+|+++++|++.+.+-.
T Consensus        20 ~~~~~~~~~~~~lt~~~~~iL~~l~~---~~~~~~~~la~~l~~~~~tvs~~l~~L~   73 (138)
T 1jgs_A           20 DRLLNEYLSPLDITAAQFKVLCSIRC---AACITPVELKKVLSVDLGALTRMLDRLV   73 (138)
T ss_dssp             HHHHHHHHTTTTSCHHHHHHHHHHHH---HSSBCHHHHHHHHTCCHHHHHHHHHHHH
T ss_pred             HHHHHHHhhhcCCCHHHHHHHHHHHh---cCCCCHHHHHHHHCCChHHHHHHHHHHH
Confidence            344555554  589999998887653   2468999999999999999988765543

>3hsr_A HTH-type transcriptional regulator SARZ; helix-turn-helix, cysteine disulfide, MARR-family transcript regulator, DNA-binding; 1.90A {Staphylococcus aureus subsp} PDB: 3hse_A 3hrm_A 4gxo_A

Probab=89.40  E-value=0.81  Score=37.12  Aligned_cols=50  Identities=12%  Similarity=0.123  Sum_probs=38.3

Q ss_pred             HHHHHHHh--cCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 046578          309 QELKELLQ--TLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIA  361 (379)
Q Consensus       309 ~~L~~~L~--~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rA  361 (379)
                      ..+...+.  .|++.|..|+...+.   ..+.|..|||+.+|+++++|++.+.+-
T Consensus        23 ~~~~~~~~~~glt~~q~~vL~~l~~---~~~~t~~eLa~~l~~~~~tvs~~l~~L   74 (140)
T 3hsr_A           23 KKYTNYLKEYDLTYTGYIVLMAIEN---DEKLNIKKLGERVFLDSGTLTPLLKKL   74 (140)
T ss_dssp             HHHHHHHGGGTCCHHHHHHHHHSCT---TCEEEHHHHHHHHTCCHHHHHHHHHHH
T ss_pred             HHHHHHHHHcCCCHHHHHHHHHHHH---cCCcCHHHHHHHHCCChhhHHHHHHHH
Confidence            34555554  589999888876542   367999999999999999998776654

>2ia0_A Putative HTH-type transcriptional regulator PF086; ASNC, PSI, structural genomics, southeast collaboratory for structural genomics; 2.37A {Pyrococcus furiosus}

Probab=89.26  E-value=0.66  Score=39.75  Aligned_cols=42  Identities=21%  Similarity=0.213  Sum_probs=32.9

Q ss_pred             hcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 046578          316 QTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGI  360 (379)
Q Consensus       316 ~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~r  360 (379)
                      ..|++.++.|+.+..- +  ...|+.|||+.+|+|+++|++++.+
T Consensus        13 ~~ld~~d~~IL~~L~~-~--~~~s~~eLA~~lglS~~tv~~~l~~   54 (171)
T 2ia0_A           13 IHLDDLDRNILRLLKK-D--ARLTISELSEQLKKPESTIHFRIKK   54 (171)
T ss_dssp             -CCCHHHHHHHHHHHH-C--TTCCHHHHHHHHTSCHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHHHHH-c--CCCCHHHHHHHHCcCHHHHHHHHHH
Confidence            3588888888886542 2  4589999999999999999877554

>2fa5_A Transcriptional regulator MARR/EMRR family; multiple antibiotics resistance repressor, XCC structural genomics, X-RAY diffraction; 1.80A {Xanthomonas campestris}

Probab=89.23  E-value=1.5  Score=36.17  Aligned_cols=51  Identities=8%  Similarity=0.077  Sum_probs=39.0

Q ss_pred             HHHHHHH---hcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHH
Q 046578          309 QELKELL---QTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIAL  362 (379)
Q Consensus       309 ~~L~~~L---~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl  362 (379)
                      ..+...+   ..|++.|..|+...+.   ..+.|..|||+.+|++.++|++.+.+-.
T Consensus        35 ~~~~~~l~~~~~lt~~~~~iL~~l~~---~~~~t~~ela~~l~is~~tvs~~l~~Le   88 (162)
T 2fa5_A           35 GNIAKVYGDRYGMAIPEWRVITILAL---YPGSSASEVSDRTAMDKVAVSRAVARLL   88 (162)
T ss_dssp             HHHHHHHHHHHCCCHHHHHHHHHHHH---STTCCHHHHHHHHTCCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHhcCCCHHHHHHHHHHHh---CCCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence            3344444   3799999999887653   2579999999999999999988766543

>2rdp_A Putative transcriptional regulator MARR; PFAM PF01047, winged-helix binding motif, structural genomics, PSI-2; 2.30A {Geobacillus stearothermophilus}

Probab=89.11  E-value=1.3  Score=36.10  Aligned_cols=50  Identities=10%  Similarity=0.121  Sum_probs=38.2

Q ss_pred             HHHHHHh--cCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHH
Q 046578          310 ELKELLQ--TLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIAL  362 (379)
Q Consensus       310 ~L~~~L~--~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl  362 (379)
                      .+...+.  .|++.|..|+...+.   ..+.|..|||+.+|+++++|++.+.+-.
T Consensus        30 ~~~~~~~~~~l~~~~~~iL~~l~~---~~~~t~~ela~~l~~~~~tvs~~l~~Le   81 (150)
T 2rdp_A           30 RGREILTNYPITPPQFVALQWLLE---EGDLTVGELSNKMYLACSTTTDLVDRME   81 (150)
T ss_dssp             HHHHHHTTSSSCHHHHHHHHHHHH---HCSBCHHHHHHHHTCCHHHHHHHHHHHH
T ss_pred             HHHHHHHhCCCCHHHHHHHHHHHH---cCCCCHHHHHHHHCCCchhHHHHHHHHH
Confidence            3445554  589999998886653   2469999999999999999988765543

>1p6r_A Penicillinase repressor; transcription regulation, DNA-binding, winged helix protein, bacterial resistance to antibiotics; NMR {Bacillus licheniformis} SCOP: a.4.5.39 PDB: 2p7c_B

Probab=89.06  E-value=0.55  Score=34.74  Aligned_cols=43  Identities=16%  Similarity=0.295  Sum_probs=34.6

Q ss_pred             hcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhC----CCHHHHHHHHHHH
Q 046578          316 QTLSEREADILRLHFGLDGQTPVSCKEIGRLLS----LSRERIRQIRGIA  361 (379)
Q Consensus       316 ~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~Lg----iS~~~Vr~~~~rA  361 (379)
                      ..|++.|..|+...+-   ..+.|..||++.++    ++.+||.+.+.+-
T Consensus         5 ~~lt~~e~~vL~~L~~---~~~~t~~ei~~~l~~~~~~s~~Tv~~~l~rL   51 (82)
T 1p6r_A            5 PQISDAELEVMKVIWK---HSSINTNEVIKELSKTSTWSPKTIQTMLLRL   51 (82)
T ss_dssp             CCCCHHHHHHHHHHHT---SSSEEHHHHHHHHHHHSCCCHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHHHHc---CCCCCHHHHHHHHhhcCCccHHHHHHHHHHH
Confidence            4689999999987653   25799999999997    7999998776553

>3g3z_A NMB1585, transcriptional regulator, MARR family; transcription factor, structur genomics, oxford protein production facility; 2.10A {Neisseria meningitidis serogroup B}

Probab=89.05  E-value=1.2  Score=36.03  Aligned_cols=50  Identities=14%  Similarity=0.135  Sum_probs=37.9

Q ss_pred             HHHHHHHh--cCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 046578          309 QELKELLQ--TLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIA  361 (379)
Q Consensus       309 ~~L~~~L~--~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rA  361 (379)
                      ..+...+.  .|++.|..||...+.   ..+.|..|||+.+|++.++|++.+.+-
T Consensus        18 ~~~~~~~~~~~lt~~q~~iL~~l~~---~~~~t~~eLa~~l~~~~~tvs~~l~~L   69 (145)
T 3g3z_A           18 NVFDKWIGQQDLNYNLFAVLYTLAT---EGSRTQKHIGEKWSLPKQTVSGVCKTL   69 (145)
T ss_dssp             HHHHHHHHTTTCCHHHHHHHHHHHH---HCSBCHHHHHHHHTCCHHHHHHHHHHH
T ss_pred             HHHHHHHHHcCCCHHHHHHHHHHHH---CCCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence            33444443  589999999887653   245999999999999999998776553

>2qww_A Transcriptional regulator, MARR family; YP_013417.1, multiple antibiotic-resistance repressor (MARR) structural genomics; HET: MSE; 2.07A {Listeria monocytogenes str}

Probab=89.05  E-value=1.3  Score=36.36  Aligned_cols=42  Identities=7%  Similarity=0.128  Sum_probs=34.8

Q ss_pred             cCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 046578          317 TLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIA  361 (379)
Q Consensus       317 ~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rA  361 (379)
                      .|++.|..|+...+.   ..+.|..|||+.+|++.++|++.+.+-
T Consensus        38 ~lt~~~~~iL~~l~~---~~~~t~~eLa~~l~~~~~tvs~~l~~L   79 (154)
T 2qww_A           38 GLTIQQLAMINVIYS---TPGISVADLTKRLIITGSSAAANVDGL   79 (154)
T ss_dssp             TCCHHHHHHHHHHHH---STTEEHHHHHHHHTCCHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHH---CCCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence            699999999887653   256999999999999999998876654

>3bj6_A Transcriptional regulator, MARR family; helix-turn-helix, trasnscription regulator, STR genomics, PSI-2, protein structure initiative; 2.01A {Silicibacter pomeroyi dss-3}

Probab=88.81  E-value=1.3  Score=36.02  Aligned_cols=42  Identities=17%  Similarity=0.157  Sum_probs=34.5

Q ss_pred             cCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 046578          317 TLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIA  361 (379)
Q Consensus       317 ~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rA  361 (379)
                      .|++.|..|+...+.   ..+.|..+||+.+|+++++|++.+.+-
T Consensus        37 ~lt~~~~~iL~~l~~---~~~~t~~ela~~l~~~~~~vs~~l~~L   78 (152)
T 3bj6_A           37 GVTVGQRAILEGLSL---TPGATAPQLGAALQMKRQYISRILQEV   78 (152)
T ss_dssp             TCCHHHHHHHHHHHH---STTEEHHHHHHHHTCCHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHh---CCCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence            689999999887653   246999999999999999998776553

>3nrv_A Putative transcriptional regulator (MARR/EMRR FAM; PSI-2, protein structure initiati structural genomics; HET: MSE; 2.00A {Acinetobacter SP}

Probab=88.78  E-value=0.81  Score=37.28  Aligned_cols=43  Identities=14%  Similarity=0.170  Sum_probs=35.0

Q ss_pred             cCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHH
Q 046578          317 TLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIAL  362 (379)
Q Consensus       317 ~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl  362 (379)
                      .|++.|..|+...+.   ..+.|..|||+.+|+++++|++.+.+-.
T Consensus        37 ~l~~~~~~iL~~l~~---~~~~t~~ela~~l~~~~~tvs~~l~~Le   79 (148)
T 3nrv_A           37 GIGMTEWRIISVLSS---ASDCSVQKISDILGLDKAAVSRTVKKLE   79 (148)
T ss_dssp             TCCHHHHHHHHHHHH---SSSBCHHHHHHHHTCCHHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHc---CCCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence            588999888887653   2479999999999999999988766543

>2p5k_A Arginine repressor; DNA-binding domain, winged helix-turn-helix (WHTH), DNA binding protein; 1.00A {Bacillus subtilis} SCOP: a.4.5.3 PDB: 2p5l_C*

Probab=88.75  E-value=0.59  Score=32.61  Aligned_cols=24  Identities=8%  Similarity=0.091  Sum_probs=22.2

Q ss_pred             CCCCHHHHHHHh-----CCCHHHHHHHHH
Q 046578          336 TPVSCKEIGRLL-----SLSRERIRQIRG  359 (379)
Q Consensus       336 e~~S~~EIAe~L-----giS~~~Vr~~~~  359 (379)
                      ...|.+||++.|     ++|..||++.+.
T Consensus        18 ~~~t~~el~~~l~~~~~~vs~~Tv~R~L~   46 (64)
T 2p5k_A           18 EIETQDELVDMLKQDGYKVTQATVSRDIK   46 (64)
T ss_dssp             CCCSHHHHHHHHHHTTCCCCHHHHHHHHH
T ss_pred             CCCCHHHHHHHHHHhCCCcCHHHHHHHHH
Confidence            579999999999     999999998877

>2htj_A P fimbrial regulatory protein KS71A; winged helix-turn-helix, PAP PILI, transcription activator; NMR {Escherichia coli} SCOP: a.4.5.73

Probab=88.74  E-value=0.97  Score=33.38  Aligned_cols=25  Identities=16%  Similarity=0.092  Sum_probs=21.4

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHHH
Q 046578          336 TPVSCKEIGRLLSLSRERIRQIRGI  360 (379)
Q Consensus       336 e~~S~~EIAe~LgiS~~~Vr~~~~r  360 (379)
                      .+.|..|||+.+|+|+++|++.+.+
T Consensus        13 ~~~s~~eLa~~lgvs~~tv~r~L~~   37 (81)
T 2htj_A           13 NGGKTAEIAEALAVTDYQARYYLLL   37 (81)
T ss_dssp             CCCCHHHHHHHHTSCHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHCcCHHHHHHHHHH
Confidence            4589999999999999999776554

>2gxg_A 146AA long hypothetical transcriptional regulator; winged helix; 1.45A {Sulfolobus tokodaii} PDB: 2eb7_A 2yr2_A 3gez_A 3gf2_A* 3gfi_A 3gfm_A 3gfj_A 3gfl_A

Probab=88.72  E-value=1.6  Score=35.14  Aligned_cols=47  Identities=17%  Similarity=0.105  Sum_probs=36.5

Q ss_pred             HHHHHh--cCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 046578          311 LKELLQ--TLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIA  361 (379)
Q Consensus       311 L~~~L~--~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rA  361 (379)
                      +...+.  .|++.|..|+...+    ..+.|..|||+.+|+++++|++.+.+-
T Consensus        26 ~~~~~~~~~l~~~~~~iL~~l~----~~~~~~~ela~~l~~s~~tvs~~l~~L   74 (146)
T 2gxg_A           26 LNRRLGELNLSYLDFLVLRATS----DGPKTMAYLANRYFVTQSAITASVDKL   74 (146)
T ss_dssp             HHHHHHTTTCCHHHHHHHHHHT----TSCBCHHHHHHHTTCCHHHHHHHHHHH
T ss_pred             HHHHHHhcCCCHHHHHHHHHHh----cCCcCHHHHHHHhCCCchhHHHHHHHH
Confidence            444443  58999999887655    256999999999999999998776553

>2x4h_A Hypothetical protein SSO2273; transcription; 2.30A {Sulfolobus solfataricus}

Probab=88.70  E-value=0.8  Score=37.17  Aligned_cols=47  Identities=17%  Similarity=0.121  Sum_probs=33.5

Q ss_pred             HhcCCHHHHHHHHHHhhc-CCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 046578          315 LQTLSEREADILRLHFGL-DGQTPVSCKEIGRLLSLSRERIRQIRGIA  361 (379)
Q Consensus       315 L~~L~~rer~Vl~l~ygL-~g~e~~S~~EIAe~LgiS~~~Vr~~~~rA  361 (379)
                      +..|++.+..++...+.+ ....+.|..+||+.+|+++++|++.+.+-
T Consensus         8 ~~~lt~~~~~~L~~l~~l~~~~~~~s~~ela~~l~is~~tv~~~l~~L   55 (139)
T 2x4h_A            8 MSNLSRREFSYLLTIKRYNDSGEGAKINRIAKDLKIAPSSVFEEVSHL   55 (139)
T ss_dssp             ---CCHHHHHHHHHHHHHHTTTSCBCHHHHHHHHTCCHHHHHHHHHHH
T ss_pred             HhhcCHHHHHHHHHHHHHHhcCCCcCHHHHHHHhCCChHHHHHHHHHH
Confidence            346888888887755432 11257899999999999999998776553

>1jhf_A LEXA repressor; LEXA SOS repressor, hydrolase; 1.80A {Escherichia coli} SCOP: a.4.5.2 b.87.1.1 PDB: 1jhh_A 3jso_A* 3jsp_A* 3k3r_E* 1jhc_A 1jhe_A 1lea_A 1leb_A

Probab=88.66  E-value=0.31  Score=42.74  Aligned_cols=45  Identities=18%  Similarity=0.200  Sum_probs=32.6

Q ss_pred             hcCCHHHHHHHHHHhhcCCCCCC--CHHHHHHHhCCC-HHHHHHHHHH
Q 046578          316 QTLSEREADILRLHFGLDGQTPV--SCKEIGRLLSLS-RERIRQIRGI  360 (379)
Q Consensus       316 ~~L~~rer~Vl~l~ygL~g~e~~--S~~EIAe~LgiS-~~~Vr~~~~r  360 (379)
                      ..|+++|+.++...-.+-...++  |++|+|+.+|++ +++|++++.+
T Consensus         2 ~~lt~~q~~i~~~i~~~~~~~g~~ps~~elA~~lgiss~~tv~~~~~~   49 (202)
T 1jhf_A            2 KALTARQQEVFDLIRDHISQTGMPPTRAEIAQRLGFRSPNAAEEHLKA   49 (202)
T ss_dssp             CCCCHHHHHHHHHHHHHHHHHSSCCCHHHHHHHTTCSSHHHHHHHHHH
T ss_pred             CccCHHHHHHHHHHHHHHHHhCCCccHHHHHHHhCCCChHHHHHHHHH
Confidence            35888888877643211111357  999999999999 9999988663

>2k27_A Paired box protein PAX-8; paired domain, solution structure, triple frequency, 3D NMR, induced FIT, alternative splicing, developmental protein; NMR {Homo sapiens}

Probab=88.65  E-value=0.26  Score=41.48  Aligned_cols=40  Identities=23%  Similarity=0.127  Sum_probs=30.0

Q ss_pred             cCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 046578          317 TLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGI  360 (379)
Q Consensus       317 ~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~r  360 (379)
                      .++..++.-+...+-    +++|..+||+.||||++||++++.+
T Consensus        25 ~~s~e~r~~ii~l~~----~G~s~~~IA~~lgis~~TV~rwl~r   64 (159)
T 2k27_A           25 PLPEVVRQRIVDLAH----QGVRPCDISRQLRVSHGCVSKILGR   64 (159)
T ss_dssp             SSCHHHHHHHHHHHH----HTCCHHHHHHHHTCCSHHHHHHHCC
T ss_pred             CCCHHHHHHHHHHHH----cCCCHHHHHHHHCcCHHHHHHHHHH
Confidence            355555554444442    5699999999999999999998765

>2pex_A Transcriptional regulator OHRR; transcription regulator; 1.90A {Xanthomonas campestris} PDB: 2pfb_A

Probab=88.63  E-value=1.2  Score=36.57  Aligned_cols=51  Identities=18%  Similarity=0.191  Sum_probs=38.4

Q ss_pred             HHHHHHHh--cCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHH
Q 046578          309 QELKELLQ--TLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIAL  362 (379)
Q Consensus       309 ~~L~~~L~--~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl  362 (379)
                      ..+...+.  .|++.|..|+...+.   ..+.|..|||+.+|++.++|++.+.+-.
T Consensus        34 ~~~~~~~~~~~l~~~~~~iL~~l~~---~~~~t~~ela~~l~~s~~tvs~~l~~Le   86 (153)
T 2pex_A           34 KLYRGLLKALDLTYPQYLVMLVLWE---TDERSVSEIGERLYLDSATLTPLLKRLQ   86 (153)
T ss_dssp             HHHHHHTTTTTCCHHHHHHHHHHHH---SCSEEHHHHHHHHTCCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHCCCCHHHHHHHHHHHh---CCCcCHHHHHHHhCCCcccHHHHHHHHH
Confidence            34444443  588999988876653   2569999999999999999988766543

>3oop_A LIN2960 protein; protein structure initiative, PSI-2, structural genomics, MI center for structural genomics, MCSG, unknown function; 1.78A {Listeria innocua}

Probab=88.52  E-value=0.98  Score=36.59  Aligned_cols=50  Identities=16%  Similarity=0.149  Sum_probs=38.0

Q ss_pred             HHHHHHHh--cCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 046578          309 QELKELLQ--TLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIA  361 (379)
Q Consensus       309 ~~L~~~L~--~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rA  361 (379)
                      ..+...+.  .|++.|..|+...+.   ..+.|..|||+.+|+++++|.+.+.+-
T Consensus        24 ~~~~~~~~~~~lt~~~~~iL~~l~~---~~~~t~~eLa~~l~~~~~~vs~~l~~L   75 (143)
T 3oop_A           24 LFLMRSIASYDVTPEQWSVLEGIEA---NEPISQKEIALWTKKDTPTVNRIVDVL   75 (143)
T ss_dssp             HHHHHHTTTSSSCHHHHHHHHHHHH---HSSEEHHHHHHHHTCCHHHHHHHHHHH
T ss_pred             HHHHHHhhhCCCCHHHHHHHHHHHH---cCCcCHHHHHHHHCCCHhhHHHHHHHH
Confidence            34444444  589999999887653   256999999999999999998776553

>2lkp_A Transcriptional regulator, ARSR family; symmetric homodimer, NI(II) binding protein, DNA binding Pro transcription regulator; NMR {Mycobacterium tuberculosis}

Probab=88.51  E-value=1.8  Score=34.13  Aligned_cols=40  Identities=8%  Similarity=0.164  Sum_probs=31.6

Q ss_pred             CCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 046578          318 LSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIA  361 (379)
Q Consensus       318 L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rA  361 (379)
                      .++.+..||....-    .+.|..|||+.+|+|+++|++.+.+-
T Consensus        30 ~~~~~~~il~~L~~----~~~s~~ela~~l~is~stvsr~l~~L   69 (119)
T 2lkp_A           30 ATPSRLMILTQLRN----GPLPVTDLAEAIGMEQSAVSHQLRVL   69 (119)
T ss_dssp             CCHHHHHHHHHHHH----CCCCHHHHHHHHSSCHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHH----CCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence            45777778776552    36999999999999999998876553

>3jth_A Transcription activator HLYU; transcription factor, RTXA, DNA-binding, transcription regulation; 2.00A {Vibrio vulnificus}

Probab=88.39  E-value=0.84  Score=34.83  Aligned_cols=46  Identities=26%  Similarity=0.290  Sum_probs=31.5

Q ss_pred             HHHHHhcCC-HHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 046578          311 LKELLQTLS-EREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGI  360 (379)
Q Consensus       311 L~~~L~~L~-~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~r  360 (379)
                      +..++..|. +....|+.+..   . .+.|..|||+.+|+|+++|++.+..
T Consensus        13 ~~~~~~~l~~~~r~~Il~~L~---~-~~~~~~ela~~l~is~~tvs~~L~~   59 (98)
T 3jth_A           13 AVVLLKAMANERRLQILCMLH---N-QELSVGELCAKLQLSQSALSQHLAW   59 (98)
T ss_dssp             HHHHHHHHCSHHHHHHHHHTT---T-SCEEHHHHHHHHTCCHHHHHHHHHH
T ss_pred             HHHHHHHcCCHHHHHHHHHHh---c-CCCCHHHHHHHHCcCHHHHHHHHHH
Confidence            444455454 55555554432   2 5699999999999999999876543

>1sfu_A 34L protein; protein/Z-DNA complex, DNA binding protein/DNA complex; 2.00A {Yaba-like disease virus} SCOP: a.4.5.19

Probab=88.25  E-value=0.95  Score=33.53  Aligned_cols=27  Identities=11%  Similarity=0.085  Sum_probs=22.3

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHHHHH
Q 046578          336 TPVSCKEIGRLLSLSRERIRQIRGIAL  362 (379)
Q Consensus       336 e~~S~~EIAe~LgiS~~~Vr~~~~rAl  362 (379)
                      +..|..+||.+||++.+.|.+.+++-.
T Consensus        28 ~~~Ta~~IAkkLg~sK~~vNr~LY~L~   54 (75)
T 1sfu_A           28 DYTTAISLSNRLKINKKKINQQLYKLQ   54 (75)
T ss_dssp             CEECHHHHHHHTTCCHHHHHHHHHHHH
T ss_pred             cchHHHHHHHHHCCCHHHHHHHHHHHH
Confidence            448999999999999988887776643

>3k0l_A Repressor protein; helix-turn-helix, structural genomics, PSI-2, protein structure initiative, midwest center for structural genomics, MCSG; 2.35A {Acinetobacter SP}

Probab=87.99  E-value=1.3  Score=36.88  Aligned_cols=50  Identities=14%  Similarity=0.076  Sum_probs=38.5

Q ss_pred             HHHHHHHh--cCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 046578          309 QELKELLQ--TLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIA  361 (379)
Q Consensus       309 ~~L~~~L~--~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rA  361 (379)
                      ..+...+.  .|++.|..||...+.   ..+.|..|||+.+|++.++|.+.+.+-
T Consensus        33 ~~~~~~l~~~glt~~q~~iL~~l~~---~~~~t~~eLa~~l~~~~~tvs~~l~~L   84 (162)
T 3k0l_A           33 KYLTEHLSALEISLPQFTALSVLAA---KPNLSNAKLAERSFIKPQSANKILQDL   84 (162)
T ss_dssp             HHHHHHHHTTTCCHHHHHHHHHHHH---CTTCCHHHHHHHHTSCGGGHHHHHHHH
T ss_pred             HHHHHHhhhcCCCHHHHHHHHHHHH---CCCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence            34444444  689999999987653   256999999999999999998776553

>3s2w_A Transcriptional regulator, MARR family; structural genomics, PSI-biology, protein structure initiati midwest center for structural genomics; 2.45A {Methanosarcina mazei}

Probab=87.96  E-value=0.98  Score=37.43  Aligned_cols=51  Identities=4%  Similarity=0.090  Sum_probs=39.2

Q ss_pred             HHHHHHHHh--cCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 046578          308 KQELKELLQ--TLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIA  361 (379)
Q Consensus       308 ~~~L~~~L~--~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rA  361 (379)
                      ...+...+.  .|++.|..||...+.   ..+.|..|||+.+|+++++|++.+.+-
T Consensus        36 ~~~~~~~l~~~~lt~~q~~vL~~l~~---~~~~t~~eLa~~l~~~~~tvs~~l~~L   88 (159)
T 3s2w_A           36 QIYIGKKIEPYGIGSGQFPFLMRLYR---EDGINQESLSDYLKIDKGTTARAIQKL   88 (159)
T ss_dssp             HHHHHHHHGGGTCCTTTHHHHHHHHH---SCSEEHHHHHHHHTCCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHcCCCHHHHHHHHHHHH---CCCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence            344555554  589999998886653   356999999999999999998876654

>2nyx_A Probable transcriptional regulatory protein, RV14; alpha/beta, structural genomics, PSI-2; 2.30A {Mycobacterium tuberculosis}

Probab=87.92  E-value=1.2  Score=37.49  Aligned_cols=42  Identities=10%  Similarity=0.153  Sum_probs=34.6

Q ss_pred             cCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 046578          317 TLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIA  361 (379)
Q Consensus       317 ~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rA  361 (379)
                      .|++.|..||...+.   ..+.|..|||+.+|++.++|++.+.+-
T Consensus        42 ~lt~~~~~iL~~L~~---~~~~t~~eLa~~l~is~~tvs~~l~~L   83 (168)
T 2nyx_A           42 NITIPQFRTLVILSN---HGPINLATLATLLGVQPSATGRMVDRL   83 (168)
T ss_dssp             SCCHHHHHHHHHHHH---HCSEEHHHHHHHHTSCHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHH---cCCCCHHHHHHHhCCCHHHHHHHHHHH
Confidence            689999999887653   246999999999999999998876553

>1s3j_A YUSO protein; structural genomics, MARR transcriptional regulator family, PSI, protein structure initiative; HET: MSE; 2.25A {Bacillus subtilis} SCOP: a.4.5.28

Probab=87.76  E-value=1.2  Score=36.51  Aligned_cols=42  Identities=7%  Similarity=0.060  Sum_probs=34.6

Q ss_pred             cCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 046578          317 TLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIA  361 (379)
Q Consensus       317 ~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rA  361 (379)
                      .|++.|..|+...+.   ..+.|..+||+.+|+++++|++.+.+-
T Consensus        34 ~l~~~~~~iL~~l~~---~~~~t~~ela~~l~~s~~tvs~~l~~L   75 (155)
T 1s3j_A           34 GVTPAQLFVLASLKK---HGSLKVSEIAERMEVKPSAVTLMADRL   75 (155)
T ss_dssp             TCCHHHHHHHHHHHH---HSEEEHHHHHHHHTSCHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHH---cCCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence            799999999887652   246899999999999999998776553

>3pqk_A Biofilm growth-associated repressor; helix-turn-helix motif, winged-helix fold, transcriptional R DNA binding, transcription; 2.09A {Xylella fastidiosa} PDB: 3pqj_A

Probab=87.67  E-value=1.5  Score=33.63  Aligned_cols=46  Identities=20%  Similarity=0.287  Sum_probs=31.5

Q ss_pred             HHHHHhcCC-HHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 046578          311 LKELLQTLS-EREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGI  360 (379)
Q Consensus       311 L~~~L~~L~-~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~r  360 (379)
                      +..++..|. |.-..|+.+..  +  .+.+..|||+.+|+|+++|++++.+
T Consensus        13 ~~~~~~~l~~~~r~~Il~~L~--~--~~~~~~ela~~l~is~~tvs~~L~~   59 (102)
T 3pqk_A           13 VANLLKTLSHPVRLMLVCTLV--E--GEFSVGELEQQIGIGQPTLSQQLGV   59 (102)
T ss_dssp             HHHHHHHHCSHHHHHHHHHHH--T--CCBCHHHHHHHHTCCTTHHHHHHHH
T ss_pred             HHHHHHHcCCHHHHHHHHHHH--h--CCCCHHHHHHHHCcCHHHHHHHHHH
Confidence            445555554 44555555433  2  4599999999999999999876543

>3cuo_A Uncharacterized HTH-type transcriptional regulato; DNA-binding transcriptional regulator, structural genomics, MCSG; 2.00A {Escherichia coli K12}

Probab=87.66  E-value=0.9  Score=34.34  Aligned_cols=45  Identities=22%  Similarity=0.203  Sum_probs=32.0

Q ss_pred             HHHhcC-CHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 046578          313 ELLQTL-SEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGI  360 (379)
Q Consensus       313 ~~L~~L-~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~r  360 (379)
                      .++..| ++.+..|+....  . ..+.|..|||+.+|+|+++|++.+.+
T Consensus        16 ~~~~~l~~~~~~~il~~l~--~-~~~~s~~ela~~l~is~~tvs~~l~~   61 (99)
T 3cuo_A           16 ALLKAMSHPKRLLILCMLS--G-SPGTSAGELTRITGLSASATSQHLAR   61 (99)
T ss_dssp             HHHHHHCSHHHHHHHHHHT--T-CCSEEHHHHHHHHCCCHHHHHHHHHH
T ss_pred             HHHHHhCChHHHHHHHHHH--h-CCCcCHHHHHHHHCcCHHHHHHHHHH
Confidence            334434 466777776543  2 24799999999999999999877554

>3fm5_A Transcriptional regulator; MCSG, PF04017, PSI, MARR, structu genomics, protein structure initiative, midwest center for structural genomics; HET: GOL; 2.00A {Rhodococcus jostii}

Probab=87.60  E-value=1.5  Score=35.84  Aligned_cols=51  Identities=16%  Similarity=0.165  Sum_probs=38.2

Q ss_pred             HHHHHHHHh--cCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 046578          308 KQELKELLQ--TLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGI  360 (379)
Q Consensus       308 ~~~L~~~L~--~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~r  360 (379)
                      ...+...+.  .|++.|..||...+. . .++.|..|||+.+|+++++|++.+.+
T Consensus        25 ~~~~~~~l~~~glt~~q~~vL~~l~~-~-~~~~t~~eLa~~l~i~~~tvs~~l~~   77 (150)
T 3fm5_A           25 LGAVNKALVPTGLRVRSYSVLVLACE-Q-AEGVNQRGVAATMGLDPSQIVGLVDE   77 (150)
T ss_dssp             HHHHHHHHGGGTCCHHHHHHHHHHHH-S-TTCCCSHHHHHHHTCCHHHHHHHHHH
T ss_pred             HHHHHHHHHHcCCCHHHHHHHHHHHh-C-CCCcCHHHHHHHHCCCHhHHHHHHHH
Confidence            344555554  589999999886542 2 24689999999999999999887655

>2fbh_A Transcriptional regulator PA3341; MARR, transcription regulator, APC5857, structural genomics, protein structure initiative; 1.80A {Pseudomonas aeruginosa} SCOP: a.4.5.28

Probab=87.44  E-value=1.4  Score=35.59  Aligned_cols=51  Identities=14%  Similarity=0.113  Sum_probs=37.6

Q ss_pred             HHHHHHHh--cCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 046578          309 QELKELLQ--TLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIA  361 (379)
Q Consensus       309 ~~L~~~L~--~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rA  361 (379)
                      ..+...+.  .|++.|..|+...+. . ..+.|..+||+.+|+++++|++.+.+-
T Consensus        24 ~~~~~~~~~~~l~~~~~~iL~~l~~-~-~~~~t~~~la~~l~~s~~~vs~~l~~L   76 (146)
T 2fbh_A           24 AELDRRLSHLGLSQARWLVLLHLAR-H-RDSPTQRELAQSVGVEGPTLARLLDGL   76 (146)
T ss_dssp             HHHHHHTGGGCCTTTHHHHHHHHHH-C-SSCCBHHHHHHHHTCCHHHHHHHHHHH
T ss_pred             HHHHHHHHHCCCCHHHHHHHHHHHH-c-CCCCCHHHHHHHhCCChhhHHHHHHHH
Confidence            33444444  588889888876621 2 267999999999999999998776553

>1lj9_A Transcriptional regulator SLYA; HTH DNA binding protein, structural genomics, PSI, protein structure initiative; 1.60A {Enterococcus faecalis} SCOP: a.4.5.28

Probab=87.42  E-value=1.1  Score=36.20  Aligned_cols=50  Identities=10%  Similarity=0.021  Sum_probs=37.6

Q ss_pred             HHHHHHHh--cCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 046578          309 QELKELLQ--TLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIA  361 (379)
Q Consensus       309 ~~L~~~L~--~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rA  361 (379)
                      ..+...+.  .|++.+..|+...+.   ..+.|..+||+.+|+++++|++.+.+-
T Consensus        16 ~~~~~~~~~~~lt~~~~~iL~~l~~---~~~~t~~~la~~l~~s~~~vs~~l~~L   67 (144)
T 1lj9_A           16 SISNIEFKELSLTRGQYLYLVRVCE---NPGIIQEKIAELIKVDRTTAARAIKRL   67 (144)
T ss_dssp             HHHHHHTGGGTCTTTHHHHHHHHHH---STTEEHHHHHHHHTCCHHHHHHHHHHH
T ss_pred             HHHHHHHHHcCCCHHHHHHHHHHHH---CcCcCHHHHHHHHCCCHhHHHHHHHHH
Confidence            33444444  588889888876653   246899999999999999998776554

>3cjn_A Transcriptional regulator, MARR family; silicibacter pomeroy structural genomics, PSI-2, protein structure initiative; 1.95A {Silicibacter pomeroyi dss-3}

Probab=87.28  E-value=0.86  Score=37.81  Aligned_cols=42  Identities=10%  Similarity=0.093  Sum_probs=34.7

Q ss_pred             cCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 046578          317 TLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIA  361 (379)
Q Consensus       317 ~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rA  361 (379)
                      .|++.|..|+...+.   ..+.|..|||+.+|+++++|++.+.+-
T Consensus        49 ~lt~~~~~iL~~l~~---~~~~t~~ela~~l~is~~tvs~~l~~L   90 (162)
T 3cjn_A           49 GLSTAKMRALAILSA---KDGLPIGTLGIFAVVEQSTLSRALDGL   90 (162)
T ss_dssp             TCCHHHHHHHHHHHH---SCSEEHHHHHHHHTCCHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHH---CCCCCHHHHHHHHCCChhHHHHHHHHH
Confidence            589999999887653   256999999999999999998876553

>2a61_A Transcriptional regulator TM0710; APC4350, MCSG, midwest center for structural genomics, PSI, protein structure initiative, MARR; 1.80A {Thermotoga maritima} SCOP: a.4.5.28

Probab=87.26  E-value=0.91  Score=36.70  Aligned_cols=42  Identities=17%  Similarity=0.241  Sum_probs=34.3

Q ss_pred             cCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 046578          317 TLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIA  361 (379)
Q Consensus       317 ~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rA  361 (379)
                      .|++.|..|+...+.   ..+.|..+||+.+|+++++|++.+.+-
T Consensus        30 ~l~~~~~~iL~~l~~---~~~~~~~~la~~l~~s~~tvs~~l~~L   71 (145)
T 2a61_A           30 GITPAQFDILQKIYF---EGPKRPGELSVLLGVAKSTVTGLVKRL   71 (145)
T ss_dssp             TCCHHHHHHHHHHHH---HCCBCHHHHHHHHTCCHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHH---cCCCCHHHHHHHHCCCchhHHHHHHHH
Confidence            589999988887653   246999999999999999998776553

>2zkz_A Transcriptional repressor PAGR; protein-DNA, HTH motif, dimer, DN binding, transcription regulation; 2.00A {Bacillus anthracis}

Probab=87.14  E-value=1.1  Score=34.53  Aligned_cols=39  Identities=13%  Similarity=0.170  Sum_probs=29.0

Q ss_pred             CHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 046578          319 SEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGI  360 (379)
Q Consensus       319 ~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~r  360 (379)
                      +|....|+.....   ..+.+..|||+.+|+|+++|++++..
T Consensus        26 ~~~Rl~IL~~l~~---~~~~~~~ela~~l~is~stvs~hL~~   64 (99)
T 2zkz_A           26 HPMRLKIVNELYK---HKALNVTQIIQILKLPQSTVSQHLCK   64 (99)
T ss_dssp             SHHHHHHHHHHHH---HSCEEHHHHHHHHTCCHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHH---CCCcCHHHHHHHHCcCHHHHHHHHHH
Confidence            4666677733221   14699999999999999999988553

>2l0k_A Stage III sporulation protein D; SPOIIID, solution structure, DNA binding, bacillus subti transcription factor, transcription; NMR {Bacillus subtilis}

Probab=86.88  E-value=0.7  Score=35.75  Aligned_cols=38  Identities=16%  Similarity=0.161  Sum_probs=28.5

Q ss_pred             HHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 046578          320 EREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIA  361 (379)
Q Consensus       320 ~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rA  361 (379)
                      +++..|+.+..-    .+.|..+||+.+|+|..||++.+..-
T Consensus         7 ~R~~~I~~~l~~----~~~ti~dlA~~~gVS~~TVsR~L~~~   44 (93)
T 2l0k_A            7 ERTIKIGKYIVE----TKKTVRVIAKEFGVSKSTVHKDLTER   44 (93)
T ss_dssp             HHHHHHHHHHHH----HCCCHHHHHHHHTSCHHHHHHHHTTH
T ss_pred             HHHHHHHHHHHH----cCCCHHHHHHHHCCCHHHHHHHHcCC
Confidence            345555554431    34899999999999999999988753

>2fbi_A Probable transcriptional regulator; MARR, APC5816, structural genomic protein structure initiative; 2.10A {Pseudomonas aeruginosa} SCOP: a.4.5.28

Probab=86.73  E-value=0.79  Score=36.85  Aligned_cols=42  Identities=12%  Similarity=0.176  Sum_probs=34.3

Q ss_pred             cCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 046578          317 TLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIA  361 (379)
Q Consensus       317 ~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rA  361 (379)
                      .|++.|..|+...+.   ..+.|..|||+.+|+++++|++.+.+-
T Consensus        33 ~lt~~~~~iL~~l~~---~~~~t~~ela~~l~~s~~~vs~~l~~L   74 (142)
T 2fbi_A           33 GLTEQQWRVIRILRQ---QGEMESYQLANQACILRPSMTGVLARL   74 (142)
T ss_dssp             TCCHHHHHHHHHHHH---HCSEEHHHHHHHTTCCHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHH---cCCCCHHHHHHHHCCCHhHHHHHHHHH
Confidence            589999988887653   246999999999999999998776553

>3f3x_A Transcriptional regulator, MARR family, putative; DNA binding protein, DNA-binding, transcription regulation; 1.90A {Sulfolobus solfataricus}

Probab=86.59  E-value=2.1  Score=34.53  Aligned_cols=42  Identities=14%  Similarity=0.033  Sum_probs=34.0

Q ss_pred             cCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHH
Q 046578          317 TLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIAL  362 (379)
Q Consensus       317 ~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl  362 (379)
                      .|++.|..||...+.   ..+ |..|||+.+|+++++|++.+.+-.
T Consensus        34 ~lt~~~~~iL~~l~~---~~~-~~~~la~~l~~~~~tvs~~l~~Le   75 (144)
T 3f3x_A           34 NLSYLDFSILKATSE---EPR-SMVYLANRYFVTQSAITAAVDKLE   75 (144)
T ss_dssp             SCCHHHHHHHHHHHH---SCE-EHHHHHHHHTCCHHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHH---CCC-CHHHHHHHHCCChhHHHHHHHHHH
Confidence            689999999987653   234 999999999999999988766543

>3sqn_A Conserved domain protein; structural genomics, PSI-biology, midwest center for structu genomics, MCSG, MGA family; 2.31A {Enterococcus faecalis}

Probab=86.54  E-value=1.4  Score=44.17  Aligned_cols=108  Identities=13%  Similarity=0.079  Sum_probs=60.4

Q ss_pred             CCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCccc-cCCCCcccccCCCCCCCChHHHHHHHHHHHHHHHHHhcCCH
Q 046578          242 RRMPTDSEIAEMLNIHVSTVRLAIERTRHPISLDGAVT-DRGCMTMQDIIPGPDETMPERMVQKQLMKQELKELLQTLSE  320 (379)
Q Consensus       242 gr~pt~~eia~~Lgis~~~~~~~l~~~~~~iSLd~~~~-~~~~~~l~d~i~~~~~~~pe~~~~~~e~~~~L~~~L~~L~~  320 (379)
                      +...+..++|+.+|+|..+++.-+...+....-...+. ...+..+.    ........+          +   ...+.+
T Consensus        30 ~~~it~~eLA~~L~VS~RTIr~dI~~In~~L~~~~~I~~~~~Gy~L~----~~~~~~~~~----------~---~~~~~~   92 (485)
T 3sqn_A           30 VPQLTAKRLAAQIQTTERTVFSDLQYIRSQLPADWSIETDSSGIRLR----NQGNAQTNE----------L---WSLFLP   92 (485)
T ss_dssp             CCSCBCGGGHHHHTSCHHHHHHHHHHHHTTCCTTEEEEEETTEEEEE----EC---CTHH----------H---HHHHGG
T ss_pred             CCCcCHHHHHHHhCCCHHHHHHHHHHHHHhcccCcEEEEcCCEEEEe----cCcHHHHHH----------H---HHhcCH
Confidence            34478899999999999999987766433331000010 11111111    110001000          1   112233


Q ss_pred             HHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHh
Q 046578          321 READILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQ  367 (379)
Q Consensus       321 rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~  367 (379)
                      .+|....+.+.+.. +..+..++|+.+.||++||.+-+.+..+.|++
T Consensus        93 ~eR~~~Il~~LL~~-~~isi~~Lae~l~VS~sTi~~DLk~i~~~L~~  138 (485)
T 3sqn_A           93 QSISIQLLKELLFT-KELVTTSFLSTSGVSYETLKRHIKKMNQALRD  138 (485)
T ss_dssp             GSHHHHHHHHHHHC-SEEEHHHHHHHHTCCHHHHHHHHHHHHHHHGG
T ss_pred             HHHHHHHHHHHHhC-CCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence            34433333332332 57999999999999999999887777666654

>3bja_A Transcriptional regulator, MARR family, putative; NP_978771.1, putative MARR-like transcription regulator, MAR structural genomics; 2.38A {Bacillus cereus}

Probab=86.53  E-value=0.93  Score=36.27  Aligned_cols=49  Identities=8%  Similarity=0.087  Sum_probs=37.7

Q ss_pred             HHHHHHh--cCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 046578          310 ELKELLQ--TLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIA  361 (379)
Q Consensus       310 ~L~~~L~--~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rA  361 (379)
                      .+...+.  .|++.|..|+...+.   ..+.|..|||+.+|+++++|++.+.+-
T Consensus        21 ~~~~~~~~~~l~~~~~~iL~~l~~---~~~~~~~ela~~l~~~~~tvs~~l~~L   71 (139)
T 3bja_A           21 NLDKAIEQYDISYVQFGVIQVLAK---SGKVSMSKLIENMGCVPSNMTTMIQRM   71 (139)
T ss_dssp             HHHHHTGGGTCCHHHHHHHHHHHH---SCSEEHHHHHHHCSSCCTTHHHHHHHH
T ss_pred             HHHhhhhhcCCCHHHHHHHHHHHH---cCCcCHHHHHHHHCCChhHHHHHHHHH
Confidence            3444444  589999999887653   256999999999999999998876554

>3kp7_A Transcriptional regulator TCAR; multiple drug resistance, biofilm, transcription regulation, binding, transcription regulator; 2.30A {Staphylococcus epidermidis RP62A} PDB: 3kp3_A* 3kp4_A* 3kp5_A* 3kp2_A* 3kp6_A

Probab=86.48  E-value=1.3  Score=36.22  Aligned_cols=41  Identities=7%  Similarity=0.155  Sum_probs=34.2

Q ss_pred             cCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 046578          317 TLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIA  361 (379)
Q Consensus       317 ~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rA  361 (379)
                      .|++.|..|+... .   ..+.|..|||+.+|+++++|++.+.+-
T Consensus        35 ~lt~~q~~iL~~l-~---~~~~t~~eLa~~l~~~~~~vs~~l~~L   75 (151)
T 3kp7_A           35 GISAEQSHVLNML-S---IEALTVGQITEKQGVNKAAVSRRVKKL   75 (151)
T ss_dssp             TCCHHHHHHHHHH-H---HSCBCHHHHHHHHCSCSSHHHHHHHHH
T ss_pred             CCCHHHHHHHHHH-H---cCCcCHHHHHHHHCCCHHHHHHHHHHH
Confidence            6899999888765 2   367999999999999999998776553

>3e6m_A MARR family transcriptional regulator; APC88769, silicibacter pomeroyi DSS, structural genomics, PSI-2, protein structure initiative; 2.20A {Silicibacter pomeroyi}

Probab=86.48  E-value=1.5  Score=36.37  Aligned_cols=42  Identities=7%  Similarity=0.045  Sum_probs=34.8

Q ss_pred             cCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 046578          317 TLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIA  361 (379)
Q Consensus       317 ~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rA  361 (379)
                      .|++.|..||...+.   ..+.|..|||+.+|++.++|++.+.+-
T Consensus        50 glt~~q~~vL~~l~~---~~~~t~~eLa~~l~~~~~~vs~~l~~L   91 (161)
T 3e6m_A           50 KLPTPKLRLLSSLSA---YGELTVGQLATLGVMEQSTTSRTVDQL   91 (161)
T ss_dssp             TCCHHHHHHHHHHHH---HSEEEHHHHHHHTTCCHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHh---CCCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence            699999999887653   246999999999999999998876653

>2eth_A Transcriptional regulator, putative, MAR family; MARR family, structural genomics, joint center for structura genomics, JCSG; 2.30A {Thermotoga maritima} SCOP: a.4.5.28

Probab=86.40  E-value=0.91  Score=37.41  Aligned_cols=43  Identities=16%  Similarity=0.128  Sum_probs=34.1

Q ss_pred             cCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHH
Q 046578          317 TLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIAL  362 (379)
Q Consensus       317 ~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl  362 (379)
                      .|++.|..||...+.   ..+.|..|||+.+|+++++|++.+.+-.
T Consensus        41 ~lt~~~~~iL~~l~~---~~~~t~~ela~~l~is~~tvs~~l~~Le   83 (154)
T 2eth_A           41 DMKTTELYAFLYVAL---FGPKKMKEIAEFLSTTKSNVTNVVDSLE   83 (154)
T ss_dssp             HSBHHHHHHHHHHHH---HCCBCHHHHHHHTTSCHHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHH---cCCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence            478888888876652   2469999999999999999988765543

>2oqg_A Possible transcriptional regulator, ARSR family P; winged-helix-turn-helix, structural genomics, PSI-2, protein structure initiative; 1.54A {Rhodococcus SP}

Probab=86.35  E-value=2  Score=33.35  Aligned_cols=46  Identities=24%  Similarity=0.229  Sum_probs=32.6

Q ss_pred             HHHHHhcCC-HHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 046578          311 LKELLQTLS-EREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGI  360 (379)
Q Consensus       311 L~~~L~~L~-~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~r  360 (379)
                      +..++..|. +....|+....  +  .+.+..|||+.+|+|+++|++.+.+
T Consensus        11 ~~~~~~~l~~~~r~~IL~~L~--~--~~~~~~ela~~l~is~~tv~~~l~~   57 (114)
T 2oqg_A           11 LASVFAALSDETRWEILTELG--R--ADQSASSLATRLPVSRQAIAKHLNA   57 (114)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHH--H--SCBCHHHHHHHSSSCHHHHHHHHHH
T ss_pred             HHHHHHHhCChHHHHHHHHHH--c--CCCCHHHHHHHHCcCHHHHHHHHHH
Confidence            334455454 56666766442  2  4599999999999999999877654

>2fu4_A Ferric uptake regulation protein; DNA binding domain, helix-turn-helix, DNA binding protein; 1.80A {Escherichia coli}

Probab=85.97  E-value=2.2  Score=31.37  Aligned_cols=42  Identities=12%  Similarity=0.178  Sum_probs=32.2

Q ss_pred             cCCHHHHHHHHHHhhcCCC-CCCCHHHHHHHh-----CCCHHHHHHHHHH
Q 046578          317 TLSEREADILRLHFGLDGQ-TPVSCKEIGRLL-----SLSRERIRQIRGI  360 (379)
Q Consensus       317 ~L~~rer~Vl~l~ygL~g~-e~~S~~EIAe~L-----giS~~~Vr~~~~r  360 (379)
                      +++++...|+.+..  ... ...|..||++.+     ++|.+||++.+..
T Consensus        14 ~~t~~r~~IL~~l~--~~~~~~~s~~el~~~l~~~~~~is~~TVyR~L~~   61 (83)
T 2fu4_A           14 KVTLPRLKILEVLQ--EPDNHHVSAEDLYKRLIDMGEEIGLATVYRVLNQ   61 (83)
T ss_dssp             CCCHHHHHHHHHHT--SGGGSSBCHHHHHHHHHHTTCCCCHHHHHHHHHH
T ss_pred             CcCHHHHHHHHHHH--hCCCCCCCHHHHHHHHHHhCCCCCHhhHHHHHHH
Confidence            58888888887654  211 469999999999     9999999876543

>3o9x_A Uncharacterized HTH-type transcriptional regulato; HTH-XRE DNA binding motif, transcriptional regulator, bacter antitoxin, Zn binding protein, transcription regulator-DNA; HET: DNA; 2.10A {Escherichia coli} PDB: 3gn5_A* 3gn5_B* 2kz8_A

Probab=85.87  E-value=2.5  Score=34.09  Aligned_cols=39  Identities=10%  Similarity=0.073  Sum_probs=30.4

Q ss_pred             hcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 046578          316 QTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGI  360 (379)
Q Consensus       316 ~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~r  360 (379)
                      ..+++.+-.-++...      ++|++|+|+.+|+|+++|+++.+-
T Consensus        69 ~~~~~~~l~~~R~~~------glsq~~la~~~g~s~~~i~~~E~g  107 (133)
T 3o9x_A           69 ETVAPEFIVKVRKKL------SLTQKEASEIFGGGVNAFSRYEKG  107 (133)
T ss_dssp             TTCCHHHHHHHHHHT------TCCHHHHHHHHCSCTTHHHHHHHT
T ss_pred             cCCCHHHHHHHHHHc------CCCHHHHHHHHCCCHHHHHHHHCC
Confidence            346666655555554      499999999999999999998763

>2qvo_A Uncharacterized protein AF_1382; PSI, structural genomics, southeast collaboratory for structural genomics; 1.85A {Archaeoglobus fulgidus dsm 4304} PDB: 3o3k_A 3ov8_A

Probab=85.82  E-value=0.73  Score=35.12  Aligned_cols=45  Identities=16%  Similarity=0.099  Sum_probs=33.2

Q ss_pred             cCCHHHHHHHHHHhhcC-CCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 046578          317 TLSEREADILRLHFGLD-GQTPVSCKEIGRLLSLSRERIRQIRGIA  361 (379)
Q Consensus       317 ~L~~rer~Vl~l~ygL~-g~e~~S~~EIAe~LgiS~~~Vr~~~~rA  361 (379)
                      .|+..+..||...+.-. +....|..|||+.+|+++++|.+++.+-
T Consensus         9 ~l~~~~~~iL~~l~~~~~~~~~~t~~eLa~~l~i~~~tvs~~l~~L   54 (95)
T 2qvo_A            9 LFKEKALEILMTIYYESLGGNDVYIQYIASKVNSPHSYVWLIIKKF   54 (95)
T ss_dssp             HSCHHHHHHHHHHHHHHHTTCCEEHHHHHHHSSSCHHHHHHHHHHH
T ss_pred             CCchhHHHHHHHHHHccCCCCCcCHHHHHHHHCcCHHHHHHHHHHH
Confidence            47888888877654221 1123899999999999999998876553

>1q1h_A TFE, transcription factor E, TFE; TFIIE, transcription initiation, preinitiation complex, RNA polymerase II, transcription bubble; 2.90A {Sulfolobus solfataricus} SCOP: a.4.5.41

Probab=85.63  E-value=0.79  Score=35.85  Aligned_cols=42  Identities=24%  Similarity=0.396  Sum_probs=30.1

Q ss_pred             cCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 046578          317 TLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGI  360 (379)
Q Consensus       317 ~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~r  360 (379)
                      .+.+....|+...+ -.| +.+|..|||+.+|+|+++|++.+.+
T Consensus        15 ~~~~~~l~Il~~l~-~~g-~~~s~~eLa~~lgvs~~tV~~~L~~   56 (110)
T 1q1h_A           15 LLGDDVIDVLRILL-DKG-TEMTDEEIANQLNIKVNDVRKKLNL   56 (110)
T ss_dssp             TSCSTTHHHHHHHH-HHC-SCBCHHHHHHTTTSCHHHHHHHHHH
T ss_pred             HcChHHHHHHHHHH-HcC-CCCCHHHHHHHHCcCHHHHHHHHHH
Confidence            34556667776543 123 5699999999999999999765443

>1uly_A Hypothetical protein PH1932; helix-turn-helix, structural genomics, DNA binding protein; 2.50A {Pyrococcus horikoshii} SCOP: a.4.5.58 PDB: 2cwe_A

Probab=85.36  E-value=1.5  Score=38.34  Aligned_cols=39  Identities=15%  Similarity=0.249  Sum_probs=32.2

Q ss_pred             CCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 046578          318 LSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGI  360 (379)
Q Consensus       318 L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~r  360 (379)
                      +++.++.|+.+..  +  .+.|..|||+.+|+|.++|++++.+
T Consensus        18 ~d~~~~~IL~~L~--~--~~~s~~eLA~~lglS~stv~~~l~~   56 (192)
T 1uly_A           18 LEDTRRKILKLLR--N--KEMTISQLSEILGKTPQTIYHHIEK   56 (192)
T ss_dssp             HSHHHHHHHHHHT--T--CCBCHHHHHHHHTCCHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHH--c--CCCCHHHHHHHHCcCHHHHHHHHHH
Confidence            6788888887654  2  4699999999999999999887654

>3hyi_A Protein DUF199/WHIA; laglidadg, homing endonuclease, helix-turn-helix, HTH, trans regulator; 2.34A {Thermotoga maritima} PDB: 3hyj_A

Probab=85.24  E-value=1.3  Score=41.63  Aligned_cols=50  Identities=22%  Similarity=0.311  Sum_probs=41.0

Q ss_pred             HHHHHH--HhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 046578          309 QELKEL--LQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIA  361 (379)
Q Consensus       309 ~~L~~~--L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rA  361 (379)
                      +.+.+.  ++.||+.-+++-.+|.-   .++.|++|+|+.+++|.+.|..++.|.
T Consensus       233 ~~i~e~~Gl~~Lp~~L~e~a~lRl~---~pdaSL~ELge~l~isKSgVnhRlrKL  284 (295)
T 3hyi_A          233 ELIKENMGLENLPEDLRRVALVRLR---NKELSLRELGKKLNLTKSQIYSKLKRI  284 (295)
T ss_dssp             HHHHHHTCGGGSCHHHHHHHHHHHH---CTTSCHHHHHHTTTCCHHHHHHHHHHH
T ss_pred             HHHHHhcCcccCCHHHHHHHHHHHH---CccccHHHHHHHhCcCHHHHHHHHHHH
Confidence            334443  36899999999999863   488999999999999999999887764

>2jt1_A PEFI protein; solution structure, winged helix-turn-helix, transcripti regulatory protein, structural genomics, PSI-2; NMR {Salmonella typhimurium LT2}

Probab=85.18  E-value=1.3  Score=32.88  Aligned_cols=25  Identities=24%  Similarity=0.295  Sum_probs=21.1

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHHH
Q 046578          336 TPVSCKEIGRLLSLSRERIRQIRGI  360 (379)
Q Consensus       336 e~~S~~EIAe~LgiS~~~Vr~~~~r  360 (379)
                      ...|.+|||+.||+|..||++.+..
T Consensus        23 ~~psv~EIa~~lgvS~~TVrr~L~~   47 (77)
T 2jt1_A           23 APVKTRDIADAAGLSIYQVRLYLEQ   47 (77)
T ss_dssp             SCEEHHHHHHHHTCCHHHHHHHHHH
T ss_pred             CCcCHHHHHHHHCCCHHHHHHHHHH
Confidence            3579999999999999999877544

>2kko_A Possible transcriptional regulatory protein (possibly ARSR-family); NESG, DNA-binding, transcription regulation, WHTH, homodimer; NMR {Mycobacterium bovis} PDB: 3gw2_A

Probab=85.13  E-value=1.2  Score=34.86  Aligned_cols=46  Identities=13%  Similarity=0.096  Sum_probs=30.8

Q ss_pred             HHHHHhcCC-HHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 046578          311 LKELLQTLS-EREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGI  360 (379)
Q Consensus       311 L~~~L~~L~-~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~r  360 (379)
                      +..++..|. +....|+.+..  +  .+.|..|||+.+|+|+++|++.+.+
T Consensus        15 ~~~~~~al~~~~r~~IL~~L~--~--~~~s~~eLa~~lgis~stvs~~L~~   61 (108)
T 2kko_A           15 VARVGKALANGRRLQILDLLA--Q--GERAVEAIATATGMNLTTASANLQA   61 (108)
T ss_dssp             HHHHHHHHTTSTTHHHHHHHT--T--CCEEHHHHHHHHTCCHHHHHHHHHH
T ss_pred             HHHHHHHhCCHHHHHHHHHHH--c--CCcCHHHHHHHHCcCHHHHHHHHHH
Confidence            334444444 33455665433  2  5689999999999999999877544

>2bv6_A MGRA, HTH-type transcriptional regulator MGRA; multidrug resistance regulator, virulence determinant, transcriptional factors; 2.8A {Staphylococcus aureus} SCOP: a.4.5.28

Probab=85.11  E-value=1.2  Score=35.94  Aligned_cols=42  Identities=17%  Similarity=0.264  Sum_probs=34.3

Q ss_pred             cCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 046578          317 TLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIA  361 (379)
Q Consensus       317 ~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rA  361 (379)
                      .|++.|..|+...+.   ..+.|..|||+.+|+++++|++.+.+-
T Consensus        34 ~l~~~~~~iL~~l~~---~~~~~~~ela~~l~~~~~tvs~~l~~L   75 (142)
T 2bv6_A           34 NLTYPQFLVLTILWD---ESPVNVKKVVTELALDTGTVSPLLKRM   75 (142)
T ss_dssp             TCCHHHHHHHHHHHH---SSEEEHHHHHHHTTCCTTTHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHH---cCCcCHHHHHHHHCCChhhHHHHHHHH
Confidence            689999998887653   246999999999999999998766553

>1tbx_A ORF F-93, hypothetical 11.0 kDa protein; sulfolobus spindle virus, winged helix, fusellovirus; 2.70A {Sulfolobus virus 1} SCOP: a.4.5.48

Probab=85.09  E-value=0.78  Score=35.02  Aligned_cols=42  Identities=10%  Similarity=0.149  Sum_probs=32.8

Q ss_pred             cCCHHHHHHHHHHhhcCCCCCCCHHHH----HHHhCCCHHHHHHHHHHH
Q 046578          317 TLSEREADILRLHFGLDGQTPVSCKEI----GRLLSLSRERIRQIRGIA  361 (379)
Q Consensus       317 ~L~~rer~Vl~l~ygL~g~e~~S~~EI----Ae~LgiS~~~Vr~~~~rA  361 (379)
                      .|++.|..||...+.   ..+.+..||    |+.+|++.++|++.+.+-
T Consensus         5 ~lt~~q~~iL~~l~~---~~~~~~~el~~~la~~l~is~~tvs~~l~~L   50 (99)
T 1tbx_A            5 PFFYPEAIVLAYLYD---NEGIATYDLYKKVNAEFPMSTATFYDAKKFL   50 (99)
T ss_dssp             SSBCHHHHHHHHHTT---CTTCBHHHHHHHHHTTSCCCHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHH---cCCcCHHHHHHHHHHHcCCCHHHHHHHHHHH
Confidence            477788888876552   256999999    899999999998876554

>4aik_A Transcriptional regulator SLYA; transcription, transcription factor; 1.85A {Yersinia pseudotuberculosis} PDB: 4aih_A 4aij_A 3qpt_A* 3q5f_A*

Probab=85.07  E-value=3  Score=34.48  Aligned_cols=50  Identities=10%  Similarity=0.048  Sum_probs=37.0

Q ss_pred             HHHHHHh--cCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 046578          310 ELKELLQ--TLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIA  361 (379)
Q Consensus       310 ~L~~~L~--~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rA  361 (379)
                      .+...+.  .|++.|..||...+..  .++.+..|||+.+|++.++|.+.+.+-
T Consensus        19 ~~~~~l~~~gLt~~q~~vL~~L~~~--~~~~~~~eLa~~l~~~~~tvs~~v~~L   70 (151)
T 4aik_A           19 LIDHRLKPLELTQTHWVTLYNINRL--PPEQSQIQLAKAIGIEQPSLVRTLDQL   70 (151)
T ss_dssp             HHHHHTGGGCCCHHHHHHHHHHHHS--CTTSCHHHHHHHHTSCHHHHHHHHHHH
T ss_pred             HHHHHHHHcCCCHHHHHHHHHHHHc--CCCCcHHHHHHHHCcCHHHHHHHHHHH
Confidence            3444554  5899998888755421  256899999999999999998876553

>2frh_A SARA, staphylococcal accessory regulator A; winged-helix protein, divalent metal binding, transcription; 2.50A {Staphylococcus aureus} SCOP: a.4.5.28 PDB: 2fnp_A 1fzp_D

Probab=85.03  E-value=0.85  Score=36.65  Aligned_cols=50  Identities=14%  Similarity=0.080  Sum_probs=37.7

Q ss_pred             HHHHHHh--cCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 046578          310 ELKELLQ--TLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGI  360 (379)
Q Consensus       310 ~L~~~L~--~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~r  360 (379)
                      .+...+.  .|++.|..|+...+. .+..+.|..|||+.+|++.++|.+.+.+
T Consensus        25 ~~~~~~~~~~lt~~q~~vL~~l~~-~~~~~~t~~eLa~~l~~~~~tvs~~l~~   76 (127)
T 2frh_A           25 LKSLIKKEFSISFEEFAVLTYISE-NKEKEYYLKDIINHLNYKQPQVVKAVKI   76 (127)
T ss_dssp             HHHHHHHTTCCCHHHHHHHHHHHH-TCCSEEEHHHHHHHSSSHHHHHHHHHHH
T ss_pred             HHHHHHHHcCCCHHHHHHHHHHHh-ccCCCcCHHHHHHHHCCCHHHHHHHHHH
Confidence            3444444  689999999887663 2125699999999999999999877655

>3deu_A Transcriptional regulator SLYA; MARR, WING-helix, transcription regulator, activator, DNA-binding, repressor; HET: SAL; 2.30A {Salmonella typhimurium} SCOP: a.4.5.28

Probab=84.93  E-value=2.4  Score=35.57  Aligned_cols=51  Identities=10%  Similarity=0.077  Sum_probs=37.9

Q ss_pred             HHHHHHHh--cCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 046578          309 QELKELLQ--TLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIA  361 (379)
Q Consensus       309 ~~L~~~L~--~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rA  361 (379)
                      ..+...+.  .|++.|..||...+..+  .+.|..|||+.+|++.++|.+.+.+-
T Consensus        40 ~~~~~~l~~~glt~~q~~vL~~L~~~~--~~~t~~eLa~~l~i~~~tvs~~l~~L   92 (166)
T 3deu_A           40 ALIDHRLKPLELTQTHWVTLHNIHQLP--PDQSQIQLAKAIGIEQPSLVRTLDQL   92 (166)
T ss_dssp             HHHHHHTTTTTCCHHHHHHHHHHHHSC--SSEEHHHHHHHHTSCHHHHHHHHHHH
T ss_pred             HHHHHHHhhcCCCHHHHHHHHHHHHcC--CCCCHHHHHHHHCCCHhhHHHHHHHH
Confidence            34444444  58999988888665212  56999999999999999998776553

>4fx0_A Probable transcriptional repressor protein; helix-turn-helix, DNA binding, transcription regulator; 2.70A {Mycobacterium tuberculosis} PDB: 4fx4_A*

Probab=84.93  E-value=3  Score=34.32  Aligned_cols=53  Identities=13%  Similarity=0.190  Sum_probs=36.4

Q ss_pred             HHHHHHHh--cCCHHHHHHHHHHhhcCC--CCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 046578          309 QELKELLQ--TLSEREADILRLHFGLDG--QTPVSCKEIGRLLSLSRERIRQIRGIA  361 (379)
Q Consensus       309 ~~L~~~L~--~L~~rer~Vl~l~ygL~g--~e~~S~~EIAe~LgiS~~~Vr~~~~rA  361 (379)
                      ..+...+.  .|++.|..|+...+...|  ..++|..|||+.+|+++++|.+.+.+-
T Consensus        20 ~~~~~~l~~~gLt~~q~~vL~~l~~~~~~~~~~~t~~eLa~~l~~~~~tvsr~v~~L   76 (148)
T 4fx0_A           20 QAYDRALRPSGLTNTQFSTLAVISLSEGSAGIDLTMSELAARIGVERTTLTRNLEVM   76 (148)
T ss_dssp             HHHHHHHGGGTCCHHHHHHHHHHHC---------CHHHHHHHHTCCHHHHHHHHHHH
T ss_pred             HHHHHHHHHcCCCHHHHHHHHHHHHhcCCCCCCcCHHHHHHHHCCChhhHHHHHHHH
Confidence            34455554  589999998876653222  135899999999999999998877663

>1u2w_A CADC repressor, cadmium efflux system accessory protein; LEAD, SOFT metal ION resistance, ARSR/SM family, DNA binding protein; 1.90A {Staphylococcus aureus} SCOP: a.4.5.5 PDB: 3f72_A

Probab=84.84  E-value=2.5  Score=33.79  Aligned_cols=39  Identities=15%  Similarity=0.147  Sum_probs=29.5

Q ss_pred             CHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 046578          319 SEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGI  360 (379)
Q Consensus       319 ~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~r  360 (379)
                      ++....||.+... +  .+.|..|||+.+|+|+++|++++..
T Consensus        41 ~~~rl~IL~~L~~-~--~~~s~~eLa~~l~is~stvs~~L~~   79 (122)
T 1u2w_A           41 DENRAKITYALCQ-D--EELCVCDIANILGVTIANASHHLRT   79 (122)
T ss_dssp             SHHHHHHHHHHHH-S--SCEEHHHHHHHHTCCHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHH-C--CCcCHHHHHHHHCcCHHHHHHHHHH
Confidence            4556667765431 1  4689999999999999999987654

>1xmk_A Double-stranded RNA-specific adenosine deaminase; winged helix-turn-helix, RNA editing, interferon, ADAR1, hydrolase; 0.97A {Homo sapiens} SCOP: a.4.5.19

Probab=84.77  E-value=0.74  Score=34.51  Aligned_cols=38  Identities=16%  Similarity=0.188  Sum_probs=27.9

Q ss_pred             HHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHH-HHHHHHHH
Q 046578          320 EREADILRLHFGLDGQTPVSCKEIGRLLSLSRE-RIRQIRGI  360 (379)
Q Consensus       320 ~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~-~Vr~~~~r  360 (379)
                      +.+..|+.+-.-   ..+.|..+||+.||||.. .|++.+++
T Consensus        11 ~~~~~IL~~Lk~---~g~~ta~eiA~~Lgit~~~aVr~hL~~   49 (79)
T 1xmk_A           11 EIKEKICDYLFN---VSDSSALNLAKNIGLTKARDINAVLID   49 (79)
T ss_dssp             HHHHHHHHHHHH---TCCEEHHHHHHHHCGGGHHHHHHHHHH
T ss_pred             hHHHHHHHHHHH---cCCcCHHHHHHHcCCCcHHHHHHHHHH
Confidence            344555554332   246999999999999999 99888665

>2xi8_A Putative transcription regulator; HTH DNA-binding motif; HET: GOL; 1.21A {Enterococcus faecalis} PDB: 2gzu_A 1utx_A* 2xj3_A 2xiu_A

Probab=84.62  E-value=0.7  Score=31.94  Aligned_cols=24  Identities=33%  Similarity=0.470  Sum_probs=22.0

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHH
Q 046578          336 TPVSCKEIGRLLSLSRERIRQIRG  359 (379)
Q Consensus       336 e~~S~~EIAe~LgiS~~~Vr~~~~  359 (379)
                      .++|++++|+.+|+|+++|+++.+
T Consensus        13 ~g~s~~~lA~~~gis~~~i~~~e~   36 (66)
T 2xi8_A           13 KKISQSELAALLEVSRQTINGIEK   36 (66)
T ss_dssp             TTCCHHHHHHHHTSCHHHHHHHHT
T ss_pred             cCCCHHHHHHHHCcCHHHHHHHHc
Confidence            459999999999999999999876

>1okr_A MECI, methicillin resistance regulatory protein MECI; bacterial antibiotic resistance, MECI protein, transcriptional regulatory element; 2.4A {Staphylococcus aureus} SCOP: a.4.5.39 PDB: 1sax_A 1sd7_A 2d45_A 1sd6_A

Probab=84.55  E-value=1.2  Score=35.31  Aligned_cols=45  Identities=16%  Similarity=0.152  Sum_probs=35.6

Q ss_pred             HhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhC----CCHHHHHHHHHHHH
Q 046578          315 LQTLSEREADILRLHFGLDGQTPVSCKEIGRLLS----LSRERIRQIRGIAL  362 (379)
Q Consensus       315 L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~Lg----iS~~~Vr~~~~rAl  362 (379)
                      +..|++.|..|+...+-   ..+.|..|||+.++    ++.++|++.+.+-.
T Consensus         5 ~~~lt~~~~~vL~~l~~---~~~~t~~ela~~l~~~~~~s~~tv~~~l~~L~   53 (123)
T 1okr_A            5 TYEISSAEWEVMNIIWM---KKYASANNIIEEIQMQKDWSPKTIRTLITRLY   53 (123)
T ss_dssp             CCCCCHHHHHHHHHHHH---HSSEEHHHHHHHHHHHCCCCHHHHHHHHHHHH
T ss_pred             cccCCHHHHHHHHHHHh---CCCcCHHHHHHHHhccCCCcHhhHHHHHHHHH
Confidence            34689999998876542   25699999999999    89999988766643

>3u2r_A Regulatory protein MARR; structural genomics, PSI-biology, midwest center for structu genomics, MCSG, helix-turn-helix; 2.20A {Planctomyces limnophilus}

Probab=84.54  E-value=1.5  Score=36.72  Aligned_cols=53  Identities=19%  Similarity=0.172  Sum_probs=36.6

Q ss_pred             HHHHHHHHh--cCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 046578          308 KQELKELLQ--TLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIA  361 (379)
Q Consensus       308 ~~~L~~~L~--~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rA  361 (379)
                      ...+...+.  .|++.|..||...+.. |.++.|..|||+.+|++.++|.+.+.+-
T Consensus        32 ~~~~~~~~~~~glt~~q~~vL~~l~~~-~~~~~t~~eLa~~l~~~~~tvs~~l~~L   86 (168)
T 3u2r_A           32 KAIEEEIFSQFELSAQQYNTLRLLRSV-HPEGMATLQIADRLISRAPDITRLIDRL   86 (168)
T ss_dssp             HHHHHHHHHTTTCCHHHHHHHHHHHHH-TTSCEEHHHHHHHC---CTHHHHHHHHH
T ss_pred             HHHHHHHhhhcCCCHHHHHHHHHHHhc-CCCCcCHHHHHHHHCCChhhHHHHHHHH
Confidence            344555554  5899999998876532 1257999999999999999998776653

>3kz3_A Repressor protein CI; five helix bundle, DNA-binding, transcription, transcription regulation; 1.64A {Enterobacteria phage lambda}

Probab=84.48  E-value=0.64  Score=34.05  Aligned_cols=24  Identities=4%  Similarity=0.183  Sum_probs=21.7

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHH
Q 046578          336 TPVSCKEIGRLLSLSRERIRQIRG  359 (379)
Q Consensus       336 e~~S~~EIAe~LgiS~~~Vr~~~~  359 (379)
                      .++|+.|+|+.+|||+++|+++.+
T Consensus        24 ~gltq~~lA~~~gvs~~~is~~e~   47 (80)
T 3kz3_A           24 LGLSYESVADKMGMGQSAVAALFN   47 (80)
T ss_dssp             HTCCHHHHHHHTTSCHHHHHHHHT
T ss_pred             cCCCHHHHHHHhCcCHHHHHHHHc
Confidence            349999999999999999999875

>1ub9_A Hypothetical protein PH1061; helix-turn-helix motif, winged helix motif, structural genom transcription; 2.05A {Pyrococcus horikoshii} SCOP: a.4.5.28

Probab=84.32  E-value=1.1  Score=33.90  Aligned_cols=39  Identities=10%  Similarity=0.182  Sum_probs=29.5

Q ss_pred             CHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 046578          319 SEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGI  360 (379)
Q Consensus       319 ~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~r  360 (379)
                      ++.+..||.....   ..+.|..|||+.+|+|.++|++++.+
T Consensus        15 ~~~~~~iL~~L~~---~~~~~~~ela~~l~is~~tvs~~l~~   53 (100)
T 1ub9_A           15 NPVRLGIMIFLLP---RRKAPFSQIQKVLDLTPGNLDSHIRV   53 (100)
T ss_dssp             SHHHHHHHHHHHH---HSEEEHHHHHHHTTCCHHHHHHHHHH
T ss_pred             ChHHHHHHHHHHh---cCCcCHHHHHHHHCcCHHHHHHHHHH
Confidence            5666677764431   15699999999999999999877554

>1r1t_A Transcriptional repressor SMTB; zinc, transcriptional regulation, winged HTH protein, DNA binding, transcription repressor; 1.70A {Synechococcus elongatus pcc 7942} SCOP: a.4.5.5 PDB: 1r23_A 1smt_A 1r22_A

Probab=84.30  E-value=2.7  Score=33.74  Aligned_cols=38  Identities=8%  Similarity=0.158  Sum_probs=29.3

Q ss_pred             CHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 046578          319 SEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGI  360 (379)
Q Consensus       319 ~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~r  360 (379)
                      ++....||.+..  .  .+.+..|||+.+|+|+++|++++.+
T Consensus        45 ~~~rl~IL~~L~--~--~~~s~~ela~~lgis~stvs~~L~~   82 (122)
T 1r1t_A           45 DPNRLRLLSLLA--R--SELCVGDLAQAIGVSESAVSHQLRS   82 (122)
T ss_dssp             CHHHHHHHHHHT--T--CCBCHHHHHHHHTCCHHHHHHHHHH
T ss_pred             CHHHHHHHHHHH--c--CCCCHHHHHHHHCcCHHHHHHHHHH
Confidence            566667776543  2  4689999999999999999887554

>2fxa_A Protease production regulatory protein HPR; protease porduction, regulation, STR genomics, PSI, protein structure initiative; HET: PGE P6G 1PE; 2.40A {Bacillus subtilis} SCOP: a.4.5.28

Probab=83.93  E-value=2.5  Score=37.06  Aligned_cols=42  Identities=17%  Similarity=0.144  Sum_probs=34.5

Q ss_pred             cCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 046578          317 TLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIA  361 (379)
Q Consensus       317 ~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rA  361 (379)
                      .|++.|..||...+.   ..+.|..|||+.+|++.++|.+.+.+-
T Consensus        45 gLt~~q~~iL~~L~~---~~~~t~~eLa~~l~i~~stvs~~l~~L   86 (207)
T 2fxa_A           45 DLNINEHHILWIAYQ---LNGASISEIAKFGVMHVSTAFNFSKKL   86 (207)
T ss_dssp             TCCHHHHHHHHHHHH---HTSEEHHHHHHHTTCCHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHH---CCCcCHHHHHHHHCCCHHHHHHHHHHH
Confidence            689999999886653   246999999999999999998876553

>1z91_A Organic hydroperoxide resistance transcriptional; OHRR, MARR family, bacterial transcription factor, DNA bindi protein; 2.50A {Bacillus subtilis} SCOP: a.4.5.28 PDB: 1z9c_A*

Probab=83.83  E-value=1.1  Score=36.26  Aligned_cols=44  Identities=14%  Similarity=0.157  Sum_probs=34.6

Q ss_pred             cCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 046578          317 TLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALT  363 (379)
Q Consensus       317 ~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~  363 (379)
                      .|++.|..|+...+.   ..+.|..+||+.+|+++++|++.+.+-.+
T Consensus        37 ~l~~~~~~iL~~l~~---~~~~~~~~la~~l~~~~~tvs~~l~~L~~   80 (147)
T 1z91_A           37 NITYPQYLALLLLWE---HETLTVKKMGEQLYLDSGTLTPMLKRMEQ   80 (147)
T ss_dssp             CCCHHHHHHHHHHHH---HSEEEHHHHHHTTTCCHHHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHH---CCCCCHHHHHHHHCCCcCcHHHHHHHHHH
Confidence            488888888876552   24689999999999999999887665443

>1u78_A TC3 transposase, transposable element TC3 transposase; transposon DNA, bipartite DNA-binding, HTH- motif, DNA binding protein/DNA complex; 2.69A {Caenorhabditis elegans} SCOP: a.4.1.2 a.4.1.2

Probab=83.73  E-value=14  Score=29.28  Aligned_cols=77  Identities=13%  Similarity=0.145  Sum_probs=47.5

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHHhcCCccccCCccccCCCCcccccCCCCCCCChHHHHHHHHHHHHHHHHHhcCCHHHH-
Q 046578          245 PTDSEIAEMLNIHVSTVRLAIERTRHPISLDGAVTDRGCMTMQDIIPGPDETMPERMVQKQLMKQELKELLQTLSEREA-  323 (379)
Q Consensus       245 pt~~eia~~Lgis~~~~~~~l~~~~~~iSLd~~~~~~~~~~l~d~i~~~~~~~pe~~~~~~e~~~~L~~~L~~L~~rer-  323 (379)
                      -+..+||+.+|++..++...+......       +   ...    ..+..                     ..|++.+. 
T Consensus        23 ~s~~~ia~~lgis~~Tv~r~~~~~~~~-------g---~~~----~~gr~---------------------~~l~~~~~~   67 (141)
T 1u78_A           23 VSLHEMSRKISRSRHCIRVYLKDPVSY-------G---TSK----RAPRR---------------------KALSVRDER   67 (141)
T ss_dssp             CCHHHHHHHHTCCHHHHHHHHHSGGGT-------T---CCC----CCCCC---------------------CSSCHHHHH
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHccccc-------C---CcC----CCCCC---------------------CcCCHHHHH
Confidence            578999999999999999887653211       0   000    01100                     01222222 


Q ss_pred             HHHHHHhhcCCCCCCCHHHHHHHhC--CCHHHHHHHHHH
Q 046578          324 DILRLHFGLDGQTPVSCKEIGRLLS--LSRERIRQIRGI  360 (379)
Q Consensus       324 ~Vl~l~ygL~g~e~~S~~EIAe~Lg--iS~~~Vr~~~~r  360 (379)
                      .|+.+.-    ....|..+|+..+|  +|.+||++++.+
T Consensus        68 ~i~~~~~----~~~~s~~~i~~~lg~~~s~~tV~r~l~~  102 (141)
T 1u78_A           68 NVIRAAS----NSCKTARDIRNELQLSASKRTILNVIKR  102 (141)
T ss_dssp             HHHHHHH----HCCCCHHHHHHHTTCCSCHHHHHHHHHH
T ss_pred             HHHHHHh----CCCCCHHHHHHHHCCCccHHHHHHHHHH
Confidence            2222211    13489999999999  899999999876

>3omt_A Uncharacterized protein; structural genomics, PSI-2, protein structure initiative, MI center for structural genomics, MCSG; 1.65A {Cytophaga hutchinsonii}

Probab=83.58  E-value=0.77  Score=32.85  Aligned_cols=25  Identities=4%  Similarity=-0.089  Sum_probs=22.3

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHHH
Q 046578          336 TPVSCKEIGRLLSLSRERIRQIRGI  360 (379)
Q Consensus       336 e~~S~~EIAe~LgiS~~~Vr~~~~r  360 (379)
                      .++|++|+|+.+|+|+++|+++.+-
T Consensus        20 ~glsq~~lA~~~gis~~~is~~e~g   44 (73)
T 3omt_A           20 KGKTNLWLTETLDKNKTTVSKWCTN   44 (73)
T ss_dssp             HTCCHHHHHHHTTCCHHHHHHHHTT
T ss_pred             cCCCHHHHHHHHCcCHHHHHHHHcC
Confidence            3499999999999999999998763

>2wte_A CSA3; antiviral protein, viral resistance, winged helix-turn-helix prnai nucleotide-binding domain; HET: MSE; 1.80A {Sulfolobus solfataricus}

Probab=83.38  E-value=2.2  Score=38.86  Aligned_cols=44  Identities=16%  Similarity=0.280  Sum_probs=35.3

Q ss_pred             HHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 046578          314 LLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGI  360 (379)
Q Consensus       314 ~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~r  360 (379)
                      .-..|++.+..||.....   ..+.|..|||+.+|++++||++++.+
T Consensus       146 ~~~~L~~~~~~IL~~L~~---~~~~s~~eLA~~lglsksTv~r~L~~  189 (244)
T 2wte_A          146 LMRDYSREEMKLLNVLYE---TKGTGITELAKMLDKSEKTLINKIAE  189 (244)
T ss_dssp             HHSCCCHHHHHHHHHHHH---HTCBCHHHHHHHHTCCHHHHHHHHHH
T ss_pred             ccCCCCHHHHHHHHHHHH---cCCCCHHHHHHHHCcCHHHHHHHHHH
Confidence            445799999999986432   25699999999999999999877554

>1r69_A Repressor protein CI; gene regulating protein; 2.00A {Phage 434} SCOP: a.35.1.2 PDB: 1pra_A 1per_L 1rpe_L* 2or1_L* 1r63_A 2r63_A 1sq8_A

Probab=83.37  E-value=0.8  Score=32.01  Aligned_cols=25  Identities=12%  Similarity=0.201  Sum_probs=22.1

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHHH
Q 046578          336 TPVSCKEIGRLLSLSRERIRQIRGI  360 (379)
Q Consensus       336 e~~S~~EIAe~LgiS~~~Vr~~~~r  360 (379)
                      .++|+.++|+.+|+|+++|+++.+.
T Consensus        13 ~glsq~~lA~~~gis~~~i~~~e~g   37 (69)
T 1r69_A           13 LGLNQAELAQKVGTTQQSIEQLENG   37 (69)
T ss_dssp             TTCCHHHHHHHHTSCHHHHHHHHTT
T ss_pred             cCCCHHHHHHHHCcCHHHHHHHHcC
Confidence            4599999999999999999998653

>1hlv_A CENP-B, major centromere autoantigen B; helix-turn-helix, protein-DNA complex, riken structural genomics/proteomics initiative, RSGI; 2.50A {Homo sapiens} SCOP: a.4.1.7 a.4.1.7 PDB: 1bw6_A

Probab=83.30  E-value=1.5  Score=35.15  Aligned_cols=45  Identities=22%  Similarity=0.189  Sum_probs=31.3

Q ss_pred             cCCHHHH-HHHHHHhhcCCCCCC-CHHHHHHHhCCCHHHHHHHHHHHHHHH
Q 046578          317 TLSEREA-DILRLHFGLDGQTPV-SCKEIGRLLSLSRERIRQIRGIALTKL  365 (379)
Q Consensus       317 ~L~~rer-~Vl~l~ygL~g~e~~-S~~EIAe~LgiS~~~Vr~~~~rAl~kL  365 (379)
                      .+++.++ +|+.++.-    .+. +..+||+.|||++++|+++++..-..+
T Consensus         7 ~~t~e~K~~iv~~~~~----~g~~~~~~~A~~~gvs~stl~~~~~~~~~~~   53 (131)
T 1hlv_A            7 QLTFREKSRIIQEVEE----NPDLRKGEIARRFNIPPSTLSTILKNKRAIL   53 (131)
T ss_dssp             CCCHHHHHHHHHHHHH----CTTSCHHHHHHHHTCCHHHHHHHHHTHHHHH
T ss_pred             eCCHHHHHHHHHHHHH----CCCCcHHHHHHHhCCCHHHHHHHHhchhhhc
Confidence            4677776 45555432    334 455999999999999999987754433

>1zug_A Phage 434 CRO protein; gene regulating protein, transcription regulation; NMR {Phage 434} SCOP: a.35.1.2 PDB: 2cro_A 3cro_L*

Probab=83.09  E-value=0.82  Score=32.14  Aligned_cols=24  Identities=13%  Similarity=0.230  Sum_probs=21.8

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHH
Q 046578          336 TPVSCKEIGRLLSLSRERIRQIRG  359 (379)
Q Consensus       336 e~~S~~EIAe~LgiS~~~Vr~~~~  359 (379)
                      .++|+.++|+.+|+|+++|+++.+
T Consensus        15 ~glsq~~lA~~~gis~~~i~~~e~   38 (71)
T 1zug_A           15 LKMTQTELATKAGVKQQSIQLIEA   38 (71)
T ss_dssp             TTCCHHHHHHHHTSCHHHHHHHHT
T ss_pred             cCCCHHHHHHHhCCCHHHHHHHHc
Confidence            459999999999999999999875

>3boq_A Transcriptional regulator, MARR family; MARR famil structural genomics, PSI-2, protein structure initiative; 2.39A {Silicibacter pomeroyi dss-3}

Probab=83.06  E-value=1.8  Score=35.60  Aligned_cols=44  Identities=11%  Similarity=0.108  Sum_probs=35.3

Q ss_pred             cCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHH
Q 046578          317 TLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIAL  362 (379)
Q Consensus       317 ~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl  362 (379)
                      .|++.|..||...+. . ..+.|..|||+.+|++.++|++.+.+-.
T Consensus        44 ~l~~~~~~iL~~L~~-~-~~~~~~~ela~~l~i~~~tvs~~l~~Le   87 (160)
T 3boq_A           44 GLSLAKFDAMAQLAR-N-PDGLSMGKLSGALKVTNGNVSGLVNRLI   87 (160)
T ss_dssp             SCCHHHHHHHHHHHH-C-TTCEEHHHHHHHCSSCCSCHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHH-c-CCCCCHHHHHHHHCCChhhHHHHHHHHH
Confidence            699999999887632 1 2579999999999999999988766543

>2r1j_L Repressor protein C2; protein-DNA complex, helix-turn-helix, DNA-binding, transcription, transcription regulation; 1.53A {Enterobacteria phage P22} SCOP: a.35.1.2 PDB: 3jxb_C 3jxc_L 3jxd_L

Probab=82.97  E-value=0.85  Score=31.69  Aligned_cols=24  Identities=17%  Similarity=0.296  Sum_probs=21.7

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHH
Q 046578          336 TPVSCKEIGRLLSLSRERIRQIRG  359 (379)
Q Consensus       336 e~~S~~EIAe~LgiS~~~Vr~~~~  359 (379)
                      .++|+.++|+.+|+|+++|+++.+
T Consensus        17 ~g~s~~~lA~~~gis~~~i~~~e~   40 (68)
T 2r1j_L           17 LKIRQAALGKMVGVSNVAISQWER   40 (68)
T ss_dssp             HTCCHHHHHHHHTSCHHHHHHHHT
T ss_pred             cCCCHHHHHHHHCCCHHHHHHHHc
Confidence            349999999999999999999876

>3fmy_A HTH-type transcriptional regulator MQSA (YGIT/B3021); helix-turn-helix, DNA-binding, transcription regulation, DNA binding protein; HET: MEQ; 1.40A {Escherichia coli k-12}

Probab=82.89  E-value=1.2  Score=32.12  Aligned_cols=37  Identities=8%  Similarity=0.039  Sum_probs=27.5

Q ss_pred             CCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 046578          318 LSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGI  360 (379)
Q Consensus       318 L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~r  360 (379)
                      +++..-.-++...      ++|++|+|+.+|||+++|+++..-
T Consensus        11 ~~g~~lr~~R~~~------gltq~elA~~~gvs~~tis~~E~G   47 (73)
T 3fmy_A           11 VAPEFIVKVRKKL------SLTQKEASEIFGGGVNAFSRYEKG   47 (73)
T ss_dssp             CCHHHHHHHHHHT------TCCHHHHHHHHCSCTTHHHHHHTT
T ss_pred             CCHHHHHHHHHHc------CCCHHHHHHHhCcCHHHHHHHHcC
Confidence            4444444444443      499999999999999999998753

>1gdt_A GD resolvase, protein (gamma delta resolvase); protein-DNA complex, double helix, overhanging base, DNA binding protein/DNA complex; 3.00A {Escherichia coli} SCOP: a.4.1.2 c.53.1.1 PDB: 1zr4_A 1zr2_A 2gm4_A 1res_A 1ret_A

Probab=82.83  E-value=1.2  Score=38.36  Aligned_cols=24  Identities=8%  Similarity=0.329  Sum_probs=21.6

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHH
Q 046578          336 TPVSCKEIGRLLSLSRERIRQIRG  359 (379)
Q Consensus       336 e~~S~~EIAe~LgiS~~~Vr~~~~  359 (379)
                      +|+|..+||+.||+|++||++++.
T Consensus       157 ~G~s~~~Ia~~l~is~~tv~r~l~  180 (183)
T 1gdt_A          157 QGLGASHISKTMNIARSTVYKVIN  180 (183)
T ss_dssp             TTCCHHHHHHHHTCCHHHHHHHHH
T ss_pred             CCCCHHHHHHHHCcCHHHHHHHHh
Confidence            569999999999999999988764

>2r0q_C Putative transposon TN552 DNA-invertase BIN3; site-specific recombinase, resolvase, DNA-binding protein, protein-DNA complex, DNA integration, DNA invertase, DNA recombination; 3.20A {Staphylococcus aureus}

Probab=82.82  E-value=1  Score=39.70  Aligned_cols=32  Identities=9%  Similarity=0.262  Sum_probs=25.7

Q ss_pred             HHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 046578          323 ADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRG  359 (379)
Q Consensus       323 r~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~  359 (379)
                      +.|+.++.     +|+|..+||+.||+|++||++++.
T Consensus       166 ~~i~~~~~-----~G~s~~~Ia~~l~is~~tv~r~l~  197 (209)
T 2r0q_C          166 HRVVEMLE-----EGQAISKIAKEVNITRQTVYRIKH  197 (209)
T ss_dssp             HHHHHHHH-----TTCCHHHHHHHHTCCHHHHHHHHT
T ss_pred             HHHHHHHH-----cCCCHHHHHHHHCcCHHHHHHHHh
Confidence            45666543     569999999999999999988764

>2a6c_A Helix-turn-helix motif; putative transcriptional regulator, structural genomics, JOI for structural genomics, JCSG; HET: CIT; 1.90A {Nitrosomonas europaea} SCOP: a.35.1.13

Probab=82.75  E-value=1.5  Score=32.31  Aligned_cols=24  Identities=13%  Similarity=0.281  Sum_probs=22.1

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHH
Q 046578          336 TPVSCKEIGRLLSLSRERIRQIRG  359 (379)
Q Consensus       336 e~~S~~EIAe~LgiS~~~Vr~~~~  359 (379)
                      .++|++|+|+.+|+|+++|+++++
T Consensus        30 ~glsq~elA~~~gis~~~is~~e~   53 (83)
T 2a6c_A           30 SGLTQFKAAELLGVTQPRVSDLMR   53 (83)
T ss_dssp             TTCCHHHHHHHHTSCHHHHHHHHT
T ss_pred             cCCCHHHHHHHHCcCHHHHHHHHc
Confidence            459999999999999999999876

>2k9q_A Uncharacterized protein; all helix, helix-turn-helix, plasmid, structural genomics, PSI-2, protein structure initiative; NMR {Bacteroides thetaiotaomicron}

Probab=82.72  E-value=0.85  Score=33.03  Aligned_cols=24  Identities=17%  Similarity=0.394  Sum_probs=21.8

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHH
Q 046578          336 TPVSCKEIGRLLSLSRERIRQIRG  359 (379)
Q Consensus       336 e~~S~~EIAe~LgiS~~~Vr~~~~  359 (379)
                      .++|++++|+.+|||+++|+++.+
T Consensus        14 ~glsq~~lA~~~gis~~~i~~~e~   37 (77)
T 2k9q_A           14 LSLTAKSVAEEMGISRQQLCNIEQ   37 (77)
T ss_dssp             HTCCHHHHHHHHTSCHHHHHHHHT
T ss_pred             cCCCHHHHHHHhCCCHHHHHHHHc
Confidence            459999999999999999999875

>3qq6_A HTH-type transcriptional regulator SINR; helix-turn-helix motif, biofilm, repressor, SINI; 1.90A {Bacillus subtilis}

Probab=82.63  E-value=0.92  Score=33.21  Aligned_cols=25  Identities=12%  Similarity=0.135  Sum_probs=22.6

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHHH
Q 046578          336 TPVSCKEIGRLLSLSRERIRQIRGI  360 (379)
Q Consensus       336 e~~S~~EIAe~LgiS~~~Vr~~~~r  360 (379)
                      .++|++++|+.+|||+++|+++.+-
T Consensus        22 ~gltq~elA~~~gis~~~is~~E~G   46 (78)
T 3qq6_A           22 KGYSLSELAEKAGVAKSYLSSIERN   46 (78)
T ss_dssp             TTCCHHHHHHHHTCCHHHHHHHHTT
T ss_pred             cCCCHHHHHHHHCcCHHHHHHHHcC
Confidence            5699999999999999999998764

>2g9w_A Conserved hypothetical protein; DNA-binding domain, bacterial transcription repressor, DNA B protein; 1.80A {Mycobacterium tuberculosis} SCOP: a.4.5.39

Probab=82.46  E-value=2  Score=35.08  Aligned_cols=45  Identities=16%  Similarity=0.257  Sum_probs=35.9

Q ss_pred             HhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhC----CCHHHHHHHHHHH
Q 046578          315 LQTLSEREADILRLHFGLDGQTPVSCKEIGRLLS----LSRERIRQIRGIA  361 (379)
Q Consensus       315 L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~Lg----iS~~~Vr~~~~rA  361 (379)
                      +..|++.|..|+...+..+  .+.|..||++.++    ++.+||.+.+.+-
T Consensus         4 ~~~lt~~e~~vL~~L~~~~--~~~t~~el~~~l~~~~~~~~~Tvt~~l~rL   52 (138)
T 2g9w_A            4 LTRLGDLERAVMDHLWSRT--EPQTVRQVHEALSARRDLAYTTVMAVLQRL   52 (138)
T ss_dssp             GGGCCHHHHHHHHHHHTCS--SCEEHHHHHHHHTTTCCCCHHHHHHHHHHH
T ss_pred             cccCCHHHHHHHHHHHhcC--CCCCHHHHHHHHhccCCCCHHHHHHHHHHH
Confidence            3579999999998765211  4699999999998    8999998877664

>2o0m_A Transcriptional regulator, SORC family; structural genomics, protein structure initiative, midwest center for structural genomics, MCSG; 1.60A {Enterococcus faecalis} SCOP: c.124.1.8

Probab=82.26  E-value=0.26  Score=47.20  Aligned_cols=43  Identities=12%  Similarity=0.260  Sum_probs=0.0

Q ss_pred             CCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 046578          318 LSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALT  363 (379)
Q Consensus       318 L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~  363 (379)
                      +.+++..|+...|.   .++.|++|||+.||+|+.||++.+.+..+
T Consensus        18 ~~~r~~~iL~~l~~---~~~~t~~eLa~~l~vs~~Tv~r~l~~Le~   60 (345)
T 2o0m_A           18 VLQERFQILRNIYW---MQPIGRRSLSETMGITERVLRTETDVLKQ   60 (345)
T ss_dssp             ----------------------------------------------
T ss_pred             hhHHHHHHHHHHHH---cCCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence            56677777776553   35799999999999999999988776543

>2l8n_A Transcriptional repressor CYTR; bacterial gene repressor, helix turn helix binding domain, L family, transcription regulation, binding protein; NMR {Escherichia coli} PDB: 2lcv_A

Probab=82.15  E-value=0.59  Score=33.76  Aligned_cols=22  Identities=9%  Similarity=0.098  Sum_probs=20.3

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHH
Q 046578          338 VSCKEIGRLLSLSRERIRQIRG  359 (379)
Q Consensus       338 ~S~~EIAe~LgiS~~~Vr~~~~  359 (379)
                      .|++|||+..|+|..||++.++
T Consensus        10 ~t~~diA~~aGVS~sTVSr~ln   31 (67)
T 2l8n_A           10 ATMKDVALKAKVSTATVSRALM   31 (67)
T ss_dssp             CCHHHHHHHTTCCHHHHHHTTT
T ss_pred             CCHHHHHHHHCCCHHHHHHHHc
Confidence            6999999999999999998865

>1sd4_A Penicillinase repressor; BLAI, MECI, methicillin, B-lactam, DNA binding PR; 2.00A {Staphylococcus aureus} SCOP: a.4.5.39 PDB: 1xsd_A

Probab=82.04  E-value=1.7  Score=34.41  Aligned_cols=43  Identities=23%  Similarity=0.285  Sum_probs=34.8

Q ss_pred             hcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhC----CCHHHHHHHHHHH
Q 046578          316 QTLSEREADILRLHFGLDGQTPVSCKEIGRLLS----LSRERIRQIRGIA  361 (379)
Q Consensus       316 ~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~Lg----iS~~~Vr~~~~rA  361 (379)
                      ..|++.|..|+...+-   ..+.|..|||+.++    ++.+||...+.|-
T Consensus         6 ~~Lt~~q~~vL~~L~~---~~~~t~~el~~~l~~~~~~~~~Tvt~~l~rL   52 (126)
T 1sd4_A            6 VEISMAEWDVMNIIWD---KKSVSANEIVVEIQKYKEVSDKTIRTLITRL   52 (126)
T ss_dssp             CCCCHHHHHHHHHHHH---SSSEEHHHHHHHHHTTSCCCHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHHHHh---cCCCCHHHHHHHHhhcCCCChhhHHHHHHHH
Confidence            3689999999987663   24699999999997    5899998877664

>2fbk_A Transcriptional regulator, MARR family; winged-helix-turn-helix; 2.30A {Deinococcus radiodurans} SCOP: a.4.5.28

Probab=82.02  E-value=1.9  Score=36.65  Aligned_cols=53  Identities=13%  Similarity=0.073  Sum_probs=38.5

Q ss_pred             HHHHHHHh--cCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 046578          309 QELKELLQ--TLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIA  361 (379)
Q Consensus       309 ~~L~~~L~--~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rA  361 (379)
                      ..+...+.  .|++.|..||...+.-++..+.|..|||+.+|++.++|++.+.+-
T Consensus        56 ~~~~~~l~~~glt~~~~~iL~~L~~~~~~~~~t~~eLa~~l~is~~tvs~~l~~L  110 (181)
T 2fbk_A           56 REIERTYAASGLNAAGWDLLLTLYRSAPPEGLRPTELSALAAISGPSTSNRIVRL  110 (181)
T ss_dssp             HHHHHHHHTTTCCHHHHHHHHHHHHHCCSSCBCHHHHHHHCSCCSGGGSSHHHHH
T ss_pred             HHHHHHHHHcCCCHHHHHHHHHHHHcCCCCCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence            34444554  589999999887663221124899999999999999998876553

>3jw4_A Transcriptional regulator, MARR/EMRR family; DNA-binding protein, structural genomics, PSI-2, protein structure initiative; HET: MSE; 2.10A {Clostridium acetobutylicum} SCOP: a.4.5.0

Probab=82.01  E-value=0.96  Score=36.91  Aligned_cols=44  Identities=7%  Similarity=0.188  Sum_probs=29.3

Q ss_pred             cCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 046578          317 TLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIA  361 (379)
Q Consensus       317 ~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rA  361 (379)
                      .|++.|..|+...+. .+..+.|..|||+.+|+++++|++.+.+-
T Consensus        38 glt~~q~~vL~~l~~-~~~~~~t~~eLa~~l~~~~~~vs~~l~~L   81 (148)
T 3jw4_A           38 GLNSQQGRMIGYIYE-NQESGIIQKDLAQFFGRRGASITSMLQGL   81 (148)
T ss_dssp             TCCHHHHHHHHHHHH-HTTTCCCHHHHHHC------CHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHh-CCCCCCCHHHHHHHHCCChhHHHHHHHHH
Confidence            699999999887663 21257999999999999999998776553

>1on2_A Transcriptional regulator MNTR; helix-turn-helix, DNA-binding protein, metalloregulatory protein; 1.61A {Bacillus subtilis} SCOP: a.4.5.24 a.76.1.1 PDB: 2ev0_A 1on1_A 2ev5_A 2ev6_A* 2f5c_A 2f5d_A 2f5e_A 2f5f_A 2hyf_A* 2hyg_D 3r60_A* 3r61_A*

Probab=81.95  E-value=1.6  Score=35.40  Aligned_cols=43  Identities=7%  Similarity=0.095  Sum_probs=28.8

Q ss_pred             CCHHHHHHHHHHhhc-CCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 046578          318 LSEREADILRLHFGL-DGQTPVSCKEIGRLLSLSRERIRQIRGI  360 (379)
Q Consensus       318 L~~rer~Vl~l~ygL-~g~e~~S~~EIAe~LgiS~~~Vr~~~~r  360 (379)
                      |++.+..++...+.+ ....+.|..+||+.+|+|+++|++.+.+
T Consensus         2 ls~~~~~~L~~i~~l~~~~~~~~~~ela~~l~vs~~tvs~~l~~   45 (142)
T 1on2_A            2 TTPSMEMYIEQIYMLIEEKGYARVSDIAEALAVHPSSVTKMVQK   45 (142)
T ss_dssp             CCHHHHHHHHHHHHHHHHHSSCCHHHHHHHHTSCHHHHHHHHHH
T ss_pred             CChHHHHHHHHHHHHHhhcCCCCHHHHHHHhCCCHHHHHHHHHH
Confidence            445554444433322 1125699999999999999999877654

>2hr3_A Probable transcriptional regulator; MCSG, structural genomics, PSI-2, protein structure initiati midwest center for structural genomics; 2.40A {Pseudomonas aeruginosa} SCOP: a.4.5.28

Probab=81.35  E-value=1.7  Score=35.16  Aligned_cols=42  Identities=10%  Similarity=-0.001  Sum_probs=31.8

Q ss_pred             CCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 046578          318 LSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIA  361 (379)
Q Consensus       318 L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rA  361 (379)
                      |++.+..||...+.-.  .+.|..+||+.+|+++++|++.+.+-
T Consensus        33 l~~~~~~iL~~l~~~~--~~~~~~~la~~l~i~~~~vs~~l~~L   74 (147)
T 2hr3_A           33 VQFSQLVVLGAIDRLG--GDVTPSELAAAERMRSSNLAALLREL   74 (147)
T ss_dssp             HHHHHHHHHHHHHHTT--SCBCHHHHHHHTTCCHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHcC--CCCCHHHHHHHhCCChhhHHHHHHHH
Confidence            5677777776554101  56999999999999999998876554

>3f6w_A XRE-family like protein; helix-turn-helix, DNA binding protein, xenobiotic response E family of transcriptional regulators; HET: MSE BTB; 1.85A {Pseudomonas syringae PV}

Probab=81.34  E-value=1  Score=32.98  Aligned_cols=24  Identities=13%  Similarity=0.199  Sum_probs=21.9

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHH
Q 046578          336 TPVSCKEIGRLLSLSRERIRQIRG  359 (379)
Q Consensus       336 e~~S~~EIAe~LgiS~~~Vr~~~~  359 (379)
                      .++|++|+|+.+|+|+++|+++.+
T Consensus        26 ~gltq~elA~~~gis~~~is~~e~   49 (83)
T 3f6w_A           26 AGITQKELAARLGRPQSFVSKTEN   49 (83)
T ss_dssp             HTCCHHHHHHHHTSCHHHHHHHHT
T ss_pred             cCCCHHHHHHHHCcCHHHHHHHHC
Confidence            459999999999999999999875

>1neq_A DNA-binding protein NER; NMR {Enterobacteria phage MU} SCOP: a.35.1.2 PDB: 1ner_A

Probab=81.30  E-value=1.1  Score=32.97  Aligned_cols=25  Identities=8%  Similarity=0.097  Sum_probs=22.7

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHHH
Q 046578          336 TPVSCKEIGRLLSLSRERIRQIRGI  360 (379)
Q Consensus       336 e~~S~~EIAe~LgiS~~~Vr~~~~r  360 (379)
                      .|+|+.++|+.+|+|+++|++.+.+
T Consensus        21 ~glT~~~LA~~~Gvs~stls~~~~~   45 (74)
T 1neq_A           21 RKLSLSALSRQFGYAPTTLANALER   45 (74)
T ss_dssp             TSCCHHHHHHHHSSCHHHHHHTTTS
T ss_pred             cCCCHHHHHHHHCcCHHHHHHHHcC
Confidence            6699999999999999999988764

>2hin_A GP39, repressor protein; transcription factor, dimer interface, helix-turn-helix; 1.05A {Enterobacteria phage N15} PDB: 3qws_A

Probab=81.21  E-value=1.3  Score=32.38  Aligned_cols=22  Identities=5%  Similarity=-0.034  Sum_probs=20.1

Q ss_pred             CHHHHHHHhCCCHHHHHHHHHH
Q 046578          339 SCKEIGRLLSLSRERIRQIRGI  360 (379)
Q Consensus       339 S~~EIAe~LgiS~~~Vr~~~~r  360 (379)
                      +..++|+.||||+.+|++++..
T Consensus        12 ~~~~lA~~lGVs~~aVs~W~~g   33 (71)
T 2hin_A           12 DVEKAAVGVGVTPGAVYQWLQA   33 (71)
T ss_dssp             SHHHHHHHHTSCHHHHHHHHHH
T ss_pred             CHHHHHHHHCCCHHHHHHHHhC
Confidence            6999999999999999999754

>1adr_A P22 C2 repressor; transcription regulation; NMR {Enterobacteria phage P22} SCOP: a.35.1.2

Probab=81.16  E-value=1.1  Score=32.02  Aligned_cols=24  Identities=17%  Similarity=0.296  Sum_probs=21.7

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHH
Q 046578          336 TPVSCKEIGRLLSLSRERIRQIRG  359 (379)
Q Consensus       336 e~~S~~EIAe~LgiS~~~Vr~~~~  359 (379)
                      .++|++++|+.+|+|+++|+++.+
T Consensus        17 ~gls~~~lA~~~gis~~~i~~~e~   40 (76)
T 1adr_A           17 LKIRQAALGKMVGVSNVAISQWER   40 (76)
T ss_dssp             HTCCHHHHHHHHTSCHHHHHHHHT
T ss_pred             cCCCHHHHHHHHCcCHHHHHHHHc
Confidence            349999999999999999999876

>2b5a_A C.BCLI; helix-turn-helix motif, gene regulation; 1.54A {Bacillus caldolyticus} SCOP: a.35.1.3

Probab=81.15  E-value=1.1  Score=32.13  Aligned_cols=24  Identities=29%  Similarity=0.380  Sum_probs=21.9

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHH
Q 046578          336 TPVSCKEIGRLLSLSRERIRQIRG  359 (379)
Q Consensus       336 e~~S~~EIAe~LgiS~~~Vr~~~~  359 (379)
                      .++|+.++|+.+|+|+++|+++.+
T Consensus        22 ~glsq~~lA~~~gis~~~i~~~e~   45 (77)
T 2b5a_A           22 KGVSQEELADLAGLHRTYISEVER   45 (77)
T ss_dssp             TTCCHHHHHHHHTCCHHHHHHHHT
T ss_pred             cCCCHHHHHHHHCCCHHHHHHHHC
Confidence            459999999999999999999875

>1y7y_A C.AHDI; helix-turn-helix, DNA-binding protein, transcriptional regulator, transcription regulator; 1.69A {Aeromonas hydrophila} SCOP: a.35.1.3

Probab=81.12  E-value=1.1  Score=31.63  Aligned_cols=25  Identities=16%  Similarity=0.139  Sum_probs=22.2

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHHH
Q 046578          336 TPVSCKEIGRLLSLSRERIRQIRGI  360 (379)
Q Consensus       336 e~~S~~EIAe~LgiS~~~Vr~~~~r  360 (379)
                      .++|++++|+.+|+|+++|+++.+-
T Consensus        25 ~g~s~~~lA~~~gis~~~i~~~e~g   49 (74)
T 1y7y_A           25 KGLSQETLAFLSGLDRSYVGGVERG   49 (74)
T ss_dssp             TTCCHHHHHHHHTCCHHHHHHHHTT
T ss_pred             cCCCHHHHHHHHCcCHHHHHHHHCC
Confidence            4599999999999999999998753

>2da4_A Hypothetical protein DKFZP686K21156; homeobox domain, three helices with the DNA binding helix- turn-helix motif, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=80.82  E-value=4.4  Score=29.85  Aligned_cols=51  Identities=16%  Similarity=0.143  Sum_probs=37.0

Q ss_pred             CCHHHHHHHHHHhhcCC---C--CCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhH
Q 046578          318 LSEREADILRLHFGLDG---Q--TPVSCKEIGRLLSLSRERIRQIRGIALTKLQQT  368 (379)
Q Consensus       318 L~~rer~Vl~l~ygL~g---~--e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~~  368 (379)
                      +++.|..+|...|--++   .  ......+||..+|++...|..+....+.|.|+.
T Consensus        15 ft~~Q~~~Le~~F~~~~~~~~yp~~~~r~~La~~lgL~~~qV~vWFqNrR~k~rk~   70 (80)
T 2da4_A           15 FSDRDLATLKKYWDNGMTSLGSVCREKIEAVATELNVDCEIVRTWIGNRRRKYRLM   70 (80)
T ss_dssp             CCHHHHHHHHHHHTTTTTCCSHHHHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHhCCCCCCCcCHHHHHHHHHHhCCCHHHhhHhHHHHHHHHhhc
Confidence            67777888877762110   0  001356899999999999999999988888774

>1z4h_A TORI, TOR inhibition protein; winged helix, reverse turn, protein binding, DNA binding protein; NMR {Escherichia coli}

Probab=80.75  E-value=1.3  Score=31.51  Aligned_cols=24  Identities=17%  Similarity=-0.075  Sum_probs=22.1

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHHHH
Q 046578          338 VSCKEIGRLLSLSRERIRQIRGIA  361 (379)
Q Consensus       338 ~S~~EIAe~LgiS~~~Vr~~~~rA  361 (379)
                      ++.+|+|+.+|+|++||+++.+++
T Consensus        11 l~~~eva~~lgvsrstiy~~~~~g   34 (66)
T 1z4h_A           11 VDLKFIMADTGFGKTFIYDRIKSG   34 (66)
T ss_dssp             ECHHHHHHHHSSCHHHHHHHHHHH
T ss_pred             cCHHHHHHHHCcCHHHHHHHHHCC
Confidence            789999999999999999988765

>2cw1_A SN4M; lambda CRO fold, de novo protein; NMR {Synthetic} SCOP: k.46.1.1

Probab=80.67  E-value=1.1  Score=32.22  Aligned_cols=22  Identities=23%  Similarity=0.237  Sum_probs=20.3

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHH
Q 046578          338 VSCKEIGRLLSLSRERIRQIRG  359 (379)
Q Consensus       338 ~S~~EIAe~LgiS~~~Vr~~~~  359 (379)
                      .|+.++|+.||+|+++|++++.
T Consensus        14 ~sq~~~A~~Lgvsq~aVS~~~~   35 (65)
T 2cw1_A           14 KNQEYAARALGLSQKLIEEVLK   35 (65)
T ss_dssp             SCHHHHHHHSSSCHHHHHHHHH
T ss_pred             cCHHHHHHHhCCCHHHHHHHHH
Confidence            4999999999999999999874

>2wiu_B HTH-type transcriptional regulator HIPB; transferase transcription complex, serine kinase, DNA-bindin mercury derivative, repressor; 2.35A {Escherichia coli} PDB: 3dnv_B* 3dnw_B* 3hzi_B*

Probab=80.60  E-value=1.4  Score=32.51  Aligned_cols=25  Identities=8%  Similarity=0.187  Sum_probs=22.5

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHHH
Q 046578          336 TPVSCKEIGRLLSLSRERIRQIRGI  360 (379)
Q Consensus       336 e~~S~~EIAe~LgiS~~~Vr~~~~r  360 (379)
                      .++|++++|+.+|+|+++|+++.+-
T Consensus        24 ~glsq~~lA~~~gis~~~i~~~e~g   48 (88)
T 2wiu_B           24 NGWTQSELAKKIGIKQATISNFENN   48 (88)
T ss_dssp             TTCCHHHHHHHHTCCHHHHHHHHHC
T ss_pred             cCCCHHHHHHHhCCCHHHHHHHHcC
Confidence            4599999999999999999998863

>3bs3_A Putative DNA-binding protein; XRE-family, structural genomics, PSI-2, protein structure initiative; HET: MSE; 1.65A {Bacteroides fragilis}

Probab=80.50  E-value=1.2  Score=31.71  Aligned_cols=24  Identities=8%  Similarity=0.061  Sum_probs=21.9

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHH
Q 046578          336 TPVSCKEIGRLLSLSRERIRQIRG  359 (379)
Q Consensus       336 e~~S~~EIAe~LgiS~~~Vr~~~~  359 (379)
                      .++|++++|+.+|+|+++|+++.+
T Consensus        22 ~g~s~~~lA~~~gis~~~i~~~e~   45 (76)
T 3bs3_A           22 KQRTNRWLAEQMGKSENTISRWCS   45 (76)
T ss_dssp             TTCCHHHHHHHHTCCHHHHHHHHT
T ss_pred             cCCCHHHHHHHHCcCHHHHHHHHc
Confidence            459999999999999999999876

>3bd1_A CRO protein; transcription factor, helix-turn-helix, prophage, structural evolution, transcription; 1.40A {Xylella fastidiosa}

Probab=80.46  E-value=1.4  Score=32.10  Aligned_cols=24  Identities=17%  Similarity=0.177  Sum_probs=22.0

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHHH
Q 046578          336 TPVSCKEIGRLLSLSRERIRQIRGI  360 (379)
Q Consensus       336 e~~S~~EIAe~LgiS~~~Vr~~~~r  360 (379)
                      .| |+.++|+.+|||+++|+++.+.
T Consensus        11 ~g-sq~~lA~~lgvs~~~is~~e~g   34 (79)
T 3bd1_A           11 LG-SVSALAASLGVRQSAISNWRAR   34 (79)
T ss_dssp             HS-SHHHHHHHHTCCHHHHHHHHHH
T ss_pred             hC-CHHHHHHHHCCCHHHHHHHHHC
Confidence            46 9999999999999999999875

>3eus_A DNA-binding protein; structural genomics, PSI2,MCSG, protein structure initiative, midwest center for structural genomic binding; 1.80A {Silicibacter pomeroyi}

Probab=80.37  E-value=1.1  Score=33.32  Aligned_cols=24  Identities=4%  Similarity=0.160  Sum_probs=22.0

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHH
Q 046578          336 TPVSCKEIGRLLSLSRERIRQIRG  359 (379)
Q Consensus       336 e~~S~~EIAe~LgiS~~~Vr~~~~  359 (379)
                      .++|++|+|+.+|+|+++|+++.+
T Consensus        26 ~gltq~elA~~~gis~~~is~~E~   49 (86)
T 3eus_A           26 AGLTQADLAERLDKPQSFVAKVET   49 (86)
T ss_dssp             TTCCHHHHHHHTTCCHHHHHHHHT
T ss_pred             cCCCHHHHHHHhCcCHHHHHHHHC
Confidence            559999999999999999999875

>2ao9_A Phage protein; structural genomics, nine-fold NCS., PSI, protein structure initiative, midwest center for structural genomics, MCSG, U function; 1.90A {Bacillus cereus} SCOP: a.4.1.17

Probab=80.35  E-value=4.5  Score=34.22  Aligned_cols=47  Identities=19%  Similarity=0.203  Sum_probs=32.1

Q ss_pred             HHhcCCHHHHHHHHHH--hhcC---CCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 046578          314 LLQTLSEREADILRLH--FGLD---GQTPVSCKEIGRLLSLSRERIRQIRGI  360 (379)
Q Consensus       314 ~L~~L~~rer~Vl~l~--ygL~---g~e~~S~~EIAe~LgiS~~~Vr~~~~r  360 (379)
                      +=.++++..+.-..+.  -++.   +.+++|..|||+.+|||++|++++...
T Consensus        20 ~~r~yt~EfK~aAv~l~~~~~~~p~~~~~lTv~eIA~~LGIS~~TLyrW~k~   71 (155)
T 2ao9_A           20 LKQKLTAKQIQAAYLLVENELMESNNEEKRTQDEMANELGINRTTLWEWRTK   71 (155)
T ss_dssp             HHTTSCHHHHHHHHHHHHHHHCC---CCCCCHHHHHHHHTCCHHHHHHHHHH
T ss_pred             hhhhcCHHHHHHHHHHHHccccccccccCCCHHHHHHHhCCCHHHHHHHHHc
Confidence            3446777766655432  1111   113699999999999999999998773

>1r71_A Transcriptional repressor protein KORB; INCP, plasmid partitioning, protein-DNA complex, heilx-turn- helix motif, transcription factor; HET: BRU; 2.20A {Escherichia coli} SCOP: a.4.14.1

Probab=80.29  E-value=2  Score=37.17  Aligned_cols=42  Identities=19%  Similarity=0.065  Sum_probs=33.6

Q ss_pred             hcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 046578          316 QTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGI  360 (379)
Q Consensus       316 ~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~r  360 (379)
                      ..|+|.|+......+ ++  .|+|..+||+.+|+|+++|++++.-
T Consensus        34 edL~piE~A~a~~~L-~~--~G~t~eeiA~~lG~s~s~V~~~LrL   75 (178)
T 1r71_A           34 NELTPREIADFIGRE-LA--KGKKKGDIAKEIGKSPAFITQHVTL   75 (178)
T ss_dssp             TCCCHHHHHHHHHHH-HH--TTCCHHHHHHHHTCCHHHHHHHHGG
T ss_pred             CCCCHHHHHHHHHHH-HH--cCCCHHHHHHHHCcCHHHHHHHHHH
Confidence            368998887776655 33  5699999999999999999987653

>3b7h_A Prophage LP1 protein 11; structural genomics, PSI2, MCSG, protein structure initiative, midwest center for structural genomics; 2.00A {Lactobacillus plantarum WCFS1}

Probab=80.16  E-value=1.5  Score=31.46  Aligned_cols=25  Identities=8%  Similarity=0.171  Sum_probs=22.3

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHHH
Q 046578          336 TPVSCKEIGRLLSLSRERIRQIRGI  360 (379)
Q Consensus       336 e~~S~~EIAe~LgiS~~~Vr~~~~r  360 (379)
                      .++|+.++|+.+|+|+++|+++.+.
T Consensus        19 ~g~sq~~lA~~~gis~~~i~~~e~g   43 (78)
T 3b7h_A           19 QNLTINRVATLAGLNQSTVNAMFEG   43 (78)
T ss_dssp             TTCCHHHHHHHHTCCHHHHHHHHCT
T ss_pred             cCCCHHHHHHHHCcCHHHHHHHHcC
Confidence            4599999999999999999998753

---

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	379
d1siga_	334	a.177.1.1 (A:) Sigma70 {Escherichia coli [TaxId: 5	1e-27
d1ku2a2	180	a.177.1.1 (A:93-272) Sigma factor SigA {Thermus aq	8e-21
d1ttya_	87	a.4.13.2 (A:) Sigma70 (SigA, RpoD) {Thermotoga mar	9e-20
d1rp3a3	87	a.177.1.1 (A:0-86) Sigma factor sigma-28 (FliA) {A	8e-17
d2p7vb1	68	a.4.13.2 (B:546-613) Sigma70 (SigA, RpoD) {Escheri	7e-16
d1ku3a_	61	a.4.13.2 (A:) Sigma70 (SigA, RpoD) {Thermus aquati	3e-15
d1rp3a2	71	a.4.13.2 (A:164-234) Sigma factor sigma-28 (FliA)	8e-08
d1rp3a1	77	a.4.13.1 (A:87-163) Sigma factor sigma-28 (FliA) {	3e-07
d1l0oc_	57	a.4.13.2 (C:) SigmaF {Bacillus stearothermophilus	1e-05
d1ku2a1	60	a.4.13.1 (A:273-332) Sigma factor SigA {Thermus aq	2e-05
d1yioa1	70	a.4.6.2 (A:131-200) Response regulatory protein St	9e-05

>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 =  109 bits (272), Expect = 1e-27
 Identities = 48/177 (27%), Positives = 80/177 (45%)

Query: 37  CSNKYNININLVTNEALALHPVIESATDAAALASAAVRTAKDAVSFANGAEEVCFDDGEC 96
            ++   +   + T E L +   +E                + + ++ N A  +     E 
Sbjct: 158 VNSMRVMMDRVRTQERLIMKLCVEQCKMPKKNFITLFTGNETSDTWFNAAIAMNKPWSEK 217

Query: 97  ESVLKMMRRRSRRKKRTKESDFLDKENGELDYNLVKYKILCKERESQERIIRSYRSLVVS 156
              +     R+ +K +  E +         D N        K R +++ ++ +   LV+S
Sbjct: 218 LHDVSEEVHRALQKLQQIEEETGLTIEQVKDINRRMSIGEAKARRAKKEMVEANLRLVIS 277

Query: 157 IATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYWWIKQAIIRAIANK 213
           IA  Y  +GL   DLIQEG+IGL++   +F   RGYK STY  WWI+QAI R+IA++
Sbjct: 278 IAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQ 334

>d1ku2a2 a.177.1.1 (A:93-272) Sigma factor SigA {Thermus aquaticus [TaxId: 271]} Length = 180

class: All alpha proteins
fold: Sigma2 domain of RNA polymerase sigma factors
superfamily: Sigma2 domain of RNA polymerase sigma factors
family: Sigma2 domain of RNA polymerase sigma factors
domain: Sigma factor SigA
species: Thermus aquaticus [TaxId: 271]

 Score = 86.8 bits (214), Expect = 8e-21
 Identities = 39/77 (50%), Positives = 55/77 (71%)

Query: 140 RESQERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVY 199
             +++ +I +   LVVSIA  Y G+GLS  DLIQEG+ GL+R  ++F  +R +K STY  
Sbjct: 104 EAARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQEGNQGLIRAVEKFEYKRRFKFSTYAT 163

Query: 200 WWIKQAIIRAIANKSRT 216
           WWI+QAI RAIA+++RT
Sbjct: 164 WWIRQAINRAIADQART 180

>d1ttya_ a.4.13.2 (A:) Sigma70 (SigA, RpoD) {Thermotoga maritima [TaxId: 2336]} Length = 87

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Sigma3 and sigma4 domains of RNA polymerase sigma factors
family: Sigma4 domain
domain: Sigma70 (SigA, RpoD)
species: Thermotoga maritima [TaxId: 2336]

 Score = 80.9 bits (200), Expect = 9e-20
 Identities = 31/77 (40%), Positives = 51/77 (66%)

Query: 302 VQKQLMKQELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIA 361
             + LM++EL+++L+TLS REA +LR+ +GL    P + +E+G+  +++RERIRQI   A
Sbjct: 3   AMRMLMREELEKVLKTLSPREAMVLRMRYGLLDGKPKTLEEVGQYFNVTRERIRQIEVKA 62

Query: 362 LTKLQQTNILNNLKVYM 378
           L KL+  +    LK  +
Sbjct: 63  LRKLRHPSRSKYLKSLL 79

>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 = 72.6 bits (178), Expect = 8e-17
 Identities = 21/76 (27%), Positives = 35/76 (46%), Gaps = 3/76 (3%)

Query: 138 KERESQERIIRSYRSLVVSIATGYQGK---GLSLKDLIQEGSIGLLRGAKRFNPERGYKL 194
             +  +E +I  Y  LV +IAT  +      + ++DLI  G IGL++     + E   + 
Sbjct: 7   SNQIEREELILKYLPLVKAIATNIKKHLPEDVDIRDLISYGVIGLIKAVDNLSTENPKRA 66

Query: 195 STYVYWWIKQAIIRAI 210
             Y+   IK AI   +
Sbjct: 67  EAYIKLRIKGAIYDYL 82

>d2p7vb1 a.4.13.2 (B:546-613) Sigma70 (SigA, RpoD) {Escherichia coli [TaxId: 562]} Length = 68

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Sigma3 and sigma4 domains of RNA polymerase sigma factors
family: Sigma4 domain
domain: Sigma70 (SigA, RpoD)
species: Escherichia coli [TaxId: 562]

 Score = 69.4 bits (170), Expect = 7e-16
 Identities = 25/66 (37%), Positives = 42/66 (63%)

Query: 313 ELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQTNILN 372
           ++L  L+ REA +LR+ FG+D  T  + +E+G+   ++RERIRQI   AL KL+  +   
Sbjct: 1   DVLAGLTAREAKVLRMRFGIDMNTDYTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSE 60

Query: 373 NLKVYM 378
            L+ ++
Sbjct: 61  VLRSFL 66

>d1ku3a_ a.4.13.2 (A:) Sigma70 (SigA, RpoD) {Thermus aquaticus [TaxId: 271]} Length = 61

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Sigma3 and sigma4 domains of RNA polymerase sigma factors
family: Sigma4 domain
domain: Sigma70 (SigA, RpoD)
species: Thermus aquaticus [TaxId: 271]

 Score = 67.4 bits (165), Expect = 3e-15
 Identities = 25/58 (43%), Positives = 36/58 (62%)

Query: 310 ELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQ 367
           EL++ L  LSEREA +L++  GL      + +E+G    ++RERIRQI   AL KL+ 
Sbjct: 1   ELEKALSKLSEREAMVLKMRKGLIDGREHTLEEVGAYFGVTRERIRQIENKALRKLKY 58

>d1rp3a2 a.4.13.2 (A:164-234) Sigma factor sigma-28 (FliA) {Aquifex aeolicus [TaxId: 63363]} Length = 71

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Sigma3 and sigma4 domains of RNA polymerase sigma factors
family: Sigma4 domain
domain: Sigma factor sigma-28 (FliA)
species: Aquifex aeolicus [TaxId: 63363]

 Score = 46.8 bits (111), Expect = 8e-08
 Identities = 20/70 (28%), Positives = 39/70 (55%), Gaps = 4/70 (5%)

Query: 298 PERMVQKQLMKQELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQI 357
            E  V K+ + +++KE +  L ERE  +++L F       +  KE+ ++L  S  R+ Q+
Sbjct: 2   VEEEVIKRELTEKVKEAVSKLPEREKLVIQLIFYE----ELPAKEVAKILETSVSRVSQL 57

Query: 358 RGIALTKLQQ 367
           +  AL +L++
Sbjct: 58  KAKALERLRE 67

>d1rp3a1 a.4.13.1 (A:87-163) Sigma factor sigma-28 (FliA) {Aquifex aeolicus [TaxId: 63363]} Length = 77

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Sigma3 and sigma4 domains of RNA polymerase sigma factors
family: Sigma3 domain
domain: Sigma factor sigma-28 (FliA)
species: Aquifex aeolicus [TaxId: 63363]

 Score = 45.5 bits (108), Expect = 3e-07
 Identities = 21/80 (26%), Positives = 32/80 (40%), Gaps = 9/80 (11%)

Query: 214 SRTIRLPGSMAGMVAKIAEANNVLSRRLRRMPTDSEIAEMLNIHVSTVR--LAIERTRHP 271
           SR +R          +I E    L  +L R PTD E+A+ L I    +   L      + 
Sbjct: 2   SRQVRE------KERRIKEVVEKLKEKLGREPTDEEVAKELGISTEELFKTLDKINFSYI 55

Query: 272 ISLDGAVTDRGCMTMQDIIP 291
           +SL+    D       ++IP
Sbjct: 56  LSLEEVFRDFA-RDYSELIP 74

>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 = 40.4 bits (95), Expect = 1e-05
 Identities = 21/55 (38%), Positives = 30/55 (54%)

Query: 215 RTIRLPGSMAGMVAKIAEANNVLSRRLRRMPTDSEIAEMLNIHVSTVRLAIERTR 269
            T+++  S+  M  KI +A + LS+   R PT +EIA+ L I    V LA E  R
Sbjct: 2   GTVKVSRSLKEMGNKIRKAKDELSKTRGRAPTVTEIADHLGISPEDVVLAQEAVR 56

>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 = 40.0 bits (94), Expect = 2e-05
 Identities = 17/60 (28%), Positives = 28/60 (46%), Gaps = 2/60 (3%)

Query: 217 IRLPGSMAGMVAKIAEANNVLSRRLRRMPTDSEIAEMLNIHVST--VRLAIERTRHPISL 274
           IR+P  M   + K++     L + L R P+  EIAE +        V   ++  + P+SL
Sbjct: 1   IRIPVHMVETINKLSRTARQLQQELGREPSYEEIAEAMGPGWDAKRVEETLKIAQEPVSL 60

>d1yioa1 a.4.6.2 (A:131-200) Response regulatory protein StyR, C-terminal domain {Pseudomonas fluorescens [TaxId: 294]} Length = 70

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: C-terminal effector domain of the bipartite response regulators
family: GerE-like (LuxR/UhpA family of transcriptional regulators)
domain: Response regulatory protein StyR, C-terminal domain
species: Pseudomonas fluorescens [TaxId: 294]

 Score = 38.1 bits (89), Expect = 9e-05
 Identities = 14/62 (22%), Positives = 30/62 (48%), Gaps = 5/62 (8%)

Query: 308 KQELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQ 367
           + +L++L  +L+ RE  +L+L   + G      K+I   L ++   ++  R   + KL  
Sbjct: 3   QDQLEQLFSSLTGREQQVLQLT--IRGLMN---KQIAGELGIAEVTVKVHRHNIMQKLNV 57

Query: 368 TN 369
            +
Sbjct: 58  RS 59

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	379
d1ku2a2	180	Sigma factor SigA {Thermus aquaticus [TaxId: 271]}	99.75
d1rp3a3	87	Sigma factor sigma-28 (FliA) {Aquifex aeolicus [Ta	99.71
d1siga_	334	Sigma70 {Escherichia coli [TaxId: 562]}	99.7
d1or7a2	113	SigmaE factor (RpoE) {Escherichia coli [TaxId: 562	99.63
d2p7vb1	68	Sigma70 (SigA, RpoD) {Escherichia coli [TaxId: 562	99.53
d1ttya_	87	Sigma70 (SigA, RpoD) {Thermotoga maritima [TaxId:	99.5
d1rp3a2	71	Sigma factor sigma-28 (FliA) {Aquifex aeolicus [Ta	99.47
d1ku3a_	61	Sigma70 (SigA, RpoD) {Thermus aquaticus [TaxId: 27	99.44
d1or7a1	68	SigmaE factor (RpoE) {Escherichia coli [TaxId: 562	99.33
d1h3la_	75	Sigma factor SigR {Streptomyces coelicolor a3(2) [	99.12
d1xsva_	106	Hypothetical protein SAV1236 {Staphylococcus aureu	98.97
d1s7oa_	106	Hypothetical protein SPy1201 {Streptococcus pyogen	98.95
d1ku2a1	60	Sigma factor SigA {Thermus aquaticus [TaxId: 271]}	98.81
d1l0oc_	57	SigmaF {Bacillus stearothermophilus [TaxId: 1422]}	98.73
d1yioa1	70	Response regulatory protein StyR, C-terminal domai	98.58
d1rp3a1	77	Sigma factor sigma-28 (FliA) {Aquifex aeolicus [Ta	98.43
d1a04a1	67	Nitrate/nitrite response regulator (NarL) {Escheri	98.4
d1l3la1	65	Quorum-sensing transcription factor TraR, C-termin	98.24
d1fsea_	67	Germination protein GerE {Bacillus subtilis [TaxId	98.2
d1p4wa_	87	Transcriptional regulator RcsB {Erwinia amylovora	97.95
d1ijwc_	47	HIN recombinase (DNA-binding domain) {Synthetic}	96.33
d1gdta1	43	gamma,delta resolvase (C-terminal domain) {Escheri	95.49
d1jhfa1	71	LexA repressor, N-terminal DNA-binding domain {Esc	95.45
d2cg4a1	63	Regulatory protein AsnC {Escherichia coli [TaxId:	94.99
d2cfxa1	63	Transcriptional regulator LrpC {Bacillus subtilis	94.79
d1i1ga1	60	LprA {Archaeon Pyrococcus furiosus [TaxId: 2261]}	94.64
d2cyya1	60	Putative transcriptional regulator PH1519 {Archaeo	94.37
d1hlva1	66	DNA-binding domain of centromere binding protein B	94.26
d1k78a1	63	Pax-5 {Human (Homo sapiens) [TaxId: 9606]}	93.54
d1ku9a_	151	DNA-binding protein Mj223 {Archaeon Methanococcus	93.01
d2jn6a1	89	Uncharacterized protein Cgl2762 {Corynebacterium g	92.61
d1pdnc_	123	Paired protein (prd) {Fruit fly (Drosophila melano	92.26
d1nr3a_	122	DNA-binding protein Tfx {Archaeon Methanobacterium	92.18
d1biaa1	63	Biotin repressor, N-terminal domain {Escherichia c	91.91
d2ppxa1	62	Uncharacterized protein Atu1735 {Agrobacterium tum	91.23
d2o3fa1	83	Putative transcriptional regulator YbbH {Bacillus	90.98
d1dpua_	69	C-terminal domain of RPA32 {Human (Homo sapiens) [	90.86
d3broa1	135	Transcriptional regulator OEOE1854 {Oenococcus oen	90.73
d1sfxa_	109	Hypothetical protein AF2008 {Archaeoglobus fulgidu	90.41
d1r1ta_	98	SmtB repressor {Cyanobacteria (Synechococcus), pcc	90.4
d2d1ha1	109	Hypothetical transcriptional regulator ST1889 {Sul	90.33
d1stza1	87	Heat-inducible transcription repressor HrcA, N-ter	89.51
d1z05a1	71	Transcriptional regulator VC2007 N-terminal domain	89.44
d1le8a_	53	Mating type protein A1 Homeodomain {Baker's yeast	89.34
d1r71a_	114	Transcriptional repressor protein KorB DNA-binding	89.25
d1vz0a1	93	Putative partitioning protein ParB/Spo0J {Thermus	89.03
d1r1ua_	94	Metal-sensing transcriptional repressor CzrA {Stap	88.97
d1yz8p1	60	Pituitary homeobox 2 {Human (Homo sapiens) [TaxId:	88.87
d1qpza1	57	Purine repressor (PurR), N-terminal domain {Escher	88.41
d2auwa1	67	Hypothetical protein NE0471 C-terminal domain {Nit	88.31
d2ecca1	76	Homeobox-leucine zipper protein Homez {Human (Homo	87.99
d1s3ja_	143	Putative transcriptional regulator YusO {Bacillus	87.84
d1uxda_	59	Fructose repressor (FruR), N-terminal domain {Esch	87.72
d1jhfa1	71	LexA repressor, N-terminal DNA-binding domain {Esc	87.53
d1uhsa_	72	Homeodomain-only protein, Hop {Mouse (Mus musculus	87.44
d2isya1	63	Iron-dependent regulator IdeR {Mycobacterium tuber	87.16
d1i5za1	69	Catabolite gene activator protein (CAP), C-termina	87.15
d1hsja1	115	Staphylococcal accessory regulator A homolog, SarR	87.14
d2hsga1	57	Glucose-resistance amylase regulator CcpA, N-termi	87.03
d1ig7a_	58	Msx-1 homeodomain {Mouse (Mus musculus) [TaxId: 10	86.75
d1e3oc1	57	Oct-1 POU Homeodomain {Human (Homo sapiens) [TaxId	86.69
d1utxa_	66	Putative transcription regulator CylR2 {Enterococc	86.51
d1au7a1	58	Pit-1 POU homeodomain {Rat (Rattus norvegicus) [Ta	86.36
d1lnwa_	141	MexR repressor {Pseudomonas aeruginosa [TaxId: 287	86.35
d1j5ya1	65	Putative transcriptional regulator TM1602, N-termi	86.33
d2a6ca1	69	HTH-motif protein NE1354 {Nitrosomonas europaea [T	86.24
d1p4xa2	125	Staphylococcal accessory regulator A homolog, SarS	86.19
d1fjla_	65	Paired protein {Fruit fly (Drosophila melanogaster	86.13
d2a61a1	139	Transcriptional regulator TM0710 {Thermotoga marit	85.98
d1ub9a_	100	Hypothetical protein PH1061 {Archaeon Pyrococcus h	85.93
d2croa_	65	cro 434 {Bacteriophage 434 [TaxId: 10712]}	85.91
d1jgsa_	138	Multiple antibiotic resistance repressor, MarR {Es	85.89
d1jhga_	101	Trp repressor, TrpR {Escherichia coli [TaxId: 562]	85.84
d1ft9a1	80	CO-sensing protein CooA, C-terminal domain {Rhodos	85.81
d2o38a1	89	Hypothetical protein RPA3824 {Rhodopseudomonas pal	85.49
d1x2na1	62	Homeobox protein pknox1 {Human (Homo sapiens) [Tax	85.34
d2etha1	140	Putative transcriptional regulator TM0816 {Thermot	85.11
d1z6ra1	70	Mlc protein N-terminal domain {Escherichia coli [T	84.62
d1rr7a_	94	Middle operon regulator, Mor {Bacteriophage Mu [Ta	84.58
d2frha1	115	Pleiotropic regulator of virulence genes, SarA {St	84.55
d3e5ua1	80	Chlorophenol reduction protein CprK {Desulfitobact	84.45
d1z91a1	137	Organic hydroperoxide resistance transcriptional r	84.44
d2fxaa1	162	Protease production regulatory protein Hpr {Bacill	84.38
d2fbka1	172	Transcriptional regulator DR1159 {Deinococcus radi	84.32
d1efaa1	59	Lac repressor (LacR), N-terminal domain {Escherich	84.17
d1lj9a_	144	Transcriptional regulator SlyA {Enterococcus faeca	84.13
d2e1oa1	57	Homeobox protein prh {Human (Homo sapiens) [TaxId:	84.07
d2fbha1	137	Transcriptional regulator PA3341 {Pseudomonas aeru	83.94
d2ao9a1	120	Phage protein BC1890 {Bacillus cereus [TaxId: 1396	83.94
d2gaua1	81	Transcriptional regulator PG0396, C-terminal domai	83.88
d1y7ya1	69	Restriction-modification controller protein C.AhdI	83.86
d1zyba1	73	Probable transcription regulator BT4300, C-termina	83.83
d1r69a_	63	434 C1 repressor, DNA-binding domain {Bacteriophag	83.81
d1zq3p1	67	Homeotic bicoid protein {Fruit fly (Drosophila mel	83.76
d1mkma1	75	Transcriptional regulator IclR, N-terminal domain	83.17
d1wi3a_	71	DNA-binding protein SATB2 {Human (Homo sapiens) [T	83.1
d1jgga_	57	Even-skipped homeodomain {Fruit fly (Drosophila me	82.97
d1pufb_	73	pbx1 {Human (Homo sapiens) [TaxId: 9606]}	82.94
d2icta1	87	Antitoxin HigA {Escherichia coli [TaxId: 562]}	82.8
d1b0na2	68	SinR repressor, DNA-binding domain {Bacillus subti	82.76
d2g9wa1	122	Hypothetical protein Rv1846c {Mycobacterium tuberc	82.63
d1bw5a_	66	Insulin gene enhancer protein isl-1 {Rat (Rattus n	82.59
d1x57a1	78	Endothelial differentiation-related factor 1, EDF1	81.99
d2cuea1	68	Paired box protein pax6 {Human (Homo sapiens) [Tax	81.88
d1k61a_	60	mat alpha2 Homeodomain {Baker's yeast (Saccharomyc	81.86
d3deua1	140	Transcriptional regulator SlyA {Salmonella typhimu	81.79
d1ftta_	68	Thyroid transcription factor 1 homeodomain {Rat (R	81.14
d2r1jl1	66	P22 C2 repressor, DNA-binding domain {Salmonella b	80.91
d1lmb3_	87	lambda C1 repressor, DNA-binding domain {Bacteriop	80.73
d2fbia1	136	Probable transcriptional regulator PA4135 {Pseudom	80.68
d1ulya_	190	Hypothetical protein PH1932 {Pyrococcus horikoshii	80.66
d2ev0a1	61	Manganese transport regulator MntR {Bacillus subti	80.65
d9anta_	56	Antennapedia Homeodomain {Drosophila melanogaster	80.47
d1ic8a2	94	Hepatocyte nuclear factor 1a (LFB1/HNF1) {Human (H	80.4
d1umqa_	60	Photosynthetic apparatus regulatory protein PprA (	80.4

>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=99.75  E-value=1.1e-18  Score=153.32  Aligned_cols=83  Identities=47%  Similarity=0.811  Sum_probs=77.3

Q ss_pred             HHHhcccHHHHHHHHHHhHHHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHhccCCCCCCCchhHHHHHHHHHHHHHHHh
Q 046578          133 YKILCKERESQERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYWWIKQAIIRAIAN  212 (379)
Q Consensus       133 ~~~~~Gd~~A~e~Li~~y~~lV~~ia~r~~~~~~d~eDLvQEg~i~L~~ai~~fD~~~g~~FsTYa~~~Ir~~i~~~lr~  212 (379)
                      .+.......|+++|+..|.++|+++|++|.+.+.+++||+|||++||++|+++|||++|++|+|||+|||++.|.+++++
T Consensus        97 ~~~~~~~~~a~~~li~~~~~lv~~~a~~~~~~~~~~~dl~q~g~~gl~~a~~~fd~~~g~~f~tya~~~i~~~i~~~~~~  176 (180)
T d1ku2a2          97 LHIAREGEAARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQEGNQGLIRAVEKFEYKRRFKFSTYATWWIRQAINRAIAD  176 (180)
T ss_dssp             HHHHHHHHHHHHHHHHTTHHHHHHHHHTTCSSSSCHHHHHHHHHHHHHHHHHHCCGGGCSCHHHHHHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHhcccCCCcCHHHHHHHHHHHHHHHHHHcCCCCCCCHHHHHHHHHHHHHHHHHHH
Confidence            34445557799999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             hcC
Q 046578          213 KSR  215 (379)
Q Consensus       213 ~~r  215 (379)
                      +.|
T Consensus       177 ~~r  179 (180)
T d1ku2a2         177 QAR  179 (180)
T ss_dssp             SCC
T ss_pred             hCC
Confidence            775

>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=99.71  E-value=1.3e-17  Score=129.01  Aligned_cols=74  Identities=28%  Similarity=0.448  Sum_probs=68.6

Q ss_pred             HHHHHHHHHHhHHHHHHHHHhccCC---CCCHHHHHHHHHHHHHHHHhccCCCCCCCchhHHHHHHHHHHHHHHHhh
Q 046578          140 RESQERIIRSYRSLVVSIATGYQGK---GLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYWWIKQAIIRAIANK  213 (379)
Q Consensus       140 ~~A~e~Li~~y~~lV~~ia~r~~~~---~~d~eDLvQEg~i~L~~ai~~fD~~~g~~FsTYa~~~Ir~~i~~~lr~~  213 (379)
                      +..+++|+..|.|+|.++|+++.++   +.+.|||+|+|++||++|+++|||++|.+|+|||.++|+++|++++|+.
T Consensus         9 ~~~re~li~~~~~LV~~ia~~~~~~~~~~~e~eDL~q~G~igL~~A~~~yd~~~g~~F~tYA~~~Irgai~d~lRk~   85 (87)
T d1rp3a3           9 QIEREELILKYLPLVKAIATNIKKHLPEDVDIRDLISYGVIGLIKAVDNLSTENPKRAEAYIKLRIKGAIYDYLRSL   85 (87)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHTTSCTTSCHHHHHHHHHHHHHHHHHTCCCCCTHHHHHHHHHHHHHHHHHHHHTS
T ss_pred             HHHHHHHHHHhHHHHHHHHHHHhccCCCCCCHHHHHHHHHHHHHHHHHhhCCCCCCCHHHHHHHHHHHHHHHHHHhC
Confidence            3456899999999999999998653   7899999999999999999999999999999999999999999999975

>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=99.70  E-value=8.9e-18  Score=160.73  Aligned_cols=133  Identities=30%  Similarity=0.445  Sum_probs=106.6

Q ss_pred             hhhcCCcccccchhHHHHHHHHHHHHHhhhcccccccchhh----------------hcCcC---cHHHHHHHHhcccH-
Q 046578           81 SFANGAEEVCFDDGECESVLKMMRRRSRRKKRTKESDFLDK----------------ENGEL---DYNLVKYKILCKER-  140 (379)
Q Consensus        81 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----------------~~~~~---~~~eLi~~~~~Gd~-  140 (379)
                      +...|+++..|.+.+.+.+....|..+..+..+.+..+...                ...++   ++.+++.++..|.. 
T Consensus       180 ~~~~~~~r~~fik~~~~~e~~~~wl~~~~k~~~~~~~~l~~~~~~I~~~q~kl~~ie~~~gl~~~elk~i~~~i~~ge~~  259 (334)
T d1siga_         180 VEQCKMPKKNFITLFTGNETSDTWFNAAIAMNKPWSEKLHDVSEEVHRALQKLQQIEEETGLTIEQVKDINRRMSIGEAK  259 (334)
T ss_dssp             HTTSCCCHHHHHHHHTTTCSSGGGTHHHHTTCSHHHHHGGGTHHHHHHHHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHH
T ss_pred             HhccccchHHHHHHHhhhhhhHHHHHHHHhhchhHHHHHHhhHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHhh
Confidence            35689999999998888887777755544443333322110                01112   35677777777765 


Q ss_pred             --HHHHHHHHHhHHHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHhccCCCCCCCchhHHHHHHHHHHHHHHHhh
Q 046578          141 --ESQERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYWWIKQAIIRAIANK  213 (379)
Q Consensus       141 --~A~e~Li~~y~~lV~~ia~r~~~~~~d~eDLvQEg~i~L~~ai~~fD~~~g~~FsTYa~~~Ir~~i~~~lr~~  213 (379)
                        .|.++|+..|++||.++|++|.++|.+++||+|+|++||++|+++|||.+|++|+|||+|||+++|.++++++
T Consensus       260 ~~~ak~~~~~~~~~lv~~~~~~~~~~~~~~~dl~~~~~~~l~~~~~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~  334 (334)
T d1siga_         260 ARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQ  334 (334)
T ss_dssp             HHHHHHHHHHHTHHHHHHHHTTSTTSSSCHHHHHHHHHHHHHHHHHHCCGGGCCCHHHHHHHHHHHHHHHHHHHC
T ss_pred             ccchHHHHHHhHHHHHHHHHHhccCCCCCHHHHHHhhHHHHHHHHHhcCCCCCCchHhhhHHHHHHHHHHHHhCC
Confidence              5779999999999999999999999999999999999999999999999999999999999999999999864

>d2p7vb1 a.4.13.2 (B:546-613) Sigma70 (SigA, RpoD) {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Sigma3 and sigma4 domains of RNA polymerase sigma factors
family: Sigma4 domain
domain: Sigma70 (SigA, RpoD)
species: Escherichia coli [TaxId: 562]

Probab=99.53  E-value=2.2e-15  Score=110.26  Aligned_cols=65  Identities=38%  Similarity=0.661  Sum_probs=62.2

Q ss_pred             HHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHHhhchhhhhc
Q 046578          314 LLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQTNILNNLKVYM  378 (379)
Q Consensus       314 ~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~~l~~~~L~~y~  378 (379)
                      +|+.|+|+|+.||.++|||+|.+++|++|||+.||||+++|+|+..+|++|||+......|++|+
T Consensus         2 ~L~~L~~rE~~Ii~~rfGl~~~~~~tl~eI~~~lgiSrerVrqie~~al~kLr~~~~~~~L~~yl   66 (68)
T d2p7vb1           2 VLAGLTAREAKVLRMRFGIDMNTDYTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRSFL   66 (68)
T ss_dssp             CSCCCCHHHHHHHHHHTTTTSSSCCCHHHHHHHHTCCHHHHHHHHHHHHHGGGSCCGGGGGSCTT
T ss_pred             hhhcCCHHHHHHHHHHcCCCCCCcCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhhHHHHHHHHHh
Confidence            46789999999999999999889999999999999999999999999999999999999999997

>d1ttya_ a.4.13.2 (A:) Sigma70 (SigA, RpoD) {Thermotoga maritima [TaxId: 2336]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Sigma3 and sigma4 domains of RNA polymerase sigma factors
family: Sigma4 domain
domain: Sigma70 (SigA, RpoD)
species: Thermotoga maritima [TaxId: 2336]

Probab=99.50  E-value=1.8e-14  Score=110.47  Aligned_cols=70  Identities=41%  Similarity=0.636  Sum_probs=66.2

Q ss_pred             HHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHHhhchhhhhc
Q 046578          309 QELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQTNILNNLKVYM  378 (379)
Q Consensus       309 ~~L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~~l~~~~L~~y~  378 (379)
                      +.|..+++.|+|+|+.||.++|||+|.+++|+.|||+.||||+++|+|+..+|++|||.......|++|+
T Consensus        10 ~~l~~~l~~L~~rE~~Ii~~rfGl~~~~~~tl~eI~~~lgiSrERVRQie~~al~kLr~~~~~~~L~~~l   79 (87)
T d1ttya_          10 EELEKVLKTLSPREAMVLRMRYGLLDGKPKTLEEVGQYFNVTRERIRQIEVKALRKLRHPSRSKYLKSLL   79 (87)
T ss_dssp             SHHHHHHTTSCHHHHHHHHHHHTTTTSSCCCHHHHHHHHTCCHHHHHHHHHHHHHHHBTTBSSHHHHHHH
T ss_pred             HHHHHHHhcCCHHHHHHHHHHcCCCCCCcCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcHHHHHHHHHH
Confidence            4578899999999999999999999889999999999999999999999999999999999888898885

>d1rp3a2 a.4.13.2 (A:164-234) Sigma factor sigma-28 (FliA) {Aquifex aeolicus [TaxId: 63363]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Sigma3 and sigma4 domains of RNA polymerase sigma factors
family: Sigma4 domain
domain: Sigma factor sigma-28 (FliA)
species: Aquifex aeolicus [TaxId: 63363]

Probab=99.47  E-value=9.6e-14  Score=102.58  Aligned_cols=69  Identities=29%  Similarity=0.432  Sum_probs=64.8

Q ss_pred             hHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHHh
Q 046578          298 PERMVQKQLMKQELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQTNI  370 (379)
Q Consensus       298 pe~~~~~~e~~~~L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~~l~  370 (379)
                      |++.+...+....|..+|+.|||++|.||.++|+    +|+|++|||+.||+|.++|+++++||+++||+.+.
T Consensus         2 ~e~~~~~~e~~~~l~~~l~~L~~~~r~v~~l~~~----~~~s~~eIA~~lgis~~tv~~~~~ra~~~Lr~~L~   70 (71)
T d1rp3a2           2 VEEEVIKRELTEKVKEAVSKLPEREKLVIQLIFY----EELPAKEVAKILETSVSRVSQLKAKALERLREMLS   70 (71)
T ss_dssp             HHHHHHHHHHHHHHHHHHTTSCHHHHHHHHHHHT----SCCCHHHHHHHTTSCHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHh----HhCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHcc
Confidence            6777888888999999999999999999999995    77999999999999999999999999999999875

>d1ku3a_ a.4.13.2 (A:) Sigma70 (SigA, RpoD) {Thermus aquaticus [TaxId: 271]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Sigma3 and sigma4 domains of RNA polymerase sigma factors
family: Sigma4 domain
domain: Sigma70 (SigA, RpoD)
species: Thermus aquaticus [TaxId: 271]

Probab=99.44  E-value=3.5e-14  Score=101.68  Aligned_cols=57  Identities=40%  Similarity=0.560  Sum_probs=54.0

Q ss_pred             HHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhH
Q 046578          312 KELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQT  368 (379)
Q Consensus       312 ~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~~  368 (379)
                      ..+|+.|+++|+.||.++||++|.+++|++|||+.||||+++|+++..+|++|||+.
T Consensus         3 ~~~L~~L~~rer~Ii~~ryGl~~~~~~tl~eIa~~lgiS~erVrqi~~~al~kLR~~   59 (61)
T d1ku3a_           3 EKALSKLSEREAMVLKMRKGLIDGREHTLEEVGAYFGVTRERIRQIENKALRKLKYH   59 (61)
T ss_dssp             SSSTTTSCHHHHHHHHHHHTTTTSSCCCHHHHHHHHTCCHHHHHHHHHHHHHHHHHT
T ss_pred             HHHHhcCCHHHHHHHHHHhCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHhcC
Confidence            456889999999999999999988999999999999999999999999999999975

>d1or7a1 a.4.13.2 (A:120-187) SigmaE factor (RpoE) {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Sigma3 and sigma4 domains of RNA polymerase sigma factors
family: Sigma4 domain
domain: SigmaE factor (RpoE)
species: Escherichia coli [TaxId: 562]

Probab=99.33  E-value=2.2e-12  Score=94.40  Aligned_cols=63  Identities=14%  Similarity=0.086  Sum_probs=57.9

Q ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHHh
Q 046578          304 KQLMKQELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQTNI  370 (379)
Q Consensus       304 ~~e~~~~L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~~l~  370 (379)
                      .++....|..+|+.||+++|+||.++|+    +|+|++|||+.||+|.++|+++++||+++||+.++
T Consensus         5 ~~e~~~~l~~~l~~Lp~~~r~v~~l~~~----~~~s~~eIA~~lgis~~tv~~~l~ra~~~Lr~~l~   67 (68)
T d1or7a1           5 SEELRQIVFRTIESLPEDLRMAITLREL----DGLSYEEIAAIMDCPVGTVRSRIFRAREAIDNKVQ   67 (68)
T ss_dssp             HHHHHHHHHHHHHHSCHHHHHHHHHHHT----TCCCHHHHHHHTTSCHHHHHHHHHHHHHHHHHHHC
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHH----hCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHcC
Confidence            3456678999999999999999999995    77999999999999999999999999999999864

>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=99.12  E-value=2.1e-11  Score=90.66  Aligned_cols=72  Identities=17%  Similarity=0.197  Sum_probs=66.1

Q ss_pred             ccHHHHHHHHHHhHHHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHhccCCCCCCCchhHHHHHHHHHHHHHHH
Q 046578          138 KERESQERIIRSYRSLVVSIATGYQGKGLSLKDLIQEGSIGLLRGAKRFNPERGYKLSTYVYWWIKQAIIRAIA  211 (379)
Q Consensus       138 Gd~~A~e~Li~~y~~lV~~ia~r~~~~~~d~eDLvQEg~i~L~~ai~~fD~~~g~~FsTYa~~~Ir~~i~~~lr  211 (379)
                      ++.+++++++..|.+.++++|.++.++..++||++||+|+.+|+..++|++.  .+|.+|++++++|.+++++|
T Consensus         4 ~~~~~f~~~~~~y~~~l~~~~~~~~~d~~~aeDivQd~f~~~~~~~~~~~~~--~~~~~wl~~i~~n~~~d~~R   75 (75)
T d1h3la_           4 ERSARFERDALEFLDQMYSAALRMTRNPADAEDLVQETYAKAYASFHQFREG--TNLKAWLYRILTNTFINSYR   75 (75)
T ss_dssp             HHHHHHHHHHHHTHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHGGGCCSS--SCHHHHHHHHHHHHHHHTCC
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhhhhcCCC--CCHHHHHHHHHHHHHHHHhC
Confidence            4567899999999999999999999999999999999999999999999864  37999999999999998754

>d1xsva_ a.4.13.3 (A:) Hypothetical protein SAV1236 {Staphylococcus aureus, strain Mu50 / ATCC 700699 [TaxId: 1280]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Sigma3 and sigma4 domains of RNA polymerase sigma factors
family: YlxM/p13-like
domain: Hypothetical protein SAV1236
species: Staphylococcus aureus, strain Mu50 / ATCC 700699 [TaxId: 1280]

Probab=98.97  E-value=1.2e-09  Score=86.20  Aligned_cols=54  Identities=17%  Similarity=0.164  Sum_probs=49.3

Q ss_pred             cCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHHhhchh
Q 046578          317 TLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQTNILNNL  374 (379)
Q Consensus       317 ~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~~l~~~~L  374 (379)
                      -||++||.||.++|+    +++|+.|||+.||||+++|+++++||+++||+......+
T Consensus        18 LLpe~QR~vl~L~~~----e~ls~~EIA~~lgiS~~aV~~~l~Ra~~~L~~ye~kL~l   71 (106)
T d1xsva_          18 LLTNKQRNYLELFYL----EDYSLSEIADTFNVSRQAVYDNIRRTGDLVEDYEKKLEL   71 (106)
T ss_dssp             GSCHHHHHHHHHHHT----SCCCHHHHHHHTTCCHHHHHHHHHHHHHHHHHHHHHHCH
T ss_pred             hCCHHHHHHHHHHHH----hCCcHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHHCh
Confidence            499999999999995    779999999999999999999999999999997665554

>d1s7oa_ a.4.13.3 (A:) Hypothetical protein SPy1201 {Streptococcus pyogenes [TaxId: 1314]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Sigma3 and sigma4 domains of RNA polymerase sigma factors
family: YlxM/p13-like
domain: Hypothetical protein SPy1201
species: Streptococcus pyogenes [TaxId: 1314]

Probab=98.95  E-value=1.2e-09  Score=86.42  Aligned_cols=54  Identities=15%  Similarity=0.210  Sum_probs=49.2

Q ss_pred             cCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHHhhchh
Q 046578          317 TLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQTNILNNL  374 (379)
Q Consensus       317 ~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~~l~~~~L  374 (379)
                      -|||+||.||.++|+    +++|++|||+.||||+++|+++++||+++||+...+.++
T Consensus        16 lLp~~qR~v~~L~y~----~~ls~~EIA~~lgiS~~aV~~~l~RA~~~L~~~e~kL~l   69 (106)
T d1s7oa_          16 LLTDKQMNYIELYYA----DDYSLAEIADEFGVSRQAVYDNIKRTEKILETYEMKLHM   69 (106)
T ss_dssp             GSCHHHHHHHHHHHH----TCCCHHHHHHHHTCCHHHHHHHHHHHHHHHHHHHHHHCH
T ss_pred             hCCHHHHHHHHHHHH----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHHCh
Confidence            499999999999996    779999999999999999999999999999997655444

>d1ku2a1 a.4.13.1 (A:273-332) Sigma factor SigA {Thermus aquaticus [TaxId: 271]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Sigma3 and sigma4 domains of RNA polymerase sigma factors
family: Sigma3 domain
domain: Sigma factor SigA
species: Thermus aquaticus [TaxId: 271]

Probab=98.81  E-value=4.8e-09  Score=74.16  Aligned_cols=58  Identities=29%  Similarity=0.466  Sum_probs=53.9

Q ss_pred             ccCCcchHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCC--HHHHHHHHHhcCCcccc
Q 046578          217 IRLPGSMAGMVAKIAEANNVLSRRLRRMPTDSEIAEMLNIH--VSTVRLAIERTRHPISL  274 (379)
Q Consensus       217 irip~~~~~~~~ki~~a~~~l~~~lgr~pt~~eia~~Lgis--~~~~~~~l~~~~~~iSL  274 (379)
                      +|+|.|+.+.++++.++.+++.+++||+||.+|||+.+|++  ++++..++.....++||
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            68999999999999999999999999999999999999755  78999999988888876

>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=98.73  E-value=6.9e-09  Score=72.66  Aligned_cols=53  Identities=38%  Similarity=0.438  Sum_probs=50.4

Q ss_pred             CcccCCcchHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHh
Q 046578          215 RTIRLPGSMAGMVAKIAEANNVLSRRLRRMPTDSEIAEMLNIHVSTVRLAIER  267 (379)
Q Consensus       215 r~irip~~~~~~~~ki~~a~~~l~~~lgr~pt~~eia~~Lgis~~~~~~~l~~  267 (379)
                      +++++|+++.+..+++.++.+.+.+++||+||.+|||+.||++.+++..++..
T Consensus         2 g~IrvPr~~~e~~~ki~~~~~~l~q~lgRePT~~EiA~~l~~~~e~V~~~l~a   54 (57)
T d1l0oc_           2 GTVKVSRSLKEMGNKIRKAKDELSKTRGRAPTVTEIADHLGISPEDVVLAQEA   54 (57)
T ss_dssp             CCCTTHHHHHHHHHHHHHHHHHHHHHHTSCCBHHHHHHHHTSCHHHHHHHHHH
T ss_pred             CCEeCcHHHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHHCcCHHHHHHHHHH
Confidence            47899999999999999999999999999999999999999999999988865

>d1yioa1 a.4.6.2 (A:131-200) Response regulatory protein StyR, C-terminal domain {Pseudomonas fluorescens [TaxId: 294]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: C-terminal effector domain of the bipartite response regulators
family: GerE-like (LuxR/UhpA family of transcriptional regulators)
domain: Response regulatory protein StyR, C-terminal domain
species: Pseudomonas fluorescens [TaxId: 294]

Probab=98.58  E-value=7.6e-08  Score=70.10  Aligned_cols=55  Identities=24%  Similarity=0.399  Sum_probs=49.4

Q ss_pred             HHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHh
Q 046578          308 KQELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQ  367 (379)
Q Consensus       308 ~~~L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~  367 (379)
                      .+.+...++.|+|+|++|+.+..     +|+|.+|||+.||+|..||+..+.++++||.-
T Consensus         3 ~~~~~~~~~~LT~rE~~vl~~l~-----~G~s~~eIA~~l~iS~~TV~~~~~~i~~Klgv   57 (70)
T d1yioa1           3 QDQLEQLFSSLTGREQQVLQLTI-----RGLMNKQIAGELGIAEVTVKVHRHNIMQKLNV   57 (70)
T ss_dssp             HHHHHHHHHTSCHHHHHHHHHHT-----TTCCHHHHHHHHTCCHHHHHHHHHHHHHHTTC
T ss_pred             HHHHHHHHccCCHHHHHHHHHHH-----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHcCC
Confidence            45677888899999999999875     77999999999999999999999999999853

>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=98.43  E-value=2.1e-08  Score=74.55  Aligned_cols=70  Identities=24%  Similarity=0.349  Sum_probs=56.9

Q ss_pred             cchHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHh--cCCccccCCccccCCCCcccccCC
Q 046578          221 GSMAGMVAKIAEANNVLSRRLRRMPTDSEIAEMLNIHVSTVRLAIER--TRHPISLDGAVTDRGCMTMQDIIP  291 (379)
Q Consensus       221 ~~~~~~~~ki~~a~~~l~~~lgr~pt~~eia~~Lgis~~~~~~~l~~--~~~~iSLd~~~~~~~~~~l~d~i~  291 (379)
                      +.++...+++.++...|.+++||+|+.+|||+.||++.+++..++..  ....+|||.++.+++. .+.+.++
T Consensus         3 Rs~r~~~~ki~~a~~~L~~~lGR~Pt~~EiA~~lg~s~~e~~~~l~~~~~~~~~SLD~~~~d~~~-~~~e~lp   74 (77)
T d1rp3a1           3 RQVREKERRIKEVVEKLKEKLGREPTDEEVAKELGISTEELFKTLDKINFSYILSLEEVFRDFAR-DYSELIP   74 (77)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHSSCCCHHHHHHHHTSCHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHTTTGG
T ss_pred             hHHHHHHHHHHHHHHHHHHHHCcCCCHHHHHHHHCcCHHHHHHHHHHHhcCCceecccCccCCCC-chhccCC
Confidence            45667889999999999999999999999999999999999998865  4477899987654432 3444444

>d1a04a1 a.4.6.2 (A:150-216) Nitrate/nitrite response regulator (NarL) {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: C-terminal effector domain of the bipartite response regulators
family: GerE-like (LuxR/UhpA family of transcriptional regulators)
domain: Nitrate/nitrite response regulator (NarL)
species: Escherichia coli [TaxId: 562]

Probab=98.40  E-value=2.8e-07  Score=66.35  Aligned_cols=48  Identities=27%  Similarity=0.365  Sum_probs=44.3

Q ss_pred             HhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHh
Q 046578          315 LQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQ  367 (379)
Q Consensus       315 L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~  367 (379)
                      +..|+|+|++|+.+..     +|+|.+|||+.||+|..||++.+.++++||.-
T Consensus         4 l~~LT~rE~~vl~ll~-----~G~s~~eIA~~l~iS~~TV~~~~~~i~~Klgv   51 (67)
T d1a04a1           4 VNQLTPRERDILKLIA-----QGLPNKMIARRLDITESTVKVHVKHMLKKMKL   51 (67)
T ss_dssp             GGGSCHHHHHHHHHHH-----TTCCHHHHHHHHTCCHHHHHHHHHHHHHHHTC
T ss_pred             cccCCHHHHHHHHHHH-----hCCCHHHHHHHHCCCHHHHHHHHHHHHHHhCC
Confidence            5689999999999876     78999999999999999999999999999864

>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=98.24  E-value=1.1e-06  Score=62.72  Aligned_cols=47  Identities=19%  Similarity=0.186  Sum_probs=43.1

Q ss_pred             cCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhH
Q 046578          317 TLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQT  368 (379)
Q Consensus       317 ~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~~  368 (379)
                      .|+++|++|+.+.-     +|+|.+|||+.||+|..||+..+.++++||.-.
T Consensus         4 ~Lt~rE~~vl~l~~-----~G~s~~eIA~~l~iS~~TV~~~~~~i~~Klgv~   50 (65)
T d1l3la1           4 WLDPKEATYLRWIA-----VGKTMEEIADVEGVKYNSVRVKLREAMKRFDVR   50 (65)
T ss_dssp             CCCHHHHHHHHHHT-----TTCCHHHHHHHHTCCHHHHHHHHHHHHHHHTCS
T ss_pred             ccCHHHHHHHHHHH-----hcCCHHHHHHHHCCCHHHHHHHHHHHHHHcCCC
Confidence            69999999999875     789999999999999999999999999998643

>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=98.20  E-value=1.4e-06  Score=62.49  Aligned_cols=47  Identities=28%  Similarity=0.352  Sum_probs=42.7

Q ss_pred             cCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhH
Q 046578          317 TLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQT  368 (379)
Q Consensus       317 ~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~~  368 (379)
                      .|+++|++|+.+..     +|+|.+|||+.||+|..||+..+.++.+||--.
T Consensus         4 ~LT~rE~~vl~l~~-----~G~s~~eIA~~L~is~~TV~~~~~~i~~Kl~v~   50 (67)
T d1fsea_           4 LLTKREREVFELLV-----QDKTTKEIASELFISEKTVRNHISNAMQKLGVK   50 (67)
T ss_dssp             CCCHHHHHHHHHHT-----TTCCHHHHHHHHTSCHHHHHHHHHHHHHHHTCS
T ss_pred             CCCHHHHHHHHHHH-----ccCCHHHHHHHHCCCHHHHHHHHHHHHHHcCCC
Confidence            49999999999865     789999999999999999999999999998543

>d1p4wa_ a.4.6.2 (A:) Transcriptional regulator RcsB {Erwinia amylovora [TaxId: 552]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: C-terminal effector domain of the bipartite response regulators
family: GerE-like (LuxR/UhpA family of transcriptional regulators)
domain: Transcriptional regulator RcsB
species: Erwinia amylovora [TaxId: 552]

Probab=97.95  E-value=6.5e-06  Score=62.09  Aligned_cols=46  Identities=30%  Similarity=0.355  Sum_probs=42.8

Q ss_pred             cCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHh
Q 046578          317 TLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQ  367 (379)
Q Consensus       317 ~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~  367 (379)
                      .|+++|++|+.+..     .|++.+|||+.|++|..||+..+.++++||.-
T Consensus        22 ~LT~rE~~vl~ll~-----~G~s~~eIA~~l~iS~~TV~~~~~~i~~Kl~~   67 (87)
T d1p4wa_          22 RLSPKESEVLRLFA-----EGFLVTEIAKKLNRSIKTISSQKKSAMMKLGV   67 (87)
T ss_dssp             SCCHHHHHHHHHHH-----HTCCHHHHHHHHTSCHHHHHHHHHHHHHHHTC
T ss_pred             CCCHHHHHHHHHHH-----cCCCHHHHHHHhCCCHHHHHHHHHHHHHHcCC
Confidence            59999999999886     77999999999999999999999999999853

>d1ijwc_ a.4.1.2 (C:) HIN recombinase (DNA-binding domain) {Synthetic}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Recombinase DNA-binding domain
domain: HIN recombinase (DNA-binding domain)
species: Synthetic

Probab=96.33  E-value=0.0021  Score=41.99  Aligned_cols=38  Identities=3%  Similarity=0.145  Sum_probs=31.2

Q ss_pred             cCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHH
Q 046578          317 TLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIR  358 (379)
Q Consensus       317 ~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~  358 (379)
                      .|++.|.+-+.-.+    ..|.|..+||+.||||+.|+++.+
T Consensus         5 ~lt~~q~~~a~~l~----~~G~s~~~iA~~~gVSr~TiYry~   42 (47)
T d1ijwc_           5 AINKHEQEQISRLL----EKGHPRQQLAIIFGIGVSTLYRYF   42 (47)
T ss_dssp             SSCHHHHHHHHHHH----HTTCCHHHHHHHHTCCHHHHHHHS
T ss_pred             cCCHHHHHHHHHHH----HCCCCHHHHHHHHCcCHHHHHhhC
Confidence            57888777777665    267999999999999999998864

>d1gdta1 a.4.1.2 (A:141-183) gamma,delta resolvase (C-terminal domain) {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Recombinase DNA-binding domain
domain: gamma,delta resolvase (C-terminal domain)
species: Escherichia coli [TaxId: 562]

Probab=95.49  E-value=0.007  Score=38.37  Aligned_cols=32  Identities=9%  Similarity=0.287  Sum_probs=27.2

Q ss_pred             HHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 046578          324 DILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGI  360 (379)
Q Consensus       324 ~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~r  360 (379)
                      +|..|+-     +|++-.+||++|||++.+|++++..
T Consensus        10 ~V~~L~~-----~G~gat~IAk~lgI~R~SVYR~L~~   41 (43)
T d1gdta1          10 AVLNMWQ-----QGLGASHISKTMNIARSTVYKVINE   41 (43)
T ss_dssp             HHHHHHH-----TTCCHHHHHHHHTCCHHHHHHHHHS
T ss_pred             HHHHHHH-----cCCCHHHHHHHHCCCHHHHHHHHhh
Confidence            4666764     8899999999999999999988754

>d1jhfa1 a.4.5.2 (A:2-72) LexA repressor, N-terminal DNA-binding domain {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: LexA repressor, N-terminal DNA-binding domain
domain: LexA repressor, N-terminal DNA-binding domain
species: Escherichia coli [TaxId: 562]

Probab=95.45  E-value=0.0098  Score=42.18  Aligned_cols=44  Identities=18%  Similarity=0.215  Sum_probs=34.1

Q ss_pred             cCCHHHHHHHHHH--hhcCCCCCCCHHHHHHHhCC-CHHHHHHHHHH
Q 046578          317 TLSEREADILRLH--FGLDGQTPVSCKEIGRLLSL-SRERIRQIRGI  360 (379)
Q Consensus       317 ~L~~rer~Vl~l~--ygL~g~e~~S~~EIAe~Lgi-S~~~Vr~~~~r  360 (379)
                      .|+++|++|+...  |....+-.-|++|||+.+|+ |.++|++.+..
T Consensus         2 ~LT~rQ~~vL~~I~~~~~~~G~~Ps~rei~~~~g~~S~stv~~~l~~   48 (71)
T d1jhfa1           2 ALTARQQEVFDLIRDHISQTGMPPTRAEIAQRLGFRSPNAAEEHLKA   48 (71)
T ss_dssp             CCCHHHHHHHHHHHHHHHHHSSCCCHHHHHHHTTCSSHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCCHHHHHHHHHH
Confidence            5999999999863  32222266899999999999 79999887543

>d2cg4a1 a.4.5.32 (A:4-66) Regulatory protein AsnC {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Lrp/AsnC-like transcriptional regulator N-terminal domain
domain: Regulatory protein AsnC
species: Escherichia coli [TaxId: 562]

Probab=94.99  E-value=0.035  Score=38.09  Aligned_cols=40  Identities=18%  Similarity=0.272  Sum_probs=33.0

Q ss_pred             CCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 046578          318 LSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGI  360 (379)
Q Consensus       318 L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~r  360 (379)
                      |++.+++||...-. +  ..+|+.|||+.+|+|.++|++++.+
T Consensus         3 lD~~D~~IL~~L~~-~--~r~s~~eiA~~l~ls~~~v~~Ri~r   42 (63)
T d2cg4a1           3 IDNLDRGILEALMG-N--ARTAYAELAKQFGVSPETIHVRVEK   42 (63)
T ss_dssp             CCHHHHHHHHHHHH-C--TTSCHHHHHHHHTSCHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHH-c--CCCCHHHHHHHHCcCHHHHHHHHHH
Confidence            67888999887652 2  5699999999999999999887655

>d2cfxa1 a.4.5.32 (A:1-63) Transcriptional regulator LrpC {Bacillus subtilis [TaxId: 1423]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Lrp/AsnC-like transcriptional regulator N-terminal domain
domain: Transcriptional regulator LrpC
species: Bacillus subtilis [TaxId: 1423]

Probab=94.79  E-value=0.041  Score=37.77  Aligned_cols=41  Identities=22%  Similarity=0.304  Sum_probs=33.4

Q ss_pred             cCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 046578          317 TLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGI  360 (379)
Q Consensus       317 ~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~r  360 (379)
                      +|++.++.|+...-. +  ...|+.|||+.+|+|+++|.+++.+
T Consensus         2 klD~~D~~IL~~L~~-n--~r~s~~~iA~~lgis~~tv~~Ri~~   42 (63)
T d2cfxa1           2 KLDQIDLNIIEELKK-D--SRLSMRELGRKIKLSPPSVTERVRQ   42 (63)
T ss_dssp             CCCHHHHHHHHHHHH-C--SCCCHHHHHHHHTCCHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHH-c--CCCCHHHHHHHHCcCHHHHHHHHHH
Confidence            478888999886542 2  5689999999999999999887554

>d1i1ga1 a.4.5.32 (A:2-61) LprA {Archaeon Pyrococcus furiosus [TaxId: 2261]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Lrp/AsnC-like transcriptional regulator N-terminal domain
domain: LprA
species: Archaeon Pyrococcus furiosus [TaxId: 2261]

Probab=94.64  E-value=0.037  Score=37.60  Aligned_cols=40  Identities=25%  Similarity=0.329  Sum_probs=31.3

Q ss_pred             CCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 046578          318 LSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGI  360 (379)
Q Consensus       318 L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~r  360 (379)
                      |++.+++|+.+.-- +  ...|+.|||+.+|+|+++|.+++.+
T Consensus         1 lD~~D~kIl~~L~~-n--~r~s~~~lA~~~gls~~~v~~Ri~~   40 (60)
T d1i1ga1           1 IDERDKIILEILEK-D--ARTPFTEIAKKLGISETAVRKRVKA   40 (60)
T ss_dssp             CCSHHHHHHHHHHH-C--TTCCHHHHHHHHTSCHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHH-c--CCCCHHHHHHHHCcCHHHHHHHHHH
Confidence            45677888876542 2  5689999999999999999877554

>d2cyya1 a.4.5.32 (A:5-64) Putative transcriptional regulator PH1519 {Archaeon Pyrococcus horikoshii [TaxId: 53953]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Lrp/AsnC-like transcriptional regulator N-terminal domain
domain: Putative transcriptional regulator PH1519
species: Archaeon Pyrococcus horikoshii [TaxId: 53953]

Probab=94.37  E-value=0.063  Score=36.30  Aligned_cols=40  Identities=18%  Similarity=0.286  Sum_probs=31.0

Q ss_pred             CCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 046578          318 LSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGI  360 (379)
Q Consensus       318 L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~r  360 (379)
                      |++.++.||...--   ....|+.|||+.+|+|+++|..++.+
T Consensus         1 lD~~D~~Il~~L~~---n~r~s~~eiA~~l~ls~~~v~~Ri~~   40 (60)
T d2cyya1           1 LDEIDKKIIKILQN---DGKAPLREISKITGLAESTIHERIRK   40 (60)
T ss_dssp             CCHHHHHHHHHHHH---CTTCCHHHHHHHHCSCHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHH---cCCCCHHHHHHHHCcCHHHHHHHHHH
Confidence            45667788876532   25689999999999999999877554

>d1hlva1 a.4.1.7 (A:1-66) DNA-binding domain of centromere binding protein B (CENP-B) {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Centromere-binding
domain: DNA-binding domain of centromere binding protein B (CENP-B)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=94.26  E-value=0.033  Score=38.72  Aligned_cols=50  Identities=14%  Similarity=0.155  Sum_probs=34.9

Q ss_pred             cCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHH
Q 046578          317 TLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQTN  369 (379)
Q Consensus       317 ~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~~l  369 (379)
                      .|+..++.=+..+| -.| +.++..|||..|||+++||+.++.+- .++....
T Consensus         7 ~LT~~eK~~ii~~~-e~g-~k~sq~eIA~~fGv~~STvs~IlKnK-~kil~~~   56 (66)
T d1hlva1           7 QLTFREKSRIIQEV-EEN-PDLRKGEIARRFNIPPSTLSTILKNK-RAILASE   56 (66)
T ss_dssp             CCCHHHHHHHHHHH-HHC-TTSCHHHHHHHHTCCHHHHHHHHHTH-HHHHHHH
T ss_pred             cCCHHHHHHHHHHH-HcC-CcchHHHHHHHhCCChhHHHHHHHHH-HHHHHHH
Confidence            46666665555454 122 55789999999999999999998873 4444433

>d1k78a1 a.4.1.5 (A:19-81) Pax-5 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Paired domain
domain: Pax-5
species: Human (Homo sapiens) [TaxId: 9606]

Probab=93.54  E-value=0.057  Score=37.10  Aligned_cols=33  Identities=27%  Similarity=0.289  Sum_probs=27.3

Q ss_pred             HHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 046578          324 DILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIA  361 (379)
Q Consensus       324 ~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rA  361 (379)
                      .|+.+..     +++|..+||+.|+||.++|.+++.+=
T Consensus        22 Riv~~~~-----~G~s~r~aA~rf~VS~s~v~k~l~r~   54 (63)
T d1k78a1          22 RIVELAH-----QGVRPCDISRQLRVSHGCVSKILGRY   54 (63)
T ss_dssp             HHHHHHH-----TTCCHHHHHHHHTCCHHHHHHHHHHH
T ss_pred             HHHHHHH-----cCCCHHHHHHHhCCCHHHHHHHHHHH
Confidence            3556544     77999999999999999999987764

>d1ku9a_ a.4.5.36 (A:) DNA-binding protein Mj223 {Archaeon Methanococcus jannaschii [TaxId: 2190]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: DNA-binding protein Mj223
domain: DNA-binding protein Mj223
species: Archaeon Methanococcus jannaschii [TaxId: 2190]

Probab=93.01  E-value=0.13  Score=40.74  Aligned_cols=50  Identities=16%  Similarity=0.281  Sum_probs=39.4

Q ss_pred             HHHHHHHh--cCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 046578          309 QELKELLQ--TLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGI  360 (379)
Q Consensus       309 ~~L~~~L~--~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~r  360 (379)
                      +.+...+.  .|++.+-.|+.+.+ +.| +++|..|||+.+|+|+++|++.+.+
T Consensus        13 ~~~~~~~~~~Gl~~~~~~i~~~L~-~~~-~plt~~ela~~l~vsk~~vs~~l~~   64 (151)
T d1ku9a_          13 ELFSELAKIHGLNKSVGAVYAILY-LSD-KPLTISDIMEELKISKGNVSMSLKK   64 (151)
T ss_dssp             HHHHHHHHHTTCCHHHHHHHHHHH-HCS-SCEEHHHHHHHHTCCHHHHHHHHHH
T ss_pred             HHHHHHHHHcCCCHHHHHHHHHHH-hCC-CCcCHHHHHHHhCCCcchHHHHHHH
Confidence            34444444  57999999998887 454 5699999999999999999877655

>d2jn6a1 a.4.1.19 (A:1-89) Uncharacterized protein Cgl2762 {Corynebacterium glutamicum [TaxId: 1718]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Cgl2762-like
domain: Uncharacterized protein Cgl2762
species: Corynebacterium glutamicum [TaxId: 1718]

Probab=92.61  E-value=0.074  Score=38.89  Aligned_cols=36  Identities=17%  Similarity=0.112  Sum_probs=28.4

Q ss_pred             HHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 046578          323 ADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIA  361 (379)
Q Consensus       323 r~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rA  361 (379)
                      ++++.++.  . .+|.|..+||+.|||+.++|++++.+.
T Consensus        12 ~~aV~l~~--~-~~g~s~~~vA~~lGIs~~tl~~W~k~~   47 (89)
T d2jn6a1          12 RDAVALYE--N-SDGASLQQIANDLGINRVTLKNWIIKY   47 (89)
T ss_dssp             HHHHHHHT--T-GGGSCHHHHHHHHTSCHHHHHHHHHHH
T ss_pred             HHHHHHHH--H-cCCCcHHHHHHHHCCCHHHHHHHHHHH
Confidence            35566654  1 146999999999999999999998765

>d1pdnc_ a.4.1.5 (C:) Paired protein (prd) {Fruit fly (Drosophila melanogaster) [TaxId: 7227]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Paired domain
domain: Paired protein (prd)
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

Probab=92.26  E-value=0.095  Score=40.86  Aligned_cols=40  Identities=15%  Similarity=-0.008  Sum_probs=29.5

Q ss_pred             CCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 046578          318 LSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIA  361 (379)
Q Consensus       318 L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rA  361 (379)
                      |+...|.-|.-.+    .+|++..+||+.||||.++|++++.+=
T Consensus        17 Ls~dlR~rIv~~~----~~G~s~r~iA~~~~VS~~tV~k~l~r~   56 (123)
T d1pdnc_          17 LPNNIRLKIVEMA----ADGIRPCVISRQLRVSHGCVSKILNRY   56 (123)
T ss_dssp             CCHHHHHHHHHHH----HTTCCHHHHHHHHTCCHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHH----HhcCCHHHHHHHHCcCHHHHHHHHHHH
Confidence            5544444343334    267999999999999999999987763

>d1nr3a_ d.236.1.1 (A:) DNA-binding protein Tfx {Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262]}

class: Alpha and beta proteins (a+b)
fold: DNA-binding protein Tfx
superfamily: DNA-binding protein Tfx
family: DNA-binding protein Tfx
domain: DNA-binding protein Tfx
species: Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262]

Probab=92.18  E-value=0.0014  Score=51.46  Aligned_cols=34  Identities=24%  Similarity=0.344  Sum_probs=31.7

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHH
Q 046578          336 TPVSCKEIGRLLSLSRERIRQIRGIALTKLQQTN  369 (379)
Q Consensus       336 e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~~l  369 (379)
                      .|+|++|||+.||.|+.+|+.+.++|++.++++-
T Consensus         4 kGltQ~eIA~~LgTSraNIs~IEk~A~eNIekAr   37 (122)
T d1nr3a_           4 RGWSQKKIARELKTTRQNVSAIERKAMENIEKSR   37 (122)
T ss_dssp             CSCSSCSTHHHHHHCCSSSCCHHHHHHTTCSSSS
T ss_pred             ccCCHHHHHHHHCccHHHHHHHHHHHHHHHHHHH
Confidence            6799999999999999999999999999988763

>d1biaa1 a.4.5.1 (A:1-63) Biotin repressor, N-terminal domain {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Biotin repressor-like
domain: Biotin repressor, N-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=91.91  E-value=0.17  Score=34.41  Aligned_cols=39  Identities=18%  Similarity=0.195  Sum_probs=28.8

Q ss_pred             CHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 046578          319 SEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGI  360 (379)
Q Consensus       319 ~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~r  360 (379)
                      +....+|+.+-   ......|.+|+|+.||||+.||++.+..
T Consensus         4 ~~~~~~iL~~L---~~~~~~s~~eLa~~l~vS~~ti~r~i~~   42 (63)
T d1biaa1           4 NTVPLKLIALL---ANGEFHSGEQLGETLGMSRAAINKHIQT   42 (63)
T ss_dssp             CHHHHHHHHHH---TTSSCBCHHHHHHHHTSCHHHHHHHHHH
T ss_pred             cHHHHHHHHHH---HHCCcCCHHHHHHHHCcCHHHHHHHHHH
Confidence            44555666543   2236689999999999999999887543

>d2ppxa1 a.35.1.3 (A:30-91) Uncharacterized protein Atu1735 {Agrobacterium tumefaciens [TaxId: 358]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: SinR domain-like
domain: Uncharacterized protein Atu1735
species: Agrobacterium tumefaciens [TaxId: 358]

Probab=91.23  E-value=0.067  Score=36.43  Aligned_cols=24  Identities=8%  Similarity=0.116  Sum_probs=22.1

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHH
Q 046578          336 TPVSCKEIGRLLSLSRERIRQIRG  359 (379)
Q Consensus       336 e~~S~~EIAe~LgiS~~~Vr~~~~  359 (379)
                      .|+|++|+|+.+|||+++|+++.+
T Consensus        11 ~gltQ~elA~~lGvs~~tvs~~E~   34 (62)
T d2ppxa1          11 LKLTQEEFSARYHIPLGTLRDWEQ   34 (62)
T ss_dssp             TTCCHHHHHHHHTCCHHHHHHHHT
T ss_pred             cCCCHHHHHHHhCCCHHHHHHHHC
Confidence            349999999999999999999886

>d2o3fa1 a.4.1.20 (A:1-83) Putative transcriptional regulator YbbH {Bacillus subtilis [TaxId: 1423]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: RpiR-like
domain: Putative transcriptional regulator YbbH
species: Bacillus subtilis [TaxId: 1423]

Probab=90.98  E-value=0.19  Score=36.29  Aligned_cols=52  Identities=12%  Similarity=0.128  Sum_probs=40.1

Q ss_pred             HHHHHHHhcCCHHHHHHHHHHhh-cCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 046578          309 QELKELLQTLSEREADILRLHFG-LDGQTPVSCKEIGRLLSLSRERIRQIRGI  360 (379)
Q Consensus       309 ~~L~~~L~~L~~rer~Vl~l~yg-L~g~e~~S~~EIAe~LgiS~~~Vr~~~~r  360 (379)
                      ..|......|++.|+.|.....- .+....+|.+|||+..|+|.+||.+..++
T Consensus         7 ~~i~~~~~~Ls~~e~~ia~yil~~~~~~~~~si~~lA~~~~vS~sTi~Rf~kk   59 (83)
T d2o3fa1           7 AIIQSMKHKLPPSERKLADYILAHPHKAIESTVNEISALANSSDAAVIRLCKS   59 (83)
T ss_dssp             HHHHHHGGGSCHHHHHHHHHHHHCHHHHHTCCHHHHHHHTTCCHHHHHHHHHH
T ss_pred             HHHHHHHhhCCHHHHHHHHHHHcCHHHHHHccHHHHHHHHCCCHHHHHHHHHH
Confidence            45778889999999998864320 00124699999999999999999887665

>d1dpua_ a.4.5.16 (A:) C-terminal domain of RPA32 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: C-terminal domain of RPA32
domain: C-terminal domain of RPA32
species: Human (Homo sapiens) [TaxId: 9606]

Probab=90.86  E-value=0.18  Score=35.12  Aligned_cols=43  Identities=16%  Similarity=0.204  Sum_probs=36.6

Q ss_pred             hcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHh-CCCHHHHHHHH
Q 046578          316 QTLSEREADILRLHFGLDGQTPVSCKEIGRLL-SLSRERIRQIR  358 (379)
Q Consensus       316 ~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~L-giS~~~Vr~~~  358 (379)
                      +.|+|.++.|+.+.-.-.+.+|++..||+.+| |++...|++.+
T Consensus         2 nGLs~~q~~V~~~i~s~~~~eGi~~~el~~~l~~~~~~~i~~ai   45 (69)
T d1dpua_           2 NGLTVAQNQVLNLIKACPRPEGLNFQDLKNQLKHMSVSSIKQAV   45 (69)
T ss_dssp             CCSCHHHHHHHHHHHHCCCTTTEEHHHHHHHSTTSCHHHHHHHH
T ss_pred             CCCCHHHHHHHHHHHhCCCccCcCHHHHHHHccCCCHHHHHHHH
Confidence            35899999999987666677899999999999 89999887654

>d3broa1 a.4.5.28 (A:3-137) Transcriptional regulator OEOE1854 {Oenococcus oeni [TaxId: 1247]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MarR-like transcriptional regulators
domain: Transcriptional regulator OEOE1854
species: Oenococcus oeni [TaxId: 1247]

Probab=90.73  E-value=0.51  Score=36.35  Aligned_cols=50  Identities=8%  Similarity=0.079  Sum_probs=37.5

Q ss_pred             HHHHHHh--cCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 046578          310 ELKELLQ--TLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGI  360 (379)
Q Consensus       310 ~L~~~L~--~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~r  360 (379)
                      .+...+.  .|++.|..||...+.-. ..+.|..|||+.++++.++|++.+.+
T Consensus        17 ~~~~~l~~~glt~~q~~vL~~l~~~~-~~~it~~ela~~~~~~~~~vs~~l~~   68 (135)
T d3broa1          17 RFDIFAKKYDLTGTQMTIIDYLSRNK-NKEVLQRDLESEFSIKSSTATVLLQR   68 (135)
T ss_dssp             HHHHHHHTTTCCHHHHHHHHHHHHTT-TSCCBHHHHHHHHTCCHHHHHHHHHH
T ss_pred             HHHHHHHHcCCCHHHHHHHHHHHHcC-CCCCCHHHHHHHHCcCHhHHHHHHHH
Confidence            3444444  58999999998766322 25699999999999999999765444

>d1sfxa_ a.4.5.50 (A:) Hypothetical protein AF2008 {Archaeoglobus fulgidus [TaxId: 2234]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: TrmB-like
domain: Hypothetical protein AF2008
species: Archaeoglobus fulgidus [TaxId: 2234]

Probab=90.41  E-value=0.38  Score=36.14  Aligned_cols=41  Identities=22%  Similarity=0.296  Sum_probs=33.4

Q ss_pred             cCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 046578          317 TLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGI  360 (379)
Q Consensus       317 ~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~r  360 (379)
                      .|++.|..|+..-+-   ..+.|..|||+.+|+++++|+..+.+
T Consensus        17 Glt~~e~~v~~~L~~---~g~~t~~eia~~~~i~~~~v~~~l~~   57 (109)
T d1sfxa_          17 SFKPSDVRIYSLLLE---RGGMRVSEIARELDLSARFVRDRLKV   57 (109)
T ss_dssp             CCCHHHHHHHHHHHH---HCCBCHHHHHHHHTCCHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHh---cCCCCHHHHHHHhCCCcchHHHHHHH
Confidence            688999999876553   24699999999999999999876554

>d1r1ta_ a.4.5.5 (A:) SmtB repressor {Cyanobacteria (Synechococcus), pcc7942 [TaxId: 1129]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: ArsR-like transcriptional regulators
domain: SmtB repressor
species: Cyanobacteria (Synechococcus), pcc7942 [TaxId: 1129]

Probab=90.40  E-value=0.34  Score=35.89  Aligned_cols=46  Identities=13%  Similarity=0.258  Sum_probs=31.8

Q ss_pred             HHHHHhcCCHH-HHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 046578          311 LKELLQTLSER-EADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGI  360 (379)
Q Consensus       311 L~~~L~~L~~r-er~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~r  360 (379)
                      +.+++..|... -..|+.+-.  +  .+++..|||+.+|+|+++|++++..
T Consensus        13 la~~~kaL~~p~Rl~Il~~L~--~--~~~~v~ela~~l~is~stvS~HL~~   59 (98)
T d1r1ta_          13 LAEFFAVLADPNRLRLLSLLA--R--SELCVGDLAQAIGVSESAVSHQLRS   59 (98)
T ss_dssp             HHHHHHHHCCHHHHHHHHHHT--T--CCBCHHHHHHHHTCCHHHHHHHHHH
T ss_pred             HHHHHHHhCCHHHHHHHHHHH--c--CCcCHHHHHHHHCcCHHHHHHHHHH
Confidence            44555556544 444544332  2  5699999999999999999988543

>d2d1ha1 a.4.5.50 (A:1-109) Hypothetical transcriptional regulator ST1889 {Sulfolobus tokodaii [TaxId: 111955]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: TrmB-like
domain: Hypothetical transcriptional regulator ST1889
species: Sulfolobus tokodaii [TaxId: 111955]

Probab=90.33  E-value=0.19  Score=37.75  Aligned_cols=43  Identities=12%  Similarity=0.352  Sum_probs=34.5

Q ss_pred             cCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 046578          317 TLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIA  361 (379)
Q Consensus       317 ~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rA  361 (379)
                      .|++.+..||...+.-+  .++|..|||+.+|+++++|++.+.+-
T Consensus        18 gLs~~~~~iL~~L~~~~--~~~t~~eLa~~~~i~~~tvs~~l~~L   60 (109)
T d2d1ha1          18 KITDTDVAVLLKMVEIE--KPITSEELADIFKLSKTTVENSLKKL   60 (109)
T ss_dssp             TCCHHHHHHHHHHHHHC--SCEEHHHHHHHHTCCHHHHHHHHHHH
T ss_pred             CcCHHHHHHHHHHHHcC--CCCCHHHHHHHHCccHhHHHHHHHHH
Confidence            69999999997554212  45899999999999999998876653

>d1stza1 a.4.5.51 (A:14-100) Heat-inducible transcription repressor HrcA, N-terminal domain {Thermotoga maritima [TaxId: 2336]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Heat-inducible transcription repressor HrcA, N-terminal domain
domain: Heat-inducible transcription repressor HrcA, N-terminal domain
species: Thermotoga maritima [TaxId: 2336]

Probab=89.51  E-value=0.21  Score=36.37  Aligned_cols=44  Identities=20%  Similarity=0.264  Sum_probs=33.5

Q ss_pred             cCCHHHHHHHHHH--hhcCCCCCCCHHHHHHHhC--CCHHHHHHHHHH
Q 046578          317 TLSEREADILRLH--FGLDGQTPVSCKEIGRLLS--LSRERIRQIRGI  360 (379)
Q Consensus       317 ~L~~rer~Vl~l~--ygL~g~e~~S~~EIAe~Lg--iS~~~Vr~~~~r  360 (379)
                      +|+++|++||...  .++..+.+.+.++||+.+|  +|.+||++.+..
T Consensus         1 ~Lt~Rq~~IL~~Ive~y~~~g~Pv~s~~i~~~~~l~~S~aTIRn~m~~   48 (87)
T d1stza1           1 KLNDRQRKVLYCIVREYIENKKPVSSQRVLEVSNIEFSSATIRNDMKK   48 (87)
T ss_dssp             CCCHHHHHHHHHHHHHHHHHCSCBCHHHHHHHSCCCSCHHHHHHHHHH
T ss_pred             CcCHHHHHHHHHHHHHHHHcCCccCHHHHHHHhCCCCCHHHHHHHHHH
Confidence            5899999998753  1144348899999999966  579999987643

>d1z05a1 a.4.5.63 (A:10-80) Transcriptional regulator VC2007 N-terminal domain {Vibrio cholerae [TaxId: 666]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: ROK associated domain
domain: Transcriptional regulator VC2007 N-terminal domain
species: Vibrio cholerae [TaxId: 666]

Probab=89.44  E-value=0.29  Score=33.81  Aligned_cols=37  Identities=16%  Similarity=0.238  Sum_probs=28.6

Q ss_pred             HHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHH
Q 046578          323 ADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIAL  362 (379)
Q Consensus       323 r~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl  362 (379)
                      ..|+.+.+-   ..+.|-.|||+.+|+|..||++++.+-.
T Consensus         9 ~~Il~~l~~---~g~~sr~eLa~~~glS~~Tv~~~l~~L~   45 (71)
T d1z05a1           9 GRVYKLIDQ---KGPISRIDLSKESELAPASITKITRELI   45 (71)
T ss_dssp             HHHHHHHHH---HCSBCHHHHHHHHTCCHHHHHHHHHHHH
T ss_pred             HHHHHHHHH---cCCcCHHHHHHHHCCCHHHHHHHHHHHH
Confidence            456665542   2469999999999999999998876643

>d1le8a_ a.4.1.1 (A:) Mating type protein A1 Homeodomain {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Mating type protein A1 Homeodomain
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=89.34  E-value=0.19  Score=33.05  Aligned_cols=49  Identities=10%  Similarity=0.070  Sum_probs=37.5

Q ss_pred             cCCHHHHHHHHHHhhcCCC-CCCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Q 046578          317 TLSEREADILRLHFGLDGQ-TPVSCKEIGRLLSLSRERIRQIRGIALTKL  365 (379)
Q Consensus       317 ~L~~rer~Vl~l~ygL~g~-e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kL  365 (379)
                      .|+|.+..+|.-.|-.+.. .....++||+.+|++...|+.+...-+.+.
T Consensus         3 ~~s~~q~~~Le~~F~~~~~P~~~~~~~LA~~lgl~~~qV~~WFqNrR~k~   52 (53)
T d1le8a_           3 SISPQARAFLEQVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMRS   52 (53)
T ss_dssp             CCCHHHHHHHHHHHHHCSCCCHHHHHHHHHHTTSCHHHHHHHHHHHHHTT
T ss_pred             CCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHCCCHHHHHHHHHhhhhcc
Confidence            5899999999988854421 223457799999999999999988766553

>d1r71a_ a.4.14.1 (A:) Transcriptional repressor protein KorB DNA-binding domain {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: KorB DNA-binding domain-like
family: KorB DNA-binding domain-like
domain: Transcriptional repressor protein KorB DNA-binding domain
species: Escherichia coli [TaxId: 562]

Probab=89.25  E-value=0.23  Score=37.85  Aligned_cols=41  Identities=20%  Similarity=0.061  Sum_probs=33.1

Q ss_pred             cCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 046578          317 TLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGI  360 (379)
Q Consensus       317 ~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~r  360 (379)
                      .|+|-|.-...-++ ++  .|.|.++||+.+|.|+++|++++.-
T Consensus        13 ~L~p~e~A~a~~~l-~~--~g~s~~eiA~~~G~s~~~V~~~l~L   53 (114)
T d1r71a_          13 ELTPREIADFIGRE-LA--KGKKKGDIAKEIGKSPAFITQHVTL   53 (114)
T ss_dssp             CCCHHHHHHHHHHH-HH--TTCCHHHHHHHHTCCHHHHHHHHGG
T ss_pred             CCCHHHHHHHHHHH-HH--hCCCHHHHHHHHCCcHHHHHHHHHH
Confidence            58888877666555 32  5689999999999999999998763

>d1vz0a1 a.4.14.1 (A:116-208) Putative partitioning protein ParB/Spo0J {Thermus thermophilus [TaxId: 274]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: KorB DNA-binding domain-like
family: KorB DNA-binding domain-like
domain: Putative partitioning protein ParB/Spo0J
species: Thermus thermophilus [TaxId: 274]

Probab=89.03  E-value=0.31  Score=35.89  Aligned_cols=35  Identities=9%  Similarity=0.080  Sum_probs=26.0

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHHHHHH--HHHHhHHhh
Q 046578          337 PVSCKEIGRLLSLSRERIRQIRGIAL--TKLQQTNIL  371 (379)
Q Consensus       337 ~~S~~EIAe~LgiS~~~Vr~~~~rAl--~kLR~~l~~  371 (379)
                      ++|..+||+.+|.|+++|++++.-.-  ..+++.+..
T Consensus        19 g~t~~~iA~~~Gks~~~V~~~LrLl~L~~~v~~~l~~   55 (93)
T d1vz0a1          19 GLTQEEVARRVGKARSTVANALRLLQLPPEALEALER   55 (93)
T ss_dssp             TCCHHHHHHHHTCCHHHHHHHHHGGGSCHHHHHHHHT
T ss_pred             CCCHHHHHHHHccchHHHHHHHHHHHHHHHHHHHHHc
Confidence            48999999999999999999876422  344444433

>d1r1ua_ a.4.5.5 (A:) Metal-sensing transcriptional repressor CzrA {Staphylococcus aureus [TaxId: 1280]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: ArsR-like transcriptional regulators
domain: Metal-sensing transcriptional repressor CzrA
species: Staphylococcus aureus [TaxId: 1280]

Probab=88.97  E-value=0.6  Score=34.21  Aligned_cols=47  Identities=19%  Similarity=0.295  Sum_probs=34.6

Q ss_pred             HHHHHHHhcCCHHHH-HHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 046578          309 QELKELLQTLSEREA-DILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRG  359 (379)
Q Consensus       309 ~~L~~~L~~L~~rer-~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~  359 (379)
                      +.+.+++..|...-| .|+.+..  .  .+++..||++.+|+|+++|++.++
T Consensus         6 e~~a~~fkaL~d~~Rl~Il~~L~--~--~~~~v~el~~~l~~s~~~vS~HL~   53 (94)
T d1r1ua_           6 ERVTEIFKALGDYNRIRIMELLS--V--SEASVGHISHQLNLSQSNVSHQLK   53 (94)
T ss_dssp             HHHHHHHHHTCSHHHHHHHHHHH--H--CCBCHHHHHHHHTCCHHHHHHHHH
T ss_pred             HHHHHHHHHhCCHHHHHHHHHHH--c--CCccHHHHHHHHCCCHHHHHHHHH
Confidence            446677788876655 4444332  2  569999999999999999998854

>d1yz8p1 a.4.1.1 (P:1-60) Pituitary homeobox 2 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Pituitary homeobox 2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=88.87  E-value=0.68  Score=30.94  Aligned_cols=51  Identities=16%  Similarity=0.159  Sum_probs=40.5

Q ss_pred             cCCHHHHHHHHHHhhcCCC-CCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHh
Q 046578          317 TLSEREADILRLHFGLDGQ-TPVSCKEIGRLLSLSRERIRQIRGIALTKLQQ  367 (379)
Q Consensus       317 ~L~~rer~Vl~l~ygL~g~-e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~  367 (379)
                      .+++.|..+|...|-.+.. ......+||..+|+|...|..+...-+.+.|+
T Consensus         7 ~ft~~Q~~~Le~~F~~~~yP~~~~r~~LA~~l~l~~~~V~~WFqNrR~k~kr   58 (60)
T d1yz8p1           7 HFTSQQLQQLEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRK   58 (60)
T ss_dssp             CCCHHHHHHHHHHHTTCSSCCTTTTTHHHHHTTSCHHHHHHHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHHHcCCCChHHHHHHHHHHCCChHHHHHHhHHHHHHHHh
Confidence            3678888888888754421 34567889999999999999999998888775

>d1qpza1 a.35.1.5 (A:2-58) Purine repressor (PurR), N-terminal domain {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: GalR/LacI-like bacterial regulator
domain: Purine repressor (PurR), N-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=88.41  E-value=0.18  Score=33.80  Aligned_cols=22  Identities=9%  Similarity=0.255  Sum_probs=20.3

Q ss_pred             CHHHHHHHhCCCHHHHHHHHHH
Q 046578          339 SCKEIGRLLSLSRERIRQIRGI  360 (379)
Q Consensus       339 S~~EIAe~LgiS~~~Vr~~~~r  360 (379)
                      |++|||+..|+|..||++.++.
T Consensus         2 Ti~dvA~~agVS~sTVSr~ln~   23 (57)
T d1qpza1           2 TIKDVAKRANVSTTTVSHVINK   23 (57)
T ss_dssp             CHHHHHHHHTSCHHHHHHHHHT
T ss_pred             CHHHHHHHHCcCHHHHHHHHCC
Confidence            7899999999999999998875

>d2auwa1 a.35.1.10 (A:88-154) Hypothetical protein NE0471 C-terminal domain {Nitrosomonas europaea [TaxId: 915]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: NE0471 C-terminal domain-like
domain: Hypothetical protein NE0471 C-terminal domain
species: Nitrosomonas europaea [TaxId: 915]

Probab=88.31  E-value=0.35  Score=33.40  Aligned_cols=24  Identities=21%  Similarity=0.250  Sum_probs=21.7

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHH
Q 046578          336 TPVSCKEIGRLLSLSRERIRQIRG  359 (379)
Q Consensus       336 e~~S~~EIAe~LgiS~~~Vr~~~~  359 (379)
                      .|+|++|+|+.||||+.+|.++..
T Consensus        13 ~gltQ~elA~~LGvs~~ti~~yE~   36 (67)
T d2auwa1          13 NNLSLTTAAEALGISRRMVSYYRT   36 (67)
T ss_dssp             TTCCHHHHHHHHTSCHHHHHHHHT
T ss_pred             cCCCHHHHHHHhCCCHHHHHHHHc
Confidence            459999999999999999998765

>d2ecca1 a.4.1.1 (A:1-76) Homeobox-leucine zipper protein Homez {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Homeobox-leucine zipper protein Homez
species: Human (Homo sapiens) [TaxId: 9606]

Probab=87.99  E-value=0.43  Score=33.61  Aligned_cols=52  Identities=17%  Similarity=0.140  Sum_probs=40.9

Q ss_pred             cCCHHHHHHHHHHhhcCCC-CCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhH
Q 046578          317 TLSEREADILRLHFGLDGQ-TPVSCKEIGRLLSLSRERIRQIRGIALTKLQQT  368 (379)
Q Consensus       317 ~L~~rer~Vl~l~ygL~g~-e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~~  368 (379)
                      .+++.|..||...|-.+-. ......+||+.+|++...|+.+....+.++|+.
T Consensus         9 r~T~eQ~~~Le~~F~~n~~Ps~~~~~~La~~~gL~~~qV~~WF~NrR~k~k~~   61 (76)
T d2ecca1           9 RKTKEQLAILKSFFLQCQWARREDYQKLEQITGLPRPEIIQWFGDTRYALKHG   61 (76)
T ss_dssp             CCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTCCCHHHHHHHHHHHHHHHHHT
T ss_pred             CCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHHccCHHHHHHHHHHHHHHHHhc
Confidence            4678888888877754311 234567899999999999999999999999864

>d1s3ja_ a.4.5.28 (A:) Putative transcriptional regulator YusO {Bacillus subtilis [TaxId: 1423]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MarR-like transcriptional regulators
domain: Putative transcriptional regulator YusO
species: Bacillus subtilis [TaxId: 1423]

Probab=87.84  E-value=0.5  Score=36.88  Aligned_cols=50  Identities=10%  Similarity=0.118  Sum_probs=38.4

Q ss_pred             HHHHHHHh--cCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 046578          309 QELKELLQ--TLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIA  361 (379)
Q Consensus       309 ~~L~~~L~--~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rA  361 (379)
                      ..+.+.+.  .|++.|..||...+.   ..+.|..+||+.+++++++|.+.+.+-
T Consensus        22 ~~~~~~l~~~glt~~q~~iL~~l~~---~~~~t~~~la~~~~i~~~~vs~~l~~L   73 (143)
T d1s3ja_          22 PEMLESMEKQGVTPAQLFVLASLKK---HGSLKVSEIAERMEVKPSAVTLMADRL   73 (143)
T ss_dssp             HHHHHHHHHTTCCHHHHHHHHHHHH---HSEEEHHHHHHHHTSCHHHHHHHHHHH
T ss_pred             HHHHHHHHHcCCCHHHHHHHHHHHH---CCCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence            33445554  499999999887663   246999999999999999998776653

>d1uxda_ a.35.1.5 (A:) Fructose repressor (FruR), N-terminal domain {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: GalR/LacI-like bacterial regulator
domain: Fructose repressor (FruR), N-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=87.72  E-value=0.14  Score=34.63  Aligned_cols=22  Identities=27%  Similarity=0.357  Sum_probs=20.4

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHH
Q 046578          338 VSCKEIGRLLSLSRERIRQIRG  359 (379)
Q Consensus       338 ~S~~EIAe~LgiS~~~Vr~~~~  359 (379)
                      +|++|||+..|+|.+||++.++
T Consensus         1 vTl~diA~~agvS~sTVSrvLn   22 (59)
T d1uxda_           1 MKLDEIARLAGVSRTTASYVIN   22 (59)
T ss_dssp             CCHHHHHHHHTSCTTHHHHHHH
T ss_pred             CCHHHHHHHHCcCHHHHHHHHc
Confidence            4899999999999999999886

>d1jhfa1 a.4.5.2 (A:2-72) LexA repressor, N-terminal DNA-binding domain {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: LexA repressor, N-terminal DNA-binding domain
domain: LexA repressor, N-terminal DNA-binding domain
species: Escherichia coli [TaxId: 562]

Probab=87.53  E-value=0.83  Score=31.57  Aligned_cols=42  Identities=14%  Similarity=0.097  Sum_probs=34.7

Q ss_pred             HHHHHHHHHHHHHHHhCCCCCHHHHHHHhCC-CHHHHHHHHHh
Q 046578          226 MVAKIAEANNVLSRRLRRMPTDSEIAEMLNI-HVSTVRLAIER  267 (379)
Q Consensus       226 ~~~ki~~a~~~l~~~lgr~pt~~eia~~Lgi-s~~~~~~~l~~  267 (379)
                      .-.++..+........|..|+..|||+.+|+ |...+...+..
T Consensus         6 rQ~~vL~~I~~~~~~~G~~Ps~rei~~~~g~~S~stv~~~l~~   48 (71)
T d1jhfa1           6 RQQEVFDLIRDHISQTGMPPTRAEIAQRLGFRSPNAAEEHLKA   48 (71)
T ss_dssp             HHHHHHHHHHHHHHHHSSCCCHHHHHHHTTCSSHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCCHHHHHHHHHH
Confidence            4456667777788889999999999999999 78888877654

>d1uhsa_ a.4.1.1 (A:) Homeodomain-only protein, Hop {Mouse (Mus musculus) [TaxId: 10090]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Homeodomain-only protein, Hop
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=87.44  E-value=0.6  Score=32.57  Aligned_cols=52  Identities=19%  Similarity=0.303  Sum_probs=41.6

Q ss_pred             cCCHHHHHHHHHHhhc-CC-CCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhH
Q 046578          317 TLSEREADILRLHFGL-DG-QTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQT  368 (379)
Q Consensus       317 ~L~~rer~Vl~l~ygL-~g-~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~~  368 (379)
                      .+++.|..+|...|-- +- ......++||..+|++...|..+...-+.++|+.
T Consensus         7 ~fT~~Ql~~Le~~F~~~n~yP~~~~r~~LA~~lgL~~~~VqvWFqNrRak~rk~   60 (72)
T d1uhsa_           7 TMTEDQVEILEYNFNKVNKHPDPTTLCLIAAEAGLTEEQTQKWFKQRLAEWRRS   60 (72)
T ss_dssp             CCCHHHHHHHHHHHHSSCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHHHccccCCHHHHHHHHHHhCCCHHHHHHHHHHHHHHHHhc
Confidence            5789999999988742 21 1334678899999999999999999988888875

>d2isya1 a.4.5.24 (A:2-64) Iron-dependent regulator IdeR {Mycobacterium tuberculosis [TaxId: 1773]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Iron-dependent repressor protein
domain: Iron-dependent regulator IdeR
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=87.16  E-value=0.45  Score=32.33  Aligned_cols=25  Identities=16%  Similarity=0.017  Sum_probs=20.9

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHHH
Q 046578          336 TPVSCKEIGRLLSLSRERIRQIRGI  360 (379)
Q Consensus       336 e~~S~~EIAe~LgiS~~~Vr~~~~r  360 (379)
                      ..-+..+||+.||+++++|...++|
T Consensus        22 ~~v~~~~iA~~L~vs~~SVt~mvkr   46 (63)
T d2isya1          22 VTPLRARIAERLDQSGPTVSQTVSR   46 (63)
T ss_dssp             CCCCHHHHHHHHTCCHHHHHHHHHH
T ss_pred             CCCcHHHHHHHhCCCchhHHHHHHH
Confidence            4588999999999999999766443

>d1i5za1 a.4.5.4 (A:138-206) Catabolite gene activator protein (CAP), C-terminal domain {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: CAP C-terminal domain-like
domain: Catabolite gene activator protein (CAP), C-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=87.15  E-value=0.22  Score=34.24  Aligned_cols=23  Identities=30%  Similarity=0.538  Sum_probs=19.8

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHHH
Q 046578          337 PVSCKEIGRLLSLSRERIRQIRG  359 (379)
Q Consensus       337 ~~S~~EIAe~LgiS~~~Vr~~~~  359 (379)
                      .+|.+|||..+|+|+.+|++.++
T Consensus        29 ~lt~~~lA~~~G~sRetvsr~L~   51 (69)
T d1i5za1          29 KITRQEIGQIVGCSRETVGRILK   51 (69)
T ss_dssp             ECCHHHHHHHHTCCHHHHHHHHH
T ss_pred             CCCHHHHHHHHCCCHHHHHHHHH
Confidence            38999999999999999976543

>d1hsja1 a.4.5.28 (A:373-487) Staphylococcal accessory regulator A homolog, SarR {Staphylococcus aureus [TaxId: 1280]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MarR-like transcriptional regulators
domain: Staphylococcal accessory regulator A homolog, SarR
species: Staphylococcus aureus [TaxId: 1280]

Probab=87.14  E-value=0.41  Score=36.29  Aligned_cols=52  Identities=17%  Similarity=0.169  Sum_probs=39.2

Q ss_pred             HHHHHHHHh--cCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 046578          308 KQELKELLQ--TLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGI  360 (379)
Q Consensus       308 ~~~L~~~L~--~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~r  360 (379)
                      ...+...+.  .|+..|-.||...+... ..+.|..|||+.++++.++|.+.+.+
T Consensus        18 ~~~~~~~~~~~~Lt~~q~~vL~~l~~~~-~~~~t~~ela~~l~~~~~~vs~~i~~   71 (115)
T d1hsja1          18 KKFFRDTKKKFNLNYEEIYILNHILRSE-SNEISSKEIAKCSEFKPYYLTKALQK   71 (115)
T ss_dssp             HHHHHHHSSSCCCCHHHHHHHHHHHTCS-CSEEEHHHHHHSSCCCHHHHHHHHHH
T ss_pred             HHHHHHHHhhcCCCHHHHHHHHHHHccC-CCCcCHHHHHHHHCCChhhHHHHHHH
Confidence            344555554  68999999998766323 25799999999999999999876554

>d2hsga1 a.35.1.5 (A:2-58) Glucose-resistance amylase regulator CcpA, N-terminal domain {Bacillus megaterium [TaxId: 1404]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: GalR/LacI-like bacterial regulator
domain: Glucose-resistance amylase regulator CcpA, N-terminal domain
species: Bacillus megaterium [TaxId: 1404]

Probab=87.03  E-value=0.21  Score=33.42  Aligned_cols=23  Identities=17%  Similarity=0.211  Sum_probs=20.9

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHHH
Q 046578          338 VSCKEIGRLLSLSRERIRQIRGI  360 (379)
Q Consensus       338 ~S~~EIAe~LgiS~~~Vr~~~~r  360 (379)
                      .|++|||+..|+|..||++.++.
T Consensus         2 vTi~dvA~~agvS~~TVSr~Ln~   24 (57)
T d2hsga1           2 VTIYDVAREASVSMATVSRVVNG   24 (57)
T ss_dssp             CCHHHHHHHTTSCHHHHHHHHTT
T ss_pred             cCHHHHHHHHCcCHHHHHHHhCC
Confidence            68999999999999999998764

>d1ig7a_ a.4.1.1 (A:) Msx-1 homeodomain {Mouse (Mus musculus) [TaxId: 10090]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Msx-1 homeodomain
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=86.75  E-value=0.62  Score=30.91  Aligned_cols=50  Identities=14%  Similarity=0.097  Sum_probs=38.5

Q ss_pred             CCHHHHHHHHHHhhcCCC-CCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHh
Q 046578          318 LSEREADILRLHFGLDGQ-TPVSCKEIGRLLSLSRERIRQIRGIALTKLQQ  367 (379)
Q Consensus       318 L~~rer~Vl~l~ygL~g~-e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~  367 (379)
                      .++.|..+|...|-.+.. ....-++||+.+|++...|..+...-+.++|+
T Consensus         7 ft~~Ql~~Le~~F~~~~yP~~~~r~~LA~~l~l~~~~V~~WFqNrR~k~kr   57 (58)
T d1ig7a_           7 FTTAQLLALERKFRQKQYLSIAERAEFSSSLSLTETQVKIWFQNRRAKAKR   57 (58)
T ss_dssp             CCHHHHHHHHHHHHHCSCCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhCCChhheeecCcchHhHhcc
Confidence            578888888887743311 22356789999999999999999988888775

>d1e3oc1 a.4.1.1 (C:104-160) Oct-1 POU Homeodomain {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Oct-1 POU Homeodomain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=86.69  E-value=0.56  Score=31.07  Aligned_cols=51  Identities=18%  Similarity=0.112  Sum_probs=39.4

Q ss_pred             cCCHHHHHHHHHHhhcCCC-CCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHh
Q 046578          317 TLSEREADILRLHFGLDGQ-TPVSCKEIGRLLSLSRERIRQIRGIALTKLQQ  367 (379)
Q Consensus       317 ~L~~rer~Vl~l~ygL~g~-e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~  367 (379)
                      .+++.++.+|.-.|-.+-. ......+||..+|++...|..+...-+.+.|+
T Consensus         4 ~~~~~q~~~Le~~F~~~~~P~~~~~~~LA~~lgL~~~qV~~WFqNrR~k~kk   55 (57)
T d1e3oc1           4 SIETNIRVALEKSFMENQKPTSEDITLIAEQLNMEKEVIRVWFSNRRQKEKR   55 (57)
T ss_dssp             CCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHTS
T ss_pred             CCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHc
Confidence            4678888888887754311 22346789999999999999999998888775

>d1utxa_ a.35.1.3 (A:) Putative transcription regulator CylR2 {Enterococcus faecalis [TaxId: 1351]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: SinR domain-like
domain: Putative transcription regulator CylR2
species: Enterococcus faecalis [TaxId: 1351]

Probab=86.51  E-value=0.23  Score=33.80  Aligned_cols=24  Identities=33%  Similarity=0.470  Sum_probs=22.2

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHH
Q 046578          336 TPVSCKEIGRLLSLSRERIRQIRG  359 (379)
Q Consensus       336 e~~S~~EIAe~LgiS~~~Vr~~~~  359 (379)
                      .++|++|+|+.+|||+++++++.+
T Consensus        13 ~g~tq~elA~~~gis~~~is~~e~   36 (66)
T d1utxa_          13 KKISQSELAALLEVSRQTINGIEK   36 (66)
T ss_dssp             TTCCHHHHHHHHTSCHHHHHHHHT
T ss_pred             cCCCHHHHHHhcccCHHHHHHHHc
Confidence            569999999999999999999876

>d1au7a1 a.4.1.1 (A:103-160) Pit-1 POU homeodomain {Rat (Rattus norvegicus) [TaxId: 10116]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Pit-1 POU homeodomain
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=86.36  E-value=0.47  Score=31.57  Aligned_cols=51  Identities=22%  Similarity=0.251  Sum_probs=39.5

Q ss_pred             cCCHHHHHHHHHHhhcCCC-CCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHh
Q 046578          317 TLSEREADILRLHFGLDGQ-TPVSCKEIGRLLSLSRERIRQIRGIALTKLQQ  367 (379)
Q Consensus       317 ~L~~rer~Vl~l~ygL~g~-e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~  367 (379)
                      .+++.+..+|...|-.+.. ......+||+.+|++...|+.+...-+.+.|+
T Consensus         5 ~~s~~q~~~Le~~F~~~~~P~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kr   56 (58)
T d1au7a1           5 TISIAAKDALERHFGEHSKPSSQEIMRMAEELNLEKEVVRVWFCNRRQREKR   56 (58)
T ss_dssp             CCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHTTS
T ss_pred             CCCHHHHHHHHHHHHHccCCCHHHHHHHHHHhCCCHHHHHHHHHHHhHHHHh
Confidence            3678888898888754421 22346789999999999999999998887765

>d1lnwa_ a.4.5.28 (A:) MexR repressor {Pseudomonas aeruginosa [TaxId: 287]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MarR-like transcriptional regulators
domain: MexR repressor
species: Pseudomonas aeruginosa [TaxId: 287]

Probab=86.35  E-value=0.62  Score=36.34  Aligned_cols=42  Identities=17%  Similarity=0.240  Sum_probs=34.9

Q ss_pred             cCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 046578          317 TLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIA  361 (379)
Q Consensus       317 ~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rA  361 (379)
                      .|++.|..||...+.   .++.|..|||+.+++++++|++.+.+-
T Consensus        33 ~lt~~q~~vL~~l~~---~~~~t~~~la~~l~~~~~~vsr~l~~L   74 (141)
T d1lnwa_          33 DLTPPDVHVLKLIDE---QRGLNLQDLGRQMCRDKALITRKIREL   74 (141)
T ss_dssp             CCCHHHHHHHHHHHS---STTCBHHHHHHHTTCCHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHH---CCCCCHHHHHHHHCccHhHHHHHHHHH
Confidence            589999999976653   356999999999999999998876653

>d1j5ya1 a.4.5.1 (A:3-67) Putative transcriptional regulator TM1602, N-terminal domain {Thermotoga maritima [TaxId: 2336]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Biotin repressor-like
domain: Putative transcriptional regulator TM1602, N-terminal domain
species: Thermotoga maritima [TaxId: 2336]

Probab=86.33  E-value=0.62  Score=31.58  Aligned_cols=39  Identities=33%  Similarity=0.351  Sum_probs=27.8

Q ss_pred             HHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 046578          320 EREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGI  360 (379)
Q Consensus       320 ~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~r  360 (379)
                      ++...|+.+-.  ......|..|+|+.||||+.||++-+..
T Consensus         7 eR~~~Il~~L~--~~~~~vs~~~La~~l~VS~~TI~rdi~~   45 (65)
T d1j5ya1           7 ERLKSIVRILE--RSKEPVSGAQLAEELSVSRQVIVQDIAY   45 (65)
T ss_dssp             HHHHHHHHHHH--HCSSCBCHHHHHHHHTSCHHHHHHHHHH
T ss_pred             HHHHHHHHHHH--HcCCCCcHHHHHHHHCCCHHHHHHHHHH
Confidence            44556665432  2123479999999999999999887654

>d2a6ca1 a.35.1.13 (A:1-69) HTH-motif protein NE1354 {Nitrosomonas europaea [TaxId: 915]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: NE1354
domain: HTH-motif protein NE1354
species: Nitrosomonas europaea [TaxId: 915]

Probab=86.24  E-value=0.43  Score=32.71  Aligned_cols=25  Identities=12%  Similarity=0.279  Sum_probs=23.0

Q ss_pred             CCCCCHHHHHHHhCCCHHHHHHHHH
Q 046578          335 QTPVSCKEIGRLLSLSRERIRQIRG  359 (379)
Q Consensus       335 ~e~~S~~EIAe~LgiS~~~Vr~~~~  359 (379)
                      ..++|++|+|+.+||++++|+++.+
T Consensus        17 ~~gltq~elA~~~gv~~~~is~ie~   41 (69)
T d2a6ca1          17 NSGLTQFKAAELLGVTQPRVSDLMR   41 (69)
T ss_dssp             TTTCCHHHHHHHHTSCHHHHHHHHT
T ss_pred             HcCCCHHHHHHHHHcCHhHHHHHHc
Confidence            3779999999999999999999886

>d1p4xa2 a.4.5.28 (A:126-250) Staphylococcal accessory regulator A homolog, SarS {Staphylococcus aureus [TaxId: 1280]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MarR-like transcriptional regulators
domain: Staphylococcal accessory regulator A homolog, SarS
species: Staphylococcus aureus [TaxId: 1280]

Probab=86.19  E-value=0.65  Score=35.76  Aligned_cols=44  Identities=18%  Similarity=0.051  Sum_probs=35.4

Q ss_pred             cCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 046578          317 TLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIA  361 (379)
Q Consensus       317 ~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rA  361 (379)
                      .|+..|-.|+...+. .+..+++..+||+.+|++.++|++.+.+-
T Consensus        30 ~Ls~~q~~vL~~l~~-~~~~~~~~~~ia~~l~~~~~~vs~~v~~L   73 (125)
T d1p4xa2          30 TLSFVEFTILAIITS-QNKNIVLLKDLIETIHHKYPQTVRALNNL   73 (125)
T ss_dssp             SSCHHHHHHHHHHHT-TTTCCEEHHHHHHHSSSCHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHH-ccCCCccHHHHHHHHCCCcchHHHHHHHH
Confidence            789999999876653 22356899999999999999998876653

>d1fjla_ a.4.1.1 (A:) Paired protein {Fruit fly (Drosophila melanogaster) [TaxId: 7227]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Paired protein
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

Probab=86.13  E-value=0.73  Score=31.35  Aligned_cols=52  Identities=19%  Similarity=0.179  Sum_probs=40.7

Q ss_pred             cCCHHHHHHHHHHhhcCCC-CCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhH
Q 046578          317 TLSEREADILRLHFGLDGQ-TPVSCKEIGRLLSLSRERIRQIRGIALTKLQQT  368 (379)
Q Consensus       317 ~L~~rer~Vl~l~ygL~g~-e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~~  368 (379)
                      .+++.|..+|...|-.+.. ......+||..+|++...|+.+....+.+.|+.
T Consensus         8 ~ft~~Q~~~Le~~F~~n~yPs~~~r~~LA~~lgl~~~~V~~WFqNrR~k~kk~   60 (65)
T d1fjla_           8 TFSASQLDELERAFERTQYPDIYTREELAQRTNLTEARIQVWFQNRRARLRKQ   60 (65)
T ss_dssp             CCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHHHcCCCChHHHHHHHHHhCCCHHHhhHhhhhHHHHHHhc
Confidence            3678888888888754421 234567899999999999999999999988875

>d2a61a1 a.4.5.28 (A:5-143) Transcriptional regulator TM0710 {Thermotoga maritima [TaxId: 2336]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MarR-like transcriptional regulators
domain: Transcriptional regulator TM0710
species: Thermotoga maritima [TaxId: 2336]

Probab=85.98  E-value=0.55  Score=36.48  Aligned_cols=42  Identities=17%  Similarity=0.249  Sum_probs=34.6

Q ss_pred             cCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 046578          317 TLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIA  361 (379)
Q Consensus       317 ~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rA  361 (379)
                      .|++.|..||...+. .  .+.|..+||+.+|++.++|.+.+.+-
T Consensus        27 glt~~q~~iL~~i~~-~--~~~t~~~la~~l~i~~~tvs~~l~~L   68 (139)
T d2a61a1          27 GITPAQFDILQKIYF-E--GPKRPGELSVLLGVAKSTVTGLVKRL   68 (139)
T ss_dssp             TCCHHHHHHHHHHHH-H--CCBCHHHHHHHHTCCHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHH-c--CCCCHHHHHHHhCCCcccchHHHHHH
Confidence            589999888887663 2  46999999999999999998876654

>d1ub9a_ a.4.5.28 (A:) Hypothetical protein PH1061 {Archaeon Pyrococcus horikoshii [TaxId: 53953]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MarR-like transcriptional regulators
domain: Hypothetical protein PH1061
species: Archaeon Pyrococcus horikoshii [TaxId: 53953]

Probab=85.93  E-value=0.36  Score=35.48  Aligned_cols=39  Identities=10%  Similarity=0.182  Sum_probs=31.2

Q ss_pred             CHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 046578          319 SEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGI  360 (379)
Q Consensus       319 ~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~r  360 (379)
                      +|.+..|+.+.+-   ..++|..|||+.+|++.++|++++.+
T Consensus        15 ~p~r~~IL~~L~~---~~~~~~~eLa~~l~is~~~vs~~l~~   53 (100)
T d1ub9a_          15 NPVRLGIMIFLLP---RRKAPFSQIQKVLDLTPGNLDSHIRV   53 (100)
T ss_dssp             SHHHHHHHHHHHH---HSEEEHHHHHHHTTCCHHHHHHHHHH
T ss_pred             CHHHHHHHHHhcc---CCCeeHHHHHHHHhhccccccHHHHH
Confidence            6878888876542   25699999999999999999887544

>d2croa_ a.35.1.2 (A:) cro 434 {Bacteriophage 434 [TaxId: 10712]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: Phage repressors
domain: cro 434
species: Bacteriophage 434 [TaxId: 10712]

Probab=85.91  E-value=0.25  Score=33.50  Aligned_cols=24  Identities=13%  Similarity=0.230  Sum_probs=22.1

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHH
Q 046578          336 TPVSCKEIGRLLSLSRERIRQIRG  359 (379)
Q Consensus       336 e~~S~~EIAe~LgiS~~~Vr~~~~  359 (379)
                      .++|++|+|+.+|||+++|+++.+
T Consensus        15 ~gltq~~lA~~~gvs~~ti~~~E~   38 (65)
T d2croa_          15 LKMTQTELATKAGVKQQSIQLIEA   38 (65)
T ss_dssp             TTCCHHHHHHHHTSCHHHHHHHHT
T ss_pred             cCCCHHHHHHHHCcCHhHHHHHHC
Confidence            559999999999999999999875

>d1jgsa_ a.4.5.28 (A:) Multiple antibiotic resistance repressor, MarR {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MarR-like transcriptional regulators
domain: Multiple antibiotic resistance repressor, MarR
species: Escherichia coli [TaxId: 562]

Probab=85.89  E-value=1.4  Score=33.97  Aligned_cols=52  Identities=13%  Similarity=0.144  Sum_probs=39.7

Q ss_pred             HHHHHHHHHh--cCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 046578          307 MKQELKELLQ--TLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIA  361 (379)
Q Consensus       307 ~~~~L~~~L~--~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rA  361 (379)
                      ....+...+.  .|+..|..++...+.   ..+.|..|||+.++++.++|++.+.+-
T Consensus        19 ~~~~~~~~l~~~~Lt~~q~~vL~~l~~---~~~~t~~ela~~~~i~~~~vs~~v~~L   72 (138)
T d1jgsa_          19 KDRLLNEYLSPLDITAAQFKVLCSIRC---AACITPVELKKVLSVDLGALTRMLDRL   72 (138)
T ss_dssp             HHHHHHHHHTTTTSCHHHHHHHHHHHH---HSSBCHHHHHHHHTCCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHcCCCHHHHHHHHhHHh---CcCCCHHHHHHHHCCCHhHHHHHHHHH
Confidence            3445555564  689999888887653   246999999999999999998776553

>d1jhga_ a.4.12.1 (A:) Trp repressor, TrpR {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: TrpR-like
family: Trp repressor, TrpR
domain: Trp repressor, TrpR
species: Escherichia coli [TaxId: 562]

Probab=85.84  E-value=0.69  Score=34.43  Aligned_cols=46  Identities=17%  Similarity=0.123  Sum_probs=30.9

Q ss_pred             cCCHHHHHHHHHHhhcCC--CCC-CCHHHHHHHhCCCHHHHHHHHHHHHH
Q 046578          317 TLSEREADILRLHFGLDG--QTP-VSCKEIGRLLSLSRERIRQIRGIALT  363 (379)
Q Consensus       317 ~L~~rer~Vl~l~ygL~g--~e~-~S~~EIAe~LgiS~~~Vr~~~~rAl~  363 (379)
                      -|+|.|+.-|..|+-+-.  .+| +|++||++.+|+|..||.+. .+.|+
T Consensus        35 LlT~~E~~~la~R~~ia~~L~~G~~s~reI~~~~gvs~aTItR~-s~~Lk   83 (101)
T d1jhga_          35 MLTPDEREALGTRVRIIEELLRGEMSQRELKNELGAGIATITRG-SNSLK   83 (101)
T ss_dssp             HSCHHHHHHHHHHHHHHHHHHHCCSCHHHHHHHHCCCHHHHHHH-HHHHH
T ss_pred             hCCHHHHHHHHHHHHHHHHHHcCCcCHHHHHHHhCCChHHHHHH-HHHHH
Confidence            478888776665542210  034 89999999999999988653 44443

>d1ft9a1 a.4.5.4 (A:134-213) CO-sensing protein CooA, C-terminal domain {Rhodospirillum rubrum [TaxId: 1085]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: CAP C-terminal domain-like
domain: CO-sensing protein CooA, C-terminal domain
species: Rhodospirillum rubrum [TaxId: 1085]

Probab=85.81  E-value=0.32  Score=34.37  Aligned_cols=28  Identities=25%  Similarity=0.364  Sum_probs=22.7

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhH
Q 046578          337 PVSCKEIGRLLSLSRERIRQIRGIALTKLQQT  368 (379)
Q Consensus       337 ~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~~  368 (379)
                      ++|.+|||..+|+|+.+|.+.    +++|++.
T Consensus        30 ~~t~~eiA~~lG~sretvsr~----l~~l~~~   57 (80)
T d1ft9a1          30 DFTVEEIANLIGSSRQTTSTA----LNSLIKE   57 (80)
T ss_dssp             CCCHHHHHHHHCSCHHHHHHH----HHHHHHT
T ss_pred             CCCHHHHHHHHCCCHHHHHHH----HHHHHHC
Confidence            589999999999999999655    5556554

>d2o38a1 a.35.1.13 (A:28-116) Hypothetical protein RPA3824 {Rhodopseudomonas palustris [TaxId: 1076]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: NE1354
domain: Hypothetical protein RPA3824
species: Rhodopseudomonas palustris [TaxId: 1076]

Probab=85.49  E-value=0.37  Score=34.94  Aligned_cols=37  Identities=11%  Similarity=0.140  Sum_probs=28.8

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHH-H----HHHHHHhHHhhc
Q 046578          336 TPVSCKEIGRLLSLSRERIRQIRG-I----ALTKLQQTNILN  372 (379)
Q Consensus       336 e~~S~~EIAe~LgiS~~~Vr~~~~-r----Al~kLR~~l~~~  372 (379)
                      .|+|++++|+.+|+|+.+|+++++ +    .+.+|.+.+...
T Consensus        23 ~gltq~~lA~~~gis~~~is~ie~G~~~~~~~~~L~~ia~~L   64 (89)
T d2o38a1          23 ARLSQAAAAARLGINQPKVSALRNYKLEGFSVERLMTLLNAL   64 (89)
T ss_dssp             TTCCHHHHHHHHTCCHHHHHHHHTTCCTTCCHHHHHHHHHHT
T ss_pred             cCCCHHHHHHHHHhhHhHHHHHHcCCCCCCcHHHHHHHHHHc
Confidence            669999999999999999999986 2    245555555443

>d1x2na1 a.4.1.1 (A:6-67) Homeobox protein pknox1 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Homeobox protein pknox1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=85.34  E-value=0.81  Score=30.81  Aligned_cols=51  Identities=16%  Similarity=0.076  Sum_probs=38.5

Q ss_pred             cCCHHHHHHHHHHhhcCC----CCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHh
Q 046578          317 TLSEREADILRLHFGLDG----QTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQ  367 (379)
Q Consensus       317 ~L~~rer~Vl~l~ygL~g----~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~  367 (379)
                      .+|+.+..||.-.|.-.-    .......+||+.+|+|...|+.+...++++|.+
T Consensus         8 ~~~~~~~~iL~~wf~~~~~nPyPs~~e~~~La~~~~l~~~qI~~WF~N~R~R~lq   62 (62)
T d1x2na1           8 VLPKHATNVMRSWLFQHIGHPYPTEDEKKQIAAQTNLTLLQVNNWFINARRRILQ   62 (62)
T ss_dssp             CCCHHHHHHHHHHHHHTTTSCCCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHHHhccCCCcCHHHHHHHHHHHCcCHHHhHHHHHHHHHHhcC
Confidence            478888999887663110    012245679999999999999999999988753

>d2etha1 a.4.5.28 (A:1-140) Putative transcriptional regulator TM0816 {Thermotoga maritima [TaxId: 2336]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MarR-like transcriptional regulators
domain: Putative transcriptional regulator TM0816
species: Thermotoga maritima [TaxId: 2336]

Probab=85.11  E-value=0.55  Score=36.46  Aligned_cols=43  Identities=16%  Similarity=0.128  Sum_probs=35.2

Q ss_pred             cCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHH
Q 046578          317 TLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIAL  362 (379)
Q Consensus       317 ~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl  362 (379)
                      .|+..|..||...+.   ..+.|..+||+.+|+++++|.+.+.+-.
T Consensus        29 ~lt~~q~~iL~~l~~---~~~~t~~~La~~l~i~~~~vs~~v~~L~   71 (140)
T d2etha1          29 DMKTTELYAFLYVAL---FGPKKMKEIAEFLSTTKSNVTNVVDSLE   71 (140)
T ss_dssp             HSBHHHHHHHHHHHH---HCCBCHHHHHHHTTSCHHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHH---cCCcCHHHHHHHHCcCHHHHHHHHHHHH
Confidence            588888888876653   2569999999999999999988876643

>d1z6ra1 a.4.5.63 (A:12-81) Mlc protein N-terminal domain {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: ROK associated domain
domain: Mlc protein N-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=84.62  E-value=1.1  Score=30.65  Aligned_cols=38  Identities=29%  Similarity=0.305  Sum_probs=29.8

Q ss_pred             HHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHH
Q 046578          322 EADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIAL  362 (379)
Q Consensus       322 er~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl  362 (379)
                      .+.|+.+.+-   ..+.|-.|||+.+|+|..||.++...-+
T Consensus         7 ~~~Il~~i~~---~g~~sr~eLa~~~gLS~~Tvs~iv~~L~   44 (70)
T d1z6ra1           7 AGAVYRLIDQ---LGPVSRIDLSRLAQLAPASITKIVHEML   44 (70)
T ss_dssp             HHHHHHHHHS---SCSCCHHHHHHHTTCCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHH---cCCcCHHHHHHHHCcCHHHHHHHHHHHH
Confidence            3456666652   3679999999999999999999877643

>d1rr7a_ a.4.1.14 (A:) Middle operon regulator, Mor {Bacteriophage Mu [TaxId: 10677]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Middle operon regulator, Mor
domain: Middle operon regulator, Mor
species: Bacteriophage Mu [TaxId: 10677]

Probab=84.58  E-value=0.82  Score=33.53  Aligned_cols=37  Identities=11%  Similarity=0.071  Sum_probs=30.4

Q ss_pred             HHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 046578          321 READILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALT  363 (379)
Q Consensus       321 rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~  363 (379)
                      +.++|... |     .|.+..|+|.++|+|..+|++++++..+
T Consensus        56 Rn~~I~~e-f-----~G~n~~eLA~kY~lS~~~I~~Ii~~~rk   92 (94)
T d1rr7a_          56 RDLRIWND-F-----NGRNVSELTTRYGVTFNTVYKAIRRMRR   92 (94)
T ss_dssp             HHHHHHHH-C-----CSSCHHHHHHHHTCCHHHHHHHHHHHHH
T ss_pred             HHHHHHHH-h-----CCCCHHHHHHHHCCCHHHHHHHHHHHHc
Confidence            66777764 4     4689999999999999999999887643

>d2frha1 a.4.5.28 (A:102-216) Pleiotropic regulator of virulence genes, SarA {Staphylococcus aureus [TaxId: 1280]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MarR-like transcriptional regulators
domain: Pleiotropic regulator of virulence genes, SarA
species: Staphylococcus aureus [TaxId: 1280]

Probab=84.55  E-value=0.48  Score=35.84  Aligned_cols=44  Identities=16%  Similarity=0.122  Sum_probs=34.8

Q ss_pred             cCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 046578          317 TLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIA  361 (379)
Q Consensus       317 ~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rA  361 (379)
                      .|+..|-.|+...+. ....++|..|||+.++++.++|++.+.+-
T Consensus        30 ~Ls~~q~~vL~~l~~-~~~~~~t~~~la~~l~~~~~tvs~~i~~L   73 (115)
T d2frha1          30 SISFEEFAVLTYISE-NKEKEYYLKDIINHLNYKQPQVVKAVKIL   73 (115)
T ss_dssp             CCCHHHHHHHHHHHH-TCCSEEEHHHHHHHSSSHHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHc-CCCCCCCHHHHHHHHCCCHhHHHHHHHHH
Confidence            699999999876653 22245899999999999999998876653

>d3e5ua1 a.4.5.4 (A:148-227) Chlorophenol reduction protein CprK {Desulfitobacterium hafniense [TaxId: 49338]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: CAP C-terminal domain-like
domain: Chlorophenol reduction protein CprK
species: Desulfitobacterium hafniense [TaxId: 49338]

Probab=84.45  E-value=0.41  Score=33.74  Aligned_cols=28  Identities=25%  Similarity=0.533  Sum_probs=22.5

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhH
Q 046578          337 PVSCKEIGRLLSLSRERIRQIRGIALTKLQQT  368 (379)
Q Consensus       337 ~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~~  368 (379)
                      .+|.+|||..+|+|+.+|.+.    +++|++.
T Consensus        30 ~lt~~elA~~~g~sretvsr~----l~~l~~~   57 (80)
T d3e5ua1          30 PLSQKSIGEITGVHHVTVSRV----LASLKRE   57 (80)
T ss_dssp             CCCHHHHHHHHTCCHHHHHHH----HHHHHHT
T ss_pred             CCCHHHHHHHHCCCHHHHHHH----HHHHHHC
Confidence            589999999999999999655    5555554

>d1z91a1 a.4.5.28 (A:8-144) Organic hydroperoxide resistance transcriptional regulator OhrR {Bacillus subtilis [TaxId: 1423]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MarR-like transcriptional regulators
domain: Organic hydroperoxide resistance transcriptional regulator OhrR
species: Bacillus subtilis [TaxId: 1423]

Probab=84.44  E-value=0.49  Score=36.74  Aligned_cols=41  Identities=15%  Similarity=0.197  Sum_probs=33.6

Q ss_pred             cCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 046578          317 TLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGI  360 (379)
Q Consensus       317 ~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~r  360 (379)
                      .|++.|..|+...+.   .++.|..|||+.+++++++|.+.+.+
T Consensus        30 gLt~~q~~vL~~l~~---~~~~t~~~La~~~~i~~~~vsr~i~~   70 (137)
T d1z91a1          30 NITYPQYLALLLLWE---HETLTVKKMGEQLYLDSGTLTPMLKR   70 (137)
T ss_dssp             CCCHHHHHHHHHHHH---HSEEEHHHHHHTTTCCHHHHHHHHHH
T ss_pred             CcCHHHHHHHHHHHc---CCCCCHHHHHHHHCcCHHHHHHHHHH
Confidence            588888888876653   36799999999999999999876554

>d2fxaa1 a.4.5.28 (A:6-167) Protease production regulatory protein Hpr {Bacillus subtilis [TaxId: 1423]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MarR-like transcriptional regulators
domain: Protease production regulatory protein Hpr
species: Bacillus subtilis [TaxId: 1423]

Probab=84.38  E-value=1.2  Score=35.75  Aligned_cols=43  Identities=16%  Similarity=0.119  Sum_probs=35.4

Q ss_pred             cCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHH
Q 046578          317 TLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIAL  362 (379)
Q Consensus       317 ~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl  362 (379)
                      .|+..|..||...+-   .++.|..+||+.++++.++|++.+.+-.
T Consensus        38 ~Lt~~q~~vL~~l~~---~~~~t~~~la~~~~l~~~tvs~~i~rL~   80 (162)
T d2fxaa1          38 DLNINEHHILWIAYQ---LNGASISEIAKFGVMHVSTAFNFSKKLE   80 (162)
T ss_dssp             TCCHHHHHHHHHHHH---HTSEEHHHHHHHTTCCHHHHHHHHHHHH
T ss_pred             CCCHHHHHHHhhhcc---CCCcCHHHHHHHHcCCchhhHHHHHHHH
Confidence            689999998877653   2569999999999999999988776643

>d2fbka1 a.4.5.28 (A:8-179) Transcriptional regulator DR1159 {Deinococcus radiodurans [TaxId: 1299]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MarR-like transcriptional regulators
domain: Transcriptional regulator DR1159
species: Deinococcus radiodurans [TaxId: 1299]

Probab=84.32  E-value=0.63  Score=37.73  Aligned_cols=52  Identities=13%  Similarity=0.082  Sum_probs=39.3

Q ss_pred             HHHHHHHh--cCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 046578          309 QELKELLQ--TLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGI  360 (379)
Q Consensus       309 ~~L~~~L~--~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~r  360 (379)
                      ..+...+.  .|++.|..||..-+..++.+++|..|||+.+|+++++|.+.+.+
T Consensus        49 ~~~~~~l~~~gLt~~q~~vL~~L~~~~~~~~lt~~eLa~~l~i~~~tvsr~l~~  102 (172)
T d2fbka1          49 REIERTYAASGLNAAGWDLLLTLYRSAPPEGLRPTELSALAAISGPSTSNRIVR  102 (172)
T ss_dssp             HHHHHHHHTTTCCHHHHHHHHHHHHHCCSSCBCHHHHHHHCSCCSGGGSSHHHH
T ss_pred             HHHHHHHHHcCCCHHHHHHHHHHHhhCCCCCcCHHHHHHHHCcCHhHHHHHHHH
Confidence            44555554  58999998887665333335699999999999999999877665

>d1efaa1 a.35.1.5 (A:2-60) Lac repressor (LacR), N-terminal domain {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: GalR/LacI-like bacterial regulator
domain: Lac repressor (LacR), N-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=84.17  E-value=0.29  Score=32.93  Aligned_cols=24  Identities=13%  Similarity=0.314  Sum_probs=21.3

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHHHH
Q 046578          337 PVSCKEIGRLLSLSRERIRQIRGI  360 (379)
Q Consensus       337 ~~S~~EIAe~LgiS~~~Vr~~~~r  360 (379)
                      ..|++|||+..|+|.+||++.++.
T Consensus         2 ~~Ti~diA~~agvS~sTVSr~l~~   25 (59)
T d1efaa1           2 PVTLYDVAEYAGVSYQTVSRVVNQ   25 (59)
T ss_dssp             CCCHHHHHHTTTSCHHHHHHHHTT
T ss_pred             CCCHHHHHHHHCCCHHHHHHHHCC
Confidence            368999999999999999998854

>d1lj9a_ a.4.5.28 (A:) Transcriptional regulator SlyA {Enterococcus faecalis [TaxId: 1351]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MarR-like transcriptional regulators
domain: Transcriptional regulator SlyA
species: Enterococcus faecalis [TaxId: 1351]

Probab=84.13  E-value=1  Score=35.08  Aligned_cols=42  Identities=12%  Similarity=0.071  Sum_probs=34.1

Q ss_pred             cCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 046578          317 TLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIA  361 (379)
Q Consensus       317 ~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rA  361 (379)
                      .|+..|..+|...+.   .++.|..+||+.++++.++|++.+.+-
T Consensus        26 ~lt~~q~~iL~~i~~---~~~~t~~~la~~l~i~~~tvs~~l~~L   67 (144)
T d1lj9a_          26 SLTRGQYLYLVRVCE---NPGIIQEKIAELIKVDRTTAARAIKRL   67 (144)
T ss_dssp             TCTTTHHHHHHHHHH---STTEEHHHHHHHHTCCHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHh---CCCCCHHHHHHHHCccHhhHHHHHHHH
Confidence            578888888876553   357999999999999999998876654

>d2e1oa1 a.4.1.1 (A:8-64) Homeobox protein prh {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Homeobox protein prh
species: Human (Homo sapiens) [TaxId: 9606]

Probab=84.07  E-value=1  Score=29.69  Aligned_cols=51  Identities=18%  Similarity=0.244  Sum_probs=37.9

Q ss_pred             cCCHHHHHHHHHHhhcCCC-CCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHh
Q 046578          317 TLSEREADILRLHFGLDGQ-TPVSCKEIGRLLSLSRERIRQIRGIALTKLQQ  367 (379)
Q Consensus       317 ~L~~rer~Vl~l~ygL~g~-e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~  367 (379)
                      .+++.|..+|...|-.+.. ......+||..+|++...|..+...-+.+.|+
T Consensus         6 ~ft~~Q~~~Le~~F~~n~yp~~~~r~~LA~~l~L~~~qV~~WFqNrR~k~kk   57 (57)
T d2e1oa1           6 RFSNDQTIELEKKFETQKYLSPPERKRLAKMLQLSERQVKTWFQNRRAKWRR   57 (57)
T ss_dssp             CCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHH
T ss_pred             cCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCHHHhhHhhhhhhhhccC
Confidence            4678888888887744321 22345679999999999999999887776653

>d2fbha1 a.4.5.28 (A:8-144) Transcriptional regulator PA3341 {Pseudomonas aeruginosa [TaxId: 287]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MarR-like transcriptional regulators
domain: Transcriptional regulator PA3341
species: Pseudomonas aeruginosa [TaxId: 287]

Probab=83.94  E-value=1.3  Score=34.00  Aligned_cols=53  Identities=13%  Similarity=0.100  Sum_probs=38.5

Q ss_pred             HHHHHHHh--cCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 046578          309 QELKELLQ--TLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIALT  363 (379)
Q Consensus       309 ~~L~~~L~--~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~  363 (379)
                      ..+...+.  .|++.|..||...+. . .++.|..+||+.+++++++|++.+.+..+
T Consensus        15 ~~~~~~l~~~glt~~q~~iL~~l~~-~-~~~~t~~~la~~~~~~~~~vs~~v~~L~~   69 (137)
T d2fbha1          15 AELDRRLSHLGLSQARWLVLLHLAR-H-RDSPTQRELAQSVGVEGPTLARLLDGLES   69 (137)
T ss_dssp             HHHHHHTGGGCCTTTHHHHHHHHHH-C-SSCCBHHHHHHHHTCCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHcCCCHHHHHHHHHHHH-c-CCCCcHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            34455554  588888888765432 1 25699999999999999999888766443

>d2ao9a1 a.4.1.17 (A:13-132) Phage protein BC1890 {Bacillus cereus [TaxId: 1396]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Nanomeric phage protein-like
domain: Phage protein BC1890
species: Bacillus cereus [TaxId: 1396]

Probab=83.94  E-value=2.1  Score=31.83  Aligned_cols=48  Identities=21%  Similarity=0.257  Sum_probs=34.7

Q ss_pred             HHHHHhcCCHHHHHHHHHHh----hcC-CCCCCCHHHHHHHhCCCHHHHHHHH
Q 046578          311 LKELLQTLSEREADILRLHF----GLD-GQTPVSCKEIGRLLSLSRERIRQIR  358 (379)
Q Consensus       311 L~~~L~~L~~rer~Vl~l~y----gL~-g~e~~S~~EIAe~LgiS~~~Vr~~~  358 (379)
                      +.++-.+|+-.+++.-.+.-    -.. |.+..|+.|||+.+|||+.+..++.
T Consensus         5 ~~el~~~L~~~q~~AA~~l~~Ne~~~~~~~ekktqeqiAeelGisr~tLyrWr   57 (120)
T d2ao9a1           5 LDELKQKLTAKQIQAAYLLVENELMESNNEEKRTQDEMANELGINRTTLWEWR   57 (120)
T ss_dssp             HHHHHTTSCHHHHHHHHHHHHHHHCC---CCCCCHHHHHHHHTCCHHHHHHHH
T ss_pred             HHHHHHHhhHHHHHHHHHHhhchhccccchhhhhHHHHHHHhChhHHHHHHHh
Confidence            45556688877776554432    122 3377899999999999999999987

>d2gaua1 a.4.5.4 (A:152-232) Transcriptional regulator PG0396, C-terminal domain {Porphyromonas gingivalis [TaxId: 837]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: CAP C-terminal domain-like
domain: Transcriptional regulator PG0396, C-terminal domain
species: Porphyromonas gingivalis [TaxId: 837]

Probab=83.88  E-value=0.43  Score=33.59  Aligned_cols=28  Identities=14%  Similarity=0.194  Sum_probs=22.3

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhH
Q 046578          337 PVSCKEIGRLLSLSRERIRQIRGIALTKLQQT  368 (379)
Q Consensus       337 ~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~~  368 (379)
                      .+|.+|||..+|+|+.+|++.    +++|++.
T Consensus        29 ~lt~~eLA~~~G~sretvsr~----L~~l~~~   56 (81)
T d2gaua1          29 YLSREELATLSNMTVSNAIRT----LSTFVSE   56 (81)
T ss_dssp             CCCHHHHHHHTTSCHHHHHHH----HHHHHHT
T ss_pred             cCCHHHHHHHHCCCHHHHHHH----HHHHHHC
Confidence            489999999999999998655    5555543

>d1y7ya1 a.35.1.3 (A:5-73) Restriction-modification controller protein C.AhdI {Aeromonas hydrophila [TaxId: 644]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: SinR domain-like
domain: Restriction-modification controller protein C.AhdI
species: Aeromonas hydrophila [TaxId: 644]

Probab=83.86  E-value=0.37  Score=32.97  Aligned_cols=24  Identities=17%  Similarity=0.207  Sum_probs=22.1

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHH
Q 046578          336 TPVSCKEIGRLLSLSRERIRQIRG  359 (379)
Q Consensus       336 e~~S~~EIAe~LgiS~~~Vr~~~~  359 (379)
                      .++|++++|+.+|+|+++++++.+
T Consensus        21 ~gltq~~lA~~~gis~~~i~~~E~   44 (69)
T d1y7ya1          21 KGLSQETLAFLSGLDRSYVGGVER   44 (69)
T ss_dssp             TTCCHHHHHHHHTCCHHHHHHHHT
T ss_pred             cCCCHHHHHhHhCCCHHHHHHHHC
Confidence            569999999999999999999875

>d1zyba1 a.4.5.4 (A:148-220) Probable transcription regulator BT4300, C-terminal domain {Bacteroides thetaiotaomicron [TaxId: 818]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: CAP C-terminal domain-like
domain: Probable transcription regulator BT4300, C-terminal domain
species: Bacteroides thetaiotaomicron [TaxId: 818]

Probab=83.83  E-value=0.39  Score=33.50  Aligned_cols=27  Identities=30%  Similarity=0.448  Sum_probs=21.9

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHHHHHHHHHhH
Q 046578          338 VSCKEIGRLLSLSRERIRQIRGIALTKLQQT  368 (379)
Q Consensus       338 ~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~~  368 (379)
                      +|.+|||+.+|+|+.+|++    ++++|++.
T Consensus        28 lt~~elA~~lg~sr~tvsr----~l~~l~~~   54 (73)
T d1zyba1          28 VKMDDLARCLDDTRLNISK----TLNELQDN   54 (73)
T ss_dssp             CCHHHHHHHHTSCHHHHHH----HHHHHHHT
T ss_pred             cCHHHHHHHHCCCHHHHHH----HHHHHHHC
Confidence            7999999999999999865    45666553

>d1r69a_ a.35.1.2 (A:) 434 C1 repressor, DNA-binding domain {Bacteriophage 434 [TaxId: 10712]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: Phage repressors
domain: 434 C1 repressor, DNA-binding domain
species: Bacteriophage 434 [TaxId: 10712]

Probab=83.81  E-value=0.38  Score=32.23  Aligned_cols=24  Identities=13%  Similarity=0.271  Sum_probs=22.3

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHH
Q 046578          336 TPVSCKEIGRLLSLSRERIRQIRG  359 (379)
Q Consensus       336 e~~S~~EIAe~LgiS~~~Vr~~~~  359 (379)
                      .++|++|+|+.+|||+++|+++.+
T Consensus        13 ~g~sq~elA~~~gvs~~~is~~E~   36 (63)
T d1r69a_          13 LGLNQAELAQKVGTTQQSIEQLEN   36 (63)
T ss_dssp             TTCCHHHHHHHHTSCHHHHHHHHT
T ss_pred             cCCcHHHHHHHhCcCHHHHHHHHC
Confidence            569999999999999999999975

>d1zq3p1 a.4.1.1 (P:2-68) Homeotic bicoid protein {Fruit fly (Drosophila melanogaster) [TaxId: 7227]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Homeotic bicoid protein
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

Probab=83.76  E-value=1.4  Score=30.09  Aligned_cols=54  Identities=13%  Similarity=0.086  Sum_probs=41.3

Q ss_pred             cCCHHHHHHHHHHhhcCCC-CCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHHh
Q 046578          317 TLSEREADILRLHFGLDGQ-TPVSCKEIGRLLSLSRERIRQIRGIALTKLQQTNI  370 (379)
Q Consensus       317 ~L~~rer~Vl~l~ygL~g~-e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~~l~  370 (379)
                      .+++.|..+|...|-.+.. ....-.+||+.||++...|..+...-+.+.|+...
T Consensus         7 ~ft~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~~V~iWFqNrR~k~kk~~~   61 (67)
T d1zq3p1           7 TFTSSQIAELEQHFLQGRYLTAPRLADLSAKLALGTAQVKIWFKNRRRRHKIQSD   61 (67)
T ss_dssp             CCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHHHH
T ss_pred             cCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhCCCccceeeccccHHHhHhhhhh
Confidence            3678888888888743311 22346789999999999999999998888887654

>d1mkma1 a.4.5.33 (A:1-75) Transcriptional regulator IclR, N-terminal domain {Thermotoga maritima [TaxId: 2336]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Transcriptional regulator IclR, N-terminal domain
domain: Transcriptional regulator IclR, N-terminal domain
species: Thermotoga maritima [TaxId: 2336]

Probab=83.17  E-value=0.83  Score=31.80  Aligned_cols=26  Identities=19%  Similarity=0.166  Sum_probs=22.4

Q ss_pred             CCCCCHHHHHHHhCCCHHHHHHHHHH
Q 046578          335 QTPVSCKEIGRLLSLSRERIRQIRGI  360 (379)
Q Consensus       335 ~e~~S~~EIAe~LgiS~~~Vr~~~~r  360 (379)
                      ..++|..|||+.+|+++++|++++.-
T Consensus        18 ~~~~s~~eia~~~~~~~st~~rll~t   43 (75)
T d1mkma1          18 PGDVSVSEIAEKFNMSVSNAYKYMVV   43 (75)
T ss_dssp             SSCBCHHHHHHHTTCCHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHCcCHHHHHHHHHH
Confidence            36799999999999999999877543

>d1wi3a_ a.4.1.1 (A:) DNA-binding protein SATB2 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: DNA-binding protein SATB2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=83.10  E-value=0.46  Score=32.97  Aligned_cols=52  Identities=12%  Similarity=0.107  Sum_probs=36.8

Q ss_pred             cCCHHHHHHHHHHhh-cCC-CCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhH
Q 046578          317 TLSEREADILRLHFG-LDG-QTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQT  368 (379)
Q Consensus       317 ~L~~rer~Vl~l~yg-L~g-~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~~  368 (379)
                      .+++.|..+|...|- .+- .......+||+.+|++...|..+....+.+.|+.
T Consensus        13 ~~t~~Q~~~Le~~F~~~~~~P~~~~~~~La~~lgl~~~qV~~WFqNrR~k~kk~   66 (71)
T d1wi3a_          13 KISLEALGILQSFIHDVGLYPDQEAIHTLSAQLDLPKHTIIKFFQNQRYHVKHS   66 (71)
T ss_dssp             CCCSHHHHHHHHHHHHHCSCCCHHHHHHHHHHSCCCHHHHHHHHHHHHHHCCSS
T ss_pred             cCCHHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCHHHHHHHhHhhHhhhccc
Confidence            356666677766552 121 1223455799999999999999999999988763

>d1jgga_ a.4.1.1 (A:) Even-skipped homeodomain {Fruit fly (Drosophila melanogaster) [TaxId: 7227]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Even-skipped homeodomain
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

Probab=82.97  E-value=1.2  Score=29.38  Aligned_cols=50  Identities=14%  Similarity=0.069  Sum_probs=38.0

Q ss_pred             CCHHHHHHHHHHhhcCCC-CCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHh
Q 046578          318 LSEREADILRLHFGLDGQ-TPVSCKEIGRLLSLSRERIRQIRGIALTKLQQ  367 (379)
Q Consensus       318 L~~rer~Vl~l~ygL~g~-e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~  367 (379)
                      .++.|..+|.-.|-.+.. ......+||+.+|+|...|..+...-+.+.|+
T Consensus         6 fT~~Ql~~Le~~F~~~~yp~~~~r~~LA~~lgl~~~qV~vWFqNrR~k~kk   56 (57)
T d1jgga_           6 FTRDQLGRLEKEFYKENYVSRPRRCELAAQLNLPESTIKVWFQNRRMKDKR   56 (57)
T ss_dssp             CCHHHHHHHHHHHHHCSCCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhCCChhHhhhcchhhhhhhhc
Confidence            578888888877743321 22345789999999999999999988877775

>d1pufb_ a.4.1.1 (B:) pbx1 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: pbx1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=82.94  E-value=1.1  Score=31.15  Aligned_cols=53  Identities=9%  Similarity=0.134  Sum_probs=40.6

Q ss_pred             cCCHHHHHHHHHHhhcCC----CCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHH
Q 046578          317 TLSEREADILRLHFGLDG----QTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQTN  369 (379)
Q Consensus       317 ~L~~rer~Vl~l~ygL~g----~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~~l  369 (379)
                      .+++.+..+|.-.|.-..    .....-.+||..+|+|...|..+....+.+.++..
T Consensus         7 ~~t~~q~~~Le~~f~~~~~~pYPs~~~k~~La~~~gl~~~qv~~WF~N~R~r~k~~~   63 (73)
T d1pufb_           7 NFNKQATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIRYKKNI   63 (73)
T ss_dssp             CCCHHHHHHHHHHHHHTTTSCCCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHCT
T ss_pred             CCCHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHCcCHHHhHHHHHHHHHHhcccc
Confidence            478899999998773110    11233457999999999999999999999988654

>d2icta1 a.35.1.3 (A:8-94) Antitoxin HigA {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: SinR domain-like
domain: Antitoxin HigA
species: Escherichia coli [TaxId: 562]

Probab=82.80  E-value=0.48  Score=34.14  Aligned_cols=25  Identities=16%  Similarity=0.198  Sum_probs=22.3

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHHH
Q 046578          336 TPVSCKEIGRLLSLSRERIRQIRGI  360 (379)
Q Consensus       336 e~~S~~EIAe~LgiS~~~Vr~~~~r  360 (379)
                      .++|+.++|+.+|||+++|+++++-
T Consensus        13 ~glsq~~LA~~lGvs~~~is~ie~g   37 (87)
T d2icta1          13 LNVSLREFARAMEIAPSTASRLLTG   37 (87)
T ss_dssp             HTCCHHHHHHHHTCCHHHHHHHHHT
T ss_pred             cCCCHHHHHHHHhhcHHHHHHHHHh
Confidence            3599999999999999999998763

>d1b0na2 a.35.1.3 (A:1-68) SinR repressor, DNA-binding domain {Bacillus subtilis [TaxId: 1423]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: SinR domain-like
domain: SinR repressor, DNA-binding domain
species: Bacillus subtilis [TaxId: 1423]

Probab=82.76  E-value=0.44  Score=32.44  Aligned_cols=24  Identities=13%  Similarity=0.180  Sum_probs=22.3

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHH
Q 046578          336 TPVSCKEIGRLLSLSRERIRQIRG  359 (379)
Q Consensus       336 e~~S~~EIAe~LgiS~~~Vr~~~~  359 (379)
                      .++|+.|+|+.+|||+++|+++.+
T Consensus        13 ~gltq~~la~~~gis~~~i~~~E~   36 (68)
T d1b0na2          13 KGYSLSELAEKAGVAKSYLSSIER   36 (68)
T ss_dssp             TTCCHHHHHHHHTCCHHHHHHHHT
T ss_pred             cCCCHHHHHHHHCCCHHHHHHHHc
Confidence            569999999999999999999886

>d2g9wa1 a.4.5.39 (A:3-124) Hypothetical protein Rv1846c {Mycobacterium tuberculosis [TaxId: 1773]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Penicillinase repressor
domain: Hypothetical protein Rv1846c
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=82.63  E-value=1  Score=34.42  Aligned_cols=47  Identities=13%  Similarity=0.219  Sum_probs=37.5

Q ss_pred             HhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHh----CCCHHHHHHHHHHHHH
Q 046578          315 LQTLSEREADILRLHFGLDGQTPVSCKEIGRLL----SLSRERIRQIRGIALT  363 (379)
Q Consensus       315 L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~L----giS~~~Vr~~~~rAl~  363 (379)
                      +.+|++.|.+|+...+-. | ++.|.+||.+.|    +++.+||+..+.|-.+
T Consensus         2 ~~~L~~~E~~IM~~lW~~-g-~~~t~~eI~~~l~~~~~~~~sTV~T~L~rL~~   52 (122)
T d2g9wa1           2 LTRLGDLERAVMDHLWSR-T-EPQTVRQVHEALSARRDLAYTTVMAVLQRLAK   52 (122)
T ss_dssp             GGGCCHHHHHHHHHHHTC-S-SCEEHHHHHHHHTTTCCCCHHHHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHHcC-C-CCccHHHHHHHHhccCCCcHHHHHHHHHHHHH
Confidence            457999999999988732 2 567999999999    5788999988777554

>d1bw5a_ a.4.1.1 (A:) Insulin gene enhancer protein isl-1 {Rat (Rattus norvegicus) [TaxId: 10116]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Insulin gene enhancer protein isl-1
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=82.59  E-value=0.67  Score=31.64  Aligned_cols=52  Identities=17%  Similarity=0.180  Sum_probs=39.7

Q ss_pred             cCCHHHHHHHHHHhhcCCC-CCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhH
Q 046578          317 TLSEREADILRLHFGLDGQ-TPVSCKEIGRLLSLSRERIRQIRGIALTKLQQT  368 (379)
Q Consensus       317 ~L~~rer~Vl~l~ygL~g~-e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~~  368 (379)
                      .+++.|..+|...|-.+.. .....++||..+|++...|..+...-+.+.|+.
T Consensus         9 ~~t~~Q~~~Le~~F~~n~~Ps~~~~~~LA~~l~l~~~~V~~WFqNrR~k~kk~   61 (66)
T d1bw5a_           9 VLNEKQLHTLRTCYAANPRPDALMKEQLVEMTGLSPRVIRVWFQNKRCKDKKR   61 (66)
T ss_dssp             CCSHHHHHHHHHHHHHCSCCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHCSSC
T ss_pred             CcCHHHHHHHHHHHHHCCCCCHHHHHHHHHHcCcCHHHhhhhhHhHHHHHHHH
Confidence            4688899999988865422 122345799999999999999999888776653

>d1x57a1 a.35.1.12 (A:8-85) Endothelial differentiation-related factor 1, EDF1 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: EDF1-like
domain: Endothelial differentiation-related factor 1, EDF1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=81.99  E-value=1  Score=31.56  Aligned_cols=25  Identities=8%  Similarity=0.082  Sum_probs=22.8

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHHH
Q 046578          336 TPVSCKEIGRLLSLSRERIRQIRGI  360 (379)
Q Consensus       336 e~~S~~EIAe~LgiS~~~Vr~~~~r  360 (379)
                      .++|++++|+.+|||.++|+++.+-
T Consensus        18 ~gltq~~lA~~~gis~~~is~~E~G   42 (78)
T d1x57a1          18 KGLTQKDLATKINEKPQVIADYESG   42 (78)
T ss_dssp             TTCCHHHHHHHHTSCHHHHHHHHHT
T ss_pred             cCCChhHHHHcCCCCHHHHHHHHcc
Confidence            6699999999999999999998764

>d2cuea1 a.4.1.1 (A:7-74) Paired box protein pax6 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Paired box protein pax6
species: Human (Homo sapiens) [TaxId: 9606]

Probab=81.88  E-value=1.7  Score=29.70  Aligned_cols=53  Identities=11%  Similarity=0.145  Sum_probs=41.0

Q ss_pred             CCHHHHHHHHHHhhcCCC-CCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHHh
Q 046578          318 LSEREADILRLHFGLDGQ-TPVSCKEIGRLLSLSRERIRQIRGIALTKLQQTNI  370 (379)
Q Consensus       318 L~~rer~Vl~l~ygL~g~-e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~~l~  370 (379)
                      .++.|..+|...|-.+.+ ....-.+||..+|++...|..+....+.+.|+...
T Consensus         8 ft~~Ql~~Le~~F~~n~yP~~~~r~~LA~~l~L~~~~V~~WFqNrR~k~kr~~~   61 (68)
T d2cuea1           8 FTQEQIEALEKEFERTHYPDVFARERLAAKIDLPEARIQVWFSNRRAKWRREEK   61 (68)
T ss_dssp             SCHHHHHHHHHHHTTCSSCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHHcCCCCHHHHHHHHHHhCcChhheeecCcchhHHHHhhhh
Confidence            678888999988743321 22456789999999999999999998888887543

>d1k61a_ a.4.1.1 (A:) mat alpha2 Homeodomain {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: mat alpha2 Homeodomain
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=81.86  E-value=1.3  Score=29.45  Aligned_cols=51  Identities=18%  Similarity=0.144  Sum_probs=37.9

Q ss_pred             cCCHHHHHHHHHHhhcCC----CCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHh
Q 046578          317 TLSEREADILRLHFGLDG----QTPVSCKEIGRLLSLSRERIRQIRGIALTKLQQ  367 (379)
Q Consensus       317 ~L~~rer~Vl~l~ygL~g----~e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~  367 (379)
                      ++++.+..+|...|.-+.    ....-..+||..+|++...|..+...++.+.|.
T Consensus         4 Rft~~q~~~L~~~f~~~~~~pyPs~~e~~~La~~~gL~~~qV~~WF~N~R~r~K~   58 (60)
T d1k61a_           4 RFTKENVRILESWFAKNIENPYLDTKGLENLMKNTSLSRIQIKNWVSNRRRKEKT   58 (60)
T ss_dssp             SCCHHHHHHHHHHHHHTTTSCCCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHC
T ss_pred             CCCHHHHHHHHHHHHHcCCCCCcCHHHHHHHHHHHCcCHHHHhHHhHhhcccccc
Confidence            578889999887763211    011224569999999999999999999988764

>d3deua1 a.4.5.28 (A:2-141) Transcriptional regulator SlyA {Salmonella typhimurium [TaxId: 90371]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MarR-like transcriptional regulators
domain: Transcriptional regulator SlyA
species: Salmonella typhimurium [TaxId: 90371]

Probab=81.79  E-value=1.9  Score=33.05  Aligned_cols=51  Identities=10%  Similarity=0.080  Sum_probs=37.8

Q ss_pred             HHHHHHHh--cCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 046578          309 QELKELLQ--TLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIA  361 (379)
Q Consensus       309 ~~L~~~L~--~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rA  361 (379)
                      ..+.+.+.  .|++.|..++...+-.  .++.|..+||+.+++++++|++.+.+-
T Consensus        18 ~~~~~~l~~~glt~~~~~~L~~l~~~--~~~~t~~~la~~l~i~~~~vs~~l~~L   70 (140)
T d3deua1          18 ALIDHRLKPLELTQTHWVTLHNIHQL--PPDQSQIQLAKAIGIEQPSLVRTLDQL   70 (140)
T ss_dssp             HHHHHHTTTTTCCHHHHHHHHHHHHS--CSSEEHHHHHHHHTSCHHHHHHHHHHH
T ss_pred             HHHHHHHHHcCCCHHHHHHHHHHHHc--CCCccHHHHHHHHCCCHhHHHHHHHHH
Confidence            34555555  5888888888765421  257999999999999999998765553

>d1ftta_ a.4.1.1 (A:) Thyroid transcription factor 1 homeodomain {Rat (Rattus norvegicus) [TaxId: 10116]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Thyroid transcription factor 1 homeodomain
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=81.14  E-value=1.4  Score=30.12  Aligned_cols=54  Identities=9%  Similarity=0.103  Sum_probs=41.5

Q ss_pred             cCCHHHHHHHHHHhhcCCC-CCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhHHh
Q 046578          317 TLSEREADILRLHFGLDGQ-TPVSCKEIGRLLSLSRERIRQIRGIALTKLQQTNI  370 (379)
Q Consensus       317 ~L~~rer~Vl~l~ygL~g~-e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~~l~  370 (379)
                      .+++.|..+|.-.|-.+-+ ....-.+||..+|++...|..+...-+.+.|+...
T Consensus         8 ~ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~l~L~~~~V~~WFqNrR~k~kk~~~   62 (68)
T d1ftta_           8 LFSQAQVYELERRFKQQKYLSAPEREHLASMIHLTPTQVKIWFQNHRYKMKRQAK   62 (68)
T ss_dssp             SCCHHHHHHHHHHHHHSSSCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHTTS
T ss_pred             CCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhCCCccceeeecccHHHHHhhccc
Confidence            3678888888887743321 22345789999999999999999999999987643

>d2r1jl1 a.35.1.2 (L:3-68) P22 C2 repressor, DNA-binding domain {Salmonella bacteriophage P22 [TaxId: 10754]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: Phage repressors
domain: P22 C2 repressor, DNA-binding domain
species: Salmonella bacteriophage P22 [TaxId: 10754]

Probab=80.91  E-value=0.53  Score=31.76  Aligned_cols=24  Identities=17%  Similarity=0.296  Sum_probs=21.9

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHH
Q 046578          336 TPVSCKEIGRLLSLSRERIRQIRG  359 (379)
Q Consensus       336 e~~S~~EIAe~LgiS~~~Vr~~~~  359 (379)
                      .++|+.++|+.+|+|+++++++.+
T Consensus        15 ~g~tq~~lA~~~gvs~~~i~~~e~   38 (66)
T d2r1jl1          15 LKIRQAALGKMVGVSNVAISQWER   38 (66)
T ss_dssp             HTCCHHHHHHHHTSCHHHHHHHHT
T ss_pred             cCCCHHHHHHHHCCCHHHHHHHHc
Confidence            459999999999999999999875

>d1lmb3_ a.35.1.2 (3:) lambda C1 repressor, DNA-binding domain {Bacteriophage lambda [TaxId: 10710]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: Phage repressors
domain: lambda C1 repressor, DNA-binding domain
species: Bacteriophage lambda [TaxId: 10710]

Probab=80.73  E-value=0.51  Score=34.00  Aligned_cols=24  Identities=4%  Similarity=0.145  Sum_probs=21.8

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHH
Q 046578          336 TPVSCKEIGRLLSLSRERIRQIRG  359 (379)
Q Consensus       336 e~~S~~EIAe~LgiS~~~Vr~~~~  359 (379)
                      .|+|++++|+.+|+|.++|+++.+
T Consensus        24 ~gltq~~lA~~lgis~~~is~~E~   47 (87)
T d1lmb3_          24 LGLSQESVADKMGMGQSGVGALFN   47 (87)
T ss_dssp             HTCCHHHHHHHHTSCHHHHHHHHT
T ss_pred             cCCCHHHHHHHhCccHHHHHHHHh
Confidence            459999999999999999999874

>d2fbia1 a.4.5.28 (A:5-140) Probable transcriptional regulator PA4135 {Pseudomonas aeruginosa [TaxId: 287]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MarR-like transcriptional regulators
domain: Probable transcriptional regulator PA4135
species: Pseudomonas aeruginosa [TaxId: 287]

Probab=80.68  E-value=0.95  Score=34.84  Aligned_cols=42  Identities=12%  Similarity=0.176  Sum_probs=34.9

Q ss_pred             cCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 046578          317 TLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIA  361 (379)
Q Consensus       317 ~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rA  361 (379)
                      .|++.|..||.....   ..+.|..|||+.++++.++|++.+.+-
T Consensus        27 glt~~q~~vL~~l~~---~~~~t~~~la~~~~i~~~~vs~~i~~L   68 (136)
T d2fbia1          27 GLTEQQWRVIRILRQ---QGEMESYQLANQACILRPSMTGVLARL   68 (136)
T ss_dssp             TCCHHHHHHHHHHHH---HCSEEHHHHHHHTTCCHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHH---cCCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence            699999999986553   256999999999999999998876654

>d1ulya_ a.4.5.58 (A:) Hypothetical protein PH1932 {Pyrococcus horikoshii [TaxId: 53953]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Hypothetical protein PH1932
domain: Hypothetical protein PH1932
species: Pyrococcus horikoshii [TaxId: 53953]

Probab=80.66  E-value=1.1  Score=36.57  Aligned_cols=38  Identities=13%  Similarity=0.207  Sum_probs=29.4

Q ss_pred             CHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 046578          319 SEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGI  360 (379)
Q Consensus       319 ~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~r  360 (379)
                      +|.-++||.+..    ..++|..|||+.+|+|+++|++++..
T Consensus        18 ~p~R~~Il~~L~----~~~~s~~ela~~lg~s~~~v~~hl~~   55 (190)
T d1ulya_          18 EDTRRKILKLLR----NKEMTISQLSEILGKTPQTIYHHIEK   55 (190)
T ss_dssp             SHHHHHHHHHHT----TCCBCHHHHHHHHTCCHHHHHHHHHH
T ss_pred             CHHHHHHHHHHH----hCCCCHHHHHHHHCcCHHHHHHHHHH
Confidence            456666776543    25799999999999999999987543

>d2ev0a1 a.4.5.24 (A:2-62) Manganese transport regulator MntR {Bacillus subtilis [TaxId: 1423]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Iron-dependent repressor protein
domain: Manganese transport regulator MntR
species: Bacillus subtilis [TaxId: 1423]

Probab=80.65  E-value=1.2  Score=29.83  Aligned_cols=25  Identities=8%  Similarity=0.133  Sum_probs=20.8

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHHH
Q 046578          336 TPVSCKEIGRLLSLSRERIRQIRGI  360 (379)
Q Consensus       336 e~~S~~EIAe~LgiS~~~Vr~~~~r  360 (379)
                      ..-+..+||+.||+|+.+|...++|
T Consensus        20 ~~v~~~~iA~~L~vs~~SVs~mikr   44 (61)
T d2ev0a1          20 GYARVSDIAEALAVHPSSVTKMVQK   44 (61)
T ss_dssp             SSCCHHHHHHHHTCCHHHHHHHHHH
T ss_pred             CCccHHHHHHHhCCCchhHHHHHHH
Confidence            4578999999999999999766443

>d9anta_ a.4.1.1 (A:) Antennapedia Homeodomain {Drosophila melanogaster [TaxId: 7227]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Antennapedia Homeodomain
species: Drosophila melanogaster [TaxId: 7227]

Probab=80.47  E-value=1.9  Score=28.24  Aligned_cols=50  Identities=20%  Similarity=0.137  Sum_probs=38.0

Q ss_pred             CCHHHHHHHHHHhhcCCC-CCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHh
Q 046578          318 LSEREADILRLHFGLDGQ-TPVSCKEIGRLLSLSRERIRQIRGIALTKLQQ  367 (379)
Q Consensus       318 L~~rer~Vl~l~ygL~g~-e~~S~~EIAe~LgiS~~~Vr~~~~rAl~kLR~  367 (379)
                      .++.|..+|...|-.+-. ....-.+||..+|++...|..+...-+.|.|+
T Consensus         4 ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~~V~iWFQNrRak~kk   54 (56)
T d9anta_           4 YTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKK   54 (56)
T ss_dssp             CCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCChhHeeeccccchhhhhh
Confidence            577888888887743311 12335689999999999999999998888775

>d1ic8a2 a.35.1.1 (A:87-180) Hepatocyte nuclear factor 1a (LFB1/HNF1) {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: POU-specific domain
domain: Hepatocyte nuclear factor 1a (LFB1/HNF1)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=80.40  E-value=3.6  Score=29.74  Aligned_cols=60  Identities=20%  Similarity=0.225  Sum_probs=42.9

Q ss_pred             CChHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 046578          296 TMPERMVQKQLMKQELKELLQTLSEREADILRLHFGLDGQTPVSCKEIGRLLSLSRERIRQIRGIA  361 (379)
Q Consensus       296 ~~pe~~~~~~e~~~~L~~~L~~L~~rer~Vl~l~ygL~g~e~~S~~EIAe~LgiS~~~Vr~~~~rA  361 (379)
                      .+|++..+.   ...|.+++..=+..-.+.|..+..   ....++.+||+..|+|.+.|++.+.++
T Consensus         6 ~~~eE~~~~---~~eVE~llr~d~~~v~~~IK~Fl~---~h~I~Q~~Va~~TGlsQS~iSq~L~~g   65 (94)
T d1ic8a2           6 LSPEEAAHQ---KAVVETLLQEDPWRVAKMVKSYLQ---QHNIPQREVVDTTGLNQSHLSQHLNKG   65 (94)
T ss_dssp             CCHHHHHHH---HHHHHHHTTSCHHHHHHHHHHHHH---HTTCCHHHHHHHHCCCHHHHHHHHHSB
T ss_pred             cCchhHhHH---HHHHHHHHhcCHHHHHHHHHHHHH---HcCCcHHHHHHHHcccHHHHHHHHhCC
Confidence            356664443   335667666656666666665442   366999999999999999999998874

>d1umqa_ a.4.1.12 (A:) Photosynthetic apparatus regulatory protein PprA (RegA), DNA-binding domain {Rhodobacter sphaeroides [TaxId: 1063]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: FIS-like
domain: Photosynthetic apparatus regulatory protein PprA (RegA), DNA-binding domain
species: Rhodobacter sphaeroides [TaxId: 1063]

Probab=80.40  E-value=0.72  Score=30.82  Aligned_cols=23  Identities=22%  Similarity=0.361  Sum_probs=19.4

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHHH
Q 046578          337 PVSCKEIGRLLSLSRERIRQIRG  359 (379)
Q Consensus       337 ~~S~~EIAe~LgiS~~~Vr~~~~  359 (379)
                      +-...+.|+.||||+.|+++.+.
T Consensus        33 ~gn~~~aA~~LGIsR~TL~rkmk   55 (60)
T d1umqa_          33 DRNVSETARRLNMHRRTLQRILA   55 (60)
T ss_dssp             TSCHHHHHHHHTSCHHHHHHHHH
T ss_pred             cCcHHHHHHHHCCCHHHHHHHHH
Confidence            36788999999999999987654