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Conserved domains on  [gi|15607323|ref|NP_214696|]
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ECF RNA polymerase sigma factor SigG [Mycobacterium tuberculosis H37Rv]

Protein Classification

sigma-70 family RNA polymerase sigma factor( domain architecture ID 11483180)

sigma-70 family RNA polymerase sigma factor such as Mycobacterium tuberculosis ECF RNA polymerase sigma factor SigG; sigma factors are initiation factors that promote the attachment of RNA polymerase to specific initiation sites and are then released

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PRK08241 PRK08241
RNA polymerase subunit sigma-70;
49-370 0e+00

RNA polymerase subunit sigma-70;


:

Pssm-ID: 236196 [Multi-domain]  Cd Length: 339  Bit Score: 524.12  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15607323   49 EPADERRGDFSAHTEPYRRELLAHCYRMTGSLHDAEDLVQETLLRAWKAYEGFAGKSSLRTWLHRIATNTCLTALEGRRR 128
Cdd:PRK08241  12 RAAAGDRDAFAALVEPHRRELLAHCYRMLGSVHDAEDAVQETLLRAWRGYDRFEGRSSLRTWLYRIATNVCLDALEGRAR 91

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15607323  129 RPLPTGLGRPSADPSGELVERREVSWLEPLPDVTDDP--ADPSTIVGNRESVRLAFVAALQHLSPRQRAVLLLRDVLQWK 206
Cdd:PRK08241  92 RPLPTDLGAPAADPVDELVERPEVPWLEPYPDALLDPaaADPAARVVARESVRLAFVAALQHLPPRQRAVLILRDVLGWS 171

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15607323  207 SAEVADAIGTSTVAVNSLLQRARSQLQTVRPSAADRLSAPDSPEAQDLLARYIAAFEAYDIDRLVELFTAEAIWEMPPYT 286
Cdd:PRK08241 172 AAEVAELLDTSVAAVNSALQRARATLAERGPSAADTLREPDDPEERALLARYVAAFEAYDVDALVALLTEDATWSMPPFP 251

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15607323  287 GWYQGAQAIVTLIHQQCPAYSPGDMRLISLIANGQPAAAMYMRAGD--VHLPFQLHVLDMAADRVSHVVAFLDTTLFPKF 364
Cdd:PRK08241 252 LWYRGRDAIAAFLAGQCPGAGCGGSRLVPTRANGQPAFAQYMRDPDggGHRPWALHVLELRGGRIAHVTSFLDTTLFPRF 331


                 ....*.
gi 15607323  365 GLPDSL 370
Cdd:PRK08241 332 GLPATL 337
 
Name Accession Description Interval E-value
PRK08241 PRK08241
RNA polymerase subunit sigma-70;
49-370 0e+00

RNA polymerase subunit sigma-70;


Pssm-ID: 236196 [Multi-domain]  Cd Length: 339  Bit Score: 524.12  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15607323   49 EPADERRGDFSAHTEPYRRELLAHCYRMTGSLHDAEDLVQETLLRAWKAYEGFAGKSSLRTWLHRIATNTCLTALEGRRR 128
Cdd:PRK08241  12 RAAAGDRDAFAALVEPHRRELLAHCYRMLGSVHDAEDAVQETLLRAWRGYDRFEGRSSLRTWLYRIATNVCLDALEGRAR 91

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15607323  129 RPLPTGLGRPSADPSGELVERREVSWLEPLPDVTDDP--ADPSTIVGNRESVRLAFVAALQHLSPRQRAVLLLRDVLQWK 206
Cdd:PRK08241  92 RPLPTDLGAPAADPVDELVERPEVPWLEPYPDALLDPaaADPAARVVARESVRLAFVAALQHLPPRQRAVLILRDVLGWS 171

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15607323  207 SAEVADAIGTSTVAVNSLLQRARSQLQTVRPSAADRLSAPDSPEAQDLLARYIAAFEAYDIDRLVELFTAEAIWEMPPYT 286
Cdd:PRK08241 172 AAEVAELLDTSVAAVNSALQRARATLAERGPSAADTLREPDDPEERALLARYVAAFEAYDVDALVALLTEDATWSMPPFP 251

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15607323  287 GWYQGAQAIVTLIHQQCPAYSPGDMRLISLIANGQPAAAMYMRAGD--VHLPFQLHVLDMAADRVSHVVAFLDTTLFPKF 364
Cdd:PRK08241 252 LWYRGRDAIAAFLAGQCPGAGCGGSRLVPTRANGQPAFAQYMRDPDggGHRPWALHVLELRGGRIAHVTSFLDTTLFPRF 331


                 ....*.
gi 15607323  365 GLPDSL 370
Cdd:PRK08241 332 GLPATL 337
SigX5 TIGR02960
RNA polymerase sigma-70 factor, TIGR02960 family; This group of sigma factors are members of ...
 55-366 1.93e-156

RNA polymerase sigma-70 factor, TIGR02960 family; 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.


Pssm-ID: 132005 [Multi-domain]  Cd Length: 324  Bit Score: 442.38  E-value: 1.93e-156
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15607323    55 RGDFSAHTEPYRRELLAHCYRMTGSLHDAEDLVQETLLRAWKAYEGFAGKSSLRTWLHRIATNTCLTALEGRRRRPLPTG 134
Cdd:TIGR02960   4 GAAFTALAEPHRRELLAHCYRMLGSLHEAEDLVQETLLRAWRARDRFEGRSSVRTWLYRIATNACLDALEARQRRPRPVG 83

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15607323   135 LGRPSADPSGELVERREVSWLEPLPDVT---DDP--ADPSTIVGNRESVRLAFVAALQHLSPRQRAVLLLRDVLQWKSAE 209
Cdd:TIGR02960  84 LGAPSADGTAAASEAAEVTWLEPLPDLTldlDDPaaADPSVAAGSRESVRLAFVAAIQYLPPRQRAVLLLRDVLGWRAAE 163

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15607323   210 VADAIGTSTVAVNSLLQRARSQLQTVRPSA-ADRLSAPDSPEAQDLLARYIAAFEAYDIDRLVELFTAEAIWEMPPYTGW 288
Cdd:TIGR02960 164 TAELLGTSTASVNSALQRARATLDEVGPSArDDQLAQPPSPEEQDLLERYIAAFESYDLDALTALLHEDAIWEMPPYTLW 243

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15607323   289 YQGAQAIVTLIHQQCPAYSPGDMRLISLIANGQPAAAMYMRAGDV--HLPFQLHVLDMAADRVSHVVAFLDT-TLFPKFG 365
Cdd:TIGR02960 244 YQGRPAIVGFIHTVCPGEGAAGMRLLPTIANGQPAAAMYMRRPDAerHTAFQLHVLEIRGGRITHVTAFLDGpSLFAAFG 323


                  .
gi 15607323   366 L 366
Cdd:TIGR02960 324 L 324
RpoE COG1595
DNA-directed RNA polymerase specialized sigma subunit, sigma24 family [Transcription]; ...
 54-233 6.45e-38

DNA-directed RNA polymerase specialized sigma subunit, sigma24 family [Transcription]; DNA-directed RNA polymerase specialized sigma subunit, sigma24 family is part of the Pathway/BioSystem: RNA polymerase


Pssm-ID: 441203 [Multi-domain]  Cd Length: 181  Bit Score: 134.35  E-value: 6.45e-38
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15607323  54 RRGD---FSAHTEPYRRELLAHCYRMTGSLHDAEDLVQETLLRAWKAYEGFAGKSSLRTWLHRIATNTCLTALegRRRRp 130
Cdd:COG1595  12 RAGDeaaFEELYERYRPRLYRYARRLLGDRADAEDLVQETFLRLWRKLDSFRGRGSFRAWLYRIARNLAIDHL--RKRR- 88

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15607323 131 lptglgrpsadpsgelveRREVSWLEPLPDVTDDPADPSTIVGNREsVRLAFVAALQHLSPRQRAVLLLRDVLQWKSAEV 210
Cdd:COG1595  89 ------------------RRRELLDELAEELPDEAADPEEALEAEE-LLEALLAALERLPPRQREVLVLRYLEGLSYAEI 149

                       170       180
                ....*....|....*....|...
gi 15607323 211 ADAIGTSTVAVNSLLQRARSQLQ 233
Cdd:COG1595 150 AEILGISEGTVKSRLSRARKKLR 172
Sigma70_r2 pfam04542
Sigma-70 region 2; Region 2 of sigma-70 is the most conserved region of the entire protein. ...
 63-129 3.42e-16

Sigma-70 region 2; 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.


Pssm-ID: 427998 [Multi-domain]  Cd Length: 71  Bit Score: 72.24  E-value: 3.42e-16
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 15607323    63 EPYRRELLAHCYRMTGSLHDAEDLVQETLLRAWKAYEGF--AGKSSLRTWLHRIATNTCLTALEGRRRR 129
Cdd:pfam04542   3 ERYLPLVYSLARRYLGDGADAEDLVQEGFLGLWRAIERFdpERGVSFSTWLYTIIRNAIIDYLRKQRRT 71
Sigma70_r4 cd06171
Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in ...
 185-233 7.06e-08

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). 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).


Pssm-ID: 100119 [Multi-domain]  Cd Length: 55  Bit Score: 48.64  E-value: 7.06e-08
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*....
gi 15607323 185 ALQHLSPRQRAVLLLRDVLQWKSAEVADAIGTSTVAVNSLLQRARSQLQ 233
Cdd:cd06171   7 ALDKLPEREREVILLRFGEGLSYEEIAEILGISRSTVRQRLHRALKKLR 55
 
Name Accession Description Interval E-value
PRK08241 PRK08241
RNA polymerase subunit sigma-70;
49-370 0e+00

RNA polymerase subunit sigma-70;


Pssm-ID: 236196 [Multi-domain]  Cd Length: 339  Bit Score: 524.12  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15607323   49 EPADERRGDFSAHTEPYRRELLAHCYRMTGSLHDAEDLVQETLLRAWKAYEGFAGKSSLRTWLHRIATNTCLTALEGRRR 128
Cdd:PRK08241  12 RAAAGDRDAFAALVEPHRRELLAHCYRMLGSVHDAEDAVQETLLRAWRGYDRFEGRSSLRTWLYRIATNVCLDALEGRAR 91

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15607323  129 RPLPTGLGRPSADPSGELVERREVSWLEPLPDVTDDP--ADPSTIVGNRESVRLAFVAALQHLSPRQRAVLLLRDVLQWK 206
Cdd:PRK08241  92 RPLPTDLGAPAADPVDELVERPEVPWLEPYPDALLDPaaADPAARVVARESVRLAFVAALQHLPPRQRAVLILRDVLGWS 171

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15607323  207 SAEVADAIGTSTVAVNSLLQRARSQLQTVRPSAADRLSAPDSPEAQDLLARYIAAFEAYDIDRLVELFTAEAIWEMPPYT 286
Cdd:PRK08241 172 AAEVAELLDTSVAAVNSALQRARATLAERGPSAADTLREPDDPEERALLARYVAAFEAYDVDALVALLTEDATWSMPPFP 251

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15607323  287 GWYQGAQAIVTLIHQQCPAYSPGDMRLISLIANGQPAAAMYMRAGD--VHLPFQLHVLDMAADRVSHVVAFLDTTLFPKF 364
Cdd:PRK08241 252 LWYRGRDAIAAFLAGQCPGAGCGGSRLVPTRANGQPAFAQYMRDPDggGHRPWALHVLELRGGRIAHVTSFLDTTLFPRF 331


                 ....*.
gi 15607323  365 GLPDSL 370
Cdd:PRK08241 332 GLPATL 337
SigX5 TIGR02960
RNA polymerase sigma-70 factor, TIGR02960 family; This group of sigma factors are members of ...
 55-366 1.93e-156

RNA polymerase sigma-70 factor, TIGR02960 family; 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.


Pssm-ID: 132005 [Multi-domain]  Cd Length: 324  Bit Score: 442.38  E-value: 1.93e-156
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15607323    55 RGDFSAHTEPYRRELLAHCYRMTGSLHDAEDLVQETLLRAWKAYEGFAGKSSLRTWLHRIATNTCLTALEGRRRRPLPTG 134
Cdd:TIGR02960   4 GAAFTALAEPHRRELLAHCYRMLGSLHEAEDLVQETLLRAWRARDRFEGRSSVRTWLYRIATNACLDALEARQRRPRPVG 83

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15607323   135 LGRPSADPSGELVERREVSWLEPLPDVT---DDP--ADPSTIVGNRESVRLAFVAALQHLSPRQRAVLLLRDVLQWKSAE 209
Cdd:TIGR02960  84 LGAPSADGTAAASEAAEVTWLEPLPDLTldlDDPaaADPSVAAGSRESVRLAFVAAIQYLPPRQRAVLLLRDVLGWRAAE 163

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15607323   210 VADAIGTSTVAVNSLLQRARSQLQTVRPSA-ADRLSAPDSPEAQDLLARYIAAFEAYDIDRLVELFTAEAIWEMPPYTGW 288
Cdd:TIGR02960 164 TAELLGTSTASVNSALQRARATLDEVGPSArDDQLAQPPSPEEQDLLERYIAAFESYDLDALTALLHEDAIWEMPPYTLW 243

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15607323   289 YQGAQAIVTLIHQQCPAYSPGDMRLISLIANGQPAAAMYMRAGDV--HLPFQLHVLDMAADRVSHVVAFLDT-TLFPKFG 365
Cdd:TIGR02960 244 YQGRPAIVGFIHTVCPGEGAAGMRLLPTIANGQPAAAMYMRRPDAerHTAFQLHVLEIRGGRITHVTAFLDGpSLFAAFG 323


                  .
gi 15607323   366 L 366
Cdd:TIGR02960 324 L 324
RpoE COG1595
DNA-directed RNA polymerase specialized sigma subunit, sigma24 family [Transcription]; ...
 54-233 6.45e-38

DNA-directed RNA polymerase specialized sigma subunit, sigma24 family [Transcription]; DNA-directed RNA polymerase specialized sigma subunit, sigma24 family is part of the Pathway/BioSystem: RNA polymerase


Pssm-ID: 441203 [Multi-domain]  Cd Length: 181  Bit Score: 134.35  E-value: 6.45e-38
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15607323  54 RRGD---FSAHTEPYRRELLAHCYRMTGSLHDAEDLVQETLLRAWKAYEGFAGKSSLRTWLHRIATNTCLTALegRRRRp 130
Cdd:COG1595  12 RAGDeaaFEELYERYRPRLYRYARRLLGDRADAEDLVQETFLRLWRKLDSFRGRGSFRAWLYRIARNLAIDHL--RKRR- 88

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15607323 131 lptglgrpsadpsgelveRREVSWLEPLPDVTDDPADPSTIVGNREsVRLAFVAALQHLSPRQRAVLLLRDVLQWKSAEV 210
Cdd:COG1595  89 ------------------RRRELLDELAEELPDEAADPEEALEAEE-LLEALLAALERLPPRQREVLVLRYLEGLSYAEI 149

                       170       180
                ....*....|....*....|...
gi 15607323 211 ADAIGTSTVAVNSLLQRARSQLQ 233
Cdd:COG1595 150 AEILGISEGTVKSRLSRARKKLR 172
SigX4 TIGR02957
RNA polymerase sigma-70 factor, TIGR02957 family; This group of sigma factors are members of ...
 63-327 3.85e-33

RNA polymerase sigma-70 factor, TIGR02957 family; 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.


Pssm-ID: 132002 [Multi-domain]  Cd Length: 281  Bit Score: 124.77  E-value: 3.85e-33
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15607323    63 EPYRRELLAHCYRMTGSLHDAEDLVQETLLRAWKAYEgfAGKSSLRTWLHRIATNTCLTALEGRRRrplptglgrpsadp 142
Cdd:TIGR02957   4 EALRPLLFSLAYRMLGSVADAEDIVQETFLRWQEADR--AQIENPKAYLTKVVTRRCIDVLRSARA-------------- 67

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15607323   143 sgelveRREV---SWL-EPLPdvtDDPADPSTIVGNRESVRLAFVAALQHLSPRQRAVLLLRDVLQWKSAEVADAIGTST 218
Cdd:TIGR02957  68 ------RREVyvgPWLpEPLL---TTSADPAESVELAESLSMAYLLLLERLSPLERAVFVLREVFDYPYEEIASIVGKSE 138

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15607323   219 VAVNSLLQRARSQLQTVRPSaadrlSAPDSPEAQDLLARYIAAFEAYDIDRLVELFTAEAI-----------WEMPPYTG 287
Cdd:TIGR02957 139 ANCRQLVSRARRHLDARRPR-----FEVSREESRQLLERFVEAAQTGDLDGLLELLAEDVVlygdgggkvraALRPIYGA 213

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|
gi 15607323   288 wYQGAQAIVTLIHQQCPayspgDMRLISLIANGQPAAAMY 327
Cdd:TIGR02957 214 -DRVARFFFGLVRRLGP-----GGRVDPVDVNGQPAVLVR 247
PRK09636 PRK09636
RNA polymerase sigma factor SigJ; Provisional
 50-279 1.54e-32

RNA polymerase sigma factor SigJ; Provisional


Pssm-ID: 236600 [Multi-domain]  Cd Length: 293  Bit Score: 123.49  E-value: 1.54e-32
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15607323   50 PADERRGDFsahtEPYRRELLAHCYRMTGSLHDAEDLVQETLLRaWKAYEGfAGKSSLRTWLHRIATNTCLTALEGRRRR 129
Cdd:PRK09636   2 TMADAAAEF----EPLRPHLLSVAYRMLGSVADAEDIVQEAWLR-WNNADR-AQIRDPRAWLTRVVTRLCLDRLRSARHR 75

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15607323  130 plptglgrpsadpsgelverREV---SWLePLPDVTDDpADPSTIVGNRESVRLAFVAALQHLSPRQRAVLLLRDVLQWK 206
Cdd:PRK09636  76 --------------------RETyvgPWL-PEPVVEEL-DDPLEAVVAAEDLSLALMLALERLSPLERAAFLLHDVFGVP 133

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 15607323  207 SAEVADAIGTSTVAVNSLLQRARSQLQTVRPSaadrlSAPDSPEAQDLLARYIAAFEAYDIDRLVELFTAEAI 279
Cdd:PRK09636 134 FDEIASTLGRSPAACRQLASRARKHVRAARPR-----FPVSDEEGAELVEAFFAALASGDLDALVALLAPDVV 201
sigma70-ECF TIGR02937
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ...
 65-233 2.19e-30

RNA polymerase sigma factor, sigma-70 family; 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.


Pssm-ID: 274357 [Multi-domain]  Cd Length: 158  Bit Score: 113.60  E-value: 2.19e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15607323    65 YRRELLAHCYRMTGSLHDAEDLVQETLLRAWKAYEGFAGKSSLRTWLHRIATNTCLTALegRRRRplptglgrpsadpsg 144
Cdd:TIGR02937  10 YLPLVYRYARRYLGDDADAEDLVQEAFLKLLEALDRFDPEGSFKAWLFRIARNLILDYL--RRKR--------------- 72

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15607323   145 elVERREVSWLEPLPDVTDDPADPSTivgnRESVRLAFVAALQHLSPRQRAVLLLRDVLQWKSAEVADAIGTSTVAVNSL 224
Cdd:TIGR02937  73 --RLRRELDLLEELLDSDPSPEEELE----QEEEREALREALEKLPEREREVLVLRYLEGLSYKEIAEILGISVGTVKRR 146


                  ....*....
gi 15607323   225 LQRARSQLQ 233
Cdd:TIGR02937 147 LKRARKKLR 155
PRK11924 PRK11924
RNA polymerase sigma factor; Provisional
 63-232 2.93e-22

RNA polymerase sigma factor; Provisional


Pssm-ID: 183384 [Multi-domain]  Cd Length: 179  Bit Score: 92.34  E-value: 2.93e-22
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15607323   63 EPYRRELLAHCYRMTGSLHDAEDLVQETLLRAWKAYEGFAGKSSLRTWLHRIATNTCLTALEGRRRRPLptglgrpsadp 142
Cdd:PRK11924  20 RPHAPDLLRYARRQLGDRALAEDAVQEAFLRAWRKADLFNGKGSARTWLLTIARNVCYDLLRRRRREKA----------- 88

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15607323  143 sgelverrEVSWLEPLPDVTDDPADPSTIVGNRESVRlAFVAALQHLSPRQRAVLLLRDVLQWKSAEVADAIGTSTVAVN 222
Cdd:PRK11924  89 --------VLSDDALEPEFAETAETPEAALLAKDDLA-RIDRCLDALPVKQREVFLLRYVEGLSYREIAEILGVPVGTVK 159

                        170
                 ....*....|
gi 15607323  223 SLLQRARSQL 232
Cdd:PRK11924 160 SRLRRARQLL 169
PRK09652 PRK09652
RNA polymerase sigma factor RpoE; Provisional
 64-241 1.79e-21

RNA polymerase sigma factor RpoE; Provisional


Pssm-ID: 236608 [Multi-domain]  Cd Length: 182  Bit Score: 90.25  E-value: 1.79e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15607323   64 PYRRELLAHCYRMTGSLHDAEDLVQETLLRAWKAYEGFAGKSSLRTWLHRIATNTCLTALEGRRRRPlptglgrPSADPS 143
Cdd:PRK09652  18 RYQPRVKRLLSRLTRDPADAEDLVQETFIKAYRALHSFRGGAAFYTWLYRIARNTAINYLRKQGRRP-------PASDVD 90

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15607323  144 GELVERREVSwleplpDVTDDPADPSTIVGNRE---SVRlafvAALQHLSPRQRAVLLLRDVLQWKSAEVADAIGTSTVA 220
Cdd:PRK09652  91 AEEAEDFDLA------DALRDISTPENELLSAEleqRVR----AAIESLPEELRTAITLREIEGLSYEEIAEIMGCPIGT 160

                        170       180
                 ....*....|....*....|..
gi 15607323  221 VNSLLQRARSQLQT-VRPSAAD 241
Cdd:PRK09652 161 VRSRIFRAREALRAkLQPLLDE 182
SigE-fam_strep TIGR02983
RNA polymerase sigma-70 factor, sigma-E family; This group of similar sigma-70 factors ...
 51-234 1.05e-18

RNA polymerase sigma-70 factor, sigma-E family; 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.


Pssm-ID: 132028 [Multi-domain]  Cd Length: 162  Bit Score: 82.05  E-value: 1.05e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15607323    51 ADERRGDFSAHTEPYRRELLAHCYRMTGSLHDAEDLVQETLLRAWKAYEGFAGKSSLRTWLHRIATNTCLTALEGRRRRP 130
Cdd:TIGR02983   1 RSATEEEFTAFVAARYPRLLRTAYLLTGDPHEAEDLVQEALVRTYVRWDRIRDPDAPDAYVRRVLVNLARSRWRRRRLLE 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15607323   131 LPTglgrpsadpsgelverrevswlEPLPDVTDDPADPSTivgnreSVRLAFVAALQHLSPRQRAVLLLRDVLQWKSAEV 210
Cdd:TIGR02983  81 LPT----------------------RELPDAAAPDPAPDV------ALRAALARALRRLPARQRAVVVLRYYEDLSEAQV 132

                         170       180
                  ....*....|....*....|....
gi 15607323   211 ADAIGTSTVAVNSLLQRARSQLQT 234
Cdd:TIGR02983 133 AEALGISVGTVKSRLSRALARLRE 156
PRK05602 PRK05602
RNA polymerase sigma factor; Reviewed
 69-234 8.91e-18

RNA polymerase sigma factor; Reviewed


Pssm-ID: 235530 [Multi-domain]  Cd Length: 186  Bit Score: 80.47  E-value: 8.91e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15607323   69 LLAHCYRMTGSLHDAEDLVQETLLRAWKAYEGF-AGKSSLRTWLHRIATNTCLTALegRRRRPLPTglgrpsadpsgelv 147
Cdd:PRK05602  33 LLALATRMLGDPAEAEDVAQETFLRIWKQAPSWrPGEARFDTWLHRVVLNLCYDRL--RRRREVPV-------------- 96

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15607323  148 errevswlEPLPDVTDD-PADPSTIVGNRESVRLAfvAALQHLSPRQRAVLLLRDVLQWKSAEVADAIGTSTVAVNSLLQ 226
Cdd:PRK05602  97 --------EDAPDVPDPaPGPDAGLEARQRARRVE--QALAALPERQREAIVLQYYQGLSNIEAAAVMDISVDALESLLA 166


                 ....*...
gi 15607323  227 RARSQLQT 234
Cdd:PRK05602 167 RGRRALRA 174
Sig70_famx1 TIGR02943
RNA polymerase sigma-70 factor, TIGR02943 family; This group of sigma factors are members of ...
 59-234 1.32e-17

RNA polymerase sigma-70 factor, TIGR02943 family; 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.


Pssm-ID: 274359 [Multi-domain]  Cd Length: 188  Bit Score: 79.81  E-value: 1.32e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15607323    59 SAHTEPYRRELLaHCYRMtgSLHD---AEDLVQETLLRAWKAYEGFAGKSSLRTWLHRIATNTCLTALEGRRRRPLPTGL 135
Cdd:TIGR02943   5 PQELEQLRRDLL-RFARL--QLRDrdlAEDAVQETLLAALSHRDSFAGRSALKTWLFAILKNKIIDALRAKGREVKVSDL 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15607323   136 GRPSADPSGELVERREVSWleplpDVTDDPAD---PSTIVGNRESVRLaFVAALQHLSPRQRAVLLLRDVLQWKSAEVAD 212
Cdd:TIGR02943  82 DDELDDEAFNALFTQNGHW-----AQHGQPQHwntPEKQLENKEFWEV-FEACLYHLPEQTARVFMMREVLGFESDEICQ 155

                         170       180
                  ....*....|....*....|..
gi 15607323   213 AIGTSTVAVNSLLQRARSQLQT 234
Cdd:TIGR02943 156 ELEISTSNCHVLLYRARLSLRA 177
PRK09640 PRK09640
RNA polymerase sigma factor SigX; Reviewed
 64-233 6.16e-17

RNA polymerase sigma factor SigX; Reviewed


Pssm-ID: 236603 [Multi-domain]  Cd Length: 188  Bit Score: 78.06  E-value: 6.16e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15607323   64 PYRRELLAHCYRMTGSLHDAEDLVQETLLRAWKAYEGFAGKSSLRTWLHRIATNTCLTALEGRRRRplptglgrpsadps 143
Cdd:PRK09640  34 RYQRTLFNVCARYLGNDRDADDVCQEVMLKVLYGLKNFEGKSKFKTWLYSITYNECITQYRKERRK-------------- 99

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15607323  144 gelveRREVS--WLEPLPDVTDDPADpstivgnRESVRLAFVAALQHLSPRQRAVLLLRDVLQWKSAEVADAIGTSTVAV 221
Cdd:PRK09640 100 -----RRLMDalSLDPLEEASEEKAP-------KPEERGGLDRWLVHVNPIDREILVLRFVAELEFQEIADIMHMGLSAT 167

                        170
                 ....*....|..
gi 15607323  222 NSLLQRARSQLQ 233
Cdd:PRK09640 168 KMRYKRALDKLR 179
PRK11922 PRK11922
RNA polymerase sigma factor; Provisional
 82-232 1.69e-16

RNA polymerase sigma factor; Provisional


Pssm-ID: 237024 [Multi-domain]  Cd Length: 231  Bit Score: 77.70  E-value: 1.69e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15607323   82 DAEDLVQETLLRAWKAYEGFAGKSSLRTWLHRIATNTCLTALEGRRRRPLPtglgrpsADPSGELVERREVSWLEPLPDv 161
Cdd:PRK11922  56 EAEDVVQEAYLRAFRALGTFRGDASLSTWLSRIVLNEALGRLRRRRRLVNL-------AEMVMASTIAGGERTPLADPA- 127

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 15607323  162 tddpADPSTIVGNRESVRLaFVAALQHLSPRQRAVLLLRDVLQWKSAEVADAIGTSTVAVNSLLQRARSQL 232
Cdd:PRK11922 128 ----EDPERAAARREIRAL-LERAIDALPDAFRAVFVLRVVEELSVEETAQALGLPEETVKTRLHRARRLL 193
Sigma70_r2 pfam04542
Sigma-70 region 2; Region 2 of sigma-70 is the most conserved region of the entire protein. ...
 63-129 3.42e-16

Sigma-70 region 2; 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.


Pssm-ID: 427998 [Multi-domain]  Cd Length: 71  Bit Score: 72.24  E-value: 3.42e-16
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 15607323    63 EPYRRELLAHCYRMTGSLHDAEDLVQETLLRAWKAYEGF--AGKSSLRTWLHRIATNTCLTALEGRRRR 129
Cdd:pfam04542   3 ERYLPLVYSLARRYLGDGADAEDLVQEGFLGLWRAIERFdpERGVSFSTWLYTIIRNAIIDYLRKQRRT 71
Sig-70_gvs1 TIGR02989
RNA polymerase sigma-70 factor, Rhodopirellula/Verrucomicrobium family; This group of sigma ...
 65-234 3.06e-15

RNA polymerase sigma-70 factor, Rhodopirellula/Verrucomicrobium family; 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).


Pssm-ID: 274379 [Multi-domain]  Cd Length: 159  Bit Score: 72.35  E-value: 3.06e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15607323    65 YRRELLAHCYRMTGSLHDAEDLVQETLLRAWKAYEGFAGKSSLRTWLHRIATNTCLTALEGRRRRplptglgrpsadpsg 144
Cdd:TIGR02989  10 HERALRAFVRSLVADRDDVDDVLQETFVVAWRKFDQFDPGTNFVAWARGIARNKVLNYRRKLGRD--------------- 74

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15607323   145 ELVERREVswLEPLPDVTDDPADPStivgnRESVRLAFVAALQHLSPRQRAVLLLRDVLQWKSAEVADAIGTSTVAVNSL 224
Cdd:TIGR02989  75 RLVFDDDL--LEALAAEAEPTEAER-----LSDDRQALEGCLEKLPERQRELLDLRYQRGQKATALAEQTGRTVNAVYKA 147

                         170
                  ....*....|
gi 15607323   225 LQRARSQLQT 234
Cdd:TIGR02989 148 LQRIRVSLRE 157
PRK09641 PRK09641
RNA polymerase sigma factor SigW; Provisional
 54-130 5.96e-15

RNA polymerase sigma factor SigW; Provisional


Pssm-ID: 182012 [Multi-domain]  Cd Length: 187  Bit Score: 72.42  E-value: 5.96e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15607323   54 RRGD---FSAHTEPYRRELLAHCYRMTGSLHDAEDLVQETLLRAWKAYEGFAGKSSLRTWLHRIATNTCLTALegRRRRP 130
Cdd:PRK09641  13 KKGDqnaFAELVDLYKDKIYQLCYRMLGNRHEAEDAAQEAFIRAYVNIDSYDINRKFSTWLYRIATNLTIDRL--RKRKP 90
YesE COG3631
Ketosteroid isomerase-related protein [General function prediction only];
250-358 8.56e-15

Ketosteroid isomerase-related protein [General function prediction only];


Pssm-ID: 442849  Cd Length: 126  Bit Score: 70.34  E-value: 8.56e-15
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15607323 250 EAQDLLARYIAAFEAYDIDRLVELFTAEAIWEMP--PYTGWYQGAQAIVTLIHQQCPAYSPGDMRLISLIANGQPAAA-- 325
Cdd:COG3631   1 TNRELVRRFYAAFNAGDVDALLALLAEDVVWEDPggPGAGTYRGKEAVRAFFARLAAAFEDLRFEVRRVVADGDRVVVeg 80

                        90       100       110
                ....*....|....*....|....*....|....*...
gi 15607323 326 ----MYMRAG-DVHLPFqLHVLDMAADRVSHVVAFLDT 358
Cdd:COG3631  81 tvrgTVLATGkPYENRY-ADVFTVRDGKIVRVREYFDT 117
PRK09643 PRK09643
RNA polymerase sigma factor SigM; Reviewed
 65-233 2.14e-14

RNA polymerase sigma factor SigM; Reviewed


Pssm-ID: 236604 [Multi-domain]  Cd Length: 192  Bit Score: 70.89  E-value: 2.14e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15607323   65 YRRELLAHCYRMTGSLHDAEDLVQETLLRAWKAYEGFAGKSSLRTWLHRIATNTCLTALegRRRRPLPTglgrpsadpsg 144
Cdd:PRK09643  36 HHRRLWAVARRTSGTREDAADALQDAMLSAHRAAGSFRGDAAVSSWLHRIVVNACLDRL--RRAKARPT----------- 102

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15607323  145 elverrevswlEPLPDVTDDPADPSTIVGnRESVRLAFVAALQHLSPRQRAVLLLRDVLQWKSAEVADAIGTSTVAVNSL 224
Cdd:PRK09643 103 -----------VPLDDVYPVAQLERDPTA-RVETALAVQRALMRLPVEQRAALVAVDMQGYSVADAARMLGVAEGTVKSR 170


                 ....*....
gi 15607323  225 LQRARSQLQ 233
Cdd:PRK09643 171 CARGRARLA 179
PRK09647 PRK09647
RNA polymerase sigma factor SigE; Reviewed
 74-256 3.47e-14

RNA polymerase sigma factor SigE; Reviewed


Pssm-ID: 236606 [Multi-domain]  Cd Length: 203  Bit Score: 70.59  E-value: 3.47e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15607323   74 YRMTGSLHDAEDLVQETLLRAWKAYEGFAgKSSLRTWLHRIATNTCLTALegRRRrplptglGRPSADPSGELVERREVS 153
Cdd:PRK09647  46 YRLSGNQHDAEDLTQETFIRVFRSLQNYQ-PGTFEGWLHRITTNLFLDMV--RRR-------ARIRMEALPEDYDRVPGD 115

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15607323  154 WLEPLPDVTDDPADPstivgnresvrlAFVAALQHLSPRQRAVLLLRDVLQWKSAEVADAIGTSTVAVNSLLQRARSQLq 233
Cdd:PRK09647 116 EPNPEQIYHDARLDP------------DLQAALDSLPPEFRAAVVLCDIEGLSYEEIAATLGVKLGTVRSRIHRGRQQL- 182

                        170       180
                 ....*....|....*....|...
gi 15607323  234 tvRPSAADRlsAPDSPEAQDLLA 256
Cdd:PRK09647 183 --RAALAAH--APHAECAALLNP 201
PRK12524 PRK12524
RNA polymerase sigma factor; Provisional
 42-232 4.84e-14

RNA polymerase sigma factor; Provisional


Pssm-ID: 183573 [Multi-domain]  Cd Length: 196  Bit Score: 69.92  E-value: 4.84e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15607323   42 LAENSGREPADER------RGDFSAHTEPYRR---ELLAHCYRMTGSLHDAEDLVQETLLRAWKAYEGF-AGKSSLRTWL 111
Cdd:PRK12524   3 MPFDALSDVSDEAllvlyaNGDPAAARALTLRlapRALAVATRVLGDRAEAEDVTQEAMLRLWRIAPDWrQGEARVSTWL 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15607323  112 HRIATNTCLTALEGRRRRplptglgrpSADpsgelverrevswLEPLPDVTDD--PADPSTIVGNResvRLAFVAALQHL 189
Cdd:PRK12524  83 YRVVCNLCTDRLRRRRRA---------SVD-------------LDDAPEPADAapGAEEALIEGDR---MRALDAALAAL 137

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|...
gi 15607323  190 SPRQRAVLLLRDVLQWKSAEVADAIGTSTVAVNSLLQRARSQL 232
Cdd:PRK12524 138 PERQRQAVVLRHIEGLSNPEIAEVMEIGVEAVESLTARGKRAL 180
SigW_bacill TIGR02948
RNA polymerase sigma-W factor; This sigma factor is restricted to certain lineages of the ...
 54-233 7.02e-14

RNA polymerase sigma-W factor; This sigma factor is restricted to certain lineages of the order Bacillales.


Pssm-ID: 131993 [Multi-domain]  Cd Length: 187  Bit Score: 69.54  E-value: 7.02e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15607323    54 RRGD---FSAHTEPYRRELLAHCYRMTGSLHDAEDLVQETLLRAWKAYEGFAGKSSLRTWLHRIATNTCLTALegRRRRP 130
Cdd:TIGR02948  13 RKGDenaFADLVDLYKDKIYQLCYRMLGNVHEAEDVAQEAFIRAYTNIDTYDIQRKFSTWLYRIATNLTIDRL--RKRKP 90

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15607323   131 lPTGLGRPSADPSGELVERREVSWLEPlpdvtddPADPSTIVGNRESVRlafvAALQHLSPRQRAVLLLRDVLQWKSAEV 210
Cdd:TIGR02948  91 -DFYLDDEVQGTDGLTMESQLAADEAP-------PEDQVISLELRDTIQ----QEIQALPPKYRMVIVLKYMEDLSLKEI 158

                         170       180
                  ....*....|....*....|...
gi 15607323   211 ADAIGTSTVAVNSLLQRARSQLQ 233
Cdd:TIGR02948 159 SEILDLPVGTVKTRIHRGREALR 181
sigI PRK09635
RNA polymerase sigma factor SigI; Provisional
 65-273 8.75e-14

RNA polymerase sigma factor SigI; Provisional


Pssm-ID: 182008 [Multi-domain]  Cd Length: 290  Bit Score: 71.15  E-value: 8.75e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15607323   65 YRRELLAHCYRMTGSLHDAEDLVQETLLRAWKAYEGfaGKSSLRTWLHRIATNTCLTALE-GRRRRPLPTGLGrpsadps 143
Cdd:PRK09635  14 HRAYLVDLAFRMVGDIGVAEDMVQEAFSRLLRAPVG--DIDDERGWLIVVTSRLCLDHIKsASTRRERPQDIA------- 84

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15607323  144 gelverrEVSWLEPLPDVTDdPADPSTIvgnRESVRLAFVAALQHLSPRQRAVLLLRDVLQWKSAEVADAIGTSTVAVNS 223
Cdd:PRK09635  85 -------AWHDGDASVSSVD-PADRVTL---DDEVRLALLIMLERLGPAERVVFVLHEIFGLPYQQIATTIGSQASTCRQ 153

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|
gi 15607323  224 LLQRARSQLQTVRPSAadrlsAPDSPEAQDLLARYIAAFEAYDIDRLVEL 273
Cdd:PRK09635 154 LAHRARRKINESRIAA-----SVEPAQHRVVTRAFIEACSNGDLDTLLEV 198
PRK12533 PRK12533
RNA polymerase sigma factor; Provisional
 76-251 1.23e-13

RNA polymerase sigma factor; Provisional


Pssm-ID: 237129 [Multi-domain]  Cd Length: 216  Bit Score: 69.37  E-value: 1.23e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15607323   76 MTGSLHDAEDLVQETLLRAWKAYEGFAGKSSlRTWLHRIATNTCLTalEGRRRRplptglgrpsadPSGELVERREVSWL 155
Cdd:PRK12533  38 LCGNASDADDVVQEACMRALRFFDSFRGDNA-RPWLLAIVRHTWYS--EWRRRA------------NAHEVAAPDTLDDA 102

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15607323  156 EPLPDVTDDPADPSTIVGNRESVRLAFvAALQHLSPRQRAVLLLRDV--LQWKS-AEVADA-IGTstvaVNSLLQRARSQ 231
Cdd:PRK12533 103 DSLDDWQPAGEDPLALLLRAEDVRLVN-AALAKLPVEYREVLVLRELedMSYREiAAIADVpVGT----VMSRLARARRR 177

                        170       180
                 ....*....|....*....|...
gi 15607323  232 LQTV---RPSAADRLSAPDSPEA 251
Cdd:PRK12533 178 LAALlggASAAQAAPGERAAGRP 200
Sig70_bacteroi1 TIGR02985
RNA polymerase sigma-70 factor, Bacteroides expansion family 1; This group of sigma factors ...
 65-232 1.04e-12

RNA polymerase sigma-70 factor, Bacteroides expansion family 1; 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.


Pssm-ID: 274376 [Multi-domain]  Cd Length: 161  Bit Score: 65.28  E-value: 1.04e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15607323    65 YRRELLAHCYRMTGSLHDAEDLVQETLLRAWKAYEGFAGKSSLRTWLHRIATNTCLTALEGRRRRplptglgrpsadpsg 144
Cdd:TIGR02985  10 YYPKLCAFARRYVKDEEDAEDIVQDVFLKLWENRETLEISESIKAYLFTIVKNRCLNYLRHKQVE--------------- 74

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15607323   145 elvERREVSWLEPLPDVTDDPADPSTIvgNRESVRLAFVAALQHLSPRQRAVLLLRDVLQWKSAEVADAIGTSTVAVNSL 224
Cdd:TIGR02985  75 ---EKYQEELAEIEERELSEADPEEEL--EAKELEEIIEEAIEKLPEQCREIFILSRFEGLSNKEIAEELGISVKTVEYH 149


                  ....*...
gi 15607323   225 LQRARSQL 232
Cdd:TIGR02985 150 ITKALKFL 157
PRK12538 PRK12538
RNA polymerase sigma factor; Provisional
 75-233 1.67e-12

RNA polymerase sigma factor; Provisional


Pssm-ID: 139048 [Multi-domain]  Cd Length: 233  Bit Score: 66.42  E-value: 1.67e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15607323   75 RMTGSLHDAEDLVQETLLRAWKAYEGFA-GKSSLRTWLHRIATNTCLTAlegrRRRPlptglgrpsadpsgelveRREVs 153
Cdd:PRK12538  82 RIVGNRADAEDVVQDTMLKVWTHRGRWQhGRAKFSTWLYRVVSNRCIDL----RRKP------------------RTEN- 138

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15607323  154 wLEPLPDVTDDPADPSTIVgNRESVRLAFVAALQHLSPRQRAVLLLRDVLQWKSAEVADAIGTSTVAVNSLLQRARSQLQ 233
Cdd:PRK12538 139 -VDAVPEVADGKPDAVSVI-ERNELSDLLEAAMQRLPEQQRIAVILSYHENMSNGEIAEVMDTTVAAVESLLKRGRQQLR 216
PRK12516 PRK12516
RNA polymerase sigma factor; Provisional
 63-251 2.97e-12

RNA polymerase sigma factor; Provisional


Pssm-ID: 183568 [Multi-domain]  Cd Length: 187  Bit Score: 64.60  E-value: 2.97e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15607323   63 EPYRRELL-------AHCYRMTGSLHDAEDLVQETLLRAWKAYEGFAGKSSLRTWLHRIATNTCLTALegRRRrplptgl 135
Cdd:PRK12516  10 PPFKRELLaalpslrAFAVSLIGRHDRADDLVQDTIMKAWAKQDHFEVGTNMKAWLFTILRNEFYSQM--RKR------- 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15607323  136 GRPSADPSGELVERREVswlEPLPDVTDDPADpstivgnresvrlaFVAALQHLSPRQRAVLLLRDVLQWKSAEVADAIG 215
Cdd:PRK12516  81 GREVQDTDGMFTEQLAV---HPSQYGTLDLQD--------------FRAALDQLPDDQREAIILVGASGFAYEEAAEICG 143

                        170       180       190
                 ....*....|....*....|....*....|....*.
gi 15607323  216 TSTVAVNSLLQRARSQLQTVRPSAADRLSAPDSPEA 251
Cdd:PRK12516 144 CAVGTIKSRVNRARQRLQEILQIEGEADYGPDADSA 179
PRK12544 PRK12544
RNA polymerase factor sigma-70;
66-233 3.05e-12

RNA polymerase factor sigma-70;


Pssm-ID: 183583 [Multi-domain]  Cd Length: 206  Bit Score: 65.21  E-value: 3.05e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15607323   66 RRELLAHCYRMTGSLHDAEDLVQETLLRAWKAYEGFAGKSSLRTWLHRIATNTCLTALEGRRRRPLPTGLGRpsADPSGE 145
Cdd:PRK12544  28 RKQMIKFATLQLSDLHLAEDAVQEALIGALKNADSFAGRAAFKTWVFAILKNKIIDLLRQKKRHVSASSLLR--DEEEEE 105

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15607323  146 LVE------------RREVSWLEPlpdvtDDPADpstivgnRESVRLAFVAALQHLSPRQRAVLLLRDVLQWKSAEVADA 213
Cdd:PRK12544 106 DFEelfdesghwqkdERPQAWGNP-----EESLE-------QEQFWRIFEACLDGLPAKYARVFMMREFIELETNEICHA 173

                        170       180
                 ....*....|....*....|
gi 15607323  214 IGTSTVAVNSLLQRARSQLQ 233
Cdd:PRK12544 174 VDLSVSNLNVLLYRARLRLR 193
PRK12530 PRK12530
RNA polymerase sigma factor; Provisional
 83-233 4.09e-12

RNA polymerase sigma factor; Provisional


Pssm-ID: 237128 [Multi-domain]  Cd Length: 189  Bit Score: 64.40  E-value: 4.09e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15607323   83 AEDLVQETLLRAWKAYEGFAGKSSLRTWLHRIATNTCLTALEGRRRRPLptglgrpsadpSGELVERREV-SWLEPLPDV 161
Cdd:PRK12530  34 AEDVVQEALVSAYKNADSFKGQSALKTWIFAILKNKIIDLIRYRKRFVN-----------ESELIEEDSPnSFFDEKGHW 102

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 15607323  162 TDDPADPSTIVGNRESVR-----LAFVAALQHLSPRQRAVLLLRDVLQWKSAEVADAIGTSTVAVNSLLQRARSQLQ 233
Cdd:PRK12530 103 KPEYYEPSEWQEVENTVYkeefwLIFEACLNHLPAQQARVFMMREYLELSSEQICQECDISTSNLHVLLYRARLQLQ 179
PRK09639 PRK09639
RNA polymerase sigma factor SigX; Provisional
 83-232 4.27e-12

RNA polymerase sigma factor SigX; Provisional


Pssm-ID: 236602 [Multi-domain]  Cd Length: 166  Bit Score: 63.81  E-value: 4.27e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15607323   83 AEDLVQETLLRAWKayEGFAGKSSLRTWLHRIATNTCLTAL--EGRRRRPlptglgrpsadpsgelvERREVSWLEplpd 160
Cdd:PRK09639  30 AEDLAQEVFLRLYR--SDFKGIENEKGWLIKSARNVAYNYLrsEKRRRAR-----------------ILGEFQWQE---- 86

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 15607323  161 VTDDPaDPSTIVGNRESVRLAFvAALQHLSPRQRAVLLLRdvLQWKS-AEVADAIGTSTVAVNSLLQRARSQL 232
Cdd:PRK09639  87 VDNEP-SPEEIWIRKEEITKVQ-EVLAKMTERDRTVLLLR--FSGYSyKEIAEALGIKESSVGTTLARAKKKF 155
SigM_subfam TIGR02950
RNA polymerase sigma factor, SigM family; This family of RNA polymerase sigma factors is a ...
 65-233 5.53e-12

RNA polymerase sigma factor, SigM family; 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:


Pssm-ID: 274361 [Multi-domain]  Cd Length: 154  Bit Score: 63.24  E-value: 5.53e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15607323    65 YRRELLAHCYRMTGSLHDAEDLVQETLLRAWKAYEGFAGkSSLRTWLHRIATNTCLTALEGRRRRPLptglgrPSADPSG 144
Cdd:TIGR02950   4 YMHDVFRYLYRLTKDKHLAEDLLQETFLKAYIHLHSFKD-SSIKPWLFRIARNAFIDWYRKDKKIQT------IDDDAIG 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15607323   145 ELverrevsWLEPLPdvtdDPADPSTIVGNRESVRLafvaALQHLSPRQRAVLLLRDVLQWKSAEVADAIGTSTVAVNSL 224
Cdd:TIGR02950  77 DL-------EQHPVE----SPEHHLLIKIEQEEITH----HLSRLPENYRTVLILREFKEFSYKEIAELLNLSLAKVKSN 141


                  ....*....
gi 15607323   225 LQRARSQLQ 233
Cdd:TIGR02950 142 LFRARKELK 150
PRK12513 PRK12513
RNA polymerase sigma factor; Provisional
 43-233 6.16e-12

RNA polymerase sigma factor; Provisional


Pssm-ID: 183566 [Multi-domain]  Cd Length: 194  Bit Score: 63.94  E-value: 6.16e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15607323   43 AENSGREPADE------RRGDFSAHTEPYRRE---LLAHCYRMTGSLHDAEDLVQETLLRAWKAYEGFAGKSSLRTWLHR 113
Cdd:PRK12513   4 GAMSTAAASDEalmlryRAGDAAAFEALYARHrtgLYRFLLRLARDRALAEDIFQETWLRVIRARAQYQPRARFRTWLYQ 83

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15607323  114 IATNTCLTALEGRRRRPLPTglgrPSADPSGELverrevswleplpdVTDDPADPSTIVGNREsVRLAFVAALQHLSPRQ 193
Cdd:PRK12513  84 IARNLLIDHWRRHGARQAPS----LDADEQLHA--------------LADDGAAPEQQLSLFR-DRRRLQAALETLPDEQ 144

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|
gi 15607323  194 RAVLLLRDVLQWKSAEVADAIGTSTVAVNSLLQRARSQLQ 233
Cdd:PRK12513 145 REVFLLREHGDLELEEIAELTGVPEETVKSRLRYALQKLR 184
PRK09415 PRK09415
RNA polymerase factor sigma C; Reviewed
 65-234 9.78e-12

RNA polymerase factor sigma C; Reviewed


Pssm-ID: 181835 [Multi-domain]  Cd Length: 179  Bit Score: 63.23  E-value: 9.78e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15607323   65 YRRELLAHCYRMTGSLHDAEDLVQETLLRAWKAYEGFAGKSSLRTWLHRIATNTCLTALEG-RRRRPLPTglgrpsadps 143
Cdd:PRK09415  25 YGQEVLQLVYSYVKNKEVAEDLTQEIFVKCYKSLHTYKGKSSLKTWLYRIAINHCKDYLKSwHNKKVIVT---------- 94

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15607323  144 gelverrEVSWLEpLPDVTDDPAdpSTIVGNRESVRLAfvAALQHLSPRQRAVLLLRDVLQWKSAEVADAIGTSTVAVNS 223
Cdd:PRK09415  95 -------EDIFTY-MESQKESVE--EEVIQNAEDERLA--SAVMSLPIKYREVIYLFYYEELSIKEIAEVTGVNENTVKT 162

                        170
                 ....*....|.
gi 15607323  224 LLQRARSQLQT 234
Cdd:PRK09415 163 RLKKAKELLKK 173
PRK09638 PRK09638
RNA polymerase sigma factor SigY; Reviewed
 49-232 1.98e-11

RNA polymerase sigma factor SigY; Reviewed


Pssm-ID: 182010 [Multi-domain]  Cd Length: 176  Bit Score: 61.96  E-value: 1.98e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15607323   49 EPADE-------RRGDFSAHTEPYRRE---LLAHCYRMTGSLHDAEDLVQETLLRAWKAYEGFAGKSSLRTWLHRIATNT 118
Cdd:PRK09638   1 MQMDEkeliqkaKKGDDAALTTLFQQHysfLYKYLLKLTLDPDLAEDLVQETMLKAIENLSSFQGRSKFSTWLISIASRL 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15607323  119 CLTALEGRRRRPLptglgrpSADPSGELVERREvSWLEPLPDvtddpADPSTIVgnresvrlafvAALQHLSPRQRAVLL 198
Cdd:PRK09638  81 YKDHLRKQKREKL-------RLQRAKEETLRKE-KWEAAIKG-----AEWSEML-----------DALSKLDPEFRAPVI 136

                        170       180       190
                 ....*....|....*....|....*....|....
gi 15607323  199 LRDVLQWKSAEVADAIGTSTVAVNSLLQRARSQL 232
Cdd:PRK09638 137 LKHYYGYTYEEIAKMLNIPEGTVKSRVHHGIKQL 170
PRK09645 PRK09645
ECF RNA polymerase sigma factor SigL;
67-215 6.01e-11

ECF RNA polymerase sigma factor SigL;


Pssm-ID: 236605 [Multi-domain]  Cd Length: 173  Bit Score: 60.48  E-value: 6.01e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15607323   67 RELLAHCYRMTGSLHDAEDLVQETLLRAWKAYEGFAGK-SSLRTWLHRIATNTCLTALEGRRRRPlptglgrPSADPSGE 145
Cdd:PRK09645  20 APLWRYALRLTGDRARAEDVVQETLLRAWQHPEVLADTgRSARAWLFTVARNLVIDERRSARARP-------VEGGDDVL 92

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15607323  146 LVERRevswleplpdVTDDPADpstivgnRESVRLAFVAALQHLSPRQRAVLLLRDVLQWKSAEVADAIG 215
Cdd:PRK09645  93 GVPEQ----------SAPDEVD-------RALDRLLVADALAQLSPEHRAVLVRSYYRGWSTAQIAADLG 145
Sigma70_r4_2 pfam08281
Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 ...
 179-232 7.72e-11

Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 promoter element via a helix-turn-helix motif.


Pssm-ID: 400535 [Multi-domain]  Cd Length: 54  Bit Score: 56.70  E-value: 7.72e-11
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 15607323   179 RLAFVAALQHLSPRQRAVLLLRDVLQWKSAEVADAIGTSTVAVNSLLQRARSQL 232
Cdd:pfam08281   1 LEALLRALEELPPRQREVFLLRYLEGLSYAEIAELLGISEGTVKSRLSRARKKL 54
PRK12546 PRK12546
RNA polymerase sigma factor; Provisional
 83-232 8.73e-11

RNA polymerase sigma factor; Provisional


Pssm-ID: 139055 [Multi-domain]  Cd Length: 188  Bit Score: 60.62  E-value: 8.73e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15607323   83 AEDLVQETLLRAWKAYEGFAGKSSLRTWLHRIATNTCLTAlegRRRRplptglGRPSADPSGELVERREVSwleplpdvt 162
Cdd:PRK12546  34 ADDLVQDTIVKAWTNFDKFQEGTNLRAWLFTILRNTFYSD---RRKH------KREVPDPEGVHAASLAVK--------- 95

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 15607323  163 ddPADPStivgnresvRLA---FVAALQHLSPRQRAVLLLRDVLQWKSAEVADAIGTSTVAVNSLLQRARSQL 232
Cdd:PRK12546  96 --PAHDG---------RLAmsdFRAAFAQLPDEQREALILVGASGFSYEEAAEMCGVAVGTVKSRANRARARL 157
PRK12532 PRK12532
RNA polymerase sigma factor; Provisional
 67-233 9.83e-11

RNA polymerase sigma factor; Provisional


Pssm-ID: 171564 [Multi-domain]  Cd Length: 195  Bit Score: 60.33  E-value: 9.83e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15607323   67 RELLAHCYRMtgSLHD----AEDLVQETLLRAWKAYEGFAGKSSLRTWLHRIATNTCLTALEGR-RRRPLPTGLGRPSAD 141
Cdd:PRK12532  15 RKLLLHFARL--QLPDhpdlAEDLVQETLLSAYSAGDSFQGRALVNSWLFAILKNKIIDALRQIgRQRKVFTLLDDELLD 92

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15607323  142 PSGELVERREVSWlepLPDvtDDPA---DPSTIVGNRESVRLaFVAALQHLSPRQRAVLLLRDVLQWKSAEVADAIGTST 218
Cdd:PRK12532  93 EAFESHFSQNGHW---TPE--GQPQhwnTPEKSLNNNEFQKI-LQSCLYNLPENTARVFTLKEILGFSSDEIQQMCGIST 166

                        170
                 ....*....|....*
gi 15607323  219 VAVNSLLQRARSQLQ 233
Cdd:PRK12532 167 SNYHTIMHRARESLR 181
PRK12545 PRK12545
RNA polymerase factor sigma-70;
59-234 1.20e-10

RNA polymerase factor sigma-70;


Pssm-ID: 183584 [Multi-domain]  Cd Length: 201  Bit Score: 60.35  E-value: 1.20e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15607323   59 SAHTEP-----YRRELLAHCYRMTGSLHDAEDLVQETLLRAWKAYEGFAGKSSLRTWLHRIATNTCLTALEGRRRRPLPT 133
Cdd:PRK12545   6 SAHDDPaylaqLRHDLLRFARLQLRDADAAEDAVQEALAAAWSQAGRFAGQSAHKTWVFGILRNKLIDTLRARQRTVNLS 85

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15607323  134 GLgrpSADPSGELVERREV-----SW---LEPLPDVTddpadPSTIVGNRESVRLaFVAALQHLSPRQRAVLLLRDVLQW 205
Cdd:PRK12545  86 AL---DAELDGEALLDRELfkdngHWaahAKPRPWPK-----PETILQQQQFWTL-FETCLDHLPEQIGRVFMMREFLDF 156

                        170       180
                 ....*....|....*....|....*....
gi 15607323  206 KSAEVADAIGTSTVAVNSLLQRARSQLQT 234
Cdd:PRK12545 157 EIDDICTELTLTANHCSVLLYRARTRLRT 185
PRK12518 PRK12518
RNA polymerase sigma factor; Provisional
 55-234 2.96e-10

RNA polymerase sigma factor; Provisional


Pssm-ID: 237124 [Multi-domain]  Cd Length: 175  Bit Score: 58.58  E-value: 2.96e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15607323   55 RGDFSAHTEPYRR---ELLAHCYRMTGSlHDAEDLVQETLLRAWKAYEGFAGKSSLRTWLHRIATNtclTALEGRRRRPl 131
Cdd:PRK12518   7 RGDRQSFRQLYRRyqqKVRSTLYQLCGR-ELLDDLVQEVFLRVWKGLPKLRNPAYFSTWLYRITWN---VATDARRQFA- 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15607323  132 ptglGRPSADPSGElverrevSWLEPLPDVTDDPAdpstivgnresVRLAF----VAALQHLSPRQRAVLLLRDVLQWKS 207
Cdd:PRK12518  82 ----QRPSRIQDDS-------LNDQPSRPSDTPDL-----------MQLHYqdlvQQGLQTLSLEHRAVLVLHDLEDLPQ 139

                        170       180
                 ....*....|....*....|....*..
gi 15607323  208 AEVADAIGTSTVAVNSLLQRARSQLQT 234
Cdd:PRK12518 140 KEIAEILNIPVGTVKSRLFYARRQLRK 166
algU PRK11923
RNA polymerase sigma factor AlgU; Provisional
 54-229 9.23e-10

RNA polymerase sigma factor AlgU; Provisional


Pssm-ID: 171347 [Multi-domain]  Cd Length: 193  Bit Score: 57.50  E-value: 9.23e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15607323   54 RRGD---FSAHTEPYRRELLAHCYRMTGSLHDAEDLVQETLLRAWKAYEGFAGKSSLRTWLHRIATNTCLTALEGRRRRP 130
Cdd:PRK11923  15 QRGDkraFDLLVLKYQHKILGLIVRFVHDTAEAQDVAQEAFIKAYRALGNFRGDSAFYTWLYRIAINTAKNHLVSRGRRP 94

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15607323  131 lptglgrPSADPSGELVERREVSwleplpDVTDDPADPSTIVgNRESVRLAFVAALQHLSPRQRAVLLLRDVLQWKSAEV 210
Cdd:PRK11923  95 -------PDSDVSSEDAEFYDGD------HALKDIESPERAL-LRDEIEGTVHRTIQQLPEDLRTALTLREFDGLSYEDI 160

                        170
                 ....*....|....*....
gi 15607323  211 ADAIGTSTVAVNSLLQRAR 229
Cdd:PRK11923 161 ASVMQCPVGTVRSRIFRAR 179
PRK12541 PRK12541
RNA polymerase sigma factor; Provisional
 58-236 9.82e-10

RNA polymerase sigma factor; Provisional


Pssm-ID: 183580 [Multi-domain]  Cd Length: 161  Bit Score: 56.87  E-value: 9.82e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15607323   58 FSAHTEPYRRELLAhcyrMTGSLHDAEDLVQETLLRAWKAYEGFAGKsSLRTWLHRIATNTCLTALEGRRRRP------- 130
Cdd:PRK12541  11 YSEHMQDLFRYLLS----LTGDSHFAEDLMQETFYRMLVHIDYYKGE-EIRPWLFTIAYNAFIDWYRKEKKYKtttieef 85

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15607323  131 -LPTglgRPSADPSgELVERREVSWLEplpdvtddpadpstivgnresvrlafvaALQHLSPRQRAVLLLRDVLQWKSAE 209
Cdd:PRK12541  86 hLPN---VPSTEHE-YFIKHEIASWLD----------------------------SLSSLPLERRNVLLLRDYYGFSYKE 133

                        170       180
                 ....*....|....*....|....*..
gi 15607323  210 VADAIGTSTVAVNSLLQRARSQLQTVR 236
Cdd:PRK12541 134 IAEMTGLSLAKVKIELHRGRKETKSIK 160
PRK12520 PRK12520
RNA polymerase sigma factor; Provisional
 83-233 1.19e-09

RNA polymerase sigma factor; Provisional


Pssm-ID: 237126 [Multi-domain]  Cd Length: 191  Bit Score: 57.43  E-value: 1.19e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15607323   83 AEDLVQETLLRAWKAYEGFAGKSSLRTWLHRIATNTCLTALE-GRRRRPLPTGLGRPSADpsGELVER---REVSWLEPl 158
Cdd:PRK12520  29 AEDAVSETLLAVLEHPERFAGQSSLKTYLVGILKHKIIDAIRsGRREVRLSLDDADEQSD--DDLFDAlfaADGHYREP- 105

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 15607323  159 pdvTDDPADPSTIVGNRESVRLaFVAALQHLSPRQRAVLLLRDVLQWKSAEVADAIGTSTVAVNSLLQRARSQLQ 233
Cdd:PRK12520 106 ---PSDWGDPDAALSRREFFEV-LQACVDRLPPRTGRVFMMREWLELETEEICQELQITATNAWVLLYRARMRLR 176
PRK09649 PRK09649
RNA polymerase sigma factor SigC; Reviewed
 74-232 4.38e-09

RNA polymerase sigma factor SigC; Reviewed


Pssm-ID: 137458 [Multi-domain]  Cd Length: 185  Bit Score: 55.43  E-value: 4.38e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15607323   74 YRMTGSLHD---AEDLVQETLLRAWKAYEGFAGKSSLRTWLHRIATNTCLTALEGRRRRPLPTGLGrpsaDPSGELVERR 150
Cdd:PRK09649  38 WRFVAYLSDvgsADDLTQETFLRAIGAIPRFSARSSARTWLLAIARHVVADHIRHVRSRPRTTRGA----RPEHLIDGDR 113

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15607323  151 EVSWLEPLPDVTddpadpsTIVGNresvrlafvaalqhLSPRQRAVLLLRDVLQWKSAEVADAIGTSTVAVNSLLQRARS 230
Cdd:PRK09649 114 HARGFEDLVEVT-------TMIAD--------------LTTDQREALLLTQLLGLSYADAAAVCGCPVGTIRSRVARARD 172


                 ..
gi 15607323  231 QL 232
Cdd:PRK09649 173 AL 174
PRK12547 PRK12547
RNA polymerase sigma factor; Provisional
 65-233 2.71e-08

RNA polymerase sigma factor; Provisional


Pssm-ID: 139056 [Multi-domain]  Cd Length: 164  Bit Score: 52.96  E-value: 2.71e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15607323   65 YRRELL-------AHCYRMTGSLHDAEDLVQETLLRAWKAYEGFAGKSSLRTWLHRIATNTCLTALEGRrrrplptglGR 137
Cdd:PRK12547   8 FKQELLlalpalrAFAVSLSSKHDKAEDLVQDTLMKAWAKQDSFEMGTNLKAWLFTILRNEFYSQMRKR---------GR 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15607323  138 PSADPSGELVERREVswlEPLPDVTDDPADpstivgnresvrlaFVAALQHLSPRQRAVLLLRDVLQWKSAEVADAIGTS 217
Cdd:PRK12547  79 EVQDSDGVFTARVAV---HPAQYGSLDLQD--------------FKKALNLLSADQREAIILIGASGFSYEDAAAICGCA 141

                        170
                 ....*....|....*.
gi 15607323  218 TVAVNSLLQRARSQLQ 233
Cdd:PRK12547 142 VGTIKSRVSRARNRLQ 157
PRK12515 PRK12515
RNA polymerase sigma factor; Provisional
 75-232 4.26e-08

RNA polymerase sigma factor; Provisional


Pssm-ID: 183567 [Multi-domain]  Cd Length: 189  Bit Score: 52.81  E-value: 4.26e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15607323   75 RMTGSLHDAEDLVQETLLRAWKAYEGFAGKSSLRTWLHRIATNTCLTALegRRRRplptglgrpsadpsGELVERREVSW 154
Cdd:PRK12515  41 RLVRDEQTAEDLVSEVFLDVWRQAGQFEGRSQVSTWLLSIARFKALSAL--RRRK--------------HEEIDDEAAAA 104

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 15607323  155 LEplpdvtdDPADPSTIVGNRESVRLAFVAALQHLSPRQRAVLLLRDVLQWKSAEVADAIGTSTVAVNSLLQRARSQL 232
Cdd:PRK12515 105 IE-------DGADTPEVALQKSDTSAALRACLAKLSPAHREIIDLVYYHEKSVEEVGEIVGIPESTVKTRMFYARKKL 175
PRK12511 PRK12511
RNA polymerase sigma factor; Provisional
 52-233 6.07e-08

RNA polymerase sigma factor; Provisional


Pssm-ID: 237123 [Multi-domain]  Cd Length: 182  Bit Score: 52.10  E-value: 6.07e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15607323   52 DERRGDFSAHTEPYRRellaHCYRMTGSLHDAEDLVQETLLRAWKAYEGFAGKSSLRTWLHRIATNTCLTALegRRRRPL 131
Cdd:PRK12511   4 KSKRFDVLDQLVPLRR----YARSLTRDSAEAEDLVHDALVRALERRASFRSGGNLRTWLMSILHNAFIDEL--RRRRVE 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15607323  132 PtglgrpsadpsgelveRREvswleplpDVTDDPADPSTIVGNRESVRLAFV-AALQHLSPRQRAVLLLRDVLQWKSAEV 210
Cdd:PRK12511  78 A----------------RRA--------DELAVLADASLPAAQEHAVRLAQIrDAFFDLPEEQRAALHLVAIEGLSYQEA 133

                        170       180
                 ....*....|....*....|...
gi 15607323  211 ADAIGTSTVAVNSLLQRARSQLQ 233
Cdd:PRK12511 134 AAVLGIPIGTLMSRIGRARAALR 156
Sigma70_r4 cd06171
Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in ...
 185-233 7.06e-08

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). 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).


Pssm-ID: 100119 [Multi-domain]  Cd Length: 55  Bit Score: 48.64  E-value: 7.06e-08
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*....
gi 15607323 185 ALQHLSPRQRAVLLLRDVLQWKSAEVADAIGTSTVAVNSLLQRARSQLQ 233
Cdd:cd06171   7 ALDKLPEREREVILLRFGEGLSYEEIAEILGISRSTVRQRLHRALKKLR 55
PRK06704 PRK06704
RNA polymerase subunit sigma-70;
68-235 1.38e-07

RNA polymerase subunit sigma-70;


Pssm-ID: 180663 [Multi-domain]  Cd Length: 228  Bit Score: 51.95  E-value: 1.38e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15607323   68 ELLAHCYRMTGSLHDAEDLVQETLLRAWKAYegfAGKSSLRTWLHRIATNTCLTALEGRRRRplptglgrpsadpsgELV 147
Cdd:PRK06704  29 ELKRYCTFLTKNKWDGEDLAQETVCKVLQKY---SNKDICMTLVYKIARNRWLDQIKSKSVH---------------EKI 90

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15607323  148 ERrEVSWLEPLPDVtddpADPSTIVGNresvrlafvaALQHLSPRQRAVLLLRDVLQWKSAEVADAIGTSTVAVNSLLQR 227
Cdd:PRK06704  91 RD-QITFEEPHEKI----ADLHEMVGK----------VLSSLNVQQSAILLLKDVFQYSIADIAKVCSVSEGAVKASLFR 155


                 ....*...
gi 15607323  228 ARSQLQTV 235
Cdd:PRK06704 156 SRNRLKTV 163
PRK12517 PRK12517
RNA polymerase sigma factor; Provisional
 58-253 2.05e-07

RNA polymerase sigma factor; Provisional


Pssm-ID: 183569 [Multi-domain]  Cd Length: 188  Bit Score: 50.84  E-value: 2.05e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15607323   58 FSAHTEPYRRELLAHCYRMTGSLHDAEDLVQETLLRAWKAYEGF----AGKSSLRTWLHRiatntcltalEGRRRrplpt 133
Cdd:PRK12517  25 YEALVKALHADIYRYAYWLCKDKHIAEDLVQETFLRAWRSLDSLkdekAAKAWLITILRR----------ENARR----- 89

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15607323  134 glgrpsadpsgelVERREVSwlepLPDVTDDPADPSTIVGNRESVRLAFV-AALQHLSPRQRAVLLLRDVLQWKSAEVAD 212
Cdd:PRK12517  90 -------------FERKQFD----LVDIEDDSIEDDASHSSEEEMEQEWLrRQIAKLDPEYREPLLLQVIGGFSGEEIAE 152

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|.
gi 15607323  213 AIGTSTVAVNSLLQRARSQLQtvrpsaaDRLSAPDSPEAQD 253
Cdd:PRK12517 153 ILDLNKNTVMTRLFRARNQLK-------EALEKPDVQRGQS 186
PRK12540 PRK12540
RNA polymerase sigma factor; Provisional
 69-232 6.54e-07

RNA polymerase sigma factor; Provisional


Pssm-ID: 183579 [Multi-domain]  Cd Length: 182  Bit Score: 49.19  E-value: 6.54e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15607323   69 LLAHCYRMTGSLHDAEDLVQETLLRAWKAYEGFAGKSSLRTWLHRIATNTCLTALEGRRRRplptglgrpsadpsgelVE 148
Cdd:PRK12540  18 LRAFAISLSGNGDRADDLVQETLLRALANIDSFQPGSNLPAWLFTILRNLFRSDYRKRRRE-----------------VE 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15607323  149 RREVSWLEPLpdvTDDPADPSTIVGNResvrlaFVAALQHLSPRQRAVLLLRDVLQWKSAEVADAIGTSTVAVNSLLQRA 228
Cdd:PRK12540  81 DADGSYAKTL---KSQPGQNAHLEFEE------FRAALDKLPQDQREALILVGASGFSYEDAAAICGCAVGTIKSRVNRA 151


                 ....
gi 15607323  229 RSQL 232
Cdd:PRK12540 152 RSKL 155
PRK09637 PRK09637
RNA polymerase sigma factor SigZ; Provisional
 65-232 7.55e-07

RNA polymerase sigma factor SigZ; Provisional


Pssm-ID: 236601 [Multi-domain]  Cd Length: 181  Bit Score: 48.83  E-value: 7.55e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15607323   65 YRRELLAHCYRMTGSLHDAEDLVQETLLRAWKAYEGFAGKSSLRTWLHRIATNTCLTALEGRRRRP-LPTGLGRPSADPS 143
Cdd:PRK09637  10 YKAQLKAFLHSRVSNEADVDDLLQEVLIKTHSNLHSLKDGSSIKSWLYQIANNTIIDFYRKKNRSEeLPDDLLFEDEERE 89

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15607323  144 GELveRREVS-WLEPLpdvtddpadpstivgnresvrlafvaaLQHLSPRQRAVLLLRDvLQWKS-AEVADAIGTSTVAV 221
Cdd:PRK09637  90 ENA--KKELApCLRPF---------------------------IDALPEKYAEALRLTE-LEGLSqKEIAEKLGLSLSGA 139

                        170
                 ....*....|.
gi 15607323  222 NSLLQRARSQL 232
Cdd:PRK09637 140 KSRVQRGRVKL 150
PRK12535 PRK12535
RNA polymerase sigma factor; Provisional
 55-232 1.05e-06

RNA polymerase sigma factor; Provisional


Pssm-ID: 237130 [Multi-domain]  Cd Length: 196  Bit Score: 48.74  E-value: 1.05e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15607323   55 RGDFSAHTEPYRR------ELLAHcyrmTGSLHDAEDLVQETLLRAWKAYEGFAGKSSLRTWLHRIAtntcltalegrrR 128
Cdd:PRK12535  21 RGDRAALTEFIREtqddvwRLLAH----LGGHDIADDLTQETYLRVMSALPRFAARSSARTWLLSLA------------R 84

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15607323  129 RPLPTGLGRPSADPSGELVERREVswleplpdvtdDPADPSTIVGNRESVRLAFVAALQHLSPRQRAVLLLRDVLQWKSA 208
Cdd:PRK12535  85 RVWVDNIRHDMARPRKSATEYEDA-----------AATTASNETTGSWSEWIDVRTLIDALPPERREALILTQVLGYTYE 153

                        170       180
                 ....*....|....*....|....
gi 15607323  209 EVADAIGTSTVAVNSLLQRARSQL 232
Cdd:PRK12535 154 EAAKIADVRVGTIRSRVARARADL 177
SnoaL_2 pfam12680
SnoaL-like domain; This family contains a large number of proteins that share the SnoaL fold.
 255-333 1.05e-06

SnoaL-like domain; This family contains a large number of proteins that share the SnoaL fold.


Pssm-ID: 432716 [Multi-domain]  Cd Length: 100  Bit Score: 46.51  E-value: 1.05e-06
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 15607323   255 LARYIAAFEAYDIDRLVELFTAEAIWEMPPYTgwYQGAQAIVTLIHQQCPAYSPGDMRLISLIANGQPAAAMYMRAGDV 333
Cdd:pfam12680   1 VRRFYEALNAGDLDALAALFAPDAVFHDPGGP--LRGRDAIRAFFAALFAAFPDLRFEIHDVIADGDRVAVRWTVTGTI 77
PRK09047 PRK09047
RNA polymerase factor sigma-70; Validated
 77-234 2.21e-06

RNA polymerase factor sigma-70; Validated


Pssm-ID: 236367 [Multi-domain]  Cd Length: 161  Bit Score: 47.27  E-value: 2.21e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15607323   77 TGSLHDAEDLVQETLLRAWKAYegfaGKSSLRTW---LHRIATNTCLTALEGRRRRPLPTGL-GRPSADPSGElvERREV 152
Cdd:PRK09047   1 VRDDDAALDIVQDAMIKLAEKY----GDRPAAEWpplFQRILQNRIHDWFRRQKVRNTWVSLfSSFSDDDDDD--DFDPL 74

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15607323  153 SWLEPLPDVTDDPADPStivgNRESVRLAFVAALQHLSPRQRAVLLLR-----DVlqwksAEVADAIGTSTVAVNSLLQR 227
Cdd:PRK09047  75 ETLDSADEGAESPADKL----ERAQVLQLIEEAIQKLPARQREAFLLRywedmDV-----AETAAAMGCSEGSVKTHCSR 145


                 ....*..
gi 15607323  228 ARSQLQT 234
Cdd:PRK09047 146 ATHALAK 152
PRK13919 PRK13919
putative RNA polymerase sigma E protein; Provisional
 55-235 2.21e-06

putative RNA polymerase sigma E protein; Provisional


Pssm-ID: 184395 [Multi-domain]  Cd Length: 186  Bit Score: 47.60  E-value: 2.21e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15607323   55 RGDFSAHTEPYRR---ELLAHCYRMTGSLHDAEDLVQETLLRAWKAYEGF-AGKSSLRTWLHRIATNTCLTALEGRRRRP 130
Cdd:PRK13919  19 RGEEEALRALFRRyagAFLALARRMGLDGAAAEDVVQEVFIRVWKKAKEFdPRRGSARAWLLALAHHAAVDHVRRRAARP 98

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15607323  131 LPTglgrpsadpsgELVERREVSWLEPLPDVTDDpadpstivGNRESVRLAfvAALQHLSPRQRAVLLLRDVLQWKSAEV 210
Cdd:PRK13919  99 QPL-----------EPDEREPEAFDLPGPGLDEE--------GHLDRTRLG--RALKALSPEERRVIEVLYYQGYTHREA 157

                        170       180
                 ....*....|....*....|....*
gi 15607323  211 ADAIGTSTVAVNSLLQRARSQLQTV 235
Cdd:PRK13919 158 AQLLGLPLGTLKTRARRALSRLKEV 182
PRK09644 PRK09644
RNA polymerase sigma factor SigM; Provisional
 65-233 4.92e-05

RNA polymerase sigma factor SigM; Provisional


Pssm-ID: 170033 [Multi-domain]  Cd Length: 165  Bit Score: 43.33  E-value: 4.92e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15607323   65 YRRELLAHCYRMTGSLHDAEDLVQETLLRAWKAYEGFAgKSSLRTWLHRIATNTCLTALegRRrrplptglgrpsadpsg 144
Cdd:PRK09644  10 YINDVYRYLFSLTKSHHAAEDLLQETFYRAYIYLEDYD-NQKVKPWLFKVAYHTFIDFV--RK----------------- 69

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15607323  145 elvERREVSwleplpdVTDDPAD------PSTIVGNRESvRLAFVAALQHLSPRQRAVLLLRDVLQWKSAEVADAIGTST 218
Cdd:PRK09644  70 ---EKKVSF-------VGTDEIEaiqaesTEEYVVAKNS-YEKLIQIIHTLPVIEAQAILLCDVHELTYEEAASVLDLKL 138

                        170
                 ....*....|....*
gi 15607323  219 VAVNSLLQRARSQLQ 233
Cdd:PRK09644 139 NTYKSHLFRGRKRLK 153
YybH COG4319
Ketosteroid isomerase homolog YybH [General function prediction only];
242-316 7.52e-05

Ketosteroid isomerase homolog YybH [General function prediction only];


Pssm-ID: 443460 [Multi-domain]  Cd Length: 131  Bit Score: 42.05  E-value: 7.52e-05
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 15607323 242 RLSAPDSPEAQDLLARYIAAFEAYDIDRLVELFTAEAIWeMPPYTGWYQGAQAIVTLIHQQCPAYSPGDMRLISL 316
Cdd:COG4319   2 KRSAEDEAAIRALLAAFAEAFNAGDADALAALYAEDAVF-FDPGGPPVRGREAIRAAWAAAFAAGPRVTFEVEDV 75
Sigma70_r4 pfam04545
Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 ...
 185-233 1.54e-04

Sigma-70, region 4; 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.


Pssm-ID: 461347 [Multi-domain]  Cd Length: 50  Bit Score: 38.95  E-value: 1.54e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 15607323   185 ALQHLSPRQRAVLLLRDVLQWKSAEVADAIGTSTVAVNSLLQRARSQLQ 233
Cdd:pfam04545   1 ALASLPPRERQVLVLRYGEGLTLEEIGERLGISRERVRQIEKRALRKLR 49
PRK12531 PRK12531
RNA polymerase sigma factor; Provisional
 65-131 1.84e-04

RNA polymerase sigma factor; Provisional


Pssm-ID: 105726 [Multi-domain]  Cd Length: 194  Bit Score: 42.23  E-value: 1.84e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 15607323   65 YRRELLAHCYRMTGSLHDAEDLVQETLLRAWKAYEGFAG-KSSLRTWLHRIATNTCLTALEGRRRRPL 131
Cdd:PRK12531  36 YAPKLKQFAMKHVGNEQVAMEMVQETMSTVWQKAHLFDGqKSALSTWIYTIIRNLCFDLLRKQKGKDL 103
PRK12527 PRK12527
RNA polymerase sigma factor; Reviewed
 63-228 6.40e-04

RNA polymerase sigma factor; Reviewed


Pssm-ID: 171560 [Multi-domain]  Cd Length: 159  Bit Score: 39.76  E-value: 6.40e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15607323   63 EPYRRELLAHCYRMTGSLHDAEDLVQETLLRAWKAYEGFAGKSSlRTWLHRIATNTCltaLEGRRRRplptgLGRpSADP 142
Cdd:PRK12527   2 ENYYRELVRFLSARLGNRQAAEDVAHDAYLRVLERSSSAQIEHP-RAFLYRTALNLV---VDRHRRH-----RVR-QAEP 71

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15607323  143 SGELVErrEVSWLEPLPDVTDDpadpstivgnrESVRLAFVA-ALQHLSPRQRAVLLLRDVLQWKSAEVADAIGTSTVAV 221
Cdd:PRK12527  72 LEVLDE--EERLHSPSPQTRLD-----------LGQRLALLQrALAELPPACRDSFLLRKLEGLSHQQIAEHLGISRSLV 138


                 ....*..
gi 15607323  222 NSLLQRA 228
Cdd:PRK12527 139 EKHIVNA 145
NTF2 pfam02136
Nuclear transport factor 2 (NTF2) domain; This family includes the NTF2-like ...
 250-303 9.79e-04

Nuclear transport factor 2 (NTF2) domain; This family includes the NTF2-like Delta-5-3-ketosteroid isomerase proteins.


Pssm-ID: 396625  Cd Length: 116  Bit Score: 38.49  E-value: 9.79e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 15607323   250 EAQDLLARYIAAFEAYDIDRLVELFTAEAIWEMPPYTGWYQGAQAIV----TLIHQQC 303
Cdd:pfam02136   1 VGNAFVQQYYAALDAHDPEGLHALYADDASMLTPPGSDPVVGLEAINeffdSLPFTRI 58
PRK09648 PRK09648
RNA polymerase sigma factor ShbA;
78-232 1.23e-03

RNA polymerase sigma factor ShbA;


Pssm-ID: 236607 [Multi-domain]  Cd Length: 189  Bit Score: 39.57  E-value: 1.23e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15607323   78 GSLHDAEDLVQETLLRAWKAYEGF--AGKSSLrTWLHRIATNTCLTALEGRrrrplptglGRPSADPSGELverrevswl 155
Cdd:PRK09648  50 RPGLSADDVAQEVCLAVITALPRYrdQGRPFL-AFVYGIAAHKVADAHRAA---------GRDKAVPTEEV--------- 110

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 15607323  156 eplPDVTDDPADP-STIVGNRESVRLAfvAALQHLSPRQRAVLLLRDVLQWKSAEVADAIGTSTVAVNSLLQRARSQL 232
Cdd:PRK09648 111 ---PERPSDDAGPeERALRSESSNRMR--ELLDTLPEKQREILILRVVVGLSAEETAEAVGSTPGAVRVAQHRALARL 183
PRK12514 PRK12514
RNA polymerase sigma factor; Provisional
 56-151 1.75e-03

RNA polymerase sigma factor; Provisional


Pssm-ID: 105710 [Multi-domain]  Cd Length: 179  Bit Score: 39.03  E-value: 1.75e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15607323   56 GDFSAHTEPYRR---ELLAHCYRMTGSLHDAEDLVQETLLRAWKAYEGFA-GKSSLRTWLHRIATNTCLTALegRRRRPL 131
Cdd:PRK12514  16 GDRDAFSSLYDAtsaKLFGICLRVLKDRSEAEEALQDVYVKIWTKADRFAvSGLSPMTWLITIARNHAIDRL--RARKAV 93

                         90       100
                 ....*....|....*....|....*.
gi 15607323  132 PTG------LGRPSADPSGELVERRE 151
Cdd:PRK12514  94 AVDideahdLADPSPGPEAEVIAGDE 119
PRK12519 PRK12519
RNA polymerase sigma factor; Provisional
 43-232 1.84e-03

RNA polymerase sigma factor; Provisional


Pssm-ID: 237125 [Multi-domain]  Cd Length: 194  Bit Score: 38.89  E-value: 1.84e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15607323   43 AENSGREPADE------RRGDFSAHTEPYRREL-----LAhcYRMTGSLHDAEDLVQETLLRAW--KAYEGFAGksSLRT 109
Cdd:PRK12519   7 APTSLSSRSDAelfsalKAGQSAALGVLYDRHAglvygLA--LKILGNSQEAEDLTQEIFLSLWrkSSYDPKRG--SLSS 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15607323  110 WLHRIATNTCLTALEGRRRRplptglgrpsadpsGELVERREVSWLEPLPDVTddPADPSTIVGNRESVRlafvAALQHL 189
Cdd:PRK12519  83 YLLTLTRSRAIDRLRSRRSR--------------QRLLERWQQELLGEASEDT--PLEQASLAERSQRVQ----TALAQL 142

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|...
gi 15607323  190 SPRQRAVLLLRDVLQWKSAEVADAIGTSTVAVNSLLQRARSQL 232
Cdd:PRK12519 143 PESQRQVLELAYYEGLSQSEIAKRLGIPLGTVKARARQGLLKL 185
PRK12522 PRK12522
RNA polymerase sigma factor; Provisional
 65-234 5.94e-03

RNA polymerase sigma factor; Provisional


Pssm-ID: 183571 [Multi-domain]  Cd Length: 173  Bit Score: 37.16  E-value: 5.94e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15607323   65 YRRELLAHCYRMTGSLHDAEDLVQETLLRAWKAYEGFAGKSSLRTWLHRIATNTCLTALEGRRRrplptglgrpsadpsg 144
Cdd:PRK12522  12 YKQQIYSLCYKLAKTKEDAEDIFQETWIKVFSSRHQLSYVENYKKWITTICVRTFYDFYRKKKR---------------- 75

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15607323  145 elverrevsWLEPLPDVTDD--------PAD---PSTIVGNRESVRLAfvAALQHLSPRQRAVLLLRDVLQWKSAEVADA 213
Cdd:PRK12522  76 ---------WKDRILDLFHKedggeiefADDvniSEEFIQKVEAEMIR--EVIQLLNEKYKTVLVLYYYEQYSYKEMSEI 144

                        170       180
                 ....*....|....*....|.
gi 15607323  214 IGTSTVAVNSLLQRARSQLQT 234
Cdd:PRK12522 145 LNIPIGTVKYRLNYAKKQMRE 165
PRK06930 PRK06930
positive control sigma-like factor; Validated
 160-233 6.06e-03

positive control sigma-like factor; Validated


Pssm-ID: 180757 [Multi-domain]  Cd Length: 170  Bit Score: 37.40  E-value: 6.06e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 15607323  160 DVTDDPADPSTIVGNRESVRLAfvAALQHLSPRQRAVLLLRDVLQWKSAEVADAIGTSTVAVNSLLQRARSQLQ 233
Cdd:PRK06930  88 DLEWDIEEPESVISEWDKIRIE--DALSVLTEREKEVYLMHRGYGLSYSEIADYLNIKKSTVQSMIERAEKKIA 159
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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