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Conserved domains on  [gi|750432401|ref|WP_040714291|]
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RNA polymerase sigma factor [Paenibacillus curdlanolyticus]

Protein Classification

RNA polymerase sigma factor( domain architecture ID 11471810)

RNA polymerase sigma factor; sigma factors are initiation factors that promote the attachment of RNA polymerase to specific initiation sites and are then released; contains a DUF6596 domain

Gene Ontology:  GO:0016987
PubMed:  26131973

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
COG4941 COG4941
Predicted RNA polymerase sigma factor, contains C-terminal TPR domain [Transcription];
3-417 0e+00

Predicted RNA polymerase sigma factor, contains C-terminal TPR domain [Transcription];


:

Pssm-ID: 443968 [Multi-domain]  Cd Length: 412  Bit Score: 536.60  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 750432401   3 QTVQRTIDAIWRIESAKLIAGLARMLRDLGAAEDLAQDVLVTALERWPETGIPDNPGAWLMTAAKRRAIDLIRRNKKQSE 82
Cdd:COG4941    2 SDARRAIEALFREESGRLVAALARRFGDLDLAEDAVQDAFLAALEQWPRDGVPDNPAAWLYTVARRRAIDRLRREARRRR 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 750432401  83 KYEELGRSGATftEDEADLAMEGEVGDDLLRLIFATCHPSLSQEARVALTLRLLGGLTTEEIARAFLLAESTIAQRIVRA 162
Cdd:COG4941   82 KEAELAADLEA--EAPAEDADDDDIPDDRLRLLFTCCHPALSPEAQVALTLRLVGGLTTAEIARAFLVPEATMAQRIVRA 159

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 750432401 163 KRTLSAQRAAFEVPTDkEELKARLTAVFEVIYLMFNEGYAATSGGSWTRPLLCQEALRLGRILAEVAPAEPEVHGLVALM 242
Cdd:COG4941  160 KRKIREAGIPFEVPDA-AELPERLDAVLAVIYLIFNEGYAASSGDDLVRADLCDEAIRLARLLAELLPDEPEVHGLLALM 238

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 750432401 243 EIQSSRLRTRVNAAGEPILLMDQNRALWDHLLIRRGLAALERAQSLGQPlGPYALQASIAACHARACTAADTDWVRIAAL 322
Cdd:COG4941  239 LLHAARRPARTDADGELVLLEDQDRSRWDRALIAEGLALLERALAGGRP-GPYQLQAAIAAVHARAPSAEDTDWPQILAL 317

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 750432401 323 YEALLRIMPSPVVELNRAVAIAMAFGPAFGLQLIDELMDMQALRDYHLLPSVRGDLLAKLGRMDEAREAFERAAMLTSNA 402
Cdd:COG4941  318 YDALLRLAPSPVVALNRAVAVAMADGPEAGLALLDALAAEPRLAGYHLLHAVRADLLRRLGRRAEARAAYRRALALTRNE 397

                        410
                 ....*....|....*
gi 750432401 403 PERELMLRRAADCHS 417
Cdd:COG4941  398 AERAFLRRRLAALAA 412
 
Name Accession Description Interval E-value
COG4941 COG4941
Predicted RNA polymerase sigma factor, contains C-terminal TPR domain [Transcription];
3-417 0e+00

Predicted RNA polymerase sigma factor, contains C-terminal TPR domain [Transcription];


Pssm-ID: 443968 [Multi-domain]  Cd Length: 412  Bit Score: 536.60  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 750432401   3 QTVQRTIDAIWRIESAKLIAGLARMLRDLGAAEDLAQDVLVTALERWPETGIPDNPGAWLMTAAKRRAIDLIRRNKKQSE 82
Cdd:COG4941    2 SDARRAIEALFREESGRLVAALARRFGDLDLAEDAVQDAFLAALEQWPRDGVPDNPAAWLYTVARRRAIDRLRREARRRR 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 750432401  83 KYEELGRSGATftEDEADLAMEGEVGDDLLRLIFATCHPSLSQEARVALTLRLLGGLTTEEIARAFLLAESTIAQRIVRA 162
Cdd:COG4941   82 KEAELAADLEA--EAPAEDADDDDIPDDRLRLLFTCCHPALSPEAQVALTLRLVGGLTTAEIARAFLVPEATMAQRIVRA 159

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 750432401 163 KRTLSAQRAAFEVPTDkEELKARLTAVFEVIYLMFNEGYAATSGGSWTRPLLCQEALRLGRILAEVAPAEPEVHGLVALM 242
Cdd:COG4941  160 KRKIREAGIPFEVPDA-AELPERLDAVLAVIYLIFNEGYAASSGDDLVRADLCDEAIRLARLLAELLPDEPEVHGLLALM 238

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 750432401 243 EIQSSRLRTRVNAAGEPILLMDQNRALWDHLLIRRGLAALERAQSLGQPlGPYALQASIAACHARACTAADTDWVRIAAL 322
Cdd:COG4941  239 LLHAARRPARTDADGELVLLEDQDRSRWDRALIAEGLALLERALAGGRP-GPYQLQAAIAAVHARAPSAEDTDWPQILAL 317

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 750432401 323 YEALLRIMPSPVVELNRAVAIAMAFGPAFGLQLIDELMDMQALRDYHLLPSVRGDLLAKLGRMDEAREAFERAAMLTSNA 402
Cdd:COG4941  318 YDALLRLAPSPVVALNRAVAVAMADGPEAGLALLDALAAEPRLAGYHLLHAVRADLLRRLGRRAEARAAYRRALALTRNE 397

                        410
                 ....*....|....*
gi 750432401 403 PERELMLRRAADCHS 417
Cdd:COG4941  398 AERAFLRRRLAALAA 412
DUF6596 pfam20239
Family of unknown function (DUF6596); This presumed domain is found at the C-terminus of ...
 185-285 3.49e-40

Family of unknown function (DUF6596); This presumed domain is found at the C-terminus of bacterial RNA polymerase ECF sigma factor proteins.


Pssm-ID: 466390  Cd Length: 102  Bit Score: 138.45  E-value: 3.49e-40
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 750432401  185 RLTAVFEVIYLMFNEGYAATSGGSWTRPLLCQEALRLGRILAEVAPAEPEVHGLVALMEIQSSRLRTRVNAAGEPILLMD 264
Cdd:pfam20239   1 RLDAVLEVLYLLFNEGYAATSGDQLIREDLCSEALRLARLLAELLPDEPEVLGLLALMLLHAARRPARVDADGELVPLAE 80

                          90       100
                  ....*....|....*....|.
gi 750432401  265 QNRALWDHLLIRRGLAALERA 285
Cdd:pfam20239  81 QDRSLWDRALIAEGLALLERA 101
sigma70-ECF TIGR02937
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ...
 24-169 2.20e-11

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: 61.59  E-value: 2.20e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 750432401   24 LARMLRDLGAAEDLAQDVLVTALERWPETGIPDNPGAWLMTAAKRRAIDLIRRNKKQSEKYEELgrsgatFTEDEADLAM 103
Cdd:TIGR02937  18 ARRYLGDDADAEDLVQEAFLKLLEALDRFDPEGSFKAWLFRIARNLILDYLRRKRRLRRELDLL------EELLDSDPSP 91

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 750432401  104 EGEVGDDLLRLIFATCHPSLSQEARVALTLRLLGGLTTEEIARAFLLAESTIAQRIVRAKRTLSAQ 169
Cdd:TIGR02937  92 EEELEQEEEREALREALEKLPEREREVLVLRYLEGLSYKEIAEILGISVGTVKRRLKRARKKLREL 157
sigI PRK09635
RNA polymerase sigma factor SigI; Provisional
 3-175 2.11e-06

RNA polymerase sigma factor SigI; Provisional


Pssm-ID: 182008 [Multi-domain]  Cd Length: 290  Bit Score: 49.19  E-value: 2.11e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 750432401   3 QTVQRTIDAIWRIESAKLIAGLARMLRDLGAAEDLAQDVLVTaLERWPETGIpDNPGAWLMTAAKRRAIDLIRRNKKQSE 82
Cdd:PRK09635   1 MSQHDPVSAAWRAHRAYLVDLAFRMVGDIGVAEDMVQEAFSR-LLRAPVGDI-DDERGWLIVVTSRLCLDHIKSASTRRE 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 750432401  83 KYEELG----RSGATFTEDEAD-LAMEGEVGDDLLRLIfatchPSLSQEARVALTLRLLGGLTTEEIARAFLLAESTIAQ 157
Cdd:PRK09635  79 RPQDIAawhdGDASVSSVDPADrVTLDDEVRLALLIML-----ERLGPAERVVFVLHEIFGLPYQQIATTIGSQASTCRQ 153

                        170
                 ....*....|....*...
gi 750432401 158 RIVRAKRTLSAQRAAFEV 175
Cdd:PRK09635 154 LAHRARRKINESRIAASV 171
 
Name Accession Description Interval E-value
COG4941 COG4941
Predicted RNA polymerase sigma factor, contains C-terminal TPR domain [Transcription];
3-417 0e+00

Predicted RNA polymerase sigma factor, contains C-terminal TPR domain [Transcription];


Pssm-ID: 443968 [Multi-domain]  Cd Length: 412  Bit Score: 536.60  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 750432401   3 QTVQRTIDAIWRIESAKLIAGLARMLRDLGAAEDLAQDVLVTALERWPETGIPDNPGAWLMTAAKRRAIDLIRRNKKQSE 82
Cdd:COG4941    2 SDARRAIEALFREESGRLVAALARRFGDLDLAEDAVQDAFLAALEQWPRDGVPDNPAAWLYTVARRRAIDRLRREARRRR 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 750432401  83 KYEELGRSGATftEDEADLAMEGEVGDDLLRLIFATCHPSLSQEARVALTLRLLGGLTTEEIARAFLLAESTIAQRIVRA 162
Cdd:COG4941   82 KEAELAADLEA--EAPAEDADDDDIPDDRLRLLFTCCHPALSPEAQVALTLRLVGGLTTAEIARAFLVPEATMAQRIVRA 159

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 750432401 163 KRTLSAQRAAFEVPTDkEELKARLTAVFEVIYLMFNEGYAATSGGSWTRPLLCQEALRLGRILAEVAPAEPEVHGLVALM 242
Cdd:COG4941  160 KRKIREAGIPFEVPDA-AELPERLDAVLAVIYLIFNEGYAASSGDDLVRADLCDEAIRLARLLAELLPDEPEVHGLLALM 238

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 750432401 243 EIQSSRLRTRVNAAGEPILLMDQNRALWDHLLIRRGLAALERAQSLGQPlGPYALQASIAACHARACTAADTDWVRIAAL 322
Cdd:COG4941  239 LLHAARRPARTDADGELVLLEDQDRSRWDRALIAEGLALLERALAGGRP-GPYQLQAAIAAVHARAPSAEDTDWPQILAL 317

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 750432401 323 YEALLRIMPSPVVELNRAVAIAMAFGPAFGLQLIDELMDMQALRDYHLLPSVRGDLLAKLGRMDEAREAFERAAMLTSNA 402
Cdd:COG4941  318 YDALLRLAPSPVVALNRAVAVAMADGPEAGLALLDALAAEPRLAGYHLLHAVRADLLRRLGRRAEARAAYRRALALTRNE 397

                        410
                 ....*....|....*
gi 750432401 403 PERELMLRRAADCHS 417
Cdd:COG4941  398 AERAFLRRRLAALAA 412
DUF6596 pfam20239
Family of unknown function (DUF6596); This presumed domain is found at the C-terminus of ...
 185-285 3.49e-40

Family of unknown function (DUF6596); This presumed domain is found at the C-terminus of bacterial RNA polymerase ECF sigma factor proteins.


Pssm-ID: 466390  Cd Length: 102  Bit Score: 138.45  E-value: 3.49e-40
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 750432401  185 RLTAVFEVIYLMFNEGYAATSGGSWTRPLLCQEALRLGRILAEVAPAEPEVHGLVALMEIQSSRLRTRVNAAGEPILLMD 264
Cdd:pfam20239   1 RLDAVLEVLYLLFNEGYAATSGDQLIREDLCSEALRLARLLAELLPDEPEVLGLLALMLLHAARRPARVDADGELVPLAE 80

                          90       100
                  ....*....|....*....|.
gi 750432401  265 QNRALWDHLLIRRGLAALERA 285
Cdd:pfam20239  81 QDRSLWDRALIAEGLALLERA 101
RpoE COG1595
DNA-directed RNA polymerase specialized sigma subunit, sigma24 family [Transcription]; ...
 1-175 8.89e-17

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: 77.73  E-value: 8.89e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 750432401   1 MPQTVQRTIDAIWRIESAKLIAGLARMLRDLGAAEDLAQDVLVTALERWPETGIPDNPGAWLMTAAKRRAIDLIRRNKKQ 80
Cdd:COG1595   11 LRAGDEAAFEELYERYRPRLYRYARRLLGDRADAEDLVQETFLRLWRKLDSFRGRGSFRAWLYRIARNLAIDHLRKRRRR 90

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 750432401  81 SEKYEELGRSGATFTEDEADLAMEGEVGDDLLRLIFAtchpsLSQEARVALTLRLLGGLTTEEIARAFLLAESTIAQRIV 160
Cdd:COG1595   91 RELLDELAEELPDEAADPEEALEAEELLEALLAALER-----LPPRQREVLVLRYLEGLSYAEIAEILGISEGTVKSRLS 165

                        170
                 ....*....|....*
gi 750432401 161 RAKRTLSAQRAAFEV 175
Cdd:COG1595  166 RARKKLREALEEEGA 180
sigma70-ECF TIGR02937
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ...
 24-169 2.20e-11

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: 61.59  E-value: 2.20e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 750432401   24 LARMLRDLGAAEDLAQDVLVTALERWPETGIPDNPGAWLMTAAKRRAIDLIRRNKKQSEKYEELgrsgatFTEDEADLAM 103
Cdd:TIGR02937  18 ARRYLGDDADAEDLVQEAFLKLLEALDRFDPEGSFKAWLFRIARNLILDYLRRKRRLRRELDLL------EELLDSDPSP 91

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 750432401  104 EGEVGDDLLRLIFATCHPSLSQEARVALTLRLLGGLTTEEIARAFLLAESTIAQRIVRAKRTLSAQ 169
Cdd:TIGR02937  92 EEELEQEEEREALREALEKLPEREREVLVLRYLEGLSYKEIAEILGISVGTVKRRLKRARKKLREL 157
Sigma70_r2 pfam04542
Sigma-70 region 2; Region 2 of sigma-70 is the most conserved region of the entire protein. ...
 18-79 3.65e-08

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: 49.89  E-value: 3.65e-08
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 750432401   18 AKLIAGLA-RMLRDLGAAEDLAQDVLVTALERWP--ETGIPDNPGAWLMTAAKRRAIDLIRRNKK 79
Cdd:pfam04542   6 LPLVYSLArRYLGDGADAEDLVQEGFLGLWRAIErfDPERGVSFSTWLYTIIRNAIIDYLRKQRR 70
SigX4 TIGR02957
RNA polymerase sigma-70 factor, TIGR02957 family; This group of sigma factors are members of ...
 26-181 8.73e-08

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: 53.13  E-value: 8.73e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 750432401   26 RMLRDLGAAEDLAQDVLVtaleRWPETGI--PDNPGAWLMTAAKRRAIDLIRRNKKQSEKYeelgrSGATFTE----DEA 99
Cdd:TIGR02957  16 RMLGSVADAEDIVQETFL----RWQEADRaqIENPKAYLTKVVTRRCIDVLRSARARREVY-----VGPWLPEplltTSA 86

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 750432401  100 DLAMEGEVGDDlLRLIFATCHPSLSQEARVALTLRLLGGLTTEEIARAFLLAESTIAQRIVRAKRTLSAQRAAFEVPTDK 179
Cdd:TIGR02957  87 DPAESVELAES-LSMAYLLLLERLSPLERAVFVLREVFDYPYEEIASIVGKSEANCRQLVSRARRHLDARRPRFEVSREE 165


                  ..
gi 750432401  180 EE 181
Cdd:TIGR02957 166 SR 167
sigI PRK09635
RNA polymerase sigma factor SigI; Provisional
 3-175 2.11e-06

RNA polymerase sigma factor SigI; Provisional


Pssm-ID: 182008 [Multi-domain]  Cd Length: 290  Bit Score: 49.19  E-value: 2.11e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 750432401   3 QTVQRTIDAIWRIESAKLIAGLARMLRDLGAAEDLAQDVLVTaLERWPETGIpDNPGAWLMTAAKRRAIDLIRRNKKQSE 82
Cdd:PRK09635   1 MSQHDPVSAAWRAHRAYLVDLAFRMVGDIGVAEDMVQEAFSR-LLRAPVGDI-DDERGWLIVVTSRLCLDHIKSASTRRE 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 750432401  83 KYEELG----RSGATFTEDEAD-LAMEGEVGDDLLRLIfatchPSLSQEARVALTLRLLGGLTTEEIARAFLLAESTIAQ 157
Cdd:PRK09635  79 RPQDIAawhdGDASVSSVDPADrVTLDDEVRLALLIML-----ERLGPAERVVFVLHEIFGLPYQQIATTIGSQASTCRQ 153

                        170
                 ....*....|....*...
gi 750432401 158 RIVRAKRTLSAQRAAFEV 175
Cdd:PRK09635 154 LAHRARRKINESRIAASV 171
PRK12514 PRK12514
RNA polymerase sigma factor; Provisional
 10-113 6.59e-06

RNA polymerase sigma factor; Provisional


Pssm-ID: 105710 [Multi-domain]  Cd Length: 179  Bit Score: 46.35  E-value: 6.59e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 750432401  10 DAIWRIESAKLIAGLARMLRDLGAAEDLAQDVLVTALERWPETGIPD-NPGAWLMTAAKRRAIDLIRRNKKQSEKYEELG 88
Cdd:PRK12514  22 SSLYDATSAKLFGICLRVLKDRSEAEEALQDVYVKIWTKADRFAVSGlSPMTWLITIARNHAIDRLRARKAVAVDIDEAH 101

                         90       100
                 ....*....|....*....|....*..
gi 750432401  89 R--SGATFTEDEADLAMEGEVGDDLLR 113
Cdd:PRK12514 102 DlaDPSPGPEAEVIAGDEGQRIDACLE 128
PRK09639 PRK09639
RNA polymerase sigma factor SigX; Provisional
 24-101 4.36e-05

RNA polymerase sigma factor SigX; Provisional


Pssm-ID: 236602 [Multi-domain]  Cd Length: 166  Bit Score: 43.78  E-value: 4.36e-05
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 750432401  24 LARMLRDLGAAEDLAQDVLVTALeRWPETGIpDNPGAWLMTAAKRRAIDLIRRNKKQSEKYEElgrsgaTFTEDEADL 101
Cdd:PRK09639  20 IFYIVKDRTQAEDLAQEVFLRLY-RSDFKGI-ENEKGWLIKSARNVAYNYLRSEKRRRARILG------EFQWQEVDN 89
Sig70_bacteroi1 TIGR02985
RNA polymerase sigma-70 factor, Bacteroides expansion family 1; This group of sigma factors ...
 26-102 2.57e-04

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: 41.39  E-value: 2.57e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 750432401   26 RMLRDLGAAEDLAQDVLVTALERWPETGIPDNPGAWLMTAAKRRAIDLIRRNKKQSEKYEELgrsgATFTEDEADLA 102
Cdd:TIGR02985  20 RYVKDEEDAEDIVQDVFLKLWENRETLEISESIKAYLFTIVKNRCLNYLRHKQVEEKYQEEL----AEIEERELSEA 92
PRK12515 PRK12515
RNA polymerase sigma factor; Provisional
 24-167 2.78e-04

RNA polymerase sigma factor; Provisional


Pssm-ID: 183567 [Multi-domain]  Cd Length: 189  Bit Score: 41.64  E-value: 2.78e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 750432401  24 LARMLRDLGAAEDLAQDVLvtaLERWPETGIPDNPGA---WLMTAAKRRAIDLIRRnkkqsEKYEELGRSGATFTEDEAD 100
Cdd:PRK12515  39 GLRLVRDEQTAEDLVSEVF---LDVWRQAGQFEGRSQvstWLLSIARFKALSALRR-----RKHEEIDDEAAAAIEDGAD 110

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 750432401 101 ---LAMEGEVGDDLLRlifaTCHPSLSQEARVALTLRLLGGLTTEEIARAFLLAESTIAQRIVRAKRTLS 167
Cdd:PRK12515 111 tpeVALQKSDTSAALR----ACLAKLSPAHREIIDLVYYHEKSVEEVGEIVGIPESTVKTRMFYARKKLA 176
PRK11924 PRK11924
RNA polymerase sigma factor; Provisional
 21-166 4.05e-04

RNA polymerase sigma factor; Provisional


Pssm-ID: 183384 [Multi-domain]  Cd Length: 179  Bit Score: 41.11  E-value: 4.05e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 750432401  21 IAGLARM-LRDLGAAEDLAQDVLVTALERWPETGIPDNPGAWLMTAAKRRAIDLIRRNKKQSEKyeelgrsgATFTEDEA 99
Cdd:PRK11924  26 LLRYARRqLGDRALAEDAVQEAFLRAWRKADLFNGKGSARTWLLTIARNVCYDLLRRRRREKAV--------LSDDALEP 97

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 750432401 100 DLAMEGE-VGDDLLRLIFA----TCHPSLSQEARVALTLRLLGGLTTEEIARAFLLAESTIAQRIVRAKRTL 166
Cdd:PRK11924  98 EFAETAEtPEAALLAKDDLaridRCLDALPVKQREVFLLRYVEGLSYREIAEILGVPVGTVKSRLRRARQLL 169
PRK12511 PRK12511
RNA polymerase sigma factor; Provisional
 25-189 1.65e-03

RNA polymerase sigma factor; Provisional


Pssm-ID: 237123 [Multi-domain]  Cd Length: 182  Bit Score: 39.38  E-value: 1.65e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 750432401  25 ARML-RDLGAAEDLAQDVLVTALERWPETGIPDNPGAWLMTAAKRRAIDLIRRNKKQSEKYEELGRsgatFTEDEADLAM 103
Cdd:PRK12511  21 ARSLtRDSAEAEDLVHDALVRALERRASFRSGGNLRTWLMSILHNAFIDELRRRRVEARRADELAV----LADASLPAAQ 96

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 750432401 104 EGEVGDDLLRLIFAtchpSLSQEARVALTLRLLGGLTTEEIARAFLLAESTIAQRIVRAKrtlsAQRAAFEVPTDKEELK 183
Cdd:PRK12511  97 EHAVRLAQIRDAFF----DLPEEQRAALHLVAIEGLSYQEAAAVLGIPIGTLMSRIGRAR----AALRAFEEGTGPARGR 168


                 ....*.
gi 750432401 184 ARLTAV 189
Cdd:PRK12511 169 AHLRVV 174
PRK09645 PRK09645
ECF RNA polymerase sigma factor SigL;
1-166 1.95e-03

ECF RNA polymerase sigma factor SigL;


Pssm-ID: 236605 [Multi-domain]  Cd Length: 173  Bit Score: 38.91  E-value: 1.95e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 750432401   1 MPQTVQRTIDAIWRIESAKLIAGLARMLRDLGAAEDLAQDVLVTALERWPETGIPDNPG-AWLMTAAKRRAIDLIRRNKK 79
Cdd:PRK09645   3 MATAEAALMRALYDEHAAPLWRYALRLTGDRARAEDVVQETLLRAWQHPEVLADTGRSArAWLFTVARNLVIDERRSARA 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 750432401  80 QSEkyeelgrSGATFTEDEADLAMEGEVGDDLLRLIFATCHPSLSQEARVALTLRLLGGLTTEEIARAFLLAESTIAQRI 159
Cdd:PRK09645  83 RPV-------EGGDDVLGVPEQSAPDEVDRALDRLLVADALAQLSPEHRAVLVRSYYRGWSTAQIAADLGIPEGTVKSRL 155


                 ....*..
gi 750432401 160 VRAKRTL 166
Cdd:PRK09645 156 HYALRAL 162
PRK09646 PRK09646
ECF RNA polymerase sigma factor SigK;
26-83 3.24e-03

ECF RNA polymerase sigma factor SigK;


Pssm-ID: 182015 [Multi-domain]  Cd Length: 194  Bit Score: 38.50  E-value: 3.24e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 750432401  26 RMLRDLGAAEDLAQDVLV----TALERWPETGipdNPGAWLMTAAKRRAIDLIRRNKKQSEK 83
Cdd:PRK09646  49 RVLRDPGYSEETTQEVYLevwrTASRFDPARG---SALAWLLTLAHRRAVDRVRSEQAASQR 107
Sig-70_gvs1 TIGR02989
RNA polymerase sigma-70 factor, Rhodopirellula/Verrucomicrobium family; This group of sigma ...
 20-80 3.25e-03

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: 38.07  E-value: 3.25e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 750432401   20 LIAGLARMLRDLGAAEDLAQDVLVTALERWPETGIPDNPGAWLMTAAKRRAIDLIRRNKKQ 80
Cdd:TIGR02989  14 LRAFVRSLVADRDDVDDVLQETFVVAWRKFDQFDPGTNFVAWARGIARNKVLNYRRKLGRD 74
 
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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