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Conserved domains on  [gi|1125296280|gb|OLC39886|]
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MAG: RNA polymerase subunit sigma-24 [Candidatus Rokubacteria bacterium 13_1_40CM_4_69_5]

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];
4-404 0e+00

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


:

Pssm-ID: 443968 [Multi-domain]  Cd Length: 412  Bit Score: 532.36  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125296280   4 TDTHRAIEAVWRIESAKVIAGLTRITGDVGLAEDLAQDALVAALERWPESGVPDNPGAWLMTTAKRRAIDLFRRGKLLER 83
Cdd:COG4941     2 SDARRAIEALFREESGRLVAALARRFGDLDLAEDAVQDAFLAALEQWPRDGVPDNPAAWLYTVARRRAIDRLRREARRRR 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125296280  84 KHAELGHDLvarqeSPEPGLAAAIDDHVGDDLLGLMFTTCHPVLGTEARAALTLRLLGGLTTDEIARAFLVPEPTVAQRI 163
Cdd:COG4941    82 KEAELAADL-----EAEAPAEDADDDDIPDDRLRLLFTCCHPALSPEAQVALTLRLVGGLTTAEIARAFLVPEATMAQRI 156

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125296280 164 VRAKRTLREAHVPFDVPRGAELTARLSSVLEVIYLIFNEGYSATAGDDWVRPALCEDALRLGRILAELAPDDPEVHGLVA 243
Cdd:COG4941   157 VRAKRKIREAGIPFEVPDAAELPERLDAVLAVIYLIFNEGYAASSGDDLVRADLCDEAIRLARLLAELLPDEPEVHGLLA 236

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125296280 244 LMEIQASRLKARVGPAGEPILLLDQDRARWDQLLVRRGLAALERAQQLaGALGPYALQAAIAACHARARTPEETDWTRIT 323
Cdd:COG4941   237 LMLLHAARRPARTDADGELVLLEDQDRSRWDRALIAEGLALLERALAG-GRPGPYQLQAAIAAVHARAPSAEDTDWPQIL 315

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125296280 324 ALYNALAQLTQSPIVELNRAVAYSMAFGPAAGLEIVDALTSEPALQSYHLLPSVRGDFLAKLGRFDEARKELERAASLTQ 403
Cdd:COG4941   316 ALYDALLRLAPSPVVALNRAVAVAMADGPEAGLALLDALAAEPRLAGYHLLHAVRADLLRRLGRRAEARAAYRRALALTR 395


                  .
gi 1125296280 404 N 404
Cdd:COG4941   396 N 396
 
Name Accession Description Interval E-value
COG4941 COG4941
Predicted RNA polymerase sigma factor, contains C-terminal TPR domain [Transcription];
4-404 0e+00

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


Pssm-ID: 443968 [Multi-domain]  Cd Length: 412  Bit Score: 532.36  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125296280   4 TDTHRAIEAVWRIESAKVIAGLTRITGDVGLAEDLAQDALVAALERWPESGVPDNPGAWLMTTAKRRAIDLFRRGKLLER 83
Cdd:COG4941     2 SDARRAIEALFREESGRLVAALARRFGDLDLAEDAVQDAFLAALEQWPRDGVPDNPAAWLYTVARRRAIDRLRREARRRR 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125296280  84 KHAELGHDLvarqeSPEPGLAAAIDDHVGDDLLGLMFTTCHPVLGTEARAALTLRLLGGLTTDEIARAFLVPEPTVAQRI 163
Cdd:COG4941    82 KEAELAADL-----EAEAPAEDADDDDIPDDRLRLLFTCCHPALSPEAQVALTLRLVGGLTTAEIARAFLVPEATMAQRI 156

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125296280 164 VRAKRTLREAHVPFDVPRGAELTARLSSVLEVIYLIFNEGYSATAGDDWVRPALCEDALRLGRILAELAPDDPEVHGLVA 243
Cdd:COG4941   157 VRAKRKIREAGIPFEVPDAAELPERLDAVLAVIYLIFNEGYAASSGDDLVRADLCDEAIRLARLLAELLPDEPEVHGLLA 236

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125296280 244 LMEIQASRLKARVGPAGEPILLLDQDRARWDQLLVRRGLAALERAQQLaGALGPYALQAAIAACHARARTPEETDWTRIT 323
Cdd:COG4941   237 LMLLHAARRPARTDADGELVLLEDQDRSRWDRALIAEGLALLERALAG-GRPGPYQLQAAIAAVHARAPSAEDTDWPQIL 315

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125296280 324 ALYNALAQLTQSPIVELNRAVAYSMAFGPAAGLEIVDALTSEPALQSYHLLPSVRGDFLAKLGRFDEARKELERAASLTQ 403
Cdd:COG4941   316 ALYDALLRLAPSPVVALNRAVAVAMADGPEAGLALLDALAAEPRLAGYHLLHAVRADLLRRLGRRAEARAAYRRALALTR 395


                  .
gi 1125296280 404 N 404
Cdd:COG4941   396 N 396
DUF6596 pfam20239
Family of unknown function (DUF6596); This presumed domain is found at the C-terminus of ...
 188-288 5.53e-44

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: 148.85  E-value: 5.53e-44
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125296280 188 RLSSVLEVIYLIFNEGYSATAGDDWVRPALCEDALRLGRILAELAPDDPEVHGLVALMEIQASRLKARVGPAGEPILLLD 267
Cdd:pfam20239   1 RLDAVLEVLYLLFNEGYAATSGDQLIREDLCSEALRLARLLAELLPDEPEVLGLLALMLLHAARRPARVDADGELVPLAE 80

                          90       100
                  ....*....|....*....|.
gi 1125296280 268 QDRARWDQLLVRRGLAALERA 288
Cdd:pfam20239  81 QDRSLWDRALIAEGLALLERA 101
sigma70-ECF TIGR02937
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ...
 8-173 1.57e-12

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: 65.06  E-value: 1.57e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125296280   8 RAIEAVWRIESAKVIAGLTRITGDVGLAEDLAQDALVAALERWPESGVPDNPGAWLMTTAKRRAIDLFRRgklleRKHAE 87
Cdd:TIGR02937   1 EAFEELYERYLPLVYRYARRYLGDDADAEDLVQEAFLKLLEALDRFDPEGSFKAWLFRIARNLILDYLRR-----KRRLR 75

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125296280  88 LGHDLVARQESPEPGLAAAIDDHVGDDLLGLMFTTchpvLGTEARAALTLRLLGGLTTDEIARAFLVPEPTVAQRIVRAK 167
Cdd:TIGR02937  76 RELDLLEELLDSDPSPEEELEQEEEREALREALEK----LPEREREVLVLRYLEGLSYKEIAEILGISVGTVKRRLKRAR 151


                  ....*.
gi 1125296280 168 RTLREA 173
Cdd:TIGR02937 152 KKLREL 157
PRK11924 PRK11924
RNA polymerase sigma factor; Provisional
 1-173 2.40e-09

RNA polymerase sigma factor; Provisional


Pssm-ID: 183384 [Multi-domain]  Cd Length: 179  Bit Score: 56.52  E-value: 2.40e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125296280   1 MTATDTHRAIEAVWRIESAKVIAGLTRITGDVGLAEDLAQDALVAALERWPESGVPDNPGAWLMTTAKRRAIDLFRRGKL 80
Cdd:PRK11924    6 VDATGDKEAFSELFRPHAPDLLRYARRQLGDRALAEDAVQEAFLRAWRKADLFNGKGSARTWLLTIARNVCYDLLRRRRR 85

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125296280  81 --LERKHAELGHDLVARQESPEPGLAAAIDdhvgddllGLMFTTCHPVLGTEARAALTLRLLGGLTTDEIARAFLVPEPT 158
Cdd:PRK11924   86 ekAVLSDDALEPEFAETAETPEAALLAKDD--------LARIDRCLDALPVKQREVFLLRYVEGLSYREIAEILGVPVGT 157

                         170
                  ....*....|....*
gi 1125296280 159 VAQRIVRAKRTLREA 173
Cdd:PRK11924  158 VKSRLRRARQLLREC 172
 
Name Accession Description Interval E-value
COG4941 COG4941
Predicted RNA polymerase sigma factor, contains C-terminal TPR domain [Transcription];
4-404 0e+00

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


Pssm-ID: 443968 [Multi-domain]  Cd Length: 412  Bit Score: 532.36  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125296280   4 TDTHRAIEAVWRIESAKVIAGLTRITGDVGLAEDLAQDALVAALERWPESGVPDNPGAWLMTTAKRRAIDLFRRGKLLER 83
Cdd:COG4941     2 SDARRAIEALFREESGRLVAALARRFGDLDLAEDAVQDAFLAALEQWPRDGVPDNPAAWLYTVARRRAIDRLRREARRRR 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125296280  84 KHAELGHDLvarqeSPEPGLAAAIDDHVGDDLLGLMFTTCHPVLGTEARAALTLRLLGGLTTDEIARAFLVPEPTVAQRI 163
Cdd:COG4941    82 KEAELAADL-----EAEAPAEDADDDDIPDDRLRLLFTCCHPALSPEAQVALTLRLVGGLTTAEIARAFLVPEATMAQRI 156

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125296280 164 VRAKRTLREAHVPFDVPRGAELTARLSSVLEVIYLIFNEGYSATAGDDWVRPALCEDALRLGRILAELAPDDPEVHGLVA 243
Cdd:COG4941   157 VRAKRKIREAGIPFEVPDAAELPERLDAVLAVIYLIFNEGYAASSGDDLVRADLCDEAIRLARLLAELLPDEPEVHGLLA 236

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125296280 244 LMEIQASRLKARVGPAGEPILLLDQDRARWDQLLVRRGLAALERAQQLaGALGPYALQAAIAACHARARTPEETDWTRIT 323
Cdd:COG4941   237 LMLLHAARRPARTDADGELVLLEDQDRSRWDRALIAEGLALLERALAG-GRPGPYQLQAAIAAVHARAPSAEDTDWPQIL 315

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125296280 324 ALYNALAQLTQSPIVELNRAVAYSMAFGPAAGLEIVDALTSEPALQSYHLLPSVRGDFLAKLGRFDEARKELERAASLTQ 403
Cdd:COG4941   316 ALYDALLRLAPSPVVALNRAVAVAMADGPEAGLALLDALAAEPRLAGYHLLHAVRADLLRRLGRRAEARAAYRRALALTR 395


                  .
gi 1125296280 404 N 404
Cdd:COG4941   396 N 396
DUF6596 pfam20239
Family of unknown function (DUF6596); This presumed domain is found at the C-terminus of ...
 188-288 5.53e-44

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: 148.85  E-value: 5.53e-44
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125296280 188 RLSSVLEVIYLIFNEGYSATAGDDWVRPALCEDALRLGRILAELAPDDPEVHGLVALMEIQASRLKARVGPAGEPILLLD 267
Cdd:pfam20239   1 RLDAVLEVLYLLFNEGYAATSGDQLIREDLCSEALRLARLLAELLPDEPEVLGLLALMLLHAARRPARVDADGELVPLAE 80

                          90       100
                  ....*....|....*....|.
gi 1125296280 268 QDRARWDQLLVRRGLAALERA 288
Cdd:pfam20239  81 QDRSLWDRALIAEGLALLERA 101
RpoE COG1595
DNA-directed RNA polymerase specialized sigma subunit, sigma24 family [Transcription]; ...
 7-173 3.81e-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: 78.88  E-value: 3.81e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125296280   7 HRAIEAVWRIESAKVIAGLTRITGDVGLAEDLAQDALVAALERWPESGVPDNPGAWLMTTAKRRAIDLFRRGKLLERKHA 86
Cdd:COG1595    16 EAAFEELYERYRPRLYRYARRLLGDRADAEDLVQETFLRLWRKLDSFRGRGSFRAWLYRIARNLAIDHLRKRRRRRELLD 95

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125296280  87 ELGHDLVARQESPEpglAAAIDDHVGDDLLGLMFTtchpvLGTEARAALTLRLLGGLTTDEIARAFLVPEPTVAQRIVRA 166
Cdd:COG1595    96 ELAEELPDEAADPE---EALEAEELLEALLAALER-----LPPRQREVLVLRYLEGLSYAEIAEILGISEGTVKSRLSRA 167


                  ....*..
gi 1125296280 167 KRTLREA 173
Cdd:COG1595   168 RKKLREA 174
sigma70-ECF TIGR02937
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ...
 8-173 1.57e-12

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: 65.06  E-value: 1.57e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125296280   8 RAIEAVWRIESAKVIAGLTRITGDVGLAEDLAQDALVAALERWPESGVPDNPGAWLMTTAKRRAIDLFRRgklleRKHAE 87
Cdd:TIGR02937   1 EAFEELYERYLPLVYRYARRYLGDDADAEDLVQEAFLKLLEALDRFDPEGSFKAWLFRIARNLILDYLRR-----KRRLR 75

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125296280  88 LGHDLVARQESPEPGLAAAIDDHVGDDLLGLMFTTchpvLGTEARAALTLRLLGGLTTDEIARAFLVPEPTVAQRIVRAK 167
Cdd:TIGR02937  76 RELDLLEELLDSDPSPEEELEQEEEREALREALEK----LPEREREVLVLRYLEGLSYKEIAEILGISVGTVKRRLKRAR 151


                  ....*.
gi 1125296280 168 RTLREA 173
Cdd:TIGR02937 152 KKLREL 157
PRK11924 PRK11924
RNA polymerase sigma factor; Provisional
 1-173 2.40e-09

RNA polymerase sigma factor; Provisional


Pssm-ID: 183384 [Multi-domain]  Cd Length: 179  Bit Score: 56.52  E-value: 2.40e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125296280   1 MTATDTHRAIEAVWRIESAKVIAGLTRITGDVGLAEDLAQDALVAALERWPESGVPDNPGAWLMTTAKRRAIDLFRRGKL 80
Cdd:PRK11924    6 VDATGDKEAFSELFRPHAPDLLRYARRQLGDRALAEDAVQEAFLRAWRKADLFNGKGSARTWLLTIARNVCYDLLRRRRR 85

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125296280  81 --LERKHAELGHDLVARQESPEPGLAAAIDdhvgddllGLMFTTCHPVLGTEARAALTLRLLGGLTTDEIARAFLVPEPT 158
Cdd:PRK11924   86 ekAVLSDDALEPEFAETAETPEAALLAKDD--------LARIDRCLDALPVKQREVFLLRYVEGLSYREIAEILGVPVGT 157

                         170
                  ....*....|....*
gi 1125296280 159 VAQRIVRAKRTLREA 173
Cdd:PRK11924  158 VKSRLRRARQLLREC 172
Sigma70_r2 pfam04542
Sigma-70 region 2; Region 2 of sigma-70 is the most conserved region of the entire protein. ...
 21-77 2.67e-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: 50.28  E-value: 2.67e-08
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1125296280  21 VIAGLTRITGDVGLAEDLAQDALVAALERWP--ESGVPDNPGAWLMTTAKRRAIDLFRR 77
Cdd:pfam04542   9 VYSLARRYLGDGADAEDLVQEGFLGLWRAIErfDPERGVSFSTWLYTIIRNAIIDYLRK 67
SigE-fam_strep TIGR02983
RNA polymerase sigma-70 factor, sigma-E family; This group of similar sigma-70 factors ...
 27-172 6.39e-08

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: 52.01  E-value: 6.39e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125296280  27 RITGDVGLAEDLAQDALVAALERWPESGVPDNPGAWLMTTAKRRAIDLFRRGKLLERKHAELghdlvarQESPEPGLAAA 106
Cdd:TIGR02983  25 LLTGDPHEAEDLVQEALVRTYVRWDRIRDPDAPDAYVRRVLVNLARSRWRRRRLLELPTREL-------PDAAAPDPAPD 97

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1125296280 107 IDDHvgDDLLGLMfttchPVLGTEARAALTLRLLGGLTTDEIARAFLVPEPTVAQRIVRAKRTLRE 172
Cdd:TIGR02983  98 VALR--AALARAL-----RRLPARQRAVVVLRYYEDLSEAQVAEALGISVGTVKSRLSRALARLRE 156
PRK12523 PRK12523
RNA polymerase sigma factor; Reviewed
 10-168 3.84e-07

RNA polymerase sigma factor; Reviewed


Pssm-ID: 183572 [Multi-domain]  Cd Length: 172  Bit Score: 49.85  E-value: 3.84e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125296280  10 IEAVWRIESAKVIAGLTRITGDVGLAEDLAQDALVAALERwPESGVPDNPGAWLMTTAKRRAIDLFRRGKLLERKHAELG 89
Cdd:PRK12523   12 VGALYRDHRGWLLAWLRRNVACRQRAEDLSQDTFVRLLGR-PELPTPREPRAFLAAVAKGLMFDHFRRAALEQAYLAELA 90

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1125296280  90 HDLVARQESPEPGLAAAIDDHVGDDLLGlmfttchpVLGTEARAALTLRLLGGLTTDEIARAFLVPEPTVAQRIVRAKR 168
Cdd:PRK12523   91 LVPEAEQPSPEEQHLILEDLKAIDRLLG--------KLSSKARAAFLYNRLDGMGHAEIAERLGVSVSRVRQYLAQGLR 161
PRK09645 PRK09645
ECF RNA polymerase sigma factor SigL;
1-173 1.64e-06

ECF RNA polymerase sigma factor SigL;


Pssm-ID: 236605 [Multi-domain]  Cd Length: 173  Bit Score: 48.15  E-value: 1.64e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125296280   1 MTATDTHRaIEAVWRIESAKVIAGLTRITGDVGLAEDLAQDALVAAlerWPESGVPDNPG----AWLMTTAKRRAIDLFR 76
Cdd:PRK09645    3 MATAEAAL-MRALYDEHAAPLWRYALRLTGDRARAEDVVQETLLRA---WQHPEVLADTGrsarAWLFTVARNLVIDERR 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125296280  77 RGKLlerKHAELGHDLVARQESPEPglaaaidDHVGDDLLGLMFTTCHPVLGTEARAALTLRLLGGLTTDEIARAFLVPE 156
Cdd:PRK09645   79 SARA---RPVEGGDDVLGVPEQSAP-------DEVDRALDRLLVADALAQLSPEHRAVLVRSYYRGWSTAQIAADLGIPE 148

                         170
                  ....*....|....*..
gi 1125296280 157 PTVAQRIVRAKRTLREA 173
Cdd:PRK09645  149 GTVKSRLHYALRALRLA 165
PRK12511 PRK12511
RNA polymerase sigma factor; Provisional
 25-172 2.66e-05

RNA polymerase sigma factor; Provisional


Pssm-ID: 237123 [Multi-domain]  Cd Length: 182  Bit Score: 44.78  E-value: 2.66e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125296280  25 LTRITGDvglAEDLAQDALVAALERWPESGVPDNPGAWLMTTAKRRAIDLFRRGKLLERKHAELGHdlvarqeSPEPGLA 104
Cdd:PRK12511   24 LTRDSAE---AEDLVHDALVRALERRASFRSGGNLRTWLMSILHNAFIDELRRRRVEARRADELAV-------LADASLP 93

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1125296280 105 AAIDDHVGDDLLGLMFTTchpvLGTEARAALTLRLLGGLTTDEIARAFLVPEPTVAQRIVRAKRTLRE 172
Cdd:PRK12511   94 AAQEHAVRLAQIRDAFFD----LPEEQRAALHLVAIEGLSYQEAAAVLGIPIGTLMSRIGRARAALRA 157
PRK09638 PRK09638
RNA polymerase sigma factor SigY; Reviewed
 25-171 4.46e-05

RNA polymerase sigma factor SigY; Reviewed


Pssm-ID: 182010 [Multi-domain]  Cd Length: 176  Bit Score: 43.86  E-value: 4.46e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125296280  25 LTRITGDVGLAEDLAQDALVAALERW----PESGVpdnpGAWLMTTAKRRAIDLFRRGKlLERKHAELGHDLVARQESPE 100
Cdd:PRK09638   35 LLKLTLDPDLAEDLVQETMLKAIENLssfqGRSKF----STWLISIASRLYKDHLRKQK-REKLRLQRAKEETLRKEKWE 109

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1125296280 101 pglaAAIDDHVGDDLLGLMFTtchpvLGTEARAALTLRLLGGLTTDEIARAFLVPEPTVAQRIVRAKRTLR 171
Cdd:PRK09638  110 ----AAIKGAEWSEMLDALSK-----LDPEFRAPVILKHYYGYTYEEIAKMLNIPEGTVKSRVHHGIKQLR 171
sigI PRK09635
RNA polymerase sigma factor SigI; Provisional
 7-179 6.51e-05

RNA polymerase sigma factor SigI; Provisional


Pssm-ID: 182008 [Multi-domain]  Cd Length: 290  Bit Score: 44.57  E-value: 6.51e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125296280   7 HRAIEAVWRIESAKVIAGLTRITGDVGLAEDLAQDALVaALERWPESGVpDNPGAWLMTTAKRRAIDLFRRGKLLERKHA 86
Cdd:PRK09635    4 HDPVSAAWRAHRAYLVDLAFRMVGDIGVAEDMVQEAFS-RLLRAPVGDI-DDERGWLIVVTSRLCLDHIKSASTRRERPQ 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125296280  87 ELG--HDLVARQESPEPGLAAAIDDHVGDDLLGLMFTtchpvLGTEARAALTLRLLGGLTTDEIARAFLVPEPTVAQRIV 164
Cdd:PRK09635   82 DIAawHDGDASVSSVDPADRVTLDDEVRLALLIMLER-----LGPAERVVFVLHEIFGLPYQQIATTIGSQASTCRQLAH 156

                         170
                  ....*....|....*
gi 1125296280 165 RAKRTLREAHVPFDV 179
Cdd:PRK09635  157 RARRKINESRIAASV 171
PRK09639 PRK09639
RNA polymerase sigma factor SigX; Provisional
 20-100 1.04e-03

RNA polymerase sigma factor SigX; Provisional


Pssm-ID: 236602 [Multi-domain]  Cd Length: 166  Bit Score: 39.55  E-value: 1.04e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125296280  20 KVIAGLTRITGDVGLAEDLAQDALVAALERWPESgvPDNPGAWLMTTAKRRAIDLFRRGKLLERKHAEL-GHDLVARQES 98
Cdd:PRK09639   15 DVVQQIFYIVKDRTQAEDLAQEVFLRLYRSDFKG--IENEKGWLIKSARNVAYNYLRSEKRRRARILGEfQWQEVDNEPS 92


                  ..
gi 1125296280  99 PE 100
Cdd:PRK09639   93 PE 94
PRK12514 PRK12514
RNA polymerase sigma factor; Provisional
 9-172 1.23e-03

RNA polymerase sigma factor; Provisional


Pssm-ID: 105710 [Multi-domain]  Cd Length: 179  Bit Score: 39.80  E-value: 1.23e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125296280   9 AIEAVWRIESAKVIAGLTRITGDVGLAEDLAQDALVAALERWPESGVPD-NPGAWLMTTAKRRAIDLFRRGKLLERKHAE 87
Cdd:PRK12514   20 AFSSLYDATSAKLFGICLRVLKDRSEAEEALQDVYVKIWTKADRFAVSGlSPMTWLITIARNHAIDRLRARKAVAVDIDE 99

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125296280  88 LgHDLVARQESPEPGLAAAIDDHVGDDllglmfttCHPVLGTEARAALTLRLLGGLTTDEIARAFLVPEPTVAQRIVRAK 167
Cdd:PRK12514  100 A-HDLADPSPGPEAEVIAGDEGQRIDA--------CLEELEKDRAAAVRRAYLEGLSYKELAERHDVPLNTMRTWLRRSL 170


                  ....*
gi 1125296280 168 RTLRE 172
Cdd:PRK12514  171 LKLRE 175
Sig-70_gvs1 TIGR02989
RNA polymerase sigma-70 factor, Rhodopirellula/Verrucomicrobium family; This group of sigma ...
 8-77 9.27e-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: 36.53  E-value: 9.27e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125296280   8 RAIEAVWRIESAKVIAGLTRITGDVGLAEDLAQDALVAALERWPESGVPDNPGAWLMTTAKRRAIDLFRR 77
Cdd:TIGR02989   1 KAFVRLLTRHERALRAFVRSLVADRDDVDDVLQETFVVAWRKFDQFDPGTNFVAWARGIARNKVLNYRRK 70
 
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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