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Conserved domains on  [gi|1756724307|gb|QFG23054|]
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RNA polymerase sigma factor [Actinomadura sp. WMMB 499]

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];
4-409 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 1756724307   4 PDARASVEAIFREERGRLLAALVRRFGDLDLAEDVAADAIEAALVHWPERGVPPSPGGWLMTTARRKAVDRLRRDRAQAA 83
Cdd:COG4941     2 SDARRAIEALFREESGRLVAALARRFGDLDLAEDAVQDAFLAALEQWPRDGVPDNPAAWLYTVARRRAIDRLRREARRRR 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1756724307  84 RLALLHVEMERAAPVPAPDPDGgLPDERLLLFFTCAHPALAAEDRTALTLRCLAGLTTPEVARAFLVPAATMAKRIVRAK 163
Cdd:COG4941    82 KEAELAADLEAEAPAEDADDDD-IPDDRLRLLFTCCHPALSPEAQVALTLRLVGGLTTAEIARAFLVPEATMAQRIVRAK 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1756724307 164 HRIREARIPFRVPDPGELPERLPGVLQVLYSIFTEGYAAA------RRDLADEAVRLARILRRLLPDEREVAGLLALMLL 237
Cdd:COG4941   161 RKIREAGIPFEVPDAAELPERLDAVLAVIYLIFNEGYAASsgddlvRADLCDEAIRLARLLAELLPDEPEVHGLLALMLL 240

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1756724307 238 THARFDARTAPDGGLLLLEEQDRARWDRAAIEEGRGLAEEALTGGPPGPYGVQAAIAALHGEAADVASTDWPQIVALYDV 317
Cdd:COG4941   241 HAARRPARTDADGELVLLEDQDRSRWDRALIAEGLALLERALAGGRPGPYQLQAAIAAVHARAPSAEDTDWPQILALYDA 320

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1756724307 318 LLALTPSPVVALNRAVAVAMRDGPEAGLALLDDLAAEPRLRGYHPYAAARADLLRRLGRPAESAAAYREAISLAATAPER 397
Cdd:COG4941   321 LLRLAPSPVVALNRAVAVAMADGPEAGLALLDALAAEPRLAGYHLLHAVRADLLRRLGRRAEARAAYRRALALTRNEAER 400

                         410
                  ....*....|..
gi 1756724307 398 ALLRRMLAAVEP 409
Cdd:COG4941   401 AFLRRRLAALAA 412
 
Name Accession Description Interval E-value
COG4941 COG4941
Predicted RNA polymerase sigma factor, contains C-terminal TPR domain [Transcription];
4-409 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 1756724307   4 PDARASVEAIFREERGRLLAALVRRFGDLDLAEDVAADAIEAALVHWPERGVPPSPGGWLMTTARRKAVDRLRRDRAQAA 83
Cdd:COG4941     2 SDARRAIEALFREESGRLVAALARRFGDLDLAEDAVQDAFLAALEQWPRDGVPDNPAAWLYTVARRRAIDRLRREARRRR 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1756724307  84 RLALLHVEMERAAPVPAPDPDGgLPDERLLLFFTCAHPALAAEDRTALTLRCLAGLTTPEVARAFLVPAATMAKRIVRAK 163
Cdd:COG4941    82 KEAELAADLEAEAPAEDADDDD-IPDDRLRLLFTCCHPALSPEAQVALTLRLVGGLTTAEIARAFLVPEATMAQRIVRAK 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1756724307 164 HRIREARIPFRVPDPGELPERLPGVLQVLYSIFTEGYAAA------RRDLADEAVRLARILRRLLPDEREVAGLLALMLL 237
Cdd:COG4941   161 RKIREAGIPFEVPDAAELPERLDAVLAVIYLIFNEGYAASsgddlvRADLCDEAIRLARLLAELLPDEPEVHGLLALMLL 240

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1756724307 238 THARFDARTAPDGGLLLLEEQDRARWDRAAIEEGRGLAEEALTGGPPGPYGVQAAIAALHGEAADVASTDWPQIVALYDV 317
Cdd:COG4941   241 HAARRPARTDADGELVLLEDQDRSRWDRALIAEGLALLERALAGGRPGPYQLQAAIAAVHARAPSAEDTDWPQILALYDA 320

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1756724307 318 LLALTPSPVVALNRAVAVAMRDGPEAGLALLDDLAAEPRLRGYHPYAAARADLLRRLGRPAESAAAYREAISLAATAPER 397
Cdd:COG4941   321 LLRLAPSPVVALNRAVAVAMADGPEAGLALLDALAAEPRLAGYHLLHAVRADLLRRLGRRAEARAAYRRALALTRNEAER 400

                         410
                  ....*....|..
gi 1756724307 398 ALLRRMLAAVEP 409
Cdd:COG4941   401 AFLRRRLAALAA 412
DUF6596 pfam20239
Family of unknown function (DUF6596); This presumed domain is found at the C-terminus of ...
 184-279 9.06e-27

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: 103.02  E-value: 9.06e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1756724307 184 RLPGVLQVLYSIFTEGYAAA------RRDLADEAVRLARILRRLLPDEREVAGLLALMLLTHARFDARTAPDGGLLLLEE 257
Cdd:pfam20239   1 RLDAVLEVLYLLFNEGYAATsgdqliREDLCSEALRLARLLAELLPDEPEVLGLLALMLLHAARRPARVDADGELVPLAE 80

                          90       100
                  ....*....|....*....|..
gi 1756724307 258 QDRARWDRAAIEEGRGLAEEAL 279
Cdd:pfam20239  81 QDRSLWDRALIAEGLALLERAA 102
sigma70-ECF TIGR02937
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ...
 11-169 1.54e-13

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: 67.76  E-value: 1.54e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1756724307  11 EAIFREERGRLLAALVRRFGDLDLAEDVAADAIEAALVHWPERGVPPSPGGWLMTTARRKAVDRLRRdraQAARLALLHV 90
Cdd:TIGR02937   4 EELYERYLPLVYRYARRYLGDDADAEDLVQEAFLKLLEALDRFDPEGSFKAWLFRIARNLILDYLRR---KRRLRRELDL 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1756724307  91 EMERAAPVPAPDPDGGLPDERLLLFFTCAHpaLAAEDRTALTLRCLAGLTTPEVARAFLVPAATMAKRIVRAKHRIREA 169
Cdd:TIGR02937  81 LEELLDSDPSPEEELEQEEEREALREALEK--LPEREREVLVLRYLEGLSYKEIAEILGISVGTVKRRLKRARKKLREL 157
PRK11924 PRK11924
RNA polymerase sigma factor; Provisional
 4-169 6.07e-13

RNA polymerase sigma factor; Provisional


Pssm-ID: 183384 [Multi-domain]  Cd Length: 179  Bit Score: 66.92  E-value: 6.07e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1756724307   4 PDARASVEAIFREERGRLLAALVRRFGDLDLAEDVAADAIEAALVHWPERGVPPSPGGWLMTTARRKAVDRLRRDRAQAA 83
Cdd:PRK11924    9 TGDKEAFSELFRPHAPDLLRYARRQLGDRALAEDAVQEAFLRAWRKADLFNGKGSARTWLLTIARNVCYDLLRRRRREKA 88

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1756724307  84 RLALLhvEMERAAPVPAPDPDGGLPDERLLLFFTCAHPALAAEDRTALTLRCLAGLTTPEVARAFLVPAATMAKRIVRAK 163
Cdd:PRK11924   89 VLSDD--ALEPEFAETAETPEAALLAKDDLARIDRCLDALPVKQREVFLLRYVEGLSYREIAEILGVPVGTVKSRLRRAR 166


                  ....*.
gi 1756724307 164 HRIREA 169
Cdd:PRK11924  167 QLLREC 172
 
Name Accession Description Interval E-value
COG4941 COG4941
Predicted RNA polymerase sigma factor, contains C-terminal TPR domain [Transcription];
4-409 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 1756724307   4 PDARASVEAIFREERGRLLAALVRRFGDLDLAEDVAADAIEAALVHWPERGVPPSPGGWLMTTARRKAVDRLRRDRAQAA 83
Cdd:COG4941     2 SDARRAIEALFREESGRLVAALARRFGDLDLAEDAVQDAFLAALEQWPRDGVPDNPAAWLYTVARRRAIDRLRREARRRR 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1756724307  84 RLALLHVEMERAAPVPAPDPDGgLPDERLLLFFTCAHPALAAEDRTALTLRCLAGLTTPEVARAFLVPAATMAKRIVRAK 163
Cdd:COG4941    82 KEAELAADLEAEAPAEDADDDD-IPDDRLRLLFTCCHPALSPEAQVALTLRLVGGLTTAEIARAFLVPEATMAQRIVRAK 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1756724307 164 HRIREARIPFRVPDPGELPERLPGVLQVLYSIFTEGYAAA------RRDLADEAVRLARILRRLLPDEREVAGLLALMLL 237
Cdd:COG4941   161 RKIREAGIPFEVPDAAELPERLDAVLAVIYLIFNEGYAASsgddlvRADLCDEAIRLARLLAELLPDEPEVHGLLALMLL 240

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1756724307 238 THARFDARTAPDGGLLLLEEQDRARWDRAAIEEGRGLAEEALTGGPPGPYGVQAAIAALHGEAADVASTDWPQIVALYDV 317
Cdd:COG4941   241 HAARRPARTDADGELVLLEDQDRSRWDRALIAEGLALLERALAGGRPGPYQLQAAIAAVHARAPSAEDTDWPQILALYDA 320

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1756724307 318 LLALTPSPVVALNRAVAVAMRDGPEAGLALLDDLAAEPRLRGYHPYAAARADLLRRLGRPAESAAAYREAISLAATAPER 397
Cdd:COG4941   321 LLRLAPSPVVALNRAVAVAMADGPEAGLALLDALAAEPRLAGYHLLHAVRADLLRRLGRRAEARAAYRRALALTRNEAER 400

                         410
                  ....*....|..
gi 1756724307 398 ALLRRMLAAVEP 409
Cdd:COG4941   401 AFLRRRLAALAA 412
DUF6596 pfam20239
Family of unknown function (DUF6596); This presumed domain is found at the C-terminus of ...
 184-279 9.06e-27

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: 103.02  E-value: 9.06e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1756724307 184 RLPGVLQVLYSIFTEGYAAA------RRDLADEAVRLARILRRLLPDEREVAGLLALMLLTHARFDARTAPDGGLLLLEE 257
Cdd:pfam20239   1 RLDAVLEVLYLLFNEGYAATsgdqliREDLCSEALRLARLLAELLPDEPEVLGLLALMLLHAARRPARVDADGELVPLAE 80

                          90       100
                  ....*....|....*....|..
gi 1756724307 258 QDRARWDRAAIEEGRGLAEEAL 279
Cdd:pfam20239  81 QDRSLWDRALIAEGLALLERAA 102
RpoE COG1595
DNA-directed RNA polymerase specialized sigma subunit, sigma24 family [Transcription]; ...
 7-169 1.46e-19

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: 85.43  E-value: 1.46e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1756724307   7 RASVEAIFREERGRLLAALVRRFGDLDLAEDVAADAIEAALVHWPERGVPPSPGGWLMTTARRKAVDRLRRDRAQAARLA 86
Cdd:COG1595    16 EAAFEELYERYRPRLYRYARRLLGDRADAEDLVQETFLRLWRKLDSFRGRGSFRAWLYRIARNLAIDHLRKRRRRRELLD 95

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1756724307  87 llhvEMERAAPVPAPDPDGGLPDERLLLFFTCAHPALAAEDRTALTLRCLAGLTTPEVARAFLVPAATMAKRIVRAKHRI 166
Cdd:COG1595    96 ----ELAEELPDEAADPEEALEAEELLEALLAALERLPPRQREVLVLRYLEGLSYAEIAEILGISEGTVKSRLSRARKKL 171


                  ...
gi 1756724307 167 REA 169
Cdd:COG1595   172 REA 174
sigma70-ECF TIGR02937
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ...
 11-169 1.54e-13

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: 67.76  E-value: 1.54e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1756724307  11 EAIFREERGRLLAALVRRFGDLDLAEDVAADAIEAALVHWPERGVPPSPGGWLMTTARRKAVDRLRRdraQAARLALLHV 90
Cdd:TIGR02937   4 EELYERYLPLVYRYARRYLGDDADAEDLVQEAFLKLLEALDRFDPEGSFKAWLFRIARNLILDYLRR---KRRLRRELDL 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1756724307  91 EMERAAPVPAPDPDGGLPDERLLLFFTCAHpaLAAEDRTALTLRCLAGLTTPEVARAFLVPAATMAKRIVRAKHRIREA 169
Cdd:TIGR02937  81 LEELLDSDPSPEEELEQEEEREALREALEK--LPEREREVLVLRYLEGLSYKEIAEILGISVGTVKRRLKRARKKLREL 157
PRK11924 PRK11924
RNA polymerase sigma factor; Provisional
 4-169 6.07e-13

RNA polymerase sigma factor; Provisional


Pssm-ID: 183384 [Multi-domain]  Cd Length: 179  Bit Score: 66.92  E-value: 6.07e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1756724307   4 PDARASVEAIFREERGRLLAALVRRFGDLDLAEDVAADAIEAALVHWPERGVPPSPGGWLMTTARRKAVDRLRRDRAQAA 83
Cdd:PRK11924    9 TGDKEAFSELFRPHAPDLLRYARRQLGDRALAEDAVQEAFLRAWRKADLFNGKGSARTWLLTIARNVCYDLLRRRRREKA 88

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1756724307  84 RLALLhvEMERAAPVPAPDPDGGLPDERLLLFFTCAHPALAAEDRTALTLRCLAGLTTPEVARAFLVPAATMAKRIVRAK 163
Cdd:PRK11924   89 VLSDD--ALEPEFAETAETPEAALLAKDDLARIDRCLDALPVKQREVFLLRYVEGLSYREIAEILGVPVGTVKSRLRRAR 166


                  ....*.
gi 1756724307 164 HRIREA 169
Cdd:PRK11924  167 QLLREC 172
Sigma70_r2 pfam04542
Sigma-70 region 2; Region 2 of sigma-70 is the most conserved region of the entire protein. ...
 13-79 2.60e-06

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: 44.89  E-value: 2.60e-06
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1756724307  13 IFREERGRLLAALVRRFGDLDLAEDVAADAIEAALVHWP--ERGVPPSPGGWLMTTARRKAVDRLRRDR 79
Cdd:pfam04542   1 LVERYLPLVYSLARRYLGDGADAEDLVQEGFLGLWRAIErfDPERGVSFSTWLYTIIRNAIIDYLRKQR 69
PRK12511 PRK12511
RNA polymerase sigma factor; Provisional
 21-168 9.62e-06

RNA polymerase sigma factor; Provisional


Pssm-ID: 237123 [Multi-domain]  Cd Length: 182  Bit Score: 45.93  E-value: 9.62e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1756724307  21 LLAALVRRFGDLDLAEDVAADAIEAALVHWPERGVPPSPGG----WLMTTARRKAVDRLRRDRAQAARLALLHVEMERAA 96
Cdd:PRK12511   13 QLVPLRRYARSLTRDSAEAEDLVHDALVRALERRASFRSGGnlrtWLMSILHNAFIDELRRRRVEARRADELAVLADASL 92

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1756724307  97 PvPAPDPDGGLPDERLLLFftcahpALAAEDRTALTLRCLAGLTTPEVARAFLVPAATMAKRIVRAKHRIRE 168
Cdd:PRK12511   93 P-AAQEHAVRLAQIRDAFF------DLPEEQRAALHLVAIEGLSYQEAAAVLGIPIGTLMSRIGRARAALRA 157
sigI PRK09635
RNA polymerase sigma factor SigI; Provisional
 6-171 3.98e-04

RNA polymerase sigma factor SigI; Provisional


Pssm-ID: 182008 [Multi-domain]  Cd Length: 290  Bit Score: 41.88  E-value: 3.98e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1756724307   6 ARASVEAIFREERGRLLAALVRRFGDLDLAEDVAADAIEAALvhWPERGVPPSPGGWLMTTARRKAVDRLRRDRAQAARL 85
Cdd:PRK09635    3 QHDPVSAAWRAHRAYLVDLAFRMVGDIGVAEDMVQEAFSRLL--RAPVGDIDDERGWLIVVTSRLCLDHIKSASTRRERP 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1756724307  86 ALLHVEMERAAPVPAPDP-DGGLPDERLLLFFTCAHPALAAEDRTALTLRCLAGLTTPEVARAFLVPAATMAKRIVRAKH 164
Cdd:PRK09635   81 QDIAAWHDGDASVSSVDPaDRVTLDDEVRLALLIMLERLGPAERVVFVLHEIFGLPYQQIATTIGSQASTCRQLAHRARR 160


                  ....*..
gi 1756724307 165 RIREARI 171
Cdd:PRK09635  161 KINESRI 167
PRK12527 PRK12527
RNA polymerase sigma factor; Reviewed
 21-168 4.81e-04

RNA polymerase sigma factor; Reviewed


Pssm-ID: 171560 [Multi-domain]  Cd Length: 159  Bit Score: 40.53  E-value: 4.81e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1756724307  21 LLAALVRRFGDLDLAEDVAADAI--------EAALVHwpergvppsPGGWLMTTARRKAVDRLRRDRA-QAARLALLHVE 91
Cdd:PRK12527    8 LVRFLSARLGNRQAAEDVAHDAYlrvlerssSAQIEH---------PRAFLYRTALNLVVDRHRRHRVrQAEPLEVLDEE 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1756724307  92 MERAAPVPAPDPDgglPDERLLLfFTCAHPALAAEDRTALTLRCLAGLTTPEVARAFLVPAATMAKRIVRA-KH---RIR 167
Cdd:PRK12527   79 ERLHSPSPQTRLD---LGQRLAL-LQRALAELPPACRDSFLLRKLEGLSHQQIAEHLGISRSLVEKHIVNAmKHcrvRMR 154


                  .
gi 1756724307 168 E 168
Cdd:PRK12527  155 Q 155
PRK09646 PRK09646
ECF RNA polymerase sigma factor SigK;
51-168 6.49e-04

ECF RNA polymerase sigma factor SigK;


Pssm-ID: 182015 [Multi-domain]  Cd Length: 194  Bit Score: 40.42  E-value: 6.49e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1756724307  51 PERGvppSPGGWLMTTARRKAVDRLRRDRAQAARLALLHV-EMERAAPVPAPDPDGGLPDERLllffTCAHPALAAEDRT 129
Cdd:PRK09646   77 PARG---SALAWLLTLAHRRAVDRVRSEQAASQREVRYGArNVDPAFDQVAEEVEARLERERV----RDCLDALTDTQRE 149

                          90       100       110
                  ....*....|....*....|....*....|....*....
gi 1756724307 130 ALTLRCLAGLTTPEVARAFLVPAATMAKRIVRAKHRIRE 168
Cdd:PRK09646  150 SVTLAYYGGLTYREVAERLAVPLGTVKTRMRDGLIRLRD 188
COG3903 COG3903
Predicted ATPase [General function prediction only];
17-413 6.55e-04

Predicted ATPase [General function prediction only];


Pssm-ID: 443109 [Multi-domain]  Cd Length: 933  Bit Score: 41.93  E-value: 6.55e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1756724307  17 ERGRLLAALVRRFGDLDLAEDVAADAIEAALVHWPERGVppspggwlmttARRKAVDRLRRDRAQAARLALLHVEMERAA 96
Cdd:COG3903   542 ELALRLAAALAPFWFLRGLLREGRRWLERALAAAGEAAA-----------ALAAAAALAAAAAAARAAAAAAAAAAAAAA 610

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1756724307  97 PVPAPDPDGGLPDERLLLFFTCAHPALAAEDRTALTLRCLAGLTTPEVARAFLVPAATMAKRIVRAKHRIREARIPFRVP 176
Cdd:COG3903   611 AAAAAAAAAAAALLLLAALAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAALAAAAAAAAAAAAAAAAAAAALAAA 690

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1756724307 177 DPGELPERLPGVLQVLYSIFTEGYAAARRDLADEAVRLARILRRLLPDEREVAGLLALMLLTHARFDARTAPDGGLLLLE 256
Cdd:COG3903   691 AAALAAAAAAAALAAAAAAALAAAAAAAAAAAAAAALLAAAAAAALAAAAAAAALALAAAAAAAAAAAAAAALAAAAAAA 770

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1756724307 257 EQDRARWDRAAIEEGRGLAEEALTGGPPGPYGVQAAIAALHGEAADVASTDWPQIVALYDVLLALTPSPVVALNRAVAVA 336
Cdd:COG3903   771 ALAALLLALAAAAAALAAAAAAAAAAAAAAAAAAAAAAAAAAAAALAAAAAAAAAAAAALAAALAAAAAAAAAAAAAAAA 850

                         330       340       350       360       370       380       390
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1756724307 337 MRDGPEAGLALLDDLAAEPRLRGYHPYAAARADLLRRLGRPAESAAAYREAISLAATAPERALLRRMLAAVEPSGRA 413
Cdd:COG3903   851 AAALAAALAAAAAAAAAAALAAAAAAAAAAAAALLAAAAAAAAAAAAAAAAAAALAAAAAAAAAAALAAAAAAAAAA 927
Spy COG3914
Predicted O-linked N-acetylglucosamine transferase, SPINDLY family [Posttranslational ...
 252-407 9.14e-04

Predicted O-linked N-acetylglucosamine transferase, SPINDLY family [Posttranslational modification, protein turnover, chaperones];


Pssm-ID: 443119 [Multi-domain]  Cd Length: 658  Bit Score: 41.52  E-value: 9.14e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1756724307 252 LLLLEEQDRARWDRAAIEEGRGLAEEALTGGPPGPYGVQAAIAALHGEAADVAST---------DWPQIVALYDVLLALT 322
Cdd:COG3914    29 AAELEAAALAAALGLALLLLAALAEAAAAALLALAAGEAAAAAAALLLLAALLELaalllqalgRYEEALALYRRALALN 108

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1756724307 323 PSPVVAL-NRAVAVAMRDGPEAGLALLDD-LAAEPRlrgYHPYAAARADLLRRLGRPAESAAAYREAISLaatAPERALL 400
Cdd:COG3914   109 PDNAEALfNLGNLLLALGRLEEALAALRRaLALNPD---FAEAYLNLGEALRRLGRLEEAIAALRRALEL---DPDNAEA 182


                  ....*..
gi 1756724307 401 RRMLAAV 407
Cdd:COG3914   183 LNNLGNA 189
Sigma70_r4_2 pfam08281
Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 ...
 116-163 1.41e-03

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: 36.67  E-value: 1.41e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 1756724307 116 FTCAHPALAAEDRTALTLRCLAGLTTPEVARAFLVPAATMAKRIVRAK 163
Cdd:pfam08281   4 LLRALEELPPRQREVFLLRYLEGLSYAEIAELLGISEGTVKSRLSRAR 51
PRK12535 PRK12535
RNA polymerase sigma factor; Provisional
 20-170 2.51e-03

RNA polymerase sigma factor; Provisional


Pssm-ID: 237130 [Multi-domain]  Cd Length: 196  Bit Score: 38.72  E-value: 2.51e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1756724307  20 RLLAALvrrfGDLDLAEDVAADAIEAALVHWPERGVPPSPGGWLMTTARRKAVDRLRRDRAQAARLAllhVEMERAAP-V 98
Cdd:PRK12535   40 RLLAHL----GGHDIADDLTQETYLRVMSALPRFAARSSARTWLLSLARRVWVDNIRHDMARPRKSA---TEYEDAAAtT 112

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1756724307  99 PAPDPDGGLP---DERLLLfftcahPALAAEDRTALTLRCLAGLTTPEVARAFLVPAATMAKRIVRAKHRIREAR 170
Cdd:PRK12535  113 ASNETTGSWSewiDVRTLI------DALPPERREALILTQVLGYTYEEAAKIADVRVGTIRSRVARARADLIAAT 181
PRK13919 PRK13919
putative RNA polymerase sigma E protein; Provisional
 8-168 6.52e-03

putative RNA polymerase sigma E protein; Provisional


Pssm-ID: 184395 [Multi-domain]  Cd Length: 186  Bit Score: 37.59  E-value: 6.52e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1756724307   8 ASVEAIFREERGRLLAaLVRRFG-DLDLAEDVAADAI----EAALVHWPERGvppSPGGWLMTTARRKAVDRLRRDRAQA 82
Cdd:PRK13919   23 EALRALFRRYAGAFLA-LARRMGlDGAAAEDVVQEVFirvwKKAKEFDPRRG---SARAWLLALAHHAAVDHVRRRAARP 98

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1756724307  83 arLALLHVEMERAA---PVPAPDPDGGLPDERLllffTCAHPALAAEDRTALTLRCLAGLTTPEVARAFLVPAATMAKRI 159
Cdd:PRK13919   99 --QPLEPDEREPEAfdlPGPGLDEEGHLDRTRL----GRALKALSPEERRVIEVLYYQGYTHREAAQLLGLPLGTLKTRA 172


                  ....*....
gi 1756724307 160 VRAKHRIRE 168
Cdd:PRK13919  173 RRALSRLKE 181
PRK09645 PRK09645
ECF RNA polymerase sigma factor SigL;
1-158 6.78e-03

ECF RNA polymerase sigma factor SigL;


Pssm-ID: 236605 [Multi-domain]  Cd Length: 173  Bit Score: 37.37  E-value: 6.78e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1756724307   1 MTGPDARAS-VEAIFREERGRLLAALVRRFGDLDLAEDVAADAIEAALVHWPERGVPP-SPGGWLMTTARRKAVD--RLR 76
Cdd:PRK09645    1 SGMATAEAAlMRALYDEHAAPLWRYALRLTGDRARAEDVVQETLLRAWQHPEVLADTGrSARAWLFTVARNLVIDerRSA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1756724307  77 RDRAQAARLALLHVemerAAPVPAPDPDGGLpdERLLLffTCAHPALAAEDRTALTLRCLAGLTTPEVARAFLVPAATMA 156
Cdd:PRK09645   81 RARPVEGGDDVLGV----PEQSAPDEVDRAL--DRLLV--ADALAQLSPEHRAVLVRSYYRGWSTAQIAADLGIPEGTVK 152


                  ..
gi 1756724307 157 KR 158
Cdd:PRK09645  153 SR 154
 
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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