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Conserved domains on  [gi|505916344|ref|WP_015715732|]
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MULTISPECIES: sigma-70 family RNA polymerase sigma factor [Bacillus]

Protein Classification

PRK06930 family protein( domain architecture ID 11482500)

PRK06930 family protein

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PRK06930 PRK06930
positive control sigma-like factor; Validated
 1-169 6.81e-78

positive control sigma-like factor; Validated


:

Pssm-ID: 180757 [Multi-domain]  Cd Length: 170  Bit Score: 229.23  E-value: 6.81e-78
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505916344   1 MQDLLFEYKRTLKQTRIQYKPLAEADEsvlsaEELKDKKIIRNMITDLEYVTEWLEKGRQPGIRRAIDRRDAYQRLMIKD 80
Cdd:PRK06930   1 MQDLLKEYKRTLKQLRKMYKDAQEEID-----EQLKDKKIIRSMISDLEYVIEWMEKGRQPGNRRGIDRRAAYQREVICD 75

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505916344  81 PRIIESFSSAM------MFEPDGQVSEEDRDRIREALALLTDREKEMFLLHKVECFSYERIADLLGVKKSTVQTTIKRAS 154
Cdd:PRK06930  76 PLLIQRYFRSMedlewdIEEPESVISEWDKIRIEDALSVLTEREKEVYLMHRGYGLSYSEIADYLNIKKSTVQSMIERAE 155

                        170
                 ....*....|....*
gi 505916344 155 LKMQRQQEDMNRSLA 169
Cdd:PRK06930 156 KKIARQINESLFCMA 170
 
Name Accession Description Interval E-value
PRK06930 PRK06930
positive control sigma-like factor; Validated
 1-169 6.81e-78

positive control sigma-like factor; Validated


Pssm-ID: 180757 [Multi-domain]  Cd Length: 170  Bit Score: 229.23  E-value: 6.81e-78
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505916344   1 MQDLLFEYKRTLKQTRIQYKPLAEADEsvlsaEELKDKKIIRNMITDLEYVTEWLEKGRQPGIRRAIDRRDAYQRLMIKD 80
Cdd:PRK06930   1 MQDLLKEYKRTLKQLRKMYKDAQEEID-----EQLKDKKIIRSMISDLEYVIEWMEKGRQPGNRRGIDRRAAYQREVICD 75

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505916344  81 PRIIESFSSAM------MFEPDGQVSEEDRDRIREALALLTDREKEMFLLHKVECFSYERIADLLGVKKSTVQTTIKRAS 154
Cdd:PRK06930  76 PLLIQRYFRSMedlewdIEEPESVISEWDKIRIEDALSVLTEREKEVYLMHRGYGLSYSEIADYLNIKKSTVQSMIERAE 155

                        170
                 ....*....|....*
gi 505916344 155 LKMQRQQEDMNRSLA 169
Cdd:PRK06930 156 KKIARQINESLFCMA 170
Sigma70_r4 cd06171
Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in ...
 104-158 1.71e-11

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: 56.34  E-value: 1.71e-11
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 505916344 104 RDRIREALALLTDREKEMFLLHKVECFSYERIADLLGVKKSTVQTTIKRASLKMQ 158
Cdd:cd06171    1 RERLEEALDKLPEREREVILLRFGEGLSYEEIAEILGISRSTVRQRLHRALKKLR 55
RpoE COG1595
DNA-directed RNA polymerase specialized sigma subunit, sigma24 family [Transcription]; ...
 64-160 7.86e-11

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: 57.70  E-value: 7.86e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505916344  64 RRAIDRRDAYQRLMIKDPRIIESFSSAMMFEPDGQVSEEDRDRIREALALLTDREKEMFLLHKVECFSYERIADLLGVKK 143
Cdd:COG1595   78 NLAIDHLRKRRRRRELLDELAEELPDEAADPEEALEAEELLEALLAALERLPPRQREVLVLRYLEGLSYAEIAEILGISE 157

                         90
                 ....*....|....*..
gi 505916344 144 STVQTTIKRASLKMQRQ 160
Cdd:COG1595  158 GTVKSRLSRARKKLREA 174
sigma70-ECF TIGR02937
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ...
 63-160 3.40e-10

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: 55.43  E-value: 3.40e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505916344   63 IRRAIDRRDAYQRLMIKDPRIIESFSSAMMFEpdgqVSEEDRDRIREALALLTDREKEMFLLHKVECFSYERIADLLGVK 142
Cdd:TIGR02937  64 ILDYLRRKRRLRRELDLLEELLDSDPSPEEEL----EQEEEREALREALEKLPEREREVLVLRYLEGLSYKEIAEILGIS 139

                          90
                  ....*....|....*...
gi 505916344  143 KSTVQTTIKRASLKMQRQ 160
Cdd:TIGR02937 140 VGTVKRRLKRARKKLREL 157
Sigma70_r4_2 pfam08281
Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 ...
 104-157 7.49e-10

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: 52.07  E-value: 7.49e-10
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 505916344  104 RDRIREALALLTDREKEMFLLHKVECFSYERIADLLGVKKSTVQTTIKRASLKM 157
Cdd:pfam08281   1 LEALLRALEELPPRQREVFLLRYLEGLSYAEIAELLGISEGTVKSRLSRARKKL 54
 
Name Accession Description Interval E-value
PRK06930 PRK06930
positive control sigma-like factor; Validated
 1-169 6.81e-78

positive control sigma-like factor; Validated


Pssm-ID: 180757 [Multi-domain]  Cd Length: 170  Bit Score: 229.23  E-value: 6.81e-78
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505916344   1 MQDLLFEYKRTLKQTRIQYKPLAEADEsvlsaEELKDKKIIRNMITDLEYVTEWLEKGRQPGIRRAIDRRDAYQRLMIKD 80
Cdd:PRK06930   1 MQDLLKEYKRTLKQLRKMYKDAQEEID-----EQLKDKKIIRSMISDLEYVIEWMEKGRQPGNRRGIDRRAAYQREVICD 75

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505916344  81 PRIIESFSSAM------MFEPDGQVSEEDRDRIREALALLTDREKEMFLLHKVECFSYERIADLLGVKKSTVQTTIKRAS 154
Cdd:PRK06930  76 PLLIQRYFRSMedlewdIEEPESVISEWDKIRIEDALSVLTEREKEVYLMHRGYGLSYSEIADYLNIKKSTVQSMIERAE 155

                        170
                 ....*....|....*
gi 505916344 155 LKMQRQQEDMNRSLA 169
Cdd:PRK06930 156 KKIARQINESLFCMA 170
Sigma70_r4 cd06171
Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in ...
 104-158 1.71e-11

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: 56.34  E-value: 1.71e-11
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 505916344 104 RDRIREALALLTDREKEMFLLHKVECFSYERIADLLGVKKSTVQTTIKRASLKMQ 158
Cdd:cd06171    1 RERLEEALDKLPEREREVILLRFGEGLSYEEIAEILGISRSTVRQRLHRALKKLR 55
RpoE COG1595
DNA-directed RNA polymerase specialized sigma subunit, sigma24 family [Transcription]; ...
 64-160 7.86e-11

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: 57.70  E-value: 7.86e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505916344  64 RRAIDRRDAYQRLMIKDPRIIESFSSAMMFEPDGQVSEEDRDRIREALALLTDREKEMFLLHKVECFSYERIADLLGVKK 143
Cdd:COG1595   78 NLAIDHLRKRRRRRELLDELAEELPDEAADPEEALEAEELLEALLAALERLPPRQREVLVLRYLEGLSYAEIAEILGISE 157

                         90
                 ....*....|....*..
gi 505916344 144 STVQTTIKRASLKMQRQ 160
Cdd:COG1595  158 GTVKSRLSRARKKLREA 174
sigma70-ECF TIGR02937
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ...
 63-160 3.40e-10

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: 55.43  E-value: 3.40e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505916344   63 IRRAIDRRDAYQRLMIKDPRIIESFSSAMMFEpdgqVSEEDRDRIREALALLTDREKEMFLLHKVECFSYERIADLLGVK 142
Cdd:TIGR02937  64 ILDYLRRKRRLRRELDLLEELLDSDPSPEEEL----EQEEEREALREALEKLPEREREVLVLRYLEGLSYKEIAEILGIS 139

                          90
                  ....*....|....*...
gi 505916344  143 KSTVQTTIKRASLKMQRQ 160
Cdd:TIGR02937 140 VGTVKRRLKRARKKLREL 157
Sigma70_r4_2 pfam08281
Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 ...
 104-157 7.49e-10

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: 52.07  E-value: 7.49e-10
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 505916344  104 RDRIREALALLTDREKEMFLLHKVECFSYERIADLLGVKKSTVQTTIKRASLKM 157
Cdd:pfam08281   1 LEALLRALEELPPRQREVFLLRYLEGLSYAEIAELLGISEGTVKSRLSRARKKL 54
PRK09639 PRK09639
RNA polymerase sigma factor SigX; Provisional
 102-164 4.10e-06

RNA polymerase sigma factor SigX; Provisional


Pssm-ID: 236602 [Multi-domain]  Cd Length: 166  Bit Score: 44.55  E-value: 4.10e-06
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 505916344 102 EDRDRIREALALLTDREKeMFLLHKVECFSYERIADLLGVKKSTVQTTIKRASLKMQRQQEDM 164
Cdd:PRK09639 101 EEITKVQEVLAKMTERDR-TVLLLRFSGYSYKEIAEALGIKESSVGTTLARAKKKFRKIYEQM 162
PRK09191 PRK09191
two-component response regulator; Provisional
 95-160 8.19e-06

two-component response regulator; Provisional


Pssm-ID: 236402 [Multi-domain]  Cd Length: 261  Bit Score: 44.45  E-value: 8.19e-06
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 505916344  95 PDGQVSEEDRDRIREALALLTDREKEMFLLHKVECFSYERIADLLGVKKSTVQTTIKRASLKMQRQ 160
Cdd:PRK09191  70 NDPEPGSPFEARAERRLAGLTPLPRQAFLLTALEGFSVEEAAEILGVDPAEAEALLDDARAEIARQ 135
CsgD COG2771
DNA-binding transcriptional regulator, CsgD family [Transcription];
16-157 4.20e-04

DNA-binding transcriptional regulator, CsgD family [Transcription];


Pssm-ID: 442052 [Multi-domain]  Cd Length: 188  Bit Score: 39.35  E-value: 4.20e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505916344  16 RIQYKPLAEADESVLSAEELKDKKIIRNMITDLEYVTEWLEKGRQPGIRRAIDRRDAYQRLMIKDPRIIESFSSAMMFEP 95
Cdd:COG2771   30 AALLLLLALLLLAALLLLAAAAAALAAALAAALLLGLLLLLLIALLLLLLLLLALLLLLALLALLAALLARLAALLLALA 109

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 505916344  96 DGQVSEEDRDRIREALALLTDREKEMfLLHKVECFSYERIADLLGVKKSTVQTTIKRASLKM 157
Cdd:COG2771  110 LAALLLAALARLLARAPGLTPREREV-LRLLAEGLTLKEIARILGISERTVRTHLKRIYRKL 170
PRK12517 PRK12517
RNA polymerase sigma factor; Provisional
 101-167 5.85e-04

RNA polymerase sigma factor; Provisional


Pssm-ID: 183569 [Multi-domain]  Cd Length: 188  Bit Score: 38.51  E-value: 5.85e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 505916344 101 EEDRDRIREALALLTDREKEMFLLHKVECFSYERIADLLGVKKSTVQTTIKRA--SLKMQRQQEDMNRS 167
Cdd:PRK12517 116 EMEQEWLRRQIAKLDPEYREPLLLQVIGGFSGEEIAEILDLNKNTVMTRLFRArnQLKEALEKPDVQRG 184
PRK12513 PRK12513
RNA polymerase sigma factor; Provisional
 95-159 8.23e-04

RNA polymerase sigma factor; Provisional


Pssm-ID: 183566 [Multi-domain]  Cd Length: 194  Bit Score: 38.13  E-value: 8.23e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 505916344  95 PDGQVSE-EDRDRIREALALLTDREKEMFLLHKVECFSYERIADLLGVKKSTVQTTIKRASLKMQR 159
Cdd:PRK12513 120 PEQQLSLfRDRRRLQAALETLPDEQREVFLLREHGDLELEEIAELTGVPEETVKSRLRYALQKLRE 185
PRK12546 PRK12546
RNA polymerase sigma factor; Provisional
 96-153 9.11e-04

RNA polymerase sigma factor; Provisional


Pssm-ID: 139055 [Multi-domain]  Cd Length: 188  Bit Score: 38.28  E-value: 9.11e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 505916344  96 DGQVSEEDrdrIREALALLTDREKEMFLLHKVECFSYERIADLLGVKKSTVQTTIKRA 153
Cdd:PRK12546  99 DGRLAMSD---FRAAFAQLPDEQREALILVGASGFSYEEAAEMCGVAVGTVKSRANRA 153
PRK09652 PRK09652
RNA polymerase sigma factor RpoE; Provisional
 100-164 1.13e-03

RNA polymerase sigma factor RpoE; Provisional


Pssm-ID: 236608 [Multi-domain]  Cd Length: 182  Bit Score: 37.86  E-value: 1.13e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 505916344 100 SEEDRDRIREALALLTDREKEMFLLHKVECFSYERIADLLGVKKSTVQTTIKRASLKMQRQQEDM 164
Cdd:PRK09652 115 SAELEQRVRAAIESLPEELRTAITLREIEGLSYEEIAEIMGCPIGTVRSRIFRAREALRAKLQPL 179
PRK11924 PRK11924
RNA polymerase sigma factor; Provisional
 96-157 1.26e-03

RNA polymerase sigma factor; Provisional


Pssm-ID: 183384 [Multi-domain]  Cd Length: 179  Bit Score: 37.64  E-value: 1.26e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 505916344  96 DGQVSEEDRDRIREALALLTDREKEMFLLHKVECFSYERIADLLGVKKSTVQTTIKRASLKM 157
Cdd:PRK11924 108 AALLAKDDLARIDRCLDALPVKQREVFLLRYVEGLSYREIAEILGVPVGTVKSRLRRARQLL 169
FliA COG1191
DNA-directed RNA polymerase specialized sigma subunit [Transcription]; DNA-directed RNA ...
 101-146 2.80e-03

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


Pssm-ID: 440804 [Multi-domain]  Cd Length: 236  Bit Score: 36.73  E-value: 2.80e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*.
gi 505916344 101 EEDRDRIREALALLTDREKEMFLLHKVECFSYERIADLLGVKKSTV 146
Cdd:COG1191  174 EELREALAEAIEQLPERERLVLSLYYFEELTLKEIAEVLGVSESRV 219
PRK09647 PRK09647
RNA polymerase sigma factor SigE; Reviewed
 64-161 3.31e-03

RNA polymerase sigma factor SigE; Reviewed


Pssm-ID: 236606 [Multi-domain]  Cd Length: 203  Bit Score: 36.69  E-value: 3.31e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505916344  64 RRAIDRRDA----YQRLMIKDPRIIESFSSAMmFEPDGQvseedrdrirEALALLTDREKEMFLLHKVECFSYERIADLL 139
Cdd:PRK09647  96 RRARIRMEAlpedYDRVPGDEPNPEQIYHDAR-LDPDLQ----------AALDSLPPEFRAAVVLCDIEGLSYEEIAATL 164

                         90       100
                 ....*....|....*....|..
gi 505916344 140 GVKKSTVQTTIKRAslkmqRQQ 161
Cdd:PRK09647 165 GVKLGTVRSRIHRG-----RQQ 181
PRK12547 PRK12547
RNA polymerase sigma factor; Provisional
 98-158 4.49e-03

RNA polymerase sigma factor; Provisional


Pssm-ID: 139056 [Multi-domain]  Cd Length: 164  Bit Score: 36.01  E-value: 4.49e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 505916344  98 QVSEEDRDRIREALALLTDREKEMFLLHKVECFSYERIADLLGVKKSTVQTTIKRASLKMQ 158
Cdd:PRK12547  97 QYGSLDLQDFKKALNLLSADQREAIILIGASGFSYEDAAAICGCAVGTIKSRVSRARNRLQ 157
PRK09646 PRK09646
ECF RNA polymerase sigma factor SigK;
64-151 5.38e-03

ECF RNA polymerase sigma factor SigK;


Pssm-ID: 182015 [Multi-domain]  Cd Length: 194  Bit Score: 35.80  E-value: 5.38e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505916344  64 RRAIDRRDAYQRLMIKDPRiiesFSSAMMFEPDGQVSEE-----DRDRIREALALLTDREKEMFLLHKVECFSYERIADL 138
Cdd:PRK09646  92 RRAVDRVRSEQAASQREVR----YGARNVDPAFDQVAEEvearlERERVRDCLDALTDTQRESVTLAYYGGLTYREVAER 167

                         90
                 ....*....|...
gi 505916344 139 LGVKKSTVQTTIK 151
Cdd:PRK09646 168 LAVPLGTVKTRMR 180
Sigma70_r4 pfam04545
Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 ...
 110-159 5.98e-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. 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: 33.56  E-value: 5.98e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 505916344  110 ALALLTDREKEMFLLHKVECFSYERIADLLGVKKSTVQTTIKRASLKMQR 159
Cdd:pfam04545   1 ALASLPPRERQVLVLRYGEGLTLEEIGERLGISRERVRQIEKRALRKLRK 50
PRK09415 PRK09415
RNA polymerase factor sigma C; Reviewed
 99-158 8.93e-03

RNA polymerase factor sigma C; Reviewed


Pssm-ID: 181835 [Multi-domain]  Cd Length: 179  Bit Score: 35.11  E-value: 8.93e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 505916344  99 VSEEDRDRIREALALLTDREKEMFLLHKVECFSYERIADLLGVKKSTVQTTIKRASLKMQ 158
Cdd:PRK09415 113 IQNAEDERLASAVMSLPIKYREVIYLFYYEELSIKEIAEVTGVNENTVKTRLKKAKELLK 172
 
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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