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Conserved domains on  [gi|291514096|emb|CBK63306|]
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RNA polymerase sigma factor, sigma-70 family/RNA polymerase sigma-70 factor, Bacteroides expansion family 1 [Alistipes shahii WAL 8301]

Protein Classification

sigma-70 family RNA polymerase sigma factor( domain architecture ID 1001859)

sigma-70 family RNA polymerase sigma factor is a general transcription factor that reversibly binds RNA polymerase and mediates transcription

Gene Ontology:  GO:0016987|GO:0003677
PubMed:  28117604

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
Sig70_bacteroi1 super family cl37203
RNA polymerase sigma-70 factor, Bacteroides expansion family 1; This group of sigma factors ...
 8-174 9.06e-40

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.


The actual alignment was detected with superfamily member TIGR02985:

Pssm-ID: 274376 [Multi-domain]  Cd Length: 161  Bit Score: 133.07  E-value: 9.06e-40
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 291514096    8 SFEELYNCYKVRFERFAISYIQDRSVAEDIVTDSFVYWWEHRDRVgSKDENPAAYILATIRHKCLNHLRALQVRLRSHNE 87
Cdd:TIGR02985   2 AFEQLYRRYYPKLCAFARRYVKDEEDAEDIVQDVFLKLWENRETL-EISESIKAYLFTIVKNRCLNYLRHKQVEEKYQEE 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 291514096   88 IRESQSRIVQENirslelCDPVHLFAGEVEALVRQSLEELPELTRYIFIDQRLKGKSYRDIAVEYAISERRVETELARAL 167
Cdd:TIGR02985  81 LAEIEERELSEA------DPEEELEAKELEEIIEEAIEKLPEQCREIFILSRFEGLSNKEIAEELGISVKTVEYHITKAL 154


                  ....*..
gi 291514096  168 DKLRRRL 174
Cdd:TIGR02985 155 KFLRKEL 161
 
Name Accession Description Interval E-value
Sig70_bacteroi1 TIGR02985
RNA polymerase sigma-70 factor, Bacteroides expansion family 1; This group of sigma factors ...
 8-174 9.06e-40

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: 133.07  E-value: 9.06e-40
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 291514096    8 SFEELYNCYKVRFERFAISYIQDRSVAEDIVTDSFVYWWEHRDRVgSKDENPAAYILATIRHKCLNHLRALQVRLRSHNE 87
Cdd:TIGR02985   2 AFEQLYRRYYPKLCAFARRYVKDEEDAEDIVQDVFLKLWENRETL-EISESIKAYLFTIVKNRCLNYLRHKQVEEKYQEE 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 291514096   88 IRESQSRIVQENirslelCDPVHLFAGEVEALVRQSLEELPELTRYIFIDQRLKGKSYRDIAVEYAISERRVETELARAL 167
Cdd:TIGR02985  81 LAEIEERELSEA------DPEEELEAKELEEIIEEAIEKLPEQCREIFILSRFEGLSNKEIAEELGISVKTVEYHITKAL 154


                  ....*..
gi 291514096  168 DKLRRRL 174
Cdd:TIGR02985 155 KFLRKEL 161
RpoE COG1595
DNA-directed RNA polymerase specialized sigma subunit, sigma24 family [Transcription]; ...
 9-179 5.16e-25

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: 95.83  E-value: 5.16e-25
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 291514096   9 FEELYNCYKVRFERFAISYIQDRSVAEDIVTDSFVYWWEHRDRVgSKDENPAAYILATIRHKCLNHLRALQVRLRSHNEI 88
Cdd:COG1595   19 FEELYERYRPRLYRYARRLLGDRADAEDLVQETFLRLWRKLDSF-RGRGSFRAWLYRIARNLAIDHLRKRRRRRELLDEL 97

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 291514096  89 RESQSRIVQENIRSLElcdpvhlfAGEVEALVRQSLEELPELTRYIFIDQRLKGKSYRDIAVEYAISERRVETELARALD 168
Cdd:COG1595   98 AEELPDEAADPEEALE--------AEELLEALLAALERLPPRQREVLVLRYLEGLSYAEIAEILGISEGTVKSRLSRARK 169

                        170
                 ....*....|.
gi 291514096 169 KLRRRLKDYLP 179
Cdd:COG1595  170 KLREALEEEGA 180
PRK11924 PRK11924
RNA polymerase sigma factor; Provisional
 1-176 2.43e-13

RNA polymerase sigma factor; Provisional


Pssm-ID: 183384 [Multi-domain]  Cd Length: 179  Bit Score: 64.99  E-value: 2.43e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 291514096   1 MMRKADVSFEELYNCYKVRFERFAISYIQDRSVAEDIVTDSFVYWWEHRDRVGSKdENPAAYILATIRHKCLNHLRALQV 80
Cdd:PRK11924   7 DATGDKEAFSELFRPHAPDLLRYARRQLGDRALAEDAVQEAFLRAWRKADLFNGK-GSARTWLLTIARNVCYDLLRRRRR 85

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 291514096  81 RL--RSHNEIRESQSRIVQENIRSLElcdpVHLFAGEVEALvrqsLEELPELTRYIFIDQRLKGKSYRDIAVEYAISERR 158
Cdd:PRK11924  86 EKavLSDDALEPEFAETAETPEAALL----AKDDLARIDRC----LDALPVKQREVFLLRYVEGLSYREIAEILGVPVGT 157

                        170
                 ....*....|....*...
gi 291514096 159 VETELARALDKLRRRLKD 176
Cdd:PRK11924 158 VKSRLRRARQLLRECLEA 175
Sigma70_r4_2 pfam08281
Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 ...
 120-170 1.60e-06

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: 43.60  E-value: 1.60e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 291514096  120 VRQSLEELPELTRYIFIDQRLKGKSYRDIAVEYAISERRVETELARALDKL 170
Cdd:pfam08281   4 LLRALEELPPRQREVFLLRYLEGLSYAEIAELLGISEGTVKSRLSRARKKL 54
Sigma70_r4 cd06171
Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in ...
 118-171 5.41e-05

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: 39.40  E-value: 5.41e-05
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 291514096 118 ALVRQSLEELPELTRYIFIDQRLKGKSYRDIAVEYAISERRVETELARALDKLR 171
Cdd:cd06171    2 ERLEEALDKLPEREREVILLRFGEGLSYEEIAEILGISRSTVRQRLHRALKKLR 55
 
Name Accession Description Interval E-value
Sig70_bacteroi1 TIGR02985
RNA polymerase sigma-70 factor, Bacteroides expansion family 1; This group of sigma factors ...
 8-174 9.06e-40

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: 133.07  E-value: 9.06e-40
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 291514096    8 SFEELYNCYKVRFERFAISYIQDRSVAEDIVTDSFVYWWEHRDRVgSKDENPAAYILATIRHKCLNHLRALQVRLRSHNE 87
Cdd:TIGR02985   2 AFEQLYRRYYPKLCAFARRYVKDEEDAEDIVQDVFLKLWENRETL-EISESIKAYLFTIVKNRCLNYLRHKQVEEKYQEE 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 291514096   88 IRESQSRIVQENirslelCDPVHLFAGEVEALVRQSLEELPELTRYIFIDQRLKGKSYRDIAVEYAISERRVETELARAL 167
Cdd:TIGR02985  81 LAEIEERELSEA------DPEEELEAKELEEIIEEAIEKLPEQCREIFILSRFEGLSNKEIAEELGISVKTVEYHITKAL 154


                  ....*..
gi 291514096  168 DKLRRRL 174
Cdd:TIGR02985 155 KFLRKEL 161
RpoE COG1595
DNA-directed RNA polymerase specialized sigma subunit, sigma24 family [Transcription]; ...
 9-179 5.16e-25

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: 95.83  E-value: 5.16e-25
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 291514096   9 FEELYNCYKVRFERFAISYIQDRSVAEDIVTDSFVYWWEHRDRVgSKDENPAAYILATIRHKCLNHLRALQVRLRSHNEI 88
Cdd:COG1595   19 FEELYERYRPRLYRYARRLLGDRADAEDLVQETFLRLWRKLDSF-RGRGSFRAWLYRIARNLAIDHLRKRRRRRELLDEL 97

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 291514096  89 RESQSRIVQENIRSLElcdpvhlfAGEVEALVRQSLEELPELTRYIFIDQRLKGKSYRDIAVEYAISERRVETELARALD 168
Cdd:COG1595   98 AEELPDEAADPEEALE--------AEELLEALLAALERLPPRQREVLVLRYLEGLSYAEIAEILGISEGTVKSRLSRARK 169

                        170
                 ....*....|.
gi 291514096 169 KLRRRLKDYLP 179
Cdd:COG1595  170 KLREALEEEGA 180
sigma70-ECF TIGR02937
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ...
 8-174 9.66e-19

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: 78.54  E-value: 9.66e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 291514096    8 SFEELYNCYKVRFERFAISYIQDRSVAEDIVTDSFVYWWEHRDRVgSKDENPAAYILATIRHKCLNHLRALQVRLRSHNE 87
Cdd:TIGR02937   2 AFEELYERYLPLVYRYARRYLGDDADAEDLVQEAFLKLLEALDRF-DPEGSFKAWLFRIARNLILDYLRRKRRLRRELDL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 291514096   88 IRESQSRIVQENIrslelcdpvHLFAGEVEALVRQSLEELPELTRYIFIDQRLKGKSYRDIAVEYAISERRVETELARAL 167
Cdd:TIGR02937  81 LEELLDSDPSPEE---------ELEQEEEREALREALEKLPEREREVLVLRYLEGLSYKEIAEILGISVGTVKRRLKRAR 151


                  ....*..
gi 291514096  168 DKLRRRL 174
Cdd:TIGR02937 152 KKLRELL 158
PRK11924 PRK11924
RNA polymerase sigma factor; Provisional
 1-176 2.43e-13

RNA polymerase sigma factor; Provisional


Pssm-ID: 183384 [Multi-domain]  Cd Length: 179  Bit Score: 64.99  E-value: 2.43e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 291514096   1 MMRKADVSFEELYNCYKVRFERFAISYIQDRSVAEDIVTDSFVYWWEHRDRVGSKdENPAAYILATIRHKCLNHLRALQV 80
Cdd:PRK11924   7 DATGDKEAFSELFRPHAPDLLRYARRQLGDRALAEDAVQEAFLRAWRKADLFNGK-GSARTWLLTIARNVCYDLLRRRRR 85

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 291514096  81 RL--RSHNEIRESQSRIVQENIRSLElcdpVHLFAGEVEALvrqsLEELPELTRYIFIDQRLKGKSYRDIAVEYAISERR 158
Cdd:PRK11924  86 EKavLSDDALEPEFAETAETPEAALL----AKDDLARIDRC----LDALPVKQREVFLLRYVEGLSYREIAEILGVPVGT 157

                        170
                 ....*....|....*...
gi 291514096 159 VETELARALDKLRRRLKD 176
Cdd:PRK11924 158 VKSRLRRARQLLRECLEA 175
PRK09639 PRK09639
RNA polymerase sigma factor SigX; Provisional
 6-171 2.05e-11

RNA polymerase sigma factor SigX; Provisional


Pssm-ID: 236602 [Multi-domain]  Cd Length: 166  Bit Score: 59.58  E-value: 2.05e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 291514096   6 DVSFEELYNCYKVRFERFAISYIQDRSVAEDIVTDsfVYWWEHRDRVGSKdENPAAYILATIRHKCLNHLRAlQVRLRSH 85
Cdd:PRK09639   2 DETFEDLFEQYYPDVVQQIFYIVKDRTQAEDLAQE--VFLRLYRSDFKGI-ENEKGWLIKSARNVAYNYLRS-EKRRRAR 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 291514096  86 nEIRESQsrivQENIRSLELCDPVHLFAGEVEaLVRQSLEELPELTRYIFIdQRLKGKSYRDIAVEYAISERRVETELAR 165
Cdd:PRK09639  78 -ILGEFQ----WQEVDNEPSPEEIWIRKEEIT-KVQEVLAKMTERDRTVLL-LRFSGYSYKEIAEALGIKESSVGTTLAR 150


                 ....*.
gi 291514096 166 ALDKLR 171
Cdd:PRK09639 151 AKKKFR 156
PRK09652 PRK09652
RNA polymerase sigma factor RpoE; Provisional
 9-179 2.73e-08

RNA polymerase sigma factor RpoE; Provisional


Pssm-ID: 236608 [Multi-domain]  Cd Length: 182  Bit Score: 51.35  E-value: 2.73e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 291514096   9 FEELYNCYKVRFERFAISYIQDRSVAEDIVTDSFVYWWE--HRDRVGSkdeNPAAYI--LATIRHKclNHLRALQVRL-R 83
Cdd:PRK09652  12 FALLVRRYQPRVKRLLSRLTRDPADAEDLVQETFIKAYRalHSFRGGA---AFYTWLyrIARNTAI--NYLRKQGRRPpA 86

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 291514096  84 SHNEIRESQSRIVQENIRSLELCDpVHLFAGEVEALVRQSLEELPELTRYIFIDQRLKGKSYRDIAVEYAISERRVETEL 163
Cdd:PRK09652  87 SDVDAEEAEDFDLADALRDISTPE-NELLSAELEQRVRAAIESLPEELRTAITLREIEGLSYEEIAEIMGCPIGTVRSRI 165

                        170
                 ....*....|....*.
gi 291514096 164 ARALDKLRRRLKDYLP 179
Cdd:PRK09652 166 FRAREALRAKLQPLLD 181
PRK12519 PRK12519
RNA polymerase sigma factor; Provisional
 12-178 2.67e-07

RNA polymerase sigma factor; Provisional


Pssm-ID: 237125 [Multi-domain]  Cd Length: 194  Bit Score: 48.52  E-value: 2.67e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 291514096  12 LYNCYKVRFERFAISYIQDRSVAEDIVTDSFVYWWEHRDrVGSKDENPAAYILATIRHKCLNHLRALQVRLRShneIRES 91
Cdd:PRK12519  34 LYDRHAGLVYGLALKILGNSQEAEDLTQEIFLSLWRKSS-YDPKRGSLSSYLLTLTRSRAIDRLRSRRSRQRL---LERW 109

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 291514096  92 QSRIVQENIRSLELcdpVHLFAGEVEALVRQSLEELPELTRYIFIDQRLKGKSYRDIAVEYAISERRVETELARALDKLR 171
Cdd:PRK12519 110 QQELLGEASEDTPL---EQASLAERSQRVQTALAQLPESQRQVLELAYYEGLSQSEIAKRLGIPLGTVKARARQGLLKLR 186


                 ....*..
gi 291514096 172 RRLKDYL 178
Cdd:PRK12519 187 ELLQDLL 193
Sigma70_r4_2 pfam08281
Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 ...
 120-170 1.60e-06

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: 43.60  E-value: 1.60e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 291514096  120 VRQSLEELPELTRYIFIDQRLKGKSYRDIAVEYAISERRVETELARALDKL 170
Cdd:pfam08281   4 LLRALEELPPRQREVFLLRYLEGLSYAEIAELLGISEGTVKSRLSRARKKL 54
PRK12514 PRK12514
RNA polymerase sigma factor; Provisional
 8-171 4.02e-06

RNA polymerase sigma factor; Provisional


Pssm-ID: 105710 [Multi-domain]  Cd Length: 179  Bit Score: 45.20  E-value: 4.02e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 291514096   8 SFEELYNCYKVRFERFAISYIQDRSVAEDIVTDSFVYWWEHRDRVGSKDENPAAYILATIRHKCLNHLRAlqvRLRSHNE 87
Cdd:PRK12514  20 AFSSLYDATSAKLFGICLRVLKDRSEAEEALQDVYVKIWTKADRFAVSGLSPMTWLITIARNHAIDRLRA---RKAVAVD 96

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 291514096  88 IREsqsrivqenirSLELCDPV-----HLFAGEVEALVRQSLEELPELTRYIFIDQRLKGKSYRDIAVEYAISERRVETE 162
Cdd:PRK12514  97 IDE-----------AHDLADPSpgpeaEVIAGDEGQRIDACLEELEKDRAAAVRRAYLEGLSYKELAERHDVPLNTMRTW 165


                 ....*....
gi 291514096 163 LARALDKLR 171
Cdd:PRK12514 166 LRRSLLKLR 174
Sigma70_r2 pfam04542
Sigma-70 region 2; Region 2 of sigma-70 is the most conserved region of the entire protein. ...
 12-79 1.05e-05

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: 41.80  E-value: 1.05e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 291514096   12 LYNCYKVRFERFAISYIQDRSVAEDIVTDSFVYWWEHRDRV-GSKDENPAAYILATIRHKCLNHLRALQ 79
Cdd:pfam04542   1 LVERYLPLVYSLARRYLGDGADAEDLVQEGFLGLWRAIERFdPERGVSFSTWLYTIIRNAIIDYLRKQR 69
Sigma70_r4 cd06171
Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in ...
 118-171 5.41e-05

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: 39.40  E-value: 5.41e-05
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 291514096 118 ALVRQSLEELPELTRYIFIDQRLKGKSYRDIAVEYAISERRVETELARALDKLR 171
Cdd:cd06171    2 ERLEEALDKLPEREREVILLRFGEGLSYEEIAEILGISRSTVRQRLHRALKKLR 55
PRK12527 PRK12527
RNA polymerase sigma factor; Reviewed
 22-177 6.68e-05

RNA polymerase sigma factor; Reviewed


Pssm-ID: 171560 [Multi-domain]  Cd Length: 159  Bit Score: 41.30  E-value: 6.68e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 291514096  22 RFAISYIQDRSVAEDIVTDSFVYWWEHRDrvGSKDENPAAYILATirhkCLNhlraLQVRLRSHNEIRESQSRIVQENIR 101
Cdd:PRK12527  10 RFLSARLGNRQAAEDVAHDAYLRVLERSS--SAQIEHPRAFLYRT----ALN----LVVDRHRRHRVRQAEPLEVLDEEE 79

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 291514096 102 SLELCDPVH-LFAGEVEALVRQSLEELPELTRYIFIDQRLKGKSYRDIAVEYAISERRVETELARALDKLRRRLKDY 177
Cdd:PRK12527  80 RLHSPSPQTrLDLGQRLALLQRALAELPPACRDSFLLRKLEGLSHQQIAEHLGISRSLVEKHIVNAMKHCRVRMRQW 156
PRK07037 PRK07037
extracytoplasmic-function sigma-70 factor; Validated
 31-174 6.80e-05

extracytoplasmic-function sigma-70 factor; Validated


Pssm-ID: 180803 [Multi-domain]  Cd Length: 163  Bit Score: 41.59  E-value: 6.80e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 291514096  31 RSVAEDIVTDSFVYWWEHRDRVGSKdeNPAAYILATIRHKCLNHLRALQVRLRSHNEIRESqsrivqenirsleLCDPVH 110
Cdd:PRK07037  22 RSRAEDVVQDAFVKLVEAPNQDAVK--QPVAYLFRIVRNLAIDHYRRQALENKYHGDEEDG-------------LDVPSP 86

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 291514096 111 LFAGEVEALVRQSLE-------ELPELTRYIFIDQRLKGKSYRDIAVEYAISERRVETELARALDKLRRRL 174
Cdd:PRK07037  87 EASPEAALINRDTLRhvadalsELPARTRYAFEMYRLHGETQKDIARELGVSPTLVNFMIRDALVHCRKCL 157
PRK12515 PRK12515
RNA polymerase sigma factor; Provisional
 12-175 3.59e-04

RNA polymerase sigma factor; Provisional


Pssm-ID: 183567 [Multi-domain]  Cd Length: 189  Bit Score: 39.71  E-value: 3.59e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 291514096  12 LYNCYKVRFERFAISYIQDRSVAEDIVTDSFVYWW------EHRDRVgskdenpAAYILATIRHKCLNHLRAlqvrlRSH 85
Cdd:PRK12515  27 LYGRHHVRVYRFGLRLVRDEQTAEDLVSEVFLDVWrqagqfEGRSQV-------STWLLSIARFKALSALRR-----RKH 94

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 291514096  86 NEIRESQSRIVQENIRSLElcdpVHLFAGEVEALVRQSLEELPELTRYIFIDQRLKGKSYRDIAVEYAISERRVETELAR 165
Cdd:PRK12515  95 EEIDDEAAAAIEDGADTPE----VALQKSDTSAALRACLAKLSPAHREIIDLVYYHEKSVEEVGEIVGIPESTVKTRMFY 170

                        170
                 ....*....|
gi 291514096 166 ALDKLRRRLK 175
Cdd:PRK12515 171 ARKKLAELLK 180
PRK12542 PRK12542
RNA polymerase sigma factor; Provisional
 10-171 1.26e-03

RNA polymerase sigma factor; Provisional


Pssm-ID: 183581 [Multi-domain]  Cd Length: 185  Bit Score: 38.11  E-value: 1.26e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 291514096  10 EELYNCYKVRFERFAISYIQDRSVAEDIVTDSFVYWWEHRDRVGSKD-ENPAAYILATIRHKCLNHLRALQVRLRSHNEI 88
Cdd:PRK12542  12 EELYELYEQKVYYVAYSILNNIQQAEDAVQETFITLYKNLEKLHSLNtQELKRYILRVAKNKAIDSYRKNKRHETFLEEY 91

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 291514096  89 RESQSRIVQENIRSLElcdpvHLFAGEVEalVRQSLEELPELTRYIFIDQRLKGKSYRDIAVEYAISERRVETELARALD 168
Cdd:PRK12542  92 ERESIEAVDENIEEWE-----KRKMSEVQ--IDTLLKELNESNRQVFKYKVFYNLTYQEISSVMGITEANVRKQFERARK 164


                 ...
gi 291514096 169 KLR 171
Cdd:PRK12542 165 RVQ 167
PRK12513 PRK12513
RNA polymerase sigma factor; Provisional
 9-177 1.65e-03

RNA polymerase sigma factor; Provisional


Pssm-ID: 183566 [Multi-domain]  Cd Length: 194  Bit Score: 37.75  E-value: 1.65e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 291514096   9 FEELYNCYKVRFERFAISYIQDRSVAEDIVTDSFVYW------WEHRDRVGSkdenpaaYILATIRHKCLNHLRALQVRL 82
Cdd:PRK12513  28 FEALYARHRTGLYRFLLRLARDRALAEDIFQETWLRViraraqYQPRARFRT-------WLYQIARNLLIDHWRRHGARQ 100

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 291514096  83 RSHNEIRESQSRIVQENIRSLELcdpvhLFAGEVEALVRQSLEELPELTRYIFIDQRLKGKSYRDIAVEYAISERRVETE 162
Cdd:PRK12513 101 APSLDADEQLHALADDGAAPEQQ-----LSLFRDRRRLQAALETLPDEQREVFLLREHGDLELEEIAELTGVPEETVKSR 175

                        170
                 ....*....|....*
gi 291514096 163 LARALDKLRRRLKDY 177
Cdd:PRK12513 176 LRYALQKLRELLAEE 190
Sigma70_r4 pfam04545
Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 ...
 124-172 2.09e-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: 34.71  E-value: 2.09e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 291514096  124 LEELPELTRYIFIDQRLKGKSYRDIAVEYAISERRVETELARALDKLRR 172
Cdd:pfam04545   2 LASLPPRERQVLVLRYGEGLTLEEIGERLGISRERVRQIEKRALRKLRK 50
PRK09642 PRK09642
RNA polymerase sigma factor;
97-176 3.69e-03

RNA polymerase sigma factor;


Pssm-ID: 170031 [Multi-domain]  Cd Length: 160  Bit Score: 36.62  E-value: 3.69e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 291514096  97 QENIRSLELCDPVhLFAGEVEALVRQSLEELPELTRYIFIDQRLKGKSYRDIAVEYAISERRVETELARALDKLRRRLKD 176
Cdd:PRK09642  78 EENIKSSHNIEDL-LLTKEQKLLIAQKLRELPENYRDVVLAHYLEEKSYQEIALQEKIEVKTVEMKLYRARKWIKKHWKE 156
Sig70_famx1 TIGR02943
RNA polymerase sigma-70 factor, TIGR02943 family; This group of sigma factors are members of ...
 22-171 5.64e-03

RNA polymerase sigma-70 factor, TIGR02943 family; This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family.


Pssm-ID: 274359 [Multi-domain]  Cd Length: 188  Bit Score: 36.28  E-value: 5.64e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 291514096   22 RFAISYIQDRSVAEDIVTDSFVYWWEHRDRVGSKDENpAAYILATIRHKCLNHLRALQVRLRSHNEIRESQSrivqENIR 101
Cdd:TIGR02943  17 RFARLQLRDRDLAEDAVQETLLAALSHRDSFAGRSAL-KTWLFAILKNKIIDALRAKGREVKVSDLDDELDD----EAFN 91

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 291514096  102 SL-------ELCDPVHLFAGEVEALVRQS--------LEELPELTRYIFIDQRLKGKSYRDIAVEYAISERRVETELARA 166
Cdd:TIGR02943  92 ALftqnghwAQHGQPQHWNTPEKQLENKEfwevfeacLYHLPEQTARVFMMREVLGFESDEICQELEISTSNCHVLLYRA 171


                  ....*
gi 291514096  167 LDKLR 171
Cdd:TIGR02943 172 RLSLR 176
FliA COG1191
DNA-directed RNA polymerase specialized sigma subunit [Transcription]; DNA-directed RNA ...
 115-176 5.84e-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: 36.34  E-value: 5.84e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 291514096 115 EVEALVRQSLEELPELTRYIFIDQRLKGKSYRDIAVEYAISERRVETELARALDKLRRRLKD 176
Cdd:COG1191  175 ELREALAEAIEQLPERERLVLSLYYFEELTLKEIAEVLGVSESRVSRLHKKALARLREYLKE 236
PRK12537 PRK12537
RNA polymerase sigma factor; Provisional
 10-76 9.06e-03

RNA polymerase sigma factor; Provisional


Pssm-ID: 171568 [Multi-domain]  Cd Length: 182  Bit Score: 35.52  E-value: 9.06e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 291514096  10 EELYNCYKVRFERFAISYIQDRSVAEDIVTDSFVYWWEHRDRVGSKDENPAAYILATIRHKCLNHLR 76
Cdd:PRK12537  26 QALYQQESARLLGVARRIVRDRALAEDIVHDAFIKIWTGAASFDPARGSARGWIYSVTRHLALNVLR 92
 
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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