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Conserved domains on  [gi|1277893426|gb|PIU98925|]
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hypothetical protein COS60_00440 [Candidatus Wolfebacteria bacterium CG03_land_8_20_14_0_80_39_317]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
RpoD super family cl33954
DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32) [Transcription]; DNA-directed RNA ...
 1-68 1.38e-18

DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32) [Transcription]; DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32) is part of the Pathway/BioSystem: RNA polymerase


The actual alignment was detected with superfamily member COG0568:

Pssm-ID: 440334 [Multi-domain]  Cd Length: 268  Bit Score: 83.95  E-value: 1.38e-18
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1277893426   1 MISSTINNLISDLKPRQQEILNGRFGLANGEKKTLASLGEKYDITRERVRQIEEEALRMARARIAKEK 68
Cdd:COG0568   195 LLREELREALDTLTEREREILRLRFGLDDGEPHTLEEIGKEFGVSRERVRQIEAKALRKLRHPLRSRK 262
HARE-HTH super family cl46430
HB1, ASXL, restriction endonuclease HTH domain; A winged helix-turn-helix domain present in ...
 216-278 3.69e-06

HB1, ASXL, restriction endonuclease HTH domain; A winged helix-turn-helix domain present in the plant HB1, vertebrate ASXL, the H. pylori restriction endonuclease HpyAIII(HgrA), the RNA polymerase delta subunit(RpoE) of Gram positive bacteria and several restriction endonucleases. The domain is distinguished by the presence of a conserved one-turn helix between helix-3 and the preceding conserved turn. Its diverse architectures in eukaryotic species with extensive gene body methylation is suggestive of a chromatin function. The genetic interaction of the HARE-HTH containing ASXL with the methyl cytosine hydroxylating Tet2 protein is suggestive of a role for the domain in discriminating sequences with DNA modifications such as hmC. Bacterial versions include fusions to diverse restriction endonucleases, and a DNA glycosylase where it may play a similar role in detecting modified DNA. Certain bacterial version of the HARE-HTH domain show fusions to the helix-hairpin-helix domain of the RNA polymerase alpha subunit and the HTH domains found in regions 3 and 4 of the sigma factors. These versions are predicted to function as a novel inhibitor of the binding of RNA polymerase to transcription start sites, similar to the Bacillus delta protein.


The actual alignment was detected with superfamily member pfam05066:

Pssm-ID: 480770  Cd Length: 71  Bit Score: 44.22  E-value: 3.69e-06
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1277893426 216 TVREKAYLILKKQDKPLHFREISEAINRTNFVGR--AAHPQTV----HNELIKDPRFVLVGRGIYGLTE 278
Cdd:pfam05066   2 TLKEAAFQVLEEEGRPLHFKEIAEEIQEKGLISLsgKTPEATLaaqlYTDIKEDSLFVRVGPGTFGLRS 70
 
Name Accession Description Interval E-value
RpoD COG0568
DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32) [Transcription]; DNA-directed RNA ...
 1-68 1.38e-18

DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32) [Transcription]; DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32) is part of the Pathway/BioSystem: RNA polymerase


Pssm-ID: 440334 [Multi-domain]  Cd Length: 268  Bit Score: 83.95  E-value: 1.38e-18
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1277893426   1 MISSTINNLISDLKPRQQEILNGRFGLANGEKKTLASLGEKYDITRERVRQIEEEALRMARARIAKEK 68
Cdd:COG0568   195 LLREELREALDTLTEREREILRLRFGLDDGEPHTLEEIGKEFGVSRERVRQIEAKALRKLRHPLRSRK 262
PRK07405 PRK07405
RNA polymerase sigma factor SigD; Validated
 2-65 3.53e-13

RNA polymerase sigma factor SigD; Validated


Pssm-ID: 180963 [Multi-domain]  Cd Length: 317  Bit Score: 69.40  E-value: 3.53e-13
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1277893426   2 ISSTINNLISDLKPRQQEILNGRFGLANGEKKTLASLGEKYDITRERVRQIEEEALRMARARIA 65
Cdd:PRK07405  246 LQLDLERLMEDLTPQQKEVIALRFGLEDGQPLTLAKIGERLNISRERVRQIEREALSKLRKRKA 309
Sigma70_r4 pfam04545
Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 ...
 9-58 8.41e-09

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: 50.89  E-value: 8.41e-09
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 1277893426   9 LISDLKPRQQEILNGRFGlangEKKTLASLGEKYDITRERVRQIEEEALR 58
Cdd:pfam04545   1 ALASLPPRERQVLVLRYG----EGLTLEEIGERLGISRERVRQIEKRALR 46
HARE-HTH pfam05066
HB1, ASXL, restriction endonuclease HTH domain; A winged helix-turn-helix domain present in ...
 216-278 3.69e-06

HB1, ASXL, restriction endonuclease HTH domain; A winged helix-turn-helix domain present in the plant HB1, vertebrate ASXL, the H. pylori restriction endonuclease HpyAIII(HgrA), the RNA polymerase delta subunit(RpoE) of Gram positive bacteria and several restriction endonucleases. The domain is distinguished by the presence of a conserved one-turn helix between helix-3 and the preceding conserved turn. Its diverse architectures in eukaryotic species with extensive gene body methylation is suggestive of a chromatin function. The genetic interaction of the HARE-HTH containing ASXL with the methyl cytosine hydroxylating Tet2 protein is suggestive of a role for the domain in discriminating sequences with DNA modifications such as hmC. Bacterial versions include fusions to diverse restriction endonucleases, and a DNA glycosylase where it may play a similar role in detecting modified DNA. Certain bacterial version of the HARE-HTH domain show fusions to the helix-hairpin-helix domain of the RNA polymerase alpha subunit and the HTH domains found in regions 3 and 4 of the sigma factors. These versions are predicted to function as a novel inhibitor of the binding of RNA polymerase to transcription start sites, similar to the Bacillus delta protein.


Pssm-ID: 461541  Cd Length: 71  Bit Score: 44.22  E-value: 3.69e-06
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1277893426 216 TVREKAYLILKKQDKPLHFREISEAINRTNFVGR--AAHPQTV----HNELIKDPRFVLVGRGIYGLTE 278
Cdd:pfam05066   2 TLKEAAFQVLEEEGRPLHFKEIAEEIQEKGLISLsgKTPEATLaaqlYTDIKEDSLFVRVGPGTFGLRS 70
Sigma70_r4 cd06171
Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in ...
 6-58 4.52e-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: 40.55  E-value: 4.52e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1277893426   6 INNLISDLKPRQQEILNGRFGlangEKKTLASLGEKYDITRERVRQIEEEALR 58
Cdd:cd06171     4 LEEALDKLPEREREVILLRFG----EGLSYEEIAEILGISRSTVRQRLHRALK 52
RpoE COG3343
DNA-directed RNA polymerase, delta subunit [Transcription]; DNA-directed RNA polymerase, delta ...
 219-278 3.53e-04

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


Pssm-ID: 442572  Cd Length: 90  Bit Score: 39.11  E-value: 3.53e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1277893426 219 EKAYLILKKQDKPLHFREISEAI----NRTNFVGRAAHPQtVHNELIKDPRFVLVGRGIYGLTE 278
Cdd:COG3343    16 ELAYEILEEKGEPMSFRDLIKEVaelkGLSDEELKERIAQ-FYTDLNIDGRFVSLGENRWGLRE 78
sigma70-ECF TIGR02937
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ...
 6-64 8.85e-03

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: 36.56  E-value: 8.85e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1277893426   6 INNLISDLKPRQQEILNGRFGlangEKKTLASLGEKYDITRERVRQIEEEALRMARARI 64
Cdd:TIGR02937 104 LREALEKLPEREREVLVLRYL----EGLSYKEIAEILGISVGTVKRRLKRARKKLRELL 158
 
Name Accession Description Interval E-value
RpoD COG0568
DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32) [Transcription]; DNA-directed RNA ...
 1-68 1.38e-18

DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32) [Transcription]; DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32) is part of the Pathway/BioSystem: RNA polymerase


Pssm-ID: 440334 [Multi-domain]  Cd Length: 268  Bit Score: 83.95  E-value: 1.38e-18
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1277893426   1 MISSTINNLISDLKPRQQEILNGRFGLANGEKKTLASLGEKYDITRERVRQIEEEALRMARARIAKEK 68
Cdd:COG0568   195 LLREELREALDTLTEREREILRLRFGLDDGEPHTLEEIGKEFGVSRERVRQIEAKALRKLRHPLRSRK 262
PRK07405 PRK07405
RNA polymerase sigma factor SigD; Validated
 2-65 3.53e-13

RNA polymerase sigma factor SigD; Validated


Pssm-ID: 180963 [Multi-domain]  Cd Length: 317  Bit Score: 69.40  E-value: 3.53e-13
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1277893426   2 ISSTINNLISDLKPRQQEILNGRFGLANGEKKTLASLGEKYDITRERVRQIEEEALRMARARIA 65
Cdd:PRK07405  246 LQLDLERLMEDLTPQQKEVIALRFGLEDGQPLTLAKIGERLNISRERVRQIEREALSKLRKRKA 309
PRK05949 PRK05949
RNA polymerase sigma factor; Validated
 6-68 4.96e-13

RNA polymerase sigma factor; Validated


Pssm-ID: 180321 [Multi-domain]  Cd Length: 327  Bit Score: 68.72  E-value: 4.96e-13
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1277893426   6 INNLISDLKPRQQEILNGRFGLANGEKKTLASLGEKYDITRERVRQIEEEALRMARARIAKEK 68
Cdd:PRK05949  260 LNNLLAELTPQQREVLTLRFGLEDGKELSLAKVGERLNLSRERVRQLEHQALAHLRRRRANVK 322
PRK07406 PRK07406
RNA polymerase sigma factor RpoD; Validated
 8-61 1.01e-10

RNA polymerase sigma factor RpoD; Validated


Pssm-ID: 236012 [Multi-domain]  Cd Length: 373  Bit Score: 62.11  E-value: 1.01e-10
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1277893426   8 NLISDLKPRQQEILNGRFGLANGEKKTLASLGEKYDITRERVRQIEEEALRMAR 61
Cdd:PRK07406  307 GVLATLSPRERDVLRLRYGLDDGRMKTLEEIGQIFNVTRERIRQIEAKALRKLR 360
PRK07598 PRK07598
RNA polymerase sigma factor SigC; Validated
 9-61 5.33e-10

RNA polymerase sigma factor SigC; Validated


Pssm-ID: 236067 [Multi-domain]  Cd Length: 415  Bit Score: 60.27  E-value: 5.33e-10
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1277893426   9 LISDLKPRQQEILNGRFGLANGEKKTLASLGEKYDITRERVRQIEEEALRMAR 61
Cdd:PRK07598  347 LLADLTSRERDVIRMRFGLADGHTYSLAEIGRALDLSRERVRQIESKALQKLR 399
PRK09210 PRK09210
RNA polymerase sigma factor RpoD; Validated
 13-61 3.01e-09

RNA polymerase sigma factor RpoD; Validated


Pssm-ID: 236413 [Multi-domain]  Cd Length: 367  Bit Score: 57.69  E-value: 3.01e-09
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 1277893426  13 LKPRQQEILNGRFGLANGEKKTLASLGEKYDITRERVRQIEEEALRMAR 61
Cdd:PRK09210  306 LTDREENVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLR 354
PRK05901 PRK05901
RNA polymerase sigma factor; Provisional
 6-58 3.25e-09

RNA polymerase sigma factor; Provisional


Pssm-ID: 235640 [Multi-domain]  Cd Length: 509  Bit Score: 58.08  E-value: 3.25e-09
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1277893426   6 INNLISDLKPRQQEILNGRFGLANGEKKTLASLGEKYDITRERVRQIEEEALR 58
Cdd:PRK05901  441 LQEVLETLSEREAGVIRMRFGLTDGQPKTLDEIGQVYGVTRERIRQIESKTLR 493
PRK07921 PRK07921
RNA polymerase sigma factor SigB; Reviewed
 1-62 5.58e-09

RNA polymerase sigma factor SigB; Reviewed


Pssm-ID: 181169 [Multi-domain]  Cd Length: 324  Bit Score: 56.66  E-value: 5.58e-09
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1277893426   1 MISSTINNLISDLKPRQQEILNGRFGLANGEKKTLASLGEKYDITRERVRQIEEEALRMARA 62
Cdd:PRK07921  251 LLHTDIRSVLATLDEREQQVIRLRFGLDDGQPRTLDQIGKLFGLSRERVRQIEREVMSKLRN 312
PRK05657 PRK05657
RNA polymerase sigma factor RpoS; Validated
 2-67 7.93e-09

RNA polymerase sigma factor RpoS; Validated


Pssm-ID: 235548 [Multi-domain]  Cd Length: 325  Bit Score: 56.12  E-value: 7.93e-09
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1277893426   2 ISSTINNLISDLKPRQQEILNGRFGLANGEKKTLASLGEKYDITRERVRQIEEEALRMARARIAKE 67
Cdd:PRK05657  252 MKQSIVKWLFELNDKQREVLARRFGLLGYEAATLEDVAREIGLTRERVRQIQVEALRRLREILQTQ 317
Sigma70_r4 pfam04545
Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 ...
 9-58 8.41e-09

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: 50.89  E-value: 8.41e-09
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 1277893426   9 LISDLKPRQQEILNGRFGlangEKKTLASLGEKYDITRERVRQIEEEALR 58
Cdd:pfam04545   1 ALASLPPRERQVLVLRYG----EGLTLEEIGERLGISRERVRQIEKRALR 46
PRK06596 PRK06596
RNA polymerase factor sigma-32; Reviewed
 6-67 1.91e-06

RNA polymerase factor sigma-32; Reviewed


Pssm-ID: 235838 [Multi-domain]  Cd Length: 284  Bit Score: 48.63  E-value: 1.91e-06
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1277893426   6 INNLISDLKPRQQEILNGRFgLANgEKKTLASLGEKYDITRERVRQIEEEALRMARARIAKE 67
Cdd:PRK06596  224 LADALEGLDERSRDIIEARW-LDD-DKSTLQELAAEYGVSAERVRQIEKNAMKKLKAAIEAA 283
PRK05658 PRK05658
RNA polymerase sigma factor RpoD; Validated
 13-58 2.18e-06

RNA polymerase sigma factor RpoD; Validated


Pssm-ID: 235549 [Multi-domain]  Cd Length: 619  Bit Score: 49.41  E-value: 2.18e-06
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 1277893426  13 LKPRQQEILNGRFGLANGEKKTLASLGEKYDITRERVRQIEEEALR 58
Cdd:PRK05658  557 LTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALR 602
HARE-HTH pfam05066
HB1, ASXL, restriction endonuclease HTH domain; A winged helix-turn-helix domain present in ...
 216-278 3.69e-06

HB1, ASXL, restriction endonuclease HTH domain; A winged helix-turn-helix domain present in the plant HB1, vertebrate ASXL, the H. pylori restriction endonuclease HpyAIII(HgrA), the RNA polymerase delta subunit(RpoE) of Gram positive bacteria and several restriction endonucleases. The domain is distinguished by the presence of a conserved one-turn helix between helix-3 and the preceding conserved turn. Its diverse architectures in eukaryotic species with extensive gene body methylation is suggestive of a chromatin function. The genetic interaction of the HARE-HTH containing ASXL with the methyl cytosine hydroxylating Tet2 protein is suggestive of a role for the domain in discriminating sequences with DNA modifications such as hmC. Bacterial versions include fusions to diverse restriction endonucleases, and a DNA glycosylase where it may play a similar role in detecting modified DNA. Certain bacterial version of the HARE-HTH domain show fusions to the helix-hairpin-helix domain of the RNA polymerase alpha subunit and the HTH domains found in regions 3 and 4 of the sigma factors. These versions are predicted to function as a novel inhibitor of the binding of RNA polymerase to transcription start sites, similar to the Bacillus delta protein.


Pssm-ID: 461541  Cd Length: 71  Bit Score: 44.22  E-value: 3.69e-06
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1277893426 216 TVREKAYLILKKQDKPLHFREISEAINRTNFVGR--AAHPQTV----HNELIKDPRFVLVGRGIYGLTE 278
Cdd:pfam05066   2 TLKEAAFQVLEEEGRPLHFKEIAEEIQEKGLISLsgKTPEATLaaqlYTDIKEDSLFVRVGPGTFGLRS 70
Sigma70_r4 cd06171
Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in ...
 6-58 4.52e-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: 40.55  E-value: 4.52e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1277893426   6 INNLISDLKPRQQEILNGRFGlangEKKTLASLGEKYDITRERVRQIEEEALR 58
Cdd:cd06171     4 LEEALDKLPEREREVILLRFG----EGLSYEEIAEILGISRSTVRQRLHRALK 52
RpoE COG3343
DNA-directed RNA polymerase, delta subunit [Transcription]; DNA-directed RNA polymerase, delta ...
 219-278 3.53e-04

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


Pssm-ID: 442572  Cd Length: 90  Bit Score: 39.11  E-value: 3.53e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1277893426 219 EKAYLILKKQDKPLHFREISEAI----NRTNFVGRAAHPQtVHNELIKDPRFVLVGRGIYGLTE 278
Cdd:COG3343    16 ELAYEILEEKGEPMSFRDLIKEVaelkGLSDEELKERIAQ-FYTDLNIDGRFVSLGENRWGLRE 78
rpoH2 PRK07500
RNA polymerase factor sigma-32; Reviewed
 13-69 6.68e-04

RNA polymerase factor sigma-32; Reviewed


Pssm-ID: 236033 [Multi-domain]  Cd Length: 289  Bit Score: 40.79  E-value: 6.68e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1277893426  13 LKPRQQEILngRFGLANGEKKTLASLGEKYDITRERVRQIEEEAlrMARARIAKEKA 69
Cdd:PRK07500  228 LNERELRII--RERRLREDGATLEALGEELGISKERVRQIEARA--LEKLRRALLSQ 280
sigma70-ECF TIGR02937
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ...
 6-64 8.85e-03

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: 36.56  E-value: 8.85e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1277893426   6 INNLISDLKPRQQEILNGRFGlangEKKTLASLGEKYDITRERVRQIEEEALRMARARI 64
Cdd:TIGR02937 104 LREALEKLPEREREVLVLRYL----EGLSYKEIAEILGISVGTVKRRLKRARKKLRELL 158
 
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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