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Conserved domains on  [gi|985380394|gb|KXA61779|]
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sigma-70, region 4 [Veillonella atypica]

Protein Classification

sigma-70 family RNA polymerase sigma factor( domain architecture ID 11495650)

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

Gene Ontology:  GO:0003677|GO:0016987|GO:0006352
PubMed:  28117604

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
sigma70-ECF TIGR02937
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ...
 54-223 9.07e-09

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: 52.73  E-value: 9.07e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 985380394   54 ELCRRYRPLIVKY-ERLLVNRTVEDDVEAMLWLTFIESIYTYNlaGTVPFAGYVKSAIHFKHLNHYKRIKqqwnhefHIP 132
Cdd:TIGR02937   5 ELYERYLPLVYRYaRRYLGDDADAEDLVQEAFLKLLEALDRFD--PEGSFKAWLFRIARNLILDYLRRKR-------RLR 75

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 985380394  133 DTADGDEQLamdqipdtIDVANQTVHREERVEQHQLLRRALRLLKVDQQQLITDIYGRGCNLSDLARQQNCSRQSVQQRH 212
Cdd:TIGR02937  76 RELDLLEEL--------LDSDPSPEEELEQEEEREALREALEKLPEREREVLVLRYLEGLSYKEIAEILGISVGTVKRRL 147

                         170
                  ....*....|.
gi 985380394  213 KRILDVLREYM 223
Cdd:TIGR02937 148 KRARKKLRELL 158
 
Name Accession Description Interval E-value
sigma70-ECF TIGR02937
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ...
 54-223 9.07e-09

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: 52.73  E-value: 9.07e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 985380394   54 ELCRRYRPLIVKY-ERLLVNRTVEDDVEAMLWLTFIESIYTYNlaGTVPFAGYVKSAIHFKHLNHYKRIKqqwnhefHIP 132
Cdd:TIGR02937   5 ELYERYLPLVYRYaRRYLGDDADAEDLVQEAFLKLLEALDRFD--PEGSFKAWLFRIARNLILDYLRRKR-------RLR 75

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 985380394  133 DTADGDEQLamdqipdtIDVANQTVHREERVEQHQLLRRALRLLKVDQQQLITDIYGRGCNLSDLARQQNCSRQSVQQRH 212
Cdd:TIGR02937  76 RELDLLEEL--------LDSDPSPEEELEQEEEREALREALEKLPEREREVLVLRYLEGLSYKEIAEILGISVGTVKRRL 147

                         170
                  ....*....|.
gi 985380394  213 KRILDVLREYM 223
Cdd:TIGR02937 148 KRARKKLRELL 158
RpoE COG1595
DNA-directed RNA polymerase specialized sigma subunit, sigma24 family [Transcription]; ...
 54-226 3.73e-04

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: 39.98  E-value: 3.73e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 985380394  54 ELCRRYRPLIVKY-ERLLVNRTVEDDVEAMLWLTFIESIYTYNlaGTVPFAGYVKSAIHFKHLNHYKRikqQWNHEFHIP 132
Cdd:COG1595   21 ELYERYRPRLYRYaRRLLGDRADAEDLVQETFLRLWRKLDSFR--GRGSFRAWLYRIARNLAIDHLRK---RRRRRELLD 95

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 985380394 133 DTADgdeqlamdQIPDTIDVANQTVHREERveqHQLLRRALRLLKVDQQQLITDIYGRGCNLSDLARQQNCSRQSVQQRH 212
Cdd:COG1595   96 ELAE--------ELPDEAADPEEALEAEEL---LEALLAALERLPPRQREVLVLRYLEGLSYAEIAEILGISEGTVKSRL 164

                        170
                 ....*....|....
gi 985380394 213 KRILDVLREYMYRY 226
Cdd:COG1595  165 SRARKKLREALEEE 178
Sigma70_r4 pfam04545
Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 ...
 180-221 1.53e-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: 35.48  E-value: 1.53e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 985380394  180 QQQLITDIYGRGCNLSDLARQQNCSRQSVQQRHKRILDVLRE 221
Cdd:pfam04545   9 ERQVLVLRYGEGLTLEEIGERLGISRERVRQIEKRALRKLRK 50
 
Name Accession Description Interval E-value
sigma70-ECF TIGR02937
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ...
 54-223 9.07e-09

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: 52.73  E-value: 9.07e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 985380394   54 ELCRRYRPLIVKY-ERLLVNRTVEDDVEAMLWLTFIESIYTYNlaGTVPFAGYVKSAIHFKHLNHYKRIKqqwnhefHIP 132
Cdd:TIGR02937   5 ELYERYLPLVYRYaRRYLGDDADAEDLVQEAFLKLLEALDRFD--PEGSFKAWLFRIARNLILDYLRRKR-------RLR 75

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 985380394  133 DTADGDEQLamdqipdtIDVANQTVHREERVEQHQLLRRALRLLKVDQQQLITDIYGRGCNLSDLARQQNCSRQSVQQRH 212
Cdd:TIGR02937  76 RELDLLEEL--------LDSDPSPEEELEQEEEREALREALEKLPEREREVLVLRYLEGLSYKEIAEILGISVGTVKRRL 147

                         170
                  ....*....|.
gi 985380394  213 KRILDVLREYM 223
Cdd:TIGR02937 148 KRARKKLRELL 158
RpoE COG1595
DNA-directed RNA polymerase specialized sigma subunit, sigma24 family [Transcription]; ...
 54-226 3.73e-04

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: 39.98  E-value: 3.73e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 985380394  54 ELCRRYRPLIVKY-ERLLVNRTVEDDVEAMLWLTFIESIYTYNlaGTVPFAGYVKSAIHFKHLNHYKRikqQWNHEFHIP 132
Cdd:COG1595   21 ELYERYRPRLYRYaRRLLGDRADAEDLVQETFLRLWRKLDSFR--GRGSFRAWLYRIARNLAIDHLRK---RRRRRELLD 95

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 985380394 133 DTADgdeqlamdQIPDTIDVANQTVHREERveqHQLLRRALRLLKVDQQQLITDIYGRGCNLSDLARQQNCSRQSVQQRH 212
Cdd:COG1595   96 ELAE--------ELPDEAADPEEALEAEEL---LEALLAALERLPPRQREVLVLRYLEGLSYAEIAEILGISEGTVKSRL 164

                        170
                 ....*....|....
gi 985380394 213 KRILDVLREYMYRY 226
Cdd:COG1595  165 SRARKKLREALEEE 178
Sigma70_r4 pfam04545
Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 ...
 180-221 1.53e-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: 35.48  E-value: 1.53e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 985380394  180 QQQLITDIYGRGCNLSDLARQQNCSRQSVQQRHKRILDVLRE 221
Cdd:pfam04545   9 ERQVLVLRYGEGLTLEEIGERLGISRERVRQIEKRALRKLRK 50
 
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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