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Conserved domains on  [gi|1525942373|ref|WP_124562135|]
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sigma-70 family RNA polymerase sigma factor [Pedobacter sp. KBW01]

Protein Classification

sigma-70 RNA polymerase sigma factor region 4 domain-containing protein( domain architecture ID 1001861)

sigma-70 RNA polymerase sigma factor region 4 domain-containing protein which may or may not bind DNA or function as a sigma factor.

Gene Ontology:  GO:0003677|GO:0016987|GO:0006352
PubMed:  1597408

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
sigma70-ECF super family cl37189
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ...
 25-196 7.42e-06

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.


The actual alignment was detected with superfamily member TIGR02937:

Pssm-ID: 274357 [Multi-domain]  Cd Length: 158  Bit Score: 45.03  E-value: 7.42e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1525942373  25 LEFFYKLLYPRTYYYGFRYIKDDVNAGCIVNEAFLRLWLCRNNITCPDHIETFVKKLTSDGCKAYYKtsgnrfhRNMLRL 104
Cdd:TIGR02937   3 FEELYERYLPLVYRYARRYLGDDADAEDLVQEAFLKLLEALDRFDPEGSFKAWLFRIARNLILDYLR-------RKRRLR 75

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1525942373 105 DEIENYQDfIGGYDPNQEDErdilyqhepgEEEKKQWERVQTVLPNLSHDQQLFVRLCIKYSFNYGQMAwHIGGISDYQV 184
Cdd:TIGR02937  76 RELDLLEE-LLDSDPSPEEE----------LEQEEEREALREALEKLPEREREVLVLRYLEGLSYKEIA-EILGISVGTV 143

                         170
                  ....*....|..
gi 1525942373 185 ARKVEKTLECLK 196
Cdd:TIGR02937 144 KRRLKRARKKLR 155
 
Name Accession Description Interval E-value
sigma70-ECF TIGR02937
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ...
 25-196 7.42e-06

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: 45.03  E-value: 7.42e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1525942373  25 LEFFYKLLYPRTYYYGFRYIKDDVNAGCIVNEAFLRLWLCRNNITCPDHIETFVKKLTSDGCKAYYKtsgnrfhRNMLRL 104
Cdd:TIGR02937   3 FEELYERYLPLVYRYARRYLGDDADAEDLVQEAFLKLLEALDRFDPEGSFKAWLFRIARNLILDYLR-------RKRRLR 75

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1525942373 105 DEIENYQDfIGGYDPNQEDErdilyqhepgEEEKKQWERVQTVLPNLSHDQQLFVRLCIKYSFNYGQMAwHIGGISDYQV 184
Cdd:TIGR02937  76 RELDLLEE-LLDSDPSPEEE----------LEQEEEREALREALEKLPEREREVLVLRYLEGLSYKEIA-EILGISVGTV 143

                         170
                  ....*....|..
gi 1525942373 185 ARKVEKTLECLK 196
Cdd:TIGR02937 144 KRRLKRARKKLR 155
RpoE COG1595
DNA-directed RNA polymerase specialized sigma subunit, sigma24 family [Transcription]; ...
 15-173 1.02e-05

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: 44.99  E-value: 1.02e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1525942373  15 TKFKEGNEKGLEFFYKLLYPRTYYYGFRYIKDDVNAGCIVNEAFLRLWLCRNNITCPDHIETFVKKLTsdgckayYKTSG 94
Cdd:COG1595     9 ERLRAGDEAAFEELYERYRPRLYRYARRLLGDRADAEDLVQETFLRLWRKLDSFRGRGSFRAWLYRIA-------RNLAI 81

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1525942373  95 NRFHRNMLRLDEIENYQDFIGGYDPNQEDErdilyqhepgEEEKKQWERVQTVLPNLSHDQQLFVRLCIKYSFNYGQMA 173
Cdd:COG1595    82 DHLRKRRRRRELLDELAEELPDEAADPEEA----------LEAEELLEALLAALERLPPRQREVLVLRYLEGLSYAEIA 150
 
Name Accession Description Interval E-value
sigma70-ECF TIGR02937
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ...
 25-196 7.42e-06

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: 45.03  E-value: 7.42e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1525942373  25 LEFFYKLLYPRTYYYGFRYIKDDVNAGCIVNEAFLRLWLCRNNITCPDHIETFVKKLTSDGCKAYYKtsgnrfhRNMLRL 104
Cdd:TIGR02937   3 FEELYERYLPLVYRYARRYLGDDADAEDLVQEAFLKLLEALDRFDPEGSFKAWLFRIARNLILDYLR-------RKRRLR 75

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1525942373 105 DEIENYQDfIGGYDPNQEDErdilyqhepgEEEKKQWERVQTVLPNLSHDQQLFVRLCIKYSFNYGQMAwHIGGISDYQV 184
Cdd:TIGR02937  76 RELDLLEE-LLDSDPSPEEE----------LEQEEEREALREALEKLPEREREVLVLRYLEGLSYKEIA-EILGISVGTV 143

                         170
                  ....*....|..
gi 1525942373 185 ARKVEKTLECLK 196
Cdd:TIGR02937 144 KRRLKRARKKLR 155
RpoE COG1595
DNA-directed RNA polymerase specialized sigma subunit, sigma24 family [Transcription]; ...
 15-173 1.02e-05

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: 44.99  E-value: 1.02e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1525942373  15 TKFKEGNEKGLEFFYKLLYPRTYYYGFRYIKDDVNAGCIVNEAFLRLWLCRNNITCPDHIETFVKKLTsdgckayYKTSG 94
Cdd:COG1595     9 ERLRAGDEAAFEELYERYRPRLYRYARRLLGDRADAEDLVQETFLRLWRKLDSFRGRGSFRAWLYRIA-------RNLAI 81

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1525942373  95 NRFHRNMLRLDEIENYQDFIGGYDPNQEDErdilyqhepgEEEKKQWERVQTVLPNLSHDQQLFVRLCIKYSFNYGQMA 173
Cdd:COG1595    82 DHLRKRRRRRELLDELAEELPDEAADPEEA----------LEAEELLEALLAALERLPPRQREVLVLRYLEGLSYAEIA 150
Sig70_bacteroi1 TIGR02985
RNA polymerase sigma-70 factor, Bacteroides expansion family 1; This group of sigma factors ...
 28-96 1.08e-04

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: 41.78  E-value: 1.08e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1525942373  28 FYKLLYPRTYYYGFRYIKDDVNAGCIVNEAFLRLWLCRNNITCPDHIETFVKKLTSDGCKAYYKTSGNR 96
Cdd:TIGR02985   6 LYRRYYPKLCAFARRYVKDEEDAEDIVQDVFLKLWENRETLEISESIKAYLFTIVKNRCLNYLRHKQVE 74
 
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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