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Conserved domains on  [gi|518093924|ref|WP_019264132|]
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MULTISPECIES: DUF134 domain-containing protein [Methanobrevibacter]

Protein Classification

COG1342 family protein( domain architecture ID 10003558)

COG1342 family protein

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
COG1342 COG1342
Predicted DNA-binding protein, UPF0251 family [General function prediction only];
1-86 6.95e-32

Predicted DNA-binding protein, UPF0251 family [General function prediction only];


:

Pssm-ID: 440953  Cd Length: 99  Bit Score: 110.23  E-value: 6.95e-32
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518093924   1 MVRPKRMRRVvtCHRHELN---------KNLKPIELSVDEFEAIRFKDYHNIKQTESAEFMGISQSTFHRILNSARHKLS 71
Cdd:COG1342    1 MPRPKKCRRV--CFLPEVRcfkpagiplRELEEVVLTVDELEAIRLVDLEGLTQEEAAEKMGVSRPTFQRILKSARKKVA 78

                         90
                 ....*....|....*
gi 518093924  72 TSLIEGRPIVIVKGD 86
Cdd:COG1342   79 DALVNGKAIRIEGGN 93
 
Name Accession Description Interval E-value
COG1342 COG1342
Predicted DNA-binding protein, UPF0251 family [General function prediction only];
1-86 6.95e-32

Predicted DNA-binding protein, UPF0251 family [General function prediction only];


Pssm-ID: 440953  Cd Length: 99  Bit Score: 110.23  E-value: 6.95e-32
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518093924   1 MVRPKRMRRVvtCHRHELN---------KNLKPIELSVDEFEAIRFKDYHNIKQTESAEFMGISQSTFHRILNSARHKLS 71
Cdd:COG1342    1 MPRPKKCRRV--CFLPEVRcfkpagiplRELEEVVLTVDELEAIRLVDLEGLTQEEAAEKMGVSRPTFQRILKSARKKVA 78

                         90
                 ....*....|....*
gi 518093924  72 TSLIEGRPIVIVKGD 86
Cdd:COG1342   79 DALVNGKAIRIEGGN 93
DUF134 pfam02001
Protein of unknown function DUF134; This family of archaeal proteins has no known function. A ...
 3-90 1.34e-26

Protein of unknown function DUF134; This family of archaeal proteins has no known function. A study suggests that some members may be G-quadruplex binding proteins.


Pssm-ID: 280223  Cd Length: 98  Bit Score: 96.91  E-value: 1.34e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518093924    3 RPKRMRRV-----VTCHRHELNKNLKPIELSVDEFEAIRFKDYHNIKQTESAEFMGISQSTFHRILNSARHKLSTSLIEG 77
Cdd:pfam02001   6 RPRILRDIseepaVRAFIPEGVPGTGKVAINLDEAEAIRLVDYEDMSQDDAAAKMGISKATLWRLLTAARKKIADALFEG 85

                          90
                  ....*....|...
gi 518093924   78 RPIVIVKGDTMID 90
Cdd:pfam02001  86 RAIIIKGGEYEIL 98
PRK04217 PRK04217
hypothetical protein; Provisional
 23-83 2.75e-15

hypothetical protein; Provisional


Pssm-ID: 235258  Cd Length: 110  Bit Score: 67.98  E-value: 2.75e-15
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 518093924  23 KPIELSVDEFEAIRFKDYHNIKQTESAEFMGISQSTFHRILNSARHKLSTSLIEGRPIVIV 83
Cdd:PRK04217  39 PPIFMTYEEFEALRLVDYEGLTQEEAGKRMGVSRGTVWRALTSARKKVAQMLVEGRELIIL 99
sigma70-ECF TIGR02937
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ...
 14-74 1.36e-04

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: 40.41  E-value: 1.36e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 518093924   14 HRHELNKNLKPI--ELSVDEFEAIRFKDYHNIKQTESAEFMGISQSTFHRILNSARHKLSTSL 74
Cdd:TIGR02937  96 EQEEEREALREAleKLPEREREVLVLRYLEGLSYKEIAEILGISVGTVKRRLKRARKKLRELL 158
Sigma70_r4 cd06171
Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in ...
 26-70 1.95e-03

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: 34.77  E-value: 1.95e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*
gi 518093924  26 ELSVDEFEAIRFKDYHNIKQTESAEFMGISQSTFHRILNSARHKL 70
Cdd:cd06171   10 KLPEREREVILLRFGEGLSYEEIAEILGISRSTVRQRLHRALKKL 54
 
Name Accession Description Interval E-value
COG1342 COG1342
Predicted DNA-binding protein, UPF0251 family [General function prediction only];
1-86 6.95e-32

Predicted DNA-binding protein, UPF0251 family [General function prediction only];


Pssm-ID: 440953  Cd Length: 99  Bit Score: 110.23  E-value: 6.95e-32
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518093924   1 MVRPKRMRRVvtCHRHELN---------KNLKPIELSVDEFEAIRFKDYHNIKQTESAEFMGISQSTFHRILNSARHKLS 71
Cdd:COG1342    1 MPRPKKCRRV--CFLPEVRcfkpagiplRELEEVVLTVDELEAIRLVDLEGLTQEEAAEKMGVSRPTFQRILKSARKKVA 78

                         90
                 ....*....|....*
gi 518093924  72 TSLIEGRPIVIVKGD 86
Cdd:COG1342   79 DALVNGKAIRIEGGN 93
DUF134 pfam02001
Protein of unknown function DUF134; This family of archaeal proteins has no known function. A ...
 3-90 1.34e-26

Protein of unknown function DUF134; This family of archaeal proteins has no known function. A study suggests that some members may be G-quadruplex binding proteins.


Pssm-ID: 280223  Cd Length: 98  Bit Score: 96.91  E-value: 1.34e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518093924    3 RPKRMRRV-----VTCHRHELNKNLKPIELSVDEFEAIRFKDYHNIKQTESAEFMGISQSTFHRILNSARHKLSTSLIEG 77
Cdd:pfam02001   6 RPRILRDIseepaVRAFIPEGVPGTGKVAINLDEAEAIRLVDYEDMSQDDAAAKMGISKATLWRLLTAARKKIADALFEG 85

                          90
                  ....*....|...
gi 518093924   78 RPIVIVKGDTMID 90
Cdd:pfam02001  86 RAIIIKGGEYEIL 98
PRK04217 PRK04217
hypothetical protein; Provisional
 23-83 2.75e-15

hypothetical protein; Provisional


Pssm-ID: 235258  Cd Length: 110  Bit Score: 67.98  E-value: 2.75e-15
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 518093924  23 KPIELSVDEFEAIRFKDYHNIKQTESAEFMGISQSTFHRILNSARHKLSTSLIEGRPIVIV 83
Cdd:PRK04217  39 PPIFMTYEEFEALRLVDYEGLTQEEAGKRMGVSRGTVWRALTSARKKVAQMLVEGRELIIL 99
sigma70-ECF TIGR02937
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ...
 14-74 1.36e-04

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: 40.41  E-value: 1.36e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 518093924   14 HRHELNKNLKPI--ELSVDEFEAIRFKDYHNIKQTESAEFMGISQSTFHRILNSARHKLSTSL 74
Cdd:TIGR02937  96 EQEEEREALREAleKLPEREREVLVLRYLEGLSYKEIAEILGISVGTVKRRLKRARKKLRELL 158
Sigma70_r4 cd06171
Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in ...
 26-70 1.95e-03

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: 34.77  E-value: 1.95e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*
gi 518093924  26 ELSVDEFEAIRFKDYHNIKQTESAEFMGISQSTFHRILNSARHKL 70
Cdd:cd06171   10 KLPEREREVILLRFGEGLSYEEIAEILGISRSTVRQRLHRALKKL 54
 
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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