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Conserved domains on  [gi|1779413597|emb|VUD39585|]
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Cox [Peduovirus P24C9]

Protein Classification

regulatory phage cox family protein( domain architecture ID 10566637)

regulatory phage cox family protein similar to the multifunctional Cox protein of bacteriophage P2 that is involved in site-specific recombination leading to P2 prophage excision and functions as a transcriptional repressor of the P2 Pc promoter

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
Phage_Cox pfam10743
Regulatory phage protein cox; This family of phage Cox proteins is expressed by Enterobacteria ...
 1-80 5.52e-45

Regulatory phage protein cox; This family of phage Cox proteins is expressed by Enterobacteria phages. The Cox protein is a 79-residue basic protein with a predicted strong helix-turn-helix DNA-binding motif. It inhibits integrative recombination and it activates site-specific excision of the HP1 genome from the Haemophilus influenzae chromosome, Hp1. Cox appears to function as a tetramer. Cox binding sites consist of two direct repeats of the consensus motif 5'-GGTMAWWWWA, one Cox tetramer binding to each motif. Cox binding interferes with the interaction of HP1 integrase with one of its binding sites, IBS5. This competition is central to directional control. Both Cox binding sites are needed for full inhibition of integration and for activating excision, because it plays a positive role in assembling the nucleoprotein complexes that produce excisive recombination, by inducing the formation of a critical conformation in those complexes.


:

Pssm-ID: 431468  Cd Length: 87  Bit Score: 139.29  E-value: 5.52e-45
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1779413597  1 MTDAIPYQEFAKLIGKSTGAVRRMIDKGKLPVIDMTDPQSASGRAGEYWVYLPAWNNGLKLAYESRPKEIRDGWLMWLGL 80
Cdd:pfam10743  8 PADAVTKEKFAELIGKTTSAIRAMIKAGKLPVVEMTDPLKAGGRNGEYWVYLPEWNKGLKLAYESRPPEERDGWLGWLGL 87
 
Name Accession Description Interval E-value
Phage_Cox pfam10743
Regulatory phage protein cox; This family of phage Cox proteins is expressed by Enterobacteria ...
 1-80 5.52e-45

Regulatory phage protein cox; This family of phage Cox proteins is expressed by Enterobacteria phages. The Cox protein is a 79-residue basic protein with a predicted strong helix-turn-helix DNA-binding motif. It inhibits integrative recombination and it activates site-specific excision of the HP1 genome from the Haemophilus influenzae chromosome, Hp1. Cox appears to function as a tetramer. Cox binding sites consist of two direct repeats of the consensus motif 5'-GGTMAWWWWA, one Cox tetramer binding to each motif. Cox binding interferes with the interaction of HP1 integrase with one of its binding sites, IBS5. This competition is central to directional control. Both Cox binding sites are needed for full inhibition of integration and for activating excision, because it plays a positive role in assembling the nucleoprotein complexes that produce excisive recombination, by inducing the formation of a critical conformation in those complexes.


Pssm-ID: 431468  Cd Length: 87  Bit Score: 139.29  E-value: 5.52e-45
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1779413597  1 MTDAIPYQEFAKLIGKSTGAVRRMIDKGKLPVIDMTDPQSASGRAGEYWVYLPAWNNGLKLAYESRPKEIRDGWLMWLGL 80
Cdd:pfam10743  8 PADAVTKEKFAELIGKTTSAIRAMIKAGKLPVVEMTDPLKAGGRNGEYWVYLPEWNKGLKLAYESRPPEERDGWLGWLGL 87
COG2452 COG2452
Predicted site-specific integrase-resolvase [Mobilome: prophages, transposons];
8-33 3.87e-03

Predicted site-specific integrase-resolvase [Mobilome: prophages, transposons];


Pssm-ID: 441988 [Multi-domain]  Cd Length: 178  Bit Score: 33.81  E-value: 3.87e-03
                          10        20
                  ....*....|....*....|....*.
gi 1779413597   8 QEFAKLIGKSTGAVRRMIDKGKLPVI 33
Cdd:COG2452     4 GEAAELLGVSPKTLRRWEKEGKLPAI 29
 
Name Accession Description Interval E-value
Phage_Cox pfam10743
Regulatory phage protein cox; This family of phage Cox proteins is expressed by Enterobacteria ...
 1-80 5.52e-45

Regulatory phage protein cox; This family of phage Cox proteins is expressed by Enterobacteria phages. The Cox protein is a 79-residue basic protein with a predicted strong helix-turn-helix DNA-binding motif. It inhibits integrative recombination and it activates site-specific excision of the HP1 genome from the Haemophilus influenzae chromosome, Hp1. Cox appears to function as a tetramer. Cox binding sites consist of two direct repeats of the consensus motif 5'-GGTMAWWWWA, one Cox tetramer binding to each motif. Cox binding interferes with the interaction of HP1 integrase with one of its binding sites, IBS5. This competition is central to directional control. Both Cox binding sites are needed for full inhibition of integration and for activating excision, because it plays a positive role in assembling the nucleoprotein complexes that produce excisive recombination, by inducing the formation of a critical conformation in those complexes.


Pssm-ID: 431468  Cd Length: 87  Bit Score: 139.29  E-value: 5.52e-45
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1779413597  1 MTDAIPYQEFAKLIGKSTGAVRRMIDKGKLPVIDMTDPQSASGRAGEYWVYLPAWNNGLKLAYESRPKEIRDGWLMWLGL 80
Cdd:pfam10743  8 PADAVTKEKFAELIGKTTSAIRAMIKAGKLPVVEMTDPLKAGGRNGEYWVYLPEWNKGLKLAYESRPPEERDGWLGWLGL 87
COG2452 COG2452
Predicted site-specific integrase-resolvase [Mobilome: prophages, transposons];
8-33 3.87e-03

Predicted site-specific integrase-resolvase [Mobilome: prophages, transposons];


Pssm-ID: 441988 [Multi-domain]  Cd Length: 178  Bit Score: 33.81  E-value: 3.87e-03
                          10        20
                  ....*....|....*....|....*.
gi 1779413597   8 QEFAKLIGKSTGAVRRMIDKGKLPVI 33
Cdd:COG2452     4 GEAAELLGVSPKTLRRWEKEGKLPAI 29
TMP_3 pfam20155
Tape measure protein; This entry represents phage tape measure proteins that are required to ...
 1-30 6.65e-03

Tape measure protein; This entry represents phage tape measure proteins that are required to assemble the page tail. The protein serves as a base for tail tube protein polymerization and acts as a template for tail length determination.


Pssm-ID: 466312 [Multi-domain]  Cd Length: 192  Bit Score: 33.35  E-value: 6.65e-03
                          10        20        30
                  ....*....|....*....|....*....|..
gi 1779413597   1 MTDAIPY--QEFAKLIGKSTGAVRRMIDKGKL 30
Cdd:pfam20155 114 VLEQAPGllQALAKGLGVSTGELRKMASDGKL 145
 
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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