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Conserved domains on  [gi|2045876395|ref|WP_214057464|]
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AlpA family transcriptional regulator [Nocardioides aquaticus]

Protein Classification

helix-turn-helix transcriptional regulator( domain architecture ID 10007181)

helix-turn-helix DNA-binding protein similar to Mycobacterium phage excisionase, which is necessary for the excision of prophage from the host genome by site-specific recombination at the attachment site

CATH:  1.10.10.10
Gene Ontology:  GO:0003677|GO:0003700|GO:0006355
PubMed:  15808743|10473770|8831795

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
AlpA COG3311
DNA-binding transcriptional regulator AlpA [Transcription, Mobilome: prophages, transposons];
60-109 1.18e-09

DNA-binding transcriptional regulator AlpA [Transcription, Mobilome: prophages, transposons];


:

Pssm-ID: 442540 [Multi-domain]  Cd Length: 64  Bit Score: 50.31  E-value: 1.18e-09
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 2045876395  60 PDGLWDIDAVATYLNVPRQTIYAWRQKGYGPHGFRVG-KHLRWRAATVVAW 109
Cdd:COG3311     5 PDRLLRLKEVAELLGVSRSTIYRLIKKGEFPKPVKLGgRSVRWRESEVEAW 55
 
Name Accession Description Interval E-value
AlpA COG3311
DNA-binding transcriptional regulator AlpA [Transcription, Mobilome: prophages, transposons];
60-109 1.18e-09

DNA-binding transcriptional regulator AlpA [Transcription, Mobilome: prophages, transposons];


Pssm-ID: 442540 [Multi-domain]  Cd Length: 64  Bit Score: 50.31  E-value: 1.18e-09
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 2045876395  60 PDGLWDIDAVATYLNVPRQTIYAWRQKGYGPHGFRVG-KHLRWRAATVVAW 109
Cdd:COG3311     5 PDRLLRLKEVAELLGVSRSTIYRLIKKGEFPKPVKLGgRSVRWRESEVEAW 55
HTH_17 pfam12728
Helix-turn-helix domain; This domain is a DNA-binding helix-turn-helix domain.
 63-109 2.12e-07

Helix-turn-helix domain; This domain is a DNA-binding helix-turn-helix domain.


Pssm-ID: 463684 [Multi-domain]  Cd Length: 51  Bit Score: 43.99  E-value: 2.12e-07
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 2045876395  63 LWDIDAVATYLNVPRQTIYAWRQKGYGPHgFRVGKHLRWRAATVVAW 109
Cdd:pfam12728   1 LLTVEEAAELLGVSRRTVYRLIRSGELPA-AKIGRRWRIRKSDLEEW 46
excise TIGR01764
DNA binding domain, excisionase family; An excisionase, or Xis protein, is a small protein ...
 66-109 3.05e-04

DNA binding domain, excisionase family; An excisionase, or Xis protein, is a small protein that binds and promotes excisive recombination; it is not enzymatically active. This model represents a number of putative excisionases and related proteins from temperate phage, plasmids, and transposons, as well as DNA binding domains of other proteins, such as a DNA modification methylase. This model identifies mostly small proteins and N-terminal regions of large proteins, but some proteins appear to have two copies. This domain appears similar, in both sequence and predicted secondary structure (PSIPRED) to the MerR family of transcriptional regulators (pfam00376). [Unknown function, General]


Pssm-ID: 200128  Cd Length: 49  Bit Score: 36.04  E-value: 3.05e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 2045876395  66 IDAVATYLNVPRQTIYAWRQKGYGPHgFRVGKHLRWRAATVVAW 109
Cdd:TIGR01764   4 VEEAAEYLGVSKSTVYRLIEEGELPA-YRVGRHYRIPREDVDEY 46
 
Name Accession Description Interval E-value
AlpA COG3311
DNA-binding transcriptional regulator AlpA [Transcription, Mobilome: prophages, transposons];
60-109 1.18e-09

DNA-binding transcriptional regulator AlpA [Transcription, Mobilome: prophages, transposons];


Pssm-ID: 442540 [Multi-domain]  Cd Length: 64  Bit Score: 50.31  E-value: 1.18e-09
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 2045876395  60 PDGLWDIDAVATYLNVPRQTIYAWRQKGYGPHGFRVG-KHLRWRAATVVAW 109
Cdd:COG3311     5 PDRLLRLKEVAELLGVSRSTIYRLIKKGEFPKPVKLGgRSVRWRESEVEAW 55
HTH_17 pfam12728
Helix-turn-helix domain; This domain is a DNA-binding helix-turn-helix domain.
 63-109 2.12e-07

Helix-turn-helix domain; This domain is a DNA-binding helix-turn-helix domain.


Pssm-ID: 463684 [Multi-domain]  Cd Length: 51  Bit Score: 43.99  E-value: 2.12e-07
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 2045876395  63 LWDIDAVATYLNVPRQTIYAWRQKGYGPHgFRVGKHLRWRAATVVAW 109
Cdd:pfam12728   1 LLTVEEAAELLGVSRRTVYRLIRSGELPA-AKIGRRWRIRKSDLEEW 46
excise TIGR01764
DNA binding domain, excisionase family; An excisionase, or Xis protein, is a small protein ...
 66-109 3.05e-04

DNA binding domain, excisionase family; An excisionase, or Xis protein, is a small protein that binds and promotes excisive recombination; it is not enzymatically active. This model represents a number of putative excisionases and related proteins from temperate phage, plasmids, and transposons, as well as DNA binding domains of other proteins, such as a DNA modification methylase. This model identifies mostly small proteins and N-terminal regions of large proteins, but some proteins appear to have two copies. This domain appears similar, in both sequence and predicted secondary structure (PSIPRED) to the MerR family of transcriptional regulators (pfam00376). [Unknown function, General]


Pssm-ID: 200128  Cd Length: 49  Bit Score: 36.04  E-value: 3.05e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 2045876395  66 IDAVATYLNVPRQTIYAWRQKGYGPHgFRVGKHLRWRAATVVAW 109
Cdd:TIGR01764   4 VEEAAEYLGVSKSTVYRLIEEGELPA-YRVGRHYRIPREDVDEY 46
 
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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