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Conserved domains on  [gi|2720679307|ref|WP_342029870|]
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AlpA family phage regulatory protein [Pseudomonas borbori]

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];
17-86 5.43e-14

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


:

Pssm-ID: 442540 [Multi-domain]  Cd Length: 64  Bit Score: 61.48  E-value: 5.43e-14
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2720679307  17 NQSPLVMLRLTQVVQRTGLSRSTIYSKLDTNsvhydsTFPKQVRLGRGSaVRFIEAEVNAWLEQCVYSSR 86
Cdd:COG3311     2 SLPPDRLLRLKEVAELLGVSRSTIYRLIKKG------EFPKPVKLGGRS-VRWRESEVEAWLAARIAASR 64
 
Name Accession Description Interval E-value
AlpA COG3311
DNA-binding transcriptional regulator AlpA [Transcription, Mobilome: prophages, transposons];
17-86 5.43e-14

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


Pssm-ID: 442540 [Multi-domain]  Cd Length: 64  Bit Score: 61.48  E-value: 5.43e-14
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2720679307  17 NQSPLVMLRLTQVVQRTGLSRSTIYSKLDTNsvhydsTFPKQVRLGRGSaVRFIEAEVNAWLEQCVYSSR 86
Cdd:COG3311     2 SLPPDRLLRLKEVAELLGVSRSTIYRLIKKG------EFPKPVKLGGRS-VRWRESEVEAWLAARIAASR 64
Phage_AlpA pfam05930
Prophage CP4-57 regulatory protein (AlpA); This family consists of several short bacterial and ...
 24-78 3.29e-13

Prophage CP4-57 regulatory protein (AlpA); This family consists of several short bacterial and phage proteins which are related to the E. coli protein AlpA. AlpA suppress two phenotypes of a delta lon protease mutant, overproduction of capsular polysaccharide and sensitivity to UV light. Several of the sequences in this family are thought to be DNA-binding proteins.


Pssm-ID: 399137  Cd Length: 51  Bit Score: 58.88  E-value: 3.29e-13
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 2720679307  24 LRLTQVVQRTGLSRSTIYSKLDtnsvhyDSTFPKQVRLGrGSAVRFIEAEVNAWL 78
Cdd:pfam05930   4 LRLREVEQKTGLSRSSIYRLMK------EGEFPKPVRLG-VRAVAWVESEIDQWI 51
excise TIGR01764
DNA binding domain, excisionase family; An excisionase, or Xis protein, is a small protein ...
 24-80 4.49e-03

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: 32.96  E-value: 4.49e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 2720679307  24 LRLTQVVQRTGLSRSTIYSKLDTNSVHYdstfpkqVRLGRGsaVRFIEAEVNAWLEQ 80
Cdd:TIGR01764   2 LTVEEAAEYLGVSKSTVYRLIEEGELPA-------YRVGRH--YRIPREDVDEYLEQ 49
 
Name Accession Description Interval E-value
AlpA COG3311
DNA-binding transcriptional regulator AlpA [Transcription, Mobilome: prophages, transposons];
17-86 5.43e-14

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


Pssm-ID: 442540 [Multi-domain]  Cd Length: 64  Bit Score: 61.48  E-value: 5.43e-14
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2720679307  17 NQSPLVMLRLTQVVQRTGLSRSTIYSKLDTNsvhydsTFPKQVRLGRGSaVRFIEAEVNAWLEQCVYSSR 86
Cdd:COG3311     2 SLPPDRLLRLKEVAELLGVSRSTIYRLIKKG------EFPKPVKLGGRS-VRWRESEVEAWLAARIAASR 64
Phage_AlpA pfam05930
Prophage CP4-57 regulatory protein (AlpA); This family consists of several short bacterial and ...
 24-78 3.29e-13

Prophage CP4-57 regulatory protein (AlpA); This family consists of several short bacterial and phage proteins which are related to the E. coli protein AlpA. AlpA suppress two phenotypes of a delta lon protease mutant, overproduction of capsular polysaccharide and sensitivity to UV light. Several of the sequences in this family are thought to be DNA-binding proteins.


Pssm-ID: 399137  Cd Length: 51  Bit Score: 58.88  E-value: 3.29e-13
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 2720679307  24 LRLTQVVQRTGLSRSTIYSKLDtnsvhyDSTFPKQVRLGrGSAVRFIEAEVNAWL 78
Cdd:pfam05930   4 LRLREVEQKTGLSRSSIYRLMK------EGEFPKPVRLG-VRAVAWVESEIDQWI 51
HTH_17 pfam12728
Helix-turn-helix domain; This domain is a DNA-binding helix-turn-helix domain.
 23-81 3.83e-03

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


Pssm-ID: 463684 [Multi-domain]  Cd Length: 51  Bit Score: 32.82  E-value: 3.83e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 2720679307  23 MLRLTQVVQRTGLSRSTIYSKLDTNSVHYdstfpkqvrLGRGSAVRFIEAEVNAWLEQC 81
Cdd:pfam12728   1 LLTVEEAAELLGVSRRTVYRLIRSGELPA---------AKIGRRWRIRKSDLEEWLERR 50
excise TIGR01764
DNA binding domain, excisionase family; An excisionase, or Xis protein, is a small protein ...
 24-80 4.49e-03

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: 32.96  E-value: 4.49e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 2720679307  24 LRLTQVVQRTGLSRSTIYSKLDTNSVHYdstfpkqVRLGRGsaVRFIEAEVNAWLEQ 80
Cdd:TIGR01764   2 LTVEEAAEYLGVSKSTVYRLIEEGELPA-------YRVGRH--YRIPREDVDEYLEQ 49
 
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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