NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|2574381292|ref|WP_308690742|]
View 

AlpA family transcriptional regulator [uncultured Sutterella sp.]

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

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

 Name Accession Description Interval E-value
AlpA COG3311
DNA-binding transcriptional regulator AlpA [Transcription, Mobilome: prophages, transposons];
18-79 1.57e-11

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


:

Pssm-ID: 442540 [Multi-domain]  Cd Length: 64  Bit Score: 53.78  E-value: 1.57e-11
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2574381292 18 EEYVSPKEAAEILSVSVRTIWNWAADPLkkqagFPTAIKLSRTATRFPRSELEAFAEAMRAA 79
Cdd:COG3311    6 DRLLRLKEVAELLGVSRSTIYRLIKKGE-----FPKPVKLGGRSVRWRESEVEAWLAARIAA 62
 
Name Accession Description Interval E-value
AlpA COG3311
DNA-binding transcriptional regulator AlpA [Transcription, Mobilome: prophages, transposons];
18-79 1.57e-11

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


Pssm-ID: 442540 [Multi-domain]  Cd Length: 64  Bit Score: 53.78  E-value: 1.57e-11
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2574381292 18 EEYVSPKEAAEILSVSVRTIWNWAADPLkkqagFPTAIKLSRTATRFPRSELEAFAEAMRAA 79
Cdd:COG3311    6 DRLLRLKEVAELLGVSRSTIYRLIKKGE-----FPKPVKLGGRSVRWRESEVEAWLAARIAA 62
HTH_17 pfam12728
Helix-turn-helix domain; This domain is a DNA-binding helix-turn-helix domain.
 20-77 1.01e-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: 43.60  E-value: 1.01e-07
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 2574381292 20 YVSPKEAAEILSVSVRTIWNWAadplkKQAGFPtAIKLSRtATRFPRSELEAFAEAMR 77
Cdd:pfam12728  1 LLTVEEAAELLGVSRRTVYRLI-----RSGELP-AAKIGR-RWRIRKSDLEEWLERRR 51
HTH_MerR-trunc cd04762
Helix-Turn-Helix DNA binding domain of truncated MerR-like proteins; Proteins in this family ...
 21-74 1.10e-05

Helix-Turn-Helix DNA binding domain of truncated MerR-like proteins; Proteins in this family mostly have a truncated helix-turn-helix (HTH) MerR-like domain. They lack a portion of the C-terminal region, called Wing 2 and the long dimerization helix that is typically present in MerR-like proteins. These truncated domains are found in response regulator receiver (REC) domain proteins (i.e., CheY), cytosine-C5 specific DNA methylases, IS607 transposase-like proteins, and RacA, a bacterial protein that anchors chromosomes to cell poles.


Pssm-ID: 133390 [Multi-domain]  Cd Length: 49  Bit Score: 38.72  E-value: 1.10e-05
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 2574381292 21 VSPKEAAEILSVSVRTIWNWAadplkkQAGfptAIKLSRTAT---RFPRSELEAFAE 74
Cdd:cd04762    1 LTTKEAAELLGVSPSTLRRWV------KEG---KLKAIRTPGghrRFPEEDLERLLG 48
excise TIGR01764
DNA binding domain, excisionase family; An excisionase, or Xis protein, is a small protein ...
 20-75 2.88e-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: 32.19  E-value: 2.88e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 2574381292 20 YVSPKEAAEILSVSVRTIWNWAADplkkqaGFPTAIKLSRTaTRFPRSELEAFAEA 75
Cdd:TIGR01764  1 YLTVEEAAEYLGVSKSTVYRLIEE------GELPAYRVGRH-YRIPREDVDEYLEQ 49
 
Name Accession Description Interval E-value
AlpA COG3311
DNA-binding transcriptional regulator AlpA [Transcription, Mobilome: prophages, transposons];
18-79 1.57e-11

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


Pssm-ID: 442540 [Multi-domain]  Cd Length: 64  Bit Score: 53.78  E-value: 1.57e-11
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2574381292 18 EEYVSPKEAAEILSVSVRTIWNWAADPLkkqagFPTAIKLSRTATRFPRSELEAFAEAMRAA 79
Cdd:COG3311    6 DRLLRLKEVAELLGVSRSTIYRLIKKGE-----FPKPVKLGGRSVRWRESEVEAWLAARIAA 62
HTH_17 pfam12728
Helix-turn-helix domain; This domain is a DNA-binding helix-turn-helix domain.
 20-77 1.01e-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: 43.60  E-value: 1.01e-07
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 2574381292 20 YVSPKEAAEILSVSVRTIWNWAadplkKQAGFPtAIKLSRtATRFPRSELEAFAEAMR 77
Cdd:pfam12728  1 LLTVEEAAELLGVSRRTVYRLI-----RSGELP-AAKIGR-RWRIRKSDLEEWLERRR 51
COG2452 COG2452
Predicted site-specific integrase-resolvase [Mobilome: prophages, transposons];
21-72 2.89e-06

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


Pssm-ID: 441988 [Multi-domain]  Cd Length: 178  Bit Score: 42.29  E-value: 2.89e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 2574381292  21 VSPKEAAEILSVSVRTIWNWAadplkkQAGFPTAIKLSRTATRFPRSELEAF 72
Cdd:COG2452     1 LTPGEAAELLGVSPKTLRRWE------KEGKLPAIRTPGGHRRYPESEVERL 46
HTH_MerR-trunc cd04762
Helix-Turn-Helix DNA binding domain of truncated MerR-like proteins; Proteins in this family ...
 21-74 1.10e-05

Helix-Turn-Helix DNA binding domain of truncated MerR-like proteins; Proteins in this family mostly have a truncated helix-turn-helix (HTH) MerR-like domain. They lack a portion of the C-terminal region, called Wing 2 and the long dimerization helix that is typically present in MerR-like proteins. These truncated domains are found in response regulator receiver (REC) domain proteins (i.e., CheY), cytosine-C5 specific DNA methylases, IS607 transposase-like proteins, and RacA, a bacterial protein that anchors chromosomes to cell poles.


Pssm-ID: 133390 [Multi-domain]  Cd Length: 49  Bit Score: 38.72  E-value: 1.10e-05
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 2574381292 21 VSPKEAAEILSVSVRTIWNWAadplkkQAGfptAIKLSRTAT---RFPRSELEAFAE 74
Cdd:cd04762    1 LTTKEAAELLGVSPSTLRRWV------KEG---KLKAIRTPGghrRFPEEDLERLLG 48
excise TIGR01764
DNA binding domain, excisionase family; An excisionase, or Xis protein, is a small protein ...
 20-75 2.88e-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: 32.19  E-value: 2.88e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 2574381292 20 YVSPKEAAEILSVSVRTIWNWAADplkkqaGFPTAIKLSRTaTRFPRSELEAFAEA 75
Cdd:TIGR01764  1 YLTVEEAAEYLGVSKSTVYRLIEE------GELPAYRVGRH-YRIPREDVDEYLEQ 49
HTH_11 pfam08279
HTH domain; This family includes helix-turn-helix domains in a wide variety of proteins.
 16-39 3.29e-03

HTH domain; This family includes helix-turn-helix domains in a wide variety of proteins.


Pssm-ID: 429896 [Multi-domain]  Cd Length: 52  Bit Score: 32.40  E-value: 3.29e-03
                         10        20
                 ....*....|....*....|....
gi 2574381292 16 KKEEYVSPKEAAEILSVSVRTIWN 39
Cdd:pfam08279  9 EARGPISGQELAEKLGVSRRTIRR 32
 
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.
Help | Disclaimer | Write to the Help Desk
NCBI | NLM | NIH