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Conserved domains on  [gi|593776132|ref|YP_009013931|]
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excisionase family DNA-binding protein [Mycobacterium phage Turbido]

Protein Classification

helix-turn-helix domain-containing protein( domain architecture ID 10578545)

helix-turn-helix (HTH) domain-containing protein may function in DNA binding; similar to excisionase

CATH:  1.10.1660.10
Gene Ontology:  GO:0003677
PubMed:  15808743

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
HTH_17 pfam12728
Helix-turn-helix domain; This domain is a DNA-binding helix-turn-helix domain.
 6-52 4.31e-10

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


:

Pssm-ID: 463684 [Multi-domain]  Cd Length: 51  Bit Score: 48.61  E-value: 4.31e-10
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 593776132   6 SIQQTADYLGVSTRTVRNYIADGKLKAVRLGpRLIRVERDSVEALMR 52
Cdd:pfam12728  3 TVEEAAELLGVSRRTVYRLIRSGELPAAKIG-RRWRIRKSDLEEWLE 48
 
Name Accession Description Interval E-value
HTH_17 pfam12728
Helix-turn-helix domain; This domain is a DNA-binding helix-turn-helix domain.
 6-52 4.31e-10

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


Pssm-ID: 463684 [Multi-domain]  Cd Length: 51  Bit Score: 48.61  E-value: 4.31e-10
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 593776132   6 SIQQTADYLGVSTRTVRNYIADGKLKAVRLGpRLIRVERDSVEALMR 52
Cdd:pfam12728  3 TVEEAAELLGVSRRTVYRLIRSGELPAAKIG-RRWRIRKSDLEEWLE 48
COG2452 COG2452
Predicted site-specific integrase-resolvase [Mobilome: prophages, transposons];
6-52 1.61e-08

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


Pssm-ID: 441988 [Multi-domain]  Cd Length: 178  Bit Score: 47.29  E-value: 1.61e-08
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 593776132   6 SIQQTADYLGVSTRTVRNYIADGKLKAVRLGPRLIRVERDSVEALMR 52
Cdd:COG2452    2 TPGEAAELLGVSPKTLRRWEKEGKLPAIRTPGGHRRYPESEVERLER 48
excise TIGR01764
DNA binding domain, excisionase family; An excisionase, or Xis protein, is a small protein ...
 6-53 6.42e-08

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: 43.36  E-value: 6.42e-08
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*...
gi 593776132   6 SIQQTADYLGVSTRTVRNYIADGKLKAVRLGpRLIRVERDSVEALMRP 53
Cdd:TIGR01764  3 TVEEAAEYLGVSKSTVYRLIEEGELPAYRVG-RHYRIPREDVDEYLEQ 49
HTH_MerR-trunc cd04762
Helix-Turn-Helix DNA binding domain of truncated MerR-like proteins; Proteins in this family ...
 6-52 1.60e-07

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: 42.19  E-value: 1.60e-07
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*..
gi 593776132  6 SIQQTADYLGVSTRTVRNYIADGKLKAVRLGPRLIRVERDSVEALMR 52
Cdd:cd04762   2 TTKEAAELLGVSPSTLRRWVKEGKLKAIRTPGGHRRFPEEDLERLLG 48
 
Name Accession Description Interval E-value
HTH_17 pfam12728
Helix-turn-helix domain; This domain is a DNA-binding helix-turn-helix domain.
 6-52 4.31e-10

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


Pssm-ID: 463684 [Multi-domain]  Cd Length: 51  Bit Score: 48.61  E-value: 4.31e-10
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 593776132   6 SIQQTADYLGVSTRTVRNYIADGKLKAVRLGpRLIRVERDSVEALMR 52
Cdd:pfam12728  3 TVEEAAELLGVSRRTVYRLIRSGELPAAKIG-RRWRIRKSDLEEWLE 48
COG2452 COG2452
Predicted site-specific integrase-resolvase [Mobilome: prophages, transposons];
6-52 1.61e-08

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


Pssm-ID: 441988 [Multi-domain]  Cd Length: 178  Bit Score: 47.29  E-value: 1.61e-08
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 593776132   6 SIQQTADYLGVSTRTVRNYIADGKLKAVRLGPRLIRVERDSVEALMR 52
Cdd:COG2452    2 TPGEAAELLGVSPKTLRRWEKEGKLPAIRTPGGHRRYPESEVERLER 48
AlpA COG3311
DNA-binding transcriptional regulator AlpA [Transcription, Mobilome: prophages, transposons];
6-52 1.74e-08

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


Pssm-ID: 442540 [Multi-domain]  Cd Length: 64  Bit Score: 44.92  E-value: 1.74e-08
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*...
gi 593776132  6 SIQQTADYLGVSTRTVRNYIADGKL-KAVRLGPRLIRVERDSVEALMR 52
Cdd:COG3311  10 RLKEVAELLGVSRSTIYRLIKKGEFpKPVKLGGRSVRWRESEVEAWLA 57
excise TIGR01764
DNA binding domain, excisionase family; An excisionase, or Xis protein, is a small protein ...
 6-53 6.42e-08

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: 43.36  E-value: 6.42e-08
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*...
gi 593776132   6 SIQQTADYLGVSTRTVRNYIADGKLKAVRLGpRLIRVERDSVEALMRP 53
Cdd:TIGR01764  3 TVEEAAEYLGVSKSTVYRLIEEGELPAYRVG-RHYRIPREDVDEYLEQ 49
HTH_MerR-trunc cd04762
Helix-Turn-Helix DNA binding domain of truncated MerR-like proteins; Proteins in this family ...
 6-52 1.60e-07

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: 42.19  E-value: 1.60e-07
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*..
gi 593776132  6 SIQQTADYLGVSTRTVRNYIADGKLKAVRLGPRLIRVERDSVEALMR 52
Cdd:cd04762   2 TTKEAAELLGVSPSTLRRWVKEGKLKAIRTPGGHRRFPEEDLERLLG 48
HTH_11 pfam08279
HTH domain; This family includes helix-turn-helix domains in a wide variety of proteins.
 6-27 5.00e-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: 30.86  E-value: 5.00e-03
                         10        20
                 ....*....|....*....|..
gi 593776132   6 SIQQTADYLGVSTRTVRNYIAD 27
Cdd:pfam08279 15 SGQELAEKLGVSRRTIRRDIKI 36
BglG COG3711
Transcriptional antiterminator [Transcription];
6-25 5.72e-03

Transcriptional antiterminator [Transcription];


Pssm-ID: 442925 [Multi-domain]  Cd Length: 618  Bit Score: 32.52  E-value: 5.72e-03
                         10        20
                 ....*....|....*....|
gi 593776132   6 SIQQTADYLGVSTRTVRNYI 25
Cdd:COG3711   13 TAKELAKKLNVSERTIRYDI 32
HTH_MerR-SF cd04761
Helix-Turn-Helix DNA binding domain of transcription regulators from the MerR superfamily; ...
 6-34 6.99e-03

Helix-Turn-Helix DNA binding domain of transcription regulators from the MerR superfamily; Helix-turn-helix (HTH) transcription regulator MerR superfamily, N-terminal domain. The MerR family transcription regulators have been shown to mediate responses to stress including exposure to heavy metals, drugs, or oxygen radicals in eubacterial and some archaeal species. They regulate transcription of multidrug/metal ion transporter genes and oxidative stress regulons by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.


Pssm-ID: 133389 [Multi-domain]  Cd Length: 49  Bit Score: 30.64  E-value: 6.99e-03
                        10        20
                ....*....|....*....|....*....
gi 593776132  6 SIQQTADYLGVSTRTVRNYIADGKLKAVR 34
Cdd:cd04761   2 TIGELAKLTGVSPSTLRYYERIGLLSPAR 30
 
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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