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Conserved domains on  [gi|1232993992|gb|OZB89950.1|]
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hypothetical protein B7X41_00045 [Microbacterium sp. 14-71-5]

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.
 36-83 1.69e-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: 51.69  E-value: 1.69e-10
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 1232993992  36 LLTVVEAARRLGIGRSSLYRLLDGGQIRSIHVGRSHRIPVEALVDFIA 83
Cdd:pfam12728   1 LLTVEEAAELLGVSRRTVYRLIRSGELPAAKIGRRWRIRKSDLEEWLE 48
 
Name Accession Description Interval E-value
HTH_17 pfam12728
Helix-turn-helix domain; This domain is a DNA-binding helix-turn-helix domain.
 36-83 1.69e-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: 51.69  E-value: 1.69e-10
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 1232993992  36 LLTVVEAARRLGIGRSSLYRLLDGGQIRSIHVGRSHRIPVEALVDFIA 83
Cdd:pfam12728   1 LLTVEEAAELLGVSRRTVYRLIRSGELPAAKIGRRWRIRKSDLEEWLE 48
excise TIGR01764
DNA binding domain, excisionase family; An excisionase, or Xis protein, is a small protein ...
 36-84 3.10e-09

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: 48.37  E-value: 3.10e-09
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 1232993992  36 LLTVVEAARRLGIGRSSLYRLLDGGQIRSIHVGRSHRIPVEALVDFIAT 84
Cdd:TIGR01764   1 YLTVEEAAEYLGVSKSTVYRLIEEGELPAYRVGRHYRIPREDVDEYLEQ 49
AlpA COG3311
DNA-binding transcriptional regulator AlpA [Transcription, Mobilome: prophages, transposons];
36-83 8.12e-05

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


Pssm-ID: 442540 [Multi-domain]  Cd Length: 64  Bit Score: 37.60  E-value: 8.12e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 1232993992  36 LLTVVEAARRLGIGRSSLYRLLDGGQI-RSIHVG-RSHRIPVEALVDFIA 83
Cdd:COG3311     8 LLRLKEVAELLGVSRSTIYRLIKKGEFpKPVKLGgRSVRWRESEVEAWLA 57
 
Name Accession Description Interval E-value
HTH_17 pfam12728
Helix-turn-helix domain; This domain is a DNA-binding helix-turn-helix domain.
 36-83 1.69e-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: 51.69  E-value: 1.69e-10
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 1232993992  36 LLTVVEAARRLGIGRSSLYRLLDGGQIRSIHVGRSHRIPVEALVDFIA 83
Cdd:pfam12728   1 LLTVEEAAELLGVSRRTVYRLIRSGELPAAKIGRRWRIRKSDLEEWLE 48
excise TIGR01764
DNA binding domain, excisionase family; An excisionase, or Xis protein, is a small protein ...
 36-84 3.10e-09

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: 48.37  E-value: 3.10e-09
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 1232993992  36 LLTVVEAARRLGIGRSSLYRLLDGGQIRSIHVGRSHRIPVEALVDFIAT 84
Cdd:TIGR01764   1 YLTVEEAAEYLGVSKSTVYRLIEEGELPAYRVGRHYRIPREDVDEYLEQ 49
AlpA COG3311
DNA-binding transcriptional regulator AlpA [Transcription, Mobilome: prophages, transposons];
36-83 8.12e-05

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


Pssm-ID: 442540 [Multi-domain]  Cd Length: 64  Bit Score: 37.60  E-value: 8.12e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 1232993992  36 LLTVVEAARRLGIGRSSLYRLLDGGQI-RSIHVG-RSHRIPVEALVDFIA 83
Cdd:COG3311     8 LLRLKEVAELLGVSRSTIYRLIKKGEFpKPVKLGgRSVRWRESEVEAWLA 57
COG2452 COG2452
Predicted site-specific integrase-resolvase [Mobilome: prophages, transposons];
37-78 2.59e-03

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


Pssm-ID: 441988 [Multi-domain]  Cd Length: 178  Bit Score: 35.35  E-value: 2.59e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 1232993992  37 LTVVEAARRLGIGRSSLYRLLDGGQIRSIHV-GRSHRIPVEAL 78
Cdd:COG2452     1 LTPGEAAELLGVSPKTLRRWEKEGKLPAIRTpGGHRRYPESEV 43
RocR COG3829
RocR-type transcriptional regulator, contains PAS, AAA-type ATPase, and DNA-binding Fis ...
 38-57 3.66e-03

RocR-type transcriptional regulator, contains PAS, AAA-type ATPase, and DNA-binding Fis domains [Transcription, Signal transduction mechanisms];


Pssm-ID: 443041 [Multi-domain]  Cd Length: 448  Bit Score: 35.13  E-value: 3.66e-03
                          10        20
                  ....*....|....*....|
gi 1232993992  38 TVVEAARRLGIGRSSLYRLL 57
Cdd:COG3829   423 NKSKAAKALGISRSTLYRKL 442
AcoR COG3284
Transcriptional regulator DhaR of acetoin/glycerol metabolism [Transcription];
39-55 5.06e-03

Transcriptional regulator DhaR of acetoin/glycerol metabolism [Transcription];


Pssm-ID: 442514 [Multi-domain]  Cd Length: 625  Bit Score: 34.88  E-value: 5.06e-03
                          10
                  ....*....|....*..
gi 1232993992  39 VVEAARRLGIGRSSLYR 55
Cdd:COG3284   603 VSAAARALGISRSTLYR 619
 
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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