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Conserved domains on  [gi|1864365439|ref|WP_176747182|]
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transposase family protein, partial [Actinomyces sp. HMSC075C01]

Protein Classification

helix-turn-helix domain-containing protein( domain architecture ID 82772)

helix-turn-helix domain-containing protein binds DNA

CATH:  1.10.10.10
Gene Ontology:  GO:0003677
PubMed:  20885819|15808743|8831795

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
HTH_Tnp_4 super family cl16321
Helix-turn-helix of DDE superfamily endonuclease; This domain is the probable DNA-binding ...
 1-29 1.74e-05

Helix-turn-helix of DDE superfamily endonuclease; This domain is the probable DNA-binding region of transposase enzymes, necessary for efficient DNA transposition. Most of the members derive from the IS superfamily IS5 and rather fewer from IS4.


The actual alignment was detected with superfamily member pfam13613:

Pssm-ID: 463934  Cd Length: 53  Bit Score: 37.50  E-value: 1.74e-05
                         10        20
                 ....*....|....*....|....*....
gi 1864365439  1 TYLRHNLPQAAIGELLGVSQPTVSRAVKA 29
Cdd:pfam13613 14 VYLRLNLTFQDLAYRFGVSESTASRIFHK 42
 
Name Accession Description Interval E-value
HTH_Tnp_4 pfam13613
Helix-turn-helix of DDE superfamily endonuclease; This domain is the probable DNA-binding ...
 1-29 1.74e-05

Helix-turn-helix of DDE superfamily endonuclease; This domain is the probable DNA-binding region of transposase enzymes, necessary for efficient DNA transposition. Most of the members derive from the IS superfamily IS5 and rather fewer from IS4.


Pssm-ID: 463934  Cd Length: 53  Bit Score: 37.50  E-value: 1.74e-05
                         10        20
                 ....*....|....*....|....*....
gi 1864365439  1 TYLRHNLPQAAIGELLGVSQPTVSRAVKA 29
Cdd:pfam13613 14 VYLRLNLTFQDLAYRFGVSESTASRIFHK 42
PRK09775 PRK09775
type II toxin-antitoxin system HipA family toxin YjjJ;
3-36 7.12e-05

type II toxin-antitoxin system HipA family toxin YjjJ;


Pssm-ID: 236623 [Multi-domain]  Cd Length: 442  Bit Score: 38.41  E-value: 7.12e-05
                          10        20        30
                  ....*....|....*....|....*....|....*
gi 1864365439   3 LRHNLPQAAIGELLGVSQPTVSRAVKA-RPELVTR 36
Cdd:PRK09775   10 LQGPLSAAELAARLGVSQATLSRLLAAlGDQVVRF 44
FliA COG1191
DNA-directed RNA polymerase specialized sigma subunit [Transcription]; DNA-directed RNA ...
 2-25 2.48e-04

DNA-directed RNA polymerase specialized sigma subunit [Transcription]; DNA-directed RNA polymerase specialized sigma subunit is part of the Pathway/BioSystem: RNA polymerase


Pssm-ID: 440804 [Multi-domain]  Cd Length: 236  Bit Score: 36.73  E-value: 2.48e-04
                          10        20
                  ....*....|....*....|....
gi 1864365439   2 YLRHNLPQAAIGELLGVSQPTVSR 25
Cdd:COG1191   198 YYFEELTLKEIAEVLGVSESRVSR 221
 
Name Accession Description Interval E-value
HTH_Tnp_4 pfam13613
Helix-turn-helix of DDE superfamily endonuclease; This domain is the probable DNA-binding ...
 1-29 1.74e-05

Helix-turn-helix of DDE superfamily endonuclease; This domain is the probable DNA-binding region of transposase enzymes, necessary for efficient DNA transposition. Most of the members derive from the IS superfamily IS5 and rather fewer from IS4.


Pssm-ID: 463934  Cd Length: 53  Bit Score: 37.50  E-value: 1.74e-05
                         10        20
                 ....*....|....*....|....*....
gi 1864365439  1 TYLRHNLPQAAIGELLGVSQPTVSRAVKA 29
Cdd:pfam13613 14 VYLRLNLTFQDLAYRFGVSESTASRIFHK 42
PRK09775 PRK09775
type II toxin-antitoxin system HipA family toxin YjjJ;
3-36 7.12e-05

type II toxin-antitoxin system HipA family toxin YjjJ;


Pssm-ID: 236623 [Multi-domain]  Cd Length: 442  Bit Score: 38.41  E-value: 7.12e-05
                          10        20        30
                  ....*....|....*....|....*....|....*
gi 1864365439   3 LRHNLPQAAIGELLGVSQPTVSRAVKA-RPELVTR 36
Cdd:PRK09775   10 LQGPLSAAELAARLGVSQATLSRLLAAlGDQVVRF 44
FliA COG1191
DNA-directed RNA polymerase specialized sigma subunit [Transcription]; DNA-directed RNA ...
 2-25 2.48e-04

DNA-directed RNA polymerase specialized sigma subunit [Transcription]; DNA-directed RNA polymerase specialized sigma subunit is part of the Pathway/BioSystem: RNA polymerase


Pssm-ID: 440804 [Multi-domain]  Cd Length: 236  Bit Score: 36.73  E-value: 2.48e-04
                          10        20
                  ....*....|....*....|....
gi 1864365439   2 YLRHNLPQAAIGELLGVSQPTVSR 25
Cdd:COG1191   198 YYFEELTLKEIAEVLGVSESRVSR 221
AF0184 COG2522
Predicted transcriptional regulator, contains XRE-type HTH domain [Transcription];
4-28 2.22e-03

Predicted transcriptional regulator, contains XRE-type HTH domain [Transcription];


Pssm-ID: 442012 [Multi-domain]  Cd Length: 99  Bit Score: 33.26  E-value: 2.22e-03
                         10        20
                 ....*....|....*....|....*
gi 1864365439  4 RHNLPQAAIGELLGVSQPTVSRAVK 28
Cdd:COG2522   26 ERGLSQSEIAKLLGITQAAVSQYLS 50
COG5606 COG5606
Predicted DNA-binding protein, XRE-type HTH domain [General function prediction only];
4-35 2.52e-03

Predicted DNA-binding protein, XRE-type HTH domain [General function prediction only];


Pssm-ID: 444337  Cd Length: 105  Bit Score: 33.32  E-value: 2.52e-03
                          10        20        30
                  ....*....|....*....|....*....|..
gi 1864365439   4 RHNLPQAAIGELLGVSQPTVSRAVKARPELVT 35
Cdd:COG5606    43 ERGLTQAEAAELLGITQPRVSDLLRGKISKFS 74
DeoR COG2390
DNA-binding transcriptional regulator LsrR, DeoR family [Transcription];
2-30 2.94e-03

DNA-binding transcriptional regulator LsrR, DeoR family [Transcription];


Pssm-ID: 441955 [Multi-domain]  Cd Length: 301  Bit Score: 33.56  E-value: 2.94e-03
                          10        20        30
                  ....*....|....*....|....*....|
gi 1864365439   2 YLRHNLPQAAIGELLGVSQPTVSRAVK-AR 30
Cdd:COG2390     6 YYVEGLTQREIAERLGISRRTVSRLLAeAR 35
 
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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