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Conserved domains on  [gi|186492184|ref|NP_176311|]
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retrotransposon gag [Arabidopsis thaliana]

Protein Classification

retrotransposon gag family protein( domain architecture ID 1903551)

retrotransposon gag family protein

PubMed:  11600699|25573958

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
Retrotrans_gag super family cl46289
Retrotransposon gag protein; Gag or Capsid-like proteins from LTR retrotransposons. There is a ...
 63-105 1.62e-03

Retrotransposon gag protein; Gag or Capsid-like proteins from LTR retrotransposons. There is a central motif QGXXEXXXXXFXXLXXH that is common to Retroviridae gag-proteins, but is poorly conserved.


The actual alignment was detected with superfamily member pfam03732:

Pssm-ID: 480629  Cd Length: 97  Bit Score: 36.54  E-value: 1.62e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 186492184   63 FEVKQGTETVREYYNEFLKKVKNLGRELEEEQ-LACLFQEGLRE 105
Cdd:pfam03732  54 RSLRQGTESVREYVERFKRLARQLPHHGRDEEaLISAFLRGLRP 97
 
Name Accession Description Interval E-value
Retrotrans_gag pfam03732
Retrotransposon gag protein; Gag or Capsid-like proteins from LTR retrotransposons. There is a ...
 63-105 1.62e-03

Retrotransposon gag protein; Gag or Capsid-like proteins from LTR retrotransposons. There is a central motif QGXXEXXXXXFXXLXXH that is common to Retroviridae gag-proteins, but is poorly conserved.


Pssm-ID: 367628  Cd Length: 97  Bit Score: 36.54  E-value: 1.62e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 186492184   63 FEVKQGTETVREYYNEFLKKVKNLGRELEEEQ-LACLFQEGLRE 105
Cdd:pfam03732  54 RSLRQGTESVREYVERFKRLARQLPHHGRDEEaLISAFLRGLRP 97
 
Name Accession Description Interval E-value
Retrotrans_gag pfam03732
Retrotransposon gag protein; Gag or Capsid-like proteins from LTR retrotransposons. There is a ...
 63-105 1.62e-03

Retrotransposon gag protein; Gag or Capsid-like proteins from LTR retrotransposons. There is a central motif QGXXEXXXXXFXXLXXH that is common to Retroviridae gag-proteins, but is poorly conserved.


Pssm-ID: 367628  Cd Length: 97  Bit Score: 36.54  E-value: 1.62e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 186492184   63 FEVKQGTETVREYYNEFLKKVKNLGRELEEEQ-LACLFQEGLRE 105
Cdd:pfam03732  54 RSLRQGTESVREYVERFKRLARQLPHHGRDEEaLISAFLRGLRP 97
 
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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