NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|197245393|ref|NP_001127793|]
View 

retrotransposon Gag-like protein 8A isoform 2 [Homo sapiens]

Protein Classification

Graphical summary

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

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 ...
 2-64 1.36e-30

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 pfam16297:

Pssm-ID: 480629  Cd Length: 112  Bit Score: 103.84  E-value: 1.36e-30
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 197245393    2 DGRVQLMKALLAGPlRPAARRWRNPIPFPETFDGDTDRLPEFIVQTSSYMFVDENTFSNDALK 64
Cdd:pfam16297   1 DQRKQLRILVMEWP-RLQVRRWSNPIPFPERFSGESGRLPEFIVQTMSYMLVDEKTFCNDAMK 62
 
Name Accession Description Interval E-value
DUF4939 pfam16297
Domain of unknown function (DUF4939); This family consists of uncharacterized proteins around ...
 2-64 1.36e-30

Domain of unknown function (DUF4939); This family consists of uncharacterized proteins around 110 residues in length and is mainly found in various mammalia species. LDOC1, a member of this family and a novel MZF-1-interacting protein, inhibits NF-kappaB activation and relates with cancer and some other diseases. But the specific function of this family is still unknown.


Pssm-ID: 465086  Cd Length: 112  Bit Score: 103.84  E-value: 1.36e-30
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 197245393    2 DGRVQLMKALLAGPlRPAARRWRNPIPFPETFDGDTDRLPEFIVQTSSYMFVDENTFSNDALK 64
Cdd:pfam16297   1 DQRKQLRILVMEWP-RLQVRRWSNPIPFPERFSGESGRLPEFIVQTMSYMLVDEKTFCNDAMK 62
 
Name Accession Description Interval E-value
DUF4939 pfam16297
Domain of unknown function (DUF4939); This family consists of uncharacterized proteins around ...
 2-64 1.36e-30

Domain of unknown function (DUF4939); This family consists of uncharacterized proteins around 110 residues in length and is mainly found in various mammalia species. LDOC1, a member of this family and a novel MZF-1-interacting protein, inhibits NF-kappaB activation and relates with cancer and some other diseases. But the specific function of this family is still unknown.


Pssm-ID: 465086  Cd Length: 112  Bit Score: 103.84  E-value: 1.36e-30
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 197245393    2 DGRVQLMKALLAGPlRPAARRWRNPIPFPETFDGDTDRLPEFIVQTSSYMFVDENTFSNDALK 64
Cdd:pfam16297   1 DQRKQLRILVMEWP-RLQVRRWSNPIPFPERFSGESGRLPEFIVQTMSYMLVDEKTFCNDAMK 62
 
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