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Conserved domains on  [gi|3063657|gb|AAC14131|]
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putative retrovirus-related gag protein [Rattus norvegicus]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
Gag_p10 super family cl03546
Retroviral GAG p10 protein; This family consists of various retroviral GAG (core) polyproteins ...
 10-86 7.85e-21

Retroviral GAG p10 protein; This family consists of various retroviral GAG (core) polyproteins and encompasses the p10 region producing the p10 protein upon proteolytic cleavage of GAG by retroviral protease. The p10 or matrix protein (MA) is associated with the virus envelope glycoproteins in most mammalian retroviruses and may be involved in virus particle assembly, transport and budding. Some of the GAG polyproteins have alternate cleavage sites leading to the production of alternative and longer cleavage products (e.g. p19) the alignment of this family only covers the approximately N-terminal (GAG) 100 amino acid region of homology to p10.


The actual alignment was detected with superfamily member pfam02337:

Pssm-ID: 426727  Cd Length: 85  Bit Score: 80.08  E-value: 7.85e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3063657     10 LTALQELLNRRKLKVERKILSSFLDECDRCAPWFIVSGSLTLRAWDKLGRDLDKEATE---GKLRPGSKPLWRIVRACLE 86
Cdd:pfam02337   6 LTALQALLKERGLKVSKSSLIKFLQFVEEVCPWFPEEGTLNLETWKKVGRELKTQATEhgpKNIPVDTWPIWALIRAVLD 85
 
Name Accession Description Interval E-value
Gag_p10 pfam02337
Retroviral GAG p10 protein; This family consists of various retroviral GAG (core) polyproteins ...
 10-86 7.85e-21

Retroviral GAG p10 protein; This family consists of various retroviral GAG (core) polyproteins and encompasses the p10 region producing the p10 protein upon proteolytic cleavage of GAG by retroviral protease. The p10 or matrix protein (MA) is associated with the virus envelope glycoproteins in most mammalian retroviruses and may be involved in virus particle assembly, transport and budding. Some of the GAG polyproteins have alternate cleavage sites leading to the production of alternative and longer cleavage products (e.g. p19) the alignment of this family only covers the approximately N-terminal (GAG) 100 amino acid region of homology to p10.


Pssm-ID: 426727  Cd Length: 85  Bit Score: 80.08  E-value: 7.85e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3063657     10 LTALQELLNRRKLKVERKILSSFLDECDRCAPWFIVSGSLTLRAWDKLGRDLDKEATE---GKLRPGSKPLWRIVRACLE 86
Cdd:pfam02337   6 LTALQALLKERGLKVSKSSLIKFLQFVEEVCPWFPEEGTLNLETWKKVGRELKTQATEhgpKNIPVDTWPIWALIRAVLD 85
 
Name Accession Description Interval E-value
Gag_p10 pfam02337
Retroviral GAG p10 protein; This family consists of various retroviral GAG (core) polyproteins ...
 10-86 7.85e-21

Retroviral GAG p10 protein; This family consists of various retroviral GAG (core) polyproteins and encompasses the p10 region producing the p10 protein upon proteolytic cleavage of GAG by retroviral protease. The p10 or matrix protein (MA) is associated with the virus envelope glycoproteins in most mammalian retroviruses and may be involved in virus particle assembly, transport and budding. Some of the GAG polyproteins have alternate cleavage sites leading to the production of alternative and longer cleavage products (e.g. p19) the alignment of this family only covers the approximately N-terminal (GAG) 100 amino acid region of homology to p10.


Pssm-ID: 426727  Cd Length: 85  Bit Score: 80.08  E-value: 7.85e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3063657     10 LTALQELLNRRKLKVERKILSSFLDECDRCAPWFIVSGSLTLRAWDKLGRDLDKEATE---GKLRPGSKPLWRIVRACLE 86
Cdd:pfam02337   6 LTALQALLKERGLKVSKSSLIKFLQFVEEVCPWFPEEGTLNLETWKKVGRELKTQATEhgpKNIPVDTWPIWALIRAVLD 85
 
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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