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Conserved domains on  [gi|210071|gb|AAA42547|]
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gag polyprotein, partial [Rous-associated virus type 2]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
Retro_M super family cl03726
Retroviral M domain; Retroviruses contain a small protein, MA (matrix), which forms a protein ...
 1-47 2.74e-15

Retroviral M domain; Retroviruses contain a small protein, MA (matrix), which forms a protein lining immediately beneath the phospholipid membrane of the mature virus particle. MA is located in the N-terminal region of the Gag precursor polyprotein. The N-terminal segment of MA proteins directs the Gag protein to the plasma membrane where budding takes place, and has been called the M domain. This domain forms an alpha helical bundle structure.


The actual alignment was detected with superfamily member pfam02813:

Pssm-ID: 460707  Cd Length: 86  Bit Score: 62.48  E-value: 2.74e-15
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 210071      1 MEAVIKVISSACKTYCGKTSPSKKEIGAMLSLLQKEGLLTSPSDLYS 47
Cdd:pfam02813  1 EAAIIKIISAACKTCCGKSPPKKEEGAALLLLLKEEGLLMPPDDLSP 47
 
Name Accession Description Interval E-value
Retro_M pfam02813
Retroviral M domain; Retroviruses contain a small protein, MA (matrix), which forms a protein ...
 1-47 2.74e-15

Retroviral M domain; Retroviruses contain a small protein, MA (matrix), which forms a protein lining immediately beneath the phospholipid membrane of the mature virus particle. MA is located in the N-terminal region of the Gag precursor polyprotein. The N-terminal segment of MA proteins directs the Gag protein to the plasma membrane where budding takes place, and has been called the M domain. This domain forms an alpha helical bundle structure.


Pssm-ID: 460707  Cd Length: 86  Bit Score: 62.48  E-value: 2.74e-15
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 210071      1 MEAVIKVISSACKTYCGKTSPSKKEIGAMLSLLQKEGLLTSPSDLYS 47
Cdd:pfam02813  1 EAAIIKIISAACKTCCGKSPPKKEEGAALLLLLKEEGLLMPPDDLSP 47
 
Name Accession Description Interval E-value
Retro_M pfam02813
Retroviral M domain; Retroviruses contain a small protein, MA (matrix), which forms a protein ...
 1-47 2.74e-15

Retroviral M domain; Retroviruses contain a small protein, MA (matrix), which forms a protein lining immediately beneath the phospholipid membrane of the mature virus particle. MA is located in the N-terminal region of the Gag precursor polyprotein. The N-terminal segment of MA proteins directs the Gag protein to the plasma membrane where budding takes place, and has been called the M domain. This domain forms an alpha helical bundle structure.


Pssm-ID: 460707  Cd Length: 86  Bit Score: 62.48  E-value: 2.74e-15
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 210071      1 MEAVIKVISSACKTYCGKTSPSKKEIGAMLSLLQKEGLLTSPSDLYS 47
Cdd:pfam02813  1 EAAIIKIISAACKTCCGKSPPKKEEGAALLLLLKEEGLLMPPDDLSP 47
 
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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