NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|469830376|emb|CCN26472|]
View 

gag polyprotein, p17 region, partial [HIV-1 M:CRF13_MP1034]

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
Gag_p17 super family cl02892
gag gene protein p17 (matrix protein); The matrix protein forms an icosahedral shell ...
 1-98 2.04e-38

gag gene protein p17 (matrix protein); The matrix protein forms an icosahedral shell associated with the inner membrane of the mature immunodeficiency virus.


The actual alignment was detected with superfamily member pfam00540:

Pssm-ID: 249943  Cd Length: 140  Bit Score: 126.59  E-value: 2.04e-38
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 469830376    1 VWASRELERFALNPGLLETAEGCQQIM*QLQPALQTGSEELKSL*NTVATLYCVHQRIEVRDTKEALDEV---------E 71
Cdd:pfam00540  34 VWASRELERFAVNPGLLETSEGCRKILGQLQPSLQTGSEGLRSLYNTVAVLYCVHQRIDVKDTKEALEKIeeeqnkskkK 113

                          90       100
                  ....*....|....*....|....*..
gi 469830376   72 KIQKKSQQKTQQAAKDEGNSKQVSQNY 98
Cdd:pfam00540 114 KTAVPPGAQQAANTGGTGNSSGVSQNY 140
 
Name Accession Description Interval E-value
Gag_p17 pfam00540
gag gene protein p17 (matrix protein); The matrix protein forms an icosahedral shell ...
 1-98 2.04e-38

gag gene protein p17 (matrix protein); The matrix protein forms an icosahedral shell associated with the inner membrane of the mature immunodeficiency virus.


Pssm-ID: 249943  Cd Length: 140  Bit Score: 126.59  E-value: 2.04e-38
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 469830376    1 VWASRELERFALNPGLLETAEGCQQIM*QLQPALQTGSEELKSL*NTVATLYCVHQRIEVRDTKEALDEV---------E 71
Cdd:pfam00540  34 VWASRELERFAVNPGLLETSEGCRKILGQLQPSLQTGSEGLRSLYNTVAVLYCVHQRIDVKDTKEALEKIeeeqnkskkK 113

                          90       100
                  ....*....|....*....|....*..
gi 469830376   72 KIQKKSQQKTQQAAKDEGNSKQVSQNY 98
Cdd:pfam00540 114 KTAVPPGAQQAANTGGTGNSSGVSQNY 140
 
Name Accession Description Interval E-value
Gag_p17 pfam00540
gag gene protein p17 (matrix protein); The matrix protein forms an icosahedral shell ...
 1-98 2.04e-38

gag gene protein p17 (matrix protein); The matrix protein forms an icosahedral shell associated with the inner membrane of the mature immunodeficiency virus.


Pssm-ID: 249943  Cd Length: 140  Bit Score: 126.59  E-value: 2.04e-38
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 469830376    1 VWASRELERFALNPGLLETAEGCQQIM*QLQPALQTGSEELKSL*NTVATLYCVHQRIEVRDTKEALDEV---------E 71
Cdd:pfam00540  34 VWASRELERFAVNPGLLETSEGCRKILGQLQPSLQTGSEGLRSLYNTVAVLYCVHQRIDVKDTKEALEKIeeeqnkskkK 113

                          90       100
                  ....*....|....*....|....*..
gi 469830376   72 KIQKKSQQKTQQAAKDEGNSKQVSQNY 98
Cdd:pfam00540 114 KTAVPPGAQQAANTGGTGNSSGVSQNY 140
 
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