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Conserved domains on  [gi|158536663|gb|ABW72881|]
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vpu protein [Human immunodeficiency virus 1]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
Vpu super family cl02898
Vpu protein; The Vpu protein contains an N-terminal transmembrane spanning region and a ...
 23-78 3.95e-21

Vpu protein; The Vpu protein contains an N-terminal transmembrane spanning region and a C-terminal cytoplasmic region. The HIV-1 Vpu protein stimulates virus production by enhancing the release of viral particles from infected cells. The VPU protein binds specifically to CD4.


The actual alignment was detected with superfamily member pfam00558:

Pssm-ID: 109608  Cd Length: 81  Bit Score: 78.54  E-value: 3.95e-21
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 158536663  23 WSIVLIEYRKILKQRKIDRLIARISERAEDSGNESDGDHEE-LSALVE-MGHHAPWDI 78
Cdd:pfam00558 23 WTIVYREYRKIKKQREILRLIKRIRERAEDSGNESNGDEEEeLADLVHsHGFDNPMFE 80
 
Name Accession Description Interval E-value
Vpu pfam00558
Vpu protein; The Vpu protein contains an N-terminal transmembrane spanning region and a ...
 23-78 3.95e-21

Vpu protein; The Vpu protein contains an N-terminal transmembrane spanning region and a C-terminal cytoplasmic region. The HIV-1 Vpu protein stimulates virus production by enhancing the release of viral particles from infected cells. The VPU protein binds specifically to CD4.


Pssm-ID: 109608  Cd Length: 81  Bit Score: 78.54  E-value: 3.95e-21
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 158536663  23 WSIVLIEYRKILKQRKIDRLIARISERAEDSGNESDGDHEE-LSALVE-MGHHAPWDI 78
Cdd:pfam00558 23 WTIVYREYRKIKKQREILRLIKRIRERAEDSGNESNGDEEEeLADLVHsHGFDNPMFE 80
 
Name Accession Description Interval E-value
Vpu pfam00558
Vpu protein; The Vpu protein contains an N-terminal transmembrane spanning region and a ...
 23-78 3.95e-21

Vpu protein; The Vpu protein contains an N-terminal transmembrane spanning region and a C-terminal cytoplasmic region. The HIV-1 Vpu protein stimulates virus production by enhancing the release of viral particles from infected cells. The VPU protein binds specifically to CD4.


Pssm-ID: 109608  Cd Length: 81  Bit Score: 78.54  E-value: 3.95e-21
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 158536663  23 WSIVLIEYRKILKQRKIDRLIARISERAEDSGNESDGDHEE-LSALVE-MGHHAPWDI 78
Cdd:pfam00558 23 WTIVYREYRKIKKQREILRLIKRIRERAEDSGNESNGDEEEeLADLVHsHGFDNPMFE 80
 
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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