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Conserved domains on  [gi|14530239|gb|AAK65972|]
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vif protein [Human immunodeficiency virus 1]

Protein Classification

virion infectivity factor( domain architecture ID 138)

virion infectivity factor forms a complex with host APOBEC3F and APOBEC3G thus preventing the entry of these lethally hypermutating enzymes into progeny virions

Gene Ontology:  GO:0019058|GO:0003723

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
Vif super family cl02899
Retroviral Vif (Viral infectivity) protein; Human immunodeficiency virus type 1 (HIV-1) Vif is ...
 1-191 6.33e-99

Retroviral Vif (Viral infectivity) protein; Human immunodeficiency virus type 1 (HIV-1) Vif is required for productive infection of T lymphocytes and macrophages. Virions produced in the absence of Vif have abnormal core morphology and those produced in primary T cells carry immature core proteins and low levels of mature capsid.


The actual alignment was detected with superfamily member pfam00559:

Pssm-ID: 278957  Cd Length: 200  Bit Score: 284.70  E-value: 6.33e-99
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 14530239     1 MENRWQVMIVWQVDRMRIRTWNSLVKHHMYISRKAKGWVYKHHYESRNPRIS------SEVHIPL-GEARIIVRTYWGLH 73
Cdd:pfam00559   1 DENRWIVMITWQVDGMRIEKWHALVKHHKYRSGDAEEVFYRHHYESPHHKIGwawwtcSEVHFPLqGDAHLEIQAYWGLH 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 14530239    74 IGEKDWHLGHGVSIEWRQNRYHTQIDPDLADHLIHLYYFDCFSESAIRKAIIGEIVSPRCEY-QAGHNKVGSLQYLALKA 152
Cdd:pfam00559  81 TGEKDWHLGHAVRIEWRKEKFSTDVDPDCADILIHLTYFDCFSAGAIRKAILGEILLPCCEYpQAGHAKVGSLQYLALAA 160

                         170       180       190
                  ....*....|....*....|....*....|....*....
gi 14530239   153 VVASTRTKPPLPSVRKLVEDRWNKPQKTKGHRGSHTMNG 191
Cdd:pfam00559 161 LIQNDKIKPKGPARKKLREDHWNGLQKAKEDHGSHKMGG 199
 
Name Accession Description Interval E-value
Vif pfam00559
Retroviral Vif (Viral infectivity) protein; Human immunodeficiency virus type 1 (HIV-1) Vif is ...
 1-191 6.33e-99

Retroviral Vif (Viral infectivity) protein; Human immunodeficiency virus type 1 (HIV-1) Vif is required for productive infection of T lymphocytes and macrophages. Virions produced in the absence of Vif have abnormal core morphology and those produced in primary T cells carry immature core proteins and low levels of mature capsid.


Pssm-ID: 278957  Cd Length: 200  Bit Score: 284.70  E-value: 6.33e-99
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 14530239     1 MENRWQVMIVWQVDRMRIRTWNSLVKHHMYISRKAKGWVYKHHYESRNPRIS------SEVHIPL-GEARIIVRTYWGLH 73
Cdd:pfam00559   1 DENRWIVMITWQVDGMRIEKWHALVKHHKYRSGDAEEVFYRHHYESPHHKIGwawwtcSEVHFPLqGDAHLEIQAYWGLH 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 14530239    74 IGEKDWHLGHGVSIEWRQNRYHTQIDPDLADHLIHLYYFDCFSESAIRKAIIGEIVSPRCEY-QAGHNKVGSLQYLALKA 152
Cdd:pfam00559  81 TGEKDWHLGHAVRIEWRKEKFSTDVDPDCADILIHLTYFDCFSAGAIRKAILGEILLPCCEYpQAGHAKVGSLQYLALAA 160

                         170       180       190
                  ....*....|....*....|....*....|....*....
gi 14530239   153 VVASTRTKPPLPSVRKLVEDRWNKPQKTKGHRGSHTMNG 191
Cdd:pfam00559 161 LIQNDKIKPKGPARKKLREDHWNGLQKAKEDHGSHKMGG 199
 
Name Accession Description Interval E-value
Vif pfam00559
Retroviral Vif (Viral infectivity) protein; Human immunodeficiency virus type 1 (HIV-1) Vif is ...
 1-191 6.33e-99

Retroviral Vif (Viral infectivity) protein; Human immunodeficiency virus type 1 (HIV-1) Vif is required for productive infection of T lymphocytes and macrophages. Virions produced in the absence of Vif have abnormal core morphology and those produced in primary T cells carry immature core proteins and low levels of mature capsid.


Pssm-ID: 278957  Cd Length: 200  Bit Score: 284.70  E-value: 6.33e-99
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 14530239     1 MENRWQVMIVWQVDRMRIRTWNSLVKHHMYISRKAKGWVYKHHYESRNPRIS------SEVHIPL-GEARIIVRTYWGLH 73
Cdd:pfam00559   1 DENRWIVMITWQVDGMRIEKWHALVKHHKYRSGDAEEVFYRHHYESPHHKIGwawwtcSEVHFPLqGDAHLEIQAYWGLH 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 14530239    74 IGEKDWHLGHGVSIEWRQNRYHTQIDPDLADHLIHLYYFDCFSESAIRKAIIGEIVSPRCEY-QAGHNKVGSLQYLALKA 152
Cdd:pfam00559  81 TGEKDWHLGHAVRIEWRKEKFSTDVDPDCADILIHLTYFDCFSAGAIRKAILGEILLPCCEYpQAGHAKVGSLQYLALAA 160

                         170       180       190
                  ....*....|....*....|....*....|....*....
gi 14530239   153 VVASTRTKPPLPSVRKLVEDRWNKPQKTKGHRGSHTMNG 191
Cdd:pfam00559 161 LIQNDKIKPKGPARKKLREDHWNGLQKAKEDHGSHKMGG 199
DNA_pol3_delta2 pfam13177
DNA polymerase III, delta subunit; DNA polymerase III, delta subunit (EC 2.7.7.7) is required ...
 1-26 8.90e-03

DNA polymerase III, delta subunit; DNA polymerase III, delta subunit (EC 2.7.7.7) is required for, along with delta' subunit, the assembly of the processivity factor beta(2) onto primed DNA in the DNA polymerase III holoenzyme-catalyzed reaction. The delta subunit is also known as HolA.


Pssm-ID: 433013 [Multi-domain]  Cd Length: 161  Bit Score: 35.26  E-value: 8.90e-03
                          10        20
                  ....*....|....*....|....*.
gi 14530239     1 MENRWQVMIVWQVDRMRIRTWNSLVK 26
Cdd:pfam13177  98 YEGKKKVYIIEDAEKMTASAANSLLK 123
 
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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