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Conserved domains on  [gi|19172948|ref|NP_579880|]
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capsid [Human immunodeficiency virus 1]

Protein Classification

gag protein( domain architecture ID 18158590)

HIV-1 gag protein functions in assembly of virus-like particles, virion maturation after particle release, and early post-entry steps in virus replication; gag protein (p24), or CA (capsid) forms the HIV nucleocapsid

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
Gag_p24_C pfam19317
Gag protein p24 C-terminal domain; p24 forms inner protein layer of the nucleocapsid. ELISA ...
 144-217 2.83e-42

Gag protein p24 C-terminal domain; p24 forms inner protein layer of the nucleocapsid. ELISA tests for p24 is the most commonly used method to demonstrate virus replication both in vivo and in vitro.


:

Pssm-ID: 466038  Cd Length: 74  Bit Score: 138.00  E-value: 2.83e-42
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 19172948   144 MYSPTSILDIRQGPKEPFRDYVDRFYKTLRAEQASQEVKNWMTETLLVQNANPDCKTILKALGPAATLEEMMTA 217
Cdd:pfam19317   1 GYKPTSLADIRQGPKEPYQDFVARLYDALRKEMPDGKAKDVITKQLAYENANPECQDLLKPLGKTGTLSDMIRA 74
Gag_p24 pfam00607
gag protein p24 N-terminal domain; p24 forms inner protein layer of the nucleocapsid. ELISA ...
 11-118 1.57e-13

gag protein p24 N-terminal domain; p24 forms inner protein layer of the nucleocapsid. ELISA tests for p24 is the most commonly used method to demonstrate virus replication both in vivo and in vitro.


:

Pssm-ID: 459864  Cd Length: 128  Bit Score: 64.99  E-value: 1.57e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19172948    11 VHQAISPRTLNAWVKVVEEKAF-SPEVIPMFSALSEG--ATPQDLNTMLNTVGGHqAAMQMLKETINEEAAEWDRvHPVH 87
Cdd:pfam00607   1 VWEPLDFKLLKELKKAVKQYGPnSPYTMQLLEALASSnaLTPYDWRTLAKAVLSP-GQYLLWKAEWQELAQEQAR-RNQR 78

                          90       100       110
                  ....*....|....*....|....*....|....
gi 19172948    88 AGPIapgqmrEPRGSD-IAGTT--STLQEQIGWM 118
Cdd:pfam00607  79 AGPD------RGITLDmLTGTGqyATPQAQAQLP 106
 
Name Accession Description Interval E-value
Gag_p24_C pfam19317
Gag protein p24 C-terminal domain; p24 forms inner protein layer of the nucleocapsid. ELISA ...
 144-217 2.83e-42

Gag protein p24 C-terminal domain; p24 forms inner protein layer of the nucleocapsid. ELISA tests for p24 is the most commonly used method to demonstrate virus replication both in vivo and in vitro.


Pssm-ID: 466038  Cd Length: 74  Bit Score: 138.00  E-value: 2.83e-42
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 19172948   144 MYSPTSILDIRQGPKEPFRDYVDRFYKTLRAEQASQEVKNWMTETLLVQNANPDCKTILKALGPAATLEEMMTA 217
Cdd:pfam19317   1 GYKPTSLADIRQGPKEPYQDFVARLYDALRKEMPDGKAKDVITKQLAYENANPECQDLLKPLGKTGTLSDMIRA 74
Gag_p24 pfam00607
gag protein p24 N-terminal domain; p24 forms inner protein layer of the nucleocapsid. ELISA ...
 11-118 1.57e-13

gag protein p24 N-terminal domain; p24 forms inner protein layer of the nucleocapsid. ELISA tests for p24 is the most commonly used method to demonstrate virus replication both in vivo and in vitro.


Pssm-ID: 459864  Cd Length: 128  Bit Score: 64.99  E-value: 1.57e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19172948    11 VHQAISPRTLNAWVKVVEEKAF-SPEVIPMFSALSEG--ATPQDLNTMLNTVGGHqAAMQMLKETINEEAAEWDRvHPVH 87
Cdd:pfam00607   1 VWEPLDFKLLKELKKAVKQYGPnSPYTMQLLEALASSnaLTPYDWRTLAKAVLSP-GQYLLWKAEWQELAQEQAR-RNQR 78

                          90       100       110
                  ....*....|....*....|....*....|....
gi 19172948    88 AGPIapgqmrEPRGSD-IAGTT--STLQEQIGWM 118
Cdd:pfam00607  79 AGPD------RGITLDmLTGTGqyATPQAQAQLP 106
 
Name Accession Description Interval E-value
Gag_p24_C pfam19317
Gag protein p24 C-terminal domain; p24 forms inner protein layer of the nucleocapsid. ELISA ...
 144-217 2.83e-42

Gag protein p24 C-terminal domain; p24 forms inner protein layer of the nucleocapsid. ELISA tests for p24 is the most commonly used method to demonstrate virus replication both in vivo and in vitro.


Pssm-ID: 466038  Cd Length: 74  Bit Score: 138.00  E-value: 2.83e-42
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 19172948   144 MYSPTSILDIRQGPKEPFRDYVDRFYKTLRAEQASQEVKNWMTETLLVQNANPDCKTILKALGPAATLEEMMTA 217
Cdd:pfam19317   1 GYKPTSLADIRQGPKEPYQDFVARLYDALRKEMPDGKAKDVITKQLAYENANPECQDLLKPLGKTGTLSDMIRA 74
Gag_p24 pfam00607
gag protein p24 N-terminal domain; p24 forms inner protein layer of the nucleocapsid. ELISA ...
 11-118 1.57e-13

gag protein p24 N-terminal domain; p24 forms inner protein layer of the nucleocapsid. ELISA tests for p24 is the most commonly used method to demonstrate virus replication both in vivo and in vitro.


Pssm-ID: 459864  Cd Length: 128  Bit Score: 64.99  E-value: 1.57e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19172948    11 VHQAISPRTLNAWVKVVEEKAF-SPEVIPMFSALSEG--ATPQDLNTMLNTVGGHqAAMQMLKETINEEAAEWDRvHPVH 87
Cdd:pfam00607   1 VWEPLDFKLLKELKKAVKQYGPnSPYTMQLLEALASSnaLTPYDWRTLAKAVLSP-GQYLLWKAEWQELAQEQAR-RNQR 78

                          90       100       110
                  ....*....|....*....|....*....|....
gi 19172948    88 AGPIapgqmrEPRGSD-IAGTT--STLQEQIGWM 118
Cdd:pfam00607  79 AGPD------RGITLDmLTGTGqyATPQAQAQLP 106
 
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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