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Conserved domains on  [gi|407227254|emb|CCA62399|]
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polyprotein, partial [HIV-1 M:G_PT919]

Protein Classification

gag protein( domain architecture ID 13284203)

gag polyprotein is processed during maturation to matrix protein (MA), capsid protein (CA), spacer peptides (SP1, SP2), nucleocapsid protein (NC) and p6

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
Gag_p6 pfam08705
Gag protein p6; HIV protein p6 contains two late-budding domains (L domains) which are short ...
 102-138 1.82e-19

Gag protein p6; HIV protein p6 contains two late-budding domains (L domains) which are short sequence motifs essential for viral particle release. p6 interacts with the endosomal sorting complex and represents a docking site for several cellular and binding factors. The PTAP motif interacts with the cellular budding factor TSG101. This domain is also found in some chimpanzee immunodeficiency virus (SIV-cpz) proteins.


:

Pssm-ID: 312289  Cd Length: 37  Bit Score: 75.72  E-value: 1.82e-19
                          10        20        30
                  ....*....|....*....|....*....|....*..
gi 407227254  102 LQNRPEPTAPPAESFGFGEEIAPSPKLEPKEKELYPL 138
Cdd:pfam08705   1 LQSRPEPTAPPAESFGFGEEITPSPKQEQKDKELYPL 37
PTZ00368 super family cl31762
universal minicircle sequence binding protein (UMSBP); Provisional
 37-82 1.73e-08

universal minicircle sequence binding protein (UMSBP); Provisional


The actual alignment was detected with superfamily member PTZ00368:

Pssm-ID: 173561 [Multi-domain]  Cd Length: 148  Bit Score: 50.19  E-value: 1.73e-08
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 407227254  37 KGPRRQIKCFNCGKEGHLARNCRAPRKKG-----CWKCGKEGHQMKDCTER 82
Cdd:PTZ00368  98 KGGAARRACYNCGGEGHISRDCPNAGKRPggdktCYNCGQTGHLSRDCPDK 148
 
Name Accession Description Interval E-value
Gag_p6 pfam08705
Gag protein p6; HIV protein p6 contains two late-budding domains (L domains) which are short ...
 102-138 1.82e-19

Gag protein p6; HIV protein p6 contains two late-budding domains (L domains) which are short sequence motifs essential for viral particle release. p6 interacts with the endosomal sorting complex and represents a docking site for several cellular and binding factors. The PTAP motif interacts with the cellular budding factor TSG101. This domain is also found in some chimpanzee immunodeficiency virus (SIV-cpz) proteins.


Pssm-ID: 312289  Cd Length: 37  Bit Score: 75.72  E-value: 1.82e-19
                          10        20        30
                  ....*....|....*....|....*....|....*..
gi 407227254  102 LQNRPEPTAPPAESFGFGEEIAPSPKLEPKEKELYPL 138
Cdd:pfam08705   1 LQSRPEPTAPPAESFGFGEEITPSPKQEQKDKELYPL 37
PTZ00368 PTZ00368
universal minicircle sequence binding protein (UMSBP); Provisional
 37-82 1.73e-08

universal minicircle sequence binding protein (UMSBP); Provisional


Pssm-ID: 173561 [Multi-domain]  Cd Length: 148  Bit Score: 50.19  E-value: 1.73e-08
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 407227254  37 KGPRRQIKCFNCGKEGHLARNCRAPRKKG-----CWKCGKEGHQMKDCTER 82
Cdd:PTZ00368  98 KGGAARRACYNCGGEGHISRDCPNAGKRPggdktCYNCGQTGHLSRDCPDK 148
AIR1 COG5082
Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational ...
 39-82 1.62e-06

Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion];


Pssm-ID: 227414 [Multi-domain]  Cd Length: 190  Bit Score: 45.61  E-value: 1.62e-06
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 407227254  39 PRRQIKCFNCGKEGHLARNC----------------RAPRKKGCWKCGKEGHQMKDCTER 82
Cdd:COG5082   57 REENPVCFNCGQNGHLRRDCphsicyncswdghrsnHCPKPKKCYNCGETGHLSRDCNPS 116
ZnF_C2HC smart00343
zinc finger;
44-59 6.97e-04

zinc finger;


Pssm-ID: 197667 [Multi-domain]  Cd Length: 17  Bit Score: 35.11  E-value: 6.97e-04
                           10
                   ....*....|....*.
gi 407227254    44 KCFNCGKEGHLARNCR 59
Cdd:smart00343   1 KCYNCGKEGHIARDCP 16
zf-CCHC pfam00098
Zinc knuckle; The zinc knuckle is a zinc binding motif composed of the the following ...
 43-58 1.33e-03

Zinc knuckle; The zinc knuckle is a zinc binding motif composed of the the following CX2CX4HX4C where X can be any amino acid. The motifs are mostly from retroviral gag proteins (nucleocapsid). Prototype structure is from HIV. Also contains members involved in eukaryotic gene regulation, such as C. elegans GLH-1. Structure is an 18-residue zinc finger.


Pssm-ID: 395050 [Multi-domain]  Cd Length: 18  Bit Score: 34.43  E-value: 1.33e-03
                          10
                  ....*....|....*.
gi 407227254   43 IKCFNCGKEGHLARNC 58
Cdd:pfam00098   1 GKCYNCGEPGHIARDC 16
 
Name Accession Description Interval E-value
Gag_p6 pfam08705
Gag protein p6; HIV protein p6 contains two late-budding domains (L domains) which are short ...
 102-138 1.82e-19

Gag protein p6; HIV protein p6 contains two late-budding domains (L domains) which are short sequence motifs essential for viral particle release. p6 interacts with the endosomal sorting complex and represents a docking site for several cellular and binding factors. The PTAP motif interacts with the cellular budding factor TSG101. This domain is also found in some chimpanzee immunodeficiency virus (SIV-cpz) proteins.


Pssm-ID: 312289  Cd Length: 37  Bit Score: 75.72  E-value: 1.82e-19
                          10        20        30
                  ....*....|....*....|....*....|....*..
gi 407227254  102 LQNRPEPTAPPAESFGFGEEIAPSPKLEPKEKELYPL 138
Cdd:pfam08705   1 LQSRPEPTAPPAESFGFGEEITPSPKQEQKDKELYPL 37
PTZ00368 PTZ00368
universal minicircle sequence binding protein (UMSBP); Provisional
 37-82 1.73e-08

universal minicircle sequence binding protein (UMSBP); Provisional


Pssm-ID: 173561 [Multi-domain]  Cd Length: 148  Bit Score: 50.19  E-value: 1.73e-08
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 407227254  37 KGPRRQIKCFNCGKEGHLARNCRAPRKKG-----CWKCGKEGHQMKDCTER 82
Cdd:PTZ00368  98 KGGAARRACYNCGGEGHISRDCPNAGKRPggdktCYNCGQTGHLSRDCPDK 148
PTZ00368 PTZ00368
universal minicircle sequence binding protein (UMSBP); Provisional
 45-114 9.29e-08

universal minicircle sequence binding protein (UMSBP); Provisional


Pssm-ID: 173561 [Multi-domain]  Cd Length: 148  Bit Score: 48.26  E-value: 9.29e-08
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 407227254  45 CFNCGKEGHLARNCRAPRKKG----CWKCGKEGHQMKDCTERQANFLGKIWPSNKGRPGNFLQNRPEPTAPPAE 114
Cdd:PTZ00368  55 CYNCGKTGHLSRECPEAPPGSgprsCYNCGQTGHISRECPNRAKGGAARRACYNCGGEGHISRDCPNAGKRPGG 128
PTZ00368 PTZ00368
universal minicircle sequence binding protein (UMSBP); Provisional
 43-79 5.66e-07

universal minicircle sequence binding protein (UMSBP); Provisional


Pssm-ID: 173561 [Multi-domain]  Cd Length: 148  Bit Score: 46.34  E-value: 5.66e-07
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|..
gi 407227254  43 IKCFNCGKEGHLARNCRAPRKKG-----CWKCGKEGHQMKDC 79
Cdd:PTZ00368  78 RSCYNCGQTGHISRECPNRAKGGaarraCYNCGGEGHISRDC 119
AIR1 COG5082
Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational ...
 39-82 1.62e-06

Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion];


Pssm-ID: 227414 [Multi-domain]  Cd Length: 190  Bit Score: 45.61  E-value: 1.62e-06
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 407227254  39 PRRQIKCFNCGKEGHLARNC----------------RAPRKKGCWKCGKEGHQMKDCTER 82
Cdd:COG5082   57 REENPVCFNCGQNGHLRRDCphsicyncswdghrsnHCPKPKKCYNCGETGHLSRDCNPS 116
AIR1 COG5082
Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational ...
 43-101 1.89e-04

Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion];


Pssm-ID: 227414 [Multi-domain]  Cd Length: 190  Bit Score: 39.83  E-value: 1.89e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 407227254  43 IKCFNCGKEGHLARNC--RAPRKKGCWKCGKEGHQMKDCTErqanflgkIWPSNKGRPGNF 101
Cdd:COG5082   98 KKCYNCGETGHLSRDCnpSKDQQKSCFDCNSTRHSSEDCPS--------IWKHYVLNNGDG 150
ZnF_C2HC smart00343
zinc finger;
44-59 6.97e-04

zinc finger;


Pssm-ID: 197667 [Multi-domain]  Cd Length: 17  Bit Score: 35.11  E-value: 6.97e-04
                           10
                   ....*....|....*.
gi 407227254    44 KCFNCGKEGHLARNCR 59
Cdd:smart00343   1 KCYNCGKEGHIARDCP 16
AIR1 COG5082
Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational ...
 39-82 1.16e-03

Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion];


Pssm-ID: 227414 [Multi-domain]  Cd Length: 190  Bit Score: 37.52  E-value: 1.16e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 407227254  39 PRRQIKCFNCGKEGHLARNCRA-------------PRKKGCWKCGKEGHQMKDCTER 82
Cdd:COG5082  117 KDQQKSCFDCNSTRHSSEDCPSiwkhyvlnngdghPIKKFCYSCGSAGHFGDDCKEP 173
zf-CCHC pfam00098
Zinc knuckle; The zinc knuckle is a zinc binding motif composed of the the following ...
 43-58 1.33e-03

Zinc knuckle; The zinc knuckle is a zinc binding motif composed of the the following CX2CX4HX4C where X can be any amino acid. The motifs are mostly from retroviral gag proteins (nucleocapsid). Prototype structure is from HIV. Also contains members involved in eukaryotic gene regulation, such as C. elegans GLH-1. Structure is an 18-residue zinc finger.


Pssm-ID: 395050 [Multi-domain]  Cd Length: 18  Bit Score: 34.43  E-value: 1.33e-03
                          10
                  ....*....|....*.
gi 407227254   43 IKCFNCGKEGHLARNC 58
Cdd:pfam00098   1 GKCYNCGEPGHIARDC 16
ZnF_C2HC smart00343
zinc finger;
65-81 1.58e-03

zinc finger;


Pssm-ID: 197667 [Multi-domain]  Cd Length: 17  Bit Score: 34.34  E-value: 1.58e-03
                           10
                   ....*....|....*..
gi 407227254    65 GCWKCGKEGHQMKDCTE 81
Cdd:smart00343   1 KCYNCGKEGHIARDCPS 17
zf-CCHC pfam00098
Zinc knuckle; The zinc knuckle is a zinc binding motif composed of the the following ...
 64-81 8.50e-03

Zinc knuckle; The zinc knuckle is a zinc binding motif composed of the the following CX2CX4HX4C where X can be any amino acid. The motifs are mostly from retroviral gag proteins (nucleocapsid). Prototype structure is from HIV. Also contains members involved in eukaryotic gene regulation, such as C. elegans GLH-1. Structure is an 18-residue zinc finger.


Pssm-ID: 395050 [Multi-domain]  Cd Length: 18  Bit Score: 32.11  E-value: 8.50e-03
                          10
                  ....*....|....*...
gi 407227254   64 KGCWKCGKEGHQMKDCTE 81
Cdd:pfam00098   1 GKCYNCGEPGHIARDCPK 18
 
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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