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Conserved domains on  [gi|407227292|emb|CCA62418|]
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polyprotein, partial [HIV-1 M:B/A/CR14_BG_PT107]

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 ...
 87-110 9.21e-13

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: 58.39  E-value: 9.21e-13
                          10        20
                  ....*....|....*....|....
gi 407227292   87 LQNRPEPTAPPAESFGFGEEIAPS 110
Cdd:pfam08705   1 LQSRPEPTAPPAESFGFGEEITPS 24
PTZ00368 super family cl31762
universal minicircle sequence binding protein (UMSBP); Provisional
 22-67 6.45e-09

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: 50.96  E-value: 6.45e-09
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 407227292  22 RNQRKTVKCFNCGKEGHIARNCRAPRKKG-----CWKCGKEGHQMKDCTER 67
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 ...
 87-110 9.21e-13

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: 58.39  E-value: 9.21e-13
                          10        20
                  ....*....|....*....|....
gi 407227292   87 LQNRPEPTAPPAESFGFGEEIAPS 110
Cdd:pfam08705   1 LQSRPEPTAPPAESFGFGEEITPS 24
PTZ00368 PTZ00368
universal minicircle sequence binding protein (UMSBP); Provisional
 22-67 6.45e-09

universal minicircle sequence binding protein (UMSBP); Provisional


Pssm-ID: 173561 [Multi-domain]  Cd Length: 148  Bit Score: 50.96  E-value: 6.45e-09
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 407227292  22 RNQRKTVKCFNCGKEGHIARNCRAPRKKG-----CWKCGKEGHQMKDCTER 67
Cdd:PTZ00368  98 KGGAARRACYNCGGEGHISRDCPNAGKRPggdktCYNCGQTGHLSRDCPDK 148
AIR1 COG5082
Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational ...
 29-67 4.86e-05

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: 40.99  E-value: 4.86e-05
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 407227292  29 KCFNCGKEGHIARNC----------------RAPRKKGCWKCGKEGHQMKDCTER 67
Cdd:COG5082   62 VCFNCGQNGHLRRDCphsicyncswdghrsnHCPKPKKCYNCGETGHLSRDCNPS 116
ZnF_C2HC smart00343
zinc finger;
29-44 4.34e-04

zinc finger;


Pssm-ID: 197667 [Multi-domain]  Cd Length: 17  Bit Score: 35.50  E-value: 4.34e-04
                           10
                   ....*....|....*.
gi 407227292    29 KCFNCGKEGHIARNCR 44
Cdd:smart00343   1 KCYNCGKEGHIARDCP 16
zf-CCHC pfam00098
Zinc knuckle; The zinc knuckle is a zinc binding motif composed of the the following ...
 28-43 1.20e-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: 1.20e-03
                          10
                  ....*....|....*.
gi 407227292   28 VKCFNCGKEGHIARNC 43
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 ...
 87-110 9.21e-13

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: 58.39  E-value: 9.21e-13
                          10        20
                  ....*....|....*....|....
gi 407227292   87 LQNRPEPTAPPAESFGFGEEIAPS 110
Cdd:pfam08705   1 LQSRPEPTAPPAESFGFGEEITPS 24
PTZ00368 PTZ00368
universal minicircle sequence binding protein (UMSBP); Provisional
 22-67 6.45e-09

universal minicircle sequence binding protein (UMSBP); Provisional


Pssm-ID: 173561 [Multi-domain]  Cd Length: 148  Bit Score: 50.96  E-value: 6.45e-09
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 407227292  22 RNQRKTVKCFNCGKEGHIARNCRAPRKKG-----CWKCGKEGHQMKDCTER 67
Cdd:PTZ00368  98 KGGAARRACYNCGGEGHISRDCPNAGKRPggdktCYNCGQTGHLSRDCPDK 148
PTZ00368 PTZ00368
universal minicircle sequence binding protein (UMSBP); Provisional
 30-99 6.28e-08

universal minicircle sequence binding protein (UMSBP); Provisional


Pssm-ID: 173561 [Multi-domain]  Cd Length: 148  Bit Score: 48.26  E-value: 6.28e-08
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 407227292  30 CFNCGKEGHIARNCRAPRKKG----CWKCGKEGHQMKDCTERQANFLGKIWPSNKGRPGNFLQNRPEPTAPPAE 99
Cdd:PTZ00368  55 CYNCGKTGHLSRECPEAPPGSgprsCYNCGQTGHISRECPNRAKGGAARRACYNCGGEGHISRDCPNAGKRPGG 128
PTZ00368 PTZ00368
universal minicircle sequence binding protein (UMSBP); Provisional
 20-64 6.35e-08

universal minicircle sequence binding protein (UMSBP); Provisional


Pssm-ID: 173561 [Multi-domain]  Cd Length: 148  Bit Score: 48.26  E-value: 6.35e-08
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|
gi 407227292  20 NFRNQRKTVKCFNCGKEGHIARNCRAPRKKG-----CWKCGKEGHQMKDC 64
Cdd:PTZ00368  70 EAPPGSGPRSCYNCGQTGHISRECPNRAKGGaarraCYNCGGEGHISRDC 119
PTZ00368 PTZ00368
universal minicircle sequence binding protein (UMSBP); Provisional
 25-68 3.18e-07

universal minicircle sequence binding protein (UMSBP); Provisional


Pssm-ID: 173561 [Multi-domain]  Cd Length: 148  Bit Score: 46.34  E-value: 3.18e-07
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*...
gi 407227292  25 RKTVKCFNCGKEGHIARNCRAPRKKG----CWKCGKEGHQMKDCTERQ 68
Cdd:PTZ00368  25 AKARPCYKCGEPGHLSRECPSAPGGRgersCYNCGKTGHLSRECPEAP 72
AIR1 COG5082
Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational ...
 29-67 4.86e-05

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: 40.99  E-value: 4.86e-05
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 407227292  29 KCFNCGKEGHIARNC----------------RAPRKKGCWKCGKEGHQMKDCTER 67
Cdd:COG5082   62 VCFNCGQNGHLRRDCphsicyncswdghrsnHCPKPKKCYNCGETGHLSRDCNPS 116
PTZ00368 PTZ00368
universal minicircle sequence binding protein (UMSBP); Provisional
 30-68 5.78e-05

universal minicircle sequence binding protein (UMSBP); Provisional


Pssm-ID: 173561 [Multi-domain]  Cd Length: 148  Bit Score: 40.56  E-value: 5.78e-05
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*
gi 407227292  30 CFNCGKEGHIARNCRAPRKKG------CWKCGKEGHQMKDCTERQ 68
Cdd:PTZ00368   3 CYRCGGVGHQSRECPNSAPAGaakarpCYKCGEPGHLSRECPSAP 47
AIR1 COG5082
Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational ...
 26-86 2.30e-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: 39.06  E-value: 2.30e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 407227292  26 KTVKCFNCGKEGHIARNC--RAPRKKGCWKCGKEGHQMKDCTErqanflgkIWPSNKGRPGNF 86
Cdd:COG5082   96 KPKKCYNCGETGHLSRDCnpSKDQQKSCFDCNSTRHSSEDCPS--------IWKHYVLNNGDG 150
ZnF_C2HC smart00343
zinc finger;
29-44 4.34e-04

zinc finger;


Pssm-ID: 197667 [Multi-domain]  Cd Length: 17  Bit Score: 35.50  E-value: 4.34e-04
                           10
                   ....*....|....*.
gi 407227292    29 KCFNCGKEGHIARNCR 44
Cdd:smart00343   1 KCYNCGKEGHIARDCP 16
zf-CCHC pfam00098
Zinc knuckle; The zinc knuckle is a zinc binding motif composed of the the following ...
 28-43 1.20e-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: 1.20e-03
                          10
                  ....*....|....*.
gi 407227292   28 VKCFNCGKEGHIARNC 43
Cdd:pfam00098   1 GKCYNCGEPGHIARDC 16
ZnF_C2HC smart00343
zinc finger;
50-66 1.74e-03

zinc finger;


Pssm-ID: 197667 [Multi-domain]  Cd Length: 17  Bit Score: 33.96  E-value: 1.74e-03
                           10
                   ....*....|....*..
gi 407227292    50 GCWKCGKEGHQMKDCTE 66
Cdd:smart00343   1 KCYNCGKEGHIARDCPS 17
AIR1 COG5082
Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational ...
 23-67 2.78e-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: 35.98  E-value: 2.78e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 407227292  23 NQRKTVKCFNCGKEGHIARNCRA-------------PRKKGCWKCGKEGHQMKDCTER 67
Cdd:COG5082  116 SKDQQKSCFDCNSTRHSSEDCPSiwkhyvlnngdghPIKKFCYSCGSAGHFGDDCKEP 173
zf-CCHC pfam00098
Zinc knuckle; The zinc knuckle is a zinc binding motif composed of the the following ...
 49-66 9.83e-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: 31.73  E-value: 9.83e-03
                          10
                  ....*....|....*...
gi 407227292   49 KGCWKCGKEGHQMKDCTE 66
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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