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Conserved domains on  [gi|407227256|emb|CCA62400|]
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polyprotein, partial [HIV-1 M:G_PT13]

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 ...
 106-141 1.36e-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: 1.36e-19
                          10        20        30
                  ....*....|....*....|....*....|....*.
gi 407227256  106 LQNRPEPTAPPAESFGFGEEIAPSQKQEPKQEELYP 141
Cdd:pfam08705   1 LQSRPEPTAPPAESFGFGEEITPSPKQEQKDKELYP 36
PTZ00368 super family cl31762
universal minicircle sequence binding protein (UMSBP); Provisional
 41-83 2.90e-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: 49.42  E-value: 2.90e-08
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*...
gi 407227256  41 KGPRRTIKCFKCGKEGHLARNCRAPRKKG-----CWKCGKEGHQMKDC 83
Cdd:PTZ00368  98 KGGAARRACYNCGGEGHISRDCPNAGKRPggdktCYNCGQTGHLSRDC 145
 
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 ...
 106-141 1.36e-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: 1.36e-19
                          10        20        30
                  ....*....|....*....|....*....|....*.
gi 407227256  106 LQNRPEPTAPPAESFGFGEEIAPSQKQEPKQEELYP 141
Cdd:pfam08705   1 LQSRPEPTAPPAESFGFGEEITPSPKQEQKDKELYP 36
PTZ00368 PTZ00368
universal minicircle sequence binding protein (UMSBP); Provisional
 41-83 2.90e-08

universal minicircle sequence binding protein (UMSBP); Provisional


Pssm-ID: 173561 [Multi-domain]  Cd Length: 148  Bit Score: 49.42  E-value: 2.90e-08
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*...
gi 407227256  41 KGPRRTIKCFKCGKEGHLARNCRAPRKKG-----CWKCGKEGHQMKDC 83
Cdd:PTZ00368  98 KGGAARRACYNCGGEGHISRDCPNAGKRPggdktCYNCGQTGHLSRDC 145
AIR1 COG5082
Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational ...
 43-86 3.67e-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: 41.37  E-value: 3.67e-05
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....
gi 407227256  43 PRRTIKCFKCGKEGHLARNCRAprkKGCWKCGKEGHQMKDCTQG 86
Cdd:COG5082   57 REENPVCFNCGQNGHLRRDCPH---SICYNCSWDGHRSNHCPKP 97
ZnF_C2HC smart00343
zinc finger;
48-63 1.59e-03

zinc finger;


Pssm-ID: 197667 [Multi-domain]  Cd Length: 17  Bit Score: 33.96  E-value: 1.59e-03
                           10
                   ....*....|....*.
gi 407227256    48 KCFKCGKEGHLARNCR 63
Cdd:smart00343   1 KCYNCGKEGHIARDCP 16
zf-CCHC pfam00098
Zinc knuckle; The zinc knuckle is a zinc binding motif composed of the the following ...
 47-62 4.53e-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: 32.88  E-value: 4.53e-03
                          10
                  ....*....|....*.
gi 407227256   47 IKCFKCGKEGHLARNC 62
Cdd:pfam00098   1 GKCYNCGEPGHIARDC 16
COG5222 COG5222
Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only];
70-137 8.01e-03

Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only];


Pssm-ID: 227547 [Multi-domain]  Cd Length: 427  Bit Score: 35.11  E-value: 8.01e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 407227256  70 CWKCGKEGHQMKDC-TQGQANFLGKIWLSNKGRPGNFLQNRPEPTAPPAESFGFGEEIAPSQKQEPKQE 137
Cdd:COG5222  179 CYRCGQKGHWIQNCpTNQDPNFDGKRIRRTTGIPKDFLKPVEGPNEPSNAAIMITPEGGYVVAQPDVQS 247
 
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 ...
 106-141 1.36e-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: 1.36e-19
                          10        20        30
                  ....*....|....*....|....*....|....*.
gi 407227256  106 LQNRPEPTAPPAESFGFGEEIAPSQKQEPKQEELYP 141
Cdd:pfam08705   1 LQSRPEPTAPPAESFGFGEEITPSPKQEQKDKELYP 36
PTZ00368 PTZ00368
universal minicircle sequence binding protein (UMSBP); Provisional
 41-83 2.90e-08

universal minicircle sequence binding protein (UMSBP); Provisional


Pssm-ID: 173561 [Multi-domain]  Cd Length: 148  Bit Score: 49.42  E-value: 2.90e-08
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*...
gi 407227256  41 KGPRRTIKCFKCGKEGHLARNCRAPRKKG-----CWKCGKEGHQMKDC 83
Cdd:PTZ00368  98 KGGAARRACYNCGGEGHISRDCPNAGKRPggdktCYNCGQTGHLSRDC 145
PTZ00368 PTZ00368
universal minicircle sequence binding protein (UMSBP); Provisional
 42-118 3.00e-07

universal minicircle sequence binding protein (UMSBP); Provisional


Pssm-ID: 173561 [Multi-domain]  Cd Length: 148  Bit Score: 46.72  E-value: 3.00e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 407227256  42 GPRRTIKCFKCGKEGHLARNCRAPRKKG----CWKCGKEGHQMKDCTQGQANFLGKIWLSNKGRPGNFLQNRPEPTAPPA 117
Cdd:PTZ00368  48 GGRGERSCYNCGKTGHLSRECPEAPPGSgprsCYNCGQTGHISRECPNRAKGGAARRACYNCGGEGHISRDCPNAGKRPG 127


                 .
gi 407227256 118 E 118
Cdd:PTZ00368 128 G 128
PTZ00368 PTZ00368
universal minicircle sequence binding protein (UMSBP); Provisional
 39-83 4.91e-07

universal minicircle sequence binding protein (UMSBP); Provisional


Pssm-ID: 173561 [Multi-domain]  Cd Length: 148  Bit Score: 45.95  E-value: 4.91e-07
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|
gi 407227256  39 NFKGPRRTIKCFKCGKEGHLARNCRAPRKKG-----CWKCGKEGHQMKDC 83
Cdd:PTZ00368  70 EAPPGSGPRSCYNCGQTGHISRECPNRAKGGaarraCYNCGGEGHISRDC 119
AIR1 COG5082
Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational ...
 43-86 3.67e-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: 41.37  E-value: 3.67e-05
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....
gi 407227256  43 PRRTIKCFKCGKEGHLARNCRAprkKGCWKCGKEGHQMKDCTQG 86
Cdd:COG5082   57 REENPVCFNCGQNGHLRRDCPH---SICYNCSWDGHRSNHCPKP 97
AIR1 COG5082
Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational ...
 46-105 3.55e-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: 38.68  E-value: 3.55e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 407227256  46 TIKCFKCGKEGHLARNC--RAPRKKGCWKCGKEGHQMKDCTQgqanflgkIWLSNKGRPGNF 105
Cdd:COG5082   97 PKKCYNCGETGHLSRDCnpSKDQQKSCFDCNSTRHSSEDCPS--------IWKHYVLNNGDG 150
ZnF_C2HC smart00343
zinc finger;
48-63 1.59e-03

zinc finger;


Pssm-ID: 197667 [Multi-domain]  Cd Length: 17  Bit Score: 33.96  E-value: 1.59e-03
                           10
                   ....*....|....*.
gi 407227256    48 KCFKCGKEGHLARNCR 63
Cdd:smart00343   1 KCYNCGKEGHIARDCP 16
ZnF_C2HC smart00343
zinc finger;
69-85 2.53e-03

zinc finger;


Pssm-ID: 197667 [Multi-domain]  Cd Length: 17  Bit Score: 33.57  E-value: 2.53e-03
                           10
                   ....*....|....*..
gi 407227256    69 GCWKCGKEGHQMKDCTQ 85
Cdd:smart00343   1 KCYNCGKEGHIARDCPS 17
zf-CCHC pfam00098
Zinc knuckle; The zinc knuckle is a zinc binding motif composed of the the following ...
 47-62 4.53e-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: 32.88  E-value: 4.53e-03
                          10
                  ....*....|....*.
gi 407227256   47 IKCFKCGKEGHLARNC 62
Cdd:pfam00098   1 GKCYNCGEPGHIARDC 16
COG5222 COG5222
Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only];
70-137 8.01e-03

Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only];


Pssm-ID: 227547 [Multi-domain]  Cd Length: 427  Bit Score: 35.11  E-value: 8.01e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 407227256  70 CWKCGKEGHQMKDC-TQGQANFLGKIWLSNKGRPGNFLQNRPEPTAPPAESFGFGEEIAPSQKQEPKQE 137
Cdd:COG5222  179 CYRCGQKGHWIQNCpTNQDPNFDGKRIRRTTGIPKDFLKPVEGPNEPSNAAIMITPEGGYVVAQPDVQS 247
 
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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