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Conserved domains on  [gi|209156860|gb|ACI39914|]
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gag protein [Human immunodeficiency virus 1]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
Gag_p17 super family cl02892
gag gene protein p17 (matrix protein); The matrix protein forms an icosahedral shell ...
 2-107 1.80e-60

gag gene protein p17 (matrix protein); The matrix protein forms an icosahedral shell associated with the inner membrane of the mature immunodeficiency virus.


The actual alignment was detected with superfamily member pfam00540:

Pssm-ID: 249943  Cd Length: 140  Bit Score: 194.77  E-value: 1.80e-60
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 209156860    2 GARASVLSGGKLDTWEKIRLRPGGKKKYKLKHLVWASRELERFAVNPGLLETTEGCRKIIGQLQPSIQTGSEELKSLYNT 81
Cdd:pfam00540   1 GARASVLSGGELDKWEKIRLRPGGKKKYKLKHLVWASRELERFAVNPGLLETSEGCRKILGQLQPSLQTGSEGLRSLYNT 80

                          90       100
                  ....*....|....*....|....*.
gi 209156860   82 VAVLYYVHQGVEVKDTKEALDKLEEE 107
Cdd:pfam00540  81 VAVLYCVHQRIDVKDTKEALEKIEEE 106
Gag_p24_C super family cl44748
Gag protein p24 C-terminal domain; p24 forms inner protein layer of the nucleocapsid. ELISA ...
 272-345 2.70e-33

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.


The actual alignment was detected with superfamily member pfam19317:

Pssm-ID: 466038  Cd Length: 74  Bit Score: 120.66  E-value: 2.70e-33
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 209156860  272 MYSPVSILDIRQGPKEPFRDYVDRFFKVLRAEQATQEVKGWMTDTLLVQNANPDCKTILKALGTGATLEEMMAA 345
Cdd:pfam19317   1 GYKPTSLADIRQGPKEPYQDFVARLYDALRKEMPDGKAKDVITKQLAYENANPECQDLLKPLGKTGTLSDMIRA 74
Gag_p24 pfam00607
gag protein p24 N-terminal domain; p24 forms inner protein layer of the nucleocapsid. ELISA ...
 139-264 3.76e-15

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: 71.93  E-value: 3.76e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 209156860  139 VHQPISPRTLNAWVKVVEEKAF-SPEVIPMFSALSEG--ATPQDLNTMLNTVGGHqAAMQMLKDTINEEAADWDRlHPVH 215
Cdd:pfam00607   1 VWEPLDFKLLKELKKAVKQYGPnSPYTMQLLEALASSnaLTPYDWRTLAKAVLSP-GQYLLWKAEWQELAQEQAR-RNQR 78

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 209156860  216 AGPIppgqmrEPRGSD-IAGTT--STLQEQIQWmtsNPPV--PVGEI-YKRWIIL 264
Cdd:pfam00607  79 AGPD------RGITLDmLTGTGqyATPQAQAQL---PPEVleQIKALaLRAWKKL 124
PTZ00368 super family cl31762
universal minicircle sequence binding protein (UMSBP); Provisional
 344-422 8.38e-12

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: 62.90  E-value: 8.38e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 209156860 344 AACQGVGGPGHKARVLAEAmsqvtstavmmqnsnfKGQRKIVKCFNCGKQGHIARNCKAPRKKG-----CWKCGGEGHQM 418
Cdd:PTZ00368  53 RSCYNCGKTGHLSRECPEA----------------PPGSGPRSCYNCGQTGHISRECPNRAKGGaarraCYNCGGEGHIS 116


                 ....
gi 209156860 419 KDCP 422
Cdd:PTZ00368 117 RDCP 120
 
Name Accession Description Interval E-value
Gag_p17 pfam00540
gag gene protein p17 (matrix protein); The matrix protein forms an icosahedral shell ...
 2-107 1.80e-60

gag gene protein p17 (matrix protein); The matrix protein forms an icosahedral shell associated with the inner membrane of the mature immunodeficiency virus.


Pssm-ID: 249943  Cd Length: 140  Bit Score: 194.77  E-value: 1.80e-60
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 209156860    2 GARASVLSGGKLDTWEKIRLRPGGKKKYKLKHLVWASRELERFAVNPGLLETTEGCRKIIGQLQPSIQTGSEELKSLYNT 81
Cdd:pfam00540   1 GARASVLSGGELDKWEKIRLRPGGKKKYKLKHLVWASRELERFAVNPGLLETSEGCRKILGQLQPSLQTGSEGLRSLYNT 80

                          90       100
                  ....*....|....*....|....*.
gi 209156860   82 VAVLYYVHQGVEVKDTKEALDKLEEE 107
Cdd:pfam00540  81 VAVLYCVHQRIDVKDTKEALEKIEEE 106
Gag_p24_C pfam19317
Gag protein p24 C-terminal domain; p24 forms inner protein layer of the nucleocapsid. ELISA ...
 272-345 2.70e-33

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: 120.66  E-value: 2.70e-33
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 209156860  272 MYSPVSILDIRQGPKEPFRDYVDRFFKVLRAEQATQEVKGWMTDTLLVQNANPDCKTILKALGTGATLEEMMAA 345
Cdd:pfam19317   1 GYKPTSLADIRQGPKEPYQDFVARLYDALRKEMPDGKAKDVITKQLAYENANPECQDLLKPLGKTGTLSDMIRA 74
Gag_p24 pfam00607
gag protein p24 N-terminal domain; p24 forms inner protein layer of the nucleocapsid. ELISA ...
 139-264 3.76e-15

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: 71.93  E-value: 3.76e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 209156860  139 VHQPISPRTLNAWVKVVEEKAF-SPEVIPMFSALSEG--ATPQDLNTMLNTVGGHqAAMQMLKDTINEEAADWDRlHPVH 215
Cdd:pfam00607   1 VWEPLDFKLLKELKKAVKQYGPnSPYTMQLLEALASSnaLTPYDWRTLAKAVLSP-GQYLLWKAEWQELAQEQAR-RNQR 78

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 209156860  216 AGPIppgqmrEPRGSD-IAGTT--STLQEQIQWmtsNPPV--PVGEI-YKRWIIL 264
Cdd:pfam00607  79 AGPD------RGITLDmLTGTGqyATPQAQAQL---PPEVleQIKALaLRAWKKL 124
PTZ00368 PTZ00368
universal minicircle sequence binding protein (UMSBP); Provisional
 344-422 8.38e-12

universal minicircle sequence binding protein (UMSBP); Provisional


Pssm-ID: 173561 [Multi-domain]  Cd Length: 148  Bit Score: 62.90  E-value: 8.38e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 209156860 344 AACQGVGGPGHKARVLAEAmsqvtstavmmqnsnfKGQRKIVKCFNCGKQGHIARNCKAPRKKG-----CWKCGGEGHQM 418
Cdd:PTZ00368  53 RSCYNCGKTGHLSRECPEA----------------PPGSGPRSCYNCGQTGHISRECPNRAKGGaarraCYNCGGEGHIS 116


                 ....
gi 209156860 419 KDCP 422
Cdd:PTZ00368 117 RDCP 120
AIR1 COG5082
Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational ...
 344-443 7.90e-08

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: 52.55  E-value: 7.90e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 209156860 344 AACQGVGGPGHKARvlaeamsqvTSTAVMMQNSNFKGQRKI-----VKCFNCGKQGHIARNC--KAPRKKGCWKCGGEGH 416
Cdd:COG5082   61 PVCFNCGQNGHLRR---------DCPHSICYNCSWDGHRSNhcpkpKKCYNCGETGHLSRDCnpSKDQQKSCFDCNSTRH 131

                         90       100
                 ....*....|....*....|....*..
gi 209156860 417 QMKDCPggqanflgKIWPSNKGRPGNF 443
Cdd:COG5082  132 SSEDCP--------SIWKHYVLNNGDG 150
ZnF_C2HC smart00343
zinc finger;
407-422 7.37e-05

zinc finger;


Pssm-ID: 197667 [Multi-domain]  Cd Length: 17  Bit Score: 39.73  E-value: 7.37e-05
                           10
                   ....*....|....*.
gi 209156860   407 GCWKCGGEGHQMKDCP 422
Cdd:smart00343   1 KCYNCGKEGHIARDCP 16
zf-CCHC pfam00098
Zinc knuckle; The zinc knuckle is a zinc binding motif composed of the the following ...
 385-401 1.68e-04

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: 38.66  E-value: 1.68e-04
                          10
                  ....*....|....*..
gi 209156860  385 VKCFNCGKQGHIARNCK 401
Cdd:pfam00098   1 GKCYNCGEPGHIARDCP 17
 
Name Accession Description Interval E-value
Gag_p17 pfam00540
gag gene protein p17 (matrix protein); The matrix protein forms an icosahedral shell ...
 2-107 1.80e-60

gag gene protein p17 (matrix protein); The matrix protein forms an icosahedral shell associated with the inner membrane of the mature immunodeficiency virus.


Pssm-ID: 249943  Cd Length: 140  Bit Score: 194.77  E-value: 1.80e-60
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 209156860    2 GARASVLSGGKLDTWEKIRLRPGGKKKYKLKHLVWASRELERFAVNPGLLETTEGCRKIIGQLQPSIQTGSEELKSLYNT 81
Cdd:pfam00540   1 GARASVLSGGELDKWEKIRLRPGGKKKYKLKHLVWASRELERFAVNPGLLETSEGCRKILGQLQPSLQTGSEGLRSLYNT 80

                          90       100
                  ....*....|....*....|....*.
gi 209156860   82 VAVLYYVHQGVEVKDTKEALDKLEEE 107
Cdd:pfam00540  81 VAVLYCVHQRIDVKDTKEALEKIEEE 106
Gag_p24_C pfam19317
Gag protein p24 C-terminal domain; p24 forms inner protein layer of the nucleocapsid. ELISA ...
 272-345 2.70e-33

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: 120.66  E-value: 2.70e-33
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 209156860  272 MYSPVSILDIRQGPKEPFRDYVDRFFKVLRAEQATQEVKGWMTDTLLVQNANPDCKTILKALGTGATLEEMMAA 345
Cdd:pfam19317   1 GYKPTSLADIRQGPKEPYQDFVARLYDALRKEMPDGKAKDVITKQLAYENANPECQDLLKPLGKTGTLSDMIRA 74
Gag_p24 pfam00607
gag protein p24 N-terminal domain; p24 forms inner protein layer of the nucleocapsid. ELISA ...
 139-264 3.76e-15

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: 71.93  E-value: 3.76e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 209156860  139 VHQPISPRTLNAWVKVVEEKAF-SPEVIPMFSALSEG--ATPQDLNTMLNTVGGHqAAMQMLKDTINEEAADWDRlHPVH 215
Cdd:pfam00607   1 VWEPLDFKLLKELKKAVKQYGPnSPYTMQLLEALASSnaLTPYDWRTLAKAVLSP-GQYLLWKAEWQELAQEQAR-RNQR 78

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 209156860  216 AGPIppgqmrEPRGSD-IAGTT--STLQEQIQWmtsNPPV--PVGEI-YKRWIIL 264
Cdd:pfam00607  79 AGPD------RGITLDmLTGTGqyATPQAQAQL---PPEVleQIKALaLRAWKKL 124
PTZ00368 PTZ00368
universal minicircle sequence binding protein (UMSBP); Provisional
 344-422 8.38e-12

universal minicircle sequence binding protein (UMSBP); Provisional


Pssm-ID: 173561 [Multi-domain]  Cd Length: 148  Bit Score: 62.90  E-value: 8.38e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 209156860 344 AACQGVGGPGHKARVLAEAmsqvtstavmmqnsnfKGQRKIVKCFNCGKQGHIARNCKAPRKKG-----CWKCGGEGHQM 418
Cdd:PTZ00368  53 RSCYNCGKTGHLSRECPEA----------------PPGSGPRSCYNCGQTGHISRECPNRAKGGaarraCYNCGGEGHIS 116


                 ....
gi 209156860 419 KDCP 422
Cdd:PTZ00368 117 RDCP 120
PTZ00368 PTZ00368
universal minicircle sequence binding protein (UMSBP); Provisional
 345-422 9.05e-12

universal minicircle sequence binding protein (UMSBP); Provisional


Pssm-ID: 173561 [Multi-domain]  Cd Length: 148  Bit Score: 62.90  E-value: 9.05e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 209156860 345 ACQGVGGPGHKARVLAEAMsqvtstavmmqnsnfKGQRKIVKCFNCGKQGHIARNCKAPRKKG-----CWKCGGEGHQMK 419
Cdd:PTZ00368  79 SCYNCGQTGHISRECPNRA---------------KGGAARRACYNCGGEGHISRDCPNAGKRPggdktCYNCGQTGHLSR 143


                 ...
gi 209156860 420 DCP 422
Cdd:PTZ00368 144 DCP 146
PTZ00368 PTZ00368
universal minicircle sequence binding protein (UMSBP); Provisional
 346-443 1.83e-10

universal minicircle sequence binding protein (UMSBP); Provisional


Pssm-ID: 173561 [Multi-domain]  Cd Length: 148  Bit Score: 59.05  E-value: 1.83e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 209156860 346 CQGVGGPGHKARVLAeamsqvtstavmmqNSNFKGQRKIVKCFNCGKQGHIARNCKAPRKKG----CWKCGGEGHQMKDC 421
Cdd:PTZ00368   3 CYRCGGVGHQSRECP--------------NSAPAGAAKARPCYKCGEPGHLSRECPSAPGGRgersCYNCGKTGHLSREC 68

                         90       100
                 ....*....|....*....|..
gi 209156860 422 PGGQANFlGKIWPSNKGRPGNF 443
Cdd:PTZ00368  69 PEAPPGS-GPRSCYNCGQTGHI 89
PTZ00368 PTZ00368
universal minicircle sequence binding protein (UMSBP); Provisional
 387-427 3.76e-09

universal minicircle sequence binding protein (UMSBP); Provisional


Pssm-ID: 173561 [Multi-domain]  Cd Length: 148  Bit Score: 55.20  E-value: 3.76e-09
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*
gi 209156860 387 CFNCGKQGHIARNC-KAPRKKG---CWKCGGEGHQMKDCPGGQAN 427
Cdd:PTZ00368  55 CYNCGKTGHLSRECpEAPPGSGprsCYNCGQTGHISRECPNRAKG 99
AIR1 COG5082
Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational ...
 344-443 7.90e-08

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: 52.55  E-value: 7.90e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 209156860 344 AACQGVGGPGHKARvlaeamsqvTSTAVMMQNSNFKGQRKI-----VKCFNCGKQGHIARNC--KAPRKKGCWKCGGEGH 416
Cdd:COG5082   61 PVCFNCGQNGHLRR---------DCPHSICYNCSWDGHRSNhcpkpKKCYNCGETGHLSRDCnpSKDQQKSCFDCNSTRH 131

                         90       100
                 ....*....|....*....|....*..
gi 209156860 417 QMKDCPggqanflgKIWPSNKGRPGNF 443
Cdd:COG5082  132 SSEDCP--------SIWKHYVLNNGDG 150
ZnF_C2HC smart00343
zinc finger;
407-422 7.37e-05

zinc finger;


Pssm-ID: 197667 [Multi-domain]  Cd Length: 17  Bit Score: 39.73  E-value: 7.37e-05
                           10
                   ....*....|....*.
gi 209156860   407 GCWKCGGEGHQMKDCP 422
Cdd:smart00343   1 KCYNCGKEGHIARDCP 16
ZnF_C2HC smart00343
zinc finger;
386-401 8.29e-05

zinc finger;


Pssm-ID: 197667 [Multi-domain]  Cd Length: 17  Bit Score: 39.35  E-value: 8.29e-05
                           10
                   ....*....|....*.
gi 209156860   386 KCFNCGKQGHIARNCK 401
Cdd:smart00343   1 KCYNCGKEGHIARDCP 16
zf-CCHC pfam00098
Zinc knuckle; The zinc knuckle is a zinc binding motif composed of the the following ...
 385-401 1.68e-04

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: 38.66  E-value: 1.68e-04
                          10
                  ....*....|....*..
gi 209156860  385 VKCFNCGKQGHIARNCK 401
Cdd:pfam00098   1 GKCYNCGEPGHIARDCP 17
zf-CCHC pfam00098
Zinc knuckle; The zinc knuckle is a zinc binding motif composed of the the following ...
 406-422 6.01e-04

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: 37.12  E-value: 6.01e-04
                          10
                  ....*....|....*..
gi 209156860  406 KGCWKCGGEGHQMKDCP 422
Cdd:pfam00098   1 GKCYNCGEPGHIARDCP 17
 
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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