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Conserved domains on  [gi|2655133|gb|AAB87876|]
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gag protein, partial [Human immunodeficiency virus 2]

Protein Classification

gag protein( domain architecture ID 10255561)

HIV-1 gag protein functions in assembly of virus-like particles, virion maturation after particle release, and early post-entry steps in virus replication

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 ...
 3-98 4.00e-30

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: 109.64  E-value: 4.00e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2655133      3 ELDRFGLADNLLESKEGCQKILKALDPLVPTGSENLKSLYNTTCVIWCLHAEEKVKDTEEAKQIIQRH-------LVAGT 75
Cdd:pfam00540  39 ELERFAVNPGLLETSEGCRKILGQLQPSLQTGSEGLRSLYNTVAVLYCVHQRIDVKDTKEALEKIEEEqnkskkkKTAVP 118

                          90       100
                  ....*....|....*....|...
gi 2655133     76 GTAEKMPNTSrPTAPPSGKGGNF 98
Cdd:pfam00540 119 PGAQQAANTG-GTGNSSGVSQNY 140
Gag_p24 pfam00607
gag protein p24 N-terminal domain; p24 forms inner protein layer of the nucleocapsid. ELISA ...
 108-237 9.39e-14

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: 66.15  E-value: 9.39e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2655133    108 THMPLSPRTLNAWVKLVEDKKFGAE-VVPGFQALSEG--CTPYDINQMLNCVGDHqAAMQIIREIINEEAADWDTAHPIP 184
Cdd:pfam00607   1 VWEPLDFKLLKELKKAVKQYGPNSPyTMQLLEALASSnaLTPYDWRTLAKAVLSP-GQYLLWKAEWQELAQEQARRNQRA 79

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 2655133    185 GPLpagqlrEPRGSD-IAGTT--STVEEQIQWMFRAQNPIPvGNIYRRWIQIGLQK 237
Cdd:pfam00607  80 GPD------RGITLDmLTGTGqyATPQAQAQLPPEVLEQIK-ALALRAWKKLPPPG 128
Gag_p24_C super family cl44748
Gag protein p24 C-terminal domain; p24 forms inner protein layer of the nucleocapsid. ELISA ...
 241-260 1.08e-04

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: 39.77  E-value: 1.08e-04
                          10        20
                  ....*....|....*....|
gi 2655133    241 MYNPTNILDIKQGPKESFQS 260
Cdd:pfam19317   1 GYKPTSLADIRQGPKEPYQD 20
 
Name Accession Description Interval E-value
Gag_p17 pfam00540
gag gene protein p17 (matrix protein); The matrix protein forms an icosahedral shell ...
 3-98 4.00e-30

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: 109.64  E-value: 4.00e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2655133      3 ELDRFGLADNLLESKEGCQKILKALDPLVPTGSENLKSLYNTTCVIWCLHAEEKVKDTEEAKQIIQRH-------LVAGT 75
Cdd:pfam00540  39 ELERFAVNPGLLETSEGCRKILGQLQPSLQTGSEGLRSLYNTVAVLYCVHQRIDVKDTKEALEKIEEEqnkskkkKTAVP 118

                          90       100
                  ....*....|....*....|...
gi 2655133     76 GTAEKMPNTSrPTAPPSGKGGNF 98
Cdd:pfam00540 119 PGAQQAANTG-GTGNSSGVSQNY 140
Gag_p24 pfam00607
gag protein p24 N-terminal domain; p24 forms inner protein layer of the nucleocapsid. ELISA ...
 108-237 9.39e-14

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: 66.15  E-value: 9.39e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2655133    108 THMPLSPRTLNAWVKLVEDKKFGAE-VVPGFQALSEG--CTPYDINQMLNCVGDHqAAMQIIREIINEEAADWDTAHPIP 184
Cdd:pfam00607   1 VWEPLDFKLLKELKKAVKQYGPNSPyTMQLLEALASSnaLTPYDWRTLAKAVLSP-GQYLLWKAEWQELAQEQARRNQRA 79

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 2655133    185 GPLpagqlrEPRGSD-IAGTT--STVEEQIQWMFRAQNPIPvGNIYRRWIQIGLQK 237
Cdd:pfam00607  80 GPD------RGITLDmLTGTGqyATPQAQAQLPPEVLEQIK-ALALRAWKKLPPPG 128
Gag_p24_C pfam19317
Gag protein p24 C-terminal domain; p24 forms inner protein layer of the nucleocapsid. ELISA ...
 241-260 1.08e-04

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: 39.77  E-value: 1.08e-04
                          10        20
                  ....*....|....*....|
gi 2655133    241 MYNPTNILDIKQGPKESFQS 260
Cdd:pfam19317   1 GYKPTSLADIRQGPKEPYQD 20
 
Name Accession Description Interval E-value
Gag_p17 pfam00540
gag gene protein p17 (matrix protein); The matrix protein forms an icosahedral shell ...
 3-98 4.00e-30

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: 109.64  E-value: 4.00e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2655133      3 ELDRFGLADNLLESKEGCQKILKALDPLVPTGSENLKSLYNTTCVIWCLHAEEKVKDTEEAKQIIQRH-------LVAGT 75
Cdd:pfam00540  39 ELERFAVNPGLLETSEGCRKILGQLQPSLQTGSEGLRSLYNTVAVLYCVHQRIDVKDTKEALEKIEEEqnkskkkKTAVP 118

                          90       100
                  ....*....|....*....|...
gi 2655133     76 GTAEKMPNTSrPTAPPSGKGGNF 98
Cdd:pfam00540 119 PGAQQAANTG-GTGNSSGVSQNY 140
Gag_p24 pfam00607
gag protein p24 N-terminal domain; p24 forms inner protein layer of the nucleocapsid. ELISA ...
 108-237 9.39e-14

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: 66.15  E-value: 9.39e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2655133    108 THMPLSPRTLNAWVKLVEDKKFGAE-VVPGFQALSEG--CTPYDINQMLNCVGDHqAAMQIIREIINEEAADWDTAHPIP 184
Cdd:pfam00607   1 VWEPLDFKLLKELKKAVKQYGPNSPyTMQLLEALASSnaLTPYDWRTLAKAVLSP-GQYLLWKAEWQELAQEQARRNQRA 79

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 2655133    185 GPLpagqlrEPRGSD-IAGTT--STVEEQIQWMFRAQNPIPvGNIYRRWIQIGLQK 237
Cdd:pfam00607  80 GPD------RGITLDmLTGTGqyATPQAQAQLPPEVLEQIK-ALALRAWKKLPPPG 128
Gag_p24_C pfam19317
Gag protein p24 C-terminal domain; p24 forms inner protein layer of the nucleocapsid. ELISA ...
 241-260 1.08e-04

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: 39.77  E-value: 1.08e-04
                          10        20
                  ....*....|....*....|
gi 2655133    241 MYNPTNILDIKQGPKESFQS 260
Cdd:pfam19317   1 GYKPTSLADIRQGPKEPYQD 20
 
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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