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Conserved domains on  [gi|9627205|ref|NP_054369|]
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gag protein [Simian immunodeficiency virus]

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 ...
 2-135 9.05e-57

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: 185.91  E-value: 9.05e-57
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9627205      2 GGGHSALSGRSLDTFEKIRLRPNGKKKYQIKHLIWAGKEMERFGLHEKLLETKEGCQKIIEVLTPLEPTGSEGLKALFNL 81
Cdd:pfam00540   1 GARASVLSGGELDKWEKIRLRPGGKKKYKLKHLVWASRELERFAVNPGLLETSEGCRKILGQLQPSLQTGSEGLRSLYNT 80

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 9627205     82 CCVIWCIHAEQKVKDTEEAVVTVKQHYHLVDKNEKAAKKKNE------TTAPPGGESRNY 135
Cdd:pfam00540  81 VAVLYCVHQRIDVKDTKEALEKIEEEQNKSKKKKTAVPPGAQqaantgGTGNSSGVSQNY 140
Gag_p24_C pfam19317
Gag protein p24 C-terminal domain; p24 forms inner protein layer of the nucleocapsid. ELISA ...
 279-352 1.77e-35

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: 126.83  E-value: 1.77e-35
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 9627205    279 MYNPQKVLDIRQGPKEPFQDYVDRFYKALRAEQAPQDVKNWMTQTLLIQNANPDCKLILKGLGMNPTLEEMLIA 352
Cdd:pfam19317   1 GYKPTSLADIRQGPKEPYQDFVARLYDALRKEMPDGKAKDVITKQLAYENANPECQDLLKPLGKTGTLSDMIRA 74
PTZ00368 super family cl31762
universal minicircle sequence binding protein (UMSBP); Provisional
 381-428 1.47e-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: 65.21  E-value: 1.47e-12
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 9627205   381 PQKKGPRGPLKCFNCGKFGHMQRECKAPRQ-----IKCFKCGKIGHMAKDCKN 428
Cdd:PTZ00368  69 PEAPPGSGPRSCYNCGQTGHISRECPNRAKggaarRACYNCGGEGHISRDCPN 121
Gag_p24 super family cl02908
gag protein p24 N-terminal domain; p24 forms inner protein layer of the nucleocapsid. ELISA ...
 145-275 3.84e-09

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.


The actual alignment was detected with superfamily member pfam00607:

Pssm-ID: 459864  Cd Length: 128  Bit Score: 54.98  E-value: 3.84e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9627205    145 VHQPLSPRTLNAWVKCVEEKRWGAE-VVPMFQALSEG--CLSYDVNQMLNVIGDHqGALQILKEVINEEAAEWDRTHRpp 221
Cdd:pfam00607   1 VWEPLDFKLLKELKKAVKQYGPNSPyTMQLLEALASSnaLTPYDWRTLAKAVLSP-GQYLLWKAEWQELAQEQARRNQ-- 77

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 9627205    222 agplPAGQLRDPTGSDIAGTT--SSIQEQIEWTFNANPRIDvGAQYRKWVILGLQK 275
Cdd:pfam00607  78 ----RAGPDRGITLDMLTGTGqyATPQAQAQLPPEVLEQIK-ALALRAWKKLPPPG 128
 
Name Accession Description Interval E-value
Gag_p17 pfam00540
gag gene protein p17 (matrix protein); The matrix protein forms an icosahedral shell ...
 2-135 9.05e-57

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: 185.91  E-value: 9.05e-57
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9627205      2 GGGHSALSGRSLDTFEKIRLRPNGKKKYQIKHLIWAGKEMERFGLHEKLLETKEGCQKIIEVLTPLEPTGSEGLKALFNL 81
Cdd:pfam00540   1 GARASVLSGGELDKWEKIRLRPGGKKKYKLKHLVWASRELERFAVNPGLLETSEGCRKILGQLQPSLQTGSEGLRSLYNT 80

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 9627205     82 CCVIWCIHAEQKVKDTEEAVVTVKQHYHLVDKNEKAAKKKNE------TTAPPGGESRNY 135
Cdd:pfam00540  81 VAVLYCVHQRIDVKDTKEALEKIEEEQNKSKKKKTAVPPGAQqaantgGTGNSSGVSQNY 140
Gag_p24_C pfam19317
Gag protein p24 C-terminal domain; p24 forms inner protein layer of the nucleocapsid. ELISA ...
 279-352 1.77e-35

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: 126.83  E-value: 1.77e-35
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 9627205    279 MYNPQKVLDIRQGPKEPFQDYVDRFYKALRAEQAPQDVKNWMTQTLLIQNANPDCKLILKGLGMNPTLEEMLIA 352
Cdd:pfam19317   1 GYKPTSLADIRQGPKEPYQDFVARLYDALRKEMPDGKAKDVITKQLAYENANPECQDLLKPLGKTGTLSDMIRA 74
PTZ00368 PTZ00368
universal minicircle sequence binding protein (UMSBP); Provisional
 381-428 1.47e-12

universal minicircle sequence binding protein (UMSBP); Provisional


Pssm-ID: 173561 [Multi-domain]  Cd Length: 148  Bit Score: 65.21  E-value: 1.47e-12
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 9627205   381 PQKKGPRGPLKCFNCGKFGHMQRECKAPRQ-----IKCFKCGKIGHMAKDCKN 428
Cdd:PTZ00368  69 PEAPPGSGPRSCYNCGQTGHISRECPNRAKggaarRACYNCGGEGHISRDCPN 121
Gag_p24 pfam00607
gag protein p24 N-terminal domain; p24 forms inner protein layer of the nucleocapsid. ELISA ...
 145-275 3.84e-09

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: 54.98  E-value: 3.84e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9627205    145 VHQPLSPRTLNAWVKCVEEKRWGAE-VVPMFQALSEG--CLSYDVNQMLNVIGDHqGALQILKEVINEEAAEWDRTHRpp 221
Cdd:pfam00607   1 VWEPLDFKLLKELKKAVKQYGPNSPyTMQLLEALASSnaLTPYDWRTLAKAVLSP-GQYLLWKAEWQELAQEQARRNQ-- 77

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 9627205    222 agplPAGQLRDPTGSDIAGTT--SSIQEQIEWTFNANPRIDvGAQYRKWVILGLQK 275
Cdd:pfam00607  78 ----RAGPDRGITLDMLTGTGqyATPQAQAQLPPEVLEQIK-ALALRAWKKLPPPG 128
AIR1 COG5082
Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational ...
 391-426 4.72e-07

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: 50.23  E-value: 4.72e-07
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|..
gi 9627205  391 KCFNCGKFGHMQRECKA----------------PRQIKCFKCGKIGHMAKDC 426
Cdd:COG5082  62 VCFNCGQNGHLRRDCPHsicyncswdghrsnhcPKPKKCYNCGETGHLSRDC 113
zf-CCHC pfam00098
Zinc knuckle; The zinc knuckle is a zinc binding motif composed of the the following ...
 411-428 9.75e-05

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: 39.43  E-value: 9.75e-05
                          10
                  ....*....|....*...
gi 9627205    411 IKCFKCGKIGHMAKDCKN 428
Cdd:pfam00098   1 GKCYNCGEPGHIARDCPK 18
ZnF_C2HC smart00343
zinc finger;
412-428 1.37e-04

zinc finger;


Pssm-ID: 197667 [Multi-domain]  Cd Length: 17  Bit Score: 38.96  E-value: 1.37e-04
                           10
                   ....*....|....*..
gi 9627205     412 KCFKCGKIGHMAKDCKN 428
Cdd:smart00343   1 KCYNCGKEGHIARDCPS 17
 
Name Accession Description Interval E-value
Gag_p17 pfam00540
gag gene protein p17 (matrix protein); The matrix protein forms an icosahedral shell ...
 2-135 9.05e-57

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: 185.91  E-value: 9.05e-57
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9627205      2 GGGHSALSGRSLDTFEKIRLRPNGKKKYQIKHLIWAGKEMERFGLHEKLLETKEGCQKIIEVLTPLEPTGSEGLKALFNL 81
Cdd:pfam00540   1 GARASVLSGGELDKWEKIRLRPGGKKKYKLKHLVWASRELERFAVNPGLLETSEGCRKILGQLQPSLQTGSEGLRSLYNT 80

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 9627205     82 CCVIWCIHAEQKVKDTEEAVVTVKQHYHLVDKNEKAAKKKNE------TTAPPGGESRNY 135
Cdd:pfam00540  81 VAVLYCVHQRIDVKDTKEALEKIEEEQNKSKKKKTAVPPGAQqaantgGTGNSSGVSQNY 140
Gag_p24_C pfam19317
Gag protein p24 C-terminal domain; p24 forms inner protein layer of the nucleocapsid. ELISA ...
 279-352 1.77e-35

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: 126.83  E-value: 1.77e-35
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 9627205    279 MYNPQKVLDIRQGPKEPFQDYVDRFYKALRAEQAPQDVKNWMTQTLLIQNANPDCKLILKGLGMNPTLEEMLIA 352
Cdd:pfam19317   1 GYKPTSLADIRQGPKEPYQDFVARLYDALRKEMPDGKAKDVITKQLAYENANPECQDLLKPLGKTGTLSDMIRA 74
PTZ00368 PTZ00368
universal minicircle sequence binding protein (UMSBP); Provisional
 381-428 1.47e-12

universal minicircle sequence binding protein (UMSBP); Provisional


Pssm-ID: 173561 [Multi-domain]  Cd Length: 148  Bit Score: 65.21  E-value: 1.47e-12
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 9627205   381 PQKKGPRGPLKCFNCGKFGHMQRECKAPRQ-----IKCFKCGKIGHMAKDCKN 428
Cdd:PTZ00368  69 PEAPPGSGPRSCYNCGQTGHISRECPNRAKggaarRACYNCGGEGHISRDCPN 121
PTZ00368 PTZ00368
universal minicircle sequence binding protein (UMSBP); Provisional
 381-438 1.96e-12

universal minicircle sequence binding protein (UMSBP); Provisional


Pssm-ID: 173561 [Multi-domain]  Cd Length: 148  Bit Score: 64.83  E-value: 1.96e-12
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 9627205   381 PQKKGPRGPLKCFNCGKFGHMQRECKAPRQ----IKCFKCGKIGHMAKDCKNGQANFLGYGH 438
Cdd:PTZ00368  44 PSAPGGRGERSCYNCGKTGHLSRECPEAPPgsgpRSCYNCGQTGHISRECPNRAKGGAARRA 105
PTZ00368 PTZ00368
universal minicircle sequence binding protein (UMSBP); Provisional
 383-430 4.12e-10

universal minicircle sequence binding protein (UMSBP); Provisional


Pssm-ID: 173561 [Multi-domain]  Cd Length: 148  Bit Score: 58.28  E-value: 4.12e-10
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 9627205   383 KKGPRGPLKCFNCGKFGHMQRECKAPRQIK----CFKCGKIGHMAKDCKNGQ 430
Cdd:PTZ00368  21 PAGAAKARPCYKCGEPGHLSRECPSAPGGRgersCYNCGKTGHLSRECPEAP 72
PTZ00368 PTZ00368
universal minicircle sequence binding protein (UMSBP); Provisional
 384-427 4.53e-10

universal minicircle sequence binding protein (UMSBP); Provisional


Pssm-ID: 173561 [Multi-domain]  Cd Length: 148  Bit Score: 57.89  E-value: 4.53e-10
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*....
gi 9627205   384 KGPRGPLKCFNCGKFGHMQRECKAPRQI-----KCFKCGKIGHMAKDCK 427
Cdd:PTZ00368  98 KGGAARRACYNCGGEGHISRDCPNAGKRpggdkTCYNCGQTGHLSRDCP 146
Gag_p24 pfam00607
gag protein p24 N-terminal domain; p24 forms inner protein layer of the nucleocapsid. ELISA ...
 145-275 3.84e-09

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: 54.98  E-value: 3.84e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9627205    145 VHQPLSPRTLNAWVKCVEEKRWGAE-VVPMFQALSEG--CLSYDVNQMLNVIGDHqGALQILKEVINEEAAEWDRTHRpp 221
Cdd:pfam00607   1 VWEPLDFKLLKELKKAVKQYGPNSPyTMQLLEALASSnaLTPYDWRTLAKAVLSP-GQYLLWKAEWQELAQEQARRNQ-- 77

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 9627205    222 agplPAGQLRDPTGSDIAGTT--SSIQEQIEWTFNANPRIDvGAQYRKWVILGLQK 275
Cdd:pfam00607  78 ----RAGPDRGITLDMLTGTGqyATPQAQAQLPPEVLEQIK-ALALRAWKKLPPPG 128
PTZ00368 PTZ00368
universal minicircle sequence binding protein (UMSBP); Provisional
 392-430 1.52e-07

universal minicircle sequence binding protein (UMSBP); Provisional


Pssm-ID: 173561 [Multi-domain]  Cd Length: 148  Bit Score: 50.58  E-value: 1.52e-07
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*
gi 9627205   392 CFNCGKFGHMQRECKAPRQ------IKCFKCGKIGHMAKDCKNGQ 430
Cdd:PTZ00368   3 CYRCGGVGHQSRECPNSAPagaakaRPCYKCGEPGHLSRECPSAP 47
AIR1 COG5082
Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational ...
 391-426 4.72e-07

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: 50.23  E-value: 4.72e-07
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|..
gi 9627205  391 KCFNCGKFGHMQRECKA----------------PRQIKCFKCGKIGHMAKDC 426
Cdd:COG5082  62 VCFNCGQNGHLRRDCPHsicyncswdghrsnhcPKPKKCYNCGETGHLSRDC 113
AIR1 COG5082
Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational ...
 389-426 2.41e-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: 45.23  E-value: 2.41e-05
                        10        20        30        40
                ....*....|....*....|....*....|....*....|
gi 9627205  389 PLKCFNCGKFGHMQREC--KAPRQIKCFKCGKIGHMAKDC 426
Cdd:COG5082  97 PKKCYNCGETGHLSRDCnpSKDQQKSCFDCNSTRHSSEDC 136
zf-CCHC pfam00098
Zinc knuckle; The zinc knuckle is a zinc binding motif composed of the the following ...
 411-428 9.75e-05

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: 39.43  E-value: 9.75e-05
                          10
                  ....*....|....*...
gi 9627205    411 IKCFKCGKIGHMAKDCKN 428
Cdd:pfam00098   1 GKCYNCGEPGHIARDCPK 18
ZnF_C2HC smart00343
zinc finger;
412-428 1.37e-04

zinc finger;


Pssm-ID: 197667 [Multi-domain]  Cd Length: 17  Bit Score: 38.96  E-value: 1.37e-04
                           10
                   ....*....|....*..
gi 9627205     412 KCFKCGKIGHMAKDCKN 428
Cdd:smart00343   1 KCYNCGKEGHIARDCPS 17
AIR1 COG5082
Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational ...
 386-427 5.17e-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: 41.37  E-value: 5.17e-04
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*
gi 9627205  386 PRGPLKCFNCGKFGHMQREC-------------KAPRQIKCFKCGKIGHMAKDCK 427
Cdd:COG5082 117 KDQQKSCFDCNSTRHSSEDCpsiwkhyvlnngdGHPIKKFCYSCGSAGHFGDDCK 171
ZnF_C2HC smart00343
zinc finger;
391-406 6.99e-04

zinc finger;


Pssm-ID: 197667 [Multi-domain]  Cd Length: 17  Bit Score: 37.04  E-value: 6.99e-04
                           10
                   ....*....|....*.
gi 9627205     391 KCFNCGKFGHMQRECK 406
Cdd:smart00343   1 KCYNCGKEGHIARDCP 16
zf-CCHC pfam00098
Zinc knuckle; The zinc knuckle is a zinc binding motif composed of the the following ...
 391-406 1.89e-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: 35.58  E-value: 1.89e-03
                          10
                  ....*....|....*.
gi 9627205    391 KCFNCGKFGHMQRECK 406
Cdd:pfam00098   2 KCYNCGEPGHIARDCP 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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