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Conserved domains on  [gi|1127546997|gb|APS24114|]
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gag protein [synthetic HIV-2]

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 7.31e-49

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: 165.11  E-value: 7.31e-49
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1127546997   2 GARNSVLRGKKADELERIRLRPGGKKKYRLKHIVWAANKLDRFGLAESLLESKEGCQKILTVLDPMVPTGSENLKSLFNT 81
Cdd:pfam00540   1 GARASVLSGGELDKWEKIRLRPGGKKKYKLKHLVWASRELERFAVNPGLLETSEGCRKILGQLQPSLQTGSEGLRSLYNT 80

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1127546997  82 VCVIWCIHAEEKVKDTEGAKQIVRRH-------LVAETGTAEKMPSTSrPTAPSSEKGGNY 135
Cdd:pfam00540  81 VAVLYCVHQRIDVKDTKEALEKIEEEqnkskkkKTAVPPGAQQAANTG-GTGNSSGVSQNY 140
Gag_p24_C pfam19317
Gag protein p24 C-terminal domain; p24 forms inner protein layer of the nucleocapsid. ELISA ...
 278-351 5.66e-39

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: 136.46  E-value: 5.66e-39
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1127546997 278 MYNPTNILDIKQGPKEPFQSYVDRFYKSLRAEQTDPAVKNWMTQTLLVQNANPDCKLVLKGLGMNPTLEEMLTA 351
Cdd:pfam19317   1 GYKPTSLADIRQGPKEPYQDFVARLYDALRKEMPDGKAKDVITKQLAYENANPECQDLLKPLGKTGTLSDMIRA 74
Gag_p24 pfam00607
gag protein p24 N-terminal domain; p24 forms inner protein layer of the nucleocapsid. ELISA ...
 145-274 1.70e-11

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: 61.53  E-value: 1.70e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1127546997 145 THIPLSPRTLNAWVKLVEEKKFGAE-VVPGFQALSEG--CTPYDINQMLNCVGDHqAAMQIIREIINEEAAEWDVQHPIP 221
Cdd:pfam00607   1 VWEPLDFKLLKELKKAVKQYGPNSPyTMQLLEALASSnaLTPYDWRTLAKAVLSP-GQYLLWKAEWQELAQEQARRNQRA 79

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1127546997 222 GPLpagqlrEPRGSD-IAGTT--STVEEQIQWMFRPQNPVPvGNIYRRWIQIGLQK 274
Cdd:pfam00607  80 GPD------RGITLDmLTGTGqyATPQAQAQLPPEVLEQIK-ALALRAWKKLPPPG 128
PTZ00368 super family cl31762
universal minicircle sequence binding protein (UMSBP); Provisional
 350-431 3.09e-10

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: 58.66  E-value: 3.09e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1127546997 350 TACQGVGGPGQKARLMAEAlkevigpapipfAAAQQRKAFKCWNCGKEGHSARQCraPRRQG------CWKCGKPGHIMT 423
Cdd:PTZ00368    1 MVCYRCGGVGHQSRECPNS------------APAGAAKARPCYKCGEPGHLSREC--PSAPGgrgersCYNCGKTGHLSR 66


                  ....*...
gi 1127546997 424 NCPDRQAG 431
Cdd:PTZ00368   67 ECPEAPPG 74
 
Name Accession Description Interval E-value
Gag_p17 pfam00540
gag gene protein p17 (matrix protein); The matrix protein forms an icosahedral shell ...
 2-135 7.31e-49

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: 165.11  E-value: 7.31e-49
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1127546997   2 GARNSVLRGKKADELERIRLRPGGKKKYRLKHIVWAANKLDRFGLAESLLESKEGCQKILTVLDPMVPTGSENLKSLFNT 81
Cdd:pfam00540   1 GARASVLSGGELDKWEKIRLRPGGKKKYKLKHLVWASRELERFAVNPGLLETSEGCRKILGQLQPSLQTGSEGLRSLYNT 80

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1127546997  82 VCVIWCIHAEEKVKDTEGAKQIVRRH-------LVAETGTAEKMPSTSrPTAPSSEKGGNY 135
Cdd:pfam00540  81 VAVLYCVHQRIDVKDTKEALEKIEEEqnkskkkKTAVPPGAQQAANTG-GTGNSSGVSQNY 140
Gag_p24_C pfam19317
Gag protein p24 C-terminal domain; p24 forms inner protein layer of the nucleocapsid. ELISA ...
 278-351 5.66e-39

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: 136.46  E-value: 5.66e-39
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1127546997 278 MYNPTNILDIKQGPKEPFQSYVDRFYKSLRAEQTDPAVKNWMTQTLLVQNANPDCKLVLKGLGMNPTLEEMLTA 351
Cdd:pfam19317   1 GYKPTSLADIRQGPKEPYQDFVARLYDALRKEMPDGKAKDVITKQLAYENANPECQDLLKPLGKTGTLSDMIRA 74
Gag_p24 pfam00607
gag protein p24 N-terminal domain; p24 forms inner protein layer of the nucleocapsid. ELISA ...
 145-274 1.70e-11

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: 61.53  E-value: 1.70e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1127546997 145 THIPLSPRTLNAWVKLVEEKKFGAE-VVPGFQALSEG--CTPYDINQMLNCVGDHqAAMQIIREIINEEAAEWDVQHPIP 221
Cdd:pfam00607   1 VWEPLDFKLLKELKKAVKQYGPNSPyTMQLLEALASSnaLTPYDWRTLAKAVLSP-GQYLLWKAEWQELAQEQARRNQRA 79

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1127546997 222 GPLpagqlrEPRGSD-IAGTT--STVEEQIQWMFRPQNPVPvGNIYRRWIQIGLQK 274
Cdd:pfam00607  80 GPD------RGITLDmLTGTGqyATPQAQAQLPPEVLEQIK-ALALRAWKKLPPPG 128
PTZ00368 PTZ00368
universal minicircle sequence binding protein (UMSBP); Provisional
 350-431 3.09e-10

universal minicircle sequence binding protein (UMSBP); Provisional


Pssm-ID: 173561 [Multi-domain]  Cd Length: 148  Bit Score: 58.66  E-value: 3.09e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1127546997 350 TACQGVGGPGQKARLMAEAlkevigpapipfAAAQQRKAFKCWNCGKEGHSARQCraPRRQG------CWKCGKPGHIMT 423
Cdd:PTZ00368    1 MVCYRCGGVGHQSRECPNS------------APAGAAKARPCYKCGEPGHLSREC--PSAPGgrgersCYNCGKTGHLSR 66


                  ....*...
gi 1127546997 424 NCPDRQAG 431
Cdd:PTZ00368   67 ECPEAPPG 74
AIR1 COG5082
Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational ...
 387-426 3.54e-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: 44.84  E-value: 3.54e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 1127546997 387 KAFKCWNCGKEGHSARQCRAPRRQG--CWKCGKPGHIMTNCP 426
Cdd:COG5082    96 KPKKCYNCGETGHLSRDCNPSKDQQksCFDCNSTRHSSEDCP 137
ZnF_C2HC smart00343
zinc finger;
390-405 8.94e-05

zinc finger;


Pssm-ID: 197667 [Multi-domain]  Cd Length: 17  Bit Score: 39.35  E-value: 8.94e-05
                           10
                   ....*....|....*.
gi 1127546997  390 KCWNCGKEGHSARQCR 405
Cdd:smart00343   1 KCYNCGKEGHIARDCP 16
zf-CCHC pfam00098
Zinc knuckle; The zinc knuckle is a zinc binding motif composed of the the following ...
 390-404 3.20e-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: 35.20  E-value: 3.20e-03
                          10
                  ....*....|....*
gi 1127546997 390 KCWNCGKEGHSARQC 404
Cdd:pfam00098   2 KCYNCGEPGHIARDC 16
 
Name Accession Description Interval E-value
Gag_p17 pfam00540
gag gene protein p17 (matrix protein); The matrix protein forms an icosahedral shell ...
 2-135 7.31e-49

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: 165.11  E-value: 7.31e-49
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1127546997   2 GARNSVLRGKKADELERIRLRPGGKKKYRLKHIVWAANKLDRFGLAESLLESKEGCQKILTVLDPMVPTGSENLKSLFNT 81
Cdd:pfam00540   1 GARASVLSGGELDKWEKIRLRPGGKKKYKLKHLVWASRELERFAVNPGLLETSEGCRKILGQLQPSLQTGSEGLRSLYNT 80

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1127546997  82 VCVIWCIHAEEKVKDTEGAKQIVRRH-------LVAETGTAEKMPSTSrPTAPSSEKGGNY 135
Cdd:pfam00540  81 VAVLYCVHQRIDVKDTKEALEKIEEEqnkskkkKTAVPPGAQQAANTG-GTGNSSGVSQNY 140
Gag_p24_C pfam19317
Gag protein p24 C-terminal domain; p24 forms inner protein layer of the nucleocapsid. ELISA ...
 278-351 5.66e-39

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: 136.46  E-value: 5.66e-39
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1127546997 278 MYNPTNILDIKQGPKEPFQSYVDRFYKSLRAEQTDPAVKNWMTQTLLVQNANPDCKLVLKGLGMNPTLEEMLTA 351
Cdd:pfam19317   1 GYKPTSLADIRQGPKEPYQDFVARLYDALRKEMPDGKAKDVITKQLAYENANPECQDLLKPLGKTGTLSDMIRA 74
Gag_p24 pfam00607
gag protein p24 N-terminal domain; p24 forms inner protein layer of the nucleocapsid. ELISA ...
 145-274 1.70e-11

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: 61.53  E-value: 1.70e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1127546997 145 THIPLSPRTLNAWVKLVEEKKFGAE-VVPGFQALSEG--CTPYDINQMLNCVGDHqAAMQIIREIINEEAAEWDVQHPIP 221
Cdd:pfam00607   1 VWEPLDFKLLKELKKAVKQYGPNSPyTMQLLEALASSnaLTPYDWRTLAKAVLSP-GQYLLWKAEWQELAQEQARRNQRA 79

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1127546997 222 GPLpagqlrEPRGSD-IAGTT--STVEEQIQWMFRPQNPVPvGNIYRRWIQIGLQK 274
Cdd:pfam00607  80 GPD------RGITLDmLTGTGqyATPQAQAQLPPEVLEQIK-ALALRAWKKLPPPG 128
PTZ00368 PTZ00368
universal minicircle sequence binding protein (UMSBP); Provisional
 350-431 3.09e-10

universal minicircle sequence binding protein (UMSBP); Provisional


Pssm-ID: 173561 [Multi-domain]  Cd Length: 148  Bit Score: 58.66  E-value: 3.09e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1127546997 350 TACQGVGGPGQKARLMAEAlkevigpapipfAAAQQRKAFKCWNCGKEGHSARQCraPRRQG------CWKCGKPGHIMT 423
Cdd:PTZ00368    1 MVCYRCGGVGHQSRECPNS------------APAGAAKARPCYKCGEPGHLSREC--PSAPGgrgersCYNCGKTGHLSR 66


                  ....*...
gi 1127546997 424 NCPDRQAG 431
Cdd:PTZ00368   67 ECPEAPPG 74
PTZ00368 PTZ00368
universal minicircle sequence binding protein (UMSBP); Provisional
 379-428 4.63e-10

universal minicircle sequence binding protein (UMSBP); Provisional


Pssm-ID: 173561 [Multi-domain]  Cd Length: 148  Bit Score: 57.89  E-value: 4.63e-10
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1127546997 379 PFAAAQQRKAFKCWNCGKEGHSARQCRAPRRQG-----CWKCGKPGHIMTNCPDR 428
Cdd:PTZ00368   94 PNRAKGGAARRACYNCGGEGHISRDCPNAGKRPggdktCYNCGQTGHLSRDCPDK 148
PTZ00368 PTZ00368
universal minicircle sequence binding protein (UMSBP); Provisional
 390-426 2.95e-08

universal minicircle sequence binding protein (UMSBP); Provisional


Pssm-ID: 173561 [Multi-domain]  Cd Length: 148  Bit Score: 52.89  E-value: 2.95e-08
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 1127546997 390 KCWNCGKEGHSARQCRAPRRQG-----CWKCGKPGHIMTNCP 426
Cdd:PTZ00368   79 SCYNCGQTGHISRECPNRAKGGaarraCYNCGGEGHISRDCP 120
PTZ00368 PTZ00368
universal minicircle sequence binding protein (UMSBP); Provisional
 391-437 3.54e-08

universal minicircle sequence binding protein (UMSBP); Provisional


Pssm-ID: 173561 [Multi-domain]  Cd Length: 148  Bit Score: 52.50  E-value: 3.54e-08
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1127546997 391 CWNCGKEGHSARQCraPRRQG------CWKCGKPGHIMTNCPDRQAGFLGLGP 437
Cdd:PTZ00368   55 CYNCGKTGHLSREC--PEAPPgsgprsCYNCGQTGHISRECPNRAKGGAARRA 105
AIR1 COG5082
Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational ...
 387-426 3.54e-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: 44.84  E-value: 3.54e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 1127546997 387 KAFKCWNCGKEGHSARQCRAPRRQG--CWKCGKPGHIMTNCP 426
Cdd:COG5082    96 KPKKCYNCGETGHLSRDCNPSKDQQksCFDCNSTRHSSEDCP 137
AIR1 COG5082
Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational ...
 382-426 7.69e-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: 43.69  E-value: 7.69e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 1127546997 382 AAQQRKAFKCWNCGKEGHSARQCraPRRQgCWKCGKPGHIMTNCP 426
Cdd:COG5082    54 SAIREENPVCFNCGQNGHLRRDC--PHSI-CYNCSWDGHRSNHCP 95
ZnF_C2HC smart00343
zinc finger;
390-405 8.94e-05

zinc finger;


Pssm-ID: 197667 [Multi-domain]  Cd Length: 17  Bit Score: 39.35  E-value: 8.94e-05
                           10
                   ....*....|....*.
gi 1127546997  390 KCWNCGKEGHSARQCR 405
Cdd:smart00343   1 KCYNCGKEGHIARDCP 16
ZnF_C2HC smart00343
zinc finger;
411-426 4.72e-04

zinc finger;


Pssm-ID: 197667 [Multi-domain]  Cd Length: 17  Bit Score: 37.42  E-value: 4.72e-04
                           10
                   ....*....|....*.
gi 1127546997  411 GCWKCGKPGHIMTNCP 426
Cdd:smart00343   1 KCYNCGKEGHIARDCP 16
zf-CCHC pfam00098
Zinc knuckle; The zinc knuckle is a zinc binding motif composed of the the following ...
 390-404 3.20e-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: 35.20  E-value: 3.20e-03
                          10
                  ....*....|....*
gi 1127546997 390 KCWNCGKEGHSARQC 404
Cdd:pfam00098   2 KCYNCGEPGHIARDC 16
 
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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