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Conserved domains on  [gi|1316032224|sp|P25058|]
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RecName: Full=Gag polyprotein; Contains: RecName: Full=Matrix protein p15; Short=MA; Contains: RecName: Full=Capsid protein p24; Short=CA; Contains: RecName: Full=Nucleocapsid protein p12-gag

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
Gag_p24_C super family cl44748
Gag protein p24 C-terminal domain; p24 forms inner protein layer of the nucleocapsid. ELISA ...
 241-297 5.30e-17

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: 74.82  E-value: 5.30e-17
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1316032224 241 WSTIVQGPAESYVEFVNRLQISLADNLPDGVPKEPIIDSLSYANANKECQQILQGRG 297
Cdd:pfam19317   7 LADIRQGPKEPYQDFVARLYDALRKEMPDGKAKDVITKQLAYENANPECQDLLKPLG 63
Gag_p19 super family cl03491
Major core protein p19; p19 is a component of the inner protein layer of the viral ...
 4-44 1.67e-05

Major core protein p19; p19 is a component of the inner protein layer of the viral nucleocapsid.


The actual alignment was detected with superfamily member pfam02228:

Pssm-ID: 460500  Cd Length: 92  Bit Score: 43.02  E-value: 1.67e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|.
gi 1316032224   4 SPSYNPPAGISPSDWLNLLQSAQRLNPRPSPSDFTDLKNYI 44
Cdd:pfam02228  10 SPIPRPPRGLAAHHWLNFLQAAYRLEPGPSSYDFHQLKKFL 50
PTZ00368 super family cl31762
universal minicircle sequence binding protein (UMSBP); Provisional
 334-387 2.56e-05

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: 44.03  E-value: 2.56e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1316032224 334 PRQPAPKRPPPGPCYRCLKEGHWARDCPTKTTGPPPGPCPICKDPSHWKRDCPT 387
Cdd:PTZ00368   17 PNSAPAGAAKARPCYKCGEPGHLSRECPSAPGGRGERSCYNCGKTGHLSRECPE 70
Gag_p24 super family cl02908
gag protein p24 N-terminal domain; p24 forms inner protein layer of the nucleocapsid. ELISA ...
 119-233 6.83e-05

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: 42.27  E-value: 6.83e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1316032224 119 RHRAWALRELQDIKKEIENKAPGSQVWIQTLRLAILQADPTPADLEQLCQYIASPVDQT---------AHMTSLTAAIAA 189
Cdd:pfam00607   1 VWEPLDFKLLKELKKAVKQYGPNSPYTMQLLEALASSNALTPYDWRTLAKAVLSPGQYLlwkaewqelAQEQARRNQRAG 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*...
gi 1316032224 190 EAANT----LQGFNPkMGTLTQQSAQPNagDLRSQYQNLWLQAWKNLP 233
Cdd:pfam00607  81 PDRGItldmLTGTGQ-YATPQAQAQLPP--EVLEQIKALALRAWKKLP 125
 
Name Accession Description Interval E-value
Gag_p24_C pfam19317
Gag protein p24 C-terminal domain; p24 forms inner protein layer of the nucleocapsid. ELISA ...
 241-297 5.30e-17

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: 74.82  E-value: 5.30e-17
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1316032224 241 WSTIVQGPAESYVEFVNRLQISLADNLPDGVPKEPIIDSLSYANANKECQQILQGRG 297
Cdd:pfam19317   7 LADIRQGPKEPYQDFVARLYDALRKEMPDGKAKDVITKQLAYENANPECQDLLKPLG 63
Gag_p19 pfam02228
Major core protein p19; p19 is a component of the inner protein layer of the viral ...
 4-44 1.67e-05

Major core protein p19; p19 is a component of the inner protein layer of the viral nucleocapsid.


Pssm-ID: 460500  Cd Length: 92  Bit Score: 43.02  E-value: 1.67e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|.
gi 1316032224   4 SPSYNPPAGISPSDWLNLLQSAQRLNPRPSPSDFTDLKNYI 44
Cdd:pfam02228  10 SPIPRPPRGLAAHHWLNFLQAAYRLEPGPSSYDFHQLKKFL 50
PTZ00368 PTZ00368
universal minicircle sequence binding protein (UMSBP); Provisional
 334-387 2.56e-05

universal minicircle sequence binding protein (UMSBP); Provisional


Pssm-ID: 173561 [Multi-domain]  Cd Length: 148  Bit Score: 44.03  E-value: 2.56e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1316032224 334 PRQPAPKRPPPGPCYRCLKEGHWARDCPTKTTGPPPGPCPICKDPSHWKRDCPT 387
Cdd:PTZ00368   17 PNSAPAGAAKARPCYKCGEPGHLSRECPSAPGGRGERSCYNCGKTGHLSRECPE 70
ZnF_C2HC smart00343
zinc finger;
347-361 2.74e-05

zinc finger;


Pssm-ID: 197667 [Multi-domain]  Cd Length: 17  Bit Score: 40.50  E-value: 2.74e-05
                           10
                   ....*....|....*
gi 1316032224  347 CYRCLKEGHWARDCP 361
Cdd:smart00343   2 CYNCGKEGHIARDCP 16
Gag_p24 pfam00607
gag protein p24 N-terminal domain; p24 forms inner protein layer of the nucleocapsid. ELISA ...
 119-233 6.83e-05

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: 42.27  E-value: 6.83e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1316032224 119 RHRAWALRELQDIKKEIENKAPGSQVWIQTLRLAILQADPTPADLEQLCQYIASPVDQT---------AHMTSLTAAIAA 189
Cdd:pfam00607   1 VWEPLDFKLLKELKKAVKQYGPNSPYTMQLLEALASSNALTPYDWRTLAKAVLSPGQYLlwkaewqelAQEQARRNQRAG 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*...
gi 1316032224 190 EAANT----LQGFNPkMGTLTQQSAQPNagDLRSQYQNLWLQAWKNLP 233
Cdd:pfam00607  81 PDRGItldmLTGTGQ-YATPQAQAQLPP--EVLEQIKALALRAWKKLP 125
zf-CCHC pfam00098
Zinc knuckle; The zinc knuckle is a zinc binding motif composed of the the following ...
 347-361 4.09e-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: 4.09e-04
                          10
                  ....*....|....*
gi 1316032224 347 CYRCLKEGHWARDCP 361
Cdd:pfam00098   3 CYNCGEPGHIARDCP 17
 
Name Accession Description Interval E-value
Gag_p24_C pfam19317
Gag protein p24 C-terminal domain; p24 forms inner protein layer of the nucleocapsid. ELISA ...
 241-297 5.30e-17

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: 74.82  E-value: 5.30e-17
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1316032224 241 WSTIVQGPAESYVEFVNRLQISLADNLPDGVPKEPIIDSLSYANANKECQQILQGRG 297
Cdd:pfam19317   7 LADIRQGPKEPYQDFVARLYDALRKEMPDGKAKDVITKQLAYENANPECQDLLKPLG 63
Gag_p19 pfam02228
Major core protein p19; p19 is a component of the inner protein layer of the viral ...
 4-44 1.67e-05

Major core protein p19; p19 is a component of the inner protein layer of the viral nucleocapsid.


Pssm-ID: 460500  Cd Length: 92  Bit Score: 43.02  E-value: 1.67e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|.
gi 1316032224   4 SPSYNPPAGISPSDWLNLLQSAQRLNPRPSPSDFTDLKNYI 44
Cdd:pfam02228  10 SPIPRPPRGLAAHHWLNFLQAAYRLEPGPSSYDFHQLKKFL 50
PTZ00368 PTZ00368
universal minicircle sequence binding protein (UMSBP); Provisional
 334-387 2.56e-05

universal minicircle sequence binding protein (UMSBP); Provisional


Pssm-ID: 173561 [Multi-domain]  Cd Length: 148  Bit Score: 44.03  E-value: 2.56e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1316032224 334 PRQPAPKRPPPGPCYRCLKEGHWARDCPTKTTGPPPGPCPICKDPSHWKRDCPT 387
Cdd:PTZ00368   17 PNSAPAGAAKARPCYKCGEPGHLSRECPSAPGGRGERSCYNCGKTGHLSRECPE 70
ZnF_C2HC smart00343
zinc finger;
347-361 2.74e-05

zinc finger;


Pssm-ID: 197667 [Multi-domain]  Cd Length: 17  Bit Score: 40.50  E-value: 2.74e-05
                           10
                   ....*....|....*
gi 1316032224  347 CYRCLKEGHWARDCP 361
Cdd:smart00343   2 CYNCGKEGHIARDCP 16
Gag_p24 pfam00607
gag protein p24 N-terminal domain; p24 forms inner protein layer of the nucleocapsid. ELISA ...
 119-233 6.83e-05

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: 42.27  E-value: 6.83e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1316032224 119 RHRAWALRELQDIKKEIENKAPGSQVWIQTLRLAILQADPTPADLEQLCQYIASPVDQT---------AHMTSLTAAIAA 189
Cdd:pfam00607   1 VWEPLDFKLLKELKKAVKQYGPNSPYTMQLLEALASSNALTPYDWRTLAKAVLSPGQYLlwkaewqelAQEQARRNQRAG 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*...
gi 1316032224 190 EAANT----LQGFNPkMGTLTQQSAQPNagDLRSQYQNLWLQAWKNLP 233
Cdd:pfam00607  81 PDRGItldmLTGTGQ-YATPQAQAQLPP--EVLEQIKALALRAWKKLP 125
zf-CCHC pfam00098
Zinc knuckle; The zinc knuckle is a zinc binding motif composed of the the following ...
 347-361 4.09e-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: 4.09e-04
                          10
                  ....*....|....*
gi 1316032224 347 CYRCLKEGHWARDCP 361
Cdd:pfam00098   3 CYNCGEPGHIARDCP 17
PTZ00368 PTZ00368
universal minicircle sequence binding protein (UMSBP); Provisional
 347-386 1.96e-03

universal minicircle sequence binding protein (UMSBP); Provisional


Pssm-ID: 173561 [Multi-domain]  Cd Length: 148  Bit Score: 38.25  E-value: 1.96e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|
gi 1316032224 347 CYRCLKEGHWARDCPTKTTGPPPGPCPICKDPSHWKRDCP 386
Cdd:PTZ00368   55 CYNCGKTGHLSRECPEAPPGSGPRSCYNCGQTGHISRECP 94
PTZ00368 PTZ00368
universal minicircle sequence binding protein (UMSBP); Provisional
 347-386 2.83e-03

universal minicircle sequence binding protein (UMSBP); Provisional


Pssm-ID: 173561 [Multi-domain]  Cd Length: 148  Bit Score: 37.86  E-value: 2.83e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|.
gi 1316032224 347 CYRCLKEGHWARDCPTKTTGPPPGPC-PICKDPSHWKRDCP 386
Cdd:PTZ00368  106 CYNCGGEGHISRDCPNAGKRPGGDKTcYNCGQTGHLSRDCP 146
PTZ00368 PTZ00368
universal minicircle sequence binding protein (UMSBP); Provisional
 347-387 7.11e-03

universal minicircle sequence binding protein (UMSBP); Provisional


Pssm-ID: 173561 [Multi-domain]  Cd Length: 148  Bit Score: 36.71  E-value: 7.11e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 1316032224 347 CYRCLKEGHWARDCPTKTTGPPPGPCPICK--DPSHWKRDCPT 387
Cdd:PTZ00368    3 CYRCGGVGHQSRECPNSAPAGAAKARPCYKcgEPGHLSRECPS 45
 
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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