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Conserved domains on  [gi|120855|sp|P03345|]
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RecName: Full=Gag polyprotein; AltName: Full=Pr53Gag; Contains: RecName: Full=Matrix protein p19; Short=MA; Contains: RecName: Full=Capsid protein p24; Short=CA; Contains: RecName: Full=Nucleocapsid protein p15-gag; Short=NC-gag

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
Gag_p19 super family cl03491
Major core protein p19; p19 is a component of the inner protein layer of the viral ...
 1-92 2.18e-53

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: 173.22  E-value: 2.18e-53
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 120855       1 MGQIFSRSASPIPRPPRGLAAHHWLNFLQAAYRLEPGPSSYDFHQLKKFLKIALETPARICPINYSLLASLLPKGYPGRV 80
Cdd:pfam02228   1 MGKIFSRSASPIPRPPRGLAAHHWLNFLQAAYRLEPGPSSYDFHQLKKFLKIALETPVWICPINYSLLASLLPKGYPGRV 80

                          90
                  ....*....|..
gi 120855      81 NEILHILIQTQA 92
Cdd:pfam02228  81 NEILHILIQTQA 92
Gag_p24_C pfam19317
Gag protein p24 C-terminal domain; p24 forms inner protein layer of the nucleocapsid. ELISA ...
 257-331 4.78e-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: 124.51  E-value: 4.78e-35
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 120855     257 SAKDPSWASILQGLEEPYHAFVERLNIALDNGLPEGTPKDPILRSLAYSNANKECQKLLQARGHTnSPLGDMLRA 331
Cdd:pfam19317   1 GYKPTSLADIRQGPKEPYQDFVARLYDALRKEMPDGKAKDVITKQLAYENANPECQDLLKPLGKT-GTLSDMIRA 74
Gag_p24 pfam00607
gag protein p24 N-terminal domain; p24 forms inner protein layer of the nucleocapsid. ELISA ...
 141-258 6.95e-13

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: 65.38  E-value: 6.95e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 120855     141 NHRPWQMKDLQAIKQEVSQAAPGSPQFMQTIRLAVQQFDPTAKDLQDLLQyLCSS-----LVASLHHQQLDSLISEAETR 215
Cdd:pfam00607   1 VWEPLDFKLLKELKKAVKQYGPNSPYTMQLLEALASSNALTPYDWRTLAK-AVLSpgqylLWKAEWQELAQEQARRNQRA 79

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|..
gi 120855     216 G---------ITGYNPLAGPlRVQANNPqqQGLRREYQQLWLAAFAALPGSA 258
Cdd:pfam00607  80 GpdrgitldmLTGTGQYATP-QAQAQLP--PEVLEQIKALALRAWKKLPPPG 128
PTZ00368 super family cl31762
universal minicircle sequence binding protein (UMSBP); Provisional
 357-398 3.50e-06

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: 46.72  E-value: 3.50e-06
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....
gi 120855    357 CFRCGKAGHWSRDCTQPRPPPGPCPL--CQDPTHWKRDCPRLKP 398
Cdd:PTZ00368  30 CYKCGEPGHLSRECPSAPGGRGERSCynCGKTGHLSRECPEAPP 73
 
Name Accession Description Interval E-value
Gag_p19 pfam02228
Major core protein p19; p19 is a component of the inner protein layer of the viral ...
 1-92 2.18e-53

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: 173.22  E-value: 2.18e-53
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 120855       1 MGQIFSRSASPIPRPPRGLAAHHWLNFLQAAYRLEPGPSSYDFHQLKKFLKIALETPARICPINYSLLASLLPKGYPGRV 80
Cdd:pfam02228   1 MGKIFSRSASPIPRPPRGLAAHHWLNFLQAAYRLEPGPSSYDFHQLKKFLKIALETPVWICPINYSLLASLLPKGYPGRV 80

                          90
                  ....*....|..
gi 120855      81 NEILHILIQTQA 92
Cdd:pfam02228  81 NEILHILIQTQA 92
Gag_p24_C pfam19317
Gag protein p24 C-terminal domain; p24 forms inner protein layer of the nucleocapsid. ELISA ...
 257-331 4.78e-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: 124.51  E-value: 4.78e-35
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 120855     257 SAKDPSWASILQGLEEPYHAFVERLNIALDNGLPEGTPKDPILRSLAYSNANKECQKLLQARGHTnSPLGDMLRA 331
Cdd:pfam19317   1 GYKPTSLADIRQGPKEPYQDFVARLYDALRKEMPDGKAKDVITKQLAYENANPECQDLLKPLGKT-GTLSDMIRA 74
Gag_p24 pfam00607
gag protein p24 N-terminal domain; p24 forms inner protein layer of the nucleocapsid. ELISA ...
 141-258 6.95e-13

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: 65.38  E-value: 6.95e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 120855     141 NHRPWQMKDLQAIKQEVSQAAPGSPQFMQTIRLAVQQFDPTAKDLQDLLQyLCSS-----LVASLHHQQLDSLISEAETR 215
Cdd:pfam00607   1 VWEPLDFKLLKELKKAVKQYGPNSPYTMQLLEALASSNALTPYDWRTLAK-AVLSpgqylLWKAEWQELAQEQARRNQRA 79

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|..
gi 120855     216 G---------ITGYNPLAGPlRVQANNPqqQGLRREYQQLWLAAFAALPGSA 258
Cdd:pfam00607  80 GpdrgitldmLTGTGQYATP-QAQAQLP--PEVLEQIKALALRAWKKLPPPG 128
PTZ00368 PTZ00368
universal minicircle sequence binding protein (UMSBP); Provisional
 357-398 3.50e-06

universal minicircle sequence binding protein (UMSBP); Provisional


Pssm-ID: 173561 [Multi-domain]  Cd Length: 148  Bit Score: 46.72  E-value: 3.50e-06
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....
gi 120855    357 CFRCGKAGHWSRDCTQPRPPPGPCPL--CQDPTHWKRDCPRLKP 398
Cdd:PTZ00368  30 CYKCGEPGHLSRECPSAPGGRGERSCynCGKTGHLSRECPEAPP 73
ZnF_C2HC smart00343
zinc finger;
357-372 3.89e-05

zinc finger;


Pssm-ID: 197667 [Multi-domain]  Cd Length: 17  Bit Score: 40.12  E-value: 3.89e-05
                           10
                   ....*....|....*.
gi 120855      357 CFRCGKAGHWSRDCTQ 372
Cdd:smart00343   2 CYNCGKEGHIARDCPS 17
zf-CCHC pfam00098
Zinc knuckle; The zinc knuckle is a zinc binding motif composed of the the following ...
 357-372 8.38e-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: 8.38e-05
                          10
                  ....*....|....*.
gi 120855     357 CFRCGKAGHWSRDCTQ 372
Cdd:pfam00098   3 CYNCGEPGHIARDCPK 18
AIR1 COG5082
Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational ...
 357-397 2.58e-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: 41.76  E-value: 2.58e-04
                        10        20        30        40
                ....*....|....*....|....*....|....*....|.
gi 120855   357 CFRCGKAGHWSRDCTQPRPPPGPCPLCQDPTHWKRDCPRLK 397
Cdd:COG5082 100 CYNCGETGHLSRDCNPSKDQQKSCFDCNSTRHSSEDCPSIW 140
 
Name Accession Description Interval E-value
Gag_p19 pfam02228
Major core protein p19; p19 is a component of the inner protein layer of the viral ...
 1-92 2.18e-53

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: 173.22  E-value: 2.18e-53
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 120855       1 MGQIFSRSASPIPRPPRGLAAHHWLNFLQAAYRLEPGPSSYDFHQLKKFLKIALETPARICPINYSLLASLLPKGYPGRV 80
Cdd:pfam02228   1 MGKIFSRSASPIPRPPRGLAAHHWLNFLQAAYRLEPGPSSYDFHQLKKFLKIALETPVWICPINYSLLASLLPKGYPGRV 80

                          90
                  ....*....|..
gi 120855      81 NEILHILIQTQA 92
Cdd:pfam02228  81 NEILHILIQTQA 92
Gag_p24_C pfam19317
Gag protein p24 C-terminal domain; p24 forms inner protein layer of the nucleocapsid. ELISA ...
 257-331 4.78e-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: 124.51  E-value: 4.78e-35
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 120855     257 SAKDPSWASILQGLEEPYHAFVERLNIALDNGLPEGTPKDPILRSLAYSNANKECQKLLQARGHTnSPLGDMLRA 331
Cdd:pfam19317   1 GYKPTSLADIRQGPKEPYQDFVARLYDALRKEMPDGKAKDVITKQLAYENANPECQDLLKPLGKT-GTLSDMIRA 74
Gag_p24 pfam00607
gag protein p24 N-terminal domain; p24 forms inner protein layer of the nucleocapsid. ELISA ...
 141-258 6.95e-13

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: 65.38  E-value: 6.95e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 120855     141 NHRPWQMKDLQAIKQEVSQAAPGSPQFMQTIRLAVQQFDPTAKDLQDLLQyLCSS-----LVASLHHQQLDSLISEAETR 215
Cdd:pfam00607   1 VWEPLDFKLLKELKKAVKQYGPNSPYTMQLLEALASSNALTPYDWRTLAK-AVLSpgqylLWKAEWQELAQEQARRNQRA 79

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|..
gi 120855     216 G---------ITGYNPLAGPlRVQANNPqqQGLRREYQQLWLAAFAALPGSA 258
Cdd:pfam00607  80 GpdrgitldmLTGTGQYATP-QAQAQLP--PEVLEQIKALALRAWKKLPPPG 128
PTZ00368 PTZ00368
universal minicircle sequence binding protein (UMSBP); Provisional
 357-398 3.50e-06

universal minicircle sequence binding protein (UMSBP); Provisional


Pssm-ID: 173561 [Multi-domain]  Cd Length: 148  Bit Score: 46.72  E-value: 3.50e-06
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....
gi 120855    357 CFRCGKAGHWSRDCTQPRPPPGPCPL--CQDPTHWKRDCPRLKP 398
Cdd:PTZ00368  30 CYKCGEPGHLSRECPSAPGGRGERSCynCGKTGHLSRECPEAPP 73
ZnF_C2HC smart00343
zinc finger;
357-372 3.89e-05

zinc finger;


Pssm-ID: 197667 [Multi-domain]  Cd Length: 17  Bit Score: 40.12  E-value: 3.89e-05
                           10
                   ....*....|....*.
gi 120855      357 CFRCGKAGHWSRDCTQ 372
Cdd:smart00343   2 CYNCGKEGHIARDCPS 17
zf-CCHC pfam00098
Zinc knuckle; The zinc knuckle is a zinc binding motif composed of the the following ...
 357-372 8.38e-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: 8.38e-05
                          10
                  ....*....|....*.
gi 120855     357 CFRCGKAGHWSRDCTQ 372
Cdd:pfam00098   3 CYNCGEPGHIARDCPK 18
PTZ00368 PTZ00368
universal minicircle sequence binding protein (UMSBP); Provisional
 357-395 1.10e-04

universal minicircle sequence binding protein (UMSBP); Provisional


Pssm-ID: 173561 [Multi-domain]  Cd Length: 148  Bit Score: 42.10  E-value: 1.10e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|.
gi 120855    357 CFRCGKAGHWSRDCTQPRPPPGPCPL--CQDPTHWKRDCPR 395
Cdd:PTZ00368  55 CYNCGKTGHLSRECPEAPPGSGPRSCynCGQTGHISRECPN 95
PTZ00368 PTZ00368
universal minicircle sequence binding protein (UMSBP); Provisional
 357-395 1.24e-04

universal minicircle sequence binding protein (UMSBP); Provisional


Pssm-ID: 173561 [Multi-domain]  Cd Length: 148  Bit Score: 42.10  E-value: 1.24e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|...
gi 120855    357 CFRCGKAGHWSRDCTQPRPPPGPCPL----CQDPTHWKRDCPR 395
Cdd:PTZ00368   3 CYRCGGVGHQSRECPNSAPAGAAKARpcykCGEPGHLSRECPS 45
PTZ00368 PTZ00368
universal minicircle sequence binding protein (UMSBP); Provisional
 309-394 2.32e-04

universal minicircle sequence binding protein (UMSBP); Provisional


Pssm-ID: 173561 [Multi-domain]  Cd Length: 148  Bit Score: 41.33  E-value: 2.32e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 120855    309 KECQKLLQARG-----HTNSPlGDMLRACQTWTPKDKTKvlvvqpkkpppnqPCFRCGKAGHWSRDCTQPRPPPGPCP-- 381
Cdd:PTZ00368  41 RECPSAPGGRGerscyNCGKT-GHLSRECPEAPPGSGPR-------------SCYNCGQTGHISRECPNRAKGGAARRac 106

                         90
                 ....*....|....
gi 120855    382 -LCQDPTHWKRDCP 394
Cdd:PTZ00368 107 yNCGGEGHISRDCP 120
AIR1 COG5082
Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational ...
 357-397 2.58e-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: 41.76  E-value: 2.58e-04
                        10        20        30        40
                ....*....|....*....|....*....|....*....|.
gi 120855   357 CFRCGKAGHWSRDCTQPRPPPGPCPLCQDPTHWKRDCPRLK 397
Cdd:COG5082 100 CYNCGETGHLSRDCNPSKDQQKSCFDCNSTRHSSEDCPSIW 140
PTZ00368 PTZ00368
universal minicircle sequence binding protein (UMSBP); Provisional
 357-394 9.75e-04

universal minicircle sequence binding protein (UMSBP); Provisional


Pssm-ID: 173561 [Multi-domain]  Cd Length: 148  Bit Score: 39.40  E-value: 9.75e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|.
gi 120855    357 CFRCGKAGHWSRDCTQPRPPPGPCPLCQ---DPTHWKRDCP 394
Cdd:PTZ00368 106 CYNCGGEGHISRDCPNAGKRPGGDKTCYncgQTGHLSRDCP 146
 
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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