NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|91772079|ref|YP_567048|]
View 

gag protein [Simian T-lymphotropic virus 2]

Protein Classification

Graphical summary

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

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 ...
 1-91 5.00e-47

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: 156.66  E-value: 5.00e-47
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 91772079     1 MGQTYGLSSSPIPKAPRGLSTHHWLNFLQAAYRLQPGPSDFDFQQLRRFLKLALKTPIWLNPIDYSLLASLIPKGYPGRT 80
Cdd:pfam02228   1 MGKIFSRSASPIPRPPRGLAAHHWLNFLQAAYRLEPGPSSYDFHQLKKFLKIALETPVWICPINYSLLASLLPKGYPGRV 80

                          90
                  ....*....|.
gi 91772079    81 IEIINVLIKNQ 91
Cdd:pfam02228  81 NEILHILIQTQ 91
Gag_p24_C super family cl44748
Gag protein p24 C-terminal domain; p24 forms inner protein layer of the nucleocapsid. ELISA ...
 263-336 9.31e-31

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: 112.96  E-value: 9.31e-31
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 91772079   263 TRDPSWAAILQGLEEPYCAFVERLNVALDNGLPEGTPKEPILRSLAYSNANKDCQKLLQARGHTnSPLGDMLRA 336
Cdd:pfam19317   2 YKPTSLADIRQGPKEPYQDFVARLYDALRKEMPDGKAKDVITKQLAYENANPECQDLLKPLGKT-GTLSDMIRA 74
Gag_p24 pfam00607
gag protein p24 N-terminal domain; p24 forms inner protein layer of the nucleocapsid. ELISA ...
 146-263 2.70e-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: 69.23  E-value: 2.70e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 91772079   146 AHSPWQMKDLQAIKQEVSTSAPGSPQFMQTVRLAIQQFDPTAKDLQDLLQyLCSS-----LVVSLHHQQFHTLITEAETR 220
Cdd:pfam00607   1 VWEPLDFKLLKELKKAVKQYGPNSPYTMQLLEALASSNALTPYDWRTLAK-AVLSpgqylLWKAEWQELAQEQARRNQRA 79

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|..
gi 91772079   221 G---------MTGYNPMAGPlRMQANNPaqQGLRREYQNLWLAAFSALPGNT 263
Cdd:pfam00607  80 GpdrgitldmLTGTGQYATP-QAQAQLP--PEVLEQIKALALRAWKKLPPPG 128
PTZ00368 super family cl31762
universal minicircle sequence binding protein (UMSBP); Provisional
 353-407 2.36e-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: 47.11  E-value: 2.36e-06
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 91772079  353 PRKPPPT----QPCFRCGKTGHWSRDCTLPRPPPGPCPLCK--DPSHWKRDCPQfKPPPTE 407
Cdd:PTZ00368  17 PNSAPAGaakaRPCYKCGEPGHLSRECPSAPGGRGERSCYNcgKTGHLSRECPE-APPGSG 76
 
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 ...
 1-91 5.00e-47

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: 156.66  E-value: 5.00e-47
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 91772079     1 MGQTYGLSSSPIPKAPRGLSTHHWLNFLQAAYRLQPGPSDFDFQQLRRFLKLALKTPIWLNPIDYSLLASLIPKGYPGRT 80
Cdd:pfam02228   1 MGKIFSRSASPIPRPPRGLAAHHWLNFLQAAYRLEPGPSSYDFHQLKKFLKIALETPVWICPINYSLLASLLPKGYPGRV 80

                          90
                  ....*....|.
gi 91772079    81 IEIINVLIKNQ 91
Cdd:pfam02228  81 NEILHILIQTQ 91
Gag_p24_C pfam19317
Gag protein p24 C-terminal domain; p24 forms inner protein layer of the nucleocapsid. ELISA ...
 263-336 9.31e-31

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: 112.96  E-value: 9.31e-31
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 91772079   263 TRDPSWAAILQGLEEPYCAFVERLNVALDNGLPEGTPKEPILRSLAYSNANKDCQKLLQARGHTnSPLGDMLRA 336
Cdd:pfam19317   2 YKPTSLADIRQGPKEPYQDFVARLYDALRKEMPDGKAKDVITKQLAYENANPECQDLLKPLGKT-GTLSDMIRA 74
Gag_p24 pfam00607
gag protein p24 N-terminal domain; p24 forms inner protein layer of the nucleocapsid. ELISA ...
 146-263 2.70e-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: 69.23  E-value: 2.70e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 91772079   146 AHSPWQMKDLQAIKQEVSTSAPGSPQFMQTVRLAIQQFDPTAKDLQDLLQyLCSS-----LVVSLHHQQFHTLITEAETR 220
Cdd:pfam00607   1 VWEPLDFKLLKELKKAVKQYGPNSPYTMQLLEALASSNALTPYDWRTLAK-AVLSpgqylLWKAEWQELAQEQARRNQRA 79

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|..
gi 91772079   221 G---------MTGYNPMAGPlRMQANNPaqQGLRREYQNLWLAAFSALPGNT 263
Cdd:pfam00607  80 GpdrgitldmLTGTGQYATP-QAQAQLP--PEVLEQIKALALRAWKKLPPPG 128
PTZ00368 PTZ00368
universal minicircle sequence binding protein (UMSBP); Provisional
 353-407 2.36e-06

universal minicircle sequence binding protein (UMSBP); Provisional


Pssm-ID: 173561 [Multi-domain]  Cd Length: 148  Bit Score: 47.11  E-value: 2.36e-06
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 91772079  353 PRKPPPT----QPCFRCGKTGHWSRDCTLPRPPPGPCPLCK--DPSHWKRDCPQfKPPPTE 407
Cdd:PTZ00368  17 PNSAPAGaakaRPCYKCGEPGHLSRECPSAPGGRGERSCYNcgKTGHLSRECPE-APPGSG 76
ZnF_C2HC smart00343
zinc finger;
362-376 2.81e-05

zinc finger;


Pssm-ID: 197667 [Multi-domain]  Cd Length: 17  Bit Score: 40.50  E-value: 2.81e-05
                           10
                   ....*....|....*
gi 91772079    362 CFRCGKTGHWSRDCT 376
Cdd:smart00343   2 CYNCGKEGHIARDCP 16
zf-CCHC pfam00098
Zinc knuckle; The zinc knuckle is a zinc binding motif composed of the the following ...
 360-376 4.60e-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: 40.20  E-value: 4.60e-05
                          10
                  ....*....|....*..
gi 91772079   360 QPCFRCGKTGHWSRDCT 376
Cdd:pfam00098   1 GKCYNCGEPGHIARDCP 17
AIR1 COG5082
Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational ...
 353-400 5.56e-03

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: 37.91  E-value: 5.56e-03
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*...
gi 91772079 353 PRKPPPTQPCFRCGKTGHWSRDCTLPRPPPGPCplckdPSHWKRDCPQ 400
Cdd:COG5082  54 SAIREENPVCFNCGQNGHLRRDCPHSICYNCSW-----DGHRSNHCPK 96
 
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 ...
 1-91 5.00e-47

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: 156.66  E-value: 5.00e-47
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 91772079     1 MGQTYGLSSSPIPKAPRGLSTHHWLNFLQAAYRLQPGPSDFDFQQLRRFLKLALKTPIWLNPIDYSLLASLIPKGYPGRT 80
Cdd:pfam02228   1 MGKIFSRSASPIPRPPRGLAAHHWLNFLQAAYRLEPGPSSYDFHQLKKFLKIALETPVWICPINYSLLASLLPKGYPGRV 80

                          90
                  ....*....|.
gi 91772079    81 IEIINVLIKNQ 91
Cdd:pfam02228  81 NEILHILIQTQ 91
Gag_p24_C pfam19317
Gag protein p24 C-terminal domain; p24 forms inner protein layer of the nucleocapsid. ELISA ...
 263-336 9.31e-31

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: 112.96  E-value: 9.31e-31
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 91772079   263 TRDPSWAAILQGLEEPYCAFVERLNVALDNGLPEGTPKEPILRSLAYSNANKDCQKLLQARGHTnSPLGDMLRA 336
Cdd:pfam19317   2 YKPTSLADIRQGPKEPYQDFVARLYDALRKEMPDGKAKDVITKQLAYENANPECQDLLKPLGKT-GTLSDMIRA 74
Gag_p24 pfam00607
gag protein p24 N-terminal domain; p24 forms inner protein layer of the nucleocapsid. ELISA ...
 146-263 2.70e-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: 69.23  E-value: 2.70e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 91772079   146 AHSPWQMKDLQAIKQEVSTSAPGSPQFMQTVRLAIQQFDPTAKDLQDLLQyLCSS-----LVVSLHHQQFHTLITEAETR 220
Cdd:pfam00607   1 VWEPLDFKLLKELKKAVKQYGPNSPYTMQLLEALASSNALTPYDWRTLAK-AVLSpgqylLWKAEWQELAQEQARRNQRA 79

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|..
gi 91772079   221 G---------MTGYNPMAGPlRMQANNPaqQGLRREYQNLWLAAFSALPGNT 263
Cdd:pfam00607  80 GpdrgitldmLTGTGQYATP-QAQAQLP--PEVLEQIKALALRAWKKLPPPG 128
PTZ00368 PTZ00368
universal minicircle sequence binding protein (UMSBP); Provisional
 353-407 2.36e-06

universal minicircle sequence binding protein (UMSBP); Provisional


Pssm-ID: 173561 [Multi-domain]  Cd Length: 148  Bit Score: 47.11  E-value: 2.36e-06
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 91772079  353 PRKPPPT----QPCFRCGKTGHWSRDCTLPRPPPGPCPLCK--DPSHWKRDCPQfKPPPTE 407
Cdd:PTZ00368  17 PNSAPAGaakaRPCYKCGEPGHLSRECPSAPGGRGERSCYNcgKTGHLSRECPE-APPGSG 76
ZnF_C2HC smart00343
zinc finger;
362-376 2.81e-05

zinc finger;


Pssm-ID: 197667 [Multi-domain]  Cd Length: 17  Bit Score: 40.50  E-value: 2.81e-05
                           10
                   ....*....|....*
gi 91772079    362 CFRCGKTGHWSRDCT 376
Cdd:smart00343   2 CYNCGKEGHIARDCP 16
zf-CCHC pfam00098
Zinc knuckle; The zinc knuckle is a zinc binding motif composed of the the following ...
 360-376 4.60e-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: 40.20  E-value: 4.60e-05
                          10
                  ....*....|....*..
gi 91772079   360 QPCFRCGKTGHWSRDCT 376
Cdd:pfam00098   1 GKCYNCGEPGHIARDCP 17
PTZ00368 PTZ00368
universal minicircle sequence binding protein (UMSBP); Provisional
 353-399 7.73e-05

universal minicircle sequence binding protein (UMSBP); Provisional


Pssm-ID: 173561 [Multi-domain]  Cd Length: 148  Bit Score: 42.49  E-value: 7.73e-05
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*....
gi 91772079  353 PRKPPPTQPCFRCGKTGHWSRDCTLPRPPPGPCPLCK--DPSHWKRDCP 399
Cdd:PTZ00368  46 APGGRGERSCYNCGKTGHLSRECPEAPPGSGPRSCYNcgQTGHISRECP 94
PTZ00368 PTZ00368
universal minicircle sequence binding protein (UMSBP); Provisional
 362-407 5.10e-04

universal minicircle sequence binding protein (UMSBP); Provisional


Pssm-ID: 173561 [Multi-domain]  Cd Length: 148  Bit Score: 40.18  E-value: 5.10e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|
gi 91772079  362 CFRCGKTGHWSRDCTLPRPPPGPCPLC----KDPSHWKRDCPQFKPPPTE 407
Cdd:PTZ00368   3 CYRCGGVGHQSRECPNSAPAGAAKARPcykcGEPGHLSRECPSAPGGRGE 52
PTZ00368 PTZ00368
universal minicircle sequence binding protein (UMSBP); Provisional
 353-408 1.18e-03

universal minicircle sequence binding protein (UMSBP); Provisional


Pssm-ID: 173561 [Multi-domain]  Cd Length: 148  Bit Score: 39.40  E-value: 1.18e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 91772079  353 PRKPPPTQP--CFRCGKTGHWSRDCTLPRPPPGPCPL---CKDPSHWKRDCPQFKPPPTEE 408
Cdd:PTZ00368  69 PEAPPGSGPrsCYNCGQTGHISRECPNRAKGGAARRAcynCGGEGHISRDCPNAGKRPGGD 129
AIR1 COG5082
Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational ...
 353-400 5.56e-03

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: 37.91  E-value: 5.56e-03
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*...
gi 91772079 353 PRKPPPTQPCFRCGKTGHWSRDCTLPRPPPGPCplckdPSHWKRDCPQ 400
Cdd:COG5082  54 SAIREENPVCFNCGQNGHLRRDCPHSICYNCSW-----DGHRSNHCPK 96
PTZ00368 PTZ00368
universal minicircle sequence binding protein (UMSBP); Provisional
 353-399 6.14e-03

universal minicircle sequence binding protein (UMSBP); Provisional


Pssm-ID: 173561 [Multi-domain]  Cd Length: 148  Bit Score: 37.09  E-value: 6.14e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|
gi 91772079  353 PRKPPPTQPCFRCGKTGHWSRDCTLPRPPPGPCPLCK---DPSHWKRDCP 399
Cdd:PTZ00368  97 AKGGAARRACYNCGGEGHISRDCPNAGKRPGGDKTCYncgQTGHLSRDCP 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.
Help | Disclaimer | Write to the Help Desk
NCBI | NLM | NIH