NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|995585|gb|AAC54466|]
View 

core protein [Human immunodeficiency 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_p17 super family cl02892
gag gene protein p17 (matrix protein); The matrix protein forms an icosahedral shell ...
 2-139 5.07e-46

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: 157.41  E-value: 5.07e-46
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 995585       2 GARGSVLSGKKTDELEKVRLRPGGKKRYMLKHIVWAVNELERFGLAESRLGSKEGCRKIRKVLGPLVPTGSENLKSLYNT 81
Cdd:pfam00540   1 GARASVLSGGELDKWEKIRLRPGGKKKYKLKHLVWASRELERFAVNPGLLETSEGCRKILGQLQPSLQTGSEGLRSLYNT 80

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 995585      82 VCVIFCLHAEEKVKDTEEAKKIAQRH---LAADTEKMPAMSKPSKPTSRLAYPvQQIAGNY 139
Cdd:pfam00540  81 VAVLYCVHQRIDVKDTKEALEKIEEEqnkSKKKKTAVPPGAQQAANTGGTGNS-SGVSQNY 140
Gag_p24_C pfam19317
Gag protein p24 C-terminal domain; p24 forms inner protein layer of the nucleocapsid. ELISA ...
 273-346 6.83e-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: 136.07  E-value: 6.83e-39
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 995585     273 MYNPTNILDIKQGPKEPFQSYVDRFYKSLRAEQTDPAVKNWMTQTLLIQNANPDCKLVLKGLGMNPTLEEMLTA 346
Cdd:pfam19317   1 GYKPTSLADIRQGPKEPYQDFVARLYDALRKEMPDGKAKDVITKQLAYENANPECQDLLKPLGKTGTLSDMIRA 74
Gag_p24 pfam00607
gag protein p24 N-terminal domain; p24 forms inner protein layer of the nucleocapsid. ELISA ...
 141-269 5.55e-12

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: 63.07  E-value: 5.55e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 995585     141 HLPLSPRTLNAWVKLVEEKKFGAE-VVPGFQALSEG--CTPYDINQMLNCVGEHqAAMQIIREIINEEAADWDQQHPSPG 217
Cdd:pfam00607   2 WEPLDFKLLKELKKAVKQYGPNSPyTMQLLEALASSnaLTPYDWRTLAKAVLSP-GQYLLWKAEWQELAQEQARRNQRAG 80

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 995585     218 PMpagqlrEPRGSD-IAGTT--STVEEQIQWMYRPQNPVPvGNIYRRWIQLGLQK 269
Cdd:pfam00607  81 PD------RGITLDmLTGTGqyATPQAQAQLPPEVLEQIK-ALALRAWKKLPPPG 128
PTZ00368 super family cl31762
universal minicircle sequence binding protein (UMSBP); Provisional
 380-435 7.81e-11

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: 60.21  E-value: 7.81e-11
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 995585    380 PRAGKRTVTCWNCGKAGHTARQCkaPRRQG------CWKCGQQGHIMSKCPERQAGFLGFGP 435
Cdd:PTZ00368  46 APGGRGERSCYNCGKTGHLSREC--PEAPPgsgprsCYNCGQTGHISRECPNRAKGGAARRA 105
 
Name Accession Description Interval E-value
Gag_p17 pfam00540
gag gene protein p17 (matrix protein); The matrix protein forms an icosahedral shell ...
 2-139 5.07e-46

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: 157.41  E-value: 5.07e-46
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 995585       2 GARGSVLSGKKTDELEKVRLRPGGKKRYMLKHIVWAVNELERFGLAESRLGSKEGCRKIRKVLGPLVPTGSENLKSLYNT 81
Cdd:pfam00540   1 GARASVLSGGELDKWEKIRLRPGGKKKYKLKHLVWASRELERFAVNPGLLETSEGCRKILGQLQPSLQTGSEGLRSLYNT 80

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 995585      82 VCVIFCLHAEEKVKDTEEAKKIAQRH---LAADTEKMPAMSKPSKPTSRLAYPvQQIAGNY 139
Cdd:pfam00540  81 VAVLYCVHQRIDVKDTKEALEKIEEEqnkSKKKKTAVPPGAQQAANTGGTGNS-SGVSQNY 140
Gag_p24_C pfam19317
Gag protein p24 C-terminal domain; p24 forms inner protein layer of the nucleocapsid. ELISA ...
 273-346 6.83e-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: 136.07  E-value: 6.83e-39
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 995585     273 MYNPTNILDIKQGPKEPFQSYVDRFYKSLRAEQTDPAVKNWMTQTLLIQNANPDCKLVLKGLGMNPTLEEMLTA 346
Cdd:pfam19317   1 GYKPTSLADIRQGPKEPYQDFVARLYDALRKEMPDGKAKDVITKQLAYENANPECQDLLKPLGKTGTLSDMIRA 74
Gag_p24 pfam00607
gag protein p24 N-terminal domain; p24 forms inner protein layer of the nucleocapsid. ELISA ...
 141-269 5.55e-12

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: 63.07  E-value: 5.55e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 995585     141 HLPLSPRTLNAWVKLVEEKKFGAE-VVPGFQALSEG--CTPYDINQMLNCVGEHqAAMQIIREIINEEAADWDQQHPSPG 217
Cdd:pfam00607   2 WEPLDFKLLKELKKAVKQYGPNSPyTMQLLEALASSnaLTPYDWRTLAKAVLSP-GQYLLWKAEWQELAQEQARRNQRAG 80

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 995585     218 PMpagqlrEPRGSD-IAGTT--STVEEQIQWMYRPQNPVPvGNIYRRWIQLGLQK 269
Cdd:pfam00607  81 PD------RGITLDmLTGTGqyATPQAQAQLPPEVLEQIK-ALALRAWKKLPPPG 128
PTZ00368 PTZ00368
universal minicircle sequence binding protein (UMSBP); Provisional
 380-435 7.81e-11

universal minicircle sequence binding protein (UMSBP); Provisional


Pssm-ID: 173561 [Multi-domain]  Cd Length: 148  Bit Score: 60.21  E-value: 7.81e-11
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 995585    380 PRAGKRTVTCWNCGKAGHTARQCkaPRRQG------CWKCGQQGHIMSKCPERQAGFLGFGP 435
Cdd:PTZ00368  46 APGGRGERSCYNCGKTGHLSREC--PEAPPgsgprsCYNCGQTGHISRECPNRAKGGAARRA 105
AIR1 COG5082
Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational ...
 386-425 2.41e-06

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: 48.31  E-value: 2.41e-06
                        10        20        30        40
                ....*....|....*....|....*....|....*....|..
gi 995585   386 TVTCWNCGKAGHTARQCKAPRRQG--CWKCGQQGHIMSKCPE 425
Cdd:COG5082  97 PKKCYNCGETGHLSRDCNPSKDQQksCFDCNSTRHSSEDCPS 138
ZnF_C2HC smart00343
zinc finger;
388-403 1.12e-03

zinc finger;


Pssm-ID: 197667 [Multi-domain]  Cd Length: 17  Bit Score: 36.27  E-value: 1.12e-03
                           10
                   ....*....|....*.
gi 995585      388 TCWNCGKAGHTARQCK 403
Cdd:smart00343   1 KCYNCGKEGHIARDCP 16
zf-CCHC pfam00098
Zinc knuckle; The zinc knuckle is a zinc binding motif composed of the the following ...
 387-403 7.04e-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: 34.04  E-value: 7.04e-03
                          10
                  ....*....|....*..
gi 995585     387 VTCWNCGKAGHTARQCK 403
Cdd:pfam00098   1 GKCYNCGEPGHIARDCP 17
 
Name Accession Description Interval E-value
Gag_p17 pfam00540
gag gene protein p17 (matrix protein); The matrix protein forms an icosahedral shell ...
 2-139 5.07e-46

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: 157.41  E-value: 5.07e-46
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 995585       2 GARGSVLSGKKTDELEKVRLRPGGKKRYMLKHIVWAVNELERFGLAESRLGSKEGCRKIRKVLGPLVPTGSENLKSLYNT 81
Cdd:pfam00540   1 GARASVLSGGELDKWEKIRLRPGGKKKYKLKHLVWASRELERFAVNPGLLETSEGCRKILGQLQPSLQTGSEGLRSLYNT 80

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 995585      82 VCVIFCLHAEEKVKDTEEAKKIAQRH---LAADTEKMPAMSKPSKPTSRLAYPvQQIAGNY 139
Cdd:pfam00540  81 VAVLYCVHQRIDVKDTKEALEKIEEEqnkSKKKKTAVPPGAQQAANTGGTGNS-SGVSQNY 140
Gag_p24_C pfam19317
Gag protein p24 C-terminal domain; p24 forms inner protein layer of the nucleocapsid. ELISA ...
 273-346 6.83e-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: 136.07  E-value: 6.83e-39
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 995585     273 MYNPTNILDIKQGPKEPFQSYVDRFYKSLRAEQTDPAVKNWMTQTLLIQNANPDCKLVLKGLGMNPTLEEMLTA 346
Cdd:pfam19317   1 GYKPTSLADIRQGPKEPYQDFVARLYDALRKEMPDGKAKDVITKQLAYENANPECQDLLKPLGKTGTLSDMIRA 74
Gag_p24 pfam00607
gag protein p24 N-terminal domain; p24 forms inner protein layer of the nucleocapsid. ELISA ...
 141-269 5.55e-12

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: 63.07  E-value: 5.55e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 995585     141 HLPLSPRTLNAWVKLVEEKKFGAE-VVPGFQALSEG--CTPYDINQMLNCVGEHqAAMQIIREIINEEAADWDQQHPSPG 217
Cdd:pfam00607   2 WEPLDFKLLKELKKAVKQYGPNSPyTMQLLEALASSnaLTPYDWRTLAKAVLSP-GQYLLWKAEWQELAQEQARRNQRAG 80

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 995585     218 PMpagqlrEPRGSD-IAGTT--STVEEQIQWMYRPQNPVPvGNIYRRWIQLGLQK 269
Cdd:pfam00607  81 PD------RGITLDmLTGTGqyATPQAQAQLPPEVLEQIK-ALALRAWKKLPPPG 128
PTZ00368 PTZ00368
universal minicircle sequence binding protein (UMSBP); Provisional
 380-435 7.81e-11

universal minicircle sequence binding protein (UMSBP); Provisional


Pssm-ID: 173561 [Multi-domain]  Cd Length: 148  Bit Score: 60.21  E-value: 7.81e-11
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 995585    380 PRAGKRTVTCWNCGKAGHTARQCkaPRRQG------CWKCGQQGHIMSKCPERQAGFLGFGP 435
Cdd:PTZ00368  46 APGGRGERSCYNCGKTGHLSREC--PEAPPgsgprsCYNCGQTGHISRECPNRAKGGAARRA 105
PTZ00368 PTZ00368
universal minicircle sequence binding protein (UMSBP); Provisional
 380-426 3.25e-10

universal minicircle sequence binding protein (UMSBP); Provisional


Pssm-ID: 173561 [Multi-domain]  Cd Length: 148  Bit Score: 58.66  E-value: 3.25e-10
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 995585    380 PRAGKRTVTCWNCGKAGHTARQCKAPRRQG-----CWKCGQQGHIMSKCPER 426
Cdd:PTZ00368  97 AKGGAARRACYNCGGEGHISRDCPNAGKRPggdktCYNCGQTGHLSRDCPDK 148
PTZ00368 PTZ00368
universal minicircle sequence binding protein (UMSBP); Provisional
 381-435 3.03e-09

universal minicircle sequence binding protein (UMSBP); Provisional


Pssm-ID: 173561 [Multi-domain]  Cd Length: 148  Bit Score: 55.58  E-value: 3.03e-09
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 995585    381 RAGKRTVTCWNCGKAGHTARQCKAPRRQG-----CWKCGQQGHIMSKCPErqAGFLGFGP 435
Cdd:PTZ00368  72 PPGSGPRSCYNCGQTGHISRECPNRAKGGaarraCYNCGGEGHISRDCPN--AGKRPGGD 129
PTZ00368 PTZ00368
universal minicircle sequence binding protein (UMSBP); Provisional
 345-429 1.22e-08

universal minicircle sequence binding protein (UMSBP); Provisional


Pssm-ID: 173561 [Multi-domain]  Cd Length: 148  Bit Score: 54.04  E-value: 1.22e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 995585    345 TACQGIGGPGQKARLmaealkealTPSTNPFAAAQPRagkrtvTCWNCGKAGHTARQCKAPRR----QGCWKCGQQGHIM 420
Cdd:PTZ00368   1 MVCYRCGGVGHQSRE---------CPNSAPAGAAKAR------PCYKCGEPGHLSRECPSAPGgrgeRSCYNCGKTGHLS 65


                 ....*....
gi 995585    421 SKCPERQAG 429
Cdd:PTZ00368  66 RECPEAPPG 74
AIR1 COG5082
Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational ...
 386-425 2.41e-06

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: 48.31  E-value: 2.41e-06
                        10        20        30        40
                ....*....|....*....|....*....|....*....|..
gi 995585   386 TVTCWNCGKAGHTARQCKAPRRQG--CWKCGQQGHIMSKCPE 425
Cdd:COG5082  97 PKKCYNCGETGHLSRDCNPSKDQQksCFDCNSTRHSSEDCPS 138
AIR1 COG5082
Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational ...
 371-441 1.99e-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: 45.61  E-value: 1.99e-05
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 995585   371 STNPFAAAQPRAGKRtvtCWNCGKAGHTARQCKA----------------PRRQGCWKCGQQGHIMSKCPERqagflgfg 434
Cdd:COG5082  48 RSVEDVSAIREENPV---CFNCGQNGHLRRDCPHsicyncswdghrsnhcPKPKKCYNCGETGHLSRDCNPS-------- 116


                ....*..
gi 995585   435 PWGKKPR 441
Cdd:COG5082 117 KDQQKSC 123
ZnF_C2HC smart00343
zinc finger;
388-403 1.12e-03

zinc finger;


Pssm-ID: 197667 [Multi-domain]  Cd Length: 17  Bit Score: 36.27  E-value: 1.12e-03
                           10
                   ....*....|....*.
gi 995585      388 TCWNCGKAGHTARQCK 403
Cdd:smart00343   1 KCYNCGKEGHIARDCP 16
ZnF_C2HC smart00343
zinc finger;
409-425 1.74e-03

zinc finger;


Pssm-ID: 197667 [Multi-domain]  Cd Length: 17  Bit Score: 35.88  E-value: 1.74e-03
                           10
                   ....*....|....*..
gi 995585      409 GCWKCGQQGHIMSKCPE 425
Cdd:smart00343   1 KCYNCGKEGHIARDCPS 17
zf-CCHC pfam00098
Zinc knuckle; The zinc knuckle is a zinc binding motif composed of the the following ...
 387-403 7.04e-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: 34.04  E-value: 7.04e-03
                          10
                  ....*....|....*..
gi 995585     387 VTCWNCGKAGHTARQCK 403
Cdd:pfam00098   1 GKCYNCGEPGHIARDCP 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.
Help | Disclaimer | Write to the Help Desk
NCBI | NLM | NIH