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Conserved domains on  [gi|187371944|gb|ACD02839|]
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gag protein, partial [Human immunodeficiency virus 1]

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 ...
 1-95 1.59e-57

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: 187.07  E-value: 1.59e-57
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 187371944    1 ARASVLSGGELDRWEKIRLRPGGKKKYKLKHIVWASRELERFAVNPGLLETSEGCRKIIAQLQPSLQTGSEELRSLYNTV 80
Cdd:pfam00540   2 ARASVLSGGELDKWEKIRLRPGGKKKYKLKHLVWASRELERFAVNPGLLETSEGCRKILGQLQPSLQTGSEGLRSLYNTV 81

                          90
                  ....*....|....*
gi 187371944   81 AVLYCVHQKVEVKDT 95
Cdd:pfam00540  82 AVLYCVHQRIDVKDT 96
Gag_p24_C pfam19317
Gag protein p24 C-terminal domain; p24 forms inner protein layer of the nucleocapsid. ELISA ...
 270-343 6.30e-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: 124.90  E-value: 6.30e-35
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 187371944  270 MYSPVSILDIKQGPKEPFRDYVDRFFKTLRAEQATQEVKGWMTETLLVQNANPDCKTILRALGSGATLEEMMTA 343
Cdd:pfam19317   1 GYKPTSLADIRQGPKEPYQDFVARLYDALRKEMPDGKAKDVITKQLAYENANPECQDLLKPLGKTGTLSDMIRA 74
Gag_p6 pfam08705
Gag protein p6; HIV protein p6 contains two late-budding domains (L domains) which are short ...
 442-477 5.21e-17

Gag protein p6; HIV protein p6 contains two late-budding domains (L domains) which are short sequence motifs essential for viral particle release. p6 interacts with the endosomal sorting complex and represents a docking site for several cellular and binding factors. The PTAP motif interacts with the cellular budding factor TSG101. This domain is also found in some chimpanzee immunodeficiency virus (SIV-cpz) proteins.


:

Pssm-ID: 312289  Cd Length: 37  Bit Score: 74.18  E-value: 5.21e-17
                          10        20        30
                  ....*....|....*....|....*....|....*.
gi 187371944  442 LQNRTEPTAPPLESFGFGEKITPDPKQEQKDEGQYP 477
Cdd:pfam08705   1 LQSRPEPTAPPAESFGFGEEITPSPKQEQKDKELYP 36
Gag_p24 pfam00607
gag protein p24 N-terminal domain; p24 forms inner protein layer of the nucleocapsid. ELISA ...
 137-262 1.89e-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: 70.00  E-value: 1.89e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 187371944  137 VHQSLSPRTLNAWVKVIEEKGFN-PEVIPMFTALSEG--ATPQDLNTMLNTVGGHqAAMQMLKDTINEEAAEWDRlHPVQ 213
Cdd:pfam00607   1 VWEPLDFKLLKELKKAVKQYGPNsPYTMQLLEALASSnaLTPYDWRTLAKAVLSP-GQYLLWKAEWQELAQEQAR-RNQR 78

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 187371944  214 AGPIppgqmrEPRGSD-IAGTT--SNLQEQIQWmtsNPPV--PVGEI-YKRWIIL 262
Cdd:pfam00607  79 AGPD------RGITLDmLTGTGqyATPQAQAQL---PPEVleQIKALaLRAWKKL 124
PTZ00368 super family cl31762
universal minicircle sequence binding protein (UMSBP); Provisional
 343-422 3.97e-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: 58.28  E-value: 3.97e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 187371944 343 ACQGVGGPGHKARVLAEAMsqvtgttvmmqksnfKGQRRIVKCFNCGREGHIAKNCRAPRKKG-----CWKCGREGHQMK 417
Cdd:PTZ00368  79 SCYNCGQTGHISRECPNRA---------------KGGAARRACYNCGGEGHISRDCPNAGKRPggdktCYNCGQTGHLSR 143


                 ....*
gi 187371944 418 DCTER 422
Cdd:PTZ00368 144 DCPDK 148
 
Name Accession Description Interval E-value
Gag_p17 pfam00540
gag gene protein p17 (matrix protein); The matrix protein forms an icosahedral shell ...
 1-95 1.59e-57

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: 187.07  E-value: 1.59e-57
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 187371944    1 ARASVLSGGELDRWEKIRLRPGGKKKYKLKHIVWASRELERFAVNPGLLETSEGCRKIIAQLQPSLQTGSEELRSLYNTV 80
Cdd:pfam00540   2 ARASVLSGGELDKWEKIRLRPGGKKKYKLKHLVWASRELERFAVNPGLLETSEGCRKILGQLQPSLQTGSEGLRSLYNTV 81

                          90
                  ....*....|....*
gi 187371944   81 AVLYCVHQKVEVKDT 95
Cdd:pfam00540  82 AVLYCVHQRIDVKDT 96
Gag_p24_C pfam19317
Gag protein p24 C-terminal domain; p24 forms inner protein layer of the nucleocapsid. ELISA ...
 270-343 6.30e-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: 124.90  E-value: 6.30e-35
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 187371944  270 MYSPVSILDIKQGPKEPFRDYVDRFFKTLRAEQATQEVKGWMTETLLVQNANPDCKTILRALGSGATLEEMMTA 343
Cdd:pfam19317   1 GYKPTSLADIRQGPKEPYQDFVARLYDALRKEMPDGKAKDVITKQLAYENANPECQDLLKPLGKTGTLSDMIRA 74
Gag_p6 pfam08705
Gag protein p6; HIV protein p6 contains two late-budding domains (L domains) which are short ...
 442-477 5.21e-17

Gag protein p6; HIV protein p6 contains two late-budding domains (L domains) which are short sequence motifs essential for viral particle release. p6 interacts with the endosomal sorting complex and represents a docking site for several cellular and binding factors. The PTAP motif interacts with the cellular budding factor TSG101. This domain is also found in some chimpanzee immunodeficiency virus (SIV-cpz) proteins.


Pssm-ID: 312289  Cd Length: 37  Bit Score: 74.18  E-value: 5.21e-17
                          10        20        30
                  ....*....|....*....|....*....|....*.
gi 187371944  442 LQNRTEPTAPPLESFGFGEKITPDPKQEQKDEGQYP 477
Cdd:pfam08705   1 LQSRPEPTAPPAESFGFGEEITPSPKQEQKDKELYP 36
Gag_p24 pfam00607
gag protein p24 N-terminal domain; p24 forms inner protein layer of the nucleocapsid. ELISA ...
 137-262 1.89e-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: 70.00  E-value: 1.89e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 187371944  137 VHQSLSPRTLNAWVKVIEEKGFN-PEVIPMFTALSEG--ATPQDLNTMLNTVGGHqAAMQMLKDTINEEAAEWDRlHPVQ 213
Cdd:pfam00607   1 VWEPLDFKLLKELKKAVKQYGPNsPYTMQLLEALASSnaLTPYDWRTLAKAVLSP-GQYLLWKAEWQELAQEQAR-RNQR 78

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 187371944  214 AGPIppgqmrEPRGSD-IAGTT--SNLQEQIQWmtsNPPV--PVGEI-YKRWIIL 262
Cdd:pfam00607  79 AGPD------RGITLDmLTGTGqyATPQAQAQL---PPEVleQIKALaLRAWKKL 124
PTZ00368 PTZ00368
universal minicircle sequence binding protein (UMSBP); Provisional
 343-422 3.97e-10

universal minicircle sequence binding protein (UMSBP); Provisional


Pssm-ID: 173561 [Multi-domain]  Cd Length: 148  Bit Score: 58.28  E-value: 3.97e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 187371944 343 ACQGVGGPGHKARVLAEAMsqvtgttvmmqksnfKGQRRIVKCFNCGREGHIAKNCRAPRKKG-----CWKCGREGHQMK 417
Cdd:PTZ00368  79 SCYNCGQTGHISRECPNRA---------------KGGAARRACYNCGGEGHISRDCPNAGKRPggdktCYNCGQTGHLSR 143


                 ....*
gi 187371944 418 DCTER 422
Cdd:PTZ00368 144 DCPDK 148
AIR1 COG5082
Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational ...
 384-422 5.22e-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: 47.15  E-value: 5.22e-06
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 187371944 384 KCFNCGREGHIAKNC----------------RAPRKKGCWKCGREGHQMKDCTER 422
Cdd:COG5082   62 VCFNCGQNGHLRRDCphsicyncswdghrsnHCPKPKKCYNCGETGHLSRDCNPS 116
ZnF_C2HC smart00343
zinc finger;
384-399 1.74e-04

zinc finger;


Pssm-ID: 197667 [Multi-domain]  Cd Length: 17  Bit Score: 38.58  E-value: 1.74e-04
                           10
                   ....*....|....*.
gi 187371944   384 KCFNCGREGHIAKNCR 399
Cdd:smart00343   1 KCYNCGKEGHIARDCP 16
zf-CCHC pfam00098
Zinc knuckle; The zinc knuckle is a zinc binding motif composed of the the following ...
 383-398 2.04e-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: 38.28  E-value: 2.04e-04
                          10
                  ....*....|....*.
gi 187371944  383 VKCFNCGREGHIAKNC 398
Cdd:pfam00098   1 GKCYNCGEPGHIARDC 16
 
Name Accession Description Interval E-value
Gag_p17 pfam00540
gag gene protein p17 (matrix protein); The matrix protein forms an icosahedral shell ...
 1-95 1.59e-57

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: 187.07  E-value: 1.59e-57
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 187371944    1 ARASVLSGGELDRWEKIRLRPGGKKKYKLKHIVWASRELERFAVNPGLLETSEGCRKIIAQLQPSLQTGSEELRSLYNTV 80
Cdd:pfam00540   2 ARASVLSGGELDKWEKIRLRPGGKKKYKLKHLVWASRELERFAVNPGLLETSEGCRKILGQLQPSLQTGSEGLRSLYNTV 81

                          90
                  ....*....|....*
gi 187371944   81 AVLYCVHQKVEVKDT 95
Cdd:pfam00540  82 AVLYCVHQRIDVKDT 96
Gag_p24_C pfam19317
Gag protein p24 C-terminal domain; p24 forms inner protein layer of the nucleocapsid. ELISA ...
 270-343 6.30e-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: 124.90  E-value: 6.30e-35
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 187371944  270 MYSPVSILDIKQGPKEPFRDYVDRFFKTLRAEQATQEVKGWMTETLLVQNANPDCKTILRALGSGATLEEMMTA 343
Cdd:pfam19317   1 GYKPTSLADIRQGPKEPYQDFVARLYDALRKEMPDGKAKDVITKQLAYENANPECQDLLKPLGKTGTLSDMIRA 74
Gag_p6 pfam08705
Gag protein p6; HIV protein p6 contains two late-budding domains (L domains) which are short ...
 442-477 5.21e-17

Gag protein p6; HIV protein p6 contains two late-budding domains (L domains) which are short sequence motifs essential for viral particle release. p6 interacts with the endosomal sorting complex and represents a docking site for several cellular and binding factors. The PTAP motif interacts with the cellular budding factor TSG101. This domain is also found in some chimpanzee immunodeficiency virus (SIV-cpz) proteins.


Pssm-ID: 312289  Cd Length: 37  Bit Score: 74.18  E-value: 5.21e-17
                          10        20        30
                  ....*....|....*....|....*....|....*.
gi 187371944  442 LQNRTEPTAPPLESFGFGEKITPDPKQEQKDEGQYP 477
Cdd:pfam08705   1 LQSRPEPTAPPAESFGFGEEITPSPKQEQKDKELYP 36
Gag_p24 pfam00607
gag protein p24 N-terminal domain; p24 forms inner protein layer of the nucleocapsid. ELISA ...
 137-262 1.89e-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: 70.00  E-value: 1.89e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 187371944  137 VHQSLSPRTLNAWVKVIEEKGFN-PEVIPMFTALSEG--ATPQDLNTMLNTVGGHqAAMQMLKDTINEEAAEWDRlHPVQ 213
Cdd:pfam00607   1 VWEPLDFKLLKELKKAVKQYGPNsPYTMQLLEALASSnaLTPYDWRTLAKAVLSP-GQYLLWKAEWQELAQEQAR-RNQR 78

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 187371944  214 AGPIppgqmrEPRGSD-IAGTT--SNLQEQIQWmtsNPPV--PVGEI-YKRWIIL 262
Cdd:pfam00607  79 AGPD------RGITLDmLTGTGqyATPQAQAQL---PPEVleQIKALaLRAWKKL 124
PTZ00368 PTZ00368
universal minicircle sequence binding protein (UMSBP); Provisional
 343-422 3.97e-10

universal minicircle sequence binding protein (UMSBP); Provisional


Pssm-ID: 173561 [Multi-domain]  Cd Length: 148  Bit Score: 58.28  E-value: 3.97e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 187371944 343 ACQGVGGPGHKARVLAEAMsqvtgttvmmqksnfKGQRRIVKCFNCGREGHIAKNCRAPRKKG-----CWKCGREGHQMK 417
Cdd:PTZ00368  79 SCYNCGQTGHISRECPNRA---------------KGGAARRACYNCGGEGHISRDCPNAGKRPggdktCYNCGQTGHLSR 143


                 ....*
gi 187371944 418 DCTER 422
Cdd:PTZ00368 144 DCPDK 148
PTZ00368 PTZ00368
universal minicircle sequence binding protein (UMSBP); Provisional
 343-439 1.32e-09

universal minicircle sequence binding protein (UMSBP); Provisional


Pssm-ID: 173561 [Multi-domain]  Cd Length: 148  Bit Score: 56.74  E-value: 1.32e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 187371944 343 ACQGVGGPGHKARVLAEAMSQVTGttvmmqksnfkgqrriVKCFNCGREGHIAKNCRAPRKKG-----CWKCGREGHQMK 417
Cdd:PTZ00368  54 SCYNCGKTGHLSRECPEAPPGSGP----------------RSCYNCGQTGHISRECPNRAKGGaarraCYNCGGEGHISR 117

                         90       100
                 ....*....|....*....|..
gi 187371944 418 DCterqanflgkvwPSNRGRPG 439
Cdd:PTZ00368 118 DC------------PNAGKRPG 127
PTZ00368 PTZ00368
universal minicircle sequence binding protein (UMSBP); Provisional
 342-441 4.62e-09

universal minicircle sequence binding protein (UMSBP); Provisional


Pssm-ID: 173561 [Multi-domain]  Cd Length: 148  Bit Score: 55.20  E-value: 4.62e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 187371944 342 TACQGVGGPGHKARVLAEAmsqvtgTTVMMQKSnfkgqrriVKCFNCGREGHIAKNCRAPRKKG----CWKCGREGHQMK 417
Cdd:PTZ00368   1 MVCYRCGGVGHQSRECPNS------APAGAAKA--------RPCYKCGEPGHLSRECPSAPGGRgersCYNCGKTGHLSR 66

                         90       100
                 ....*....|....*....|....
gi 187371944 418 DCTERQANFlGKVWPSNRGRPGNF 441
Cdd:PTZ00368  67 ECPEAPPGS-GPRSCYNCGQTGHI 89
AIR1 COG5082
Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational ...
 384-422 5.22e-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: 47.15  E-value: 5.22e-06
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 187371944 384 KCFNCGREGHIAKNC----------------RAPRKKGCWKCGREGHQMKDCTER 422
Cdd:COG5082   62 VCFNCGQNGHLRRDCphsicyncswdghrsnHCPKPKKCYNCGETGHLSRDCNPS 116
AIR1 COG5082
Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational ...
 312-441 3.21e-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: 3.21e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 187371944 312 TETLLVQNANPdckTILRALGSGATLEEMMT-----------ACQGVGGPGHKARvlaeamsqvTGTTVMMQKSNFKGQR 380
Cdd:COG5082   23 ANSIEESSSNP---NELRSLRSSGRYEDRSVedvsaireenpVCFNCGQNGHLRR---------DCPHSICYNCSWDGHR 90

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 187371944 381 RI-----VKCFNCGREGHIAKNC--RAPRKKGCWKCGREGHQMKDCTErqanflgkVWPSNRGRPGNF 441
Cdd:COG5082   91 SNhcpkpKKCYNCGETGHLSRDCnpSKDQQKSCFDCNSTRHSSEDCPS--------IWKHYVLNNGDG 150
ZnF_C2HC smart00343
zinc finger;
384-399 1.74e-04

zinc finger;


Pssm-ID: 197667 [Multi-domain]  Cd Length: 17  Bit Score: 38.58  E-value: 1.74e-04
                           10
                   ....*....|....*.
gi 187371944   384 KCFNCGREGHIAKNCR 399
Cdd:smart00343   1 KCYNCGKEGHIARDCP 16
zf-CCHC pfam00098
Zinc knuckle; The zinc knuckle is a zinc binding motif composed of the the following ...
 383-398 2.04e-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: 38.28  E-value: 2.04e-04
                          10
                  ....*....|....*.
gi 187371944  383 VKCFNCGREGHIAKNC 398
Cdd:pfam00098   1 GKCYNCGEPGHIARDC 16
ZnF_C2HC smart00343
zinc finger;
405-421 4.75e-04

zinc finger;


Pssm-ID: 197667 [Multi-domain]  Cd Length: 17  Bit Score: 37.42  E-value: 4.75e-04
                           10
                   ....*....|....*..
gi 187371944   405 GCWKCGREGHQMKDCTE 421
Cdd:smart00343   1 KCYNCGKEGHIARDCPS 17
AIR1 COG5082
Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational ...
 380-422 7.14e-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: 40.60  E-value: 7.14e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 187371944 380 RRIVKCFNCGREGHIAKNCRA-------------PRKKGCWKCGREGHQMKDCTER 422
Cdd:COG5082  118 DQQKSCFDCNSTRHSSEDCPSiwkhyvlnngdghPIKKFCYSCGSAGHFGDDCKEP 173
zf-CCHC pfam00098
Zinc knuckle; The zinc knuckle is a zinc binding motif composed of the the following ...
 404-421 1.07e-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: 36.35  E-value: 1.07e-03
                          10
                  ....*....|....*...
gi 187371944  404 KGCWKCGREGHQMKDCTE 421
Cdd:pfam00098   1 GKCYNCGEPGHIARDCPK 18
 
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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