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Conserved domains on  [gi|41353552|gb|AAS01339|]
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gag protein [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 ...
 2-132 7.04e-67

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: 211.72  E-value: 7.04e-67
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41353552     2 GARASVLSGGKLDAWEKIRLRPGGKKKYRIKHLVWASRELERFALNPSLLETSEGCQQILEQLQPTLKTGSEELKSLYNT 81
Cdd:pfam00540   1 GARASVLSGGELDKWEKIRLRPGGKKKYKLKHLVWASRELERFAVNPGLLETSEGCRKILGQLQPSLQTGSEGLRSLYNT 80

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 41353552    82 VATLYCVHQRIEIKDTKEALDKIEEIQNENKQKT-------QQAAT--GTGSSSKVSQNY 132
Cdd:pfam00540  81 VAVLYCVHQRIDVKDTKEALEKIEEEQNKSKKKKtavppgaQQAANtgGTGNSSGVSQNY 140
Gag_p24_C pfam19317
Gag protein p24 C-terminal domain; p24 forms inner protein layer of the nucleocapsid. ELISA ...
 276-349 2.22e-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: 126.44  E-value: 2.22e-35
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 41353552   276 MYSPVSILDIRQGPKEPFRDYVDRFFKTLRAEQATQDVKNWMTETLLVQNANPDCKTILRALGSGATLEEMMTA 349
Cdd:pfam19317   1 GYKPTSLADIRQGPKEPYQDFVARLYDALRKEMPDGKAKDVITKQLAYENANPECQDLLKPLGKTGTLSDMIRA 74
Gag_p6 pfam08705
Gag protein p6; HIV protein p6 contains two late-budding domains (L domains) which are short ...
 447-482 5.80e-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: 5.80e-17
                          10        20        30
                  ....*....|....*....|....*....|....*.
gi 41353552   447 PQSRPEPSAPPAE*FGM*EEITPSLKQEQKDREQRP 482
Cdd:pfam08705   1 LQSRPEPTAPPAESFGFGEEITPSPKQEQKDKELYP 36
Gag_p24 pfam00607
gag protein p24 N-terminal domain; p24 forms inner protein layer of the nucleocapsid. ELISA ...
 143-250 1.70e-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: 64.22  E-value: 1.70e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41353552   143 THQSISPRTLNAWVKVIEEKAF-SPEVIPMFSALSEG--ATPQDLNMMLNIVGGHqAAMQMLKDTINEEAAEWDRlHPTQ 219
Cdd:pfam00607   1 VWEPLDFKLLKELKKAVKQYGPnSPYTMQLLEALASSnaLTPYDWRTLAKAVLSP-GQYLLWKAEWQELAQEQAR-RNQR 78

                          90       100       110
                  ....*....|....*....|....*....|....
gi 41353552   220 AGPfppgqmREPRGSD-IAGTT--STLQEQIGWM 250
Cdd:pfam00607  79 AGP------DRGITLDmLTGTGqyATPQAQAQLP 106
PTZ00368 super family cl31762
universal minicircle sequence binding protein (UMSBP); Provisional
 349-427 2.78e-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: 61.36  E-value: 2.78e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41353552  349 ACQGVGGPGHKARVLAEAMSQvqnanimmqkssfrGPKRIKCFNCGREGHLARNCRAPRKKG-----CWKCGKEGHQMKD 423
Cdd:PTZ00368  79 SCYNCGQTGHISRECPNRAKG--------------GAARRACYNCGGEGHISRDCPNAGKRPggdktCYNCGQTGHLSRD 144


                 ....
gi 41353552  424 CTER 427
Cdd:PTZ00368 145 CPDK 148
 
Name Accession Description Interval E-value
Gag_p17 pfam00540
gag gene protein p17 (matrix protein); The matrix protein forms an icosahedral shell ...
 2-132 7.04e-67

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: 211.72  E-value: 7.04e-67
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41353552     2 GARASVLSGGKLDAWEKIRLRPGGKKKYRIKHLVWASRELERFALNPSLLETSEGCQQILEQLQPTLKTGSEELKSLYNT 81
Cdd:pfam00540   1 GARASVLSGGELDKWEKIRLRPGGKKKYKLKHLVWASRELERFAVNPGLLETSEGCRKILGQLQPSLQTGSEGLRSLYNT 80

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 41353552    82 VATLYCVHQRIEIKDTKEALDKIEEIQNENKQKT-------QQAAT--GTGSSSKVSQNY 132
Cdd:pfam00540  81 VAVLYCVHQRIDVKDTKEALEKIEEEQNKSKKKKtavppgaQQAANtgGTGNSSGVSQNY 140
Gag_p24_C pfam19317
Gag protein p24 C-terminal domain; p24 forms inner protein layer of the nucleocapsid. ELISA ...
 276-349 2.22e-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: 126.44  E-value: 2.22e-35
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 41353552   276 MYSPVSILDIRQGPKEPFRDYVDRFFKTLRAEQATQDVKNWMTETLLVQNANPDCKTILRALGSGATLEEMMTA 349
Cdd:pfam19317   1 GYKPTSLADIRQGPKEPYQDFVARLYDALRKEMPDGKAKDVITKQLAYENANPECQDLLKPLGKTGTLSDMIRA 74
Gag_p6 pfam08705
Gag protein p6; HIV protein p6 contains two late-budding domains (L domains) which are short ...
 447-482 5.80e-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: 5.80e-17
                          10        20        30
                  ....*....|....*....|....*....|....*.
gi 41353552   447 PQSRPEPSAPPAE*FGM*EEITPSLKQEQKDREQRP 482
Cdd:pfam08705   1 LQSRPEPTAPPAESFGFGEEITPSPKQEQKDKELYP 36
Gag_p24 pfam00607
gag protein p24 N-terminal domain; p24 forms inner protein layer of the nucleocapsid. ELISA ...
 143-250 1.70e-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: 64.22  E-value: 1.70e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41353552   143 THQSISPRTLNAWVKVIEEKAF-SPEVIPMFSALSEG--ATPQDLNMMLNIVGGHqAAMQMLKDTINEEAAEWDRlHPTQ 219
Cdd:pfam00607   1 VWEPLDFKLLKELKKAVKQYGPnSPYTMQLLEALASSnaLTPYDWRTLAKAVLSP-GQYLLWKAEWQELAQEQAR-RNQR 78

                          90       100       110
                  ....*....|....*....|....*....|....
gi 41353552   220 AGPfppgqmREPRGSD-IAGTT--STLQEQIGWM 250
Cdd:pfam00607  79 AGP------DRGITLDmLTGTGqyATPQAQAQLP 106
PTZ00368 PTZ00368
universal minicircle sequence binding protein (UMSBP); Provisional
 349-427 2.78e-11

universal minicircle sequence binding protein (UMSBP); Provisional


Pssm-ID: 173561 [Multi-domain]  Cd Length: 148  Bit Score: 61.36  E-value: 2.78e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41353552  349 ACQGVGGPGHKARVLAEAMSQvqnanimmqkssfrGPKRIKCFNCGREGHLARNCRAPRKKG-----CWKCGKEGHQMKD 423
Cdd:PTZ00368  79 SCYNCGQTGHISRECPNRAKG--------------GAARRACYNCGGEGHISRDCPNAGKRPggdktCYNCGQTGHLSRD 144


                 ....
gi 41353552  424 CTER 427
Cdd:PTZ00368 145 CPDK 148
AIR1 COG5082
Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational ...
 318-462 5.47e-10

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: 58.71  E-value: 5.47e-10
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41353552 318 TETLLVQNANPdckTILRALGSGATLEEMMT-----------ACQGVGGPGHKAR----VLAEAMSQVQNanimmqkSSF 382
Cdd:COG5082  23 ANSIEESSSNP---NELRSLRSSGRYEDRSVedvsaireenpVCFNCGQNGHLRRdcphSICYNCSWDGH-------RSN 92

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41353552 383 RGPKRIKCFNCGREGHLARNC--RAPRKKGCWKCGKEGHQMKDCTErqanflgrIWPSSKGRPGNF-PQSRPEPSAPPAE 459
Cdd:COG5082  93 HCPKPKKCYNCGETGHLSRDCnpSKDQQKSCFDCNSTRHSSEDCPS--------IWKHYVLNNGDGhPIKKFCYSCGSAG 164


                ...
gi 41353552 460 *FG 462
Cdd:COG5082 165 HFG 167
ZnF_C2HC smart00343
zinc finger;
410-426 6.19e-05

zinc finger;


Pssm-ID: 197667 [Multi-domain]  Cd Length: 17  Bit Score: 39.73  E-value: 6.19e-05
                           10
                   ....*....|....*..
gi 41353552    410 GCWKCGKEGHQMKDCTE 426
Cdd:smart00343   1 KCYNCGKEGHIARDCPS 17
zf-CCHC pfam00098
Zinc knuckle; The zinc knuckle is a zinc binding motif composed of the the following ...
 388-403 1.06e-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: 39.05  E-value: 1.06e-04
                          10
                  ....*....|....*.
gi 41353552   388 IKCFNCGREGHLARNC 403
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 ...
 2-132 7.04e-67

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: 211.72  E-value: 7.04e-67
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41353552     2 GARASVLSGGKLDAWEKIRLRPGGKKKYRIKHLVWASRELERFALNPSLLETSEGCQQILEQLQPTLKTGSEELKSLYNT 81
Cdd:pfam00540   1 GARASVLSGGELDKWEKIRLRPGGKKKYKLKHLVWASRELERFAVNPGLLETSEGCRKILGQLQPSLQTGSEGLRSLYNT 80

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 41353552    82 VATLYCVHQRIEIKDTKEALDKIEEIQNENKQKT-------QQAAT--GTGSSSKVSQNY 132
Cdd:pfam00540  81 VAVLYCVHQRIDVKDTKEALEKIEEEQNKSKKKKtavppgaQQAANtgGTGNSSGVSQNY 140
Gag_p24_C pfam19317
Gag protein p24 C-terminal domain; p24 forms inner protein layer of the nucleocapsid. ELISA ...
 276-349 2.22e-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: 126.44  E-value: 2.22e-35
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 41353552   276 MYSPVSILDIRQGPKEPFRDYVDRFFKTLRAEQATQDVKNWMTETLLVQNANPDCKTILRALGSGATLEEMMTA 349
Cdd:pfam19317   1 GYKPTSLADIRQGPKEPYQDFVARLYDALRKEMPDGKAKDVITKQLAYENANPECQDLLKPLGKTGTLSDMIRA 74
Gag_p6 pfam08705
Gag protein p6; HIV protein p6 contains two late-budding domains (L domains) which are short ...
 447-482 5.80e-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: 5.80e-17
                          10        20        30
                  ....*....|....*....|....*....|....*.
gi 41353552   447 PQSRPEPSAPPAE*FGM*EEITPSLKQEQKDREQRP 482
Cdd:pfam08705   1 LQSRPEPTAPPAESFGFGEEITPSPKQEQKDKELYP 36
Gag_p24 pfam00607
gag protein p24 N-terminal domain; p24 forms inner protein layer of the nucleocapsid. ELISA ...
 143-250 1.70e-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: 64.22  E-value: 1.70e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41353552   143 THQSISPRTLNAWVKVIEEKAF-SPEVIPMFSALSEG--ATPQDLNMMLNIVGGHqAAMQMLKDTINEEAAEWDRlHPTQ 219
Cdd:pfam00607   1 VWEPLDFKLLKELKKAVKQYGPnSPYTMQLLEALASSnaLTPYDWRTLAKAVLSP-GQYLLWKAEWQELAQEQAR-RNQR 78

                          90       100       110
                  ....*....|....*....|....*....|....
gi 41353552   220 AGPfppgqmREPRGSD-IAGTT--STLQEQIGWM 250
Cdd:pfam00607  79 AGP------DRGITLDmLTGTGqyATPQAQAQLP 106
PTZ00368 PTZ00368
universal minicircle sequence binding protein (UMSBP); Provisional
 349-427 2.78e-11

universal minicircle sequence binding protein (UMSBP); Provisional


Pssm-ID: 173561 [Multi-domain]  Cd Length: 148  Bit Score: 61.36  E-value: 2.78e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41353552  349 ACQGVGGPGHKARVLAEAMSQvqnanimmqkssfrGPKRIKCFNCGREGHLARNCRAPRKKG-----CWKCGKEGHQMKD 423
Cdd:PTZ00368  79 SCYNCGQTGHISRECPNRAKG--------------GAARRACYNCGGEGHISRDCPNAGKRPggdktCYNCGQTGHLSRD 144


                 ....
gi 41353552  424 CTER 427
Cdd:PTZ00368 145 CPDK 148
PTZ00368 PTZ00368
universal minicircle sequence binding protein (UMSBP); Provisional
 349-444 3.57e-11

universal minicircle sequence binding protein (UMSBP); Provisional


Pssm-ID: 173561 [Multi-domain]  Cd Length: 148  Bit Score: 61.36  E-value: 3.57e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41353552  349 ACQGVGGPGHKARVLAEAMSqvqnanimmqkssfrGPKRIKCFNCGREGHLARNCRAPRKKG-----CWKCGKEGHQMKD 423
Cdd:PTZ00368  54 SCYNCGKTGHLSRECPEAPP---------------GSGPRSCYNCGQTGHISRECPNRAKGGaarraCYNCGGEGHISRD 118

                         90       100
                 ....*....|....*....|.
gi 41353552  424 CterqanflgriwPSSKGRPG 444
Cdd:PTZ00368 119 C------------PNAGKRPG 127
PTZ00368 PTZ00368
universal minicircle sequence binding protein (UMSBP); Provisional
 348-428 6.25e-11

universal minicircle sequence binding protein (UMSBP); Provisional


Pssm-ID: 173561 [Multi-domain]  Cd Length: 148  Bit Score: 60.59  E-value: 6.25e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41353552  348 TACQGVGGPGHKARVLAEAmsqvQNANIMmqkssfrgpKRIKCFNCGREGHLARNCRAPRKKG----CWKCGKEGHQMKD 423
Cdd:PTZ00368   1 MVCYRCGGVGHQSRECPNS----APAGAA---------KARPCYKCGEPGHLSRECPSAPGGRgersCYNCGKTGHLSRE 67


                 ....*
gi 41353552  424 CTERQ 428
Cdd:PTZ00368  68 CPEAP 72
AIR1 COG5082
Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational ...
 318-462 5.47e-10

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: 58.71  E-value: 5.47e-10
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41353552 318 TETLLVQNANPdckTILRALGSGATLEEMMT-----------ACQGVGGPGHKAR----VLAEAMSQVQNanimmqkSSF 382
Cdd:COG5082  23 ANSIEESSSNP---NELRSLRSSGRYEDRSVedvsaireenpVCFNCGQNGHLRRdcphSICYNCSWDGH-------RSN 92

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41353552 383 RGPKRIKCFNCGREGHLARNC--RAPRKKGCWKCGKEGHQMKDCTErqanflgrIWPSSKGRPGNF-PQSRPEPSAPPAE 459
Cdd:COG5082  93 HCPKPKKCYNCGETGHLSRDCnpSKDQQKSCFDCNSTRHSSEDCPS--------IWKHYVLNNGDGhPIKKFCYSCGSAG 164


                ...
gi 41353552 460 *FG 462
Cdd:COG5082 165 HFG 167
ZnF_C2HC smart00343
zinc finger;
410-426 6.19e-05

zinc finger;


Pssm-ID: 197667 [Multi-domain]  Cd Length: 17  Bit Score: 39.73  E-value: 6.19e-05
                           10
                   ....*....|....*..
gi 41353552    410 GCWKCGKEGHQMKDCTE 426
Cdd:smart00343   1 KCYNCGKEGHIARDCPS 17
zf-CCHC pfam00098
Zinc knuckle; The zinc knuckle is a zinc binding motif composed of the the following ...
 388-403 1.06e-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: 39.05  E-value: 1.06e-04
                          10
                  ....*....|....*.
gi 41353552   388 IKCFNCGREGHLARNC 403
Cdd:pfam00098   1 GKCYNCGEPGHIARDC 16
ZnF_C2HC smart00343
zinc finger;
389-404 1.41e-04

zinc finger;


Pssm-ID: 197667 [Multi-domain]  Cd Length: 17  Bit Score: 38.96  E-value: 1.41e-04
                           10
                   ....*....|....*.
gi 41353552    389 KCFNCGREGHLARNCR 404
Cdd:smart00343   1 KCYNCGKEGHIARDCP 16
zf-CCHC pfam00098
Zinc knuckle; The zinc knuckle is a zinc binding motif composed of the the following ...
 409-426 5.41e-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: 5.41e-04
                          10
                  ....*....|....*...
gi 41353552   409 KGCWKCGKEGHQMKDCTE 426
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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