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Conserved domains on  [gi|270381459|emb|CBI68307|]
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gag polyprotein, partial [HIV-1 M:B 2007_HIV_010]

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 ...
 2-133 1.65e-68

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: 215.96  E-value: 1.65e-68
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 270381459    2 GARASILSGGQLDRWEKIRLRPGGKKQYKLKHLVWASRELERFAVNPGLLETSEGCKQILKQLYPSLQTGSEELKSLYNT 81
Cdd:pfam00540   1 GARASVLSGGELDKWEKIRLRPGGKKKYKLKHLVWASRELERFAVNPGLLETSEGCRKILGQLQPSLQTGSEGLRSLYNT 80

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 270381459   82 VAVLYCVHQRIGIKDTKEALDKIEEEQNKSKQKAQ------QAAADTGDSS--SKVSQNY 133
Cdd:pfam00540  81 VAVLYCVHQRIDVKDTKEALEKIEEEQNKSKKKKTavppgaQQAANTGGTGnsSGVSQNY 140
Gag_p24_C pfam19317
Gag protein p24 C-terminal domain; p24 forms inner protein layer of the nucleocapsid. ELISA ...
 277-350 8.91e-38

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: 132.99  E-value: 8.91e-38
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 270381459  277 MYSPTSILDIKQGPKEPFRDYVDRFYKTLRAEQASQDVKNWMTETLMIQNANPDCKTILKALGPGATLEEMMTA 350
Cdd:pfam19317   1 GYKPTSLADIRQGPKEPYQDFVARLYDALRKEMPDGKAKDVITKQLAYENANPECQDLLKPLGKTGTLSDMIRA 74
Gag_p6 pfam08705
Gag protein p6; HIV protein p6 contains two late-budding domains (L domains) which are short ...
 451-488 1.40e-16

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: 73.03  E-value: 1.40e-16
                          10        20        30
                  ....*....|....*....|....*....|....*...
gi 270381459  451 PQSRTEPTAPPEESFRFGEETTaPSQKQEKIDKEPYPL 488
Cdd:pfam08705   1 LQSRPEPTAPPAESFGFGEEIT-PSPKQEQKDKELYPL 37
Gag_p24 pfam00607
gag protein p24 N-terminal domain; p24 forms inner protein layer of the nucleocapsid. ELISA ...
 144-251 1.70e-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: 67.30  E-value: 1.70e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 270381459  144 VHQAISPRTLNAWVKVVEEKAF-SPEVIPMFSALSEG--ATPQDLNTMLNTVGGHqAAMQMLKETINEEAAEWDRlHPVH 220
Cdd:pfam00607   1 VWEPLDFKLLKELKKAVKQYGPnSPYTMQLLEALASSnaLTPYDWRTLAKAVLSP-GQYLLWKAEWQELAQEQAR-RNQR 78

                          90       100       110
                  ....*....|....*....|....*....|....
gi 270381459  221 AGPIapgqmrEPRGSD-IAGTT--STLQEQIGWM 251
Cdd:pfam00607  79 AGPD------RGITLDmLTGTGqyATPQAQAQLP 106
PTZ00368 super family cl31762
universal minicircle sequence binding protein (UMSBP); Provisional
 350-431 1.26e-12

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: 65.21  E-value: 1.26e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 270381459 350 ACQGVGGPSHKARVLAEAMSQVTNQSATIMMQKGNY--------RNQRKTVKCFNCGKEGHVARNCRAPRKKG-----CW 416
Cdd:PTZ00368  54 SCYNCGKTGHLSRECPEAPPGSGPRSCYNCGQTGHIsrecpnraKGGAARRACYNCGGEGHISRDCPNAGKRPggdktCY 133

                         90
                 ....*....|....*
gi 270381459 417 KCGKEGHQMKDCPER 431
Cdd:PTZ00368 134 NCGQTGHLSRDCPDK 148
 
Name Accession Description Interval E-value
Gag_p17 pfam00540
gag gene protein p17 (matrix protein); The matrix protein forms an icosahedral shell ...
 2-133 1.65e-68

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: 215.96  E-value: 1.65e-68
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 270381459    2 GARASILSGGQLDRWEKIRLRPGGKKQYKLKHLVWASRELERFAVNPGLLETSEGCKQILKQLYPSLQTGSEELKSLYNT 81
Cdd:pfam00540   1 GARASVLSGGELDKWEKIRLRPGGKKKYKLKHLVWASRELERFAVNPGLLETSEGCRKILGQLQPSLQTGSEGLRSLYNT 80

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 270381459   82 VAVLYCVHQRIGIKDTKEALDKIEEEQNKSKQKAQ------QAAADTGDSS--SKVSQNY 133
Cdd:pfam00540  81 VAVLYCVHQRIDVKDTKEALEKIEEEQNKSKKKKTavppgaQQAANTGGTGnsSGVSQNY 140
Gag_p24_C pfam19317
Gag protein p24 C-terminal domain; p24 forms inner protein layer of the nucleocapsid. ELISA ...
 277-350 8.91e-38

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: 132.99  E-value: 8.91e-38
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 270381459  277 MYSPTSILDIKQGPKEPFRDYVDRFYKTLRAEQASQDVKNWMTETLMIQNANPDCKTILKALGPGATLEEMMTA 350
Cdd:pfam19317   1 GYKPTSLADIRQGPKEPYQDFVARLYDALRKEMPDGKAKDVITKQLAYENANPECQDLLKPLGKTGTLSDMIRA 74
Gag_p6 pfam08705
Gag protein p6; HIV protein p6 contains two late-budding domains (L domains) which are short ...
 451-488 1.40e-16

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: 73.03  E-value: 1.40e-16
                          10        20        30
                  ....*....|....*....|....*....|....*...
gi 270381459  451 PQSRTEPTAPPEESFRFGEETTaPSQKQEKIDKEPYPL 488
Cdd:pfam08705   1 LQSRPEPTAPPAESFGFGEEIT-PSPKQEQKDKELYPL 37
Gag_p24 pfam00607
gag protein p24 N-terminal domain; p24 forms inner protein layer of the nucleocapsid. ELISA ...
 144-251 1.70e-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: 67.30  E-value: 1.70e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 270381459  144 VHQAISPRTLNAWVKVVEEKAF-SPEVIPMFSALSEG--ATPQDLNTMLNTVGGHqAAMQMLKETINEEAAEWDRlHPVH 220
Cdd:pfam00607   1 VWEPLDFKLLKELKKAVKQYGPnSPYTMQLLEALASSnaLTPYDWRTLAKAVLSP-GQYLLWKAEWQELAQEQAR-RNQR 78

                          90       100       110
                  ....*....|....*....|....*....|....
gi 270381459  221 AGPIapgqmrEPRGSD-IAGTT--STLQEQIGWM 251
Cdd:pfam00607  79 AGPD------RGITLDmLTGTGqyATPQAQAQLP 106
PTZ00368 PTZ00368
universal minicircle sequence binding protein (UMSBP); Provisional
 350-431 1.26e-12

universal minicircle sequence binding protein (UMSBP); Provisional


Pssm-ID: 173561 [Multi-domain]  Cd Length: 148  Bit Score: 65.21  E-value: 1.26e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 270381459 350 ACQGVGGPSHKARVLAEAMSQVTNQSATIMMQKGNY--------RNQRKTVKCFNCGKEGHVARNCRAPRKKG-----CW 416
Cdd:PTZ00368  54 SCYNCGKTGHLSRECPEAPPGSGPRSCYNCGQTGHIsrecpnraKGGAARRACYNCGGEGHISRDCPNAGKRPggdktCY 133

                         90
                 ....*....|....*
gi 270381459 417 KCGKEGHQMKDCPER 431
Cdd:PTZ00368 134 NCGQTGHLSRDCPDK 148
AIR1 COG5082
Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational ...
 381-454 8.80e-07

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: 49.46  E-value: 8.80e-07
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 270381459 381 QKGNYRNQR-KTVKCFNCGKEGHVARNC--RAPRKKGCWKCGKEGHQMKDCPErqanflgkIWPSHKGRPGNFPQSR 454
Cdd:COG5082   86 WDGHRSNHCpKPKKCYNCGETGHLSRDCnpSKDQQKSCFDCNSTRHSSEDCPS--------IWKHYVLNNGDGHPIK 154
ZnF_C2HC smart00343
zinc finger;
414-430 1.88e-05

zinc finger;


Pssm-ID: 197667 [Multi-domain]  Cd Length: 17  Bit Score: 41.27  E-value: 1.88e-05
                           10
                   ....*....|....*..
gi 270381459   414 GCWKCGKEGHQMKDCPE 430
Cdd:smart00343   1 KCYNCGKEGHIARDCPS 17
zf-CCHC pfam00098
Zinc knuckle; The zinc knuckle is a zinc binding motif composed of the the following ...
 392-407 1.42e-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: 38.66  E-value: 1.42e-04
                          10
                  ....*....|....*.
gi 270381459  392 VKCFNCGKEGHVARNC 407
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 ...
 2-133 1.65e-68

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: 215.96  E-value: 1.65e-68
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 270381459    2 GARASILSGGQLDRWEKIRLRPGGKKQYKLKHLVWASRELERFAVNPGLLETSEGCKQILKQLYPSLQTGSEELKSLYNT 81
Cdd:pfam00540   1 GARASVLSGGELDKWEKIRLRPGGKKKYKLKHLVWASRELERFAVNPGLLETSEGCRKILGQLQPSLQTGSEGLRSLYNT 80

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 270381459   82 VAVLYCVHQRIGIKDTKEALDKIEEEQNKSKQKAQ------QAAADTGDSS--SKVSQNY 133
Cdd:pfam00540  81 VAVLYCVHQRIDVKDTKEALEKIEEEQNKSKKKKTavppgaQQAANTGGTGnsSGVSQNY 140
Gag_p24_C pfam19317
Gag protein p24 C-terminal domain; p24 forms inner protein layer of the nucleocapsid. ELISA ...
 277-350 8.91e-38

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: 132.99  E-value: 8.91e-38
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 270381459  277 MYSPTSILDIKQGPKEPFRDYVDRFYKTLRAEQASQDVKNWMTETLMIQNANPDCKTILKALGPGATLEEMMTA 350
Cdd:pfam19317   1 GYKPTSLADIRQGPKEPYQDFVARLYDALRKEMPDGKAKDVITKQLAYENANPECQDLLKPLGKTGTLSDMIRA 74
Gag_p6 pfam08705
Gag protein p6; HIV protein p6 contains two late-budding domains (L domains) which are short ...
 451-488 1.40e-16

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: 73.03  E-value: 1.40e-16
                          10        20        30
                  ....*....|....*....|....*....|....*...
gi 270381459  451 PQSRTEPTAPPEESFRFGEETTaPSQKQEKIDKEPYPL 488
Cdd:pfam08705   1 LQSRPEPTAPPAESFGFGEEIT-PSPKQEQKDKELYPL 37
Gag_p24 pfam00607
gag protein p24 N-terminal domain; p24 forms inner protein layer of the nucleocapsid. ELISA ...
 144-251 1.70e-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: 67.30  E-value: 1.70e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 270381459  144 VHQAISPRTLNAWVKVVEEKAF-SPEVIPMFSALSEG--ATPQDLNTMLNTVGGHqAAMQMLKETINEEAAEWDRlHPVH 220
Cdd:pfam00607   1 VWEPLDFKLLKELKKAVKQYGPnSPYTMQLLEALASSnaLTPYDWRTLAKAVLSP-GQYLLWKAEWQELAQEQAR-RNQR 78

                          90       100       110
                  ....*....|....*....|....*....|....
gi 270381459  221 AGPIapgqmrEPRGSD-IAGTT--STLQEQIGWM 251
Cdd:pfam00607  79 AGPD------RGITLDmLTGTGqyATPQAQAQLP 106
PTZ00368 PTZ00368
universal minicircle sequence binding protein (UMSBP); Provisional
 350-431 1.26e-12

universal minicircle sequence binding protein (UMSBP); Provisional


Pssm-ID: 173561 [Multi-domain]  Cd Length: 148  Bit Score: 65.21  E-value: 1.26e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 270381459 350 ACQGVGGPSHKARVLAEAMSQVTNQSATIMMQKGNY--------RNQRKTVKCFNCGKEGHVARNCRAPRKKG-----CW 416
Cdd:PTZ00368  54 SCYNCGKTGHLSRECPEAPPGSGPRSCYNCGQTGHIsrecpnraKGGAARRACYNCGGEGHISRDCPNAGKRPggdktCY 133

                         90
                 ....*....|....*
gi 270381459 417 KCGKEGHQMKDCPER 431
Cdd:PTZ00368 134 NCGQTGHLSRDCPDK 148
PTZ00368 PTZ00368
universal minicircle sequence binding protein (UMSBP); Provisional
 349-432 1.56e-11

universal minicircle sequence binding protein (UMSBP); Provisional


Pssm-ID: 173561 [Multi-domain]  Cd Length: 148  Bit Score: 62.13  E-value: 1.56e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 270381459 349 TACQGVGGPSHKARvlaeamsQVTNQSATIMMqkgnyrnqrKTVKCFNCGKEGHVARNCRAPRKKG----CWKCGKEGHQ 424
Cdd:PTZ00368   1 MVCYRCGGVGHQSR-------ECPNSAPAGAA---------KARPCYKCGEPGHLSRECPSAPGGRgersCYNCGKTGHL 64


                 ....*...
gi 270381459 425 MKDCPERQ 432
Cdd:PTZ00368  65 SRECPEAP 72
PTZ00368 PTZ00368
universal minicircle sequence binding protein (UMSBP); Provisional
 394-460 1.02e-09

universal minicircle sequence binding protein (UMSBP); Provisional


Pssm-ID: 173561 [Multi-domain]  Cd Length: 148  Bit Score: 57.12  E-value: 1.02e-09
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 270381459 394 CFNCGKEGHVARNC-RAPRKKG---CWKCGKEGHQMKDCPERQANFLGKIWPSHKGRPGNFpqSRTEPTAP 460
Cdd:PTZ00368  55 CYNCGKTGHLSRECpEAPPGSGprsCYNCGQTGHISRECPNRAKGGAARRACYNCGGEGHI--SRDCPNAG 123
AIR1 COG5082
Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational ...
 381-454 8.80e-07

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: 49.46  E-value: 8.80e-07
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 270381459 381 QKGNYRNQR-KTVKCFNCGKEGHVARNC--RAPRKKGCWKCGKEGHQMKDCPErqanflgkIWPSHKGRPGNFPQSR 454
Cdd:COG5082   86 WDGHRSNHCpKPKKCYNCGETGHLSRDCnpSKDQQKSCFDCNSTRHSSEDCPS--------IWKHYVLNNGDGHPIK 154
AIR1 COG5082
Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational ...
 393-431 7.21e-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: 46.77  E-value: 7.21e-06
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 270381459 393 KCFNCGKEGHVARNC----------------RAPRKKGCWKCGKEGHQMKDCPER 431
Cdd:COG5082   62 VCFNCGQNGHLRRDCphsicyncswdghrsnHCPKPKKCYNCGETGHLSRDCNPS 116
ZnF_C2HC smart00343
zinc finger;
414-430 1.88e-05

zinc finger;


Pssm-ID: 197667 [Multi-domain]  Cd Length: 17  Bit Score: 41.27  E-value: 1.88e-05
                           10
                   ....*....|....*..
gi 270381459   414 GCWKCGKEGHQMKDCPE 430
Cdd:smart00343   1 KCYNCGKEGHIARDCPS 17
ZnF_C2HC smart00343
zinc finger;
393-408 4.20e-05

zinc finger;


Pssm-ID: 197667 [Multi-domain]  Cd Length: 17  Bit Score: 40.12  E-value: 4.20e-05
                           10
                   ....*....|....*.
gi 270381459   393 KCFNCGKEGHVARNCR 408
Cdd:smart00343   1 KCYNCGKEGHIARDCP 16
zf-CCHC pfam00098
Zinc knuckle; The zinc knuckle is a zinc binding motif composed of the the following ...
 392-407 1.42e-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: 38.66  E-value: 1.42e-04
                          10
                  ....*....|....*.
gi 270381459  392 VKCFNCGKEGHVARNC 407
Cdd:pfam00098   1 GKCYNCGEPGHIARDC 16
zf-CCHC pfam00098
Zinc knuckle; The zinc knuckle is a zinc binding motif composed of the the following ...
 413-430 2.63e-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: 37.89  E-value: 2.63e-04
                          10
                  ....*....|....*...
gi 270381459  413 KGCWKCGKEGHQMKDCPE 430
Cdd:pfam00098   1 GKCYNCGEPGHIARDCPK 18
zf-MYND pfam01753
MYND finger;
394-444 5.65e-03

MYND finger;


Pssm-ID: 460312  Cd Length: 39  Bit Score: 34.70  E-value: 5.65e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 270381459  394 CFNCGKEGHVARNCraPRKKGCWKCGKEgHQMKDcperqanflgkiWPSHK 444
Cdd:pfam01753   1 CAVCGKEALKLLRC--SRCKSVYYCSKE-CQKAD------------WPYHK 36
 
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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