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Conserved domains on  [gi|41054992|ref|NP_955762|]
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retrotransposon Gag-like protein 3 [Mus musculus]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PTZ00449 super family cl33186
104 kDa microneme/rhoptry antigen; Provisional
 41-277 5.32e-08

104 kDa microneme/rhoptry antigen; Provisional


The actual alignment was detected with superfamily member PTZ00449:

Pssm-ID: 185628 [Multi-domain]  Cd Length: 943  Bit Score: 55.85  E-value: 5.32e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41054992   41 QKSGAVKEHEPLRKPSEAQEP--PESPEFPaaRESQNPWEPPATTEPGEPTKIREPREPSAISELREPPEIKEPQEP--- 115
Cdd:PTZ00449 559 KKPGPAKEHKPSKIPTLSKKPefPKDPKHP--KDPEEPKKPKRPRSAQRPTRPKSPKLPELLDIPKSPKRPESPKSPkrp 636

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41054992  116 -----PETNESGESSAITEFRGSPEIKEPHLPPKSKEYWGPQELPMVKESWEppealDSTAWKPPAVKESQEIQKALESP 190
Cdd:PTZ00449 637 pppqrPSSPERPEGPKIIKSPKPPKSPKPPFDPKFKEKFYDDYLDAAAKSKE-----TKTTVVLDESFESILKETLPETP 711

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41054992  191 ATqrPQASPRgyDLPAVceaEPTDNQGT-PALKELQSPQlhnpTNDEESQTVPEYQETSSQLEPLEHPPP----QETLEP 265
Cdd:PTZ00449 712 GT--PFTTPR--PLPPK---LPRDEEFPfEPIGDPDAEQ----PDDIEFFTPPEEERTFFHETPADTPLPdilaEEFKEE 780

                        250
                 ....*....|..
gi 41054992  266 RVPQEPLDPSDA 277
Cdd:PTZ00449 781 DIHAETGEPDEA 792
Retrotrans_gag super family cl46289
Retrotransposon gag protein; Gag or Capsid-like proteins from LTR retrotransposons. There is a ...
 313-390 7.23e-05

Retrotransposon gag protein; Gag or Capsid-like proteins from LTR retrotransposons. There is a central motif QGXXEXXXXXFXXLXXH that is common to Retroviridae gag-proteins, but is poorly conserved.


The actual alignment was detected with superfamily member pfam16297:

Pssm-ID: 480629  Cd Length: 112  Bit Score: 42.21  E-value: 7.23e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41054992   313 PLEYPLAFSEDFQKLSEFLVQLTSYL--RSRGYPTEAALVSFVGSFFSGEAGRMFQPLLDSQPPLVEQFERLLRALQDTF 390
Cdd:pfam16297  24 PIPFPERFSGESGRLPEFIVQTMSYMlvDEKTFCNDAMKVAFLITRLSGRALEWVMPYIQSDSPILNNYRAFLNEMKQYF 103
PTZ00368 super family cl31762
universal minicircle sequence binding protein (UMSBP); Provisional
 508-539 7.97e-04

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: 40.18  E-value: 7.97e-04
                         10        20        30
                 ....*....|....*....|....*....|....*
gi 41054992  508 HLSE---AERARRREGHLCLYCGHPGHFARDCPVK 539
Cdd:PTZ00368 114 HISRdcpNAGKRPGGDKTCYNCGQTGHLSRDCPDK 148
 
Name Accession Description Interval E-value
PTZ00449 PTZ00449
104 kDa microneme/rhoptry antigen; Provisional
 41-277 5.32e-08

104 kDa microneme/rhoptry antigen; Provisional


Pssm-ID: 185628 [Multi-domain]  Cd Length: 943  Bit Score: 55.85  E-value: 5.32e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41054992   41 QKSGAVKEHEPLRKPSEAQEP--PESPEFPaaRESQNPWEPPATTEPGEPTKIREPREPSAISELREPPEIKEPQEP--- 115
Cdd:PTZ00449 559 KKPGPAKEHKPSKIPTLSKKPefPKDPKHP--KDPEEPKKPKRPRSAQRPTRPKSPKLPELLDIPKSPKRPESPKSPkrp 636

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41054992  116 -----PETNESGESSAITEFRGSPEIKEPHLPPKSKEYWGPQELPMVKESWEppealDSTAWKPPAVKESQEIQKALESP 190
Cdd:PTZ00449 637 pppqrPSSPERPEGPKIIKSPKPPKSPKPPFDPKFKEKFYDDYLDAAAKSKE-----TKTTVVLDESFESILKETLPETP 711

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41054992  191 ATqrPQASPRgyDLPAVceaEPTDNQGT-PALKELQSPQlhnpTNDEESQTVPEYQETSSQLEPLEHPPP----QETLEP 265
Cdd:PTZ00449 712 GT--PFTTPR--PLPPK---LPRDEEFPfEPIGDPDAEQ----PDDIEFFTPPEEERTFFHETPADTPLPdilaEEFKEE 780

                        250
                 ....*....|..
gi 41054992  266 RVPQEPLDPSDA 277
Cdd:PTZ00449 781 DIHAETGEPDEA 792
DUF4939 pfam16297
Domain of unknown function (DUF4939); This family consists of uncharacterized proteins around ...
 313-390 7.23e-05

Domain of unknown function (DUF4939); This family consists of uncharacterized proteins around 110 residues in length and is mainly found in various mammalia species. LDOC1, a member of this family and a novel MZF-1-interacting protein, inhibits NF-kappaB activation and relates with cancer and some other diseases. But the specific function of this family is still unknown.


Pssm-ID: 465086  Cd Length: 112  Bit Score: 42.21  E-value: 7.23e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41054992   313 PLEYPLAFSEDFQKLSEFLVQLTSYL--RSRGYPTEAALVSFVGSFFSGEAGRMFQPLLDSQPPLVEQFERLLRALQDTF 390
Cdd:pfam16297  24 PIPFPERFSGESGRLPEFIVQTMSYMlvDEKTFCNDAMKVAFLITRLSGRALEWVMPYIQSDSPILNNYRAFLNEMKQYF 103
PTZ00368 PTZ00368
universal minicircle sequence binding protein (UMSBP); Provisional
 508-539 7.97e-04

universal minicircle sequence binding protein (UMSBP); Provisional


Pssm-ID: 173561 [Multi-domain]  Cd Length: 148  Bit Score: 40.18  E-value: 7.97e-04
                         10        20        30
                 ....*....|....*....|....*....|....*
gi 41054992  508 HLSE---AERARRREGHLCLYCGHPGHFARDCPVK 539
Cdd:PTZ00368 114 HISRdcpNAGKRPGGDKTCYNCGQTGHLSRDCPDK 148
ZnF_C2HC smart00343
zinc finger;
523-537 3.23e-03

zinc finger;


Pssm-ID: 197667 [Multi-domain]  Cd Length: 17  Bit Score: 35.11  E-value: 3.23e-03
                           10
                   ....*....|....*
gi 41054992    523 CLYCGHPGHFARDCP 537
Cdd:smart00343   2 CYNCGKEGHIARDCP 16
zf-CCHC pfam00098
Zinc knuckle; The zinc knuckle is a zinc binding motif composed of the the following ...
 523-537 3.59e-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: 34.81  E-value: 3.59e-03
                          10
                  ....*....|....*
gi 41054992   523 CLYCGHPGHFARDCP 537
Cdd:pfam00098   3 CYNCGEPGHIARDCP 17
 
Name Accession Description Interval E-value
PTZ00449 PTZ00449
104 kDa microneme/rhoptry antigen; Provisional
 41-277 5.32e-08

104 kDa microneme/rhoptry antigen; Provisional


Pssm-ID: 185628 [Multi-domain]  Cd Length: 943  Bit Score: 55.85  E-value: 5.32e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41054992   41 QKSGAVKEHEPLRKPSEAQEP--PESPEFPaaRESQNPWEPPATTEPGEPTKIREPREPSAISELREPPEIKEPQEP--- 115
Cdd:PTZ00449 559 KKPGPAKEHKPSKIPTLSKKPefPKDPKHP--KDPEEPKKPKRPRSAQRPTRPKSPKLPELLDIPKSPKRPESPKSPkrp 636

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41054992  116 -----PETNESGESSAITEFRGSPEIKEPHLPPKSKEYWGPQELPMVKESWEppealDSTAWKPPAVKESQEIQKALESP 190
Cdd:PTZ00449 637 pppqrPSSPERPEGPKIIKSPKPPKSPKPPFDPKFKEKFYDDYLDAAAKSKE-----TKTTVVLDESFESILKETLPETP 711

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41054992  191 ATqrPQASPRgyDLPAVceaEPTDNQGT-PALKELQSPQlhnpTNDEESQTVPEYQETSSQLEPLEHPPP----QETLEP 265
Cdd:PTZ00449 712 GT--PFTTPR--PLPPK---LPRDEEFPfEPIGDPDAEQ----PDDIEFFTPPEEERTFFHETPADTPLPdilaEEFKEE 780

                        250
                 ....*....|..
gi 41054992  266 RVPQEPLDPSDA 277
Cdd:PTZ00449 781 DIHAETGEPDEA 792
PTZ00449 PTZ00449
104 kDa microneme/rhoptry antigen; Provisional
 22-279 5.06e-07

104 kDa microneme/rhoptry antigen; Provisional


Pssm-ID: 185628 [Multi-domain]  Cd Length: 943  Bit Score: 52.77  E-value: 5.06e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41054992   22 QVKRLMEENaalQAQIPELQKSGAVKEHEPLRKPSEAQEPPESP--------EFPAARESQNPWE--PPATTEPGEPTKI 91
Cdd:PTZ00449 484 EIKKLIKKS---KKKLAPIEEEDSDKHDEPPEGPEASGLPPKAPgdkegeegEHEDSKESDEPKEggKPGETKEGEVGKK 560

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41054992   92 REP---REPSAISELREPPEI-KEPQEP--PETNESGESSAITEFRGSPeiKEPHLPPKSKEYWGPQELPMVKESWEPPe 165
Cdd:PTZ00449 561 PGPakeHKPSKIPTLSKKPEFpKDPKHPkdPEEPKKPKRPRSAQRPTRP--KSPKLPELLDIPKSPKRPESPKSPKRPP- 637

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41054992  166 aldstawkPPAVKESQEIQKALESPATQRPQASPRGYDLPAVCEaEPTDNQGTPALKELQSPQLHNPTNDEESQTVPEYQ 245
Cdd:PTZ00449 638 --------PPQRPSSPERPEGPKIIKSPKPPKSPKPPFDPKFKE-KFYDDYLDAAAKSKETKTTVVLDESFESILKETLP 708

                        250       260       270
                 ....*....|....*....|....*....|....*
gi 41054992  246 ETSSQLEPLEHP-PPQETLEPRVPQEPLDPSDAEE 279
Cdd:PTZ00449 709 ETPGTPFTTPRPlPPKLPRDEEFPFEPIGDPDAEQ 743
PTZ00449 PTZ00449
104 kDa microneme/rhoptry antigen; Provisional
 42-291 2.79e-06

104 kDa microneme/rhoptry antigen; Provisional


Pssm-ID: 185628 [Multi-domain]  Cd Length: 943  Bit Score: 50.46  E-value: 2.79e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41054992   42 KSGAVKEHEPLR---KPSEAQEPPESPEFPA------ARESQNPWEPPATTEPGEPTKIREPREPSAISELREPPEIKEP 112
Cdd:PTZ00449 527 KEGEEGEHEDSKesdEPKEGGKPGETKEGEVgkkpgpAKEHKPSKIPTLSKKPEFPKDPKHPKDPEEPKKPKRPRSAQRP 606

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41054992  113 QEPPETNESgESSAITEFRGSPEI-KEPHLPPKSKEYWGPQ--ELPMVKESWEPPEALdstawKPPAVKESQE------I 183
Cdd:PTZ00449 607 TRPKSPKLP-ELLDIPKSPKRPESpKSPKRPPPPQRPSSPErpEGPKIIKSPKPPKSP-----KPPFDPKFKEkfyddyL 680

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41054992  184 QKALESPATQRPQASPRGYDlpAVCEAEPTDNQGTPALKELQSPQLHnPTnDEESQTVPEYQETSSQLEPLEHPPPQETL 263
Cdd:PTZ00449 681 DAAAKSKETKTTVVLDESFE--SILKETLPETPGTPFTTPRPLPPKL-PR-DEEFPFEPIGDPDAEQPDDIEFFTPPEEE 756

                        250       260       270
                 ....*....|....*....|....*....|..
gi 41054992  264 EPRVPQEPLDPSD----AEEFLELSVPEESLE 291
Cdd:PTZ00449 757 RTFFHETPADTPLpdilAEEFKEEDIHAETGE 788
DUF4939 pfam16297
Domain of unknown function (DUF4939); This family consists of uncharacterized proteins around ...
 313-390 7.23e-05

Domain of unknown function (DUF4939); This family consists of uncharacterized proteins around 110 residues in length and is mainly found in various mammalia species. LDOC1, a member of this family and a novel MZF-1-interacting protein, inhibits NF-kappaB activation and relates with cancer and some other diseases. But the specific function of this family is still unknown.


Pssm-ID: 465086  Cd Length: 112  Bit Score: 42.21  E-value: 7.23e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41054992   313 PLEYPLAFSEDFQKLSEFLVQLTSYL--RSRGYPTEAALVSFVGSFFSGEAGRMFQPLLDSQPPLVEQFERLLRALQDTF 390
Cdd:pfam16297  24 PIPFPERFSGESGRLPEFIVQTMSYMlvDEKTFCNDAMKVAFLITRLSGRALEWVMPYIQSDSPILNNYRAFLNEMKQYF 103
Ty3_capsid pfam19259
Ty3 transposon capsid-like protein; This entry corresponds to the capsid protein found in the ...
 310-457 3.47e-04

Ty3 transposon capsid-like protein; This entry corresponds to the capsid protein found in the Ty3 transposons of yeast as well as other transposable elements.


Pssm-ID: 437091 [Multi-domain]  Cd Length: 197  Bit Score: 42.07  E-value: 3.47e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41054992   310 TTLPLEY--PLAF--SEDFQKLSEFLVQLTSYLRSRGYPTEAALVSFVGSFFSGEAGRMFQPLLDSQPPLVEQFERLLRA 385
Cdd:pfam19259   5 TLPNFMIqvILPFrgRKDVLKLKSFISEIMLQMSMIFWPNDAERIVFCARHLTGPAAQWFHDFVQEQGILDATFDTFIKA 84

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 41054992   386 LQDTFDNPESLEVANQGLPQLRQGEGLAPRYSTRFHLIAQELD---LGESTLCIQFQEELASSIQNELSCTSPAT 457
Cdd:pfam19259  85 FKQHFYGKPDINKLFNDIVNLSEAKLGIERYNSHFNRLWDLLPpdfLSEKAAIMFYIRGLKPETYIIVRLAKPST 159
PRK07764 PRK07764
DNA polymerase III subunits gamma and tau; Validated
 53-280 4.47e-04

DNA polymerase III subunits gamma and tau; Validated


Pssm-ID: 236090 [Multi-domain]  Cd Length: 824  Bit Score: 43.05  E-value: 4.47e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41054992   53 RKPSEAQEPPESPEFPAARESQNPWEPPATTEPGEPTKIREPREPSAISELREPPEIkepqePPETNESGESSAITEFRG 132
Cdd:PRK07764 592 PGAAGGEGPPAPASSGPPEEAARPAAPAAPAAPAAPAPAGAAAAPAEASAAPAPGVA-----APEHHPKHVAVPDASDGG 666

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41054992  133 SPEIKEPHLPPKSKEYWGPQELPMVKESWEPPEALDSTAWKPPAVKESQeiQKALESPATQRPQASPRGYDLPAVCEAEP 212
Cdd:PRK07764 667 DGWPAKAGGAAPAAPPPAPAPAAPAAPAGAAPAQPAPAPAATPPAGQAD--DPAAQPPQAAQGASAPSPAADDPVPLPPE 744

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 41054992  213 TDNQGTPALKELQSPQlhnptndeeSQTVPEYQETSSQLEPLEHPPPQETL-EPRVPQEPLDPSDAEEF 280
Cdd:PRK07764 745 PDDPPDPAGAPAQPPP---------PPAPAPAAAPAAAPPPSPPSEEEEMAeDDAPSMDDEDRRDAEEV 804
PTZ00368 PTZ00368
universal minicircle sequence binding protein (UMSBP); Provisional
 508-539 7.97e-04

universal minicircle sequence binding protein (UMSBP); Provisional


Pssm-ID: 173561 [Multi-domain]  Cd Length: 148  Bit Score: 40.18  E-value: 7.97e-04
                         10        20        30
                 ....*....|....*....|....*....|....*
gi 41054992  508 HLSE---AERARRREGHLCLYCGHPGHFARDCPVK 539
Cdd:PTZ00368 114 HISRdcpNAGKRPGGDKTCYNCGQTGHLSRDCPDK 148
PHA03247 PHA03247
large tegument protein UL36; Provisional
 38-276 1.33e-03

large tegument protein UL36; Provisional


Pssm-ID: 223021 [Multi-domain]  Cd Length: 3151  Bit Score: 41.85  E-value: 1.33e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41054992    38 PELQKSGAVKEHEPLRKPSEAQEPPESP----EFPAARESQNPWEPPATTEPGEPTKIREPREPSAISELREPPEIK--- 110
Cdd:PHA03247 2848 PSLPLGGSVAPGGDVRRRPPSRSPAAKPaapaRPPVRRLARPAVSRSTESFALPPDQPERPPQPQAPPPPQPQPQPPppp 2927

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41054992   111 EPQEPPETnesgessaitefrgsPEIKEPHLPPKSKEYWGPQELPMVKESWeppeaLDSTAWKPPAVKESQEIQKALESP 190
Cdd:PHA03247 2928 QPQPPPPP---------------PPRPQPPLAPTTDPAGAGEPSGAVPQPW-----LGALVPGRVAVPRFRVPQPAPSRE 2987

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41054992   191 ATQRPQASPRGYDLPAVceaepTDNQGTPALKELQSP-------QLHNPTNDEESQTVPEYQETS--SQLEPLEHPPPQE 261
Cdd:PHA03247 2988 APASSTPPLTGHSLSRV-----SSWASSLALHEETDPppvslkqTLWPPDDTEDSDADSLFDSDSerSDLEALDPLPPEP 3062

                         250
                  ....*....|....*
gi 41054992   262 TLEPRVPQEPLDPSD 276
Cdd:PHA03247 3063 HDPFAHEPDPATPEA 3077
PHA03247 PHA03247
large tegument protein UL36; Provisional
 50-230 2.03e-03

large tegument protein UL36; Provisional


Pssm-ID: 223021 [Multi-domain]  Cd Length: 3151  Bit Score: 41.08  E-value: 2.03e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41054992    50 EPLRKPSEAQEPPESPEFPAARESQNPWEPPATTEPGEPTkirEPREPSAISELREPPEIKEPQEPPETNESGE----SS 125
Cdd:PHA03247 2896 ESFALPPDQPERPPQPQAPPPPQPQPQPPPPPQPQPPPPP---PPRPQPPLAPTTDPAGAGEPSGAVPQPWLGAlvpgRV 2972

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41054992   126 AITEFRGSP-----EIKEPHLPPKSKEY------WGpQELPMVKESWEPPEALDSTAWKPPAVKESQEIQKALESPA--- 191
Cdd:PHA03247 2973 AVPRFRVPQpapsrEAPASSTPPLTGHSlsrvssWA-SSLALHEETDPPPVSLKQTLWPPDDTEDSDADSLFDSDSErsd 3051

                         170       180       190
                  ....*....|....*....|....*....|....*....
gi 41054992   192 TQRPQASPRGYDLPAVCEAEPtdnqGTPALKELQSPQLH 230
Cdd:PHA03247 3052 LEALDPLPPEPHDPFAHEPDP----ATPEAGARESPSSQ 3086
ZnF_C2HC smart00343
zinc finger;
523-537 3.23e-03

zinc finger;


Pssm-ID: 197667 [Multi-domain]  Cd Length: 17  Bit Score: 35.11  E-value: 3.23e-03
                           10
                   ....*....|....*
gi 41054992    523 CLYCGHPGHFARDCP 537
Cdd:smart00343   2 CYNCGKEGHIARDCP 16
zf-CCHC pfam00098
Zinc knuckle; The zinc knuckle is a zinc binding motif composed of the the following ...
 523-537 3.59e-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: 34.81  E-value: 3.59e-03
                          10
                  ....*....|....*
gi 41054992   523 CLYCGHPGHFARDCP 537
Cdd:pfam00098   3 CYNCGEPGHIARDCP 17
PHA03321 PHA03321
tegument protein VP11/12; Provisional
 30-205 4.31e-03

tegument protein VP11/12; Provisional


Pssm-ID: 223041 [Multi-domain]  Cd Length: 694  Bit Score: 39.94  E-value: 4.31e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41054992   30 NAALQaqiPELQKSGAVKEHEPLRKPSEAQEPPesPEFPAARESQNPWEPPATTEPGEPTKIREPR-------EPSAISE 102
Cdd:PHA03321 401 EAALA---TELFRTGVPSEHYEASLRLLSSRQP--PGAPAPRRDNDPPPPPRARPGSTPACARRARaqrardaGPEYVDP 475

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41054992  103 LREPPEIKEPQEPPETNESGESSA--ITEFRGSPeikePHLPPKSKeywgpqELPMVKESWEPPEALDSTAWKPPAVKES 180
Cdd:PHA03321 476 LGALRRLPAGAAPPPEPAAAPSPAtyYTRMGGGP----PRLPPRNR------ATETLRPDWGPPAAAPPEQMEDPYLEPD 545

                        170       180
                 ....*....|....*....|....*...
gi 41054992  181 QEIQKALE---SPATQRPQASPRGYDLP 205
Cdd:PHA03321 546 DDRFDRRDgaaAAATSHPREAPAPDDDP 573
PTZ00368 PTZ00368
universal minicircle sequence binding protein (UMSBP); Provisional
 508-540 7.20e-03

universal minicircle sequence binding protein (UMSBP); Provisional


Pssm-ID: 173561 [Multi-domain]  Cd Length: 148  Bit Score: 37.48  E-value: 7.20e-03
                         10        20        30
                 ....*....|....*....|....*....|....*
gi 41054992  508 HLS-EAERARR-REGHLCLYCGHPGHFARDCPVKP 540
Cdd:PTZ00368  38 HLSrECPSAPGgRGERSCYNCGKTGHLSRECPEAP 72
 
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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