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Conserved domains on  [gi|281362576|ref|NP_001163731|]
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nuclear protein localization 4, isoform D [Drosophila melanogaster]

Protein Classification

zinc finger Ran-binding domain-containing protein( domain architecture ID 11189535)

zinc finger Ran-binding domain-containing protein; similar to human zinc finger Ran-binding domain-containing protein 2 (ZRANB2) which is a splice factor required for alternative splicing of TRA2B/SFRS10 transcripts and whose zinc finger domains bind single-stranded RNA, and to the zinc finger domain of human TAK1-binding protein 2 (TAB2) which binds Lys 63-linked polyubiquitin chains

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
NPL4 pfam05021
NPL4 family; The HRD4 gene was identical to NPL4, a gene previously implicated in nuclear ...
 254-565 1.73e-176

NPL4 family; The HRD4 gene was identical to NPL4, a gene previously implicated in nuclear transport. Using a diverse set of substrates and direct ubiquitination assays, analysis revealed that HRD4/NPL4 is required for a poorly characterized step in ER-associated degradation after ubiquitination of target proteins but before their recognition by the 26S proteasome. Npl4p physically associates with Cdc48p via Ufd1p to form a Cdc48p-Ufd1p-Npl4p complex. The Cdc48-Ufd1-Npl4 complex functions in the recognition of several polyubiquitin-tagged proteins and facilitates their presentation to the 26S proteasome for processive degradation or even more specific processing.


:

Pssm-ID: 461524  Cd Length: 309  Bit Score: 502.57  E-value: 1.73e-176
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281362576  254 RMGYLYGTYEQHTDVPLGIRAKVAAIYEPPQESTRDSINIQPDEFADDVDAVASALGLKKIGWIFTDLITDDASIGTVKQ 333
Cdd:pfam05021   1 RFGYLYGRYEEYDEVPLGIKAVVEAIYEPPQHDELDGITLLPWENEKDVDEIARELGLERVGVIFTDLTDAGAGDGTVLC 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281362576  334 IRGIESHFITAQECITAGELQNRHPNPCKYASNGVFGSKFVTICVTGDKTKQVHMEGYAVSAQCMALVRDNCLIPTKDaP 413
Cdd:pfam05021  81 KRHKDSYFLSSLEVIMAARLQARHPNPTKYSETGRFGSKFVTCVVSGDLNGEIDISSYQVSNQAEALVRADIIEPSTD-P 159

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281362576  414 ELGYVRESTDKQYVPDVFYKEKDLYGNEVQRLARP-LPVEYLLVDVPASTPLQPIYTFteyDKRQPFPIENRYIDGHLQD 492
Cdd:pfam05021 160 SVAYVRESSDERYVPEVFYSKINEYGLEVKENAKPaFPVEYLLVTLTHGFPLEPSPTF---SANNGFPIENREAMGELQD 236

                         250       260       270       280       290       300       310
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 281362576  493 FNALSCYLSAWG-EEEFLEAISDFHLLVYLYKMDMLPlRQHMGPLLEAVRTKNPNQAAQFKVVDVWKLLESLIQ 565
Cdd:pfam05021 237 LSALAKYLKSSAdPNDFLEALSNFHLLLYLHSLGILS-KDEESLLCRAATQKDTEDLLQLIESPGWQTLVTILQ 309
zf-NPL4 pfam05020
NPL4 family, putative zinc binding region; The HRD4 gene was identical to NPL4, a gene ...
 113-251 2.63e-87

NPL4 family, putative zinc binding region; The HRD4 gene was identical to NPL4, a gene previously implicated in nuclear transport. Using a diverse set of substrates and direct ubiquitination assays, analysis revealed that HRD4/NPL4 is required for a poorly characterized step in ER-associated degradation after ubiquitination of target proteins but before their recognition by the 26S proteasome. This region of the protein contains possibly two zinc binding motifs (Bateman A pers. obs.). Npl4p physically associates with Cdc48p via Ufd1p to form a Cdc48p-Ufd1p-Npl4p complex. The Cdc48-Ufd1-Npl4 complex functions in the recognition of several polyubiquitin-tagged proteins and facilitates their presentation to the 26S proteasome for processive degradation or even more specific processing.


:

Pssm-ID: 461523  Cd Length: 145  Bit Score: 267.92  E-value: 2.63e-87
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281362576  113 VIEDDVDQALSKADGTIKRERDSKLCHHNANGRCVHCSALEPYDESYLKEHNIKHLSFHSYIRKQTSGMD-----QGKYF 187
Cdd:pfam05020   1 VKEDPVDDYLDKQDGKIPRKRDPKLCRHGPKGMCDYCSPLEPYDEEYLKEHKIKHLSFHAYLRKLNSGTNkkesgSSYIP 80

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 281362576  188 VFDDINCRIKPGCRE-HPPWPKGICSKCQPSAITLNRQTYRHVDNVMFENTKIVERFLNYWRTTG 251
Cdd:pfam05020  81 PLEEPSYKVKPGCPSgHPPWPKGICSKCQPSAITLQRQPFRMVDHVEFANSEIVNRFLDFWRKTG 145
UN_NPL4 pfam11543
Nuclear pore localization protein NPL4; Npl4 is part of the heterodimer UN along with Ufd1 ...
 6-77 1.91e-27

Nuclear pore localization protein NPL4; Npl4 is part of the heterodimer UN along with Ufd1 which is involved in the recruitment of p97, an AAA ATPase, for tasks involving the ubiquitin pathway. Npl4 has a ubiquitin-like domain which has within its structure a beta-grasp fold with a helical insert.


:

Pssm-ID: 431926  Cd Length: 80  Bit Score: 105.64  E-value: 1.91e-27
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 281362576    6 ILIRVQSAEGIKRIEISPKSNLKHLYDSVQNALKVD--GFGLFKERNFLTELQASGSQLVG-TSLRHGDMVYLKQ 77
Cdd:pfam11543   5 IIIRVQSADGIKRIEISSDSTLSTLLSKVAEELGFPnnGFSLYLERNKTTELVSSGSKRVSlVGLKHGDSLYLFP 79
ZnF_RBZ smart00547
Zinc finger domain; Zinc finger domain in Ran-binding proteins (RanBPs), and other proteins. ...
 599-623 1.55e-04

Zinc finger domain; Zinc finger domain in Ran-binding proteins (RanBPs), and other proteins. In RanBPs, this domain binds RanGDP.


:

Pssm-ID: 197784 [Multi-domain]  Cd Length: 25  Bit Score: 39.22  E-value: 1.55e-04
                           10        20
                   ....*....|....*....|....*
gi 281362576   599 NTWTCNHCTFINRGELTSCEICSLP 623
Cdd:smart00547   1 GDWECPACTFLNFASRSKCFACGAP 25
 
Name Accession Description Interval E-value
NPL4 pfam05021
NPL4 family; The HRD4 gene was identical to NPL4, a gene previously implicated in nuclear ...
 254-565 1.73e-176

NPL4 family; The HRD4 gene was identical to NPL4, a gene previously implicated in nuclear transport. Using a diverse set of substrates and direct ubiquitination assays, analysis revealed that HRD4/NPL4 is required for a poorly characterized step in ER-associated degradation after ubiquitination of target proteins but before their recognition by the 26S proteasome. Npl4p physically associates with Cdc48p via Ufd1p to form a Cdc48p-Ufd1p-Npl4p complex. The Cdc48-Ufd1-Npl4 complex functions in the recognition of several polyubiquitin-tagged proteins and facilitates their presentation to the 26S proteasome for processive degradation or even more specific processing.


Pssm-ID: 461524  Cd Length: 309  Bit Score: 502.57  E-value: 1.73e-176
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281362576  254 RMGYLYGTYEQHTDVPLGIRAKVAAIYEPPQESTRDSINIQPDEFADDVDAVASALGLKKIGWIFTDLITDDASIGTVKQ 333
Cdd:pfam05021   1 RFGYLYGRYEEYDEVPLGIKAVVEAIYEPPQHDELDGITLLPWENEKDVDEIARELGLERVGVIFTDLTDAGAGDGTVLC 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281362576  334 IRGIESHFITAQECITAGELQNRHPNPCKYASNGVFGSKFVTICVTGDKTKQVHMEGYAVSAQCMALVRDNCLIPTKDaP 413
Cdd:pfam05021  81 KRHKDSYFLSSLEVIMAARLQARHPNPTKYSETGRFGSKFVTCVVSGDLNGEIDISSYQVSNQAEALVRADIIEPSTD-P 159

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281362576  414 ELGYVRESTDKQYVPDVFYKEKDLYGNEVQRLARP-LPVEYLLVDVPASTPLQPIYTFteyDKRQPFPIENRYIDGHLQD 492
Cdd:pfam05021 160 SVAYVRESSDERYVPEVFYSKINEYGLEVKENAKPaFPVEYLLVTLTHGFPLEPSPTF---SANNGFPIENREAMGELQD 236

                         250       260       270       280       290       300       310
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 281362576  493 FNALSCYLSAWG-EEEFLEAISDFHLLVYLYKMDMLPlRQHMGPLLEAVRTKNPNQAAQFKVVDVWKLLESLIQ 565
Cdd:pfam05021 237 LSALAKYLKSSAdPNDFLEALSNFHLLLYLHSLGILS-KDEESLLCRAATQKDTEDLLQLIESPGWQTLVTILQ 309
NPL4 COG5100
Nuclear pore protein [Nuclear structure];
6-527 2.76e-132

Nuclear pore protein [Nuclear structure];


Pssm-ID: 227431 [Multi-domain]  Cd Length: 571  Bit Score: 399.76  E-value: 2.76e-132
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281362576   6 ILIRVQSAEGIKRIEISPKSNL-----KHLYDSVQNAlKVDGFGLFKERN----FLTELQASGSQLVGtsLRHGDMVYLK 76
Cdd:COG5100    1 MIFRFRSKEGQRRVEVQESDVLgmlspKLLAFFEVNY-SPEQISVCSAPDgqgeIFSLLKDQTPDDLG--LRHGQMLYLE 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281362576  77 QMAGTSSRRTSTTVldsqAFKTSTISNPN--SARPSFNVIEDDVDQALSKADGTIKRERdSKLCHHNANGRCVHCSALEP 154
Cdd:COG5100   78 YSDIASNNEKKRDV----PGKPKQDCSKGikREKDSMPVIQDPIDDSLEKEDGLIRRSM-TMLCQHGSNGMCSYCSPLDP 152

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281362576 155 YDESYLKEHNIKHLSFHSYIRKQTSGMDQ---GKYFV--FDDINCRIKPGCRE-HPPWPKGICSKCQPSAITLNRQTYRH 228
Cdd:COG5100  153 WDEKYYKDNKIKHLSFHSYLEKMNSNKNKlgsVESYIvpLEEPSFTVKETCEDgHGPWPHGICNKCQPSNIILAPQVFRM 232

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281362576 229 VDNVMFENTKIVERFLNYWRTTGHQRMGYLYGTYEQHTDVPLGIRAKVAAIYEPPQESTRDSINIQPDEFADDVDAVASA 308
Cdd:COG5100  233 VDHVEFDGKHIVENFIRNWRESGRQRFGYLYGRYMDYENIPLGIKAVVEAIYEPPQEDEPDGFTIEEWADEGLMDAPASG 312

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281362576 309 LGLKKIGWIFTDLITDDASIGTVKQIRGIESHFITAQECITAGELQNRHPNPCKYASNGVFGSKFVTICVTGDKTKQVHM 388
Cdd:COG5100  313 TGLERIGMIFTDLLDEGSNRGSVTCKRHADSYFLSSLEVEFIAKMQTMHPNTVKDSREGEFGSKFVTIVISGNLDGEIGL 392

                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281362576 389 EGYAVSAQCMALVRDNCLIPTKDaPELGYVRESTDKQYVPDVFYKEKDLYGNEVQRLARP-LPVEYLLVDVPASTPLQPI 467
Cdd:COG5100  393 QSYQVSNQCMALVKADYILPSED-PRRFLATKEDQTRYVPDIFYRYTDTYGEEVMENAKPaFPVEFLLVTLTHGFPEKPN 471

                        490       500       510       520       530       540
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 281362576 468 YTFTEYDKrqpFPIENRYIDGHLQDFNALSCYL--SAWGEEEFLEAISDFHLLVYLYKMDML 527
Cdd:COG5100  472 PLFRSIDF---IPKKFGDRKMAEYFGGDLSKELfsNFTLLTRIQGVFSNFKDLLKIIVLRIL 530
MPN_NPL4 cd08061
Mov34/MPN/PAD-1 family: nuclear protein localization-4 (Npl4) domain; Npl4p (nuclear protein ...
 220-521 3.73e-131

Mov34/MPN/PAD-1 family: nuclear protein localization-4 (Npl4) domain; Npl4p (nuclear protein localization-4) is identical to Hmg-CoA reductase degradation 4 (HRD4) protein and contains a domain that is part of the pfam clan MPN/Mov34-like. Npl4 plays an intermediate role between endoplasmic reticulum-associated degradation (ERAD) substrate ubiquitylation and proteasomal degradation. Npl4p associates with Cdc48p (Cdc48 in yeast and p97 or valosin-containing protein (VCP) in higher eukaryotes), the highly conserved ATPase of the AAA family, via ubiquitin fusion degradation-1 protein (Ufd1p) to form a Cdc48p-Ufd1p-Npl4p complex which then functions in the recognition of several polyubiquitin-tagged proteins and facilitates their presentation to the 26S proteasome for processive degradation. This family of eukaryotic MPN-like domains lacks the key residues that coordinate a metal ion and therefore does not show catalytic isopeptidase activity.


Pssm-ID: 163692  Cd Length: 274  Bit Score: 385.94  E-value: 3.73e-131
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281362576 220 TLNRQTYRHVDNVMFENTKIVERFLN-YWRTTGHQRMGYLYGTYEQHTDVPLGIRAKVAAIYEPPQESTRDSINIQPDEF 298
Cdd:cd08061    1 TLKRQKYRHVDHVEFDNPSIVEFFLYvFWRKTGQQRIGFLYGRYDEDEDVPLGIKAVVEAIYEPPQEGTPDGFELLEDPN 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281362576 299 ADDVDAVASALGLKKIGWIFTDLITDDasigtvkqirgIESHFITAQECITAGELQNRHPnpckyasNGVFGSKFVTICV 378
Cdd:cd08061   81 ADTVDAIAAALGLERVGWIFTDLPRED-----------KDGYFLSAEEVILAAKFQLKHP-------TGKFGSKFVTVVV 142

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281362576 379 TGDKTKQVHMEGYAVSAQCMALVRDNCLIPTKDAPELgYVRESTDKQYVPDVFYKEKDLYGneVQRLARPLPVEYLLVDV 458
Cdd:cd08061  143 TGDKDGQIHFEAYQVSDQAMALVRDGLLLPTKDADEL-YVREPTLERYVPDVFYSGKDKYG--KTKAVPEVDVEYFLVDV 219

                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 281362576 459 PASTPLQPIytfteYDKRQPFPIENRY-IDGHLQDFNALSCYLSawgeEEFLEAISDFHLLVYL 521
Cdd:cd08061  220 PHGFPLSPS-----SFKSSDFPIENRPpSLGELQDLDALARYLG----KPFLERLSDFHLLLYL 274
zf-NPL4 pfam05020
NPL4 family, putative zinc binding region; The HRD4 gene was identical to NPL4, a gene ...
 113-251 2.63e-87

NPL4 family, putative zinc binding region; The HRD4 gene was identical to NPL4, a gene previously implicated in nuclear transport. Using a diverse set of substrates and direct ubiquitination assays, analysis revealed that HRD4/NPL4 is required for a poorly characterized step in ER-associated degradation after ubiquitination of target proteins but before their recognition by the 26S proteasome. This region of the protein contains possibly two zinc binding motifs (Bateman A pers. obs.). Npl4p physically associates with Cdc48p via Ufd1p to form a Cdc48p-Ufd1p-Npl4p complex. The Cdc48-Ufd1-Npl4 complex functions in the recognition of several polyubiquitin-tagged proteins and facilitates their presentation to the 26S proteasome for processive degradation or even more specific processing.


Pssm-ID: 461523  Cd Length: 145  Bit Score: 267.92  E-value: 2.63e-87
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281362576  113 VIEDDVDQALSKADGTIKRERDSKLCHHNANGRCVHCSALEPYDESYLKEHNIKHLSFHSYIRKQTSGMD-----QGKYF 187
Cdd:pfam05020   1 VKEDPVDDYLDKQDGKIPRKRDPKLCRHGPKGMCDYCSPLEPYDEEYLKEHKIKHLSFHAYLRKLNSGTNkkesgSSYIP 80

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 281362576  188 VFDDINCRIKPGCRE-HPPWPKGICSKCQPSAITLNRQTYRHVDNVMFENTKIVERFLNYWRTTG 251
Cdd:pfam05020  81 PLEEPSYKVKPGCPSgHPPWPKGICSKCQPSAITLQRQPFRMVDHVEFANSEIVNRFLDFWRKTG 145
UN_NPL4 pfam11543
Nuclear pore localization protein NPL4; Npl4 is part of the heterodimer UN along with Ufd1 ...
 6-77 1.91e-27

Nuclear pore localization protein NPL4; Npl4 is part of the heterodimer UN along with Ufd1 which is involved in the recruitment of p97, an AAA ATPase, for tasks involving the ubiquitin pathway. Npl4 has a ubiquitin-like domain which has within its structure a beta-grasp fold with a helical insert.


Pssm-ID: 431926  Cd Length: 80  Bit Score: 105.64  E-value: 1.91e-27
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 281362576    6 ILIRVQSAEGIKRIEISPKSNLKHLYDSVQNALKVD--GFGLFKERNFLTELQASGSQLVG-TSLRHGDMVYLKQ 77
Cdd:pfam11543   5 IIIRVQSADGIKRIEISSDSTLSTLLSKVAEELGFPnnGFSLYLERNKTTELVSSGSKRVSlVGLKHGDSLYLFP 79
Ubl_AtNPL4_like cd17055
ubiquitin-like (Ubl) domain found in Arabidopsis thaliana NPL4-like proteins NPL4-1, NPL4-2, ...
 7-75 2.98e-08

ubiquitin-like (Ubl) domain found in Arabidopsis thaliana NPL4-like proteins NPL4-1, NPL4-2, and similar proteins; The family includes a group of uncharacterized plant ubiquitin-like (Ubl) domain-containing proteins, including Arabidopsis thaliana NPL4-like protein 1 and NPL4-like protein 2.


Pssm-ID: 340575  Cd Length: 73  Bit Score: 50.68  E-value: 2.98e-08
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 281362576   7 LIRVQSAEGIKRIEISPKSNLKHLYDSVQNALKV--DGFGL--FKERNFLTEL-QASGSQLvgtSLRHGDMVYL 75
Cdd:cd17055    2 LLRVRSRDGTERVEVPDDATVGDLKEKIAEQLSVpvSDQTLslDPGPDLLTAKsSATLSQL---GLKHGDMVFL 72
ZnF_RBZ smart00547
Zinc finger domain; Zinc finger domain in Ran-binding proteins (RanBPs), and other proteins. ...
 599-623 1.55e-04

Zinc finger domain; Zinc finger domain in Ran-binding proteins (RanBPs), and other proteins. In RanBPs, this domain binds RanGDP.


Pssm-ID: 197784 [Multi-domain]  Cd Length: 25  Bit Score: 39.22  E-value: 1.55e-04
                           10        20
                   ....*....|....*....|....*
gi 281362576   599 NTWTCNHCTFINRGELTSCEICSLP 623
Cdd:smart00547   1 GDWECPACTFLNFASRSKCFACGAP 25
zf-RanBP pfam00641
Zn-finger in Ran binding protein and others;
601-624 8.07e-04

Zn-finger in Ran binding protein and others;


Pssm-ID: 395516 [Multi-domain]  Cd Length: 30  Bit Score: 36.95  E-value: 8.07e-04
                          10        20
                  ....*....|....*....|....
gi 281362576  601 WTCNHCTFINRGELTSCEICSLPR 624
Cdd:pfam00641   5 WDCSKCLVQNFATSTKCVACQAPK 28
 
Name Accession Description Interval E-value
NPL4 pfam05021
NPL4 family; The HRD4 gene was identical to NPL4, a gene previously implicated in nuclear ...
 254-565 1.73e-176

NPL4 family; The HRD4 gene was identical to NPL4, a gene previously implicated in nuclear transport. Using a diverse set of substrates and direct ubiquitination assays, analysis revealed that HRD4/NPL4 is required for a poorly characterized step in ER-associated degradation after ubiquitination of target proteins but before their recognition by the 26S proteasome. Npl4p physically associates with Cdc48p via Ufd1p to form a Cdc48p-Ufd1p-Npl4p complex. The Cdc48-Ufd1-Npl4 complex functions in the recognition of several polyubiquitin-tagged proteins and facilitates their presentation to the 26S proteasome for processive degradation or even more specific processing.


Pssm-ID: 461524  Cd Length: 309  Bit Score: 502.57  E-value: 1.73e-176
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281362576  254 RMGYLYGTYEQHTDVPLGIRAKVAAIYEPPQESTRDSINIQPDEFADDVDAVASALGLKKIGWIFTDLITDDASIGTVKQ 333
Cdd:pfam05021   1 RFGYLYGRYEEYDEVPLGIKAVVEAIYEPPQHDELDGITLLPWENEKDVDEIARELGLERVGVIFTDLTDAGAGDGTVLC 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281362576  334 IRGIESHFITAQECITAGELQNRHPNPCKYASNGVFGSKFVTICVTGDKTKQVHMEGYAVSAQCMALVRDNCLIPTKDaP 413
Cdd:pfam05021  81 KRHKDSYFLSSLEVIMAARLQARHPNPTKYSETGRFGSKFVTCVVSGDLNGEIDISSYQVSNQAEALVRADIIEPSTD-P 159

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281362576  414 ELGYVRESTDKQYVPDVFYKEKDLYGNEVQRLARP-LPVEYLLVDVPASTPLQPIYTFteyDKRQPFPIENRYIDGHLQD 492
Cdd:pfam05021 160 SVAYVRESSDERYVPEVFYSKINEYGLEVKENAKPaFPVEYLLVTLTHGFPLEPSPTF---SANNGFPIENREAMGELQD 236

                         250       260       270       280       290       300       310
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 281362576  493 FNALSCYLSAWG-EEEFLEAISDFHLLVYLYKMDMLPlRQHMGPLLEAVRTKNPNQAAQFKVVDVWKLLESLIQ 565
Cdd:pfam05021 237 LSALAKYLKSSAdPNDFLEALSNFHLLLYLHSLGILS-KDEESLLCRAATQKDTEDLLQLIESPGWQTLVTILQ 309
NPL4 COG5100
Nuclear pore protein [Nuclear structure];
6-527 2.76e-132

Nuclear pore protein [Nuclear structure];


Pssm-ID: 227431 [Multi-domain]  Cd Length: 571  Bit Score: 399.76  E-value: 2.76e-132
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281362576   6 ILIRVQSAEGIKRIEISPKSNL-----KHLYDSVQNAlKVDGFGLFKERN----FLTELQASGSQLVGtsLRHGDMVYLK 76
Cdd:COG5100    1 MIFRFRSKEGQRRVEVQESDVLgmlspKLLAFFEVNY-SPEQISVCSAPDgqgeIFSLLKDQTPDDLG--LRHGQMLYLE 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281362576  77 QMAGTSSRRTSTTVldsqAFKTSTISNPN--SARPSFNVIEDDVDQALSKADGTIKRERdSKLCHHNANGRCVHCSALEP 154
Cdd:COG5100   78 YSDIASNNEKKRDV----PGKPKQDCSKGikREKDSMPVIQDPIDDSLEKEDGLIRRSM-TMLCQHGSNGMCSYCSPLDP 152

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281362576 155 YDESYLKEHNIKHLSFHSYIRKQTSGMDQ---GKYFV--FDDINCRIKPGCRE-HPPWPKGICSKCQPSAITLNRQTYRH 228
Cdd:COG5100  153 WDEKYYKDNKIKHLSFHSYLEKMNSNKNKlgsVESYIvpLEEPSFTVKETCEDgHGPWPHGICNKCQPSNIILAPQVFRM 232

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281362576 229 VDNVMFENTKIVERFLNYWRTTGHQRMGYLYGTYEQHTDVPLGIRAKVAAIYEPPQESTRDSINIQPDEFADDVDAVASA 308
Cdd:COG5100  233 VDHVEFDGKHIVENFIRNWRESGRQRFGYLYGRYMDYENIPLGIKAVVEAIYEPPQEDEPDGFTIEEWADEGLMDAPASG 312

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281362576 309 LGLKKIGWIFTDLITDDASIGTVKQIRGIESHFITAQECITAGELQNRHPNPCKYASNGVFGSKFVTICVTGDKTKQVHM 388
Cdd:COG5100  313 TGLERIGMIFTDLLDEGSNRGSVTCKRHADSYFLSSLEVEFIAKMQTMHPNTVKDSREGEFGSKFVTIVISGNLDGEIGL 392

                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281362576 389 EGYAVSAQCMALVRDNCLIPTKDaPELGYVRESTDKQYVPDVFYKEKDLYGNEVQRLARP-LPVEYLLVDVPASTPLQPI 467
Cdd:COG5100  393 QSYQVSNQCMALVKADYILPSED-PRRFLATKEDQTRYVPDIFYRYTDTYGEEVMENAKPaFPVEFLLVTLTHGFPEKPN 471

                        490       500       510       520       530       540
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 281362576 468 YTFTEYDKrqpFPIENRYIDGHLQDFNALSCYL--SAWGEEEFLEAISDFHLLVYLYKMDML 527
Cdd:COG5100  472 PLFRSIDF---IPKKFGDRKMAEYFGGDLSKELfsNFTLLTRIQGVFSNFKDLLKIIVLRIL 530
MPN_NPL4 cd08061
Mov34/MPN/PAD-1 family: nuclear protein localization-4 (Npl4) domain; Npl4p (nuclear protein ...
 220-521 3.73e-131

Mov34/MPN/PAD-1 family: nuclear protein localization-4 (Npl4) domain; Npl4p (nuclear protein localization-4) is identical to Hmg-CoA reductase degradation 4 (HRD4) protein and contains a domain that is part of the pfam clan MPN/Mov34-like. Npl4 plays an intermediate role between endoplasmic reticulum-associated degradation (ERAD) substrate ubiquitylation and proteasomal degradation. Npl4p associates with Cdc48p (Cdc48 in yeast and p97 or valosin-containing protein (VCP) in higher eukaryotes), the highly conserved ATPase of the AAA family, via ubiquitin fusion degradation-1 protein (Ufd1p) to form a Cdc48p-Ufd1p-Npl4p complex which then functions in the recognition of several polyubiquitin-tagged proteins and facilitates their presentation to the 26S proteasome for processive degradation. This family of eukaryotic MPN-like domains lacks the key residues that coordinate a metal ion and therefore does not show catalytic isopeptidase activity.


Pssm-ID: 163692  Cd Length: 274  Bit Score: 385.94  E-value: 3.73e-131
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281362576 220 TLNRQTYRHVDNVMFENTKIVERFLN-YWRTTGHQRMGYLYGTYEQHTDVPLGIRAKVAAIYEPPQESTRDSINIQPDEF 298
Cdd:cd08061    1 TLKRQKYRHVDHVEFDNPSIVEFFLYvFWRKTGQQRIGFLYGRYDEDEDVPLGIKAVVEAIYEPPQEGTPDGFELLEDPN 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281362576 299 ADDVDAVASALGLKKIGWIFTDLITDDasigtvkqirgIESHFITAQECITAGELQNRHPnpckyasNGVFGSKFVTICV 378
Cdd:cd08061   81 ADTVDAIAAALGLERVGWIFTDLPRED-----------KDGYFLSAEEVILAAKFQLKHP-------TGKFGSKFVTVVV 142

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281362576 379 TGDKTKQVHMEGYAVSAQCMALVRDNCLIPTKDAPELgYVRESTDKQYVPDVFYKEKDLYGneVQRLARPLPVEYLLVDV 458
Cdd:cd08061  143 TGDKDGQIHFEAYQVSDQAMALVRDGLLLPTKDADEL-YVREPTLERYVPDVFYSGKDKYG--KTKAVPEVDVEYFLVDV 219

                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 281362576 459 PASTPLQPIytfteYDKRQPFPIENRY-IDGHLQDFNALSCYLSawgeEEFLEAISDFHLLVYL 521
Cdd:cd08061  220 PHGFPLSPS-----SFKSSDFPIENRPpSLGELQDLDALARYLG----KPFLERLSDFHLLLYL 274
zf-NPL4 pfam05020
NPL4 family, putative zinc binding region; The HRD4 gene was identical to NPL4, a gene ...
 113-251 2.63e-87

NPL4 family, putative zinc binding region; The HRD4 gene was identical to NPL4, a gene previously implicated in nuclear transport. Using a diverse set of substrates and direct ubiquitination assays, analysis revealed that HRD4/NPL4 is required for a poorly characterized step in ER-associated degradation after ubiquitination of target proteins but before their recognition by the 26S proteasome. This region of the protein contains possibly two zinc binding motifs (Bateman A pers. obs.). Npl4p physically associates with Cdc48p via Ufd1p to form a Cdc48p-Ufd1p-Npl4p complex. The Cdc48-Ufd1-Npl4 complex functions in the recognition of several polyubiquitin-tagged proteins and facilitates their presentation to the 26S proteasome for processive degradation or even more specific processing.


Pssm-ID: 461523  Cd Length: 145  Bit Score: 267.92  E-value: 2.63e-87
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281362576  113 VIEDDVDQALSKADGTIKRERDSKLCHHNANGRCVHCSALEPYDESYLKEHNIKHLSFHSYIRKQTSGMD-----QGKYF 187
Cdd:pfam05020   1 VKEDPVDDYLDKQDGKIPRKRDPKLCRHGPKGMCDYCSPLEPYDEEYLKEHKIKHLSFHAYLRKLNSGTNkkesgSSYIP 80

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 281362576  188 VFDDINCRIKPGCRE-HPPWPKGICSKCQPSAITLNRQTYRHVDNVMFENTKIVERFLNYWRTTG 251
Cdd:pfam05020  81 PLEEPSYKVKPGCPSgHPPWPKGICSKCQPSAITLQRQPFRMVDHVEFANSEIVNRFLDFWRKTG 145
UN_NPL4 pfam11543
Nuclear pore localization protein NPL4; Npl4 is part of the heterodimer UN along with Ufd1 ...
 6-77 1.91e-27

Nuclear pore localization protein NPL4; Npl4 is part of the heterodimer UN along with Ufd1 which is involved in the recruitment of p97, an AAA ATPase, for tasks involving the ubiquitin pathway. Npl4 has a ubiquitin-like domain which has within its structure a beta-grasp fold with a helical insert.


Pssm-ID: 431926  Cd Length: 80  Bit Score: 105.64  E-value: 1.91e-27
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 281362576    6 ILIRVQSAEGIKRIEISPKSNLKHLYDSVQNALKVD--GFGLFKERNFLTELQASGSQLVG-TSLRHGDMVYLKQ 77
Cdd:pfam11543   5 IIIRVQSADGIKRIEISSDSTLSTLLSKVAEELGFPnnGFSLYLERNKTTELVSSGSKRVSlVGLKHGDSLYLFP 79
Ubl_AtNPL4_like cd17055
ubiquitin-like (Ubl) domain found in Arabidopsis thaliana NPL4-like proteins NPL4-1, NPL4-2, ...
 7-75 2.98e-08

ubiquitin-like (Ubl) domain found in Arabidopsis thaliana NPL4-like proteins NPL4-1, NPL4-2, and similar proteins; The family includes a group of uncharacterized plant ubiquitin-like (Ubl) domain-containing proteins, including Arabidopsis thaliana NPL4-like protein 1 and NPL4-like protein 2.


Pssm-ID: 340575  Cd Length: 73  Bit Score: 50.68  E-value: 2.98e-08
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 281362576   7 LIRVQSAEGIKRIEISPKSNLKHLYDSVQNALKV--DGFGL--FKERNFLTEL-QASGSQLvgtSLRHGDMVYL 75
Cdd:cd17055    2 LLRVRSRDGTERVEVPDDATVGDLKEKIAEQLSVpvSDQTLslDPGPDLLTAKsSATLSQL---GLKHGDMVFL 72
MPN cd07767
Mpr1p, Pad1p N-terminal (MPN) domains; MPN (also known as Mov34, PAD-1, JAMM, JAB, MPN+) ...
 248-391 1.40e-07

Mpr1p, Pad1p N-terminal (MPN) domains; MPN (also known as Mov34, PAD-1, JAMM, JAB, MPN+) domains are found in the N-terminal termini of proteins with a variety of functions; they are components of the proteasome regulatory subunits, the signalosome (CSN), eukaryotic translation initiation factor 3 (eIF3) complexes, and regulators of transcription factors. These domains are isopeptidases that release ubiquitin from ubiquitinated proteins (thus having deubiquitinating (DUB) activity) that are tagged for degradation. Catalytically active MPN domains contain a metalloprotease signature known as the JAB1/MPN/Mov34 metalloenzyme (JAMM) motif. For example, Rpn11 (also known as POH1 or PSMD14), a subunit of the 19S proteasome lid is involved in the ATP-dependent degradation of ubiquitinated proteins, contains the conserved JAMM motif involved in zinc ion coordination. Poh1 is a regulator of c-Jun, an important regulator of cell proliferation, differentiation, survival and death. JAB1 is a component of the COP9 signalosome (CSN), a regulatory particle of the ubiquitin (Ub)/26S proteasome system occurring in all eukaryotic cells; it cleaves the ubiquitin-like protein NEDD8 from the cullin subunit of the SCF (Skp1, Cullins, F-box proteins) family of E3 ubiquitin ligases. AMSH (associated molecule with the SH3 domain of STAM, also known as STAMBP), a member of JAMM/MPN+ deubiquitinases (DUBs), specifically cleaves Lys 63-linked polyubiquitin (poly-Ub) chains, thus facilitating the recycling and subsequent trafficking of receptors to the cell surface. Similarly, BRCC36, part of the nuclear complex that includes BRCA1 protein and is targeted to DNA damage foci after irradiation, specifically disassembles K63-linked polyUb. BRCC36 is aberrantly expressed in sporadic breast tumors, indicative of a potential role in the pathogenesis of the disease. Some variants of the JAB1/MPN domains lack key residues in their JAMM motif and are unable to coordinate a metal ion. Comparisons of key catalytic and metal binding residues explain why the MPN-containing proteins Mov34/PSMD7, Rpn8, CSN6, Prp8p, and the translation initiation factor 3 subunits f (p47) and h (p40) do not show catalytic isopeptidase activity. It has been proposed that the MPN domain in these proteins has a primarily structural function.


Pssm-ID: 163686 [Multi-domain]  Cd Length: 116  Bit Score: 50.20  E-value: 1.40e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281362576 248 RTTGHQRMGYLYGTYEQHtdvpLGIRAKVAAIYEPPQESTRDSiniqpdEFADDVDAVASALGLKKIGWIFTDLitddas 327
Cdd:cd07767   10 SINGKEVIGLLYGSKTKK----VLDVDEVIAVPFDEGDKDDNV------WFLMYLDFKKLNAGLRIVGWYHTHP------ 73

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 281362576 328 igtvkqirgIESHFITAQECITAGELQNRhpnpckyasngvFGSKFVTICVTGDKTKQVHMEGY 391
Cdd:cd07767   74 ---------KPSCFLSPNDLATHELFQRY------------FPEKVMIIVDVKPKDLGNSWKCY 116
ZnF_RBZ smart00547
Zinc finger domain; Zinc finger domain in Ran-binding proteins (RanBPs), and other proteins. ...
 599-623 1.55e-04

Zinc finger domain; Zinc finger domain in Ran-binding proteins (RanBPs), and other proteins. In RanBPs, this domain binds RanGDP.


Pssm-ID: 197784 [Multi-domain]  Cd Length: 25  Bit Score: 39.22  E-value: 1.55e-04
                           10        20
                   ....*....|....*....|....*
gi 281362576   599 NTWTCNHCTFINRGELTSCEICSLP 623
Cdd:smart00547   1 GDWECPACTFLNFASRSKCFACGAP 25
zf-RanBP pfam00641
Zn-finger in Ran binding protein and others;
601-624 8.07e-04

Zn-finger in Ran binding protein and others;


Pssm-ID: 395516 [Multi-domain]  Cd Length: 30  Bit Score: 36.95  E-value: 8.07e-04
                          10        20
                  ....*....|....*....|....
gi 281362576  601 WTCNHCTFINRGELTSCEICSLPR 624
Cdd:pfam00641   5 WDCSKCLVQNFATSTKCVACQAPK 28
 
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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