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Conserved domains on  [gi|1845972123|ref|NP_001370453|]
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Nuclear protein localization protein 4 homolog 1 [Caenorhabditis elegans]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
NPL4 super family cl47910
NPL4 family; The HRD4 gene was identical to NPL4, a gene previously implicated in nuclear ...
 151-470 6.08e-165

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.


The actual alignment was detected with superfamily member pfam05021:

Pssm-ID: 461524  Cd Length: 309  Bit Score: 469.83  E-value: 6.08e-165
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1845972123 151 RVGFLIGQYQPHLEVPLGIKATVAAIYEPPQHCREDGIEFLEDKNQKTIDNLLEMLGLQRVGWIFTDCWTANSAEGTVHY 230
Cdd:pfam05021   1 RFGYLYGRYEEYDEVPLGIKAVVEAIYEPPQHDELDGITLLPWENEKDVDEIARELGLERVGVIFTDLTDAGAGDGTVLC 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1845972123 231 TRHKDSFFLSAEECITAAMLQNQHPNITEYSMDRHYGSKFVTVVASGDESMHVNFHGYQVSNQCAAMVEADILCPTLYtP 310
Cdd:pfam05021  81 KRHKDSYFLSSLEVIMAARLQARHPNPTKYSETGRFGSKFVTCVVSGDLNGEIDISSYQVSNQAEALVRADIIEPSTD-P 159

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1845972123 311 ELAYVRETplSEEHYITDVQFSMKNEYGAEVMKNGRP-LPVEYLLVDVPAGMPKEPHYTFhvgtsnkSKSAKFNVENRQA 389
Cdd:pfam05021 160 SVAYVRES--SDERYVPEVFYSKINEYGLEVKENAKPaFPVEYLLVTLTHGFPLEPSPTF-------SANNGFPIENREA 230

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1845972123 390 IGQLQGGANLIQYSSEFS-KNQFLEQATNFHFLLYLVTNDQVqiSDEWMKRLCDAVKAQDRGTAMEWaQECEDWHQLMAL 468
Cdd:pfam05021 231 MGELQDLSALAKYLKSSAdPNDFLEALSNFHLLLYLHSLGIL--SKDEESLLCRAATQKDTEDLLQL-IESPGWQTLVTI 307


                  ..
gi 1845972123 469 AH 470
Cdd:pfam05021 308 LQ 309
zf-NPL4 pfam05020
NPL4 family, putative zinc binding region; The HRD4 gene was identical to NPL4, a gene ...
 13-148 3.00e-69

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: 218.61  E-value: 3.00e-69
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1845972123  13 DVDVFLSTQDGQIQRPKGPN-CRHPVRQKCTNCLPVDPFDEEYLKEKDIKHMSFHAHVRKLLGSQGK---GTTLKKPLEN 88
Cdd:pfam05020   5 PVDDYLDKQDGKIPRKRDPKlCRHGPKGMCDYCSPLEPYDEEYLKEHKIKHLSFHAYLRKLNSGTNKkesGSSYIPPLEE 84

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1845972123  89 FRCSLKPNC-DAHKPFPKGICTKCKPQVVTLNRQKFRHVDNIQIENQELVNQFLDYWRLSG 148
Cdd:pfam05020  85 PSYKVKPGCpSGHPPWPKGICSKCQPSAITLQRQPFRMVDHVEFANSEIVNRFLDFWRKTG 145
ZnF_RBZ smart00547
Zinc finger domain; Zinc finger domain in Ran-binding proteins (RanBPs), and other proteins. ...
 502-524 7.84e-05

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: 39.61  E-value: 7.84e-05
                           10        20
                   ....*....|....*....|...
gi 1845972123  502 WNCGHCTFQNEAARQDCSMCGLP 524
Cdd:smart00547   3 WECPACTFLNFASRSKCFACGAP 25
 
Name Accession Description Interval E-value
NPL4 pfam05021
NPL4 family; The HRD4 gene was identical to NPL4, a gene previously implicated in nuclear ...
 151-470 6.08e-165

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: 469.83  E-value: 6.08e-165
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1845972123 151 RVGFLIGQYQPHLEVPLGIKATVAAIYEPPQHCREDGIEFLEDKNQKTIDNLLEMLGLQRVGWIFTDCWTANSAEGTVHY 230
Cdd:pfam05021   1 RFGYLYGRYEEYDEVPLGIKAVVEAIYEPPQHDELDGITLLPWENEKDVDEIARELGLERVGVIFTDLTDAGAGDGTVLC 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1845972123 231 TRHKDSFFLSAEECITAAMLQNQHPNITEYSMDRHYGSKFVTVVASGDESMHVNFHGYQVSNQCAAMVEADILCPTLYtP 310
Cdd:pfam05021  81 KRHKDSYFLSSLEVIMAARLQARHPNPTKYSETGRFGSKFVTCVVSGDLNGEIDISSYQVSNQAEALVRADIIEPSTD-P 159

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1845972123 311 ELAYVRETplSEEHYITDVQFSMKNEYGAEVMKNGRP-LPVEYLLVDVPAGMPKEPHYTFhvgtsnkSKSAKFNVENRQA 389
Cdd:pfam05021 160 SVAYVRES--SDERYVPEVFYSKINEYGLEVKENAKPaFPVEYLLVTLTHGFPLEPSPTF-------SANNGFPIENREA 230

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1845972123 390 IGQLQGGANLIQYSSEFS-KNQFLEQATNFHFLLYLVTNDQVqiSDEWMKRLCDAVKAQDRGTAMEWaQECEDWHQLMAL 468
Cdd:pfam05021 231 MGELQDLSALAKYLKSSAdPNDFLEALSNFHLLLYLHSLGIL--SKDEESLLCRAATQKDTEDLLQL-IESPGWQTLVTI 307


                  ..
gi 1845972123 469 AH 470
Cdd:pfam05021 308 LQ 309
MPN_NPL4 cd08061
Mov34/MPN/PAD-1 family: nuclear protein localization-4 (Npl4) domain; Npl4p (nuclear protein ...
 117-424 6.57e-119

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: 351.28  E-value: 6.57e-119
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1845972123 117 TLNRQKFRHVDNIQIENQELVNQFLD-YWRLSGHQRVGFLIGQYQPHLEVPLGIKATVAAIYEPPQHCREDGIEFLEDKN 195
Cdd:cd08061     1 TLKRQKYRHVDHVEFDNPSIVEFFLYvFWRKTGQQRIGFLYGRYDEDEDVPLGIKAVVEAIYEPPQEGTPDGFELLEDPN 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1845972123 196 QKTIDNLLEMLGLQRVGWIFTDCWtansaegtvhyTRHKDSFFLSAEECITAAMLQNQHPniteysmDRHYGSKFVTVVA 275
Cdd:cd08061    81 ADTVDAIAAALGLERVGWIFTDLP-----------REDKDGYFLSAEEVILAAKFQLKHP-------TGKFGSKFVTVVV 142

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1845972123 276 SGDESMHVNFHGYQVSNQCAAMVEADILCPTLYTPELaYVRETPlsEEHYITDVQFSMKNEYGaeVMKNGRPLPVEYLLV 355
Cdd:cd08061   143 TGDKDGQIHFEAYQVSDQAMALVRDGLLLPTKDADEL-YVREPT--LERYVPDVFYSGKDKYG--KTKAVPEVDVEYFLV 217

                         250       260       270       280       290       300       310
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1845972123 356 DVPAGMPKEPHYtfhvgtsnkSKSAKFNVENRQA-IGQLQGGANLIQYssefSKNQFLEQATNFHFLLYL 424
Cdd:cd08061   218 DVPHGFPLSPSS---------FKSSDFPIENRPPsLGELQDLDALARY----LGKPFLERLSDFHLLLYL 274
NPL4 COG5100
Nuclear pore protein [Nuclear structure];
14-436 5.27e-114

Nuclear pore protein [Nuclear structure];


Pssm-ID: 227431 [Multi-domain]  Cd Length: 571  Bit Score: 349.30  E-value: 5.27e-114
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1845972123  14 VDVFLSTQDGQIQRPKGPNCRHPVRQKCTNCLPVDPFDEEYLKEKDIKHMSFHAHVRKL---LGSQGKGTTLKKPLENFR 90
Cdd:COG5100   117 IDDSLEKEDGLIRRSMTMLCQHGSNGMCSYCSPLDPWDEKYYKDNKIKHLSFHSYLEKMnsnKNKLGSVESYIVPLEEPS 196

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1845972123  91 CSLKPNC-DAHKPFPKGICTKCKPQVVTLNRQKFRHVDNIQIENQELVNQFLDYWRLSGHQRVGFLIGQYQPHLEVPLGI 169
Cdd:COG5100   197 FTVKETCeDGHGPWPHGICNKCQPSNIILAPQVFRMVDHVEFDGKHIVENFIRNWRESGRQRFGYLYGRYMDYENIPLGI 276

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1845972123 170 KATVAAIYEPPQHCREDGIEFLEDKNQKTIDNLLEMLGLQRVGWIFTDCWTANSAEGTVHYTRHKDSFFLSAEECITAAM 249
Cdd:COG5100   277 KAVVEAIYEPPQEDEPDGFTIEEWADEGLMDAPASGTGLERIGMIFTDLLDEGSNRGSVTCKRHADSYFLSSLEVEFIAK 356

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1845972123 250 LQNQHPNITEYSMDRHYGSKFVTVVASGDESMHVNFHGYQVSNQCAAMVEADILCPTLYtPELAYVRETplSEEHYITDV 329
Cdd:COG5100   357 MQTMHPNTVKDSREGEFGSKFVTIVISGNLDGEIGLQSYQVSNQCMALVKADYILPSED-PRRFLATKE--DQTRYVPDI 433

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1845972123 330 QFSMKNEYGAEVMKNGRP-LPVEYLLVDVPAGMPKEPHYTFhvgtsnkSKSAKFNVENRQAIGQLQGGANLIQYssEFSK 408
Cdd:COG5100   434 FYRYTDTYGEEVMENAKPaFPVEFLLVTLTHGFPEKPNPLF-------RSIDFIPKKFGDRKMAEYFGGDLSKE--LFSN 504

                         410       420       430
                  ....*....|....*....|....*....|..
gi 1845972123 409 NQFL----EQATNFHFLLYLVTnDQVQISDEW 436
Cdd:COG5100   505 FTLLtriqGVFSNFKDLLKIIV-LRILDKFDF 535
zf-NPL4 pfam05020
NPL4 family, putative zinc binding region; The HRD4 gene was identical to NPL4, a gene ...
 13-148 3.00e-69

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: 218.61  E-value: 3.00e-69
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1845972123  13 DVDVFLSTQDGQIQRPKGPN-CRHPVRQKCTNCLPVDPFDEEYLKEKDIKHMSFHAHVRKLLGSQGK---GTTLKKPLEN 88
Cdd:pfam05020   5 PVDDYLDKQDGKIPRKRDPKlCRHGPKGMCDYCSPLEPYDEEYLKEHKIKHLSFHAYLRKLNSGTNKkesGSSYIPPLEE 84

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1845972123  89 FRCSLKPNC-DAHKPFPKGICTKCKPQVVTLNRQKFRHVDNIQIENQELVNQFLDYWRLSG 148
Cdd:pfam05020  85 PSYKVKPGCpSGHPPWPKGICSKCQPSAITLQRQPFRMVDHVEFANSEIVNRFLDFWRKTG 145
ZnF_RBZ smart00547
Zinc finger domain; Zinc finger domain in Ran-binding proteins (RanBPs), and other proteins. ...
 502-524 7.84e-05

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: 39.61  E-value: 7.84e-05
                           10        20
                   ....*....|....*....|...
gi 1845972123  502 WNCGHCTFQNEAARQDCSMCGLP 524
Cdd:smart00547   3 WECPACTFLNFASRSKCFACGAP 25
zf-RanBP pfam00641
Zn-finger in Ran binding protein and others;
502-525 2.65e-03

Zn-finger in Ran binding protein and others;


Pssm-ID: 395516 [Multi-domain]  Cd Length: 30  Bit Score: 35.41  E-value: 2.65e-03
                          10        20
                  ....*....|....*....|....
gi 1845972123 502 WNCGHCTFQNEAARQDCSMCGLPA 525
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 ...
 151-470 6.08e-165

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: 469.83  E-value: 6.08e-165
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1845972123 151 RVGFLIGQYQPHLEVPLGIKATVAAIYEPPQHCREDGIEFLEDKNQKTIDNLLEMLGLQRVGWIFTDCWTANSAEGTVHY 230
Cdd:pfam05021   1 RFGYLYGRYEEYDEVPLGIKAVVEAIYEPPQHDELDGITLLPWENEKDVDEIARELGLERVGVIFTDLTDAGAGDGTVLC 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1845972123 231 TRHKDSFFLSAEECITAAMLQNQHPNITEYSMDRHYGSKFVTVVASGDESMHVNFHGYQVSNQCAAMVEADILCPTLYtP 310
Cdd:pfam05021  81 KRHKDSYFLSSLEVIMAARLQARHPNPTKYSETGRFGSKFVTCVVSGDLNGEIDISSYQVSNQAEALVRADIIEPSTD-P 159

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1845972123 311 ELAYVRETplSEEHYITDVQFSMKNEYGAEVMKNGRP-LPVEYLLVDVPAGMPKEPHYTFhvgtsnkSKSAKFNVENRQA 389
Cdd:pfam05021 160 SVAYVRES--SDERYVPEVFYSKINEYGLEVKENAKPaFPVEYLLVTLTHGFPLEPSPTF-------SANNGFPIENREA 230

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1845972123 390 IGQLQGGANLIQYSSEFS-KNQFLEQATNFHFLLYLVTNDQVqiSDEWMKRLCDAVKAQDRGTAMEWaQECEDWHQLMAL 468
Cdd:pfam05021 231 MGELQDLSALAKYLKSSAdPNDFLEALSNFHLLLYLHSLGIL--SKDEESLLCRAATQKDTEDLLQL-IESPGWQTLVTI 307


                  ..
gi 1845972123 469 AH 470
Cdd:pfam05021 308 LQ 309
MPN_NPL4 cd08061
Mov34/MPN/PAD-1 family: nuclear protein localization-4 (Npl4) domain; Npl4p (nuclear protein ...
 117-424 6.57e-119

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: 351.28  E-value: 6.57e-119
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1845972123 117 TLNRQKFRHVDNIQIENQELVNQFLD-YWRLSGHQRVGFLIGQYQPHLEVPLGIKATVAAIYEPPQHCREDGIEFLEDKN 195
Cdd:cd08061     1 TLKRQKYRHVDHVEFDNPSIVEFFLYvFWRKTGQQRIGFLYGRYDEDEDVPLGIKAVVEAIYEPPQEGTPDGFELLEDPN 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1845972123 196 QKTIDNLLEMLGLQRVGWIFTDCWtansaegtvhyTRHKDSFFLSAEECITAAMLQNQHPniteysmDRHYGSKFVTVVA 275
Cdd:cd08061    81 ADTVDAIAAALGLERVGWIFTDLP-----------REDKDGYFLSAEEVILAAKFQLKHP-------TGKFGSKFVTVVV 142

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1845972123 276 SGDESMHVNFHGYQVSNQCAAMVEADILCPTLYTPELaYVRETPlsEEHYITDVQFSMKNEYGaeVMKNGRPLPVEYLLV 355
Cdd:cd08061   143 TGDKDGQIHFEAYQVSDQAMALVRDGLLLPTKDADEL-YVREPT--LERYVPDVFYSGKDKYG--KTKAVPEVDVEYFLV 217

                         250       260       270       280       290       300       310
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1845972123 356 DVPAGMPKEPHYtfhvgtsnkSKSAKFNVENRQA-IGQLQGGANLIQYssefSKNQFLEQATNFHFLLYL 424
Cdd:cd08061   218 DVPHGFPLSPSS---------FKSSDFPIENRPPsLGELQDLDALARY----LGKPFLERLSDFHLLLYL 274
NPL4 COG5100
Nuclear pore protein [Nuclear structure];
14-436 5.27e-114

Nuclear pore protein [Nuclear structure];


Pssm-ID: 227431 [Multi-domain]  Cd Length: 571  Bit Score: 349.30  E-value: 5.27e-114
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1845972123  14 VDVFLSTQDGQIQRPKGPNCRHPVRQKCTNCLPVDPFDEEYLKEKDIKHMSFHAHVRKL---LGSQGKGTTLKKPLENFR 90
Cdd:COG5100   117 IDDSLEKEDGLIRRSMTMLCQHGSNGMCSYCSPLDPWDEKYYKDNKIKHLSFHSYLEKMnsnKNKLGSVESYIVPLEEPS 196

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1845972123  91 CSLKPNC-DAHKPFPKGICTKCKPQVVTLNRQKFRHVDNIQIENQELVNQFLDYWRLSGHQRVGFLIGQYQPHLEVPLGI 169
Cdd:COG5100   197 FTVKETCeDGHGPWPHGICNKCQPSNIILAPQVFRMVDHVEFDGKHIVENFIRNWRESGRQRFGYLYGRYMDYENIPLGI 276

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1845972123 170 KATVAAIYEPPQHCREDGIEFLEDKNQKTIDNLLEMLGLQRVGWIFTDCWTANSAEGTVHYTRHKDSFFLSAEECITAAM 249
Cdd:COG5100   277 KAVVEAIYEPPQEDEPDGFTIEEWADEGLMDAPASGTGLERIGMIFTDLLDEGSNRGSVTCKRHADSYFLSSLEVEFIAK 356

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1845972123 250 LQNQHPNITEYSMDRHYGSKFVTVVASGDESMHVNFHGYQVSNQCAAMVEADILCPTLYtPELAYVRETplSEEHYITDV 329
Cdd:COG5100   357 MQTMHPNTVKDSREGEFGSKFVTIVISGNLDGEIGLQSYQVSNQCMALVKADYILPSED-PRRFLATKE--DQTRYVPDI 433

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1845972123 330 QFSMKNEYGAEVMKNGRP-LPVEYLLVDVPAGMPKEPHYTFhvgtsnkSKSAKFNVENRQAIGQLQGGANLIQYssEFSK 408
Cdd:COG5100   434 FYRYTDTYGEEVMENAKPaFPVEFLLVTLTHGFPEKPNPLF-------RSIDFIPKKFGDRKMAEYFGGDLSKE--LFSN 504

                         410       420       430
                  ....*....|....*....|....*....|..
gi 1845972123 409 NQFL----EQATNFHFLLYLVTnDQVQISDEW 436
Cdd:COG5100   505 FTLLtriqGVFSNFKDLLKIIV-LRILDKFDF 535
zf-NPL4 pfam05020
NPL4 family, putative zinc binding region; The HRD4 gene was identical to NPL4, a gene ...
 13-148 3.00e-69

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: 218.61  E-value: 3.00e-69
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1845972123  13 DVDVFLSTQDGQIQRPKGPN-CRHPVRQKCTNCLPVDPFDEEYLKEKDIKHMSFHAHVRKLLGSQGK---GTTLKKPLEN 88
Cdd:pfam05020   5 PVDDYLDKQDGKIPRKRDPKlCRHGPKGMCDYCSPLEPYDEEYLKEHKIKHLSFHAYLRKLNSGTNKkesGSSYIPPLEE 84

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1845972123  89 FRCSLKPNC-DAHKPFPKGICTKCKPQVVTLNRQKFRHVDNIQIENQELVNQFLDYWRLSG 148
Cdd:pfam05020  85 PSYKVKPGCpSGHPPWPKGICSKCQPSAITLQRQPFRMVDHVEFANSEIVNRFLDFWRKTG 145
MPN cd07767
Mpr1p, Pad1p N-terminal (MPN) domains; MPN (also known as Mov34, PAD-1, JAMM, JAB, MPN+) ...
 148-277 2.81e-06

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: 46.35  E-value: 2.81e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1845972123 148 GHQRVGFLIGQYQPHLevplGIKATVAAIYEPPQHcREDGIEFLedknqKTIDNLLEMLGLQRVGWIFTDcwtansaegt 227
Cdd:cd07767    13 GKEVIGLLYGSKTKKV----LDVDEVIAVPFDEGD-KDDNVWFL-----MYLDFKKLNAGLRIVGWYHTH---------- 72

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|
gi 1845972123 228 vhytrHKDSFFLSAEECITAAMLQNqhpniteysmdrHYGSKFVTVVASG 277
Cdd:cd07767    73 -----PKPSCFLSPNDLATHELFQR------------YFPEKVMIIVDVK 105
ZnF_RBZ smart00547
Zinc finger domain; Zinc finger domain in Ran-binding proteins (RanBPs), and other proteins. ...
 502-524 7.84e-05

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: 39.61  E-value: 7.84e-05
                           10        20
                   ....*....|....*....|...
gi 1845972123  502 WNCGHCTFQNEAARQDCSMCGLP 524
Cdd:smart00547   3 WECPACTFLNFASRSKCFACGAP 25
zf-RanBP pfam00641
Zn-finger in Ran binding protein and others;
502-525 2.65e-03

Zn-finger in Ran binding protein and others;


Pssm-ID: 395516 [Multi-domain]  Cd Length: 30  Bit Score: 35.41  E-value: 2.65e-03
                          10        20
                  ....*....|....*....|....
gi 1845972123 502 WNCGHCTFQNEAARQDCSMCGLPA 525
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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