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Conserved domains on  [gi|2038324413|ref|XP_041501840|]
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nuclear protein localization protein 4 homolog [Microtus oregoni]

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 super family cl47910
NPL4 family; The HRD4 gene was identical to NPL4, a gene previously implicated in nuclear ...
 249-555 1.05e-153

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: 444.02  E-value: 1.05e-153
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2038324413 249 FGYLYGRYTEHKDIPLGIRAEVAAIYEPPQIGTQNSLELLEDPKAEVVDEIAAKLGLRKVGWIFTDLVSEDTRKGTVRYS 328
Cdd:pfam05021   2 FGYLYGRYEEYDEVPLGIKAVVEAIYEPPQHDELDGITLLPWENEKDVDEIARELGLERVGVIFTDLTDAGAGDGTVLCK 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2038324413 329 RNKDTYFLSSEECITAGDFQNKHPNICRLSPDGHFGSKFVTAVATGGPDNQVHFEGYQVSNQCMALVRDECLLPCKDaPE 408
Cdd:pfam05021  82 RHKDSYFLSSLEVIMAARLQARHPNPTKYSETGRFGSKFVTCVVSGDLNGEIDISSYQVSNQAEALVRADIIEPSTD-PS 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2038324413 409 LGYAKESSSEQYVPDVFYKDIDKFGNEITQLARP-LPVEYLIIDITTTFPKDPVYTFSiSQNPFPIENRDVLGETQDFHS 487
Cdd:pfam05021 161 VAYVRESSDERYVPEVFYSKINEYGLEVKENAKPaFPVEYLLVTLTHGFPLEPSPTFS-ANNGFPIENREAMGELQDLSA 239

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2038324413 488 LATYLSQN-TSSMFLDTISDFHLLLFLVTNEVMPlQDSISLLLEAVRTRNEELAQTWKKSEQWATIEQL 555
Cdd:pfam05021 240 LAKYLKSSaDPNDFLEALSNFHLLLYLHSLGILS-KDEESLLCRAATQKDTEDLLQLIESPGWQTLVTI 307
zf-NPL4 pfam05020
NPL4 family, putative zinc binding region; The HRD4 gene was identical to NPL4, a gene ...
 105-245 1.31e-92

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: 281.40  E-value: 1.31e-92
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2038324413 105 VVEDEIDQYLSKQDGKIYRSRDPQLCRHGPLGKCVHCVPLEPFDEDYLNhlEPPVKHMSFHAYIRKLTGGADK-----GK 179
Cdd:pfam05020   1 VKEDPVDDYLDKQDGKIPRKRDPKLCRHGPKGMCDYCSPLEPYDEEYLK--EHKIKHLSFHAYLRKLNSGTNKkesgsSY 78

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2038324413 180 FVALENISCKIKSGC-EGHLPWPNGICTKCQPSAITLNRQKYRHVDNIMFENHTVADRFLDFWRKTG 245
Cdd:pfam05020  79 IPPLEEPSYKVKPGCpSGHPPWPKGICSKCQPSAITLQRQPFRMVDHVEFANSEIVNRFLDFWRKTG 145
UN_NPL4 pfam11543
Nuclear pore localization protein NPL4; Npl4 is part of the heterodimer UN along with Ufd1 ...
 1-80 1.79e-37

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: 133.75  E-value: 1.79e-37
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2038324413   1 MAESIIIRVQSPDGVKRITATKRETAATFLKKVAKEFGFQNNGFSVYINRNKTGEITASSSKSLHLLKIKHGDLLFLFPS 80
Cdd:pfam11543   1 MAEEIIIRVQSADGIKRIEISSDSTLSTLLSKVAEELGFPNNGFSLYLERNKTTELVSSGSKRVSLVGLKHGDSLYLFPG 80
ZnF_RBZ smart00547
Zinc finger domain; Zinc finger domain in Ran-binding proteins (RanBPs), and other proteins. ...
 584-606 9.73e-03

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: 33.83  E-value: 9.73e-03
                           10        20
                   ....*....|....*....|...
gi 2038324413  584 WACQHCTFMNQPGTGHCEMCSLP 606
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 ...
 249-555 1.05e-153

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: 444.02  E-value: 1.05e-153
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2038324413 249 FGYLYGRYTEHKDIPLGIRAEVAAIYEPPQIGTQNSLELLEDPKAEVVDEIAAKLGLRKVGWIFTDLVSEDTRKGTVRYS 328
Cdd:pfam05021   2 FGYLYGRYEEYDEVPLGIKAVVEAIYEPPQHDELDGITLLPWENEKDVDEIARELGLERVGVIFTDLTDAGAGDGTVLCK 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2038324413 329 RNKDTYFLSSEECITAGDFQNKHPNICRLSPDGHFGSKFVTAVATGGPDNQVHFEGYQVSNQCMALVRDECLLPCKDaPE 408
Cdd:pfam05021  82 RHKDSYFLSSLEVIMAARLQARHPNPTKYSETGRFGSKFVTCVVSGDLNGEIDISSYQVSNQAEALVRADIIEPSTD-PS 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2038324413 409 LGYAKESSSEQYVPDVFYKDIDKFGNEITQLARP-LPVEYLIIDITTTFPKDPVYTFSiSQNPFPIENRDVLGETQDFHS 487
Cdd:pfam05021 161 VAYVRESSDERYVPEVFYSKINEYGLEVKENAKPaFPVEYLLVTLTHGFPLEPSPTFS-ANNGFPIENREAMGELQDLSA 239

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2038324413 488 LATYLSQN-TSSMFLDTISDFHLLLFLVTNEVMPlQDSISLLLEAVRTRNEELAQTWKKSEQWATIEQL 555
Cdd:pfam05021 240 LAKYLKSSaDPNDFLEALSNFHLLLYLHSLGILS-KDEESLLCRAATQKDTEDLLQLIESPGWQTLVTI 307
MPN_NPL4 cd08061
Mov34/MPN/PAD-1 family: nuclear protein localization-4 (Npl4) domain; Npl4p (nuclear protein ...
 214-513 2.24e-146

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: 424.08  E-value: 2.24e-146
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2038324413 214 TLNRQKYRHVDNIMFENHTVADRFLD-FWRKTGNQHFGYLYGRYTEHKDIPLGIRAEVAAIYEPPQIGTQNSLELLEDPK 292
Cdd:cd08061     1 TLKRQKYRHVDHVEFDNPSIVEFFLYvFWRKTGQQRIGFLYGRYDEDEDVPLGIKAVVEAIYEPPQEGTPDGFELLEDPN 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2038324413 293 AEVVDEIAAKLGLRKVGWIFTDLVSEDtrkgtvrysrnKDTYFLSSEECITAGDFQNKHpnicrlsPDGHFGSKFVTAVA 372
Cdd:cd08061    81 ADTVDAIAAALGLERVGWIFTDLPRED-----------KDGYFLSAEEVILAAKFQLKH-------PTGKFGSKFVTVVV 142

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2038324413 373 TGGPDNQVHFEGYQVSNQCMALVRDECLLPCKDAPELgYAKESSSEQYVPDVFYKDIDKFGneITQLARPLPVEYLIIDI 452
Cdd:cd08061   143 TGDKDGQIHFEAYQVSDQAMALVRDGLLLPTKDADEL-YVREPTLERYVPDVFYSGKDKYG--KTKAVPEVDVEYFLVDV 219

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2038324413 453 TTTFPKDPVYTFSIsqnPFPIENRD-VLGETQDFHSLATYLsqntSSMFLDTISDFHLLLFL 513
Cdd:cd08061   220 PHGFPLSPSSFKSS---DFPIENRPpSLGELQDLDALARYL----GKPFLERLSDFHLLLYL 274
NPL4 COG5100
Nuclear pore protein [Nuclear structure];
5-560 9.22e-142

Nuclear pore protein [Nuclear structure];


Pssm-ID: 227431 [Multi-domain]  Cd Length: 571  Bit Score: 423.64  E-value: 9.22e-142
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2038324413   5 IIIRVQSPDGVKRITATKRETAATFLKKVAKEF--GFQNNGFSVYINRNKTGEITAS-SSKSLHLLKIKHGDLLFLFPSS 81
Cdd:COG5100     1 MIFRFRSKEGQRRVEVQESDVLGMLSPKLLAFFevNYSPEQISVCSAPDGQGEIFSLlKDQTPDDLGLRHGQMLYLEYSD 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2038324413  82 LAGPSTEMET---------STSVGLKAFGAPnVVEDEIDQYLSKQDGKIYRSRDpQLCRHGPLGKCVHCVPLEPFDEDYl 152
Cdd:COG5100    81 IASNNEKKRDvpgkpkqdcSKGIKREKDSMP-VIQDPIDDSLEKEDGLIRRSMT-MLCQHGSNGMCSYCSPLDPWDEKY- 157

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2038324413 153 nHLEPPVKHMSFHAYIRKLTGGADK-----GKFVALENISCKIKSGCE-GHLPWPNGICTKCQPSAITLNRQKYRHVDNI 226
Cdd:COG5100   158 -YKDNKIKHLSFHSYLEKMNSNKNKlgsveSYIVPLEEPSFTVKETCEdGHGPWPHGICNKCQPSNIILAPQVFRMVDHV 236

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2038324413 227 MFENHTVADRFLDFWRKTGNQHFGYLYGRYTEHKDIPLGIRAEVAAIYEPPQIGTQNSLELLEDPKAEVVDEIAAKLGLR 306
Cdd:COG5100   237 EFDGKHIVENFIRNWRESGRQRFGYLYGRYMDYENIPLGIKAVVEAIYEPPQEDEPDGFTIEEWADEGLMDAPASGTGLE 316

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2038324413 307 KVGWIFTDLVSEDTRKGTVRYSRNKDTYFLSSEECITAGDFQNKHPNICRLSPDGHFGSKFVTAVATGGPDNQVHFEGYQ 386
Cdd:COG5100   317 RIGMIFTDLLDEGSNRGSVTCKRHADSYFLSSLEVEFIAKMQTMHPNTVKDSREGEFGSKFVTIVISGNLDGEIGLQSYQ 396

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2038324413 387 VSNQCMALVRDECLLPCKDaPELGYAKESSSEQYVPDVFYKDIDKFGNEITQLARP-LPVEYLIIDITTTFPKDPVYTFS 465
Cdd:COG5100   397 VSNQCMALVKADYILPSED-PRRFLATKEDQTRYVPDIFYRYTDTYGEEVMENAKPaFPVEFLLVTLTHGFPEKPNPLFR 475

                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2038324413 466 iSQNPFPIENRDVLGETQDFHSLATYLSQNTSSMFL--DTISDFHLLLFLVTNEVMPLQDSISLLLEAVRTRNEELAQTW 543
Cdd:COG5100   476 -SIDFIPKKFGDRKMAEYFGGDLSKELFSNFTLLTRiqGVFSNFKDLLKIIVLRILDKFDFKSFISSMERYRWECKMCTF 554

                         570
                  ....*....|....*..
gi 2038324413 544 KKSEQWATIEQLCSTVG 560
Cdd:COG5100   555 INEKNSCTCEMCNSTRD 571
zf-NPL4 pfam05020
NPL4 family, putative zinc binding region; The HRD4 gene was identical to NPL4, a gene ...
 105-245 1.31e-92

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: 281.40  E-value: 1.31e-92
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2038324413 105 VVEDEIDQYLSKQDGKIYRSRDPQLCRHGPLGKCVHCVPLEPFDEDYLNhlEPPVKHMSFHAYIRKLTGGADK-----GK 179
Cdd:pfam05020   1 VKEDPVDDYLDKQDGKIPRKRDPKLCRHGPKGMCDYCSPLEPYDEEYLK--EHKIKHLSFHAYLRKLNSGTNKkesgsSY 78

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2038324413 180 FVALENISCKIKSGC-EGHLPWPNGICTKCQPSAITLNRQKYRHVDNIMFENHTVADRFLDFWRKTG 245
Cdd:pfam05020  79 IPPLEEPSYKVKPGCpSGHPPWPKGICSKCQPSAITLQRQPFRMVDHVEFANSEIVNRFLDFWRKTG 145
UN_NPL4 pfam11543
Nuclear pore localization protein NPL4; Npl4 is part of the heterodimer UN along with Ufd1 ...
 1-80 1.79e-37

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: 133.75  E-value: 1.79e-37
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2038324413   1 MAESIIIRVQSPDGVKRITATKRETAATFLKKVAKEFGFQNNGFSVYINRNKTGEITASSSKSLHLLKIKHGDLLFLFPS 80
Cdd:pfam11543   1 MAEEIIIRVQSADGIKRIEISSDSTLSTLLSKVAEELGFPNNGFSLYLERNKTTELVSSGSKRVSLVGLKHGDSLYLFPG 80
Ubl_AtNPL4_like cd17055
ubiquitin-like (Ubl) domain found in Arabidopsis thaliana NPL4-like proteins NPL4-1, NPL4-2, ...
 6-77 1.97e-12

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: 62.62  E-value: 1.97e-12
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2038324413   6 IIRVQSPDGVKRITATKRETAATFLKKVAKEFGFQNNGFSVYINRNKtGEITASSSKSLHLLKIKHGDLLFL 77
Cdd:cd17055     2 LLRVRSRDGTERVEVPDDATVGDLKEKIAEQLSVPVSDQTLSLDPGP-DLLTAKSSATLSQLGLKHGDMVFL 72
ZnF_RBZ smart00547
Zinc finger domain; Zinc finger domain in Ran-binding proteins (RanBPs), and other proteins. ...
 584-606 9.73e-03

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: 33.83  E-value: 9.73e-03
                           10        20
                   ....*....|....*....|...
gi 2038324413  584 WACQHCTFMNQPGTGHCEMCSLP 606
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 ...
 249-555 1.05e-153

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: 444.02  E-value: 1.05e-153
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2038324413 249 FGYLYGRYTEHKDIPLGIRAEVAAIYEPPQIGTQNSLELLEDPKAEVVDEIAAKLGLRKVGWIFTDLVSEDTRKGTVRYS 328
Cdd:pfam05021   2 FGYLYGRYEEYDEVPLGIKAVVEAIYEPPQHDELDGITLLPWENEKDVDEIARELGLERVGVIFTDLTDAGAGDGTVLCK 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2038324413 329 RNKDTYFLSSEECITAGDFQNKHPNICRLSPDGHFGSKFVTAVATGGPDNQVHFEGYQVSNQCMALVRDECLLPCKDaPE 408
Cdd:pfam05021  82 RHKDSYFLSSLEVIMAARLQARHPNPTKYSETGRFGSKFVTCVVSGDLNGEIDISSYQVSNQAEALVRADIIEPSTD-PS 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2038324413 409 LGYAKESSSEQYVPDVFYKDIDKFGNEITQLARP-LPVEYLIIDITTTFPKDPVYTFSiSQNPFPIENRDVLGETQDFHS 487
Cdd:pfam05021 161 VAYVRESSDERYVPEVFYSKINEYGLEVKENAKPaFPVEYLLVTLTHGFPLEPSPTFS-ANNGFPIENREAMGELQDLSA 239

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2038324413 488 LATYLSQN-TSSMFLDTISDFHLLLFLVTNEVMPlQDSISLLLEAVRTRNEELAQTWKKSEQWATIEQL 555
Cdd:pfam05021 240 LAKYLKSSaDPNDFLEALSNFHLLLYLHSLGILS-KDEESLLCRAATQKDTEDLLQLIESPGWQTLVTI 307
MPN_NPL4 cd08061
Mov34/MPN/PAD-1 family: nuclear protein localization-4 (Npl4) domain; Npl4p (nuclear protein ...
 214-513 2.24e-146

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: 424.08  E-value: 2.24e-146
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2038324413 214 TLNRQKYRHVDNIMFENHTVADRFLD-FWRKTGNQHFGYLYGRYTEHKDIPLGIRAEVAAIYEPPQIGTQNSLELLEDPK 292
Cdd:cd08061     1 TLKRQKYRHVDHVEFDNPSIVEFFLYvFWRKTGQQRIGFLYGRYDEDEDVPLGIKAVVEAIYEPPQEGTPDGFELLEDPN 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2038324413 293 AEVVDEIAAKLGLRKVGWIFTDLVSEDtrkgtvrysrnKDTYFLSSEECITAGDFQNKHpnicrlsPDGHFGSKFVTAVA 372
Cdd:cd08061    81 ADTVDAIAAALGLERVGWIFTDLPRED-----------KDGYFLSAEEVILAAKFQLKH-------PTGKFGSKFVTVVV 142

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2038324413 373 TGGPDNQVHFEGYQVSNQCMALVRDECLLPCKDAPELgYAKESSSEQYVPDVFYKDIDKFGneITQLARPLPVEYLIIDI 452
Cdd:cd08061   143 TGDKDGQIHFEAYQVSDQAMALVRDGLLLPTKDADEL-YVREPTLERYVPDVFYSGKDKYG--KTKAVPEVDVEYFLVDV 219

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2038324413 453 TTTFPKDPVYTFSIsqnPFPIENRD-VLGETQDFHSLATYLsqntSSMFLDTISDFHLLLFL 513
Cdd:cd08061   220 PHGFPLSPSSFKSS---DFPIENRPpSLGELQDLDALARYL----GKPFLERLSDFHLLLYL 274
NPL4 COG5100
Nuclear pore protein [Nuclear structure];
5-560 9.22e-142

Nuclear pore protein [Nuclear structure];


Pssm-ID: 227431 [Multi-domain]  Cd Length: 571  Bit Score: 423.64  E-value: 9.22e-142
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2038324413   5 IIIRVQSPDGVKRITATKRETAATFLKKVAKEF--GFQNNGFSVYINRNKTGEITAS-SSKSLHLLKIKHGDLLFLFPSS 81
Cdd:COG5100     1 MIFRFRSKEGQRRVEVQESDVLGMLSPKLLAFFevNYSPEQISVCSAPDGQGEIFSLlKDQTPDDLGLRHGQMLYLEYSD 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2038324413  82 LAGPSTEMET---------STSVGLKAFGAPnVVEDEIDQYLSKQDGKIYRSRDpQLCRHGPLGKCVHCVPLEPFDEDYl 152
Cdd:COG5100    81 IASNNEKKRDvpgkpkqdcSKGIKREKDSMP-VIQDPIDDSLEKEDGLIRRSMT-MLCQHGSNGMCSYCSPLDPWDEKY- 157

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2038324413 153 nHLEPPVKHMSFHAYIRKLTGGADK-----GKFVALENISCKIKSGCE-GHLPWPNGICTKCQPSAITLNRQKYRHVDNI 226
Cdd:COG5100   158 -YKDNKIKHLSFHSYLEKMNSNKNKlgsveSYIVPLEEPSFTVKETCEdGHGPWPHGICNKCQPSNIILAPQVFRMVDHV 236

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2038324413 227 MFENHTVADRFLDFWRKTGNQHFGYLYGRYTEHKDIPLGIRAEVAAIYEPPQIGTQNSLELLEDPKAEVVDEIAAKLGLR 306
Cdd:COG5100   237 EFDGKHIVENFIRNWRESGRQRFGYLYGRYMDYENIPLGIKAVVEAIYEPPQEDEPDGFTIEEWADEGLMDAPASGTGLE 316

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2038324413 307 KVGWIFTDLVSEDTRKGTVRYSRNKDTYFLSSEECITAGDFQNKHPNICRLSPDGHFGSKFVTAVATGGPDNQVHFEGYQ 386
Cdd:COG5100   317 RIGMIFTDLLDEGSNRGSVTCKRHADSYFLSSLEVEFIAKMQTMHPNTVKDSREGEFGSKFVTIVISGNLDGEIGLQSYQ 396

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2038324413 387 VSNQCMALVRDECLLPCKDaPELGYAKESSSEQYVPDVFYKDIDKFGNEITQLARP-LPVEYLIIDITTTFPKDPVYTFS 465
Cdd:COG5100   397 VSNQCMALVKADYILPSED-PRRFLATKEDQTRYVPDIFYRYTDTYGEEVMENAKPaFPVEFLLVTLTHGFPEKPNPLFR 475

                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2038324413 466 iSQNPFPIENRDVLGETQDFHSLATYLSQNTSSMFL--DTISDFHLLLFLVTNEVMPLQDSISLLLEAVRTRNEELAQTW 543
Cdd:COG5100   476 -SIDFIPKKFGDRKMAEYFGGDLSKELFSNFTLLTRiqGVFSNFKDLLKIIVLRILDKFDFKSFISSMERYRWECKMCTF 554

                         570
                  ....*....|....*..
gi 2038324413 544 KKSEQWATIEQLCSTVG 560
Cdd:COG5100   555 INEKNSCTCEMCNSTRD 571
zf-NPL4 pfam05020
NPL4 family, putative zinc binding region; The HRD4 gene was identical to NPL4, a gene ...
 105-245 1.31e-92

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: 281.40  E-value: 1.31e-92
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2038324413 105 VVEDEIDQYLSKQDGKIYRSRDPQLCRHGPLGKCVHCVPLEPFDEDYLNhlEPPVKHMSFHAYIRKLTGGADK-----GK 179
Cdd:pfam05020   1 VKEDPVDDYLDKQDGKIPRKRDPKLCRHGPKGMCDYCSPLEPYDEEYLK--EHKIKHLSFHAYLRKLNSGTNKkesgsSY 78

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2038324413 180 FVALENISCKIKSGC-EGHLPWPNGICTKCQPSAITLNRQKYRHVDNIMFENHTVADRFLDFWRKTG 245
Cdd:pfam05020  79 IPPLEEPSYKVKPGCpSGHPPWPKGICSKCQPSAITLQRQPFRMVDHVEFANSEIVNRFLDFWRKTG 145
UN_NPL4 pfam11543
Nuclear pore localization protein NPL4; Npl4 is part of the heterodimer UN along with Ufd1 ...
 1-80 1.79e-37

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: 133.75  E-value: 1.79e-37
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2038324413   1 MAESIIIRVQSPDGVKRITATKRETAATFLKKVAKEFGFQNNGFSVYINRNKTGEITASSSKSLHLLKIKHGDLLFLFPS 80
Cdd:pfam11543   1 MAEEIIIRVQSADGIKRIEISSDSTLSTLLSKVAEELGFPNNGFSLYLERNKTTELVSSGSKRVSLVGLKHGDSLYLFPG 80
MPN cd07767
Mpr1p, Pad1p N-terminal (MPN) domains; MPN (also known as Mov34, PAD-1, JAMM, JAB, MPN+) ...
 225-385 1.43e-21

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: 90.26  E-value: 1.43e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2038324413 225 NIMFENHTVADRfldfwrktGNQHFGYLYGRYTEHkdipLGIRAEVAAIYEPPQIGTQNSLELledpkaEVVDEIAAKLG 304
Cdd:cd07767     1 LKMFLDAAKSIN--------GKEVIGLLYGSKTKK----VLDVDEVIAVPFDEGDKDDNVWFL------MYLDFKKLNAG 62

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2038324413 305 LRKVGWIFTDLVSedtrkgtvrysrnkdTYFLSSEECITAGDFQNkhpnicrlspdgHFGSKFVTAVATGGPDNQVHFEG 384
Cdd:cd07767    63 LRIVGWYHTHPKP---------------SCFLSPNDLATHELFQR------------YFPEKVMIIVDVKPKDLGNSWKC 115


                  .
gi 2038324413 385 Y 385
Cdd:cd07767   116 Y 116
Ubl_AtNPL4_like cd17055
ubiquitin-like (Ubl) domain found in Arabidopsis thaliana NPL4-like proteins NPL4-1, NPL4-2, ...
 6-77 1.97e-12

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: 62.62  E-value: 1.97e-12
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2038324413   6 IIRVQSPDGVKRITATKRETAATFLKKVAKEFGFQNNGFSVYINRNKtGEITASSSKSLHLLKIKHGDLLFL 77
Cdd:cd17055     2 LLRVRSRDGTERVEVPDDATVGDLKEKIAEQLSVPVSDQTLSLDPGP-DLLTAKSSATLSQLGLKHGDMVFL 72
ZnF_RBZ smart00547
Zinc finger domain; Zinc finger domain in Ran-binding proteins (RanBPs), and other proteins. ...
 584-606 9.73e-03

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: 33.83  E-value: 9.73e-03
                           10        20
                   ....*....|....*....|...
gi 2038324413  584 WACQHCTFMNQPGTGHCEMCSLP 606
Cdd:smart00547   3 WECPACTFLNFASRSKCFACGAP 25
 
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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