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Conserved domains on  [gi|18407495|ref|NP_566118|]
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Nuclear pore localization protein NPL4 [Arabidopsis thaliana]

Protein Classification

NPL4 family protein( domain architecture ID 13018412)

NPL4 (nuclear protein localization-4) family protein similar to Arabidopsis thaliana NPL4-like proteins 1 and 2

Gene Ontology:  GO:0043130|GO:0031625|GO:0006511
PubMed:  12015140|11598205

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
MPN_NPL4 cd08061
Mov34/MPN/PAD-1 family: nuclear protein localization-4 (Npl4) domain; Npl4p (nuclear protein ...
 120-375 3.37e-77

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: 240.34  E-value: 3.37e-77
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18407495 120 RVTRQETSHCDSVSFDRDAANAFQHYVnESLAFAVKRGGFMYGTVTEE------GQVEVDFIYEPPQQGTEANLILMRDA 193
Cdd:cd08061   1 TLKRQKYRHVDHVEFDNPSIVEFFLYV-FWRKTGQQRIGFLYGRYDEDedvplgIKAVVEAIYEPPQEGTPDGFELLEDP 79

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18407495 194 DEEKrVDAIAMGLGMRRVGFIFNQTVVQDKTEYTLSNAEVLQAAELHAE----SELKEWVTAVVKLevNEDGgaDVHFEA 269
Cdd:cd08061  80 NADT-VDAIAAALGLERVGWIFTDLPREDKDGYFLSAEEVILAAKFQLKhptgKFGSKFVTVVVTG--DKDG--QIHFEA 154

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18407495 270 FQMSDMCIRLFKEEWFETEIMPD----DDPKLSKMKKEVVVGVKDL-------KEVDNDFFLVlvrILDHQGPL------ 332
Cdd:cd08061 155 YQVSDQAMALVRDGLLLPTKDADelyvREPTLERYVPDVFYSGKDKygktkavPEVDVEYFLV---DVPHGFPLspssfk 231

                       250       260       270       280
                ....*....|....*....|....*....|....*....|....*
gi 18407495 333 SSTFPIENRSsrATMRALKTH--LDRAKSLPLVKKMSDFHLLLFV 375
Cdd:cd08061 232 SSDFPIENRP--PSLGELQDLdaLARYLGKPFLERLSDFHLLLYL 274
Ubl_AtNPL4_like cd17055
ubiquitin-like (Ubl) domain found in Arabidopsis thaliana NPL4-like proteins NPL4-1, NPL4-2, ...
 2-85 1.54e-23

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: 93.05  E-value: 1.54e-23
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18407495   2 MMLRIRSRDGLERVTAEgAHITVSQLKTLIADQLQIPLHKQTLSTNRdlllaktPADLLaftdLTDPNLPLSSLNLGHGS 81
Cdd:cd17055   1 MLLRVRSRDGTERVEVP-DDATVGDLKEKIAEQLSVPVSDQTLSLDP-------GPDLL----TAKSSATLSQLGLKHGD 68


                ....
gi 18407495  82 MLYL 85
Cdd:cd17055  69 MVFL 72
 
Name Accession Description Interval E-value
MPN_NPL4 cd08061
Mov34/MPN/PAD-1 family: nuclear protein localization-4 (Npl4) domain; Npl4p (nuclear protein ...
 120-375 3.37e-77

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: 240.34  E-value: 3.37e-77
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18407495 120 RVTRQETSHCDSVSFDRDAANAFQHYVnESLAFAVKRGGFMYGTVTEE------GQVEVDFIYEPPQQGTEANLILMRDA 193
Cdd:cd08061   1 TLKRQKYRHVDHVEFDNPSIVEFFLYV-FWRKTGQQRIGFLYGRYDEDedvplgIKAVVEAIYEPPQEGTPDGFELLEDP 79

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18407495 194 DEEKrVDAIAMGLGMRRVGFIFNQTVVQDKTEYTLSNAEVLQAAELHAE----SELKEWVTAVVKLevNEDGgaDVHFEA 269
Cdd:cd08061  80 NADT-VDAIAAALGLERVGWIFTDLPREDKDGYFLSAEEVILAAKFQLKhptgKFGSKFVTVVVTG--DKDG--QIHFEA 154

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18407495 270 FQMSDMCIRLFKEEWFETEIMPD----DDPKLSKMKKEVVVGVKDL-------KEVDNDFFLVlvrILDHQGPL------ 332
Cdd:cd08061 155 YQVSDQAMALVRDGLLLPTKDADelyvREPTLERYVPDVFYSGKDKygktkavPEVDVEYFLV---DVPHGFPLspssfk 231

                       250       260       270       280
                ....*....|....*....|....*....|....*....|....*
gi 18407495 333 SSTFPIENRSsrATMRALKTH--LDRAKSLPLVKKMSDFHLLLFV 375
Cdd:cd08061 232 SSDFPIENRP--PSLGELQDLdaLARYLGKPFLERLSDFHLLLYL 274
Ubl_AtNPL4_like cd17055
ubiquitin-like (Ubl) domain found in Arabidopsis thaliana NPL4-like proteins NPL4-1, NPL4-2, ...
 2-85 1.54e-23

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: 93.05  E-value: 1.54e-23
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18407495   2 MMLRIRSRDGLERVTAEgAHITVSQLKTLIADQLQIPLHKQTLSTNRdlllaktPADLLaftdLTDPNLPLSSLNLGHGS 81
Cdd:cd17055   1 MLLRVRSRDGTERVEVP-DDATVGDLKEKIAEQLSVPVSDQTLSLDP-------GPDLL----TAKSSATLSQLGLKHGD 68


                ....
gi 18407495  82 MLYL 85
Cdd:cd17055  69 MVFL 72
NPL4 pfam05021
NPL4 family; The HRD4 gene was identical to NPL4, a gene previously implicated in nuclear ...
 156-377 2.51e-22

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: 96.57  E-value: 2.51e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18407495   156 RGGFMYGTVTEEGQVE------VDFIYEPPQQGtEANLILMRDADEEKRVDAIAMGLGMRRVGFIF---------NQTVV 220
Cdd:pfam05021   1 RFGYLYGRYEEYDEVPlgikavVEAIYEPPQHD-ELDGITLLPWENEKDVDEIARELGLERVGVIFtdltdagagDGTVL 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18407495   221 Q--DKTEYTLSNAEVLQAAELHAE-------SELKEW----VTAVVklEVNEDGGadVHFEAFQMSDMCIRLFKEEWfet 287
Cdd:pfam05021  80 CkrHKDSYFLSSLEVIMAARLQARhpnptkySETGRFgskfVTCVV--SGDLNGE--IDISSYQVSNQAEALVRADI--- 152

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18407495   288 eIMPDDDPKL----SKMKKEVVVGV--KDLKEVDN------------DFFLVlvrILDHQGPL--------SSTFPIENR 341
Cdd:pfam05021 153 -IEPSTDPSVayvrESSDERYVPEVfySKINEYGLevkenakpafpvEYLLV---TLTHGFPLepsptfsaNNGFPIENR 228

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|...
gi 18407495   342 -------SSRATMRALKTHLDrakSLPLVKKMSDFHLLLFVAQ 377
Cdd:pfam05021 229 eamgelqDLSALAKYLKSSAD---PNDFLEALSNFHLLLYLHS 268
NPL4 COG5100
Nuclear pore protein [Nuclear structure];
124-384 1.61e-10

Nuclear pore protein [Nuclear structure];


Pssm-ID: 227431 [Multi-domain]  Cd Length: 571  Bit Score: 62.71  E-value: 1.61e-10
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18407495 124 QETSHCDSVSFDRdaanafQHYVNESL----AFAVKRGGFMYGTVTEEGQVE------VDFIYEPPQQgTEANLILMRDA 193
Cdd:COG5100 228 QVFRMVDHVEFDG------KHIVENFIrnwrESGRQRFGYLYGRYMDYENIPlgikavVEAIYEPPQE-DEPDGFTIEEW 300

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18407495 194 DEEKRVDAIAMGLGMRRVGFIFNQ---------TVVQDKTE--YTLSNAEVLQAAELHAE-------SELKEW----VTA 251
Cdd:COG5100 301 ADEGLMDAPASGTGLERIGMIFTDlldegsnrgSVTCKRHAdsYFLSSLEVEFIAKMQTMhpntvkdSREGEFgskfVTI 380

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18407495 252 VVKleVNEDGGADVhfEAFQMSDMCIRLFKEEWfeteIMPDDDP--------------------KLSKMKKEVVVGVKDL 311
Cdd:COG5100 381 VIS--GNLDGEIGL--QSYQVSNQCMALVKADY----ILPSEDPrrflatkedqtryvpdifyrYTDTYGEEVMENAKPA 452

                       250       260       270       280       290       300       310       320
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18407495 312 KEVdnDFFLVlvrILDHQGPL--------SSTFPIENRSSRAT---MRALKTHL-DRAKSLPLVK-KMSDFHLLLFVAQF 378
Cdd:COG5100 453 FPV--EFLLV---TLTHGFPEkpnplfrsIDFIPKKFGDRKMAeyfGGDLSKELfSNFTLLTRIQgVFSNFKDLLKIIVL 527


                ....*.
gi 18407495 379 LDVSSD 384
Cdd:COG5100 528 RILDKF 533
UN_NPL4 pfam11543
Nuclear pore localization protein NPL4; Npl4 is part of the heterodimer UN along with Ufd1 ...
 2-85 4.17e-06

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: 44.39  E-value: 4.17e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18407495     2 MMLRIRSRDGLERVTAEgAHITVSQLKTLIADQLQIPLHKQTLSTNRDLLLAKTPADllaftdltdpNLPLSSLNLGHGS 81
Cdd:pfam11543   5 IIIRVQSADGIKRIEIS-SDSTLSTLLSKVAEELGFPNNGFSLYLERNKTTELVSSG----------SKRVSLVGLKHGD 73


                  ....
gi 18407495    82 MLYL 85
Cdd:pfam11543  74 SLYL 77
 
Name Accession Description Interval E-value
MPN_NPL4 cd08061
Mov34/MPN/PAD-1 family: nuclear protein localization-4 (Npl4) domain; Npl4p (nuclear protein ...
 120-375 3.37e-77

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: 240.34  E-value: 3.37e-77
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18407495 120 RVTRQETSHCDSVSFDRDAANAFQHYVnESLAFAVKRGGFMYGTVTEE------GQVEVDFIYEPPQQGTEANLILMRDA 193
Cdd:cd08061   1 TLKRQKYRHVDHVEFDNPSIVEFFLYV-FWRKTGQQRIGFLYGRYDEDedvplgIKAVVEAIYEPPQEGTPDGFELLEDP 79

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18407495 194 DEEKrVDAIAMGLGMRRVGFIFNQTVVQDKTEYTLSNAEVLQAAELHAE----SELKEWVTAVVKLevNEDGgaDVHFEA 269
Cdd:cd08061  80 NADT-VDAIAAALGLERVGWIFTDLPREDKDGYFLSAEEVILAAKFQLKhptgKFGSKFVTVVVTG--DKDG--QIHFEA 154

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18407495 270 FQMSDMCIRLFKEEWFETEIMPD----DDPKLSKMKKEVVVGVKDL-------KEVDNDFFLVlvrILDHQGPL------ 332
Cdd:cd08061 155 YQVSDQAMALVRDGLLLPTKDADelyvREPTLERYVPDVFYSGKDKygktkavPEVDVEYFLV---DVPHGFPLspssfk 231

                       250       260       270       280
                ....*....|....*....|....*....|....*....|....*
gi 18407495 333 SSTFPIENRSsrATMRALKTH--LDRAKSLPLVKKMSDFHLLLFV 375
Cdd:cd08061 232 SSDFPIENRP--PSLGELQDLdaLARYLGKPFLERLSDFHLLLYL 274
Ubl_AtNPL4_like cd17055
ubiquitin-like (Ubl) domain found in Arabidopsis thaliana NPL4-like proteins NPL4-1, NPL4-2, ...
 2-85 1.54e-23

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: 93.05  E-value: 1.54e-23
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18407495   2 MMLRIRSRDGLERVTAEgAHITVSQLKTLIADQLQIPLHKQTLSTNRdlllaktPADLLaftdLTDPNLPLSSLNLGHGS 81
Cdd:cd17055   1 MLLRVRSRDGTERVEVP-DDATVGDLKEKIAEQLSVPVSDQTLSLDP-------GPDLL----TAKSSATLSQLGLKHGD 68


                ....
gi 18407495  82 MLYL 85
Cdd:cd17055  69 MVFL 72
NPL4 pfam05021
NPL4 family; The HRD4 gene was identical to NPL4, a gene previously implicated in nuclear ...
 156-377 2.51e-22

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: 96.57  E-value: 2.51e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18407495   156 RGGFMYGTVTEEGQVE------VDFIYEPPQQGtEANLILMRDADEEKRVDAIAMGLGMRRVGFIF---------NQTVV 220
Cdd:pfam05021   1 RFGYLYGRYEEYDEVPlgikavVEAIYEPPQHD-ELDGITLLPWENEKDVDEIARELGLERVGVIFtdltdagagDGTVL 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18407495   221 Q--DKTEYTLSNAEVLQAAELHAE-------SELKEW----VTAVVklEVNEDGGadVHFEAFQMSDMCIRLFKEEWfet 287
Cdd:pfam05021  80 CkrHKDSYFLSSLEVIMAARLQARhpnptkySETGRFgskfVTCVV--SGDLNGE--IDISSYQVSNQAEALVRADI--- 152

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18407495   288 eIMPDDDPKL----SKMKKEVVVGV--KDLKEVDN------------DFFLVlvrILDHQGPL--------SSTFPIENR 341
Cdd:pfam05021 153 -IEPSTDPSVayvrESSDERYVPEVfySKINEYGLevkenakpafpvEYLLV---TLTHGFPLepsptfsaNNGFPIENR 228

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|...
gi 18407495   342 -------SSRATMRALKTHLDrakSLPLVKKMSDFHLLLFVAQ 377
Cdd:pfam05021 229 eamgelqDLSALAKYLKSSAD---PNDFLEALSNFHLLLYLHS 268
NPL4 COG5100
Nuclear pore protein [Nuclear structure];
124-384 1.61e-10

Nuclear pore protein [Nuclear structure];


Pssm-ID: 227431 [Multi-domain]  Cd Length: 571  Bit Score: 62.71  E-value: 1.61e-10
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18407495 124 QETSHCDSVSFDRdaanafQHYVNESL----AFAVKRGGFMYGTVTEEGQVE------VDFIYEPPQQgTEANLILMRDA 193
Cdd:COG5100 228 QVFRMVDHVEFDG------KHIVENFIrnwrESGRQRFGYLYGRYMDYENIPlgikavVEAIYEPPQE-DEPDGFTIEEW 300

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18407495 194 DEEKRVDAIAMGLGMRRVGFIFNQ---------TVVQDKTE--YTLSNAEVLQAAELHAE-------SELKEW----VTA 251
Cdd:COG5100 301 ADEGLMDAPASGTGLERIGMIFTDlldegsnrgSVTCKRHAdsYFLSSLEVEFIAKMQTMhpntvkdSREGEFgskfVTI 380

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18407495 252 VVKleVNEDGGADVhfEAFQMSDMCIRLFKEEWfeteIMPDDDP--------------------KLSKMKKEVVVGVKDL 311
Cdd:COG5100 381 VIS--GNLDGEIGL--QSYQVSNQCMALVKADY----ILPSEDPrrflatkedqtryvpdifyrYTDTYGEEVMENAKPA 452

                       250       260       270       280       290       300       310       320
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18407495 312 KEVdnDFFLVlvrILDHQGPL--------SSTFPIENRSSRAT---MRALKTHL-DRAKSLPLVK-KMSDFHLLLFVAQF 378
Cdd:COG5100 453 FPV--EFLLV---TLTHGFPEkpnplfrsIDFIPKKFGDRKMAeyfGGDLSKELfSNFTLLTRIQgVFSNFKDLLKIIVL 527


                ....*.
gi 18407495 379 LDVSSD 384
Cdd:COG5100 528 RILDKF 533
UN_NPL4 pfam11543
Nuclear pore localization protein NPL4; Npl4 is part of the heterodimer UN along with Ufd1 ...
 2-85 4.17e-06

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: 44.39  E-value: 4.17e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18407495     2 MMLRIRSRDGLERVTAEgAHITVSQLKTLIADQLQIPLHKQTLSTNRDLLLAKTPADllaftdltdpNLPLSSLNLGHGS 81
Cdd:pfam11543   5 IIIRVQSADGIKRIEIS-SDSTLSTLLSKVAEELGFPNNGFSLYLERNKTTELVSSG----------SKRVSLVGLKHGD 73


                  ....
gi 18407495    82 MLYL 85
Cdd:pfam11543  74 SLYL 77
Ubl_ubiquitin_like cd17039
ubiquitin-like (Ubl) domain found in ubiquitin and ubiquitin-like Ubl proteins; Ubiquitin-like ...
 4-85 1.11e-03

ubiquitin-like (Ubl) domain found in ubiquitin and ubiquitin-like Ubl proteins; Ubiquitin-like (Ubl) proteins have a similar ubiquitin (Ub) beta-grasp fold and attach to other proteins in a Ubl manner but with biochemically distinct roles. Ub and Ubl proteins conjugate and deconjugate via ligases and peptidases to covalently modify target polypeptides. Some Ubl domains have adaptor roles in Ub-signaling by mediating protein-protein interaction. Prokaryotic sulfur carrier proteins are Ub-related proteins that can be activated in an ATP-dependent manner. Polyubiquitination signals for a diverse set of cellular events via different isopeptide linkages formed between the C terminus of one ubiquitin (Ub) and the epsilon-amine of K6, K11, K27, K29, K33, K48, or K63 of a second Ub. One of these seven lysine residues (K27, Ub numbering) is conserved in this Ubl_ubiquitin_like family. K27-linked Ub chains are versatile and can be recognized by several downstream receptor proteins. K27 has roles beyond chain linkage, such as in Ubl NEDD8 (which contains many of the same lysines (K6, K11, K27, K33, K48) as Ub) where K27 has a role (other than conjugation) in the mechanism of protein neddylation.


Pssm-ID: 340559 [Multi-domain]  Cd Length: 68  Bit Score: 37.19  E-value: 1.11e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18407495   4 LRIRSRDGLERVTAEGAHITVSQLKTLIADQLQIPLHKQTLSTNRDLLlaktpadllaftdltDPNLPLSSLNLGHGSML 83
Cdd:cd17039   1 ITVKTLDGKTYTVEVDPDDTVADLKEKIEEKTGIPVEQQRLIYNGKEL---------------KDDKTLSDYGIKDGSTI 65


                ..
gi 18407495  84 YL 85
Cdd:cd17039  66 HL 67
Ubl_OTU1 cd17059
ubiquitin-like (Ubl) domain found in ubiquitin thioesterase OTU1 and similar proteins; OTU1 ...
 2-85 1.54e-03

ubiquitin-like (Ubl) domain found in ubiquitin thioesterase OTU1 and similar proteins; OTU1 (EC 3.4.19.12), also termed YOD1, or DUBA-8, or HIV-1-induced protease 7 (HIN-7), or OTU domain-containing protein 2 (OTUD2), is a p97-associated deubiquitinylase that functions as a key player in endoplasmic reticulum-associated degradation (ERAD). Its deubiquitinylase activity is also required for negatively regulating cholera toxin A1 (CTA1) retro-translocation. OTU1 contains a conserved ubiquitin-like (Ubl) domain with a beta-grasp Ubl fold, a C2H2-type zinc finger, and an OTU domain.


Pssm-ID: 340579  Cd Length: 75  Bit Score: 37.19  E-value: 1.54e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18407495   2 MMLRIRSRDGLERVTAEGAHITVSQLKTLIADQLQIPLHKQTlstnrdlLLAKTPADLLaftDLTDPNLPLSSLNLGHGS 81
Cdd:cd17059   1 MRLRVRSKGGQHVLSLLTDTSTVGELQDRIAALTGIPPSSQK-------ILYGFPPKPL---DLSDEEASLESLGIQSGD 70


                ....
gi 18407495  82 MLYL 85
Cdd:cd17059  71 TLIV 74
Ubl_USP48 cd01795
ubiquitin-like (Ubl) domain found in ubiquitin-specific-processing protease 48 (USP48) and ...
 20-96 6.13e-03

ubiquitin-like (Ubl) domain found in ubiquitin-specific-processing protease 48 (USP48) and similar proteins; USP48, also termed USP31, or deubiquitinating enzyme 48, or ubiquitin thioesterase 48, or ubiquitin carboxyl-terminal hydrolase 48, belongs to the ubiquitin specific protease (USP) family that is one of at least seven deubiquitylating enzyme (DUB) families capable of deconjugating ubiquitin (Ub)and ubiquitin-like (Ubl) adducts. While the USP proteins have a conserved catalytic core domain, USP48 differs in its domain architecture. It contains an N-terminal USP domain, three DUSP (domain present in ubiquitin-specific protease) domains, and a C-terminal Ubl domain with a beta-grasp Ubl fold, a common structure involved in protein-protein interactions. USP48 is a deubiquitinating enzyme that interacts with TNF receptor-associated factor 2 (TRAF2) and has been implicated in activation of nuclear factor-kappaB (NF-kappaB). Moreover, as a nuclear deubiquitinase regulated by casein kinase 2 (CK2), USP48 controls the ubiquitin/proteasome-system (UPS)-dependent turnover of activated NF-kappaB/RelA in the nucleus together with the COP9 signalosome, suggesting a role of USP48 in a timely control of immune responses.


Pssm-ID: 340493 [Multi-domain]  Cd Length: 99  Bit Score: 36.11  E-value: 6.13e-03
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 18407495  20 AHITVSQLKTLIADQLQIPLHKQTLSTNRDlllaktpadllaftDLTDPNLPLSSLNLGHGSMLYLAYDGERSIPGA 96
Cdd:cd01795  14 STTTLKELKLQIMEKFSVAPFDQHLYFNGR--------------ELTDDSATLADLGILPGDVLYLKVDEPPDDPDD 76
Ubl2_FAT10 cd17053
ubiquitin-like (Ubl) domain 2 found in leukocyte antigen F (HLA-F) adjacent transcript 10 ...
 23-86 6.25e-03

ubiquitin-like (Ubl) domain 2 found in leukocyte antigen F (HLA-F) adjacent transcript 10 (FAT10) and similar proteins; FAT10, also termed ubiquitin D (UBD), or diubiquitin, is a cytokine-inducible ubiquitin-like (Ubl) modifer that is highly expressed in the thymus, and targets substrates covalently for 26S proteasomal degradation. It is also associated with cancer development, antigen processing and antimicrobial defense, chromosomal stability and cell cycle regulation. FAT10 is presented on immune cells and under the inflammatory conditions, is synergistically induced by interferon gamma (IFNgamma) and tumor necrosis factor (TNFalpha) in the non-immune (liver parenchymal) cells. FAT10 contains two Ubl domains. The family corresponds to the second Ubl domain of FAT10. Some family members contain only one Ubl domain.


Pssm-ID: 340573  Cd Length: 71  Bit Score: 35.40  E-value: 6.25e-03
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 18407495  23 TVSQLKTLIADQLQIPLHKQTLSTNRdlllaktpadllafTDLTDPNLPLSSLNLGHGSMLYLA 86
Cdd:cd17053  22 TVAQVKAMIEDQSGVPPNEQILVYNG--------------KRLEDGDKTLGEYGIKTGDTLYLL 71
 
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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