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Conserved domains on  [gi|339241073|ref|XP_003376462|]
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ubiquitin fusion degradation protein 1-like protein [Trichinella spiralis]

Protein Classification

ubiquitin fusion degradation UFD1 family protein( domain architecture ID 11152413)

ubiquitin fusion degradation UFD1 family protein similar to human ubiquitin recognition factor in ER-associated degradation protein 1 (UFD1), an essential component of the ubiquitin-dependent proteolytic pathway which degrades ubiquitin fusion proteins

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
UFD1 pfam03152
Ubiquitin fusion degradation protein UFD1; Post-translational ubiquitin-protein conjugates are ...
 211-386 2.41e-92

Ubiquitin fusion degradation protein UFD1; Post-translational ubiquitin-protein conjugates are recognized for degradation by the ubiquitin fusion degradation (UFD) pathway. Several proteins involved in this pathway have been identified. This family includes UFD1, a 40kD protein that is essential for vegetative cell viability. The human UFD1 gene is expressed at high levels during embryogenesis, especially in the eyes and in the inner ear primordia and is thought to be important in the determination of ectoderm-derived structures, including neural crest cells. In addition, this gene is deleted in the CATCH-22 (cardiac defects, abnormal facies, thymic hypoplasia, cleft palate and hypocalcaemia with deletions on chromosome 22) syndrome. This clinical syndrome is associated with a variety of developmental defects, all characterized by microdeletions on 22q11.2. Two such developmental defects are the DiGeorge syndrome OMIM:188400, and the velo-cardio- facial syndrome OMIM:145410. Several of the abnormalities associated with these conditions are thought to be due to defective neural crest cell differentiation.


:

Pssm-ID: 460828  Cd Length: 174  Bit Score: 280.53  E-value: 2.41e-92
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 339241073  211 YNTRYRCFSVAMCPSSVSIErtrNIDYGGKVLLPHSALDWLTRLHISYPMLFKITNSNKdvKRSTHCGVLEFHQEEGKCY 290
Cdd:pfam03152   1 FDEYYRCYPVSMLDKGNERE---DLNYGGKIILPPSALDKLTRLNIEYPMLFELSNPNK--EKSTHCGVLEFTAEEGRVY 75

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 339241073  291 IPHWMMRNLLLCEGDMIQIESVDLPVGTYVKLKPQDSRFVGLANPSVLLELKLRNYACLTKGDMIAIEYNDKVMEFLVQE 370
Cdd:pfam03152  76 LPYWMMQNLGLQEGDLVQIKSASLPKGTFVKLQPQSTDFLDISNPKAVLENALRNFSTLTKGDIIAINYNDKIYELDVLE 155

                         170
                  ....*....|....*.
gi 339241073  371 LRPTDAVSIIECDINV 386
Cdd:pfam03152 156 VKPSNAISIIETDLEV 171
P16-Arc pfam04699
ARP2/3 complex 16 kDa subunit (p16-Arc); The Arp2/3 protein complex has been implicated in the ...
 50-186 5.75e-47

ARP2/3 complex 16 kDa subunit (p16-Arc); The Arp2/3 protein complex has been implicated in the control of actin polymerization. The human complex consists of seven subunits which include the actin related proteins Arp2 and Arp3, and five others referred to as p41-Arc, p34-Arc, p21-Arc, p20-Arc, and p16-Arc. The precise function of p16-Arc is currently unknown. Its structure consists of a single domain containing a bundle of seven alpha helices.


:

Pssm-ID: 461399  Cd Length: 146  Bit Score: 161.14  E-value: 5.75e-47
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 339241073   50 SFRNIDVDVQNEEIFGDE------ADVETAYVGPNESAINNLLHNNRLSEALQACLKNPPFRSKSQESKDKCTQLVIRVL 123
Cdd:pfam04699   1 DFRKIDIDAYDPDSFTEEdlypppSEVSLAEAQPLASQVRSLLSSGDAEGALKLALDNPPYGADEQAAKDLHLQTVLEVL 80

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 339241073  124 CSFKQSDVQKAVNNLDVDQLDILMKYIYKGFEFGQDGSSPALLFWHKIVFGKAGDGAIMRAVS 186
Cdd:pfam04699  81 SSIKSSDITNIVKSLDSEQQDVLMKYLYKGMSLPSEKSGSVLLSWHEKLVEVAGVGCIVRVLT 143
 
Name Accession Description Interval E-value
UFD1 pfam03152
Ubiquitin fusion degradation protein UFD1; Post-translational ubiquitin-protein conjugates are ...
 211-386 2.41e-92

Ubiquitin fusion degradation protein UFD1; Post-translational ubiquitin-protein conjugates are recognized for degradation by the ubiquitin fusion degradation (UFD) pathway. Several proteins involved in this pathway have been identified. This family includes UFD1, a 40kD protein that is essential for vegetative cell viability. The human UFD1 gene is expressed at high levels during embryogenesis, especially in the eyes and in the inner ear primordia and is thought to be important in the determination of ectoderm-derived structures, including neural crest cells. In addition, this gene is deleted in the CATCH-22 (cardiac defects, abnormal facies, thymic hypoplasia, cleft palate and hypocalcaemia with deletions on chromosome 22) syndrome. This clinical syndrome is associated with a variety of developmental defects, all characterized by microdeletions on 22q11.2. Two such developmental defects are the DiGeorge syndrome OMIM:188400, and the velo-cardio- facial syndrome OMIM:145410. Several of the abnormalities associated with these conditions are thought to be due to defective neural crest cell differentiation.


Pssm-ID: 460828  Cd Length: 174  Bit Score: 280.53  E-value: 2.41e-92
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 339241073  211 YNTRYRCFSVAMCPSSVSIErtrNIDYGGKVLLPHSALDWLTRLHISYPMLFKITNSNKdvKRSTHCGVLEFHQEEGKCY 290
Cdd:pfam03152   1 FDEYYRCYPVSMLDKGNERE---DLNYGGKIILPPSALDKLTRLNIEYPMLFELSNPNK--EKSTHCGVLEFTAEEGRVY 75

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 339241073  291 IPHWMMRNLLLCEGDMIQIESVDLPVGTYVKLKPQDSRFVGLANPSVLLELKLRNYACLTKGDMIAIEYNDKVMEFLVQE 370
Cdd:pfam03152  76 LPYWMMQNLGLQEGDLVQIKSASLPKGTFVKLQPQSTDFLDISNPKAVLENALRNFSTLTKGDIIAINYNDKIYELDVLE 155

                         170
                  ....*....|....*.
gi 339241073  371 LRPTDAVSIIECDINV 386
Cdd:pfam03152 156 VKPSNAISIIETDLEV 171
UFD1 COG5140
Ubiquitin fusion-degradation protein [Posttranslational modification, protein turnover, ...
 192-406 1.45e-53

Ubiquitin fusion-degradation protein [Posttranslational modification, protein turnover, chaperones];


Pssm-ID: 227469  Cd Length: 331  Bit Score: 185.14  E-value: 1.45e-53
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 339241073 192 GAESTMFDLTALFpqeirpyNTRYRCFSVAMCPSsvsiERTRNIDYGGKVLLPHSALDWLTRLHISYPMLFKITNSnkDV 271
Cdd:COG5140   10 GGNGFLNDLFQLF-------GEKPRCYPRAMKFD----GCRQNANFGGKVILPPSALVKLSSLNIQYPMLFEISHS--DG 76

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 339241073 272 KRSTHCGVLEFHQEEGKCYIPHWMMRNLLLCEGDMIQIESVDLPVGTYVKLKPQDSRFVGLANPSVLLELKLRNYACLTK 351
Cdd:COG5140   77 IYRTHGGVLEFIAEEGRVYLPSWMMQTLSMEPGDLVVLRYTDFPLGKFVKLIPQSVDFLDIEDPKAVLENCLRNFSTLTE 156

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 339241073 352 GDMIAIEYNDKVMEFLVQELRPTDavsiiecdinvrrSAKSVCFTDEYL-VDFDVP 406
Cdd:COG5140  157 GDEIEIQYNDEVGSIKFTVVHPEP-------------SANAIYVVETDLvVDFLPP 199
P16-Arc pfam04699
ARP2/3 complex 16 kDa subunit (p16-Arc); The Arp2/3 protein complex has been implicated in the ...
 50-186 5.75e-47

ARP2/3 complex 16 kDa subunit (p16-Arc); The Arp2/3 protein complex has been implicated in the control of actin polymerization. The human complex consists of seven subunits which include the actin related proteins Arp2 and Arp3, and five others referred to as p41-Arc, p34-Arc, p21-Arc, p20-Arc, and p16-Arc. The precise function of p16-Arc is currently unknown. Its structure consists of a single domain containing a bundle of seven alpha helices.


Pssm-ID: 461399  Cd Length: 146  Bit Score: 161.14  E-value: 5.75e-47
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 339241073   50 SFRNIDVDVQNEEIFGDE------ADVETAYVGPNESAINNLLHNNRLSEALQACLKNPPFRSKSQESKDKCTQLVIRVL 123
Cdd:pfam04699   1 DFRKIDIDAYDPDSFTEEdlypppSEVSLAEAQPLASQVRSLLSSGDAEGALKLALDNPPYGADEQAAKDLHLQTVLEVL 80

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 339241073  124 CSFKQSDVQKAVNNLDVDQLDILMKYIYKGFEFGQDGSSPALLFWHKIVFGKAGDGAIMRAVS 186
Cdd:pfam04699  81 SSIKSSDITNIVKSLDSEQQDVLMKYLYKGMSLPSEKSGSVLLSWHEKLVEVAGVGCIVRVLT 143
PLN03086 PLN03086
PRLI-interacting factor K; Provisional
 259-386 1.23e-20

PRLI-interacting factor K; Provisional


Pssm-ID: 178635 [Multi-domain]  Cd Length: 567  Bit Score: 95.71  E-value: 1.23e-20
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 339241073 259 PMLFKI---------TNSNKDVKRSTHCGVLEFHQEEGKCYIPHWMMRNLLLC---EGDMIQIESVDLPVGTYVKLKPQD 326
Cdd:PLN03086 114 PLYFRLsvvhqegsgEMKDTDSQKTTHSGVLEFTAEEGSVGLPPHVWSNLFPSdppDVPLVEVRYIWLPKGTYAKLQPDG 193

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 339241073 327 SRFVGLANPSVLLELKLRNYACLTKGDMIAIEYNDKVMEFLVQELRPTDAVSIIECDINV 386
Cdd:PLN03086 194 VGFSDLPNHKAVLETALRQHATLSEDDVLVVNYGQLTYKLKVLELKPASSVSVLETDIEV 253
 
Name Accession Description Interval E-value
UFD1 pfam03152
Ubiquitin fusion degradation protein UFD1; Post-translational ubiquitin-protein conjugates are ...
 211-386 2.41e-92

Ubiquitin fusion degradation protein UFD1; Post-translational ubiquitin-protein conjugates are recognized for degradation by the ubiquitin fusion degradation (UFD) pathway. Several proteins involved in this pathway have been identified. This family includes UFD1, a 40kD protein that is essential for vegetative cell viability. The human UFD1 gene is expressed at high levels during embryogenesis, especially in the eyes and in the inner ear primordia and is thought to be important in the determination of ectoderm-derived structures, including neural crest cells. In addition, this gene is deleted in the CATCH-22 (cardiac defects, abnormal facies, thymic hypoplasia, cleft palate and hypocalcaemia with deletions on chromosome 22) syndrome. This clinical syndrome is associated with a variety of developmental defects, all characterized by microdeletions on 22q11.2. Two such developmental defects are the DiGeorge syndrome OMIM:188400, and the velo-cardio- facial syndrome OMIM:145410. Several of the abnormalities associated with these conditions are thought to be due to defective neural crest cell differentiation.


Pssm-ID: 460828  Cd Length: 174  Bit Score: 280.53  E-value: 2.41e-92
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 339241073  211 YNTRYRCFSVAMCPSSVSIErtrNIDYGGKVLLPHSALDWLTRLHISYPMLFKITNSNKdvKRSTHCGVLEFHQEEGKCY 290
Cdd:pfam03152   1 FDEYYRCYPVSMLDKGNERE---DLNYGGKIILPPSALDKLTRLNIEYPMLFELSNPNK--EKSTHCGVLEFTAEEGRVY 75

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 339241073  291 IPHWMMRNLLLCEGDMIQIESVDLPVGTYVKLKPQDSRFVGLANPSVLLELKLRNYACLTKGDMIAIEYNDKVMEFLVQE 370
Cdd:pfam03152  76 LPYWMMQNLGLQEGDLVQIKSASLPKGTFVKLQPQSTDFLDISNPKAVLENALRNFSTLTKGDIIAINYNDKIYELDVLE 155

                         170
                  ....*....|....*.
gi 339241073  371 LRPTDAVSIIECDINV 386
Cdd:pfam03152 156 VKPSNAISIIETDLEV 171
UFD1 COG5140
Ubiquitin fusion-degradation protein [Posttranslational modification, protein turnover, ...
 192-406 1.45e-53

Ubiquitin fusion-degradation protein [Posttranslational modification, protein turnover, chaperones];


Pssm-ID: 227469  Cd Length: 331  Bit Score: 185.14  E-value: 1.45e-53
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 339241073 192 GAESTMFDLTALFpqeirpyNTRYRCFSVAMCPSsvsiERTRNIDYGGKVLLPHSALDWLTRLHISYPMLFKITNSnkDV 271
Cdd:COG5140   10 GGNGFLNDLFQLF-------GEKPRCYPRAMKFD----GCRQNANFGGKVILPPSALVKLSSLNIQYPMLFEISHS--DG 76

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 339241073 272 KRSTHCGVLEFHQEEGKCYIPHWMMRNLLLCEGDMIQIESVDLPVGTYVKLKPQDSRFVGLANPSVLLELKLRNYACLTK 351
Cdd:COG5140   77 IYRTHGGVLEFIAEEGRVYLPSWMMQTLSMEPGDLVVLRYTDFPLGKFVKLIPQSVDFLDIEDPKAVLENCLRNFSTLTE 156

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 339241073 352 GDMIAIEYNDKVMEFLVQELRPTDavsiiecdinvrrSAKSVCFTDEYL-VDFDVP 406
Cdd:COG5140  157 GDEIEIQYNDEVGSIKFTVVHPEP-------------SANAIYVVETDLvVDFLPP 199
P16-Arc pfam04699
ARP2/3 complex 16 kDa subunit (p16-Arc); The Arp2/3 protein complex has been implicated in the ...
 50-186 5.75e-47

ARP2/3 complex 16 kDa subunit (p16-Arc); The Arp2/3 protein complex has been implicated in the control of actin polymerization. The human complex consists of seven subunits which include the actin related proteins Arp2 and Arp3, and five others referred to as p41-Arc, p34-Arc, p21-Arc, p20-Arc, and p16-Arc. The precise function of p16-Arc is currently unknown. Its structure consists of a single domain containing a bundle of seven alpha helices.


Pssm-ID: 461399  Cd Length: 146  Bit Score: 161.14  E-value: 5.75e-47
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 339241073   50 SFRNIDVDVQNEEIFGDE------ADVETAYVGPNESAINNLLHNNRLSEALQACLKNPPFRSKSQESKDKCTQLVIRVL 123
Cdd:pfam04699   1 DFRKIDIDAYDPDSFTEEdlypppSEVSLAEAQPLASQVRSLLSSGDAEGALKLALDNPPYGADEQAAKDLHLQTVLEVL 80

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 339241073  124 CSFKQSDVQKAVNNLDVDQLDILMKYIYKGFEFGQDGSSPALLFWHKIVFGKAGDGAIMRAVS 186
Cdd:pfam04699  81 SSIKSSDITNIVKSLDSEQQDVLMKYLYKGMSLPSEKSGSVLLSWHEKLVEVAGVGCIVRVLT 143
PLN03086 PLN03086
PRLI-interacting factor K; Provisional
 259-386 1.23e-20

PRLI-interacting factor K; Provisional


Pssm-ID: 178635 [Multi-domain]  Cd Length: 567  Bit Score: 95.71  E-value: 1.23e-20
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 339241073 259 PMLFKI---------TNSNKDVKRSTHCGVLEFHQEEGKCYIPHWMMRNLLLC---EGDMIQIESVDLPVGTYVKLKPQD 326
Cdd:PLN03086 114 PLYFRLsvvhqegsgEMKDTDSQKTTHSGVLEFTAEEGSVGLPPHVWSNLFPSdppDVPLVEVRYIWLPKGTYAKLQPDG 193

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 339241073 327 SRFVGLANPSVLLELKLRNYACLTKGDMIAIEYNDKVMEFLVQELRPTDAVSIIECDINV 386
Cdd:PLN03086 194 VGFSDLPNHKAVLETALRQHATLSEDDVLVVNYGQLTYKLKVLELKPASSVSVLETDIEV 253
 
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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