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Conserved domains on  [gi|392920390|ref|NP_001256227|]
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Vacuolar protein sorting-associated protein 54 [Caenorhabditis elegans]

Protein Classification

vacuolar protein sorting-associated protein 54( domain architecture ID 10996507)

vacuolar protein sorting-associated protein 54 is a component of the GARP complex that is involved in retrograde transport from early and late endosomes to the trans-Golgi network

Gene Ontology:  GO:0000938|GO:0006896|GO:0019905|GO:0006886

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
Vps54 pfam07928
Vps54-like protein; This family contains various proteins that are homologs of the yeast Vps54 ...
 510-638 1.89e-49

Vps54-like protein; This family contains various proteins that are homologs of the yeast Vps54 protein, such as the rat homolog, the human homolog, and the mouse homolog. In yeast, Vps54 associates with Vps52 and Vps53 proteins to form a trimolecular complex that is involved in protein transport between Golgi, endosomal, and vacuolar compartments. All Vps54 homologs contain a coiled coil region (not found in the region featured in this family) and multiple dileucine motifs.


:

Pssm-ID: 462318  Cd Length: 131  Bit Score: 169.62  E-value: 1.89e-49
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392920390  510 ENYVVVGSSITMIQLLSDYCEAISEMPSFSQDWNSRVVELLKTFNSRCCQLILGAGALQLVGLKTISVRNLALAGRSLEL 589
Cdd:pfam07928   1 EKFIVVNSALLLLKMLSDYLHLAANFPSLASDILSRLLELLKLFNSRTCQLILGAGATRTAGLKNITAKHLALASQALSF 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*....
gi 392920390  590 VCRFIPMVHDEMDRVLPENRKSLLRYFKQVESEYRDHVNEIAAKLISVI 638
Cdd:pfam07928  81 VIALIPYIREFFRRHLGPKQALLLSEFDKVKRDYQEHQSEIHSKLVSIM 129
COG2 super family cl19297
COG (conserved oligomeric Golgi) complex component, COG2; The COG complex comprises eight ...
 3-140 3.82e-04

COG (conserved oligomeric Golgi) complex component, COG2; The COG complex comprises eight proteins COG1-8. The COG complex plays critical roles in Golgi structure and function. The proposed function of the complex is to mediate the initial physical contact between transport vesicles and their membrane targets. A comparable role in tethering vesicles has been suggested for at least six additional large multisubunit complexes, including the exocyst, a complex that mediates trafficking to the plasma membrane. COG2 structure reveals a six-helix bundle with few conserved surface features but a general resemblance to recently determined crystal structures of four different exocyst subunits. These bundles inCOG2 may act as platforms for interaction with other trafficing proteins including SNAREs (soluble N-ethylmaleimide factor attachment protein receptors) and Rabs.


The actual alignment was detected with superfamily member pfam10475:

Pssm-ID: 473160  Cd Length: 291  Bit Score: 43.11  E-value: 3.82e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392920390    3 HDVVDGRLAGKLVAKTDDFWQVVRSYSGLQEQLANALQCVMVVRKNLkrvdelvcDQSKKIV-----EVHERYEQK---K 74
Cdd:pfam10475  44 HDVVSKKLSQLIMEQYNEFVQGMSQVREIEKDLQHSAVMCTNGRRYL--------DSAKKNLtrtslGLLAKYRKRqllK 115

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 392920390   75 KLLAKLHDISCLREAQSTVQMMLSQGDYPKAIE-CIETSldVLSKELNGVTCFRHLASQLRELYTVI 140
Cdd:pfam10475 116 KLLMTLTTIKEIRDTDVRLQELLEDGNYPQAIQlLLECQ--QLATGYSHYNCVQELSSKLQETLLLT 180
 
Name Accession Description Interval E-value
Vps54 pfam07928
Vps54-like protein; This family contains various proteins that are homologs of the yeast Vps54 ...
 510-638 1.89e-49

Vps54-like protein; This family contains various proteins that are homologs of the yeast Vps54 protein, such as the rat homolog, the human homolog, and the mouse homolog. In yeast, Vps54 associates with Vps52 and Vps53 proteins to form a trimolecular complex that is involved in protein transport between Golgi, endosomal, and vacuolar compartments. All Vps54 homologs contain a coiled coil region (not found in the region featured in this family) and multiple dileucine motifs.


Pssm-ID: 462318  Cd Length: 131  Bit Score: 169.62  E-value: 1.89e-49
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392920390  510 ENYVVVGSSITMIQLLSDYCEAISEMPSFSQDWNSRVVELLKTFNSRCCQLILGAGALQLVGLKTISVRNLALAGRSLEL 589
Cdd:pfam07928   1 EKFIVVNSALLLLKMLSDYLHLAANFPSLASDILSRLLELLKLFNSRTCQLILGAGATRTAGLKNITAKHLALASQALSF 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*....
gi 392920390  590 VCRFIPMVHDEMDRVLPENRKSLLRYFKQVESEYRDHVNEIAAKLISVI 638
Cdd:pfam07928  81 VIALIPYIREFFRRHLGPKQALLLSEFDKVKRDYQEHQSEIHSKLVSIM 129
Vps54_N pfam10475
Vacuolar-sorting protein 54, of GARP complex; This is a family of vacuolar-sorting proteins 54, ...
 3-140 3.82e-04

Vacuolar-sorting protein 54, of GARP complex; This is a family of vacuolar-sorting proteins 54, from eukaryotes. Along with VPS52 and VPS53 this forms the Golgi-associated retrograde protein complex GARP. VPS54 is separated into N- and C-terminal regions each of which has a different function. This N-terminal family of is important for GARP complex assembly and stability, whereas the C-terminal domain, pfam07928, brings about localization to an early endocytic compartment.


Pssm-ID: 431303  Cd Length: 291  Bit Score: 43.11  E-value: 3.82e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392920390    3 HDVVDGRLAGKLVAKTDDFWQVVRSYSGLQEQLANALQCVMVVRKNLkrvdelvcDQSKKIV-----EVHERYEQK---K 74
Cdd:pfam10475  44 HDVVSKKLSQLIMEQYNEFVQGMSQVREIEKDLQHSAVMCTNGRRYL--------DSAKKNLtrtslGLLAKYRKRqllK 115

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 392920390   75 KLLAKLHDISCLREAQSTVQMMLSQGDYPKAIE-CIETSldVLSKELNGVTCFRHLASQLRELYTVI 140
Cdd:pfam10475 116 KLLMTLTTIKEIRDTDVRLQELLEDGNYPQAIQlLLECQ--QLATGYSHYNCVQELSSKLQETLLLT 180
 
Name Accession Description Interval E-value
Vps54 pfam07928
Vps54-like protein; This family contains various proteins that are homologs of the yeast Vps54 ...
 510-638 1.89e-49

Vps54-like protein; This family contains various proteins that are homologs of the yeast Vps54 protein, such as the rat homolog, the human homolog, and the mouse homolog. In yeast, Vps54 associates with Vps52 and Vps53 proteins to form a trimolecular complex that is involved in protein transport between Golgi, endosomal, and vacuolar compartments. All Vps54 homologs contain a coiled coil region (not found in the region featured in this family) and multiple dileucine motifs.


Pssm-ID: 462318  Cd Length: 131  Bit Score: 169.62  E-value: 1.89e-49
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392920390  510 ENYVVVGSSITMIQLLSDYCEAISEMPSFSQDWNSRVVELLKTFNSRCCQLILGAGALQLVGLKTISVRNLALAGRSLEL 589
Cdd:pfam07928   1 EKFIVVNSALLLLKMLSDYLHLAANFPSLASDILSRLLELLKLFNSRTCQLILGAGATRTAGLKNITAKHLALASQALSF 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*....
gi 392920390  590 VCRFIPMVHDEMDRVLPENRKSLLRYFKQVESEYRDHVNEIAAKLISVI 638
Cdd:pfam07928  81 VIALIPYIREFFRRHLGPKQALLLSEFDKVKRDYQEHQSEIHSKLVSIM 129
Vps54_N pfam10475
Vacuolar-sorting protein 54, of GARP complex; This is a family of vacuolar-sorting proteins 54, ...
 3-140 3.82e-04

Vacuolar-sorting protein 54, of GARP complex; This is a family of vacuolar-sorting proteins 54, from eukaryotes. Along with VPS52 and VPS53 this forms the Golgi-associated retrograde protein complex GARP. VPS54 is separated into N- and C-terminal regions each of which has a different function. This N-terminal family of is important for GARP complex assembly and stability, whereas the C-terminal domain, pfam07928, brings about localization to an early endocytic compartment.


Pssm-ID: 431303  Cd Length: 291  Bit Score: 43.11  E-value: 3.82e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392920390    3 HDVVDGRLAGKLVAKTDDFWQVVRSYSGLQEQLANALQCVMVVRKNLkrvdelvcDQSKKIV-----EVHERYEQK---K 74
Cdd:pfam10475  44 HDVVSKKLSQLIMEQYNEFVQGMSQVREIEKDLQHSAVMCTNGRRYL--------DSAKKNLtrtslGLLAKYRKRqllK 115

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 392920390   75 KLLAKLHDISCLREAQSTVQMMLSQGDYPKAIE-CIETSldVLSKELNGVTCFRHLASQLRELYTVI 140
Cdd:pfam10475 116 KLLMTLTTIKEIRDTDVRLQELLEDGNYPQAIQlLLECQ--QLATGYSHYNCVQELSSKLQETLLLT 180
 
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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