Vps54-like protein; This family contains various proteins that are homologs of the yeast Vps54 ...
990-1120
4.59e-66
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: 219.31 E-value: 4.59e-66
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: 41.19 E-value: 3.65e-03
Vps54-like protein; This family contains various proteins that are homologs of the yeast Vps54 ...
990-1120
4.59e-66
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: 219.31 E-value: 4.59e-66
Ribosomal protein S3AE [Translation, ribosomal structure and biogenesis]; Ribosomal protein ...
1285-1487
5.34e-51
Ribosomal protein S3AE [Translation, ribosomal structure and biogenesis]; Ribosomal protein S3AE is part of the Pathway/BioSystem: Archaeal ribosomal proteins
Pssm-ID: 441494 Cd Length: 208 Bit Score: 179.28 E-value: 5.34e-51
Vacuolar-sorting protein 54, of GARP complex; This is a family of vacuolar-sorting proteins 54, ...
270-429
3.65e-03
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: 41.19 E-value: 3.65e-03
Vps54-like protein; This family contains various proteins that are homologs of the yeast Vps54 ...
990-1120
4.59e-66
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: 219.31 E-value: 4.59e-66
Ribosomal protein S3AE [Translation, ribosomal structure and biogenesis]; Ribosomal protein ...
1285-1487
5.34e-51
Ribosomal protein S3AE [Translation, ribosomal structure and biogenesis]; Ribosomal protein S3AE is part of the Pathway/BioSystem: Archaeal ribosomal proteins
Pssm-ID: 441494 Cd Length: 208 Bit Score: 179.28 E-value: 5.34e-51
Vacuolar-sorting protein 54, of GARP complex; This is a family of vacuolar-sorting proteins 54, ...
270-429
3.65e-03
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: 41.19 E-value: 3.65e-03
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.
of the residues that compose this conserved feature have been mapped to the query sequence.
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Functional characterization of the conserved domain architecture found on the query.
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This image shows a graphical summary of conserved domains identified on the query sequence.
The Show Concise/Full Display button at the top of the page can be used to select the desired level of detail: only top scoring hits
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if a domain or superfamily has been annotated with functional sites (conserved features),
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click on the bars or triangles to view your query sequence embedded in a multiple sequence alignment of the proteins used to develop the corresponding domain model.
The table lists conserved domains identified on the query sequence. Click on the plus sign (+) on the left to display full descriptions, alignments, and scores.
Click on the domain model's accession number to view the multiple sequence alignment of the proteins used to develop the corresponding domain model.
To view your query sequence embedded in that multiple sequence alignment, click on the colored bars in the Graphical Summary portion of the search results page,
or click on the triangles, if present, that represent functional sites (conserved features)
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Concise Display shows only the best scoring domain model, in each hit category listed below except non-specific hits, for each region on the query sequence.
(labeled illustration) Standard Display shows only the best scoring domain model from each source, in each hit category listed below for each region on the query sequence.
(labeled illustration) Full Display shows all domain models, in each hit category below, that meet or exceed the RPS-BLAST threshold for statistical significance.
(labeled illustration) Four types of hits can be shown, as available,
for each region on the query sequence:
specific hits meet or exceed a domain-specific e-value threshold
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and represent a very high confidence that the query sequence belongs to the same protein family as the sequences use to create the domain model
non-specific hits
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the domain superfamily to which the specific and non-specific hits belong
multi-domain models that were computationally detected and are likely to contain multiple single domains
Retrieve proteins that contain one or more of the domains present in the query sequence, using the Conserved Domain Architecture Retrieval Tool
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