Vacuolar sorting protein 39 domain 1; This domain is found on the vacuolar sorting protein ...
460-562
4.87e-39
Vacuolar sorting protein 39 domain 1; This domain is found on the vacuolar sorting protein Vps39 which is a component of the C-Vps complex. Vps39 is thought to be required for the fusion of endosomes and other types of transport intermediates with the vacuole. In Saccharomyces cerevisiae, Vps39 has been shown to stimulate nucleotide exchange. The precise function of this domain has not been characterized.
:
Pssm-ID: 371008 Cd Length: 108 Bit Score: 140.45 E-value: 4.87e-39
Vacuolar sorting protein 39 domain 2; This domain is found on the vacuolar sorting protein ...
772-862
6.09e-30
Vacuolar sorting protein 39 domain 2; This domain is found on the vacuolar sorting protein Vps39 which is a component of the C-Vps complex. Vps39 is thought to be required for the fusion of endosomes and other types of transport intermediates with the vacuole. In Saccharomyces cerevisiae, Vps39 has been shown to stimulate nucleotide exchange. This domain is involved in localization and in mediating the interactions of Vps39 with Vps11.
The actual alignment was detected with superfamily member pfam10367:
Pssm-ID: 402126 Cd Length: 109 Bit Score: 114.27 E-value: 6.09e-30
Region in Clathrin and VPS; Each region is about 140 amino acids long. The regions are ...
595-746
5.44e-04
Region in Clathrin and VPS; Each region is about 140 amino acids long. The regions are composed of multiple alpha helical repeats. They occur in the arm region of the Clathrin heavy chain.
The actual alignment was detected with superfamily member pfam00637:
Pssm-ID: 459884 [Multi-domain] Cd Length: 142 Bit Score: 41.09 E-value: 5.44e-04
Vacuolar sorting protein 39 domain 1; This domain is found on the vacuolar sorting protein ...
460-562
4.87e-39
Vacuolar sorting protein 39 domain 1; This domain is found on the vacuolar sorting protein Vps39 which is a component of the C-Vps complex. Vps39 is thought to be required for the fusion of endosomes and other types of transport intermediates with the vacuole. In Saccharomyces cerevisiae, Vps39 has been shown to stimulate nucleotide exchange. The precise function of this domain has not been characterized.
Pssm-ID: 371008 Cd Length: 108 Bit Score: 140.45 E-value: 4.87e-39
Vacuolar sorting protein 39 domain 2; This domain is found on the vacuolar sorting protein ...
772-862
6.09e-30
Vacuolar sorting protein 39 domain 2; This domain is found on the vacuolar sorting protein Vps39 which is a component of the C-Vps complex. Vps39 is thought to be required for the fusion of endosomes and other types of transport intermediates with the vacuole. In Saccharomyces cerevisiae, Vps39 has been shown to stimulate nucleotide exchange. This domain is involved in localization and in mediating the interactions of Vps39 with Vps11.
Pssm-ID: 402126 Cd Length: 109 Bit Score: 114.27 E-value: 6.09e-30
Region in Clathrin and VPS; Each region is about 140 amino acids long. The regions are ...
595-746
5.44e-04
Region in Clathrin and VPS; Each region is about 140 amino acids long. The regions are composed of multiple alpha helical repeats. They occur in the arm region of the Clathrin heavy chain.
Pssm-ID: 459884 [Multi-domain] Cd Length: 142 Bit Score: 41.09 E-value: 5.44e-04
Vacuolar sorting protein 39 domain 1; This domain is found on the vacuolar sorting protein ...
460-562
4.87e-39
Vacuolar sorting protein 39 domain 1; This domain is found on the vacuolar sorting protein Vps39 which is a component of the C-Vps complex. Vps39 is thought to be required for the fusion of endosomes and other types of transport intermediates with the vacuole. In Saccharomyces cerevisiae, Vps39 has been shown to stimulate nucleotide exchange. The precise function of this domain has not been characterized.
Pssm-ID: 371008 Cd Length: 108 Bit Score: 140.45 E-value: 4.87e-39
Vacuolar sorting protein 39 domain 2; This domain is found on the vacuolar sorting protein ...
772-862
6.09e-30
Vacuolar sorting protein 39 domain 2; This domain is found on the vacuolar sorting protein Vps39 which is a component of the C-Vps complex. Vps39 is thought to be required for the fusion of endosomes and other types of transport intermediates with the vacuole. In Saccharomyces cerevisiae, Vps39 has been shown to stimulate nucleotide exchange. This domain is involved in localization and in mediating the interactions of Vps39 with Vps11.
Pssm-ID: 402126 Cd Length: 109 Bit Score: 114.27 E-value: 6.09e-30
Region in Clathrin and VPS; Each region is about 140 amino acids long. The regions are ...
595-746
5.44e-04
Region in Clathrin and VPS; Each region is about 140 amino acids long. The regions are composed of multiple alpha helical repeats. They occur in the arm region of the Clathrin heavy chain.
Pssm-ID: 459884 [Multi-domain] Cd Length: 142 Bit Score: 41.09 E-value: 5.44e-04
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.
Click on the triangle to view details about the feature, including a multiple sequence alignment
of your query sequence and the protein sequences used to curate the domain model,
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The thumbnail image, if present, provides an approximate view of the feature's location in 3 dimensions.
Click on the triangle for interactive 3D structure viewing options.
Functional characterization of the conserved domain architecture found on the query.
Click here to see more details.
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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Domains are color coded according to superfamilies
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Others (non-specific hits) and
superfamily placeholders are drawn in pastel colors.
if a domain or superfamily has been annotated with functional sites (conserved features),
they are mapped to the query sequence and indicated through sets of triangles
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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)
mapped to the query sequence.
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
(illustrated example)
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
meet or exceed the RPS-BLAST threshold for statistical significance (default E-value cutoff of 0.01, or an E-value selected by user via the
advanced search options)
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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Modify your query to search against a different database and/or use advanced search options
