VAriation effect on
PROtein Structure and function TABLE
VaProS Table
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General
acc
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acc
UniProt accession (e.g., P11499)
uniprot_id
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uniprot_id
UniProt ID (e.g., HS90B_MOUSE)
gene
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gene
protein
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protein
Protein name
length
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length
Sequence length
location
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location
Subcellular location
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PDB
num_pdb_entries
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num_pdb_entries
Number of PDB entries corresponding to the UniProt entry
exptl_methods
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exptl_methods
Experimental method for structure determination
coverage_pdb_union
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coverage_pdb_union
Fraction of amino acid residues covered by corresponding PDB entries (union)
coverage_pdb_top
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coverage_pdb_top
Fraction of amino acid residues covered by the closest corresponding PDB homolog
coverage_pdb_union_wo_diso
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coverage_pdb_union_wo_diso
Fraction of amino acid residues covered by corresponding PDB entries excluding disordered regions (union)
pdb_mutant
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pdb_mutant
Number of mutants annonated in the PDB, including (1) those annotated as "MUTATION" in SEQADV, and (2) MODRES (modified residue)
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PDB Homolog
num_pdb_homolog
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num_pdb_homolog
Number of PDB homologs detected by BLAST
coverage_homolog_union
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coverage_homolog_union
Fraction of residues covered by PDB homologs (union).
identity_homolog_union
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identity_homolog_union
Weighted average of sequence identity.
coverage_homolog_union_coverage
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coverage_homolog_union_coverage
Fraction of residues covered by PDB homologs (union) excluding disordered regions.
coverage_homolog_top
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coverage_homolog_top
Fraction of residues covered by the closest PDB homolog.
identity_homolog_top
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identity_homolog_top
Sequence identity of the closest PDB homolog.
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Disorder
num_id_region
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num_id_region
Number of (contiguous) disordered regions.
frac_id_region
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frac_id_region
Fraction of residues in disoredered regions.
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Secondary Structure
frac_alpha
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frac_alpha
Fraction of residues in predicted alpha helices.
frac_beta
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frac_beta
Fraction of residues in predictied beta strands.
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Domain
num_domain_variety
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num_domain_variety
Number of unique domains (i.e., repeated domains are counted once).
num_domains
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num_domains
Number of domains (i.e., repeated domains are multiply counted).
pfam_ids
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pfam_ids
Pfam domain identifier(s).
pfam_domains
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pfam_domains
Pfam domain name(s).
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Complex
ligand_state
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ligand_state
Whether a ligand is bound or not.
num_homolog_complex_compound
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num_homolog_complex_compound
Number of chemical compounds found in PDB homologs.
num_homolog_complex_metal
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num_homolog_complex_metal
Number of metals found in PDB homologs.
num_homolog_complex_nucleotide
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num_homolog_complex_nucleotide
Number of nucleotides found in PDB homologs.
num_homolog_complex_otherpoly
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num_homolog_complex_otherpoly
Number of "other" polymers found in PDB homologs.
num_homolog_complex_precipitant
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num_homolog_complex_precipitant
Number of (supposed) precipitants found in PDB homologs.
ligands
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ligands
Ligand names found in PDB homologs.
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Compound
num_monomer
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num_monomer
Number of monomeric structures in PDB homologs.
num_homomer
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num_homomer
Number of homomeric structures in PDB homologs.
num_heteromer
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num_heteromer
Number of heteromeric structures in PDB homologs.
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Organism Homolog
div_hum
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div_hum
Number of homologs in the "HUM" (human) division.
div_pri
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div_pri
Number of homologs in the "PRI" (primates) division.
div_rod
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div_rod
Number of homologs in the "ROD" (rodents) division.
div_mam
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div_mam
Number of homologs in the "MAM" (mammals) division.
div_vrt
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div_vrt
Number of homologs in the "VRT" (vertebrates) division.
div_inv
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div_inv
Number of homologs in the "INV" (invertebrates) division.
div_pln
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div_pln
Number of homologs in the "PLN" (plants) division.
div_bct
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div_bct
Number of homologs in the "BCT" (bacteria) division.
div_arc
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div_arc
Number of homologs in the "ARC" (archeae) division.
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Variants
num_splice_variants
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num_splice_variants
Number of splice variants (isoforms).
num_variant_sites
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num_variant_sites
Number of variant sites.
num_variants
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num_variants
Number of sequence variants.
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Disease
num_related_disease
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num_related_disease
Number of related diseases.
diseases
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diseases
List of related diseases.
num_pubmed
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num_pubmed
Number of related PubMed entries.
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Other
num_ppi_others
num_potential_compounds
alt_frequency
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