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Collapse Statistics
226 human active and 11 inactive phosphatases in total;
194 phosphatases have substrate data;
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305 protein substrates;
89 non-protein substrates;
1114 dephosphorylation interactions;
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213 KEGG pathways;
206 NCI Nature PID pathways
560 Reactome pathways;
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last update: 18 Feb, 2016

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DEPOD User Manual


Tips: When you explore DEPOD, you can [1] put your mouse over icon to show hints; [2] conveniently search phosphatases, substrates, or pathways via "Quick Search".

1. Search the database

Search human phosphatases with gene name, protein name, UniProt accession number, Ensembl gene ID, or Entrez gene ID.
search phosphatase
Phosphatase search result:
phosphatase search result


2. Browse the database

Browse human phosphatases
Browse human phosphatases browse phosphatases part 1
browse phosphatases part 2
browse phosphatases part 3


3. Phosphatase data page

Gene Name Gene name is the approved gene symbol from HGNC (HUGO Gene Nomenclature Committee). Click the link to see gene name information in HGNC. Click the link "QuickGO" to see Gene Ontology terms and annotations provided by the UniProtKB-GOA group at the EBI.
Synonyms Gene synonyms
Protein Name Protein name
Alternative Name(s) Protein names from UniProt annotation
Ensembl Gene ID Gene ID in the Ensembl database
EntrezGene ID Gene ID in the EntrezGene database
UniProt AC (Human) Protein entry in the UniProt database (Homo sapiens)
Enzyme Class Enzyme Commission number (links to the BRENDA database - the main collection of enzyme functional data available to the scientific community.)
Molecular Weight Molecular wight of the protein
Protein Length Protein length (number of amino acids)
Protein Domain Protein domain composition information in the InterPro database (an integrated database of predictive protein "signatures" used for the classification and automatic annotation of proteins and genomes) and the Pfam database (a large collection of protein families, each represented by multiple sequence alignments and hidden Markov models (HMMs)).
Structure of phosphatase catalytic domain PDB Structure of the phosphatase catalytic domain. The incomplete structures like fragments and the structures of domains other than catalytic domain are rejected here.
3D Structure Links to PDB and PDBe (experimental structure databases); DrugPort (providing an analysis of the structural information available in PDB relating to drug molecules and their protein targets); ModBase and SwissModel (theoretical structure model databases).
Structure-based Family Structure-based family of the phosphatase (click the link to see all the phosphatases within the family in DEPOD) and CATH code of catalytic domain.
Historical Class Historical class of the phosphatase
Localization The localizations are retrieved from both UniProt annotations and the LocDB database. Only experimental annotations with original literature information are considered here.
Localization The localizations are retrieved from both UniProt annotations and the LocDB database. Only experimental annotations with original literature information are considered here. Click the links to PubMed to see original literatures.
Catalytic Site Link to the Catalytic Site Atlas (CSA) - a database documenting enzyme active sites and catalytic residues in enzymes of 3D structure.
Target by Small Molecules Link to the ChEMBL database - a database of bioactive drug-like small molecules, it contains 2-D structures, calculated properties (e.g. logP, Molecular Weight, Lipinski Parameters, etc.) and abstracted bioactivities (e.g. binding constants, pharmacology and ADMET data).
Gene Expression Link to the Gene Expression Atlas, which is a semantically enriched database of meta-analysis based summary statistics over a curated subset of ArrayExpress Archive, servicing queries for condition-specific gene expression patterns as well as broader exploratory searches for biologically interesting genes/samples.
Function and Disease Link to the OMIM - Online Mendelian Inheritance in Man. OMIM is a comprehensive, authoritative, and timely compendium of human genes and genetic phenotypes. The full-text, referenced overviews in OMIM contain information on all known mendelian disorders and over 12,000 genes. OMIM focuses on the relationship between phenotype and genotype. It is updated daily, and the entries contain copious links to other genetics resources.
Protein-protein Interaction Database Click the links to three popular protein-protein interaction databases (STRING, IntAct and MINT). The interacting partners can be easily explored to find potential dephosphorylation interactions and study the phosphatase in a systematic way.
Kinase Database Click the links to three popular kinase databases (Phospho.ELM, PhosphoSite and NetworKIN) to see which kinases can phosphorylate this phosphatase.
Function (UniProt annotation) Protein functions from UniProt annotations
Catalytic Activity (UniProt annotation) Protein catalytic activities from UniProt annotations
Gene Ontology ID Gene Ontology IDs
Gene Ontology Term Gene Ontology terms
Protein Sequence Protein sequence of the UniProt entry


4. Substrate data page

Protein substrate
Gene Name Gene name is the approved gene symbol from HGNC (HUGO Gene Nomenclature Committee). Click the link to see gene name information in HGNC. Click the link "QuickGO" to see Gene Ontology terms and annotations provided by the UniProtKB-GOA group at the EBI.
Synonyms Gene synonyms
Protein Name Protein name
Alternative name(s) Protein names from UniProt annotation
Protein Family Protein family information from UniProt annotation
EntrezGene ID Gene ID in the EntrezGene database
UniProt AC (Human) Protein entry in the UniProt database (Homo sapiens)
Enzyme Class Enzyme Commission number (links to the BRENDA database - the main collection of enzyme functional data available to the scientific community.)
Molecular Weight Molecular wight of the protein
Protein Length Protein length (number of amino acids)
Protein Domain Protein domain composition information in the InterPro database (an integrated database of predictive protein "signatures" used for the classification and automatic annotation of proteins and genomes) and the Pfam database (a large collection of protein families, each represented by multiple sequence alignments and hidden Markov models (HMMs)).
3D Structure Links to PDB and PDBe (experimental structure databases); DrugPort (providing an analysis of the structural information available in PDB relating to drug molecules and their protein targets); ModBase and SwissModel (theoretical structure model databases).
Localization (UniProt annotation) Localization information from UniProt annotation
Gene Expression Link to the Gene Expression Atlas, which is a semantically enriched database of meta-analysis based summary statistics over a curated subset of ArrayExpress Archive, servicing queries for condition-specific gene expression patterns as well as broader exploratory searches for biologically interesting genes/samples.
Function and Disease Link to the OMIM - Online Mendelian Inheritance in Man. OMIM is a comprehensive, authoritative, and timely compendium of human genes and genetic phenotypes. The full-text, referenced overviews in OMIM contain information on all known mendelian disorders and over 12,000 genes. OMIM focuses on the relationship between phenotype and genotype. It is updated daily, and the entries contain copious links to other genetics resources.
Protein-protein Interaction Database Click the links to three popular protein-protein interaction databases (STRING, IntAct and MINT). The interacting partners can be easily explored to find potential dephosphorylation interactions and study the substrate in a systematic way.
Kinase Database Click the links to three popular kinase databases (Phospho.ELM, PhosphoSite and NetworKIN) to see which kinases can phosphorylate this substrate.
Function (UniProt annotation) Protein functions from UniProt annotations
Catalytic Activity (UniProt annotation) Protein catalytic activities from UniProt annotations
Gene Ontology ID Gene Ontology IDs
Gene Ontology Term Gene Ontology terms
Protein Sequence Protein sequence of the UniProt entry
Non-protein substrate
Name Substrate name in DEPOD.
IUPAC Name IUPAC name of the substrate
Synonyms Synonyms of the substrate
Molecular Weight Molecular weight of the substrate
KEGG Compound ID KEGG Compound ID of the substrate. Link to the KEGG Compound database.
ChEBI ID ChEBI ID of the substrate. Link to the ChEBI database.
ChEBI Ontology ChEBI Ontology of the substrate. The ChEBI Ontology is a structured classification of the entities contained within ChEBI.


5. Pathway mapping result page

pathway mapping result in DEPOD
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