Collapse Statistics
241 human active and 13 inactive phosphatases in total;
194 phosphatases have substrate data;
336 protein substrates;
83 non-protein substrates;
1215 dephosphorylation interactions;
299 KEGG pathways;
876 Reactome pathways;
last update: 11 Mar, 2019


DEPOD User Manual


1. Mouse-over icon to get hints about various fields while exploring DEPOD-2019
2. Use Quick Search to search for phosphatases, substrates, or pathways in DEPOD-2019.



1. Search DEPOD-2019

2. Browse DEPOD-2019

3. Protein annotations in DEPOD-2019

4. Non-protein annotations in DEPOD-2019

5. Pathway-mapping in DEPOD-2019

1. Search DEPOD-2019

DEPOD-2019 allows you to search for - phosphatases, substrates (both protein and non-protein), dephosphosites, pathways and protein sequences. It also provides a Quick Search utility on every page in the top-right corner.

    Click on the following tabs to see the search-interface and the output.

Search Interface

search phosphatase


phosphatase search result

Click of the entry name to go to the corresponding protein entry

2. Browse the database

    Click on the following tabs to see the browsing interfaces of DEPOD-2019.

Browse human phosphatasesHuman phosphatases can be accessed using their historical classification, structure-based (CATH) classification or EC-number based classes
Browse human phosphatases browse phosphatases part 1
browse phosphatases part 1
browse phosphatases part 1

3. Protein entry in DEPOD

    Click on the following tabs to see the annotations provided under each tab in DEPOD-2019.

Gene NameGene 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.
SynonymsGene synonyms
Protein NameProtein name
Alternative Name(s)Protein names from UniProt annotation
EntrezGene IDGene ID in the EntrezGene database
Comparative ToxicogenomicsLink to the manually curated information about chemical–gene/protein interactions, chemical–disease and gene–disease relationships in CTD database
UniProt AC (Human)Protein entry in the UniProt database (Homo sapiens)
Enzyme ClassEnzyme Commission number (links to the BRENDA database - the main collection of enzyme functional data available to the scientific community.)
Molecular WeightMolecular weight of the protein in Daltons
Protein LengthProtein length (number of amino acids)
Genome BrowsersVisualize the gene in four genome browsers - NCBI, Ensembl, UCSC and 1000Genomes
CrosslinkingAnnotations from 69 external databases
OrthologuesEvolutionary conservation of the protein across different species from Quest for Orthologues (QFO), Genetree and eggNOG (if available) visualized in ProViz
ClassificationFamily-level classification of protein phosphatases. Historical class of the phosphatase and the CATH-based classification as implemented in DEPOD along with the CATH and SCOP IDs
Phosphatase activity statusAnnotations whether the phosphatases are catalytically active or not as reported in Alonso A and Oulido R, 2015, FEBS J. Catalytic signature motifs in protein Tyr-phosphatases (PTPs) are annotated as such.
Phosphonetwork visualizationCytoscape visualization of the phosphatase-substrate-kinase network in a random layout. Protein kinases (purple squares) phosphorylating the protein of interest (blue triangle) and the phosphatases (orange circles) that dephosphorylate it can be visualized here. Nodes are connected via non-directed non-weighted edges. Click on these nodes to get information about that gene from the NCBI-Gene database. Drag and/or scroll the network using your mouse.
Protein DomainProtein domain composition as defined in InterPro (an integrated database of predictive protein "signatures" used for the classification and automatic annotation of proteins and genomes), the SMART database (focuses on signaling domains, uses their own individual models and domain-specific cut-offs to define domain boundaries) and the Pfam database (a large collection of protein families, each represented by multiple sequence alignments and hidden Markov models (HMMs)).
Polypeptide organizationSchematic representation of the Pfam domains within the protein of interest. Click on a domain to see additional information about it in Pfam.
Interactive structure visualizationPDB Structures of proteins as reported in UniProt can be loaded one-by-one using the load button and visualized in Web3DMol.
3D StructureLinks to PDB (experimental structure database); 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).
Catalytic SiteLink to the Catalytic Site Atlas (CSA) - a database documenting enzyme active sites and catalytic residues in enzymes of 3D structure.
Gene ExpressionLink 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.
DiseasesLink to the OMIM - Online Mendelian Inheritance in Man (a comprehensive compendium of human genes and genetic phenotypes focusing on their inter-relationships. It is updated daily, and the entries contain copious links to other genetics resources), DisGeNet (discovery platform containing genes and variants in them associated to human diseases), COSMIC - Catalogue Of Somatic Mutations In Cancer (a comprehensive resource for exploring the impact of somatic mutations in human cancer) and ClinVar (a public archive of reports of the relationships among human variations and phenotypes, with supporting evidence).
Protein-protein Interaction DatabaseLinks to four popular protein-protein interaction databases (BioGRID, STRING, IntAct and MINT). The interacting partners can be easily explored to find potential dephosphorylation interactions and study the phosphatase in a systematic way.
PhosphositesLinks to two major phosphosite databases - PhosphoSitePlus and PhosphoELM - so as to see which sites in the given proteins are experimentally characterized phosphosites and potential kinases in some of these cases.
LocalizationThe localizations are retrieved from UniProt annotations.
Function (UniProt annotation)Protein functions from UniProt annotations
Catalytic Activity (UniProt annotation)Protein catalytic activities from UniProt annotations
Protein SequenceProtein sequence in FASTA format.
ELM MotifsShort Linear Motifs (SLiMs) occurring in the protein predicted as true positive hots according to the Eukaryotic Linear Motif (ELM) database. The boundaries of the motif instance in that protein along with the general regular expression of the motif is also provided. Click on the motif instance to visualize its conservation using ProViz.
Gene Ontology IDGene Ontology IDs
Gene Ontology TermGene Ontology terms. P: Biological processes, MF: Molecular function terms and C: Cellular component terms.

4. Non-protein Substrate Entry in DEPOD

    Click on the following tabs to see the annotations provided under each tab in DEPOD-2019.

Name ChEBI ASCII nomenclature of the chemical substrate name in DEPOD.
Synonyms Other nomenclatures used for the substrate
Definition A brief description of the chemical substrate as provided in ChEBI
Molecular Weight Molecular weight of the substrate
Molecular Formula Molecular formula of the substrate
SMILEs Simplified Molecular Input Line Entry System (SMILES) notation for the substrate
InChI IUPAC International Chemical Indentifier (InChI) of the substrate
InChI Key InChI-based compact hashed code of a chemical compound having fixed length.
Crosslinking annotations Links to other databases are provided.

5. Pathway mapping result page

For a given pathway, DEPOD provides phosphatase and their substrates (both protein and non-proteins) involved in that pathway. Following is an example of pathway mapping using one of the reactome pathways.

pathway mapping result in DEPOD