(Search by UniProt ID, AC and keywords of gene/protein names) - eg.: CHK2_HUMAN / Histone
Recent Update History
The updated dbPTM 2019 is now accessible.


Time 10:00 am at 29th june

PTM Data Updated.


Time 2:00 pm at 1st june

Welcome to dbPTM

dbPTM is an integrated resource for protein post-translational modifications (PTMs). Due to the importance of protein post-translational modifications (PTMs) in regulating biological processes, the dbPTM was developed as a comprehensive database by integrating experimentally verified PTMs from several databases and annotating the potential PTMs for all UniProtKB protein entries. The dbPTM has been maintained for over ten years with an attempt to provide comprehensively functional and structural analyses for post-translational modifications (PTMs). In this update, dbPTM not only integrate more experimentally validated PTMs from available databases and manual curation of literature, but also provide disease association based on non-synonymous single nucleotide polymorphisms (nsSNPs). - [Data Statistics Page]

The high-throughput deep sequencing technology has leaded the analysis of association between SNPs and diseases into a data surge in both growth and scope. This update thus integrated disease-associated nsSNPs from dbSNP based on Genome-Wide Association Studies (GWAS). The PTM substrate sites locating in a specified distance of the amino acids encoded from nsSNPs were referred to having an association with its involving diseases (Figure 1). In recent years, an increasing evidence for crosstalk between PTMs has been reported.

Although mass spectrometry (MS)-based proteomics has substantially improved our knowledge about substrate site specificity of single PTM, this neglects the fact that the crosstalk of combinatorial PTMs may act in concert in the regulation of protein function. Due to the relatively limited information about the frequency and functional relevance of PTM crosstalk, in this update, the PTM sites neighbouring with other PTM sites in a specified window length were subjected to motif discovery and functional enrichment analysis. This update confronts the current state of PTM crosstalk research and breaks the bottleneck of how proteomics may contribute to understanding PTM codes, revealing the next level of data complexity and proteomic limitation in prospective PTM research.

Summary Table of PTM Sites

All of the experimentally validated PTM instances were categorized by their PTM types and further grouped by the modified amino acid. The number of experimentally validated PTM substrate sites is provided in the following summary table. Users can investigate into the substrate peptide specificity of each categorized PTM.

PTM Type Ala(A)Arg(R)Asn(N)Asp(D)Cys(C)Gly(G)Glu(E)Gln(Q)His(H)Ile(I) Leu(L)Lys(K)Met(M)Phe(F)Pro(P)Ser(S)Thr(T)Trp(W)Tyr(Y)Val(V)
C-linked Glycosylation-----------------255--
Gamma-carboxyglutamic acid------439-------------
N-linked Glycosylation1278741-----1-29---223-1
O-linked Glycosylation------1----41--9521014073-29-
Pyrrolidone carboxylic acid------8900------------
S-linked Glycosylation----6---------------

PTM Analysis Resource Portal

dbPTM is updated as an integrated resource for PTMs, providing not only a comprehensive dataset of experimentally verified PTMs that are supported by the literature but also an integrative platform for accessing all available databases and tools that are associated with PTM analysis.

#Database NameDescriptionURLReference
1GlycoEpitopeCarbohydrate chains occupy truly significant positions in various fields of life sciences and biotechnology. Recently, the wide-ranging involvement of carbohydrate chains in life sciences has been extended to such diverse functions as cell to cell recognition and communication in neuronal tissues and immune systems, pathogen recognition, sperm-egg recognition and fertilization, regulating hormonal half-lives in the blood, directing embryonic development and differentiation, and directing distribution of various cells and proteins throughout the body. A large number of polyclonal or monoclonal antibodies have been used as very important tools for analyzing expression of various carbohydrate chains and their functions. In this database, useful information on these carbohydrate antigens, i.e. glyco-epitopes, and antibodies has been assembled as a compact encyclopedia.http://www.glycoepitope.jp/
2GlycomeDBCarbohydrates are the third major class of biological macromolecules, besides proteins and DNA molecules. They are involved in numerous biological processes, among them protein folding and inter/intra cell recognition. In contrast to DNA and proteins neither a comprehensive database for carbohydrate structures nor a universal nomenclature for computational purposes exists. After the cease of funding for the Complex Carbohydrate Structure Database (CCSDB, often referred as CarbBank) in 1997, four initiatives developed independent databases with partially overlapping foci. For each database, a proprietary encoding scheme for residues and topology of the structures was designed. As a result it is virtually impossible to get an overview of all existing structures, and to compare the contents of the different databases. We have analysed all of the existing public databases and defined a sequence format based on XML (GlycoCT) capable of storing all structural information of carbohydrate sequences. We have implemented a library of parsers for the interpretation of the different encoding schemes for carbohydrates. With this library we have translated the carbohydrate sequences of all freely available databases (CFG , KEGG, GLYCOSCIENCES.de, BCSDB and Carbbank) to GlycoCT, and created a new database (GlycomeDB) containing all structures and annotations. During the process of data integration we found multiple inconsistencies in the existing databases which were corrected in collaboration with the responsible curators. With the new database, GlycomeDB, it is possible to get an overview of all carbohydrate structures in the different databases and to crosslink common structures in the different databases. Scientists are now able to search for a particular structure in the meta database and get information about the occurrence of this structure in the five carbohydrate structure databases.http://www.glycome-db.org/21045056
3UnicarbKBUniCarbKB is an initiative that aims to promote the creation of an online information storage and search platform for glycomics and glycobiology research. The knowledgebase will offer a freely accessible and information-rich resource supported by querying interfaces, annotation technologies and the adoption of common standards to integrate structural, experimental and functional data.http://unicarbkb.org24234447
4GLYCOSCIENCES.deThe human genome seems to encode for not more than 30,000 to 40,000 proteins. A major challenge is to understand how posttranslational events, such as glycosylation, affect the activities and functions of these proteins in health and disease. The importance of protein glycosylation is becoming widely realized through studies on protein folding, protein localization and trafficking, protein solubility, biological half-life as well as studies on cell-cell interactions. The progressing Glycomics projects will dramatically accelerate the understanding of the roles of carbohydrates in cell communication and lead to novel therapeutic approaches for treatment of human disease. The MIT's magazine of innovation (January 21 2003) has identified Glycomics as one of the top ten technologies that will change the future.http://www.glycosciences.de/16239495
5GlycoSuiteDBUniCarbKB is an initiative that aims to promote the creation of an online information storage and search platform for glycomics and glycobiology research. The knowledgebase will offer a freely accessible and information-rich resource supported by querying interfaces, annotation technologies and the adoption of common standards to integrate structural, experimental and functional data.http://www.unicarbkb.org/12520065
6CFGThe CFG's Glycan Structures Database offers detailed structural and chemical information for thousands of glycans, including both synthetic glycans and glycans isolated from biological sources. Each glycan structure in the database is linked to relevant entries in CFG and external databases (including primary data and information about binding proteins, where available). Links are also provided to a 3-D modeling feature, references, and other information.http://www.functionalglycomics.org/glycomics/molecule/jsp/carbohydrate/carbMoleculeHome.jsp25753711
7ProGlycProtProGlycProt (Prokaryotic Glycoproteins) is a manually curated, comprehensive repository of experimentally characterized bacterial glycoproteins and archaeal glycoproteins, generated from an exhaustive literature search. This is the focused beginning of an effort to provide concise relevant information derived from rapidly expanding literature on prokaryotic glycoproteins, their glycosylating enzyme(s), glycosylation linked genes, and genomic context thereof, in a cross-referenced manner. ProGlycProt is an extensive online collection of experimentally verified glycosites and glycoproteins of the prokaryotes. For users’ benefit, the database under menu ProGlycProtdb is arranged into two sections namely, ProCGP and ProUGP. ProCGP is the main section containing characterized prokaryotic glycoproteins, defined as entries with at least one experimentally known "glycosylated residue (glycosite)". Whereas, ProUGP is the supplementary section, presenting uncharacterized prokaryotic glycoproteins, defined as entries with experimentally identified glycosylation but unidentified glycosites. The ProGlycProt has been developed with an aim to aid and advance the emerging scientific interests in understanding the mechanisms, implications, and novelties of protein glycosylation in prokaryotes that include many pathogenic as well as economically important bacterial species. A general data update policy is once in three months. Existing entries are updated in real-time.http://www.proglycprot.org/22039152
#Database NameDescriptionURLReference
1CPLACPLM (Compendium of Protein Lysine Modifications) is an online data resource specifically designed for protein lysine modifications (PLMs). The CPLM database was extended and adapted from our CPLA 1.0 (Compendium of Protein Lysine Acetylation) database (Liu et al., 2011), and the 2.0 release contains 203,972 modification events on 189,919 modified lysines in 45,748 proteins for 12 types of PLMs, including N?-lysine acetylation (Yang et al., 2007; Shahbazian et al., 2007; Smith et al., 2009), ubiquitination (Gao, et al., 2013), methylation (Chen, et al., 2006), sumoylation (Ren, et al., 2009; Xue, et al., 2006), glycation (Priego-Capote, et al., 2010), butyrylation (Chen, et al., 2007; Cheng, et al., 2009; Zhang, et al., 2009), crotonylation (Tan, et al., 2011), malonylation (Xie, et al., 2012), propionylation (Chen, et al., 2007; Cheng, et al., 2009; Zhang, et al., 2009), succinylation (Xie, et al., 2012; Zhang, et al., 2011), phosphoglycerylation (Moellering, R. E. and B. F. Cravatt, 2013) and prokaryotic Pupylation (Liu, et al., 2011).http://cpla.biocuckoo.org21059677
#Database NameDescriptionURLReference
1CPLMCPLM (Compendium of Protein Lysine Modifications) is an online data resource specifically designed for protein lysine modifications (PLMs). The CPLM database was extended and adapted from our CPLA 1.0 (Compendium of Protein Lysine Acetylation) database (Liu et al., 2011), and the 2.0 release contains 203,972 modification events on 189,919 modified lysines in 45,748 proteins for 12 types of PLMs, including N?-lysine acetylation (Yang et al., 2007; Shahbazian et al., 2007; Smith et al., 2009), ubiquitination (Gao, et al., 2013), methylation (Chen, et al., 2006), sumoylation (Ren, et al., 2009; Xue, et al., 2006), glycation (Priego-Capote, et al., 2010), butyrylation (Chen, et al., 2007; Cheng, et al., 2009; Zhang, et al., 2009), crotonylation (Tan, et al., 2011), malonylation (Xie, et al., 2012), propionylation (Chen, et al., 2007; Cheng, et al., 2009; Zhang, et al., 2009), succinylation (Xie, et al., 2012; Zhang, et al., 2011), phosphoglycerylation (Moellering, R. E. and B. F. Cravatt, 2013) and prokaryotic Pupylation (Liu, et al., 2011).http://cplm.biocuckoo.org/24214993
2CrosstalkDBThis database aims to collect mass spectrometry data of multiply modified histones or histone tails. You can search, analyze and download data from this database without having to log in. Quantification can be based on either spectral counting or peak intensities. We recommend isoScale and Histone Coder for spectra validation and quantification. For details of the database, see Schwämmle, V.; Aspalter, C.-M.; Sidoli, S. and Jensen, O. N. Large-scale analysis of co-existing post-translational modifications on histone tails reveals global fine-structure of crosstalk Mol Cell Proteomics, 2014, 13, 1855-1865 We encourage users to register and upload their data from mass spectrometry experiments. Registration is only formal and no private data (not even your email) will be required. After uploading your data, you will still be able to correct errors or delete selected entries. As special feature, the statistical part includes calculation of interaction patterns between different histone modifications. With this tool, it should be possible to reveal the crosstalk between multiple histone modifications. We are sure that this software is not exempt from bugs. Please send us a message (at the Impressum / Feedback page) describing your problem(s).http://crosstalkdb.bmb.sdu.dk/24741113
3dbPTMProtein modification is an extremely important post-translational regulation that adjusts the physical and chemical properties, conformation, stability and activity of a protein; thus altering protein function. Due to the high-throughput of mass spectrometry-based methods in identifying site-specific post-translational modifications (PTMs), dbPTM is updated to integrate experimental PTMs obtained from public resources as well as manually curated MS/MS peptides associated with PTMs from research articles. The new version of dbPTM aims to be an informative resource for investigating the substrate specificity of PTM sites and functional association of PTMs between substrates and their interacting proteins. In order to investigate the substrate specificity for modification sites, a newly developed statistical method has been applied to identify the significant substrate motifs for each type of PTMs containing sufficient experimental data. According to the data statistics in dbPTM, over 60% of PTM sites are located in the functional domains of proteins. It is known that most PTMs can create binding sites for specific protein-interaction domains that work together for cellular function. Thus, this update integrates protein-protein interaction and domain-domain interaction to determine the functional association of PTM sites located in protein-interacting domains. Additionally, the information of structural topologies on transmembrane proteins is integrated in dbPTM in order to delineate the structural correlation between the reported PTM sites and transmembrane topologies. To facilitate the investigation of PTMs on transmembrane proteins, the PTM substrate sites and the structural topology are graphically represented. Also, literature information related to PTMs, orthologous conservations and substrate motifs of PTMs are also provided in the resource. Lastly, this version features an improved web interface to facilitate convenient access to the resource.http://dbptm.mbc.nctu.edu.tw/index.php23193290
4HIstomePost-translational modification (PTM) of histones is a crucial step in epigenetic regulation of a gene. N-terminal tails of histones are the most accessible regions of these peptide as they protrude from the nucleosome and possess no specific structure. These tails are subjected to various modifications such as acetylation, methylation, phosphorylation, ubiquitination etc. by the 'writers'. PTMs are believed to function in a combinatorial pattern referred to as the 'histone code'. The major function of PTMs is to either create sites for the recruitment of specific factors or modify existing sites so as to abolish previous interactions. This alters the expression states of associated loci by multiple ways thus enabling gene regulation. PTMs can recruite enzymes that can ‘write’, ‘erase’ or ‘read’ modifications and the repertoire of such modifiers is found to be fairly large in number (~150 different enzymes in humans). Certain modifications such as acetylation, phosphorylation, change the overall charge on basic histone proteins and thereby interfere with the histone-DNA interaction essential for nucleosome stability. In terms of molecular weight, these modifications range from light (acetylation, methylation, phosphorylation) to heavy (ubiquitination, poly ADP ribosylation). Here we include 8 different types of modifications that exist on all histone peptides. PTMs are often found to be cell cycle dependent. Role of various histone PTMs has been evaluated in many important cellular processes such as demarcating euchromatin and hetrochromatin regions, transcriptional regulation of Hox gene clusters, maintainance of stemness, cell cycle control etc. Presence or absence of certain PTMs is shown to be a hallmark of different cancers.http://www.actrec.gov.in/histome/ptm_main.php22140112
5novPTMenzySeveral attempts have been made to catalog the wealth of available information on Post-Translational Modification(PTMs) for easy retrieval and analysis. However, the tools and databases available mainly focus on modified sites or enzymes of well-known PTMs. Tools for newly discovered PTMs like AMPylation and Eliminylation or unusual PTMs like sulfation,hydroxylation,deamidation etc are not yet available. novPTMenzy is a step towards cataloging information about novel and unusual PTMs and using this information for genome mining of ezymes involved in these PTMs and understanding the pathways in which they are involved. novPTMenzy provides a database Using novPTMenzy user can search for enzymes involved in five PTMs namely AMPylation, Eliminylation, Sulfation, Hydroxylation and Deamidation.The search tool also links the protein to closest experimentally characterized neighbor and closest structural neighbor.http://www.nii.ac.in/novptmenzy.html25931459
6ProteomeScoutProteomeScout is a database of proteins and post-translational modifications. There are two main data types in ProteomeScout. 1) Proteins: Visualize proteins or annotate your own proteins. 2) Experiments: You can load a new experiment or browse and analyze an existing experiment.https://proteomescout.wustl.edu/25414335
7PSPPhosphoSitePlus® (PSP) is an online systems biology resource providing comprehensive information and tools for the study of protein post-translational modifications (PTMs) including phosphorylation, ubiquitination, acetylation and methylation. See About PhosphoSite above for more information. Please cite the following reference for this resource: Hornbeck PV, et al (2015) PhosphoSitePlus, 2014: mutations, PTMs and recalibrations. Nucleic Acids Res. 43:D512-20. [reprint]http://www.phosphosite.org/homeAction.do25514926
8PTMCodePTMCode is a resource of known and predicted functional associations between protein post-translational modifications (PTMs) within and between interacting proteins. It currently contains 316,546 modified sites from 69 different PTM types which are also propagated through ortholgs between 19 different eukaryotic species. A total of 1.6 million sites and 17 million functional associations more than 100,000 proteins can currently be explored.http://ptmcode.embl.de/25361965
9PTMfuncPTMfunc is a repository of functional predictions for protein post-translational modifications (PTMs). To find predictions for your protein of interest just search using a protein name or ID in the search box above. We rely mostly on ids from ENSEMBL but also have protein names for most species. For more info click on documentation.http://ptmfunc.com/22817900
10PTM-SDPosttranslational modifications (PTMs) define covalent and chemical modifications of protein residues. They play important roles in modulating various biological functions. Current PTM databases contain important sequence annotations but do not provide informative 3D structural resource about these modifications. Posttranslational modification structural database (PTM-SD) provides access to structurally solved modified residues, which are experimentally annotated as PTMs. It combines different PTM information and annotation gathered from other databases, e.g. Protein DataBank for the protein structures and dbPTM and PTMCuration for fine sequence annotation. PTM-SD gives an accurate detection of PTMs in structural data. PTM-SD can be browsed by PDB id, UniProt accession number, organism and classic PTM annotation. Advanced queries can also be performed, i.e. detailed PTM annotations, amino acid type, secondary structure, SCOP class classification, PDB chain length and number of PTMs by chain. Statistics and analyses can be computed on a selected dataset of PTMs. Each PTM entry is detailed in a dedicated page with information on the protein sequence, local conformation with secondary structure and Protein Blocks. PTM-SD gives valuable information on observed PTMs in protein 3D structure, which is of great interest for studying sequence-structure- function relationships at the light of PTMs, and could provide insights for comparative modeling and PTM predictions protocols. Database URL: PTM-SD can be accessed at http://www.dsimb.inserm.fr/dsimb_tools/PTM-SD/. © The Author(s) 2014. Published by Oxford University Press.http://www.dsimb.inserm.fr/dsimb_tools/PTM-SD/24857970
11RedoxDBSUMMARY: Redox regulation and signaling, which are involved in various cellular processes, have become one of the research focuses in the past decade. Cysteine thiol groups are particularly susceptible to post-translational modification, and their reversible oxidation is of critical role in redox regulation and signaling. With the tremendous improvement of techniques, hundreds of redox proteins along with their redox-sensitive cysteines have been reported, and the number is still fast growing. However, until now there is no database to accommodate the rapid accumulation of information on protein oxidative modification. Here we present RedoxDB-a manually curated database for experimentally validated redox proteins. RedoxDB (version 1.0) consists of two datasets (A and B, for proteins with or without verified modified cysteines, respectively) and includes 2157 redox proteins containing 2203 cysteine residues with oxidative modification. For each modified cysteine, the exact position, modification type and flanking sequence are provided. Additional information, including gene name, organism, sequence, literature references and links to UniProt and PDB, is also supplied. The database supports several functions including data search, blast and browsing. Bulk download of the entire dataset is also available. We expect that RedoxDB will be useful for both experimental studies and computational analyses of protein oxidative modification. AVAILABILITY: The database is freely available at: http://biocomputer.bio.cuhk.edu.hk/RedoxDB.http://biocomputer.bio.cuhk.edu.hk/RedoxDB/22833525
12RESIDThe RESID Database of Protein Modifications is a comprehensive collection of annotations and structures for protein modifications including amino-terminal, carboxyl-terminal and peptide chain cross-link post-translational modifications.http://pir.georgetown.edu/resid/12520062
13SysPTM SysPTM Version 2.0, updated June 15th, 2013. Visits: 110. SysPTM provides a systematic and sophisticated platform for proteomic PTM research, equipped not only with a knowledge base of manually curated multi-type modification data, but also with four fully developed, in-depth data mining tools. Currently, SysPTM contains data detailing 471109 experimentally determined PTM sites on 53235 proteins, covering more than 50 modification types, curated from public resources including five databases and four webservers and more than three hundred peer-reviewed mass spectrometry papers. Protein annotations including Pfam domains, KEGG pathways, GO functional classification, and ortholog groups are integrated into the database. Five online tools have been developed and incorporated, including: PTMBlast, PTMPathway, PTMPhylog, PTMCluster and PTMGO.In SysPTM, the roles of single-type and multi-type modifications can be systematically investigated in a full biological context. SysPTM could be an important contribution to modificomics research.http://lifecenter.sgst.cn/SysPTM/24705204
14topPTMtopPTM is a database that integrates experimentally verified post-translational modifications (PTMs) from available databases and research articles, and annotates the PTM sites on transmembrane proteins with structural topology. The biological effects of PTMs on transmembrane proteins include phosphorylation for signal transduction and ion transport, acetylation for structure stability, attachment of fatty acids for membrane anchoring and association, as well as the glycosylation for substrates targeting, cell-cell interactions, and viruses infection. The experimentally verified PTMs are mainly collected from public resources including dbPTM, Phospho.ELM, PhosphoSite, OGlycBase, and UbiProt. For transmembrane proteins, the information of membrane topologies is collected from TMPad, TOPDB, PDBTM, and OPM. In order to fully investigate the PTMs on transmembrane proteins, the UniProtKB protein entries containing the annotation of membrane protein and the information of membrane topology are regarded as potential transmembrane proteins. To delineate the structural correlation and consensus motif of these reported PTM sites, the topPTM database also provide structural analyses, including the membrane accessibility of PTM substrate sites, protein secondary and tertiary structures, protein domains, and cross-species conservations of each entry.http://topptm.cse.yzu.edu.tw/24302577
#Database NameDescriptionURLReference
1PubMethEpigenetics, and more specifically DNA methylation is a fast evolving research area. In almost every cancer type, each month new publications confirm the differentiated regulation of specific genes due to methylation and mention the discovery of novel methylation markers. Therefore, it would be extremely useful to have an annotated, reviewed, sorted and summarized overview of all available data. PubMeth is a cancer methylation database that includes genes that are reported to be methylated in various cancer types. A query can be based either on genes (to check in which cancer types the genes are reported as being methylated) or on cancer types (which genes are reported to be methylated in the cancer (sub) types of interest). The database is freely accessible at http://www.pubmeth.org. PubMeth is based on text-mining of Medline/PubMed abstracts, combined with manual reading and annotation of preselected abstracts. The text-mining approach results in increased speed and selectivity (as for instance many different aliases of a gene are searched at once), while the manual screening significantly raises the specificity and quality of the database. The summarized overview of the results is very useful in case more genes or cancer types are searched at the same time.http://www.pubmeth.org17932060
#Database NameDescriptionURLReference
1MYRbaseMyristoylation is a common lipid modification of proteins in Eukaryotes and their Viruses as well as some Bacteria and essential for the function of several important proteins (such as G proteins, SRC and related kinases, ADP ribosylation factors, HIV gag, HIV nef,...). The saturated 14-carbon fatty acid (Myristate) is attached most often co-translationally by the enzyme NMT (MyristoylCoA:Protein N-Myristoyltransferase) to N-terminal glycines or glycines that become N-terminal after proteolytic cleavage. Based on sequence variability of known substrate proteins, physical property profiles and structural models of NMT-substrate interactions (J Mol Biol. 2002 Apr 5;317[4]:523-40), we developed a powerful prediction tool for glycine myristoylation (J Mol Biol. 2002 Apr 5;317[4]:541-57) that is available as webserver (http://mendel.imp.univie.ac.at/myristate/) and whose sensitivity allows large-scale database runs. To facilitate selection of targets for experimental verification of our predictions, we evaluate the evolutionary conservation of the predicted myristoylation motif within close homologues (EvOluation). If a sequence is predicted to be myristoylated and the same applies to its homologues (preferably in a series of different organisms), we not only add another dimension of credibility to our prediction but derive that the lipid anchor might play an essential role for that protein's function. Such an analysis has been applied in a large-scale approach to the proteins included in the SwissProt and Genbank databases. The corresponding predicted entries and their homologues were annotated and summarized in tabular form accessible from MYRbase.http://mendel.imp.ac.at/myristate/myrbase/15003124
#Database NameDescriptionURLReference
1GlycoFishLIPID PROFILING & CELL ENGINEERING POST-DOCTORAL SCIENTIST An opening for a motivated and talented post-doctoral scientist in lipid profiling/ lipidomics and cellular engineering is available in the laboratory of Dr. Betenbaugh. Candidates should have a PhD in biochemistry, molecular biology, bioengineering, chemical engineering, or a related discipline with a strong record of publication and experience. Previous work experience in one or more of the following specialties is highly desirable: identifi