FAQ

  • What is KMetHub?

    KMetHub is a curated database of experimentally identified lysine methylation sites in human non-histone proteins. It brings together methylation site records from the scientific literature in a single, searchable resource with protein, modification, enzyme, cellular context, and reference information.

  • What does "non-histone" mean?

    Lysine methylation is mostly studied on histone proteins, where it regulates chromatin and gene expression. "Non-histone" refers to all other proteins in the proteome that can also carry lysine methylation. KMetHub focuses on these non-histone sites rather than histone tail modifications.

  • What information is provided for each methylation site?

    Each entry includes the substrate protein (UniProt ID, gene and protein name), the position of the modified lysine in the canonical sequence, the methylation degree (Kme1, Kme2, Kme3 or Kme if the degree is unknown), the local peptide sequence (±7 aa), the modifying KMT enzyme when known, cell type where the methylation event was identified, protein domain, Gene Ontology annotations, literature references (HTP/LTP), and optional notes.

  • How were the data collected? Where do the data come from?

    Data were curated from published experimental studies, both high-throughput and low-throughput proteomics and affinity-based enrichment experiments reported in the literature. Only experimentally reported sites are included; sources are linked via PubMed identifiers for each methylated lysine site.

  • Are computational predictions included?

    No. KMetHub contains experimentally reported methylation sites only. Computational or in silico predictions are not included in the database.

  • How reliable are the data?

    Entries are based on published experimental evidence. References are classified as high-throughput (HTP) or low-throughput (LTP). LTP studies typically provide stronger site-level evidence and often include information on the methyltransferase, whereas HTP studies contribute breadth across the proteome. We encourage you to consult the original publications for full experimental details.

  • Can one site have multiple methylation states?

    Yes. The same lysine position can appear as separate entries when different methylation degrees (mono-, di-, or tri-methylation) have been reported, or when reported in different experimental contexts. Each combination of protein, position, degree, and sequence context is stored as its own record.

  • Why is the modifying enzyme unknown for some sites?

    The methyltransferase (KMT) is listed only when it was identified or confidently assigned in the source study. Many proteomic surveys detect methylation on substrate proteins without establishing the responsible enzyme, so the enzyme field is left unknown for those entries.

  • Can I download the data?

    Yes. Data files are available from the Downloads page. You can export or retrieve the current release of KMetHub data for offline analysis.

  • How should I cite KMetHub?

    Please cite KMetHub and the original publications for the methylation sites you use. A dedicated KMetHub publication will be listed here when available. Until then, acknowledge the database as "KMetHub, Non-Coding Genome Research Group" and cite the primary literature references linked to each site.

  • How often is KMetHub updated?

    The database is updated when new curated datasets become available from the literature. Update frequency depends on the release of new experimental data and curation cycles. Check the Downloads page or site statistics for the current dataset version.

  • I found an error. How can I report it?

    If you notice incorrect or missing information, please contact the KMetHub curators at kmethub@ttk.hu and include the UniProt ID, site position, and the reference or correction details so the entry can be reviewed.

  • Can I submit new data?

    Contributions of newly published experimental methylation sites are welcome. Please contact the KMetHub team at kmethub@ttk.hu with publication details (PMID), accession information, and supporting evidence so curators can review and incorporate validated entries.

  • What organisms are included?

    KMetHub currently focuses on human proteins. All substrate UniProt IDs refer to human entries in UniProtKB.

  • How can I search the database?

    The search bar at the top of the page allows you to search in the protein names, UniProt IDs and gene names. Under the Advanced Search options you have the ability to search among any fields of the database.

  • How can the data be filtered?

    Use the Browser to browse and sort all methylation sites, the Advanced Search page to query by keyword or filter by KMT enzyme and cell type, and the navbar search box for quick text searches across the site.