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ToxoEntityNet Toxoplasma gondii ME49
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ToxoEntityNet

Toxoplasma gondii ME49 proteins, metabolites and published experimental data

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Help and methods

Search

Search by TGME49 gene ID, syntenic GT1/VEG ortholog ID (e.g. TGGT1_215490), UniProt or RefSeq accession, ToxoDB gene name or alias (e.g. SAG1, CDPK1), ToxoDB or UniProt protein name, metabolite name or GO ID. A GO ID (e.g. GO:0020009) lists every protein annotated with that term together with its evidence codes. Press / to focus the search box.

Data and methods

  1. Experimental data: source values, p-values and citations from 11 published datasets (CRISPR fitness screens, RNA-seq, TMT proteomics, ChIP/CUT&RUN, AP-MS, phosphoproteomics). Each dataset states whether the protein was within its assay range; "not assayed" or "not in the published selected list" is not a negative result. Scales differ between datasets and are not directly comparable.
  2. Homology inference: annotations with experimental evidence codes (EXP/IDA/IPI/IMP/IGI/IEP/HTP and related) in UniProtKB/Swiss-Prot 2026_02 are transferred to ME49 proteins through DIAMOND sequence or Foldseek structure matches. Each transfer shows its precision measured by leave-one-lineage-out testing (Wilson 95% interval); transferred locations agree with hyperLOPIT for 46% of 2,359 comparable location records (14% expected by chance).
  3. ToxoDB: gene–publication links, community comments, GO evidence, hyperLOPIT probabilities, mass-spectrometry detection and stage-specific transcript levels (TPM / RMA) from ToxoDB release 71 (2026-08-20). Publications linked to more than 50 genes are listed as genome-wide studies; community comments are not verified. Gene models that ToxoDB merged, split or removed are flagged.
  4. Functional annotation: function, GO (three columns, coloured by evidence code), subcellular location, sequence features, AlphaFold structure and families, in the order of a UniProt entry. GO combines InterPro2GO (electronic), ToxoDB GO and homology transfers; obsolete terms are replaced following GO 2026-07-26. Every annotation carries its source and an ECO evidence term (ECO 2026-07-10).
  5. CRISPR values: GT1 loci are assigned to ME49 genes through ToxoDB syntenic orthology; 19 of 147,185 gene-by-variable pairs differ from ToxoDB, and corrected values are marked on the entry page.
  6. Names: the displayed name is the ToxoDB product name with experimental support, otherwise the literature-curated name, the ToxoDB product name, RefSeq or UniProt; the source is shown on the entry.
  7. Network: recorded relations between entries, filterable by evidence type. An edge does not imply direct physical interaction; rank scores are ordinal, not probabilities.
  8. Cross-species comparison: best DIAMOND matches in both directions; these are not confirmed orthologs.
  9. Membrane proteins follow the integrated membrane-topology classification (TMbed, TMHMM, UniProtKB, hyperLOPIT membrane clusters and membrane annotations); proteins with only a signal peptide are listed as predicted secretory proteins. On 1,343 hyperLOPIT soluble proteins this classification has 94% specificity; recall cannot be assessed independently because hyperLOPIT is an input. Transporter flags are predictions (sequence homology, HMMs, topology prediction, Foldseek, with TCDB and Parker et al. 2019).

Tools

Batch search lists proteins by ID list or combined criteria and exports TSV. Downloads offers the derived data tables with SHA-256 checksums. Saved and recent entries are stored only in this browser.

Release 2026-10 contains published measurements and database records; it has no computed interaction rankings, vulnerability scores, transport-hypothesis rankings or human selectivity tiers. Details: Methods.