L-tryptophan biosynthesis

Backbone and characterized-protein groundings were mined from GapMind trp.steps and ModelSEED (see modules/experimental/gapmind-mining/), then curated: GO molecular-function terms were verified via QuickGO, reaction chemistry and channeling/fusion notes were added, and the GapMind anthranilate-synthase OR-rule (two-component vs single-protein) was curated into an EXACTLY_ONE variant set. EC numbers that GapMind records only as ignore_other (the true reaction ECs 4.1.3.27, 4.1.2.8, 4.2.1.20) were reinstated as reaction evidence. In the P. putida KT2440 ppu00400 batch, the narrow module is fully satisfied by trpE, PP_0420/trpG-like amidotransferase, trpD, trpF, trpC, trpA, and trpB. Upstream shikimate genes, phenylalanine/tyrosine branch enzymes, and quinate-catabolic genes are outside this module. ALIGN with YeastPathways (2026-10): the five YeastCyc TRPSYN-PWY-1 reactions map one-to-one onto the five parts and the YeastCyc catalysts (TRP2 + TRP3, TRP4, TRP1, TRP3, TRP5) are all correct; no enzymes are missing. Scope widened from "microbial" to bacteria, archaea, fungi and plants (the title no longer says microbial). Because the reaction chain is fixed but the fungal fusion pattern differs from bacteria, architecture variant sets were added: a fungal anthranilate synthase variant (TrpE = S. cerevisiae TRP2 / S. pombe trp3, plus the TrpG domain of S. cerevisiae TRP3 or S. pombe trp1); a PRAI variant set (monofunctional TrpF, including S. cerevisiae TRP1, versus the TrpF domain of TrpCF-type fusions, including E. coli TrpCF and S. pombe trp1); an IGPS variant set (standalone TrpC or TrpCF-type fusions in PTHR22854, versus the TRP3-type TrpG-TrpC protein in PTHR43418:SF4); and a tryptophan synthase variant set (TrpA2-TrpB2 complex versus single-chain TrpA-TrpB, S. cerevisiae TRP5 / S. pombe trp2, PTHR48077:SF3). Fusion choices are correlated across steps: budding yeast uses the fungal anthranilate synthase, monofunctional TrpF, TrpG-TrpC IGPS and fused tryptophan synthase variants; fission yeast uses the fungal anthranilate synthase, TrpCF-type PRAI, TrpCF-type IGPS and fused tryptophan synthase variants. Glutaminase (TrpG) annotons carry GO:0004049 as a contributing subunit, consistent with the S. cerevisiae TRP3 review (contributes_to GO:0004049, part of GO:0005950); the anthranilate-synthase connection to the next step was changed from PROVIDES_INPUT_FOR to PRECEDES for consistency with the other steps. Compartment - every activity is cytosolic in both GO-CAMs and in bacteria, but the plant pathway is plastid-localised, so no module-level compartment is asserted (the previous cytosol context was removed for that reason). GO-CAM disagreements - neither model has causal edges (activities are linked only by shared input/output molecules); the PomBase model (67369e7600004623) shows S. pombe trp3 alone enabling GO:0004049 and does not represent the TrpG glutaminase contribution of trp1 or an anthranilate synthase complex, whereas the SGD model attributes GO:0004049 to the TRP2-TRP3 complex (CPX-1850). The PomBase model is a whole-network aromatic amino acid model, and only its four tryptophan-branch activities map to this module. S. pombe assignments (trp1, trp2, trp3, trp4) are sequence-based (UniProt, PomBase); the trifunctional TrpG-TrpC-TrpF architecture of trp1 is supported by the Neurospora trp-1 precedent (PMID:6221060).

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