The accepted intake preserves genuine source acquisitions and the unsuccessful provider attempt. The following manual-source notes record the biological assessment; no provider-authored report is fabricated.
The 13 assigned source contexts were reviewed manually: 11 ACCEPT, one MODIFY (cytoplasm to cytosol), and one KEEP_AS_NON_CORE (the reported minor alpha-granule lumen pool). The 34 direct-evidence contexts remain PENDING in this lane candidate. All 47 imported source objects, initial description/status, product representation and original reference identities/findings are preserved; no core, NEW annotation or publication quotation is added.
The actual PAINT tree/MSA and IBD support the ancestral enzyme and fibrin-clot claims. The inconsistent generic negative tree GO-slim display is explicitly separate from IBD; target self-WITH is valid. Human F13A1's executed chemistry was independently read in the complete PMID:27363989 article and supplement reproduced in an author thesis. Mouse donor originals remain abstract-only and are not represented as human experiments.
The human platelet evidence in PMID:25331118 and PMID:39116293 distinguishes soluble intracellular protein from surface/released material. The minor A2B2 granule finding in PMID:8360253 is positive at abstract scope; it is not disproven by the dominant cytoplasmic pool. Detailed uptake routing and granule fraction purity remain unverified. The source guide records original-access boundaries and public section/figure locators; the private read ledger preserves exact inspected text and failed image/supplement requests.
All six Reactome target routes were replayed from raw objects, including regulator branches. F13A1 is the substrate of activating cleavage, the cargo of exocytosis, and the product of expression in the corresponding events; it is the cross-linking catalyst in the fibrin reactions. Literal coordinate/display differences are preserved. These are distinct roles, not new process assertions.
Five genuine additive publication fetches completed successfully with 253 preimages unchanged and no restoration. The provisional normal union is 44 objects (39 original plus five additions), with 23 selected normal dependencies and two machine inputs; 21 unused normal sources remain private. Publication availability flags follow actual complete-original availability rather than cache fullness. This checkpoint is private and requires ROOT integration and later canonical validation.
Human F13A1 chemistry is supported by the complete 2016 article and supplement reproduced in the official author thesis. Its sequence-checked human constructs, COS-1 host and lysate assays are kept distinct. Thrombin is the activating protease; F13A1 subsequently cross-links proteins. The older activation-peptide kinetics and structural papers are not represented as additional F13A1 catalytic assays. The specific fibrin-clot process captures the performed stabilization step within coagulation. PMID:27363989(https://pubmed.ncbi.nlm.nih.gov/27363989/), PMID:10801785(https://pubmed.ncbi.nlm.nih.gov/10801785/)
Twenty-two Haenig/NeuroNet physical associations remain non-core after inspecting the original screening Methods, bait table and literal pair records. A historical bait clone does not establish current product identity, and a positive yeast reporter does not identify a physiological cross-linking substrate or an adaptor activity. The separate HuRI study is not their source. PMID:32814053(https://pubmed.ncbi.nlm.nih.gov/32814053/)
Target-level proteomic tables support F13A1 in ECM-enriched colon, bone-marrow and omental fractions, retained as contextual locations. These observations are distinct from catalytic activity or a cancer mechanism. The human-plasma microparticle context remains undecided because its target table and operative main text could not be recovered. This access limit is not evidence against the annotation. PMID:25037231(https://pubmed.ncbi.nlm.nih.gov/25037231/), PMID:28344315(https://pubmed.ncbi.nlm.nih.gov/28344315/), PMID:28675934(https://pubmed.ncbi.nlm.nih.gov/28675934/), PMID:22516433(https://pubmed.ncbi.nlm.nih.gov/22516433/)
The displayed 732-residue sequence and processed chains remain distinct from alternative transcript models. No splice-product equivalence, new publication quotation, or additional GO assertion is inferred. Database-source decisions and eventual core synthesis are separate checkpoints.
The two accepted evidence lanes cover all 47 imported contexts: 18 ACCEPT, two MODIFY, 26 KEEP_AS_NON_CORE and one UNDECIDED. All source objects and 19 original reference identities/findings are preserved. Five genuinely acquired references are appended, giving 24 references. Shared PMID:27363989 retains both labeled reading scopes. F13A1 performs protein cross-linking; thrombin performs its proteolytic activation. Soluble cytosolic platelet F13A1 is distinguished from the positive minor granule-associated pool. The microparticle context remains undecided because target-specific source evidence was unavailable. Description and core synthesis follow this annotation checkpoint.
F13A1 supplies the catalytic A subunit that cross-links fibrin chains and incorporates alpha2-antiplasmin. The complete human-expression article and supplementary recipes distinguish measured amine incorporation and fibrin-chain products from activation by thrombin. The COS-1 cells are the host of the human construct, and the deficient-plasma assays test the expressed preparation rather than every natural transcript. Plasma A2B2 describes the B-containing zymogen assembly; activation changes that assembly, and no single active stoichiometry is imposed. PMID:27363989(https://doi.org/10.1002/humu.23041)
The single core places performed protein cross-linking in fibrin-clot formation. Those two current process terms are not ancestors of each other. Cytosolic residence remains a supported part of the biological description and annotation review, but the core's extracellular catalytic location does not assert fibrin cross-linking inside intact platelets. The major soluble A-subunit pool, smaller exposed/released pools and reported minor granule A2B2 pool remain distinct. Antigen, ex vivo activity and intracellular substrate chemistry are separate measurements. The paired questions address this remaining functional separation without presupposing export or uptake. PMID:25331118(https://doi.org/10.1182/blood-2014-06-583070), PMID:39116293(https://pmc.ncbi.nlm.nih.gov/articles/PMC11459904/), PMID:8360253(https://doi.org/10.1002/jcp.1041560302)
This phase changes only description, the single core and two paired questions/experiments, with this append and the source-guide append. All 47 accepted source/review objects, all 24 references, source product representation and INITIALIZED checkpoint status remain exact. No new annotation or publication quotation is introduced. Canonical status and rendering remain a later validation step.
F13A1 directly binds calcium, beyond requiring it in an activation or activity assay. The 1999 crystallography study reports a calcium site per A-subunit monomer, and its primary 1GGU deposition contains two modeled calcium ions in a recombinant human A2 crystal. The deposited polymer sequence matches current P00488 residues 2–732 and was expressed in yeast. UniProt's experimentally supported side-chain positions 437, 439, 486 and 491 correspond to paper positions 436, 438, 485 and 490; the paper's backbone Ala457 corresponds to current Ala458. The complete article remains inaccessible, but its abstract, primary structural data and curated UniProt binding features together support the new calcium-binding annotation. This does not assign a universal calcium stoichiometry, affinity or active conformation to every F13A1 preparation.
The current calcium ion binding term describes the measured interaction. An exact-term query found human TGM2 and TGM3 IDA assertions and no TGM1 or F13A1 assertion; thus there is no systematic family-wide convention against this binding term. The target's structural evidence, not the comparator count or the reviewer's request, justifies the new molecular-function assertion. Calcium binding is described within the existing catalytic core rather than duplicated as a separate enzymatic unit. The revision retains all 47 imported review objects and appends one NEW row; all 24 existing reference objects remain exact and two source references are added. No publication quotation is added.
The circulating A2B2 precursor and activated A-subunit assemblies are distinct states. The broad transferase-complex context does not assert retention of B subunits in active A preparations. Two exact OLS complex-name searches found no match; broader QuickGO searches were limited to their first 100 ranked results and do not prove global absence. A focused representation question records this unresolved specificity without inventing a GO complex identifier.
The blood-microparticle row remains UNDECIDED because the target-level evidence in PMID:22516433 has not been inspected. Abundant plasma proteins or possible carryover do not by themselves disprove a curated experimental target observation. Availability flags continue to describe access to the original paper, whereas the separate immutable cache metadata describes cached text: the complete external originals already inspected for PMIDs 10801785, 27363989 and 28344315 remain available despite abstract-only normal caches. No new whole-article access is claimed for those papers here. Earlier journal entries retain their historical acquisition and validation scope; this appendix records the focused biological clarification.