The full-length RHOJ/TCL protein is an active, rapidly exchanging GTPase, contrary to a generic GTPase-deficient Rho-family description. However, G3V4H1 is a substantially altered short product, so its activity cannot be decided from the full-length result in either direction.
G3V4H1 and Q9H4E5 share HGNC:688. The first 103 residues match exactly; the remainder is highly divergent. The reference guanine-binding residue 136 is not aligned to the target, reference binding residue 177 is not conserved, and the terminal lipidation region is absent from the conserved segment. Retaining the P-loop and switch-region segment alone does not establish a functional G-domain.
In vitro, TCL shows rapid GDP/GTP
exchange and displays higher GTP dissociation and hydolysis rates than TC10.
Chimeras of TCL and TC10
revealed amino acids 121-129 of TCL contributed to the differences in nucleotide
loading.
The complete emitted record is preserved in RHOJ-protnlm-source.json. Assessments below address the selected protein product; evidence on longer products is identified explicitly.
Cell division control protein 42 homolog
LSP (CS 2) if “homolog” is read as a broad relationship: RHOJ is demonstrably Cdc42-related. The name is less informative than RHOJ/TCL and must not be read as identifying the CDC42 paralog or guaranteeing an intact Cdc42-like enzyme. PMID:10967094(https://pubmed.ncbi.nlm.nih.gov/10967094/).
Binds GTP but lacks intrinsic GTPase activity and is resistant to Rho-specific GTPase-activating proteins
UNC (CS 1) for the selected G3V4H1 product. The “lacks intrinsic GTPase activity” description is contradicted for full-length RHOJ by direct hydrolysis measurements, but the target has a divergent, incomplete G-domain. The conjunction “binds GTP but lacks hydrolysis and resists GAPs” requires binding, hydrolysis and GAP assays of this exact product; a truncation alone does not establish an atypical GTPase mechanism. PMID:10967094(https://pubmed.ncbi.nlm.nih.gov/10967094/); sequence mapping.
Membrane
UNC (CS 1). The selected product does not retain the reference C-terminal membrane-targeting region, and RHOJ membrane association is sensitive to sequence-dependent nucleotide loading. Partner-mediated membrane association remains possible, so no exclusively cytosolic alternative is asserted. PMID:27660391(https://pubmed.ncbi.nlm.nih.gov/27660391/).
No GO or EC term was emitted in this record; the name, function and location assessments above constitute its prediction review.
PTHR24072 establishes Rho-family ancestry but includes paralogs with different nucleotide cycling properties. The experimentally characterized RHOJ branch is catalytically active. The selected altered product creates an additional product-integrity boundary beyond family membership.
The original RHOJ paper is abstract-only in the cache; the 2016 mechanistic study has full text. Neither tests G3V4H1. A confident pseudoenzyme designation would conflate a potentially incomplete product with a stable, evolved GTPase-deficient signaling protein.
Exact sequence mapping: RHOJ-bioinformatics/RESULTS.md. Global alignments can place nonhomologous alternative tails opposite gaps or distant residues; only conserved segments and explicitly retained feature intervals support functional transfer.
The genuine Falcon report is retained. Its gene-level synthesis is interpreted through the exact product sequence and the primary sources above; the truncation boundary and paralog distinctions are assessed independently.
Scope: G3V4H1 (ProtNLM2 benchmark target, cohort MOD_EVOLUTION20). No ProtNLM2 file or prediction output was opened or used. New analysis: RHOJ-bioinformatics/compare_sequences_rereview.py -> RESULTS-rereview.txt / RESULTS-rereview.md, which fetch sequences and transcript models live from UniProt and Ensembl. The earlier RESULTS.md and its scripts are unchanged.
interpro/panther/PTHR24072/PTHR24072-review.yaml) already names G3V4H1 as an altered same-gene product and does not dispute subfamily placement. I found no disagreement.All three IEAs (GTPase activity, G protein activity, GTP binding) changed from UNDECIDED to MARK_AS_OVER_ANNOTATED. They are true of the gene and of Q9H4E5 PMID:10967094. They are not supported for an NMD-transcript product that lacks the guanine-base motifs and half the fold. I did not use REMOVE, because no assay of this product exists and the claims are correct at gene level. The description was rewritten so that it gives the gene-level biology [PMID:21628409; PMID:30158707] and then the product-identity boundary. core_functions stays empty, since no function is established for this product. No NEW terms were proposed.
The canonical product of the same gene, Q9H4E5 (RHOJ_HUMAN, reviewed). genes/human/RHOJ is keyed to G3V4H1, and no review of Q9H4E5 exists in the repo, so the next folder would be genes/human/RHOJ__Q9H4E5. No module names RHOJ or Q9H4E5. These modules use PTHR24072 Rho-family descriptors and are context only: modules/rho_gprotein_signaling.yaml, modules/ephrin_receptor_signaling.yaml, modules/chemokine_signaling.yaml, modules/phagocytic_engulfment.yaml.
The function narrative (RHOJ-protnlm-function-review.md) now scores "binds GTP" as NPI
(DOMAIN_ARCHITECTURE_MISMATCH) for G3V4H1. GTP binding is true of the gene, but guanine binding needs
the G4 (TQID) and G5 (CSAL) motifs, and G3V4H1 keeps only the P-loop, switch I and switch II before
diverging after residue 103. "Lacks intrinsic GTPase activity and is resistant to Rho-specific GAPs"
stays UNC. This supersedes the single UNC given under "Exact non-GO claims" above.
The GO row for GTP binding (GO:0005525) stays MARK_AS_OVER_ANNOTATED, not REMOVE. The two calls rest
on different grounds and are consistent: the narrative score judges whether this exact product can do
what the text says, and the missing G4/G5 motifs refute that; the GO action judges an annotation that
is correct for the gene, and no assay of G3V4H1 exists to justify removing it.