gltX

Summary: gltX recognizes the tRNA substrate as an integral enzymatic role.

Reason: Curated tRNA substrate recognition and the conserved binding/catalytic architecture support this core capability. Its co-occurrence with ligase activity is not grounds for marking it peripheral.

Summary: gltX binds ATP as part of its aminoacylation machinery.

Reason: Nucleotide binding is true but broad. The curated glutamate reaction and relevant subunit architecture support the more specific ATP-binding claim; this is integral substrate recognition, not a peripheral role.

Proposed replacements: ATP binding

Summary: gltX has a defined role in the substrate-specific catalytic reaction.

Reason: Refine the broad activity to the supported glutamate-tRNA ligase activity. The exact KT2440 curated family/rule assignment supports function by homology, not a purified-target experiment.

Proposed replacements: glutamate-tRNA ligase activity

Summary: gltX supports its substrate-specific tRNA-ligase activity.

Reason: The exact native protein has the corresponding curated HAMAP family/domain and reaction assignment. This supports conserved catalytic capability by homology, not direct KT2440 purification.

Summary: gltX contributes integral ATP recognition to its enzymatic reaction.

Reason: ATP binding is an integral biochemical property, not a non-core activity merely because it is binding. The curated reaction/architecture supports it by homology for KT2440.

Summary: gltX acts in the soluble intracellular tRNA-processing system.

Reason: The soluble intracellular synthetase acts on cellular tRNAs; refine cytoplasm to the already retained cytosol term. This is a conserved biochemical/localization inference, not native microscopy.

Proposed replacements: cytosol

Summary: gltX acts in the bacterial cytosol.

Reason: The conserved soluble enzyme architecture and curated intracellular localization support this core location. Direct KT2440 imaging is not claimed; lack of such an experiment does not make the supported core location peripheral.

Summary: gltX directly supplies aminoacyl-tRNA for protein translation.

Reason: The curated glutamate–tRNA reaction forms the amino-acid–tRNA ester bond used in translation. This is the current process term, not overannotation merely because a former substrate-specific BP was more detailed.

Summary: gltX contributes to translational tRNA aminoacylation; the old substrate-specific BP is obsolete.

Reason: Current QuickGO marks this substrate-specific process obsolete because it restates a molecular function. Preserve the original GOA term while replacing it with GO:0006418; retain substrate specificity in the supported ligase molecular function.

Proposed replacements: tRNA aminoacylation for protein translation

Summary: KT2440 GltX loses canonical zinc ligands, but native binding remains unresolved.

Reason: The reproduced three-protein alignment maps E. coli C98/C100/C125/H127 and PAO1 C107/C109/C134/H136 to KT2440 C107/C109/A134/L136. Thus the actual three-cysteine/one-histidine site has lost its last two ligands. This establishes divergence of the canonical site, not a negative native zinc-binding assay. Full PMID:25686371 separates zinc occupancy, transplanted-domain binding and catalytic requirement; alternative coordination motifs exist. No native KT2440 metal-content or affinity measurement was found, so the broader zinc-binding claim remains unresolved rather than categorically excluded.

Summary: gltX performs a defined chemical step supplying translation substrates.

Reason: gltX directly participates in ATP-dependent glutamate attachment to tRNA for protein translation. Use the precise translational charging process rather than the broader parent; do not retain obsolete substrate-specific BP terms.

Proposed replacements: tRNA aminoacylation for protein translation