Gene Ontology annotation through association of InterPro records with GO terms

Manual transfer of experimentally-verified manual GO annotation data to orthologs by curator judgment of sequence similarity

GO_REF:0000118

TreeGrafter-generated GO annotations

GO_REF:0000120

Combined Automated Annotation using Multiple IEA Methods

file:PSEPK/mdh/mdh-deep-research-falcon.md

Deep research report on P. putida KT2440 mdh (PP_0654), synthesizing Nikel et al. 2015 (J Biol Chem; NAD+ cofactor specificity), de Lorenzo et al. 2024 (Essays Biochem; MDH catalytic mechanism), and 2023-2024 P. putida systems/engineering studies

P. putida KT2440 Mdh (PP_0654) is a canonical NAD-dependent malate dehydrogenase acting at the malate/oxaloacetate node of the TCA cycle; cell-free extract assays show ~98% NAD+ vs ~2% NADP+ cofactor preference.

PMID:12534463

Complete genome sequence and comparative analysis of the metabolically versatile Pseudomonas putida KT2440

file:PSEPK/mdh/mdh-deep-research-openscientist.md

OpenScientist gene report on Pseudomonas putida KT2440 mdh

The OpenScientist report supports Q88Q44 as the PP_0654 malate dehydrogenase.

"The core identity of the gene product is firmly established. UniProt entry Q88Q44 assigns gene *mdh*, ordered locus name PP_0654, the description "Probable malate dehydrogenase," EC number 1.1.1.37"