PTN000656921 is the LivG ATPase node. Its 25 leaves (15 taxa) include
E. coli/Salmonella/Yersinia LivG, P. aeruginosa BraF and its paralog PA4910,
seven Bradyrhizobium japonicum HAAT ATPases, three Geobacter, two Deinococcus,
and Thermotoga, Chloroflexus, Streptomyces, Fusobacterium and Streptococcus
members. The same node already carries E. coli-seeded (P0A9S7) IBDs for
L-valine, L-isoleucine and L-phenylalanine transmembrane transporter activity.
| PTN node | node term | n_seeds | leaf IBAs | seed annotation (term, evidence, PMID) | verdict | rationale |
|---|---|---|---|---|---|---|
| PTN000656921 | GO:1903805 L-valine import across plasma membrane | 1 (sole) | 25 (15 taxa) | GO:1903805, IMP, PMID:18833300 (PseudoCAP) | SOUND | The screen shows only a partial N-source growth defect on L-Val, which on its own is an indirect phenotype. But LIV-I Val transport is established biochemically (PMID:113383, PMID:1400443), and the term matches the E. coli-seeded L-valine transporter activity IBD on the same node. Clade caveat: substrate specificity is set by each system's binding protein, and the node includes several paralogous HAAT ATPases per genome (7 in B. japonicum) whose substrates are unknown. This is the same caveat that applies to the existing MF IBDs. |
| PTN000656921 | GO:1903806 L-isoleucine import across plasma membrane | 1 (sole) | 25 (15 taxa) | GO:1903806, IMP, PMID:18833300 (PseudoCAP) | SOUND | Reduced growth on L-Ile as a C source, corroborated by the LIV-I reconstitution and binding data. It matches the E. coli-seeded L-isoleucine transporter activity IBD. The same clade caveat applies as for valine. |
| PTN000656921 | GO:0015808 L-alanine transport | 1 (sole) | 25 (15 taxa) | GO:0015808, IMP, PMID:18833300 (PseudoCAP) | SOUND | The claim is correct for P. aeruginosa LIV-I, which transports Ala in proteoliposomes (PMID:1400443). Ala is a secondary LIV-I substrate, though, and none of the E. coli seeds supports it. Propagating it to the whole LivG clade, including uncharacterised paralogs, is a stretch. GO:1904273 L-alanine import across plasma membrane is the more precise term. |
| PTN000656921 | GO:0042941 D-alanine transmembrane transport | 2 (PA1071, PA4910) | 25 (15 taxa) | GO:0042941, IMP, PMID:18833300 (PseudoCAP) | INDIRECT-PHENOTYPE | Both seeds rest on partial growth defects on D-Ala in the same Biolog screen. No D-Ala uptake or binding has been shown for LIV-I or BraC. D-Ala transport is plausible but not established, and the node propagates it to 25 proteins. |
The PseudoCAP rows are not wrong enough to file as defects: the L-Ile, L-Val
and L-Ala claims are true of the bra system. The D-Ala rows are recorded as
UNDECIDED, with a suggested question, rather than as a defect.