thiI (PA5118, Q9HU66) notes

Identity

tRNA sulfurtransferase ThiI, 484 aa, Swiss-Prot entry annotated entirely by
HAMAP-Rule MF_00021 (no P. aeruginosa experimental evidence in UniProt).
Domain architecture (UniProt FT, HAMAP): N-terminal ferredoxin-like domain,
THUMP domain 63..167 (tRNA binding), PP-loop/AANH adenylation domain (ATP
binding 185..186, 267, 289, 298), and a C-terminal rhodanese domain 405..483
with the persulfide active-site Cys457 and the redox-active Cys346-Cys457
disulfide. NCBIfam TIGR04271 (ThiI_C_thiazole) and InterPro IPR026340
(thiazole biosynthesis domain) match: P. aeruginosa ThiI is the long,
rhodanese-containing "E. coli / Salmonella type" ThiI.
Pa Cys457 and Cys346 correspond to E. coli Cys456 and Cys344
PMID:10722656
PMID:11443125

4-thiouridine (s4U8) in tRNA: ThiI adenylates U8 and transfers the IscS
persulfide sulfur
PMID:10753862
PMID:10753862
Thiazole moiety of thiamine: Salmonella thiI mutants require thiazole
PMID:9209060
and the rhodanese domain alone suffices for this role
PMID:21724998
PMID:21724998
Mechanism of sulfur delivery to ThiS is not settled:
PMID:21724998
The thiazole role is lineage-specific. ThiI without the rhodanese domain
(Firmicutes, many archaea) makes s4U but is not needed for thiamine:
PMID:22773787
PMID:22904325
PMID:21724998

No P. aeruginosa thiI paper found (PubMed: thiI AND Pseudomonas in
title/abstract returns nothing).
P. putida KT2440 thiI deletion: PMID:37891428
This is the closest genus-level experimental support (s4U only; thiamine not
tested).

Webb, Claas & Downs 1997 J Bacteriol. The title and abstract are about
Salmonella typhimurium: PMID:9209060.
Full text is not in PMC text form (PMC179266 is scanned page images; not
read). From the abstract the study is genetic (thiI mutant, thiazole
requirement, mapping, ORF sequence, transcriptional regulation). The title
and abstract name Salmonella typhimurium as the organism and mention no
P. aeruginosa work, and the paper predates the PAO1 genome (2000), so it is
very unlikely to have assayed PA5118 (audit 2026-10-29: the evidence-code
defect stays CONFIRMED on the organism stated in the abstract). The PseudoCAP IDA is therefore an
orthology transfer coded as direct evidence; the correct code would be ISS
(with Salmonella ThiI), or the row should be dropped.
The term itself is plausible for PA5118, because PA5118 has the rhodanese
domain and Cys457 that Salmonella needs for thiazole synthesis.

PTN001804941 is the root (AN0) of PTHR43209 (ThiI family; LUCA-level
speciation node per projects/TREEGRAFTER/graft_paths_all.tsv). The family
file lists 289 members, mostly Firmicutes (Streptococcus, Bacillus,
Staphylococcus, Listeria, Clostridium, Lactobacillus, Mycoplasma) and
archaea (Saccharolobus, Methanocaldococcus, Methanosarcina, Thermococcus,
Halobacterium), plus Gammaproteobacteria. 165/289 members are <=440 aa,
i.e. short ThiI lacking the rhodanese domain.
IBDs at this node: GO:0002937, GO:0016783, GO:1990228 seeded by E. coli
P77718 (sound; E. coli has EXP/IMP/IDA for s4U and sulfurtransferase), and
GO:0052837 thiazole biosynthetic process seeded only by Q9HU66.
E. coli ThiI itself has GO:0009228 thiamine biosynthetic process IMP
(PMID:9632726, EcoCyc) in GOA, so a genuine experimental seed for a
thiamine/thiazole IBD exists, but it belongs at a rhodanese-domain
(Proteobacteria) subclade, not the family root.

PTN node	node term	n_seeds	leaf IBAs	seed annotation (term, evidence, PMID)	verdict	rationale
PTN001804941	GO:0052837 thiazole biosynthetic process	1 (sole seed)	25 (22 taxa)	GO:0052837 thiazole biosynthetic process, IDA, PMID:9209060 (PseudoCAP)	WRONG	The seed paper is a Salmonella typhimurium genetics study (thiI mutant requires thiazole); it does not assay P. aeruginosa ThiI, so the IDA is a mis-coded orthology transfer and is not experimental evidence for PA5118. The claim is plausible for PA5118 (rhodanese domain with Cys457, TIGR04271), but the node is the family root, which is dominated by short Firmicutes and archaeal ThiI proteins lacking the rhodanese domain; B. subtilis and M. maripaludis thiI mutants make no s4U yet still make thiamine. The IBD should be withdrawn from the root and, if wanted, re-placed at the rhodanese-domain (proteobacterial) clade with Salmonella/E. coli experimental seeds.

ACCEPT: tRNA 4-thiouridine biosynthesis (IBA), tRNA-uracil-4
sulfurtransferase activity (IEA), tRNA binding (IEA), cytoplasm (IEA).
MODIFY: sulfurtransferase activity (IBA, IEA) -> tRNA-uracil-4
sulfurtransferase activity; RNA binding -> tRNA binding; tRNA
thio-modification -> tRNA 4-thiouridine biosynthesis; sulfur compound
biosynthetic process -> thiazole biosynthetic process.
KEEP_AS_NON_CORE: thiazole biosynthetic process (IDA, IBA, IEA; plausible by
domain architecture, unshown in P. aeruginosa), thiamine diphosphate
biosynthetic process, ATP binding, sulfurtransferase complex.
REMOVE: CCA tRNA nucleotidyltransferase activity (InterPro2GO mapping of the
AANH/PP-loop domain; ThiI is not a CCA-adding enzyme).