cysB (PA1754, G3XCU6) notes

Identity

Locus PA1754 (UniProt G3XCU6 GN Name=cysB; OrderedLocusNames=PA1754). The task brief guessed PA0281;
the worklist and UniProt agree on PA1754, which is used here.
LysR-family regulator: LysR HTH (IPR000847), CysB-type substrate-binding domain (IPR037423 CysB_PBP2),
PANTHER PTHR30126:SF6 "HTH-TYPE TRANSCRIPTIONAL REGULATOR CYSB-RELATED". Adjacent, divergent cysH
(PAPS reductase).

Literature

PMID:9218775 — work in mucoid strain CHA; the protein is 63% identical to E. coli /
S. typhimurium CysB.
PMID:9218775 — this is the basis
of the PseudoCAP IMP to L-cysteine biosynthetic process: a mutant phenotype (auxotrophy).
PMID:9218775
PMID:20370820 — basis for the PseudoCAP IDA to positive regulation of
DNA-templated transcription.
PMID:20370820
Both cached papers are abstract-only.

Regulator vs participant (CLAUDE.md "Do not add what curators deliberately declined to add")

Which entity performs the steps of L-cysteine biosynthesis? Serine acetyltransferase (CysE) and
O-acetylserine sulfhydrylase (CysK/CysM), with sulfide supplied by the sulfate-assimilation enzymes
(CysDNC, CysH, CysIJ). CysB catalyses none of these; it activates their genes. The cysteine auxotrophy
of the cysB mutant shows necessity, not participation.
Comparator check (QuickGO, 2026-10-28): E. coli CysB (P0A9F3) has EcoCyc experimental annotations to
DNA binding, transcription and regulation but no experimental GO:0019344; its only GO:0019344 is the IBA
from PTN002824317, which is seeded by P. aeruginosa CysB alone.
The node PTN002824317 passes GO:0019344 (IBA) to 10 leaves: CysB of P. aeruginosa, S. typhimurium
(P06614), E. coli (P0A9F3), H. influenzae (P45105), Y. pestis (Q0WEU7), S. oneidensis (Q8EDU4),
X. campestris (Q8P602), N. meningitidis (Q9K116), V. cholerae VC_1907 (Q9KQU1), and E. coli Cbl
(Q47083), a CysB paralog that activates taurine/sulfonate-utilisation genes. Every leaf is a
transcriptional regulator. The same node also feeds TreeGrafter IEAs (about 1,200 GO:0019344 rows in
QuickGO withFrom PTN002824317).
GO's "regulation of cysteine metabolic process" terms are obsolete; the live GO:1900059 positive
regulation of sulfate assimilation is the nearest regulatory term, but the P. aeruginosa papers do not
test sulfate-assimilation gene expression, so I do not propose it as NEW. CysB's own process is captured
by GO:0045893 positive regulation of DNA-templated transcription (IDA, PMID:20370820).

Annotation decisions

GO:0019344 L-cysteine biosynthetic process (IMP PseudoCAP; IBA PTN002824317): MARK_AS_OVER_ANNOTATED.
PSEUDOCAP and GO_CENTRAL defects recorded.
GO:0045893 positive regulation of DNA-templated transcription (IDA PseudoCAP, PMID:20370820): ACCEPT.
GO:0006355 regulation of DNA-templated transcription (IBA PTN001248394; IEA): ACCEPT.
GO:0000976 transcription cis-regulatory region binding (IBA): ACCEPT (binds the algD and pvdS
promoters).
GO:0003677 DNA binding (IEA): MODIFY to GO:0000976.
GO:0003700 DNA-binding transcription factor activity (IEA): ACCEPT, core MF.
GO:0006351 DNA-templated transcription (IEA): MARK_AS_OVER_ANNOTATED.

PseudoCAP IBA-seed assessment

PTN node	node term	n_seeds	leaf IBAs	seed annotation (term, evidence, PMID)	verdict	rationale
PTN001248394	GO:0006355 regulation of DNA-templated transcription	7	202 (30 taxa)	GO:0045893, IDA, PMID:20370820 (PseudoCAP)	SOUND	Purified CysB binds the pvdS promoter and activates pvdS expression in vivo; direct evidence for transcriptional regulation. The generic regulation term suits a 202-leaf LysR clade; six further seeds (E. coli, B. subtilis, P. aeruginosa paralogs) also support it.
PTN002824317	GO:0019344 L-cysteine biosynthetic process	1 (sole)	10 (9 taxa)	GO:0019344, IMP, PMID:9218775 (PseudoCAP)	INDIRECT-PHENOTYPE	The seed is the cysteine auxotrophy of a cysB insertion mutant. CysB is the transcriptional activator of the cys regulon and performs no step of cysteine synthesis; the enzymes (CysE, CysK/M) do. Every leaf of the node is a CysB/Cbl-type regulator, none with experimental support for the process (E. coli CysB has none in EcoCyc). The term is wrong for the whole clade as a participation claim.

Leaf evidence check (2026-11-06)

Audit of the "all 10 IBA leaves are CysB or Cbl regulators" claim in the
GO_CENTRAL source defect on PTN002824317. Membership confirmed with
uv run python projects/PSEUDOCAP/panther_tree.py node PTN002824317 --leaves
(10 leaves, all PTHR30126:SF6); UniProt flat files fetched for all ten.

All 10 have exactly the two-domain LysR architecture and nothing else (Pfam
PF00126 HTH_1 + PF03466 LysR_substrate), all 10 match a CysB-type NCBIfam
profile (NF009327 PRK12684, or NF009325 PRK12680 for Q8P602), and none carries a
cysteine-biosynthetic enzyme domain (no CysE serine acetyltransferase, no
CysK/CysM O-acetylserine sulfhydrylase).

Leaf	Name and its evidence	Experimental annotations	Verdict
P0A9F3 (E. coli CysB)	RecName, curated (Reviewed); PE 3	GO:0003677 DNA binding (IDA), GO:0005829 cytosol (IDA), GO:0006351 (EXP), GO:0010165 (IMP); no experimental GO:0019344	Regulator, confirmed experimentally; confirms the "no experimental GO:0019344 on E. coli CysB" claim
Q47083 (E. coli Cbl)	RecName, curated; PE 1	GO:0045883 positive regulation of sulfur utilization (IDA)	Regulator, confirmed experimentally
P06614 (S. typhimurium CysB)	RecName, curated; PE 1	none	Curated regulator; identity rests on curation + architecture
P45105 (H. influenzae CysB)	RecName, curated; PE 3	none; FUNCTION by ECO:0000250	Same
G3XCU6 (P. aeruginosa CysB)	RecName (this gene)	PseudoCAP IMP/IDA rows under review	Seed
Q9K116, Q8EDU4, Q9KQU1, Q8P602, Q0WEU7	SubName {ECO:0000313\|EMBL}; PE 3	none	"Cys regulon transcriptional activator" wording is a predicted name, not evidence; the regulator claim for these five now rests on the PF00126+PF03466 architecture and the CysB-type NCBIfam match

Outcome: the leaf claim survives, but reworded so it rests on domain
architecture plus two verified experimental regulator annotations rather than on
names. The entry's core argument (CysB is a LysR activator that performs no step
of cysteine synthesis; auxotrophy shows necessity, not participation) is
independent of the leaf list, and the explanation now says so explicitly.
Confidence held at CONFIRMED, now resting on that core argument.