sufB (A2RMK5, llmg_1969) notes

Source of request

Reviewed from the KBase Dark Protein Atlas item
https://gene-annotate-dashboard.kbase.us/review/NZ_LKLC01000161.1_58
(Lactococcus lactis, 470 aa). That protein is 100% identical over its full
length to UniProt A2RMK5 (MG1363 llmg_1969), so the review is filed under
genes/LACLM/sufB.

Dashboard call (tier A): "SufB iron–sulfur cluster assembly scaffold protein of
the SUF system", GO:0051536 iron-sulfur cluster binding and GO:0016226
iron-sulfur cluster assembly. Prior annotations: eggNOG "Uncharacterized protein
family (UPF0051)", Pfam PF19295, KEGG K09014.

Dashboard verdict: supported. The call agrees with, and refines, the older
UPF0051 label. It does not assign an EC number, rightly, because SufB is a
scaffold, not an enzyme. Rejecting the transporter and cysteine-desulfurase
labels on distant hits is also right: "ABC transporter" names on SufB homologs
come from the SufC ATPase partner, and the desulfurase labels belong to SufS.

Evidence

• Identity: the dashboard sequence is exactly equal to A2RMK5 (470/470;
  sufB-bioinformatics/identity_and_family.py).
• Full-length TIGR01980 (SufB-specific) match: residues 14-461, 95.3% coverage,
  E=1.6e-224 by local hmmsearch (dashboard InterProScan: 15-461, E=1.1e-216);
  SufBD N-terminal (PF19295) and core (PF01458) domains (UniProt A2RMK5).
• E. coli SufB residues conserved: C254→C236 (sulfur acceptor), C405→C380 and
  E434→E409 (cluster site) PMID:28839209; see sufB-bioinformatics/RESULTS.md.
• Operon llmg_1974-1969 = sufC, sufD, sufS, (llmg_1971 unknown), sufU, sufB
  (KEGG), the Firmicute arrangement in which SufU replaces SufE
  PMID:24321018.
• E. coli SufB is the site of cluster assembly PMID:17350958.
• Only L. lactis literature: sufB used as a prophage-integration landmark
  PMID:24009606. Close homolog data: E. faecalis EF2390 operon induced by H2O2
  (PMID:24936909) and important for growth in Tn-seq (PMID:33234689).

Caveats

• No direct experimental work on the lactococcal protein.
• The MF stays at the generic GO:0051536 because the cluster species on the
  donor E. coli SufB is not settled: E. coli SufB has IDA rows for both
  [4Fe-4S] (PMID:17350958) and [2Fe-2S] (PMID:25485887) binding, and the
  anaerobically isolated SufBCD cluster differs spectroscopically from the
  in vitro [4Fe-4S] one PMID:28839209.
• The dashboard's fitness homologs (37-39% identity, Enterobacterales) are too
  distant to add anything specific.