sufB (A2RMK5, llmg_1969) bioinformatics results

Reproduce with:

uv run --no-project --with pyhmmer --with biopython python identity_and_family.py
uv run --project ../../../.. python map_ecoli_residues.py
bash fetch_neighborhood.sh

Query identity

identity_and_family.py (identity_and_family_output.txt) aligns the KBase Dark
Protein Atlas protein NZ_LKLC01000161.1_58 (kbase_NZ_LKLC01000161.1_58.fasta,
saved from the dashboard's sequence panel on 2026-10-30) with UniProtKB A2RMK5
(llmg_1969, L. lactis subsp. cremoris MG1363):

KBase length 470; A2RMK5 length 470
aligned columns: 470; identical: 470; identity: 100.0%
sequences exactly equal: True

So the KBase protein is reviewed here as A2RMK5.

SufB family model

The same script runs hmmsearch (pyhmmer) with NCBIfam TIGR01980 (sufB, model
length 448, downloaded from the InterPro API) against A2RMK5:

full-sequence E-value 1.6e-224, score 731.5
domain envelope 14-461 (query coverage 95.3%), HMM 2-448 of 448 (HMM coverage 99.8%), i-Evalue 1.8e-224

This agrees with the dashboard's InterProScan hit (15-461, E=1.1e-216); the
E-values differ because of database size.

Essential E. coli SufB residues are conserved

map_ecoli_residues.py aligns A2RMK5 with E. coli SufB (P77522; global, BLOSUM62).
Output (alignment_output.txt):

aligned columns: 466; identity: 39.9%
E. coli C254 -> query C236 (E.coli SYIEGCSAPVR / query QYVEGCTAPTY)
E. coli C405 -> query C380 (E.coli RNFTQCDSMLI / query ASHIECDTILM)
E. coli E434 -> query E409 (E.coli AQLEHEATTSR / query VALEHEAKVSK)

C254 is the E. coli SufB sulfur-acceptor cysteine, and C405/E434 form part of the
de novo cluster site at the SufB-SufD interface (PMID:28839209). All three are
conserved in the L. lactis protein, consistent with a functional SufB scaffold
subunit rather than a degenerate paralog.

Operon context (KEGG, MG1363)

fetch_neighborhood.sh (neighborhood_output.txt), all on the minus strand:

locus	KEGG KO	assignment
llmg_1974	K09013	Fe-S cluster assembly ATP-binding protein (SufC)
llmg_1973	K09015	Fe-S cluster assembly protein SufD
llmg_1972	K11717	cysteine desulfurase (SufS)
llmg_1971	none	unknown protein
llmg_1970	K04488	NifU-related (SufU)
llmg_1969	K09014	Fe-S cluster assembly protein SufB (query)

This is the Firmicute-type sufCDSUB operon, with SufU (not SufE) as the sulfur
transfer partner of SufS.