Msed_1695 (A4YHE8) paralog assignment: results

Analyses run 2026-10-15. Sequences, family memberships and neighbour annotations were
fetched live from UniProt REST; nothing is hardcoded.

1. Cdv ESCRT-III family members in M. sedula DSM 5348 (UniProt REST query)

Only A4YHE8 is also matched by IPR005024 (Snf7 family, Pfam PF03357), which is why it
is the only M. sedula Cdv protein that carries the InterPro2GO vacuolar transport row.

2. Pairwise global alignment (paralog_assignment.py; BLOSUM62, gap -10/-0.5)

Output in paralog_assignment_output.tsv.

• Msed_1695 vs Saci_1416 CdvB2: 64.8% identity; vs Saci_0451 CdvB1: 60.5%;
  vs Saci_1373 CdvB: 31.9%; vs Saci_1601 CdvB3: 26.7%.
• Msed_2179 vs Saci_0451 CdvB1: 61.1%; vs Saci_1416 CdvB2: 57.0%.
• Best S. acidocaldarius hit: Msed_1695 -> Saci_1416 CdvB2; Msed_2179 -> Saci_0451 CdvB1;
  Msed_1671 -> Saci_1373 CdvB; Msed_1969 -> Saci_1601 CdvB3 (reciprocal best-hit pairs).
• The sequence margin between B1 and B2 is small (CdvB1 and CdvB2 are close paralogs,
  65.0% identical to each other in S. acidocaldarius), so identity alone is not decisive.

3. Conserved gene neighbourhood (synteny.py, +/-3 loci)

Output in synteny_output.txt.

• Msed_1695 neighbourhood shares 5 arCOGs with the Saci_1416 (cdvB2) neighbourhood
  (arCOG01111 PEP synthase, arCOG01434 threonine synthase, arCOG01671 UbiD-family
  decarboxylase, arCOG04213 inositol-1-phosphate synthase, arCOG07220 conserved protein)
  and 0 with the Saci_0451 (cdvB1) neighbourhood.
• Msed_2179 neighbourhood shares 4 arCOGs with Saci_0451 (cdvB1) (arCOG01887 TrpRS,
  arCOG01947, arCOG03358, arCOG04273) and 0 with Saci_1416.

Conclusion

Msed_1695 is the CdvB2 ortholog of M. sedula: it is in the CdvB1/B2 family
(NF041005), is the reciprocal best hit of S. acidocaldarius CdvB2 (Saci_1416), and lies
in the conserved cdvB2 gene neighbourhood. The other CdvB1/B2-family protein, Msed_2179,
is the CdvB1 ortholog, consistent with its independent designation as M. sedula CdvB1
in the literature (PMID:35238034).