Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | superoxide dismutase |
|---|
| MTBC0 PGAP re-annotation | superoxide dismutase |
|---|
| Revised (this work) | Superoxide dismutase. Pfam: Sod_Fe_N (PF00081.28), Sod_Fe_C (PF02777.24). |
|---|
Auto-curated: this verdict and function were generated by rules from
PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WGE7
SwissProt · reviewed
· Evidence at protein level
|
|---|
| UniProt name | Superoxide dismutase [Fe] |
|---|
| EC (curated) |
EC 1.15.1.1
|
|---|
| Curated function | Destroys superoxide anion radicals which are normally produced within the cells and which are toxic to biological systems. |
|---|
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
C Energy production and conversion
|
|---|
| Preferred name | sodA |
|---|
| eggNOG description | radicals which are normally produced within the cells and which are toxic to biological systems |
|---|
| Orthologous group | COG0605 |
|---|
| EC number |
EC 1.15.1.1
|
|---|
| KEGG orthology |
K04564
|
|---|
| KEGG pathways |
map04013, map04068, map04146, map04211, map04212, map04213, map05016
|
|---|
| Gene Ontology (81) |
GO:0000302, GO:0000303, GO:0000305, GO:0003674, GO:0003824, GO:0004784, GO:0005488, GO:0005506, GO:0005575, GO:0005576, GO:0005622, GO:0005623 +69 more
|
|---|
Orthology-based transfer (eggNOG 5.0.2, diamond). EC/KO/GO/CAZy are
computed annotations, not manual curation; cross-check against the primary literature
before treating a specific reaction as established.
Conservation & selection (intra-MTBC, 145 209 strains)
| pN/pS |
0.442 · purifying
|
|---|
| Polymorphic sites (≥ 0.1% of strains) |
2 synonymous, 3 missense, 0 nonsense, 1 frameshift
|
|---|
| Disruption |
1 distinct premature-stop/frameshift site(s); most common in
0.19% of strains
(273) · clonal
|
|---|
pN/pS from segregating SNPs (singletons removed) normalised by possible sites.
Low pN/pS = purifying selection (a strong signal that a "hypothetical" is a real, constrained gene).
A high pN/pS is ambiguous: relaxed constraint or positive selection (drug resistance, antigenic
variation) inflate it; e.g. rpoB/katG/pncA score high here for resistance, not loss of function. A
clonal disruption (one allele over a clade) suggests lineage pseudogenisation; a
convergent one (many independent alleles) is typical of resistance loss-of-function.
Domains (Pfam, hmmscan --cut_ga)
| Pfam | Accession | i-Evalue | Residues | Description |
|---|
Sod_Fe_N | PF00081.28 |
1.1e-31 | 3–84 |
Iron/manganese superoxide dismutases, alpha-hairpin domain |
Sod_Fe_C | PF02777.24 |
4.7e-35 | 91–193 |
Iron/manganese superoxide dismutases, C-terminal domain |
Functional interaction network (STRING v12, guilt-by-association)
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|
Rv3456c rplQ |
50S ribosomal protein L17 |
936 |
936 |
experimental:919 |
Rv0723 rplO |
50S ribosomal protein L15 |
929 |
925 |
experimental:911 |
Rv0710 rpsQ |
30S ribosomal protein S17 |
928 |
925 |
experimental:920 |
Rv3443c rplM |
50S ribosomal protein L13 |
932 |
922 |
experimental:910 |
Rv0701 rplC |
50S ribosomal protein L3 |
926 |
921 |
experimental:910 |
Rv2367c ybeY |
endoribonuclease |
919 |
907 |
experimental:903 |
Rv0640 rplK |
50S ribosomal protein L11 |
907 |
907 |
experimental:902 |
Rv0714 rplN |
50S ribosomal protein L14 |
906 |
901 |
experimental:887 |
Rv0704 rplB |
50S ribosomal protein L2 |
897 |
898 |
experimental:887 |
Rv1475c acn |
iron-regulated aconitate hydratase |
921 |
897 |
experimental:830 |
Rv2909c rpsP |
30S ribosomal protein S16 |
893 |
889 |
experimental:869 |
Rv2904c rplS |
50S ribosomal protein L19 |
892 |
889 |
experimental:838 |
Rv0721 rpsE |
30S ribosomal protein S5 |
889 |
883 |
experimental:850 |
Rv2441c rpmA |
50S ribosomal protein L27 |
887 |
875 |
experimental:838 |
Rv3442c rpsI |
30S ribosomal protein S9 |
882 |
865 |
experimental:838 |
STRING combines evidence channels (neighborhood, fusion, cooccurrence, coexpression,
experimental, database, text-mining) into a 0–1000 score. The ctx
badge marks edges carried by the genomic-context channels (conserved neighborhood, fusion,
phylogenetic co-occurrence), which are independent of orthology and structure and the strongest signal for an
unknown gene. The no text-mining column recomputes the score from data alone, so a link that does not
depend on the literature is visible. Association is a function hypothesis, not proof: corroborate with
the operon context and the primary literature before assigning a function.
Evidence
- Legacy H37Rv annotation: superoxide dismutase
- MTBC0 PGAP product: superoxide dismutase
- Pfam (hmmscan --cut_ga): Sod_Fe_N PF00081.28 (E=1e-31), Sod_Fe_C PF02777.24 (E=5e-35)
- (auto-curated by rules from PGAP + Pfam + Foldseek; not hand-reviewed)
Sources
- Ancestral sequence & coordinates: Harrison LB et al. (2024),
An imputed ancestral reference genome for the MTBC,
doi:10.1101/2023.09.07.556366
- Product annotation: NCBI PGAP on MTBC0; legacy from H37Rv NC_000962.3 (RefSeq NP_218363.1)
- Domains: Pfam-A via hmmscan --cut_ga — Sod_Fe_N (PF00081.28), Sod_Fe_C (PF02777.24)
- Sequence-level signal: ESM Atlas (EvolutionaryScale × BioHub) — exploratory
- Controlled vocabulary: eggNOG-mapper 2.1.12 (Cantalapiedra et al. 2021,
doi:10.1093/molbev/msab293), eggNOG 5.0 DB
(Huerta-Cepas et al. 2019) — OG
COG0605
- Curated reference: UniProt
P9WGE7
(SwissProt, reviewed; Evidence at protein level)
- Intra-MTBC selection: pN/pS and disruption from SPDI variants of
145 209 MTBC strains (this work, local collection vs H37Rv NC_000962.3)
- Interaction network: STRING v12.0 (Szklarczyk et al. 2023,
doi:10.1093/nar/gkac1000), taxon 83332, CC-BY 4.0 —
258 functional partner(s)
- Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_004079|Rv3846|sodA
MAEYTLPDLDWDYGALEPHISGQINELHHSKHHATYVKGANDAVAKLEEARAKEDHSAILLNEKNLAFNLAGHVNHTIWWKNLSPNGGDKPTGELAAAIADAFGSFDKFRAQFHAAATTVQGSGWAALGWDTLGNKLLIFQVYDHQTNFPLGIVPLLLLDMWEHAFYLQYKNVKVDFAKAFWNVVNWADVQSRYAAATSQTKGLIFG
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