sodC Family assigned · medium auto-curated
H37Rv Rv0432 · MTBC0 mtbc0_000454 ·
240 aa · 522965–523687 (+) ·
RefSeq NP_214946.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | superoxide dismutase |
|---|---|
| MTBC0 PGAP re-annotation | superoxide dismutase family protein |
| Revised (this work) | Superoxide dismutase family protein. Pfam: Sod_Cu (PF00080.26). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WGE9
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Superoxide dismutase [Cu-Zn] |
| EC (curated) |
EC 1.15.1.1
|
| Curated function | Destroys radicals which are normally produced within the cells and which are toxic to biological systems. May play a role in favoring mycobacterial survival in phagocytes (By similarity). |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
P Inorganic ion transport and metabolism
|
|---|---|
| Preferred name | sodC |
| eggNOG description | Destroys radicals which are normally produced within the cells and which are toxic to biological systems |
| Orthologous group | COG2032 |
| EC number |
EC 1.15.1.1
|
| KEGG orthology |
K04565
|
| KEGG pathways |
map04146, map04213, map05014, map05016, map05020
|
| Gene Ontology (84) |
GO:0000302, GO:0000303, GO:0000305, GO:0003674, GO:0003824, GO:0004784, GO:0005575, GO:0005576, GO:0005615, GO:0005618, GO:0005623, GO:0005886 +72 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 | 0.146 · strong purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 5 synonymous, 2 missense, 0 nonsense, 0 frameshift |
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_Cu | PF00080.26 | 2.0e-24 | 86–237 | Copper/zinc superoxide dismutase (SODC) |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv0433 (carboxylate-amine ligase), high confidence from genomic context alone (score 907 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2876 |
transmembrane protein | 997 | 998 | experimental:997 |
Rv2195 qcrA |
ubiquinol-cytochrome C reductase rieske iron-sulfur subunit | 997 | 997 | experimental:997 |
Rv2196 qcrB |
ubiquinol-cytochrome C reductase cytochrome subunit B | 997 | 997 | experimental:997 |
Rv0433 |
carboxylate-amine ligase | 907 | 907 ctx | neighborhood:882 |
Rv3043c ctaD |
cytochrome C oxidase cytochrome 1 | 907 | 877 | experimental:870 |
Rv2200c ctaC |
cytochrome C oxidase subunit II | 880 | 874 | experimental:870 |
Rv2193 ctaE |
cytochrome C oxidase subunit III | 876 | 872 | experimental:870 |
Rv2194 qcrC |
ubiquinol-cytochrome C reductase cytochrome subunit C | 871 | 872 | experimental:870 |
Rv2199c ctaF |
cytochrome c oxidase polypeptide 4 | 871 | 872 | experimental:870 |
Rv3846 sodA |
superoxide dismutase | 985 | 841 | experimental:788 textmining:914 |
Rv0431 |
tuberculin-like peptide | 835 | 835 ctx | neighborhood:833 |
Rv3584 lpqE |
lipoprotein LpqE | 823 | 824 | experimental:790 |
Rv0434 hyp |
hypothetical protein | 804 | 804 ctx | neighborhood:801 |
Rv0430 hyp |
hypothetical protein | 797 | 797 ctx | neighborhood:795 |
Rv0428c |
GCN5-like N-acetyltransferase | 669 | 669 ctx | neighborhood:664 |
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 family protein
- Pfam (hmmscan --cut_ga): Sod_Cu PF00080.26 (E=2e-24)
- (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_214946.1)
- Domains: Pfam-A via hmmscan --cut_ga — Sod_Cu (PF00080.26)
- 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
COG2032 - Curated reference: UniProt P9WGE9 (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 —
77 functional partner(s); context anchor
Rv0433 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_000454|Rv0432|sodC MPKPADHRNHAAVSTSVLSALFLGAGAALLSACSSPQHASTVPGTTPSIWTGSPAPSGLSGHDEESPGAQSLTSTLTAPDGTKVATAKFEFANGYATVTIATTGVGKLTPGFHGLHIHQVGKCEPNSVAPTGGAPGNFLSAGGHYHVPGHTGTPASGDLASLQVRGDGSAMLVTTTDAFTMDDLLSGAKTAIIIHAGADNFANIPPERYVQVNGTPGPDETTLTTGDAGKRVACGVIGSG