Rv2454c Family assigned · medium auto-curated
H37Rv Rv2454c · MTBC0 mtbc0_002613 ·
373 aa · 2777873–2778994 (-) ·
RefSeq NP_216970.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | 2-oxoglutarate oxidoreductase subunit KorB |
|---|---|
| MTBC0 PGAP re-annotation | 2-oxoacid:ferredoxin oxidoreductase subunit beta |
| Revised (this work) | 2-oxoacid:ferredoxin oxidoreductase subunit beta. Pfam: TPP_enzyme_C (PF02775.27). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
O53181
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | 2-oxoglutarate oxidoreductase subunit KorB |
| EC (curated) |
EC 1.2.7.3
|
| Curated function | Component of KG oxidoreductase (KOR) that catalyzes the CoA-dependent oxidative decarboxylation of 2-oxoglutarate (alpha-ketoglutarate, KG) to succinyl-CoA. Methyl viologen can act as electron acceptor in vitro; the physiologic electron acceptor is unknown. Is involved in the alternative TCA pathway that functions concurrently with fatty acid beta-oxidation. Since a growing body of evidence indicates that lipids (for example cholesterol and fatty acids) are a predominant growth substrate for M.tuberculosis during infection, flux through KOR likely represents an important step in intermediary m. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
C Energy production and conversion
|
|---|---|
| Preferred name | korB |
| eggNOG description | ferredoxin oxidoreductase |
| Orthologous group | COG1013 |
| EC number |
EC 1.2.7.11, EC 1.2.7.3
|
| KEGG orthology |
K00175
|
| KEGG pathways |
map00010, map00020, map00620, map00650, map00720, map01100, map01120, map01130, map01200
|
| KEGG modules |
M00009, M00011, M00173, M00620
|
| Gene Ontology (42) |
GO:0000287, GO:0003674, GO:0003824, GO:0005488, GO:0005575, GO:0005618, GO:0005622, GO:0005623, GO:0005737, GO:0005829, GO:0006082, GO:0006091 +30 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 | 0.138 · 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 |
|---|---|---|---|---|
TPP_enzyme_C | PF02775.27 | 4.0e-30 | 88–235 | Thiamine pyrophosphate enzyme, C-terminal TPP binding domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: korA (2-oxoglutarate oxidoreductase subunit KorA), high confidence from genomic context alone (score 1000 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2455c korA |
2-oxoglutarate oxidoreductase subunit KorA | 999 | 1000 ctx | neighborhood:881 cooccurence:774 coexpression:989 experimental:999 database:900 textmining:932 |
Rv2453c mobA |
molybdenum cofactor guanylyltransferase | 995 | 979 ctx | neighborhood:881 coexpression:829 textmining:803 |
Rv0066c icd2 |
isocitrate dehydrogenase | 946 | 944 | coexpression:417 database:900 |
Rv0408 pta |
phosphate acetyltransferase | 961 | 924 | database:900 textmining:518 |
Rv1617 pykA |
pyruvate kinase | 945 | 918 | database:900 |
Rv0952 sucD |
succinyl-CoA ligase subunit alpha | 945 | 916 | database:900 |
Rv0951 sucC |
succinyl-CoA ligase subunit beta | 944 | 912 | database:900 |
Rv3667 acs |
acetyl-CoAsynthetase | 921 | 909 | database:900 |
Rv3509c ilvX |
acetohydroxyacid synthase large subunit | 911 | 906 | database:900 |
Rv3002c ilvN |
acetolactate synthase small subunit | 905 | 906 | database:900 |
Rv0889c citA |
citrate synthase 2 | 939 | 905 | database:900 |
Rv0896 gltA2 |
citrate synthase 1 | 924 | 905 | database:900 |
Rv1131 prpC |
methylcitrate synthase PrpC | 913 | 905 | database:900 |
Rv1820 ilvG |
acetolactate synthase large subunit IlvG | 911 | 905 | database:900 |
Rv3003c ilvB1 |
acetolactate synthase large subunit IlvB | 910 | 905 | database:900 |
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: 2-oxoglutarate oxidoreductase subunit KorB
- MTBC0 PGAP product: 2-oxoacid:ferredoxin oxidoreductase subunit beta
- Pfam (hmmscan --cut_ga): TPP_enzyme_C PF02775.27 (E=4e-30)
- (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_216970.1)
- Domains: Pfam-A via hmmscan --cut_ga — TPP_enzyme_C (PF02775.27)
- 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
COG1013 - Curated reference: UniProt O53181 (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 —
83 functional partner(s); context anchor
korA - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002613|Rv2454c| MTRSGDEAQLMTGVTGDLAGTELGLTPSLTKNAGVPTTDQPQKGKDFTSDQEVRWCPGCGDYVILNTIRNFLPELGLRRENIVFISGIGCSSRFPYYLETYGFHSIHGRAPAIATGLALAREDLSVWVVTGDGDALSIGGNHLIHALRRNINVTILLFNNRIYGLTKGQYSPTSEVGKVTKSTPMGSLDHPFNPVSLALGAEATFVGRALDSDRNGLTEVLRAAAQHRGAALVEILQDCPIFNDGSFDALRKEGAEERVIKVRHGEPIVFGANGEYCVVKSGFGLEVAKTADVAIDEIIVHDAQVDDPAYAFALSRLSDQNLDHTVLGIFRHISRPTYDDAARSQVVAARNAAPSGTAALQSLLHGRDTWTVD