Rv2313c Family assigned · low auto-curated
H37Rv Rv2313c · MTBC0 mtbc0_002461 ·
284 aa · 2609801–2610655 (-) ·
RefSeq NP_216829.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | carboxymuconolactone decarboxylase family protein |
| Revised (this work) | Carboxymuconolactone decarboxylase family protein. |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WLB7
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Uncharacterized protein Rv2313c |
UniProt still lists this protein as Uncharacterized protein Rv2313c; the revised annotation above is ahead of the current UniProt record.
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| eggNOG description | Antioxidant protein with alkyl hydroperoxidase activity. Required for the reduction of the AhpC active site cysteine residues and for the regeneration of the AhpC enzyme activity |
| Orthologous group | COG2128 |
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 | 0.716 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 2 synonymous, 4 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)
No Pfam-A domain above the gathering threshold (or not yet scanned).
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: uspB (sugar ABC transporter permease UspB), high confidence from genomic context alone (score 788 excluding text-mining). This association is the citable seed of a function hypothesis for this hypothetical protein.
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2315c hyp |
hypothetical protein | 879 | 880 ctx | neighborhood:879 |
Rv2314c hyp |
hypothetical protein | 879 | 880 ctx | neighborhood:879 |
Rv2317 uspB |
sugar ABC transporter permease UspB | 787 | 788 ctx | neighborhood:788 |
Rv2316 uspA |
sugar ABC transporter permease UspA | 779 | 779 ctx | neighborhood:779 |
Rv2318 uspC |
sugar ABC transporter substrate-binding lipoprotein UspC | 719 | 720 ctx | neighborhood:719 |
Rv1286 cysC |
adenylyl-sulfate kinase | 474 | 474 | coexpression:474 |
Rv0433 |
carboxylate-amine ligase | 405 | 406 | coexpression:406 |
Rv1859 modC |
molybdenum ABC transporter ATP-binding protein ModC | 405 | 406 | coexpression:406 |
Rv2399c cysT |
sulfate ABC transporter permease CysT | 403 | 403 | coexpression:403 |
Rv3736 |
AraC/XylS family transcriptional regulator | 494 | 67 | textmining:480 |
Rv1519 hyp |
hypothetical protein | 870 | 41 | textmining:870 |
Rv3651 hyp |
hypothetical protein | 870 | 41 | textmining:870 |
Rv3737 |
transmembrane protein | 652 | 41 | textmining:652 |
Rv3517 hyp |
hypothetical protein | 540 | 41 | textmining:540 |
Rv3022A PE29 |
PE family protein PE29 | 446 | 41 | textmining:446 |
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: hypothetical protein
- MTBC0 PGAP product: carboxymuconolactone decarboxylase family protein
- (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_216829.1)
- Domains: Pfam-A via hmmscan --cut_ga — none above threshold
- 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
COG2128 - Curated reference: UniProt P9WLB7 (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 —
15 functional partner(s); context anchor
uspB - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002461|Rv2313c| MPAPVSVRDDLCRLVALSPGDGRIAGLVRQVCARALSLPSLPCEVAVNEPESPAEAVVAEFAEQFSVDVSAITGEQRSLLWTHLGEDAFGAVVAMYIADFVPRVRAGLEALGVGKEYLGWVTGPISWDHNTDLSAAVFNGFLPAVARMRALDPVTSELVRLRGAAQHNCRVCKSLREVSALDAGGSETLYGEIERFDTSVLLDVRAKAALRYADALIWTPAHLAVDVAVEVRSRFSDDEAVELTFDIMRNASNKVAVSLGADAPRVQQGTERYRIGLDGQTVFG