Rv2159c Family assigned · medium auto-curated
H37Rv Rv2159c · MTBC0 mtbc0_002295 ·
344 aa · 2448010–2449044 (-) ·
RefSeq NP_216675.1
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. Pfam: CMD (PF02627.26). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
O06218
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Alkyl hydroperoxide reductase Rv2159c |
| EC (curated) |
EC 1.11.1.-
|
| Curated function | Involved in protection against oxidative stresses. May play a significant role in maintaining the cellular homeostasis during stress and virulence of M.tuberculosis. In vitro, catalyzes the decomposition of cumene hydroperoxide (CHP) to acetophenone. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
O Post-translational modification, protein turnover, chaperones
|
|---|---|
| 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 | 0.959 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 4 synonymous, 10 missense, 0 nonsense, 1 frameshift |
| Disruption | 1 distinct premature-stop/frameshift site(s); most common in 0.14% of strains (199) · 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 |
|---|---|---|---|---|
CMD | PF02627.26 | 3.0e-09 | 49–121 | Carboxymuconolactone decarboxylase family |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv2160A (Rv2160A, len: 211 aa. Conserved hypothetical protein, possibly a TetR-family transcriptional regulator,similar to N-terminal half of AL51266), high confidence from genomic context alone (score 966 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) |
|---|---|---|---|---|
Rv2160A |
Rv2160A, len: 211 aa. Conserved hypothetical protein, possibly a TetR-family transcriptional regulator,similar to N-terminal half of AL51266 | 965 | 966 ctx | neighborhood:799 coexpression:836 |
Rv2160c |
Rv2160c, (MTCY270.08), len: 113 aa. Conserved hypothetical protein, possibly a TetR-family transcriptional regulator, similar to C-terminal | 978 | 843 | coexpression:799 textmining:870 |
Rv2161c hyp |
hypothetical protein | 978 | 842 | coexpression:819 textmining:870 |
Rv2158c murE |
UDP-N-acetylmuramoylalanyl-D-glutamate--2,6-diaminopimelate ligase | 847 | 784 ctx | neighborhood:709 |
Rv2151c ftsQ |
cell division protein FtsQ | 823 | 750 ctx | neighborhood:700 |
Rv2156c murX |
phospho-N-acetylmuramoyl-pentappeptidetransferase | 747 | 747 ctx | neighborhood:709 |
Rv2157c murF |
UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase | 752 | 746 ctx | neighborhood:709 |
Rv2155c murD |
UDP-N-acetylmuramoylalanine--D-glutamate ligase | 730 | 730 ctx | neighborhood:709 |
Rv2153c murG |
UDP-N-acetylglucosamine--N-acetylmuramyl-(pentapeptide) pyrophosphoryl-undecaprenol-N-acetylglucosamine transferase | 713 | 712 ctx | neighborhood:699 |
Rv2154c ftsW |
lipid II flippase FtsW | 711 | 703 ctx | neighborhood:699 |
Rv2152c murC |
UDP-N-acetylmuramate--alanine ligase | 703 | 703 ctx | neighborhood:700 |
Rv2797c hyp |
hypothetical protein | 586 | 586 ctx | cooccurence:585 |
Rv3347c PPE55 |
PPE family protein PPE55 | 584 | 585 ctx | cooccurence:582 |
Rv0355c PPE8 |
PPE family protein PPE8 | 575 | 575 ctx | cooccurence:573 |
Rv1004c |
membrane protein | 570 | 568 ctx | cooccurence:540 |
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
- Pfam (hmmscan --cut_ga): CMD PF02627.26 (E=3e-09)
- (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_216675.1)
- Domains: Pfam-A via hmmscan --cut_ga — CMD (PF02627.26)
- 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
COG2128 - Curated reference: UniProt O06218 (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 —
66 functional partner(s); context anchor
Rv2160A - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002295|Rv2159c| MKFVNHIEPVAPRRAGGAVAEVYAEARREFGRLPEPLAMLSPDEGLLTAGWATLRETLLVGQVPRGRKEAVAAAVAASLRCPWCVDAHTTMLYAAGQTDTAAAILAGTAPAAGDPNAPYVAWAAGTGTPAGPPAPFGPDVAAEYLGTAVQFHFIARLVLVLLDETFLPGGPRAQQLMRRAGGLVFARKVRAEHRPGRSTRRLEPRTLPDDLAWATPSEPIATAFAALSHHLDTAPHLPPPTRQVVRRVVGSWHGEPMPMSSRWTNEHTAELPADLHAPTRLALLTGLAPHQVTDDDVAAARSLLDTDAALVGALAWAAFTAARRIGTWIGAAAEGQVSRQNPTG