Rv2499c Family assigned · medium auto-curated
H37Rv Rv2499c · MTBC0 mtbc0_002661 ·
185 aa · 2836063–2836620 (-) ·
RefSeq NP_217015.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | oxidase regulatory-like protein |
|---|---|
| MTBC0 PGAP re-annotation | MaoC family dehydratase |
| Revised (this work) | MaoC family dehydratase. Pfam: MC_hydratase (PF19315.6), MaoC_dehydratas (PF01575.26). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
I6Y9H2
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Possible oxidase regulatory-related protein |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
I Lipid transport and metabolism
|
|---|---|
| eggNOG description | dehydratase |
| Orthologous group | COG2030 |
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 | 0.068 · strong purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 5 synonymous, 1 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 |
|---|---|---|---|---|
MC_hydratase | PF19315.6 | 9.5e-12 | 30–179 | Mesaconyl-CoA hydratase |
MaoC_dehydratas | PF01575.26 | 4.0e-29 | 39–159 | MaoC like domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: citE (citrate (pro-3S)-lyase subunit beta), high confidence from genomic context alone (score 993 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2498c citE |
citrate (pro-3S)-lyase subunit beta | 998 | 993 ctx | neighborhood:882 cooccurence:760 coexpression:761 textmining:816 |
Rv2500c fadE19 |
acyl-CoA dehydrogenase FadE19 | 998 | 990 ctx | neighborhood:881 coexpression:844 textmining:815 |
Rv2502c accD1 |
acetyl-/propionyl-CoA carboxylase subunit beta | 950 | 933 ctx | neighborhood:881 |
Rv2501c accA1 |
acetyl/propionyl-CoA carboxylase subuit alpha | 939 | 933 ctx | neighborhood:881 |
Rv2503c scoB |
succinyl-CoA:3-ketoacid-CoA transferase subunit B | 935 | 889 ctx | neighborhood:881 textmining:438 |
Rv2504c scoA |
succinyl-CoA:3-ketoacid-CoA transferase subunit A | 981 | 887 ctx | neighborhood:881 textmining:845 |
Rv2506 |
TetR family transcriptional regulator | 870 | 829 ctx | neighborhood:714 cooccurence:413 |
Rv2495c bkdC |
branched-chain keto acid dehydrogenase E2 component | 845 | 815 ctx | neighborhood:723 |
Rv2497c bkdA |
3-methyl-2-oxobutanoate dehydrogenase subunit alpha | 807 | 784 ctx | neighborhood:724 |
Rv2496c bkdB |
3-methyl-2-oxobutanoate dehydrogenase subunit beta | 736 | 737 ctx | neighborhood:723 |
Rv3339c icd1 |
isocitrate dehydrogenase | 651 | 636 | database:476 |
Rv2505c fadD35 |
fatty-acid--CoA ligase FadD35 | 717 | 618 ctx | neighborhood:567 |
Rv1223 htrA |
serine protease HtrA | 575 | 576 | database:498 |
Rv0983 pepD |
serine protease PepD | 569 | 569 | database:498 |
Rv3564 fadE33 |
acyl-CoA dehydrogenase FadE33 | 584 | 568 |
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: oxidase regulatory-like protein
- MTBC0 PGAP product: MaoC family dehydratase
- Pfam (hmmscan --cut_ga): MC_hydratase PF19315.6 (E=9e-12), MaoC_dehydratas PF01575.26 (E=4e-29)
- (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_217015.1)
- Domains: Pfam-A via hmmscan --cut_ga — MC_hydratase (PF19315.6), MaoC_dehydratas (PF01575.26)
- 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
COG2030 - Curated reference: UniProt I6Y9H2 (TrEMBL, unreviewed; 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 —
134 functional partner(s); context anchor
citE - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002661|Rv2499c| MTKHAGDRESDDAVSACRVAGSTVGRRILQRGLWFEEFQIGTTYLHRPGRTVTEADNVLFTTLTMNTQSLHLDAAWAGQQPGFRGERLVNSMFTLSTMVGLSVAQLTLGTIVANLGFSEVSFPKPVFHGDTLYAETVCTGKRESKSRPGEGIVTLEHIARNQHGEVVARAVRTTLVQKQSIKEAQ