far Resolved · high auto-curated
H37Rv Rv0855 · MTBC0 mtbc0_000910 ·
359 aa · 954783–955862 (+) ·
RefSeq NP_215370.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | fatty-acid-CoA racemase |
|---|---|
| MTBC0 PGAP re-annotation | fatty-acid-CoA racemase |
| Revised (this work) | Fatty-acid-CoA racemase. Pfam: CoA_transf_3 (PF02515.23). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
I6Y8Y0
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Alpha-methylacyl-CoA racemase |
| EC (curated) |
EC 5.1.99.4
|
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
C Energy production and conversion
|
|---|---|
| Preferred name | far |
| eggNOG description | carnitine dehydratase |
| Orthologous group | COG1804 |
| EC number |
EC 5.1.99.4
|
| KEGG orthology |
K01796
|
| KEGG pathways |
map00120, map01100, map04146
|
| KEGG modules |
M00104
|
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 | 0.236 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 6 synonymous, 4 missense, 0 nonsense, 3 frameshift |
| Disruption | 3 distinct premature-stop/frameshift site(s); most common in 0.28% of strains (405) · 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 |
|---|---|---|---|---|
CoA_transf_3 | PF02515.23 | 8.6e-77 | 7–349 | CoA-transferase family III |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: pdc (alpha-keto-acid decarboxylase), medium confidence from genomic context alone (score 576 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1143 mcr |
alpha-methylacyl-CoA racemase | 903 | 903 | database:900 |
Rv0854 hyp |
hypothetical protein | 822 | 823 ctx | neighborhood:817 |
Rv0856 hyp |
hypothetical protein | 766 | 766 ctx | neighborhood:765 |
Rv0857 hyp |
hypothetical protein | 741 | 741 ctx | neighborhood:741 |
Rv0853c pdc |
alpha-keto-acid decarboxylase | 576 | 576 ctx | neighborhood:571 |
Rv3389c htdY |
3-hydroxyacyl-thioester dehydratase HtdY | 515 | 496 | |
Rv0636 hadB |
(3R)-hydroxyacyl-ACP dehydratase subunit HadB | 508 | 489 | |
Rv1934c fadE17 |
acyl-CoA dehydrogenase FadE17 | 503 | 485 | |
Rv0125 pepA |
serine protease PepA | 484 | 485 | database:482 |
Rv0118c oxcA |
oxalyl-CoA decarboxylase OxcA | 508 | 484 | |
Rv3671c marP |
serine protease | 483 | 484 | database:482 |
Rv0154c fadE2 |
acyl-CoA dehydrogenase FadE2 | 495 | 477 | |
Rv3538 |
dehydrogenase | 496 | 476 | |
Rv2724c fadE20 |
acyl-CoA dehydrogenase FadE20 | 482 | 463 | |
Rv0130 htdZ |
3-hydroxyl-thioester dehydratase | 481 | 461 |
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: fatty-acid-CoA racemase
- MTBC0 PGAP product: fatty-acid-CoA racemase
- Pfam (hmmscan --cut_ga): CoA_transf_3 PF02515.23 (E=9e-77)
- (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_215370.1)
- Domains: Pfam-A via hmmscan --cut_ga — CoA_transf_3 (PF02515.23)
- 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
COG1804 - Curated reference: UniProt I6Y8Y0 (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 —
32 functional partner(s); context anchor
pdc - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_000910|Rv0855|far MTTGGPLAGVKVIELGGIGPGPHAGMVLADLGADVVRVRRPGGLTMPSEDRDLLHRGKRIVDLDVKTQPQAMLELAAKADVLLDCFRPGTCERLGIGPDDCASVNPRLIFARITGWGQDGPLASTAGHDINYLSQTGALAAFGYADRPPMPPLNLVADFGGGSMLVLLGIVVALYERERSGVGQVVDAAMVDGVSVLAQMMWTMKGIGSLRDQRESFLLDGGAPFYRCYETSDGKYMAVGAIEPQFFAALLSGLGLSAADVPTQLDVAGYPQMYDIFAERFASRTRDEWTRVFAGTDACVTPVLAWSEAANNDHLKARSTVITAHGVQQAAPAPRFSRTPAGPVRPPPAAATPIDEINW