ephF Family assigned · medium auto-curated
H37Rv Rv0134 · MTBC0 mtbc0_000145 ·
300 aa · 162117–163019 (+) ·
RefSeq NP_214648.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | epoxide hydrolase EphF |
|---|---|
| MTBC0 PGAP re-annotation | alpha/beta hydrolase |
| Revised (this work) | Alpha/beta hydrolase. Pfam: Abhydrolase_1 (PF00561.27), Hydrolase_4 (PF12146.16), Abhydrolase_6 (PF12697.14). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P96811
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Possible epoxide hydrolase EphF |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
I Lipid transport and metabolism
|
|---|---|
| Preferred name | ephF |
| eggNOG description | epoxide hydrolase |
| Orthologous group | COG2267 |
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 | 0.66 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 3 synonymous, 5 missense, 1 nonsense, 4 frameshift |
| Disruption | 5 distinct premature-stop/frameshift site(s); most common in 38.08% of strains (55294) · convergent |
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 |
|---|---|---|---|---|
Abhydrolase_1 | PF00561.27 | 1.6e-33 | 34–281 | alpha/beta hydrolase fold |
Hydrolase_4 | PF12146.16 | 3.5e-09 | 35–144 | Serine aminopeptidase, S33 |
Abhydrolase_6 | PF12697.14 | 2.8e-19 | 36–286 | Alpha/beta hydrolase family |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: hpx (non-heme haloperoxidase Hpx), medium confidence from genomic context alone (score 698 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3171c hpx |
non-heme haloperoxidase Hpx | 697 | 698 ctx | cooccurence:696 |
Rv0554 bpoC |
non-heme bromoperoxidase BpoC | 559 | 559 ctx | cooccurence:559 |
Rv2048c pks12 |
polyketide synthase | 531 | 504 | experimental:441 |
Rv2940c mas |
multifunctional mycocerosic acid synthase | 530 | 503 | experimental:441 |
Rv2933 ppsC |
phthiocerol synthesis polyketide synthase type I PpsC | 528 | 501 | experimental:441 |
Rv1527c pks5 |
polyketide synthase | 526 | 499 | experimental:441 |
Rv3825c pks2 |
phthioceranic/hydroxyphthioceranic acid synthase | 526 | 498 | experimental:441 |
Rv0077c |
oxidoreductase | 489 | 489 ctx | cooccurence:489 |
Rv0983 pepD |
serine protease PepD | 485 | 484 | |
Rv3569c hsaD |
4,5-9,10-diseco-3-hydroxy-5,9,17-trioxoandrosta-1(10),2-diene-4-oate hydrolase | 472 | 473 ctx | cooccurence:470 |
Rv3254 hyp |
hypothetical protein | 471 | 462 ctx | fusion:446 |
Rv2946c pks1 |
polyketide synthase | 489 | 459 | |
Rv1223 htrA |
serine protease HtrA | 455 | 455 | |
Rv0132c fgd2 |
F420-dependent glucose-6-phosphate dehydrogenase | 454 | 454 | |
Rv0125 pepA |
serine protease PepA | 440 | 440 |
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: epoxide hydrolase EphF
- MTBC0 PGAP product: alpha/beta hydrolase
- Pfam (hmmscan --cut_ga): Abhydrolase_1 PF00561.27 (E=2e-33), Hydrolase_4 PF12146.16 (E=3e-09), Abhydrolase_6 PF12697.14 (E=3e-19)
- (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_214648.1)
- Domains: Pfam-A via hmmscan --cut_ga — Abhydrolase_1 (PF00561.27), Hydrolase_4 (PF12146.16), Abhydrolase_6 (PF12697.14)
- 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
COG2267 - Curated reference: UniProt P96811 (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 —
30 functional partner(s); context anchor
hpx - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_000145|Rv0134|ephF MIALPALEGVEHRHVDVAEGVRIHVADAGPADGPAVMLVHGFPQNWWEWRDLIGPLAADGNRVLCPDLRGAGWSSAPRSRYTKTEMADDLAAVLDGLGVAKVKLVAHDWGGPVAFIMMLRHPEKVTGFFGVNTVAPWVKRDLGMLRNMWRFWYQIPMSLPVIGPRVISDPKGRYFRLLTGWVGGGFRVPDDDVRLYLDCMREPGHAEAGSRWYRTFQTREMLRWLRGEYNDARVDVPVRWLHGTGDPVITPDLLDGYAERASDFEVELVDGVGHWIVEQRPELVLDRVRAFLAAGTEQRD