ephB Resolved · high auto-curated
H37Rv Rv1938 · MTBC0 mtbc0_002052 ·
356 aa · 2210143–2211213 (+) ·
RefSeq NP_216454.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | epoxide hydrolase EphB |
|---|---|
| MTBC0 PGAP re-annotation | epoxide hydrolase EphB |
| Revised (this work) | Epoxide hydrolase EphB. 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 |
I6YC03
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Epoxide hydrolase B |
| EC (curated) |
EC 3.3.2.10
|
| Curated function | Could be involved in detoxification of extraneous host-cell epoxides. Catalyzes the hydrolysis of epoxide-containing substrates. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| Preferred name | ephB |
| eggNOG description | Alpha beta hydrolase |
| Orthologous group | COG0596 |
| Gene Ontology (12) |
GO:0003674, GO:0003824, GO:0004301, GO:0005488, GO:0005515, GO:0016787, GO:0016801, GO:0016803, GO:0018742, GO:0042802, GO:0042803, GO:0046983
|
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 | 0.952 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 3 synonymous, 9 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 |
|---|---|---|---|---|
Abhydrolase_1 | PF00561.27 | 3.6e-29 | 28–129 | alpha/beta hydrolase fold |
Hydrolase_4 | PF12146.16 | 6.2e-14 | 29–128 | Serine aminopeptidase, S33 |
Abhydrolase_6 | PF12697.14 | 1.4e-13 | 30–165 | Alpha/beta hydrolase family |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv1937 (oxygenase), high confidence from genomic context alone (score 982 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1937 |
oxygenase | 983 | 982 ctx | neighborhood:774 cooccurence:437 coexpression:864 |
Rv1939 |
oxidoreductase | 968 | 968 ctx | neighborhood:786 coexpression:858 |
Rv1940 ribA1 |
riboflavin biosynthesis protein RibA | 967 | 966 ctx | neighborhood:787 coexpression:846 |
Rv1936 |
monooxygenase | 977 | 962 ctx | neighborhood:769 coexpression:799 textmining:434 |
Rv1941 |
short-chain type dehydrogenase/reductase | 815 | 815 ctx | neighborhood:787 |
Rv1934c fadE17 |
acyl-CoA dehydrogenase FadE17 | 592 | 592 ctx | neighborhood:450 |
Rv1833c dhmA2 |
haloalkane dehalogenase | 560 | 561 ctx | cooccurence:558 |
Rv1935c echA13 |
enoyl-CoA hydratase EchA13 | 552 | 552 ctx | neighborhood:464 |
Rv1933c fadE18 |
acyl-CoA dehydrogenase FadE18 | 537 | 537 ctx | neighborhood:450 |
Rv3825c pks2 |
phthioceranic/hydroxyphthioceranic acid synthase | 530 | 502 | experimental:441 |
Rv2940c mas |
multifunctional mycocerosic acid synthase | 527 | 500 | experimental:441 |
Rv2933 ppsC |
phthiocerol synthesis polyketide synthase type I PpsC | 527 | 500 | experimental:441 |
Rv2048c pks12 |
polyketide synthase | 526 | 498 | experimental:441 |
Rv1527c pks5 |
polyketide synthase | 526 | 498 | experimental:441 |
Rv2946c pks1 |
polyketide synthase | 486 | 455 |
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 EphB
- MTBC0 PGAP product: epoxide hydrolase EphB
- Pfam (hmmscan --cut_ga): Abhydrolase_1 PF00561.27 (E=4e-29), Hydrolase_4 PF12146.16 (E=6e-14), Abhydrolase_6 PF12697.14 (E=1e-13)
- (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_216454.1)
- 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
COG0596 - Curated reference: UniProt I6YC03 (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 —
41 functional partner(s); context anchor
Rv1937 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002052|Rv1938|ephB MSQVHRILNCRGTRIHAVADSPPDQQGPLVVLLHGFPESWYSWRHQIPALAGAGYRVVAIDQRGYGRSSKYRVQKAYRIKELVGDVVGVLDSYGAEQAFVVGHDWGAPVAWTFAWLHPDRCAGVVGISVPFAGRGVIGLPGSPFGERRPSDYHLELAGPGRVWYQDYFAVQDGIITEIEEDLRGWLLGLTYTVSGEGMMAATKAAVDAGVDLESMDPIDVIRAGPLCMAEGARLKDAFVYPETMPAWFTEADLDFYTGEFERSGFGGPLSFYHNIDNDWHDLADQQGKPLTPPALFIGGQYDVGTIWGAQAIERAHEVMPNYRGTHMIADVGHWIQQEAPEETNRLLLDFLGGLRP