Rv3376 Family assigned · medium auto-curated
H37Rv Rv3376 · MTBC0 mtbc0_003591 ·
217 aa · 3816873–3817526 (+) ·
RefSeq NP_217893.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | phosphatase |
|---|---|
| MTBC0 PGAP re-annotation | HAD family phosphatase |
| Revised (this work) | HAD family phosphatase. Pfam: Hydrolase (PF00702.33), HAD_2 (PF13419.13), Hydrolase_like (PF13242.13). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WMS5
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Phosphatase Rv3376 |
| EC (curated) |
EC 3.1.-.-
|
| Curated function | Able to hydrolyze geranyl diphosphate (GPP), farnesyl diphosphate (FPP) and geranylgeranyl diphosphate (GGPP) to respectively yield geraniol, farnesol and geranylgeraniol. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| eggNOG description | Haloacid dehalogenase-like hydrolase |
| Orthologous group | COG1011 |
| EC number |
EC 3.1.3.10
|
| KEGG orthology |
K07025, K20866
|
| KEGG pathways |
map00010, map01120
|
| Gene Ontology (13) |
GO:0003674, GO:0003824, GO:0006793, GO:0006796, GO:0008150, GO:0008152, GO:0009987, GO:0016311, GO:0016787, GO:0016788, GO:0016791, GO:0042578 +1 more
|
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 | 0.249 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 4 synonymous, 3 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 |
|---|---|---|---|---|
Hydrolase | PF00702.33 | 1.7e-23 | 3–185 | haloacid dehalogenase-like hydrolase |
HAD_2 | PF13419.13 | 1.1e-10 | 91–190 | Haloacid dehalogenase-like hydrolase |
Hydrolase_like | PF13242.13 | 1.4e-04 | 147–200 | HAD-hyrolase-like |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: echA18 (enoyl-CoA hydratase), medium confidence from genomic context alone (score 557 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1043c hyp |
hypothetical protein | 648 | 645 | database:543 |
Rv3671c marP |
serine protease | 575 | 572 | database:543 |
Rv1223 htrA |
serine protease HtrA | 575 | 571 | database:543 |
Rv0983 pepD |
serine protease PepD | 572 | 569 | database:543 |
Rv0125 pepA |
serine protease PepA | 571 | 567 | database:543 |
Rv3373 echA18 |
enoyl-CoA hydratase | 777 | 557 ctx | neighborhood:531 textmining:518 |
Rv3374 echA18.1 |
Probable enoyl-CoA hydratase EchA18.1 (Enoyl hydrase) (Unsaturated acyl-CoA hydratase) (Crotonase); Rv3374, (MTV004.32), len: 82 aa. Probabl | 630 | 553 ctx | neighborhood:531 |
Rv3375 amiD |
amidase | 823 | 541 ctx | neighborhood:532 textmining:630 |
Rv3372 otsB2 |
trehalose 6-phosphate phosphatase | 582 | 453 | |
Rv3554 fdxB |
electron transfer protein FdxB | 438 | 439 | |
Rv2307c hyp |
hypothetical protein | 453 | 436 | database:422 |
Rv2627c hyp |
hypothetical protein | 451 | 435 | database:422 |
Rv2524c fas |
fatty acid synthase | 431 | 399 | |
Rv0752c fadE9 |
acyl-CoA dehydrogenase FadE9 | 419 | 397 | |
Rv0033 acpA |
acyl carrier protein AcpA | 445 | 366 |
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: phosphatase
- MTBC0 PGAP product: HAD family phosphatase
- Pfam (hmmscan --cut_ga): Hydrolase PF00702.33 (E=2e-23), HAD_2 PF13419.13 (E=1e-10), Hydrolase_like PF13242.13 (E=1e-04)
- (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_217893.1)
- Domains: Pfam-A via hmmscan --cut_ga — Hydrolase (PF00702.33), HAD_2 (PF13419.13), Hydrolase_like (PF13242.13)
- 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
COG1011 - Curated reference: UniProt P9WMS5 (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 —
40 functional partner(s); context anchor
echA18 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003591|Rv3376| MSISAVVFDRDGVLTSFDWTRAEEDVRRITGLPLEEIERRWGGWLNGLTIDDAFVETQPISEFLSSLARELELGSKARDELVRLDYMAFAQGYPDARPALEEARRRGLKVGVLTNNSLLVSARSLLQCAALHDLVDVVLSSQMIGAAKPDPRAYQAIAEALGVSTTSCLFFDDIADWVEGARCAGMRAYLVDRSGQTRDGVVRDLSSLGAILDGAGP