Rv3683 Resolved · high auto-curated
H37Rv Rv3683 · MTBC0 mtbc0_003903 ·
319 aa · 4148365–4149324 (+) ·
RefSeq NP_218200.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | metallophosphoesterase |
| Revised (this work) | Metallophosphoesterase. Pfam: Metallophos (PF00149.34), Metallophos_2 (PF12850.13). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
I6X827
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Conserved protein |
UniProt still lists this protein as Conserved protein; the revised annotation above is ahead of the current UniProt record.
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| Preferred name | ykuE |
| eggNOG description | Metallophosphoesterase |
| Orthologous group | COG1408 |
| KEGG orthology |
K07098
|
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 | 0.073 · 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 |
|---|---|---|---|---|
Metallophos | PF00149.34 | 9.1e-12 | 51–234 | Calcineurin-like phosphoesterase |
Metallophos_2 | PF12850.13 | 5.3e-07 | 52–233 | Calcineurin-like phosphoesterase superfamily domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv3684 (lyase), high confidence from genomic context alone (score 808 excluding text-mining). This association is the citable seed of a function hypothesis for this hypothetical protein.
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3684 |
lyase | 950 | 808 ctx | neighborhood:799 textmining:751 |
Rv2256c hyp |
hypothetical protein | 680 | 681 ctx | cooccurence:679 |
Rv3682 ponA2 |
bifunctional penicillin-insensitive transglycosylase/penicillin-sensitive transpeptidase | 643 | 643 ctx | neighborhood:638 |
Rv2680 hyp |
hypothetical protein | 636 | 637 ctx | cooccurence:635 |
Rv0811c hyp |
hypothetical protein | 583 | 584 ctx | cooccurence:574 |
Rv1423 whiA |
transcriptional regulator WhiA | 581 | 582 ctx | cooccurence:575 |
Rv2146c |
transmembrane protein | 572 | 572 ctx | cooccurence:555 |
Rv1650 pheT |
phenylalanine--tRNA ligase subunit beta | 567 | 567 ctx | neighborhood:544 |
Rv2413c hyp |
hypothetical protein | 562 | 563 ctx | cooccurence:555 |
Rv1002c pmt |
dolichyl-phosphate-mannose--protein mannosyltransferase | 559 | 559 ctx | cooccurence:558 |
Rv3681c whiB4 |
transcriptional regulator WhiB4 | 518 | 518 ctx | neighborhood:416 |
Rv0004 hyp |
hypothetical protein | 481 | 481 ctx | cooccurence:481 |
Rv2169c |
transmembrane protein | 479 | 480 ctx | cooccurence:478 |
Rv2699c hyp |
hypothetical protein | 462 | 462 ctx | cooccurence:459 |
Rv0883c sepH hyp |
hypothetical protein | 462 | 457 ctx | cooccurence:449 |
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: hypothetical protein
- MTBC0 PGAP product: metallophosphoesterase
- Pfam (hmmscan --cut_ga): Metallophos PF00149.34 (E=9e-12), Metallophos_2 PF12850.13 (E=5e-07)
- (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_218200.1)
- Domains: Pfam-A via hmmscan --cut_ga — Metallophos (PF00149.34), Metallophos_2 (PF12850.13)
- 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
COG1408 - Curated reference: UniProt I6X827 (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 —
34 functional partner(s); context anchor
Rv3684 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003903|Rv3683| MAAVLPTLIRTGAVALGSAIAGIGYAALVERNAFVLREVTMPVLTPGSTPLRVLHISDLHMLPNQHRKQAWLRELASWEPDLVVNTGDNLAHPKAVPAVVQTLSDLLSRPGVFVFGSNDYFGPRLKNPMNYLTSPDHRVRGAALPWQDLRAAFTERGWLDLTHTRREFEVAGLHIAAAGVDDPHIDRDRYDTIAGPASPAANLRLGLTHSPEPRVLDRFAADGYQLVLAGHTHGGQLCLPLYGALVTNCGLDRSRAKGASHWGANMRLHVSAGIGTSPFAPVRFCCRPEATLLTLIATPMGGRDSSSNLGRSQPTVSVR