Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | membrane protein |
|---|
| MTBC0 PGAP re-annotation | glycosyltransferase 87 family protein |
|---|
| Revised (this work) | Glycosyltransferase 87 family protein. Pfam: GT87 (PF09594.17). |
|---|
Auto-curated: this verdict and function were generated by rules from
PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P71787
TrEMBL · unreviewed
· Evidence at protein level
|
|---|
| UniProt name | Probable membrane protein |
|---|
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|
| eggNOG description | Glycosyltransferase family 87 |
|---|
| Orthologous group | 2A18W |
|---|
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 |
1.829 · diversifying/relaxed
|
|---|
| Polymorphic sites (≥ 0.1% of strains) |
2 synonymous, 9 missense, 1 nonsense, 3 frameshift
|
|---|
| Disruption |
4 distinct premature-stop/frameshift site(s); most common in
0.24% of strains
(349) · 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 |
|---|
GT87 | PF09594.17 |
1.5e-06 | 201–433 |
Glycosyltransferase family 87 |
Functional interaction network (STRING v12, guilt-by-association)
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|
Rv1508A hyp |
hypothetical protein |
598 |
598 ctx |
neighborhood:595 |
Rv1509 hyp |
hypothetical protein |
577 |
577 ctx |
neighborhood:572 |
Rv1510 hyp |
hypothetical protein |
762 |
360 |
textmining:644 |
Rv1516c |
sugar transferase |
807 |
55 |
textmining:805 |
Rv2284 lipM |
esterase LipM |
659 |
55 |
textmining:654 |
Rv3234c tgs3 |
diacyglycerol O-acyltransferase |
440 |
52 |
textmining:434 |
Rv2536 |
transmembrane protein |
804 |
50 |
textmining:803 |
Rv0927c |
oxidoreductase |
630 |
50 |
textmining:627 |
Rv0261c narK3 |
nitrate/nitrite transporter |
546 |
47 |
textmining:544 |
Rv3707c hyp |
hypothetical protein |
428 |
44 |
textmining:427 |
Rv0559c hyp |
hypothetical protein |
651 |
41 |
textmining:651 |
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: membrane protein
- MTBC0 PGAP product: glycosyltransferase 87 family protein
- Pfam (hmmscan --cut_ga): GT87 PF09594.17 (E=2e-06)
- (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_216024.1)
- Domains: Pfam-A via hmmscan --cut_ga — GT87 (PF09594.17)
- 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
2A18W
- Curated reference: UniProt
P71787
(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 —
11 functional partner(s)
- Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001613|Rv1508c|
MIPVMSARFTGFPLLSVALRHGITSGRGCGFILDVGAQRPFGNDVLLSVATRKIRSRLPGDRVGNHGALLPFRAEPRRIQMKRPPEVLRGAVTASRERLWAIGSQSERTLMLGTILLASVISAATAYALSQWYAVDVFSTLLVVPGDCWLDWGMNIGRHCFSDYAMVAAAGIQPNPADYLISLPADYQPTAVAAWAPARIPYAIFGLPSHWLGAPRLGLICYLVALTMAVISPAIWAARGARGLERVVIFVTLGAAAIPAWGVIDRGNSTGFVVPIALAYFVALSRQRWGLATITVILAVLVKPQFVVLGVVLLAARQWRWAGIGITGVVVSNIAAFLLWPRGFPGTIAQSIHGIIKFNSSFGGLRDPRNVSFGKALLLIPDSIKNYQSGKIPEGFLTGPRTQIGFAVLVIVVVAVLALGRRIPPVMVGIVLLATATFSPADVAFYYLVFVLPIAALVARDPNGPPGAGIFDQLAAHGDRRRAVGVCVSLAVALSIVNVAVPGQPFYVPLYGQLGAKGVVGTTPLVFTTVTWAPFLWLVTCVVIIVSYARKPARPHDSHNGPTRESDQDTAASTTSCLPNPVEESSPRGPGPICQNYTP
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