Rv1508A Family assigned · medium auto-curated
H37Rv Rv1508A · MTBC0 - ·
120 aa · 1699866–1700228 (+) ·
RefSeq YP_177649.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | Contains GDP_Man_Dehyd (PF16363.12) domain(s); putative function inferred from the domain architecture. |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Annotated on the H37Rv protein: this gene has no 1:1 ancestral MTBC0 anchor (PE/PPE, paralogue, IS element, or otherwise unanchored CDS).
Curated reference (UniProt)
| UniProt |
Q79FN0
TrEMBL · unreviewed
· Predicted
|
|---|---|
| UniProt name | NAD(P)-binding domain-containing protein |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
M Cell wall / membrane / envelope biogenesis
|
|---|---|
| Preferred name | gmd |
| eggNOG description | GDP-mannose 4,6-dehydratase activity |
| Orthologous group | COG1089 |
| EC number |
EC 4.2.1.47
|
| KEGG orthology |
K01711
|
| KEGG pathways |
map00051, map00520, map01100
|
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 | 0.162 · strong purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 2 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 |
|---|---|---|---|---|
GDP_Man_Dehyd | PF16363.12 | 2.8e-09 | 34–72 | GDP-mannose 4,6 dehydratase |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: epiA (nucleotide-sugar epimerase EpiA), high confidence from genomic context alone (score 875 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) |
|---|---|---|---|---|
Rv1512 epiA |
nucleotide-sugar epimerase EpiA | 880 | 875 ctx | cooccurence:774 |
Rv1509 hyp |
hypothetical protein | 971 | 833 ctx | neighborhood:780 textmining:835 |
Rv1514c |
glycosyltransferase | 731 | 722 ctx | cooccurence:679 |
Rv0112 gca |
GDP-mannose 4,6-dehydratase | 689 | 674 ctx | cooccurence:451 |
Rv1508c |
membrane protein | 598 | 598 ctx | neighborhood:595 |
Rv1510 hyp |
hypothetical protein | 561 | 521 ctx | neighborhood:473 |
Rv0139 |
oxidoreductase | 446 | 419 | |
Rv3468c |
dTDP-glucose 4,6-dehydratase | 446 | 419 | |
Rv1106c |
3 beta-hydroxysteroid dehydrogenase/delta 5-->4-isomerase | 446 | 419 | |
Rv1868 hyp |
hypothetical protein | 445 | 419 | |
Rv3725 |
oxidoreductase | 444 | 418 | |
Rv0501 galE2 |
UDP-glucose 4-epimerase GalE | 444 | 418 | |
Rv2047c hyp |
hypothetical protein | 444 | 418 | |
Rv1417 |
membrane protein | 444 | 418 | |
Rv0536 galE3 |
UDP-glucose 4-epimerase GalE | 442 | 416 |
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
- Annotation from H37Rv (no MTBC0 1:1 anchor; H37Rv protein used): hypothetical protein
- Pfam (hmmscan --cut_ga): GDP_Man_Dehyd PF16363.12 (E=3e-09)
- (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 YP_177649.1)
- Domains: Pfam-A via hmmscan --cut_ga — GDP_Man_Dehyd (PF16363.12)
- 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
COG1089 - Curated reference: UniProt Q79FN0 (TrEMBL, unreviewed; Predicted)
- 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 —
24 functional partner(s); context anchor
epiA - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv1508A| MKRALITGITGPDGSYLAKLPLKGYVAAGSPAEVYFCWATRNYRELYGLLAVNSIWFNHESPRHGETFMTRNPAPYRGRQRGADRCADADAPAHPDRYQYWGVPASVRGVIDRAMGVCVE