Rv1109c Resolved · high auto-curated
H37Rv Rv1109c · MTBC0 mtbc0_001191 ·
212 aa · 1243897–1244535 (-) ·
RefSeq NP_215625.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | lipid droplet-associated protein |
| Revised (this work) | Lipid droplet-associated protein. Pfam: Rv1109c_N (PF27128.1), DUF8129 (PF26450.2). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WM59
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Uncharacterized protein Rv1109c |
UniProt still lists this protein as Uncharacterized protein Rv1109c; the revised annotation above is ahead of the current UniProt record.
Functional vocabulary (eggNOG-mapper, orthology transfer)
| Orthologous group | 2EATU |
|---|---|
| Gene Ontology (13) |
GO:0005575, GO:0005618, GO:0005622, GO:0005623, GO:0005737, GO:0005829, GO:0005886, GO:0016020, GO:0030312, GO:0044424, GO:0044444, GO:0044464 +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 | 1.764 · diversifying/relaxed |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 1 synonymous, 5 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 |
|---|---|---|---|---|
Rv1109c_N | PF27128.1 | 1.4e-26 | 5–63 | Rv1109c N-terminal bi-helical domain |
DUF8129 | PF26450.2 | 3.2e-14 | 154–211 | Domain of unknown function (DUF8129) |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: xseA (exodeoxyribonuclease VII large subunit), high confidence from genomic context alone (score 886 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) |
|---|---|---|---|---|
Rv1108c xseA |
exodeoxyribonuclease VII large subunit | 886 | 886 ctx | neighborhood:882 |
Rv1107c xseB |
exodeoxyribonuclease VII small subunit | 886 | 886 ctx | neighborhood:882 |
Rv1106c |
3 beta-hydroxysteroid dehydrogenase/delta 5-->4-isomerase | 882 | 882 ctx | neighborhood:882 |
Rv1110 lytB2 |
4-hydroxy-3-methylbut-2-enyl diphosphate reductase | 785 | 785 ctx | neighborhood:782 |
Rv2091c |
membrane protein | 781 | 781 ctx | cooccurence:771 |
Rv3850 hyp |
hypothetical protein | 775 | 775 ctx | cooccurence:772 |
Rv3311 hyp |
hypothetical protein | 775 | 775 ctx | cooccurence:770 |
Rv3212 hyp |
hypothetical protein | 774 | 774 ctx | cooccurence:773 |
Rv0556 |
transmembrane protein | 774 | 774 ctx | cooccurence:773 |
Rv2732c |
transmembrane protein | 774 | 774 ctx | cooccurence:773 |
Rv2446c |
integral membrane protein | 773 | 773 ctx | cooccurence:772 |
Rv3205c hyp |
hypothetical protein | 771 | 771 ctx | cooccurence:770 |
Rv3438 hyp |
hypothetical protein | 770 | 771 ctx | cooccurence:770 |
Rv1222 rseA |
anti-sigma E factor RseA | 770 | 770 ctx | cooccurence:769 |
Rv1111c hyp |
hypothetical protein | 769 | 770 ctx | cooccurence:767 |
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: lipid droplet-associated protein
- Pfam (hmmscan --cut_ga): Rv1109c_N PF27128.1 (E=1e-26), DUF8129 PF26450.2 (E=3e-14)
- (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_215625.1)
- Domains: Pfam-A via hmmscan --cut_ga — Rv1109c_N (PF27128.1), DUF8129 (PF26450.2)
- 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
2EATU - Curated reference: UniProt P9WM59 (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 —
133 functional partner(s); context anchor
xseA - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001191|Rv1109c| MATAPYGVRLLVGAATVAVEETMKLPRTILMYPMTLASQAAHVVMRFQQGLAELVIKGDNTLETLFPPKDEKPEWATFDEDLPDALEGTSIPLLGLSDASEAKNDDRRSDGRFALYSVSDTPETTTASRSADRSTNPKTAKHPKSAAKPTVPTPAVAAELDYPALTLAQLRARLHTLDVPELEALLAYEQATKARAPFQTLLANRITRATAK