Rv3165c Still unknown · low auto-curated
H37Rv Rv3165c · MTBC0 mtbc0_003364 ·
160 aa · 3558761–3559243 (-) ·
RefSeq NP_217681.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | hypothetical protein |
| Revised (this work) | Conserved hypothetical protein; no recognised domain. Function unknown. |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
O53315
TrEMBL · unreviewed
· Predicted
|
|---|---|
| UniProt name | Uncharacterized protein |
UniProt still lists this protein as Uncharacterized protein; the revised annotation above is ahead of the current UniProt record.
Functional vocabulary (eggNOG-mapper, orthology transfer)
| Orthologous group | 2A3DE |
|---|
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 | n/a |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 0 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)
No Pfam-A domain above the gathering threshold (or not yet scanned).
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: moxR3 (methanol dehydrogenase transcriptional regulator MoxR), high confidence from genomic context alone (score 882 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) |
|---|---|---|---|---|
Rv3166c hyp |
hypothetical protein | 908 | 908 ctx | neighborhood:882 |
Rv3164c moxR3 |
methanol dehydrogenase transcriptional regulator MoxR | 882 | 882 ctx | neighborhood:881 |
Rv3162c |
integral membrane protein | 843 | 843 ctx | neighborhood:841 |
Rv3163c hyp |
hypothetical protein | 841 | 841 ctx | neighborhood:841 |
Rv3167c |
TetR family transcriptional regulator | 609 | 609 ctx | neighborhood:608 |
Rv3161c |
dioxygenase | 513 | 513 ctx | neighborhood:513 |
Rv3160c |
TetR family transcriptional regulator | 512 | 512 ctx | neighborhood:510 |
Rv3168 |
aminoglycoside phosphotransferase | 439 | 440 ctx | neighborhood:436 |
Rv3169 hyp |
hypothetical protein | 424 | 424 ctx | neighborhood:418 |
Rv1174c TB8.4 |
low molecular weight T-cell antigen | 630 | 41 | textmining:630 |
Rv0475 hbhA |
heparin binding hemagglutinin HbhA | 525 | 41 | textmining:525 |
Rv0288 esxH |
ESAT-6-like protein EsxH | 440 | 41 | textmining:440 |
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: hypothetical protein
- (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_217681.1)
- Domains: Pfam-A via hmmscan --cut_ga — none above threshold
- 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
2A3DE - Curated reference: UniProt O53315 (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)
- Model confidence: ESMFold per-residue pLDDT (mean 91.2, very high)
- Interaction network: STRING v12.0 (Szklarczyk et al. 2023,
doi:10.1093/nar/gkac1000), taxon 83332, CC-BY 4.0 —
12 functional partner(s); context anchor
moxR3 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003364|Rv3165c| MKRLIALGIFLIVGIELLALILHDRRLVLAGSGLALALVLLNVRRMLGNRDELTAAPDSDDLGEGLRRWLSNTETTIRWSESTRADWDRHLRPMLARRFEIATGHRQAKDPVAFAATGRMLFGDELWEWVNPNNVTHTGDRQPGPGRAALEEILQKLEQV