Rv3163c Still unknown · low auto-curated
H37Rv Rv3163c · MTBC0 mtbc0_003362 ·
423 aa · 3556490–3557761 (-) ·
RefSeq NP_217679.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | DUF58 domain-containing protein |
| Revised (this work) | Conserved hypothetical protein; DUF domain(s) DUF58. 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 |
O53313
TrEMBL · unreviewed
· Predicted
|
|---|---|
| UniProt name | Possible conserved secreted protein |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| eggNOG description | Protein of unknown function DUF58 |
| Orthologous group | COG1721 |
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 | 0.566 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 4 synonymous, 6 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 |
|---|---|---|---|---|
DUF58 | PF01882.26 | 2.8e-18 | 193–357 | Protein of unknown function DUF58 |
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 919 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 | 961 | 962 ctx | neighborhood:841 cooccurence:769 |
Rv3164c moxR3 |
methanol dehydrogenase transcriptional regulator MoxR | 923 | 919 ctx | neighborhood:841 cooccurence:402 |
Rv3162c |
integral membrane protein | 882 | 882 ctx | neighborhood:882 |
Rv3165c hyp |
hypothetical protein | 841 | 841 ctx | neighborhood:841 |
Rv3099c hyp |
hypothetical protein | 661 | 661 ctx | cooccurence:661 |
Rv2423 hyp |
hypothetical protein | 635 | 635 ctx | cooccurence:635 |
Rv3435c |
transmembrane protein | 581 | 581 ctx | cooccurence:581 |
Rv3161c |
dioxygenase | 580 | 580 ctx | neighborhood:580 |
Rv3160c |
TetR family transcriptional regulator | 575 | 576 ctx | neighborhood:576 |
Rv0048c |
membrane protein | 565 | 565 ctx | cooccurence:561 |
Rv3847 hyp |
hypothetical protein | 556 | 556 ctx | cooccurence:556 |
Rv3899c hyp |
hypothetical protein | 519 | 519 ctx | cooccurence:519 |
Rv2525c hyp |
hypothetical protein | 502 | 502 ctx | cooccurence:501 |
Rv3167c |
TetR family transcriptional regulator | 497 | 497 ctx | neighborhood:497 |
Rv3843c |
transmembrane protein | 489 | 489 ctx | cooccurence:489 |
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: DUF58 domain-containing protein
- Pfam (hmmscan --cut_ga): DUF58 PF01882.26 (E=3e-18)
- (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_217679.1)
- Domains: Pfam-A via hmmscan --cut_ga — DUF58 (PF01882.26)
- 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
COG1721 - Curated reference: UniProt O53313 (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 —
26 functional partner(s); context anchor
moxR3 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003362|Rv3163c| MIQTCEVELRWRASQLTLAIATCAGVALAAAVVAGRWQLIAFAAPLLGVLCSISWQRPVPVIQVHGDPDSQRCFENEHVRVTVWVTTESVDAAVELTVSALAGMQFEALESVSRRTTTVSAVAQRWGRYPIRARVAVVARGGLLMGAGTVDAAEIVVFPLTPPQSTPLPQTELLDRLGAHLTRHVGPGVEYADIRPYVPGDQLRAVNWVVSARRGRLHVTRRLTDRAADVVVLIDMYRQPAGPATEATERVVRGAAQVVQTALRNGDRAGIVALGGNRPRWLGADIGQRQFYRVLDTVLGAGEGFENTTGTLAPRAAVPAGAVVIAFSTLLDTEFALALIDLRKRGHVVVAVDVLDSCPLQDQLDPLVVRMWALQRSAMYRDMATIGVDVLSWPADHSLQQSMGALPNRRRRGRGRASRARLP