Rv3108 Still unknown · low auto-curated
H37Rv Rv3108 · MTBC0 - ·
146 aa · 3477060–3477500 (+) ·
RefSeq NP_217624.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | Conserved hypothetical protein; no recognised domain. Function unknown. Foldseek best (non-significant) hit: 6qc3-assembly1_B5 Ovine respiratory supercomplex I+III2 open class 1 (prob 0.02, TM 0.19). |
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 |
O05785
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.
Conservation & selection (intra-MTBC, 145 209 strains)
| pN/pS | 1.009 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 1 synonymous, 3 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).
Structural neighbours (Foldseek on the ESMFold model, exploratory)
ESMFold model confidence: mean pLDDT 53.2 (low). Low-confidence model: the fold may be unreliable, so treat these structural hits with caution.
Best matches against the PDB, ranked by Foldseek homology probability. A high probability / TM-score suggests a shared fold; unless flagged sig (E < 0.01) these are fold hypotheses, not assignments.
| Target | Prob | TM | E-value | Description |
|---|---|---|---|---|
6qc3-assembly1_B5 |
0.02 | 0.19 | 5.6e+00 | 6qc3-assembly1_B5 Ovine respiratory supercomplex I+III2 open class 1 |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: agpS (alkyldihydroxyacetonephosphate synthase), medium confidence from genomic context alone (score 547 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) |
|---|---|---|---|---|
Rv3107c agpS |
alkyldihydroxyacetonephosphate synthase | 547 | 547 ctx | neighborhood:545 |
Rv3109 moaA1 |
cyclic pyranopterin monophosphate synthase | 742 | 489 ctx | neighborhood:476 textmining:517 |
Rv3110 moaB1 |
pterin-4-alpha-carbinolamine dehydratase | 445 | 403 | |
Rv3111 moaC1 |
cyclic pyranopterin monophosphate synthase accessory protein | 693 | 399 | textmining:511 |
Rv3112 moaD1 |
molybdenum cofactor biosynthesis protein MoaD | 690 | 381 | textmining:520 |
Rv0218 |
transmembrane protein | 621 | 50 | textmining:618 |
Rv3611 |
Rv3611, (MTCY07H7B.11c), len: 217 aa. Hypothetical unknown arg-, pro-rich protein. Possible ORF containing several direct repeats. | 632 | 47 | textmining:630 |
Rv3124 moaR1 |
transcriptional regulator MoaR | 435 | 45 | textmining:433 |
Rv1529 fadD24 |
fatty-acid--CoA ligase FadD24 | 440 | 44 | textmining:439 |
Rv2089c pepE |
dipeptidase PepE | 440 | 44 | textmining:439 |
Rv0147 |
aldehyde dehydrogenase | 435 | 42 | textmining:435 |
Rv2900c fdhF |
formate dehydrogenase subunit alpha FdhF | 625 | 41 | textmining:625 |
Rv1066 hyp |
hypothetical protein | 566 | 41 | textmining:566 |
Rv1084 hyp |
hypothetical protein | 514 | 41 | textmining:514 |
Rv3201c adnB |
ATP-dependent DNA helicase | 439 | 41 | textmining:439 |
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
- Foldseek best: 6qc3-assembly1_B5 Ovine respiratory supercomplex I+III2 open class 1 (prob 0.02, E=6e+00, TM=0.19)
- (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_217624.1)
- Domains: Pfam-A via hmmscan --cut_ga — none above threshold
- Sequence-level signal: ESM Atlas (EvolutionaryScale × BioHub) — exploratory
- Curated reference: UniProt O05785 (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 53.2, low)
- Interaction network: STRING v12.0 (Szklarczyk et al. 2023,
doi:10.1093/nar/gkac1000), taxon 83332, CC-BY 4.0 —
15 functional partner(s); context anchor
agpS - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv3108| MTPNAASTGDSAKNTITGCCLITARALVARTRSISLPGMPFRMPADYHNASSDEPTNRHPWPAPARCCRHEWRTMRRTNACDRRRFGLSLTIHEDACRIISVVPVVLEVRRAEPAHPATPYPEPLARCSRSPGLNESSHMSGRIPP