Rv3346c Still unknown · low auto-curated
H37Rv Rv3346c · MTBC0 mtbc0_003558 ·
85 aa · 3769952–3770209 (-) ·
RefSeq NP_217863.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | transmembrane protein |
|---|---|
| MTBC0 PGAP re-annotation | DUF3017 domain-containing protein |
| Revised (this work) | Conserved hypothetical protein; DUF domain(s) DUF3017. 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 |
O50377
TrEMBL · unreviewed
· Predicted
|
|---|---|
| UniProt name | Conserved transmembrane protein |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| eggNOG description | Protein of unknown function (DUF3017) |
| Orthologous group | 2DRQP |
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)
| Pfam | Accession | i-Evalue | Residues | Description |
|---|---|---|---|---|
DUF3017 | PF11222.14 | 2.5e-18 | 18–77 | Protein of unknown function (DUF3017) |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: aftC (alpha-(1->3)-arabinofuranosyltransferase), high confidence from genomic context alone (score 757 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2673 aftC |
alpha-(1->3)-arabinofuranosyltransferase | 756 | 757 ctx | cooccurence:755 |
Rv1476 |
membrane protein | 756 | 756 ctx | cooccurence:755 |
Rv3035 hyp |
hypothetical protein | 755 | 755 ctx | cooccurence:754 |
Rv3802c |
membrane protein | 748 | 749 ctx | cooccurence:748 |
Rv3805c aftB |
terminal beta-(1->2)-arabinofuranosyltransferase | 743 | 744 ctx | cooccurence:742 |
Rv1275 lprC |
lipoprotein LprC | 734 | 734 ctx | cooccurence:732 |
Rv1274 lprB |
lipoprotein LprB | 732 | 733 ctx | cooccurence:729 |
Rv0531 |
membrane protein | 732 | 733 ctx | cooccurence:732 |
Rv3668c |
protease | 723 | 724 ctx | cooccurence:722 |
Rv0466 hyp |
hypothetical protein | 716 | 716 ctx | cooccurence:715 |
Rv3635 |
transmembrane protein | 704 | 705 ctx | cooccurence:703 |
Rv0226c |
transmembrane protein | 695 | 696 ctx | cooccurence:694 |
Rv3244c lpqB |
lipoprotein LpqB | 687 | 688 ctx | cooccurence:686 |
Rv1100 hyp |
hypothetical protein | 687 | 688 ctx | cooccurence:687 |
Rv2001 hyp |
hypothetical protein | 669 | 669 ctx | cooccurence:667 |
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: transmembrane protein
- MTBC0 PGAP product: DUF3017 domain-containing protein
- Pfam (hmmscan --cut_ga): DUF3017 PF11222.14 (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_217863.1)
- Domains: Pfam-A via hmmscan --cut_ga — DUF3017 (PF11222.14)
- 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
2DRQP - Curated reference: UniProt O50377 (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 —
83 functional partner(s); context anchor
aftC - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003558|Rv3346c| MTVRAVLRRTVGAQWPILAGVNFWRRGALLIGIGVGVAAVLRLVLSEERAGLLVVRSKGIDFVTTVTVAAAMVYIASTIDPLGTG