Rv3217c Still unknown · low auto-curated
H37Rv Rv3217c · MTBC0 mtbc0_003423 ·
143 aa · 3615946–3616377 (-) ·
RefSeq NP_217733.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | integral membrane 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 |
O05849
TrEMBL · unreviewed
· Predicted
|
|---|---|
| UniProt name | Probable conserved integral membrane protein |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| Orthologous group | 2DTKM |
|---|
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, 2 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: Rv2732c (transmembrane protein), high confidence from genomic context alone (score 771 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0358 hyp |
hypothetical protein | 774 | 774 ctx | cooccurence:765 |
Rv2732c |
transmembrane protein | 771 | 771 ctx | cooccurence:765 |
Rv2446c |
integral membrane protein | 769 | 769 ctx | cooccurence:766 |
Rv0556 |
transmembrane protein | 761 | 762 ctx | cooccurence:761 |
Rv1083 hyp |
hypothetical protein | 761 | 761 ctx | cooccurence:760 |
Rv3438 hyp |
hypothetical protein | 754 | 755 ctx | cooccurence:754 |
Rv3205c hyp |
hypothetical protein | 753 | 754 ctx | cooccurence:746 |
Rv0863 hyp |
hypothetical protein | 751 | 751 ctx | cooccurence:748 |
Rv0996 |
transmembrane protein | 750 | 751 ctx | cooccurence:750 |
Rv3218 hyp |
hypothetical protein | 747 | 748 ctx | neighborhood:748 |
Rv3212 hyp |
hypothetical protein | 730 | 730 ctx | cooccurence:726 |
Rv1109c hyp |
hypothetical protein | 727 | 728 ctx | cooccurence:726 |
Rv3311 hyp |
hypothetical protein | 718 | 718 ctx | cooccurence:718 |
Rv0475 hbhA |
heparin binding hemagglutinin HbhA | 717 | 718 ctx | cooccurence:717 |
Rv3415c hyp |
hypothetical protein | 715 | 716 ctx | cooccurence:715 |
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: integral membrane 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_217733.1)
- 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
2DTKM - Curated reference: UniProt O05849 (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 —
100 functional partner(s); context anchor
Rv2732c - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003423|Rv3217c| MPVRAPAAVRGAGLIVAVQGGAALVVAAALLVRGLAGADQHIVNGLGTAGWFVLVGGAVLAAGCRLAVGKLWGRGLAVFAQLLLLPVAWYLIVGSHQPAIGIPVGIIALGVLVLLFSPPSIRWAAGRDQRGAASAANRGPDSR