Rv2169c Still unknown · low auto-curated
H37Rv Rv2169c · MTBC0 mtbc0_002303 ·
134 aa · 2457572–2457976 (-) ·
RefSeq NP_216685.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | transmembrane protein |
|---|---|
| MTBC0 PGAP re-annotation | DUF3040 domain-containing protein |
| Revised (this work) | Conserved hypothetical protein; DUF domain(s) DUF3040. 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 |
O53503
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Probable conserved transmembrane protein |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| eggNOG description | Protein of unknown function (DUF3040) |
| Orthologous group | 2E49S |
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, 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)
| Pfam | Accession | i-Evalue | Residues | Description |
|---|---|---|---|---|
DUF3040 | PF11239.14 | 1.3e-28 | 1–86 | Protein of unknown function (DUF3040) |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv2170 (GCN5-like N-acetyltransferase), high confidence from genomic context alone (score 776 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2170 |
GCN5-like N-acetyltransferase | 776 | 776 ctx | neighborhood:733 |
Rv2199c ctaF |
cytochrome c oxidase polypeptide 4 | 678 | 678 ctx | cooccurence:676 |
Rv2680 hyp |
hypothetical protein | 670 | 670 ctx | cooccurence:670 |
Rv2194 qcrC |
ubiquinol-cytochrome C reductase cytochrome subunit C | 643 | 643 ctx | cooccurence:641 |
Rv2146c |
transmembrane protein | 627 | 627 ctx | cooccurence:612 |
Rv2256c hyp |
hypothetical protein | 613 | 613 ctx | cooccurence:609 |
Rv2166c mraZ |
transcriptional regulator MraZ | 598 | 598 ctx | neighborhood:593 |
Rv2229c hyp |
hypothetical protein | 564 | 564 ctx | cooccurence:564 |
Rv2219A |
membrane protein | 534 | 535 ctx | cooccurence:532 |
Rv2708c hyp |
hypothetical protein | 533 | 534 ctx | cooccurence:527 |
Rv2195 qcrA |
ubiquinol-cytochrome C reductase rieske iron-sulfur subunit | 524 | 524 ctx | cooccurence:521 |
Rv3208A TB9.4 hyp |
hypothetical protein | 514 | 515 ctx | cooccurence:513 |
Rv2171 lppM |
lipoprotein LppM | 512 | 513 ctx | neighborhood:511 |
Rv2219 |
transmembrane protein | 511 | 512 ctx | cooccurence:505 |
Rv0883c sepH hyp |
hypothetical protein | 506 | 506 ctx | cooccurence:503 |
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: DUF3040 domain-containing protein
- Pfam (hmmscan --cut_ga): DUF3040 PF11239.14 (E=1e-28)
- (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_216685.1)
- Domains: Pfam-A via hmmscan --cut_ga — DUF3040 (PF11239.14)
- 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
2E49S - Curated reference: UniProt O53503 (TrEMBL, unreviewed; Evidence at protein level)
- 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 —
57 functional partner(s); context anchor
Rv2170 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002303|Rv2169c| MPLSDHEQRMLDQIESALYAEDPKFASSVRGGGFRAPTARRRLQGAALFIIGLGMLVSGVAFKETMIGSFPILSVFGFVVMFGGVVYAITGPRLSGRMDRGGSAAGASRQRRTKGAGGSFTSRMEDRFRRRFDE