Rv2180c Family assigned · low auto-curated
H37Rv Rv2180c · MTBC0 mtbc0_002315 ·
295 aa · 2468334–2469221 (-) ·
RefSeq NP_216696.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | integral membrane protein |
|---|---|
| MTBC0 PGAP re-annotation | integral membrane protein |
| Revised (this work) | Integral membrane protein. |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
O53514
TrEMBL · unreviewed
· Predicted
|
|---|---|
| UniProt name | Probable conserved integral membrane protein |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
M Cell wall / membrane / envelope biogenesis
|
|---|---|
| eggNOG description | Membrane |
| Orthologous group | COG4325 |
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) pseudogene candidate
| pN/pS | 0.898 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 2 synonymous, 4 missense, 1 nonsense, 0 frameshift |
| Disruption | 1 distinct premature-stop/frameshift site(s); most common in 21.20% of strains (30785) · clonal |
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: Rv2179c (3'-5' exoribonuclease), high confidence from genomic context alone (score 884 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2179c |
3'-5' exoribonuclease | 884 | 884 ctx | neighborhood:882 |
Rv2181 |
alpha-(1-2)-phosphatidylinositol mannoside mannosyltransferase | 785 | 786 ctx | neighborhood:783 |
Rv2178c aroG |
phospho-2-dehydro-3-deoxyheptonate aldolase AroG | 778 | 778 ctx | neighborhood:778 |
Rv2728c hyp |
hypothetical protein | 513 | 514 ctx | cooccurence:509 |
Rv0037c |
MFS-type transporter | 495 | 495 ctx | cooccurence:492 |
Rv0585c |
integral membrane protein | 492 | 492 ctx | cooccurence:489 |
Rv0885 hyp |
hypothetical protein | 462 | 462 ctx | cooccurence:462 |
Rv1280c oppA |
oligopeptide ABC transporter substrate-binding lipoprotein OppA | 439 | 440 ctx | cooccurence:439 |
Rv1836c hyp |
hypothetical protein | 428 | 429 ctx | cooccurence:428 |
Rv1125 hyp |
hypothetical protein | 423 | 424 ctx | cooccurence:420 |
Rv2342 hyp |
hypothetical protein | 419 | 420 ctx | cooccurence:418 |
Rv0226c |
transmembrane protein | 417 | 418 ctx | cooccurence:416 |
Rv0464c hyp |
hypothetical protein | 404 | 404 ctx | cooccurence:401 |
Rv0794c |
oxidoreductase | 421 | 201 | |
Rv0002 dnaN |
DNA polymerase III subunit beta | 446 | 157 |
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: integral membrane 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_216696.1)
- 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
COG4325 - Curated reference: UniProt O53514 (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 —
22 functional partner(s); context anchor
Rv2179c - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002315|Rv2180c| MEVFHWLQHDIVDRGRLPLLCCLVAFVLTFLVTRSFVRFIHRRAADGRPARWWQPRNVHIGSVHIHHVAFGVVLVMISGLTLVTLSVDGREPEFTIAASIFGVGAALVLDEYALILHLSDVYWEEDGRTSVDAVFAAVAVAGLLIMGLHPLIFFLPVRQGANWVVLQTTLIAGLVLTLPLAVVVLLKGKVWTGLLGMFVVVLLVVGAVRLSRPHAPWARWRYTRHPEKMRRALQRERTWRRPVVRIKLWLQYVIAGTPRMPDERAVDAQLDQDVRPAPPPERTAPILISGSVWSD