Rv1924c Family assigned · low
H37Rv Rv1924c · MTBC0 mtbc0_002038 ·
126 aa · 2195666–2196046 (-) ·
RefSeq NP_216440.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | hypothetical protein |
| Revised (this work) | Polytopic integral membrane protein with 3 predicted transmembrane helices (DeepTMHMM). RefSeq leaves it 'hypothetical protein'. A topological feature consistent with a membrane transporter/permease or membrane-embedded enzyme; the transported substrate and molecular function are undetermined. |
Curated reference (UniProt)
| UniProt |
P95289
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | TIGR02611 family protein |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| Orthologous group | 2AVU1 |
|---|
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 | n/a |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 0 synonymous, 3 missense, 0 nonsense, 1 frameshift |
| Disruption | 1 distinct premature-stop/frameshift site(s); most common in 1.60% of strains (2320) · 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).
Structural neighbours (Foldseek on the ESMFold model, exploratory)
ESMFold model confidence: mean pLDDT 80.7 (confident). A confident model makes the fold comparison meaningful.
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 |
|---|---|---|---|---|
9eom-assembly1_A-2 |
0.04 | 0.29 | 9.2e+00 | 9eom-assembly1_A-2 250A Vipp1 dL10Ala helical tubes in the presence of EPL |
9eom-assembly1_A-3 |
0.04 | 0.29 | 9.2e+00 | 9eom-assembly1_A-3 250A Vipp1 dL10Ala helical tubes in the presence of EPL |
9eom-assembly1_A-4 |
0.04 | 0.29 | 9.2e+00 | 9eom-assembly1_A-4 250A Vipp1 dL10Ala helical tubes in the presence of EPL |
9eom-assembly1_A-5 |
0.04 | 0.29 | 9.2e+00 | 9eom-assembly1_A-5 250A Vipp1 dL10Ala helical tubes in the presence of EPL |
9eom-assembly1_A-6 |
0.04 | 0.29 | 9.2e+00 | 9eom-assembly1_A-6 250A Vipp1 dL10Ala helical tubes in the presence of EPL |
9eom-assembly1_A-7 |
0.04 | 0.29 | 9.2e+00 | 9eom-assembly1_A-7 250A Vipp1 dL10Ala helical tubes in the presence of EPL |
9eom-assembly1_A-8 |
0.04 | 0.29 | 9.2e+00 | 9eom-assembly1_A-8 250A Vipp1 dL10Ala helical tubes in the presence of EPL |
9eom-assembly1_A-9 |
0.04 | 0.29 | 9.2e+00 | 9eom-assembly1_A-9 250A Vipp1 dL10Ala helical tubes in the presence of EPL |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: fadD31 (fatty-acid--CoA ligase FadD31), medium confidence from genomic context alone (score 650 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) |
|---|---|---|---|---|
Rv1925 fadD31 |
fatty-acid--CoA ligase FadD31 | 650 | 650 ctx | neighborhood:647 |
Rv0544c |
transmembrane protein | 565 | 75 | textmining:550 |
Rv3150 nuoF |
NADH-quinone oxidoreductase subunit F | 654 | 53 | textmining:650 |
Rv1626 pdtaR |
two-component system transcriptional regulator | 655 | 51 | textmining:652 |
Rv1875 hyp |
hypothetical protein | 804 | 47 | textmining:803 |
Rv1728c hyp |
hypothetical protein | 804 | 46 | textmining:803 |
Rv3003c ilvB1 |
acetolactate synthase large subunit IlvB | 627 | 46 | textmining:626 |
Rv1526c |
glycosyltransferase | 808 | 41 | textmining:808 |
Rv1937 |
oxygenase | 808 | 41 | textmining:808 |
Rv0532 PE_PGRS6 |
PE-PGRS family protein PE_PGRS6 | 801 | 41 | textmining:801 |
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
- DeepTMHMM: 3 transmembrane helices (type TM)
- Integral membrane topology (localisation feature, not a function)
- DeepTMHMM topology prediction (project 'Still unknown gene function', phase8, 2026-06-10). A topological feature, not a demonstrated molecular function.
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_216440.1)
- 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
2AVU1 - Curated reference: UniProt P95289 (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)
- Model confidence: ESMFold per-residue pLDDT (mean 80.7, confident)
- Interaction network: STRING v12.0 (Szklarczyk et al. 2023,
doi:10.1093/nar/gkac1000), taxon 83332, CC-BY 4.0 —
10 functional partner(s); context anchor
fadD31 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002038|Rv1924c| MDPADVINPTSTRDAALARVLAYRQRVRARPLLIRATLAVVGGGLFVVSLPMIVLLPELGIPALLVAFRLLAVEAQWAVRAYAWTDWRFTQLREWFHRQVLVTRAAILVGLFLAAVALVWLLVYEF