Rv1342c Family assigned · low
H37Rv Rv1342c · MTBC0 - ·
120 aa · 1508184–1508546 (-) ·
RefSeq YP_177800.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | — |
| 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. |
Annotated on the H37Rv protein: this gene has no 1:1 ancestral MTBC0 anchor (PE/PPE, paralogue, IS element, or otherwise unanchored CDS).
Curated reference (UniProt)
| UniProt |
P9WM19
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Uncharacterized protein Rv1342c |
UniProt still lists this protein as Uncharacterized protein Rv1342c; the revised annotation above is ahead of the current UniProt record.
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| eggNOG description | membrane |
| Orthologous group | 2E65S |
| Gene Ontology (14) |
GO:0005575, GO:0005623, GO:0005886, GO:0005887, GO:0008150, GO:0016020, GO:0016021, GO:0031224, GO:0031226, GO:0040007, GO:0044425, GO:0044459 +2 more
|
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 | 0.0 · strong purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 1 synonymous, 0 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 |
|---|---|---|---|---|
DUF3817 | PF12823.13 | 2.0e-22 | 28–111 | Domain of unknown function (DUF3817) |
Structural neighbours (Foldseek on the ESMFold model, exploratory)
ESMFold model confidence: mean pLDDT 86.4 (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 |
|---|---|---|---|---|
6s37-assembly1_A |
0.12 | 0.53 | 8.8e+00 | 6s37-assembly1_A Ligand binding domain of the P. putida receptor PcaY_PP in complex with salicylic acid |
1ykh-assembly1_B |
0.08 | 0.35 | 5.2e+00 | 1ykh-assembly1_B Structure of the mediator MED7/MED21 (Med7/Srb7) subcomplex |
8cok-assembly1_A |
0.06 | 0.39 | 7.9e+00 | 8cok-assembly1_A Structural analysis of ING3 protein and its binding to histone H3 |
5bw9-assembly2_g |
0.02 | 0.26 | 9.8e+00 | 5bw9-assembly2_g Crystal Structure of Yeast V1-ATPase in the Autoinhibited Form |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: lprD (lipoprotein LprD), high confidence from genomic context alone (score 888 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) |
|---|---|---|---|---|
Rv1343c lprD |
lipoprotein LprD | 888 | 888 ctx | neighborhood:882 |
Rv1345 mbtM |
long-chain-fatty-acid--ACP ligase MbtM | 593 | 593 ctx | neighborhood:574 |
Rv2199c ctaF |
cytochrome c oxidase polypeptide 4 | 590 | 590 ctx | cooccurence:584 |
Rv1346 mbtN |
acyl-[acyl-carrier-protein | 576 | 576 ctx | neighborhood:562 |
Rv1344 mbtL |
acyl carrier protein MbtL | 569 | 568 ctx | neighborhood:562 |
Rv2229c hyp |
hypothetical protein | 490 | 491 ctx | cooccurence:489 |
Rv1451 ctaB |
protoheme IX farnesyltransferase | 490 | 472 | |
Rv2195 qcrA |
ubiquinol-cytochrome C reductase rieske iron-sulfur subunit | 467 | 445 ctx | cooccurence:442 |
Rv0360c hyp |
hypothetical protein | 459 | 438 ctx | cooccurence:438 |
Rv3207c hyp |
hypothetical protein | 456 | 435 ctx | cooccurence:432 |
Rv0102 |
integral membrane protein | 432 | 433 ctx | cooccurence:429 |
Rv2219A |
membrane protein | 427 | 427 ctx | cooccurence:418 |
Rv0528 |
transmembrane protein | 423 | 423 ctx | cooccurence:423 |
Rv2194 qcrC |
ubiquinol-cytochrome C reductase cytochrome subunit C | 419 | 410 ctx | cooccurence:400 |
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 YP_177800.1)
- Domains: Pfam-A via hmmscan --cut_ga — DUF3817 (PF12823.13)
- 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
2E65S - Curated reference: UniProt P9WM19 (SwissProt, reviewed; 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 86.4, confident)
- Interaction network: STRING v12.0 (Szklarczyk et al. 2023,
doi:10.1093/nar/gkac1000), taxon 83332, CC-BY 4.0 —
14 functional partner(s); context anchor
lprD - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv1342c| MTAPETPAAQHAEPAIAVERIRTALLGYRIMAWTTGLWLIALCYEIVVRYVVKVDNPPTWIGVVHGWVYFTYLLLTLNLAVKVRWPLGKTAGVLLAGTIPLLGIVVEHFQTKEIKARFGL