Rv1742 Family assigned · low
H37Rv Rv1742 · MTBC0 mtbc0_001855 ·
245 aa · 1980245–1980982 (+) ·
RefSeq NP_216258.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | hypothetical protein |
| Revised (this work) | LolA-superfamily fold (lipoprotein / lipid carrier-like beta-barrel). RefSeq leaves it 'hypothetical protein'. The AlphaFold model superposes on a LolA-superfamily protein (PDB 3buu; Foldseek prob 1.0, E 3e-8, TM 0.57). STRING context: the toxin vapC34 (Rv1741). A carrier/periplasmic-binding fold; the cargo is undemonstrated. |
Curated reference (UniProt)
| UniProt |
O33271
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Uncharacterized protein |
UniProt still lists this protein as Uncharacterized protein; the revised annotation above is ahead of the current UniProt record.
Functional vocabulary (eggNOG-mapper, orthology transfer)
| Orthologous group | 28MQW |
|---|
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 | 0.345 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 3 synonymous, 2 missense, 1 nonsense, 1 frameshift |
| Disruption | 2 distinct premature-stop/frameshift site(s); most common in 11.98% of strains (17398) · 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 96.5 (very high). 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 |
|---|---|---|---|---|
4z48-assembly2_B |
1.00 | 0.53 | 1.3e-07 sig | 4z48-assembly2_B Crystal structure of a DUF1329 family protein (DESPIG_00262) from Desulfovibrio piger ATCC 29098 at 1.75 A resolution |
3m4w-assembly2_D |
0.92 | 0.26 | 1.1e-03 sig | 3m4w-assembly2_D Structural basis for the negative regulation of bacterial stress response by RseB |
6n5x-assembly1_A |
0.30 | 0.62 | 1.8e+00 | 6n5x-assembly1_A Crystal structure of the SNX5 PX domain in complex with the CI-MPR (space group P212121 - Form 1) |
1xks-assembly1_A |
0.30 | 0.19 | 1.1e-02 | 1xks-assembly1_A The crystal structure of the N-terminal domain of Nup133 reveals a beta-propeller fold common to several nucleoporins |
6lk8-assembly1_J |
0.23 | 0.20 | 1.8e-02 | 6lk8-assembly1_J Structure of Xenopus laevis Cytoplasmic Ring subunit. |
2l33-assembly1_A |
0.21 | 0.53 | 1.6e+00 | 2l33-assembly1_A Solution NMR Structure of DRBM 2 domain of Interleukin enhancer-binding factor 3 from Homo sapiens, Northeast Structural Genomics Consortium Target HR4527E |
6lk8-assembly1_j |
0.20 | 0.19 | 2.0e-02 | 6lk8-assembly1_j Structure of Xenopus laevis Cytoplasmic Ring subunit. |
7wb4-assembly1_P |
0.15 | 0.18 | 3.2e-02 | 7wb4-assembly1_P Cryo-EM structure of the NR subunit from X. laevis NPC |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: vapC34 (ribonuclease VapC34), high confidence from genomic context alone (score 792 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) |
|---|---|---|---|---|
Rv1741 vapC34 |
ribonuclease VapC34 | 792 | 792 ctx | neighborhood:785 |
Rv1740 vapB34 |
antitoxin VapB34 | 786 | 785 ctx | neighborhood:780 |
Rv3879c espK |
ESX-1 secretion-associated protein EspK | 609 | 609 ctx | cooccurence:609 |
Rv3882c eccE1 |
ESX-1 secretion system protein EccE1 | 595 | 595 ctx | cooccurence:595 |
Rv3877 eccD1 |
ESX-1 secretion system protein EccD1 | 577 | 578 ctx | cooccurence:575 |
Rv1739c |
sulfate ABC transporter permease | 575 | 575 ctx | neighborhood:570 |
Rv1743 pknE |
serine/threonine-protein kinase PknE | 540 | 539 ctx | neighborhood:535 |
Rv2542 hyp |
hypothetical protein | 491 | 491 ctx | cooccurence:488 |
Rv0341 iniB |
isoniazid inducible protein IniB | 457 | 457 ctx | cooccurence:457 |
Rv0304c PPE5 |
PPE family protein PPE5 | 422 | 423 ctx | cooccurence:421 |
Rv3869 eccB1 |
ESX-1 secretion system protein EccB | 414 | 415 ctx | cooccurence:414 |
Rv2317 uspB |
sugar ABC transporter permease UspB | 657 | 54 | textmining:653 |
Rv0994 moeA1 |
molybdopterin molybdenumtransferase 1 | 656 | 49 | textmining:654 |
Rv2505c fadD35 |
fatty-acid--CoA ligase FadD35 | 655 | 47 | textmining:653 |
Rv3393 iunH |
nucleoside hydrolase | 652 | 47 | textmining:650 |
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
- Foldseek -> LolA-superfamily protein (3buu), prob 1.0, E 3e-8, TM 0.57
- STRING neighbour vapC34/Rv1741
- Structural homology: AlphaFold DB model + Foldseek vs PDB (project 'Still unknown gene function', phase5-7, 2026-06-10). A fold-level family assignment, not a demonstrated activity.
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_216258.1)
- 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
28MQW - Curated reference: UniProt O33271 (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 96.5, very high)
- Interaction network: STRING v12.0 (Szklarczyk et al. 2023,
doi:10.1093/nar/gkac1000), taxon 83332, CC-BY 4.0 —
23 functional partner(s); context anchor
vapC34 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001855|Rv1742| MSALLDGVLDAHGGLQRWRAAETVHGRVRTGGLLLRTRVPGNRFADYRITVHVQQARTVLDPFPRDGYRGVFESGQVRIESHDGAVISSRAHPRAAFFGRSGLRRNIRWDPLDSVYFAGYAMWNYLTTPYLLTREGVAVEEGAPWQQEGETWRRLIVSFPPDIDTHSPRQTFYVDASGLLRRHDYVPEVVGHWARAAHYCADPVDVDGFVFPTCRWVHPIGPGNRSLPFPTLVSILLTDIRVETD