Rv3732 Still unknown · low auto-curated
H37Rv Rv3732 · MTBC0 mtbc0_003957 ·
352 aa · 4207055–4208113 (+) ·
RefSeq NP_218249.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | DUF2330 domain-containing protein |
| Revised (this work) | Conserved hypothetical protein; DUF domain(s) DUF2330. Function unknown. Foldseek best (non-significant) hit: 6oiu-assembly3_C X-ray crystal structure of the ectodomain of the Toxo (prob 0.14, TM 0.24). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
O69699
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Conserved protein |
UniProt still lists this protein as Conserved protein; the revised annotation above is ahead of the current UniProt record.
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| eggNOG description | Uncharacterized protein conserved in bacteria (DUF2330) |
| Orthologous group | COG4402 |
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 | 0.741 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 2 synonymous, 4 missense, 0 nonsense, 1 frameshift |
| Disruption | 1 distinct premature-stop/frameshift site(s); most common in 1.08% of strains (1574) · 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)
| Pfam | Accession | i-Evalue | Residues | Description |
|---|---|---|---|---|
DUF2330 | PF10092.15 | 1.6e-80 | 29–298 | Uncharacterized protein conserved in bacteria (DUF2330) |
Structural neighbours (Foldseek on the ESMFold model, exploratory)
ESMFold model confidence: mean pLDDT 87.0 (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 |
|---|---|---|---|---|
6oiu-assembly3_C |
0.14 | 0.24 | 1.3e-01 | 6oiu-assembly3_C X-ray crystal structure of the ectodomain of the Toxoplasma gondii ME49 Aminopeptidase N (TGME49_224350) |
6oiu-assembly2_B |
0.12 | 0.24 | 8.9e-02 | 6oiu-assembly2_B X-ray crystal structure of the ectodomain of the Toxoplasma gondii ME49 Aminopeptidase N (TGME49_224350) |
6oiu-assembly4_D |
0.11 | 0.24 | 1.3e-01 | 6oiu-assembly4_D X-ray crystal structure of the ectodomain of the Toxoplasma gondii ME49 Aminopeptidase N (TGME49_224350) |
6fpy-assembly1_A |
0.10 | 0.28 | 3.4e-01 | 6fpy-assembly1_A Inter-alpha-inhibitor heavy chain 1, wild type |
8agb-assembly1_E |
0.08 | 0.28 | 5.9e-01 | 8agb-assembly1_E Structure of yeast oligosaccharylransferase complex with lipid-linked oligosaccharide bound |
6oiu-assembly1_A |
0.07 | 0.22 | 4.0e-01 | 6oiu-assembly1_A X-ray crystal structure of the ectodomain of the Toxoplasma gondii ME49 Aminopeptidase N (TGME49_224350) |
5dll-assembly1_A |
0.06 | 0.23 | 4.5e-01 | 5dll-assembly1_A Aminopeptidase N (pepN) from Francisella tularensis subsp. tularensis SCHU S4 |
4qir-assembly1_A |
0.06 | 0.27 | 1.3e+00 | 4qir-assembly1_A Crystal structure of Aminopeptidase N in complex with the phosphinic dipeptide analogue LL-(R,S)-2-(pyridin-3-yl)ethylGlyP[CH2]Phe |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv0538 (membrane protein), high confidence from genomic context alone (score 716 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) |
|---|---|---|---|---|
Rv0538 |
membrane protein | 715 | 716 ctx | cooccurence:714 |
Rv1267c embR |
transcriptional regulator EmbR | 688 | 689 ctx | cooccurence:686 |
Rv2113 |
integral membrane protein | 679 | 680 ctx | cooccurence:678 |
Rv3254 hyp |
hypothetical protein | 598 | 599 ctx | cooccurence:595 |
Rv1775 hyp |
hypothetical protein | 591 | 592 ctx | cooccurence:589 |
Rv3407 vapB47 |
antitoxin VapB47 | 588 | 588 ctx | cooccurence:588 |
Rv1963c mce3R |
transcriptional repressor Mce3R | 582 | 582 ctx | cooccurence:580 |
Rv1853 ureD |
urease accessory protein UreD | 556 | 556 ctx | cooccurence:550 |
Rv3788 hyp |
hypothetical protein | 553 | 553 ctx | cooccurence:552 |
Rv3731 ligC |
DNA ligase C | 544 | 544 ctx | neighborhood:542 |
Rv1937 |
oxygenase | 544 | 544 ctx | cooccurence:543 |
Rv0339c iniR |
transcriptional regulator | 541 | 541 ctx | cooccurence:539 |
Rv2939 papA5 |
phthiocerol/phthiodiolone dimycocerosyl transferase | 493 | 494 ctx | cooccurence:491 |
Rv2560 hyp |
hypothetical protein | 488 | 489 ctx | cooccurence:487 |
Rv3903c cpnT hyp |
hypothetical protein | 486 | 487 ctx | cooccurence:484 |
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: hypothetical protein
- MTBC0 PGAP product: DUF2330 domain-containing protein
- Pfam (hmmscan --cut_ga): DUF2330 PF10092.15 (E=2e-80)
- Foldseek best: 6oiu-assembly3_C X-ray crystal structure of the ectodomain of the Toxoplasma gon (prob 0.14, E=1e-01, TM=0.24)
- (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_218249.1)
- Domains: Pfam-A via hmmscan --cut_ga — DUF2330 (PF10092.15)
- 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
COG4402 - Curated reference: UniProt O69699 (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 87.0, confident)
- Interaction network: STRING v12.0 (Szklarczyk et al. 2023,
doi:10.1093/nar/gkac1000), taxon 83332, CC-BY 4.0 —
38 functional partner(s); context anchor
Rv0538 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003957|Rv3732| MAVLPACRLGLVVCVATAVITATMVLATPSYACACGAAVTAHGSQATLNHEVALLHWDGTTETIVMQLAMNADTDNVALVVPTPTPAIVTTADQSTFGELDTLSAPLIEHQRHWSLRRGVGASGPQEAAARAPHVLNQVRLGPLEATTLTGGDLSGLQTWLSDNGYAIRPAVSAALDPYVRDGWAFVAIRLTSTDLIVGGLDPVRMTFRSSRLVYPMRLSVAAQEPQHVTIFTLSDHRQQRTDADAATQTTHVRFAGDMSTAVRDPLLRELIGNHGSYLTKVEVDIYQTSRISSDFTFGNAPNDDPYRQVVTVYDDVALPPLLLVVVSAIAVGAAGGAVVVVLRRRRRAHTG