Rv1632c Family assigned · low
H37Rv Rv1632c · MTBC0 mtbc0_001740 ·
147 aa · 1848351–1848794 (-) ·
RefSeq NP_216148.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | DUF402 domain-containing protein |
| Revised (this work) | DUF402; structure of the DUF402 family (PDB 2P12, TM 0.96); putative nucleotide-binding/phosphatase fold. |
Curated reference (UniProt)
| UniProt |
O06149
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | DUF402 domain-containing protein |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| eggNOG description | Protein of unknown function (DUF402) |
| Orthologous group | COG2306 |
| KEGG orthology |
K09146
|
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 | 0.506 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 2 synonymous, 3 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 |
|---|---|---|---|---|
DUF402 | PF04167.19 | 5.0e-26 | 3–128 | Protein of unknown function (DUF402) |
Structural neighbours (Foldseek on the ESMFold model, exploratory)
ESMFold model confidence: mean pLDDT 87.4 (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 |
|---|---|---|---|---|
2p12-assembly1_B |
1.00 | 0.96 | 1.9e-17 sig | 2p12-assembly1_B Crystal structure of protein of unknown function DUF402 from Rhodococcus sp. RHA1 |
3exm-assembly1_A |
1.00 | 0.77 | 7.4e-05 sig | 3exm-assembly1_A Crystal structure of the phosphatase SC4828 with the non-hydrolyzable nucleotide GPCP |
5zdn-assembly1_A |
1.00 | 0.63 | 4.8e-04 sig | 5zdn-assembly1_A The complex structure of FomD with CDP |
7d8q-assembly1_A |
1.00 | 0.63 | 1.3e-03 sig | 7d8q-assembly1_A The structure of nucleotide phosphatase Sa1684 complex with GDP analogue from Staphylococcus aureus |
8rza-assembly1_A-2 |
1.00 | 0.63 | 3.1e-03 sig | 8rza-assembly1_A-2 Ribonuclease W |
8wo8-assembly1_A-3 |
1.00 | 0.63 | 4.6e-03 sig | 8wo8-assembly1_A-3 Crystal Structure of an RNA-binding protein, FAU-1, from Pyrococcus furiosus |
3ew2-assembly4_G |
0.14 | 0.37 | 1.2e+00 | 3ew2-assembly4_G Crystal structure of rhizavidin-biotin complex |
8rnu-assembly1_C |
0.13 | 0.70 | 7.7e+00 | 8rnu-assembly1_C CryoEM structure of recombinant human Bri2 BRICHOS oligomers |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: lpqW (monoacyl phosphatidylinositol tetramannoside-binding protein LpqW), high confidence from genomic context alone (score 778 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) |
|---|---|---|---|---|
Rv1166 lpqW |
monoacyl phosphatidylinositol tetramannoside-binding protein LpqW | 778 | 778 ctx | cooccurence:721 |
Rv0556 |
transmembrane protein | 776 | 776 ctx | cooccurence:773 |
Rv2732c |
transmembrane protein | 772 | 773 ctx | cooccurence:772 |
Rv3438 hyp |
hypothetical protein | 769 | 769 ctx | cooccurence:768 |
Rv3212 hyp |
hypothetical protein | 767 | 767 ctx | cooccurence:765 |
Rv3850 hyp |
hypothetical protein | 763 | 763 ctx | cooccurence:761 |
Rv2446c |
integral membrane protein | 759 | 759 ctx | cooccurence:758 |
Rv1109c hyp |
hypothetical protein | 758 | 759 ctx | cooccurence:757 |
Rv3205c hyp |
hypothetical protein | 751 | 752 ctx | cooccurence:751 |
Rv0431 |
tuberculin-like peptide | 750 | 751 ctx | cooccurence:739 |
Rv0383c ttfA hyp |
hypothetical protein | 743 | 743 ctx | cooccurence:743 |
Rv2049c hyp |
hypothetical protein | 740 | 741 ctx | cooccurence:737 |
Rv2138 lppL |
lipoprotein LppL | 735 | 736 ctx | cooccurence:734 |
Rv2360c hyp |
hypothetical protein | 734 | 735 ctx | cooccurence:728 |
Rv0358 hyp |
hypothetical protein | 725 | 725 ctx | cooccurence:725 |
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
- MTBC0 PGAP product: DUF402 domain-containing protein
- Pfam: DUF402 PF04167.19
- Foldseek best: 2p12-assembly1_B Crystal structure of protein of unknown function DUF402 from Rh (prob 1.00, E=2e-17, TM=0.96)
- (structure-only promotion reviewed by hand, 2026-06-01)
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_216148.1)
- Domains: Pfam-A via hmmscan --cut_ga — DUF402 (PF04167.19)
- 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
COG2306 - Curated reference: UniProt O06149 (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 87.4, confident)
- Interaction network: STRING v12.0 (Szklarczyk et al. 2023,
doi:10.1093/nar/gkac1000), taxon 83332, CC-BY 4.0 —
94 functional partner(s); context anchor
lpqW - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001740|Rv1632c| MRAVDEYTVHPWGLYLARPTPGRAQFHYLESWLLPSLGLRATVFHFNPSHKRDHDYYLDVGEYTPGPSVWRSEDHYLDIEVRTGGGAELADVDELLDAVRHGLLTPTVAEQAVRHAVDAVEGLARNGYDLTRWLATKGMELTWRSGS