Rv0787 Still unknown · low auto-curated
H37Rv Rv0787 · MTBC0 - ·
319 aa · 881459–882418 (+) ·
RefSeq NP_215301.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | Conserved hypothetical protein; no recognised domain. Function unknown. Foldseek best (non-significant) hit: 4tmd-assembly1_A X-ray structure of Putative uncharacterized protein ( (prob 0.66, TM 0.36). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
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 |
P71840
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Metallo-beta-lactamase superfamily protein,putative |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| Orthologous group | 28Y2U |
|---|
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 | 0.454 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 3 synonymous, 4 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)
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 61.5 (low). Low-confidence model: the fold may be unreliable, so treat these structural hits with caution.
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 |
|---|---|---|---|---|
4tmd-assembly1_A |
0.66 | 0.36 | 1.1e-02 | 4tmd-assembly1_A X-ray structure of Putative uncharacterized protein (Rv0999 ortholog) from Mycobacterium smegmatis |
6vot-assembly1_A |
0.30 | 0.35 | 6.2e-02 | 6vot-assembly1_A Crystal structure of Pseudomonas aerugonisa PBP3 complexed to gamma-lactam YU253434 |
3pbn-assembly1_A |
0.28 | 0.35 | 7.0e-02 | 3pbn-assembly1_A Crystal Structure of Apo PBP3 from Pseudomonas aeruginosa |
3ocl-assembly1_A |
0.28 | 0.36 | 7.9e-02 | 3ocl-assembly1_A Crystal structure of penicillin-binding protein 3 from Pseudomonas aeruginosa in complex with carbenicillin |
3pbo-assembly1_A |
0.25 | 0.36 | 8.9e-02 | 3pbo-assembly1_A Crystal structure of PBP3 complexed with ceftazidime |
4wel-assembly1_A |
0.25 | 0.36 | 1.0e-01 | 4wel-assembly1_A Crystal structure of Pseudomonas aeruginosa PBP3 with SMC-3176 |
3pbq-assembly1_A |
0.23 | 0.35 | 9.5e-02 | 3pbq-assembly1_A Crystal structure of PBP3 complexed with imipenem |
7ly1-assembly1_A |
0.21 | 0.35 | 1.4e-01 | 7ly1-assembly1_A Crystal structure of Pseudomonas aeruginosa PBP3 in complex with vaborbactam |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: purQ (phosphoribosylformylglycinamidine synthase), high confidence from genomic context alone (score 770 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) |
|---|---|---|---|---|
Rv0786c hyp |
hypothetical protein | 794 | 793 ctx | neighborhood:792 |
Rv0787A purS hyp |
hypothetical protein | 770 | 770 ctx | neighborhood:769 |
Rv0788 purQ |
phosphoribosylformylglycinamidine synthase | 770 | 770 ctx | neighborhood:769 |
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
- Annotation from H37Rv (no MTBC0 1:1 anchor; H37Rv protein used): hypothetical protein
- Foldseek best: 4tmd-assembly1_A X-ray structure of Putative uncharacterized protein (Rv0999 ort (prob 0.66, E=1e-02, TM=0.36)
- (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_215301.1)
- 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
28Y2U - Curated reference: UniProt P71840 (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 61.5, low)
- Interaction network: STRING v12.0 (Szklarczyk et al. 2023,
doi:10.1093/nar/gkac1000), taxon 83332, CC-BY 4.0 —
3 functional partner(s); context anchor
purQ - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv0787| MHRPPWLAQLRRRLRIGVQLGSRVVLEQGRQPRDVYVIGVLVGDQDRGQTGDSLEAVRESTGIEEQAGLTELSEEAGMAEMRELHVYDCALMGAFPMRLILATMLVAGRLLATLMAAPSAQAEPETCPPICDQIPATAWISTHAVPLNSQYRWPAMAGAAVAVTRATPRFGFEQVCATPAFPHDSRDWAVAGRVTVVHPDGQWQLQAQVLHWRGDTARGGQIAASVFGTAVAALRACQLGAPLQSPSVTDDEPTRMAAVISGPVIMYTYLVAHVSSSTISELTLWSSGPPQVPWPTVADSAVLDALTAPLCEAYIGSCP