Rv0836c Family assigned · low auto-curated · to review
H37Rv Rv0836c · MTBC0 - ·
217 aa · 932279–932932 (-) ·
RefSeq NP_215351.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | No Pfam domain above threshold; Foldseek indicates a fold similar to 8an5-assembly1_B MenAT1 toxin-antitoxin complex (rv0078a-rv0078b) from Mycobacte (prob 1.00, TM 0.48). Structure-based, putative. |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed (flagged for human review).
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 |
O53848
TrEMBL · unreviewed
· Predicted
|
|---|---|
| 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)
| COG category |
S Function unknown
|
|---|---|
| eggNOG description | Protein conserved in bacteria |
| Orthologous group | COG4849 |
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 | 0.346 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 2 synonymous, 2 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 89.7 (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 |
|---|---|---|---|---|
8an5-assembly1_B |
1.00 | 0.48 | 3.6e-04 sig | 8an5-assembly1_B MenAT1 toxin-antitoxin complex (rv0078a-rv0078b) from Mycobacterium tuberculosis H37Rv |
6y8q-assembly3_C |
0.57 | 0.33 | 5.6e-02 | 6y8q-assembly3_C AbiEi antitoxin from Streptococcus agalactiae |
6y8q-assembly4_D |
0.10 | 0.34 | 1.6e+00 | 6y8q-assembly4_D AbiEi antitoxin from Streptococcus agalactiae |
6ojk-assembly1_A |
0.08 | 0.56 | 8.2e+00 | 6ojk-assembly1_A Structure of YePL2A K291W in Complex with Tetragalacturonic Acid |
2hz8-assembly1_A |
0.08 | 0.39 | 4.2e+00 | 2hz8-assembly1_A QM/MM structure refined from NMR-structure of a single chain diiron protein |
6ojl-assembly1_A |
0.08 | 0.56 | 8.7e+00 | 6ojl-assembly1_A Structure of YePL2A R194K in Complex with Pentagalacturonic Acid |
8wwm-assembly1_R |
0.07 | 0.22 | 1.4e+00 | 8wwm-assembly1_R MCH-MCHR1-Gi complex, L2 state |
5uho-assembly1_D |
0.06 | 0.33 | 3.0e+00 | 5uho-assembly1_D Crystal structure of the core catalytic domain of human O-GlcNAcase complexed with PUGNAc |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: PE_PGRS28 (PE-PGRS family protein PE_PGRS28), high confidence from genomic context alone (score 747 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) |
|---|---|---|---|---|
Rv0837c hyp |
hypothetical protein | 997 | 989 ctx | neighborhood:754 cooccurence:774 coexpression:815 textmining:758 |
Rv1452c PE_PGRS28 |
PE-PGRS family protein PE_PGRS28 | 747 | 747 ctx | cooccurence:747 |
Rv0355c PPE8 |
PPE family protein PPE8 | 747 | 747 ctx | cooccurence:747 |
Rv1004c |
membrane protein | 746 | 747 ctx | cooccurence:746 |
Rv3350c PPE56 |
PPE family protein PPE56 | 746 | 746 ctx | cooccurence:745 |
Rv3347c PPE55 |
PPE family protein PPE55 | 745 | 745 ctx | cooccurence:744 |
Rv2490c PE_PGRS43 |
PE-PGRS family protein PE_PGRS43 | 741 | 741 ctx | cooccurence:741 |
Rv0304c PPE5 |
PPE family protein PPE5 | 740 | 741 ctx | cooccurence:740 |
Rv1917c PPE34 |
PPE family protein PPE34 | 736 | 737 ctx | cooccurence:736 |
Rv2209 |
integral membrane protein | 733 | 734 ctx | cooccurence:733 |
Rv1651c PE_PGRS30 |
PE-PGRS family protein PE_PGRS30 | 731 | 731 ctx | cooccurence:731 |
Rv3343c PPE54 |
PPE family protein PPE54 | 729 | 729 ctx | cooccurence:729 |
Rv2082 hyp |
hypothetical protein | 726 | 727 ctx | cooccurence:724 |
Rv0872c PE_PGRS15 |
PE-PGRS family protein PE_PGRS15 | 717 | 717 ctx | cooccurence:717 |
Rv1753c PPE24 |
PPE family protein PPE24 | 705 | 705 ctx | cooccurence:705 |
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: 8an5-assembly1_B MenAT1 toxin-antitoxin complex (rv0078a-rv0078b) from Mycobacte (prob 1.00, E=4e-04, TM=0.48)
- (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_215351.1)
- 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
COG4849 - Curated reference: UniProt O53848 (TrEMBL, unreviewed; Predicted)
- 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 89.7, 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
PE_PGRS28 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv0836c| MLVGAQCRDLLHWRFCRGVPPRATNDTDIAGTLNNWDHFEAIRATFRALGSTGHRFLIADRAVDALPFGEVESPTGTTRHPPGNQLMNVHGCTDAYLRADVLPLPGGLTVHLPQPPNYAVLKLHAWLDRSADHDYKDGPDLALVVHWYAGDLDRLYAKPDQWALRRHDFDLRTAAAALLGHDMRASVSAPEAAVLATRATQADHDLLAQHFAVGRPG