Rv3786c Family assigned · medium auto-curated
H37Rv Rv3786c · MTBC0 mtbc0_004014 ·
407 aa · 4256495–4257718 (-) ·
RefSeq NP_218303.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | peptidoglycan DD-metalloendopeptidase family protein |
| Revised (this work) | Peptidoglycan DD-metalloendopeptidase family protein. Pfam: Peptidase_M23 (PF01551.30). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WKW9
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Uncharacterized protein Rv3786c |
UniProt still lists this protein as Uncharacterized protein Rv3786c; the revised annotation above is ahead of the current UniProt record.
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
M Cell wall / membrane / envelope biogenesis
|
|---|---|
| eggNOG description | Glycosyl transferase family 2 |
| Orthologous group | COG0739 |
| Gene Ontology (8) |
GO:0005575, GO:0005618, GO:0005623, GO:0005886, GO:0016020, GO:0030312, GO:0044464, GO:0071944
|
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 | 1.051 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 1 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 |
|---|---|---|---|---|
Peptidase_M23 | PF01551.30 | 2.7e-16 | 275–369 | Peptidase family M23 |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv3787c (S-adenosyl-L-methionine-dependent methyltransferase), high confidence from genomic context alone (score 865 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) |
|---|---|---|---|---|
Rv3787c |
S-adenosyl-L-methionine-dependent methyltransferase | 865 | 865 ctx | neighborhood:864 |
Rv2812 |
transposase | 738 | 739 ctx | cooccurence:738 |
Rv3899c hyp |
hypothetical protein | 719 | 702 ctx | cooccurence:684 |
Rv3896c hyp |
hypothetical protein | 699 | 688 ctx | cooccurence:641 |
Rv1978 hyp |
hypothetical protein | 677 | 677 ctx | cooccurence:655 |
Rv1435c hyp |
hypothetical protein | 672 | 672 ctx | cooccurence:661 |
Rv0804 hyp |
hypothetical protein | 665 | 665 ctx | cooccurence:650 |
Rv1158c hyp |
hypothetical protein | 655 | 633 ctx | cooccurence:572 |
Rv3912 rsmA |
anti-sigma-M factor RsmA | 642 | 622 ctx | cooccurence:620 |
Rv3349c |
transposase | 611 | 611 ctx | cooccurence:608 |
Rv2687c |
antibiotic ABC transporter permease | 600 | 600 ctx | cooccurence:541 |
Rv1868 hyp |
hypothetical protein | 594 | 571 ctx | cooccurence:505 |
Rv1006 hyp |
hypothetical protein | 563 | 563 ctx | cooccurence:563 |
Rv3604c |
transmembrane protein | 563 | 563 ctx | cooccurence:562 |
Rv1181 pks4 |
polyketide beta-ketoacyl synthase | 577 | 556 |
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: peptidoglycan DD-metalloendopeptidase family protein
- Pfam (hmmscan --cut_ga): Peptidase_M23 PF01551.30 (E=3e-16)
- (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_218303.1)
- Domains: Pfam-A via hmmscan --cut_ga — Peptidase_M23 (PF01551.30)
- 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
COG0739 - Curated reference: UniProt P9WKW9 (SwissProt, reviewed; 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)
- Interaction network: STRING v12.0 (Szklarczyk et al. 2023,
doi:10.1093/nar/gkac1000), taxon 83332, CC-BY 4.0 —
56 functional partner(s); context anchor
Rv3787c - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_004014|Rv3786c| MRILAMTRAHNAGRTLAATLDSLAVFSDDIYVIDDRSTDDTAEILANHPAVTNVVRARPDLPPTPWLIPESAGLELLYRMADFCRPDWVMMVDADWLVETDIDLRAVLARTPDDIVALMCPMVSRWDDPEYPDLIPVMGTAEALRGPLWRWYPGLRAGGKLMHNPHWPANITDHGRIGQLPGVRLVHSGWSTLAERILRVEHYLRLDPDYRFNFGVAYDRSLLFGYALDEVDLLKADYRRRIRGDFDPLEPGGRLPIDREPRAIGRGYGPHAGGFHPGVDFATDPGTPVYAVASGAVSAIDEVDGLVSLTIARCELDVVYVFRPGDEGRLVLGDRIAAGAQLGTIGAQGESADGYLHFEVRTQDGHVNPVRYLANMGLRPWPPPGRLRAVSGSYPPATPCTITAEDR