Rv2800 Family assigned · medium auto-curated
H37Rv Rv2800 · MTBC0 mtbc0_002979 ·
549 aa · 3130831–3132480 (+) ·
RefSeq NP_217316.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hydrolase |
|---|---|
| MTBC0 PGAP re-annotation | CocE/NonD family hydrolase |
| Revised (this work) | CocE/NonD family hydrolase. Pfam: Peptidase_S15 (PF02129.25), PepX_C (PF08530.17). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
I6YEE6
TrEMBL · unreviewed
· Predicted
|
|---|---|
| UniProt name | Possible hydrolase |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| eggNOG description | Hydrolase |
| Orthologous group | COG2936 |
| KEGG orthology |
K06978
|
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 | 0.349 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 12 synonymous, 10 missense, 1 nonsense, 1 frameshift |
| Disruption | 2 distinct premature-stop/frameshift site(s); most common in 2.84% of strains (4131) · 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 |
|---|---|---|---|---|
Peptidase_S15 | PF02129.25 | 8.1e-70 | 49–310 | X-Pro dipeptidyl-peptidase (S15 family) |
PepX_C | PF08530.17 | 1.5e-25 | 339–541 | X-Pro dipeptidyl-peptidase C-terminal non-catalytic domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv2799 (membrane protein), high confidence from genomic context alone (score 793 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2799 |
membrane protein | 793 | 793 ctx | neighborhood:787 |
Rv1215c hyp |
hypothetical protein | 690 | 691 ctx | cooccurence:686 |
Rv3433c nnr |
bifunctional ADP-dependent (S)-NAD(P)H-hydrate dehydratase/NAD(P)H-hydrate epimerase | 615 | 615 | coexpression:615 |
Rv2797c hyp |
hypothetical protein | 568 | 567 ctx | neighborhood:562 |
Rv2798c hyp |
hypothetical protein | 565 | 565 ctx | neighborhood:562 |
Rv2796c lppV |
lipoprotein LppV | 529 | 529 ctx | neighborhood:529 |
Rv2794c pptT |
4'-phosphopantetheinyl transferase | 458 | 458 ctx | neighborhood:455 |
Rv2793c truB |
tRNA pseudouridine synthase B | 458 | 458 ctx | neighborhood:455 |
Rv2795c hyp |
hypothetical protein | 475 | 456 ctx | neighborhood:456 |
Rv2790c ltp1 |
lipid-transfer protein | 449 | 450 ctx | neighborhood:430 |
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: hydrolase
- MTBC0 PGAP product: CocE/NonD family hydrolase
- Pfam (hmmscan --cut_ga): Peptidase_S15 PF02129.25 (E=8e-70), PepX_C PF08530.17 (E=1e-25)
- (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_217316.1)
- Domains: Pfam-A via hmmscan --cut_ga — Peptidase_S15 (PF02129.25), PepX_C (PF08530.17)
- 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
COG2936 - Curated reference: UniProt I6YEE6 (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)
- Interaction network: STRING v12.0 (Szklarczyk et al. 2023,
doi:10.1093/nar/gkac1000), taxon 83332, CC-BY 4.0 —
10 functional partner(s); context anchor
Rv2799 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002979|Rv2800| MSTTSARPERPKLRALTGRVGGQALGGLLGLPRATTRYTVGHVRVPMRDGVQLVADHYAPATSQPVGTLLVRGPYGRRFPFSLVFARIYAARGYHVVLQSVRGTFGSGGVFEPMVNEAADGADTVAWLREQPWFTGRFGTIGLPYLGFTQWALLHDPPPELAAAVITVGPHDFRASVWGTGSFTVNDFLGWSDLVSHQEDPGRIRAGIRQLTAPRRVARTAATLPLGESARTLLGTGAPWFESWVEHTDRDDPFWDRLRFPAALDRVQVPVLLVGGWQDIFLRQTLQQYRHLRDRGVHVALTVGPWTHTQMLTKGLATGARESLDWLDAHLGRAPALRPSPVRVFVTGQGWRHLPDWPPATTERAWYLQPGGRLGESAPASGTPPATFRYHPADPTPTTGGPLLSSNGGYRDDSRLATRADVLCFTGAPLTHDLCVHGNPVVELVHSSDNPYVDVFVRVSEVDAKGRSRNVSDGYRRLGDAPELVRVELDAIAHRFRADSRIRVLIAGSWFPRYARNLGTPEPILTGRQLKPATHAVHFGRSRLLLPVG