Rv2525c Family assigned · medium auto-curated
H37Rv Rv2525c · MTBC0 mtbc0_002689 ·
240 aa · 2872742–2873464 (-) ·
RefSeq NP_217041.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | DUF1906 domain-containing protein |
| Revised (this work) | DUF1906 domain-containing protein. Pfam: Rv2525c_GlyHyd-like (PF08924.18). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
I6XEI5
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Putative peptidoglycan hydrolase Rv2525c |
| EC (curated) |
EC 3.2.1.17
|
| Curated function | May function as a peptidoglycan hydrolase with glycosidase activity. In vitro, displays esterase activity toward p-nitrophenyl esters of various acyl chain length (C4 to C16), with a preference for p-nitrophenyl butyrate (C4). |
UniProt still lists this protein as Putative peptidoglycan hydrolase Rv2525c; 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 | Domain of unknown function (DUF1906) |
| Orthologous group | COG3757 |
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 |
|---|---|---|---|---|
Rv2525c_GlyHyd-like | PF08924.18 | 1.9e-49 | 53–230 | Rv2525c-like, glycoside hydrolase-like domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv3668c (protease), high confidence from genomic context alone (score 755 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) |
|---|---|---|---|---|
Rv3668c |
protease | 769 | 755 ctx | cooccurence:752 |
Rv1566c ripD hyp |
hypothetical protein | 761 | 750 | coexpression:745 |
Rv3810 pirG |
cell surface protein | 744 | 744 | coexpression:744 |
Rv1158c hyp |
hypothetical protein | 732 | 732 | coexpression:732 |
Rv3847 hyp |
hypothetical protein | 729 | 730 ctx | cooccurence:728 |
Rv2673 aftC |
alpha-(1->3)-arabinofuranosyltransferase | 720 | 720 ctx | cooccurence:719 |
Rv2524c fas |
fatty acid synthase | 719 | 720 ctx | neighborhood:510 cooccurence:435 |
Rv0531 |
membrane protein | 707 | 708 ctx | cooccurence:706 |
Rv0048c |
membrane protein | 704 | 703 ctx | cooccurence:697 |
Rv3805c aftB |
terminal beta-(1->2)-arabinofuranosyltransferase | 694 | 694 ctx | cooccurence:691 |
Rv3802c |
membrane protein | 727 | 687 ctx | cooccurence:678 |
Rv1275 lprC |
lipoprotein LprC | 665 | 665 ctx | cooccurence:663 |
Rv0479c |
membrane protein | 633 | 633 ctx | cooccurence:631 |
Rv0227c |
membrane protein | 631 | 631 ctx | cooccurence:629 |
Rv3244c lpqB |
lipoprotein LpqB | 622 | 622 ctx | cooccurence:618 |
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: DUF1906 domain-containing protein
- Pfam (hmmscan --cut_ga): Rv2525c_GlyHyd-like PF08924.18 (E=2e-49)
- (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_217041.1)
- Domains: Pfam-A via hmmscan --cut_ga — Rv2525c_GlyHyd-like (PF08924.18)
- 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
COG3757 - Curated reference: UniProt I6XEI5 (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 —
62 functional partner(s); context anchor
Rv3668c - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002689|Rv2525c| MSVSRRDVLKFAAATPGVLGLGVVASSLRAAPASAGSLGTLLDYAAGVIPASQIRAAGAVGAIRYVSDRRPGGAWMLGKPIQLSEARDLSGNGLKIVSCYQYGKGSTADWLGGASAGVQHARRGSELHAAAGGPTSAPIYASIDDNPSYEQYKNQIVPYLRSWESVIGHQRTGVYANSKTIDWAVNDGLGSYFWQHNWGSPKGYTHPAAHLHQVEIDKRKVGGVGVDVNQILKPQFGQWA