Rv3915 Resolved · high auto-curated
H37Rv Rv3915 · MTBC0 - ·
406 aa · 4403192–4404412 (+) ·
RefSeq YP_178027.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | peptidoglycan hydrolase |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | Peptidoglycan hydrolase. Pfam: PG_binding_1 (PF01471.24), Amidase_3 (PF01520.24). |
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 |
L7N653
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | N-acetylmuramoyl-L-alanine amidase CwlM |
| EC (curated) |
EC 3.5.1.28
|
| Curated function | Cell-wall hydrolase that hydrolyzes the amide bond between N-acetylmuramic acid and L-alanine in cell-wall glycopeptides. Is able to lyse whole mycobacteria, release peptidoglycan from the cell wall of M.luteus and M.smegmatis, and cleave N-acetylmuramoyl-L-alanyl-D-isoglutamine, releasing free N-acetylmuramic acid and dipeptide. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
M Cell wall / membrane / envelope biogenesis
|
|---|---|
| Preferred name | cwlM |
| eggNOG description | N-acetylmuramoyl-L-alanine amidase |
| Orthologous group | COG0860 |
| EC number |
EC 3.5.1.28
|
| KEGG orthology |
K01448
|
| KEGG pathways |
map01503
|
| KEGG modules |
M00727
|
| Gene Ontology (7) |
GO:0005575, GO:0005623, GO:0030288, GO:0030313, GO:0031975, GO:0042597, GO:0044464
|
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 | 0.26 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 8 synonymous, 6 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 |
|---|---|---|---|---|
PG_binding_1 | PF01471.24 | 9.4e-18 | 105–160 | Putative peptidoglycan binding domain |
Amidase_3 | PF01520.24 | 3.1e-33 | 193–370 | N-acetylmuramoyl-L-alanine amidase |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: trxC (thioredoxin TrxC), high confidence from genomic context alone (score 754 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3717 hyp |
hypothetical protein | 989 | 905 | database:900 textmining:896 |
Rv3914 trxC |
thioredoxin TrxC | 794 | 754 ctx | neighborhood:719 |
Rv0948c |
chorismate mutase | 719 | 720 ctx | cooccurence:712 |
Rv1315 murA |
UDP-N-acetylglucosamine 1-carboxyvinyltransferase | 908 | 719 ctx | cooccurence:701 textmining:686 |
Rv2179c |
3'-5' exoribonuclease | 670 | 670 ctx | cooccurence:670 |
Rv3913 trxB2 |
thioredoxin reductase | 708 | 653 ctx | neighborhood:632 |
Rv1209 hyp |
hypothetical protein | 615 | 591 ctx | cooccurence:576 |
Rv3311 hyp |
hypothetical protein | 550 | 551 ctx | cooccurence:548 |
Rv3908 mutT4 |
mutator protein MutT | 534 | 534 ctx | neighborhood:449 |
Rv2744c 35kd_ag hyp |
hypothetical protein | 520 | 521 ctx | cooccurence:516 |
Rv3911 sigM |
ECF RNA polymerase sigma factor SigM | 522 | 500 ctx | neighborhood:482 |
Rv1337 |
integral membrane protein | 648 | 498 | experimental:465 |
Rv3433c nnr |
bifunctional ADP-dependent (S)-NAD(P)H-hydrate dehydratase/NAD(P)H-hydrate epimerase | 585 | 496 ctx | neighborhood:427 |
Rv1343c lprD |
lipoprotein LprD | 495 | 496 ctx | cooccurence:494 |
Rv3912 rsmA |
anti-sigma-M factor RsmA | 514 | 495 ctx | neighborhood:489 |
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): peptidoglycan hydrolase
- Pfam (hmmscan --cut_ga): PG_binding_1 PF01471.24 (E=9e-18), Amidase_3 PF01520.24 (E=3e-33)
- (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 YP_178027.1)
- Domains: Pfam-A via hmmscan --cut_ga — PG_binding_1 (PF01471.24), Amidase_3 (PF01520.24)
- 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
COG0860 - Curated reference: UniProt L7N653 (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 —
72 functional partner(s); context anchor
trxC - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv3915| MPSPRREDGDALRCGDRSAAVTEIRAALTALGMLDHQEEDLTTGRNVALELFDAQLDQAVRAFQQHRGLLVDGIVGEATYRALKEASYRLGARTLYHQFGAPLYGDDVATLQARLQDLGFYTGLVDGHFGLQTHNALMSYQREYGLAADGICGPETLRSLYFLSSRVSGGSPHAIREEELVRSSGPKLSGKRIIIDPGRGGVDHGLIAQGPAGPISEADLLWDLASRLEGRMAAIGMETHLSRPTNRSPSDAERAATANAVGADLMISLRCETQTSLAANGVASFHFGNSHGSVSTIGRNLADFIQREVVARTGLRDCRVHGRTWDLLRLTRMPTVQVDIGYITNPHDRGMLVSTQTRDAIAEGILAAVKRLYLLGKNDRPTGTFTFAELLAHELSVERAGRLGGS