Rv3717 Family assigned · medium auto-curated
H37Rv Rv3717 · MTBC0 - ·
241 aa · 4161048–4161773 (+) ·
RefSeq NP_218234.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | Contains Amidase_3 (PF01520.24) domain(s); putative function inferred from the domain architecture. |
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 |
I6Y4D2
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | N-acetylmuramoyl-L-alanine amidase Rv3717 |
| 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 hydrolyze the cell walls of several bacterial species (i.e. Paenibacillus sp., B.avium, E.coli DH5alpha, E.aerogenes, L.acidophilus, B.thuringiensis, B.pumilus, B.subtilis and E.coli W3110), thereby showing that it is a cell-wall hydrolase with broad-spectrum activity. May have a role in peptidoglycan fragment recycling. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
M Cell wall / membrane / envelope biogenesis
|
|---|---|
| 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 (14) |
GO:0003674, GO:0003824, GO:0005575, GO:0005623, GO:0008745, GO:0016787, GO:0016810, GO:0016811, GO:0030288, GO:0030313, GO:0031975, GO:0042597 +2 more
|
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 | 0.0 · strong purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 5 synonymous, 0 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 |
|---|---|---|---|---|
Amidase_3 | PF01520.24 | 7.2e-29 | 29–230 | N-acetylmuramoyl-L-alanine amidase |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: recR (recombination protein RecR), high confidence from genomic context alone (score 774 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) |
|---|---|---|---|---|
Rv3915 cwlM |
peptidoglycan hydrolase | 989 | 905 | database:900 textmining:896 |
Rv0063 |
oxidoreductase | 837 | 837 | coexpression:834 |
Rv3209 hyp |
hypothetical protein | 804 | 804 | coexpression:804 |
Rv3096 hyp |
hypothetical protein | 797 | 797 | coexpression:797 |
Rv3716c hyp |
hypothetical protein | 776 | 776 ctx | neighborhood:775 |
Rv3715c recR |
recombination protein RecR | 873 | 774 ctx | neighborhood:772 textmining:465 |
Rv2154c ftsW |
lipid II flippase FtsW | 771 | 756 | coexpression:748 |
Rv3414c sigD |
ECF RNA polymerase sigma factor SigD | 742 | 742 | coexpression:734 |
Rv2894c xerC |
tyrosine recombinase XerC | 739 | 739 | coexpression:731 |
Rv1157c hyp |
hypothetical protein | 629 | 616 | coexpression:615 |
Rv0110 |
integral membrane protein | 499 | 500 | experimental:465 |
Rv1337 |
integral membrane protein | 497 | 497 | experimental:465 |
Rv0826 hyp |
hypothetical protein | 481 | 481 ctx | cooccurence:481 |
Rv3714c hyp |
hypothetical protein | 431 | 432 ctx | neighborhood:425 |
Rv1645c hyp |
hypothetical protein | 420 | 420 ctx | cooccurence:417 |
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
- Pfam (hmmscan --cut_ga): Amidase_3 PF01520.24 (E=7e-29)
- (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_218234.1)
- Domains: Pfam-A via hmmscan --cut_ga — 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 I6Y4D2 (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 —
38 functional partner(s); context anchor
recR - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv3717| MIVGVLVAAATPIISSASATPANIAGMVVFIDPGHNGANDASIGRQVPTGRGGTKNCQASGTSTNSGYPEHTFTWETGLRLRAALNALGVRTALSRGNDNALGPCVDERANMANALRPNAIVSLHADGGPASGRGFHVNYSAPPLNAIQAGPSVQFARIMRDQLQASGIPKANYIGQDGLYGRSDLAGLNLAQYPSILVELGNMKNPADSALMESAEGRQKYANALVRGVAGFLATQGQAR