Rv3594 Resolved · high auto-curated
H37Rv Rv3594 · MTBC0 mtbc0_003813 ·
275 aa · 4059534–4060361 (+) ·
RefSeq NP_218111.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | N-acetylmuramoyl-L-alanine amidase |
| Revised (this work) | N-acetylmuramoyl-L-alanine amidase. Pfam: Amidase_2 (PF01510.31), Rv3766_C (PF27131.1). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
I6Y3Z2
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | N-acetylmuramoyl-L-alanine amidase domain-containing protein |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
M Cell wall / membrane / envelope biogenesisV Defense mechanisms
|
|---|---|
| eggNOG description | N-acetylmuramoyl-L-alanine amidase |
| Orthologous group | COG3023 |
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 | 1.802 · diversifying/relaxed |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 2 synonymous, 11 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_2 | PF01510.31 | 2.0e-17 | 37–173 | N-acetylmuramoyl-L-alanine amidase |
Rv3766_C | PF27131.1 | 2.2e-10 | 218–256 | Rv3766 C-terminal domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv1230c (membrane protein), medium confidence from genomic context alone (score 685 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) |
|---|---|---|---|---|
Rv1230c |
membrane protein | 704 | 685 ctx | cooccurence:683 |
Rv1443c hyp |
hypothetical protein | 675 | 675 ctx | cooccurence:675 |
Rv3879c espK |
ESX-1 secretion-associated protein EspK | 673 | 672 ctx | cooccurence:669 |
Rv3877 eccD1 |
ESX-1 secretion system protein EccD1 | 629 | 630 ctx | cooccurence:628 |
Rv1288 hyp |
hypothetical protein | 669 | 627 ctx | cooccurence:622 |
Rv1921c lppF |
lipoprotein LppF | 623 | 624 ctx | cooccurence:617 |
Rv3882c eccE1 |
ESX-1 secretion system protein EccE1 | 623 | 623 ctx | cooccurence:622 |
Rv2164c hyp |
hypothetical protein | 621 | 621 ctx | cooccurence:616 |
Rv1651c PE_PGRS30 |
PE-PGRS family protein PE_PGRS30 | 597 | 595 ctx | cooccurence:592 |
Rv0341 iniB |
isoniazid inducible protein IniB | 565 | 566 ctx | cooccurence:560 |
Rv3593 lpqF |
lipoprotein LpqF | 578 | 563 ctx | neighborhood:495 |
Rv0613c hyp |
hypothetical protein | 554 | 554 ctx | cooccurence:553 |
Rv3365c hyp |
hypothetical protein | 537 | 535 ctx | cooccurence:529 |
Rv2735c hyp |
hypothetical protein | 526 | 526 ctx | cooccurence:525 |
Rv3472 hyp |
hypothetical protein | 524 | 525 ctx | cooccurence:511 |
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: N-acetylmuramoyl-L-alanine amidase
- Pfam (hmmscan --cut_ga): Amidase_2 PF01510.31 (E=2e-17), Rv3766_C PF27131.1 (E=2e-10)
- (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_218111.1)
- Domains: Pfam-A via hmmscan --cut_ga — Amidase_2 (PF01510.31), Rv3766_C (PF27131.1)
- 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
COG3023 - Curated reference: UniProt I6Y3Z2 (TrEMBL, unreviewed; 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 —
63 functional partner(s); context anchor
Rv1230c - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003813|Rv3594| MGWIGDPIWLEEVLRPALGERLRVLDGWRERGHGDFRDIRGVMWHHTGNSRETAKSIARGRPDLPGPLANLHIAHSGVVTIVAVGVCWHAGRGSYPWLPTDNANWHMIGVECAWPTIRRDGSYDAGERWPDAQIVSMRDVAAALTLKLGYGPERNIGHKEYAGAAQGKWDPGNLSMDWFRAEVAKDTRGEFDHPLTPPPAVIARPPILPKPRNPRDDRILLEEVWDQLRGIEGRGWPVLGDKTIVDYLAELGNKVDALAAKLDAREGLDRPSDTR