amiB1 Resolved · high auto-curated
H37Rv Rv3306c · MTBC0 - ·
394 aa · 3692805–3693989 (-) ·
RefSeq YP_177956.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | amidase AmiB |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | Amidase AmiB. Pfam: Peptidase_M20 (PF01546.34), M20_dimer (PF07687.20). |
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 |
L7N690
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Peptidase M20 domain-containing protein 2 |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| Preferred name | amiB1 |
| eggNOG description | overlaps another CDS with the same product name |
| Orthologous group | COG1473 |
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 | 0.821 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 4 synonymous, 9 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 |
|---|---|---|---|---|
Peptidase_M20 | PF01546.34 | 2.3e-11 | 87–344 | Peptidase family M20/M25/M40 |
M20_dimer | PF07687.20 | 4.5e-09 | 170–260 | Peptidase dimerisation domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: amiA1 (N-acyl-L-amino acid amidohydrolase AmiA), high confidence from genomic context alone (score 938 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3305c amiA1 |
N-acyl-L-amino acid amidohydrolase AmiA | 977 | 938 ctx | neighborhood:882 cooccurence:476 textmining:653 |
Rv3307 deoD |
purine nucleoside phosphorylase | 791 | 789 ctx | neighborhood:786 |
Rv3308 pmmB |
phosphomannomutase PmmB | 788 | 788 ctx | neighborhood:786 |
Rv1201c dapD |
2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase | 492 | 456 | coexpression:425 |
Rv0074 hyp |
hypothetical protein | 438 | 416 | |
Rv3304 hyp |
hypothetical protein | 572 | 161 | textmining:511 |
Rv3253c |
cationic amino acid transport integral membrane protein | 536 | 85 | textmining:514 |
Rv1477 ripA |
peptidoglycan endopeptidase RipA | 465 | 77 | textmining:445 |
Rv3375 amiD |
amidase | 813 | 66 | textmining:809 |
Rv2888c amiC |
amidase AmiC | 873 | 65 | textmining:870 |
Rv1478 ripB |
peptidoglycan endopeptidase RipB | 445 | 64 | textmining:432 |
Rv3915 cwlM |
peptidoglycan hydrolase | 697 | 63 | textmining:690 |
Rv3594 hyp |
hypothetical protein | 571 | 55 | textmining:565 |
Rv3717 hyp |
hypothetical protein | 669 | 47 | textmining:668 |
Rv3811 hyp |
hypothetical protein | 532 | 47 | textmining:530 |
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): amidase AmiB
- Pfam (hmmscan --cut_ga): Peptidase_M20 PF01546.34 (E=2e-11), M20_dimer PF07687.20 (E=4e-09)
- (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_177956.1)
- Domains: Pfam-A via hmmscan --cut_ga — Peptidase_M20 (PF01546.34), M20_dimer (PF07687.20)
- 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
COG1473 - Curated reference: UniProt L7N690 (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 —
19 functional partner(s); context anchor
amiA1 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv3306c|amiB1 MPAASASDRVEELVRRRGGELVELSHAIHAEPELAFAEHRSCAKAQALVAERGFEITTAAGGLDTAFRADYGSGPLVVGVCAEYDALPGIGHACGHNIIAASAVGTALALAEVADDLGLTVALLGTPAEESGGGKALMLQAGTFDDVAVAVMVHPGPTDIAGARSLALSEVTVRYRGKESHAAVAPHLGVNAADAVTVAQVAIGVLRQQLAPGQMVHGIVTDGGQAVNVIPGQARLQYAMRAVESDSLRELQTRMFACFAAGALAAGCEYEIDEAAPAYAELKPDPWLADVCREEMQRLGREPLLPALEAELPLGSTDMGNVTQVLPGIHPVIGLDAGAATVHQRAFTVASAGASADRAVVDGAIMLARTVVRLAQTPDERDRVLAAQQRRAAR