amiD Resolved · high auto-curated
H37Rv Rv3375 · MTBC0 mtbc0_003590 ·
475 aa · 3815338–3816765 (+) ·
RefSeq NP_217892.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | amidase |
|---|---|
| MTBC0 PGAP re-annotation | amidase |
| Revised (this work) | Amidase. Pfam: Amidase (PF01425.27). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WQ93
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Putative amidase AmiD |
| EC (curated) |
EC 3.5.1.4
|
UniProt still lists this protein as Putative amidase AmiD; the revised annotation above is ahead of the current UniProt record.
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
J Translation, ribosomal structure and biogenesis
|
|---|---|
| Preferred name | amiD |
| eggNOG description | COG0154 Asp-tRNAAsn Glu-tRNAGln amidotransferase A subunit and related amidases |
| Orthologous group | COG0154 |
| EC number |
EC 3.5.1.4, EC 6.3.5.6, EC 6.3.5.7
|
| KEGG orthology |
K01426, K02433
|
| KEGG pathways |
map00330, map00360, map00380, map00627, map00643, map00970, map01100, map01120
|
| Gene Ontology (8) |
GO:0005575, GO:0005622, GO:0005623, GO:0005737, GO:0005829, GO:0044424, GO:0044444, 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 | 0.351 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 6 synonymous, 6 missense, 0 nonsense, 1 frameshift |
| Disruption | 1 distinct premature-stop/frameshift site(s); most common in 0.20% of strains (285) · clonal |
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 | PF01425.27 | 3.3e-121 | 38–455 | Amidase |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: gatB (aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit B), high confidence from genomic context alone (score 969 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3009c gatB |
aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit B | 980 | 969 ctx | cooccurence:774 coexpression:646 experimental:629 textmining:411 |
Rv2922A acyP |
acylphosphatase | 903 | 904 | database:900 |
Rv3012c gatC |
glutamyl-tRNA(GLN) amidotransferase subunit C | 913 | 903 | coexpression:649 experimental:629 |
Rv3551 |
CoA-transferase subunit alpha | 901 | 901 | database:900 |
Rv3374 echA18.1 |
Probable enoyl-CoA hydratase EchA18.1 (Enoyl hydrase) (Unsaturated acyl-CoA hydratase) (Crotonase); Rv3374, (MTV004.32), len: 82 aa. Probabl | 931 | 808 ctx | neighborhood:799 textmining:654 |
Rv3373 echA18 |
enoyl-CoA hydratase | 902 | 805 ctx | neighborhood:799 textmining:519 |
Rv3293 pcd |
piperideine-6-carboxylic acid dehydrogenase | 676 | 664 | database:650 |
Rv0768 aldA |
aldehyde dehydrogenase AldA | 673 | 661 | database:650 |
Rv0223c |
aldehyde dehydrogenase | 672 | 660 | database:650 |
Rv0147 |
aldehyde dehydrogenase | 671 | 659 | database:650 |
Rv2572c aspS |
aspartate--tRNA ligase | 727 | 633 | experimental:405 |
Rv2992c gltS |
glutamate--tRNA ligase | 697 | 604 | experimental:549 |
Rv3376 |
phosphatase | 823 | 541 ctx | neighborhood:532 textmining:630 |
Rv2029c pfkB |
6-phosphofructokinase PfkB | 516 | 515 | coexpression:513 |
Rv1379 pyrR |
bifunctional pyrimidine operon regulatory protein/uracil phosphoribosyltransferase | 522 | 510 | coexpression:430 |
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: amidase
- MTBC0 PGAP product: amidase
- Pfam (hmmscan --cut_ga): Amidase PF01425.27 (E=3e-121)
- (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_217892.1)
- Domains: Pfam-A via hmmscan --cut_ga — Amidase (PF01425.27)
- 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
COG0154 - Curated reference: UniProt P9WQ93 (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 —
58 functional partner(s); context anchor
gatB - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003590|Rv3375|amiD MTDADSAVPPRLDEDAISKLELTEVADLIRTRQLTSAEVTESTLRRIERLDPQLKSYAFVMPETALAAARAADADIARGHYEGVLHGVPIGVKDLCYTVDAPTAAGTTIFRDFRPAYDATVVARLRAAGAVIIGKLAMTEGAYLGYHPSLPTPVNPWDPTAWAGVSSSGCGVATAAGLCFGSIGSDTGGSIRFPTSMCGVTGIKPTWGRVSRHGVVELAASYDHVGPITRSAHDAAVLLSVIAGSDIHDPSCSAEPVPDYAADLALTRIPRVGVDWSQTTSFDEDTTAMLADVVKTLDDIGWPVIDVKLPALAPMVAAFGKMRAVETAIAHADTYPARADEYGPIMRAMIDAGHRLAAVEYQTLTERRLEFTRSLRRVFHDVDILLMPSAGIASPTLETMRGLGQDPELTARLAMPTAPFNVSGNPAICLPAGTTARGTPLGVQFIGREFDEHLLVRAGHAFQQVTGYHRRRPPV