amiA2 Resolved · high auto-curated
H37Rv Rv2363 · MTBC0 mtbc0_002515 ·
484 aa · 2668513–2669967 (+) ·
RefSeq NP_216879.1
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 |
P9WQ99
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Putative amidase AmiA2 |
| EC (curated) |
EC 3.5.1.4
|
UniProt still lists this protein as Putative amidase AmiA2; 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 | amiA2 |
| eggNOG description | Belongs to the amidase family |
| Orthologous group | COG0154 |
| EC number |
EC 3.5.1.4
|
| KEGG orthology |
K01426
|
| KEGG pathways |
map00330, map00360, map00380, map00627, map00643, map01120
|
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 | 0.184 · strong purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 2 synonymous, 1 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 | PF01425.27 | 3.0e-124 | 39–460 | 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 968 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3009c gatB |
aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit B | 970 | 968 ctx | cooccurence:772 coexpression:646 experimental:629 |
Rv2922A acyP |
acylphosphatase | 903 | 904 | database:900 |
Rv3551 |
CoA-transferase subunit alpha | 900 | 900 | database:900 |
Rv3012c gatC |
glutamyl-tRNA(GLN) amidotransferase subunit C | 905 | 899 | coexpression:656 experimental:629 |
Rv2361c uppS |
decaprenyl diphosphate synthase | 794 | 794 ctx | neighborhood:786 |
Rv2362c recO |
DNA repair protein RecO | 810 | 787 ctx | neighborhood:786 |
Rv2360c hyp |
hypothetical protein | 786 | 786 ctx | neighborhood:786 |
Rv3293 pcd |
piperideine-6-carboxylic acid dehydrogenase | 673 | 661 | database:650 |
Rv0768 aldA |
aldehyde dehydrogenase AldA | 672 | 660 | database:650 |
Rv0147 |
aldehyde dehydrogenase | 671 | 659 | database:650 |
Rv0223c |
aldehyde dehydrogenase | 671 | 659 | database:650 |
Rv2572c aspS |
aspartate--tRNA ligase | 664 | 643 | coexpression:405 experimental:405 |
Rv2992c gltS |
glutamate--tRNA ligase | 626 | 602 | experimental:549 |
Rv2029c pfkB |
6-phosphofructokinase PfkB | 516 | 515 | coexpression:513 |
Rv1307 atpH |
ATP synthase subunit b/delta | 504 | 505 | coexpression:488 |
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-124)
- (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_216879.1)
- 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 P9WQ99 (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 —
41 functional partner(s); context anchor
gatB - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002515|Rv2363|amiA2 MVGASGSDAGAISGSGNQRLPTLTDLLYQLATRAVTSEELVRRSLRAIDVSQPTLNAFRVVLTESALADAAAADKRRAAGDTAPLLGIPIAVKDDVDVAGVPTAFGTQGYVAPATDDCEVVRRLKAAGAVIVGKTNTCELGQWPFTSGPGFGHTRNPWSRRHTPGGSSGGSAAAVAAGLVTAAIGSDGAGSIRIPAAWTHLVGIKPQRGRISTWPLPEAFNGVTVNGVLARTVEDAALVLDAASGNVEGDRHQPPPVTVSDFVGIAPGPLKIALSTHFPYTGFRAKLHPEILAATQRVGDQLELLGHTVVKGNPDYGLRLSWNFLARSTAGLWEWAERLGDEVTLDRRTVSNLRMGHVLSQAILRSARRHEAADQRRVGSIFDIVDVVLAPTTAQPPPMARAFDRLGSFGTDRAIIAACPSTWPWNLLGWPSINVPAGFTSDGLPIGVQLMGPANSEGMLISLAAELEAVSGWATKQPQVWWTS