argD Resolved · high auto-curated
H37Rv Rv1655 · MTBC0 mtbc0_001764 ·
400 aa · 1880765–1881967 (+) ·
RefSeq NP_216171.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | acetylornithine aminotransferase |
|---|---|
| MTBC0 PGAP re-annotation | acetylornithine transaminase |
| Revised (this work) | Acetylornithine transaminase. Pfam: Aminotran_3 (PF00202.28), Aminotran_1_2 (PF00155.28). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WPZ7
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Acetylornithine aminotransferase |
| EC (curated) |
EC 2.6.1.11
|
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
E Amino acid transport and metabolism
|
|---|---|
| Preferred name | argD |
| eggNOG description | acetylornithine aminotransferase |
| Orthologous group | COG4992 |
| EC number |
EC 2.6.1.11, EC 2.6.1.17
|
| KEGG orthology |
K00821
|
| KEGG pathways |
map00220, map00300, map01100, map01110, map01120, map01130, map01210, map01230
|
| KEGG modules |
M00016, M00028, M00845
|
| Gene Ontology (17) |
GO:0003674, GO:0005488, GO:0005515, GO:0008144, GO:0008150, GO:0019842, GO:0030170, GO:0036094, GO:0040007, GO:0042802, GO:0043167, GO:0043168 +5 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 | 0.512 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 3 synonymous, 4 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 |
|---|---|---|---|---|
Aminotran_3 | PF00202.28 | 3.1e-107 | 21–392 | Aminotransferase class-III |
Aminotran_1_2 | PF00155.28 | 4.5e-04 | 62–296 | Aminotransferase class I and II |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: argJ (bifunctional glutamate N-acetyltransferase/amino-acid acetyltransferase), high confidence from genomic context alone (score 1000 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1653 argJ |
bifunctional glutamate N-acetyltransferase/amino-acid acetyltransferase | 999 | 1000 ctx | neighborhood:881 cooccurence:571 coexpression:948 database:900 textmining:949 |
Rv1652 argC |
N-acetyl-gamma-glutamyl-phoshate reductase | 999 | 1000 ctx | neighborhood:881 cooccurence:669 coexpression:937 database:900 textmining:925 |
Rv1654 argB |
acetylglutamate kinase | 999 | 998 ctx | neighborhood:881 cooccurence:659 coexpression:954 textmining:950 |
Rv1656 argF |
ornithine carbamoyltransferase | 999 | 997 ctx | neighborhood:882 coexpression:948 textmining:868 |
Rv1658 argG |
argininosuccinate synthase | 997 | 995 ctx | neighborhood:879 coexpression:932 textmining:462 |
Rv1657 argR |
arginine repressor | 998 | 988 ctx | neighborhood:882 coexpression:905 textmining:915 |
Rv1659 argH |
argininosuccinate lyase | 995 | 988 ctx | neighborhood:783 coexpression:915 textmining:661 |
Rv1202 dapE |
succinyl-diaminopimelate desuccinylase DapE | 911 | 906 | database:900 |
Rv0858c dapC |
N-succinyldiaminopimelate aminotransferase DapC | 909 | 905 | database:900 |
Rv1201c dapD |
2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase | 911 | 904 | database:900 |
Rv1650 pheT |
phenylalanine--tRNA ligase subunit beta | 720 | 623 ctx | neighborhood:532 |
Rv1661 pks7 |
polyketide synthase | 608 | 570 ctx | neighborhood:509 |
Rv1647 |
adenylate cyclase | 541 | 542 ctx | neighborhood:539 |
Rv1651c PE_PGRS30 |
PE-PGRS family protein PE_PGRS30 | 506 | 506 ctx | neighborhood:501 |
Rv1699 pyrG |
CTP synthase | 465 | 466 |
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: acetylornithine aminotransferase
- MTBC0 PGAP product: acetylornithine transaminase
- Pfam (hmmscan --cut_ga): Aminotran_3 PF00202.28 (E=3e-107), Aminotran_1_2 PF00155.28 (E=4e-04)
- (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_216171.1)
- Domains: Pfam-A via hmmscan --cut_ga — Aminotran_3 (PF00202.28), Aminotran_1_2 (PF00155.28)
- 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
COG4992 - Curated reference: UniProt P9WPZ7 (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 —
34 functional partner(s); context anchor
argJ - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001764|Rv1655|argD MTGASTTTATMRQRWQAVMMNNYGTPPIALASGDGAVVTDVDGRTYIDLLGGIAVNVLGHRHPAVIEAVTRQMSTLGHTSNLYATEPGIALAEELVALLGADQRTRVFFCNSGAEANEAAFKLSRLTGRTKLVAAHDAFHGRTMGSLALTGQPAKQTPFAPLPGDVTHVGYGDVDALAAAVDDHTAAVFLEPIMGESGVVVPPAGYLAAARDITARRGALLVLDEVQTGMGRTGAFFAHQHDGITPDVVTLAKGLGGGLPIGACLAVGPAAELLTPGLHGSTFGGNPVCAAAALAVLRVLASDGLVRRAEVLGKSLRHGIEALGHPLIDHVRGRGLLLGIALTAPHAKDAEATARDAGYLVNAAAPDVIRLAPPLIIAEAQLDGFVAALPAILDRAVGAP