hisC2 Resolved · high auto-curated
H37Rv Rv3772 · MTBC0 mtbc0_003999 ·
353 aa · 4241255–4242316 (+) ·
RefSeq NP_218289.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | histidinol-phosphate aminotransferase |
|---|---|
| MTBC0 PGAP re-annotation | histidinol-phosphate transaminase |
| Revised (this work) | Histidinol-phosphate transaminase. Pfam: 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 |
P9WML5
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Aromatic amino acid aminotransferase |
| EC (curated) |
EC 2.6.1.57
|
| Curated function | Aminotransferase that catalyzes the conversion of aromatic amino acids and 2-oxoglutarate into corresponding aromatic oxo acids and L-glutamate. Shows excellent activity with phenylalanine, and lower activity with tyrosine and tryptophan. Has no significant activity with histidinol phosphate. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
E Amino acid transport and metabolism
|
|---|---|
| Preferred name | pat |
| eggNOG description | May catalyze the transamination reaction in phenylalanine biosynthesis |
| Orthologous group | COG0079 |
| EC number |
EC 2.6.1.9
|
| KEGG orthology |
K00817
|
| KEGG pathways |
map00340, map00350, map00360, map00400, map00401, map00960, map01100, map01110, map01130, map01230
|
| KEGG modules |
M00026
|
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 | 0.218 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 5 synonymous, 3 missense, 0 nonsense, 1 frameshift |
| Disruption | 1 distinct premature-stop/frameshift site(s); most common in 0.14% of strains (206) · 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 |
|---|---|---|---|---|
Aminotran_1_2 | PF00155.28 | 1.1e-53 | 25–338 | Aminotransferase class I and II |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: hisB (imidazole glycerol-phosphate dehydratase), high confidence from genomic context alone (score 997 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1601 hisB |
imidazole glycerol-phosphate dehydratase | 997 | 997 ctx | fusion:860 coexpression:692 database:900 |
Rv3754 tyrA |
prephenate dehydrogenase TyrA | 969 | 966 | coexpression:654 database:900 |
Rv1599 hisD |
histidinol dehydrogenase | 950 | 931 ctx | fusion:666 coexpression:692 |
Rv1600 hisC1 |
histidinol-phosphate aminotransferase | 916 | 917 | database:900 |
Rv2231c cobC |
aminotransferase | 910 | 910 | database:900 |
Rv3838c pheA |
prephenate dehydratase | 916 | 907 | database:900 |
Rv3137 hisN |
histidinol-phosphatase | 908 | 903 | database:900 |
Rv1908c katG |
catalase-peroxidase | 905 | 900 | database:900 |
Rv1605 hisF |
imidazole glycerol phosphate synthase subunit HisF | 828 | 810 | coexpression:694 |
Rv1602 hisH |
imidazole glycerol phosphate synthase subunit HisH | 827 | 809 | coexpression:693 |
Rv3215 entC |
isochorismate synthase | 812 | 805 | database:800 |
Rv2949c |
chorismate pyruvate-lyase | 800 | 800 | database:800 |
Rv1606 hisI |
phosphoribosyl-AMP cyclohydrolase | 805 | 785 | coexpression:694 |
Rv1603 hisA |
1-(5-phosphoribosyl)-5-((5-phosphoribosylamino)methylideneamino)imidazole-4-carboxamide isomerase | 791 | 769 | coexpression:692 |
Rv2121c hisG |
ATP phosphoribosyltransferase | 785 | 744 | coexpression:697 |
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: histidinol-phosphate aminotransferase
- MTBC0 PGAP product: histidinol-phosphate transaminase
- Pfam (hmmscan --cut_ga): Aminotran_1_2 PF00155.28 (E=1e-53)
- (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_218289.1)
- Domains: Pfam-A via hmmscan --cut_ga — 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
COG0079 - Curated reference: UniProt P9WML5 (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 —
53 functional partner(s); context anchor
hisB - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003999|Rv3772|hisC2 MTARLRPELAGLPVYVPGKTVPGAIKLASNETVFGPLPSVRAAIDRATDTVNRYPDNGCVQLKAALARHLGPDFAPEHVAVGCGSVSLCQQLVQVTASVGDEVVFGWRSFELYPPQVRVAGAIPIQVPLTDHTFDLYAMLAAVTDRTRLIFVCNPNNPTSTVVGPDALARFVEAVPAHILIAIDEAYVEYIRDGMRPDSLGLVRAHNNVVVLRTFSKAYGLAGLRIGYAIGHPDVITALDKVYVPFTVSSIGQAAAIASLDAADELLARTDTVVAERARVSAELRAAGFTLPPSQANFVWLPLGSRTQDFVEQAADARIVVRPYGTDGVRVTVAAPEENDAFLRFARRWRSDQ