aroG Resolved · high auto-curated
H37Rv Rv2178c · MTBC0 mtbc0_002313 ·
462 aa · 2466339–2467727 (-) ·
RefSeq NP_216694.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | phospho-2-dehydro-3-deoxyheptonate aldolase AroG |
|---|---|
| MTBC0 PGAP re-annotation | 3-deoxy-7-phosphoheptulonate synthase class II |
| Revised (this work) | 3-deoxy-7-phosphoheptulonate synthase class II. Pfam: DAHP_synth_2 (PF01474.23). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
O53512
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Phospho-2-dehydro-3-deoxyheptonate aldolase AroG |
| EC (curated) |
EC 2.5.1.54
|
| Curated function | Catalyzes an aldol-like condensation reaction between phosphoenolpyruvate (PEP) and D-erythrose 4-phosphate (E4P) to generate 3-deoxy-D-arabino-heptulosonate 7-phosphate (DAH7P) and inorganic phosphate. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
E Amino acid transport and metabolism
|
|---|---|
| Preferred name | aroG |
| eggNOG description | Belongs to the class-II DAHP synthase family |
| Orthologous group | COG3200 |
| EC number |
EC 2.5.1.54
|
| KEGG orthology |
K01626
|
| KEGG pathways |
map00400, map01100, map01110, map01130, map01230, map02024
|
| KEGG modules |
M00022
|
| Gene Ontology (52) |
GO:0003674, GO:0003824, GO:0003849, GO:0005488, GO:0005575, GO:0005618, GO:0005622, GO:0005623, GO:0005737, GO:0005829, GO:0005886, GO:0006082 +40 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 | 0.166 · strong purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 4 synonymous, 2 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 |
|---|---|---|---|---|
DAHP_synth_2 | PF01474.23 | 3.0e-190 | 30–457 | Class-II DAHP synthetase family |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv2179c (3'-5' exoribonuclease), high confidence from genomic context alone (score 779 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0948c |
chorismate mutase | 999 | 999 | experimental:999 textmining:823 |
Rv2538c aroB |
3-dehydroquinate synthase | 992 | 916 | database:900 textmining:911 |
Rv2179c |
3'-5' exoribonuclease | 789 | 779 ctx | neighborhood:779 |
Rv2180c |
integral membrane protein | 778 | 778 ctx | neighborhood:778 |
Rv2181 |
alpha-(1-2)-phosphatidylinositol mannoside mannosyltransferase | 715 | 715 ctx | neighborhood:714 |
Rv1885c |
chorismate mutase | 834 | 515 | experimental:500 textmining:674 |
Rv2177c |
transposase | 411 | 411 ctx | neighborhood:405 |
Rv0013 trpG |
anthranilate synthase component II | 410 | 324 | |
Rv2552c aroE |
shikimate 5-dehydrogenase | 629 | 278 | textmining:508 |
Rv2175c |
DNA-binding protein | 540 | 153 | textmining:479 |
Rv2540c aroF |
chorismate synthase | 837 | 99 | textmining:827 |
Rv3227 aroA |
3-phosphoshikimate 1-carboxyvinyltransferase | 584 | 96 | textmining:559 |
Rv2539c aroK |
shikimate kinase | 400 | 78 | |
Rv2537c aroD |
3-dehydroquinate dehydratase | 476 | 77 | textmining:456 |
Rv1224 tatB |
Sec-independent protein translocase protein TatB | 468 | 50 | textmining:464 |
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: phospho-2-dehydro-3-deoxyheptonate aldolase AroG
- MTBC0 PGAP product: 3-deoxy-7-phosphoheptulonate synthase class II
- Pfam (hmmscan --cut_ga): DAHP_synth_2 PF01474.23 (E=3e-190)
- (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_216694.1)
- Domains: Pfam-A via hmmscan --cut_ga — DAHP_synth_2 (PF01474.23)
- 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
COG3200 - Curated reference: UniProt O53512 (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 —
26 functional partner(s); context anchor
Rv2179c - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002313|Rv2178c|aroG MNWTVDIPIDQLPSLPPLPTDLRTRLDAALAKPAAQQPTWPADQALAMRTVLESVPPVTVPSEIVRLQEQLAQVAKGEAFLLQGGDCAETFMDNTEPHIRGNVRALLQMAVVLTYGASMPVVKVARIAGQYAKPRSADIDALGLRSYRGDMINGFAPDAAAREHDPSRLVRAYANASAAMNLVRALTSSGLASLHLVHDWNREFVRTSPAGARYEALATEIDRGLRFMSACGVADRNLQTAEIYASHEALVLDYERAMLRLSDGEDGEPQLFDLSAHTVWIGERTRQIDGAHIAFAQVIANPVGVKLGPNMTPELAVEYVERLDPHNKPGRLTLVSRMGNHKVRDLLPPIVEKVQATGHQVIWQCDPMHGNTHESSTGFKTRHFDRIVDEVQGFFEVHRALGTHPGGIHVEITGENVTECLGGAQDISETDLAGRYETACDPRLNTQQSLELAFLVAEMLRD