aroK Resolved · high auto-curated
H37Rv Rv2539c · MTBC0 mtbc0_002705 ·
176 aa · 2885563–2886093 (-) ·
RefSeq NP_217055.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | shikimate kinase |
|---|---|
| MTBC0 PGAP re-annotation | shikimate kinase AroK |
| Revised (this work) | Shikimate kinase AroK. Pfam: AAA_33 (PF13671.13), AAA_18 (PF13238.13), SKI (PF01202.29). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WPY3
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Shikimate kinase |
| EC (curated) |
EC 2.7.1.71
|
| Curated function | Catalyzes the specific phosphorylation of the 3-hydroxyl group of shikimic acid using ATP as a cosubstrate. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
F Nucleotide transport and metabolism
|
|---|---|
| Preferred name | aroK |
| eggNOG description | Catalyzes the specific phosphorylation of the 3-hydroxyl group of shikimic acid using ATP as a cosubstrate |
| Orthologous group | COG0703 |
| EC number |
EC 2.7.1.71
|
| KEGG orthology |
K00891
|
| KEGG pathways |
map00400, map01100, map01110, map01130, map01230
|
| KEGG modules |
M00022
|
| Gene Ontology (73) |
GO:0000166, GO:0000287, GO:0003674, GO:0003824, GO:0004765, GO:0005488, GO:0005524, GO:0005575, GO:0005622, GO:0005623, GO:0005737, GO:0005829 +61 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 | n/a |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 0 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 |
|---|---|---|---|---|
AAA_33 | PF13671.13 | 8.3e-08 | 6–71 | AAA domain |
AAA_18 | PF13238.13 | 1.3e-07 | 7–74 | AAA domain |
SKI | PF01202.29 | 2.1e-47 | 11–166 | Shikimate kinase |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: aroB (3-dehydroquinate synthase), high confidence from genomic context alone (score 1000 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2538c aroB |
3-dehydroquinate synthase | 999 | 1000 ctx | neighborhood:882 fusion:900 cooccurence:753 coexpression:942 textmining:929 |
Rv2540c aroF |
chorismate synthase | 997 | 980 ctx | neighborhood:882 cooccurence:756 textmining:863 |
Rv2552c aroE |
shikimate 5-dehydrogenase | 992 | 978 ctx | neighborhood:544 cooccurence:529 database:900 textmining:668 |
Rv3227 aroA |
3-phosphoshikimate 1-carboxyvinyltransferase | 988 | 977 ctx | cooccurence:562 coexpression:471 database:900 textmining:529 |
Rv2537c aroD |
3-dehydroquinate dehydratase | 952 | 919 ctx | neighborhood:882 textmining:433 |
Rv2553c mltG |
membrane protein | 610 | 611 ctx | neighborhood:544 |
Rv2551c hyp |
hypothetical protein | 640 | 604 ctx | neighborhood:543 |
Rv2541 hyp |
hypothetical protein | 573 | 573 ctx | neighborhood:569 |
Rv2554c ruvX |
Holliday junction resolvase | 564 | 565 ctx | neighborhood:544 |
Rv2555c alaS |
alanine--tRNA ligase | 560 | 561 ctx | neighborhood:544 |
Rv3859c gltB |
glutamate synthase large subunit | 545 | 546 ctx | neighborhood:544 |
Rv1390 rpoZ |
DNA-directed RNA polymerase subunit omega | 571 | 524 | coexpression:455 |
Rv3754 tyrA |
prephenate dehydrogenase TyrA | 790 | 497 | textmining:601 |
Rv2572c aspS |
aspartate--tRNA ligase | 537 | 468 | |
Rv1005c pabB |
para-aminobenzoate synthase component I | 503 | 449 ctx | cooccurence:421 |
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: shikimate kinase
- MTBC0 PGAP product: shikimate kinase AroK
- Pfam (hmmscan --cut_ga): AAA_33 PF13671.13 (E=8e-08), AAA_18 PF13238.13 (E=1e-07), SKI PF01202.29 (E=2e-47)
- (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_217055.1)
- Domains: Pfam-A via hmmscan --cut_ga — AAA_33 (PF13671.13), AAA_18 (PF13238.13), SKI (PF01202.29)
- 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
COG0703 - Curated reference: UniProt P9WPY3 (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 —
52 functional partner(s); context anchor
aroB - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002705|Rv2539c|aroK MAPKAVLVGLPGSGKSTIGRRLAKALGVGLLDTDVAIEQRTGRSIADIFATDGEQEFRRIEEDVVRAALADHDGVLSLGGGAVTSPGVRAALAGHTVVYLEISAAEGVRRTGGNTVRPLLAGPDRAEKYRALMAKRAPLYRRVATMRVDTNRRNPGAVVRHILSRLQVPSPSEAAT