coaA Resolved · high auto-curated
H37Rv Rv1092c · MTBC0 - ·
312 aa · 1219248–1220186 (-) ·
RefSeq NP_215608.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | pantothenate kinase |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | Pantothenate kinase. Pfam: PRK (PF00485.25). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Annotated on the H37Rv protein: this gene has no 1:1 ancestral MTBC0 anchor (PE/PPE, paralogue, IS element, or otherwise unanchored CDS).
Curated reference (UniProt)
| UniProt |
P9WPA7
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Pantothenate kinase |
| EC (curated) |
EC 2.7.1.33
|
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
F Nucleotide transport and metabolism
|
|---|---|
| Preferred name | coaA |
| eggNOG description | Pantothenic acid kinase |
| Orthologous group | COG0572 |
| EC number |
EC 2.7.1.33
|
| KEGG orthology |
K00867
|
| KEGG pathways |
map00770, map01100
|
| KEGG modules |
M00120
|
| Gene Ontology (76) |
GO:0003674, GO:0003824, GO:0004594, GO:0005575, GO:0005622, GO:0005623, GO:0005737, GO:0005829, GO:0005886, GO:0006139, GO:0006163, GO:0006164 +64 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 | 0.231 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 3 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 |
|---|---|---|---|---|
PRK | PF00485.25 | 5.4e-11 | 92–229 | Phosphoribulokinase / Uridine kinase family |
Functional interaction network (STRING v12, guilt-by-association)
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1391 dfp |
bifunctional phosphopantothenoylcysteine decarboxylase/phosphopantothenate--cysteine ligase | 963 | 904 | database:900 textmining:640 |
Rv3602c panC |
pantothenate synthetase | 963 | 900 | database:900 textmining:650 |
Rv2965c kdtB |
phosphopantetheine adenylyltransferase | 959 | 900 | database:900 textmining:614 |
Rv3600c coaX |
type III pantothenate kinase | 945 | 900 | database:900 textmining:482 |
Rv3433c nnr |
bifunctional ADP-dependent (S)-NAD(P)H-hydrate dehydratase/NAD(P)H-hydrate epimerase | 411 | 412 | |
Rv1093 glyA1 |
serine hydroxymethyltransferase | 407 | 398 | |
Rv3790 dprE1 |
decaprenylphosphoryl-beta-D-ribose oxidase | 532 | 200 | textmining:440 |
Rv1631 coaE |
dephospho-CoA kinase CoaE | 692 | 168 | textmining:645 |
Rv0429c def |
polypeptide deformylase | 521 | 63 | textmining:510 |
Rv0117 oxyS |
oxidative stress response regulatory protein OxyS | 435 | 51 | textmining:430 |
Rv0507 mmpL2 |
transmembrane transport protein MmpL2 | 434 | 47 | textmining:431 |
Rv1971 mce3F |
Mce family protein Mce3F | 513 | 41 | textmining:513 |
Rv2225 panB |
3-methyl-2-oxobutanoate hydroxymethyltransferase | 481 | 41 | textmining:482 |
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
- Annotation from H37Rv (no MTBC0 1:1 anchor; H37Rv protein used): pantothenate kinase
- Pfam (hmmscan --cut_ga): PRK PF00485.25 (E=5e-11)
- (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_215608.1)
- Domains: Pfam-A via hmmscan --cut_ga — PRK (PF00485.25)
- 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
COG0572 - Curated reference: UniProt P9WPA7 (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 — 13 functional partner(s)
- Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv1092c|coaA MSRLSEPSPYVEFDRRQWRALRMSTPLALTEEELVGLRGLGEQIDLLEVEEVYLPLARLIHLQVAARQRLFAATAEFLGEPQQNPDRPVPFIIGVAGSVAVGKSTTARVLQALLARWDHHPRVDLVTTDGFLYPNAELQRRNLMHRKGFPESYNRRALMRFVTSVKSGSDYACAPVYSHLHYDIIPGAEQVVRHPDILILEGLNVLQTGPTLMVSDLFDFSLYVDARIEDIEQWYVSRFLAMRTTAFADPESHFHHYAAFSDSQAVVAAREIWRTINRPNLVENILPTRPRATLVLRKDADHSINRLRLRKL