coaE Resolved · high auto-curated
H37Rv Rv1631 · MTBC0 mtbc0_001739 ·
407 aa · 1846977–1848200 (+) ·
RefSeq NP_216147.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | dephospho-CoA kinase CoaE |
|---|---|
| MTBC0 PGAP re-annotation | dephospho-CoA kinase |
| Revised (this work) | Dephospho-CoA kinase. Pfam: CoaE (PF01121.27), GrpB (PF04229.21). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WPA3
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Dephospho-CoA kinase |
| EC (curated) |
EC 2.7.1.24
|
| Curated function | Catalyzes the phosphorylation of the 3'-hydroxyl group of dephosphocoenzyme A to form coenzyme A. Can also use dATP, with lower efficiency, but cannot use GTP, dGTP or CTP. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
F Nucleotide transport and metabolism
|
|---|---|
| Preferred name | coaE |
| eggNOG description | Catalyzes the phosphorylation of the 3'-hydroxyl group of dephosphocoenzyme A to form coenzyme A |
| Orthologous group | COG0237 |
| EC number |
EC 2.7.1.24
|
| KEGG orthology |
K00859
|
| KEGG pathways |
map00770, map01100
|
| KEGG modules |
M00120
|
| Gene Ontology (96) |
GO:0000166, GO:0001882, GO:0001884, GO:0002135, GO:0003674, GO:0003824, GO:0004140, GO:0005488, GO:0005575, GO:0005622, GO:0005623, GO:0005737 +84 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 | 0.278 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 5 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 |
|---|---|---|---|---|
CoaE | PF01121.27 | 1.4e-62 | 4–178 | Dephospho-CoA kinase |
GrpB | PF04229.21 | 2.6e-36 | 211–395 | GrpB protein |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: rpsA (30S ribosomal protein S1), high confidence from genomic context alone (score 864 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2965c kdtB |
phosphopantetheine adenylyltransferase | 994 | 911 | database:900 textmining:938 |
Rv2523c acpS |
holo-ACP synthase | 915 | 907 | database:900 |
Rv1630 rpsA |
30S ribosomal protein S1 | 877 | 864 ctx | neighborhood:844 |
Rv1629 polA |
DNA polymerase I | 922 | 856 ctx | neighborhood:726 coexpression:405 textmining:488 |
Rv1870c hyp |
hypothetical protein | 811 | 812 | coexpression:801 |
Rv2902c rnhB |
ribonuclease HII | 786 | 787 | coexpression:772 |
Rv3433c nnr |
bifunctional ADP-dependent (S)-NAD(P)H-hydrate dehydratase/NAD(P)H-hydrate epimerase | 663 | 663 ctx | neighborhood:544 |
Rv0176 |
Mce associated transmembrane protein | 659 | 659 | coexpression:651 |
Rv2924c fpg |
formamidopyrimidine-DNA glycosylase | 645 | 611 | coexpression:472 |
Rv3396c guaA |
GMP synthase | 623 | 605 ctx | neighborhood:544 |
Rv2551c hyp |
hypothetical protein | 613 | 598 | coexpression:459 |
Rv1650 pheT |
phenylalanine--tRNA ligase subunit beta | 691 | 567 ctx | neighborhood:544 |
Rv2946c pks1 |
polyketide synthase | 621 | 563 ctx | neighborhood:544 |
Rv2438c nadE |
glutamine-dependent NAD(+) synthetase | 759 | 554 ctx | neighborhood:544 textmining:482 |
Rv2230c |
GTP cyclohydrolase | 547 | 548 ctx | neighborhood:544 |
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: dephospho-CoA kinase CoaE
- MTBC0 PGAP product: dephospho-CoA kinase
- Pfam (hmmscan --cut_ga): CoaE PF01121.27 (E=1e-62), GrpB PF04229.21 (E=3e-36)
- (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_216147.1)
- Domains: Pfam-A via hmmscan --cut_ga — CoaE (PF01121.27), GrpB (PF04229.21)
- 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
COG0237 - Curated reference: UniProt P9WPA3 (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 —
95 functional partner(s); context anchor
rpsA - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001739|Rv1631|coaE MLRIGLTGGIGAGKSLLSTTFSQCGGIVVDGDVLAREVVQPGTEGLASLVDAFGRDILLADGALDRQALAAKAFRDDESRGVLNGIVHPLVARRRSEIIAAVSGDAVVVEDIPLLVESGMAPLFPLVVVVHADVELRVRRLVEQRGMAEADARARIAAQASDQQRRAVADVWLDNSGSPEDLVRRARDVWNTRVQPFAHNLAQRQIARAPARLVPADPSWPDQARRIVNRLKIACGHKALRVDHIGSTAVSGFPDFLAKDVIDIQVTVESLDVADELAEPLLAAGYPRLEHITQDTEKTDARSTVGRYDHTDSAALWHKRVHASADPGRPTNVHLRVHGWPNQQFALLFVDWLAANPGAREDYLTVKCDADRRADGELARYVTAKEPWFLDAYQRAWEWADAVHWRP