kdtB Resolved · high auto-curated
H37Rv Rv2965c · MTBC0 mtbc0_003149 ·
161 aa · 3339505–3339990 (-) ·
RefSeq NP_217481.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | phosphopantetheine adenylyltransferase |
|---|---|
| MTBC0 PGAP re-annotation | pantetheine-phosphate adenylyltransferase |
| Revised (this work) | Pantetheine-phosphate adenylyltransferase. Pfam: CTP_transf_like (PF01467.33), Citrate_ly_lig (PF08218.18). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WPA5
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Phosphopantetheine adenylyltransferase |
| EC (curated) |
EC 2.7.7.3
|
| Curated function | Reversibly transfers an adenylyl group from ATP to 4'-phosphopantetheine, yielding dephospho-CoA (dPCoA) and pyrophosphate. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
F Nucleotide transport and metabolism
|
|---|---|
| Preferred name | coaD |
| eggNOG description | Reversibly transfers an adenylyl group from ATP to 4'- phosphopantetheine, yielding dephospho-CoA (dPCoA) and pyrophosphate |
| Orthologous group | COG0669 |
| EC number |
EC 2.7.7.3
|
| KEGG orthology |
K00954
|
| KEGG pathways |
map00770, map01100
|
| KEGG modules |
M00120
|
| Gene Ontology (71) |
GO:0003674, GO:0003824, GO:0004595, GO:0006139, GO:0006163, GO:0006164, GO:0006725, GO:0006732, GO:0006753, GO:0006793, GO:0006796, GO:0006807 +59 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 | 0.0 · strong purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 1 synonymous, 0 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 |
|---|---|---|---|---|
CTP_transf_like | PF01467.33 | 1.0e-24 | 5–132 | Cytidylyltransferase-like |
Citrate_ly_lig | PF08218.18 | 5.4e-07 | 11–74 | Citrate lyase ligase C-terminal domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: rsmD (methyltransferase), high confidence from genomic context alone (score 923 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1391 dfp |
bifunctional phosphopantothenoylcysteine decarboxylase/phosphopantothenate--cysteine ligase | 994 | 930 | database:900 textmining:930 |
Rv2966c rsmD |
methyltransferase | 953 | 923 ctx | neighborhood:636 coexpression:682 textmining:422 |
Rv3600c coaX |
type III pantothenate kinase | 950 | 919 | database:900 textmining:416 |
Rv1631 coaE |
dephospho-CoA kinase CoaE | 994 | 911 | database:900 textmining:938 |
Rv1092c coaA |
pantothenate kinase | 959 | 900 | database:900 textmining:614 |
Rv2786c ribF |
bifunctional riboflavin kinase /FMN adenylyltransferase | 840 | 611 ctx | cooccurence:594 textmining:608 |
Rv1712 cmk |
cytidylate kinase | 553 | 554 ctx | cooccurence:412 |
Rv3100c smpB |
SsrA-binding protein | 495 | 496 | |
Rv2967c pca |
pyruvate carboxylase | 528 | 489 ctx | neighborhood:466 |
Rv1107c xseB |
exodeoxyribonuclease VII small subunit | 470 | 470 | coexpression:426 |
Rv1392 metK |
S-adenosylmethionine synthetase | 570 | 465 ctx | cooccurence:463 |
Rv0321 dcd |
deoxycytidine triphosphate deaminase | 455 | 456 | coexpression:456 |
Rv3396c guaA |
GMP synthase | 718 | 444 | textmining:514 |
Rv2611c |
phosphatidylinositol mannoside acyltransferase | 442 | 442 | coexpression:418 |
Rv3781 rfbE |
O-antigen/lipopolysaccharide ABC transporter ATP-binding protein RfbE | 410 | 411 | coexpression:404 |
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: phosphopantetheine adenylyltransferase
- MTBC0 PGAP product: pantetheine-phosphate adenylyltransferase
- Pfam (hmmscan --cut_ga): CTP_transf_like PF01467.33 (E=1e-24), Citrate_ly_lig PF08218.18 (E=5e-07)
- (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_217481.1)
- Domains: Pfam-A via hmmscan --cut_ga — CTP_transf_like (PF01467.33), Citrate_ly_lig (PF08218.18)
- 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
COG0669 - Curated reference: UniProt P9WPA5 (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 —
54 functional partner(s); context anchor
rsmD - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003149|Rv2965c|kdtB MTGAVCPGSFDPVTLGHVDIFERAAAQFDEVVVAILVNPAKTGMFDLDERIAMVKESTTHLPNLRVQVGHGLVVDFVRSCGMTAIVKGLRTGTDFEYELQMAQMNKHIAGVDTFFVATAPRYSFVSSSLAKEVAMLGGDVSELLPEPVNRRLRDRLNTERT