panC Resolved · high auto-curated
H37Rv Rv3602c · MTBC0 mtbc0_003820 ·
309 aa · 4067985–4068914 (-) ·
RefSeq NP_218119.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | pantothenate synthetase |
|---|---|
| MTBC0 PGAP re-annotation | pantoate--beta-alanine ligase |
| Revised (this work) | Pantoate--beta-alanine ligase. Pfam: Pantoate_ligase (PF02569.22). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WIL5
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Pantothenate synthetase |
| EC (curated) |
EC 6.3.2.1
|
| Curated function | Catalyzes the condensation of pantoate with beta-alanine in an ATP-dependent reaction via a pantoyl-adenylate intermediate. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
H Coenzyme transport and metabolism
|
|---|---|
| Preferred name | panC |
| eggNOG description | Catalyzes the condensation of pantoate with beta-alanine in an ATP-dependent reaction via a pantoyl-adenylate intermediate |
| Orthologous group | COG0414 |
| EC number |
EC 6.3.2.1
|
| KEGG orthology |
K01918
|
| KEGG pathways |
map00410, map00770, map01100, map01110
|
| KEGG modules |
M00119
|
| Gene Ontology (84) |
GO:0000166, GO:0000287, GO:0001505, GO:0003674, GO:0003824, GO:0004592, GO:0005488, GO:0005524, GO:0005575, GO:0005622, GO:0005623, GO:0005737 +72 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 | 0.096 · strong purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 4 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 |
|---|---|---|---|---|
Pantoate_ligase | PF02569.22 | 7.0e-94 | 18–283 | Pantoate-beta-alanine ligase |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: panD (aspartate 1-decarboxylase), high confidence from genomic context alone (score 1000 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3601c panD |
aspartate 1-decarboxylase | 999 | 1000 ctx | neighborhood:882 cooccurence:678 coexpression:967 database:900 textmining:942 |
Rv3600c coaX |
type III pantothenate kinase | 999 | 997 ctx | neighborhood:882 coexpression:759 database:900 textmining:713 |
Rv2225 panB |
3-methyl-2-oxobutanoate hydroxymethyltransferase | 999 | 995 ctx | fusion:811 cooccurence:774 coexpression:859 textmining:917 |
Rv3603c hyp |
hypothetical protein | 997 | 986 ctx | neighborhood:881 fusion:795 cooccurence:471 textmining:806 |
Rv3432c gadB |
glutamate decarboxylase GadB | 946 | 943 | coexpression:421 database:900 |
Rv2573 |
2-dehydropantoate 2-reductase | 933 | 913 | database:900 |
Rv1712 cmk |
cytidylate kinase | 908 | 908 ctx | fusion:900 |
Rv3293 pcd |
piperideine-6-carboxylic acid dehydrogenase | 905 | 901 | database:900 |
Rv1092c coaA |
pantothenate kinase | 963 | 900 | database:900 textmining:650 |
Rv2589 gabT |
4-aminobutyrate aminotransferase | 905 | 900 | database:900 |
Rv0223c |
aldehyde dehydrogenase | 904 | 900 | database:900 |
Rv0147 |
aldehyde dehydrogenase | 903 | 900 | database:900 |
Rv0768 aldA |
aldehyde dehydrogenase AldA | 903 | 900 | database:900 |
Rv1391 dfp |
bifunctional phosphopantothenoylcysteine decarboxylase/phosphopantothenate--cysteine ligase | 927 | 866 | database:800 textmining:480 |
Rv3598c lysS |
lysine--tRNA ligase | 881 | 787 ctx | neighborhood:773 textmining:465 |
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: pantothenate synthetase
- MTBC0 PGAP product: pantoate--beta-alanine ligase
- Pfam (hmmscan --cut_ga): Pantoate_ligase PF02569.22 (E=7e-94)
- (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_218119.1)
- Domains: Pfam-A via hmmscan --cut_ga — Pantoate_ligase (PF02569.22)
- 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
COG0414 - Curated reference: UniProt P9WIL5 (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
panD - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003820|Rv3602c|panC MTIPAFHPGELNVYSAPGDVADVSRALRLTGRRVMLVPTMGALHEGHLALVRAAKRVPGSVVVVSIFVNPMQFGAGEDLDAYPRTPDDDLAQLRAEGVEIAFTPTTAAMYPDGLRTTVQPGPLAAELEGGPRPTHFAGVLTVVLKLLQIVRPDRVFFGEKDYQQLVLIRQLVADFNLDVAVVGVPTVREADGLAMSSRNRYLDPAQRAAAVALSAALTAAAHAATAGAQAALDAARAVLDAAPGVAVDYLELRDIGLGPMPLNGSGRLLVAARLGTTRLLDNIAIEIGTFAGTDRPDGYRAILESHWRN