pks10 Resolved · high auto-curated
H37Rv Rv1660 · MTBC0 mtbc0_001769 ·
353 aa · 1886202–1887263 (+) ·
RefSeq NP_216176.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | chalcone synthase |
|---|---|
| MTBC0 PGAP re-annotation | type III polyketide synthase |
| Revised (this work) | Type III polyketide synthase. Pfam: Chal_sti_synt_N (PF00195.26), FAE1_CUT1_RppA (PF08392.19), Chal_sti_synt_C (PF02797.22), ACP_syn_III_C (PF08541.17). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WPF5
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Polyketide synthase-like Pks10 |
| EC (curated) |
EC 2.3.1.-
|
| Curated function | Could catalyze the elongation of hydroxybenzoyl-CoA as well as elongation of the aliphatic precursor involved in the synthesis of phthiocerol dimycocerosate (DIM). |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
Q Secondary metabolites biosynthesis, transport and catabolism
|
|---|---|
| Preferred name | pks10 |
| eggNOG description | synthase |
| Orthologous group | COG3424 |
| KEGG orthology |
K16167
|
| Gene Ontology (30) |
GO:0005575, GO:0005622, GO:0005623, GO:0005737, GO:0005886, GO:0006629, GO:0008150, GO:0008152, GO:0008610, GO:0009058, GO:0009273, GO:0009987 +18 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) pseudogene candidate
| pN/pS | 1.828 · diversifying/relaxed |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 2 synonymous, 10 missense, 0 nonsense, 2 frameshift |
| Disruption | 2 distinct premature-stop/frameshift site(s); most common in 17.61% of strains (25567) · clonal |
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 |
|---|---|---|---|---|
Chal_sti_synt_N | PF00195.26 | 1.2e-19 | 10–196 | Chalcone and stilbene synthases, N-terminal domain |
FAE1_CUT1_RppA | PF08392.19 | 3.4e-14 | 81–198 | FAE1/Type III polyketide synthase-like protein |
Chal_sti_synt_C | PF02797.22 | 2.0e-16 | 219–351 | Chalcone and stilbene synthases, C-terminal domain |
ACP_syn_III_C | PF08541.17 | 1.0e-07 | 261–352 | 3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III C terminal |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv1138c (oxidoreductase), high confidence from genomic context alone (score 867 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1139c hyp |
hypothetical protein | 926 | 901 ctx | cooccurence:774 coexpression:532 |
Rv1138c |
oxidoreductase | 905 | 867 ctx | cooccurence:764 |
Rv2932 ppsB |
phthiocerol synthesis polyketide synthase type I PpsB | 873 | 855 | experimental:470 database:720 |
Rv2933 ppsC |
phthiocerol synthesis polyketide synthase type I PpsC | 887 | 833 | database:720 |
Rv1665 pks11 |
chalcone synthase | 812 | 810 | database:720 |
Rv1181 pks4 |
polyketide beta-ketoacyl synthase | 830 | 806 | database:720 |
Rv2931 ppsA |
phthiocerol synthesis polyketide synthase type I PpsA | 817 | 805 | database:720 |
Rv1661 pks7 |
polyketide synthase | 822 | 796 ctx | neighborhood:582 |
Rv0667 rpoB |
DNA-directed RNA polymerase subunit beta | 801 | 773 | experimental:406 database:628 |
Rv1390 rpoZ |
DNA-directed RNA polymerase subunit omega | 771 | 771 | experimental:406 database:629 |
Rv3457c rpoA |
DNA-directed RNA polymerase subunit alpha | 759 | 759 | database:626 |
Rv1305 atpE |
ATP synthase subunit C | 765 | 755 | database:610 |
Rv0736 rslA |
anti-sigma-L factor RslA | 758 | 747 | coexpression:746 |
Rv1180 pks3 |
polyketide beta-ketoacyl synthase | 746 | 736 | database:720 |
Rv1663 pks17 |
polyketide synthase | 909 | 734 ctx | neighborhood:526 textmining:676 |
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: chalcone synthase
- MTBC0 PGAP product: type III polyketide synthase
- Pfam (hmmscan --cut_ga): Chal_sti_synt_N PF00195.26 (E=1e-19), FAE1_CUT1_RppA PF08392.19 (E=3e-14), Chal_sti_synt_C PF02797.22 (E=2e-16), ACP_syn_III_C PF08541.17 (E=1e-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_216176.1)
- Domains: Pfam-A via hmmscan --cut_ga — Chal_sti_synt_N (PF00195.26), FAE1_CUT1_RppA (PF08392.19), Chal_sti_synt_C (PF02797.22), ACP_syn_III_C (PF08541.17)
- 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
COG3424 - Curated reference: UniProt P9WPF5 (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 —
49 functional partner(s); context anchor
Rv1138c - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001769|Rv1660|pks10 MSVIAGVFGALPPYRYSQRELTDSFVSIPDFEGYEDIVRQLHASAKVNSRHLVLPLEKYPKLTDFGEANKIFIEKAVDLGVQALAGALDESGLRPEDLDVLITATVTGLAVPSLDARIAGRLGLRADVRRVPLFGLGCVAGAAGVARLHDYLRGAPDGVAALVSVELCSLTYPGYKPTLPGLVGSALFADGAAAVVAAGVKRAQDIGADGPDILDSRSHLYPDSLRTMGYDVGSAGFELVLSRDLAAVVEQYLGNDVTTFLASHGLSTTDVGAWVTHPGGPKIINAITETLDLSPQALELTWRSLGEIGNLSSASVLHVLRDTIAKPPPSGSPGLMIAMGPGFCSELVLLRWH