pks9 Resolved · high auto-curated
H37Rv Rv1664 · MTBC0 mtbc0_001772 ·
1017 aa · 1900069–1903122 (+) ·
RefSeq NP_216180.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | polyketide synthase |
|---|---|
| MTBC0 PGAP re-annotation | type I polyketide synthase |
| Revised (this work) | Type I polyketide synthase. Pfam: ketoacyl-synt (PF00109.33), Ketoacyl-synt_C (PF02801.29), KAsynt_C_assoc (PF16197.12), CurL-like_PKS_C (PF22621.3), Acyl_transf_1 (PF00698.27), PP-binding (PF00550.32). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
O06586
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Probable polyketide synthase Pks9 |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
Q Secondary metabolites biosynthesis, transport and catabolism
|
|---|---|
| Preferred name | pks9 |
| eggNOG description | Acyl transferase domain in polyketide synthase (PKS) enzymes. |
| Orthologous group | COG3321 |
| EC number |
EC 2.3.1.111, EC 2.3.1.252
|
| KEGG orthology |
K11628, K12431, K12432, K12433, K12442, K12443
|
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 | 1.145 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 5 synonymous, 15 missense, 1 nonsense, 1 frameshift |
| Disruption | 2 distinct premature-stop/frameshift site(s); most common in 0.93% of strains (1353) · 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 |
|---|---|---|---|---|
ketoacyl-synt | PF00109.33 | 5.9e-57 | 36–221 | Beta-ketoacyl synthase, N-terminal domain |
Ketoacyl-synt_C | PF02801.29 | 1.3e-39 | 230–346 | Beta-ketoacyl synthase, C-terminal domain |
KAsynt_C_assoc | PF16197.12 | 3.9e-13 | 351–469 | Ketoacyl-synthetase C-terminal extension |
CurL-like_PKS_C | PF22621.3 | 2.2e-07 | 420–478 | CurL-like, PKS C-terminal |
Acyl_transf_1 | PF00698.27 | 1.1e-65 | 504–778 | Acyl transferase domain |
PP-binding | PF00550.32 | 9.8e-08 | 877–938 | Phosphopantetheine attachment site |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: pks17 (polyketide synthase), high confidence from genomic context alone (score 980 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1663 pks17 |
polyketide synthase | 987 | 980 ctx | neighborhood:781 coexpression:861 |
Rv1661 pks7 |
polyketide synthase | 978 | 978 ctx | neighborhood:855 coexpression:801 |
Rv1662 pks8 |
polyketide synthase | 967 | 965 ctx | neighborhood:781 coexpression:806 |
Rv1912c fadB5 |
oxidoreductase FadB | 891 | 890 ctx | fusion:869 |
Rv3777 |
oxidoreductase | 867 | 866 ctx | fusion:840 |
Rv2380c mbtE |
peptide synthetase | 867 | 860 ctx | fusion:562 cooccurence:558 |
Rv0101 nrp |
peptide synthetase Nrp | 865 | 857 ctx | cooccurence:580 coexpression:428 |
Rv2383c mbtB |
phenyloxazoline synthase | 847 | 814 | coexpression:408 |
Rv3141 fadB4 |
NADPH quinone oxidoreductase FadB | 752 | 751 ctx | fusion:702 |
Rv2379c mbtF |
peptide synthetase | 759 | 750 ctx | cooccurence:508 |
Rv2928 tesA |
thioesterase TesA | 757 | 747 ctx | cooccurence:696 |
Rv1185c fadD21 |
fatty-acid--CoA ligase FadD21 | 742 | 742 ctx | fusion:427 |
Rv2930 fadD26 |
fatty-acid--CoA ligase FadD26 | 734 | 735 ctx | fusion:418 |
Rv1521 fadD25 |
fatty-acid--CoA ligase FadD25 | 730 | 731 ctx | fusion:408 |
Rv1529 fadD24 |
fatty-acid--CoA ligase FadD24 | 727 | 728 |
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: polyketide synthase
- MTBC0 PGAP product: type I polyketide synthase
- Pfam (hmmscan --cut_ga): ketoacyl-synt PF00109.33 (E=6e-57), Ketoacyl-synt_C PF02801.29 (E=1e-39), KAsynt_C_assoc PF16197.12 (E=4e-13), CurL-like_PKS_C PF22621.3 (E=2e-07), Acyl_transf_1 PF00698.27 (E=1e-65), PP-binding PF00550.32 (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_216180.1)
- Domains: Pfam-A via hmmscan --cut_ga — ketoacyl-synt (PF00109.33), Ketoacyl-synt_C (PF02801.29), KAsynt_C_assoc (PF16197.12), CurL-like_PKS_C (PF22621.3), Acyl_transf_1 (PF00698.27), PP-binding (PF00550.32)
- 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
COG3321 - Curated reference: UniProt O06586 (TrEMBL, unreviewed; 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 —
71 functional partner(s); context anchor
pks17 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001772|Rv1664|pks9 MQPTGIAIIGLACRFPTVVSPGDLWDLLRDGREATGSIDNVADFDADFFNLSPREASAMDPRQRLALELTWELLEDAFVVPETLRGQPIAVYLGAMNDDYAVLTLAADRVDHHAFAGTSRAIIANRVSFAFGLRGPSVTIDSGQSSSLVAVHLACESVRTGEAPLAIAGGVHLNLARETAMLEQEFGAVSPSGHTYAFDERADGYVPGDGGGLVLLKPVQAALDDGDRIHAIIRGSAVGNAGHSATGLTVPSVAGQVDVIRRAMSGAGVDCHQVHYVEAHGTGTKIGDPIEARALGEIFAARQRRPVSVGSVKTNIGHTGGAAGIAGLLKAVLAIENAVIPPSLNYVGAPIDLDSLGLRVDTALTPWPVADEPRRAGVSSFGMGGTNAHVILEQGPTQSPEIVESVAAAGSNAPVAVPWVLAARSPQALTNQAGRLLAHLTADDGLTALDVGWSLVSTRSVFDHRAVVVGADRGRLMAGLAGLAAGEPGAGVVVGRARSVGKTVFVFPGQGSQWLGMGRQLYGRYSVFARAFDEVVAVLDGQLRLSVRQVMWGADAGLLESTEFAQPALFVVQVALAALLQDWGVLPDLVMGHSVGEIAAAYVAGALSLVDAARVVAARGRLMQALPAGGVMVAVAASEDEVAPLLTEGVCIAAVNAPESVVISGEQAAVGVVVDRLVGLGRRVRRLAVSHAFHSVLMDPMVEEFSKVLADVCVRAPRIGLVSNVTGQLAGAGYGSPAYWVEHVRKPVRFFDGVGLAESLGARVFVEVGPGAGLEASVALLARDRPEVESVLAGVGRLFAEGVAVDWSSVFAGLGGRRVELPTYGFARQRFWLGDNGELSVDQTGKDAGAIARLQSLAPPELQRQLVELVCFHAAIVLGRKSSHDIDPECAFQDLGFDSMSGVELRNRLQMAIGLPGLSLPRTLIFDYPTASALAECLGQLLGGQHESSDDESIWQLLKNIPIHQLRRTGLLDKLLLLAGQPEESLAGRTVSDEVIDSLSPEALIGLALDEDENDIR