pks17 Resolved · high auto-curated
H37Rv Rv1663 · MTBC0 - ·
502 aa · 1886512–1888020 (+) ·
RefSeq NP_216179.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | polyketide synthase |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | Polyketide synthase. Pfam: KR (PF08659.17), adh_short (PF00106.32), Epimerase (PF01370.28), Polysacc_synt_2 (PF02719.22), GDP_Man_Dehyd (PF16363.12), 3Beta_HSD (PF01073.26), adh_short_C2 (PF13561.13), PP-binding (PF00550.32). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Annotated on the H37Rv protein: this gene has no 1:1 ancestral MTBC0 anchor (PE/PPE, paralogue, IS element, or otherwise unanchored CDS).
Curated reference (UniProt)
| UniProt |
O06585
TrEMBL · unreviewed
· Predicted
|
|---|---|
| UniProt name | Probable polyketide synthase Pks17 |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
I Lipid transport and metabolismQ Secondary metabolites biosynthesis, transport and catabolism
|
|---|---|
| Preferred name | pks17 |
| eggNOG description | KR domain |
| Orthologous group | COG0236 |
| KEGG orthology |
K12439
|
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 | 0.528 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 6 synonymous, 8 missense, 1 nonsense, 1 frameshift |
| Disruption | 2 distinct premature-stop/frameshift site(s); most common in 3.08% of strains (4467) · 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 |
|---|---|---|---|---|
KR | PF08659.17 | 1.5e-58 | 64–239 | KR domain |
adh_short | PF00106.32 | 4.6e-12 | 65–220 | short chain dehydrogenase |
Epimerase | PF01370.28 | 5.4e-13 | 66–206 | NAD dependent epimerase/dehydratase family |
Polysacc_synt_2 | PF02719.22 | 3.0e-07 | 66–196 | Polysaccharide biosynthesis protein |
GDP_Man_Dehyd | PF16363.12 | 1.9e-06 | 67–151 | GDP-mannose 4,6 dehydratase |
3Beta_HSD | PF01073.26 | 2.0e-05 | 67–201 | 3-beta hydroxysteroid dehydrogenase/isomerase family |
adh_short_C2 | PF13561.13 | 2.4e-08 | 76–222 | Enoyl-(Acyl carrier protein) reductase |
PP-binding | PF00550.32 | 1.0e-14 | 349–410 | Phosphopantetheine attachment site |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: pks8 (polyketide synthase), high confidence from genomic context alone (score 1000 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1662 pks8 |
polyketide synthase | 999 | 1000 ctx | neighborhood:792 fusion:899 cooccurence:774 coexpression:816 database:900 textmining:883 |
Rv2524c fas |
fatty acid synthase | 999 | 1000 ctx | neighborhood:544 coexpression:929 experimental:999 database:604 textmining:519 |
Rv1664 pks9 |
polyketide synthase | 987 | 980 ctx | neighborhood:781 coexpression:861 |
Rv2947c pks15 |
polyketide synthase | 981 | 980 ctx | fusion:900 cooccurence:774 |
Rv2382c mbtC |
polyketide synthetase | 981 | 980 ctx | fusion:900 cooccurence:773 |
Rv1180 pks3 |
polyketide beta-ketoacyl synthase | 981 | 980 ctx | fusion:900 cooccurence:772 |
Rv3147 nuoC |
NADH-quinone oxidoreductase subunit C | 974 | 972 | coexpression:436 experimental:897 database:564 |
Rv3153 nuoI |
NADH-quinone oxidoreductase subunit I | 974 | 972 | coexpression:413 experimental:898 database:564 |
Rv3146 nuoB |
NADH-quinone oxidoreductase subunit B | 973 | 972 | coexpression:408 experimental:899 database:564 |
Rv1661 pks7 |
polyketide synthase | 974 | 970 ctx | neighborhood:749 coexpression:859 |
Rv3800c pks13 |
polyketide synthase | 977 | 968 ctx | fusion:688 cooccurence:758 coexpression:470 |
Rv2243 fabD |
malonyl CoA-acyl carrier protein transacylase | 968 | 965 | coexpression:645 experimental:787 database:549 |
Rv3148 nuoD |
NADH-quinone oxidoreductase subunit D | 965 | 963 | experimental:905 database:564 |
Rv3158 nuoN |
NADH-quinone oxidoreductase subunit N | 961 | 959 | experimental:909 database:556 |
Rv3145 nuoA |
NADH-quinone oxidoreductase subunit A | 958 | 956 | experimental:899 database:561 |
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
- Annotation from H37Rv (no MTBC0 1:1 anchor; H37Rv protein used): polyketide synthase
- Pfam (hmmscan --cut_ga): KR PF08659.17 (E=2e-58), adh_short PF00106.32 (E=5e-12), Epimerase PF01370.28 (E=5e-13), Polysacc_synt_2 PF02719.22 (E=3e-07), GDP_Man_Dehyd PF16363.12 (E=2e-06), 3Beta_HSD PF01073.26 (E=2e-05), adh_short_C2 PF13561.13 (E=2e-08), PP-binding PF00550.32 (E=1e-14)
- (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_216179.1)
- Domains: Pfam-A via hmmscan --cut_ga — KR (PF08659.17), adh_short (PF00106.32), Epimerase (PF01370.28), Polysacc_synt_2 (PF02719.22), GDP_Man_Dehyd (PF16363.12), 3Beta_HSD (PF01073.26), adh_short_C2 (PF13561.13), 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
COG0236 - Curated reference: UniProt O06585 (TrEMBL, unreviewed; Predicted)
- 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 —
413 functional partner(s); context anchor
pks8 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv1663|pks17 MEAGPQRIAQMLAELVELFKTEALHRLPVKSWDVRHAREAYRFLSQARHVGKVVLTMPDAWAAGTVLITGGTGMAGSAVARHLVSRYGVRQVVLASRAGEHTESVAALVDELGSAGARVQVVSCDVADRDAVAGLVASQPDLTAVFHAAGVLDDAVITGLTPERVDKVLRAKVDGAWNLHELTRHLDVSAFVLFSSMAGIVGAPGQANYAAANAFLDGLAAYRRSRGLAALSVAWGLWEQASAMTEHLGERDRVRMSRVGLAPLPTNQAMGFLDAALLADRPVVVAARLDRAALAGAELPALFSQLVAGPIRRIIDGADEVSGSGLASRLHGLTPEQRHRELTELVCSNAAIVLGHSGTEIDAHKAFQDLGFDSLTAVELRNRLKTATGLTLPPTLIFDYPTAAELAEHLDIQLANAPAVTVDQPNPSTRFNEVTRELQALLDQPNWNPDDKTRLIKRLQAILTDCTAPPASSGPSTTHDDEDITTATESQLFAILDDELGP