Rv1372 Family assigned · medium auto-curated
H37Rv Rv1372 · MTBC0 - ·
393 aa · 1544825–1546006 (+) ·
RefSeq YP_177803.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | alpha-pyrone synthesis polyketide synthase-like protein |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | Alpha-pyrone synthesis polyketide synthase-like protein. Pfam: Chal_sti_synt_N (PF00195.26), FAE1_CUT1_RppA (PF08392.19), ACP_syn_III (PF08545.17), 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.
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 |
P9WPF1
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Alpha-pyrone synthesis polyketide synthase-like Pks18 |
| EC (curated) |
EC 2.3.1.-
|
| Curated function | Involved in the biosynthesis of tri- and tetraketide alpha-pyrones. Pks18 catalyzes the extension of medium- and long-chain aliphatic acyl-CoA substrates by using malonyl-CoA as an extender molecule to synthesize polyketide products. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
Q Secondary metabolites biosynthesis, transport and catabolism
|
|---|---|
| Preferred name | pks18 |
| eggNOG description | Chalcone and stilbene synthases, C-terminal domain |
| Orthologous group | COG3424 |
| KEGG orthology |
K16167, K16233
|
| Gene Ontology (22) |
GO:0006725, GO:0008150, GO:0008152, GO:0009058, GO:0009698, GO:0009699, GO:0009714, GO:0009715, GO:0009987, GO:0019438, GO:0019748, GO:0042180 +10 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 | 1.463 · diversifying/relaxed |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 3 synonymous, 13 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 |
|---|---|---|---|---|
Chal_sti_synt_N | PF00195.26 | 1.7e-23 | 33–235 | Chalcone and stilbene synthases, N-terminal domain |
FAE1_CUT1_RppA | PF08392.19 | 1.2e-10 | 131–239 | FAE1/Type III polyketide synthase-like protein |
ACP_syn_III | PF08545.17 | 9.9e-09 | 174–238 | 3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III |
Chal_sti_synt_C | PF02797.22 | 3.4e-21 | 251–389 | Chalcone and stilbene synthases, C-terminal domain |
ACP_syn_III_C | PF08541.17 | 3.7e-10 | 299–389 | 3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III C terminal |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv1371 (membrane protein), high confidence from genomic context alone (score 948 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1371 |
membrane protein | 978 | 948 ctx | neighborhood:882 cooccurence:448 textmining:601 |
Rv1139c hyp |
hypothetical protein | 875 | 832 ctx | cooccurence:702 coexpression:400 |
Rv0261c narK3 |
nitrate/nitrite transporter | 810 | 810 | coexpression:810 |
Rv1373 |
glycolipid sulfotransferase | 819 | 806 ctx | neighborhood:801 |
Rv0667 rpoB |
DNA-directed RNA polymerase subunit beta | 802 | 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 | 764 | 754 | database:610 |
Rv0259c hyp |
hypothetical protein | 732 | 732 | coexpression:732 |
Rv1138c |
oxidoreductase | 753 | 654 ctx | cooccurence:613 |
Rv2267c stf3 hyp |
hypothetical protein | 661 | 648 | database:593 |
Rv3529c hyp |
hypothetical protein | 659 | 646 | database:593 |
Rv1691 hyp |
hypothetical protein | 657 | 644 | database:593 |
Rv2101 helZ |
helicase HelZ | 625 | 608 | database:480 |
Rv1369c |
Probable transposase; Rv1369c, (MTCY02B12.03c), len: 328 aa. Probable transposase subunit for IS6110. Identical to many other M. tuberculosi | 545 | 544 ctx | neighborhood:543 |
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): alpha-pyrone synthesis polyketide synthase-like protein
- Pfam (hmmscan --cut_ga): Chal_sti_synt_N PF00195.26 (E=2e-23), FAE1_CUT1_RppA PF08392.19 (E=1e-10), ACP_syn_III PF08545.17 (E=1e-08), Chal_sti_synt_C PF02797.22 (E=3e-21), ACP_syn_III_C PF08541.17 (E=4e-10)
- (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 YP_177803.1)
- Domains: Pfam-A via hmmscan --cut_ga — Chal_sti_synt_N (PF00195.26), FAE1_CUT1_RppA (PF08392.19), ACP_syn_III (PF08545.17), 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 P9WPF1 (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 —
53 functional partner(s); context anchor
Rv1371 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv1372| MNVSAESGAPRRAGQRHEVGLAQLPPAPPTTVAVIEGLATGTPRRVVNQSDAADRVAELFLDPGQRERIPRVYQKSRITTRRMAVDPLDAKFDVFRREPATIRDRMHLFYEHAVPLAVDVSKRALAGLPYRAAEIGLLVLATSTGFIAPGVDVAIVKELGLSPSISRVVVNFMGCAAAMNALGTATNYVRAHPAMKALVVCIELCSVNAVFADDINDVVIHSLFGDGCAALVIGASQVQEKLEPGKVVVRSSFSQLLDNTEDGIVLGVNHNGITCELSENLPGYIFSGVAPVVTEMLWDNGLQISDIDLWAIHPGGPKIIEQSVRSLGISAELAAQSWDVLARFGNMLSVSLIFVLETMVQQAESAKAISTGVAFAFGPGVTVEGMLFDIIRR