ppsB Resolved · high auto-curated
H37Rv Rv2932 · MTBC0 mtbc0_003115 ·
1538 aa · 3272069–3276685 (+) ·
RefSeq NP_217448.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | phthiocerol synthesis polyketide synthase type I PpsB |
|---|---|
| MTBC0 PGAP re-annotation | phthiocerol type I polyketide synthase PpsB |
| Revised (this work) | Phthiocerol type I polyketide synthase PpsB. Pfam: ketoacyl-synt (PF00109.33), Ketoacyl-synt_C (PF02801.29), KAsynt_C_assoc (PF16197.12), Acyl_transf_1 (PF00698.27), SpnB_Rossmann (PF22953.4), KR (PF08659.17), adh_short (PF00106.32), 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 |
P9WQE5
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Phenolphthiocerol/phthiocerol polyketide synthase subunit B |
| EC (curated) |
EC 2.3.1.292
|
| Curated function | Part of the PpsABCDE complex involved in the biosynthesis of the lipid core common to phthiocerols and phenolphthiocerols by successive additions of malonyl-CoA or methylmalonyl-CoA extender units. PpsA can accept as substrate the activated forms of either icosanoyl (C20), docosanoyl (C22) or lignoceroyl (C24) groups from FadD26, or a (4-hydroxyphenyl)-C17 or (4-hydroxyphenyl)-C19 fatty acyl from FadD29. PpsA initiates the biosynthesis and extends its substrate using a malonyl-CoA extender unit. The PpsB and PpsC proteins add the second and third malonyl-CoA extender units. PpsD adds an (R)-me. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
Q Secondary metabolites biosynthesis, transport and catabolism
|
|---|---|
| Preferred name | ppsB |
| eggNOG description | synthase |
| Orthologous group | COG1020 |
| EC number |
EC 2.3.1.261
|
| KEGG orthology |
K12430, K12440, K12441
|
| Gene Ontology (66) |
GO:0003674, GO:0003824, GO:0004312, GO:0004315, GO:0005575, GO:0005622, GO:0005623, GO:0005737, GO:0006066, GO:0006082, GO:0006629, GO:0006631 +54 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 | 0.164 · strong purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 17 synonymous, 8 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 |
|---|---|---|---|---|
ketoacyl-synt | PF00109.33 | 2.8e-101 | 34–283 | Beta-ketoacyl synthase, N-terminal domain |
Ketoacyl-synt_C | PF02801.29 | 2.9e-41 | 291–405 | Beta-ketoacyl synthase, C-terminal domain |
KAsynt_C_assoc | PF16197.12 | 3.2e-11 | 409–515 | Ketoacyl-synthetase C-terminal extension |
Acyl_transf_1 | PF00698.27 | 5.6e-115 | 561–882 | Acyl transferase domain |
SpnB_Rossmann | PF22953.4 | 5.8e-12 | 989–1136 | Polyketide synthase extender module SpnB, Rossmann fold domain |
KR | PF08659.17 | 1.9e-48 | 1152–1327 | KR domain |
adh_short | PF00106.32 | 3.3e-12 | 1155–1308 | short chain dehydrogenase |
PP-binding | PF00550.32 | 2.0e-12 | 1431–1494 | Phosphopantetheine attachment site |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: fas (fatty acid synthase), high confidence from genomic context alone (score 1000 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2524c fas |
fatty acid synthase | 999 | 1000 ctx | neighborhood:544 coexpression:846 experimental:994 database:549 textmining:699 |
Rv2933 ppsC |
phthiocerol synthesis polyketide synthase type I PpsC | 998 | 996 ctx | neighborhood:892 experimental:458 database:900 textmining:545 |
Rv2931 ppsA |
phthiocerol synthesis polyketide synthase type I PpsA | 997 | 996 ctx | neighborhood:800 coexpression:802 database:900 |
Rv2930 fadD26 |
fatty-acid--CoA ligase FadD26 | 995 | 993 ctx | neighborhood:801 coexpression:779 database:650 |
Rv2935 ppsE |
phthiocerol synthesis polyketide synthase type I PpsE | 990 | 988 ctx | neighborhood:798 database:900 |
Rv2934 ppsD |
phthiocerol synthesis polyketide synthase type I PpsD | 987 | 986 ctx | neighborhood:780 database:900 |
Rv2383c mbtB |
phenyloxazoline synthase | 994 | 981 ctx | neighborhood:544 coexpression:881 experimental:473 textmining:744 |
Rv0101 nrp |
peptide synthetase Nrp | 985 | 972 ctx | neighborhood:527 cooccurence:563 coexpression:768 experimental:473 textmining:501 |
Rv2243 fabD |
malonyl CoA-acyl carrier protein transacylase | 976 | 969 | coexpression:671 experimental:787 database:549 |
Rv2928 tesA |
thioesterase TesA | 937 | 919 ctx | cooccurence:719 database:500 |
Rv1181 pks4 |
polyketide beta-ketoacyl synthase | 940 | 915 ctx | neighborhood:481 database:720 |
Rv2380c mbtE |
peptide synthetase | 926 | 902 ctx | cooccurence:584 coexpression:452 experimental:473 |
Rv2948c fadD22 |
p-hydroxybenzoyl--AMP ligase | 903 | 891 | coexpression:770 |
Rv3800c pks13 |
polyketide synthase | 941 | 890 ctx | neighborhood:544 coexpression:660 textmining:484 |
Rv2950c fadD29 |
long-chain-fatty-acid--AMP ligase FadD29 | 903 | 876 | database:650 |
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: phthiocerol synthesis polyketide synthase type I PpsB
- MTBC0 PGAP product: phthiocerol type I polyketide synthase PpsB
- Pfam (hmmscan --cut_ga): ketoacyl-synt PF00109.33 (E=3e-101), Ketoacyl-synt_C PF02801.29 (E=3e-41), KAsynt_C_assoc PF16197.12 (E=3e-11), Acyl_transf_1 PF00698.27 (E=6e-115), SpnB_Rossmann PF22953.4 (E=6e-12), KR PF08659.17 (E=2e-48), adh_short PF00106.32 (E=3e-12), PP-binding PF00550.32 (E=2e-12)
- (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_217448.1)
- Domains: Pfam-A via hmmscan --cut_ga — ketoacyl-synt (PF00109.33), Ketoacyl-synt_C (PF02801.29), KAsynt_C_assoc (PF16197.12), Acyl_transf_1 (PF00698.27), SpnB_Rossmann (PF22953.4), KR (PF08659.17), adh_short (PF00106.32), 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
COG1020 - Curated reference: UniProt P9WQE5 (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 —
314 functional partner(s); context anchor
fas - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003115|Rv2932|ppsB MMRTAFSRISGMTAQQRTSLADEFDRVSRIAVAEPVAVVGIGCRFPGDVDGPESFWDFLVAGRNAISTVPADRWDAEAFYHPDPLTPGRMTTKWGGFVPDVAGFDAEFFGITPREAAAMDPQQRMLLEVAWEALEHAGIPPDSLGGTRTAVMMGVYFNEYQSMLAASPQNVDAYSGTGNAHSITVGRISYLLGLRGPAVAVDTACSSSLVAVHLACQSLRLRETDLALAGGVSITLRPETQIAISAWGLLSPQGRCAAFDAAADGFVRGEGAGVVVLKRLTDAVRDGDQVLAVVRGSAVNQDGRSNGVTAPNTAAQCDVIADALRSGDVAPDSVNYVEAHGTGTVLGDPIEFEALAATYGHGGDACALGAVKTNIGHLEAAAGIAGFIKATLAVQRATIPPNLHFSQWNPAIDAASTRFFVPTQNSPWPTAEGPRRAAVSSFGLGGTNAHVIIEQGSELAPVSEGGEDTGVSTLVVTGKTAQRMAATAQVLADWMEGPGAEVAVADVAHTVNHHRARQATFGTVVARDRAQAIAGLRALAAGQHAPGVVSHQDGSPGPGTVFVYSGRGSQWAGMGRQLLADEPAFAAAVAELEPVFVEQAGFSLRDVIATGKELVGIEQIQLGLIGMQLTLTELWRSYGVQPDLVIGHSMGEVAAAVVAGALTPAEGLRVTATRARLMAPLSGQGGMALLGLDAAATEALIADYPQVTVGIYNSPRQTVIAGPTEQIDELIARVRAQNRFASRVNIEVAPHNPAMDALQPAMRSELADLTPRTPTIGIISTTYADLHTQPIFDAEHWATNMRNPVRFQQAIASAGSGADGAYHTFIEISAHPLLTQAIADTLEDAHRPTKSAAKYLSIGTLQRDADDTVTFRTNLYTADIAHPPHTCHPPEPHPTIPTTPWQHTHHWIATTHPSTAAPEDPGSNKVVVNGQSTSESRALEDWCHQLAWPIRPAVSADPPSTAAWLVVADNELCHELARAADSRVDSLSPPALAAGSDPAALLDALRGVDNVLYAPPVPGELLDIESAYQVFHATRRLAAAMVASSATAISPPKLFIMTRNAQPISEGDRANPGHAVLWGLGRSLALEHPEIWGGIIDLDDSMPAELAVRHVLTAAHGTDGEDQVVYRSGARHVPRLQRRTLPGKPVTLNADASQLVIGATGNIGPHLIRQLARMGAKTIVAMARKPGALDELTQCLAATGTDLIAVAADATDPAAMQTLFDRFGTELPPLEGIYLAAFAGRPALLSEMTDDDVTTMFRPKLDALALLHRLSLKSPVRHFVLFSSVSGLLGSRWLAHYTATSAFLDSFAGARRTMGLPATVVDWGLWKSLADVQKDATQISAESGLQPMADEVAIGALPLVMNPDAAVATVVVAADWPLLAAAYRTRGALRIVDDLLPAPEDVGKGESEFRTSLRSCPAEKRRDMLFDHVGALAATVMGMPPTEPLDPSAGFFQLGMDSLMSVTLQRALSESLGEFLPASVVFDYPTVYSLTDYLATVLPELLEIGATAVATQQATDSYHELTEAELLEQLSERLRGTQ