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Fig. 4 | BMC Genomics

Fig. 4

From: New insights into the genome of Rhodococcus ruber strain Chol-4

Fig. 4

Gene clusters putatively involved in aromatic compounds catabolism identified in R. ruber Chol-4 and its comparison with R. jostii RHA1. Abbreviations: I) ketoadipate pathway: catR: transcriptional regulator CatR; catA: catechol 1,2 dioyxigenase; catB: muconate cycloisomerase; catC: mucolactone isomerase; pcaJ: succinyl-CoA:3-ketoacid-coenzyme A transferase subunit B; pcaI: succinyl-CoA:3-ketoacid-coenzyme A transferase subunit A; pcaH: protocatechuate 3,4-dioxygenase β chain; pcaG: protocatechuate 3,4-dioxygenase α chain; pcaB: 3-carboxy-cis,cis-muconate cycloisomerase; pcaL: 4-carboxymuconolactone decarboxylase; pcaR: Pca regulon regulatory protein; pcaF: β-ketoadipyl-CoA thiolase. III) 2-hydroxypentandienoate pathway: nit: nitrilotriacetate monooxy7genase component B; xylF: 2-hydroxymuconic semialdehyde hydrolase; hsaE: 2-hydroxypentadienoate hydratase; hsaG: acetaldehyde dehydrogenase, acetylating, it is found in gene cluster for degradation of phenols, cresols, catechol; hsaF: 4-hydroxy-2-oxovalerate aldolase; hyd: hydroxylase; bphC: 2,3-dihydroxybiphenyl 1,2-dioxygenase; hsd4B: enoyl-CoA hydratase; kstD: 3-ketosteroid-Δ1-dehydrogenase. IV) gentisate pathway: 3hb6h:3-hydroxybenzoate 6-hydroxylase; benK: benzoate MFS transporter; genR: transcriptional regulator (IclR family); genA: gentisate 1,2-dioxygenase; genB: fumarylpyruvate hydrolase; genC: maleylpyruvate isomerase, mycothiol-dependent; xylF: 2-hydroxymuconic semialdehyde hydrolase; paa-oxy: 4-hydroxyphenylacetate 3-monooxygenase; oxo-red:3-oxoacyl-[acyl-carrier protein] reductase; xylE: catechol 2,3-dioxygenase; retron: retron-type RNA-directed DNA polymerase. V) homogentisate pathway: lp: uncharacterized protein Rv2599/MT2674 precursor; lipoprotein; hmgR: transcriptional regulator (MarR family); hmgA: homogentisate 1,2-dioxygenase; hmgB: fumarylacetoacetate hydrolase; ech: enoyl-CoA hydratase; acs: acetoacetyl-CoA synthetase, long-chain-fatty-acid-CoA ligase. VI) hydroxyquinol pathway: sh: salicylate hydroxylase; lCoA: long chain fatty acid CoA ligase; ad: acyl dehydratase; fm: FAD-binding monoxigenase; dh: iron-containing alcohol dehydrogenase; dxnF: hydroxyquinol 1,2-dioxygenase. VII) homoprotocatechuate pathway: xylE, hsaG, hsaF are previously described; chdh: 5-carboxymethyl-2-hydroxymuconate semialdehyde dehydrogenase; scdh: putative short chain dehydrogenase; tau: 4-oxalocrotonate tautomerase; nit: NADH-FMN oxidoreductase-nitrilotriacetate monooxygenase component B; hpa: 4-hydroxyphenylacetate 3-monooxygenase. VIII) A central pathway with an unknown substrate described in R. jostii RHA1: duf1486: protein of unknown function DUF1486 (probable NADH dehydrogenase/NAD(P)H nitroreductase); acDH: acyl-CoA dehydrogenase, type 2, C-terminal domain; dbps:3,4-dihydroxy-2-butanone 4-phosphate synthase /GTP cyclohydrolase II; ox: NADH-FMN oxidoreductase; dhbdII: biphenyl-2,3-diol-1,2-dioxygenase II (2,3-dihydroxybiphenyl dioxygenase II); hpcE: possible fumarylacetoacetate hydrolase; hyd: FAD-binding monooxygenase (PheA/TfdB family), conserved hypothetical hydroxylase, similar to 2,4-dichlorophenol 6-monooxygenase; syn: acetoacetyl-CoA synthetase; asnC: transcriptional regulator (AsnC family); pyrDH: pyruvate dehydrogenase E1 component. All R. jostii RHA1 genes have the prefix “RHA1_” not included in the figure

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