Rhodococcus opacus DSM 1069

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Rhodococcus opacus DSM 1069

Kingdom: Bacteria
Phylum: Actinobacteria
Class: -
Type: Gram positive
Strain: DSM 1069
Origin (Details): Soil, Finland
Origin (Category): Soil
Genome Sequenced: Yes; strain PD630
Synonyms: Nocardia opaca

Empirical Data

Utilizible (lignin-derived) carbon sources (12) Empirical

NB! Always check the primary references for the experimental details; "utilizable" does not necessarily equal "growth-supporting".

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Substrate	Reference(s)	Comment(s)
3-methoxybenzoic acid	Eggeling et al (1980)	-
4-hydroxybenzoic acid	Kosa et al (2011)	-
base-catalyzed depolymerized lignin	Ravi et al (2018)	-
coniferyl alcohol	Kosa et al (2011) Eggeling et al (1980)	-
guaiacol	Ravi et al (2018)	-
kraft lignin	Wei et al (2015)	(Oxygen-pretreated)
maize straw	Trojanowski et al (1977)	-
organosolv lignin	Wells et al (2015)	(lignocellulosic pretreatment effluent)
p-anisic acid	Eggeling et al (1980)	-
vanillic acid	Kosa et al (2011)	-
vanillyl alcohol	Ravi et al (2018)	-
veratric acid	Eggeling et al (1980)	-

Pathways (1) Empirical

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Pathway Name	Reference(s)
beta-ketoadipate (all branches)	Kosa et al (2011)

Enzymes (0) Empirical

No enzymes listed for this organism.

Transporters (0) Empirical

No transporters listed for this organism.

Genes (0) Empirical

No genes listed for this organism.

Predicted Relationships Hide predicted

The sections below contain relationships inferred from the empirical data above. They are computationally predicted and have not been independently verified. Learn more about data assumptions →

Predicted pathways in Rhodococcus opacus DSM 1069 Predicted

Inferred from reported utilizable carbon sources: if the organism can utilise a compound that enters a pathway as a reactant, it may carry that pathway. Not experimentally verified. What does this mean?

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Predicted pathway	Funneling branch	Inferred via substrate	Reference
coniferyl alcohol	coniferyl branch	coniferyl alcohol	Kosa et al (2011), Eggeling et al (1980)
guaiacol	coniferyl branch	guaiacol, vanillic acid	Ravi et al (2018), Kosa et al (2011)
p-coumaric acid	p-coumaric branch	4-hydroxybenzoic acid	Kosa et al (2011)
vanillin I	coniferyl branch	vanillic acid	Kosa et al (2011)
vanillin II	coniferyl branch	vanillic acid	Kosa et al (2011)

Predicted enzymes in Rhodococcus opacus DSM 1069 Predicted

Inferred from confirmed pathways: if the organism is confirmed to carry a pathway, enzymes known to catalyse reactions in that pathway are predicted to be present. The pathway used for each inference is shown. Not experimentally verified. What does this mean?

Predicted enzyme	Inferred via pathway	Reference
3-carboxy-cis,cis-muconate cycloisomerase	beta-ketoadipate (all branches)	Kosa et al (2011)
3-oxoadipate enol-lactonase	beta-ketoadipate (all branches)	Kosa et al (2011)
4-carboxymuconolactone decarboxylase	beta-ketoadipate (all branches)	Kosa et al (2011)
Protocatechuate 3,4-dioxygenase	beta-ketoadipate (all branches)	Kosa et al (2011)
catechol 1,2-dioxygenase	beta-ketoadipate (all branches)	Kosa et al (2011)
muconate cycloisomerase	beta-ketoadipate (all branches)	Kosa et al (2011)
muconolactone isomerase	beta-ketoadipate (all branches)	Kosa et al (2011)

Culture Collections

Strain	Depository ID
DSM 1069	DSM 1069

Genome Sequencing

Strain	Status	Reference
DSM 1069	Yes; strain PD630	Holder et al (2011)

Other Databases

Database	Comment
NCBI Taxonomy	Taxonomy database

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