Name: Caballeronia choica CCUG 63063
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 156584

Type strain:

Species: Caballeronia choica

Culture col. no.: CCUG 63063, LMG 22940

NCBI tax ID(s): 326476 (species)

SI-ID 136998

LMG 22940, CCUG 63063

Section

Caballeronia choica CCUG 63063 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from Rhizosphere soil.

Gram-negative
aerobe
mesophilic
Bacteria
genome sequence

Information on the name and the taxonomic classification. Name and taxonomic classification

	Last LPSN update	14-12-2023 (DD-MM-YYYY)
	Domain	"Bacteria"
	Phylum	*Pseudomonadota*
	Class	*Betaproteobacteria*
	Order	*Burkholderiales*
	Family	*Burkholderiaceae*
	Genus	*Caballeronia*
	Species	**Caballeronia choica**
	Full Scientific Name (LPSN)	Caballeronia choica (Vandamme et al. 2013) Dobritsa and Samadpour 2016

	Synonym	"Paraburkholderia* choica"*
	Synonym	Burkholderia choica

Information on morphological and physiological properties Morphology

[Ref.: #69480]

Gram stain

negative Confidence in %99.993

[Ref.: #62941]

Incubation period

>3 days

Information on culture and growth conditions Culture and growth conditions

	Temperatures	Kind of temperature		Temperature
[Ref.: #62941]			growth	30 °C

[Ref.: #62941]

Temperature range

mesophilic

Information on physiology and metabolism Physiology and metabolism

[Ref.: #62941]

Oxygen tolerance

aerobe

[Ref.: #69480]	Ability of spore formation	no Confidence in %99.997
[Ref.: #69481]	Ability of spore formation	no Confidence in %100

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	resorcinol degradation	100	2 of 2
[Ref.: #66794]	acetate fermentation	100	4 of 4
[Ref.: #66794]	octane oxidation	100	3 of 3
[Ref.: #66794]	ethanol fermentation	100	2 of 2
[Ref.: #66794]	threonine metabolism	100	10 of 10
[Ref.: #66794]	4-hydroxymandelate degradation	100	9 of 9
[Ref.: #66794]	gallate degradation	100	5 of 5
[Ref.: #66794]	methanofuran biosynthesis	100	5 of 5
[Ref.: #66794]	Entner Doudoroff pathway	100	10 of 10
[Ref.: #66794]	cis-vaccenate biosynthesis	100	2 of 2
[Ref.: #66794]	propanol degradation	100	7 of 7
[Ref.: #66794]	photosynthesis	100	14 of 14
[Ref.: #66794]	palmitate biosynthesis	100	22 of 22
[Ref.: #66794]	valine metabolism	100	9 of 9
[Ref.: #66794]	ketogluconate metabolism	100	8 of 8
[Ref.: #66794]	butanoate fermentation	100	4 of 4
[Ref.: #66794]	quinate degradation	100	2 of 2
[Ref.: #66794]	lipoate biosynthesis	100	5 of 5
[Ref.: #66794]	ppGpp biosynthesis	100	4 of 4
[Ref.: #66794]	methylglyoxal degradation	100	5 of 5
[Ref.: #66794]	starch degradation	100	10 of 10
[Ref.: #66794]	biotin biosynthesis	100	4 of 4
[Ref.: #66794]	glycogen metabolism	100	5 of 5
[Ref.: #66794]	adipate degradation	100	2 of 2
[Ref.: #66794]	coenzyme A metabolism	100	4 of 4
[Ref.: #66794]	formaldehyde oxidation	100	3 of 3
[Ref.: #66794]	suberin monomers biosynthesis	100	2 of 2
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	cyanate degradation	100	3 of 3
[Ref.: #66794]	taurine degradation	100	1 of 1
[Ref.: #66794]	ubiquinone biosynthesis	100	7 of 7
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	ceramide biosynthesis	100	1 of 1
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	phenylacetate degradation (aerobic)	100	5 of 5
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	NAD metabolism	94.44	17 of 18
[Ref.: #66794]	citric acid cycle	92.86	13 of 14
[Ref.: #66794]	vitamin B1 metabolism	92.31	12 of 13
[Ref.: #66794]	phenylalanine metabolism	92.31	12 of 13
[Ref.: #66794]	leucine metabolism	92.31	12 of 13
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	91.67	11 of 12
[Ref.: #66794]	pentose phosphate pathway	90.91	10 of 11
[Ref.: #66794]	molybdenum cofactor biosynthesis	88.89	8 of 9
[Ref.: #66794]	chorismate metabolism	88.89	8 of 9
[Ref.: #66794]	CO2 fixation in Crenarchaeota	88.89	8 of 9
[Ref.: #66794]	serine metabolism	88.89	8 of 9
[Ref.: #66794]	dTDPLrhamnose biosynthesis	87.5	7 of 8
[Ref.: #66794]	arginine metabolism	87.5	21 of 24
[Ref.: #66794]	gluconeogenesis	87.5	7 of 8
[Ref.: #66794]	isoleucine metabolism	87.5	7 of 8
[Ref.: #66794]	3-phenylpropionate degradation	86.67	13 of 15
[Ref.: #66794]	alanine metabolism	86.21	25 of 29
[Ref.: #66794]	tetrahydrofolate metabolism	85.71	12 of 14
[Ref.: #66794]	heme metabolism	85.71	12 of 14
[Ref.: #66794]	reductive acetyl coenzyme A pathway	85.71	6 of 7
[Ref.: #66794]	glutamate and glutamine metabolism	85.71	24 of 28
[Ref.: #66794]	phenol degradation	85	17 of 20
[Ref.: #66794]	degradation of sugar acids	84	21 of 25
[Ref.: #66794]	selenocysteine biosynthesis	83.33	5 of 6
[Ref.: #66794]	vitamin B12 metabolism	82.35	28 of 34
[Ref.: #66794]	degradation of pentoses	82.14	23 of 28
[Ref.: #66794]	proline metabolism	81.82	9 of 11
[Ref.: #66794]	vitamin B6 metabolism	81.82	9 of 11
[Ref.: #66794]	tryptophan metabolism	81.58	31 of 38
[Ref.: #66794]	methionine metabolism	80.77	21 of 26
[Ref.: #66794]	myo-inositol biosynthesis	80	8 of 10
[Ref.: #66794]	ethylmalonyl-CoA pathway	80	4 of 5
[Ref.: #66794]	flavin biosynthesis	80	12 of 15
[Ref.: #66794]	3-chlorocatechol degradation	80	4 of 5
[Ref.: #66794]	4-hydroxyphenylacetate degradation	80	8 of 10
[Ref.: #66794]	hydrogen production	80	4 of 5
[Ref.: #66794]	propionate fermentation	80	8 of 10
[Ref.: #66794]	tyrosine metabolism	78.57	11 of 14
[Ref.: #66794]	lysine metabolism	78.57	33 of 42
[Ref.: #66794]	allantoin degradation	77.78	7 of 9
[Ref.: #66794]	aspartate and asparagine metabolism	77.78	7 of 9
[Ref.: #66794]	lipid A biosynthesis	77.78	7 of 9
[Ref.: #66794]	urea cycle	76.92	10 of 13
[Ref.: #66794]	sulfate reduction	76.92	10 of 13
[Ref.: #66794]	glycolysis	76.47	13 of 17
[Ref.: #66794]	bile acid biosynthesis, neutral pathway	76.47	13 of 17
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
[Ref.: #66794]	toluene degradation	75	3 of 4
[Ref.: #66794]	C4 and CAM-carbon fixation	75	6 of 8
[Ref.: #66794]	sulfopterin metabolism	75	3 of 4
[Ref.: #66794]	degradation of sugar alcohols	75	12 of 16
[Ref.: #66794]	CMP-KDO biosynthesis	75	3 of 4
[Ref.: #66794]	glycogen biosynthesis	75	3 of 4
[Ref.: #66794]	purine metabolism	74.47	70 of 94
[Ref.: #66794]	lipid metabolism	74.19	23 of 31
[Ref.: #66794]	peptidoglycan biosynthesis	73.33	11 of 15
[Ref.: #66794]	cysteine metabolism	72.22	13 of 18
[Ref.: #66794]	glutathione metabolism	71.43	10 of 14
[Ref.: #66794]	cardiolipin biosynthesis	71.43	5 of 7
[Ref.: #66794]	oxidative phosphorylation	71.43	65 of 91
[Ref.: #66794]	histidine metabolism	68.97	20 of 29
[Ref.: #66794]	androgen and estrogen metabolism	68.75	11 of 16
[Ref.: #66794]	acetyl CoA biosynthesis	66.67	2 of 3
[Ref.: #66794]	glycolate and glyoxylate degradation	66.67	4 of 6
[Ref.: #66794]	methane metabolism	66.67	2 of 3
[Ref.: #66794]	degradation of hexoses	66.67	12 of 18
[Ref.: #66794]	sulfoquinovose degradation	66.67	2 of 3
[Ref.: #66794]	IAA biosynthesis	66.67	2 of 3
[Ref.: #66794]	L-lactaldehyde degradation	66.67	2 of 3
[Ref.: #66794]	acetoin degradation	66.67	2 of 3
[Ref.: #66794]	enterobactin biosynthesis	66.67	2 of 3
[Ref.: #66794]	d-mannose degradation	66.67	6 of 9
[Ref.: #66794]	non-pathway related	65.79	25 of 38
[Ref.: #66794]	pyrimidine metabolism	64.44	29 of 45
[Ref.: #66794]	phosphatidylethanolamine bioynthesis	61.54	8 of 13
[Ref.: #66794]	coenzyme M biosynthesis	60	6 of 10
[Ref.: #66794]	creatinine degradation	60	3 of 5
[Ref.: #66794]	cellulose degradation	60	3 of 5
[Ref.: #66794]	vitamin K metabolism	60	3 of 5
[Ref.: #66794]	isoprenoid biosynthesis	57.69	15 of 26
[Ref.: #66794]	polyamine pathway	56.52	13 of 23
[Ref.: #66794]	metabolism of disaccharids	54.55	6 of 11
[Ref.: #66794]	cholesterol biosynthesis	54.55	6 of 11
[Ref.: #66794]	d-xylose degradation	54.55	6 of 11
[Ref.: #66794]	glycine metabolism	50	5 of 10
[Ref.: #66794]	ribulose monophosphate pathway	50	1 of 2
[Ref.: #66794]	carnitine metabolism	50	4 of 8
[Ref.: #66794]	phenylmercury acetate degradation	50	1 of 2
[Ref.: #66794]	cyclohexanol degradation	50	2 of 4
[Ref.: #66794]	ascorbate metabolism	50	11 of 22
[Ref.: #66794]	aminopropanol phosphate biosynthesis	50	1 of 2
[Ref.: #66794]	lactate fermentation	50	2 of 4
[Ref.: #66794]	kanosamine biosynthesis II	50	1 of 2
[Ref.: #66794]	pantothenate biosynthesis	50	3 of 6
[Ref.: #66794]	dolichol and dolichyl phosphate biosynthesis	50	1 of 2
[Ref.: #66794]	dolichyl-diphosphooligosaccharide biosynthesis	45.45	5 of 11
[Ref.: #66794]	arachidonic acid metabolism	44.44	8 of 18
[Ref.: #66794]	nitrate assimilation	44.44	4 of 9
[Ref.: #66794]	benzoyl-CoA degradation	42.86	3 of 7
[Ref.: #66794]	methanogenesis from CO2	41.67	5 of 12
[Ref.: #66794]	carotenoid biosynthesis	40.91	9 of 22
[Ref.: #66794]	metabolism of amino sugars and derivatives	40	2 of 5
[Ref.: #66794]	arachidonate biosynthesis	40	2 of 5
[Ref.: #66794]	O-antigen biosynthesis	40	2 of 5
[Ref.: #66794]	glycine betaine biosynthesis	40	2 of 5
[Ref.: #66794]	sphingosine metabolism	33.33	2 of 6
[Ref.: #66794]	chlorophyll metabolism	33.33	6 of 18
[Ref.: #66794]	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
[Ref.: #66794]	phenylpropanoid biosynthesis	30.77	4 of 13
[Ref.: #66794]	aclacinomycin biosynthesis	28.57	2 of 7
[Ref.: #66794]	vitamin E metabolism	25	1 of 4
[Ref.: #66794]	catecholamine biosynthesis	25	1 of 4
[Ref.: #66794]	daunorubicin biosynthesis	22.22	2 of 9
		Only first 10 entries are displayed. Click here to see all.

Information on isolation source, the sampling and environmental conditions Isolation, sampling and environmental information

[Ref.: #62941]	Sample type/isolated from	Rhizosphere soil
[Ref.: #62941]	Sampling date	2003
[Ref.: #62941]	Country	Netherlands
[Ref.: #62941]	Country ISO 3 Code	NLD
[Ref.: #62941]	Continent	Europe
* marker position based on {}

Isolation sources categories

#Environmental	#Terrestrial	#Soil
#Host Body-Site	#Plant	#Rhizosphere
#Host	#Plants	-

What are isolation sources categories?

Information on genomic background e.g. entries in nucleic sequence databass Sequence information

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Caballeronia choica LMG 22940	GCA_001544535	contig	GenBank	326476 tax ID	*
[Ref.: #66792]	Burkholderia choica strain LMG 22940	326476.3	wgs	PATRIC	326476 tax ID	*
[Ref.: #66792]	Caballeronia choica LMG 22940	2724679467	draft	JGI IMG/M	326476 tax ID	*

Data predicted using genome information as a basis Genome-based predictions

	Trait	Prediction	Confidence in %	In training data
	Predictions from GenomeNet Sporulation v. 1 based on: Burkholderia choica strain LMG 22940 PATRIC: 326476.3
[Ref.: #69481]	spore-forming	no	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Burkholderia choica strain LMG 22940 PATRIC: 326476.3
[Ref.: #69480]	gram-positive	no	98.135	no
[Ref.: #69480]	anaerobic	no	98.726	yes
[Ref.: #69480]	halophile	no	93.6	no
[Ref.: #69480]	spore-forming	no	92.999	no
[Ref.: #69480]	glucose-util	yes	87.937	no
[Ref.: #69480]	motile	yes	83.928	no
[Ref.: #69480]	flagellated	no	86.509	no
[Ref.: #69480]	aerobic	yes	91.606	no
[Ref.: #69480]	thermophile	no	99.49	yes
[Ref.: #69480]	glucose-ferment	no	88.594	no

Availability in culture collections External links

[Ref.: #62941]

Culture collection no.

CCUG 63063, LMG 22940

[Ref.: #109797]

SI-ID 136998

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Caballeronia ginsengisoli sp. nov., isolated from ginseng cultivating soil.	Quan XT, Liu QZ, Siddiqi MZ, Im WT	Arch Microbiol	10.1007/s00203-018-1577-0	2018	*
Phylogeny	Burkholderia jiangsuensis sp. nov., a methyl parathion degrading bacterium, isolated from methyl parathion contaminated soil.	Liu XY, Li CX, Luo XJ, Lai QL, Xu JH	Int J Syst Evol Microbiol	10.1099/ijs.0.064444-0	2014	*
Phylogeny	Burkholderia humi sp. nov., Burkholderia choica sp. nov., Burkholderia telluris sp. nov., Burkholderia terrestris sp. nov. and Burkholderia udeis sp. nov.: Burkholderia glathei-like bacteria from soil and rhizosphere soil.	Vandamme P, De Brandt E, Houf K, Salles JF, Dirk van Elsas J, Spilker T, LiPuma JJ	Int J Syst Evol Microbiol	10.1099/ijs.0.048900-0	2013	*

References

#20215

Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.: List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ. IJSEM ( DOI 10.1099/ijsem.0.004332 )

#62941 Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 63063

#66792

Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann: Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) .

#66794

Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg: BRENDA, the ELIXIR core data resource in 2021: new developments and updates. Nucleic Acids Res. 49: D498 - D508 2020 ( DOI 10.1093/nar/gkaa1025 , PubMed 33211880 )

#69480

Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann: Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) .

#69481

Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch: Predictions based on the model GenomeNet Sporulation v. 1 . ( DOI 10.21203/rs.3.rs-2527258/v1 )

#109797

Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.: StrainInfo: A central database for resolving microbial strain identifiers . ( DOI 10.60712/SI-ID136998.1 )

* These data were automatically processed and therefore are not curated

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Burkholderia choica strain LMG 22940

Burkholderia choica strain LMG 22940

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