Cite this strain

Paracoccus yeei (CCUG 32053)

Name: Paracoccus yeei (CCUG 32053)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 146746

Type strain

Culture col. no. CCUG 32053

NCBI tax ID(s) 147645

Special Collections CCUG

Links

Paracoccus yeei CCUG 32053 is an aerobe, mesophilic prokaryote that was isolated from Human eye.

aerobe mesophilic genome sequence

Name and taxonomic classification

SI-ID 52630

CCUG 32053

@ref 20215

Last LPSN update 2025-12-16 10:05:10

Domain Pseudomonadati

Phylum Pseudomonadota

Class Alphaproteobacteria

Order Rhodobacterales

Family Paracoccaceae

Genus Paracoccus

Species Paracoccus yeei

Full scientific name Paracoccus yeei corrig. Daneshvar et al. 2003

Synonyms (1)

Paracoccus yeeii

BacDive ID	Other strains from **Paracoccus yeei** (30)	Type strain
137365	P. yeei G 1212, CIP 108092, CCUG 46822, ATCC BAA-599, ... (type strain)
13723	P. yeei ES-MS9, DSM 30768
13724	P. yeei RW15/1, DSM 30795
13725	P. yeei TS1/3, DSM 30807
100204	P. yeei ST027320(HKI), F153, Nü44,
100205	P. yeei ST033152(HKI),
130618	P. yeei T2_52, DSM 31001
131137	P. yeei T4_9, DSM 100543
131138	P. yeei T4_11, DSM 100544
131139	P. yeei T4_19, DSM 100548
131140	P. yeei T4_23, DSM 100549
131141	P. yeei T3_3, DSM 31032
142638	P. yeei CCUG 13493
143200	P. yeei CCUG 17731
146745	P. yeei CCUG 32052
146747	P. yeei CCUG 32054
154523	P. yeei CCUG 54214
155543	P. yeei CCUG 58067
155889	P. yeei CCUG 59568
156680	P. yeei CCUG 64097
157131	P. yeei CCUG 69643
157195	P. yeei CCUG 70392
157408	P. yeei IMI 505656
158096	P. yeei 2eA_C30, DSM 103913
158097	P. yeei 2fA_C32, DSM 103914
158098	P. yeei Turin130318_C1, DSM 107229
158099	P. yeei TURIN130318_C8, DSM 107236
159522	P. yeei K26-10, DSM 109539
175232	P. yeei 114828, DSM 114828
175233	P. yeei 114829, DSM 114829

Morphology

Cell morphology

@ref	Gram stain	Confidence
125439	negative	99.6
125438	negative	98.482

Culture and growth conditions

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
50798	positive	growth	30-37	mesophilic

Physiology and metabolism

Oxygen tolerance

50798

Oxygen toleranceaerobe

Spore formation

@ref	Spore formation	Confidence
125439		98.7

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
68369	17128 ChEBI	adipate	-	assimilation	from API 20NE
68369	29016 ChEBI	arginine	-	hydrolysis	from API 20NE
68369	17634 ChEBI	D-glucose	-	assimilation	from API 20NE
68369	17634 ChEBI	D-glucose	-	fermentation	from API 20NE
68369	16899 ChEBI	D-mannitol	-	assimilation	from API 20NE
68369	16024 ChEBI	D-mannose	-	assimilation	from API 20NE
68369	27689 ChEBI	decanoate	-	assimilation	from API 20NE
68369	4853 ChEBI	esculin	-	hydrolysis	from API 20NE
68369	5291 ChEBI	gelatin	-	hydrolysis	from API 20NE
68369	24265 ChEBI	gluconate	-	assimilation	from API 20NE
68369	30849 ChEBI	L-arabinose	+	assimilation	from API 20NE
68369	25115 ChEBI	malate	+	assimilation	from API 20NE
68369	17306 ChEBI	maltose	-	assimilation	from API 20NE
68369	59640 ChEBI	N-acetylglucosamine	-	assimilation	from API 20NE
68369	17632 ChEBI	nitrate	+	reduction	from API 20NE
68369	27897 ChEBI	tryptophan	-	energy source	from API 20NE
68369	16199 ChEBI	urea	+	hydrolysis	from API 20NE

Metabolite production

@ref	Chebi-ID	Metabolite	Production
68369	35581 ChEBI	indole		from API 20NE

Metabolite tests

@ref	Chebi-ID	Metabolite	Indole test
68369	35581 ChEBI	indole	-	from API 20NE

Enzymes

@ref	Value	Activity	Ec
68369	arginine dihydrolase	-	3.5.3.6	from API 20NE
68369	beta-glucosidase	-	3.2.1.21	from API 20NE
68369	cytochrome oxidase	+	1.9.3.1	from API 20NE
68369	gelatinase	-		from API 20NE
68369	urease	+	3.5.1.5	from API 20NE

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	quinate degradation	100	2 of 2
66794	reductive acetyl coenzyme A pathway	100	7 of 7
66794	formaldehyde oxidation	100	3 of 3
66794	adipate degradation	100	2 of 2
66794	coenzyme A metabolism	100	4 of 4
66794	glycogen biosynthesis	100	4 of 4
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	methane metabolism	100	3 of 3
66794	molybdenum cofactor biosynthesis	100	9 of 9
66794	ppGpp biosynthesis	100	4 of 4
66794	cardiolipin biosynthesis	100	7 of 7
66794	cis-vaccenate biosynthesis	100	2 of 2
66794	Entner Doudoroff pathway	100	10 of 10
66794	enterobactin biosynthesis	100	3 of 3
66794	allantoin degradation	100	9 of 9
66794	valine metabolism	100	9 of 9
66794	methylglyoxal degradation	100	5 of 5
66794	CMP-KDO biosynthesis	100	4 of 4
66794	palmitate biosynthesis	100	22 of 22
66794	C4 and CAM-carbon fixation	100	8 of 8
66794	ethanol fermentation	100	2 of 2
66794	propanol degradation	100	7 of 7
66794	gluconeogenesis	100	8 of 8
66794	octane oxidation	100	3 of 3
66794	suberin monomers biosynthesis	100	2 of 2
66794	folate polyglutamylation	100	1 of 1
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	photosynthesis	100	14 of 14
66794	citric acid cycle	92.86	13 of 14
66794	glutathione metabolism	92.86	13 of 14
66794	leucine metabolism	92.31	12 of 13
66794	phenylalanine metabolism	92.31	12 of 13
66794	vitamin B12 metabolism	91.18	31 of 34
66794	proline metabolism	90.91	10 of 11
66794	propionate fermentation	90	9 of 10
66794	threonine metabolism	90	9 of 10
66794	chorismate metabolism	88.89	8 of 9
66794	lipid A biosynthesis	88.89	8 of 9
66794	CO2 fixation in Crenarchaeota	88.89	8 of 9
66794	serine metabolism	88.89	8 of 9
66794	4-hydroxymandelate degradation	88.89	8 of 9
66794	isoleucine metabolism	87.5	7 of 8
66794	alanine metabolism	86.21	25 of 29
66794	ubiquinone biosynthesis	85.71	6 of 7
66794	purine metabolism	85.11	80 of 94
66794	pyrimidine metabolism	84.44	38 of 45
66794	glutamate and glutamine metabolism	82.14	23 of 28
66794	glycogen metabolism	80	4 of 5
66794	peptidoglycan biosynthesis	80	12 of 15
66794	hydrogen production	80	4 of 5
66794	ethylmalonyl-CoA pathway	80	4 of 5
66794	phenylacetate degradation (aerobic)	80	4 of 5
66794	cellulose degradation	80	4 of 5
66794	starch degradation	80	8 of 10
66794	degradation of pentoses	78.57	22 of 28
66794	NAD metabolism	77.78	14 of 18
66794	aspartate and asparagine metabolism	77.78	7 of 9
66794	vitamin B1 metabolism	76.92	10 of 13
66794	histidine metabolism	75.86	22 of 29
66794	butanoate fermentation	75	3 of 4
66794	ketogluconate metabolism	75	6 of 8
66794	acetate fermentation	75	3 of 4
66794	biotin biosynthesis	75	3 of 4
66794	sulfopterin metabolism	75	3 of 4
66794	lactate fermentation	75	3 of 4
66794	flavin biosynthesis	73.33	11 of 15
66794	vitamin B6 metabolism	72.73	8 of 11
66794	pentose phosphate pathway	72.73	8 of 11
66794	oxidative phosphorylation	72.53	66 of 91
66794	cysteine metabolism	72.22	13 of 18
66794	degradation of sugar acids	72	18 of 25
66794	heme metabolism	71.43	10 of 14
66794	myo-inositol biosynthesis	70	7 of 10
66794	sulfate reduction	69.23	9 of 13
66794	urea cycle	69.23	9 of 13
66794	methionine metabolism	69.23	18 of 26
66794	lysine metabolism	69.05	29 of 42
66794	degradation of sugar alcohols	68.75	11 of 16
66794	non-pathway related	68.42	26 of 38
66794	tryptophan metabolism	68.42	26 of 38
66794	cyanate degradation	66.67	2 of 3
66794	degradation of hexoses	66.67	12 of 18
66794	glycolate and glyoxylate degradation	66.67	4 of 6
66794	acetyl CoA biosynthesis	66.67	2 of 3
66794	acetoin degradation	66.67	2 of 3
66794	selenocysteine biosynthesis	66.67	4 of 6
66794	d-mannose degradation	66.67	6 of 9
66794	L-lactaldehyde degradation	66.67	2 of 3
66794	glycolysis	64.71	11 of 17
66794	lipid metabolism	64.52	20 of 31
66794	tetrahydrofolate metabolism	64.29	9 of 14
66794	d-xylose degradation	63.64	7 of 11
66794	arginine metabolism	62.5	15 of 24
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	62.5	5 of 8
66794	isoprenoid biosynthesis	61.54	16 of 26
66794	vitamin K metabolism	60	3 of 5
66794	phenol degradation	60	12 of 20
66794	gallate degradation	60	3 of 5
66794	3-phenylpropionate degradation	60	9 of 15
66794	3-chlorocatechol degradation	60	3 of 5
66794	creatinine degradation	60	3 of 5
66794	degradation of aromatic, nitrogen containing compounds	58.33	7 of 12
66794	tyrosine metabolism	57.14	8 of 14
66794	metabolism of disaccharids	54.55	6 of 11
66794	polyamine pathway	52.17	12 of 23
66794	cyclohexanol degradation	50	2 of 4
66794	aminopropanol phosphate biosynthesis	50	1 of 2
66794	ascorbate metabolism	50	11 of 22
66794	ribulose monophosphate pathway	50	1 of 2
66794	dTDPLrhamnose biosynthesis	50	4 of 8
66794	coenzyme M biosynthesis	50	5 of 10
66794	kanosamine biosynthesis II	50	1 of 2
66794	resorcinol degradation	50	1 of 2
66794	glycine metabolism	50	5 of 10
66794	arachidonic acid metabolism	50	9 of 18
66794	phosphatidylethanolamine bioynthesis	46.15	6 of 13
66794	glycine betaine biosynthesis	40	2 of 5
66794	lipoate biosynthesis	40	2 of 5
66794	4-hydroxyphenylacetate degradation	40	4 of 10
66794	arachidonate biosynthesis	40	2 of 5
66794	phenylpropanoid biosynthesis	38.46	5 of 13
66794	androgen and estrogen metabolism	37.5	6 of 16
66794	carotenoid biosynthesis	36.36	8 of 22
66794	nitrate assimilation	33.33	3 of 9
66794	IAA biosynthesis	33.33	1 of 3
66794	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
66794	methanogenesis from CO2	33.33	4 of 12
66794	pantothenate biosynthesis	33.33	2 of 6
66794	sulfoquinovose degradation	33.33	1 of 3
66794	sphingosine metabolism	33.33	2 of 6
66794	benzoyl-CoA degradation	28.57	2 of 7
66794	mevalonate metabolism	28.57	2 of 7
66794	alginate biosynthesis	25	1 of 4
66794	carnitine metabolism	25	2 of 8
66794	toluene degradation	25	1 of 4

API 20NE

@ref	Reduction of nitratesNO3	TRP	GLU_ Ferm	ADH (Arg)	URE	ESC	GEL	PNPG	GLU_ Assim	ARA	MNE	MAN	NAG	MAL	GNT	CAP	ADI	MLT	CIT	PAC	OX
50798	+	-	-	-	+	-	-	-	-	+	-	-	-	-	-	-	-	+	-	-	+

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Host	#Human	-
#Host Body-Site	#Organ	#Eye

Isolation

@ref	Sample type	Sampling date	Geographic location	Country	Country ISO 3 Code	Continent
50798	Human eye	1981	Missouri	USA	USA	North America

Interaction and safety

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	ASM361291v1 assembly for Paracoccus yeei CCUG 32053	complete	GCA_003612915	147645.118	2843173846	147645	97.4

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Paracoccus yeei strain CCUG 32053
PATRIC: 147645.118

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	98.70	no
125439	motility	BacteriaNetⓘ	yes	65.80	no
125439	gram_stain	BacteriaNetⓘ	negative	99.60	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	88.20	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Paracoccus yeei CCUG 32053
NCBI: GCA_003612915.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	98.48	no
125438	anaerobic	anaerobicⓘ	no	95.84	no
125438	aerobic	aerobicⓘ	yes	85.62	yes
125438	spore-forming	spore-formingⓘ	no	88.38	no
125438	thermophilic	thermophileⓘ	no	95.47	no
125438	flagellated	motile2+ⓘ	no	57.57	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Genetics	Genome-wide comparative analysis of clinical and environmental strains of the opportunistic pathogen Paracoccus yeei (Alphaproteobacteria).	Szuplewska M, Sentkowska D, Lasek R, Decewicz P, Halucha M, Funk L, Chmielowska C, Bartosik D.	Front Microbiol	10.3389/fmicb.2024.1483110	2024
Genetics	Metagenome-Assembled Genomes and Metatranscriptome Analysis of Perfluorooctane Sulfonate-Reducing Bacteria Enriched From Activated Sludge.	Sorn S, Matsuura N, Honda R.	Environ Microbiol	10.1111/1462-2920.70087	2025
	A genetic toolbox to empower Paracoccus pantotrophus DSM 2944 as a metabolically versatile SynBio chassis.	Pal U, Bachmann D, Pelzer C, Christiansen J, Blank LM, Tiso T.	Microb Cell Fact	10.1186/s12934-024-02325-0	2024
	Pan-genome analysis of six Paracoccus type strain genomes reveal lifestyle traits.	Hollensteiner J, Schneider D, Poehlein A, Brinkhoff T, Daniel R.	PLoS One	10.1371/journal.pone.0287947	2023
	Genome Structure of the Opportunistic Pathogen Paracoccus yeei (Alphaproteobacteria) and Identification of Putative Virulence Factors.	Lasek R, Szuplewska M, Mitura M, Decewicz P, Chmielowska C, Pawlot A, Sentkowska D, Czarnecki J, Bartosik D	Front Microbiol	10.3389/fmicb.2018.02553	2018

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 )
#50798	Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 32053
#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 )
#68369	Automatically annotated from API 20NE .
#125438	Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann: Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets. 2024 ( DOI 10.1101/2024.08.12.607695 )
#125439	Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardy: deepG: Deep Learning for Genome Sequence Data. R package version 0.3.1 .
#126262	A. Lissin, I. Schober, J. F. Witte, H. Lüken, A. Podstawka, J. Koblitz, B. Bunk, P. Dawyndt, P. Vandamme, P. de Vos, J. Overmann, L. C. Reimer: StrainInfo—the central database for linked microbial strain identifiers. ( DOI 10.1093/database/baaf059 )

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Paracoccus yeei (CCUG 32053)

Name and taxonomic classification

Morphology

Cell morphology

Culture and growth conditions

Culture temp

Physiology and metabolism

Oxygen tolerance

Spore formation

Metabolite utilization

Metabolite production

Metabolite tests

Enzymes

Pathway annotation

API 20NE

Isolation, sampling and environmental information

Isolation source categories

Isolation

Interaction and safety

Sequence information

Genome sequences

Genome browser: GCA_003612915

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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