Name: Paracoccus sphaerophysae Zy-3
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 133615

Type strain:

Species: Paracoccus sphaerophysae

Strain Designation: Zy-3

Culture col. no.: ACCC 05413, HAMBI 3106

NCBI tax ID(s): 690417 (species)

Section

Paracoccus sphaerophysae Zy-3 is an aerobe, Gram-negative, rod-shaped bacterium that was isolated from plant associated.

Gram-negative
rod-shaped
aerobe
16S sequence
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	*Alphaproteobacteria*
	Order	*Rhodobacterales*
	Family	*Paracoccaceae*
	Genus	*Paracoccus*
	Species	**Paracoccus sphaerophysae**
	Full Scientific Name (LPSN)	Paracoccus sphaerophysae Deng et al. 2011

Information on morphological and physiological properties Morphology

[Ref.: #29792]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %99.991

[Ref.: #29792]	Cell length	1.9 µm

[Ref.: #29792]	Cell width	0.6 µm

[Ref.: #29792]	Cell shape	rod-shaped

[Ref.: #29792]	Motility	no
[Ref.: #69480]	Motility	no Confidence in %94.001

[Ref.: #29792]

Pigment production

yes

Information on culture and growth conditions Culture and growth conditions

	Temperatures	Kind of temperature		Temperature
[Ref.: #29792]			growth	04-60 °C
[Ref.: #29792]			optimum	28 °C

[Ref.: #29792]

Temperature range

mesophilic

	pH	Kind of pH		pH
[Ref.: #29792]			optimum	7.5
[Ref.: #29792]			growth	05-11

Information on physiology and metabolism Physiology and metabolism

[Ref.: #29792]

Oxygen tolerance

aerobe

[Ref.: #29792]	Ability of spore formation	no
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.996

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #29792]		NaCl		growth	01-06	%
[Ref.: #29792]		NaCl		optimum	3	%

[Ref.: #29792]

Observation

aggregates in chains

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #29792]	alanine ChEBI	+	carbon source
[Ref.: #29792]	arabinose ChEBI	+	carbon source
[Ref.: #29792]	arginine ChEBI	+	carbon source
[Ref.: #29792]	asparagine ChEBI	+	carbon source
[Ref.: #29792]	aspartate ChEBI	+	carbon source
[Ref.: #29792]	D-tryptophan ChEBI	+	carbon source
[Ref.: #29792]	fructose ChEBI	+	carbon source
[Ref.: #29792]	galactose ChEBI	+	carbon source
[Ref.: #29792]	glutamate ChEBI	+	carbon source
[Ref.: #29792]	glycerol ChEBI	+	carbon source
[Ref.: #29792]	histidine ChEBI	+	carbon source
[Ref.: #29792]	lactose ChEBI	+	carbon source
[Ref.: #29792]	leucine ChEBI	+	carbon source
[Ref.: #29792]	malonate ChEBI	+	carbon source
[Ref.: #29792]	maltose ChEBI	+	carbon source
[Ref.: #29792]	mannose ChEBI	+	carbon source
[Ref.: #29792]	melibiose ChEBI	+	carbon source
[Ref.: #29792]	pyruvate ChEBI	+	carbon source
[Ref.: #29792]	raffinose ChEBI	+	carbon source
[Ref.: #29792]	rhamnose ChEBI	+	carbon source
[Ref.: #29792]	ribose ChEBI	+	carbon source
[Ref.: #29792]	serine ChEBI	+	carbon source
[Ref.: #29792]	sorbitol ChEBI	+	carbon source
[Ref.: #29792]	succinate ChEBI	+	carbon source
[Ref.: #29792]	threonine ChEBI	+	carbon source
[Ref.: #29792]	xylose ChEBI	+	carbon source
	Only first 10 entries are displayed. Click here to see all.

	Enzyme	Enzyme activity	EC number
[Ref.: #29792]	catalase	+	1.11.1.6
[Ref.: #29792]	cytochrome oxidase	+	1.9.3.1
[Ref.: #29792]	urease	+	3.5.1.5

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	cyanate degradation	100	3 of 3
[Ref.: #66794]	adipate degradation	100	2 of 2
[Ref.: #66794]	cis-vaccenate biosynthesis	100	2 of 2
[Ref.: #66794]	gluconeogenesis	100	8 of 8
[Ref.: #66794]	methylglyoxal degradation	100	5 of 5
[Ref.: #66794]	Entner Doudoroff pathway	100	10 of 10
[Ref.: #66794]	octane oxidation	100	3 of 3
[Ref.: #66794]	palmitate biosynthesis	100	22 of 22
[Ref.: #66794]	ppGpp biosynthesis	100	4 of 4
[Ref.: #66794]	reductive acetyl coenzyme A pathway	100	7 of 7
[Ref.: #66794]	formaldehyde oxidation	100	3 of 3
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	suberin monomers biosynthesis	100	2 of 2
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	L-lactaldehyde degradation	100	3 of 3
[Ref.: #66794]	biotin biosynthesis	100	4 of 4
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	denitrification	100	2 of 2
[Ref.: #66794]	valine metabolism	100	9 of 9
[Ref.: #66794]	proline metabolism	90.91	10 of 11
[Ref.: #66794]	lipid A biosynthesis	88.89	8 of 9
[Ref.: #66794]	molybdenum cofactor biosynthesis	88.89	8 of 9
[Ref.: #66794]	allantoin degradation	88.89	8 of 9
[Ref.: #66794]	chorismate metabolism	88.89	8 of 9
[Ref.: #66794]	ketogluconate metabolism	87.5	7 of 8
[Ref.: #66794]	C4 and CAM-carbon fixation	87.5	7 of 8
[Ref.: #66794]	vitamin B12 metabolism	85.29	29 of 34
[Ref.: #66794]	leucine metabolism	84.62	11 of 13
[Ref.: #66794]	pyrimidine metabolism	82.22	37 of 45
[Ref.: #66794]	purine metabolism	80.85	76 of 94
[Ref.: #66794]	vitamin K metabolism	80	4 of 5
[Ref.: #66794]	peptidoglycan biosynthesis	80	12 of 15
[Ref.: #66794]	threonine metabolism	80	8 of 10
[Ref.: #66794]	ethylmalonyl-CoA pathway	80	4 of 5
[Ref.: #66794]	photosynthesis	78.57	11 of 14
[Ref.: #66794]	glutamate and glutamine metabolism	78.57	22 of 28
[Ref.: #66794]	serine metabolism	77.78	7 of 9
[Ref.: #66794]	CO2 fixation in Crenarchaeota	77.78	7 of 9
[Ref.: #66794]	d-mannose degradation	77.78	7 of 9
[Ref.: #66794]	vitamin B1 metabolism	76.92	10 of 13
[Ref.: #66794]	phenylalanine metabolism	76.92	10 of 13
[Ref.: #66794]	sulfopterin metabolism	75	3 of 4
[Ref.: #66794]	butanoate fermentation	75	3 of 4
[Ref.: #66794]	isoleucine metabolism	75	6 of 8
[Ref.: #66794]	lactate fermentation	75	3 of 4
[Ref.: #66794]	CMP-KDO biosynthesis	75	3 of 4
[Ref.: #66794]	acetate fermentation	75	3 of 4
[Ref.: #66794]	flavin biosynthesis	73.33	11 of 15
[Ref.: #66794]	histidine metabolism	72.41	21 of 29
[Ref.: #66794]	alanine metabolism	72.41	21 of 29
[Ref.: #66794]	glutathione metabolism	71.43	10 of 14
[Ref.: #66794]	lysine metabolism	71.43	30 of 42
[Ref.: #66794]	citric acid cycle	71.43	10 of 14
[Ref.: #66794]	cardiolipin biosynthesis	71.43	5 of 7
[Ref.: #66794]	ubiquinone biosynthesis	71.43	5 of 7
[Ref.: #66794]	oxidative phosphorylation	69.23	63 of 91
[Ref.: #66794]	selenocysteine biosynthesis	66.67	4 of 6
[Ref.: #66794]	acetoin degradation	66.67	2 of 3
[Ref.: #66794]	aspartate and asparagine metabolism	66.67	6 of 9
[Ref.: #66794]	methionine metabolism	65.38	17 of 26
[Ref.: #66794]	isoprenoid biosynthesis	65.38	17 of 26
[Ref.: #66794]	glycolysis	64.71	11 of 17
[Ref.: #66794]	degradation of pentoses	64.29	18 of 28
[Ref.: #66794]	heme metabolism	64.29	9 of 14
[Ref.: #66794]	vitamin B6 metabolism	63.64	7 of 11
[Ref.: #66794]	pentose phosphate pathway	63.64	7 of 11
[Ref.: #66794]	degradation of sugar alcohols	62.5	10 of 16
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	62.5	5 of 8
[Ref.: #66794]	urea cycle	61.54	8 of 13
[Ref.: #66794]	NAD metabolism	61.11	11 of 18
[Ref.: #66794]	tryptophan metabolism	60.53	23 of 38
[Ref.: #66794]	non-pathway related	60.53	23 of 38
[Ref.: #66794]	phenylacetate degradation (aerobic)	60	3 of 5
[Ref.: #66794]	hydrogen production	60	3 of 5
[Ref.: #66794]	propionate fermentation	60	6 of 10
[Ref.: #66794]	arginine metabolism	58.33	14 of 24
[Ref.: #66794]	tyrosine metabolism	57.14	8 of 14
[Ref.: #66794]	tetrahydrofolate metabolism	57.14	8 of 14
[Ref.: #66794]	degradation of sugar acids	56	14 of 25
[Ref.: #66794]	nitrate assimilation	55.56	5 of 9
[Ref.: #66794]	cysteine metabolism	55.56	10 of 18
[Ref.: #66794]	4-hydroxymandelate degradation	55.56	5 of 9
[Ref.: #66794]	phenol degradation	55	11 of 20
[Ref.: #66794]	aminopropanol phosphate biosynthesis	50	1 of 2
[Ref.: #66794]	carnitine metabolism	50	4 of 8
[Ref.: #66794]	kanosamine biosynthesis II	50	1 of 2
[Ref.: #66794]	toluene degradation	50	2 of 4
[Ref.: #66794]	glycolate and glyoxylate degradation	50	3 of 6
[Ref.: #66794]	cyclohexanol degradation	50	2 of 4
[Ref.: #66794]	dTDPLrhamnose biosynthesis	50	4 of 8
[Ref.: #66794]	quinate degradation	50	1 of 2
[Ref.: #66794]	glycine metabolism	50	5 of 10
[Ref.: #66794]	ethanol fermentation	50	1 of 2
[Ref.: #66794]	resorcinol degradation	50	1 of 2
[Ref.: #66794]	coenzyme A metabolism	50	2 of 4
[Ref.: #66794]	glycogen biosynthesis	50	2 of 4
[Ref.: #66794]	phenylmercury acetate degradation	50	1 of 2
[Ref.: #66794]	lipid metabolism	48.39	15 of 31
[Ref.: #66794]	3-phenylpropionate degradation	46.67	7 of 15
[Ref.: #66794]	sulfate reduction	46.15	6 of 13
[Ref.: #66794]	androgen and estrogen metabolism	43.75	7 of 16
[Ref.: #66794]	propanol degradation	42.86	3 of 7
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	41.67	5 of 12
[Ref.: #66794]	ascorbate metabolism	40.91	9 of 22
[Ref.: #66794]	glycine betaine biosynthesis	40	2 of 5
[Ref.: #66794]	coenzyme M biosynthesis	40	4 of 10
[Ref.: #66794]	arachidonate biosynthesis	40	2 of 5
[Ref.: #66794]	gallate degradation	40	2 of 5
[Ref.: #66794]	creatinine degradation	40	2 of 5
[Ref.: #66794]	lipoate biosynthesis	40	2 of 5
[Ref.: #66794]	degradation of hexoses	38.89	7 of 18
[Ref.: #66794]	polyamine pathway	34.78	8 of 23
[Ref.: #66794]	enterobactin biosynthesis	33.33	1 of 3
[Ref.: #66794]	sulfoquinovose degradation	33.33	1 of 3
[Ref.: #66794]	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
[Ref.: #66794]	sphingosine metabolism	33.33	2 of 6
[Ref.: #66794]	acetyl CoA biosynthesis	33.33	1 of 3
[Ref.: #66794]	IAA biosynthesis	33.33	1 of 3
[Ref.: #66794]	carotenoid biosynthesis	31.82	7 of 22
[Ref.: #66794]	myo-inositol biosynthesis	30	3 of 10
[Ref.: #66794]	benzoyl-CoA degradation	28.57	2 of 7
[Ref.: #66794]	mevalonate metabolism	28.57	2 of 7
[Ref.: #66794]	arachidonic acid metabolism	27.78	5 of 18
[Ref.: #66794]	d-xylose degradation	27.27	3 of 11
[Ref.: #66794]	metabolism of disaccharids	27.27	3 of 11
[Ref.: #66794]	alginate biosynthesis	25	1 of 4
		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.: #29792]	Sample type/isolated from	plant associated
* marker position based on {}

Isolation sources categories

#Host

#Plants

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence GU129567 (>99% sequence identity) for Paracoccus sphaerophysae from Microbeatlas

Aquatic Samples	518
Soil Samples	74
Animal Samples	931
Plant Samples	74
Total Samples	1597

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

16S Sequence information:

	Sequence accession description	Seq. accession number	Sequence length (bp)	Sequence database	Associated NCBI tax ID
[Ref.: #29792]	Paracoccus sphaerophysae strain Zy-3 16S ribosomal RNA gene, partial sequence	GU129567	1368	GenBank	690417 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Paracoccus sphaerophysae HAMBI 3106	GCA_000763805	contig	GenBank	690417 tax ID	*
[Ref.: #66792]	Paracoccus sphaerophysae HAMBI 3106	690417.3	wgs	PATRIC	690417 tax ID	*
[Ref.: #66792]	Paracoccus sphaerophysae HAMBI 3106	2713897090	draft	JGI IMG/M	690417 tax ID	*

[Ref.: #29792]

GC-content

67.1 mol%

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: Paracoccus sphaerophysae HAMBI 3106 PATRIC: 690417.3
[Ref.: #69481]	spore-forming	no	82	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Paracoccus sphaerophysae HAMBI 3106 PATRIC: 690417.3
[Ref.: #69480]	gram-positive	no	97.216	no
[Ref.: #69480]	anaerobic	no	98.233	no
[Ref.: #69480]	halophile	no	82.909	no
[Ref.: #69480]	spore-forming	no	95.627	yes
[Ref.: #69480]	glucose-util	yes	82.234	no
[Ref.: #69480]	flagellated	no	89.628	no
[Ref.: #69480]	thermophile	no	84.974	yes
[Ref.: #69480]	aerobic	yes	93.211	yes
[Ref.: #69480]	glucose-ferment	no	90.543	no
[Ref.: #69480]	motile	no	64.995	yes

Availability in culture collections External links

[Ref.: #29792]

Culture collection no.

ACCC 05413, HAMBI 3106

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Paracoccus sanguinis sp. nov., isolated from clinical specimens of New York State patients.	McGinnis JM, Cole JA, Dickinson MC, Mingle LA, Lapierre P, Musser KA, Wolfgang WJ	Int J Syst Evol Microbiol	10.1099/ijs.0.000193	2015	*
Phylogeny	Paracoccus panacisoli sp. nov., isolated from a forest soil cultivated with Vietnamese ginseng.	Nguyen NL, Kim YJ, Hoang VA, Tran BT, Pham HS, Yang DC	Int J Syst Evol Microbiol	10.1099/ijs.0.000125	2015	*
Phylogeny	Paracoccus sphaerophysae sp. nov., a siderophore-producing, endophytic bacterium isolated from root nodules of Sphaerophysa salsula.	Deng ZS, Zhao LF, Xu L, Kong ZY, Zhao P, Qin W, Chang JL, Wei GH	Int J Syst Evol Microbiol	10.1099/ijs.0.021071-0	2010	*

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 )

#29792

Barberan A, Caceres Velazquez H, Jones S, Fierer N.: Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information. mSphere 2: 2017 ( DOI 10.1128/mSphere.00237-17 , PubMed 28776041 ) - originally annotated from #26170 (see below)

#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 )

#69479

João F Matias Rodrigues, Janko Tackmann,Gregor Rot, Thomas SB Schmidt, Lukas Malfertheiner, Mihai Danaila,Marija Dmitrijeva, Daniela Gaio, Nicolas Näpflin and Christian von Mering. University of Zurich.: MicrobeAtlas 1.0 beta .

#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 )

#26170

IJSEM 665 2011 ( DOI 10.1099/ijs.0.021071-0 , PubMed 20400662 )

* These data were automatically processed and therefore are not curated

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Paracoccus sphaerophysae HAMBI 3106

Paracoccus sphaerophysae HAMBI 3106

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