Name: Paracoccus halophilus HN-182
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 134285

Type strain:

Species: Paracoccus halophilus

Strain Designation: HN-182

Culture col. no.: CGMCC 1.6117, JCM 14014

Strain history: S. Liu HN-182.

NCBI tax ID(s): 376733 (species)

SI-ID 323987

CGMCC 1.6117, JCM 14014

Section

Paracoccus halophilus HN-182 is an aerobe, Gram-negative, rod-shaped bacterium that was isolated from marine sediment.

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 halophilus**
	Full Scientific Name (LPSN)	Paracoccus halophilus Liu et al. 2008

Information on morphological and physiological properties Morphology

[Ref.: #32272]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %99.994

[Ref.: #32272]	Cell length	0.9 µm

[Ref.: #32272]	Cell width	0.45 µm

[Ref.: #32272]	Cell shape	rod-shaped

[Ref.: #32272]	Motility	no

Information on culture and growth conditions Culture and growth conditions

		Temperature
[Ref.: #32272]	growth	07-42 °C
[Ref.: #32272]	optimum	25 °C
[Ref.: #67770]	growth	30 °C

[Ref.: #32272]	Temperature range	mesophilic
[Ref.: #67770]	Temperature range	mesophilic

	pH	Kind of pH		pH
[Ref.: #32272]			optimum	7
[Ref.: #32272]			growth	05-09

Information on physiology and metabolism Physiology and metabolism

[Ref.: #32272]

Oxygen tolerance

aerobe

[Ref.: #32272]	Ability of spore formation	no
[Ref.: #69481]	Ability of spore formation	no Confidence in %100
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.999

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #32272]		NaCl		growth	0.5-8.5	%
[Ref.: #32272]		NaCl		optimum	4.5	%

[Ref.: #67770]

Observation

quinones: Q-10

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #32272]	arabinose ChEBI	+	carbon source
[Ref.: #32272]	cellobiose ChEBI	+	carbon source
[Ref.: #32272]	fructose ChEBI	+	carbon source
[Ref.: #32272]	galactose ChEBI	+	carbon source
[Ref.: #32272]	glucose ChEBI	+	carbon source
[Ref.: #32272]	glycerol ChEBI	+	carbon source
[Ref.: #32272]	maltose ChEBI	+	carbon source
[Ref.: #32272]	mannitol ChEBI	+	carbon source
[Ref.: #32272]	mannose ChEBI	+	carbon source
[Ref.: #32272]	rhamnose ChEBI	+	carbon source
[Ref.: #32272]	ribose ChEBI	+	carbon source
[Ref.: #32272]	sorbitol ChEBI	+	carbon source
[Ref.: #32272]	xylose ChEBI	+	carbon source
	Only first 10 entries are displayed. Click here to see all.

	Enzyme	Enzyme activity	EC number
[Ref.: #32272]	catalase	+	1.11.1.6
[Ref.: #32272]	cytochrome oxidase	+	1.9.3.1
[Ref.: #32272]	urease	+	3.5.1.5

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	methylglyoxal degradation	100	5 of 5
[Ref.: #66794]	palmitate biosynthesis	100	22 of 22
[Ref.: #66794]	cis-vaccenate biosynthesis	100	2 of 2
[Ref.: #66794]	glycogen biosynthesis	100	4 of 4
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	glycogen metabolism	100	5 of 5
[Ref.: #66794]	denitrification	100	2 of 2
[Ref.: #66794]	L-lactaldehyde degradation	100	3 of 3
[Ref.: #66794]	ppGpp biosynthesis	100	4 of 4
[Ref.: #66794]	formaldehyde oxidation	100	3 of 3
[Ref.: #66794]	adipate degradation	100	2 of 2
[Ref.: #66794]	threonine metabolism	100	10 of 10
[Ref.: #66794]	coenzyme A metabolism	100	4 of 4
[Ref.: #66794]	C4 and CAM-carbon fixation	100	8 of 8
[Ref.: #66794]	gluconeogenesis	100	8 of 8
[Ref.: #66794]	butanoate fermentation	100	4 of 4
[Ref.: #66794]	suberin monomers biosynthesis	100	2 of 2
[Ref.: #66794]	valine metabolism	100	9 of 9
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	enterobactin biosynthesis	100	3 of 3
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	octane oxidation	100	3 of 3
[Ref.: #66794]	Entner Doudoroff pathway	100	10 of 10
[Ref.: #66794]	citric acid cycle	92.86	13 of 14
[Ref.: #66794]	glutathione metabolism	92.86	13 of 14
[Ref.: #66794]	glutamate and glutamine metabolism	89.29	25 of 28
[Ref.: #66794]	serine metabolism	88.89	8 of 9
[Ref.: #66794]	chorismate metabolism	88.89	8 of 9
[Ref.: #66794]	lipid A biosynthesis	88.89	8 of 9
[Ref.: #66794]	phenylalanine metabolism	84.62	11 of 13
[Ref.: #66794]	vitamin B1 metabolism	84.62	11 of 13
[Ref.: #66794]	leucine metabolism	84.62	11 of 13
[Ref.: #66794]	NAD metabolism	83.33	15 of 18
[Ref.: #66794]	vitamin B12 metabolism	82.35	28 of 34
[Ref.: #66794]	proline metabolism	81.82	9 of 11
[Ref.: #66794]	pentose phosphate pathway	81.82	9 of 11
[Ref.: #66794]	purine metabolism	80.85	76 of 94
[Ref.: #66794]	3-chlorocatechol degradation	80	4 of 5
[Ref.: #66794]	propionate fermentation	80	8 of 10
[Ref.: #66794]	peptidoglycan biosynthesis	80	12 of 15
[Ref.: #66794]	gallate degradation	80	4 of 5
[Ref.: #66794]	vitamin K metabolism	80	4 of 5
[Ref.: #66794]	flavin biosynthesis	80	12 of 15
[Ref.: #66794]	photosynthesis	78.57	11 of 14
[Ref.: #66794]	aspartate and asparagine 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]	molybdenum cofactor biosynthesis	77.78	7 of 9
[Ref.: #66794]	4-hydroxymandelate degradation	77.78	7 of 9
[Ref.: #66794]	ketogluconate metabolism	75	6 of 8
[Ref.: #66794]	degradation of sugar alcohols	75	12 of 16
[Ref.: #66794]	sulfopterin metabolism	75	3 of 4
[Ref.: #66794]	CMP-KDO biosynthesis	75	3 of 4
[Ref.: #66794]	isoleucine metabolism	75	6 of 8
[Ref.: #66794]	lactate fermentation	75	3 of 4
[Ref.: #66794]	acetate fermentation	75	3 of 4
[Ref.: #66794]	pyrimidine metabolism	73.33	33 of 45
[Ref.: #66794]	vitamin B6 metabolism	72.73	8 of 11
[Ref.: #66794]	histidine metabolism	72.41	21 of 29
[Ref.: #66794]	degradation of sugar acids	72	18 of 25
[Ref.: #66794]	tyrosine metabolism	71.43	10 of 14
[Ref.: #66794]	degradation of pentoses	71.43	20 of 28
[Ref.: #66794]	heme metabolism	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]	reductive acetyl coenzyme A pathway	71.43	5 of 7
[Ref.: #66794]	acetoin degradation	66.67	2 of 3
[Ref.: #66794]	methane metabolism	66.67	2 of 3
[Ref.: #66794]	acetyl CoA biosynthesis	66.67	2 of 3
[Ref.: #66794]	cyanate degradation	66.67	2 of 3
[Ref.: #66794]	allantoin degradation	66.67	6 of 9
[Ref.: #66794]	tryptophan metabolism	65.79	25 of 38
[Ref.: #66794]	alanine metabolism	65.52	19 of 29
[Ref.: #66794]	methionine metabolism	65.38	17 of 26
[Ref.: #66794]	phenol degradation	65	13 of 20
[Ref.: #66794]	glycolysis	64.71	11 of 17
[Ref.: #66794]	lysine metabolism	64.29	27 of 42
[Ref.: #66794]	tetrahydrofolate metabolism	64.29	9 of 14
[Ref.: #66794]	oxidative phosphorylation	62.64	57 of 91
[Ref.: #66794]	dTDPLrhamnose biosynthesis	62.5	5 of 8
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	62.5	5 of 8
[Ref.: #66794]	urea cycle	61.54	8 of 13
[Ref.: #66794]	isoprenoid biosynthesis	61.54	16 of 26
[Ref.: #66794]	lipid metabolism	61.29	19 of 31
[Ref.: #66794]	degradation of hexoses	61.11	11 of 18
[Ref.: #66794]	creatinine degradation	60	3 of 5
[Ref.: #66794]	myo-inositol biosynthesis	60	6 of 10
[Ref.: #66794]	metabolism of amino sugars and derivatives	60	3 of 5
[Ref.: #66794]	starch degradation	60	6 of 10
[Ref.: #66794]	cellulose degradation	60	3 of 5
[Ref.: #66794]	elloramycin biosynthesis	60	3 of 5
[Ref.: #66794]	3-phenylpropionate degradation	60	9 of 15
[Ref.: #66794]	arginine metabolism	58.33	14 of 24
[Ref.: #66794]	non-pathway related	57.89	22 of 38
[Ref.: #66794]	propanol degradation	57.14	4 of 7
[Ref.: #66794]	cysteine metabolism	55.56	10 of 18
[Ref.: #66794]	nitrate assimilation	55.56	5 of 9
[Ref.: #66794]	sulfate reduction	53.85	7 of 13
[Ref.: #66794]	ribulose monophosphate pathway	50	1 of 2
[Ref.: #66794]	kanosamine biosynthesis II	50	1 of 2
[Ref.: #66794]	aminopropanol phosphate biosynthesis	50	1 of 2
[Ref.: #66794]	glycine metabolism	50	5 of 10
[Ref.: #66794]	biotin biosynthesis	50	2 of 4
[Ref.: #66794]	selenocysteine biosynthesis	50	3 of 6
[Ref.: #66794]	glycolate and glyoxylate degradation	50	3 of 6
[Ref.: #66794]	ethanol fermentation	50	1 of 2
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	50	6 of 12
[Ref.: #66794]	carnitine metabolism	50	4 of 8
[Ref.: #66794]	resorcinol degradation	50	1 of 2
[Ref.: #66794]	quinate degradation	50	1 of 2
[Ref.: #66794]	phenylmercury acetate degradation	50	1 of 2
[Ref.: #66794]	cyclohexanol degradation	50	2 of 4
[Ref.: #66794]	ascorbate metabolism	45.45	10 of 22
[Ref.: #66794]	androgen and estrogen metabolism	43.75	7 of 16
[Ref.: #66794]	polyamine pathway	43.48	10 of 23
[Ref.: #66794]	hydrogen production	40	2 of 5
[Ref.: #66794]	coenzyme M biosynthesis	40	4 of 10
[Ref.: #66794]	phenylacetate degradation (aerobic)	40	2 of 5
[Ref.: #66794]	lipoate biosynthesis	40	2 of 5
[Ref.: #66794]	ethylmalonyl-CoA pathway	40	2 of 5
[Ref.: #66794]	arachidonate biosynthesis	40	2 of 5
[Ref.: #66794]	arachidonic acid metabolism	38.89	7 of 18
[Ref.: #66794]	d-xylose degradation	36.36	4 of 11
[Ref.: #66794]	metabolism of disaccharids	36.36	4 of 11
[Ref.: #66794]	IAA biosynthesis	33.33	1 of 3
[Ref.: #66794]	sulfoquinovose degradation	33.33	1 of 3
[Ref.: #66794]	sphingosine metabolism	33.33	2 of 6
[Ref.: #66794]	pantothenate biosynthesis	33.33	2 of 6
[Ref.: #66794]	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
[Ref.: #66794]	phosphatidylethanolamine bioynthesis	30.77	4 of 13
[Ref.: #66794]	4-hydroxyphenylacetate degradation	30	3 of 10
[Ref.: #66794]	benzoyl-CoA degradation	28.57	2 of 7
[Ref.: #66794]	chlorophyll metabolism	27.78	5 of 18
[Ref.: #66794]	toluene degradation	25	1 of 4
[Ref.: #66794]	alginate biosynthesis	25	1 of 4
[Ref.: #66794]	methanogenesis from CO2	25	3 of 12
[Ref.: #66794]	phenylpropanoid biosynthesis	23.08	3 of 13
		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.: #32272]	Sample type/isolated from	marine sediment

[Ref.: #67770]	Sample type/isolated from	Marine sediment from the South China Sea
[Ref.: #67770]	Country	China
[Ref.: #67770]	Country ISO 3 Code	CHN
[Ref.: #67770]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Environmental	#Aquatic	#Marine
#Environmental	#Aquatic	#Sediment

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence DQ423482 (>99% sequence identity) for Paracoccus halophilus subclade from Microbeatlas

Aquatic Samples	306
Soil Samples	94
Animal Samples	541
Plant Samples	10
Total Samples	951

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.: #32272]	Paracoccus halophilus strain HN-182 16S ribosomal RNA gene, partial sequence	DQ423482	1428	GenBank	376733 tax ID

Genome sequence information:

Only first 5 entries are displayed. Click here to see all.

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Paracoccus halophilus CGMCC 1.6117	GCA_900111785	scaffold	GenBank	376733 tax ID
[Ref.: #67770]	Paracoccus halophilus JCM 14014	GCA_000763905	contig	GenBank	376733 tax ID
[Ref.: #66792]	Paracoccus halophilus JCM 14014	376733.3	wgs	PATRIC	376733 tax ID	*
[Ref.: #66792]	Paracoccus halophilus strain CGMCC 1.6117	376733.15	wgs	PATRIC	376733 tax ID	*
[Ref.: #66792]	Paracoccus halophilus JCM 14014	2713897088	draft	JGI IMG/M	376733 tax ID	*
[Ref.: #66792]	Paracoccus halophilus CGMCC 1.6117	2617270913	draft	JGI IMG/M	376733 tax ID	*

[Ref.: #32272]	GC-content	67.2 mol%
[Ref.: #67770]	GC-content	67.2 mol%	thermal denaturation, midpoint method (Tm)

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 halophilus CGMCC 1.6117 NCBI: GCA_900111785.1
[Ref.: #69481]	spore-forming	no	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Paracoccus halophilus JCM 14014 PATRIC: 376733.3
[Ref.: #69480]	gram-positive	no	98.677	yes
[Ref.: #69480]	anaerobic	no	98.199	yes
[Ref.: #69480]	halophile	no	50	no
[Ref.: #69480]	spore-forming	no	97.169	yes
[Ref.: #69480]	glucose-util	yes	91.546	yes
[Ref.: #69480]	aerobic	yes	86.072	yes
[Ref.: #69480]	motile	no	77.555	yes
[Ref.: #69480]	flagellated	no	89.203	yes
[Ref.: #69480]	thermophile	no	96.347	yes
[Ref.: #69480]	glucose-ferment	no	85.058	no

Availability in culture collections External links

[Ref.: #32272]

Culture collection no.

CGMCC 1.6117, JCM 14014

[Ref.: #91871]

SI-ID 323987

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Paracoccus halophilus sp. nov., isolated from marine sediment of the South China Sea, China, and emended description of genus Paracoccus Davis 1969.	Liu ZP, Wang BJ, Liu XY, Dai X, Liu YH, Liu SJ	Int J Syst Evol Microbiol	10.1099/ijs.0.65237-0	2008	*
Phylogeny	Paracoccus luteus sp. nov., isolated from the intestine of grass carp.	Ming H, Cheng LJ, Ding CL, Niu MM, Zhao ZL, Ji WL, Zhang LY, Zhang YM, Meng XL, Nie GX	Int J Syst Evol Microbiol	10.1099/ijsem.0.003790	2020	*
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 )

#32272

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 #28512 (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 )

#67770 Japan Collection of Microorganism (JCM) ; Curators of the JCM;

#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 )

#91871

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-ID323987.1 )

#28512

IJSEM 257 2008 ( DOI 10.1099/ijs.0.65237-0 , PubMed 18175718 )

* These data were automatically processed and therefore are not curated

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Paracoccus halophilus CGMCC 1.6117

Paracoccus halophilus JCM 14014

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