Name: Pseudorhodobacter antarcticus ZS3-33
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 133859

Type strain:

Species: Pseudorhodobacter antarcticus

Strain Designation: ZS3-33

Culture col. no.: CGMCC 1.10836, KCTC 23700

NCBI tax ID(s): 1077947 (species)

Section

Pseudorhodobacter antarcticus ZS3-33 is an aerobe, Gram-negative, rod-shaped bacterium that was isolated from marine sediment.

Gram-negative
rod-shaped
aerobe
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	*Pseudorhodobacter*
	Species	**Pseudorhodobacter antarcticus**
	Full Scientific Name (LPSN)	Pseudorhodobacter antarcticus Chen et al. 2013

Information on morphological and physiological properties Morphology

[Ref.: #30694]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %99.999

[Ref.: #30694]	Cell length	1.75 µm

[Ref.: #30694]	Cell width	0.65 µm

[Ref.: #30694]	Cell shape	rod-shaped

[Ref.: #30694]	Motility	no

[Ref.: #30694]

Pigment production

yes

Information on culture and growth conditions Culture and growth conditions

	Temperatures	Kind of temperature		Temperature
[Ref.: #30694]			growth	04-30 °C
[Ref.: #30694]			optimum	15 °C

[Ref.: #30694]

Temperature range

psychrophilic

	pH	Kind of pH		pH
[Ref.: #30694]			optimum	7.5
[Ref.: #30694]			growth	05-10

Information on physiology and metabolism Physiology and metabolism

[Ref.: #30694]

Oxygen tolerance

aerobe

[Ref.: #69480]

Ability of spore formation

no Confidence in %99.997

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #30694]		NaCl		growth	0-10	%
[Ref.: #30694]		NaCl		optimum	1	%

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #30694]	acetate ChEBI	+	carbon source
[Ref.: #30694]	esculin ChEBI	+	hydrolysis
[Ref.: #30694]	glucose ChEBI	+	carbon source
[Ref.: #30694]	nitrate ChEBI	+	reduction

	Metabolite production	Metabolite	Production
[Ref.: #30694]		hydrogen sulfide ChEBI	yes

	Enzymes	Enzyme	Enzyme activity	EC number
[Ref.: #30694]		acid phosphatase	+	3.1.3.2
[Ref.: #30694]		alkaline phosphatase	+	3.1.3.1

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	C4 and CAM-carbon fixation	100	8 of 8
[Ref.: #66794]	valine metabolism	100	9 of 9
[Ref.: #66794]	Entner Doudoroff pathway	100	10 of 10
[Ref.: #66794]	gluconeogenesis	100	8 of 8
[Ref.: #66794]	cis-vaccenate biosynthesis	100	2 of 2
[Ref.: #66794]	methylglyoxal degradation	100	5 of 5
[Ref.: #66794]	IAA biosynthesis	100	3 of 3
[Ref.: #66794]	threonine metabolism	100	10 of 10
[Ref.: #66794]	octane oxidation	100	3 of 3
[Ref.: #66794]	palmitate biosynthesis	100	22 of 22
[Ref.: #66794]	adipate degradation	100	2 of 2
[Ref.: #66794]	ppGpp biosynthesis	100	4 of 4
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	suberin monomers biosynthesis	100	2 of 2
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	denitrification	100	2 of 2
[Ref.: #66794]	L-lactaldehyde degradation	100	3 of 3
[Ref.: #66794]	coenzyme A metabolism	100	4 of 4
[Ref.: #66794]	formaldehyde oxidation	100	3 of 3
[Ref.: #66794]	glycine betaine biosynthesis	100	5 of 5
[Ref.: #66794]	pentose phosphate pathway	90.91	10 of 11
[Ref.: #66794]	lipid A biosynthesis	88.89	8 of 9
[Ref.: #66794]	serine metabolism	88.89	8 of 9
[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]	ketogluconate metabolism	87.5	7 of 8
[Ref.: #66794]	glutathione metabolism	85.71	12 of 14
[Ref.: #66794]	phenylalanine metabolism	84.62	11 of 13
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	83.33	10 of 12
[Ref.: #66794]	vitamin B12 metabolism	82.35	28 of 34
[Ref.: #66794]	proline metabolism	81.82	9 of 11
[Ref.: #66794]	flavin biosynthesis	80	12 of 15
[Ref.: #66794]	ethylmalonyl-CoA pathway	80	4 of 5
[Ref.: #66794]	phenylacetate degradation (aerobic)	80	4 of 5
[Ref.: #66794]	peptidoglycan biosynthesis	80	12 of 15
[Ref.: #66794]	cellulose degradation	80	4 of 5
[Ref.: #66794]	propionate fermentation	80	8 of 10
[Ref.: #66794]	photosynthesis	78.57	11 of 14
[Ref.: #66794]	heme metabolism	78.57	11 of 14
[Ref.: #66794]	allantoin degradation	77.78	7 of 9
[Ref.: #66794]	NAD metabolism	77.78	14 of 18
[Ref.: #66794]	leucine metabolism	76.92	10 of 13
[Ref.: #66794]	purine metabolism	76.6	72 of 94
[Ref.: #66794]	alanine metabolism	75.86	22 of 29
[Ref.: #66794]	pyrimidine metabolism	75.56	34 of 45
[Ref.: #66794]	glutamate and glutamine metabolism	75	21 of 28
[Ref.: #66794]	isoleucine metabolism	75	6 of 8
[Ref.: #66794]	biotin biosynthesis	75	3 of 4
[Ref.: #66794]	butanoate fermentation	75	3 of 4
[Ref.: #66794]	CMP-KDO biosynthesis	75	3 of 4
[Ref.: #66794]	vitamin B6 metabolism	72.73	8 of 11
[Ref.: #66794]	histidine metabolism	72.41	21 of 29
[Ref.: #66794]	tyrosine metabolism	71.43	10 of 14
[Ref.: #66794]	cardiolipin biosynthesis	71.43	5 of 7
[Ref.: #66794]	reductive acetyl coenzyme A pathway	71.43	5 of 7
[Ref.: #66794]	ubiquinone biosynthesis	71.43	5 of 7
[Ref.: #66794]	citric acid cycle	71.43	10 of 14
[Ref.: #66794]	propanol degradation	71.43	5 of 7
[Ref.: #66794]	tryptophan metabolism	71.05	27 of 38
[Ref.: #66794]	arginine metabolism	70.83	17 of 24
[Ref.: #66794]	myo-inositol biosynthesis	70	7 of 10
[Ref.: #66794]	vitamin B1 metabolism	69.23	9 of 13
[Ref.: #66794]	lysine metabolism	69.05	29 of 42
[Ref.: #66794]	acetoin degradation	66.67	2 of 3
[Ref.: #66794]	cyanate degradation	66.67	2 of 3
[Ref.: #66794]	aspartate and asparagine metabolism	66.67	6 of 9
[Ref.: #66794]	non-pathway related	65.79	25 of 38
[Ref.: #66794]	oxidative phosphorylation	64.84	59 of 91
[Ref.: #66794]	glycolysis	64.71	11 of 17
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	62.5	5 of 8
[Ref.: #66794]	dTDPLrhamnose biosynthesis	62.5	5 of 8
[Ref.: #66794]	degradation of sugar alcohols	62.5	10 of 16
[Ref.: #66794]	isoprenoid biosynthesis	61.54	16 of 26
[Ref.: #66794]	urea cycle	61.54	8 of 13
[Ref.: #66794]	lipid metabolism	61.29	19 of 31
[Ref.: #66794]	cysteine metabolism	61.11	11 of 18
[Ref.: #66794]	glycogen metabolism	60	3 of 5
[Ref.: #66794]	creatinine degradation	60	3 of 5
[Ref.: #66794]	degradation of sugar acids	60	15 of 25
[Ref.: #66794]	degradation of pentoses	57.14	16 of 28
[Ref.: #66794]	tetrahydrofolate metabolism	57.14	8 of 14
[Ref.: #66794]	d-mannose degradation	55.56	5 of 9
[Ref.: #66794]	methionine metabolism	53.85	14 of 26
[Ref.: #66794]	sulfate reduction	53.85	7 of 13
[Ref.: #66794]	carotenoid biosynthesis	50	11 of 22
[Ref.: #66794]	kanosamine biosynthesis II	50	1 of 2
[Ref.: #66794]	ethanol fermentation	50	1 of 2
[Ref.: #66794]	aminopropanol phosphate biosynthesis	50	1 of 2
[Ref.: #66794]	phenylmercury acetate degradation	50	1 of 2
[Ref.: #66794]	glycine metabolism	50	5 of 10
[Ref.: #66794]	ribulose monophosphate pathway	50	1 of 2
[Ref.: #66794]	cyclohexanol degradation	50	2 of 4
[Ref.: #66794]	selenocysteine biosynthesis	50	3 of 6
[Ref.: #66794]	carnitine metabolism	50	4 of 8
[Ref.: #66794]	quinate degradation	50	1 of 2
[Ref.: #66794]	sulfopterin metabolism	50	2 of 4
[Ref.: #66794]	glycogen biosynthesis	50	2 of 4
[Ref.: #66794]	acetate fermentation	50	2 of 4
[Ref.: #66794]	glycolate and glyoxylate degradation	50	3 of 6
[Ref.: #66794]	polyamine pathway	47.83	11 of 23
[Ref.: #66794]	d-xylose degradation	45.45	5 of 11
[Ref.: #66794]	phenol degradation	45	9 of 20
[Ref.: #66794]	ascorbate metabolism	40.91	9 of 22
[Ref.: #66794]	elloramycin biosynthesis	40	2 of 5
[Ref.: #66794]	vitamin K metabolism	40	2 of 5
[Ref.: #66794]	gallate degradation	40	2 of 5
[Ref.: #66794]	coenzyme M biosynthesis	40	4 of 10
[Ref.: #66794]	lipoate biosynthesis	40	2 of 5
[Ref.: #66794]	3-phenylpropionate degradation	40	6 of 15
[Ref.: #66794]	arachidonate biosynthesis	40	2 of 5
[Ref.: #66794]	metabolism of amino sugars and derivatives	40	2 of 5
[Ref.: #66794]	hydrogen production	40	2 of 5
[Ref.: #66794]	arachidonic acid metabolism	38.89	7 of 18
[Ref.: #66794]	degradation of hexoses	38.89	7 of 18
[Ref.: #66794]	androgen and estrogen metabolism	37.5	6 of 16
[Ref.: #66794]	dolichyl-diphosphooligosaccharide biosynthesis	36.36	4 of 11
[Ref.: #66794]	bile acid biosynthesis, neutral pathway	35.29	6 of 17
[Ref.: #66794]	sphingosine metabolism	33.33	2 of 6
[Ref.: #66794]	acetyl CoA 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]	enterobactin biosynthesis	33.33	1 of 3
[Ref.: #66794]	nitrate assimilation	33.33	3 of 9
[Ref.: #66794]	4-hydroxymandelate degradation	33.33	3 of 9
[Ref.: #66794]	starch degradation	30	3 of 10
[Ref.: #66794]	mevalonate metabolism	28.57	2 of 7
[Ref.: #66794]	benzoyl-CoA degradation	28.57	2 of 7
[Ref.: #66794]	cholesterol biosynthesis	27.27	3 of 11
[Ref.: #66794]	alginate biosynthesis	25	1 of 4
[Ref.: #66794]	lactate fermentation	25	1 of 4
[Ref.: #66794]	vitamin E metabolism	25	1 of 4
[Ref.: #66794]	toluene degradation	25	1 of 4
[Ref.: #66794]	phosphatidylethanolamine bioynthesis	23.08	3 of 13
[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.: #30694]	Sample type/isolated from	marine sediment
* marker position based on {}

Isolation sources categories

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

What are isolation sources categories?

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

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.: #66792]	Pseudorhodobacter antarcticus CGMCC 1.10836	GCA_900110135	scaffold	GenBank	1077947 tax ID	*
[Ref.: #66792]	Pseudorhodobacter antarcticus KCTC 23700	GCA_001202015	contig	GenBank	1077947 tax ID	*
[Ref.: #66792]	Pseudorhodobacter antarcticus strain CGMCC 1.10836	1077947.5	wgs	PATRIC	1077947 tax ID	*
[Ref.: #66792]	Pseudorhodobacter antarcticus strain KCTC 23700	1077947.4	wgs	PATRIC	1077947 tax ID	*
[Ref.: #66792]	Pseudorhodobacter antarcticus KCTC 23700	2772190751	draft	JGI IMG/M	1077947 tax ID	*
[Ref.: #66792]	Pseudorhodobacter antarcticus CGMCC 1.10836	2667527436	draft	JGI IMG/M	1077947 tax ID	*

[Ref.: #30694]

GC-content

57.1 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: Pseudorhodobacter antarcticus CGMCC 1.10836 NCBI: GCA_900110135.1
[Ref.: #69481]	spore-forming	yes	52	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Pseudorhodobacter antarcticus CGMCC 1.10836 NCBI: GCA_900110135.1
[Ref.: #69480]	glucose-ferment	no	91.021	no
[Ref.: #69480]	motile	no	74.885	yes
[Ref.: #69480]	flagellated	no	91.615	yes
[Ref.: #69480]	gram-positive	no	98.355	yes
[Ref.: #69480]	anaerobic	no	97.195	yes
[Ref.: #69480]	aerobic	yes	81.325	no
[Ref.: #69480]	halophile	no	66.976	yes
[Ref.: #69480]	spore-forming	no	96.57	no
[Ref.: #69480]	thermophile	no	96.978	yes
[Ref.: #69480]	glucose-util	yes	75.267	yes

Availability in culture collections External links

[Ref.: #30694]

Culture collection no.

CGMCC 1.10836, KCTC 23700

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Pseudorhodobacter sinensis sp. nov. and Pseudorhodobacter aquaticus sp. nov., isolated from crater lakes.	Li AH, Liu HC, Hou WG, Zhou YG	Int J Syst Evol Microbiol	10.1099/ijsem.0.001061	2016	*
Phylogeny	Pseudorhodobacter collinsensis sp. nov., isolated from a till sample of an icecap front.	Zhang Y, Jiang F, Chang X, Qiu X, Ren L, Qu Z, Deng S, Da X, Kan W, Kim M, Fang C, Peng F	Int J Syst Evol Microbiol	10.1099/ijsem.0.000693	2015	*
Phylogeny	Pseudorhodobacter antarcticus sp. nov., isolated from Antarctic intertidal sandy sediment, and emended description of the genus Pseudorhodobacter Uchino et al. 2002 emend. Jung et al. 2012.	Chen CX, Zhang XY, Liu C, Yu Y, Liu A, Li GW, Li H, Chen XL, Chen B, Zhou BC, Zhang YZ	Int J Syst Evol Microbiol	10.1099/ijs.0.042184-0	2012	*

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 )

#30694

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 #27025 (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 )

#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 )

#27025

IJSEM 849 2013 ( DOI 10.1099/ijs.0.042184-0 , PubMed 22611201 )

* These data were automatically processed and therefore are not curated

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Pseudorhodobacter antarcticus CGMCC 1.10836

Pseudorhodobacter antarcticus CGMCC 1.10836

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