Name: Sphingorhabdus contaminans JC 216
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 158562

Type strain:

Species: Sphingorhabdus contaminans

Strain Designation: JC 216

Culture col. no.: KCTC 32445, LMG 27671

Strain history: <- Ch. Sasikala

NCBI tax ID(s): 1343899 (species)

Section

Sphingorhabdus contaminans JC 216 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from From contaminated petri dishl.

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	*Alphaproteobacteria*
	Order	*Sphingomonadales*
	Family	*Sphingomonadaceae*
	Genus	*Sphingorhabdus*
	Species	**Sphingorhabdus contaminans**
	Full Scientific Name (LPSN)	Sphingorhabdus contaminans (Subhash et al. 2014) Yang et al. 2017

	Synonym	"Sphingorhabdus* contaminans"*
	Synonym	Sphingopyxis contaminans

Information on morphological and physiological properties Morphology

[Ref.: #69480]	Gram stain	negative Confidence in %99.94

Information on culture and growth conditions Culture and growth conditions

	Temperatures	Kind of temperature		Temperature
[Ref.: #67771]			growth	30 °C

[Ref.: #67771]

Temperature range

mesophilic

Information on physiology and metabolism Physiology and metabolism

[Ref.: #67771]

Oxygen tolerance

aerobe

[Ref.: #69480]	Ability of spore formation	no Confidence in %99.992
[Ref.: #69481]	Ability of spore formation	no Confidence in %100

	Metabolite utilization	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #65260]		esculin ChEBI	+	hydrolysis
[Ref.: #65260]		glucose ChEBI	-	fermentation

	Metabolite production	Metabolite	Production
[Ref.: #65260]		indole ChEBI	no

	Enzyme	Enzyme activity	EC number
[Ref.: #65260]	acid phosphatase	+	3.1.3.2
[Ref.: #65260]	alkaline phosphatase	+	3.1.3.1
[Ref.: #65260]	alpha-chymotrypsin	+	3.4.21.1
[Ref.: #65260]	alpha-fucosidase	-	3.2.1.51
[Ref.: #65260]	alpha-galactosidase	-	3.2.1.22
[Ref.: #65260]	alpha-glucosidase	+	3.2.1.20
[Ref.: #65260]	alpha-mannosidase	-	3.2.1.24
[Ref.: #65260]	arginine dihydrolase	-	3.5.3.6
[Ref.: #65260]	beta-glucosidase	+	3.2.1.21
[Ref.: #65260]	beta-glucuronidase	-	3.2.1.31
[Ref.: #65260]	catalase	-	1.11.1.6
[Ref.: #65260]	cystine arylamidase	+	3.4.11.3
[Ref.: #65260]	esterase (C 4)	+
[Ref.: #65260]	esterase Lipase (C 8)	+
[Ref.: #65260]	leucine arylamidase	+	3.4.11.1
[Ref.: #65260]	lipase (C 14)	+
[Ref.: #65260]	N-acetyl-beta-glucosaminidase	-	3.2.1.52
[Ref.: #65260]	naphthol-AS-BI-phosphohydrolase	+
[Ref.: #65260]	trypsin	+	3.4.21.4
[Ref.: #65260]	urease	-	3.5.1.5
[Ref.: #65260]	valine arylamidase	+
	Only first 10 entries are displayed. Click here to see all.

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	ppGpp biosynthesis	100	4 of 4
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	cis-vaccenate biosynthesis	100	2 of 2
[Ref.: #66794]	gluconeogenesis	100	8 of 8
[Ref.: #66794]	C4 and CAM-carbon fixation	100	8 of 8
[Ref.: #66794]	Entner Doudoroff pathway	100	10 of 10
[Ref.: #66794]	coenzyme A metabolism	100	4 of 4
[Ref.: #66794]	formaldehyde oxidation	100	3 of 3
[Ref.: #66794]	ethylmalonyl-CoA pathway	100	5 of 5
[Ref.: #66794]	adipate degradation	100	2 of 2
[Ref.: #66794]	methylglyoxal degradation	100	5 of 5
[Ref.: #66794]	taurine degradation	100	1 of 1
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	valine metabolism	100	9 of 9
[Ref.: #66794]	suberin monomers biosynthesis	100	2 of 2
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	palmitate biosynthesis	100	22 of 22
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	citric acid cycle	92.86	13 of 14
[Ref.: #66794]	threonine metabolism	90	9 of 10
[Ref.: #66794]	aspartate and asparagine metabolism	88.89	8 of 9
[Ref.: #66794]	CO2 fixation in Crenarchaeota	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]	propanol degradation	85.71	6 of 7
[Ref.: #66794]	photosynthesis	85.71	12 of 14
[Ref.: #66794]	reductive acetyl coenzyme A pathway	85.71	6 of 7
[Ref.: #66794]	leucine metabolism	84.62	11 of 13
[Ref.: #66794]	NAD metabolism	83.33	15 of 18
[Ref.: #66794]	glutamate and glutamine metabolism	82.14	23 of 28
[Ref.: #66794]	phenylacetate degradation (aerobic)	80	4 of 5
[Ref.: #66794]	peptidoglycan biosynthesis	80	12 of 15
[Ref.: #66794]	propionate fermentation	80	8 of 10
[Ref.: #66794]	glycogen metabolism	80	4 of 5
[Ref.: #66794]	heme metabolism	78.57	11 of 14
[Ref.: #66794]	serine metabolism	77.78	7 of 9
[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]	acetate fermentation	75	3 of 4
[Ref.: #66794]	flavin biosynthesis	73.33	11 of 15
[Ref.: #66794]	3-phenylpropionate degradation	73.33	11 of 15
[Ref.: #66794]	vitamin B6 metabolism	72.73	8 of 11
[Ref.: #66794]	alanine metabolism	72.41	21 of 29
[Ref.: #66794]	tetrahydrofolate 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]	purine metabolism	70.21	66 of 94
[Ref.: #66794]	starch degradation	70	7 of 10
[Ref.: #66794]	4-hydroxyphenylacetate degradation	70	7 of 10
[Ref.: #66794]	vitamin B1 metabolism	69.23	9 of 13
[Ref.: #66794]	methionine metabolism	69.23	18 of 26
[Ref.: #66794]	cyanate degradation	66.67	2 of 3
[Ref.: #66794]	acetoin degradation	66.67	2 of 3
[Ref.: #66794]	acetyl CoA biosynthesis	66.67	2 of 3
[Ref.: #66794]	d-mannose degradation	66.67	6 of 9
[Ref.: #66794]	L-lactaldehyde degradation	66.67	2 of 3
[Ref.: #66794]	octane oxidation	66.67	2 of 3
[Ref.: #66794]	non-pathway related	65.79	25 of 38
[Ref.: #66794]	glycolysis	64.71	11 of 17
[Ref.: #66794]	glutathione metabolism	64.29	9 of 14
[Ref.: #66794]	pentose phosphate pathway	63.64	7 of 11
[Ref.: #66794]	proline metabolism	63.64	7 of 11
[Ref.: #66794]	d-xylose degradation	63.64	7 of 11
[Ref.: #66794]	arginine metabolism	62.5	15 of 24
[Ref.: #66794]	androgen and estrogen metabolism	62.5	10 of 16
[Ref.: #66794]	isoleucine metabolism	62.5	5 of 8
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	62.5	5 of 8
[Ref.: #66794]	cellulose degradation	60	3 of 5
[Ref.: #66794]	gallate degradation	60	3 of 5
[Ref.: #66794]	hydrogen production	60	3 of 5
[Ref.: #66794]	histidine metabolism	58.62	17 of 29
[Ref.: #66794]	lipid metabolism	58.06	18 of 31
[Ref.: #66794]	tryptophan metabolism	57.89	22 of 38
[Ref.: #66794]	pyrimidine metabolism	57.78	26 of 45
[Ref.: #66794]	isoprenoid biosynthesis	57.69	15 of 26
[Ref.: #66794]	lysine metabolism	57.14	24 of 42
[Ref.: #66794]	polyamine pathway	56.52	13 of 23
[Ref.: #66794]	degradation of sugar alcohols	56.25	9 of 16
[Ref.: #66794]	lipid A biosynthesis	55.56	5 of 9
[Ref.: #66794]	cysteine metabolism	55.56	10 of 18
[Ref.: #66794]	phenol degradation	55	11 of 20
[Ref.: #66794]	urea cycle	53.85	7 of 13
[Ref.: #66794]	degradation of sugar acids	52	13 of 25
[Ref.: #66794]	toluene degradation	50	2 of 4
[Ref.: #66794]	biotin biosynthesis	50	2 of 4
[Ref.: #66794]	kanosamine biosynthesis II	50	1 of 2
[Ref.: #66794]	CMP-KDO biosynthesis	50	2 of 4
[Ref.: #66794]	myo-inositol biosynthesis	50	5 of 10
[Ref.: #66794]	ethanol fermentation	50	1 of 2
[Ref.: #66794]	glycogen biosynthesis	50	2 of 4
[Ref.: #66794]	quinate degradation	50	1 of 2
[Ref.: #66794]	tyrosine metabolism	50	7 of 14
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	50	6 of 12
[Ref.: #66794]	bile acid biosynthesis, neutral pathway	47.06	8 of 17
[Ref.: #66794]	phosphatidylethanolamine bioynthesis	46.15	6 of 13
[Ref.: #66794]	cholesterol biosynthesis	45.45	5 of 11
[Ref.: #66794]	metabolism of disaccharids	45.45	5 of 11
[Ref.: #66794]	nitrate assimilation	44.44	4 of 9
[Ref.: #66794]	degradation of pentoses	42.86	12 of 28
[Ref.: #66794]	benzoyl-CoA degradation	42.86	3 of 7
[Ref.: #66794]	lipoate biosynthesis	40	2 of 5
[Ref.: #66794]	3-chlorocatechol degradation	40	2 of 5
[Ref.: #66794]	glycine betaine biosynthesis	40	2 of 5
[Ref.: #66794]	arachidonate biosynthesis	40	2 of 5
[Ref.: #66794]	metabolism of amino sugars and derivatives	40	2 of 5
[Ref.: #66794]	D-cycloserine biosynthesis	40	2 of 5
[Ref.: #66794]	glycine metabolism	40	4 of 10
[Ref.: #66794]	degradation of hexoses	38.89	7 of 18
[Ref.: #66794]	arachidonic acid metabolism	38.89	7 of 18
[Ref.: #66794]	sulfate reduction	38.46	5 of 13
[Ref.: #66794]	oxidative phosphorylation	38.46	35 of 91
[Ref.: #66794]	dTDPLrhamnose biosynthesis	37.5	3 of 8
[Ref.: #66794]	ketogluconate metabolism	37.5	3 of 8
[Ref.: #66794]	carnitine metabolism	37.5	3 of 8
[Ref.: #66794]	carotenoid biosynthesis	36.36	8 of 22
[Ref.: #66794]	selenocysteine biosynthesis	33.33	2 of 6
[Ref.: #66794]	4-hydroxymandelate degradation	33.33	3 of 9
[Ref.: #66794]	sphingosine metabolism	33.33	2 of 6
[Ref.: #66794]	enterobactin biosynthesis	33.33	1 of 3
[Ref.: #66794]	pantothenate biosynthesis	33.33	2 of 6
[Ref.: #66794]	IAA biosynthesis	33.33	1 of 3
[Ref.: #66794]	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
[Ref.: #66794]	glycolate and glyoxylate degradation	33.33	2 of 6
[Ref.: #66794]	ascorbate metabolism	31.82	7 of 22
[Ref.: #66794]	ginsenoside metabolism	31.25	5 of 16
[Ref.: #66794]	aclacinomycin biosynthesis	28.57	2 of 7
[Ref.: #66794]	catecholamine biosynthesis	25	1 of 4
[Ref.: #66794]	cyclohexanol degradation	25	1 of 4
[Ref.: #66794]	lactate fermentation	25	1 of 4
[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.: #67771]	Sample type/isolated from	From contaminated petri dishl
[Ref.: #67771]	Country	India
[Ref.: #67771]	Country ISO 3 Code	IND
[Ref.: #67771]	Continent	Asia
* marker position based on {}

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]	Sphingorhabdus contaminans KCTC32445	GCA_007280415	contig	GenBank	1343899 tax ID	*
[Ref.: #66792]	Sphingorhabdus contaminans strain KCTC32445	1343899.3	wgs	PATRIC	1343899 tax ID	*
[Ref.: #66792]	Sphingorhabdus contaminans KCTC32445	2890953850	draft	JGI IMG/M	1343899 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: Sphingorhabdus contaminans strain KCTC32445 PATRIC: 1343899.3
[Ref.: #69481]	spore-forming	no	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Sphingorhabdus contaminans strain KCTC32445 PATRIC: 1343899.3
[Ref.: #69480]	motile	yes	61.039	no
[Ref.: #69480]	gram-positive	no	97.733	no
[Ref.: #69480]	anaerobic	no	99.563	yes
[Ref.: #69480]	halophile	no	90.898	no
[Ref.: #69480]	spore-forming	no	95.094	no
[Ref.: #69480]	thermophile	no	93.182	yes
[Ref.: #69480]	glucose-util	yes	83.8	no
[Ref.: #69480]	aerobic	yes	93.975	yes
[Ref.: #69480]	flagellated	no	83.114	no
[Ref.: #69480]	glucose-ferment	no	94.215	no

Availability in culture collections External links

[Ref.: #65260]

Culture collection no.

KCTC 32445, LMG 27671

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Sphingopyxis contaminans sp. nov., isolated from a contaminated Petri dish.	Subhash Y, Sasikala C, Ramana CV	Int J Syst Evol Microbiol	10.1099/ijs.0.061937-0	2014	*

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 )

#65260

Song-Zhen Yang, Xiong Xiong, Guang-Da Feng, Hua-Ping Li, Hong-Hui Zhu: Reclassification of Sphingopyxis contaminans as Sphingorhabdus contaminans comb. nov. and emended description of the genus Sphingorhabdus. IJSEM 67: 4328 - 4331 2017 ( DOI 10.1099/ijsem.0.002201 , PubMed 28884661 )

#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 )

#67771 Korean Collection for Type Cultures (KCTC) ; Curators of the KCTC;

#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 )

* These data were automatically processed and therefore are not curated

Change proposal

You found an error in BacDive? Please tell us about it!

Note that changes will be reviewed and judged. If your changes are legitimate, changes will occur within the next BacDive update. Only proposed changes supported by the according reference will be reviewed. The BacDive team reserves the right to reject proposed changes.

Search for species Sphingorhabdus contaminans in external resources:
SILVA
BRENDA
PANGAEA
StrainInfo
GBIF

Sphingorhabdus contaminans strain KCTC32445

Sphingorhabdus contaminans strain KCTC32445

Change proposal

Change proposal