Sphingorhabdus contaminans (KCTC 32445, LMG 27671, JC 216)

Name: Sphingorhabdus contaminans (KCTC 32445, LMG 27671, JC 216)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 158562

Type strain

Strain Designation JC 216

Culture col. no. KCTC 32445 LMG 27671 JC 216

NCBI tax ID(s) 1343899

Special Collections KCTC Literature strains

Links

Sphingorhabdus contaminans JC 216 is an aerobe, mesophilic prokaryote that was isolated from From contaminated petri dishl.

aerobe mesophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 273015

LMG 27671,KCTC 32445

@ref 20215

Last LPSN update 2025-12-16 10:08:03

Domain Pseudomonadati

Phylum Pseudomonadota

Class Alphaproteobacteria

Order Sphingomonadales

Family Sphingomonadaceae

Genus Sphingorhabdus

Species Sphingorhabdus contaminans

Full scientific name Sphingorhabdus contaminans (Subhash et al. 2014) Yang et al. 2017

Synonyms (2)

"Sphingorhabdus contaminans"
Sphingopyxis contaminans

Morphology

Cell morphology

@ref	Gram stain	Confidence
125438	negative	95.376
125439	negative	97.6

Culture and growth conditions

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
67771	positive	growth	30	mesophilic

Physiology and metabolism

Oxygen tolerance

67771

Oxygen toleranceaerobe

Spore formation

@ref	Spore formation	Confidence
125438		90.812
125439		95.6

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
65260	4853 ChEBI	esculin	+	hydrolysis
65260	17234 ChEBI	glucose	-	fermentation

Metabolite production

@ref	Chebi-ID	Metabolite	Production
65260	35581 ChEBI	indole

Enzymes

@ref	Value	Activity	Ec
65260	acid phosphatase	+	3.1.3.2
65260	alkaline phosphatase	+	3.1.3.1
65260	alpha-chymotrypsin	+	3.4.21.1
65260	alpha-fucosidase	-	3.2.1.51
65260	alpha-galactosidase	-	3.2.1.22
65260	alpha-glucosidase	+	3.2.1.20
65260	alpha-mannosidase	-	3.2.1.24
65260	arginine dihydrolase	-	3.5.3.6
65260	beta-glucosidase	+	3.2.1.21
65260	beta-glucuronidase	-	3.2.1.31
65260	catalase	-	1.11.1.6
65260	cystine arylamidase	+	3.4.11.3
65260	esterase (C 4)	+
65260	esterase Lipase (C 8)	+
65260	leucine arylamidase	+	3.4.11.1
65260	lipase (C 14)	+
65260	N-acetyl-beta-glucosaminidase	-	3.2.1.52
65260	naphthol-AS-BI-phosphohydrolase	+
65260	trypsin	+	3.4.21.4
65260	urease	-	3.5.1.5
65260	valine arylamidase	+

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	ppGpp biosynthesis	100	4 of 4
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	cis-vaccenate biosynthesis	100	2 of 2
66794	gluconeogenesis	100	8 of 8
66794	C4 and CAM-carbon fixation	100	8 of 8
66794	Entner Doudoroff pathway	100	10 of 10
66794	coenzyme A metabolism	100	4 of 4
66794	formaldehyde oxidation	100	3 of 3
66794	ethylmalonyl-CoA pathway	100	5 of 5
66794	adipate degradation	100	2 of 2
66794	methylglyoxal degradation	100	5 of 5
66794	taurine degradation	100	1 of 1
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	valine metabolism	100	9 of 9
66794	suberin monomers biosynthesis	100	2 of 2
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	palmitate biosynthesis	100	22 of 22
66794	folate polyglutamylation	100	1 of 1
66794	citric acid cycle	92.86	13 of 14
66794	threonine metabolism	90	9 of 10
66794	aspartate and asparagine metabolism	88.89	8 of 9
66794	CO2 fixation in Crenarchaeota	88.89	8 of 9
66794	molybdenum cofactor biosynthesis	88.89	8 of 9
66794	chorismate metabolism	88.89	8 of 9
66794	propanol degradation	85.71	6 of 7
66794	photosynthesis	85.71	12 of 14
66794	reductive acetyl coenzyme A pathway	85.71	6 of 7
66794	leucine metabolism	84.62	11 of 13
66794	NAD metabolism	83.33	15 of 18
66794	glutamate and glutamine metabolism	82.14	23 of 28
66794	phenylacetate degradation (aerobic)	80	4 of 5
66794	peptidoglycan biosynthesis	80	12 of 15
66794	propionate fermentation	80	8 of 10
66794	glycogen metabolism	80	4 of 5
66794	heme metabolism	78.57	11 of 14
66794	serine metabolism	77.78	7 of 9
66794	phenylalanine metabolism	76.92	10 of 13
66794	sulfopterin metabolism	75	3 of 4
66794	butanoate fermentation	75	3 of 4
66794	acetate fermentation	75	3 of 4
66794	flavin biosynthesis	73.33	11 of 15
66794	3-phenylpropionate degradation	73.33	11 of 15
66794	vitamin B6 metabolism	72.73	8 of 11
66794	alanine metabolism	72.41	21 of 29
66794	tetrahydrofolate metabolism	71.43	10 of 14
66794	cardiolipin biosynthesis	71.43	5 of 7
66794	ubiquinone biosynthesis	71.43	5 of 7
66794	purine metabolism	70.21	66 of 94
66794	starch degradation	70	7 of 10
66794	4-hydroxyphenylacetate degradation	70	7 of 10
66794	vitamin B1 metabolism	69.23	9 of 13
66794	methionine metabolism	69.23	18 of 26
66794	cyanate degradation	66.67	2 of 3
66794	acetoin degradation	66.67	2 of 3
66794	acetyl CoA biosynthesis	66.67	2 of 3
66794	d-mannose degradation	66.67	6 of 9
66794	L-lactaldehyde degradation	66.67	2 of 3
66794	octane oxidation	66.67	2 of 3
66794	non-pathway related	65.79	25 of 38
66794	glycolysis	64.71	11 of 17
66794	glutathione metabolism	64.29	9 of 14
66794	pentose phosphate pathway	63.64	7 of 11
66794	proline metabolism	63.64	7 of 11
66794	d-xylose degradation	63.64	7 of 11
66794	arginine metabolism	62.5	15 of 24
66794	androgen and estrogen metabolism	62.5	10 of 16
66794	isoleucine metabolism	62.5	5 of 8
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	62.5	5 of 8
66794	cellulose degradation	60	3 of 5
66794	gallate degradation	60	3 of 5
66794	hydrogen production	60	3 of 5
66794	histidine metabolism	58.62	17 of 29
66794	lipid metabolism	58.06	18 of 31
66794	tryptophan metabolism	57.89	22 of 38
66794	pyrimidine metabolism	57.78	26 of 45
66794	isoprenoid biosynthesis	57.69	15 of 26
66794	lysine metabolism	57.14	24 of 42
66794	polyamine pathway	56.52	13 of 23
66794	degradation of sugar alcohols	56.25	9 of 16
66794	lipid A biosynthesis	55.56	5 of 9
66794	cysteine metabolism	55.56	10 of 18
66794	phenol degradation	55	11 of 20
66794	urea cycle	53.85	7 of 13
66794	degradation of sugar acids	52	13 of 25
66794	toluene degradation	50	2 of 4
66794	biotin biosynthesis	50	2 of 4
66794	kanosamine biosynthesis II	50	1 of 2
66794	CMP-KDO biosynthesis	50	2 of 4
66794	myo-inositol biosynthesis	50	5 of 10
66794	ethanol fermentation	50	1 of 2
66794	glycogen biosynthesis	50	2 of 4
66794	quinate degradation	50	1 of 2
66794	tyrosine metabolism	50	7 of 14
66794	degradation of aromatic, nitrogen containing compounds	50	6 of 12
66794	bile acid biosynthesis, neutral pathway	47.06	8 of 17
66794	phosphatidylethanolamine bioynthesis	46.15	6 of 13
66794	cholesterol biosynthesis	45.45	5 of 11
66794	metabolism of disaccharids	45.45	5 of 11
66794	nitrate assimilation	44.44	4 of 9
66794	degradation of pentoses	42.86	12 of 28
66794	benzoyl-CoA degradation	42.86	3 of 7
66794	lipoate biosynthesis	40	2 of 5
66794	3-chlorocatechol degradation	40	2 of 5
66794	glycine betaine biosynthesis	40	2 of 5
66794	arachidonate biosynthesis	40	2 of 5
66794	metabolism of amino sugars and derivatives	40	2 of 5
66794	D-cycloserine biosynthesis	40	2 of 5
66794	glycine metabolism	40	4 of 10
66794	degradation of hexoses	38.89	7 of 18
66794	arachidonic acid metabolism	38.89	7 of 18
66794	sulfate reduction	38.46	5 of 13
66794	oxidative phosphorylation	38.46	35 of 91
66794	dTDPLrhamnose biosynthesis	37.5	3 of 8
66794	ketogluconate metabolism	37.5	3 of 8
66794	carnitine metabolism	37.5	3 of 8
66794	carotenoid biosynthesis	36.36	8 of 22
66794	selenocysteine biosynthesis	33.33	2 of 6
66794	4-hydroxymandelate degradation	33.33	3 of 9
66794	sphingosine metabolism	33.33	2 of 6
66794	enterobactin biosynthesis	33.33	1 of 3
66794	pantothenate biosynthesis	33.33	2 of 6
66794	IAA biosynthesis	33.33	1 of 3
66794	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
66794	glycolate and glyoxylate degradation	33.33	2 of 6
66794	ascorbate metabolism	31.82	7 of 22
66794	ginsenoside metabolism	31.25	5 of 16
66794	aclacinomycin biosynthesis	28.57	2 of 7
66794	catecholamine biosynthesis	25	1 of 4
66794	cyclohexanol degradation	25	1 of 4
66794	lactate fermentation	25	1 of 4
66794	alginate biosynthesis	25	1 of 4

Isolation, sampling and environmental information

Isolation

@ref	Sample type	Country	Country ISO 3 Code	Continent
67771	From contaminated petri dishl	India	IND	Asia

Interaction and safety

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	ASM728041v1 assembly for Sphingorhabdus contaminans KCTC32445	contig	GCA_007280415	1343899.3	2890953850	1343899	78.99

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
124043	Sphingopyxis contaminans strain KCTC 32445 16S ribosomal RNA gene, partial sequence.	KY966260	1444		1343899

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Sphingorhabdus contaminans KCTC32445
NCBI: GCA_007280415

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	95.60	no
125439	motility	BacteriaNetⓘ	no	56.20	no
125439	gram_stain	BacteriaNetⓘ	negative	97.60	no
125439	oxygen_tolerance	BacteriaNetⓘ	aerobe	89.70	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Sphingorhabdus contaminans strain KCTC32445
PATRIC: 1343899.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	95.38	no
125438	anaerobic	anaerobicⓘ	no	94.66	yes
125438	spore-forming	spore-formingⓘ	no	90.81	no
125438	aerobic	aerobicⓘ	yes	88.89	no
125438	thermophilic	thermophileⓘ	no	95.69	yes
125438	flagellated	motile2+ⓘ	yes	61.23	no

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;
#124043	Isabel Schober, Julia Koblitz: Data extracted from sequence databases, automatically matched based on designation and taxonomy .
#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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Sphingorhabdus contaminans (KCTC 32445, LMG 27671, JC 216)

Name and taxonomic classification

Morphology

Cell morphology

Culture and growth conditions

Culture temp

Physiology and metabolism

Oxygen tolerance

Spore formation

Metabolite utilization

Metabolite production

Enzymes

Pathway annotation

Isolation, sampling and environmental information

Isolation

Interaction and safety

Sequence information

Genome sequences

Genome browser: GCA_007280415

16S sequences

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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