Phenylobacterium hankyongense (KACC 18628, LMG 30081, HKS-05)

Name: Phenylobacterium hankyongense (KACC 18628, LMG 30081, HKS-05)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 158580

Type strain

Strain Designation HKS-05

Culture col. no. KACC 18628 LMG 30081 HKS-05

NCBI tax ID(s) 1813876

Special Collections Literature strains

Links

Phenylobacterium hankyongense HKS-05 is an aerobe, Gram-negative, rod-shaped bacterium that forms circular colonies and was isolated from ginseng field soil.

Gram-negative rod-shaped colony-forming aerobe genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 272478

LMG 30081

@ref 20215

Last LPSN update 2026-02-09 11:38:22

Domain Bacteria

Phylum Pseudomonadota

Class Alphaproteobacteria

Order Caulobacterales

Family Caulobacteraceae

Genus Phenylobacterium

Species Phenylobacterium hankyongense

Full scientific name Phenylobacterium hankyongense Choi et al. 2018

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Motility
65289	negative	0.8-1 µm	0.2-0.3 µm	rod-shaped

Colony morphology

@ref	Colony size	Colony color	Colony shape	Incubation period	Medium used
65289	1.5 mm	colourless	circular	3 days	R2A

Culture and growth conditions

Culture medium

@ref	Name	Growth
65289	Reasoner's 2A agar (R2A)
65289	Nutrient agar (NA)
65289	MacConkey agar
65289	tryptic soy agar

Culture temp

@ref	Growth	Type	Temperature (°C)
65289	positive	growth	10-37
65289	negative	growth	4
65289	negative	growth	40
65289	positive	optimum	25-30

Culture pH

@ref	Ability	Type	PH
65289	positive	optimum	7
65289	positive	growth	6-8

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
65289	aerobe
125439	obligate aerobe	99.3

Spore formation

65289

Spore formationno

Halophily

@ref	Salt	Growth	Tested relation	Concentration
65289	NaCl	positive	growth	0 %(w/v)
65289	NaCl	positive	growth	2 %(w/v)

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
65289	30916 ChEBI	2-oxoglutarate	-	assimilation
65289	16193 ChEBI	3-hydroxybenzoate	-	assimilation
65289	37054 ChEBI	3-hydroxybutyrate	+	assimilation
65289	17879 ChEBI	4-hydroxybenzoate	-	assimilation
65289	58143 ChEBI	5-dehydro-D-gluconate	-	assimilation
65289	30089 ChEBI	acetate	-	assimilation
65289	17128 ChEBI	adipate	-	assimilation
65289	85146 ChEBI	carboxymethylcellulose	-	hydrolysis
65289	16947 ChEBI	citrate	+	assimilation
65289	17634 ChEBI	D-glucose	+	assimilation
65289	16899 ChEBI	D-mannitol	+	assimilation
65289	16024 ChEBI	D-mannose	+	assimilation
65289	16988 ChEBI	D-ribose	-	assimilation
65289	17924 ChEBI	D-sorbitol	-	assimilation
65289	27689 ChEBI	decanoate	-	assimilation
65289	16991 ChEBI	dna	-	hydrolysis
65289	4853 ChEBI	esculin	-	hydrolysis
65289	5291 ChEBI	gelatin	-	hydrolysis
65289	24265 ChEBI	gluconate	+	assimilation
65289	17234 ChEBI	glucose	-	builds acid from
65289	28087 ChEBI	glycogen	+	assimilation
65289	17240 ChEBI	itaconate	+	assimilation
65289	16977 ChEBI	L-alanine	-	assimilation
65289	30849 ChEBI	L-arabinose	+	assimilation
65289	18287 ChEBI	L-fucose	-	assimilation
65289	15971 ChEBI	L-histidine	-	assimilation
65289	17203 ChEBI	L-proline	+	assimilation
65289	62345 ChEBI	L-rhamnose	-	assimilation
65289	17115 ChEBI	L-serine	-	assimilation
65289	24996 ChEBI	lactate	-	assimilation
65289	25115 ChEBI	malate	-	assimilation
65289	15792 ChEBI	malonate	-	assimilation
65289	17306 ChEBI	maltose	+	assimilation
65289	28053 ChEBI	melibiose	-	assimilation
65289	17268 ChEBI	myo-inositol	-	assimilation
65289	506227 ChEBI	N-acetylglucosamine	-	assimilation
65289	17632 ChEBI	nitrate	+	reduction
65289	18401 ChEBI	phenylacetate	-	assimilation
65289	17272 ChEBI	propionate	+	assimilation
65289	17814 ChEBI	salicin	-	assimilation
65289		skimmed milk	-	hydrolysis
65289	28017 ChEBI	starch	-	hydrolysis
65289	9300 ChEBI	suberic acid	-	assimilation
65289	17992 ChEBI	sucrose	-	assimilation
65289	31011 ChEBI	valerate	-	assimilation

Metabolite production

@ref	Chebi-ID	Metabolite	Production
65289	35581 ChEBI	indole

Enzymes

@ref	Value	Activity	Ec
65289	acid phosphatase	+	3.1.3.2
65289	alkaline phosphatase	+	3.1.3.1
65289	alpha-chymotrypsin	-	3.4.21.1
65289	alpha-fucosidase	-	3.2.1.51
65289	alpha-galactosidase	+	3.2.1.22
65289	alpha-glucosidase	+	3.2.1.20
65289	alpha-mannosidase	-	3.2.1.24
65289	arginine dihydrolase	-	3.5.3.6
65289	beta-glucuronidase	-	3.2.1.31
65289	catalase	+	1.11.1.6
65289	cystine arylamidase	+	3.4.11.3
65289	cytochrome oxidase	+	1.9.3.1
65289	esterase	+
65289	esterase Lipase (C 8)	+
65289	leucine arylamidase	+	3.4.11.1
65289	lipase (C 14)	-
65289	N-acetyl-beta-glucosaminidase	+	3.2.1.52
65289	naphthol-AS-BI-phosphohydrolase	+
65289	protease	-
65289	trypsin	+	3.4.21.4
65289	urease	-	3.5.1.5
65289	valine arylamidase	+

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	adipate degradation	100	2 of 2
66794	glycine betaine biosynthesis	100	5 of 5
66794	biotin biosynthesis	100	4 of 4
66794	cyanate degradation	100	3 of 3
66794	valine metabolism	100	9 of 9
66794	kanosamine biosynthesis II	100	2 of 2
66794	Entner Doudoroff pathway	100	10 of 10
66794	ethanol fermentation	100	2 of 2
66794	photosynthesis	100	14 of 14
66794	palmitate biosynthesis	100	22 of 22
66794	methylglyoxal degradation	100	5 of 5
66794	formaldehyde oxidation	100	3 of 3
66794	coenzyme A metabolism	100	4 of 4
66794	sulfopterin metabolism	100	4 of 4
66794	cis-vaccenate biosynthesis	100	2 of 2
66794	folate polyglutamylation	100	1 of 1
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	taurine degradation	100	1 of 1
66794	suberin monomers biosynthesis	100	2 of 2
66794	ppGpp biosynthesis	100	4 of 4
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	denitrification	100	2 of 2
66794	molybdenum cofactor biosynthesis	100	9 of 9
66794	tetrahydrofolate metabolism	92.86	13 of 14
66794	CO2 fixation in Crenarchaeota	88.89	8 of 9
66794	chorismate metabolism	88.89	8 of 9
66794	serine metabolism	88.89	8 of 9
66794	C4 and CAM-carbon fixation	87.5	7 of 8
66794	gluconeogenesis	87.5	7 of 8
66794	ubiquinone biosynthesis	85.71	6 of 7
66794	reductive acetyl coenzyme A pathway	85.71	6 of 7
66794	phenylalanine metabolism	84.62	11 of 13
66794	leucine metabolism	84.62	11 of 13
66794	NAD metabolism	83.33	15 of 18
66794	alanine metabolism	82.76	24 of 29
66794	vitamin B6 metabolism	81.82	9 of 11
66794	proline metabolism	81.82	9 of 11
66794	gallate degradation	80	4 of 5
66794	phenylacetate degradation (aerobic)	80	4 of 5
66794	glycogen metabolism	80	4 of 5
66794	threonine metabolism	80	8 of 10
66794	propionate fermentation	80	8 of 10
66794	peptidoglycan biosynthesis	80	12 of 15
66794	histidine metabolism	79.31	23 of 29
66794	glutamate and glutamine metabolism	78.57	22 of 28
66794	lysine metabolism	78.57	33 of 42
66794	citric acid cycle	78.57	11 of 14
66794	lipid A biosynthesis	77.78	7 of 9
66794	aspartate and asparagine metabolism	77.78	7 of 9
66794	acetate fermentation	75	3 of 4
66794	butanoate fermentation	75	3 of 4
66794	CMP-KDO biosynthesis	75	3 of 4
66794	isoleucine metabolism	75	6 of 8
66794	glycogen biosynthesis	75	3 of 4
66794	tryptophan metabolism	73.68	28 of 38
66794	flavin biosynthesis	73.33	11 of 15
66794	methionine metabolism	73.08	19 of 26
66794	pentose phosphate pathway	72.73	8 of 11
66794	purine metabolism	72.34	68 of 94
66794	propanol degradation	71.43	5 of 7
66794	glutathione metabolism	71.43	10 of 14
66794	cardiolipin biosynthesis	71.43	5 of 7
66794	tyrosine metabolism	71.43	10 of 14
66794	heme metabolism	71.43	10 of 14
66794	pyrimidine metabolism	71.11	32 of 45
66794	4-hydroxyphenylacetate degradation	70	7 of 10
66794	vitamin B1 metabolism	69.23	9 of 13
66794	non-pathway related	68.42	26 of 38
66794	lipid metabolism	67.74	21 of 31
66794	acetyl CoA biosynthesis	66.67	2 of 3
66794	L-lactaldehyde degradation	66.67	2 of 3
66794	cysteine metabolism	66.67	12 of 18
66794	octane oxidation	66.67	2 of 3
66794	acetoin degradation	66.67	2 of 3
66794	d-mannose degradation	66.67	6 of 9
66794	phenol degradation	65	13 of 20
66794	glycolysis	64.71	11 of 17
66794	d-xylose degradation	63.64	7 of 11
66794	arginine metabolism	62.5	15 of 24
66794	ketogluconate metabolism	62.5	5 of 8
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	62.5	5 of 8
66794	urea cycle	61.54	8 of 13
66794	vitamin K metabolism	60	3 of 5
66794	ethylmalonyl-CoA pathway	60	3 of 5
66794	lipoate biosynthesis	60	3 of 5
66794	starch degradation	60	6 of 10
66794	degradation of aromatic, nitrogen containing compounds	58.33	7 of 12
66794	degradation of sugar alcohols	56.25	9 of 16
66794	allantoin degradation	55.56	5 of 9
66794	chlorophyll metabolism	55.56	10 of 18
66794	metabolism of disaccharids	54.55	6 of 11
66794	3-phenylpropionate degradation	53.33	8 of 15
66794	ascorbate metabolism	50	11 of 22
66794	glycolate and glyoxylate degradation	50	3 of 6
66794	androgen and estrogen metabolism	50	8 of 16
66794	pantothenate biosynthesis	50	3 of 6
66794	ribulose monophosphate pathway	50	1 of 2
66794	dTDPLrhamnose biosynthesis	50	4 of 8
66794	catecholamine biosynthesis	50	2 of 4
66794	cyclohexanol degradation	50	2 of 4
66794	toluene degradation	50	2 of 4
66794	selenocysteine biosynthesis	50	3 of 6
66794	resorcinol degradation	50	1 of 2
66794	glycine metabolism	50	5 of 10
66794	quinate degradation	50	1 of 2
66794	dolichol and dolichyl phosphate biosynthesis	50	1 of 2
66794	isoprenoid biosynthesis	50	13 of 26
66794	carotenoid biosynthesis	45.45	10 of 22
66794	nitrate assimilation	44.44	4 of 9
66794	oxidative phosphorylation	42.86	39 of 91
66794	benzoyl-CoA degradation	42.86	3 of 7
66794	elloramycin biosynthesis	40	2 of 5
66794	3-chlorocatechol degradation	40	2 of 5
66794	arachidonate biosynthesis	40	2 of 5
66794	degradation of pentoses	39.29	11 of 28
66794	arachidonic acid metabolism	38.89	7 of 18
66794	degradation of hexoses	38.89	7 of 18
66794	sulfate reduction	38.46	5 of 13
66794	carnitine metabolism	37.5	3 of 8
66794	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
66794	sphingosine metabolism	33.33	2 of 6
66794	IAA biosynthesis	33.33	1 of 3
66794	4-hydroxymandelate degradation	33.33	3 of 9
66794	enterobactin biosynthesis	33.33	1 of 3
66794	polyamine pathway	30.43	7 of 23
66794	myo-inositol biosynthesis	30	3 of 10
66794	coenzyme M biosynthesis	30	3 of 10
66794	bile acid biosynthesis, neutral pathway	29.41	5 of 17
66794	degradation of sugar acids	28	7 of 25
66794	cholesterol biosynthesis	27.27	3 of 11
66794	lactate fermentation	25	1 of 4
66794	alginate biosynthesis	25	1 of 4
66794	phenylpropanoid biosynthesis	23.08	3 of 13
66794	vitamin B12 metabolism	20.59	7 of 34

Fatty acid profile

Metadata FA analysis

@ref

65289

Fatty acid	Percentage
C18:1ω7c/C18:1ω6c	42.6
C16:0	22
C16:1ω7c/C16:1ω6c	6.6
C17:0	4.3
C16:1ω11c	3.7
C12:0	3.6
C19:0 cyclo ω8c	3.6
C18:1ω7c 11-methyl	2.7
C17:1ω8c	2.4
C12:1 3OH	2.1
C20:0	1.3
C18:2ω6,9c/anteiso-C18:0	1.3
C18:0	1
C12:0 3OH	0.9
C17:1ω6c	0.8
C17:0 anteiso	0.5

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Engineered	#Agriculture	#Field
#Host	#Plants	#Herbaceous plants (Grass,Crops)
#Environmental	#Terrestrial	#Soil

Isolation

@ref	Sample type	Country	Country ISO 3 Code	Continent	Enrichment culture	Enrichment culture temperature
65289	ginseng field soil	Republic of Korea	KOR	Asia	R2A	25

Taxonmaps

69479

Global distribution of 16S sequence KT950746 (>99% sequence identity) for Phenylobacterium hankyongense from Microbeatlas

Aquatic Samples	347
Soil Samples	3595
Animal Samples	305
Plant Samples	538
Total Samples	4785

Interaction and safety

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	ASM325450v1 assembly for Phenylobacterium hankyongense HKS-05	contig	GCA_003254505	1813876.3	2848300489	1813876	70.93

16S sequences

@ref	Description	Accession	Database
65289	Phenylobacterium hankyongense strain HKS-05 16S ribosomal RNA gene, partial sequence	KT950746

GC content

@ref	GC-content (mol%)	Method
65289	70.4	high performance liquid chromatography (HPLC)

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Phenylobacterium hankyongense HKS-05
NCBI: GCA_003254505

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	89.40	no
125439	motility	BacteriaNetⓘ	yes	55.10	no
125439	gram_stain	BacteriaNetⓘ	positive	81.40	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	99.30	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Phenylobacterium terrae sp. nov., isolated from a soil sample of Khyber-Pakhtun-Khwa, Pakistan.	Khan IU, Habib N, Xiao M, Huang X, Khan NU, Im WT, Ahmed I, Zhi XY, Li WJ	Antonie Van Leeuwenhoek	10.1007/s10482-018-1064-2	2018
Phylogeny	Phenylobacterium hankyongense sp. nov., isolated from ginseng field soil.	Choi GM, Lee SY, Choi KD, Im WT	Int J Syst Evol Microbiol	10.1099/ijsem.0.002469	2017
Phylogeny	Phenylobacterium soli sp. nov., isolated from arsenic and cadmium contaminated farmland soil.	Li X, Yu Y, Choi L, Song Y, Wu M, Wang G, Li M	Int J Syst Evol Microbiol	10.1099/ijsem.0.003325	2019

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 )
#65289	Gyu-Min Choi, Soon-youl Lee, Kang Duk Choi, Wan-Taek Im: Phenylobacterium hankyongense sp. nov., isolated from ginseng field soil. IJSEM 68: 125 - 130 2018 ( DOI 10.1099/ijsem.0.002469 , PubMed 29116033 )
#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 .
#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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Phenylobacterium hankyongense (KACC 18628, LMG 30081, HKS-05)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Spore formation

Halophily

Metabolite utilization

Metabolite production

Enzymes

Pathway annotation

Fatty acid profile

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Sequence information

Genome sequences

Genome browser: GCA_003254505

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

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