Paraperlucidibaca baekdonensis (DSM 26022, CCUG 59307, KCTC 23145)

Name: Paraperlucidibaca baekdonensis (DSM 26022, CCUG 59307, KCTC 23145)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 8210

Type strain

Strain Designation RL-2

Culture col. no. DSM 26022 CCUG 59307 KCTC 23145 RL-2

NCBI tax ID(s) 748120

Special Collections DSMZ CCUG KCTC

History <- KCTC <- J.-H. Yoon, Korea Res. Inst. Biosci. & Biotechnol. (KRIBB), Taejon, South Korea; RL-2 <- JH Yoon, KRIBB

Links

Paraperlucidibaca baekdonensis RL-2 is an aerobe, Gram-negative bacterium that was isolated from seawater.

Gram-negative aerobe genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 407422

KCTC 23145,DSM 26022,CCUG 59307

@ref 20215

Last LPSN update 2026-02-09 11:19:39

Domain Bacteria

Phylum Pseudomonadota

Class Gammaproteobacteria

Order Pseudomonadales

Family Moraxellaceae

Genus Paraperlucidibaca

Species Paraperlucidibaca baekdonensis

Full scientific name Paraperlucidibaca baekdonensis Oh et al. 2011

Morphology

Cell morphology

@ref	Gram stain	Confidence
67771	negative
125439	negative	99.8
125438	negative	98.994

Colony morphology

@ref	Incubation period
18150	3-7 days
61900	>3 days

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
18150	REACTIVATION WITH LIQUID MEDIUM 830 (DSMZ Medium 830c)		Medium recipe at MediaDive	Name: REACTIVATION WITH LIQUID MEDIUM 830 (DSMZ Medium 830c) Composition: Agar 15.0 g/l Yeast extract 0.5 g/l Proteose peptone 0.5 g/l Casamino acids 0.5 g/l Glucose 0.5 g/l Starch 0.5 g/l K2HPO4 0.3 g/l Na-pyruvate 0.3 g/l MgSO4 x 7 H2O 0.05 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)
18150	positive	growth	20
61900	positive	growth	20-30
67771	positive	growth	20-25

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
61900	aerobe
67771	aerobe
125439	aerobe	92.3

Spore formation

@ref	Spore formation	Confidence
125439		99.6
125438		91.979

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	adipate degradation	100	2 of 2
66794	palmitate biosynthesis	100	22 of 22
66794	ppGpp biosynthesis	100	4 of 4
66794	glycine betaine biosynthesis	100	5 of 5
66794	cis-vaccenate biosynthesis	100	2 of 2
66794	valine metabolism	100	9 of 9
66794	biotin biosynthesis	100	4 of 4
66794	formaldehyde oxidation	100	3 of 3
66794	L-lactaldehyde degradation	100	3 of 3
66794	coenzyme A metabolism	100	4 of 4
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	folate polyglutamylation	100	1 of 1
66794	suberin monomers biosynthesis	100	2 of 2
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	octane oxidation	100	3 of 3
66794	tetrahydrofolate metabolism	92.86	13 of 14
66794	threonine metabolism	90	9 of 10
66794	CO2 fixation in Crenarchaeota	88.89	8 of 9
66794	chorismate metabolism	88.89	8 of 9
66794	lipid A biosynthesis	88.89	8 of 9
66794	isoleucine metabolism	87.5	7 of 8
66794	ubiquinone biosynthesis	85.71	6 of 7
66794	glutamate and glutamine metabolism	82.14	23 of 28
66794	vitamin B6 metabolism	81.82	9 of 11
66794	peptidoglycan biosynthesis	80	12 of 15
66794	methylglyoxal degradation	80	4 of 5
66794	photosynthesis	78.57	11 of 14
66794	heme metabolism	78.57	11 of 14
66794	serine metabolism	77.78	7 of 9
66794	molybdenum cofactor biosynthesis	77.78	7 of 9
66794	phenylalanine metabolism	76.92	10 of 13
66794	vitamin B1 metabolism	76.92	10 of 13
66794	acetate fermentation	75	3 of 4
66794	sulfopterin metabolism	75	3 of 4
66794	CMP-KDO biosynthesis	75	3 of 4
66794	NAD metabolism	72.22	13 of 18
66794	reductive acetyl coenzyme A pathway	71.43	5 of 7
66794	cardiolipin biosynthesis	71.43	5 of 7
66794	propionate fermentation	70	7 of 10
66794	flavin biosynthesis	66.67	10 of 15
66794	aspartate and asparagine metabolism	66.67	6 of 9
66794	acetoin degradation	66.67	2 of 3
66794	methionine metabolism	65.38	17 of 26
66794	lipid metabolism	64.52	20 of 31
66794	citric acid cycle	64.29	9 of 14
66794	gluconeogenesis	62.5	5 of 8
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	62.5	5 of 8
66794	alanine metabolism	62.07	18 of 29
66794	leucine metabolism	61.54	8 of 13
66794	purine metabolism	60.64	57 of 94
66794	non-pathway related	60.53	23 of 38
66794	Entner Doudoroff pathway	60	6 of 10
66794	cellulose degradation	60	3 of 5
66794	isoprenoid biosynthesis	57.69	15 of 26
66794	propanol degradation	57.14	4 of 7
66794	glutathione metabolism	57.14	8 of 14
66794	pyrimidine metabolism	55.56	25 of 45
66794	cysteine metabolism	55.56	10 of 18
66794	d-mannose degradation	55.56	5 of 9
66794	proline metabolism	54.55	6 of 11
66794	pentose phosphate pathway	54.55	6 of 11
66794	arginine metabolism	54.17	13 of 24
66794	sulfate reduction	53.85	7 of 13
66794	glycolysis	52.94	9 of 17
66794	histidine metabolism	51.72	15 of 29
66794	C4 and CAM-carbon fixation	50	4 of 8
66794	dTDPLrhamnose biosynthesis	50	4 of 8
66794	ketogluconate metabolism	50	4 of 8
66794	phenylmercury acetate degradation	50	1 of 2
66794	kanosamine biosynthesis II	50	1 of 2
66794	glycine metabolism	50	5 of 10
66794	pantothenate biosynthesis	50	3 of 6
66794	cyclohexanol degradation	50	2 of 4
66794	ethanol fermentation	50	1 of 2
66794	butanoate fermentation	50	2 of 4
66794	toluene degradation	50	2 of 4
66794	tryptophan metabolism	50	19 of 38
66794	tyrosine metabolism	50	7 of 14
66794	lysine metabolism	47.62	20 of 42
66794	nitrate assimilation	44.44	4 of 9
66794	degradation of aromatic, nitrogen containing compounds	41.67	5 of 12
66794	arachidonate biosynthesis	40	2 of 5
66794	vitamin K metabolism	40	2 of 5
66794	lipoate biosynthesis	40	2 of 5
66794	3-phenylpropionate degradation	40	6 of 15
66794	factor 420 biosynthesis	40	2 of 5
66794	degradation of hexoses	38.89	7 of 18
66794	phosphatidylethanolamine bioynthesis	38.46	5 of 13
66794	carnitine metabolism	37.5	3 of 8
66794	oxidative phosphorylation	35.16	32 of 91
66794	acetyl CoA biosynthesis	33.33	1 of 3
66794	selenocysteine biosynthesis	33.33	2 of 6
66794	cyanate degradation	33.33	1 of 3
66794	methane metabolism	33.33	1 of 3
66794	IAA biosynthesis	33.33	1 of 3
66794	glycolate and glyoxylate degradation	33.33	2 of 6
66794	enterobactin biosynthesis	33.33	1 of 3
66794	ascorbate metabolism	31.82	7 of 22
66794	degradation of sugar alcohols	31.25	5 of 16
66794	androgen and estrogen metabolism	31.25	5 of 16
66794	urea cycle	30.77	4 of 13
66794	phenol degradation	30	6 of 20
66794	degradation of pentoses	28.57	8 of 28
66794	arachidonic acid metabolism	27.78	5 of 18
66794	cholesterol biosynthesis	27.27	3 of 11
66794	carotenoid biosynthesis	27.27	6 of 22
66794	lactate fermentation	25	1 of 4
66794	glycogen biosynthesis	25	1 of 4
66794	bile acid biosynthesis, neutral pathway	23.53	4 of 17
66794	4-hydroxymandelate degradation	22.22	2 of 9

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Aquatic	#Marine

Isolation

@ref	Sample type	Sampling date	Geographic location	Country	Country ISO 3 Code	Continent
18150	seawater		East Sea, Baekdo Harbor	Republic of Korea	KOR	Asia
61900	Seawater	2008	East Sea,Baekdo harbor	Republic of Korea	KOR	Asia
67771	From seawater		East Sea	Republic of Korea	KOR	Asia

Taxonmaps

69479

Global distribution of 16S sequence GU731671 (>99% sequence identity) for Paraperlucidibaca baekdonensis from Microbeatlas

Aquatic Samples	297
Soil Samples	9
Animal Samples	22
Plant Samples
Total Samples	328

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
18150	1	Risk group (German classification) According to TRBA 466

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	ASM338753v1 assembly for Paraperlucidibaca baekdonensis DSM 26022	scaffold	GCA_003387535	748120.3	2770939643	748120	70.58

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
18150	Paraperlucidibaca baekdonensis strain RL-2 16S ribosomal RNA gene, partial sequence	GU731671	1460		748120

GC content

@ref	GC-content (mol%)	Method
18150	61.3	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: Paraperlucidibaca baekdonensis DSM 26022
NCBI: GCA_003387535

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	99.60	no
125439	motility	BacteriaNetⓘ	yes	89.50	no
125439	gram_stain	BacteriaNetⓘ	negative	99.80	no
125439	oxygen_tolerance	BacteriaNetⓘ	aerobe	92.30	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Paraperlucidibaca baekdonensis DSM 26022
NCBI: GCA_003387535.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	98.99	yes
125438	anaerobic	anaerobicⓘ	no	94.63	yes
125438	aerobic	aerobicⓘ	yes	75.59	yes
125438	spore-forming	spore-formingⓘ	no	91.98	no
125438	thermophilic	thermophileⓘ	no	93.68	no
125438	flagellated	motile2+ⓘ	yes	72.10	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Amnimonas aquatica gen. nov., sp. nov., Isolated from a Freshwater River.	Lee Y, Park HY, Jeon CO	Curr Microbiol	10.1007/s00284-019-01652-5	2019
Phylogeny	Paraperlucidibaca wandonensis sp. nov., isolated from seawater, and emended description of the genus Paraperlucidibaca Oh et al. 2011.	Yoon JH, Park S, Jung YT, Lee JS, Lee KC	Int J Syst Evol Microbiol	10.1099/ijs.0.048645-0	2013
Phylogeny	Paraperlucidibaca baekdonensis gen. nov., sp. nov., isolated from seawater.	Oh KH, Lee SY, Lee MH, Oh TK, Yoon JH	Int J Syst Evol Microbiol	10.1099/ijs.0.023994-0	2010

References

#18150	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 26022
#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 )
#61900	Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 59307
#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;
#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 .
#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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Paraperlucidibaca baekdonensis (DSM 26022, CCUG 59307, KCTC 23145)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Spore formation

Pathway annotation

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_003387535

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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