Dokdonella immobilis (CGMCC 1.7659, JCM 15763, LM2-5)

Name: Dokdonella immobilis (CGMCC 1.7659, JCM 15763, LM2-5)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 133856

Type strain

Strain Designation LM2-5

Culture col. no. CGMCC 1.7659 JCM 15763 LM2-5

NCBI tax ID(s) 578942

Special Collections JCM Literature strains

Links

Dokdonella immobilis LM2-5 is an aerobe, Gram-negative, rod-shaped prokaryote that was isolated from bioreactor.

Gram-negative rod-shaped aerobe genome sequence 16S sequence

Name and taxonomic classification

SI-ID 133356

JCM 15763

@ref 20215

Last LPSN update 2025-12-16 10:01:54

Domain Pseudomonadati

Phylum Pseudomonadota

Class Gammaproteobacteria

Order Lysobacterales

Family Rhodanobacteraceae

Genus Dokdonella

Species Dokdonella immobilis

Full scientific name Dokdonella immobilis Liu et al. 2013

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell shape
30686	negative	4 µm	rod-shaped
125438	negative
125439	negative

Pigmentation

30686

Productionyes

Culture and growth conditions

Culture temp

@ref	Growth	Type	Temperature (°C)
30686	positive	growth	16-37
30686	positive	optimum	25
67770	positive	growth	25

Culture pH

@ref	Ability	Type	PH
30686	positive	optimum	6.75
30686	positive	growth	6.5-7

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance
30686	aerobe
125439	obligate aerobe

Spore formation

@ref	Spore formation
30686
125439

Halophily

@ref	Salt	Growth	Tested relation	Concentration
30686	NaCl	positive	growth	0-2 %
30686	NaCl	positive	optimum	1 %

Observation

@ref	Observation
30686	aggregates in clumps
67770	quinones: Q-8

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
30686	4853 ChEBI	esculin	+	hydrolysis
30686	24265 ChEBI	gluconate	+	carbon source

Enzymes

@ref	Value	Activity	Ec
30686	acid phosphatase	+	3.1.3.2
30686	alkaline phosphatase	+	3.1.3.1
30686	cytochrome oxidase	+	1.9.3.1
30686	gelatinase	+

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	quinate degradation	100	2 of 2
66794	formaldehyde oxidation	100	3 of 3
66794	cis-vaccenate biosynthesis	100	2 of 2
66794	ppGpp biosynthesis	100	4 of 4
66794	biotin biosynthesis	100	4 of 4
66794	cardiolipin biosynthesis	100	7 of 7
66794	glycogen metabolism	100	5 of 5
66794	palmitate biosynthesis	100	22 of 22
66794	molybdenum cofactor biosynthesis	100	9 of 9
66794	adipate degradation	100	2 of 2
66794	threonine metabolism	100	10 of 10
66794	coenzyme A metabolism	100	4 of 4
66794	octane oxidation	100	3 of 3
66794	valine metabolism	100	9 of 9
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	butanoate fermentation	100	4 of 4
66794	folate polyglutamylation	100	1 of 1
66794	suberin monomers biosynthesis	100	2 of 2
66794	methylglyoxal degradation	100	5 of 5
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	sulfopterin metabolism	100	4 of 4
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	denitrification	100	2 of 2
66794	phenylalanine metabolism	92.31	12 of 13
66794	Entner Doudoroff pathway	90	9 of 10
66794	serine metabolism	88.89	8 of 9
66794	lipid A biosynthesis	88.89	8 of 9
66794	gluconeogenesis	87.5	7 of 8
66794	isoleucine metabolism	87.5	7 of 8
66794	alanine metabolism	86.21	25 of 29
66794	photosynthesis	85.71	12 of 14
66794	propanol degradation	85.71	6 of 7
66794	glutathione metabolism	85.71	12 of 14
66794	tetrahydrofolate metabolism	85.71	12 of 14
66794	glutamate and glutamine metabolism	85.71	24 of 28
66794	leucine metabolism	84.62	11 of 13
66794	purine metabolism	84.04	79 of 94
66794	lipid metabolism	80.65	25 of 31
66794	propionate fermentation	80	8 of 10
66794	pyrimidine metabolism	80	36 of 45
66794	starch degradation	80	8 of 10
66794	cellulose degradation	80	4 of 5
66794	peptidoglycan biosynthesis	80	12 of 15
66794	tryptophan metabolism	78.95	30 of 38
66794	heme metabolism	78.57	11 of 14
66794	citric acid cycle	78.57	11 of 14
66794	NAD metabolism	77.78	14 of 18
66794	CO2 fixation in Crenarchaeota	77.78	7 of 9
66794	aspartate and asparagine metabolism	77.78	7 of 9
66794	chorismate metabolism	77.78	7 of 9
66794	vitamin B1 metabolism	76.92	10 of 13
66794	C4 and CAM-carbon fixation	75	6 of 8
66794	acetate fermentation	75	3 of 4
66794	glycogen biosynthesis	75	3 of 4
66794	CMP-KDO biosynthesis	75	3 of 4
66794	methionine metabolism	73.08	19 of 26
66794	proline metabolism	72.73	8 of 11
66794	vitamin B6 metabolism	72.73	8 of 11
66794	histidine metabolism	72.41	21 of 29
66794	reductive acetyl coenzyme A pathway	71.43	5 of 7
66794	ubiquinone biosynthesis	71.43	5 of 7
66794	cyanate degradation	66.67	2 of 3
66794	d-mannose degradation	66.67	6 of 9
66794	L-lactaldehyde degradation	66.67	2 of 3
66794	flavin biosynthesis	66.67	10 of 15
66794	methane metabolism	66.67	2 of 3
66794	acetoin degradation	66.67	2 of 3
66794	glycolysis	64.71	11 of 17
66794	tyrosine metabolism	64.29	9 of 14
66794	lysine metabolism	64.29	27 of 42
66794	pentose phosphate pathway	63.64	7 of 11
66794	dTDPLrhamnose biosynthesis	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	cysteine metabolism	61.11	11 of 18
66794	phenylacetate degradation (aerobic)	60	3 of 5
66794	D-cycloserine biosynthesis	60	3 of 5
66794	lipoate biosynthesis	60	3 of 5
66794	degradation of aromatic, nitrogen containing compounds	58.33	7 of 12
66794	arginine metabolism	58.33	14 of 24
66794	non-pathway related	57.89	22 of 38
66794	degradation of sugar alcohols	56.25	9 of 16
66794	allantoin degradation	55.56	5 of 9
66794	nitrate assimilation	55.56	5 of 9
66794	arachidonic acid metabolism	55.56	10 of 18
66794	isoprenoid biosynthesis	53.85	14 of 26
66794	glycine metabolism	50	5 of 10
66794	catecholamine biosynthesis	50	2 of 4
66794	glycolate and glyoxylate degradation	50	3 of 6
66794	ketogluconate metabolism	50	4 of 8
66794	pantothenate biosynthesis	50	3 of 6
66794	ethanol fermentation	50	1 of 2
66794	phenylmercury acetate degradation	50	1 of 2
66794	polyamine pathway	47.83	11 of 23
66794	metabolism of disaccharids	45.45	5 of 11
66794	ascorbate metabolism	45.45	10 of 22
66794	oxidative phosphorylation	41.76	38 of 91
66794	vitamin K metabolism	40	2 of 5
66794	glycine betaine biosynthesis	40	2 of 5
66794	coenzyme M biosynthesis	40	4 of 10
66794	3-phenylpropionate degradation	40	6 of 15
66794	3-chlorocatechol degradation	40	2 of 5
66794	arachidonate biosynthesis	40	2 of 5
66794	hydrogen production	40	2 of 5
66794	gallate degradation	40	2 of 5
66794	degradation of hexoses	38.89	7 of 18
66794	phenylpropanoid biosynthesis	38.46	5 of 13
66794	sulfate reduction	38.46	5 of 13
66794	dolichyl-diphosphooligosaccharide biosynthesis	36.36	4 of 11
66794	degradation of pentoses	35.71	10 of 28
66794	acetyl CoA biosynthesis	33.33	1 of 3
66794	selenocysteine biosynthesis	33.33	2 of 6
66794	IAA biosynthesis	33.33	1 of 3
66794	4-hydroxymandelate degradation	33.33	3 of 9
66794	sphingosine metabolism	33.33	2 of 6
66794	sulfoquinovose degradation	33.33	1 of 3
66794	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
66794	androgen and estrogen metabolism	31.25	5 of 16
66794	phosphatidylethanolamine bioynthesis	30.77	4 of 13
66794	phenol degradation	30	6 of 20
66794	benzoyl-CoA degradation	28.57	2 of 7
66794	aclacinomycin biosynthesis	28.57	2 of 7
66794	cholesterol biosynthesis	27.27	3 of 11
66794	d-xylose degradation	27.27	3 of 11
66794	carotenoid biosynthesis	27.27	6 of 22
66794	toluene degradation	25	1 of 4
66794	cyclohexanol degradation	25	1 of 4
66794	lactate fermentation	25	1 of 4
66794	carnitine metabolism	25	2 of 8
66794	vitamin E metabolism	25	1 of 4
66794	vitamin B12 metabolism	20.59	7 of 34

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2
#Engineered	#Bioreactor

Isolation

@ref	Sample type
30686	bioreactor
67770	Activated sludge in a sequencing batch reactor use for the treatment of triphenylmethane dye effluent

Taxonmaps

69479

Global distribution of 16S sequence FJ455531 (>99% sequence identity) for Dokdonella immobilis subclade from Microbeatlas

Aquatic Samples	1781
Soil Samples	620
Animal Samples	159
Plant Samples	133
Total Samples	2693

Interaction and safety

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
67770	IMG-taxon 2667527410 annotated assembly for Dokdonella immobilis CGMCC 1.7659	scaffold	GCA_900115085	578942.3	2667527410	578942	62.05

Genome browser: GCA_900115085

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
30686	Dokdonella immobilis strain LM2-5 16S ribosomal RNA gene, partial sequence	FJ455531	1500		578942

GC content

@ref	GC-content (mol%)
30686	66.7
67770	66.7

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Dokdonella immobilis CGMCC 1.7659
NCBI: GCA_900115085

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	90.20	no
125439	motility	BacteriaNetⓘ	yes	64.60	no
125439	gram_stain	BacteriaNetⓘ	negative	93.30	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	99.00	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Dokdonella immobilis strain CGMCC 1.7659
PATRIC: 578942.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	98.49	yes
125438	anaerobic	anaerobicⓘ	no	97.06	yes
125438	spore-forming	spore-formingⓘ	no	89.92	yes
125438	aerobic	aerobicⓘ	yes	84.20	yes
125438	thermophilic	thermophileⓘ	no	94.01	yes
125438	flagellated	motile2+ⓘ	no	58.24	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Dokdonella immobilis sp. nov., isolated from a batch reactor for the treatment of triphenylmethane dye effluent.	Liu Y, Jin JH, Liu HC, Liu ZP	Int J Syst Evol Microbiol	10.1099/ijs.0.042002-0	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 )
#30686	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 #27017 (see below)
#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 )
#67770	Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#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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Dokdonella immobilis (CGMCC 1.7659, JCM 15763, LM2-5)

Name and taxonomic classification

Morphology

Cell morphology

Pigmentation

Culture and growth conditions

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Spore formation

Halophily

Observation

Metabolite utilization

Enzymes

Pathway annotation

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Sequence information

Genome sequences

Genome browser: GCA_900115085

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

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