Name: Actinomadura darangshiensis DLS-70
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 130742

Type strain:

Species: Actinomadura darangshiensis

Strain Designation: DLS-70

Culture col. no.: DSM 45941, KCTC 29224

Strain history: <- Soon Dong Lee,Jeju

NCBI tax ID(s): 705336 (species)

SI-ID 401242

DSM 45941

Section

Actinomadura darangshiensis DLS-70 is an aerobe, mesophilic bacterium that was isolated from soil from the surface of a rock collected from the peak of a volcanic cone.

aerobe
mesophilic
16S sequence
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	*Actinomycetota*
	Class	*Actinomycetes*
	Order	*Streptosporangiales*
	Family	*Thermomonosporaceae*
	Genus	*Actinomadura*
	Species	**Actinomadura darangshiensis**
	Full Scientific Name (LPSN)	Actinomadura darangshiensis Lee and Kim 2015

Information on morphological and physiological properties Morphology

Multimedia content

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Caption:

Medium 554 28°C

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Intellectual property rights:

Information on culture and growth conditions Culture and growth conditions

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Culture medium

N-Z-AMINE-MEDIUM (DSMZ Medium 554)

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Culture medium growth

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Culture medium link

Medium recipe at MediaDive

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Culture medium composition

expand / minimize

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Culture medium

GYM STREPTOMYCES MEDIUM (DSMZ Medium 65)

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Culture medium growth

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Culture medium link

Medium recipe at MediaDive

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Culture medium composition

expand / minimize

	Temperatures	Kind of temperature		Temperature
[Ref.: #22034]			growth	28 °C
[Ref.: #67771]			growth	30 °C

[Ref.: #22034]	Temperature range	mesophilic
[Ref.: #67771]	Temperature range	mesophilic

Information on physiology and metabolism Physiology and metabolism

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Oxygen tolerance

aerobe

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	urea cycle	100	13 of 13
[Ref.: #66794]	ethanol fermentation	100	2 of 2
[Ref.: #66794]	threonine metabolism	100	10 of 10
[Ref.: #66794]	propanol degradation	100	7 of 7
[Ref.: #66794]	molybdenum cofactor biosynthesis	100	9 of 9
[Ref.: #66794]	cardiolipin biosynthesis	100	7 of 7
[Ref.: #66794]	adipate degradation	100	2 of 2
[Ref.: #66794]	Entner Doudoroff pathway	100	10 of 10
[Ref.: #66794]	gallate degradation	100	5 of 5
[Ref.: #66794]	cis-vaccenate biosynthesis	100	2 of 2
[Ref.: #66794]	ethylmalonyl-CoA pathway	100	5 of 5
[Ref.: #66794]	myo-inositol biosynthesis	100	10 of 10
[Ref.: #66794]	biotin biosynthesis	100	4 of 4
[Ref.: #66794]	4-hydroxymandelate degradation	100	9 of 9
[Ref.: #66794]	starch degradation	100	10 of 10
[Ref.: #66794]	butanoate fermentation	100	4 of 4
[Ref.: #66794]	resorcinol degradation	100	2 of 2
[Ref.: #66794]	valine metabolism	100	9 of 9
[Ref.: #66794]	methylglyoxal degradation	100	5 of 5
[Ref.: #66794]	ppGpp biosynthesis	100	4 of 4
[Ref.: #66794]	palmitate biosynthesis	100	22 of 22
[Ref.: #66794]	photosynthesis	100	14 of 14
[Ref.: #66794]	3-chlorocatechol degradation	100	5 of 5
[Ref.: #66794]	enterobactin biosynthesis	100	3 of 3
[Ref.: #66794]	acetate fermentation	100	4 of 4
[Ref.: #66794]	aspartate and asparagine metabolism	100	9 of 9
[Ref.: #66794]	kanosamine biosynthesis II	100	2 of 2
[Ref.: #66794]	glycogen metabolism	100	5 of 5
[Ref.: #66794]	pentose phosphate pathway	100	11 of 11
[Ref.: #66794]	suberin monomers biosynthesis	100	2 of 2
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	vitamin K metabolism	100	5 of 5
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	denitrification	100	2 of 2
[Ref.: #66794]	sulfopterin metabolism	100	4 of 4
[Ref.: #66794]	coenzyme A metabolism	100	4 of 4
[Ref.: #66794]	formaldehyde oxidation	100	3 of 3
[Ref.: #66794]	cellulose degradation	100	5 of 5
[Ref.: #66794]	ceramide biosynthesis	100	1 of 1
[Ref.: #66794]	daunorubicin biosynthesis	100	9 of 9
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	taurine degradation	100	1 of 1
[Ref.: #66794]	glycolate and glyoxylate degradation	100	6 of 6
[Ref.: #66794]	reductive acetyl coenzyme A pathway	100	7 of 7
[Ref.: #66794]	ribulose monophosphate pathway	100	2 of 2
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	NAD metabolism	94.44	17 of 18
[Ref.: #66794]	flavin biosynthesis	93.33	14 of 15
[Ref.: #66794]	citric acid cycle	92.86	13 of 14
[Ref.: #66794]	phenylalanine metabolism	92.31	12 of 13
[Ref.: #66794]	leucine metabolism	92.31	12 of 13
[Ref.: #66794]	propionate fermentation	90	9 of 10
[Ref.: #66794]	CO2 fixation in Crenarchaeota	88.89	8 of 9
[Ref.: #66794]	serine metabolism	88.89	8 of 9
[Ref.: #66794]	chorismate metabolism	88.89	8 of 9
[Ref.: #66794]	allantoin degradation	88.89	8 of 9
[Ref.: #66794]	d-mannose degradation	88.89	8 of 9
[Ref.: #66794]	dTDPLrhamnose biosynthesis	87.5	7 of 8
[Ref.: #66794]	isoleucine metabolism	87.5	7 of 8
[Ref.: #66794]	ketogluconate metabolism	87.5	7 of 8
[Ref.: #66794]	gluconeogenesis	87.5	7 of 8
[Ref.: #66794]	C4 and CAM-carbon fixation	87.5	7 of 8
[Ref.: #66794]	purine metabolism	87.23	82 of 94
[Ref.: #66794]	3-phenylpropionate degradation	86.67	13 of 15
[Ref.: #66794]	peptidoglycan biosynthesis	86.67	13 of 15
[Ref.: #66794]	heme metabolism	85.71	12 of 14
[Ref.: #66794]	aclacinomycin biosynthesis	85.71	6 of 7
[Ref.: #66794]	glutathione metabolism	85.71	12 of 14
[Ref.: #66794]	vitamin B12 metabolism	85.29	29 of 34
[Ref.: #66794]	vitamin B1 metabolism	84.62	11 of 13
[Ref.: #66794]	tryptophan metabolism	84.21	32 of 38
[Ref.: #66794]	selenocysteine biosynthesis	83.33	5 of 6
[Ref.: #66794]	alanine metabolism	82.76	24 of 29
[Ref.: #66794]	glutamate and glutamine metabolism	82.14	23 of 28
[Ref.: #66794]	metabolism of disaccharids	81.82	9 of 11
[Ref.: #66794]	proline metabolism	81.82	9 of 11
[Ref.: #66794]	degradation of sugar alcohols	81.25	13 of 16
[Ref.: #66794]	4-hydroxyphenylacetate degradation	80	8 of 10
[Ref.: #66794]	phenylacetate degradation (aerobic)	80	4 of 5
[Ref.: #66794]	phenol degradation	80	16 of 20
[Ref.: #66794]	metabolism of amino sugars and derivatives	80	4 of 5
[Ref.: #66794]	degradation of sugar acids	80	20 of 25
[Ref.: #66794]	factor 420 biosynthesis	80	4 of 5
[Ref.: #66794]	arginine metabolism	79.17	19 of 24
[Ref.: #66794]	tetrahydrofolate metabolism	78.57	11 of 14
[Ref.: #66794]	degradation of hexoses	77.78	14 of 18
[Ref.: #66794]	methionine metabolism	76.92	20 of 26
[Ref.: #66794]	glycolysis	76.47	13 of 17
[Ref.: #66794]	histidine metabolism	75.86	22 of 29
[Ref.: #66794]	pyrimidine metabolism	75.56	34 of 45
[Ref.: #66794]	glycogen biosynthesis	75	3 of 4
[Ref.: #66794]	CMP-KDO biosynthesis	75	3 of 4
[Ref.: #66794]	toluene degradation	75	3 of 4
[Ref.: #66794]	cyclohexanol degradation	75	3 of 4
[Ref.: #66794]	oxidative phosphorylation	73.63	67 of 91
[Ref.: #66794]	cholesterol biosynthesis	72.73	8 of 11
[Ref.: #66794]	cysteine metabolism	72.22	13 of 18
[Ref.: #66794]	lysine metabolism	71.43	30 of 42
[Ref.: #66794]	tyrosine metabolism	71.43	10 of 14
[Ref.: #66794]	degradation of pentoses	71.43	20 of 28
[Ref.: #66794]	non-pathway related	71.05	27 of 38
[Ref.: #66794]	bile acid biosynthesis, neutral pathway	70.59	12 of 17
[Ref.: #66794]	ascorbate metabolism	68.18	15 of 22
[Ref.: #66794]	lipid metabolism	67.74	21 of 31
[Ref.: #66794]	acetoin degradation	66.67	2 of 3
[Ref.: #66794]	acetyl CoA biosynthesis	66.67	2 of 3
[Ref.: #66794]	L-lactaldehyde degradation	66.67	2 of 3
[Ref.: #66794]	IAA biosynthesis	66.67	2 of 3
[Ref.: #66794]	octane oxidation	66.67	2 of 3
[Ref.: #66794]	cyanate degradation	66.67	2 of 3
[Ref.: #66794]	isoprenoid biosynthesis	65.38	17 of 26
[Ref.: #66794]	d-xylose degradation	63.64	7 of 11
[Ref.: #66794]	androgen and estrogen metabolism	62.5	10 of 16
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	62.5	5 of 8
[Ref.: #66794]	sulfate reduction	61.54	8 of 13
[Ref.: #66794]	arachidonate biosynthesis	60	3 of 5
[Ref.: #66794]	lipoate biosynthesis	60	3 of 5
[Ref.: #66794]	creatinine degradation	60	3 of 5
[Ref.: #66794]	D-cycloserine biosynthesis	60	3 of 5
[Ref.: #66794]	glycine metabolism	60	6 of 10
[Ref.: #66794]	carotenoid biosynthesis	59.09	13 of 22
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	58.33	7 of 12
[Ref.: #66794]	ubiquinone biosynthesis	57.14	4 of 7
[Ref.: #66794]	phenylpropanoid biosynthesis	53.85	7 of 13
[Ref.: #66794]	polyamine pathway	52.17	12 of 23
[Ref.: #66794]	quinate degradation	50	1 of 2
[Ref.: #66794]	dolichol and dolichyl phosphate biosynthesis	50	1 of 2
[Ref.: #66794]	phenylmercury acetate degradation	50	1 of 2
[Ref.: #66794]	vitamin E metabolism	50	2 of 4
[Ref.: #66794]	pantothenate biosynthesis	50	3 of 6
[Ref.: #66794]	coenzyme M biosynthesis	50	5 of 10
[Ref.: #66794]	lactate fermentation	50	2 of 4
[Ref.: #66794]	mannosylglycerate biosynthesis	50	1 of 2
[Ref.: #66794]	aminopropanol phosphate biosynthesis	50	1 of 2
[Ref.: #66794]	lipid A biosynthesis	44.44	4 of 9
[Ref.: #66794]	nitrate assimilation	44.44	4 of 9
[Ref.: #66794]	benzoyl-CoA degradation	42.86	3 of 7
[Ref.: #66794]	hydrogen production	40	2 of 5
[Ref.: #66794]	glycine betaine biosynthesis	40	2 of 5
[Ref.: #66794]	O-antigen biosynthesis	40	2 of 5
[Ref.: #66794]	bacilysin biosynthesis	40	2 of 5
[Ref.: #66794]	arachidonic acid metabolism	38.89	7 of 18
[Ref.: #66794]	phosphatidylethanolamine bioynthesis	38.46	5 of 13
[Ref.: #66794]	carnitine metabolism	37.5	3 of 8
[Ref.: #66794]	vitamin B6 metabolism	36.36	4 of 11
[Ref.: #66794]	sphingosine metabolism	33.33	2 of 6
[Ref.: #66794]	chlorophyll metabolism	33.33	6 of 18
[Ref.: #66794]	methanogenesis from CO2	33.33	4 of 12
[Ref.: #66794]	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
[Ref.: #66794]	sulfoquinovose degradation	33.33	1 of 3
[Ref.: #66794]	mevalonate metabolism	28.57	2 of 7
[Ref.: #66794]	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
[Ref.: #66794]	catecholamine 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.: #22034]	Sample type/isolated from	soil from the surface of a rock collected from the peak of a volcanic cone
[Ref.: #22034]	Geographic location (country and/or sea, region)	Jeju, Darangshi Oreum
[Ref.: #22034]	Country	Republic of Korea
[Ref.: #22034]	Country ISO 3 Code	KOR
[Ref.: #22034]	Continent	Asia

[Ref.: #67771]	Sample type/isolated from	From volcanic ash
[Ref.: #67771]	Country	Republic of Korea
[Ref.: #67771]	Country ISO 3 Code	KOR
[Ref.: #67771]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Environmental	#Terrestrial	#Soil
#Environmental	#Terrestrial	#Volcanic

What are isolation sources categories?

Information on possible application of the strain and its possible interaction with e.g. potential hosts Safety information

[Ref.: #22034]

Biosafety level

Risk group (German classification)
According to TRBA 466

Information on genomic background e.g. entries in nucleic sequence databass Sequence information

16S Sequence information:

	Sequence accession description	Seq. accession number	Sequence length (bp)	Sequence database	Associated NCBI tax ID
[Ref.: #22034]	Actinomadura darangshiensis partial 16S rRNA gene, type strain DLS-70T	FN646682	1424	ENA	705336 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Actinomadura darangshiensis DSM 45941	GCA_004349235	contig	GenBank	705336 tax ID	*
[Ref.: #66792]	Actinomadura darangshiensis strain DSM 45941	705336.3	wgs	PATRIC	705336 tax ID	*
[Ref.: #66792]	Actinomadura darangshiensis DSM 45941	2866841126	draft	JGI IMG/M	705336 tax ID	*

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GC-content

69.9 mol%

high performance liquid chromatography (HPLC)

Data predicted using genome information as a basis Genome-based predictions

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Actinomadura darangshiensis strain DSM 45941 PATRIC: 705336.3
[Ref.: #69480]	gram-positive	yes	89.623	no
[Ref.: #69480]	anaerobic	no	98.686	yes
[Ref.: #69480]	halophile	no	89.004	no
[Ref.: #69480]	spore-forming	yes	93.269	no
[Ref.: #69480]	glucose-util	yes	88.469	no
[Ref.: #69480]	thermophile	no	97.177	yes
[Ref.: #69480]	flagellated	no	98.026	no
[Ref.: #69480]	aerobic	yes	90.761	yes
[Ref.: #69480]	glucose-ferment	no	89.741	no
[Ref.: #69480]	motile	no	92.399	no

Availability in culture collections External links

[Ref.: #22034]

Culture collection no.

DSM 45941, KCTC 29224

[Ref.: #89242]

SI-ID 401242

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Actinomadura alkaliterrae sp. nov., isolated from an alkaline soil.	Ay H, Nouioui I, Del Carmen Montero-Calasanz M, Carro L, Klenk HP, Goodfellow M, Igual JM, Cetin D, Sahin N, Isik K	Antonie Van Leeuwenhoek	10.1007/s10482-017-0850-6	2017	*
Phylogeny	Actinomadura darangshiensis sp. nov., isolated from a volcanic cone.	Lee SD, Kim SB	Int J Syst Evol Microbiol	10.1099/ijs.0.000099	2015	*

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 )

#22034

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 45941

#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) .

#89242

Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.: StrainInfo: A central database for resolving microbial strain identifiers . ( DOI 10.60712/SI-ID401242.1 )

* These data were automatically processed and therefore are not curated

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Actinomadura darangshiensis strain DSM 45941

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