Amycolatopsis arida (DSM 45648, CGMCC 4.5579, JCM 16584)

Name: Amycolatopsis arida (DSM 45648, CGMCC 4.5579, JCM 16584)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 13516

Type strain

Strain Designation RA45

Culture col. no. DSM 45648 CGMCC 4.5579 JCM 16584 RA45

NCBI tax ID(s) 587909

Special Collections DSMZ JCM Literature strains

History DSMZ <- JCM; JCM 16584 <- L.-X. Zhang; RA45 JCM <-- L.-X. Zhang RA45.

Links

Amycolatopsis arida RA45 is an aerobe, Gram-positive, rod-shaped bacterium that was isolated from soil from a desert region.

Gram-positive rod-shaped aerobe genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 399473

JCM 16584,DSM 45648

@ref 20215

Last LPSN update 2026-05-29 08:28:03

Domain Bacteria

Phylum Actinomycetota

Class Actinomycetes

Order Pseudonocardiales

Family Pseudonocardiaceae

Genus Amycolatopsis

Species Amycolatopsis arida

Full scientific name Amycolatopsis arida Nouioui et al. 2018

Synonyms (1)

Yuhushiella deserti

Morphology

Cell morphology

@ref	Gram stain	Cell shape	Confidence
29726	positive	rod-shaped
125439			90.359
125438			90.5
125439	positive		99.492

Pigmentation

29726

Productionyes

Multimedia

@ref:	17971
multimedia content:	DSM_45648.jpg
multimedia.multimedia content:	https://www.dsmz.de/microorganisms/photos/DSM_45648.jpg
caption:	Medium 65 28°C
intellectual property rights:	© Leibniz-Institut DSMZ
manual_annotation:	1

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
17971	GPHF-MEDIUM (DSMZ Medium 553)		Medium recipe at MediaDive	Name: GPHF-MEDIUM (DSMZ Medium 553) Composition: Agar 20.0 g/l Glucose 10.0 g/l Beef extract 5.0 g/l Yeast extract 5.0 g/l Casein peptone 5.0 g/l CaCl2 x 2 H2O 0.74 g/l Distilled water
17971	GYM STREPTOMYCES MEDIUM (DSMZ Medium 65)		Medium recipe at MediaDive	Name: GYM STREPTOMYCES MEDIUM (DSMZ Medium 65) Composition: Agar 18.0 g/l Malt extract 10.0 g/l Yeast extract 4.0 g/l Glucose 4.0 g/l CaCO3 2.0 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)
17971	positive	growth	28
29726	positive	optimum	37-45
67770	positive	growth	28

Culture pH

@ref	Ability	Type	PH	PH range
29726	positive	optimum	9	alkaliphile

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
29726	aerobe
125438	aerobe	91.279
125439	obligate aerobe	99.612

Spore formation

29726

Spore formationno

Halophily

@ref	Salt	Growth	Tested relation	Concentration
29726	NaCl	positive	optimum	3.5 %

Observation

67770

Observationquinones: MK-9(H₄), MK-9, MK-9(H₂)

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
68369	29016 ChEBI	arginine	-	hydrolysis	from API 20NE
68369	17634 ChEBI	D-glucose	-	fermentation	from API 20NE
68369	27689 ChEBI	decanoate	-	assimilation	from API 20NE
68369	4853 ChEBI	esculin	-	hydrolysis	from API 20NE
68369	5291 ChEBI	gelatin	-	hydrolysis	from API 20NE
68369	24265 ChEBI	gluconate	+	assimilation	from API 20NE
68369	17306 ChEBI	maltose	+	assimilation	from API 20NE
68369	59640 ChEBI	N-acetylglucosamine	+	assimilation	from API 20NE
68369	17632 ChEBI	nitrate	-	reduction	from API 20NE
68369	27897 ChEBI	tryptophan	-	energy source	from API 20NE
68369	16199 ChEBI	urea	-	hydrolysis	from API 20NE

Metabolite production

@ref	Chebi-ID	Metabolite	Production
68369	35581 ChEBI	indole		from API 20NE

Metabolite tests

@ref	Chebi-ID	Metabolite	Indole test
68369	35581 ChEBI	indole	-	from API 20NE

Enzymes

@ref	Value	Activity	Ec
68382	acid phosphatase	-	3.1.3.2	from API zym
68382	alkaline phosphatase	+	3.1.3.1	from API zym
68382	alpha-chymotrypsin	+	3.4.21.1	from API zym
68382	alpha-fucosidase	-	3.2.1.51	from API zym
68382	alpha-galactosidase	-	3.2.1.22	from API zym
68382	alpha-glucosidase	+	3.2.1.20	from API zym
68382	alpha-mannosidase	-	3.2.1.24	from API zym
68369	arginine dihydrolase	-	3.5.3.6	from API 20NE
68382	beta-galactosidase	-	3.2.1.23	from API zym
68382	beta-glucosidase	-	3.2.1.21	from API zym
68369	beta-glucosidase	-	3.2.1.21	from API 20NE
68382	beta-glucuronidase	-	3.2.1.31	from API zym
68382	esterase lipase (C 8)	+		from API zym
68369	gelatinase	-		from API 20NE
68382	leucine arylamidase	+	3.4.11.1	from API zym
68382	N-acetyl-beta-glucosaminidase	+	3.2.1.52	from API zym
68382	naphthol-AS-BI-phosphohydrolase	-		from API zym
68382	trypsin	-	3.4.21.4	from API zym
29726	urease	+	3.5.1.5
68369	urease	-	3.5.1.5	from API 20NE
68382	valine arylamidase	+		from API zym

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	enterobactin biosynthesis	100	3 of 3
66794	phenylacetate degradation (aerobic)	100	5 of 5
66794	ethanol fermentation	100	2 of 2
66794	myo-inositol biosynthesis	100	10 of 10
66794	glycogen metabolism	100	5 of 5
66794	cis-vaccenate biosynthesis	100	2 of 2
66794	phenylmercury acetate degradation	100	2 of 2
66794	adipate degradation	100	2 of 2
66794	4-hydroxymandelate degradation	100	9 of 9
66794	molybdenum cofactor biosynthesis	100	9 of 9
66794	acetate fermentation	100	4 of 4
66794	palmitate biosynthesis	100	22 of 22
66794	ppGpp biosynthesis	100	4 of 4
66794	biotin biosynthesis	100	4 of 4
66794	methylglyoxal degradation	100	5 of 5
66794	valine metabolism	100	9 of 9
66794	glycolate and glyoxylate degradation	100	6 of 6
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	vitamin K metabolism	100	5 of 5
66794	suberin monomers biosynthesis	100	2 of 2
66794	teichoic acid biosynthesis	100	1 of 1
66794	coenzyme A metabolism	100	4 of 4
66794	formaldehyde oxidation	100	3 of 3
66794	ceramide biosynthesis	100	1 of 1
66794	folate polyglutamylation	100	1 of 1
66794	aerobactin biosynthesis	100	1 of 1
66794	cellulose degradation	100	5 of 5
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	citric acid cycle	92.86	13 of 14
66794	phenylalanine metabolism	92.31	12 of 13
66794	leucine metabolism	92.31	12 of 13
66794	proline metabolism	90.91	10 of 11
66794	pentose phosphate pathway	90.91	10 of 11
66794	Entner Doudoroff pathway	90	9 of 10
66794	threonine metabolism	90	9 of 10
66794	chorismate metabolism	88.89	8 of 9
66794	serine metabolism	88.89	8 of 9
66794	CO2 fixation in Crenarchaeota	88.89	8 of 9
66794	aspartate and asparagine metabolism	88.89	8 of 9
66794	dTDPLrhamnose biosynthesis	87.5	7 of 8
66794	ketogluconate metabolism	87.5	7 of 8
66794	peptidoglycan biosynthesis	86.67	13 of 15
66794	flavin biosynthesis	86.67	13 of 15
66794	reductive acetyl coenzyme A pathway	85.71	6 of 7
66794	aclacinomycin biosynthesis	85.71	6 of 7
66794	heme metabolism	85.71	12 of 14
66794	purine metabolism	85.11	80 of 94
66794	NAD metabolism	83.33	15 of 18
66794	alanine metabolism	82.76	24 of 29
66794	glycolysis	82.35	14 of 17
66794	vitamin B12 metabolism	82.35	28 of 34
66794	glutamate and glutamine metabolism	82.14	23 of 28
66794	ethylmalonyl-CoA pathway	80	4 of 5
66794	3-chlorocatechol degradation	80	4 of 5
66794	glycine betaine biosynthesis	80	4 of 5
66794	factor 420 biosynthesis	80	4 of 5
66794	gallate degradation	80	4 of 5
66794	propionate fermentation	80	8 of 10
66794	glutathione metabolism	78.57	11 of 14
66794	photosynthesis	78.57	11 of 14
66794	d-mannose degradation	77.78	7 of 9
66794	allantoin degradation	77.78	7 of 9
66794	urea cycle	76.92	10 of 13
66794	vitamin B1 metabolism	76.92	10 of 13
66794	tryptophan metabolism	76.32	29 of 38
66794	pyrimidine metabolism	75.56	34 of 45
66794	gluconeogenesis	75	6 of 8
66794	isoleucine metabolism	75	6 of 8
66794	phenol degradation	75	15 of 20
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
66794	sulfopterin metabolism	75	3 of 4
66794	CMP-KDO biosynthesis	75	3 of 4
66794	butanoate fermentation	75	3 of 4
66794	cyclohexanol degradation	75	3 of 4
66794	glycogen biosynthesis	75	3 of 4
66794	lipid metabolism	74.19	23 of 31
66794	non-pathway related	73.68	28 of 38
66794	carotenoid biosynthesis	72.73	16 of 22
66794	metabolism of disaccharids	72.73	8 of 11
66794	vitamin B6 metabolism	72.73	8 of 11
66794	histidine metabolism	72.41	21 of 29
66794	cardiolipin biosynthesis	71.43	5 of 7
66794	tetrahydrofolate metabolism	71.43	10 of 14
66794	tyrosine metabolism	71.43	10 of 14
66794	propanol degradation	71.43	5 of 7
66794	arginine metabolism	70.83	17 of 24
66794	4-hydroxyphenylacetate degradation	70	7 of 10
66794	phosphatidylethanolamine bioynthesis	69.23	9 of 13
66794	degradation of sugar alcohols	68.75	11 of 16
66794	cyanate degradation	66.67	2 of 3
66794	lipid A biosynthesis	66.67	6 of 9
66794	acetyl CoA biosynthesis	66.67	2 of 3
66794	octane oxidation	66.67	2 of 3
66794	acetoin degradation	66.67	2 of 3
66794	L-lactaldehyde degradation	66.67	2 of 3
66794	oxidative phosphorylation	65.93	60 of 91
66794	methionine metabolism	65.38	17 of 26
66794	polyamine pathway	65.22	15 of 23
66794	androgen and estrogen metabolism	62.5	10 of 16
66794	C4 and CAM-carbon fixation	62.5	5 of 8
66794	lysine metabolism	61.9	26 of 42
66794	isoprenoid biosynthesis	61.54	16 of 26
66794	cysteine metabolism	61.11	11 of 18
66794	degradation of pentoses	60.71	17 of 28
66794	lipoate biosynthesis	60	3 of 5
66794	3-phenylpropionate degradation	60	9 of 15
66794	metabolism of amino sugars and derivatives	60	3 of 5
66794	starch degradation	60	6 of 10
66794	coenzyme M biosynthesis	60	6 of 10
66794	degradation of sugar acids	60	15 of 25
66794	degradation of aromatic, nitrogen containing compounds	58.33	7 of 12
66794	ubiquinone biosynthesis	57.14	4 of 7
66794	daunorubicin biosynthesis	55.56	5 of 9
66794	degradation of hexoses	55.56	10 of 18
66794	bile acid biosynthesis, neutral pathway	52.94	9 of 17
66794	toluene degradation	50	2 of 4
66794	glycine metabolism	50	5 of 10
66794	selenocysteine biosynthesis	50	3 of 6
66794	mannosylglycerate biosynthesis	50	1 of 2
66794	pantothenate biosynthesis	50	3 of 6
66794	resorcinol degradation	50	1 of 2
66794	aminopropanol phosphate biosynthesis	50	1 of 2
66794	lactate fermentation	50	2 of 4
66794	vitamin E metabolism	50	2 of 4
66794	ribulose monophosphate pathway	50	1 of 2
66794	kanosamine biosynthesis II	50	1 of 2
66794	sulfate reduction	46.15	6 of 13
66794	cholesterol biosynthesis	45.45	5 of 11
66794	nitrate assimilation	44.44	4 of 9
66794	benzoyl-CoA degradation	42.86	3 of 7
66794	D-cycloserine biosynthesis	40	2 of 5
66794	arachidonate biosynthesis	40	2 of 5
66794	phenylpropanoid biosynthesis	38.46	5 of 13
66794	ascorbate metabolism	36.36	8 of 22
66794	d-xylose degradation	36.36	4 of 11
66794	sulfoquinovose degradation	33.33	1 of 3
66794	methane metabolism	33.33	1 of 3
66794	sphingosine metabolism	33.33	2 of 6
66794	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
66794	IAA biosynthesis	33.33	1 of 3
66794	mevalonate metabolism	28.57	2 of 7
66794	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
66794	carnitine metabolism	25	2 of 8
66794	alginate biosynthesis	25	1 of 4
66794	catecholamine biosynthesis	25	1 of 4
66794	arachidonic acid metabolism	22.22	4 of 18

API zym

@ref	Control	Alkaline phosphatase	Esterase (C 4)	2-naphtyl caprylateEsterase Lipase (C 8)	Lipase (C 14)	L-leucyl-2-naphthylamideLeucine arylamidase	L-valyl-2-naphthylamideValine arylamidase	L-cystyl-2-naphthylamideCystine arylamidase	Trypsin	alpha- Chymotrypsin	Acid phosphatase	Naphthol-AS-BI-phosphateNaphthol-AS-BI-phosphohydrolase	alpha- Galactosidase	beta- Galactosidase	beta- Glucuronidase	alpha- Glucosidase	beta- Glucosidase	N-acetyl-beta- glucosaminidase	alpha- Mannosidase	alpha- Fucosidase
17971	-	+	+/-	+	+/-	+	+	+/-	-	+	-	-	-	-	-	+	-	+	-	-

API 20NE

@ref	Reduction of nitratesNO3	TRP	GLU_ Ferm	ADH (Arg)	URE	ESC	GEL	PNPG	GLU_ Assim	ARA	MNE	MAN	NAG	MAL	GNT	CAP	ADI	MLT	CIT	PAC	OX
17971	-	-	-	-	-	-	-	+/-	+/-	+/-	+/-	+/-	+	+	+	-	+/-	+/-	+/-	-	not determinedn.d.

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Terrestrial	#Desert
#Environmental	#Terrestrial	#Soil

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
17971	soil from a desert region	Xinjiang Uigur Autonomous Region	China	CHN	Asia
67770	Soil from a desert region	Xinjiang Uigur Autonomous Region, north-western China	China	CHN	Asia

Taxonmaps

69479

Global distribution of 16S sequence FJ526746 (>99% sequence identity) for Amycolatopsis arida subclade from Microbeatlas

Aquatic Samples	10
Soil Samples	127
Animal Samples	286
Plant Samples	19
Total Samples	442

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
17971	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
67770	IMG-taxon 2675903051 annotated assembly for Amycolatopsis arida CGMCC 4.5579	scaffold	GCA_900115565	587909.3	2675903051	587909	72.86
67770	ASM436592v1 assembly for Amycolatopsis arida DSM 45648	contig	GCA_004365925	587909.9	2731639259	587909	72.44

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
17971	Amycolatopsis arida 16S ribosomal RNA gene, partial sequence	FJ526746	1493		587909

GC content

@ref	GC-content (mol%)	Method
17971	69.9
67770	72.7	genome sequence analysis
67770	69.9	thermal denaturation, midpoint method (Tm)

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: IMG-taxon 2675903051 annotated assembly for Amycolatopsis arida CGMCC 4.5579
BV-BRC: 587909.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	99.61	no
125439	gram_stain	BacteriaNetⓘ	positive	99.49	no
125439	spore_formation	BacteriaNetⓘ	yes	78.51	no
125439	motility	BacteriaNetⓘ	no	90.36	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Yuhushiella deserti strain CGMCC 4.5579
PATRIC: 587909.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	88.99	yes
125438	anaerobic	anaerobicⓘ	no	97.93	no
125438	spore-forming	spore-formingⓘ	yes	67.67	yes
125438	thermophilic	thermophileⓘ	no	90.96	yes
125438	aerobic	aerobicⓘ	yes	91.28	yes
125438	flagellated	motile2+ⓘ	no	90.50	yes

Literature

Topic	Title	Authors	Journal	DOI	Year
Genetics	Genome-Based Taxonomic Classification of the Phylum Actinobacteria.	Nouioui I, Carro L, Garcia-Lopez M, Meier-Kolthoff JP, Woyke T, Kyrpides NC, Pukall R, Klenk HP, Goodfellow M, Goker M.	Front Microbiol	10.3389/fmicb.2018.02007	2018
Enzymology	Cytochrome P450 Mediated Cyclization in Eunicellane Derived Diterpenoid Biosynthesis.	Wang Z, Yang Q, He J, Li H, Pan X, Li Z, Xu HM, Rudolf JD, Tantillo DJ, Dong LB.	Angew Chem Int Ed Engl	10.1002/anie.202312490	2023
	Building Streptomyces albus as a chassis for synthesis of bacterial terpenoids.	Hu YL, Zhang Q, Liu SH, Sun JL, Yin FZ, Wang ZR, Shi J, Jiao RH, Ge HM.	Chem Sci	10.1039/d2sc06033g	2023
Phylogeny	Yuhushiella deserti gen. nov., sp. nov., a new member of the suborder Pseudonocardineae.	Mao J, Wang J, Dai HQ, Zhang ZD, Tang QY, Ren B, Yang N, Goodfellow M, Zhang LX, Liu ZH	Int J Syst Evol Microbiol	10.1099/ijs.0.019588-0	2010

References

#17971	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 45648
#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 )
#26109	IJSEM 621 2011 ( DOI 10.1099/ijs.0.019588-0 , PubMed 20400669 )
#29726	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 #26109
#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;
#68369	Automatically annotated from API 20NE .
#68382	Automatically annotated from API zym .
#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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Amycolatopsis arida (DSM 45648, CGMCC 4.5579, JCM 16584)

Name and taxonomic classification

Morphology

Cell morphology

Pigmentation

Multimedia

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Spore formation

Halophily

Observation

Metabolite utilization

Metabolite production

Metabolite tests

Enzymes

Pathway annotation

API zym

API 20NE

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_900115565

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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