Amycolatopsis cihanbeyliensis (DSM 45679, JCM 31029, KCTC 29065)

Name: Amycolatopsis cihanbeyliensis (DSM 45679, JCM 31029, KCTC 29065)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 24444

Type strain

Strain Designation BNT52

Culture col. no. DSM 45679 JCM 31029 KCTC 29065 NRRL B-24886 BNT52

NCBI tax ID(s) 1128664

Special Collections DSMZ JCM KCTC Literature strains

History DSMZ <- N. Sahin, Ondokuz Mayis Univ., Dept. of Biology, Samsun, Turkey; BNT52 <- M. Camas JCM <-- DSM 45679 <-- N. Sahin; Ondokuz Mayis Univ., Turkey; BNT52 <-- M. Camas. KCTC <- Nevzat Sahin, Ondokuz Mayis Univ., Turkey

Links

Amycolatopsis cihanbeyliensis BNT52 is an aerobe, Gram-positive, rod-shaped bacterium that was isolated from soil from a salt mine .

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

Name and taxonomic classification

SI-ID 405290

KCTC 29065,JCM 31029,DSM 45679

@ref 20215

Last LPSN update 2026-05-29 08:30:37

Domain Bacteria

Phylum Actinomycetota

Class Actinomycetes

Order Pseudonocardiales

Family Pseudonocardiaceae

Genus Amycolatopsis

Species Amycolatopsis cihanbeyliensis

Full scientific name Amycolatopsis cihanbeyliensis Tatar et al. 2013

Morphology

Cell morphology

@ref	Gram stain	Cell shape	Confidence
31059	positive	rod-shaped
67771	positive
125438			91
125438	positive		91.831
125439			90.954
125439	positive		94.811

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
20306	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

Culture temp

@ref	Growth	Type	Temperature (°C)
20306	positive	growth	28
31059	positive	growth	20-37
31059	positive	optimum	28
67770	positive	growth	28
67771	positive	growth	28

Culture pH

@ref	Ability	Type	PH	PH range
31059	positive	optimum	7.2
31059	positive	growth	6.0-12	alkaliphile

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
31059	aerobe
67771	aerobe
125438	aerobe	90.986
125439	facultative anaerobe	95.298

Halophily

@ref	Salt	Growth	Tested relation	Concentration
31059	NaCl	positive	growth	0-10 %

Observation

@ref	Observation
67770	quinones: MK-9(H₄)
67771	quinones: MK-9(H4)

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
68369	17128 ChEBI	adipate	-	assimilation	from API 20NE
31059	22599 ChEBI	arabinose	+	carbon source
68369	29016 ChEBI	arginine	-	hydrolysis	from API 20NE
31059	17057 ChEBI	cellobiose	+	carbon source
68369	17634 ChEBI	D-glucose	-	fermentation	from API 20NE
68369	16899 ChEBI	D-mannitol	-	assimilation	from API 20NE
68369	16024 ChEBI	D-mannose	-	assimilation	from API 20NE
68369	27689 ChEBI	decanoate	-	assimilation	from API 20NE
31059	23652 ChEBI	dextrin	+	carbon source
31059	4853 ChEBI	esculin	+	hydrolysis
68369	4853 ChEBI	esculin	+	hydrolysis	from API 20NE
31059	28757 ChEBI	fructose	+	carbon source
31059	28260 ChEBI	galactose	+	carbon source
68369	5291 ChEBI	gelatin	+	hydrolysis	from API 20NE
31059	15428 ChEBI	glycine	+	carbon source
68369	30849 ChEBI	L-arabinose	-	assimilation	from API 20NE
31059	17716 ChEBI	lactose	+	carbon source
68369	25115 ChEBI	malate	-	assimilation	from API 20NE
31059	17306 ChEBI	maltose	+	carbon source
68369	17306 ChEBI	maltose	-	assimilation	from API 20NE
31059	29864 ChEBI	mannitol	+	carbon source
31059	37684 ChEBI	mannose	+	carbon source
31059	17268 ChEBI	myo-inositol	+	carbon source
68369	17632 ChEBI	nitrate	-	reduction	from API 20NE
31059	28044 ChEBI	phenylalanine	+	carbon source
31059	26271 ChEBI	proline	+	carbon source
31059	15963 ChEBI	ribitol	+	carbon source
31059	17822 ChEBI	serine	+	carbon source
31059	30911 ChEBI	sorbitol	+	carbon source
31059	26986 ChEBI	threonine	+	carbon source
68369	27897 ChEBI	tryptophan	-	energy source	from API 20NE
68369	16199 ChEBI	urea	-	hydrolysis	from API 20NE
31059	17151 ChEBI	xylitol	+	carbon source
31059	18222 ChEBI	xylose	+	carbon source

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
31059	catalase	+	1.11.1.6
68369	gelatinase	+		from API 20NE
68382	leucine arylamidase	+	3.4.11.1	from API zym
68382	lipase (C 14)	-		from API zym
68382	N-acetyl-beta-glucosaminidase	+	3.2.1.52	from API zym
68382	trypsin	-	3.4.21.4	from API zym
31059	urease	+	3.5.1.5
68369	urease	-	3.5.1.5	from API 20NE

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	threonine metabolism	100	10 of 10
66794	ethanol fermentation	100	2 of 2
66794	enterobactin biosynthesis	100	3 of 3
66794	acetate fermentation	100	4 of 4
66794	3-chlorocatechol degradation	100	5 of 5
66794	palmitate biosynthesis	100	22 of 22
66794	ppGpp biosynthesis	100	4 of 4
66794	cis-vaccenate biosynthesis	100	2 of 2
66794	butanoate fermentation	100	4 of 4
66794	valine metabolism	100	9 of 9
66794	phenylmercury acetate degradation	100	2 of 2
66794	methylglyoxal degradation	100	5 of 5
66794	biotin biosynthesis	100	4 of 4
66794	dTDPLrhamnose biosynthesis	100	8 of 8
66794	Entner Doudoroff pathway	100	10 of 10
66794	taurine degradation	100	1 of 1
66794	ceramide biosynthesis	100	1 of 1
66794	suberin monomers biosynthesis	100	2 of 2
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	coenzyme A metabolism	100	4 of 4
66794	formaldehyde oxidation	100	3 of 3
66794	glycine betaine biosynthesis	100	5 of 5
66794	vitamin K metabolism	100	5 of 5
66794	glycolate and glyoxylate degradation	100	6 of 6
66794	phenylacetate degradation (aerobic)	100	5 of 5
66794	kanosamine biosynthesis II	100	2 of 2
66794	aclacinomycin biosynthesis	100	7 of 7
66794	propanol degradation	100	7 of 7
66794	cellulose degradation	100	5 of 5
66794	adipate degradation	100	2 of 2
66794	folate polyglutamylation	100	1 of 1
66794	flavin biosynthesis	93.33	14 of 15
66794	citric acid cycle	92.86	13 of 14
66794	urea cycle	92.31	12 of 13
66794	leucine metabolism	92.31	12 of 13
66794	phenylalanine metabolism	92.31	12 of 13
66794	proline metabolism	90.91	10 of 11
66794	pentose phosphate pathway	90.91	10 of 11
66794	serine metabolism	88.89	8 of 9
66794	chorismate metabolism	88.89	8 of 9
66794	molybdenum cofactor biosynthesis	88.89	8 of 9
66794	aspartate and asparagine metabolism	88.89	8 of 9
66794	NAD metabolism	88.89	16 of 18
66794	4-hydroxymandelate degradation	88.89	8 of 9
66794	ketogluconate metabolism	87.5	7 of 8
66794	heme metabolism	85.71	12 of 14
66794	tetrahydrofolate metabolism	85.71	12 of 14
66794	reductive acetyl coenzyme A pathway	85.71	6 of 7
66794	phenol degradation	85	17 of 20
66794	alanine metabolism	82.76	24 of 29
66794	glycolysis	82.35	14 of 17
66794	purine metabolism	80.85	76 of 94
66794	elloramycin biosynthesis	80	4 of 5
66794	factor 420 biosynthesis	80	4 of 5
66794	ethylmalonyl-CoA pathway	80	4 of 5
66794	propionate fermentation	80	8 of 10
66794	peptidoglycan biosynthesis	80	12 of 15
66794	4-hydroxyphenylacetate degradation	80	8 of 10
66794	glycogen metabolism	80	4 of 5
66794	gallate degradation	80	4 of 5
66794	tryptophan metabolism	78.95	30 of 38
66794	glutamate and glutamine metabolism	78.57	22 of 28
66794	photosynthesis	78.57	11 of 14
66794	glutathione metabolism	78.57	11 of 14
66794	tyrosine metabolism	78.57	11 of 14
66794	allantoin degradation	77.78	7 of 9
66794	d-mannose degradation	77.78	7 of 9
66794	CO2 fixation in Crenarchaeota	77.78	7 of 9
66794	vitamin B1 metabolism	76.92	10 of 13
66794	vitamin B12 metabolism	76.47	26 of 34
66794	glycogen biosynthesis	75	3 of 4
66794	cyclohexanol degradation	75	3 of 4
66794	CMP-KDO biosynthesis	75	3 of 4
66794	gluconeogenesis	75	6 of 8
66794	sulfopterin metabolism	75	3 of 4
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
66794	toluene degradation	75	3 of 4
66794	isoleucine metabolism	75	6 of 8
66794	methionine metabolism	73.08	19 of 26
66794	cysteine metabolism	72.22	13 of 18
66794	degradation of pentoses	71.43	20 of 28
66794	ubiquinone biosynthesis	71.43	5 of 7
66794	cardiolipin biosynthesis	71.43	5 of 7
66794	non-pathway related	71.05	27 of 38
66794	arginine metabolism	70.83	17 of 24
66794	oxidative phosphorylation	70.33	64 of 91
66794	myo-inositol biosynthesis	70	7 of 10
66794	polyamine pathway	69.57	16 of 23
66794	pyrimidine metabolism	68.89	31 of 45
66794	degradation of sugar alcohols	68.75	11 of 16
66794	lipid metabolism	67.74	21 of 31
66794	cyanate degradation	66.67	2 of 3
66794	octane oxidation	66.67	2 of 3
66794	acetoin degradation	66.67	2 of 3
66794	degradation of aromatic, nitrogen containing compounds	66.67	8 of 12
66794	L-lactaldehyde degradation	66.67	2 of 3
66794	3-phenylpropionate degradation	66.67	10 of 15
66794	(5R)-carbapenem carboxylate biosynthesis	66.67	2 of 3
66794	histidine metabolism	65.52	19 of 29
66794	metabolism of disaccharids	63.64	7 of 11
66794	C4 and CAM-carbon fixation	62.5	5 of 8
66794	carnitine metabolism	62.5	5 of 8
66794	phosphatidylethanolamine bioynthesis	61.54	8 of 13
66794	lipoate biosynthesis	60	3 of 5
66794	hydrogen production	60	3 of 5
66794	coenzyme M biosynthesis	60	6 of 10
66794	starch degradation	60	6 of 10
66794	metabolism of amino sugars and derivatives	60	3 of 5
66794	glycine metabolism	60	6 of 10
66794	isoprenoid biosynthesis	57.69	15 of 26
66794	lysine metabolism	57.14	24 of 42
66794	androgen and estrogen metabolism	56.25	9 of 16
66794	lipid A biosynthesis	55.56	5 of 9
66794	daunorubicin biosynthesis	55.56	5 of 9
66794	ascorbate metabolism	54.55	12 of 22
66794	aminopropanol phosphate biosynthesis	50	1 of 2
66794	selenocysteine biosynthesis	50	3 of 6
66794	resorcinol degradation	50	1 of 2
66794	pantothenate biosynthesis	50	3 of 6
66794	vitamin E metabolism	50	2 of 4
66794	ribulose monophosphate pathway	50	1 of 2
66794	degradation of hexoses	50	9 of 18
66794	quinate degradation	50	1 of 2
66794	mannosylglycerate biosynthesis	50	1 of 2
66794	bile acid biosynthesis, neutral pathway	47.06	8 of 17
66794	sulfate reduction	46.15	6 of 13
66794	phenylpropanoid biosynthesis	46.15	6 of 13
66794	vitamin B6 metabolism	45.45	5 of 11
66794	nitrate assimilation	44.44	4 of 9
66794	benzoyl-CoA degradation	42.86	3 of 7
66794	arachidonate biosynthesis	40	2 of 5
66794	D-cycloserine biosynthesis	40	2 of 5
66794	d-xylose degradation	36.36	4 of 11
66794	cholesterol biosynthesis	36.36	4 of 11
66794	sphingosine metabolism	33.33	2 of 6
66794	IAA biosynthesis	33.33	1 of 3
66794	acetyl CoA biosynthesis	33.33	1 of 3
66794	chlorophyll metabolism	33.33	6 of 18
66794	degradation of sugar acids	32	8 of 25
66794	carotenoid biosynthesis	31.82	7 of 22
66794	mevalonate metabolism	28.57	2 of 7
66794	arachidonic acid metabolism	27.78	5 of 18
66794	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
66794	catecholamine biosynthesis	25	1 of 4
66794	methanogenesis from CO2	25	3 of 12
66794	lactate fermentation	25	1 of 4

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
20306	-	+	+/-	+/-	-	+	+/-	+/-	-	+	-	+/-	-	-	-	-	-	+	-	-

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
20306	-	-	-	-	-	+	+	-	+/-	-	-	-	+/-	-	+/-	-	-	-	+/-	+/-	not determinedn.d.

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Engineered	#Other	#Mine
#Environmental	#Terrestrial	#Soil
#Condition	#Saline	-

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent	Latitude	Longitude
20306	soil from a salt mine (38° 45' 50'' N 33° 09' 26'' E)	central Anatolia region, Cihanbeyli Salt Mine	Turkey	TUR	Asia	38.7639	33.1572 38.7639/33.1572
67770	Cihanbeyli Salt Mine in the central Anatolia region of Turkey
67771	From saltern	Yavsanbeyli Saltern	Turkey	TUR	Asia

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
20306	1	Risk group (German classification)

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
67770	ASM671504v1 assembly for Amycolatopsis cihanbeyliensis DSM 45679	contig	GCA_006715045	1128664.3	2806310631	1128664	75.04

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
20306	Amycolatopsis cihanbeyliensis strain BNT52 16S ribosomal RNA gene, partial sequence	JN989302	1460		1128664

GC content

@ref	GC-content (mol%)	Method
20306	68.8	fluorimetric
31059	68.8
67770	68.8	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: ASM671504v1 assembly for Amycolatopsis cihanbeyliensis DSM 45679
NCBI: GCA_006715045

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	facultative anaerobe	95.30	no
125439	gram_stain	BacteriaNetⓘ	positive	94.81	no
125439	motility	BacteriaNetⓘ	no	90.95	no
125439	spore_formation	BacteriaNetⓘ	yes	51.07	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Amycolatopsis cihanbeyliensis strain DSM 45679
PATRIC: 1128664.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	91.83	no
125438	anaerobic	anaerobicⓘ	no	97.93	no
125438	spore-forming	spore-formingⓘ	yes	78.56	no
125438	aerobic	aerobicⓘ	yes	90.99	yes
125438	thermophilic	thermophileⓘ	no	90.80	no
125438	flagellated	motile2+ⓘ	no	91.00	yes

Literature

Topic	Title	Authors	Journal	DOI	Year
	Discovery and Biosynthesis of Cihanmycins Reveal Cytochrome P450-Catalyzed Intramolecular C-O Phenol Coupling Reactions.	Fang C, Zhang L, Wang Y, Xiong W, Yan Z, Zhang W, Zhang Q, Wang B, Zhu Y, Zhang C.	J Am Chem Soc	10.1021/jacs.4c02841	2024
	Logical Exploration of Cinnamoyl-Containing Nonribosomal Peptides via Metabologenomic Targeting and Regulator Overexpression.	Kang S, Huynh TH, Kim JM, Heo BE, Jang SC, Ock CW, Lee J, Song Y, An JS, Shen B, Kim SB, Jang J, Lee SK, Yoon YJ, Oh DC.	J Am Chem Soc	10.1021/jacs.5c13143	2025
	Mechanistic Analysis of the Biosynthesis of the Aspartimidylated Graspetide Amycolimiditide.	Choi B, Elashal HE, Cao L, Link AJ.	J Am Chem Soc	10.1021/jacs.2c09004	2022
	Discovery of Efrotomycin Congeners and Heterologous Expression-Based Insights into the Self-Resistance Mechanism.	Fang C, Zhang Q, Zhang W, Zhang C, Zhu Y	J Nat Prod	10.1021/acs.jnatprod.2c00986	2022
Phylogeny	Amycolatopsis cihanbeyliensis sp. nov., a halotolerant actinomycete isolated from a salt mine.	Tatar D, Sazak A, Guven K, Cetin D, Sahin N	Int J Syst Evol Microbiol	10.1099/ijs.0.050963-0	2013
Phylogeny	Amycolatopsis aidingensis sp. nov., a Halotolerant Actinobacterium, Produces New Secondary Metabolites.	Li R, Wang M, Ren Z, Ji Y, Yin M, Zhou H, Tang SK	Front Microbiol	10.3389/fmicb.2021.743116	2021

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 )
#20306	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 45679
#27388	IJSEM 3739 2013 ( DOI 10.1099/ijs.0.050963-0 , PubMed 23645018 )
#31059	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 #27388
#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;
#67771	Korean Collection for Type Cultures (KCTC) ; Curators of the KCTC;
#68369	Automatically annotated from API 20NE .
#68382	Automatically annotated from API zym .
#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 )

Rate our new design

Content

About us

Amycolatopsis cihanbeyliensis (DSM 45679, JCM 31029, KCTC 29065)

Name and taxonomic classification

Morphology

Cell morphology

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Halophily

Observation

Metabolite utilization

Metabolite production

Metabolite tests

Enzymes

Pathway annotation

API zym

API 20NE

Isolation, sampling and environmental information

Isolation source categories

Isolation

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_006715045

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

Help

Social Media