Name: Streptomyces palmae CMU-AB204
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 133134

Type strain:

Species: Streptomyces palmae

Strain Designation: CMU-AB204

Culture col. no.: JCM 31289, TBRC 1999, DSM 111123

Strain history: S. Lumyong; Chiang Mai Univ., Thailand; CMU-AB204.

NCBI tax ID(s): 1701085 (species)

SI-ID 399669

DSM 111123

Section

Streptomyces palmae CMU-AB204 is an aerobe, spore-forming, mesophilic bacterium that was isolated from rhizosphere soil of an oil palm .

Gram-positive
spore-forming
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	*Kitasatosporales*
	Family	*Streptomycetaceae*
	Genus	*Streptomyces*
	Species	**Streptomyces palmae**
	Full Scientific Name (LPSN)	Streptomyces palmae Sujarit et al. 2016

Information on morphological and physiological properties Morphology

[Ref.: #24896]	Gram stain	positive
[Ref.: #69480]	Gram stain	positive Confidence in %100

[Ref.: #24896]	Motility	no
[Ref.: #69480]	Motility	no Confidence in %95.141

Multimedia content

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Caption:

Medium 252 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

Yeast extract-malt extract agar (ISP2)

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Culture medium growth

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Culture medium

Inorganic salts-starch agar (ISP4)

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Culture medium growth

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Culture medium

ROLLED OATS MINERAL MEDIUM (DSMZ Medium 84)

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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

STARCH - MINERAL SALT - AGAR (STMS) (DSMZ Medium 252)

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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

	Kind of temperature		Temperature
[Ref.: #24896]		optimum	30.0-35.0 °C
[Ref.: #24896]	no	growth	10 °C
[Ref.: #24896]		growth	45 °C
[Ref.: #66469]		growth	28 °C
[Ref.: #67770]		growth	28 °C

[Ref.: #24896]	Temperature range	mesophilic
[Ref.: #24896]	Temperature range	psychrophilic
[Ref.: #24896]	Temperature range	thermophilic
[Ref.: #66469]	Temperature range	mesophilic
[Ref.: #67770]	Temperature range	mesophilic

	pH	Kind of pH		pH
[Ref.: #24896]			optimum	6.0-9.0

Information on physiology and metabolism Physiology and metabolism

[Ref.: #24896]

Oxygen tolerance

aerobe

[Ref.: #24896]	Spore description	oval-shaped, spiny to hairy surfaced,0.7-1.0x1.0-1.3 µm
[Ref.: #24896]	Type of spore	spore
[Ref.: #24896]	Ability of spore formation	yes
[Ref.: #69481]	Ability of spore formation	yes Confidence in %100
[Ref.: #69480]	Ability of spore formation	yes Confidence in %100

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #24896]		NaCl		growth	3	%(w/v)
[Ref.: #24896]		NaCl	no	growth	7	%(w/v)

[Ref.: #67770]

Observation

quinones: MK-9(H₄), MK-9(H₆), MK-9(H₂), MK-8(H₄)

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #24896]	D-fructose ChEBI	+	carbon source
[Ref.: #24896]	D-glucose ChEBI	+	carbon source
[Ref.: #24896]	D-mannitol ChEBI	-	carbon source
[Ref.: #24896]	D-xylose ChEBI	-	carbon source
[Ref.: #24896]	L-arabinose ChEBI	-	carbon source
[Ref.: #24896]	myo-inositol ChEBI	+	carbon source
[Ref.: #24896]	raffinose ChEBI	+	carbon source
[Ref.: #24896]	rhamnose ChEBI	-	carbon source
[Ref.: #24896]	sucrose ChEBI	-	carbon source

	Metabolite production	Metabolite	Production
[Ref.: #24896]		melanin ChEBI	no

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	factor 420 biosynthesis	100	5 of 5
[Ref.: #66794]	butanoate fermentation	100	4 of 4
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	valine metabolism	100	9 of 9
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	denitrification	100	2 of 2
[Ref.: #66794]	myo-inositol biosynthesis	100	10 of 10
[Ref.: #66794]	1,4-dihydroxy-6-naphthoate biosynthesis	100	6 of 6
[Ref.: #66794]	pentose phosphate pathway	100	11 of 11
[Ref.: #66794]	phenylacetate degradation (aerobic)	100	5 of 5
[Ref.: #66794]	coenzyme A metabolism	100	4 of 4
[Ref.: #66794]	formaldehyde oxidation	100	3 of 3
[Ref.: #66794]	adipate degradation	100	2 of 2
[Ref.: #66794]	cyanate degradation	100	3 of 3
[Ref.: #66794]	ribulose monophosphate pathway	100	2 of 2
[Ref.: #66794]	biotin biosynthesis	100	4 of 4
[Ref.: #66794]	molybdenum cofactor biosynthesis	100	9 of 9
[Ref.: #66794]	hydrogen production	100	5 of 5
[Ref.: #66794]	suberin monomers biosynthesis	100	2 of 2
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	cardiolipin biosynthesis	100	7 of 7
[Ref.: #66794]	palmitate biosynthesis	100	22 of 22
[Ref.: #66794]	ppGpp biosynthesis	100	4 of 4
[Ref.: #66794]	cis-vaccenate biosynthesis	100	2 of 2
[Ref.: #66794]	threonine metabolism	100	10 of 10
[Ref.: #66794]	aerobactin biosynthesis	100	1 of 1
[Ref.: #66794]	taurine degradation	100	1 of 1
[Ref.: #66794]	acetate fermentation	100	4 of 4
[Ref.: #66794]	cellulose degradation	100	5 of 5
[Ref.: #66794]	methylglyoxal degradation	100	5 of 5
[Ref.: #66794]	ceramide biosynthesis	100	1 of 1
[Ref.: #66794]	glutamate and glutamine metabolism	92.86	26 of 28
[Ref.: #66794]	phenylalanine metabolism	92.31	12 of 13
[Ref.: #66794]	proline metabolism	90.91	10 of 11
[Ref.: #66794]	starch degradation	90	9 of 10
[Ref.: #66794]	aspartate and asparagine metabolism	88.89	8 of 9
[Ref.: #66794]	CO2 fixation in Crenarchaeota	88.89	8 of 9
[Ref.: #66794]	chorismate metabolism	88.89	8 of 9
[Ref.: #66794]	serine metabolism	88.89	8 of 9
[Ref.: #66794]	gluconeogenesis	87.5	7 of 8
[Ref.: #66794]	C4 and CAM-carbon fixation	87.5	7 of 8
[Ref.: #66794]	peptidoglycan biosynthesis	86.67	13 of 15
[Ref.: #66794]	heme metabolism	85.71	12 of 14
[Ref.: #66794]	photosynthesis	85.71	12 of 14
[Ref.: #66794]	reductive acetyl coenzyme A pathway	85.71	6 of 7
[Ref.: #66794]	tetrahydrofolate metabolism	85.71	12 of 14
[Ref.: #66794]	ubiquinone biosynthesis	85.71	6 of 7
[Ref.: #66794]	citric acid cycle	85.71	12 of 14
[Ref.: #66794]	vitamin B12 metabolism	85.29	29 of 34
[Ref.: #66794]	leucine metabolism	84.62	11 of 13
[Ref.: #66794]	glycolate and glyoxylate degradation	83.33	5 of 6
[Ref.: #66794]	arginine metabolism	83.33	20 of 24
[Ref.: #66794]	NAD metabolism	83.33	15 of 18
[Ref.: #66794]	alanine metabolism	82.76	24 of 29
[Ref.: #66794]	glycolysis	82.35	14 of 17
[Ref.: #66794]	metabolism of disaccharids	81.82	9 of 11
[Ref.: #66794]	metabolism of amino sugars and derivatives	80	4 of 5
[Ref.: #66794]	propionate fermentation	80	8 of 10
[Ref.: #66794]	glycine betaine biosynthesis	80	4 of 5
[Ref.: #66794]	flavin biosynthesis	80	12 of 15
[Ref.: #66794]	ethylmalonyl-CoA pathway	80	4 of 5
[Ref.: #66794]	glycogen metabolism	80	4 of 5
[Ref.: #66794]	purine metabolism	78.72	74 of 94
[Ref.: #66794]	d-mannose degradation	77.78	7 of 9
[Ref.: #66794]	4-hydroxymandelate degradation	77.78	7 of 9
[Ref.: #66794]	allantoin degradation	77.78	7 of 9
[Ref.: #66794]	isoleucine metabolism	75	6 of 8
[Ref.: #66794]	glycogen biosynthesis	75	3 of 4
[Ref.: #66794]	sulfopterin metabolism	75	3 of 4
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
[Ref.: #66794]	lipid metabolism	74.19	23 of 31
[Ref.: #66794]	pyrimidine metabolism	73.33	33 of 45
[Ref.: #66794]	isoprenoid biosynthesis	73.08	19 of 26
[Ref.: #66794]	histidine metabolism	72.41	21 of 29
[Ref.: #66794]	propanol degradation	71.43	5 of 7
[Ref.: #66794]	tryptophan metabolism	71.05	27 of 38
[Ref.: #66794]	Entner Doudoroff pathway	70	7 of 10
[Ref.: #66794]	vitamin B1 metabolism	69.23	9 of 13
[Ref.: #66794]	methionine metabolism	69.23	18 of 26
[Ref.: #66794]	lysine metabolism	69.05	29 of 42
[Ref.: #66794]	oxidative phosphorylation	68.13	62 of 91
[Ref.: #66794]	enterobactin biosynthesis	66.67	2 of 3
[Ref.: #66794]	octane oxidation	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]	(5R)-carbapenem carboxylate biosynthesis	66.67	2 of 3
[Ref.: #66794]	methane metabolism	66.67	2 of 3
[Ref.: #66794]	cysteine metabolism	66.67	12 of 18
[Ref.: #66794]	acetyl CoA biosynthesis	66.67	2 of 3
[Ref.: #66794]	acetoin degradation	66.67	2 of 3
[Ref.: #66794]	tyrosine metabolism	64.29	9 of 14
[Ref.: #66794]	glutathione metabolism	64.29	9 of 14
[Ref.: #66794]	non-pathway related	63.16	24 of 38
[Ref.: #66794]	degradation of sugar alcohols	62.5	10 of 16
[Ref.: #66794]	ketogluconate metabolism	62.5	5 of 8
[Ref.: #66794]	sulfate reduction	61.54	8 of 13
[Ref.: #66794]	urea cycle	61.54	8 of 13
[Ref.: #66794]	3-chlorocatechol degradation	60	3 of 5
[Ref.: #66794]	lipoate biosynthesis	60	3 of 5
[Ref.: #66794]	arachidonate biosynthesis	60	3 of 5
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	58.33	7 of 12
[Ref.: #66794]	degradation of pentoses	57.14	16 of 28
[Ref.: #66794]	daunorubicin biosynthesis	55.56	5 of 9
[Ref.: #66794]	phenylpropanoid biosynthesis	53.85	7 of 13
[Ref.: #66794]	3-phenylpropionate degradation	53.33	8 of 15
[Ref.: #66794]	coenzyme M biosynthesis	50	5 of 10
[Ref.: #66794]	androgen and estrogen metabolism	50	8 of 16
[Ref.: #66794]	mannosylglycerate biosynthesis	50	1 of 2
[Ref.: #66794]	pantothenate biosynthesis	50	3 of 6
[Ref.: #66794]	cyclohexanol degradation	50	2 of 4
[Ref.: #66794]	phenylmercury acetate degradation	50	1 of 2
[Ref.: #66794]	aminopropanol phosphate biosynthesis	50	1 of 2
[Ref.: #66794]	selenocysteine biosynthesis	50	3 of 6
[Ref.: #66794]	glycine metabolism	50	5 of 10
[Ref.: #66794]	toluene degradation	50	2 of 4
[Ref.: #66794]	kanosamine biosynthesis II	50	1 of 2
[Ref.: #66794]	CMP-KDO biosynthesis	50	2 of 4
[Ref.: #66794]	vitamin E metabolism	50	2 of 4
[Ref.: #66794]	degradation of hexoses	50	9 of 18
[Ref.: #66794]	quinate degradation	50	1 of 2
[Ref.: #66794]	ethanol fermentation	50	1 of 2
[Ref.: #66794]	bile acid biosynthesis, neutral pathway	47.06	8 of 17
[Ref.: #66794]	carotenoid biosynthesis	45.45	10 of 22
[Ref.: #66794]	vitamin B6 metabolism	45.45	5 of 11
[Ref.: #66794]	cholesterol biosynthesis	45.45	5 of 11
[Ref.: #66794]	ascorbate metabolism	45.45	10 of 22
[Ref.: #66794]	phenol degradation	45	9 of 20
[Ref.: #66794]	nitrate assimilation	44.44	4 of 9
[Ref.: #66794]	lipid A biosynthesis	44.44	4 of 9
[Ref.: #66794]	polyamine pathway	43.48	10 of 23
[Ref.: #66794]	aclacinomycin biosynthesis	42.86	3 of 7
[Ref.: #66794]	benzoyl-CoA degradation	42.86	3 of 7
[Ref.: #66794]	gallate degradation	40	2 of 5
[Ref.: #66794]	bacilysin biosynthesis	40	2 of 5
[Ref.: #66794]	vitamin K metabolism	40	2 of 5
[Ref.: #66794]	carnitine metabolism	37.5	3 of 8
[Ref.: #66794]	d-xylose degradation	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]	degradation of sugar acids	32	8 of 25
[Ref.: #66794]	phosphatidylethanolamine bioynthesis	30.77	4 of 13
[Ref.: #66794]	mevalonate metabolism	28.57	2 of 7
[Ref.: #66794]	arachidonic acid metabolism	27.78	5 of 18
[Ref.: #66794]	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
[Ref.: #66794]	alginate biosynthesis	25	1 of 4
[Ref.: #66794]	dTDPLrhamnose biosynthesis	25	2 of 8
[Ref.: #66794]	lactate fermentation	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.: #24896]	Sample type/isolated from	rhizosphere soil of an oil palm (Elaeis guineensis Jacq.)
[Ref.: #24896]	Geographic location (country and/or sea, region)	Chiang Mai University, Chiang Mai Province
[Ref.: #24896]	Country	Thailand
[Ref.: #24896]	Country ISO 3 Code	THA
[Ref.: #24896]	Continent	Asia
[Ref.: #24896]	Enrichment culture	starch casein agar (SCA)
[Ref.: #24896]	Enrichment culture composition	supplemented with nalidixic acid (25 µg ml-1) and cycloheximide (50 µg ml-1)
[Ref.: #24896]	Enrichment culture duration	14 days
[Ref.: #24896]	Enrichment culture temperature	30 ̊C

[Ref.: #66469]	Sample type/isolated from	Rhizosphere of oil palm (Elaeis guineensis Jacq.)
[Ref.: #66469]	Geographic location (country and/or sea, region)	Chiang Mai Univ, Chiang Mai, Thailand
[Ref.: #66469]	Country	Thailand
[Ref.: #66469]	Country ISO 3 Code	THA
[Ref.: #66469]	Continent	Asia

[Ref.: #67770]	Sample type/isolated from	Oil palm rhizosphere soil in Chiang Mai Univ.
[Ref.: #67770]	Geographic location (country and/or sea, region)	Chiang Mai
[Ref.: #67770]	Country	Thailand
[Ref.: #67770]	Country ISO 3 Code	THA
[Ref.: #67770]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Environmental	#Terrestrial	#Soil
#Host	#Plants	#Tree
#Host Body-Site	#Plant	#Rhizosphere

What are isolation sources categories?

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

[Ref.: #66469]

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.: #24896]	Streptomyces palmae gene for 16S ribosomal RNA, partial sequence	LC073309	1451	GenBank	1701085 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Streptomyces palmae JCM 31289	GCA_004684805	contig	GenBank	1701085 tax ID
[Ref.: #66792]	Streptomyces palmae strain JCM 31289	1701085.3	wgs	PATRIC	1701085 tax ID	*
[Ref.: #66792]	Streptomyces palmae JCM 31289	2866937661	draft	JGI IMG/M	1701085 tax ID	*

[Ref.: #66469]

GC-content

70.9 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 GenomeNet Sporulation v. 1 based on: Streptomyces palmae strain JCM 31289 PATRIC: 1701085.3
[Ref.: #69481]	spore-forming	yes	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Streptomyces palmae strain JCM 31289 PATRIC: 1701085.3
[Ref.: #69480]	motile	no	94.102	no
[Ref.: #69480]	gram-positive	yes	90.837	yes
[Ref.: #69480]	anaerobic	no	98.705	yes
[Ref.: #69480]	aerobic	yes	85.276	no
[Ref.: #69480]	halophile	no	92.514	no
[Ref.: #69480]	spore-forming	yes	94.681	yes
[Ref.: #69480]	glucose-util	yes	87.642	yes
[Ref.: #69480]	flagellated	no	97.919	yes
[Ref.: #69480]	thermophile	no	95.502	no
[Ref.: #69480]	glucose-ferment	no	89.486	no

Availability in culture collections External links

[Ref.: #66469]

Culture collection no.

JCM 31289, TBRC 1999, DSM 111123

[Ref.: #91376]

SI-ID 399669

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Streptomyces benahoarensis sp. nov. Isolated From a Lava Tube of La Palma, Canary Islands, Spain.	Gonzalez-Pimentel JL, Hermosin B, Saiz-Jimenez C, Jurado V	Front Microbiol	10.3389/fmicb.2022.907816	2022	*
Phylogeny	New Antimicrobial Phenyl Alkenoic Acids Isolated from an Oil Palm Rhizosphere-Associated Actinomycete, Streptomyces palmae CMU-AB204(T).	Sujarit K, Mori M, Dobashi K, Shiomi K, Pathom-Aree W, Lumyong S	Microorganisms	10.3390/microorganisms8030350	2020	*
Phylogeny	Streptomyces lichenis sp. nov., isolated from lichen.	Saeng-In P, Phongsopitanun W, Savarajara A, Tanasupawat S	Int J Syst Evol Microbiol	10.1099/ijsem.0.003052	2018	*
Phylogeny	Streptomyces durbertensis sp. nov., isolated from saline-alkali soil.	Yu Y, Fu Y, Guo X, Yan R, Wang H, Zhao J, Wang X, Zhang J, Xiang W	Int J Syst Evol Microbiol	10.1099/ijsem.0.003047	2018	*
Phylogeny	Streptomyces palmae sp. nov., isolated from oil palm (Elaeis guineensis) rhizosphere soil.	Sujarit K, Kudo T, Ohkuma M, Pathom-Aree W, Lumyong S	Int J Syst Evol Microbiol	10.1099/ijsem.0.001298	2016	*

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 )

#24896

K. K. Sujarit, Takuji,Ohkuma, Moriya,Pathom-Aree, Wasu,Lumyong, Saisamorn: Streptomyces palmae sp. nov., isolated from oil palm (Elaeis guineensis) rhizosphere soil. IJSEM 66: 3983 - 3988 2016 ( DOI 10.1099/ijsem.0.001298 , PubMed 27405543 )

#66469

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 111123

#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 )

#67770 Japan Collection of Microorganism (JCM) ; Curators of the JCM;

#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) .

#69481

Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch: Predictions based on the model GenomeNet Sporulation v. 1 . ( DOI 10.21203/rs.3.rs-2527258/v1 )

#91376

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-ID399669.1 )

* These data were automatically processed and therefore are not curated

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Streptomyces palmae strain JCM 31289

Streptomyces palmae strain JCM 31289

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