Name: Amycolatopsis albispora WP1
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 133131

Type strain:

Species: Amycolatopsis albispora

Strain Designation: WP1

Culture col. no.: KCTC 39642, MCCC 1A10745

Strain history: <- Gaiyun Zhang

NCBI tax ID(s): 1804986 (species)

Special Collections

Section

Amycolatopsis albispora WP1 is an aerobe, spore-forming, Gram-positive bacterium that was isolated from deep-sea sediment.

Gram-positive
spore-forming
aerobe
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	*Pseudonocardiales*
	Family	*Pseudonocardiaceae*
	Genus	*Amycolatopsis*
	Species	**Amycolatopsis albispora**
	Full Scientific Name (LPSN)	Amycolatopsis albispora Zhang et al. 2016

Information on morphological and physiological properties Morphology

[Ref.: #24893]	Gram stain	positive

[Ref.: #24893]	Motility	no

Information on culture and growth conditions Culture and growth conditions

[Ref.: #24893]

Culture medium

MZ2 medium

[Ref.: #24893]

Culture medium growth

		Temperature
[Ref.: #24893]	growth	4.0-45.0 °C
[Ref.: #24893]	optimum	30.0-35.0 °C
[Ref.: #67771]	growth	30-35 °C

	pH	Kind of pH		pH
[Ref.: #24893]			optimum	8.0-9.0
[Ref.: #24893]			growth	5.0-11.0

Information on physiology and metabolism Physiology and metabolism

[Ref.: #24893]	Oxygen tolerance	aerobe
[Ref.: #67771]	Oxygen tolerance	aerobe

[Ref.: #24893]	Spore description	white spores
[Ref.: #24893]	Type of spore	spore
[Ref.: #24893]	Ability of spore formation	yes
[Ref.: #69481]	Ability of spore formation	yes Confidence in %100

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #24893]		NaCl		growth	0.0-8.0	%(w/v)
[Ref.: #24893]		NaCl		optimum	0.0-3.0	%(w/v)

[Ref.: #24893]	Murein short key	A31
[Ref.: #24893]	Murein types	A1gamma m-Dpm-direct

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #24893]	amygdalin ChEBI	-	builds acid from
[Ref.: #24893]	casein	+	hydrolysis
[Ref.: #24893]	cellulose ChEBI	+	hydrolysis
[Ref.: #24893]	D-arabinose ChEBI	-	builds acid from
[Ref.: #24893]	glucose ChEBI	-	fermentation
[Ref.: #24893]	glucose ChEBI	-	builds acid from
[Ref.: #24893]	mannitol ChEBI	-	builds acid from
[Ref.: #24893]	melibiose ChEBI	-	builds acid from
[Ref.: #24893]	myo-inositol ChEBI	-	builds acid from
[Ref.: #24893]	nitrate ChEBI	+	reduction
[Ref.: #24893]	rhamnose ChEBI	-	builds acid from
[Ref.: #24893]	sorbitol ChEBI	-	builds acid from
[Ref.: #24893]	starch ChEBI	+	hydrolysis
[Ref.: #24893]	sucrose ChEBI	-	builds acid from
[Ref.: #24893]	tryptophan ChEBI	-	energy source
	Only first 10 entries are displayed. Click here to see all.

	Metabolite	Production
[Ref.: #24893]	acetoin ChEBI	yes
[Ref.: #24893]	hydrogen sulfide ChEBI	no
[Ref.: #24893]	indole ChEBI	no
[Ref.: #24893]	melanin ChEBI	no

	Metabolite	Voges-Proskauer-test	Methylred-test	Indole test
[Ref.: #24893]	acetoin ChEBI	+
[Ref.: #24893]	glucose ChEBI		-
[Ref.: #24893]	indole ChEBI			-

	Enzyme	Enzyme activity	EC number
[Ref.: #24893]	acid phosphatase	+	3.1.3.2
[Ref.: #24893]	alkaline phosphatase	+	3.1.3.1
[Ref.: #24893]	alpha-chymotrypsin	-	3.4.21.1
[Ref.: #24893]	alpha-fucosidase	-	3.2.1.51
[Ref.: #24893]	alpha-galactosidase	-	3.2.1.22
[Ref.: #24893]	alpha-glucosidase	+	3.2.1.20
[Ref.: #24893]	alpha-mannosidase	-	3.2.1.24
[Ref.: #24893]	arginine dihydrolase	+	3.5.3.6
[Ref.: #24893]	beta-galactosidase	+	3.2.1.23
[Ref.: #24893]	beta-glucosidase	+	3.2.1.21
[Ref.: #24893]	beta-glucuronidase	-	3.2.1.31
[Ref.: #24893]	catalase	+	1.11.1.6
[Ref.: #24893]	cystine arylamidase	+	3.4.11.3
[Ref.: #24893]	cytochrome oxidase	-	1.9.3.1
[Ref.: #24893]	esterase (C 4)	+
[Ref.: #24893]	esterase lipase (C 8)	+
[Ref.: #24893]	gelatinase	+
[Ref.: #24893]	leucine arylamidase	+	3.4.11.1
[Ref.: #24893]	lipase (C 14)	-
[Ref.: #24893]	lysine decarboxylase	-	4.1.1.18
[Ref.: #24893]	N-acetyl-beta-glucosaminidase	+	3.2.1.52
[Ref.: #24893]	naphthol-AS-BI-phosphohydrolase	+
[Ref.: #24893]	ornithine decarboxylase	-	4.1.1.17
[Ref.: #24893]	trypsin	-	3.4.21.4
[Ref.: #24893]	tryptophan deaminase	-	4.1.99.1
[Ref.: #24893]	urease	+	3.5.1.5
[Ref.: #24893]	valine arylamidase	+
	Only first 10 entries are displayed. Click here to see all.

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	4-hydroxymandelate degradation	100	9 of 9
[Ref.: #66794]	palmitate biosynthesis	100	22 of 22
[Ref.: #66794]	L-lactaldehyde degradation	100	3 of 3
[Ref.: #66794]	glycolate and glyoxylate degradation	100	6 of 6
[Ref.: #66794]	propanol degradation	100	7 of 7
[Ref.: #66794]	molybdenum cofactor biosynthesis	100	9 of 9
[Ref.: #66794]	vitamin K metabolism	100	5 of 5
[Ref.: #66794]	glycine betaine biosynthesis	100	5 of 5
[Ref.: #66794]	adipate degradation	100	2 of 2
[Ref.: #66794]	formaldehyde oxidation	100	3 of 3
[Ref.: #66794]	gallate degradation	100	5 of 5
[Ref.: #66794]	coenzyme A metabolism	100	4 of 4
[Ref.: #66794]	biotin biosynthesis	100	4 of 4
[Ref.: #66794]	phenylacetate degradation (aerobic)	100	5 of 5
[Ref.: #66794]	kanosamine biosynthesis II	100	2 of 2
[Ref.: #66794]	threonine metabolism	100	10 of 10
[Ref.: #66794]	acetate fermentation	100	4 of 4
[Ref.: #66794]	dTDPLrhamnose biosynthesis	100	8 of 8
[Ref.: #66794]	ppGpp biosynthesis	100	4 of 4
[Ref.: #66794]	Entner Doudoroff pathway	100	10 of 10
[Ref.: #66794]	ethanol fermentation	100	2 of 2
[Ref.: #66794]	methylglyoxal degradation	100	5 of 5
[Ref.: #66794]	butanoate fermentation	100	4 of 4
[Ref.: #66794]	valine metabolism	100	9 of 9
[Ref.: #66794]	cis-vaccenate biosynthesis	100	2 of 2
[Ref.: #66794]	enterobactin biosynthesis	100	3 of 3
[Ref.: #66794]	glycogen metabolism	100	5 of 5
[Ref.: #66794]	sulfopterin metabolism	100	4 of 4
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	aerobactin biosynthesis	100	1 of 1
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	lactate fermentation	100	4 of 4
[Ref.: #66794]	suberin monomers biosynthesis	100	2 of 2
[Ref.: #66794]	taurine degradation	100	1 of 1
[Ref.: #66794]	cellulose degradation	100	5 of 5
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	flavin biosynthesis	93.33	14 of 15
[Ref.: #66794]	tetrahydrofolate metabolism	92.86	13 of 14
[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]	pentose phosphate pathway	90.91	10 of 11
[Ref.: #66794]	proline metabolism	90.91	10 of 11
[Ref.: #66794]	starch degradation	90	9 of 10
[Ref.: #66794]	propionate fermentation	90	9 of 10
[Ref.: #66794]	degradation of pentoses	89.29	25 of 28
[Ref.: #66794]	glutamate and glutamine metabolism	89.29	25 of 28
[Ref.: #66794]	aspartate and asparagine metabolism	88.89	8 of 9
[Ref.: #66794]	CO2 fixation in Crenarchaeota	88.89	8 of 9
[Ref.: #66794]	serine metabolism	88.89	8 of 9
[Ref.: #66794]	NAD metabolism	88.89	16 of 18
[Ref.: #66794]	allantoin degradation	88.89	8 of 9
[Ref.: #66794]	chorismate metabolism	88.89	8 of 9
[Ref.: #66794]	purine metabolism	88.3	83 of 94
[Ref.: #66794]	isoleucine metabolism	87.5	7 of 8
[Ref.: #66794]	ketogluconate metabolism	87.5	7 of 8
[Ref.: #66794]	peptidoglycan biosynthesis	86.67	13 of 15
[Ref.: #66794]	alanine metabolism	86.21	25 of 29
[Ref.: #66794]	heme metabolism	85.71	12 of 14
[Ref.: #66794]	glutathione metabolism	85.71	12 of 14
[Ref.: #66794]	reductive acetyl coenzyme A pathway	85.71	6 of 7
[Ref.: #66794]	aclacinomycin biosynthesis	85.71	6 of 7
[Ref.: #66794]	vitamin B12 metabolism	85.29	29 of 34
[Ref.: #66794]	vitamin B1 metabolism	84.62	11 of 13
[Ref.: #66794]	urea cycle	84.62	11 of 13
[Ref.: #66794]	methionine metabolism	84.62	22 of 26
[Ref.: #66794]	pyrimidine metabolism	84.44	38 of 45
[Ref.: #66794]	degradation of sugar acids	84	21 of 25
[Ref.: #66794]	glycolysis	82.35	14 of 17
[Ref.: #66794]	3-chlorocatechol degradation	80	4 of 5
[Ref.: #66794]	phenol degradation	80	16 of 20
[Ref.: #66794]	factor 420 biosynthesis	80	4 of 5
[Ref.: #66794]	myo-inositol biosynthesis	80	8 of 10
[Ref.: #66794]	ethylmalonyl-CoA pathway	80	4 of 5
[Ref.: #66794]	4-hydroxyphenylacetate degradation	80	8 of 10
[Ref.: #66794]	histidine metabolism	79.31	23 of 29
[Ref.: #66794]	arginine metabolism	79.17	19 of 24
[Ref.: #66794]	photosynthesis	78.57	11 of 14
[Ref.: #66794]	d-mannose degradation	77.78	7 of 9
[Ref.: #66794]	degradation of hexoses	77.78	14 of 18
[Ref.: #66794]	sulfate reduction	76.92	10 of 13
[Ref.: #66794]	tryptophan metabolism	76.32	29 of 38
[Ref.: #66794]	glycogen biosynthesis	75	3 of 4
[Ref.: #66794]	cyclohexanol degradation	75	3 of 4
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	75	9 of 12
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
[Ref.: #66794]	toluene degradation	75	3 of 4
[Ref.: #66794]	gluconeogenesis	75	6 of 8
[Ref.: #66794]	lipid metabolism	74.19	23 of 31
[Ref.: #66794]	polyamine pathway	73.91	17 of 23
[Ref.: #66794]	oxidative phosphorylation	73.63	67 of 91
[Ref.: #66794]	d-xylose degradation	72.73	8 of 11
[Ref.: #66794]	vitamin B6 metabolism	72.73	8 of 11
[Ref.: #66794]	cysteine metabolism	72.22	13 of 18
[Ref.: #66794]	tyrosine metabolism	71.43	10 of 14
[Ref.: #66794]	ubiquinone biosynthesis	71.43	5 of 7
[Ref.: #66794]	cardiolipin biosynthesis	71.43	5 of 7
[Ref.: #66794]	non-pathway related	71.05	27 of 38
[Ref.: #66794]	androgen and estrogen metabolism	68.75	11 of 16
[Ref.: #66794]	degradation of sugar alcohols	68.75	11 of 16
[Ref.: #66794]	octane oxidation	66.67	2 of 3
[Ref.: #66794]	cyanate degradation	66.67	2 of 3
[Ref.: #66794]	3-phenylpropionate degradation	66.67	10 of 15
[Ref.: #66794]	acetyl CoA biosynthesis	66.67	2 of 3
[Ref.: #66794]	acetoin degradation	66.67	2 of 3
[Ref.: #66794]	IAA biosynthesis	66.67	2 of 3
[Ref.: #66794]	metabolism of disaccharids	63.64	7 of 11
[Ref.: #66794]	C4 and CAM-carbon fixation	62.5	5 of 8
[Ref.: #66794]	phosphatidylethanolamine bioynthesis	61.54	8 of 13
[Ref.: #66794]	coenzyme M biosynthesis	60	6 of 10
[Ref.: #66794]	hydrogen production	60	3 of 5
[Ref.: #66794]	lipoate biosynthesis	60	3 of 5
[Ref.: #66794]	metabolism of amino sugars and derivatives	60	3 of 5
[Ref.: #66794]	arachidonate biosynthesis	60	3 of 5
[Ref.: #66794]	creatinine degradation	60	3 of 5
[Ref.: #66794]	lysine metabolism	59.52	25 of 42
[Ref.: #66794]	carotenoid biosynthesis	59.09	13 of 22
[Ref.: #66794]	bile acid biosynthesis, neutral pathway	58.82	10 of 17
[Ref.: #66794]	isoprenoid biosynthesis	57.69	15 of 26
[Ref.: #66794]	daunorubicin biosynthesis	55.56	5 of 9
[Ref.: #66794]	nitrate assimilation	55.56	5 of 9
[Ref.: #66794]	ascorbate metabolism	54.55	12 of 22
[Ref.: #66794]	phenylpropanoid biosynthesis	53.85	7 of 13
[Ref.: #66794]	carnitine metabolism	50	4 of 8
[Ref.: #66794]	mannosylglycerate biosynthesis	50	1 of 2
[Ref.: #66794]	sphingosine metabolism	50	3 of 6
[Ref.: #66794]	ribulose monophosphate pathway	50	1 of 2
[Ref.: #66794]	chlorophyll metabolism	50	9 of 18
[Ref.: #66794]	CMP-KDO biosynthesis	50	2 of 4
[Ref.: #66794]	resorcinol degradation	50	1 of 2
[Ref.: #66794]	phenylmercury acetate degradation	50	1 of 2
[Ref.: #66794]	quinate degradation	50	1 of 2
[Ref.: #66794]	pantothenate biosynthesis	50	3 of 6
[Ref.: #66794]	aminopropanol phosphate biosynthesis	50	1 of 2
[Ref.: #66794]	glycine metabolism	50	5 of 10
[Ref.: #66794]	lipid A biosynthesis	44.44	4 of 9
[Ref.: #66794]	benzoyl-CoA degradation	42.86	3 of 7
[Ref.: #66794]	elloramycin biosynthesis	40	2 of 5
[Ref.: #66794]	bacilysin biosynthesis	40	2 of 5
[Ref.: #66794]	D-cycloserine biosynthesis	40	2 of 5
[Ref.: #66794]	arachidonic acid metabolism	38.89	7 of 18
[Ref.: #66794]	methane metabolism	33.33	1 of 3
[Ref.: #66794]	sulfoquinovose degradation	33.33	1 of 3
[Ref.: #66794]	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
[Ref.: #66794]	selenocysteine biosynthesis	33.33	2 of 6
[Ref.: #66794]	1,4-dihydroxy-6-naphthoate biosynthesis	33.33	2 of 6
[Ref.: #66794]	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
[Ref.: #66794]	vitamin E metabolism	25	1 of 4
[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.: #24893]	Sample type/isolated from	deep-sea sediment
[Ref.: #24893]	Geographic location (country and/or sea, region)	Indian Ocean at site TVG1 (-2945 m)
[Ref.: #24893]	Geographic location	-27.0000°/63.0000°
[Ref.: #24893]	Enrichment culture	modified Zobell 2216E agar
[Ref.: #24893]	Enrichment culture composition	MZ2; 1.0 g yeast extract, 5.0 g tryptone, 34 g NaCl, 15 g agar and 1 l distilled water, pH 7.4–7.6
[Ref.: #24893]	Enrichment culture duration	21 days
[Ref.: #24893]	Enrichment culture temperature	28 ̊C

[Ref.: #67771]	Sample type/isolated from	Marine sediment of Indian Ocean
[Ref.: #67771]	Country	China
[Ref.: #67771]	Country ISO 3 Code	CHN
[Ref.: #67771]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Environmental	#Aquatic	#Marine
#Environmental	#Aquatic	#Sediment

What are isolation sources categories?

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.: #24893]	Amycolatopsis albispora strain WP1 16S ribosomal RNA gene, partial sequence	KT751086	1481	GenBank ENA	1804986 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Amycolatopsis albispora WP1	GCA_003312875	complete	GenBank ENA	1804986 tax ID	*
[Ref.: #66792]	Amycolatopsis albispora WP1	2856864784	complete	JGI IMG/M	1804986 tax ID	*

[Ref.: #24893]

GC-content

72.2 mol%

high performance liquid chromatography (HPLC)

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

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from GenomeNet Sporulation v. 1 based on: Amycolatopsis albispora WP1 NCBI: GCA_003312875.1
[Ref.: #69481]	spore-forming	spore-formingⓘ	yes	100	no

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Amycolatopsis albispora WP1 NCBI: GCA_003312875.1
[Ref.: #69480]	gram-positive	gram-positiveⓘ	yes	89.557	no
[Ref.: #69480]	anaerobic	anaerobicⓘ	no	98.868	yes
[Ref.: #69480]	aerobic	aerobicⓘ	yes	88.599	yes
[Ref.: #69480]	spore-forming	spore-formingⓘ	yes	78.389	no
[Ref.: #69480]	thermophilic	thermophileⓘ	no	96.994	no
[Ref.: #69480]	flagellated	motile2+ⓘ	no	88.5	no

Availability in culture collections External links

[Ref.: #24893]

Culture collection no.

KCTC 39642, MCCC 1A10745

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Amycolatopsis albispora sp. nov., isolated from deep-sea sediment.	Zhang G, Wang L, Li J, Zhou Y	Int J Syst Evol Microbiol	10.1099/ijsem.0.001277	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 )

#24893

G. W. Zhang, Lina,Li, Jinglong,Zhou, Yuan: Amycolatopsis albispora sp. nov., isolated from deep-sea sediment. IJSEM 66: 3860 - 3864 2016 ( DOI 10.1099/ijsem.0.001277 , PubMed 27380629 )

#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) .

#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 )

* These data were automatically processed and therefore are not curated

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