Name: Pseudonocardia autotrophica 394
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 13324

Type strain:

Species: Pseudonocardia autotrophica

Strain Designation: 394, Kodai

Culture col. no.: DSM 535, ATCC 19727, CBS 466.68, DSM 40011, DSM 43210, IFO 12743, ISP 5011, KCC S-0348, NBRC 12743, RIA 1008, JCM 4348, BCRC 12444, CCM 2750, CECT 3301, CGMCC 4.1211, CGMCC 4.1297, CIP 107114, IMET 7646, IMSNU 11005, IMSNU 20050, KCTC 1816, KCTC 9564, KCTC 9574, NCIMB 9810, NRRL B-11275, VKM Ac-941

Strain history: KCC S-0348 <-- IFO 12743 <-- SAJ <-- ISP 5011 <-- A. Takamiya aa-1-1.

NCBI tax ID(s): 2074 (species)

Other strains from Pseudonocardia autotrophica

Section

Pseudonocardia autotrophica 394 is a mesophilic human pathogen that was isolated from phosphate buffer.

human pathogen
mesophilic
16S sequence
Bacteria
genome sequence

Information on the name and the taxonomic classification. Name and taxonomic classification

	Last LPSN update	07-12-2022 (DD-MM-YYYY)
	Domain	"Bacteria"
	Phylum	*Actinomycetota*
	Class	*Actinomycetes*
	Order	*Pseudonocardiales*
	Family	*Pseudonocardiaceae*
	Genus	*Pseudonocardia*
	Species	**Pseudonocardia autotrophica**
	Full Scientific Name (PNU)	Pseudonocardia autotrophica (Takamiya and Tubaki 1956) Warwick et al. 1994

	Synonym	"Proactinomyces* autotrophicus"*
	Synonym	"Streptomyces* autotrophicus"*
	Synonym	Nocardia autotrophica
	Synonym	Amycolata autotrophica

Information on morphological and physiological properties Morphology

Multimedia content

[Ref.: #130]

Caption:

Medium 65 28°C

[Ref.: #130]

Intellectual property rights:

Information on culture and growth conditions Culture and growth conditions

[Ref.: #33085]

Culture medium

MEDIUM 57 - for Streptomyces, Nocardioides, Lentzea albidocapillata and Streptoverticillium reticulum

[Ref.: #33085]

Culture medium growth

[Ref.: #33085]

Culture medium composition

expand / minimize

[Ref.: #130]

Culture medium

TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)

[Ref.: #130]

Culture medium growth

[Ref.: #130]

Culture medium link

Medium recipe provided by DSMZ

[Ref.: #130]

Culture medium composition

expand / minimize

[Ref.: #130]

Culture medium

GYM STREPTOMYCES MEDIUM (DSMZ Medium 65)

[Ref.: #130]

Culture medium growth

[Ref.: #130]

Culture medium link

Medium recipe provided by DSMZ

[Ref.: #130]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #130]	growth	28 °C
[Ref.: #33085]	growth	30 °C
[Ref.: #67770]	growth	28 °C

[Ref.: #130]	Temperature range	mesophilic
[Ref.: #33085]	Temperature range	mesophilic
[Ref.: #67770]	Temperature range	mesophilic

Information on physiology and metabolism Physiology and metabolism

[Ref.: #67770]

Observation

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

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	valine metabolism	100	9 of 9
[Ref.: #66794]	adipate degradation	100	2 of 2
[Ref.: #66794]	gallate degradation	100	5 of 5
[Ref.: #66794]	methylglyoxal degradation	100	5 of 5
[Ref.: #66794]	CMP-KDO biosynthesis	100	4 of 4
[Ref.: #66794]	cardiolipin biosynthesis	100	7 of 7
[Ref.: #66794]	Entner Doudoroff pathway	100	10 of 10
[Ref.: #66794]	cis-vaccenate biosynthesis	100	2 of 2
[Ref.: #66794]	ethylmalonyl-CoA pathway	100	5 of 5
[Ref.: #66794]	ethanol fermentation	100	2 of 2
[Ref.: #66794]	octane oxidation	100	3 of 3
[Ref.: #66794]	enterobactin biosynthesis	100	3 of 3
[Ref.: #66794]	phenylmercury acetate degradation	100	2 of 2
[Ref.: #66794]	resorcinol degradation	100	2 of 2
[Ref.: #66794]	IAA biosynthesis	100	3 of 3
[Ref.: #66794]	ppGpp biosynthesis	100	4 of 4
[Ref.: #66794]	biotin biosynthesis	100	4 of 4
[Ref.: #66794]	L-lactaldehyde degradation	100	3 of 3
[Ref.: #66794]	palmitate biosynthesis	100	22 of 22
[Ref.: #66794]	photosynthesis	100	14 of 14
[Ref.: #66794]	phenylacetate degradation (aerobic)	100	5 of 5
[Ref.: #66794]	coenzyme A metabolism	100	4 of 4
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	reductive acetyl coenzyme A pathway	100	7 of 7
[Ref.: #66794]	suberin monomers biosynthesis	100	2 of 2
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	glycine betaine biosynthesis	100	5 of 5
[Ref.: #66794]	glycolate and glyoxylate degradation	100	6 of 6
[Ref.: #66794]	cyanate degradation	100	3 of 3
[Ref.: #66794]	taurine degradation	100	1 of 1
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	formaldehyde oxidation	100	3 of 3
[Ref.: #66794]	vitamin K metabolism	100	5 of 5
[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]	myo-inositol biosynthesis	90	9 of 10
[Ref.: #66794]	phenol degradation	90	18 of 20
[Ref.: #66794]	threonine metabolism	90	9 of 10
[Ref.: #66794]	serine metabolism	88.89	8 of 9
[Ref.: #66794]	CO2 fixation in Crenarchaeota	88.89	8 of 9
[Ref.: #66794]	4-hydroxymandelate degradation	88.89	8 of 9
[Ref.: #66794]	chorismate metabolism	88.89	8 of 9
[Ref.: #66794]	aspartate and asparagine metabolism	88.89	8 of 9
[Ref.: #66794]	molybdenum cofactor biosynthesis	88.89	8 of 9
[Ref.: #66794]	C4 and CAM-carbon fixation	87.5	7 of 8
[Ref.: #66794]	gluconeogenesis	87.5	7 of 8
[Ref.: #66794]	ketogluconate metabolism	87.5	7 of 8
[Ref.: #66794]	flavin biosynthesis	86.67	13 of 15
[Ref.: #66794]	tetrahydrofolate metabolism	85.71	12 of 14
[Ref.: #66794]	propanol degradation	85.71	6 of 7
[Ref.: #66794]	purine metabolism	84.04	79 of 94
[Ref.: #66794]	NAD metabolism	83.33	15 of 18
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	83.33	10 of 12
[Ref.: #66794]	glutamate and glutamine metabolism	82.14	23 of 28
[Ref.: #66794]	pentose phosphate pathway	81.82	9 of 11
[Ref.: #66794]	methionine metabolism	80.77	21 of 26
[Ref.: #66794]	3-phenylpropionate degradation	80	12 of 15
[Ref.: #66794]	factor 420 biosynthesis	80	4 of 5
[Ref.: #66794]	3-chlorocatechol degradation	80	4 of 5
[Ref.: #66794]	starch degradation	80	8 of 10
[Ref.: #66794]	cellulose degradation	80	4 of 5
[Ref.: #66794]	peptidoglycan biosynthesis	80	12 of 15
[Ref.: #66794]	glycogen metabolism	80	4 of 5
[Ref.: #66794]	hydrogen production	80	4 of 5
[Ref.: #66794]	vitamin B12 metabolism	79.41	27 of 34
[Ref.: #66794]	tryptophan metabolism	78.95	30 of 38
[Ref.: #66794]	heme metabolism	78.57	11 of 14
[Ref.: #66794]	glutathione metabolism	78.57	11 of 14
[Ref.: #66794]	pyrimidine metabolism	77.78	35 of 45
[Ref.: #66794]	vitamin B1 metabolism	76.92	10 of 13
[Ref.: #66794]	urea cycle	76.92	10 of 13
[Ref.: #66794]	glycolysis	76.47	13 of 17
[Ref.: #66794]	non-pathway related	76.32	29 of 38
[Ref.: #66794]	butanoate fermentation	75	3 of 4
[Ref.: #66794]	glycogen biosynthesis	75	3 of 4
[Ref.: #66794]	isoleucine metabolism	75	6 of 8
[Ref.: #66794]	lactate fermentation	75	3 of 4
[Ref.: #66794]	toluene degradation	75	3 of 4
[Ref.: #66794]	acetate fermentation	75	3 of 4
[Ref.: #66794]	cyclohexanol degradation	75	3 of 4
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
[Ref.: #66794]	dTDPLrhamnose biosynthesis	75	6 of 8
[Ref.: #66794]	sulfopterin metabolism	75	3 of 4
[Ref.: #66794]	lipid metabolism	74.19	23 of 31
[Ref.: #66794]	oxidative phosphorylation	73.63	67 of 91
[Ref.: #66794]	proline metabolism	72.73	8 of 11
[Ref.: #66794]	cysteine metabolism	72.22	13 of 18
[Ref.: #66794]	degradation of sugar acids	72	18 of 25
[Ref.: #66794]	aclacinomycin biosynthesis	71.43	5 of 7
[Ref.: #66794]	ubiquinone biosynthesis	71.43	5 of 7
[Ref.: #66794]	degradation of pentoses	71.43	20 of 28
[Ref.: #66794]	tyrosine metabolism	71.43	10 of 14
[Ref.: #66794]	4-hydroxyphenylacetate degradation	70	7 of 10
[Ref.: #66794]	coenzyme M biosynthesis	70	7 of 10
[Ref.: #66794]	histidine metabolism	68.97	20 of 29
[Ref.: #66794]	alanine metabolism	68.97	20 of 29
[Ref.: #66794]	degradation of sugar alcohols	68.75	11 of 16
[Ref.: #66794]	androgen and estrogen metabolism	68.75	11 of 16
[Ref.: #66794]	methane metabolism	66.67	2 of 3
[Ref.: #66794]	d-mannose degradation	66.67	6 of 9
[Ref.: #66794]	acetoin degradation	66.67	2 of 3
[Ref.: #66794]	sulfoquinovose degradation	66.67	2 of 3
[Ref.: #66794]	isoprenoid biosynthesis	65.38	17 of 26
[Ref.: #66794]	metabolism of disaccharids	63.64	7 of 11
[Ref.: #66794]	d-xylose degradation	63.64	7 of 11
[Ref.: #66794]	carotenoid biosynthesis	63.64	14 of 22
[Ref.: #66794]	sulfate reduction	61.54	8 of 13
[Ref.: #66794]	metabolism of amino sugars and derivatives	60	3 of 5
[Ref.: #66794]	lipoate biosynthesis	60	3 of 5
[Ref.: #66794]	lysine metabolism	59.52	25 of 42
[Ref.: #66794]	arginine metabolism	58.33	14 of 24
[Ref.: #66794]	degradation of hexoses	55.56	10 of 18
[Ref.: #66794]	daunorubicin biosynthesis	55.56	5 of 9
[Ref.: #66794]	glycine metabolism	50	5 of 10
[Ref.: #66794]	sphingosine metabolism	50	3 of 6
[Ref.: #66794]	dolichol and dolichyl phosphate biosynthesis	50	1 of 2
[Ref.: #66794]	selenocysteine biosynthesis	50	3 of 6
[Ref.: #66794]	ribulose monophosphate pathway	50	1 of 2
[Ref.: #66794]	aminopropanol phosphate biosynthesis	50	1 of 2
[Ref.: #66794]	quinate degradation	50	1 of 2
[Ref.: #66794]	vitamin E metabolism	50	2 of 4
[Ref.: #66794]	carnitine metabolism	50	4 of 8
[Ref.: #66794]	mannosylglycerate biosynthesis	50	1 of 2
[Ref.: #66794]	pantothenate biosynthesis	50	3 of 6
[Ref.: #66794]	bile acid biosynthesis, neutral pathway	47.06	8 of 17
[Ref.: #66794]	phosphatidylethanolamine bioynthesis	46.15	6 of 13
[Ref.: #66794]	vitamin B6 metabolism	45.45	5 of 11
[Ref.: #66794]	cholesterol biosynthesis	45.45	5 of 11
[Ref.: #66794]	nitrate assimilation	44.44	4 of 9
[Ref.: #66794]	lipid A biosynthesis	44.44	4 of 9
[Ref.: #66794]	allantoin degradation	44.44	4 of 9
[Ref.: #66794]	benzoyl-CoA degradation	42.86	3 of 7
[Ref.: #66794]	creatinine degradation	40	2 of 5
[Ref.: #66794]	arachidonate biosynthesis	40	2 of 5
[Ref.: #66794]	ascorbate metabolism	36.36	8 of 22
[Ref.: #66794]	polyamine pathway	34.78	8 of 23
[Ref.: #66794]	chlorophyll metabolism	33.33	6 of 18
[Ref.: #66794]	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
[Ref.: #66794]	acetyl CoA biosynthesis	33.33	1 of 3
[Ref.: #66794]	arachidonic acid metabolism	27.78	5 of 18
[Ref.: #66794]	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
[Ref.: #66794]	catecholamine biosynthesis	25	1 of 4
[Ref.: #66794]	methanogenesis from CO2	25	3 of 12
		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.: #130]	Sample type/isolated from	phosphate buffer
* marker position based on {}

Isolation sources categories

#Engineered

#Laboratory

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence EU928972 (>99% sequence identity) for Pseudonocardia from Microbeatlas

Aquatic Samples	61
Soil Samples	68
Animal Samples	190
Plant Samples	20
Total Samples	339

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

[Ref.: #130]	Pathogenicity (human)	yes, in single cases
[Ref.: #130]	Biosafety level	1	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.: #20218]	Pseudonocardia autotrophica 16S ribosomal RNA gene, partial sequence	EU928972	1380	ENA	2074 tax ID	*
[Ref.: #20218]	Amycolata autotrophica (Nocardia a.) partial 16S rRNA	X54288	1332	ENA	2074 tax ID	*
[Ref.: #20218]	Pseudonocardia autotrophica 16S rRNA gene, strain IMSNU 20050T	AJ252824	1512	ENA	2074 tax ID	*

Genome sequence information:

Only first 5 entries are displayed. Click here to see all.

	Sequence accession description	Seq. accession number	Assembly level (bp)	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Pseudonocardia autotrophica NBRC 12743	GCA_003945385	complete	GenBank	2074 tax ID	*
[Ref.: #66792]	Pseudonocardia autotrophica strain DSM 535	2074.6	wgs	PATRIC	2074 tax ID	*
[Ref.: #66792]	Pseudonocardia autotrophica strain DSM 535	2074.12	wgs	PATRIC	2074 tax ID	*
[Ref.: #66792]	Pseudonocardia autotrophica strain NBRC 12743	2074.11	wgs	PATRIC	2074 tax ID	*
[Ref.: #66792]	Pseudonocardia autotrophica NBRC 12743	2856823606	complete	JGI IMG/M	2074 tax ID	*
[Ref.: #66792]	Pseudonocardia autotrophica DSM 535	2756170255	draft	JGI IMG/M	2074 tax ID	*

[Ref.: #67770]	GC-content	73 mol%	genome sequence analysis
[Ref.: #67770]	GC-content	72 mol%	thermal denaturation, midpoint method (Tm)
[Ref.: #67770]	GC-content	70 mol%	thermal denaturation, midpoint method (Tm)

Availability in culture collections External links

[Ref.: #130]

Culture collection no.

DSM 535, ATCC 19727, CBS 466.68, DSM 40011, DSM 43210, IFO 12743, ISP 5011, KCC S-0348, NBRC 12743, RIA 1008, JCM 4348, BCRC 12444, CCM 2750, CECT 3301, CGMCC 4.1211, CGMCC 4.1297, CIP 107114, IMET 7646, IMSNU 11005, IMSNU 20050, KCTC 1816, KCTC 9564, KCTC 9574, NCIMB 9810, NRRL B-11275, VKM Ac-941

[Ref.: #20218]

Associated Passport(s) in StrainInfo

100393, 100389, 229116, 100394, 100395, 100396, 100390, 100399, 334371, 100402

Literature:

Only first 10 entries are displayed. Click here to see all.

Topic	Title	Authors	Journal	DOI	Year
Metabolism	A gene cluster for the fatty acid catabolism from Pseudonocardia autotrophica BCRC12444.	Chen CH, Cheng JC, Cho YC, Hsu WH	Biochem Biophys Res Commun	10.1016/j.bbrc.2005.02.052	2005	*
Phylogeny	Pseudonocardia endophytica sp. nov., isolated from the pharmaceutical plant Lobelia clavata.	Chen HH, Qin S, Li J, Zhang YQ, Xu LH, Jiang CL, Kim CJ, Li WJ	Int J Syst Evol Microbiol	10.1099/ijs.0.64740-0	2009	*
Enzymology	Purification, characterization, and directed evolution study of a vitamin D3 hydroxylase from Pseudonocardia autotrophica.	Fujii Y, Kabumoto H, Nishimura K, Fujii T, Yanai S, Takeda K, Tamura N, Arisawa A, Tamura T	Biochem Biophys Res Commun	10.1016/j.bbrc.2009.05.033	2009	*
Enzymology	Construction of a novel expression vector in Pseudonocardia autotrophica and its application to efficient biotransformation of compactin to pravastatin, a specific HMG-CoA reductase inhibitor.	Fujii Y, Norihisa K, Fujii T, Aritoku Y, Kagawa Y, Sallam KI, Johdo O, Arisawa A, Tamura T	Biochem Biophys Res Commun	10.1016/j.bbrc.2010.12.013	2010	*
Phylogeny	Pseudonocardia nantongensis sp. nov., a novel endophytic actinomycete isolated from the coastal halophyte Tamarix chinensis Lour.	Xing K, Qin S, Bian GK, Zhang YJ, Zhang WD, Dai CC, Liu CH, Li WJ, Jiang JH	Antonie Van Leeuwenhoek	10.1007/s10482-012-9764-5	2012	*
Genetics	Draft Genome Sequences of Three Actinobacteria Strains Presenting New Candidate Organisms with High Potentials for Specific P450 Cytochromes.	Grumaz C, Vainshtein Y, Kirstahler P, Luetz S, Kittelmann M, Schroer K, Eggimann FK, Czaja R, Vogel A, Hilberath T, Worsch A, Girhard M, Urlacher VB, Sandberg M, Sohn K	Genome Announc	10.1128/genomeA.00532-17	2017	*
Genetics	Complete Genome Sequence of an Efficient Vitamin D3-Hydroxylating Bacterium, Pseudonocardia autotrophica NBRC 12743.	Yoshida K, Yasutake Y, Tamura T	Microbiol Resour Announc	10.1128/MRA.01105-18	2018	*

References

#130	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 535

#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 )

#20218

Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.: StrainInfo introduces electronic passports for microorganisms.. Syst Appl Microbiol. 37: 42 - 50 2014 ( DOI 10.1016/j.syapm.2013.11.002 , PubMed 24321274 )

#33085 ; Curators of the CIP;

#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;

#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 .

#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) .

* These data were automatically processed and therefore are not curated

Change proposal

You found an error in BacDive? Please tell us about it!

Note that changes will be reviewed and judged. If your changes are legitimate, changes will occur within the next BacDive update. Only proposed changes supported by the according reference will be reviewed. The BacDive team reserves the right to reject proposed changes.

Search for species Pseudonocardia autotrophica in external resources:
SILVA
BRENDA
PANGAEA
StrainInfo
GBIF