Cite this strain

"Halopseudomonas yangmingensis" (DSM 24213, CRS 1)

BacDive ID 130581

Type strain

Culture col. no. DSM 24213 CRS 1

NCBI tax ID(s) 1720063

Special Collections DSMZ

Links

"Halopseudomonas yangmingensis" DSM 24213 is a mesophilic prokaryote that was isolated from water and soil from hot sulfur spring.

mesophilic genome sequence

Name and taxonomic classification

SI-ID 406385

BCRC 80299,DSM 24213

@ref 20215

Last LPSN update 2025-12-16 10:01:02

Domain Pseudomonadati

Phylum Pseudomonadota

Class Gammaproteobacteria

Order Pseudomonadales

Family Pseudomonadaceae

Genus Halopseudomonas

Species "Halopseudomonas yangmingensis"

Full scientific name Halopseudomonas yangmingensis (Wong and Lee 2014) Girard et al. 2023

Synonyms (1)

"Pseudomonas yangmingensis"

Morphology

Cell morphology

@ref	Gram stain	Confidence
125438	negative	98.494
125439	negative	99.9
125439		94.4

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
22031	NSC3-MEDIUM WITH ACETATE (DSMZ Medium 1246)		Medium recipe at MediaDive	Name: NSC3-MEDIUM WITH ACETATE (DSMZ Medium 1246) Composition: Agar 15.0 g/l NaCl 10.0 g/l NaHCO3 1.5 g/l Na2S x 9 H2O 1.0 g/l Na-acetate 0.44 g/l NH4Cl 0.25 g/l K2HPO4 0.25 g/l EDTA 0.0005 g/l FeSO4 x 7 H2O 0.0002 g/l H3BO3 3e-05 g/l CoCl2 x 6 H2O 2e-05 g/l ZnSO4 x 7 H2O 1e-05 g/l MnCl2 x 4 H2O 3e-06 g/l Na2MoO4 x 2 H2O 3e-06 g/l NiCl2 x 6 H2O 2e-06 g/l CuCl2 x 2 H2O 1e-06 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
22031	positive	growth	37	mesophilic

Physiology and metabolism

Spore formation

@ref	Spore formation	Confidence
125438		93.226
125439		99.9

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	denitrification	100	2 of 2
66794	biotin biosynthesis	100	4 of 4
66794	coenzyme A metabolism	100	4 of 4
66794	formaldehyde oxidation	100	3 of 3
66794	gluconeogenesis	100	8 of 8
66794	L-lactaldehyde degradation	100	3 of 3
66794	ethanol fermentation	100	2 of 2
66794	cis-vaccenate biosynthesis	100	2 of 2
66794	adipate degradation	100	2 of 2
66794	ubiquinone biosynthesis	100	7 of 7
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	palmitate biosynthesis	100	22 of 22
66794	valine metabolism	100	9 of 9
66794	ppGpp biosynthesis	100	4 of 4
66794	folate polyglutamylation	100	1 of 1
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	suberin monomers biosynthesis	100	2 of 2
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	tetrahydrofolate metabolism	92.86	13 of 14
66794	phenylalanine metabolism	92.31	12 of 13
66794	threonine metabolism	90	9 of 10
66794	chorismate metabolism	88.89	8 of 9
66794	isoleucine metabolism	87.5	7 of 8
66794	glutamate and glutamine metabolism	85.71	24 of 28
66794	reductive acetyl coenzyme A pathway	85.71	6 of 7
66794	leucine metabolism	84.62	11 of 13
66794	NAD metabolism	83.33	15 of 18
66794	vitamin B6 metabolism	81.82	9 of 11
66794	methionine metabolism	80.77	21 of 26
66794	methylglyoxal degradation	80	4 of 5
66794	Entner Doudoroff pathway	80	8 of 10
66794	peptidoglycan biosynthesis	80	12 of 15
66794	phenylacetate degradation (aerobic)	80	4 of 5
66794	photosynthesis	78.57	11 of 14
66794	heme metabolism	78.57	11 of 14
66794	lipid A biosynthesis	77.78	7 of 9
66794	serine metabolism	77.78	7 of 9
66794	molybdenum cofactor biosynthesis	77.78	7 of 9
66794	vitamin B1 metabolism	76.92	10 of 13
66794	butanoate fermentation	75	3 of 4
66794	CMP-KDO biosynthesis	75	3 of 4
66794	acetate fermentation	75	3 of 4
66794	flavin biosynthesis	73.33	11 of 15
66794	alanine metabolism	72.41	21 of 29
66794	cardiolipin biosynthesis	71.43	5 of 7
66794	purine metabolism	69.15	65 of 94
66794	cysteine metabolism	66.67	12 of 18
66794	CO2 fixation in Crenarchaeota	66.67	6 of 9
66794	octane oxidation	66.67	2 of 3
66794	nitrate assimilation	66.67	6 of 9
66794	selenocysteine biosynthesis	66.67	4 of 6
66794	IAA biosynthesis	66.67	2 of 3
66794	acetoin degradation	66.67	2 of 3
66794	methane metabolism	66.67	2 of 3
66794	glycolysis	64.71	11 of 17
66794	glutathione metabolism	64.29	9 of 14
66794	proline metabolism	63.64	7 of 11
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	62.5	5 of 8
66794	C4 and CAM-carbon fixation	62.5	5 of 8
66794	pyrimidine metabolism	62.22	28 of 45
66794	sulfate reduction	61.54	8 of 13
66794	lipid metabolism	61.29	19 of 31
66794	polyamine pathway	60.87	14 of 23
66794	factor 420 biosynthesis	60	3 of 5
66794	cellulose degradation	60	3 of 5
66794	propionate fermentation	60	6 of 10
66794	non-pathway related	57.89	22 of 38
66794	citric acid cycle	57.14	8 of 14
66794	d-mannose degradation	55.56	5 of 9
66794	aspartate and asparagine metabolism	55.56	5 of 9
66794	tryptophan metabolism	55.26	21 of 38
66794	lysine metabolism	54.76	23 of 42
66794	pentose phosphate pathway	54.55	6 of 11
66794	isoprenoid biosynthesis	53.85	14 of 26
66794	urea cycle	53.85	7 of 13
66794	histidine metabolism	51.72	15 of 29
66794	glycogen biosynthesis	50	2 of 4
66794	phenylmercury acetate degradation	50	1 of 2
66794	pantothenate biosynthesis	50	3 of 6
66794	mannosylglycerate biosynthesis	50	1 of 2
66794	glycolate and glyoxylate degradation	50	3 of 6
66794	glycine metabolism	50	5 of 10
66794	arginine metabolism	50	12 of 24
66794	sulfopterin metabolism	50	2 of 4
66794	toluene degradation	50	2 of 4
66794	oxidative phosphorylation	48.35	44 of 91
66794	propanol degradation	42.86	3 of 7
66794	degradation of aromatic, nitrogen containing compounds	41.67	5 of 12
66794	lipoate biosynthesis	40	2 of 5
66794	metabolism of amino sugars and derivatives	40	2 of 5
66794	glycogen metabolism	40	2 of 5
66794	arachidonate biosynthesis	40	2 of 5
66794	arachidonic acid metabolism	38.89	7 of 18
66794	degradation of hexoses	38.89	7 of 18
66794	phosphatidylethanolamine bioynthesis	38.46	5 of 13
66794	ketogluconate metabolism	37.5	3 of 8
66794	dTDPLrhamnose biosynthesis	37.5	3 of 8
66794	carnitine metabolism	37.5	3 of 8
66794	tyrosine metabolism	35.71	5 of 14
66794	vitamin B12 metabolism	35.29	12 of 34
66794	cyanate degradation	33.33	1 of 3
66794	acetyl CoA biosynthesis	33.33	1 of 3
66794	3-phenylpropionate degradation	33.33	5 of 15
66794	4-hydroxymandelate degradation	33.33	3 of 9
66794	sphingosine metabolism	33.33	2 of 6
66794	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
66794	degradation of pentoses	32.14	9 of 28
66794	androgen and estrogen metabolism	31.25	5 of 16
66794	benzoyl-CoA degradation	28.57	2 of 7
66794	cyclohexanol degradation	25	1 of 4
66794	lactate fermentation	25	1 of 4
66794	alginate biosynthesis	25	1 of 4
66794	degradation of sugar alcohols	25	4 of 16
66794	carotenoid biosynthesis	22.73	5 of 22

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Aquatic	#Thermal spring
#Environmental	#Terrestrial	#Soil
#Condition	#Sulfuric	-
#Condition	#Thermophilic (>45°C)	-

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
22031	water and soil from hot sulfur spring	Yang-Ming Mountain, New Taipeh City	Taiwan, Province of China	TWN	Asia

Interaction and safety

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	IMG-taxon 2663762769 annotated assembly for Halopseudomonas yangmingensis DSM 24213	scaffold	GCA_900114825	1720063.3	2663762769	1720063	62.27

Genome browser: GCA_900114825

GC content

22031

GC-content (mol%)63.7

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Halopseudomonas yangmingensis DSM 24213
NCBI: GCA_900114825

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	99.90	no
125439	motility	BacteriaNetⓘ	yes	94.40	no
125439	gram_stain	BacteriaNetⓘ	negative	99.90	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	80.60	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Pseudomonas yangmingensis DSM 24213
NCBI: GCA_900114825.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	98.49	no
125438	anaerobic	anaerobicⓘ	no	90.72	no
125438	aerobic	aerobicⓘ	yes	75.25	no
125438	spore-forming	spore-formingⓘ	no	93.23	no
125438	thermophilic	thermophileⓘ	no	95.94	yes
125438	flagellated	motile2+ⓘ	yes	85.92	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Pseudomonas yangmingensis sp. nov., an alkaliphilic denitrifying species isolated from a hot spring.	Wong BT, Lee DJ	J Biosci Bioeng	10.1016/j.jbiosc.2013.06.006	2013

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 )
#22031	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 24213
#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 )
#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

"Halopseudomonas yangmingensis" (DSM 24213, CRS 1)

Name and taxonomic classification

Morphology

Cell morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Spore formation

Pathway annotation

Isolation, sampling and environmental information

Isolation source categories

Isolation

Interaction and safety

Sequence information

Genome sequences

Genome browser: GCA_900114825

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

Help

Social Media