Cite this strain

Albimonas pacifica (KACC 16527, CGMCC 1.11030, P-50-3)

Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 133988

Type strain

Strain Designation P-50-3

Culture col. no. KACC 16527 CGMCC 1.11030 P-50-3

NCBI tax ID(s) 1114924

Special Collections Literature strains

Links

Name and taxonomic classification

Albimonas pacifica P-50-3 is an aerobe, Gram-negative, rod-shaped bacterium that was isolated from seawater.

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

Culture Collection Numbers

KACC 16527 CGMCC 1.11030 P-50-3

Last LPSN update 2024-12-09 10:49:19

Domain Bacteria

Phylum Pseudomonadota

Class Alphaproteobacteria

Order Rhodobacterales

Family Paracoccaceae

Genus Albimonas

Species Albimonas pacifica

Full scientific name Albimonas pacifica Li et al. 2013

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Motility
31012	negative	3 µm	1 µm	rod-shaped
125438	negative

Pigmentation

31012

Productionno

Culture and growth conditions

Culture temp

@ref	Growth	Type	Temperature (°C)
31012	positive	growth	10-40
31012	positive	optimum	30

Culture pH

@ref	Ability	Type	PH
31012	positive	optimum	7.5
31012	positive	growth	6.0-9.5

Physiology and metabolism

Halophily

@ref	Salt	Growth	Tested relation	Concentration
31012	NaCl	positive	growth	0-12 %
31012	NaCl	positive	optimum	2 %

Spore formation

@ref	Spore formation
31012
125438

Enzymes

@ref	Value	Activity	Ec
31012	acid phosphatase	+	3.1.3.2
31012	alkaline phosphatase	+	3.1.3.1

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
31012	17632 ChEBI	nitrate	+	reduction

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	butanoate fermentation	100	4 of 4
66794	reductive acetyl coenzyme A pathway	100	7 of 7
66794	cis-vaccenate biosynthesis	100	2 of 2
66794	Entner Doudoroff pathway	100	10 of 10
66794	ppGpp biosynthesis	100	4 of 4
66794	threonine metabolism	100	10 of 10
66794	hydrogen production	100	5 of 5
66794	ethanol fermentation	100	2 of 2
66794	propanol degradation	100	7 of 7
66794	L-lactaldehyde degradation	100	3 of 3
66794	valine metabolism	100	9 of 9
66794	biotin biosynthesis	100	4 of 4
66794	palmitate biosynthesis	100	22 of 22
66794	methylglyoxal degradation	100	5 of 5
66794	degradation of aromatic, nitrogen containing compounds	100	12 of 12
66794	lipoate biosynthesis	100	5 of 5
66794	cyanate degradation	100	3 of 3
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	C4 and CAM-carbon fixation	100	8 of 8
66794	suberin monomers biosynthesis	100	2 of 2
66794	folate polyglutamylation	100	1 of 1
66794	ceramide biosynthesis	100	1 of 1
66794	coenzyme A metabolism	100	4 of 4
66794	formaldehyde oxidation	100	3 of 3
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	gluconeogenesis	100	8 of 8
66794	adipate degradation	100	2 of 2
66794	phenylalanine metabolism	92.31	12 of 13
66794	vitamin B1 metabolism	92.31	12 of 13
66794	CO2 fixation in Crenarchaeota	88.89	8 of 9
66794	4-hydroxymandelate degradation	88.89	8 of 9
66794	serine metabolism	88.89	8 of 9
66794	aspartate and asparagine metabolism	88.89	8 of 9
66794	molybdenum cofactor biosynthesis	88.89	8 of 9
66794	chorismate metabolism	88.89	8 of 9
66794	flavin biosynthesis	86.67	13 of 15
66794	glutathione metabolism	85.71	12 of 14
66794	citric acid cycle	85.71	12 of 14
66794	glutamate and glutamine metabolism	85.71	24 of 28
66794	leucine metabolism	84.62	11 of 13
66794	NAD metabolism	83.33	15 of 18
66794	alanine metabolism	82.76	24 of 29
66794	vitamin B12 metabolism	82.35	28 of 34
66794	proline metabolism	81.82	9 of 11
66794	purine metabolism	80.85	76 of 94
66794	phenylacetate degradation (aerobic)	80	4 of 5
66794	cellulose degradation	80	4 of 5
66794	glycogen metabolism	80	4 of 5
66794	ethylmalonyl-CoA pathway	80	4 of 5
66794	propionate fermentation	80	8 of 10
66794	gallate degradation	80	4 of 5
66794	peptidoglycan biosynthesis	80	12 of 15
66794	photosynthesis	78.57	11 of 14
66794	heme metabolism	78.57	11 of 14
66794	pyrimidine metabolism	77.78	35 of 45
66794	lipid A biosynthesis	77.78	7 of 9
66794	d-mannose degradation	77.78	7 of 9
66794	allantoin degradation	77.78	7 of 9
66794	glycolysis	76.47	13 of 17
66794	toluene degradation	75	3 of 4
66794	acetate fermentation	75	3 of 4
66794	CMP-KDO biosynthesis	75	3 of 4
66794	sulfopterin metabolism	75	3 of 4
66794	glycogen biosynthesis	75	3 of 4
66794	isoleucine metabolism	75	6 of 8
66794	tryptophan metabolism	73.68	28 of 38
66794	methionine metabolism	73.08	19 of 26
66794	vitamin B6 metabolism	72.73	8 of 11
66794	pentose phosphate pathway	72.73	8 of 11
66794	cardiolipin biosynthesis	71.43	5 of 7
66794	oxidative phosphorylation	71.43	65 of 91
66794	ubiquinone biosynthesis	71.43	5 of 7
66794	arginine metabolism	70.83	17 of 24
66794	urea cycle	69.23	9 of 13
66794	degradation of sugar alcohols	68.75	11 of 16
66794	lipid metabolism	67.74	21 of 31
66794	IAA biosynthesis	66.67	2 of 3
66794	3-phenylpropionate degradation	66.67	10 of 15
66794	acetyl CoA biosynthesis	66.67	2 of 3
66794	enterobactin biosynthesis	66.67	2 of 3
66794	octane oxidation	66.67	2 of 3
66794	methane metabolism	66.67	2 of 3
66794	acetoin degradation	66.67	2 of 3
66794	glycolate and glyoxylate degradation	66.67	4 of 6
66794	non-pathway related	65.79	25 of 38
66794	bile acid biosynthesis, neutral pathway	64.71	11 of 17
66794	tetrahydrofolate metabolism	64.29	9 of 14
66794	tyrosine metabolism	64.29	9 of 14
66794	dTDPLrhamnose biosynthesis	62.5	5 of 8
66794	ketogluconate metabolism	62.5	5 of 8
66794	lysine metabolism	61.9	26 of 42
66794	isoprenoid biosynthesis	61.54	16 of 26
66794	chlorophyll metabolism	61.11	11 of 18
66794	cysteine metabolism	61.11	11 of 18
66794	degradation of pentoses	60.71	17 of 28
66794	degradation of sugar acids	60	15 of 25
66794	myo-inositol biosynthesis	60	6 of 10
66794	starch degradation	60	6 of 10
66794	histidine metabolism	58.62	17 of 29
66794	nitrate assimilation	55.56	5 of 9
66794	phenol degradation	55	11 of 20
66794	sulfate reduction	53.85	7 of 13
66794	pantothenate biosynthesis	50	3 of 6
66794	cyclohexanol degradation	50	2 of 4
66794	carnitine metabolism	50	4 of 8
66794	ribulose monophosphate pathway	50	1 of 2
66794	aminopropanol phosphate biosynthesis	50	1 of 2
66794	arachidonic acid metabolism	50	9 of 18
66794	selenocysteine biosynthesis	50	3 of 6
66794	androgen and estrogen metabolism	50	8 of 16
66794	glycine metabolism	50	5 of 10
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	50	4 of 8
66794	phenylmercury acetate degradation	50	1 of 2
66794	quinate degradation	50	1 of 2
66794	resorcinol degradation	50	1 of 2
66794	metabolism of disaccharids	45.45	5 of 11
66794	degradation of hexoses	44.44	8 of 18
66794	polyamine pathway	43.48	10 of 23
66794	ascorbate metabolism	40.91	9 of 22
66794	creatinine degradation	40	2 of 5
66794	glycine betaine biosynthesis	40	2 of 5
66794	4-hydroxyphenylacetate degradation	40	4 of 10
66794	3-chlorocatechol degradation	40	2 of 5
66794	factor 420 biosynthesis	40	2 of 5
66794	coenzyme M biosynthesis	40	4 of 10
66794	arachidonate biosynthesis	40	2 of 5
66794	vitamin K metabolism	40	2 of 5
66794	sulfoquinovose degradation	33.33	1 of 3
66794	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
66794	methanogenesis from CO2	33.33	4 of 12
66794	sphingosine metabolism	33.33	2 of 6
66794	phosphatidylethanolamine bioynthesis	30.77	4 of 13
66794	aclacinomycin biosynthesis	28.57	2 of 7
66794	benzoyl-CoA degradation	28.57	2 of 7
66794	cholesterol biosynthesis	27.27	3 of 11
66794	d-xylose degradation	27.27	3 of 11
66794	alginate biosynthesis	25	1 of 4
66794	lactate fermentation	25	1 of 4
66794	vitamin E metabolism	25	1 of 4
66794	phenylpropanoid biosynthesis	23.08	3 of 13
66794	carotenoid biosynthesis	22.73	5 of 22

Oxygen tolerance

@ref	Oxygen tolerance
31012	aerobe
125439	obligate aerobe

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Aquatic	#Marine

Isolation

31012

Sample typeseawater

Taxonmaps

69479

Global distribution of 16S sequence JN837486 (>99% sequence identity) for Albimonas pacifica subclade from Microbeatlas

Aquatic Samples	4327
Soil Samples	923
Animal Samples	333
Plant Samples	145
Total Samples	5728

Safety information

Sequence information

GC content

31012

GC-content (mol%)69

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
31012	Albimonas pacifica strain P-50-3 16S ribosomal RNA gene, partial sequence	JN837486	1427		1114924

Genome sequences

@ref	Description	Accession	Assembly level	Database	NCBI tax ID
66792	Albimonas pacifica CGMCC 1.11030	GCA_900113695	scaffold		1114924
66792	Albimonas pacifica strain CGMCC 1.11030	1114924.3	wgs	PATRIC	1114924
66792	Albimonas pacifica CGMCC 1.11030	2667527406	draft	JGI IMG/M	1114924

Genome-based predictions

Predictions

Predictions from Diaspora project based on:
Albimonas pacifica CGMCC 1.11030
NCBI: GCA_900113695

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	85.50	no
125439	motility	BacteriaNetⓘ	yes	59.90	no
125439	gram_stain	BacteriaNetⓘ	negative	84.30	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	93.50	no

Predictions from Diaspora project based on:
Albimonas pacifica CGMCC 1.11030
NCBI: GCA_900113695.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	98.50	yes
125438	anaerobic	anaerobicⓘ	no	93.42	yes
125438	aerobic	aerobicⓘ	yes	81.60	no
125438	spore-forming	spore-formingⓘ	no	92.95	yes
125438	thermophilic	thermophileⓘ	no	99.72	yes
125438	flagellated	motile2+ⓘ	yes	67.71	no

External links

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Albimonas pacifica sp. nov., isolated from seawater of the Pacific, and emended description of the genus Albimonas.	Li GW, Zhang XY, Wang CS, Zhang YJ, Xu XW, Liu C, Li H, Liu A, Xu Z, Song XY, Chen XL, Zhou BC, Zhang YZ	Int J Syst Evol Microbiol	10.1099/ijs.0.049742-0	2013

Culture collection no.

Culture collection no.
KACC 16527
CGMCC 1.11030
P-50-3

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 )
#31012	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 #27342 (see below)
#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 )
#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 .
#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 .

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Albimonas pacifica (KACC 16527, CGMCC 1.11030, P-50-3)

Name and taxonomic classification

Culture Collection Numbers

Morphology

Cell morphology

Pigmentation

Culture and growth conditions

Culture temp

Culture pH

Physiology and metabolism

Halophily

Spore formation

Enzymes

Metabolite utilization

Pathway annotation

Oxygen tolerance

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Safety information

Sequence information

GC content

16S sequences

Genome sequences

Genome-based predictions

Predictions

External links

Literature

Culture collection no.

References

BacDive

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