Paracoccus tibetensis (CGMCC 1.8925, NBRC 105667, Tibet-S9a3)

Name: Paracoccus tibetensis (CGMCC 1.8925, NBRC 105667, Tibet-S9a3)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 133854

Type strain

Strain Designation Tibet-S9a3

Culture col. no. CGMCC 1.8925 NBRC 105667 Tibet-S9a3

NCBI tax ID(s) 336292

Special Collections Literature strains

Links

Paracoccus tibetensis Tibet-S9a3 is an aerobe, Gram-negative, rod-shaped bacterium that was isolated from soil.

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

Name and taxonomic classification

SI-ID 133481

NBRC 105667

@ref 20215

Last LPSN update 2026-05-29 08:38:11

Domain Bacteria

Phylum Pseudomonadota

Class Alphaproteobacteria

Order Rhodobacterales

Family Paracoccaceae

Genus Paracoccus

Species Paracoccus tibetensis

Full scientific name Paracoccus tibetensis Zhu et al. 2013

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Confidence
30682	negative	1 µm	0.7 µm	rod-shaped
125439	negative				93.742
125438	negative				97.482

Pigmentation

30682

Productionyes

Culture and growth conditions

Culture temp

@ref	Growth	Type	Temperature (°C)
30682	positive	growth	10-35
30682	positive	optimum	28

Culture pH

@ref	Ability	Type	PH	PH range
30682	positive	optimum	9.5
30682	positive	growth	8.5-13	alkaliphile

Physiology and metabolism

Oxygen tolerance

30682

Oxygen toleranceaerobe

Spore formation

@ref	Spore formation	Confidence
30682
125439		99.066

Halophily

@ref	Salt	Growth	Tested relation	Concentration
30682	NaCl	positive	growth	0-5 %

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
30682	28644 ChEBI	2-oxopentanoate	+	carbon source
30682	30089 ChEBI	acetate	+	carbon source
30682	16449 ChEBI	alanine	+	carbon source
30682	40585 ChEBI	alpha-cyclodextrin	+	carbon source
30682	22599 ChEBI	arabinose	+	carbon source
30682	22653 ChEBI	asparagine	+	carbon source
30682	35391 ChEBI	aspartate	+	carbon source
30682	16947 ChEBI	citrate	+	carbon source
30682	4853 ChEBI	esculin	+	hydrolysis
30682	15740 ChEBI	formate	+	carbon source
30682	28757 ChEBI	fructose	+	carbon source
30682	33984 ChEBI	fucose	+	carbon source
30682	24175 ChEBI	galacturonate	+	carbon source
30682	5417 ChEBI	glucosamine	+	carbon source
30682	17234 ChEBI	glucose	+	carbon source
30682	32323 ChEBI	glucuronamide	+	carbon source
30682	29987 ChEBI	glutamate	+	carbon source
30682	17754 ChEBI	glycerol	+	carbon source
30682	28087 ChEBI	glycogen	+	carbon source
30682	17596 ChEBI	inosine	+	carbon source
30682	21217 ChEBI	L-alaninamide	+	carbon source
30682	24996 ChEBI	lactate	+	carbon source
30682	25115 ChEBI	malate	+	carbon source
30682	17306 ChEBI	maltose	+	carbon source
30682	29864 ChEBI	mannitol	+	carbon source
30682	51850 ChEBI	methyl pyruvate	+	carbon source
30682	26271 ChEBI	proline	+	carbon source
30682	17272 ChEBI	propionate	+	carbon source
30682	16634 ChEBI	raffinose	+	carbon source
30682	17822 ChEBI	serine	+	carbon source
30682	30911 ChEBI	sorbitol	+	carbon source
30682	30031 ChEBI	succinate	+	carbon source
30682	17992 ChEBI	sucrose	+	carbon source
30682	26986 ChEBI	threonine	+	carbon source
30682	27082 ChEBI	trehalose	+	carbon source
30682	16704 ChEBI	uridine	+	carbon source
30682	17151 ChEBI	xylitol	+	carbon source

Enzymes

@ref	Value	Activity	Ec
30682	acid phosphatase	+	3.1.3.2
30682	alkaline phosphatase	+	3.1.3.1
30682	catalase	+	1.11.1.6
30682	gelatinase	+

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	palmitate biosynthesis	100	22 of 22
66794	C4 and CAM-carbon fixation	100	8 of 8
66794	cis-vaccenate biosynthesis	100	2 of 2
66794	quinate degradation	100	2 of 2
66794	CMP-KDO biosynthesis	100	4 of 4
66794	methylglyoxal degradation	100	5 of 5
66794	starch degradation	100	10 of 10
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	teichoic acid biosynthesis	100	1 of 1
66794	Entner Doudoroff pathway	100	10 of 10
66794	coenzyme A metabolism	100	4 of 4
66794	formaldehyde oxidation	100	3 of 3
66794	adipate degradation	100	2 of 2
66794	gluconeogenesis	100	8 of 8
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	suberin monomers biosynthesis	100	2 of 2
66794	valine metabolism	100	9 of 9
66794	ppGpp biosynthesis	100	4 of 4
66794	folate polyglutamylation	100	1 of 1
66794	octane oxidation	100	3 of 3
66794	phenylalanine metabolism	92.31	12 of 13
66794	threonine metabolism	90	9 of 10
66794	chorismate metabolism	88.89	8 of 9
66794	molybdenum cofactor biosynthesis	88.89	8 of 9
66794	serine metabolism	88.89	8 of 9
66794	glutathione metabolism	85.71	12 of 14
66794	photosynthesis	85.71	12 of 14
66794	citric acid cycle	85.71	12 of 14
66794	reductive acetyl coenzyme A pathway	85.71	6 of 7
66794	NAD metabolism	83.33	15 of 18
66794	vitamin B12 metabolism	82.35	28 of 34
66794	proline metabolism	81.82	9 of 11
66794	peptidoglycan biosynthesis	80	12 of 15
66794	glutamate and glutamine metabolism	78.57	22 of 28
66794	allantoin degradation	77.78	7 of 9
66794	4-hydroxymandelate degradation	77.78	7 of 9
66794	lipid A biosynthesis	77.78	7 of 9
66794	CO2 fixation in Crenarchaeota	77.78	7 of 9
66794	pyrimidine metabolism	77.78	35 of 45
66794	purine metabolism	77.66	73 of 94
66794	leucine metabolism	76.92	10 of 13
66794	degradation of sugar acids	76	19 of 25
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
66794	ketogluconate metabolism	75	6 of 8
66794	isoleucine metabolism	75	6 of 8
66794	glycogen biosynthesis	75	3 of 4
66794	toluene degradation	75	3 of 4
66794	acetate fermentation	75	3 of 4
66794	pentose phosphate pathway	72.73	8 of 11
66794	alanine metabolism	72.41	21 of 29
66794	ubiquinone biosynthesis	71.43	5 of 7
66794	tyrosine metabolism	71.43	10 of 14
66794	cardiolipin biosynthesis	71.43	5 of 7
66794	tetrahydrofolate metabolism	71.43	10 of 14
66794	tryptophan metabolism	71.05	27 of 38
66794	glycolysis	70.59	12 of 17
66794	propionate fermentation	70	7 of 10
66794	vitamin B1 metabolism	69.23	9 of 13
66794	degradation of sugar alcohols	68.75	11 of 16
66794	non-pathway related	68.42	26 of 38
66794	degradation of pentoses	67.86	19 of 28
66794	oxidative phosphorylation	67.03	61 of 91
66794	arginine metabolism	66.67	16 of 24
66794	d-mannose degradation	66.67	6 of 9
66794	flavin biosynthesis	66.67	10 of 15
66794	methane metabolism	66.67	2 of 3
66794	cyanate degradation	66.67	2 of 3
66794	lysine metabolism	66.67	28 of 42
66794	acetoin degradation	66.67	2 of 3
66794	L-lactaldehyde degradation	66.67	2 of 3
66794	sulfoquinovose degradation	66.67	2 of 3
66794	heme metabolism	64.29	9 of 14
66794	vitamin B6 metabolism	63.64	7 of 11
66794	metabolism of disaccharids	63.64	7 of 11
66794	d-xylose degradation	63.64	7 of 11
66794	dTDPLrhamnose biosynthesis	62.5	5 of 8
66794	urea cycle	61.54	8 of 13
66794	degradation of hexoses	61.11	11 of 18
66794	polyamine pathway	60.87	14 of 23
66794	myo-inositol biosynthesis	60	6 of 10
66794	lipoate biosynthesis	60	3 of 5
66794	phenol degradation	60	12 of 20
66794	3-phenylpropionate degradation	60	9 of 15
66794	glycogen metabolism	60	3 of 5
66794	gallate degradation	60	3 of 5
66794	cellulose degradation	60	3 of 5
66794	lipid metabolism	58.06	18 of 31
66794	isoprenoid biosynthesis	57.69	15 of 26
66794	aspartate and asparagine metabolism	55.56	5 of 9
66794	arachidonic acid metabolism	55.56	10 of 18
66794	histidine metabolism	55.17	16 of 29
66794	methionine metabolism	53.85	14 of 26
66794	kanosamine biosynthesis II	50	1 of 2
66794	aminopropanol phosphate biosynthesis	50	1 of 2
66794	glycolate and glyoxylate degradation	50	3 of 6
66794	sphingosine metabolism	50	3 of 6
66794	ribulose monophosphate pathway	50	1 of 2
66794	sulfopterin metabolism	50	2 of 4
66794	coenzyme M biosynthesis	50	5 of 10
66794	cyclohexanol degradation	50	2 of 4
66794	biotin biosynthesis	50	2 of 4
66794	glycine metabolism	50	5 of 10
66794	butanoate fermentation	50	2 of 4
66794	resorcinol degradation	50	1 of 2
66794	alginate biosynthesis	50	2 of 4
66794	ethanol fermentation	50	1 of 2
66794	cysteine metabolism	50	9 of 18
66794	phenylmercury acetate degradation	50	1 of 2
66794	phosphatidylethanolamine bioynthesis	46.15	6 of 13
66794	sulfate reduction	46.15	6 of 13
66794	nitrate assimilation	44.44	4 of 9
66794	androgen and estrogen metabolism	43.75	7 of 16
66794	propanol degradation	42.86	3 of 7
66794	degradation of aromatic, nitrogen containing compounds	41.67	5 of 12
66794	ascorbate metabolism	40.91	9 of 22
66794	vitamin K metabolism	40	2 of 5
66794	arachidonate biosynthesis	40	2 of 5
66794	factor 420 biosynthesis	40	2 of 5
66794	ethylmalonyl-CoA pathway	40	2 of 5
66794	glycine betaine biosynthesis	40	2 of 5
66794	hydrogen production	40	2 of 5
66794	phenylacetate degradation (aerobic)	40	2 of 5
66794	carnitine metabolism	37.5	3 of 8
66794	IAA biosynthesis	33.33	1 of 3
66794	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
66794	acetyl CoA biosynthesis	33.33	1 of 3
66794	pantothenate biosynthesis	33.33	2 of 6
66794	selenocysteine biosynthesis	33.33	2 of 6
66794	carotenoid biosynthesis	31.82	7 of 22
66794	4-hydroxyphenylacetate degradation	30	3 of 10
66794	mevalonate metabolism	28.57	2 of 7
66794	benzoyl-CoA degradation	28.57	2 of 7
66794	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
66794	catecholamine biosynthesis	25	1 of 4
66794	lactate fermentation	25	1 of 4
66794	bile acid biosynthesis, neutral pathway	23.53	4 of 17

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Terrestrial	#Soil

Isolation

30682

Sample typesoil

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 2596583549 annotated assembly for Paracoccus tibetensis CGMCC 1.8925	scaffold	GCA_900102505	336292.4	2596583549	336292	70.59

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
30682	Paracoccus tibetensis strain Tibet-S9a3 16S ribosomal RNA gene, partial sequence	DQ108402	1449		336292

GC content

30682

GC-content (mol%)69.1

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: IMG-taxon 2596583549 annotated assembly for Paracoccus tibetensis CGMCC 1.8925
NCBI: GCA_900102505

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	aerobe	89.04	no
125439	motility	BacteriaNetⓘ	yes	58.06	no
125439	gram_stain	BacteriaNetⓘ	negative	93.74	no
125439	spore_formation	BacteriaNetⓘ	no	99.07	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Paracoccus tibetensis CGMCC 1.8925
NCBI: GCA_900102505.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	97.48	yes
125438	anaerobic	anaerobicⓘ	no	93.45	no
125438	aerobic	aerobicⓘ	yes	85.16	yes
125438	spore-forming	spore-formingⓘ	no	86.92	yes
125438	thermophilic	thermophileⓘ	no	96.12	yes
125438	flagellated	motile2+ⓘ	yes	65.54	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Paracoccus pueri sp. nov., isolated from Pu'er tea.	Wang YS, Yan ZF, Lin P, Gao W, Yi TH	Antonie Van Leeuwenhoek	10.1007/s10482-018-1041-9	2018
Phylogeny	Paracoccus hibisci sp. nov., isolated from the rhizosphere of Hibiscus syriacus L. (Mugunghwa flower).	Yan ZF, Moya G, Lin P, Won KH, Yang JE, Li CT, Kook M, Wang QJ, Yi TH	Int J Syst Evol Microbiol	10.1099/ijsem.0.001874	2017
Phylogeny	Paracoccus tibetensis sp. nov., isolated from Qinghai-Tibet Plateau permafrost.	Zhu S, Zhao Q, Zhang G, Jiang Z, Sheng H, Feng H, An L	Int J Syst Evol Microbiol	10.1099/ijs.0.041905-0	2012

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 )
#27013	IJSEM 1902 2013 ( DOI 10.1099/ijs.0.041905-0 , PubMed 23024140 )
#30682	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 #27013
#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 )

Content

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Paracoccus tibetensis (CGMCC 1.8925, NBRC 105667, Tibet-S9a3)

Name and taxonomic classification

Morphology

Cell morphology

Pigmentation

Culture and growth conditions

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Spore formation

Halophily

Metabolite utilization

Enzymes

Pathway annotation

Isolation, sampling and environmental information

Isolation source categories

Isolation

Interaction and safety

Sequence information

Genome sequences

Genome browser: GCA_900102505

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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