Paraburkholderia caledonica (DSM 17062, ATCC BAA-462, CCM 7150)

Name: Paraburkholderia caledonica (DSM 17062, ATCC BAA-462, CCM 7150)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 1955

Type strain

Strain Designation W50D

Culture col. no. DSM 17062 ATCC BAA-462 CCM 7150 CCUG 42236 CIP 107098 9 more

NCBI tax ID(s) 1218115 134536

Special Collections DSMZ CCUG JCM KCTC CIP

Links

Paraburkholderia caledonica W50D is an obligate aerobe, mesophilic, Gram-negative prokaryote that was isolated from rhizosphere soil.

Gram-negative motile rod-shaped obligate aerobe mesophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 12999

LMG 19076,CCUG 42236,KCTC 12919,CIP 107098,ATCC BAA-462,DSM 17062,CCM 7150,NCIMB 13884,NBRC 102488,IAM 15100,JCM 21561,VTT E-022246,JCM 13458,NCPPB 4420

@ref 20215

Last LPSN update 2025-12-16 09:47:13

Domain Pseudomonadati

Phylum Pseudomonadota

Class Betaproteobacteria

Order Burkholderiales

Family Burkholderiaceae

Genus Paraburkholderia

Species Paraburkholderia caledonica

Full scientific name Paraburkholderia caledonica (Coenye et al. 2001) Sawana et al. 2015

Synonyms (1)

Burkholderia caledonica

BacDive ID	Other strains from **Paraburkholderia caledonica** (1)	Type strain
152653	P. caledonica CCUG 47297

Morphology

Cell morphology

@ref	Gram stain	Cell shape	Confidence
117101	negative	rod-shaped
125438	negative		96.469
125439	negative		99.5

Colony morphology

6731

Type of hemolysisgamma

Pigmentation

@ref	Production	Name
117101		Pyocyanin

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
6731	R2A MEDIUM (DSMZ Medium 830)	Medium recipe at MediaDive	Name: R2A MEDIUM (DSMZ Medium 830) Composition: Agar 15.0 g/l Casamino acids 0.5 g/l Starch 0.5 g/l Glucose 0.5 g/l Proteose peptone 0.5 g/l Yeast extract 0.5 g/l K2HPO4 0.3 g/l Na-pyruvate 0.3 g/l MgSO4 x 7 H2O 0.05 g/l Distilled water
6731	CASO AGAR (MERCK 105458) (DSMZ Medium 220)	Medium recipe at MediaDive	Name: CASO AGAR (Merck 105458) (DSMZ Medium 220) Composition: Agar 15.0 g/l Casein peptone 15.0 g/l NaCl 5.0 g/l Soy peptone 5.0 g/l Distilled water
41959	MEDIUM 72- for trypto casein soja agar		Distilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
117101	CIP Medium 72	Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
6731	positive	growth	30	mesophilic
41959	positive	growth	30	mesophilic
67770	positive	growth	28	mesophilic
117101	positive	growth	10-37
117101	negative	growth	5
117101	negative	growth	41

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
117101	obligate aerobe
125439	obligate aerobe	99.9

Spore formation

@ref	Spore formation	Confidence
125439		96.3

Halophily

@ref	Salt	Growth	Tested relation	Concentration
117101	NaCl	positive	growth	0-4 %
117101	NaCl		growth	6 %
117101	NaCl		growth	8 %
117101	NaCl		growth	10 %

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
68369	29016 ChEBI	arginine	-	hydrolysis	from API 20NE
117101	16947 ChEBI	citrate	+	carbon source
68369	17634 ChEBI	D-glucose	+	assimilation	from API 20NE
68369	17634 ChEBI	D-glucose	-	fermentation	from API 20NE
68369	16899 ChEBI	D-mannitol	+	assimilation	from API 20NE
68369	16024 ChEBI	D-mannose	+	assimilation	from API 20NE
68369	27689 ChEBI	decanoate	+	assimilation	from API 20NE
117101	4853 ChEBI	esculin	-	hydrolysis
68369	4853 ChEBI	esculin	-	hydrolysis	from API 20NE
68369	5291 ChEBI	gelatin	-	hydrolysis	from API 20NE
68369	24265 ChEBI	gluconate	+	assimilation	from API 20NE
68369	30849 ChEBI	L-arabinose	+	assimilation	from API 20NE
68369	25115 ChEBI	malate	+	assimilation	from API 20NE
68369	17306 ChEBI	maltose	-	assimilation	from API 20NE
68369	59640 ChEBI	N-acetylglucosamine	+	assimilation	from API 20NE
117101	17632 ChEBI	nitrate	-	reduction
117101	17632 ChEBI	nitrate	-	respiration
68369	17632 ChEBI	nitrate	-	reduction	from API 20NE
117101	16301 ChEBI	nitrite	-	reduction
68369	27897 ChEBI	tryptophan	-	energy source	from API 20NE
68369	16199 ChEBI	urea	-	hydrolysis	from API 20NE

Antibiotic resistance

@ref	Metabolite	Is antibiotic	Is sensitive	Is resistant
117101	0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)

Metabolite production

@ref	Chebi-ID	Metabolite	Production
68369	35581 ChEBI	indole		from API 20NE
117101	35581 ChEBI	indole

Metabolite tests

@ref	Chebi-ID	Metabolite	Indole test
68369	35581 ChEBI	indole	-	from API 20NE

Enzymes

@ref	Value	Activity	Ec
68382	acid phosphatase	+	3.1.3.2	from API zym
117101	alcohol dehydrogenase	-	1.1.1.1
68382	alkaline phosphatase	-	3.1.3.1	from API zym
68382	alpha-chymotrypsin	-	3.4.21.1	from API zym
68382	alpha-fucosidase	-	3.2.1.51	from API zym
68382	alpha-galactosidase	-	3.2.1.22	from API zym
68382	alpha-glucosidase	-	3.2.1.20	from API zym
68382	alpha-mannosidase	-	3.2.1.24	from API zym
117101	amylase	-
68369	arginine dihydrolase	-	3.5.3.6	from API 20NE
68382	beta-galactosidase	-	3.2.1.23	from API zym
117101	beta-galactosidase	+	3.2.1.23
68382	beta-glucosidase	-	3.2.1.21	from API zym
68369	beta-glucosidase	-	3.2.1.21	from API 20NE
68382	beta-glucuronidase	-	3.2.1.31	from API zym
117101	caseinase	-	3.4.21.50
6731	catalase	+	1.11.1.6
117101	catalase	+	1.11.1.6
68382	cystine arylamidase	-	3.4.11.3	from API zym
68369	cytochrome oxidase	+	1.9.3.1	from API 20NE
6731	cytochrome-c oxidase	+	1.9.3.1
117101	DNase	-
68382	esterase (C 4)	+		from API zym
68382	esterase lipase (C 8)	+		from API zym
117101	gelatinase	-
68369	gelatinase	-		from API 20NE
117101	lecithinase	-
68382	leucine arylamidase	+	3.4.11.1	from API zym
117101	lipase	-
68382	lipase (C 14)	-		from API zym
117101	lysine decarboxylase	-	4.1.1.18
68382	N-acetyl-beta-glucosaminidase	-	3.2.1.52	from API zym
68382	naphthol-AS-BI-phosphohydrolase	+		from API zym
117101	ornithine decarboxylase	-	4.1.1.17
117101	oxidase	+
117101	protease	-
68382	trypsin	-	3.4.21.4	from API zym
117101	tryptophan deaminase	-
117101	tween esterase	-
117101	urease	-	3.5.1.5
68369	urease	-	3.5.1.5	from API 20NE
68382	valine arylamidase	-		from API zym

API zym

@ref	Control	Alkaline phosphatase	Esterase (C 4)	2-naphtyl caprylateEsterase Lipase (C 8)	Lipase (C 14)	L-leucyl-2-naphthylamideLeucine arylamidase	L-valyl-2-naphthylamideValine arylamidase	L-cystyl-2-naphthylamideCystine arylamidase	Trypsin	alpha- Chymotrypsin	Acid phosphatase	Naphthol-AS-BI-phosphateNaphthol-AS-BI-phosphohydrolase	alpha- Galactosidase	beta- Galactosidase	beta- Glucuronidase	alpha- Glucosidase	beta- Glucosidase	N-acetyl-beta- glucosaminidase	alpha- Mannosidase	alpha- Fucosidase
117101	-	-	+	+	-	+	-	-	-	-	+	+	-	-	-	-	-	-	-	-

API 20NE

@ref	Reduction of nitratesNO3	TRP	GLU_ Ferm	ADH (Arg)	URE	ESC	GEL	PNPG	GLU_ Assim	ARA	MNE	MAN	NAG	MAL	GNT	CAP	ADI	MLT	CIT	PAC	OX
6731	-	-	-	-	-	-	-	+	+	+	+	+	+	-	+	+	-	+	-	+	+
6731	-	-	-	-	-	-	-	+	+	+	+	+	+	-	+	+	+/-	+	-	+	+

API biotype100

@ref	ControlQ	D-glucose as carbon sourceGLU	D-fructose as carbon sourceFRU	D-galactose as carbon sourceGAL	D-trehalose as carbon sourceTRE	D-mannose as carbon sourceMNE	L-sorbose as carbon sourceSBE	D-melibiose as carbon sourceMEL	sucrose as carbon sourceSAC	D-raffinose as carbon sourceRAF	maltotriose as carbon sourceMTE	maltose as carbon sourceMAL	lactose as carbon sourceLAC	lactulose as carbon sourceLTE	1-O-methyl-beta-galactopyranoside as carbon sourceMbGa	1-O-methyl-alpha-galactopyranoside as carbon sourceMaGa	D-cellobiose as carbon sourceCEL	gentiobiose as carbon sourceGEN	1-O-methyl-beta-D-glucopyranoside as carbon sourceMbGu	esculin as carbon sourceESC	D-ribose as carbon sourceRIB	L-arabinose as carbon sourceARA	D-xylose as carbon sourceXYL	palatinose as carbon sourcePLE	L-rhamnose as carbon sourceRHA	L-fucose as carbon sourceFUC	D-melezitose as carbon sourceMLZ	D-arabitol as carbon sourceDARL	L-arabitol as carbon sourceLARL	xylitol as carbon sourceXLT	dulcitol as carbon sourceDUL	D-tagatose as carbon sourceTAG	glycerol as carbon sourceGLY	myo-inositol as carbon sourceINO	D-mannitol as carbon sourceMAN	maltitol as carbon sourceMTL	D-turanose as carbon sourceTUR	D-sorbitol as carbon sourceSOR	adonitol as carbon sourceADO	hydroxyquinoline-beta-glucuronide as carbon sourceHBG	D-lyxose as carbon sourceLYX	i-erythritol as carbon sourceERY	1-O-methyl-alpha-D-glucoside as carbon sourceMDG	3-O-methyl-D-glucose as carbon source3MDG	D-saccharate as carbon sourceSAT	mucate as carbon sourceMUC	L-tartrate as carbon sourceLTAT	D-tartrate as carbon sourceDTAT	meso-tartrate as carbon sourceMTAT	D-malate as carbon sourceDMLT	L-malate as carbon sourceLMLT	cis-aconitate as carbon sourceCATE	trans-aconitate as carbon sourceTATE	tricarballylate as carbon sourceTTE	citrate as carbon sourceCIT	D-glucuronate as carbon sourceGRT	D-galacturonate as carbon sourceGAT	2-ketogluconate as carbon source2KG	5-ketogluconate as carbon source5KG	tryptophan as carbon sourceTRY	N-acetyl-D-glucosamine as carbon sourceNAG	D-gluconate as carbon sourceGNT	phenylacetate as carbon sourcePAC	protocatechuate as carbon sourcePAT	4-hydroxybenzoate as carbon sourcepOBE	quinate as carbon sourceQAT	gentisate as carbon sourceGTE	3-hydroxybenzoate as carbon sourcemOBE	benzoate as carbon sourceBAT	3-phenylpropionate as carbon sourcePPAT	m-coumarate as carbon sourceCMT	trigonelline as carbon sourceTGE	betaine as carbon sourceBET	putrescine as carbon sourcePCE	4-aminobutyrate as carbon sourceABT	histamine as carbon sourceHIN	DL-lactate as carbon sourceLAT	caprate as carbon sourceCAP	caprylate as carbon sourceCYT	L-histidine as carbon sourceHIS	succinate as carbon sourceSUC	fumarate as carbon sourceFUM	glutarate as carbon sourceGRE	DL-glycerate as carbon sourceGYT	5-aminovalerate as carbon sourceAVT	ethanolamine as carbon sourceETN	tryptamine as carbon sourceTTN	D-glucosamine as carbon sourceGLN	itaconate as carbon sourceITA	3-hydroxybutyrate as carbon source3OBU	L-aspartate as carbon sourceAPT	L-glutamate as carbon sourceGTT	L-proline as carbon sourcePRO	D-alanine as carbon sourceDALA	L-alanine as carbon sourceLALA	L-serine as carbon sourceSER	malonate as carbon sourceMNT	propionate as carbon sourcePROP	L-tyrosine as carbon sourceTYR	2-ketoglutarate as carbon source2KT
117101	not determinedn.d.	+	+	+	+	+	-	-	-	-	-	-	+	+	+	-	+	+	-	-	+	+	+	-	+	+	-	+	+	-	-	-	+	+	+	-	-	+	+	-	+	-	-	-	+	+	+	+	+	+	+	+	+	-	+	+	+	+	-	-	+	+	+	+	+	+	-	-	+	-	-	-	+	-	+	-	+	+	+	-	+	+	+	+	+	+	-	+	-	+	+	+	+	-	+	+	+	+	+	+

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Terrestrial	#Soil
#Host Body-Site	#Plant	#Rhizosphere
#Host	#Plants	-

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent	Isolation date
6731	rhizosphere soil	Edinburgh	United Kingdom	GBR	Europe
55371	Soil rhizosphere	Edinburgh	United Kingdom	GBR	Europe
67770	Soil rhizosphere	Edinburgh	United Kingdom	GBR	Europe
117101	Environment, Soil rhizosphere		United Kingdom	GBR	Europe	1999

Taxonmaps

69479

Global distribution of 16S sequence HQ849076 (>99% sequence identity) for Paraburkholderia caledonica from Microbeatlas

Aquatic Samples	930
Soil Samples	3308
Animal Samples	719
Plant Samples	1143
Total Samples	6100

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
6731	1	Risk group (German classification) According to TRBA 466
117101	1	Risk group (French classification) According to TRBA 466

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	ASM90283363v1 assembly for Paraburkholderia caledonica LMG 19076	scaffold	GCA_902833635	134536.51	8115425697	134536	65.78
67770	ASM68509v1 assembly for Paraburkholderia caledonica NBRC 102488	contig	GCA_000685095	1218115.9	2579779093	1218115	64.29

16S sequences

@ref	Description	Accession	Length	NCBI tax ID
20218	Burkholderia caledonica strain CIP 107098 16S ribosomal RNA gene, partial sequence	EU024157	1315	134536
20218	Burkholderia caledonica strain LMG 19076 16S ribosomal RNA gene, partial sequence	HQ849076	1126	134536
6731	Burkholderia sp. LMG 19076 16S ribosomal RNA, partial sequence	AF215704	1476	134536
67770	Burkholderia caledonica gene for 16S rRNA, partial sequence, strain: NBRC 102488	AB681827	1460	134536

GC content

@ref	GC-content (mol%)	Method
67770	62.2	high performance liquid chromatography (HPLC)

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Paraburkholderia caledonica LMG 19076
NCBI: GCA_902833635

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	99.90	no
125439	gram_stain	BacteriaNetⓘ	negative	99.50	no
125439	motility	BacteriaNetⓘ	yes	64.20	no
125439	spore_formation	BacteriaNetⓘ	no	96.30	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Burkholderia caledonica NBRC 102488
PATRIC: 1218115.9

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	96.47	no
125438	anaerobic	anaerobicⓘ	no	96.19	yes
125438	spore-forming	spore-formingⓘ	no	85.60	no
125438	aerobic	aerobicⓘ	yes	89.14	yes
125438	thermophilic	thermophileⓘ	no	97.49	yes
125438	flagellated	motile2+ⓘ	yes	82.42	no

Literature

Topic	Title	Authors	Journal	DOI	Year
	Molecular signatures and phylogenomic analysis of the genus Burkholderia: proposal for division of this genus into the emended genus Burkholderia containing pathogenic organisms and a new genus Paraburkholderia gen. nov. harboring environmental species.	Sawana A, Adeolu M, Gupta RS.	Front Genet	10.3389/fgene.2014.00429	2014
	Dual Screen for Metal-Tolerant Metallophore Producers Evaluated with Soil from the Carpenter Snow Creek Site, a Heavy-Metal-Toxified Site in Montana.	Ahmed MMA, Hammers C, Boudreau PD.	ACS Omega	10.1021/acsomega.4c07306	2024
	Application of qPCR assays based on haloacids transporter gene dehp2 for discrimination of Burkholderia and Paraburkholderia.	Su X, Shi Y, Li R, Lu ZN, Zou X, Wu JX, Han ZG.	BMC Microbiol	10.1186/s12866-019-1411-0	2019
	Genomic Assemblies of Members of Burkholderia and Related Genera as a Resource for Natural Product Discovery.	Mullins AJ, Jones C, Bull MJ, Webster G, Parkhill J, Connor TR, Murray JAH, Challis GL, Mahenthiralingam E.	Microbiol Resour Announc	10.1128/mra.00485-20	2020
Transcriptome	Identification of a Gene Encoding a New Fungal Steroid 7-Hydroxylase and Its Functional Characterization in Pichia pastoris Yeast.	Kollerov V, Tarlachkov S, Shutov A, Kazantsev A, Donova M.	Int J Mol Sci	10.3390/ijms242417256	2023
	The Potato Yam Phyllosphere Ectosymbiont Paraburkholderia sp. Msb3 Is a Potent Growth Promotor in Tomato.	Herpell JB, Schindler F, Bejtovic M, Fragner L, Diallo B, Bellaire A, Kublik S, Foesel BU, Gschwendtner S, Kerou M, Schloter M, Weckwerth W.	Front Microbiol	10.3389/fmicb.2020.00581	2020
Pathogenicity	Phylotype-Level Characterization of Complex Communities of Lactobacilli Using a High-Throughput, High-Resolution Phenylalanyl-tRNA Synthetase (pheS) Gene Amplicon Sequencing Approach.	Silvaraju S, Menon N, Fan H, Lim K, Kittelmann S.	Appl Environ Microbiol	10.1128/aem.02191-20	2020
Phylogeny	Mesorhizobium koreense sp. nov., Isolated from Soil.	Lee H, Chaudhary DK, Kim DU.	J Microbiol Biotechnol	10.4014/jmb.2404.04026	2024
Phylogeny	Burkholderia dipogonis sp. nov., isolated from root nodules of Dipogon lignosus in New Zealand and Western Australia.	Sheu SY, Chen MH, Liu WYY, Andrews M, James EK, Ardley JK, De Meyer SE, James TK, Howieson JG, Coutinho BG, Chen WM	Int J Syst Evol Microbiol	10.1099/ijsem.0.000639	2015
Phylogeny	Burkholderia rhynchosiae sp. nov., isolated from Rhynchosia ferulifolia root nodules.	De Meyer SE, Cnockaert M, Ardley JK, Trengove RD, Garau G, Howieson JG, Vandamme P	Int J Syst Evol Microbiol	10.1099/ijs.0.048751-0	2013
Phylogeny	Burkholderia ginsengisoli sp. nov., a beta-glucosidase-producing bacterium isolated from soil of a ginseng field.	Kim HB, Park MJ, Yang HC, An DS, Jin HZ, Yang DC	Int J Syst Evol Microbiol	10.1099/ijs.0.64387-0	2006
Phylogeny	Burkholderia fungorum sp. nov. and Burkholderia caledonica sp. nov., two new species isolated from the environment, animals and human clinical samples.	Coenye T, Laevens S, Willems A, Ohlen M, Hannant W, Govan JR, Gillis M, Falsen E, Vandamme P	Int J Syst Evol Microbiol	10.1099/00207713-51-3-1099	2001

References

#6731	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 17062
#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 )
#41959	; Curators of the CIP;
#55371	Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 42236
#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) .
#67770	Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#68369	Automatically annotated from API 20NE .
#68382	Automatically annotated from API zym .
#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 .
#117101	Collection of Institut Pasteur ; Curators of the CIP; CIP 107098
#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 )

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Paraburkholderia caledonica (DSM 17062, ATCC BAA-462, CCM 7150)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Pigmentation

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Spore formation

Halophily

Metabolite utilization

Antibiotic resistance

Metabolite production

Metabolite tests

Enzymes

API zym

API 20NE

API biotype100

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_902833635

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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