Pseudomonas knackmussii (DSM 6978, B13, CCUG 54928)

Name: Pseudomonas knackmussii (DSM 6978, B13, CCUG 54928)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 13155

Type strain

Strain Designation B13

Culture col. no. DSM 6978 B13 CCUG 54928 CIP 109584 LMG 23759 1 more

NCBI tax ID(s) 1301098 65741

Special Collections DSMZ CCUG CIP Literature strains

History DSMZ <- K.-J. Knackmuss CIP <- 2007, DSMZ <- K.J. Knackmus, Germany: strain B13

Links

Pseudomonas knackmussii B13 is an aerobe, Gram-negative, motile bacterium that was isolated from sewage plant.

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

Name and taxonomic classification

SI-ID 48342

DSM 624,LMG 23759,DSM 6978,CIP 109584,CCUG 54928

@ref 20215

Last LPSN update 2026-05-29 08:27:58

Domain Bacteria

Phylum Pseudomonadota

Class Gammaproteobacteria

Order Pseudomonadales

Family Pseudomonadaceae

Genus Pseudomonas

Species Pseudomonas knackmussii

Full scientific name Pseudomonas knackmussii Stolz et al. 2007

Morphology

Cell morphology

@ref	Gram stain	Cell shape	Confidence
31984	negative	rod-shaped
120452	negative	rod-shaped
125438	negative		98.485
125439	negative		95.418

Pigmentation

31984

Productionno

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
2933	NUTRIENT AGAR (DSMZ Medium 1)	Medium recipe at MediaDive	Name: NUTRIENT AGAR (DSMZ Medium 1) Composition: Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water
2933	MINERAL MEDIUM (BRUNNER) (DSMZ Medium 457)	Medium recipe at MediaDive	Name: MINERAL MEDIUM (BRUNNER) (DSMZ Medium 457) Composition: Na2HPO4 2.44 g/l KH2PO4 1.52 g/l (NH4)2SO4 0.5 g/l MgSO4 x 7 H2O 0.2 g/l CaCl2 x 2 H2O 0.05 g/l EDTA 0.005 g/l FeSO4 x 7 H2O 0.002 g/l H3BO3 0.0003 g/l CoCl2 x 6 H2O 0.0002 g/l ZnSO4 x 7 H2O 0.0001 g/l MnCl2 x 4 H2O 3e-05 g/l Na2MoO4 x 2 H2O 3e-05 g/l NiCl2 x 6 H2O 2e-05 g/l CuCl2 x 2 H2O 1e-05 g/l Distilled water
37774	MEDIUM 72- for trypto casein soja agar		Distilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
120452	CIP Medium 72	Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)
2933	positive	growth	30
31984	positive	growth	20-41
31984	positive	optimum	30.5
37774	positive	growth	30
60389	positive	growth	30-37

Culture pH

@ref	Ability	Type	PH
31984	positive	optimum	7.2
31984	positive	growth	6.0-8.3

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
60389	aerobe
120452	obligate aerobe
125439	obligate aerobe	94.919

Spore formation

@ref	Spore formation	Confidence
125439		99.596

Compound production

2933

Compoundmuconat cycloisomerase II

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
31984	37054 ChEBI	3-hydroxybutyrate	+	carbon source
31984	17879 ChEBI	4-hydroxybenzoate	+	carbon source
31984	17128 ChEBI	adipate	+	carbon source
68369	17128 ChEBI	adipate	-	assimilation	from API 20NE
31984	16449 ChEBI	alanine	+	carbon source
68369	29016 ChEBI	arginine	+	hydrolysis	from API 20NE
31984	35391 ChEBI	aspartate	+	carbon source
31984	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
68369	4853 ChEBI	esculin	-	hydrolysis	from API 20NE
31984	28757 ChEBI	fructose	+	carbon source
68369	5291 ChEBI	gelatin	-	hydrolysis	from API 20NE
31984	24265 ChEBI	gluconate	+	carbon source
68369	24265 ChEBI	gluconate	+	assimilation	from API 20NE
31984	17234 ChEBI	glucose	+	carbon source
31984	27570 ChEBI	histidine	+	carbon source
31984	17240 ChEBI	itaconate	+	carbon source
68369	30849 ChEBI	L-arabinose	-	assimilation	from API 20NE
31984	24996 ChEBI	lactate	+	carbon source
31984	25017 ChEBI	leucine	+	carbon source
31984	25115 ChEBI	malate	+	carbon source
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
120452	17632 ChEBI	nitrate	+	reduction
68369	17632 ChEBI	nitrate	+	reduction	from API 20NE
120452	16301 ChEBI	nitrite	-	reduction
31984	18257 ChEBI	ornithine	+	carbon source
31984	18401 ChEBI	phenylacetate	+	carbon source
31984	26271 ChEBI	proline	+	carbon source
31984	17148 ChEBI	putrescine	+	carbon source
31984	15361 ChEBI	pyruvate	+	carbon source
31984	9300 ChEBI	suberic acid	+	carbon source
68369	27897 ChEBI	tryptophan	-	energy source	from API 20NE
68369	16199 ChEBI	urea	-	hydrolysis	from API 20NE

Metabolite production

@ref	Chebi-ID	Metabolite	Production
120452	35581 ChEBI	indole
68369	35581 ChEBI	indole		from API 20NE

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
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
68369	arginine dihydrolase	+	3.5.3.6	from API 20NE
68382	beta-galactosidase	-	3.2.1.23	from API zym
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
31984	catalase	+	1.11.1.6
120452	catalase	+	1.11.1.6
68382	cystine arylamidase	-	3.4.11.3	from API zym
31984	cytochrome oxidase	+	1.9.3.1
68369	cytochrome oxidase	+	1.9.3.1	from API 20NE
68382	esterase (C 4)	+		from API zym
68382	esterase lipase (C 8)	+		from API zym
68369	gelatinase	-		from API 20NE
68382	leucine arylamidase	+	3.4.11.1	from API zym
68382	lipase (C 14)	-		from API zym
68382	N-acetyl-beta-glucosaminidase	-	3.2.1.52	from API zym
68382	naphthol-AS-BI-phosphohydrolase	+		from API zym
120452	oxidase	+
68382	trypsin	+	3.4.21.4	from API zym
120452	urease	-	3.5.1.5
68369	urease	-	3.5.1.5	from API 20NE
68382	valine arylamidase	-		from API zym

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	phenylacetate degradation (aerobic)	100	5 of 5
66794	methylglyoxal degradation	100	5 of 5
66794	resorcinol degradation	100	2 of 2
66794	butanoate fermentation	100	4 of 4
66794	valine metabolism	100	9 of 9
66794	coenzyme A metabolism	100	4 of 4
66794	adipate degradation	100	2 of 2
66794	formaldehyde oxidation	100	3 of 3
66794	cyanate degradation	100	3 of 3
66794	ppGpp biosynthesis	100	4 of 4
66794	cis-vaccenate biosynthesis	100	2 of 2
66794	molybdenum cofactor biosynthesis	100	9 of 9
66794	biotin biosynthesis	100	4 of 4
66794	reductive acetyl coenzyme A pathway	100	7 of 7
66794	L-lactaldehyde degradation	100	3 of 3
66794	alginate biosynthesis	100	4 of 4
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	propanol degradation	100	7 of 7
66794	palmitate biosynthesis	100	22 of 22
66794	ubiquinone biosynthesis	100	7 of 7
66794	taurine degradation	100	1 of 1
66794	folate polyglutamylation	100	1 of 1
66794	tetrahydrofolate metabolism	100	14 of 14
66794	threonine metabolism	100	10 of 10
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	3-chlorocatechol degradation	100	5 of 5
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	gluconeogenesis	100	8 of 8
66794	denitrification	100	2 of 2
66794	octane oxidation	100	3 of 3
66794	flavin biosynthesis	93.33	14 of 15
66794	glutathione metabolism	92.86	13 of 14
66794	vitamin B12 metabolism	91.18	31 of 34
66794	vitamin B6 metabolism	90.91	10 of 11
66794	Entner Doudoroff pathway	90	9 of 10
66794	4-hydroxyphenylacetate degradation	90	9 of 10
66794	glutamate and glutamine metabolism	89.29	25 of 28
66794	CO2 fixation in Crenarchaeota	88.89	8 of 9
66794	lipid A biosynthesis	88.89	8 of 9
66794	aspartate and asparagine metabolism	88.89	8 of 9
66794	chorismate metabolism	88.89	8 of 9
66794	arginine metabolism	87.5	21 of 24
66794	C4 and CAM-carbon fixation	87.5	7 of 8
66794	isoleucine metabolism	87.5	7 of 8
66794	heme metabolism	85.71	12 of 14
66794	citric acid cycle	85.71	12 of 14
66794	photosynthesis	85.71	12 of 14
66794	vitamin B1 metabolism	84.62	11 of 13
66794	leucine metabolism	84.62	11 of 13
66794	NAD metabolism	83.33	15 of 18
66794	pentose phosphate pathway	81.82	9 of 11
66794	androgen and estrogen metabolism	81.25	13 of 16
66794	methionine metabolism	80.77	21 of 26
66794	creatinine degradation	80	4 of 5
66794	propionate fermentation	80	8 of 10
66794	ethylmalonyl-CoA pathway	80	4 of 5
66794	phenol degradation	80	16 of 20
66794	peptidoglycan biosynthesis	80	12 of 15
66794	gallate degradation	80	4 of 5
66794	alanine metabolism	79.31	23 of 29
66794	4-hydroxymandelate degradation	77.78	7 of 9
66794	nitrate assimilation	77.78	7 of 9
66794	serine metabolism	77.78	7 of 9
66794	phenylalanine metabolism	76.92	10 of 13
66794	urea cycle	76.92	10 of 13
66794	cyclohexanol degradation	75	3 of 4
66794	lactate fermentation	75	3 of 4
66794	CMP-KDO biosynthesis	75	3 of 4
66794	ketogluconate metabolism	75	6 of 8
66794	acetate fermentation	75	3 of 4
66794	sulfopterin metabolism	75	3 of 4
66794	lipid metabolism	74.19	23 of 31
66794	tryptophan metabolism	73.68	28 of 38
66794	purine metabolism	73.4	69 of 94
66794	proline metabolism	72.73	8 of 11
66794	histidine metabolism	72.41	21 of 29
66794	cysteine metabolism	72.22	13 of 18
66794	tyrosine metabolism	71.43	10 of 14
66794	lysine metabolism	71.43	30 of 42
66794	cardiolipin biosynthesis	71.43	5 of 7
66794	methane metabolism	66.67	2 of 3
66794	acetyl CoA biosynthesis	66.67	2 of 3
66794	glycolate and glyoxylate degradation	66.67	4 of 6
66794	acetoin degradation	66.67	2 of 3
66794	d-mannose degradation	66.67	6 of 9
66794	selenocysteine biosynthesis	66.67	4 of 6
66794	degradation of aromatic, nitrogen containing compounds	66.67	8 of 12
66794	3-phenylpropionate degradation	66.67	10 of 15
66794	IAA biosynthesis	66.67	2 of 3
66794	enterobactin biosynthesis	66.67	2 of 3
66794	glycolysis	64.71	11 of 17
66794	oxidative phosphorylation	63.74	58 of 91
66794	non-pathway related	63.16	24 of 38
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	62.5	5 of 8
66794	sulfate reduction	61.54	8 of 13
66794	polyamine pathway	60.87	14 of 23
66794	cellulose degradation	60	3 of 5
66794	lipoate biosynthesis	60	3 of 5
66794	pyrimidine metabolism	57.78	26 of 45
66794	isoprenoid biosynthesis	57.69	15 of 26
66794	degradation of sugar alcohols	56.25	9 of 16
66794	suberin monomers biosynthesis	50	1 of 2
66794	toluene degradation	50	2 of 4
66794	carnitine metabolism	50	4 of 8
66794	aminopropanol phosphate biosynthesis	50	1 of 2
66794	arachidonic acid metabolism	50	9 of 18
66794	pantothenate biosynthesis	50	3 of 6
66794	glycine metabolism	50	5 of 10
66794	phenylmercury acetate degradation	50	1 of 2
66794	quinate degradation	50	1 of 2
66794	dTDPLrhamnose biosynthesis	50	4 of 8
66794	ethanol fermentation	50	1 of 2
66794	glycogen biosynthesis	50	2 of 4
66794	phosphatidylethanolamine bioynthesis	46.15	6 of 13
66794	phenylpropanoid biosynthesis	46.15	6 of 13
66794	ascorbate metabolism	45.45	10 of 22
66794	allantoin degradation	44.44	4 of 9
66794	benzoyl-CoA degradation	42.86	3 of 7
66794	factor 420 biosynthesis	40	2 of 5
66794	glycogen metabolism	40	2 of 5
66794	arachidonate biosynthesis	40	2 of 5
66794	glycine betaine biosynthesis	40	2 of 5
66794	vitamin K metabolism	40	2 of 5
66794	hydrogen production	40	2 of 5
66794	degradation of hexoses	38.89	7 of 18
66794	carotenoid biosynthesis	36.36	8 of 22
66794	degradation of pentoses	35.71	10 of 28
66794	bile acid biosynthesis, neutral pathway	35.29	6 of 17
66794	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
66794	sphingosine metabolism	33.33	2 of 6
66794	sulfoquinovose degradation	33.33	1 of 3
66794	myo-inositol biosynthesis	30	3 of 10
66794	catecholamine biosynthesis	25	1 of 4
66794	vitamin E metabolism	25	1 of 4

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
120452	-	+	+	+	-	+	-	-	+	-	+	+	-	-	-	-	-	-	-	-

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
2933	+	-	-	+	-	-	-	-	+	-	-	-	-	-	+	+	-	+	+	+	+
2933	+	-	-	+	-	-	-	-	+	-	-	-	-	-	+	+	-	+	+	+	+

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Engineered	#Waste	#Water treatment plant

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
2933	sewage plant	Göttingen	Germany	DEU	Europe
120452	Environment, Sewage treatment plant	Göttingen	Germany	DEU	Europe

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
2933	1	Risk group (German classification) According to TRBA 466
120452	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	PKB13 assembly for Pseudomonas knackmussii B13	complete	GCA_000689415	1301098.3	2579778852	1301098	97.8

16S sequences

@ref	Description	Accession	Length	NCBI tax ID
20218	Pseudomonas sp. partial 16S rRNA gene, isolate B13	AJ272544	612	1301098
20218	Pseudomonas knackmussii strain B13 16S ribosomal RNA gene, partial sequence	HM007154	1441	1301098
20218	Pseudomonas sp. B13(2012) 16S ribosomal RNA gene, partial sequence	JF313049	1517	1156300
20218	Pseudomonas sp. B13(2012b) 16S ribosomal RNA gene, partial sequence	JQ951521	1483	1207912
20218	Pseudomonas sp. 16S ribosomal RNA (rRNA)	L40412	559	306
31984	Pseudomonas knackmussii strain B13 small subunit ribosomal RNA gene, complete sequence	AF039489	1528	1301098

GC content

@ref	GC-content (mol%)	Method
2933	67.0	thermal denaturation, midpoint method (Tm)
31984	66.8-67.8

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: PKB13 assembly for Pseudomonas knackmussii B13
BV-BRC: 1301098.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	94.92	no
125439	motility	BacteriaNetⓘ	yes	89.12	no
125439	gram_stain	BacteriaNetⓘ	negative	95.42	no
125439	spore_formation	BacteriaNetⓘ	no	99.60	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Pseudomonas knackmussii B13 B13
NCBI: GCA_000689415.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	98.49	yes
125438	anaerobic	anaerobicⓘ	no	98.42	yes
125438	aerobic	aerobicⓘ	yes	89.73	yes
125438	spore-forming	spore-formingⓘ	no	85.46	no
125438	thermophilic	thermophileⓘ	no	98.00	no
125438	flagellated	motile2+ⓘ	yes	87.93	no

Literature

Topic	Title	Authors	Journal	DOI	Year
	Computer-directed rational engineering of dioxygenase TcsAB for triclosan biodegradation under cold conditions.	Yin Y, Yu X, Tao Z, French CE, Lu Z.	Appl Environ Microbiol	10.1128/aem.00346-25	2025
	Biodegradation of 3-Chloronitrobenzene and 3-Bromonitrobenzene by Diaphorobacter sp. Strain JS3051.	Xu ZJ, Spain JC, Zhou NY, Li T.	Appl Environ Microbiol	10.1128/aem.02437-21	2022
Metabolism	A Recently Assembled Degradation Pathway for 2,3-Dichloronitrobenzene in Diaphorobacter sp. Strain JS3051.	Li T, Gao YZ, Xu J, Zhang ST, Guo Y, Spain JC, Zhou NY.	mBio	10.1128/mbio.02231-21	2021
	Functional Gene Diversity of Selected Indigenous Hydrocarbon-Degrading Bacteria in Aged Crude Oil.	Ehis-Eriakha CB, Chikere CB, Akaranta O.	Int J Microbiol	10.1155/2020/2141209	2020
	Evolution of genetic architecture and gene regulation in biphenyl/PCB-degrading bacteria.	Fujihara H, Hirose J, Suenaga H.	Front Microbiol	10.3389/fmicb.2023.1168246	2023
	Orchestrated long-distance gene activation by a ParB-like BisD-CTP DNA clamp in low-frequency transfer competence development in Pseudomonas putida.	Antar H, Carraro N, Budny H, Gruber S, van der Meer JR.	Nucleic Acids Res	10.1093/nar/gkaf802	2025
Metabolism	Factors influencing 4-fluorobenzoate degradation in biofilm cultures of Pseudomonas knackmussii B13.	Misiak K, Casey E, Murphy CD.	Water Res	10.1016/j.watres.2011.04.020	2011
Pathogenicity	Insights into Mobile Genetic Elements of the Biocide-Degrading Bacterium Pseudomonas nitroreducens HBP-1.	Carraro N, Sentchilo V, Polak L, Bertelli C, van der Meer JR.	Genes (Basel)	10.3390/genes11080930	2020
	A dual functional origin of transfer in the ICEclc genomic island of Pseudomonas knackmussii B13.	Miyazaki R, van der Meer JR.	Mol Microbiol	10.1111/j.1365-2958.2010.07484.x	2011
Genetics	Intracellular excision and reintegration dynamics of the ICEclc genomic island of Pseudomonas knackmussii sp. strain B13.	Sentchilo V, Czechowska K, Pradervand N, Minoia M, Miyazaki R, van der Meer JR.	Mol Microbiol	10.1111/j.1365-2958.2009.06726.x	2009
Metabolism	Differences of heterotrophic 13CO2 assimilation by Pseudomonas knackmussii strain B13 and Rhodococcus opacus 1CP and potential impact on biomarker stable isotope probing.	Feisthauer S, Wick LY, Kastner M, Kaschabek SR, Schlomann M, Richnow HH.	Environ Microbiol	10.1111/j.1462-2920.2008.01573.x	2008
	How can a dual oriT system contribute to efficient transfer of an integrative and conjugative element?	Miyazaki R, van der Meer JR.	Mob Genet Elements	10.4161/mge.1.1.15744	2011
	Diversity and evolution of an abundant ICEclc family of integrative and conjugative elements in Pseudomonas aeruginosa.	Benigno V, Carraro N, Sarton-Loheac G, Romano-Bertrand S, Blanc DS, van der Meer JR.	mSphere	10.1128/msphere.00517-23	2023
	A New ICEclc Subfamily Integrative and Conjugative Element Responsible for Horizontal Transfer of Biphenyl and Salicylic Acid Catabolic Pathway in the PCB-Degrading Strain Pseudomonas stutzeri KF716.	Hirose J, Watanabe T, Futagami T, Fujihara H, Kimura N, Suenaga H, Goto M, Suyama A, Furukawa K.	Microorganisms	10.3390/microorganisms9122462	2021
Metabolism	Selection of a Very Active Microbial Community for the Coupled Treatment of Tetramethylammonium Hydroxide and Photoresist in Aqueous Solutions.	Moretti G, Matteucci F, Saraullo M, Veglio F, Del Gallo M.	Int J Environ Res Public Health	10.3390/ijerph15010041	2017
Genetics	Evolution End Classification of tfd Gene Clusters Mediating Bacterial Degradation of 2,4-Dichlorophenoxyacetic Acid (2,4-D).	Iasakov T.	Int J Mol Sci	10.3390/ijms241814370	2023
Metabolism	The Integrative Conjugative Element clc (ICEclc) of Pseudomonas aeruginosa JB2.	Obi CC, Vayla S, de Gannes V, Berres ME, Walker J, Pavelec D, Hyman J, Hickey WJ.	Front Microbiol	10.3389/fmicb.2018.01532	2018
	The TetR Family Repressor HpaR Negatively Regulates the Catabolism of 5-Hydroxypicolinic Acid in Alcaligenes faecalis JQ135 by Binding to Two Unique DNA Sequences in the Promoter of Hpa Operon.	Xu S, Jiang Y, Zhang F, Wang X, Zhang K, Zhao L, Hong Q, Qiu J, He J.	Appl Environ Microbiol	10.1128/aem.02390-21	2022
Genetics	Life Within a Contaminated Niche: Comparative Genomic Analyses of an Integrative Conjugative Element ICEnahCSV86 and Two Genomic Islands From Pseudomonas bharatica CSV86^T Suggest Probable Role in Colonization and Adaptation.	Mohapatra B, Malhotra H, Phale PS.	Front Microbiol	10.3389/fmicb.2022.928848	2022
	Inducible gene expression system by 3-hydroxypropionic acid.	Zhou S, Ainala SK, Seol E, Nguyen TT, Park S.	Biotechnol Biofuels	10.1186/s13068-015-0353-5	2015
	Characterization of an atypical but widespread type IV secretion system for transfer of the integrative and conjugative element (ICEclc) in Pseudomonas putida.	Daveri A, Benigno V, van der Meer JR.	Nucleic Acids Res	10.1093/nar/gkad024	2023
	An operon of three transcriptional regulators controls horizontal gene transfer of the integrative and conjugative element ICEclc in Pseudomonas knackmussii B13.	Pradervand N, Sulser S, Delavat F, Miyazaki R, Lamas I, van der Meer JR.	PLoS Genet	10.1371/journal.pgen.1004441	2014
Metabolism	Creatine utilization as a sole nitrogen source in Pseudomonas putida KT2440 is transcriptionally regulated by CahR.	Hinkel LA, Willsey GG, Lenahan SM, Eckstrom K, Schutz KC, Wargo MJ.	Microbiology (Reading)	10.1099/mic.0.001145	2022
Enzymology	A Novel SXT/R391 Integrative and Conjugative Element Carries Two Copies of the bla_NDM-1 Gene in Proteus mirabilis.	He J, Sun L, Zhang L, Leptihn S, Yu Y, Hua X.	mSphere	10.1128/msphere.00588-21	2021
	Gains of bacterial flagellar motility in a fungal world.	Pion M, Bshary R, Bindschedler S, Filippidou S, Wick LY, Job D, Junier P.	Appl Environ Microbiol	10.1128/aem.01393-13	2013
Metabolism	The TetR-type MfsR protein of the integrative and conjugative element (ICE) ICEclc controls both a putative efflux system and initiation of ICE transfer.	Pradervand N, Delavat F, Sulser S, Miyazaki R, van der Meer JR.	J Bacteriol	10.1128/jb.02129-14	2014
Genetics	Complete Genome Sequence and Function Gene Identify of Prometryne-Degrading Strain Pseudomonas sp. DY-1.	Liang D, Xiao C, Song F, Li H, Liu R, Gao J.	Microorganisms	10.3390/microorganisms9061261	2021
Metabolism	Bacterial degradation of chlorophenols and their derivatives.	Arora PK, Bae H.	Microb Cell Fact	10.1186/1475-2859-13-31	2014
Metabolism	Two structurally different dienelactone hydrolases (TfdEI and TfdEII) from Cupriavidus necator JMP134 plasmid pJP4 catalyse cis- and trans-dienelactones with similar efficiency.	Kumar A, Pillay B, Olaniran AO.	PLoS One	10.1371/journal.pone.0101801	2014
	Improved statistical analysis of low abundance phenomena in bimodal bacterial populations.	Reinhard F, van der Meer JR.	PLoS One	10.1371/journal.pone.0078288	2013
	An epigenetic switch activates bacterial quorum sensing and horizontal transfer of an integrative and conjugative element.	Ramsay JP, Bastholm TR, Verdonk CJ, Tambalo DD, Sullivan JT, Harold LK, Panganiban BA, Colombi E, Perry BJ, Jowsey W, Morris C, Hynes MF, Bond CS, Cameron ADS, Yost CK, Ronson CW.	Nucleic Acids Res	10.1093/nar/gkab1217	2022
	Timing of integration into the chromosome is critical for the fitness of an integrative and conjugative element and its bacterial host.	McKeithen-Mead SA, Grossman AD.	PLoS Genet	10.1371/journal.pgen.1010524	2023
Metabolism	Biphenyl/PCB Degrading bph Genes of Ten Bacterial Strains Isolated from Biphenyl-Contaminated Soil in Kitakyushu, Japan: Comparative and Dynamic Features as Integrative Conjugative Elements (ICEs).	Hirose J, Fujihara H, Watanabe T, Kimura N, Suenaga H, Futagami T, Goto M, Suyama A, Furukawa K.	Genes (Basel)	10.3390/genes10050404	2019
Transcriptome	Physiological and transcriptome changes induced by Pseudomonas putida acquisition of an integrative and conjugative element.	Miyazaki R, Yano H, Sentchilo V, van der Meer JR.	Sci Rep	10.1038/s41598-018-23858-6	2018
Metabolism	Transcriptome analysis of the mobile genome ICEclc in Pseudomonas knackmussii B13.	Gaillard M, Pradervand N, Minoia M, Sentchilo V, Johnson DR, van der Meer JR.	BMC Microbiol	10.1186/1471-2180-10-153	2010
	Cellular variability of RpoS expression underlies subpopulation activation of an integrative and conjugative element.	Miyazaki R, Minoia M, Pradervand N, Sulser S, Reinhard F, van der Meer JR.	PLoS Genet	10.1371/journal.pgen.1002818	2012
	Stochasticity and bistability in horizontal transfer control of a genomic island in Pseudomonas.	Minoia M, Gaillard M, Reinhard F, Stojanov M, Sentchilo V, van der Meer JR.	Proc Natl Acad Sci U S A	10.1073/pnas.0806164106	2008
Metabolism	The missing link: Bordetella petrii is endowed with both the metabolic versatility of environmental bacteria and virulence traits of pathogenic Bordetellae.	Gross R, Guzman CA, Sebaihia M, dos Santos VA, Pieper DH, Koebnik R, Lechner M, Bartels D, Buhrmester J, Choudhuri JV, Ebensen T, Gaigalat L, Herrmann S, Khachane AN, Larisch C, Link S, Linke B, Meyer F, Mormann S, Nakunst D, Ruckert C, Schneiker-Bekel S, Schulze K, Vorholter FJ, Yevsa T, Engle JT, Goldman WE, Puhler A, Gobel UB, Goesmann A, Blocker H, Kaiser O, Martinez-Arias R.	BMC Genomics	10.1186/1471-2164-9-449	2008
	A novel system of bacterial cell division arrest implicated in horizontal transmission of an integrative and conjugative element.	Takano S, Fukuda K, Koto A, Miyazaki R.	PLoS Genet	10.1371/journal.pgen.1008445	2019
	A new large-DNA-fragment delivery system based on integrase activity from an integrative and conjugative element.	Miyazaki R, van der Meer JR.	Appl Environ Microbiol	10.1128/aem.00711-13	2013
	Transient Replication in Specialized Cells Favors Transfer of an Integrative and Conjugative Element.	Delavat F, Moritz R, van der Meer JR.	mBio	10.1128/mbio.01133-19	2019
Metabolism	The Genome of the Toluene-Degrading Pseudomonas veronii Strain 1YdBTEX2 and Its Differential Gene Expression in Contaminated Sand.	Morales M, Sentchilo V, Bertelli C, Komljenovic A, Kryuchkova-Mostacci N, Bourdilloud A, Linke B, Goesmann A, Harshman K, Segers F, Delapierre F, Fiorucci D, Seppey M, Trofimenco E, Berra P, El Taher A, Loiseau C, Roggero D, Sulfiotti M, Etienne A, Ruiz Buendia G, Pillard L, Escoriza A, Moritz R, Schneider C, Alfonso E, Ben Jeddou F, Selmoni O, Resch G, Greub G, Emery O, Dubey M, Pillonel T, Robinson-Rechavi M, van der Meer JR.	PLoS One	10.1371/journal.pone.0165850	2016
	The hidden life of integrative and conjugative elements.	Delavat F, Miyazaki R, Carraro N, Pradervand N, van der Meer JR.	FEMS Microbiol Rev	10.1093/femsre/fux008	2017
Genetics	Protein domain architectures provide a fast, efficient and scalable alternative to sequence-based methods for comparative functional genomics.	Koehorst JJ, Saccenti E, Schaap PJ, Martins Dos Santos VAP, Suarez-Diez M.	F1000Res	10.12688/f1000research.9416.3	2016
	Life history analysis of integrative and conjugative element activation in growing microcolonies of Pseudomonas.	Reinhard F, van der Meer JR.	J Bacteriol	10.1128/jb.01333-13	2014
Genetics	A distinct and divergent lineage of genomic island-associated Type IV Secretion Systems in Legionella.	Wee BA, Woolfit M, Beatson SA, Petty NK.	PLoS One	10.1371/journal.pone.0082221	2013
Metabolism	Genomic and functional analyses of the 2-aminophenol catabolic pathway and partial conversion of its substrate into picolinic acid in Burkholderia xenovorans LB400.	Chirino B, Strahsburger E, Agullo L, Gonzalez M, Seeger M.	PLoS One	10.1371/journal.pone.0075746	2013
Metabolism	Different Ancestries of R Tailocins in Rhizospheric Pseudomonas Isolates.	Ghequire MG, Dillen Y, Lambrichts I, Proost P, Wattiez R, De Mot R.	Genome Biol Evol	10.1093/gbe/evv184	2015
Metabolism	Conjugal transfer of polychlorinated biphenyl/biphenyl degradation genes in Acidovorax sp. strain KKS102, which are located on an integrative and conjugative element.	Ohtsubo Y, Ishibashi Y, Naganawa H, Hirokawa S, Atobe S, Nagata Y, Tsuda M.	J Bacteriol	10.1128/jb.00352-12	2012
Genetics	Azotobacter Genomes: The Genome of Azotobacter chroococcum NCIMB 8003 (ATCC 4412).	Robson RL, Jones R, Robson RM, Schwartz A, Richardson TH.	PLoS One	10.1371/journal.pone.0127997	2015
Phylogeny	Pseudomonas panipatensis sp. nov., isolated from an oil-contaminated site.	Gupta SK, Kumari R, Prakash O, Lal R	Int J Syst Evol Microbiol	10.1099/ijs.0.65401-0	2008
Phylogeny	Pseudomonas knackmussii sp. nov.	Stolz A, Busse HJ, Kampfer P	Int J Syst Evol Microbiol	10.1099/ijs.0.64761-0	2007

References

#2933	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 6978
#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 )
#28238	IJSEM 572 2007 ( DOI 10.1099/ijs.0.64761-0 , PubMed 17329787 )
#31984	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 #28238
#37774	; Curators of the CIP;
#60389	Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 54928
#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 )
#68369	Automatically annotated from API 20NE .
#68382	Automatically annotated from API zym .
#120452	Collection of Institut Pasteur ; Curators of the CIP; CIP 109584
#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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Pseudomonas knackmussii (DSM 6978, B13, CCUG 54928)

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