Tropicibacter phthalicicus (DSM 26923, JCM 17793, KCTC 23703)

Name: Tropicibacter phthalicicus (DSM 26923, JCM 17793, KCTC 23703)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 23238

Type strain

Strain Designation KU27E1

Culture col. no. DSM 26923 JCM 17793 KCTC 23703 KU27E1

NCBI tax ID(s) 1037362

Special Collections DSMZ JCM KCTC

History <- JCM <- H. Iwaki; KU27E1 H. Iwaki KU27E1. <- H Iwaki, Kansai Univ., Japan

Links

Tropicibacter phthalicicus KU27E1 is an aerobe, Gram-negative bacterium that was isolated from seawater.

Gram-negative aerobe genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 380604

JCM 17793,KCTC 23703,CECT 8649,DSM 26923

@ref 20215

Last LPSN update 2026-02-09 11:23:42

Domain Bacteria

Phylum Pseudomonadota

Class Alphaproteobacteria

Order Rhodobacterales

Family Roseobacteraceae

Genus Tropicibacter

Species Tropicibacter phthalicicus

Full scientific name Tropicibacter phthalicicus corrig. Iwaki et al. 2012

Synonyms (2)

Tropicibacter phthalicus
Pelagimonas phthalicica

Morphology

Cell morphology

@ref	Gram stain	Confidence
67771	negative
125439	negative	95
125438	negative	96.833

Colony morphology

19147

Incubation period2-3 days

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
19147	BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)		Medium recipe at MediaDive	Name: BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514) Composition: NaCl 19.45 g/l MgCl2 5.9 g/l Bacto peptone 5.0 g/l Na2SO4 3.24 g/l CaCl2 1.8 g/l Yeast extract 1.0 g/l KCl 0.55 g/l NaHCO3 0.16 g/l Fe(III) citrate 0.1 g/l KBr 0.08 g/l SrCl2 0.034 g/l H3BO3 0.022 g/l Na2HPO4 0.008 g/l Na-silicate 0.004 g/l NaF 0.0024 g/l (NH4)NO3 0.0016 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)
19147	positive	growth	25
67770	positive	growth	25
67771	positive	growth	25

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
67771	aerobe
125439	obligate aerobe	92.1

Spore formation

@ref	Spore formation	Confidence
125439		96.2

Observation

67770

Observationquinones: Q-10

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
68369	17128 ChEBI	adipate	-	assimilation	from API 20NE
68369	29016 ChEBI	arginine	-	hydrolysis	from API 20NE
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
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
68369	17632 ChEBI	nitrate	-	reduction	from API 20NE
68369	27897 ChEBI	tryptophan	-	energy source	from API 20NE
68369	16199 ChEBI	urea	-	hydrolysis	from API 20NE

Metabolite production

@ref	Chebi-ID	Metabolite	Production
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
68369	arginine dihydrolase	-	3.5.3.6	from API 20NE
68369	beta-glucosidase	+	3.2.1.21	from API 20NE
19147	catalase	+	1.11.1.6
19147	cytochrome-c oxidase	+	1.9.3.1
68369	gelatinase	+		from API 20NE
68369	urease	-	3.5.1.5	from API 20NE

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	gluconeogenesis	100	8 of 8
66794	valine metabolism	100	9 of 9
66794	cis-vaccenate biosynthesis	100	2 of 2
66794	C4 and CAM-carbon fixation	100	8 of 8
66794	CMP-KDO biosynthesis	100	4 of 4
66794	formaldehyde oxidation	100	3 of 3
66794	coenzyme A metabolism	100	4 of 4
66794	ppGpp biosynthesis	100	4 of 4
66794	sulfopterin metabolism	100	4 of 4
66794	biotin biosynthesis	100	4 of 4
66794	threonine metabolism	100	10 of 10
66794	octane oxidation	100	3 of 3
66794	denitrification	100	2 of 2
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	palmitate biosynthesis	100	22 of 22
66794	phenylacetate degradation (aerobic)	100	5 of 5
66794	folate polyglutamylation	100	1 of 1
66794	suberin monomers biosynthesis	100	2 of 2
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	reductive acetyl coenzyme A pathway	100	7 of 7
66794	adipate degradation	100	2 of 2
66794	ceramide biosynthesis	100	1 of 1
66794	Entner Doudoroff pathway	100	10 of 10
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	tetrahydrofolate metabolism	92.86	13 of 14
66794	phenylalanine metabolism	92.31	12 of 13
66794	allantoin degradation	88.89	8 of 9
66794	NAD metabolism	88.89	16 of 18
66794	molybdenum cofactor biosynthesis	88.89	8 of 9
66794	serine metabolism	88.89	8 of 9
66794	chorismate metabolism	88.89	8 of 9
66794	photosynthesis	85.71	12 of 14
66794	leucine metabolism	84.62	11 of 13
66794	vitamin B1 metabolism	84.62	11 of 13
66794	tryptophan metabolism	84.21	32 of 38
66794	degradation of aromatic, nitrogen containing compounds	83.33	10 of 12
66794	glycolate and glyoxylate degradation	83.33	5 of 6
66794	glutamate and glutamine metabolism	82.14	23 of 28
66794	hydrogen production	80	4 of 5
66794	methylglyoxal degradation	80	4 of 5
66794	peptidoglycan biosynthesis	80	12 of 15
66794	ethylmalonyl-CoA pathway	80	4 of 5
66794	3-chlorocatechol degradation	80	4 of 5
66794	propionate fermentation	80	8 of 10
66794	glycine betaine biosynthesis	80	4 of 5
66794	gallate degradation	80	4 of 5
66794	degradation of sugar acids	80	20 of 25
66794	vitamin B12 metabolism	79.41	27 of 34
66794	tyrosine metabolism	78.57	11 of 14
66794	heme metabolism	78.57	11 of 14
66794	citric acid cycle	78.57	11 of 14
66794	aspartate and asparagine metabolism	77.78	7 of 9
66794	4-hydroxymandelate degradation	77.78	7 of 9
66794	CO2 fixation in Crenarchaeota	77.78	7 of 9
66794	lipid A biosynthesis	77.78	7 of 9
66794	d-mannose degradation	77.78	7 of 9
66794	purine metabolism	76.6	72 of 94
66794	alanine metabolism	75.86	22 of 29
66794	butanoate fermentation	75	3 of 4
66794	cyclohexanol degradation	75	3 of 4
66794	isoleucine metabolism	75	6 of 8
66794	arginine metabolism	75	18 of 24
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
66794	dTDPLrhamnose biosynthesis	75	6 of 8
66794	glycogen biosynthesis	75	3 of 4
66794	lactate fermentation	75	3 of 4
66794	acetate fermentation	75	3 of 4
66794	toluene degradation	75	3 of 4
66794	ketogluconate metabolism	75	6 of 8
66794	phenol degradation	75	15 of 20
66794	lysine metabolism	73.81	31 of 42
66794	flavin biosynthesis	73.33	11 of 15
66794	pyrimidine metabolism	73.33	33 of 45
66794	proline metabolism	72.73	8 of 11
66794	pentose phosphate pathway	72.73	8 of 11
66794	ubiquinone biosynthesis	71.43	5 of 7
66794	cardiolipin biosynthesis	71.43	5 of 7
66794	glutathione metabolism	71.43	10 of 14
66794	lipid metabolism	70.97	22 of 31
66794	glycolysis	70.59	12 of 17
66794	4-hydroxyphenylacetate degradation	70	7 of 10
66794	sulfate reduction	69.23	9 of 13
66794	non-pathway related	68.42	26 of 38
66794	3-phenylpropionate degradation	66.67	10 of 15
66794	acetoin degradation	66.67	2 of 3
66794	L-lactaldehyde degradation	66.67	2 of 3
66794	acetyl CoA biosynthesis	66.67	2 of 3
66794	IAA biosynthesis	66.67	2 of 3
66794	oxidative phosphorylation	65.93	60 of 91
66794	degradation of pentoses	64.29	18 of 28
66794	vitamin B6 metabolism	63.64	7 of 11
66794	degradation of sugar alcohols	62.5	10 of 16
66794	histidine metabolism	62.07	18 of 29
66794	urea cycle	61.54	8 of 13
66794	glycogen metabolism	60	3 of 5
66794	myo-inositol biosynthesis	60	6 of 10
66794	isoprenoid biosynthesis	57.69	15 of 26
66794	methionine metabolism	57.69	15 of 26
66794	propanol degradation	57.14	4 of 7
66794	androgen and estrogen metabolism	56.25	9 of 16
66794	cysteine metabolism	55.56	10 of 18
66794	nitrate assimilation	55.56	5 of 9
66794	ascorbate metabolism	54.55	12 of 22
66794	phosphatidylethanolamine bioynthesis	53.85	7 of 13
66794	arachidonic acid metabolism	50	9 of 18
66794	kanosamine biosynthesis II	50	1 of 2
66794	phenylmercury acetate degradation	50	1 of 2
66794	glycine metabolism	50	5 of 10
66794	selenocysteine biosynthesis	50	3 of 6
66794	grixazone biosynthesis	50	1 of 2
66794	carnitine metabolism	50	4 of 8
66794	ethanol fermentation	50	1 of 2
66794	aminopropanol phosphate biosynthesis	50	1 of 2
66794	quinate degradation	50	1 of 2
66794	ribulose monophosphate pathway	50	1 of 2
66794	d-xylose degradation	45.45	5 of 11
66794	degradation of hexoses	44.44	8 of 18
66794	polyamine pathway	43.48	10 of 23
66794	benzoyl-CoA degradation	42.86	3 of 7
66794	aclacinomycin biosynthesis	42.86	3 of 7
66794	bile acid biosynthesis, neutral pathway	41.18	7 of 17
66794	cellulose degradation	40	2 of 5
66794	vitamin K metabolism	40	2 of 5
66794	D-cycloserine biosynthesis	40	2 of 5
66794	lipoate biosynthesis	40	2 of 5
66794	arachidonate biosynthesis	40	2 of 5
66794	coenzyme M biosynthesis	40	4 of 10
66794	metabolism of disaccharids	36.36	4 of 11
66794	pantothenate biosynthesis	33.33	2 of 6
66794	enterobactin biosynthesis	33.33	1 of 3
66794	methane metabolism	33.33	1 of 3
66794	sphingosine metabolism	33.33	2 of 6
66794	cyanate degradation	33.33	1 of 3
66794	sulfoquinovose degradation	33.33	1 of 3
66794	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
66794	starch degradation	30	3 of 10
66794	mevalonate metabolism	28.57	2 of 7
66794	chlorophyll metabolism	27.78	5 of 18
66794	catecholamine biosynthesis	25	1 of 4
66794	vitamin E metabolism	25	1 of 4
66794	alginate biosynthesis	25	1 of 4
66794	methanogenesis from CO2	25	3 of 12
66794	phenylpropanoid biosynthesis	23.08	3 of 13
66794	carotenoid biosynthesis	22.73	5 of 22

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
19147	-	-	-	-	-	+	+	+	-	-	-	-	-	-	-	-	-	-	-	-	not determinedn.d.

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Aquatic	#Marine

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
19147	seawater	coastal region of Ishigaki Island	Japan	JPN	Asia
67770	Seawater obtained from the coastal region of Ishigaki Island		Japan	JPN	Asia
67771	From seawater	Ishigaki island, Okinawa	Japan	JPN	Asia

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
19147	1	Risk group (German classification) According to TRBA 466

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
67770	ASM436480v1 assembly for Pelagimonas phthalicica DSM 26923	contig	GCA_004364805	1037362.5	2734482174	1037362	75.56

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
19147	Tropicibacter phthalicicus gene for 16S rRNA, partial sequence	AB636139	1422		1037362

GC content

@ref	GC-content (mol%)	Method
19147	58.7	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: Pelagimonas phthalicica DSM 26923
NCBI: GCA_004364805

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	96.20	no
125439	motility	BacteriaNetⓘ	yes	63.70	no
125439	gram_stain	BacteriaNetⓘ	negative	95.00	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	92.10	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Tropicibacter phthalicicus strain DSM 26923
PATRIC: 1037362.5

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	96.83	yes
125438	anaerobic	anaerobicⓘ	no	92.32	yes
125438	spore-forming	spore-formingⓘ	no	84.71	no
125438	aerobic	aerobicⓘ	yes	80.95	no
125438	thermophilic	thermophileⓘ	no	96.98	yes
125438	flagellated	motile2+ⓘ	yes	69.42	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Genetics	Analysis of 1,000+ Type-Strain Genomes Substantially Improves Taxonomic Classification of Alphaproteobacteria.	Hordt A, Lopez MG, Meier-Kolthoff JP, Schleuning M, Weinhold LM, Tindall BJ, Gronow S, Kyrpides NC, Woyke T, Goker M.	Front Microbiol	10.3389/fmicb.2020.00468	2020
Phylogeny	Tropicibacter phthalicus sp. nov., a phthalate-degrading bacterium from seawater.	Iwaki H, Nishimura A, Hasegawa Y	Curr Microbiol	10.1007/s00284-012-0085-8	2012

References

#19147	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 26923
#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 )
#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 )
#67770	Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#67771	Korean Collection for Type Cultures (KCTC) ; Curators of the KCTC;
#68369	Automatically annotated from API 20NE .
#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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Tropicibacter phthalicicus (DSM 26923, JCM 17793, KCTC 23703)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Spore formation

Observation

Metabolite utilization

Metabolite production

Metabolite tests

Enzymes

Pathway annotation

API 20NE

Isolation, sampling and environmental information

Isolation source categories

Isolation

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_004364805

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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