Phaeovulum vinaykumarii (DSM 18714, CCUG 54311, JCM 14544)

Name: Phaeovulum vinaykumarii (DSM 18714, CCUG 54311, JCM 14544)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 13822

Type strain

Strain Designation JA 123, JA123

Culture col. no. DSM 18714 CCUG 54311 JCM 14544 CIP 109721 JA 123 1 more

NCBI tax ID(s) 407234

Special Collections DSMZ CCUG JCM CIP

History <- C. Sasikala, Bacterial Discovery Lab., Centre Environment, Inst. Sci. and Technol., J. N. T. Univ., Hyderabad, India; JA 123 <- P. A. Kumar Ch. Sasikala JA123. CIP <- 2007, CCUG <- C. Sasikala, P. Anil Kumar, Jawaharlal Nehru Technological Univ. Hyderabad, India: strain JA123

Links

Phaeovulum vinaykumarii JA 123 is a Gram-negative, rod-shaped bacterium that was isolated from enrichment of tidal seawater.

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

Name and taxonomic classification

SI-ID 309553

CCUG 54311,DSM 18714,JCM 14544,CIP 109721

@ref 20215

Last LPSN update 2026-02-09 11:21:15

Domain Bacteria

Phylum Pseudomonadota

Class Alphaproteobacteria

Order Rhodobacterales

Family Paracoccaceae

Genus Phaeovulum

Species Phaeovulum vinaykumarii

Full scientific name Phaeovulum vinaykumarii (Srinivas et al. 2007) Suresh et al. 2020

Synonyms (2)

Bieblia vinaykumarii
Rhodobacter vinaykumarii

Morphology

Cell morphology

@ref	Gram stain	Cell shape	Confidence
123844	negative	rod-shaped
125438	negative		98.5
125439	negative		98.1

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link
37824	MEDIUM 698 - for Rhodobacter vinaykumarii
123844	CIP Medium 698		Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)
37824	positive	growth	30
67770	positive	growth	30

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
125439	obligate aerobe	93.7

Spore formation

@ref	Spore formation	Confidence
125438		93.95
125439		96.3

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
123844	17632 ChEBI	nitrate	-	reduction
123844	16301 ChEBI	nitrite	-	reduction

Metabolite production

@ref	Chebi-ID	Metabolite	Production
123844	35581 ChEBI	indole

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
68382	beta-galactosidase	-	3.2.1.23	from API zym
68382	beta-glucosidase	-	3.2.1.21	from API zym
68382	beta-glucuronidase	-	3.2.1.31	from API zym
123844	catalase	+	1.11.1.6
68382	cystine arylamidase	-	3.4.11.3	from API zym
68382	esterase (C 4)	+		from API zym
68382	esterase lipase (C 8)	+		from API zym
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
123844	oxidase	+
68382	trypsin	-	3.4.21.4	from API zym
123844	urease	+	3.5.1.5
68382	valine arylamidase	+		from API zym

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	C4 and CAM-carbon fixation	100	8 of 8
66794	gluconeogenesis	100	8 of 8
66794	palmitate biosynthesis	100	22 of 22
66794	cis-vaccenate biosynthesis	100	2 of 2
66794	ppGpp biosynthesis	100	4 of 4
66794	methylglyoxal degradation	100	5 of 5
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	valine metabolism	100	9 of 9
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	adipate degradation	100	2 of 2
66794	coenzyme A metabolism	100	4 of 4
66794	formaldehyde oxidation	100	3 of 3
66794	L-lactaldehyde degradation	100	3 of 3
66794	octane oxidation	100	3 of 3
66794	suberin monomers biosynthesis	100	2 of 2
66794	alginate biosynthesis	100	4 of 4
66794	CMP-KDO biosynthesis	100	4 of 4
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	folate polyglutamylation	100	1 of 1
66794	ubiquinone biosynthesis	100	7 of 7
66794	photosynthesis	92.86	13 of 14
66794	Entner Doudoroff pathway	90	9 of 10
66794	propionate fermentation	90	9 of 10
66794	threonine metabolism	90	9 of 10
66794	serine metabolism	88.89	8 of 9
66794	molybdenum cofactor biosynthesis	88.89	8 of 9
66794	lipid A biosynthesis	88.89	8 of 9
66794	chorismate metabolism	88.89	8 of 9
66794	propanol degradation	85.71	6 of 7
66794	vitamin B1 metabolism	84.62	11 of 13
66794	leucine metabolism	84.62	11 of 13
66794	pyrimidine metabolism	84.44	38 of 45
66794	glycolate and glyoxylate degradation	83.33	5 of 6
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	ethylmalonyl-CoA pathway	80	4 of 5
66794	phenylacetate degradation (aerobic)	80	4 of 5
66794	flavin biosynthesis	80	12 of 15
66794	glycogen metabolism	80	4 of 5
66794	peptidoglycan biosynthesis	80	12 of 15
66794	purine metabolism	79.79	75 of 94
66794	alanine metabolism	79.31	23 of 29
66794	glutamate and glutamine metabolism	78.57	22 of 28
66794	CO2 fixation in Crenarchaeota	77.78	7 of 9
66794	allantoin degradation	77.78	7 of 9
66794	phenylalanine metabolism	76.92	10 of 13
66794	butanoate fermentation	75	3 of 4
66794	dTDPLrhamnose biosynthesis	75	6 of 8
66794	glycogen biosynthesis	75	3 of 4
66794	sulfopterin metabolism	75	3 of 4
66794	tryptophan metabolism	73.68	28 of 38
66794	vitamin B6 metabolism	72.73	8 of 11
66794	glutathione metabolism	71.43	10 of 14
66794	citric acid cycle	71.43	10 of 14
66794	heme metabolism	71.43	10 of 14
66794	reductive acetyl coenzyme A pathway	71.43	5 of 7
66794	lipid metabolism	70.97	22 of 31
66794	methionine metabolism	69.23	18 of 26
66794	isoprenoid biosynthesis	69.23	18 of 26
66794	degradation of sugar alcohols	68.75	11 of 16
66794	oxidative phosphorylation	67.03	61 of 91
66794	arginine metabolism	66.67	16 of 24
66794	cyanate degradation	66.67	2 of 3
66794	aspartate and asparagine metabolism	66.67	6 of 9
66794	methane metabolism	66.67	2 of 3
66794	acetoin degradation	66.67	2 of 3
66794	d-mannose degradation	66.67	6 of 9
66794	lysine metabolism	66.67	28 of 42
66794	glycolysis	64.71	11 of 17
66794	tyrosine metabolism	64.29	9 of 14
66794	tetrahydrofolate metabolism	64.29	9 of 14
66794	pentose phosphate pathway	63.64	7 of 11
66794	ketogluconate metabolism	62.5	5 of 8
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	62.5	5 of 8
66794	isoleucine metabolism	62.5	5 of 8
66794	chlorophyll metabolism	61.11	11 of 18
66794	non-pathway related	60.53	23 of 38
66794	lipoate biosynthesis	60	3 of 5
66794	glycine betaine biosynthesis	60	3 of 5
66794	histidine metabolism	58.62	17 of 29
66794	degradation of pentoses	57.14	16 of 28
66794	cysteine metabolism	55.56	10 of 18
66794	metabolism of disaccharids	54.55	6 of 11
66794	phosphatidylethanolamine bioynthesis	53.85	7 of 13
66794	acetate fermentation	50	2 of 4
66794	glycine metabolism	50	5 of 10
66794	selenocysteine biosynthesis	50	3 of 6
66794	aminopropanol phosphate biosynthesis	50	1 of 2
66794	phenol degradation	50	10 of 20
66794	ethanol fermentation	50	1 of 2
66794	biotin biosynthesis	50	2 of 4
66794	cyclohexanol degradation	50	2 of 4
66794	mannosylglycerate biosynthesis	50	1 of 2
66794	sulfate reduction	46.15	6 of 13
66794	urea cycle	46.15	6 of 13
66794	degradation of hexoses	44.44	8 of 18
66794	cardiolipin biosynthesis	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	arachidonate biosynthesis	40	2 of 5
66794	metabolism of amino sugars and derivatives	40	2 of 5
66794	starch degradation	40	4 of 10
66794	factor 420 biosynthesis	40	2 of 5
66794	cellulose degradation	40	2 of 5
66794	hydrogen production	40	2 of 5
66794	3-phenylpropionate degradation	40	6 of 15
66794	coenzyme M biosynthesis	40	4 of 10
66794	vitamin K metabolism	40	2 of 5
66794	polyamine pathway	39.13	9 of 23
66794	carnitine metabolism	37.5	3 of 8
66794	androgen and estrogen metabolism	37.5	6 of 16
66794	d-xylose degradation	36.36	4 of 11
66794	degradation of sugar acids	36	9 of 25
66794	pantothenate biosynthesis	33.33	2 of 6
66794	enterobactin biosynthesis	33.33	1 of 3
66794	acetyl CoA biosynthesis	33.33	1 of 3
66794	sphingosine metabolism	33.33	2 of 6
66794	nitrate assimilation	33.33	3 of 9
66794	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
66794	IAA biosynthesis	33.33	1 of 3
66794	4-hydroxymandelate degradation	33.33	3 of 9
66794	carotenoid biosynthesis	31.82	7 of 22
66794	bile acid biosynthesis, neutral pathway	29.41	5 of 17
66794	benzoyl-CoA degradation	28.57	2 of 7
66794	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
66794	toluene degradation	25	1 of 4
66794	catecholamine biosynthesis	25	1 of 4
66794	lactate fermentation	25	1 of 4
66794	phenylpropanoid biosynthesis	23.08	3 of 13
66794	arachidonic acid metabolism	22.22	4 of 18

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
123844	-	+	+	+	-	+	+	-	-	-	+	-	-	-	-	+	-	-	-	-

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Engineered	#Laboratory	#Lab enrichment
#Environmental	#Aquatic	#Marine

Isolation

@ref	Sample type	Sampling date	Geographic location	Country	Country ISO 3 Code	Continent	Isolation date
7674	enrichment of tidal seawater		Bay of Bengal, Visakhapatnam, Ramakrishna beach	India	IND	Asia
60136	Seashore water	2005-04-16	Visakhapatnam	India	IND	Asia
67770	Marine tidal water
123844	Environment, Water, seashore		Visakhapatnam	India	IND	Asia	2005

Taxonmaps

69479

Global distribution of 16S sequence AM408117 (>99% sequence identity) for Bieblia vinaykumarii subclade from Microbeatlas

Aquatic Samples	843
Soil Samples	98
Animal Samples	171
Plant Samples	16
Total Samples	1128

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
7674	1	Risk group (German classification) According to TRBA 466
123844	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
67770	IMG-taxon 2681813513 annotated assembly for Phaeovulum vinaykumarii DSM 18714	scaffold	GCA_900156695	407234.3	2681813513	407234	73.83
67770	IMG-taxon 2740891828 annotated assembly for Phaeovulum vinaykumarii JA123	scaffold	GCA_900217755	407234.6	2740891828	407234	72.63

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
7674	Rhodobacter vinaykumarii partial 16S rRNA gene, type strain JA123T	AM408117	1387		407234

GC content

@ref	GC-content (mol%)	Method
7674	68.8	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: Phaeovulum vinaykumarii DSM 18714
NCBI: GCA_900156695

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	96.30	no
125439	motility	BacteriaNetⓘ	yes	68.70	no
125439	gram_stain	BacteriaNetⓘ	negative	98.10	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	93.70	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Rhodobacter vinaykumarii strain DSM 18714
PATRIC: 407234.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	98.50	no
125438	anaerobic	anaerobicⓘ	no	62.45	no
125438	spore-forming	spore-formingⓘ	no	93.95	no
125438	aerobic	aerobicⓘ	no	53.20	no
125438	thermophilic	thermophileⓘ	no	93.04	no
125438	flagellated	motile2+ⓘ	yes	69.60	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Limibaculum sediminis sp. nov., isolated from mangrove sediment.	Huang Y, Liu L, Li J, Pan J, Li M	Int J Syst Evol Microbiol	10.1099/ijsem.0.005580	2022

References

#7674	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 18714
#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 )
#37824	; Curators of the CIP;
#60136	Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 54311
#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;
#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 .
#123844	Collection of Institut Pasteur ; Curators of the CIP; CIP 109721
#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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Phaeovulum vinaykumarii (DSM 18714, CCUG 54311, JCM 14544)

Name and taxonomic classification

Morphology

Cell morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Spore formation

Metabolite utilization

Metabolite production

Enzymes

Pathway annotation

API zym

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_900156695

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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