Pontixanthobacter confluentis (KEM-4, KCTC 52259, NBRC 112305)

Name: Pontixanthobacter confluentis (KEM-4, KCTC 52259, NBRC 112305)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 133169

Type strain

Strain Designation KEM-4

Culture col. no. KEM-4 KCTC 52259 NBRC 112305

NCBI tax ID(s) 1849021

Special Collections KCTC Literature strains

History KCTC <- Jung-Hoon Yoon, Sungkyunkwan Univ.

Links

Pontixanthobacter confluentis KEM-4 is an aerobe, Gram-negative, ovoid-shaped bacterium that forms circular colonies and was isolated from water collected from an estuary environment where the ocean and a river meet.

Gram-negative ovoid-shaped colony-forming aerobe genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 27934

KCTC 52259,NBRC 112305

@ref 20215

Last LPSN update 2026-05-29 08:38:01

Domain Bacteria

Phylum Pseudomonadota

Class Alphaproteobacteria

Order Sphingomonadales

Family Erythrobacteraceae

Genus Pontixanthobacter

Species Pontixanthobacter confluentis

Full scientific name Pontixanthobacter confluentis (Park et al. 2016) Xu et al. 2020

Synonyms (4)

Aestuarierythrobacter confluentis
Allopontixanthobacter confluentis
Pseudopontixanthobacter confluentis
Altererythrobacter confluentis

Morphology

Cell morphology

@ref	Gram stain	Cell shape	Cell length	Cell width	Confidence
24944	negative	ovoid-shaped
24944			0.4-10.0 µm	0.2-0.4 µm
125439	negative				98.101
125438	negative				98.302

Colony morphology

@ref	Colony size	Colony color	Colony shape	Incubation period	Medium used
24944	0.5-1.0 mm	yellow	circular	5 days	MA

Pigmentation

@ref	Production	Name
24944		carotenoid pigment

Culture and growth conditions

Culture medium

@ref	Name	Growth
24944	Marine agar (MA)

Culture temp

@ref	Growth	Type	Temperature (°C)
24944	positive	growth	4-30
24944	positive	optimum	30
24944	negative	growth	35
67771	positive	growth	30

Culture pH

@ref	Ability	Type	PH
24944	positive	optimum	7.0-8.0
24944	positive	growth	6
24944		growth	5.5

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
24944	aerobe
67771	aerobe
125439	obligate aerobe	98.797

Spore formation

@ref	Spore formation	Confidence
24944
125438		90.665
125439		99.161

Halophily

@ref	Salt	Growth	Tested relation	Concentration
24944	NaCl	positive	growth	0-3.0 %(w/v)
24944	NaCl	positive	optimum	1.0-2.0 %(w/v)

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
24944	16150 ChEBI	benzoate	-	carbon source
24944	16150 ChEBI	benzoate	-	energy source
24944		casein	-	hydrolysis
24944	17057 ChEBI	cellobiose	-	carbon source
24944	17057 ChEBI	cellobiose	-	energy source
24944	16947 ChEBI	citrate	-	carbon source
24944	16947 ChEBI	citrate	-	energy source
24944	15824 ChEBI	D-fructose	-	carbon source
24944	15824 ChEBI	D-fructose	-	energy source
24944	12936 ChEBI	D-galactose	-	carbon source
24944	12936 ChEBI	D-galactose	-	energy source
24944	17634 ChEBI	D-glucose	-	carbon source
24944	17634 ChEBI	D-glucose	-	energy source
24944	16024 ChEBI	D-mannose	-	carbon source
24944	16024 ChEBI	D-mannose	-	energy source
24944	16551 ChEBI	D-trehalose	-	carbon source
24944	16551 ChEBI	D-trehalose	-	energy source
24944	65327 ChEBI	D-xylose	-	carbon source
24944	65327 ChEBI	D-xylose	-	energy source
24944	4853 ChEBI	esculin	-	hydrolysis
24944	15740 ChEBI	formate	-	carbon source
24944	15740 ChEBI	formate	-	energy source
24944	5291 ChEBI	gelatin	-	hydrolysis
24944	17368 ChEBI	hypoxanthine	-	hydrolysis
24944	30849 ChEBI	L-arabinose	-	carbon source
24944	30849 ChEBI	L-arabinose	-	energy source
24944	29985 ChEBI	L-glutamate	-	carbon source
24944	29985 ChEBI	L-glutamate	-	energy source
24944	15589 ChEBI	L-malate	-	carbon source
24944	15589 ChEBI	L-malate	-	energy source
24944	17895 ChEBI	L-tyrosine	+	hydrolysis
24944	17306 ChEBI	maltose	-	carbon source
24944	17306 ChEBI	maltose	-	energy source
24944	17632 ChEBI	nitrate	-	reduction
24944	15361 ChEBI	pyruvate	-	carbon source
24944	15361 ChEBI	pyruvate	-	energy source
24944	17814 ChEBI	salicin	-	carbon source
24944	17814 ChEBI	salicin	-	energy source
24944	32954 ChEBI	sodium acetate	-	carbon source
24944	32954 ChEBI	sodium acetate	-	energy source
24944	28017 ChEBI	starch	-	hydrolysis
24944	30031 ChEBI	succinate	-	carbon source
24944	30031 ChEBI	succinate	-	energy source
24944	17992 ChEBI	sucrose	-	carbon source
24944	17992 ChEBI	sucrose	-	energy source
24944	53426 ChEBI	tween 80	+	hydrolysis
24944	16199 ChEBI	urea	-	hydrolysis
24944	15318 ChEBI	xanthine	-	hydrolysis

Antibiotic resistance

@ref	ChEBI	Metabolite
24944	28971	ampicillin
24944	3393	carbenicillin
24944	124991	cefalotin
24944	17698	chloramphenicol
24944	17833	gentamicin
24944	6104	kanamycin
24944	6472	lincomycin
24944	7507	neomycin
24944	28368	novobiocin
24944	16869	oleandomycin
24944	18208	penicillin g
24944	8309	polymyxin b
24944	17076	streptomycin
24944	27902	tetracycline

Enzymes

@ref	Value	Activity	Ec
24944	acid phosphatase	-	3.1.3.2
24944	alkaline phosphatase	+	3.1.3.1
24944	alpha-chymotrypsin	+	3.4.21.1
24944	alpha-fucosidase	-	3.2.1.51
24944	alpha-galactosidase	-	3.2.1.22
24944	alpha-glucosidase	-	3.2.1.20
24944	alpha-mannosidase	-	3.2.1.24
24944	beta-galactosidase	+	3.2.1.23
24944	beta-glucosidase	-	3.2.1.21
24944	beta-glucuronidase	-	3.2.1.31
24944	catalase	+	1.11.1.6
24944	cystine arylamidase	+	3.4.11.3
24944	cytochrome oxidase	+	1.9.3.1
24944	esterase (C 4)	+
24944	esterase lipase (C 8)	+
24944	leucine arylamidase	+	3.4.11.1
24944	lipase (C 14)	-
24944	N-acetyl-beta-glucosaminidase	-	3.2.1.52
24944	naphthol-AS-BI-phosphohydrolase	+
24944	trypsin	+	3.4.21.4
24944	valine arylamidase	+

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Aquatic	#Estuary

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
24944	water collected from an estuary environment where the ocean and a river meet	Seocheon	Republic of Korea	KOR	Asia
67771	From water of the mouth of Keum River	Seocheon	Republic of Korea	KOR	Asia

Taxonmaps

69479

Global distribution of 16S sequence KX129915 (>99% sequence identity) for Altererythrobacter from Microbeatlas

Aquatic Samples	1200
Soil Samples	281
Animal Samples	145
Plant Samples	10
Total Samples	1636

Interaction and safety

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	ASM982761v1 assembly for Allopontixanthobacter confluentis KCTC 52259	scaffold	GCA_009827615	1849021.3	2915136994	1849021	74.42

16S sequences

@ref	Description	Accession	Database
24944	Allopontixanthobacter confluentis strain KEM-4 16S ribosomal RNA gene, partial sequence	KX129915

GC content

@ref	GC-content (mol%)	Method
24944	59.5	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: ASM982761v1 assembly for Allopontixanthobacter confluentis KCTC 52259
NCBI: GCA_009827615

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	98.80	no
125439	gram_stain	BacteriaNetⓘ	negative	98.10	no
125439	spore_formation	BacteriaNetⓘ	no	99.16	no
125439	motility	BacteriaNetⓘ	no	62.23	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Pseudopontixanthobacter confluentis KCTC 52259
NCBI: GCA_009827615.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	98.30	yes
125438	anaerobic	anaerobicⓘ	no	95.94	yes
125438	aerobic	aerobicⓘ	yes	86.03	yes
125438	spore-forming	spore-formingⓘ	no	90.67	yes
125438	thermophilic	thermophileⓘ	no	96.02	no
125438	flagellated	motile2+ⓘ	no	71.49	yes

Literature

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 )
#24944	S. J. Park, Yong-Taek,Park, Ji-Min,Yoon, Jung-Hoon: Altererythrobacter confluentis sp. nov., isolated from water of an estuary environment. IJSEM 66: 4002 - 4008 2016 ( DOI 10.1099/ijsem.0.001301 , PubMed 27411686 )
#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) .
#67771	Korean Collection for Type Cultures (KCTC) ; Curators of the KCTC;
#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 .
#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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