Name: Pedobacter heparinus DSM 2366
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 14092

Type strain:

Species: Pedobacter heparinus

Culture col. no.: DSM 2366, ATCC 13125, IFO 12017, NBRC 12017, NCIB 9290, CCUG 12810, LMG 10339, HIM 762-3, JCM 7457, BCRC 11563, CIP 104194, IAM 12655, KCTC 12437, LMG 10344, LMG 4024, LMG 8360, NCIMB 9290, NRRL B-14731

Strain history: CIP <- 1994, IFO <- Nagoya Univ., Japan <- ATCC, Cytophaga heparina <- E.K. Korn, NIH, USA, Flavobacterium heparinum

NCBI tax ID(s): 485917 (strain), 984 (species)

SI-ID 44080

LMG 10339, ATCC 13125, DSM 2366, IFO 12017, LMG 10344, LMG 4024, LMG 8360, NCIB 9290, CIP 105498, NCIMB 9290, CCUG 12810, CIP 104194, JCM 7457, CCRC 11563, IAM 12655, NBRC 12017, NRRL B-14731, BCRC 11563, KCTC 12437, KACC 10932, CGMCC 1.2820

Special Collections

Section

Pedobacter heparinus DSM 2366 is an obligate aerobe, Gram-negative bacterium that was isolated from soil.

Gram-negative
obligate aerobe
16S sequence
Bacteria
genome sequence

Information on the name and the taxonomic classification. Name and taxonomic classification

	Last LPSN update	14-12-2023 (DD-MM-YYYY)
	Domain	"Bacteria"
	Phylum	*Bacteroidota*
	Class	*Sphingobacteriia*
	Order	*Sphingobacteriales*
	Family	*Sphingobacteriaceae*
	Genus	*Pedobacter*
	Species	**Pedobacter heparinus**
	Full Scientific Name (LPSN)	Pedobacter heparinus (Payza and Korn 1956) Steyn et al. 1998

	Synonym	Flavobacterium heparinum
	Synonym	Sphingobacterium heparinum
	Synonym	Cytophaga heparina

Information on morphological and physiological properties Morphology

[Ref.: #119875]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %97.478

[Ref.: #119875]	Cell shape	rod-shaped

[Ref.: #119875]	Motility	no

Multimedia content

[Ref.: #66793]

Caption:

electron microscopic image

[Ref.: #66793]

Intellectual property rights:

Information on culture and growth conditions Culture and growth conditions

[Ref.: #1051]

Culture medium

NUTRIENT AGAR (DSMZ Medium 1)

[Ref.: #1051]

Culture medium growth

[Ref.: #1051]

Culture medium link

Medium recipe at MediaDive

[Ref.: #1051]

Culture medium composition

expand / minimize

[Ref.: #40684]

Culture medium

MEDIUM 3 - Columbia agar

[Ref.: #40684]

Culture medium growth

[Ref.: #40684]

Culture medium composition

expand / minimize

[Ref.: #119875]

Culture medium

CIP Medium 3

[Ref.: #119875]

Culture medium growth

[Ref.: #119875]

Culture medium link

Medium recipe provided by DSMZ

	Kind of temperature		Temperature
[Ref.: #1051]		growth	25-30 °C
[Ref.: #40684]		growth	30 °C
[Ref.: #67770]		growth	30 °C
[Ref.: #119875]		growth	25-30 °C
[Ref.: #119875]	no	growth	10 °C
[Ref.: #119875]	no	growth	37 °C
[Ref.: #119875]	no	growth	41 °C

Information on physiology and metabolism Physiology and metabolism

[Ref.: #119875]

Oxygen tolerance

obligate aerobe

[Ref.: #69481]

Ability of spore formation

no Confidence in %100

[Ref.: #1051]	Name of produced compound	chondroitinase (ABC and AC)
[Ref.: #1051]	Name of produced compound	alpha glucuronidase
[Ref.: #1051]	Name of produced compound	heparinase
[Ref.: #1051]	Name of produced compound	heparinitase
[Ref.: #1051]	Name of produced compound	sulfoamidases
[Ref.: #1051]	Name of produced compound	sulfoesterases

[Ref.: #67770]

Observation

quinones: MK-7

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #68371]	amygdalin ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	arbutin ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #119875]	citrate ChEBI	-	carbon source
[Ref.: #68371]	D-arabinose ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-arabitol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-fructose ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-fucose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-galactose ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-glucose ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-lyxose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-mannitol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-mannose ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-ribose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-tagatose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-xylose ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #68371]	erythritol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #119875]	esculin ChEBI	+	hydrolysis
[Ref.: #68371]	esculin ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #68371]	galactitol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	gluconate ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #119875]	glucose ChEBI	-	fermentation
[Ref.: #68371]	glycogen ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	inulin ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	L-arabinose ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #68371]	L-arabitol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	L-fucose ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #68371]	L-rhamnose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	L-sorbose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	L-xylose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #119875]	lactose ChEBI	-	fermentation
[Ref.: #68371]	melezitose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	methyl alpha-D-glucopyranoside ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	methyl alpha-D-mannoside ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	methyl beta-D-xylopyranoside ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	myo-inositol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	N-acetylglucosamine ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #119875]	nitrate ChEBI	-	reduction
[Ref.: #119875]	nitrite ChEBI	-	reduction
[Ref.: #68371]	Potassium 2-ketogluconate ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	Potassium 5-ketogluconate ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	raffinose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	ribitol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	salicin ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #119875]	sodium thiosulfate ChEBI	-	builds gas from
[Ref.: #68371]	starch ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	xylitol ChEBI	-	builds acid from	* from API 50CH acid
	Only first 10 entries are displayed. Click here to see all.

	Metabolite production	Metabolite	Production
[Ref.: #119875]		indole ChEBI	no

	Enzyme	Enzyme activity	EC number
[Ref.: #119875]	alcohol dehydrogenase	-	1.1.1.1
[Ref.: #119875]	beta-galactosidase	+	3.2.1.23
[Ref.: #119875]	catalase	+	1.11.1.6
[Ref.: #119875]	DNase	+
[Ref.: #119875]	gamma-glutamyltransferase	+	2.3.2.2
[Ref.: #119875]	gelatinase	-
[Ref.: #119875]	lysine decarboxylase	-	4.1.1.18
[Ref.: #119875]	ornithine decarboxylase	-	4.1.1.17
[Ref.: #119875]	oxidase	+
[Ref.: #119875]	phenylalanine ammonia-lyase	+	4.3.1.24
[Ref.: #119875]	tryptophan deaminase	-
[Ref.: #119875]	urease	-	3.5.1.5
	Only first 10 entries are displayed. Click here to see all.

API® 50CH acid:

Note that the displayed test results represent raw data and therefore may deviate!

	API ID	ControlQ	Acid from glycerolGLY	Acid from erythritolERY	Acid from D-arabinoseDARA	Acid from L-arabinoseLARA	Acid from D-riboseRIB	Acid from D-xyloseDXYL	Acid from L-xyloseLXYL	Acid from D-adonitolADO	Acid from methyl beta-D-xylopyranosideMDX	Acid from D-galactoseGAL	Acid from D-glucoseGLU	Acid from D-fructoseFRU	Acid from D-mannoseMNE	Acid from L-sorboseSBE	Acid from L-rhamnoseRHA	Acid from dulcitolDUL	Acid from inositolINO	Acid from D-mannitolMAN	Acid from D-sorbitolSOR	Acid from methyl alpha-D-mannopyranosideMDM	Acid from methyl alpha-D-glucopyranosideMDG	Acid from N-acetyl-glucosamineNAG	Acid from amygdalinAMY	Acid from arbutinARB	Acid from esculinESC	Acid from salicinSAL	Acid from cellobioseCEL	Acid from maltoseMAL	Acid from lactoseLAC	Acid from melibioseMEL	Acid from sucroseSAC	Acid from trehaloseTRE	Acid from inulinINU	Acid from melezitoseMLZ	Acid from raffinoseRAF	Acid from starchAMD	Acid from glycogenGLYG	Acid from xylitolXLT	Acid from gentiobioseGEN	Acid from turanoseTUR	Acid from D-lyxoseLYX	Acid from D-tagatoseTAG	Acid from D-fucoseDFUC	Acid from L-fucoseLFUC	Acid from D-arabitolDARL	Acid from L-arabitolLARL	Acid from gluconateGNT	Acid from 2-Ketogluconate2KG	Acid from 5-Ketogluconate5KG
[Ref.: #119875]	9535	not determinedn.d.	+/-	-	+	+	-	+	-	-	-	+	+	+	+	-	-	-	-	-	+/-	-	-	-	-	-	+	-	+/-	+/-	+/-	+/-	+/-	+/-	-	-	-	-	-	-	+/-	+/-	-	-	-	+	-	-	-	-	-

API® Biotype100:

Note that the displayed test results represent raw data and therefore may deviate!

	API ID	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
[Ref.: #119875]	595	not determinedn.d.	+	+	+	+	+	-	+	+	-	-	+	+	+	-	-	+	-	-	+	-	+	+	+	+	+	-	-	-	-	-	-	+	-	+	+	+	+	+	-	-	-	+	-	-	-	-	-	-	-	-	-	-	-	-	+	+	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	+	-	-	-	+	-	-	-	-

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	methylglyoxal degradation	100	5 of 5
[Ref.: #66794]	adipate degradation	100	2 of 2
[Ref.: #66794]	glycogen metabolism	100	5 of 5
[Ref.: #66794]	kanosamine biosynthesis II	100	2 of 2
[Ref.: #66794]	1,4-dihydroxy-6-naphthoate biosynthesis	100	6 of 6
[Ref.: #66794]	cis-vaccenate biosynthesis	100	2 of 2
[Ref.: #66794]	L-lactaldehyde degradation	100	3 of 3
[Ref.: #66794]	CMP-KDO biosynthesis	100	4 of 4
[Ref.: #66794]	biotin biosynthesis	100	4 of 4
[Ref.: #66794]	ppGpp biosynthesis	100	4 of 4
[Ref.: #66794]	palmitate biosynthesis	100	22 of 22
[Ref.: #66794]	butanoate fermentation	100	4 of 4
[Ref.: #66794]	gluconeogenesis	100	8 of 8
[Ref.: #66794]	sulfopterin metabolism	100	4 of 4
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	ceramide biosynthesis	100	1 of 1
[Ref.: #66794]	suberin monomers biosynthesis	100	2 of 2
[Ref.: #66794]	coenzyme A metabolism	100	4 of 4
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	cellulose degradation	100	5 of 5
[Ref.: #66794]	NAD metabolism	94.44	17 of 18
[Ref.: #66794]	photosynthesis	92.86	13 of 14
[Ref.: #66794]	Entner Doudoroff pathway	90	9 of 10
[Ref.: #66794]	threonine metabolism	90	9 of 10
[Ref.: #66794]	chorismate metabolism	88.89	8 of 9
[Ref.: #66794]	serine metabolism	88.89	8 of 9
[Ref.: #66794]	lipid A biosynthesis	88.89	8 of 9
[Ref.: #66794]	d-mannose degradation	88.89	8 of 9
[Ref.: #66794]	C4 and CAM-carbon fixation	87.5	7 of 8
[Ref.: #66794]	isoleucine metabolism	87.5	7 of 8
[Ref.: #66794]	tetrahydrofolate metabolism	85.71	12 of 14
[Ref.: #66794]	ubiquinone biosynthesis	85.71	6 of 7
[Ref.: #66794]	phenylalanine metabolism	84.62	11 of 13
[Ref.: #66794]	pentose phosphate pathway	81.82	9 of 11
[Ref.: #66794]	metabolism of amino sugars and derivatives	80	4 of 5
[Ref.: #66794]	peptidoglycan biosynthesis	80	12 of 15
[Ref.: #66794]	O-antigen biosynthesis	80	4 of 5
[Ref.: #66794]	heme metabolism	78.57	11 of 14
[Ref.: #66794]	valine metabolism	77.78	7 of 9
[Ref.: #66794]	leucine metabolism	76.92	10 of 13
[Ref.: #66794]	vitamin B1 metabolism	76.92	10 of 13
[Ref.: #66794]	glutamate and glutamine metabolism	75	21 of 28
[Ref.: #66794]	glycogen biosynthesis	75	3 of 4
[Ref.: #66794]	acetate fermentation	75	3 of 4
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
[Ref.: #66794]	purine metabolism	74.47	70 of 94
[Ref.: #66794]	flavin biosynthesis	73.33	11 of 15
[Ref.: #66794]	isoprenoid biosynthesis	73.08	19 of 26
[Ref.: #66794]	d-xylose degradation	72.73	8 of 11
[Ref.: #66794]	vitamin B6 metabolism	72.73	8 of 11
[Ref.: #66794]	cardiolipin biosynthesis	71.43	5 of 7
[Ref.: #66794]	propanol degradation	71.43	5 of 7
[Ref.: #66794]	pyrimidine metabolism	71.11	32 of 45
[Ref.: #66794]	glycolysis	70.59	12 of 17
[Ref.: #66794]	starch degradation	70	7 of 10
[Ref.: #66794]	methionine metabolism	69.23	18 of 26
[Ref.: #66794]	lysine metabolism	69.05	29 of 42
[Ref.: #66794]	histidine metabolism	68.97	20 of 29
[Ref.: #66794]	alanine metabolism	68.97	20 of 29
[Ref.: #66794]	acetyl CoA biosynthesis	66.67	2 of 3
[Ref.: #66794]	cysteine metabolism	66.67	12 of 18
[Ref.: #66794]	formaldehyde oxidation	66.67	2 of 3
[Ref.: #66794]	CO2 fixation in Crenarchaeota	66.67	6 of 9
[Ref.: #66794]	acetoin degradation	66.67	2 of 3
[Ref.: #66794]	tyrosine metabolism	64.29	9 of 14
[Ref.: #66794]	citric acid cycle	64.29	9 of 14
[Ref.: #66794]	proline metabolism	63.64	7 of 11
[Ref.: #66794]	degradation of sugar alcohols	62.5	10 of 16
[Ref.: #66794]	ketogluconate metabolism	62.5	5 of 8
[Ref.: #66794]	dTDPLrhamnose biosynthesis	62.5	5 of 8
[Ref.: #66794]	lipid metabolism	61.29	19 of 31
[Ref.: #66794]	tryptophan metabolism	60.53	23 of 38
[Ref.: #66794]	propionate fermentation	60	6 of 10
[Ref.: #66794]	degradation of sugar acids	60	15 of 25
[Ref.: #66794]	glycine betaine biosynthesis	60	3 of 5
[Ref.: #66794]	gallate degradation	60	3 of 5
[Ref.: #66794]	phenylacetate degradation (aerobic)	60	3 of 5
[Ref.: #66794]	arachidonate biosynthesis	60	3 of 5
[Ref.: #66794]	non-pathway related	57.89	22 of 38
[Ref.: #66794]	degradation of pentoses	57.14	16 of 28
[Ref.: #66794]	glutathione metabolism	57.14	8 of 14
[Ref.: #66794]	degradation of hexoses	55.56	10 of 18
[Ref.: #66794]	aspartate and asparagine metabolism	55.56	5 of 9
[Ref.: #66794]	oxidative phosphorylation	54.95	50 of 91
[Ref.: #66794]	metabolism of disaccharids	54.55	6 of 11
[Ref.: #66794]	arginine metabolism	54.17	13 of 24
[Ref.: #66794]	ethanol fermentation	50	1 of 2
[Ref.: #66794]	glycolate and glyoxylate degradation	50	3 of 6
[Ref.: #66794]	coenzyme M biosynthesis	50	5 of 10
[Ref.: #66794]	quinate degradation	50	1 of 2
[Ref.: #66794]	sulfate reduction	46.15	6 of 13
[Ref.: #66794]	phenylpropanoid biosynthesis	46.15	6 of 13
[Ref.: #66794]	androgen and estrogen metabolism	43.75	7 of 16
[Ref.: #66794]	reductive acetyl coenzyme A pathway	42.86	3 of 7
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	41.67	5 of 12
[Ref.: #66794]	ascorbate metabolism	40.91	9 of 22
[Ref.: #66794]	3-chlorocatechol degradation	40	2 of 5
[Ref.: #66794]	glycine metabolism	40	4 of 10
[Ref.: #66794]	lipoate biosynthesis	40	2 of 5
[Ref.: #66794]	myo-inositol biosynthesis	40	4 of 10
[Ref.: #66794]	ethylmalonyl-CoA pathway	40	2 of 5
[Ref.: #66794]	arachidonic acid metabolism	38.89	7 of 18
[Ref.: #66794]	urea cycle	38.46	5 of 13
[Ref.: #66794]	dolichyl-diphosphooligosaccharide biosynthesis	36.36	4 of 11
[Ref.: #66794]	cyanate degradation	33.33	1 of 3
[Ref.: #66794]	pantothenate biosynthesis	33.33	2 of 6
[Ref.: #66794]	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
[Ref.: #66794]	nitrate assimilation	33.33	3 of 9
[Ref.: #66794]	sulfoquinovose degradation	33.33	1 of 3
[Ref.: #66794]	IAA biosynthesis	33.33	1 of 3
[Ref.: #66794]	sphingosine metabolism	33.33	2 of 6
[Ref.: #66794]	octane oxidation	33.33	1 of 3
[Ref.: #66794]	molybdenum cofactor biosynthesis	33.33	3 of 9
[Ref.: #66794]	selenocysteine biosynthesis	33.33	2 of 6
[Ref.: #66794]	carotenoid biosynthesis	31.82	7 of 22
[Ref.: #66794]	polyamine pathway	30.43	7 of 23
[Ref.: #66794]	phenol degradation	30	6 of 20
[Ref.: #66794]	3-phenylpropionate degradation	26.67	4 of 15
[Ref.: #66794]	toluene degradation	25	1 of 4
[Ref.: #66794]	cyclohexanol degradation	25	1 of 4
[Ref.: #66794]	lactate fermentation	25	1 of 4
[Ref.: #66794]	vitamin E metabolism	25	1 of 4
[Ref.: #66794]	allantoin degradation	22.22	2 of 9
[Ref.: #66794]	vitamin B12 metabolism	20.59	7 of 34
		Only first 10 entries are displayed. Click here to see all.

Information on isolation source, the sampling and environmental conditions Isolation, sampling and environmental information

[Ref.: #1051]	Sample type/isolated from	soil

[Ref.: #45833]	Sample type/isolated from	Soil

[Ref.: #119875]	Sample type/isolated from	Environment, Dry soil
* marker position based on {}

Isolation sources categories

#Environmental

#Terrestrial

#Soil

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence AJ438172 (>99% sequence identity) for Pedobacter heparinus from Microbeatlas

Aquatic Samples	264
Soil Samples	529
Animal Samples	283
Plant Samples	78
Total Samples	1154

Information on possible application of the strain and its possible interaction with e.g. potential hosts Safety information

[Ref.: #1051]	Biosafety level	1	Risk group (German classification) According to TRBA 466
[Ref.: #119875]	Biosafety level	1	Risk group (French classification)

Information on genomic background e.g. entries in nucleic sequence databass Sequence information

16S Sequence information:

	Sequence accession description	Seq. accession number	Sequence length (bp)	Sequence database	Associated NCBI tax ID
[Ref.: #20218]	Pedobacter heparinus partial 16S rRNA gene, strain DSM 2366T	AJ438172	1482	GenBank ENA	485917 tax ID	*
[Ref.: #124043]	Pedobacter heparinus strain LMG 10339 16S ribosomal RNA gene, partial sequence.	AF329951	681	GenBank ENA	485917 tax ID	*
[Ref.: #124043]	Pedobacter heparinus strain LMG 10344 16S ribosomal RNA gene, partial sequence.	AF329952	681	GenBank ENA	984 tax ID	*
[Ref.: #20218]	Pedobacter heparinus gene for 16S rRNA, partial sequence, strain: NBRC 12017	AB680215	1447	GenBank ENA	984 tax ID	*

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Pedobacter heparinus DSM 2366	GCA_000410815	contig	GenBank ENA	485917 tax ID
[Ref.: #66792]	Pedobacter heparinus DSM 2366	GCA_000023825	complete	GenBank ENA	485917 tax ID	*
[Ref.: #66792]	Pedobacter heparinus DSM 2366	485917.13	wgs	PATRIC	485917 tax ID	*
[Ref.: #66792]	Pedobacter heparinus DSM 2366	485917.6	complete	PATRIC	485917 tax ID	*
[Ref.: #66792]	Pedobacter heparinus HIM 762-3, DSM 2366	644736398	draft	JGI IMG/M	485917 tax ID	*

[Ref.: #1051]	GC-content	40.4-45.0 mol%
[Ref.: #67770]	GC-content	42.3-43.0 mol%
[Ref.: #67770]	GC-content	40.4 mol%	thermal denaturation, midpoint method (Tm)

Data predicted using genome information as a basis Genome-based predictions

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from GenomeNet Sporulation v. 1 based on: Pedobacter heparinus DSM 2366 DSM 2366 NCBI: GCA_000023825.1
[Ref.: #69481]	spore-forming	spore-formingⓘ	no	100	no

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Pedobacter heparinus DSM 2366 DSM 2366 NCBI: GCA_000023825.1
[Ref.: #69480]	gram-positive	gram-positiveⓘ	no	97.478	no
[Ref.: #69480]	anaerobic	anaerobicⓘ	no	95.521	no
[Ref.: #69480]	aerobic	aerobicⓘ	yes	86.524	yes
[Ref.: #69480]	spore-forming	spore-formingⓘ	no	85.912	no
[Ref.: #69480]	thermophilic	thermophileⓘ	no	97.1	yes
[Ref.: #69480]	flagellated	motile2+ⓘ	no	83.5	no

Availability in culture collections External links

[Ref.: #1051]

Culture collection no.

DSM 2366, ATCC 13125, IFO 12017, NBRC 12017, NCIB 9290, CCUG 12810, LMG 10339, HIM 762-3, JCM 7457, BCRC 11563, CIP 104194, IAM 12655, KCTC 12437, LMG 10344, LMG 4024, LMG 8360, NCIMB 9290, NRRL B-14731

[Ref.: #83260]

SI-ID 44080

Literature:

Only first 10 entries are displayed. Click here to see all.

Topic	Title	Authors	Journal	DOI	Year
Metabolism	Expanding the Catalytic Promiscuity of Heparinase III from Pedobacter heparinus.	Gu Y, Lu M, Wang Z, Wu X, Chen Y	Chemistry	10.1002/chem.201605929	2017	*
Phylogeny	Pedobacter panacis sp. nov., isolated from Panax ginseng soil.	Singh P, Singh H, Kim YJ, Yang DC	Antonie Van Leeuwenhoek	10.1007/s10482-016-0794-2	2016	*
Phylogeny	Pedobacter nutrimenti sp. nov., isolated from chilled food.	Derichs J, Kampfer P, Lipski A	Int J Syst Evol Microbiol	10.1099/ijs.0.058677-0	2014	*
Phylogeny	Identification and characterization of cellobiose 2-epimerases from various aerobes.	Ojima T, Saburi W, Yamamoto T, Mori H, Matsui H	Biosci Biotechnol Biochem	10.1271/bbb.120742	2013	*
Genetics	Complete genome sequence of Pedobacter heparinus type strain (HIM 762-3).	Han C, Spring S, Lapidus A, Del Rio TG, Tice H, Copeland A, Cheng JF, Lucas S, Chen F, Nolan M, Bruce D, Goodwin L, Pitluck S, Ivanova N, Mavromatis K, Mikhailova N, Pati A, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CC, Saunders E, Chertkov O, Brettin T, Goker M, Rohde M, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP, Detter JC	Stand Genomic Sci	10.4056/sigs.22138	2009	*
Phylogeny	Pedobacter duraquae sp. nov., Pedobacter westerhofensis sp. nov., Pedobacter metabolipauper sp. nov., Pedobacter hartonius sp. nov. and Pedobacter steynii sp. nov., isolated from a hard-water rivulet.	Muurholm S, Cousin S, Pauker O, Brambilla E, Stackebrandt E	Int J Syst Evol Microbiol	10.1099/ijs.0.65166-0	2007	*
Phylogeny	Parapedobacter koreensis gen. nov., sp. nov.	Kim MK, Na JR, Cho DH, Soung NK, Yang DC	Int J Syst Evol Microbiol	10.1099/ijs.0.64677-0	2007	*
Phylogeny	Pedobacter panaciterrae sp. nov., isolated from soil in South Korea.	Yoon MH, Ten LN, Im WT, Lee ST	Int J Syst Evol Microbiol	10.1099/ijs.0.64693-0	2007	*
Phylogeny	Pedobacter ginsengisoli sp. nov., a DNase-producing bacterium isolated from soil of a ginseng field in South Korea.	Ten LN, Liu QM, Im WT, Lee M, Yang DC, Lee ST	Int J Syst Evol Microbiol	10.1099/ijs.0.64414-0	2006	*
Phylogeny	Pedobacter roseus sp. nov., isolated from a hypertrophic pond, and emended description of the genus Pedobacter.	Hwang CY, Choi DH, Cho BC	Int J Syst Evol Microbiol	10.1099/ijs.0.64045-0	2006	*
Enzymology	Chondroitinase-producing bacteria in natural habitats.	Kitamikado M, Lee YZ	Appl Microbiol	10.1128/am.29.3.414-421.1975	1975	*
Phylogeny	Pedobacter mucosus sp. nov., isolated from a soil sample of glacier foreland in Austre Lovenbreen, Arctic.	Huang J, Peng X, Qin K, Liu Y, Niu J, Liu J, Dong J, Zhang Y, Peng F	Int J Syst Evol Microbiol	10.1099/ijsem.0.005448	2022	*

References

#1051

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 2366

#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 )

#40684 ; Curators of the CIP;
#45833 Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 12810

#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) .

#66793

Mukherjee et al.: GEBA: 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life. 35: 676 - 683 2017 ( DOI 10.1038/nbt.3886 , PubMed 28604660 )

#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;

#68371

Automatically annotated from API 50CH acid .

#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 .

#69480

Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann: Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) .

#69481

Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch: Predictions based on the model GenomeNet Sporulation v. 1 . ( DOI 10.21203/rs.3.rs-2527258/v1 )

#83260

Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.: StrainInfo: A central database for resolving microbial strain identifiers . ( DOI 10.60712/SI-ID44080.1 )

#119875 Collection of Institut Pasteur ; Curators of the CIP; CIP 104194

#124043

Dr. Isabel Schober, Dr. Julia Koblitz: Data extracted from sequence databases, automatically matched based on designation and taxonomy .

* These data were automatically processed and therefore are not curated

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Pedobacter heparinus DSM 2366 DSM 2366

Pedobacter heparinus DSM 2366 DSM 2366

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