Gordonia paraffinivorans (DSM 44604, AS4.1730, HD321)

Name: Gordonia paraffinivorans (DSM 44604, AS4.1730, HD321)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 10607

Type strain

Strain Designation AS4.1730, HD321

Culture col. no. DSM 44604 AS4.1730 HD321 NCIMB 14305 NBRC 108238 6 more

NCBI tax ID(s) 1223543 175628

Special Collections DSMZ JCM CIP Wink compendium

History <- Y. Xue, Chinese Academy of Science, Beijing; AS4.1730 2004, Y. Xue, Beijing, China: strain HD321 AS 4.1730 <-- Y. Xue HD321. CIP <- 2004, Y. Xue, Chinese Academy Sciences, Beijing, China: strain HD321

Links

Gordonia paraffinivorans AS4.1730 is an obligate aerobe, Gram-positive, rod-shaped bacterium that was isolated from production wellhead water sample.

Gram-positive rod-shaped obligate aerobe genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 127993

NBRC 108238,AS 4.1730,DSM 44604,BCRC 16372,CCRC 16372,JCM 12461,CIP 108331,CGMCC 4.1730

@ref 20215

Last LPSN update 2026-02-09 11:20:18

Domain Bacteria

Phylum Actinomycetota

Class Actinomycetes

Order Mycobacteriales

Family Gordoniaceae

Genus Gordonia

Species Gordonia paraffinivorans

Full scientific name Gordonia paraffinivorans Xue et al. 2003

BacDive ID	Other strains from **Gordonia paraffinivorans** (1)	Type strain
8308	G. paraffinivorans DSM 751, IFO 3083, NBRC 3083

Morphology

Cell morphology

@ref	Gram stain	Cell shape	Confidence
121554	positive	rod-shaped
125438			92.5
125438	positive		92.454
125439	positive		98.9

Colony morphology

@ref	Colony color	Incubation period	Medium used	Hemolysis ability
19682	Red orange	10-14 days	ISP 2
19682	Ivory	10-14 days	ISP 3
19682	Ivory	10-14 days	ISP 4
19682	Red orange	10-14 days	ISP 5
19682	Ivory	10-14 days	ISP 6
19682	Red orange	10-14 days	ISP 7
121554				1

Multicellular morphology

@ref	Forms multicellular complex	Medium name
19682		ISP 2
19682		ISP 3
19682		ISP 4
19682		ISP 5
19682		ISP 6
19682		ISP 7

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
11919	TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)	Medium recipe at MediaDive	Name: TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Distilled water
19682	ISP 2		Name: ISP 2 / Yeast Malt Agar (5265); 5265 Composition Malt extract 10.0 g/l Yeast extract 4.0 g/l Glucose 4.0 g/l Agar 15.0 g/l Preparation: Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.0 Usage: Maintenance and Taxonomy Organisms: All Actinomycetes
19682	ISP 3		Name: ISP 3; 5315 Composition Dog oat flakes 20.0 g/l Trace element solution (5314) 2.5 ml/l Agar 18.0 g/l Preparation: Oat flakes are cooked for 20 minutes, trace element solution and agar are added (in the case of non rolled oat flakes the suspension has to bee filtrated). Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.8 Usage: Maintenance and taxonomy (e.g. SEM As liquid medium for metabolite production) Organisms: All Actinomycetes Trace element solution 5314 Name: Trace element solution 5314; 5314 Composition CaCl2 x H2O 3.0 g/l Fe-III-citrate 1.0 g/l MnSO4 0.2 g/l ZnCl2 0.1 g/l CuSO4 x 5 H2O 0.025 g/l Sodium tetra borate 0.2 g/l CoCl2 x 6 H2O 0.004 g/l Sodium molybdate 0.01 g/l Preparation: Use double destillated water. Sterilisation: 20 minutes at 121°C pH before sterilisation: Usage: Trace element solution for different media Organisms:
19682	ISP 4		Name: ISP 4; DSM 547 Solution I: Difco soluble starch, 10.0 g. Make a paste of the starch with a small amount of cold distilled water and bring to a volume of 500 ml. Solution II: CaCO3 2.0 g K2HPO4 (anhydrous) 1.0 g MgSO4 x 7 H2O 1.0 g NaCl 1.0 g (NH4)2SO4 2.0 g Distilled water 500.0 ml Trace salt solution (see below) 1.0 ml The pH should be between 7.0 and 7.4. Do not adjust if it is within this range. Mix solutions I and II together. Add 20.0 g agar. Liquify agar by steaming at 100°C for 10 to 20 min. Trace element solution: FeSO4 x 7 H2O 0.1 g MnCl2 x 4 H2O 0.1 g ZnSO4 x 7 H2O 0.1 g Distilled water 100.0 ml
19682	ISP 5		Name: ISP 5 (5323) Composition L-Asparagine 1.0 g/l Glycerol 10.0 g/l K2HPO4 1.0 g/l Salt solution (see preparation) 1.0 ml/l Agar 20.0 g/l Preparation: Salt solution 1.0 g FeSO4 x 7 H2O 1.0 g MnCl2 x 4 H2O 1.0 g ZNSO4 x 7 H2O in 100 ml water Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.2 Usage: Maintenance and taxonomy Organisms: All Actinomycetes
19682	ISP 6		Name: ISP 6 (5318) Composition Peptone 15.0 g/l Proteose peptose 5.0 g/l Ferric ammonium citrate 0.5 g/l Sodium glycerophosphate 1.0 g/l Sodium thiosulfate 0.08 g/l Yeast extract 1.0 g/l Agar 15.0 g/l Sterilisation: 20 minutes at 121°C pH before sterilisation: Usage: Production of melanoid pigments Organisms: All Actinomycetes
19682	ISP 7		Name: ISP 7 (5322) Composition Glycerol 15.0 g/l L-Tyrosine 0.5 g/l L-Asparagine 1.0 g/l K2HPO4 0.5 g/l NaCl 0.5 g/l FeSO4 x 7 H2O 0.01 g/l Trace element solution 5343 1.0 ml/l Agar 20.0 Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.3 Usage: Production of melanoid pigments Organisms: All Actinomycetes
40488	MEDIUM 72- for trypto casein soja agar		Distilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
121554	CIP Medium 72	Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)
11919	positive	growth	28
19682	positive	optimum	28
40488	positive	growth	30
67770	positive	growth	28
121554	positive	growth	25-45
121554	negative	growth	10

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
121554	obligate aerobe
125439	obligate aerobe	91.8

Halophily

@ref	Salt	Growth	Tested relation	Concentration
121554	NaCl	positive	growth	0-10 %

Observation

67770

Observationquinones: MK-9(H₂)

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
68371	27613 ChEBI	amygdalin	-	builds acid from	from API 50CH acid
19682	22599 ChEBI	arabinose	-
68371	18305 ChEBI	arbutin	-	builds acid from	from API 50CH acid
68369	29016 ChEBI	arginine	-	hydrolysis	from API 20NE
68371	17057 ChEBI	cellobiose	-	builds acid from	from API 50CH acid
19682	62968 ChEBI	cellulose	-
121554	16947 ChEBI	citrate	-	carbon source
68371	17108 ChEBI	D-arabinose	-	builds acid from	from API 50CH acid
68371	18333 ChEBI	D-arabitol	-	builds acid from	from API 50CH acid
68371	15824 ChEBI	D-fructose	-	builds acid from	from API 50CH acid
68371	28847 ChEBI	D-fucose	-	builds acid from	from API 50CH acid
68371	12936 ChEBI	D-galactose	-	builds acid from	from API 50CH acid
68371	17634 ChEBI	D-glucose	-	builds acid from	from API 50CH acid
68369	17634 ChEBI	D-glucose	-	fermentation	from API 20NE
68371	16899 ChEBI	D-mannitol	-	builds acid from	from API 50CH acid
68371	16024 ChEBI	D-mannose	-	builds acid from	from API 50CH acid
68371	16988 ChEBI	D-ribose	-	builds acid from	from API 50CH acid
68371	17924 ChEBI	D-sorbitol	-	builds acid from	from API 50CH acid
68371	16443 ChEBI	D-tagatose	-	builds acid from	from API 50CH acid
68371	65327 ChEBI	D-xylose	-	builds acid from	from API 50CH acid
68369	27689 ChEBI	decanoate	-	assimilation	from API 20NE
68371	17113 ChEBI	erythritol	-	builds acid from	from API 50CH acid
68379	4853 ChEBI	esculin	+	hydrolysis	from API Coryne
121554	4853 ChEBI	esculin	+	hydrolysis
68369	4853 ChEBI	esculin	+	hydrolysis	from API 20NE
19682	28757 ChEBI	fructose	-
68371	16813 ChEBI	galactitol	-	builds acid from	from API 50CH acid
68379	5291 ChEBI	gelatin	-	hydrolysis	from API Coryne
68369	5291 ChEBI	gelatin	-	hydrolysis	from API 20NE
68371	28066 ChEBI	gentiobiose	-	builds acid from	from API 50CH acid
68371	24265 ChEBI	gluconate	-	builds acid from	from API 50CH acid
68369	24265 ChEBI	gluconate	+	assimilation	from API 20NE
19682	17234 ChEBI	glucose	+
68371	17754 ChEBI	glycerol	-	builds acid from	from API 50CH acid
68371	28087 ChEBI	glycogen	-	builds acid from	from API 50CH acid
121554	606565 ChEBI	hippurate	-	hydrolysis
68371	15443 ChEBI	inulin	-	builds acid from	from API 50CH acid
68371	30849 ChEBI	L-arabinose	-	builds acid from	from API 50CH acid
68371	18403 ChEBI	L-arabitol	-	builds acid from	from API 50CH acid
68371	18287 ChEBI	L-fucose	-	builds acid from	from API 50CH acid
68371	62345 ChEBI	L-rhamnose	-	builds acid from	from API 50CH acid
68371	17266 ChEBI	L-sorbose	-	builds acid from	from API 50CH acid
68371	65328 ChEBI	L-xylose	-	builds acid from	from API 50CH acid
68371	17716 ChEBI	lactose	-	builds acid from	from API 50CH acid
68369	25115 ChEBI	malate	+	assimilation	from API 20NE
68371	17306 ChEBI	maltose	-	builds acid from	from API 50CH acid
19682	29864 ChEBI	mannitol	-
68371	6731 ChEBI	melezitose	-	builds acid from	from API 50CH acid
68371	28053 ChEBI	melibiose	-	builds acid from	from API 50CH acid
68371	320061 ChEBI	methyl alpha-D-glucopyranoside	-	builds acid from	from API 50CH acid
68371	43943 ChEBI	methyl alpha-D-mannoside	-	builds acid from	from API 50CH acid
68371	74863 ChEBI	methyl beta-D-xylopyranoside	-	builds acid from	from API 50CH acid
19682	17268 ChEBI	myo-inositol	-
68371	17268 ChEBI	myo-inositol	-	builds acid from	from API 50CH acid
68371	59640 ChEBI	N-acetylglucosamine	-	builds acid from	from API 50CH acid
121554	17632 ChEBI	nitrate	-	reduction
121554	17632 ChEBI	nitrate	-	respiration
68369	17632 ChEBI	nitrate	-	reduction	from API 20NE
121554	16301 ChEBI	nitrite	-	reduction
68371		Potassium 2-ketogluconate	-	builds acid from	from API 50CH acid
68371		Potassium 5-ketogluconate	-	builds acid from	from API 50CH acid
19682	16634 ChEBI	raffinose	-
68371	16634 ChEBI	raffinose	-	builds acid from	from API 50CH acid
19682	26546 ChEBI	rhamnose	-
68371	15963 ChEBI	ribitol	-	builds acid from	from API 50CH acid
68371	17814 ChEBI	salicin	-	builds acid from	from API 50CH acid
68371	28017 ChEBI	starch	-	builds acid from	from API 50CH acid
19682	17992 ChEBI	sucrose	+
68379	17992 ChEBI	sucrose	-	fermentation	from API Coryne
68371	17992 ChEBI	sucrose	-	builds acid from	from API 50CH acid
68371	27082 ChEBI	trehalose	-	builds acid from	from API 50CH acid
68369	27897 ChEBI	tryptophan	-	energy source	from API 20NE
68371	32528 ChEBI	turanose	-	builds acid from	from API 50CH acid
68379	16199 ChEBI	urea	+	hydrolysis	from API Coryne
68371	17151 ChEBI	xylitol	-	builds acid from	from API 50CH acid
19682	18222 ChEBI	xylose	-

Metabolite production

@ref	Chebi-ID	Metabolite	Production
68369	35581 ChEBI	indole		from API 20NE
121554	35581 ChEBI	indole

Metabolite tests

@ref	Chebi-ID	Metabolite	Indole test	Voges-proskauer-test	Methylred-test
121554	15688 ChEBI	acetoin		-
121554	17234 ChEBI	glucose			-
68369	35581 ChEBI	indole	-			from API 20NE

Enzymes

@ref	Value	Activity	Ec
68382	acid phosphatase	+	3.1.3.2	from API zym
121554	alcohol dehydrogenase	+	1.1.1.1
68379	alkaline phosphatase	+	3.1.3.1	from API Coryne
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
68379	alpha-glucosidase	+	3.2.1.20	from API Coryne
68382	alpha-mannosidase	-	3.2.1.24	from API zym
121554	amylase	-
68369	arginine dihydrolase	-	3.5.3.6	from API 20NE
121554	beta-galactosidase	-	3.2.1.23
68379	beta-galactosidase	-	3.2.1.23	from API Coryne
68379	beta-glucosidase	+	3.2.1.21	from API Coryne
68369	beta-glucosidase	+	3.2.1.21	from API 20NE
68382	beta-glucuronidase	-	3.2.1.31	from API zym
68379	beta-glucuronidase	-	3.2.1.31	from API Coryne
121554	caseinase	-	3.4.21.50
121554	catalase	+	1.11.1.6
121554	DNase	-
121554	gamma-glutamyltransferase	+	2.3.2.2
121554	gelatinase	-
68369	gelatinase	-		from API 20NE
68379	gelatinase	-		from API Coryne
121554	lecithinase	-
68382	leucine arylamidase	+	3.4.11.1	from API zym
121554	lipase	-
68382	lipase (C 14)	-		from API zym
121554	lysine decarboxylase	-	4.1.1.18
68382	N-acetyl-beta-glucosaminidase	-	3.2.1.52	from API zym
68379	N-acetyl-beta-glucosaminidase	-	3.2.1.52	from API Coryne
121554	ornithine decarboxylase	-	4.1.1.17
121554	protease	-
68379	pyrazinamidase	-	3.5.1.B15	from API Coryne
68379	pyrrolidonyl arylamidase	+	3.4.19.3	from API Coryne
121554	tryptophan deaminase	-
121554	tween esterase	+
121554	urease	+	3.5.1.5
68379	urease	+	3.5.1.5	from API Coryne

API coryne

@ref	Reduction of nitrateNIT	PYZ	PYRA	PAL	beta GUR	beta GAL	alpha GLU	beta NAG	ESC	URE	GEL	Control fermentationControl	GLU	RIB	XYL	MAN	MAL	LAC	SAC	GLYG	CAT
19682	not determinedn.d.	-	+	+	-	-	+	-	+	+	-	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.	-	not determinedn.d.	not determinedn.d.

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
19682	not determinedn.d.	+	+	+	-	+	+	+	+	-	+	+	-	-	-	+	+	-	-	-
11919	-	+/-	+/-	+/-	-	+	+/-	+/-	-	-	+	+/-	-	-	-	+	-	-	-	-
11919	-	-	-	+	-	+	+/-	-	-	-	+	-	-	-	-	+	+/-	-	-	-
121554	-	+	+	+	-	+	+	+	-	-	+	+	-	+	-	+	+	-	-	-

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
11919	-	-	-	-	-	+	-	-	+/-	-	+/-	-	+/-	-	+	-	+/-	+	+/-	+/-	not determinedn.d.
11919	-	-	-	-	+	+	-	+	+	+/-	+/-	+/-	-	+/-	+	-	+	+	+/-	+/-	not determinedn.d.

API 50CHac

@ref	ControlQ	GLY	ERY	DARA	LARA	RIB	DXYL	LXYL	ADO	MDX	GAL	GLU	FRU	MNE	SBE	RHA	DUL	INO	MAN	SOR	MDM	MDG	NAG	AMY	ARB	ESC	SAL	CEL	MAL	LAC	MEL	SAC	TRE	INU	MLZ	RAF	AMD	GLYG	XLT	GEN	TUR	LYX	TAG	DFUC	LFUC	DARL	LARL	GNT	2KG	5KG
121554	not determinedn.d.	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	+/-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	+/-	-	-	-	-	-	-	-	-

API biotype100

@ref	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
121554	not determinedn.d.	+	-	-	+	+	-	-	+	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	+	+	-	-	-	-	-	-	-	-	-	-	+	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	+	+	-	-	-	-	-	-	-	+	-	+	-	-	-	-	-	+	-	-

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2
#Engineered	#Industrial
#Environmental	#Aquatic

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent	Isolation date
11919	production wellhead water sample	Daqing oilfield	China	CHN	Asia
67770	Water sample from oil-producing well of Daqing oilfield		China	CHN	Asia
121554	Environment, Water sample, producing well of Daqing oilfield		China	CHN	Asia	1996

Taxonmaps

69479

Global distribution of 16S sequence AF432348 (>99% sequence identity) for Gordonia paraffinivorans subclade from Microbeatlas

Aquatic Samples	450
Soil Samples	124
Animal Samples	1012
Plant Samples	17
Total Samples	1603

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
11919	1	Risk group (German classification) According to TRBA 466
19682	1	Risk group (German classification) According to TRBA 466
121554	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	ASM34415v1 assembly for Gordonia paraffinivorans NBRC 108238	contig	GCA_000344155	1223543.3	2523231042	1223543	56.56

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
11919	Gordonia sp. HD321 16S ribosomal RNA gene, partial sequence	AF432348	1477		175628

GC content

@ref	GC-content (mol%)	Method
67770	66	thermal denaturation, midpoint method (Tm)

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Gordonia paraffinivorans NBRC 108238
NCBI: GCA_000344155

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	65.50	no
125439	motility	BacteriaNetⓘ	no	81.00	no
125439	gram_stain	BacteriaNetⓘ	positive	98.90	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	91.80	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Gordonia paraffinivorans NBRC 108238
PATRIC: 1223543.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	92.45	no
125438	anaerobic	anaerobicⓘ	no	97.21	yes
125438	spore-forming	spore-formingⓘ	no	60.02	no
125438	aerobic	aerobicⓘ	yes	88.49	no
125438	thermophilic	thermophileⓘ	no	96.50	yes
125438	flagellated	motile2+ⓘ	no	92.50	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Removal Capacities of Polycyclic Aromatic Hydrocarbons (PAHs) by a Newly Isolated Strain from Oilfield Produced Water.	Qi YB, Wang CY, Lv CY, Lun ZM, Zheng CG.	Int J Environ Res Public Health	10.3390/ijerph14020215	2017
	Gordonia species as a rare pathogen isolated from milk of dairy cows with mastitis.	Bzdil J, Slosarkova S, Fleischer P, Matiasovic J.	Sci Rep	10.1038/s41598-022-09340-4	2022
Metabolism	Characterization of novel hydrocarbon-degrading Gordonia paraffinivorans and Gordonia sihwensis strains isolated from composting.	Silva NM, de Oliveira AMSA, Pegorin S, Giusti CE, Ferrari VB, Barbosa D, Martins LF, Morais C, Setubal JC, Vasconcellos SP, da Silva AM, de Oliveira JCF, Pascon RC, Viana-Niero C.	PLoS One	10.1371/journal.pone.0215396	2019
Metabolism	First report of cis-1,4-polyisoprene degradation by Gordonia paraffinivorans.	Braga SP, Dos Santos AP, Paganini T, Barbosa D, Epamino GWC, Morais C, Martins LF, Silva AM, Setubal JC, Vallim MA, Pascon RC.	Braz J Microbiol	10.1007/s42770-019-00143-w	2019
	In silico genome analysis reveals the metabolic versatility and biotechnology potential of a halotorelant phthalic acid esters degrading Gordonia alkanivorans strain YC-RL2.	Nahurira R, Wang J, Yan Y, Jia Y, Fan S, Khokhar I, Eltoukhy A.	AMB Express	10.1186/s13568-019-0733-5	2019
Phylogeny	Gordonia paraffinivorans sp. nov., a hydrocarbon-degrading actinomycete isolated from an oil-producing well.	Xue Y, Sun X, Zhou P, Liu R, Liang F, Ma Y	Int J Syst Evol Microbiol	10.1099/ijs.0.02605-0	2003

References

#11919	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 44604
#19682	Wink, J.: Compendium of Actinobacteria. HZI-Helmholtz-Centre for Infection Research, Braunschweig .
#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 )
#40488	; Curators of the CIP;
#67770	Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#68369	Automatically annotated from API 20NE .
#68371	Automatically annotated from API 50CH acid .
#68379	Automatically annotated from API Coryne .
#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 .
#121554	Collection of Institut Pasteur ; Curators of the CIP; CIP 108331
#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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Gordonia paraffinivorans (DSM 44604, AS4.1730, HD321)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

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Culture medium

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Physiology and metabolism

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API coryne

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Genome browser: GCA_000344155

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