Hydrocarboniphaga daqingensis (CGMCC 1.7049, NBRC 104238, B2-9)

Name: Hydrocarboniphaga daqingensis (CGMCC 1.7049, NBRC 104238, B2-9)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 133605

Type strain

Strain Designation B2-9

Culture col. no. CGMCC 1.7049 NBRC 104238 B2-9

NCBI tax ID(s) 490188

Special Collections Literature strains

Links

Hydrocarboniphaga daqingensis B2-9 is an aerobe, Gram-negative, motile bacterium that was isolated from freshwater .

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

Name and taxonomic classification

SI-ID 133513

NBRC 104238

@ref 20215

Last LPSN update 2026-02-09 11:31:59

Domain Bacteria

Phylum Pseudomonadota

Class Gammaproteobacteria

Order Nevskiales

Family Nevskiaceae

Genus Hydrocarboniphaga

Species Hydrocarboniphaga daqingensis

Full scientific name Hydrocarboniphaga daqingensis Liu et al. 2011

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Confidence
29716	negative	1.25 µm	0.75 µm	rod-shaped
125438	negative				97.644
125439	negative				99.9
125439					91.6

Pigmentation

29716

Productionno

Culture and growth conditions

Culture temp

@ref	Growth	Type	Temperature (°C)
29716	positive	growth	10-37
29716	positive	optimum	22.5

Culture pH

@ref	Ability	Type	PH	PH range
29716	positive	optimum	7
29716	positive	growth	5.5-9.5	alkaliphile

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
29716	aerobe
125439	obligate aerobe	99.5

Spore formation

@ref	Spore formation	Confidence
29716
125439		98.2

Halophily

@ref	Salt	Growth	Tested relation	Concentration
29716	NaCl	positive	growth	<1 %
29716	NaCl	positive	optimum	0.5 %

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
29716	4853 ChEBI	esculin	+	hydrolysis
29716	25017 ChEBI	leucine	+	carbon source

Enzymes

@ref	Value	Activity	Ec
29716	acid phosphatase	+	3.1.3.2
29716	alkaline phosphatase	+	3.1.3.1
29716	catalase	+	1.11.1.6
29716	cytochrome oxidase	+	1.9.3.1

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	starch degradation	100	10 of 10
66794	octane oxidation	100	3 of 3
66794	gluconeogenesis	100	8 of 8
66794	valine metabolism	100	9 of 9
66794	propanol degradation	100	7 of 7
66794	palmitate biosynthesis	100	22 of 22
66794	ppGpp biosynthesis	100	4 of 4
66794	adipate degradation	100	2 of 2
66794	glycogen metabolism	100	5 of 5
66794	methylglyoxal degradation	100	5 of 5
66794	cis-vaccenate biosynthesis	100	2 of 2
66794	Entner Doudoroff pathway	100	10 of 10
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	suberin monomers biosynthesis	100	2 of 2
66794	folate polyglutamylation	100	1 of 1
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	biotin biosynthesis	100	4 of 4
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	coenzyme A metabolism	100	4 of 4
66794	formaldehyde oxidation	100	3 of 3
66794	quinate degradation	100	2 of 2
66794	tetrahydrofolate metabolism	92.86	13 of 14
66794	photosynthesis	92.86	13 of 14
66794	lipid A biosynthesis	88.89	8 of 9
66794	aspartate and asparagine metabolism	88.89	8 of 9
66794	CO2 fixation in Crenarchaeota	88.89	8 of 9
66794	chorismate metabolism	88.89	8 of 9
66794	C4 and CAM-carbon fixation	87.5	7 of 8
66794	glutathione metabolism	85.71	12 of 14
66794	reductive acetyl coenzyme A pathway	85.71	6 of 7
66794	citric acid cycle	85.71	12 of 14
66794	purine metabolism	85.11	80 of 94
66794	phenylalanine metabolism	84.62	11 of 13
66794	methionine metabolism	80.77	21 of 26
66794	phenylacetate degradation (aerobic)	80	4 of 5
66794	vitamin K metabolism	80	4 of 5
66794	ethylmalonyl-CoA pathway	80	4 of 5
66794	threonine metabolism	80	8 of 10
66794	peptidoglycan biosynthesis	80	12 of 15
66794	alanine metabolism	79.31	23 of 29
66794	heme metabolism	78.57	11 of 14
66794	molybdenum cofactor biosynthesis	77.78	7 of 9
66794	NAD metabolism	77.78	14 of 18
66794	leucine metabolism	76.92	10 of 13
66794	androgen and estrogen metabolism	75	12 of 16
66794	isoleucine metabolism	75	6 of 8
66794	acetate fermentation	75	3 of 4
66794	CMP-KDO biosynthesis	75	3 of 4
66794	glycogen biosynthesis	75	3 of 4
66794	sulfopterin metabolism	75	3 of 4
66794	glutamate and glutamine metabolism	75	21 of 28
66794	lipid metabolism	74.19	23 of 31
66794	pyrimidine metabolism	73.33	33 of 45
66794	vitamin B6 metabolism	72.73	8 of 11
66794	cardiolipin biosynthesis	71.43	5 of 7
66794	ubiquinone biosynthesis	71.43	5 of 7
66794	glycolysis	70.59	12 of 17
66794	propionate fermentation	70	7 of 10
66794	vitamin B1 metabolism	69.23	9 of 13
66794	methane metabolism	66.67	2 of 3
66794	L-lactaldehyde degradation	66.67	2 of 3
66794	serine metabolism	66.67	6 of 9
66794	acetoin degradation	66.67	2 of 3
66794	tyrosine metabolism	64.29	9 of 14
66794	metabolism of disaccharids	63.64	7 of 11
66794	proline metabolism	63.64	7 of 11
66794	pentose phosphate pathway	63.64	7 of 11
66794	tryptophan metabolism	63.16	24 of 38
66794	arginine metabolism	62.5	15 of 24
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	62.5	5 of 8
66794	dTDPLrhamnose biosynthesis	62.5	5 of 8
66794	histidine metabolism	62.07	18 of 29
66794	non-pathway related	60.53	23 of 38
66794	arachidonate biosynthesis	60	3 of 5
66794	flavin biosynthesis	60	9 of 15
66794	3-chlorocatechol degradation	60	3 of 5
66794	gallate degradation	60	3 of 5
66794	3-phenylpropionate degradation	60	9 of 15
66794	cellulose degradation	60	3 of 5
66794	degradation of aromatic, nitrogen containing compounds	58.33	7 of 12
66794	d-mannose degradation	55.56	5 of 9
66794	phenol degradation	55	11 of 20
66794	oxidative phosphorylation	54.95	50 of 91
66794	lysine metabolism	54.76	23 of 42
66794	isoprenoid biosynthesis	53.85	14 of 26
66794	phosphatidylethanolamine bioynthesis	53.85	7 of 13
66794	pantothenate biosynthesis	50	3 of 6
66794	ethanol fermentation	50	1 of 2
66794	phenylmercury acetate degradation	50	1 of 2
66794	butanoate fermentation	50	2 of 4
66794	cyclohexanol degradation	50	2 of 4
66794	ketogluconate metabolism	50	4 of 8
66794	cysteine metabolism	50	9 of 18
66794	bile acid biosynthesis, neutral pathway	47.06	8 of 17
66794	sulfate reduction	46.15	6 of 13
66794	urea cycle	46.15	6 of 13
66794	d-xylose degradation	45.45	5 of 11
66794	nitrate assimilation	44.44	4 of 9
66794	allantoin degradation	44.44	4 of 9
66794	arachidonic acid metabolism	44.44	8 of 18
66794	glycine metabolism	40	4 of 10
66794	factor 420 biosynthesis	40	2 of 5
66794	glycine betaine biosynthesis	40	2 of 5
66794	4-hydroxyphenylacetate degradation	40	4 of 10
66794	lipoate biosynthesis	40	2 of 5
66794	ascorbate metabolism	36.36	8 of 22
66794	cholesterol biosynthesis	36.36	4 of 11
66794	1,4-dihydroxy-6-naphthoate biosynthesis	33.33	2 of 6
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	selenocysteine biosynthesis	33.33	2 of 6
66794	glycolate and glyoxylate degradation	33.33	2 of 6
66794	IAA biosynthesis	33.33	1 of 3
66794	4-hydroxymandelate degradation	33.33	3 of 9
66794	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
66794	acetyl CoA biosynthesis	33.33	1 of 3
66794	phenylpropanoid biosynthesis	30.77	4 of 13
66794	polyamine pathway	30.43	7 of 23
66794	aclacinomycin biosynthesis	28.57	2 of 7
66794	degradation of hexoses	27.78	5 of 18
66794	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
66794	degradation of sugar alcohols	25	4 of 16
66794	lactate fermentation	25	1 of 4
66794	catecholamine biosynthesis	25	1 of 4
66794	alginate biosynthesis	25	1 of 4
66794	carnitine metabolism	25	2 of 8
66794	methanogenesis from CO2	25	3 of 12
66794	toluene degradation	25	1 of 4
66794	degradation of pentoses	21.43	6 of 28

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Aquatic	#Freshwater
#Environmental	#Aquatic	#Lake (large)
#Environmental	#Aquatic	#Pond (small)
#Environmental	#Aquatic	#River (Creek)

Isolation

29716

Sample typefreshwater (river, lake, pond)

Taxonmaps

69479

Global distribution of 16S sequence EU313812 (>99% sequence identity) for Hydrocarboniphaga daqingensis subclade from Microbeatlas

Aquatic Samples	2375
Soil Samples	995
Animal Samples	606
Plant Samples	139
Total Samples	4115

Interaction and safety

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	IMG-taxon 2619618894 annotated assembly for Hydrocarboniphaga daqingensis CGMCC 1.7049	scaffold	GCA_900129825	490188.4	2619618894	490188	69.78

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
29716	Hydrocarboniphaga daqingensis strain B2-9 16S ribosomal RNA gene, partial sequence	EU313812	1487		490188
124043	Hydrocarboniphaga daqingensis gene for 16S rRNA, partial sequence, strain: NBRC 104238.	AB682161	1451		490188

GC content

29716

GC-content (mol%)66

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Hydrocarboniphaga daqingensis CGMCC 1.7049
NCBI: GCA_900129825

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	98.20	no
125439	motility	BacteriaNetⓘ	yes	91.60	no
125439	gram_stain	BacteriaNetⓘ	negative	99.90	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	99.50	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Hydrocarboniphaga daqingensis CGMCC 1.7049
NCBI: GCA_900129825.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	97.64	yes
125438	anaerobic	anaerobicⓘ	no	96.34	no
125438	aerobic	aerobicⓘ	yes	87.98	yes
125438	spore-forming	spore-formingⓘ	no	88.25	no
125438	thermophilic	thermophileⓘ	no	98.00	no
125438	flagellated	motile2+ⓘ	yes	72.42	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Hydrocarboniphaga daqingensis sp. nov., isolated from a freshwater lake.	Liu Y, Song XF, Jiang JT, Liu YH, Xu CJ, Li H, Liu ZP	Int J Syst Evol Microbiol	10.1099/ijs.0.019380-0	2010

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 )
#26099	IJSEM 408 2011 ( DOI 10.1099/ijs.0.019380-0 , PubMed 20348325 )
#29716	Barberan A, Caceres Velazquez H, Jones S, Fierer N.: Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information. mSphere 2: 2017 ( DOI 10.1128/mSphere.00237-17 , PubMed 28776041 ) - originally annotated from #26099
#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) .
#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 )
#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 .
#124043	Isabel Schober, Julia Koblitz: Data extracted from sequence databases, automatically matched based on designation and taxonomy .
#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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Hydrocarboniphaga daqingensis (CGMCC 1.7049, NBRC 104238, B2-9)

Name and taxonomic classification

Morphology

Cell morphology

Pigmentation

Culture and growth conditions

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Spore formation

Halophily

Metabolite utilization

Enzymes

Pathway annotation

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Sequence information

Genome sequences

Genome browser: GCA_900129825

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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