Name: Alcanivorax hongdengensis A-11-3
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 133431

Type strain:

Species: Alcanivorax hongdengensis

Strain Designation: A-11-3

Culture col. no.: CGMCC 1.7084, LMG 24624, MCCC 1A01496

NCBI tax ID(s): 519051 (species)

SI-ID 354038

LMG 24624, CGMCC 1.7084

Special Collections

Literature strains

Section

When using BacDive for research please cite our paper

Alcanivorax hongdengensis A-11-3 is an aerobe, Gram-negative, rod-shaped bacterium that was isolated from seawater.

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

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

	Last LPSN update	09-12-2024 (DD-MM-YYYY)
	Domain	*Bacteria*
	Phylum	*Pseudomonadota*
	Class	*Gammaproteobacteria*
	Order	*Oceanospirillales*
	Family	*Alcanivoracaceae*
	Genus	*Alcanivorax*
	Species	**Alcanivorax hongdengensis**
	Full Scientific Name (LPSN)	Alcanivorax hongdengensis Wu et al. 2009

Information on morphological and physiological properties Morphology

[Ref.: #28920]	Gram stain	negative
[Ref.: #125438]	Gram stain	negative Confidence in %96.47
[Ref.: #125439]	Gram stain	negative Confidence in %99.9

[Ref.: #28920]	Cell length	2.05 µm

[Ref.: #28920]	Cell width	0.65 µm

[Ref.: #28920]	Cell shape	rod-shaped

[Ref.: #28920]	Motility	no
[Ref.: #125439]	Motility	yes Confidence in %93.6

[Ref.: #28920]

Pigment production

Information on culture and growth conditions Culture and growth conditions

	Temperatures	Kind of temperature		Temperature
[Ref.: #28920]			growth	10-42 °C
[Ref.: #28920]			optimum	26.5 °C

	pH	Kind of pH		pH
[Ref.: #28920]			optimum	7.5
[Ref.: #28920]			growth	4.0-10.0

Information on physiology and metabolism Physiology and metabolism

[Ref.: #28920]

Oxygen tolerance

aerobe

[Ref.: #28920]	Ability of spore formation	no
[Ref.: #125438]	Ability of spore formation	no Confidence in %94.793
[Ref.: #125439]	Ability of spore formation	no Confidence in %99.9

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #28920]		NaCl		growth	0.5-15	%
[Ref.: #28920]		NaCl		optimum	5.5	%

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #28920]	3-hydroxybutyrate ChEBI	+	carbon source
[Ref.: #28920]	acetate ChEBI	+	carbon source
[Ref.: #28920]	methyl pyruvate ChEBI	+	carbon source
[Ref.: #28920]	nitrate ChEBI	+	reduction
[Ref.: #28920]	propionate ChEBI	+	carbon source
[Ref.: #28920]	succinate ChEBI	+	carbon source
[Ref.: #28920]	tween 40 ChEBI	+	carbon source
[Ref.: #28920]	tween 80 ChEBI	+	carbon source

	Enzymes	Enzyme	Enzyme activity
[Ref.: #28920]		gelatinase	+

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

[Ref.: #28920]	Sample type/isolated from	seawater
* marker position based on {}

Isolation sources categories

#Environmental

#Aquatic

#Marine

What are isolation sources categories?

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.: #28920]	Alcanivorax hongdengensis strain A-11-3 16S ribosomal RNA gene, partial sequence	EU438901	1504	GenBank ENA	1177179 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Alcanivorax hongdengensis A-11-3	GCA_000300995	contig	GenBank ENA	1177179 tax ID	*
[Ref.: #66792]	Alcanivorax hongdengensis A-11-3	1177179.3	wgs	PATRIC	1177179 tax ID	*
[Ref.: #66792]	Alcanivorax hongdengensis A-11-3	2531839231	draft	JGI IMG/M	1177179 tax ID	*

[Ref.: #28920]

GC-content

54.7 mol%

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

	Model	Trait	Prediction	Confidence in %	In training data
	Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Alcanivorax hongdengensis A-11-3 PATRIC: 1177179.3
[Ref.: #125438]	gram-positive	gram-positiveⓘ	no	96.47	yes
[Ref.: #125438]	anaerobic	anaerobicⓘ	no	95.103	yes
[Ref.: #125438]	spore-forming	spore-formingⓘ	no	94.793	yes
[Ref.: #125438]	aerobic	aerobicⓘ	yes	76.876	no
[Ref.: #125438]	thermophile	thermophilicⓘ	no	97.211	yes
[Ref.: #125438]	motile2+	flagellatedⓘ	yes	56.636	no

	Model	Trait	Prediction	Confidence in %
	Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Alcanivorax hongdengensis A-11-3 NCBI: GCA_000300995
[Ref.: #125439]	BacteriaNet	spore_formationⓘ	no	99.9
[Ref.: #125439]	BacteriaNet	motilityⓘ	yes	93.6
[Ref.: #125439]	BacteriaNet	gram_stainⓘ	negative	99.9
[Ref.: #125439]	BacteriaNet	oxygen_toleranceⓘ	obligate aerobe	63.7

Availability in culture collections External links

[Ref.: #28920]

Culture collection no.

CGMCC 1.7084, LMG 24624, MCCC 1A01496

[Ref.: #91436]

SI-ID 354038

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Alcanivorax nanhaiticus sp. nov., isolated from deep sea sediment.	Lai Q, Zhou Z, Li G, Li G, Shao Z	Int J Syst Evol Microbiol	10.1099/ijsem.0.001247	2016	*
Metabolism	Genes involved in alkane degradation in the Alcanivorax hongdengensis strain A-11-3.	Wang W, Shao Z	Appl Microbiol Biotechnol	10.1007/s00253-011-3818-x	2011	*
Metabolism	[Identification of almA genes involved in long-chain alkane degradation by Alcanivorax hongdengensis A-11-3].	Wang W, Shao Z	Wei Sheng Wu Xue Bao		2010	*
Phylogeny	Alcanivorax hongdengensis sp. nov., an alkane-degrading bacterium isolated from surface seawater of the straits of Malacca and Singapore, producing a lipopeptide as its biosurfactant.	Wu Y, Lai Q, Zhou Z, Qiao N, Liu C, Shao Z	Int J Syst Evol Microbiol	10.1099/ijs.0.001552-0	2009	*
Genetics	Genome sequence of the alkane-degrading bacterium Alcanivorax hongdengensis type strain A-11-3.	Lai Q, Shao Z	J Bacteriol	10.1128/JB.01849-12	2012	*

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 )

#28920

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 #25359 (see below)

#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) .

#91436

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-ID354038.1 )

#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 .

#25359

IJSEM 1474 2009 ( DOI 10.1099/ijs.0.001552-0 , PubMed 19502338 )

* These data were automatically processed and therefore are not curated

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