Strain identifier
BacDive ID: 133431
Type strain: 
Species: Alcanivorax hongdengensis
Strain Designation: A-11-3
NCBI tax ID(s): 519051 (species)
version 9.3 (current version)
General
@ref: 28920
BacDive-ID: 133431
keywords: genome sequence, 16S sequence, Bacteria, aerobe, Gram-negative, rod-shaped
description: Alcanivorax hongdengensis A-11-3 is an aerobe, Gram-negative, rod-shaped bacterium that was isolated from seawater.
NCBI tax id
- NCBI tax id: 519051
- Matching level: species
doi: 10.13145/bacdive133431.20250331.9.3
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Gammaproteobacteria
- order: Oceanospirillales
- family: Alcanivoracaceae
- genus: Alcanivorax
- species: Alcanivorax hongdengensis
- full scientific name: Alcanivorax hongdengensis Wu et al. 2009
@ref: 28920
domain: Bacteria
phylum: Proteobacteria
class: Gammaproteobacteria
order: Oceanospirillales
family: Alcanivoracaceae
genus: Alcanivorax
species: Alcanivorax hongdengensis
strain designation: A-11-3
type strain: yes
Morphology
cell morphology
| @ref | gram stain | cell length | cell width | cell shape | motility | confidence |
|---|---|---|---|---|---|---|
| 28920 | negative | 2.05 µm | 0.65 µm | rod-shaped | no | |
| 125438 | negative | 96.47 | ||||
| 125439 | negative | 99.9 | ||||
| 125439 | yes | 93.6 |
pigmentation
- @ref: 28920
- production: no
Culture and growth conditions
culture temp
| @ref | growth | type | temperature |
|---|---|---|---|
| 28920 | positive | growth | 10-42 |
| 28920 | positive | optimum | 26.5 |
culture pH
| @ref | ability | type | pH | PH range |
|---|---|---|---|---|
| 28920 | positive | growth | 4.0-10.0 | alkaliphile |
| 28920 | positive | optimum | 7.5 |
Physiology and metabolism
oxygen tolerance
- @ref: 28920
- oxygen tolerance: aerobe
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 28920 | no | |
| 125438 | no | 94.793 |
| 125439 | no | 99.9 |
halophily
| @ref | salt | growth | tested relation | concentration |
|---|---|---|---|---|
| 28920 | NaCl | positive | growth | 0.5-15 % |
| 28920 | NaCl | positive | optimum | 5.5 % |
metabolite utilization
| @ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
|---|---|---|---|---|
| 28920 | 37054 | 3-hydroxybutyrate | + | carbon source |
| 28920 | 30089 | acetate | + | carbon source |
| 28920 | 17272 | propionate | + | carbon source |
| 28920 | 51850 | methyl pyruvate | + | carbon source |
| 28920 | 30031 | succinate | + | carbon source |
| 28920 | 53423 | tween 40 | + | carbon source |
| 28920 | 53426 | tween 80 | + | carbon source |
| 28920 | 17632 | nitrate | + | reduction |
enzymes
- @ref: 28920
- value: gelatinase
- activity: +
Isolation, sampling and environmental information
isolation
- @ref: 28920
- sample type: seawater
isolation source categories
- Cat1: #Environmental
- Cat2: #Aquatic
- Cat3: #Marine
Sequence information
16S sequences
- @ref: 28920
- description: Alcanivorax hongdengensis strain A-11-3 16S ribosomal RNA gene, partial sequence
- accession: EU438901
- length: 1504
- database: nuccore
- NCBI tax ID: 1177179
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Alcanivorax hongdengensis A-11-3 | GCA_000300995 | contig | ncbi | 1177179 |
| 66792 | Alcanivorax hongdengensis A-11-3 | 1177179.3 | wgs | patric | 1177179 |
| 66792 | Alcanivorax hongdengensis A-11-3 | 2531839231 | draft | img | 1177179 |
GC content
- @ref: 28920
- GC-content: 54.7
Genome-based predictions
predictions
| @ref | model | trait | description | prediction | confidence | training_data |
|---|---|---|---|---|---|---|
| 125438 | gram-positive | gram-positive | Positive reaction to Gram-staining | no | 96.47 | yes |
| 125438 | anaerobic | anaerobic | Ability to grow under anoxygenic conditions (including facultative anaerobes) | no | 95.103 | yes |
| 125438 | spore-forming | spore-forming | Ability to form endo- or exospores | no | 94.793 | yes |
| 125438 | aerobic | aerobic | Ability to grow under oxygenic conditions (including facultative aerobes) | yes | 76.876 | no |
| 125438 | thermophile | thermophilic | Ability to grow at temperatures above or equal to 45°C | no | 97.211 | yes |
| 125438 | motile2+ | flagellated | Ability to perform flagellated movement | yes | 56.636 | no |
| 125439 | BacteriaNet | spore_formation | Ability to form endo- or exospores | no | 99.9 | |
| 125439 | BacteriaNet | motility | Ability to perform movement | yes | 93.6 | |
| 125439 | BacteriaNet | gram_stain | Reaction to gram-staining | negative | 99.9 | |
| 125439 | BacteriaNet | oxygen_tolerance | Oxygenic conditions needed for growth | obligate aerobe | 63.7 |
External links
@ref: 28920
culture collection no.: CGMCC 1.7084, LMG 24624, MCCC 1A01496
straininfo link
- @ref: 91436
- straininfo: 354038
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 19502338 | 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 | Alcanivoraceae/*classification/genetics/isolation & purification/physiology, Alkanes/*metabolism, Bacterial Proteins/genetics, Bacterial Typing Techniques, Base Composition, Biodegradation, Environmental, China, DNA, Bacterial/analysis, DNA, Ribosomal Spacer/analysis, Fatty Acids/analysis, Lipopeptides/*biosynthesis, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, Phylogeny, Polymerase Chain Reaction/methods, RNA, Ribosomal, 16S/genetics, RNA, Ribosomal, 23S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, Species Specificity, Surface-Active Agents/metabolism | Metabolism |
| Metabolism | 20931873 | [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 | Alcanivoraceae/*genetics/metabolism, Alkanes/*metabolism, Biodegradation, Environmental, Cloning, Molecular, *Genes, Bacterial, Polymerase Chain Reaction | Enzymology | |
| Metabolism | 22207216 | 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 | Alcanivoraceae/*genetics/isolation & purification/*metabolism, Alkanes/*metabolism, Biotransformation, Cloning, Molecular, DNA, Bacterial/chemistry/genetics, Gene Expression, Metabolic Networks and Pathways/*genetics, Molecular Sequence Data, Polymerase Chain Reaction, Pseudomonas fluorescens/genetics, Pseudomonas putida/genetics, Seawater/microbiology, Sequence Analysis, DNA, Singapore | Enzymology |
| Genetics | 23209226 | 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 | Alcanivoraceae/*genetics/isolation & purification/metabolism, Alkanes/*metabolism, Base Sequence, Biodegradation, Environmental, Cytochrome P-450 Enzyme System/genetics, DNA, Bacterial/genetics, *Genome, Bacterial, Molecular Sequence Data, Petroleum/microbiology, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA | Phylogeny |
| Phylogeny | 27307296 | 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 | Alcanivoraceae/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Geologic Sediments/*microbiology, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA | Transcriptome |
Reference
| @id | authors | title | doi/url | ID_cross_reference | pubmed |
|---|---|---|---|---|---|
| 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 | 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 | 10.1128/mSphere.00237-17 | 25359 | 28776041 |
| 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) | https://diaspora-project.de/progress.html#genomes | ||
| 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 | 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 | 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 | https://github.com/GenomeNet/deepG |