Strain identifier
BacDive ID: 387
Type strain: 
Species: Paralcaligenes ureilyticus
Strain Designation: GR24-5
Strain history: <- S. W. Kwon, KACC; GR24-5
NCBI tax ID(s): 627131 (species)
version 8.1 (current version)
General
@ref: 17702
BacDive-ID: 387
DSM-Number: 24591
keywords: genome sequence, 16S sequence, Bacteria, mesophilic, motile
description: Paralcaligenes ureilyticus GR24-5 is a mesophilic, motile bacterium that was isolated from soil of ginseng field.
NCBI tax id
- NCBI tax id: 627131
- Matching level: species
strain history
- @ref: 17702
- history: <- S. W. Kwon, KACC; GR24-5
doi: 10.13145/bacdive387.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Betaproteobacteria
- order: Burkholderiales
- family: Alcaligenaceae
- genus: Paralcaligenes
- species: Paralcaligenes ureilyticus
- full scientific name: Paralcaligenes ureilyticus Kim et al. 2011
@ref: 17702
domain: Bacteria
phylum: Proteobacteria
class: Betaproteobacteria
order: Burkholderiales
family: Alcaligenaceae
genus: Paralcaligenes
species: Paralcaligenes ureilyticus
full scientific name: Paralcaligenes ureilyticus Kim et al. 2011
strain designation: GR24-5
type strain: yes
Morphology
cell morphology
| @ref | motility | confidence | gram stain |
|---|---|---|---|
| 69480 | yes | 94.537 | |
| 69480 | 99.997 | negative |
colony morphology
- @ref: 17702
- incubation period: 3-7 days
Culture and growth conditions
culture medium
- @ref: 17702
- name: REACTIVATION WITH LIQUID MEDIUM 830 (DSMZ Medium 830c)
- growth: yes
- link: https://mediadive.dsmz.de/medium/830c
- composition: Name: REACTIVATION WITH LIQUID MEDIUM 830 (DSMZ Medium 830c) Composition: Agar 15.0 g/l Yeast extract 0.5 g/l Proteose peptone 0.5 g/l Casamino acids 0.5 g/l Glucose 0.5 g/l Starch 0.5 g/l K2HPO4 0.3 g/l Na-pyruvate 0.3 g/l MgSO4 x 7 H2O 0.05 g/l Distilled water
culture temp
- @ref: 17702
- growth: positive
- type: growth
- temperature: 28
- range: mesophilic
Physiology and metabolism
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 69481 | no | 100 |
| 69480 | no | 99.905 |
metabolite utilization
| @ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
|---|---|---|---|---|
| 68369 | 25115 | malate | + | assimilation |
| 68369 | 17128 | adipate | - | assimilation |
| 68369 | 27689 | decanoate | - | assimilation |
| 68369 | 24265 | gluconate | - | assimilation |
| 68369 | 17306 | maltose | - | assimilation |
| 68369 | 59640 | N-acetylglucosamine | - | assimilation |
| 68369 | 16899 | D-mannitol | - | assimilation |
| 68369 | 16024 | D-mannose | - | assimilation |
| 68369 | 30849 | L-arabinose | - | assimilation |
| 68369 | 17634 | D-glucose | - | assimilation |
| 68369 | 5291 | gelatin | - | hydrolysis |
| 68369 | 4853 | esculin | - | hydrolysis |
| 68369 | 16199 | urea | + | hydrolysis |
| 68369 | 29016 | arginine | - | hydrolysis |
| 68369 | 17634 | D-glucose | - | fermentation |
| 68369 | 27897 | tryptophan | - | energy source |
| 68369 | 17632 | nitrate | - | reduction |
metabolite production
- @ref: 68369
- Chebi-ID: 35581
- metabolite: indole
- production: no
metabolite tests
- @ref: 68369
- Chebi-ID: 35581
- metabolite: indole
- indole test: -
enzymes
| @ref | value | activity | ec |
|---|---|---|---|
| 68369 | cytochrome oxidase | + | 1.9.3.1 |
| 68369 | gelatinase | - | |
| 68369 | beta-glucosidase | - | 3.2.1.21 |
| 68369 | urease | + | 3.5.1.5 |
| 68369 | arginine dihydrolase | - | 3.5.3.6 |
API 20NE
| @ref | NO3 | TRP | GLU_ Ferm | ADH Arg | URE | ESC | GEL | PNPG | GLU_ Assim | ARA | MNE | MAN | NAG | MAL | GNT | CAP | ADI | MLT | CIT | PAC | OX |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 17702 | - | - | - | - | + | - | - | - | - | - | - | - | - | - | - | - | - | + | - | - | + |
Isolation, sampling and environmental information
isolation
- @ref: 17702
- sample type: soil of ginseng field
- country: Republic of Korea
- origin.country: KOR
- continent: Asia
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Engineered | #Agriculture | #Field |
| #Environmental | #Terrestrial | #Soil |
| #Host | #Plants | #Herbaceous plants (Grass,Crops) |
taxonmaps
- @ref: 69479
- File name: preview.99_68706.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_7;96_2229;97_2828;98_48347;99_68706&stattab=map
- Last taxonomy: Paralcaligenes ureilyticus
- 16S sequence: FJ793551
- Sequence Identity:
- Total samples: 146
- soil counts: 102
- aquatic counts: 16
- animal counts: 18
- plant counts: 10
Safety information
risk assessment
- @ref: 17702
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 17702
- description: Paralcaligenes ureilyticus strain GR24-5 16S ribosomal RNA gene, partial sequence
- accession: FJ793551
- length: 1441
- database: ena
- NCBI tax ID: 627131
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Paralcaligenes ureilyticus DSM 24591 | GCA_004346225 | contig | ncbi | 627131 |
| 66792 | Paralcaligenes ureilyticus strain DSM 24591 | 627131.3 | wgs | patric | 627131 |
| 66792 | Paralcaligenes ureilyticus DSM 24591 | 2784746800 | draft | img | 627131 |
GC content
- @ref: 17702
- GC-content: 55.1
- method: high performance liquid chromatography (HPLC)
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | no | 100 | no |
| gram-positive | no | 97.68 | no |
| anaerobic | no | 99.268 | no |
| halophile | no | 88.162 | no |
| spore-forming | no | 93.979 | no |
| glucose-util | no | 59.774 | no |
| thermophile | no | 98.411 | no |
| flagellated | no | 71.149 | no |
| aerobic | yes | 88.081 | no |
| motile | yes | 81.02 | no |
| glucose-ferment | no | 89.226 | no |
External links
@ref: 17702
culture collection no.: DSM 24591, KACC 13888
straininfo link
- @ref: 70067
- straininfo: 401601
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 21717340 | Paralcaligenes ureilyticus gen. nov., sp. nov. isolated from soil of a Korean ginseng field. | Kim SJ, Yoo SH, Weon HY, Kim YS, Anandham R, Suh JS, Kwon SW | J Microbiol | 10.1007/s12275-011-0076-7 | 2011 | *Agriculture, Alcaligenaceae/*classification/genetics/*isolation & purification/physiology, Bacterial Typing Techniques, DNA, Bacterial/analysis/genetics, Genes, rRNA, Panax/*growth & development, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, *Soil Microbiology, Species Specificity | Phenotype |
| Phylogeny | 26122887 | Paralcaligenes ginsengisoli sp. nov., isolated from ginseng cultivated soil. | Kang JP, Nguyen NL, Kim YJ, Hoang VA, Bae KS, Yang DC | Antonie Van Leeuwenhoek | 10.1007/s10482-015-0517-0 | 2015 | Aerobiosis, Alcaligenaceae/*classification/genetics/*isolation & purification/physiology, Bacterial Typing Techniques, Base Composition, Catalase/analysis, Cluster Analysis, Cytosol/chemistry, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Korea, Locomotion, Molecular Sequence Data, Nucleic Acid Hybridization, Oxidoreductases/analysis, Panax/*growth & development, Phospholipids/analysis, Phylogeny, Putrescine/analysis, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology | Enzymology |
Reference
| @id | authors | catalogue | doi/url | title | journal | pubmed |
|---|---|---|---|---|---|---|
| 17702 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 24591) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-24591 | |||
| 20215 | Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M. | 10.1099/ijsem.0.004332 | List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ | |||
| 66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | 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 | 10.1093/nar/gkaa1025 | BRENDA, the ELIXIR core data resource in 2021: new developments and updates | Nucleic Acids Res. 49: D498-D508 2020 | 33211880 | |
| 68369 | Automatically annotated from API 20NE | |||||
| 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. | https://microbeatlas.org/ | MicrobeAtlas 1.0 beta | |||
| 69480 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | 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 | 10.21203/rs.3.rs-2527258/v1 | Predictions based on the model GenomeNet Sporulation v. 1 | |||
| 70067 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID401601.1 | StrainInfo: A central database for resolving microbial strain identifiers |