Strain identifier
BacDive ID: 133454
Type strain:
Species: Paracoccus chinensis
Strain Designation: KS-11
NCBI tax ID(s): 525640 (species)
version 8.1 (current version)
General
@ref: 29041
BacDive-ID: 133454
keywords: genome sequence, 16S sequence, Bacteria, aerobe, Gram-negative, motile, ovoid-shaped
description: Paracoccus chinensis KS-11 is an aerobe, Gram-negative, motile bacterium that was isolated from freshwater sediment .
NCBI tax id
- NCBI tax id: 525640
- Matching level: species
doi: 10.13145/bacdive133454.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Alphaproteobacteria
- order: Rhodobacterales
- family: Paracoccaceae
- genus: Paracoccus
- species: Paracoccus chinensis
- full scientific name: Paracoccus chinensis Li et al. 2009
@ref: 29041
domain: Bacteria
phylum: Proteobacteria
class: Alphaproteobacteria
order: Rhodobacterales
family: Rhodobacteraceae
genus: Paracoccus
species: Paracoccus chinensis
strain designation: KS-11
type strain: yes
Morphology
cell morphology
@ref | gram stain | cell length | cell width | cell shape | motility | confidence |
---|---|---|---|---|---|---|
29041 | negative | 1.75 µm | 1.15 µm | ovoid-shaped | yes | |
69480 | negative | 99.99 |
Culture and growth conditions
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
29041 | positive | growth | 25-40 | |
29041 | positive | optimum | 28-37 | mesophilic |
culture pH
@ref | ability | type | pH | PH range |
---|---|---|---|---|
29041 | positive | growth | 6-9.5 | alkaliphile |
29041 | positive | optimum | 7.5-9 |
Physiology and metabolism
oxygen tolerance
- @ref: 29041
- oxygen tolerance: aerobe
spore formation
@ref | spore formation | confidence |
---|---|---|
29041 | no | |
69481 | no | 100 |
69480 | no | 99.993 |
halophily
- @ref: 29041
- salt: NaCl
- growth: positive
- tested relation: growth
- concentration: 0-1 %
observation
- @ref: 29041
- observation: aggregates in chains
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
29041 | 30089 | acetate | + | carbon source |
29041 | 16449 | alanine | + | carbon source |
29041 | 22653 | asparagine | + | carbon source |
29041 | 16947 | citrate | + | carbon source |
29041 | 28757 | fructose | + | carbon source |
29041 | 33984 | fucose | + | carbon source |
29041 | 28260 | galactose | + | carbon source |
29041 | 24265 | gluconate | + | carbon source |
29041 | 17234 | glucose | + | carbon source |
29041 | 27570 | histidine | + | carbon source |
29041 | 17716 | lactose | + | carbon source |
29041 | 17306 | maltose | + | carbon source |
29041 | 37684 | mannose | + | carbon source |
29041 | 28053 | melibiose | + | carbon source |
29041 | 26271 | proline | + | carbon source |
29041 | 15361 | pyruvate | + | carbon source |
29041 | 33942 | ribose | + | carbon source |
29041 | 17814 | salicin | + | carbon source |
29041 | 30911 | sorbitol | + | carbon source |
29041 | 17992 | sucrose | + | carbon source |
29041 | 27082 | trehalose | + | carbon source |
29041 | 18222 | xylose | + | carbon source |
29041 | 17632 | nitrate | + | reduction |
enzymes
@ref | value | activity | ec |
---|---|---|---|
29041 | catalase | + | 1.11.1.6 |
29041 | cytochrome oxidase | + | 1.9.3.1 |
29041 | urease | + | 3.5.1.5 |
Isolation, sampling and environmental information
isolation
- @ref: 29041
- sample type: freshwater sediment (river, lake, pond)
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#Environmental | #Aquatic | #Freshwater |
#Environmental | #Aquatic | #Lake (large) |
#Environmental | #Aquatic | #Pond (small) |
#Environmental | #Aquatic | #River (Creek) |
taxonmaps
- @ref: 69479
- File name: preview.99_11251.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_19;96_1674;97_3137;98_8401;99_11251&stattab=map
- Last taxonomy: Paracoccus
- 16S sequence: EU660389
- Sequence Identity:
- Total samples: 16440
- soil counts: 1527
- aquatic counts: 4482
- animal counts: 9541
- plant counts: 890
Sequence information
16S sequences
- @ref: 29041
- description: Paracoccus chinensis strain KS-11 16S ribosomal RNA gene, partial sequence
- accession: EU660389
- length: 1362
- database: nuccore
- NCBI tax ID: 525640
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Paracoccus chinensis CGMCC 1.7655 | GCA_900102885 | contig | ncbi | 525640 |
66792 | Paracoccus chinensis strain CGMCC 1.7655 | 525640.3 | wgs | patric | 525640 |
66792 | Paracoccus chinensis CGMCC 1.7655 | 2617270907 | draft | img | 525640 |
GC content
- @ref: 29041
- GC-content: 69
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 100 | no |
gram-positive | no | 97.568 | yes |
anaerobic | no | 97.368 | yes |
halophile | no | 86.731 | yes |
spore-forming | no | 96.27 | yes |
glucose-util | yes | 85.293 | yes |
thermophile | no | 93.621 | no |
motile | no | 59.274 | yes |
aerobic | yes | 88.745 | yes |
flagellated | no | 91.724 | no |
glucose-ferment | no | 91.856 | no |
External links
@ref: 29041
culture collection no.: CGMCC 1.7655, NBRC 104937
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 19625438 | Paracoccus chinensis sp. nov., isolated from sediment of a reservoir. | Li HF, Qu JH, Yang JS, Li ZJ, Yuan HL | Int J Syst Evol Microbiol | 10.1099/ijs.0.004705-0 | 2009 | DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fatty Acids/chemistry/metabolism, Fresh Water/*microbiology, Molecular Sequence Data, Paracoccus/*classification/genetics/*isolation & purification/metabolism, Phylogeny, RNA, Ribosomal, 16S/genetics | Metabolism |
Phylogeny | 20936429 | Paracoccus niistensis sp. nov., isolated from forest soil, India. | Dastager SG, Deepa CK, Li WJ, Tang SK, Pandey A | Antonie Van Leeuwenhoek | 10.1007/s10482-010-9515-4 | 2010 | India, Paracoccus/classification/*genetics/*metabolism, Phylogeny, Polymerase Chain Reaction, Sequence Analysis, DNA, *Soil Microbiology, *Trees | Transcriptome |
Phylogeny | 30325298 | Paracoccus salipaludis sp. nov., isolated from saline-alkaline soil. | Dong X, Zhang G, Xiong Q, Liu D, Wang D, Liu Y, Wu G, Li P, Luo Y, Zhang R | Int J Syst Evol Microbiol | 10.1099/ijsem.0.003065 | 2018 | Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Nucleic Acid Hybridization, Paracoccus/*classification/genetics/isolation & purification, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Salinity, Sequence Analysis, DNA, *Soil Microbiology, Ubiquinone/analogs & derivatives/chemistry | Transcriptome |
Reference
@id | authors | title | doi/url | ID_cross_reference | pubmed | journal |
---|---|---|---|---|---|---|
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 | |||
29041 | 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 | 25471 | 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 | |||
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 | 10.1093/nar/gkaa1025 | 33211880 | Nucleic Acids Res. 49: D498-D508 2020 | |
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 | https://microbeatlas.org/ | |||
69480 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | https://diaspora-project.de/progress.html#genomes | |||
69481 | Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch | Predictions based on the model GenomeNet Sporulation v. 1 | 10.21203/rs.3.rs-2527258/v1 |