Strain identifier
BacDive ID: 130663
Type strain: 
Species: Parapedobacter indicus
Strain Designation: RK1
Strain history: <- R. Lal, Univ. Delhi, Dept. Zoology, India; RK1 <- R. Kumar
NCBI tax ID(s): 1477437 (species)
version 8.1 (current version)
General
@ref: 22051
BacDive-ID: 130663
DSM-Number: 28470
keywords: genome sequence, 16S sequence, Bacteria, Gram-negative
description: Parapedobacter indicus RK1 is a Gram-negative bacterium that was isolated from hexachlorocyclohexane-contaminated dumpsite soil.
NCBI tax id
- NCBI tax id: 1477437
- Matching level: species
strain history
- @ref: 22051
- history: <- R. Lal, Univ. Delhi, Dept. Zoology, India; RK1 <- R. Kumar
doi: 10.13145/bacdive130663.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/bacteroidota
- domain: Bacteria
- phylum: Bacteroidota
- class: Sphingobacteriia
- order: Sphingobacteriales
- family: Sphingobacteriaceae
- genus: Parapedobacter
- species: Parapedobacter indicus
- full scientific name: Parapedobacter indicus Kumar et al. 2015
@ref: 22051
domain: Bacteria
phylum: Bacteroidetes
class: Sphingobacteriia
order: Sphingobacteriales
family: Sphingobacteriaceae
genus: Parapedobacter
species: Parapedobacter indicus
full scientific name: Parapedobacter indicus Kumar et al. 2015
strain designation: RK1
type strain: yes
Morphology
cell morphology
- @ref: 69480
- gram stain: negative
- confidence: 99.994
Physiology and metabolism
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 69481 | no | 100 |
| 69480 | no | 99.987 |
Isolation, sampling and environmental information
isolation
- @ref: 22051
- sample type: hexachlorocyclohexane-contaminated dumpsite soil
- geographic location: Lucknow, Ummari village
- country: India
- origin.country: IND
- continent: Asia
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Engineered | #Built environment | |
| #Engineered | #Contamination | |
| #Environmental | #Terrestrial | #Soil |
taxonmaps
- @ref: 69479
- File name: preview.99_95314.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_15793;96_16039;97_19679;98_24602;99_95314&stattab=map
- Last taxonomy: Parapedobacter indicus subclade
- 16S sequence: KJ101506
- Sequence Identity:
- Total samples: 191
- soil counts: 85
- aquatic counts: 73
- animal counts: 16
- plant counts: 17
Sequence information
16S sequences
- @ref: 22051
- description: Parapedobacter indicus strain RK1 16S ribosomal RNA gene, partial sequence
- accession: KJ101506
- length: 1466
- database: ena
- NCBI tax ID: 1477437
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Parapedobacter indicus RK1 | GCA_002934635 | scaffold | ncbi | 1477437 |
| 66792 | Parapedobacter indicus RK1 | GCA_900113765 | scaffold | ncbi | 1477437 |
| 66792 | Parapedobacter indicus RK1 | 2671180231 | draft | img | 1477437 |
| 66792 | Parapedobacter indicus DSM 28470 | 2728369513 | draft | img | 1477437 |
GC content
- @ref: 22051
- GC-content: 44.5
- method: fluorimetric
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | no | 100 | no |
| flagellated | no | 97.134 | no |
| gram-positive | no | 97.728 | no |
| anaerobic | no | 99.159 | no |
| aerobic | yes | 86.582 | no |
| halophile | no | 89.542 | no |
| spore-forming | no | 94.85 | no |
| glucose-util | yes | 88.997 | no |
| motile | no | 94.041 | no |
| glucose-ferment | no | 88.16 | no |
| thermophile | no | 98.634 | no |
External links
@ref: 22051
culture collection no.: DSM 28470, MCC 2546
literature
- topic: Phylogeny
- Pubmed-ID: 25298380
- title: Parapedobacter indicus sp. nov., isolated from hexachlorocyclohexane-contaminated soil.
- authors: Kumar R, Dwivedi V, Nayyar N, Verma H, Singh AK, Rani P, Rao DLN, Lal R
- journal: Int J Syst Evol Microbiol
- DOI: 10.1099/ijs.0.069104-0
- year: 2014
- mesh: Bacterial Typing Techniques, Bacteroidetes/*classification/genetics/isolation & purification, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Hexachlorocyclohexane/analysis, India, Molecular Sequence Data, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Soil Pollutants/analysis, Spermidine/chemistry, Vitamin K 2/analogs & derivatives/chemistry
- topic2: Genetics
Reference
| @id | authors | title | doi/url | catalogue | journal | 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 | |||
| 22051 | Curators of the DSMZ | https://www.dsmz.de/collection/catalogue/details/culture/DSM-28470 | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 28470) | |||
| 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 | Nucleic Acids Res. 49: D498-D508 2020 | 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 | 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 |