@ref: 31111
BacDive-ID: 134036
keywords: genome sequence, 16S sequence, facultative anaerobe, Gram-negative, rod-shaped
description: Gemmobacter lanyuensis Orc-4 is a facultative anaerobe, Gram-negative, rod-shaped prokaryote that was isolated from freshwater .
doi: 10.13145/bacdive134036.20251217.10
@ref: 31111
domain: Bacteria
phylum: Proteobacteria
class: Alphaproteobacteria
order: Rhodobacterales
family: Rhodobacteraceae
genus: Gemmobacter
species: Gemmobacter lanyuensis
strain designation: Orc-4
type strain: yes
| @ref | gram stain | cell length | cell width | cell shape | motility | confidence |
|---|---|---|---|---|---|---|
| 31111 | negative | 2 µm | 0.45 µm | rod-shaped | no | |
| 125438 | negative | 98.5 | ||||
| 125439 | negative | 93.2 |
| @ref | growth | type | temperature |
|---|---|---|---|
| 31111 | positive | growth | 15-40 |
| 31111 | positive | optimum | 27.5 |
| @ref | ability | type | pH | PH range |
|---|---|---|---|---|
| 31111 | positive | growth | 6.0-9.0 | alkaliphile |
| 31111 | positive | optimum | 7 |
| @ref | oxygen tolerance | confidence |
|---|---|---|
| 31111 | facultative anaerobe | |
| 125439 | obligate aerobe | 93.2 |
| @ref | salt | growth | tested relation | concentration |
|---|---|---|---|---|
| 31111 | NaCl | positive | growth | 0-1 % |
| 31111 | NaCl | positive | optimum | 0.25 % |
| @ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
|---|---|---|---|---|
| 31111 | 17754 | glycerol | + | carbon source |
| 31111 | 24996 | lactate | + | carbon source |
| 31111 | 29864 | mannitol | + | carbon source |
| 31111 | 37684 | mannose | + | carbon source |
| 31111 | 51850 | methyl pyruvate | + | carbon source |
| 31111 | 4853 | esculin | + | hydrolysis |
| 31111 | 17632 | nitrate | + | reduction |
| @ref | value | activity | ec |
|---|---|---|---|
| 31111 | acid phosphatase | + | 3.1.3.2 |
| 31111 | alkaline phosphatase | + | 3.1.3.1 |
| 31111 | catalase | + | 1.11.1.6 |
| 31111 | cytochrome oxidase | + | 1.9.3.1 |
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Environmental | #Aquatic | #Freshwater |
| #Environmental | #Aquatic | #Lake (large) |
| #Environmental | #Aquatic | #Pond (small) |
| #Environmental | #Aquatic | #River (Creek) |
| @ref | description | assembly level | INSDC accession | BV-BRC accession | IMG accession | NCBI tax ID | score |
|---|---|---|---|---|---|---|---|
| 66792 | ASM1465235v1 assembly for Gemmobacter lanyuensis KCTC 23714 | scaffold | GCA_014652355 | 1054497.3 | 2995380663 | 1054497 | 67.73 |
| 124043 | ASM4266084v1 assembly for Gemmobacter lanyuensis KCTC 23714 | contig | GCA_042660845 | 1054497 | 76.19 | ||
| 124043 | ASM4268134v1 assembly for Gemmobacter lanyuensis KCTC 23714 | contig | GCA_042681345 | 1054497 |
| @ref | model | trait | description | prediction | confidence | training_data |
|---|---|---|---|---|---|---|
| 125439 | BacteriaNet | oxygen_tolerance | Oxygenic conditions needed for growth | obligate aerobe | 93.2 | |
| 125439 | BacteriaNet | gram_stain | Reaction to gram-staining | negative | 93.2 | |
| 125439 | BacteriaNet | motility | Ability to perform movement | yes | 53.4 | |
| 125439 | BacteriaNet | spore_formation | Ability to form endo- or exospores | no | 89.3 | |
| 125438 | gram-positive | gram-positive | Positive reaction to Gram-staining | no | 98.5 | yes |
| 125438 | anaerobic | anaerobic | Ability to grow under anoxygenic conditions (including facultative anaerobes) | no | 87.992 | no |
| 125438 | aerobic | aerobic | Ability to grow under oxygenic conditions (including facultative aerobes) | yes | 67.898 | yes |
| 125438 | spore-forming | spore-forming | Ability to form endo- or exospores | no | 87.185 | no |
| 125438 | thermophile | thermophilic | Ability to grow at temperatures above or equal to 45°C | no | 96.6 | yes |
| 125438 | motile2+ | flagellated | Ability to perform flagellated movement | yes | 70.606 | no |
@ref: 31111
culture collection no.: BCRC 80378, LMG 26667, KCTC 23714
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 23728371 | Gemmobacter lanyuensis sp. nov., isolated from a freshwater spring. | Sheu SY, Shiau YW, Wei YT, Chen WM | Int J Syst Evol Microbiol | 10.1099/ijs.0.052399-0 | 2013 | Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Fresh Water/*microbiology, Hydroxybutyrates, Molecular Sequence Data, Natural Springs/*microbiology, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, Polyesters, RNA, Ribosomal, 16S/genetics, Rhodobacteraceae/*classification/genetics/isolation & purification, Sequence Analysis, DNA, Taiwan, Ubiquinone/analogs & derivatives/chemistry | Genetics |
| Phylogeny | 32553048 | Gemmobacter serpentinus sp. nov., isolated from conserved forages. | Lim K, Kannan AD, Shobnam N, Mahmood M, Lee J, Im J | Int J Syst Evol Microbiol | 10.1099/ijsem.0.004276 | 2020 | Animal Feed/*microbiology, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Kansas, *Phylogeny, RNA, Ribosomal, 16S/genetics, Rhodobacteraceae/*classification/isolation & purification, Sequence Analysis, DNA, Ubiquinone/analogs & derivatives/chemistry | Transcriptome |
| @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 | ||
| 31111 | 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 | 27440 | 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 | ||
| 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/ | ||
| 124043 | Isabel Schober, Julia Koblitz | Data extracted from sequence databases, automatically matched based on designation and taxonomy | |||
| 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 | ||
| 126262 | A. Lissin, I. Schober, J. F. Witte, H. Lüken, A. Podstawka, J. Koblitz, B. Bunk, P. Dawyndt, P. Vandamme, P. de Vos, J. Overmann, L. C. Reimer | StrainInfo—the central database for linked microbial strain identifiers | 10.1093/database/baaf059 |
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