Sphingopyxis alaskensis DSM 13593 is an aerobe, mesophilic, Gram-negative prokaryote that was isolated from seawater.
Gram-negative motile rod-shaped aerobe mesophilic genome sequence 16S sequence| @ref 20215 |
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| Domain Pseudomonadati |
| Phylum Pseudomonadota |
| Class Alphaproteobacteria |
| Order Sphingomonadales |
| Family Sphingomonadaceae |
| Genus Sphingopyxis |
| Species Sphingopyxis alaskensis |
| Full scientific name Sphingopyxis alaskensis (Vancanneyt et al. 2001) Godoy et al. 2003 |
| Synonyms (1) |
| BacDive ID | Other strains from Sphingopyxis alaskensis (2) | Type strain |
|---|---|---|
| 100142 | S. alaskensis ST022281(HKI), F104, P479, DoHKI85, BI 11497, | |
| 137733 | S. alaskensis CIP 103050 |
| @ref | Name | Growth | Medium link | Composition | |
|---|---|---|---|---|---|
| 5101 | TRYPTONE SOYA BROTH (TSB) (DSMZ Medium 545) | Medium recipe at MediaDive | Name: TRYPTONE SOYA BROTH (TSB) (DSMZ Medium 545) Composition: Casein peptone 17.0 g/l NaCl 5.0 g/l Soy peptone 3.0 g/l D(+)-Glucose 2.5 g/l K2HPO4 2.5 g/l Distilled water | ||
| 37377 | MEDIUM 72- for trypto casein soja agar | Distilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g) | |||
| 116175 | CIP Medium 72 | Medium recipe at CIP |
| @ref | Spore formation | Confidence | |
|---|---|---|---|
| 125438 | 92.84 |
| @ref | Salt | Growth | Tested relation | Concentration | |
|---|---|---|---|---|---|
| 116175 | NaCl | positive | growth | 0-10 % |
| @ref | Chebi-ID | Metabolite | Utilization activity | Kind of utilization tested | |
|---|---|---|---|---|---|
| 68369 | 17128 ChEBI | adipate | - | assimilation | from API 20NE |
| 68369 | 29016 ChEBI | arginine | - | hydrolysis | from API 20NE |
| 116175 | 16947 ChEBI | citrate | - | carbon source | |
| 68369 | 17634 ChEBI | D-glucose | + | assimilation | from API 20NE |
| 68369 | 17634 ChEBI | D-glucose | - | fermentation | from API 20NE |
| 68369 | 16899 ChEBI | D-mannitol | - | assimilation | from API 20NE |
| 68369 | 16024 ChEBI | D-mannose | - | assimilation | from API 20NE |
| 68369 | 27689 ChEBI | decanoate | - | assimilation | from API 20NE |
| 116175 | 4853 ChEBI | esculin | + | hydrolysis | |
| 68369 | 4853 ChEBI | esculin | + | hydrolysis | from API 20NE |
| 68369 | 5291 ChEBI | gelatin | - | hydrolysis | from API 20NE |
| 68369 | 24265 ChEBI | gluconate | - | assimilation | from API 20NE |
| 68369 | 30849 ChEBI | L-arabinose | - | assimilation | from API 20NE |
| 68369 | 25115 ChEBI | malate | + | assimilation | from API 20NE |
| 68369 | 17306 ChEBI | maltose | + | assimilation | from API 20NE |
| 68369 | 59640 ChEBI | N-acetylglucosamine | - | assimilation | from API 20NE |
| 116175 | 17632 ChEBI | nitrate | - | reduction | |
| 116175 | 17632 ChEBI | nitrate | - | respiration | |
| 68369 | 17632 ChEBI | nitrate | - | reduction | from API 20NE |
| 116175 | 16301 ChEBI | nitrite | - | reduction | |
| 68369 | 27897 ChEBI | tryptophan | - | energy source | from API 20NE |
| 68369 | 16199 ChEBI | urea | - | hydrolysis | from API 20NE |
| @ref | Metabolite | Is antibiotic | Is sensitive | Is resistant | |
|---|---|---|---|---|---|
| 116175 | 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate) |
| @ref | Value | Activity | Ec | |
|---|---|---|---|---|
| 68382 | acid phosphatase | + | 3.1.3.2 | from API zym |
| 116175 | alcohol dehydrogenase | - | 1.1.1.1 | |
| 68382 | alkaline phosphatase | + | 3.1.3.1 | from API zym |
| 68382 | alpha-chymotrypsin | - | 3.4.21.1 | from API zym |
| 68382 | alpha-fucosidase | - | 3.2.1.51 | from API zym |
| 68382 | alpha-galactosidase | - | 3.2.1.22 | from API zym |
| 68382 | alpha-glucosidase | + | 3.2.1.20 | from API zym |
| 68382 | alpha-mannosidase | - | 3.2.1.24 | from API zym |
| 116175 | amylase | - | ||
| 68369 | arginine dihydrolase | - | 3.5.3.6 | from API 20NE |
| 68382 | beta-galactosidase | - | 3.2.1.23 | from API zym |
| 116175 | beta-galactosidase | + | 3.2.1.23 | |
| 68382 | beta-glucosidase | - | 3.2.1.21 | from API zym |
| 68369 | beta-glucosidase | + | 3.2.1.21 | from API 20NE |
| 68382 | beta-glucuronidase | + | 3.2.1.31 | from API zym |
| 116175 | caseinase | - | 3.4.21.50 | |
| 116175 | catalase | + | 1.11.1.6 | |
| 68382 | cystine arylamidase | + | 3.4.11.3 | from API zym |
| 68369 | cytochrome oxidase | - | 1.9.3.1 | from API 20NE |
| 116175 | DNase | - | ||
| 68382 | esterase (C 4) | + | from API zym | |
| 68382 | esterase lipase (C 8) | + | from API zym | |
| 116175 | gelatinase | - | ||
| 68369 | gelatinase | - | from API 20NE | |
| 116175 | lecithinase | - | ||
| 68382 | leucine arylamidase | + | 3.4.11.1 | from API zym |
| 116175 | lipase | - | ||
| 68382 | lipase (C 14) | - | from API zym | |
| 116175 | lysine decarboxylase | - | 4.1.1.18 | |
| 68382 | N-acetyl-beta-glucosaminidase | - | 3.2.1.52 | from API zym |
| 68382 | naphthol-AS-BI-phosphohydrolase | + | from API zym | |
| 116175 | ornithine decarboxylase | - | 4.1.1.17 | |
| 116175 | oxidase | + | ||
| 116175 | protease | - | ||
| 68382 | trypsin | + | 3.4.21.4 | from API zym |
| 116175 | tryptophan deaminase | - | ||
| 116175 | tween esterase | - | ||
| 116175 | urease | - | 3.5.1.5 | |
| 68369 | urease | - | 3.5.1.5 | from API 20NE |
| @ref | Sample type | Geographic location | Country | Country ISO 3 Code | Continent | Latitude | Longitude | |
|---|---|---|---|---|---|---|---|---|
| 5101 | seawater | Resurrection Bay near Seward, Alaska | USA | USA | North America | 60.05 | -149.417 60.05/-149.417 | |
| 56601 | Seawater | Alaska,near Seward,Resurrection Bay | USA | USA | North America | |||
| 116175 | Environment, Seawater | Seward, Alaska | United States of America | USA | North America |
| @ref | Description | Assembly level | INSDC accession | BV-BRC accession | IMG accession | NCBI tax ID | Score | |
|---|---|---|---|---|---|---|---|---|
| 66792 | ASM1398v1 assembly for Sphingopyxis alaskensis RB2256 | complete | 317655 | 98.76 |
| @ref | Description | Accession | Length | Database | NCBI tax ID | |
|---|---|---|---|---|---|---|
| 20218 | Sphingomonas sp. RB2256 16S ribosomal RNA gene, partial sequence | AF148812 | 1406 | 94074 | ||
| 20218 | Sphingomonas alaskensis strain RB2256 16S ribosomal RNA gene, partial sequence | AF378795 | 1413 | 317655 | ||
| 20218 | Sphingopyxis alaskensis 16S ribosomal RNA gene, partial sequence | AY337601 | 1441 | 317655 | ||
| 20218 | Alpha proteobacterium (strain RB2256) 16S rRNA gene, partial sequence | U11041 | 725 | 34025 | ||
| 20218 | Sphingopyxis alaskensis 16S rRNA gene, strain RB2256 | Z73631 | 1445 | 317655 |
| @ref | Trait | Model | Prediction | Confidence in % | In training data |
|---|---|---|---|---|---|
| 125438 | gram-positive | gram-positiveⓘ | no | 96.46 | no |
| 125438 | anaerobic | anaerobicⓘ | no | 94.97 | yes |
| 125438 | spore-forming | spore-formingⓘ | no | 92.84 | no |
| 125438 | thermophilic | thermophileⓘ | no | 94.37 | yes |
| 125438 | aerobic | aerobicⓘ | yes | 87.73 | yes |
| 125438 | flagellated | motile2+ⓘ | yes | 63.20 | no |
| Title | Authors | Journal | DOI | Year | |
|---|---|---|---|---|---|
| High-efficiency production of 5-hydroxyectoine using metabolically engineered Corynebacterium glutamicum. | Jungmann L, Hoffmann SL, Lang C, De Agazio R, Becker J, Kohlstedt M, Wittmann C. | Microb Cell Fact | 10.1186/s12934-022-02003-z | 2022 | |
| Mining of Microbial Genomes for the Novel Sources of Nitrilases. | Sharma N, Thakur N, Raj T, Savitri, Bhalla TC. | Biomed Res Int | 10.1155/2017/7039245 | 2017 | |
| How to identify cell material in a single ice grain emitted from Enceladus or Europa. | Klenner F, Bonigk J, Napoleoni M, Hillier J, Khawaja N, Olsson-Francis K, Cable ML, Malaska MJ, Kempf S, Abel B, Postberg F. | Sci Adv | 10.1126/sciadv.adl0849 | 2024 | |
| Characterization of vB_StuS_MMDA13, a Newly Discovered Bacteriophage Infecting the Agar-Degrading Species Sphingomonas turrisvirgatae. | Marmo P, Thaller MC, Di Lallo G, Henrici De Angelis L, Poerio N, De Santis F, Fraziano M, Migliore L, D'Andrea MM. | Viruses | 10.3390/v12080894 | 2020 | |
| Markerless gene deletion system for sphingomonads. | Kaczmarczyk A, Vorholt JA, Francez-Charlot A. | Appl Environ Microbiol | 10.1128/aem.07347-11 | 2012 | |
| In silico prospection of microorganisms to produce polyhydroxyalkanoate from whey: Caulobacter segnis DSM 29236 as a suitable industrial strain. | Bustamante D, Segarra S, Tortajada M, Ramon D, Del Cerro C, Auxiliadora Prieto M, Iglesias JR, Rojas A. | Microb Biotechnol | 10.1111/1751-7915.13371 | 2019 | |
| Polyhydroxyalkanoate Production by Caenibius tardaugens from Steroidal Endocrine Disruptors. | Ibero J, Rivero-Buceta V, Garcia JL, Galan B. | Microorganisms | 10.3390/microorganisms10040706 | 2022 | |
| Adaptation of an abundant Roseobacter RCA organism to pelagic systems revealed by genomic and transcriptomic analyses. | Voget S, Wemheuer B, Brinkhoff T, Vollmers J, Dietrich S, Giebel HA, Beardsley C, Sardemann C, Bakenhus I, Billerbeck S, Daniel R, Simon M. | ISME J | 10.1038/ismej.2014.134 | 2015 | |
| Distribution and characterization of N-acylhomoserine lactone (AHL)-degrading activity and AHL lactonase gene (qsdS) in Sphingopyxis. | Morohoshi T, Kamimura Y, Sato N, Iizumi T | J Biosci Bioeng | 10.1016/j.jbiosc.2018.10.005 | 2018 | |
| Structure and Mechanism of the Sphingopyxin I Lasso Peptide Isopeptidase. | Fage CD, Hegemann JD, Nebel AJ, Steinbach RM, Zhu S, Linne U, Harms K, Bange G, Marahiel MA | Angew Chem Int Ed Engl | 10.1002/anie.201605232 | 2016 | |
| In vivo and in vitro studies on the carotenoid cleavage oxygenases from Sphingopyxis alaskensis RB2256 and Plesiocystis pacifica SIR-1 revealed their substrate specificities and non-retinal-forming cleavage activities. | Hoffmann J, Bona-Lovasz J, Beuttler H, Altenbuchner J | FEBS J | 10.1111/j.1742-4658.2012.08751.x | 2012 | |
| Metagenomic analysis of 0.2-mum-passable microorganisms in deep-sea hydrothermal fluid. | Nakai R, Abe T, Takeyama H, Naganuma T | Mar Biotechnol (NY) | 10.1007/s10126-010-9351-6 | 2011 | |
| The genomic basis of trophic strategy in marine bacteria. | Lauro FM, McDougald D, Thomas T, Williams TJ, Egan S, Rice S, DeMaere MZ, Ting L, Ertan H, Johnson J, Ferriera S, Lapidus A, Anderson I, Kyrpides N, Munk AC, Detter C, Han CS, Brown MV, Robb FT, Kjelleberg S, Cavicchioli R | Proc Natl Acad Sci U S A | 10.1073/pnas.0903507106 | 2009 | |
| The response of the marine bacterium Sphingopyxis alaskensis to solar radiation assessed by quantitative proteomics. | Matallana-Surget S, Joux F, Raftery MJ, Cavicchioli R | Environ Microbiol | 10.1111/j.1462-2920.2009.01992.x | 2009 | |
| Carbon and nitrogen substrate utilization in the marine bacterium Sphingopyxis alaskensis strain RB2256. | Williams TJ, Ertan H, Ting L, Cavicchioli R | ISME J | 10.1038/ismej.2009.52 | 2009 | |
| Sphingomonas alaskensis strain AFO1, an abundant oligotrophic ultramicrobacterium from the North Pacific. | Eguchi M, Ostrowski M, Fegatella F, Bowman J, Nichols D, Nishino T, Cavicchioli R | Appl Environ Microbiol | 10.1128/AEM.67.11.4945-4954.2001 | 2001 | |
| Specific growth rate plays a critical role in hydrogen peroxide resistance of the marine oligotrophic ultramicrobacterium sphingomonas alaskensis strain RB2256. | Ostrowski M, Cavicchioli R, Blaauw M, Gottschal JC | Appl Environ Microbiol | 10.1128/AEM.67.3.1292-1299.2001 | 2001 | |
| Sphingopyxis solisilvae sp. nov., isolated from forest soil. | Chaudhary DK, Dahal RH, Kim J | Int J Syst Evol Microbiol | 10.1099/ijsem.0.001869 | 2017 | |
| Sphingopyxis italica sp. nov., isolated from Roman catacombs. | Alias-Villegas C, Jurado V, Laiz L, Saiz-Jimenez C | Int J Syst Evol Microbiol | 10.1099/ijs.0.046573-0 | 2012 | |
| Sphingopyxis panaciterrulae sp. nov., isolated from soil of a ginseng field. | Srinivasan S, Kim MK, Sathiyaraj G, Veena V, Mahalakshmi M, Kalaiselvi S, Kim YJ, Yang DC | Int J Syst Evol Microbiol | 10.1099/ijs.0.019414-0 | 2009 | |
| Sphingopyxis soli sp. nov., isolated from landfill soil. | Choi JH, Kim MS, Jung MJ, Roh SW, Shin KS, Bae JW | Int J Syst Evol Microbiol | 10.1099/ijs.0.013128-0 | 2009 | |
| Sphingopyxis chilensis sp. nov., a chlorophenol-degrading bacterium that accumulates polyhydroxyalkanoate, and transfer of Sphingomonas alaskensis to Sphingopyxis alaskensis comb. nov. | Godoy F, Vancanneyt M, Martinez M, Steinbuchel A, Swings J, Rehm BHA | Int J Syst Evol Microbiol | 10.1099/ijs.0.02375-0 | 2003 | |
| Sphingomonas alaskensis sp. nov., a dominant bacterium from a marine oligotrophic environment. | Vancanneyt M, Schut F, Snauwaert C, Goris J, Swings J, Gottschal JC | Int J Syst Evol Microbiol | 10.1099/00207713-51-1-73 | 2001 |
| #5101 | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 13593 |
| #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. IJSEM ( DOI 10.1099/ijsem.0.004332 ) |
| #20218 | Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.: StrainInfo introduces electronic passports for microorganisms.. Syst Appl Microbiol. 37: 42 - 50 2014 ( DOI 10.1016/j.syapm.2013.11.002 , PubMed 24321274 ) |
| #37377 | ; Curators of the CIP; |
| #56601 | Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 45028 |
| #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) . |
| #68369 | Automatically annotated from API 20NE . |
| #68382 | Automatically annotated from API zym . |
| #116175 | Collection of Institut Pasteur ; Curators of the CIP; CIP 106977 |
| #125438 | Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann: Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets. 2024 ( DOI 10.1101/2024.08.12.607695 ) |
| #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. ( DOI 10.1093/database/baaf059 ) |
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