Strain identifier
BacDive ID: 470
Type strain:
Species: Saccharophagus degradans
Strain Designation: 2-40
Strain history: <- R. M. Weiner <- G. Andrykovitch; 2-40. Strain shipped as an actively growing culture, but survives only 3 days in the post, making shipping outside of Europe problematic. Customers ordering from outside of Europe should inquire before ordering the strain
NCBI tax ID(s): 203122 (strain), 86304 (species)
General
@ref: 6690
BacDive-ID: 470
DSM-Number: 17024
keywords: genome sequence, 16S sequence, Bacteria, aerobe, heterotroph, mesophilic, Gram-negative, motile, rod-shaped
description: Saccharophagus degradans 2-40 is an aerobe, heterotroph, mesophilic bacterium that was isolated from decomposing marsh grass.
NCBI tax id
NCBI tax id | Matching level |
---|---|
86304 | species |
203122 | strain |
strain history
- @ref: 6690
- history: <- R. M. Weiner <- G. Andrykovitch; 2-40. Strain shipped as an actively growing culture, but survives only 3 days in the post, making shipping outside of Europe problematic. Customers ordering from outside of Europe should inquire before ordering the strain
doi: 10.13145/bacdive470.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Gammaproteobacteria
- order: Cellvibrionales
- family: Cellvibrionaceae
- genus: Saccharophagus
- species: Saccharophagus degradans
- full scientific name: Saccharophagus degradans Ekborg et al. 2005
@ref: 6690
domain: Bacteria
phylum: Proteobacteria
class: Gammaproteobacteria
order: Cellvibrionaceae, not assigned to order
family: Cellvibrionaceae
genus: Saccharophagus
species: Saccharophagus degradans
full scientific name: Saccharophagus degradans Ekborg et al. 2005
strain designation: 2-40
type strain: yes
Morphology
cell morphology
@ref | gram stain | cell length | cell width | cell shape | motility | flagellum arrangement |
---|---|---|---|---|---|---|
23294 | negative | 1.5-3.0 µm | 0.5 µm | rod-shaped | yes | monotrichous, polar |
23294 | pleomorphic-shaped |
colony morphology
- @ref: 23294
- colony color: cream
pigmentation
- @ref: 23294
- production: yes
- color: Black
- name: Eumelanin
Culture and growth conditions
culture medium
- @ref: 6690
- name: HALF STRENGTH BACTO MARINE BROTH (DSMZ Medium 514a)
- growth: yes
- link: https://mediadive.dsmz.de/medium/514a
- composition: Name: HALF STRENGTH BACTO MARINE BROTH (DSMZ Medium 514a) Composition: Agar 15.0 g/l NaCl 9.725 g/l MgCl2 2.95 g/l Bacto peptone 2.5 g/l Na2SO4 1.62 g/l CaCl2 0.9 g/l Yeast extract 0.5 g/l KCl 0.275 g/l NaHCO3 0.08 g/l Fe(III) citrate 0.05 g/l KBr 0.04 g/l SrCl2 0.017 g/l H3BO3 0.011 g/l Na2HPO4 0.004 g/l Na-silicate 0.002 g/l NaF 0.0012 g/l (NH4)NO3 0.0008 g/l Distilled water
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
6690 | positive | growth | 28 | mesophilic |
23294 | positive | growth | 4-37 | |
23294 | positive | optimum | 30 | mesophilic |
63341 | positive | growth | 30 | mesophilic |
culture pH
@ref | ability | type | pH | PH range |
---|---|---|---|---|
23294 | positive | optimum | 7.5 | |
23294 | positive | growth | 4.5-10 | alkaliphile |
Physiology and metabolism
oxygen tolerance
@ref | oxygen tolerance |
---|---|
6690 | aerobe |
23294 | aerobe |
63341 | aerobe |
nutrition type
- @ref: 23294
- type: heterotroph
halophily
@ref | salt | growth | tested relation | concentration |
---|---|---|---|---|
23294 | Sea Salts (S9883) | no | growth | 0 % |
23294 | Sea Salts (S9883) | positive | growth | 1-10 % |
23294 | Sea Salts (S9883) | positive | optimum | 3.5 % |
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
23294 | 5291 | gelatin | + | assimilation |
23294 | 2509 | agar | + | carbon source |
23294 | 58187 | alginate | + | carbon source |
23294 | 62968 | cellulose | + | carbon source |
23294 | 17029 | chitin | + | carbon source |
23294 | 5181 | fucoidan | + | carbon source |
23294 | 6364 | laminarin | + | carbon source |
23294 | 17309 | pectin | + | carbon source |
23294 | 27941 | pullulan | + | carbon source |
23294 | 28017 | starch | + | carbon source |
23294 | 37166 | xylan | + | carbon source |
23294 | 18186 | tyrosine | + | hydrolysis |
23294 | 17632 | nitrate | + | reduction |
enzymes
@ref | value | activity | ec |
---|---|---|---|
23294 | catalase | + | 1.11.1.6 |
23294 | cytochrome oxidase | + | 1.9.3.1 |
Isolation, sampling and environmental information
isolation
@ref | sample type | geographic location | country | origin.country | continent |
---|---|---|---|---|---|
6690 | decomposing marsh grass | VA, Chesapeake Bay | USA | USA | North America |
23294 | surface of degrading salt marsh cord grass, Spartina alterniflora | ||||
63341 | Decomposing marsh grass |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#Environmental | #Terrestrial | #Wetland (Swamp) |
#Environmental | #Terrestrial | #Salt marsh |
#Host | #Plants | #Decomposing plant |
#Host | #Plants | #Herbaceous plants (Grass,Crops) |
taxonmaps
- @ref: 69479
- File name: preview.99_6445.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_235;96_3051;97_3748;98_4757;99_6445&stattab=map
- Last taxonomy: Saccharophagus degradans subclade
- 16S sequence: AF055269
- Sequence Identity:
- Total samples: 1102
- soil counts: 62
- aquatic counts: 962
- animal counts: 56
- plant counts: 22
Safety information
risk assessment
- @ref: 6690
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
@ref | description | accession | length | database | NCBI tax ID |
---|---|---|---|---|---|
20218 | Bacterium 2-40 16S ribosomal RNA gene, partial sequence | AF063028 | 519 | ena | 203122 |
6690 | Saccharophagus degradans 2-40 16S ribosomal RNA gene, partial sequence | AF055269 | 1431 | ena | 203122 |
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Saccharophagus degradans 2-40 | GCA_000013665 | complete | ncbi | 203122 |
66792 | Saccharophagus degradans 2-40 | 203122.15 | complete | patric | 203122 |
66792 | Saccharophagus degradans 2-40 | 637000249 | complete | img | 86304 |
GC content
- @ref: 23294
- GC-content: 45.8
- method: genome sequence analysis
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
motile | yes | 90.715 | yes |
flagellated | yes | 93.806 | yes |
gram-positive | no | 98.898 | yes |
anaerobic | no | 99.091 | yes |
halophile | no | 60.306 | no |
spore-forming | no | 94.059 | no |
thermophile | no | 98.297 | no |
glucose-util | yes | 90.527 | no |
aerobic | yes | 87.347 | no |
glucose-ferment | no | 83.909 | no |
External links
@ref: 6690
culture collection no.: DSM 17024, ATCC 43961, CCUG 66513
straininfo link
- @ref: 70149
- straininfo: 87752
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 16014479 | Saccharophagus degradans gen. nov., sp. nov., a versatile marine degrader of complex polysaccharides. | Ekborg NA, Gonzalez JM, Howard MB, Taylor LE, Hutcheson SW, Weiner RM | Int J Syst Evol Microbiol | 10.1099/ijs.0.63627-0 | 2005 | Alteromonadaceae/*classification/genetics/metabolism/physiology, Bacterial Typing Techniques, Biodegradation, Environmental, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Genes, rRNA, Molecular Sequence Data, Phenotype, Polysaccharides/metabolism, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, Species Specificity | Metabolism |
Genetics | 16672483 | Genomic and proteomic analyses of the agarolytic system expressed by Saccharophagus degradans 2-40. | Ekborg NA, Taylor LE, Longmire AG, Henrissat B, Weiner RM, Hutcheson SW | Appl Environ Microbiol | 10.1128/AEM.72.5.3396-3405.2006 | 2006 | Alteromonadaceae/*enzymology/genetics/metabolism, Bacterial Proteins/genetics/*metabolism, Escherichia coli/enzymology/genetics, Gene Deletion, *Genome, Bacterial, Glycoside Hydrolases/*genetics/*metabolism, Molecular Sequence Data, Phylogeny, *Proteome, Sequence Analysis, DNA | Metabolism |
Metabolism | 16707677 | Complete cellulase system in the marine bacterium Saccharophagus degradans strain 2-40T. | Taylor LE 2nd, Henrissat B, Coutinho PM, Ekborg NA, Hutcheson SW, Weiner RM | J Bacteriol | 10.1128/JB.01348-05 | 2006 | Bacterial Proteins/metabolism, Base Sequence, Cellulase/*metabolism, Gammaproteobacteria/*enzymology/genetics, Genome, Bacterial, Proteome, Restriction Mapping, Seawater/*microbiology | Genetics |
Metabolism | 18193466 | Biosynthesis and characterization of polyhydroxyalkanoates in the polysaccharide-degrading marine bacterium Saccharophagus degradans ATCC 43961. | Gonzalez-Garcia Y, Nungaray J, Cordova J, Gonzalez-Reynoso O, Koller M, Atlic A, Braunegg G | J Ind Microbiol Biotechnol | 10.1007/s10295-007-0299-0 | 2008 | Alteromonadaceae/chemistry/*metabolism, Calorimetry, Differential Scanning, Chromatography, Gel, Gas Chromatography-Mass Spectrometry, Molecular Weight, Polyhydroxyalkanoates/*biosynthesis/*chemistry, Polysaccharides/*metabolism | |
Metabolism | 18383127 | Utilization of cellulosic waste from tequila bagasse and production of polyhydroxyalkanoate (PHA) bioplastics by Saccharophagus degradans. | Alva Munoz LE, Riley MR | Biotechnol Bioeng | 10.1002/bit.21854 | 2008 | Agriculture/methods, Alcoholic Beverages/*microbiology, Biodegradation, Environmental, Cellulose/*metabolism, Gammaproteobacteria/*metabolism, Industrial Waste/*prevention & control, Plastics/metabolism, Polyhydroxyalkanoates/*metabolism | Biotechnology |
Genetics | 18516288 | Complete genome sequence of the complex carbohydrate-degrading marine bacterium, Saccharophagus degradans strain 2-40 T. | Weiner RM, Taylor LE 2nd, Henrissat B, Hauser L, Land M, Coutinho PM, Rancurel C, Saunders EH, Longmire AG, Zhang H, Bayer EA, Gilbert HJ, Larimer F, Zhulin IB, Ekborg NA, Lamed R, Richardson PM, Borovok I, Hutcheson S | PLoS Genet | 10.1371/journal.pgen.1000087 | 2008 | Alteromonadaceae/chemistry/enzymology/*genetics/metabolism, Bacterial Proteins/genetics/metabolism, Base Sequence, *Chromosome Mapping, *Genome, Bacterial, Glycoside Hydrolases/genetics/metabolism, Molecular Sequence Data, Polysaccharides/chemistry/genetics/*metabolism, Protein Transport, Seawater/*microbiology, Sequence Analysis, DNA, Signal Transduction, Substrate Specificity | Metabolism |
Genetics | 18556790 | Insights into plant cell wall degradation from the genome sequence of the soil bacterium Cellvibrio japonicus. | DeBoy RT, Mongodin EF, Fouts DE, Tailford LE, Khouri H, Emerson JB, Mohamoud Y, Watkins K, Henrissat B, Gilbert HJ, Nelson KE | J Bacteriol | 10.1128/JB.01701-07 | 2008 | Alteromonadaceae/genetics, Bacterial Proteins/*genetics, Cell Wall/*metabolism, Cellvibrio/*enzymology/*genetics, Esterases/genetics, *Genome, Bacterial, Genomics, Glycoside Hydrolases/genetics, Lyases/genetics, Molecular Sequence Data, Phylogeny, Plants/*metabolism, Sequence Analysis, DNA, Sequence Homology, Amino Acid, Soil Microbiology, Synteny | Metabolism |
Metabolism | 19568419 | The complete genome of Teredinibacter turnerae T7901: an intracellular endosymbiont of marine wood-boring bivalves (shipworms). | Yang JC, Madupu R, Durkin AS, Ekborg NA, Pedamallu CS, Hostetler JB, Radune D, Toms BS, Henrissat B, Coutinho PM, Schwarz S, Field L, Trindade-Silva AE, Soares CA, Elshahawi S, Hanora A, Schmidt EW, Haygood MG, Posfai J, Benner J, Madinger C, Nove J, Anton B, Chaudhary K, Foster J, Holman A, Kumar S, Lessard PA, Luyten YA, Slatko B, Wood N, Wu B, Teplitski M, Mougous JD, Ward N, Eisen JA, Badger JH, Distel DL | PLoS One | 10.1371/journal.pone.0006085 | 2009 | Animals, Bivalvia/metabolism/*microbiology, Computational Biology, *Genome, Bacterial, *Marine Biology, Nitrogen/metabolism, Phylogeny, Polysaccharides/metabolism, Proteobacteria/classification/enzymology/*genetics/physiology, Quorum Sensing, Spectrometry, Mass, Electrospray Ionization, *Symbiosis, Tandem Mass Spectrometry, *Wood | Phylogeny |
Metabolism | 19617364 | Processive endoglucanases mediate degradation of cellulose by Saccharophagus degradans. | Watson BJ, Zhang H, Longmire AG, Moon YH, Hutcheson SW | J Bacteriol | 10.1128/JB.00481-09 | 2009 | Alteromonadaceae/*enzymology/genetics/growth & development/metabolism, *Bacterial Proteins/genetics/isolation & purification/metabolism, Cellobiose/metabolism, *Cellulase/genetics/isolation & purification/metabolism, Cellulose/chemistry/*metabolism, Cellulose 1,4-beta-Cellobiosidase/genetics/isolation & purification/metabolism, Cloning, Molecular, Computational Biology, Culture Media, Phylogeny | Enzymology |
Enzymology | 19646553 | Optimal production of a novel endo-acting beta-1,4-xylanase cloned from Saccharophagus degradans 2-40 into Escherichia coli BL21(DE3). | Ko JK, Jung MW, Kim KH, Choi IG | N Biotechnol | 10.1016/j.nbt.2009.07.009 | 2009 | Alteromonadaceae/drug effects/*enzymology, Cell Proliferation/drug effects, Chromatography, High Pressure Liquid, Chromatography, Thin Layer, Cloning, Molecular, Electrophoresis, Polyacrylamide Gel, Endo-1,4-beta Xylanases/*biosynthesis/*genetics, Escherichia coli/cytology/drug effects/*metabolism, Fermentation/drug effects, Hydrolysis/drug effects, Isopropyl Thiogalactoside/pharmacology, Recombinant Proteins/biosynthesis, Temperature, Time Factors, Xylans/metabolism | Pathogenicity |
Enzymology | 19802606 | Overexpression and molecular characterization of Aga50D from Saccharophagus degradans 2-40: an exo-type beta-agarase producing neoagarobiose. | Kim HT, Lee S, Lee D, Kim HS, Bang WG, Kim KH, Choi IG | Appl Microbiol Biotechnol | 10.1007/s00253-009-2256-5 | 2009 | Agar/metabolism, Alteromonadaceae/*enzymology/genetics, Cloning, Molecular, Disaccharides/*biosynthesis, *Glycoside Hydrolases/chemistry/genetics/isolation & purification/metabolism, Hydrogen-Ion Concentration, Kinetics, Magnetic Resonance Spectroscopy, Mass Spectrometry, Recombinant Proteins/chemistry/genetics/isolation & purification/metabolism, Temperature, Up-Regulation | Metabolism |
Metabolism | 19806675 | Global metabolic profiling of plant cell wall polysaccharide degradation by Saccharophagus degradans. | Shin MH, Lee DY, Skogerson K, Wohlgemuth G, Choi IG, Fiehn O, Kim KH | Biotechnol Bioeng | 10.1002/bit.22557 | 2010 | Alteromonadaceae/chemistry/enzymology/growth & development/*metabolism, Bacterial Proteins/analysis, Cell Wall/chemistry, Enzymes/analysis, Fatty Acids/analysis, Gas Chromatography-Mass Spectrometry, Glucuronic Acid/analysis, *Metabolomics, Nucleotides/analysis, Plants/chemistry, Polysaccharides/*metabolism | Enzymology |
Metabolism | 20023015 | Discovery and characterization of cadherin domains in Saccharophagus degradans 2-40. | Fraiberg M, Borovok I, Weiner RM, Lamed R | J Bacteriol | 10.1128/JB.01236-09 | 2009 | Alteromonadaceae/*genetics/growth & development, Bacterial Proteins/*genetics/*metabolism, Betula/chemistry, Cadherins/*genetics/*metabolism, Calcium/metabolism, Pectins/isolation & purification/metabolism, Protein Binding, Protein Interaction Mapping, Protein Structure, Tertiary, Xylans/isolation & purification/metabolism | Enzymology |
Metabolism | 20054134 | Crystallization and preliminary X-ray analysis of neoagarobiose hydrolase from Saccharophagus degradans 2-40. | Lee S, Lee JY, Ha SC, Jung J, Shin DH, Kim KH, Choi IG | Acta Crystallogr Sect F Struct Biol Cryst Commun | 10.1107/S174430910904603X | 2009 | Agar/metabolism, Alteromonadaceae/*enzymology/genetics, Base Sequence, Crystallization, Crystallography, X-Ray, DNA Primers/genetics, Disaccharidases/*chemistry/genetics/metabolism, Recombinant Proteins/chemistry/genetics | Enzymology |
Metabolism | 20215059 | Global metabolite profiling of agarose degradation by Saccharophagus degradans 2-40. | Shin MH, Lee DY, Wohlgemuth G, Choi IG, Fiehn O, Kim KH | N Biotechnol | 10.1016/j.nbt.2010.02.023 | 2010 | Alteromonadaceae/*metabolism, Bacterial Proteins/*metabolism, Gene Expression Profiling/*methods, Peptide Mapping/*methods, Proteome/*metabolism, Sepharose/*metabolism | Proteome |
Enzymology | 20696711 | CAZymes Analysis Toolkit (CAT): web service for searching and analyzing carbohydrate-active enzymes in a newly sequenced organism using CAZy database. | Park BH, Karpinets TV, Syed MH, Leuze MR, Uberbacher EC | Glycobiology | 10.1093/glycob/cwq106 | 2010 | Alteromonadaceae/*enzymology/genetics, Bacterial Proteins/chemistry/*genetics/metabolism, *Carbohydrates, Clostridium thermocellum/*enzymology/genetics, *Databases, Protein, Enzymes/chemistry/classification/*genetics, Fungal Proteins/chemistry/*genetics/metabolism, Genome, Bacterial/physiology, Genome, Fungal/physiology, Molecular Sequence Annotation, Neurospora crassa/*enzymology/genetics | Genetics |
Phylogeny | 20833889 | Pseudoteredinibacter isoporae gen. nov., sp. nov., a marine bacterium isolated from the reef-building coral Isopora palifera. | Chen MH, Sheu SY, Arun AB, Young CC, Chen CA, Wang JT, Chen WM | Int J Syst Evol Microbiol | 10.1099/ijs.0.024190-0 | 2010 | Animals, Anthozoa/*microbiology, DNA, Bacterial, DNA, Ribosomal/genetics, Fatty Acids/genetics/metabolism, Gammaproteobacteria, Gram-Negative Bacteria/*classification/genetics/*isolation & purification/metabolism, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sodium Chloride/metabolism | Metabolism |
Metabolism | 21036994 | Cadherin domains in the polysaccharide-degrading marine bacterium Saccharophagus degradans 2-40 are carbohydrate-binding modules. | Fraiberg M, Borovok I, Bayer EA, Weiner RM, Lamed R | J Bacteriol | 10.1128/JB.00842-10 | 2010 | Bacterial Proteins/genetics/metabolism, Cadherins/chemistry/genetics/*metabolism, Carbohydrate Metabolism, Gene Expression Regulation, Bacterial/physiology, Gram-Negative Aerobic Bacteria/genetics/*metabolism, Polysaccharides/*metabolism, Protein Binding, Protein Structure, Tertiary | |
Metabolism | 21327449 | Hydrolytic and phosphorolytic metabolism of cellobiose by the marine aerobic bacterium Saccharophagus degradans 2-40T. | Zhang H, Moon YH, Watson BJ, Suvorov M, Santos E, Sinnott CA, Hutcheson SW | J Ind Microbiol Biotechnol | 10.1007/s10295-011-0945-4 | 2011 | Alteromonadaceae/genetics/*metabolism, Bacteria, Aerobic/metabolism, Cellobiose/*metabolism, Cellulose/metabolism, Cellulose 1,4-beta-Cellobiosidase/metabolism, Escherichia coli/genetics, Glucosyltransferases/genetics/metabolism, Hydrolysis, Phosphorylation, beta-Glucosidase/genetics/metabolism | |
Metabolism | 21731555 | Carbohydrase systems of Saccharophagus degradans degrading marine complex polysaccharides. | Hutcheson SW, Zhang H, Suvorov M | Mar Drugs | 10.3390/md9040645 | 2011 | Alteromonadaceae/enzymology/*genetics, Bacterial Proteins/genetics/metabolism, Carbon/metabolism, *Genome, Bacterial, Glycoside Hydrolases/genetics/*metabolism, Polysaccharides/metabolism | Genetics |
Enzymology | 21810409 | Crystal structure of a key enzyme in the agarolytic pathway, alpha-neoagarobiose hydrolase from Saccharophagus degradans 2-40. | Ha SC, Lee S, Lee J, Kim HT, Ko HJ, Kim KH, Choi IG | Biochem Biophys Res Commun | 10.1016/j.bbrc.2011.07.073 | 2011 | Agar/chemistry/metabolism, Alteromonadaceae/*enzymology, Cloning, Molecular, Cytosol/enzymology, Disaccharidases/*chemistry/genetics, Protein Conformation | Metabolism |
Enzymology | 22281843 | Depolymerization of alginate into a monomeric sugar acid using Alg17C, an exo-oligoalginate lyase cloned from Saccharophagus degradans 2-40. | Kim HT, Chung JH, Wang D, Lee J, Woo HC, Choi IG, Kim KH | Appl Microbiol Biotechnol | 10.1007/s00253-012-3882-x | 2012 | Alginates/*metabolism, Alteromonadaceae/*enzymology/genetics, Cloning, Molecular, Enzyme Stability, Escherichia coli/genetics, Gene Expression, Hydrogen-Ion Concentration, Kinetics, Polysaccharide-Lyases/chemistry/genetics/isolation & purification/*metabolism, Recombinant Proteins/chemistry/genetics/isolation & purification/metabolism, Substrate Specificity, Sugar Acids/*metabolism, Temperature | Metabolism |
Enzymology | 22344647 | Functional cell surface display and controlled secretion of diverse Agarolytic enzymes by Escherichia coli with a novel ligation-independent cloning vector based on the autotransporter YfaL. | Ko HJ, Park E, Song J, Yang TH, Lee HJ, Kim KH, Choi IG | Appl Environ Microbiol | 10.1128/AEM.07004-11 | 2012 | Alteromonadaceae/enzymology/genetics, Escherichia coli/*enzymology/*genetics, Escherichia coli Proteins/*genetics/*metabolism, Genes, Reporter, Genetic Engineering/methods, *Genetic Vectors, Genetics, Microbial/methods, Glycoside Hydrolases/chemistry/*genetics/*metabolism, Luminescent Proteins/analysis/genetics, Membrane Transport Proteins/*genetics/*metabolism, Molecular Weight, Recombinant Proteins/chemistry/genetics/metabolism | Metabolism |
Enzymology | 22526785 | Agar degradation by microorganisms and agar-degrading enzymes. | Chi WJ, Chang YK, Hong SK | Appl Microbiol Biotechnol | 10.1007/s00253-012-4023-2 | 2012 | Agar/*metabolism, Alteromonadaceae/enzymology, Geologic Sediments/microbiology, Glycoside Hydrolases/chemistry/genetics/*metabolism, Hydrolysis, Protein Conformation, Seawater/microbiology, Streptomyces coelicolor/enzymology | Metabolism |
Enzymology | 22814498 | Cloning of agarase gene from non-marine agarolytic bacterium Cellvibrio sp. | Ariga O, Inoue T, Kubo H, Minami K, Nakamura M, Iwai M, Moriyama H, Yanagisawa M, Nakasaki K | J Microbiol Biotechnol | 10.4014/jmb.1202.02020 | 2012 | Amino Acid Sequence, Bacterial Proteins/chemistry/*genetics/isolation & purification/metabolism, Base Sequence, Cellvibrio/*enzymology/genetics, Cloning, Molecular, Disaccharides/analysis/metabolism, Enzyme Stability, Escherichia coli/enzymology/genetics, Galactosides/analysis/metabolism, Glycoside Hydrolases/chemistry/*genetics/isolation & purification/metabolism, Hydrogen-Ion Concentration, Hydrolysis, Molecular Sequence Data, Oligosaccharides/analysis/metabolism, Recombinant Proteins/chemistry/genetics/isolation & purification/metabolism, Sepharose/analysis/metabolism, Temperature | Metabolism |
Metabolism | 22843394 | Bacterial cadherin domains as carbohydrate binding modules: determination of affinity constants to insoluble complex polysaccharides. | Fraiberg M, Borovok I, Weiner RM, Lamed R, Bayer EA | Methods Mol Biol | 10.1007/978-1-61779-956-3_11 | 2012 | Adsorption, Alteromonadaceae/*metabolism, Bacterial Proteins/*metabolism, Cadherins/classification/*metabolism, Calcium/metabolism, Chemistry Techniques, Analytical, Electrophoresis, Polyacrylamide Gel/methods, Kinetics, Polysaccharides, Bacterial/*metabolism, Protein Structure, Tertiary | Enzymology |
Phylogeny | 22950007 | Isolation of a novel Saccharophagus species (Myt-1) capable of degrading a variety of seaweeds and polysaccharides. | Sakatoku A, Wakabayashi M, Tanaka Y, Tanaka D, Nakamura S | Microbiologyopen | 10.1002/mbo3.10 | 2012 | ||
Phylogeny | 23291764 | Identification and characterization of cellobiose 2-epimerases from various aerobes. | Ojima T, Saburi W, Yamamoto T, Mori H, Matsui H | Biosci Biotechnol Biochem | 10.1271/bbb.120742 | 2013 | Aerobiosis, Bacteria, Aerobic/chemistry/*enzymology, Bacterial Proteins/classification/*isolation & purification/*metabolism, Carbohydrate Epimerases/classification/*isolation & purification/*metabolism, Cellobiose/*metabolism, Enzyme Assays, Enzyme Stability, Escherichia coli/genetics, Glucose/metabolism, Hydrogen-Ion Concentration, Isoenzymes/classification/isolation & purification/metabolism, Kinetics, Lactose/metabolism, Mannose/metabolism, Phylogeny, Recombinant Proteins/classification/isolation & purification/metabolism, Species Specificity, Stereoisomerism, Substrate Specificity, Temperature | Enzymology |
Metabolism | 23627584 | Biochemical characterization of 4-alpha-glucanotransferase from Saccharophagus degradans 2-40 and its potential role in glycogen degradation. | Hwang S, Choi KH, Kim J, Cha J | FEMS Microbiol Lett | 10.1111/1574-6968.12167 | 2013 | Alteromonadaceae/*enzymology/genetics/metabolism, Amino Acid Sequence, Bacterial Proteins/*chemistry/genetics/*metabolism, Enzyme Stability, Glycogen/*metabolism, Glycogen Debranching Enzyme System/*chemistry/genetics/*metabolism, Hydrogen-Ion Concentration, Molecular Sequence Data, Molecular Weight, Sequence Alignment | Enzymology |
Enzymology | 23990129 | Feasibility test of utilizing Saccharophagus degradans 2-40(T) as the source of crude enzyme for the saccharification of lignocellulose. | Jung YH, Kim HK, Song DS, Choi IG, Yang TH, Lee HJ, Seung D, Kim KH | Bioprocess Biosyst Eng | 10.1007/s00449-013-1040-1 | 2013 | Alteromonadaceae/*enzymology, Bacterial Proteins/*chemistry, Cellulase/*chemistry, Endo-1,4-beta Xylanases/*chemistry, Lignin/*chemistry | |
Metabolism | 24140897 | An expansin from the marine bacterium Hahella chejuensis acts synergistically with xylanase and enhances xylan hydrolysis. | Lee HJ, Kim IJ, Kim JF, Choi IG, Kim KH | Bioresour Technol | 10.1016/j.biortech.2013.09.086 | 2013 | Bacterial Proteins/*metabolism, Endo-1,4-beta Xylanases/*metabolism, Gammaproteobacteria/*metabolism, Hydrogen-Ion Concentration, Hydrolysis, Seawater/*microbiology, Temperature, Xylans/*metabolism | |
Enzymology | 24395600 | Gene cloning, expression and characterisation of a new beta-agarase, AgWH50C, producing neoagarobiose from Agarivorans gilvus WH0801. | Liu N, Mao X, Yang M, Mu B, Wei D | World J Microbiol Biotechnol | 10.1007/s11274-013-1591-y | 2014 | Alteromonadaceae/chemistry/*enzymology/genetics, Amino Acid Sequence, Bacterial Proteins/*chemistry/genetics/metabolism, *Cloning, Molecular, Disaccharides/*metabolism, Enzyme Stability, Gene Expression, Glycoside Hydrolases/*chemistry/genetics/metabolism, Hydrogen-Ion Concentration, Kinetics, Molecular Sequence Data, Sequence Alignment | Metabolism |
Phylogeny | 25085545 | A laboratory case study of efficient polyhydoxyalkonates production by Bacillus cereus, a contaminant in Saccharophagus degradans ATCC 43961 in minimal sea salt media. | Sawant SS, Salunke BK, Kim BS | Curr Microbiol | 10.1007/s00284-014-0664-y | 2014 | Bacillus cereus/growth & development/*isolation & purification/*metabolism, Culture Media/chemistry, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Gas Chromatography-Mass Spectrometry, Molecular Sequence Data, Polyhydroxyalkanoates/*metabolism, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Spectroscopy, Fourier Transform Infrared, Sudan, Time Factors | Metabolism |
Metabolism | 25846336 | Comparative study of MnO2 nanoparticle synthesis by marine bacterium Saccharophagus degradans and yeast Saccharomyces cerevisiae. | Salunke BK, Sawant SS, Lee SI, Kim BS | Appl Microbiol Biotechnol | 10.1007/s00253-015-6559-4 | 2015 | Culture Media/chemistry, Filtration, Gammaproteobacteria/*metabolism, Manganese Compounds/*metabolism, Microscopy, Electron, Transmission, Nanoparticles/*metabolism, Oxides/*metabolism, Potassium Permanganate/metabolism, Saccharomyces cerevisiae/*metabolism, Spectrum Analysis | Cultivation |
Metabolism | 26138394 | A rapid, sensitive, simple plate assay for detection of microbial alginate lyase activity. | Sawant SS, Salunke BK, Kim BS | Enzyme Microb Technol | 10.1016/j.enzmictec.2015.05.003 | 2015 | Alginates/metabolism, Bacillus cereus/enzymology/growth & development, Bacterial Proteins/*analysis/metabolism, Bacteriological Techniques, Gammaproteobacteria/enzymology/growth & development, Glucuronic Acid/metabolism, Hexuronic Acids/metabolism, Hydrolysis, Iodine, Paracoccus/enzymology/growth & development, Polysaccharide-Lyases/*analysis/metabolism, Ponds/microbiology, Soil Microbiology, Species Specificity | Enzymology |
Metabolism | 26458373 | Putative Alginate Assimilation Process of the Marine Bacterium Saccharophagus degradans 2-40 Based on Quantitative Proteomic Analysis. | Takagi T, Morisaka H, Aburaya S, Tatsukami Y, Kuroda K, Ueda M | Mar Biotechnol (NY) | 10.1007/s10126-015-9667-3 | 2015 | Alginates/*metabolism, Aquatic Organisms/*metabolism, Bacterial Proteins/*chemistry/*metabolism, Gammaproteobacteria/*metabolism, Glucuronic Acid/metabolism, Hexuronic Acids/metabolism, Proteome/*metabolism, Signal Transduction/physiology | Proteome |
Enzymology | 26809714 | Characterization of the biochemical properties of recombinant Xyn10C from a marine bacterium, Saccharophagus degradans 2-40. | Ko JK, Ko H, Kim KH, Choi IG | Bioprocess Biosyst Eng | 10.1007/s00449-016-1548-2 | 2016 | Aquatic Organisms/*enzymology/genetics, Bacterial Proteins/*chemistry/genetics, Glycoside Hydrolases/*chemistry/genetics, Gram-Negative Aerobic Rods and Cocci/*enzymology/genetics, Hot Temperature, Hydrogen-Ion Concentration, Recombinant Proteins/chemistry/genetics, Xylans/*chemistry | Stress |
Enzymology | 27129264 | Biochemical and Structural Characterization of a Five-domain GH115 alpha-Glucuronidase from the Marine Bacterium Saccharophagus degradans 2-40T. | Wang W, Yan R, Nocek BP, Vuong TV, Di Leo R, Xu X, Cui H, Gatenholm P, Toriz G, Tenkanen M, Savchenko A, Master ER | J Biol Chem | 10.1074/jbc.M115.702944 | 2016 | Amino Acid Sequence, Circular Dichroism, Gammaproteobacteria/*enzymology, Glycoside Hydrolases/chemistry/*metabolism, Marine Biology, Models, Molecular, Protein Conformation, Sequence Homology, Amino Acid | Metabolism |
Metabolism | 27208098 | A Novel Glycoside Hydrolase Family 5 beta-1,3-1,6-Endoglucanase from Saccharophagus degradans 2-40T and Its Transglycosylase Activity. | Wang D, Kim DH, Seo N, Yun EJ, An HJ, Kim JH, Kim KH | Appl Environ Microbiol | 10.1128/AEM.00635-16 | 2016 | Cellulase/*genetics/*metabolism, Chromatography, High Pressure Liquid, Chromatography, Thin Layer, Cloning, Molecular, Escherichia coli/genetics/metabolism, Gammaproteobacteria/*enzymology/genetics, Gene Expression, Glucans/metabolism, Hydrolysis, Polysaccharides/metabolism, Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization, Substrate Specificity | Enzymology |
Enzymology | 27521023 | The first bacterial beta-1,6-endoglucanase from Saccharophagus degradans 2-40(T) for the hydrolysis of pustulan and laminarin. | Wang D, Kim DH, Yun EJ, Park YC, Seo JH, Kim KH | Appl Microbiol Biotechnol | 10.1007/s00253-016-7753-8 | 2016 | Cellulase/genetics/*isolation & purification/*metabolism, Cloning, Molecular, Disaccharides/metabolism, Escherichia coli/genetics/metabolism, Gammaproteobacteria/*enzymology/genetics, Gene Expression, Glucans/*metabolism, Glucose/metabolism, Hydrogen-Ion Concentration, Hydrolysis, Kinetics, Phaeophyta, Polysaccharides/*metabolism, Recombinant Proteins/genetics/isolation & purification/metabolism, Temperature | Metabolism |
Enzymology | 27664160 | Enzymatic liquefaction of agarose above the sol-gel transition temperature using a thermostable endo-type beta-agarase, Aga16B. | Kim JH, Yun EJ, Seo N, Yu S, Kim DH, Cho KM, An HJ, Kim JH, Choi IG, Kim KH | Appl Microbiol Biotechnol | 10.1007/s00253-016-7831-y | 2016 | Cloning, Molecular, Enzyme Stability, Gammaproteobacteria/enzymology, Glycoside Hydrolases/genetics/isolation & purification/*metabolism, Kinetics, Phase Transition, Recombinant Proteins/metabolism, Seaweed/chemistry, Sepharose/*chemistry/*metabolism, Transition Temperature | Metabolism |
Metabolism | 28216576 | Identification of 2-keto-3-deoxy-d-Gluconate Kinase and 2-keto-3-deoxy-d-Phosphogluconate Aldolase in an Alginate-Assimilating Bacterium, Flavobacterium sp. Strain UMI-01. | Nishiyama R, Inoue A, Ojima T | Mar Drugs | 10.3390/md15020037 | 2017 | Aldehyde-Lyases/*metabolism, Alginates/*metabolism, Amino Acid Sequence, Bacteroidetes/metabolism, Escherichia coli/metabolism, Flavobacterium/*metabolism, Gluconates/*metabolism, Glucuronic Acid/metabolism, Hexuronic Acids/metabolism, Oxidoreductases/*metabolism, Phosphotransferases (Alcohol Group Acceptor)/*metabolism, Phylogeny, Proteobacteria/metabolism, Sequence Alignment, Uronic Acids/metabolism | Phylogeny |
Metabolism | 29154880 | Consolidated bioprocessing for production of polyhydroxyalkanotes from red algae Gelidium amansii. | Sawant SS, Salunke BK, Kim BS | Int J Biol Macromol | 10.1016/j.ijbiomac.2017.11.084 | 2017 | Carbon/metabolism, *Fermentation, Polyhydroxyalkanoates/*biosynthesis/*chemistry, Rhodophyta/growth & development/*metabolism, Spectroscopy, Fourier Transform Infrared | Biotechnology |
29563967 | A novel beta-glucosidase from Saccharophagus degradans 2-40(T) for the efficient hydrolysis of laminarin from brown macroalgae. | Kim DH, Kim DH, Lee SH, Kim KH | Biotechnol Biofuels | 10.1186/s13068-018-1059-2 | 2018 | |||
Biotechnology | 29896965 | Model-Based Complete Enzymatic Production of 3,6-Anhydro-l-galactose from Red Algal Biomass. | Pathiraja D, Lee S, Choi IG | J Agric Food Chem | 10.1021/acs.jafc.8b01792 | 2018 | Agar/*chemistry, Bacterial Proteins/*chemistry, Biocatalysis, Galactose/*analogs & derivatives/chemistry, Gammaproteobacteria/*enzymology, Glycoside Hydrolases/*chemistry, Hydrolysis, Rhodophyta/*chemistry | Enzymology |
Enzymology | 30128580 | Identification and biochemical characterization of a novel cold-adapted 1,3-alpha-3,6-anhydro-L-galactosidase, Ahg786, from Gayadomonas joobiniege G7. | Asghar S, Lee CR, Park JS, Chi WJ, Kang DK, Hong SK | Appl Microbiol Biotechnol | 10.1007/s00253-018-9277-x | 2018 | Alteromonadaceae/chemistry/*enzymology/genetics, Amino Acid Sequence, Bacterial Proteins/*chemistry/genetics/metabolism, Enzyme Stability, Galactosidases/*chemistry/genetics/metabolism, Hydrogen-Ion Concentration, Molecular Sequence Data, Protein Sorting Signals, Sequence Alignment, Temperature | Metabolism |
Metabolism | 30788710 | Molecular Cloning and Characterization of a Novel Cold-Adapted Alkaline 1,3-alpha-3,6-Anhydro-L-galactosidase, Ahg558, from Gayadomonas joobiniege G7. | Asghar S, Lee CR, Chi WJ, Kang DK, Hong SK | Appl Biochem Biotechnol | 10.1007/s12010-019-02963-w | 2019 | Chromatography, Thin Layer, Cloning, Molecular, Disaccharides/metabolism, Galactosidases/*metabolism, Galactosides/metabolism, Hydrogen-Ion Concentration, Mass Spectrometry, Oligosaccharides/metabolism | Enzymology |
Phylogeny | 31793854 | Thalassocella blandensis gen. nov., sp. nov., a novel member of the family Cellvibrionaceae. | Lucena T, Arahal DR, Sanz-Saez I, Acinas SG, Sanchez O, Aznar R, Pedros-Alio C, Pujalte MJ | Int J Syst Evol Microbiol | 10.1099/ijsem.0.003906 | 2020 | Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Mediterranean Sea, Phospholipids/chemistry, Phyllobacteriaceae/*classification/isolation & purification, *Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, Ubiquinone/chemistry | Transcriptome |
Enzymology | 33278947 | Specific hydrolysis of curdlan with a novel glycoside hydrolase family 128 beta-1,3-endoglucanase containing a carbohydrate-binding module. | Jia X, Wang C, Du X, Peng H, Liu L, Xiao Y, He C | Carbohydr Polym | 10.1016/j.carbpol.2020.117276 | 2020 | Biocatalysis, Cellulase/*chemistry, Cloning, Molecular/methods, Escherichia coli/enzymology/genetics, Gammaproteobacteria/*enzymology/genetics, Glycoside Hydrolases/*chemistry, Hydrogen-Ion Concentration, Hydrolysis, Oligosaccharides/biosynthesis, Polysaccharides, Bacterial/*chemistry, Substrate Specificity, Temperature, beta-Glucans/*chemistry | |
Metabolism | 33527231 | Enhanced glycolic acid yield through xylose and cellobiose utilization by metabolically engineered Escherichia coli. | Cabulong RB, Banares AB, Nisola GM, Lee WK, Chung WJ | Bioprocess Biosyst Eng | 10.1007/s00449-020-02502-6 | 2021 | Cellobiose/genetics/*metabolism, *Escherichia coli/genetics/metabolism, Glycolates/*metabolism, *Metabolic Engineering, *Microorganisms, Genetically-Modified/genetics/metabolism, Xylose/genetics/*metabolism | Biotechnology |
34335544 | Carbohydrate-Binding Module and Linker Allow Cold Adaptation and Salt Tolerance of Maltopentaose-Forming Amylase From Marine Bacterium Saccharophagus degradans 2-40 (T). | Ding N, Zhao B, Ban X, Li C, Venkataram Prasad BV, Gu Z, Li Z | Front Microbiol | 10.3389/fmicb.2021.708480 | 2021 |
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6690 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 17024) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-17024 | |||
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23294 | Nathan A. Ekborg, Jose M. Gonzalez, Michael B. Howard, Larry E. Taylor, Steven W. Hutcheson, Ronald M. Weiner | 10.1099/ijs.0.63627-0 | Saccharophagus degradans gen. nov., sp. nov., a versatile marine degrader of complex polysaccharides | IJSEM 55: 1545-1549 2005 | 16014479 | |
63341 | Curators of the CCUG | Culture Collection University of Gothenburg (CCUG) (CCUG 66513) | https://www.ccug.se/strain?id=66513 | |||
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 | |
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 | |||
70149 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID87752.1 | StrainInfo: A central database for resolving microbial strain identifiers |