Saccharophagus degradans ATCC ® 43961D-5™ Designation: Genomic DNA from Saccharophagus degradans strain 2-40 TypeStrain=True Application:
General Information: This strain is a marine gamma-proteobacterium that was isolated from decaying Spartina alterniflora, a salt marsh cord grass, in the Chesapeake Bay, USA. Saccharophagus degradans 2-40 has been used to produce ethanol from plant material and may be useful for the production bioethanol. Bacterium able to degrade complex carbohydrates. Saccharophagus degradans is capable of degrading insoluble complex carbohydrates through the collective action of enzyme complexes found on its cell surfaces, utilizing the degradation products as a carbon source. This organism may be useful in bioremediation. The degradative enzymes this organism produces are typically exoenzymes that are collected and organized into large surface complexes termed cellulosomes. ...
p>The checksum is a form of redundancy check that is calculated from the sequence. It is useful for tracking sequence updates.,/p> ,p>It should be noted that while, in theory, two different sequences could have the same checksum value, the likelihood that this would happen is extremely low.,/p> ,p>However UniProtKB may contain entries with identical sequences in case of multiple genes (paralogs).,/p> ,p>The checksum is computed as the sequence 64-bit Cyclic Redundancy Check value (CRC64) using the generator polynomial: x,sup>64,/sup> + x,sup>4,/sup> + x,sup>3,/sup> + x + 1. The algorithm is described in the ISO 3309 standard. ,/p> ,p class=publication>Press W.H., Flannery B.P., Teukolsky S.A. and Vetterling W.T.,br /> ,strong>Cyclic redundancy and other checksums,/strong>,br /> ,a href=http://www.nrbook.com/b/bookcpdf.php>Numerical recipes in C 2nd ed., pp896-902, Cambridge University Press (1993),/a>),/p> Checksum:i ...
In enzymology, a poly (beta-D-mannuronate) lyase (EC 4.2.2.3) is an enzyme that catalyzes the chemical reaction:Eliminative cleavage of polysaccharides containing beta-D-
Gammaproteobacteria belonging and related to the genus Microbulbifer are an emerging group of complex carbohydrate-degrading marine bacteria. Previously, all of the representatives were placed within Microbulbifer or were unclassified. Recently, a new genus, Teredinibacter, represented by a single species, Teredinibacter turnerae, was formed to include an endosymbiotic branch of these organisms. In this study, based on 16S rRNA gene sequence similarity and phenotypic analyses, a new genus, Saccharophagus, is proposed to accommodate the most versatile marine carbohydrate degrader yet identified, Saccharophagus degradans gen. nov., sp. nov. 2-40(T) (=ATCC 43961(T)=DSM 17024(T)). S. degradans strain 2-40(T) can degrade 10 tested complex polysaccharides: agar, alginate, chitin, cellulose, fucoidan, laminarin, pectin, pullulan, starch and xylan. S. degradans 2-40(T) shares 90.5% 16S rRNA gene sequence similarity with the type strain of the Microbulbifer type species, Microbulbifer hydrolyticus ...
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SWISS-MODEL Repository entry for Q21MA1 (COAX_SACD2), Type III pantothenate kinase. Saccharophagus degradans (strain 2-40 / ATCC 43961 / DSM 17024)
SWISS-MODEL Repository entry for Q21IG1 (PDXH_SACD2), Pyridoxine/pyridoxamine 5-phosphate oxidase. Saccharophagus degradans (strain 2-40 / ATCC 43961 / DSM 17024)
Extra-cellular Compounds This rod-shaped bacteria is enclosed by two cell membranes and contains flagella for motility. Important adaptations to its survival in such cold environments include production of extracellular polysaccharides which function in protection against cold-damage, known as cryoprotection. The genome has revealed a substantial amount of coding for an extracellular subfamily of σ-70 transcription factors, which among its many roles, can regulate extracellular polymeric synthesis. Genome analysis has also shown a large amount of coding for glycosyl transferases, which are suggested to produce such extracellular polysaccharides. [2] These extracellular polymeric substances (EPS) have been shown to increase extracellular enzymatic activity and stability in C. psychrerythraea. This stabilizing effect, which can potentially benefit several microbial generations, may allow for ever-increasing extreme environments to be tolerated. [7] Genome analysis of C. psychrerythraea has also ...
Three crystal structures of GH117 family have been reported. Two are enzymes from marine bacteria, one from Saccharophagus degradans (PDB: 3R4Y) [4] and one from Zobellia galactanivorans (PDB: 3P2N) [3], the third one is from the human gut bacterium Bacteroidetes plebeius (PDB: 4AK5) [5]. GH117 adopts a five-bladed β-propeller fold and forms a dimer via domain-swapping of the N-terminal HTH (Helix-Turn-Helix) domain (Figure 3) [3]. Interestingly, previous sequences reported from Vibrio sp. JT0107 and Bacillus sp. MK03 contain the conserved domain-swapping signature SxAxxR in the HTH domain. Consistently, these proteins were reported to form multimers (a dimer and an octamer respectively), based on calibrated gel filtration estimations [1, 2]. In contrast, RB13146 (Clade B) lacks the domain-swapping signature, in which the crucial residues are missing. This enzyme from R. baltica thus likely occurs as a monomer and may represent an ancestral form of the GH117 family, which would be limited to ...
University of Maryland research that started with bacteria from the Chesapeake Bay has led to the development of a bacterium, called Saccharophagus degradans which can break down almost any source of biomass, or plant life, into sugars, which can then be converted into ethanol and other biofuels. That process, developed by University of Maryland professors Steve Hutcheson and Ron Weiner, professors of cell biology and molecular genetics, is the foundation of their incubator company Zymetis. They discovered how to produce the enzyme in their own laboratories. The result was Ethazyme, a bacterium that creates a mixture of enzymes-through a patent-pending system which degrades the tough cell walls of cellulosic materials into bio-fuel ready sugars in one step, which are then converted into ethanol and other biofuels at a significantly lower cost and with fewer caustic chemicals than current methods.
University of Maryland research that started with bacteria from the Chesapeake Bay has led to the development of a bacterium, called Saccharophagus degradans which can break down almost any source of biomass, or plant life, into sugars, which can then be converted into ethanol and other biofuels. That process, developed by University of Maryland professors Steve Hutcheson and Ron Weiner, professors of cell biology and molecular genetics, is the foundation of their incubator company Zymetis. They discovered how to produce the enzyme in their own laboratories. The result was Ethazyme, a bacterium that creates a mixture of enzymes-through a patent-pending system which degrades the tough cell walls of cellulosic materials into bio-fuel ready sugars in one step, which are then converted into ethanol and other biofuels at a significantly lower cost and with fewer caustic chemicals than current methods.
A Gram-negative, rod-shaped, moderately halophilic bacterium, designated strain YIM 91118T, motile with a single polar flagellum, was isolated from Xinjiang province in north-west China and subjected to a polyphasic taxonomic study. Strain YIM 91118T grew optimally at 37 °C, pH 7.0-8.0 and 10 % NaCl (w/v). Its major cellular fatty acids were iso-C15 : 0, iso-C17 : 0, C16 : 0 and iso-C17 : 1 ω9c. The predominant lipoquinone was Q-8. The DNA G+C content was 63.2 mol%. All of these chemotaxonomic data supported the assignment of the new isolate to the genus Microbulbifer. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain YIM 91118T belongs to the genus Microbulbifer and it formed a distinct subclade with Microbulbifer maritimus KCCM 41774T. The levels of 16S rRNA gene sequence similarity to the type strains of Microbulbifer species were in the range 93.5-95.0 %. The mean level of DNA-DNA relatedness between strain YIM 91118T and M. maritimus KCCM 41774T was 45.8 %. On the basis of
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ID H5TDX2_9ALTE Unreviewed; 474 AA. AC H5TDX2; DT 18-APR-2012, integrated into UniProtKB/TrEMBL. DT 18-APR-2012, sequence version 1. DT 20-DEC-2017, entry version 39. DE RecName: Full=Chromosomal replication initiator protein DnaA {ECO:0000256,HAMAP-Rule:MF_00377, ECO:0000256,RuleBase:RU000577, ECO:0000256,SAAS:SAAS00724181}; GN Name=dnaA {ECO:0000256,HAMAP-Rule:MF_00377, GN ECO:0000313,EMBL:GAB56499.1}; GN ORFNames=GPUN_2384 {ECO:0000313,EMBL:GAB56499.1}; OS Glaciecola punicea ACAM 611. OC Bacteria; Proteobacteria; Gammaproteobacteria; Alteromonadales; OC Alteromonadaceae; Glaciecola. OX NCBI_TaxID=1121923 {ECO:0000313,EMBL:GAB56499.1, ECO:0000313,Proteomes:UP000053586}; RN [1] {ECO:0000313,EMBL:GAB56499.1, ECO:0000313,Proteomes:UP000053586} RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. RC STRAIN=ACAM 611 {ECO:0000313,EMBL:GAB56499.1, RC ECO:0000313,Proteomes:UP000053586}; RX PubMed=22628500; DOI=10.1128/JB.00463-12; RA Qin Q.-L., Xie B.-B., Shu Y.-L., Rong J.-C., Zhao D.-L., Zhang X.-Y., ...
original description Tanaka, N., Romanenko, L.A., Frolova, G.M., and Mikhailov, V.V. 2010. Aestuariibacter litoralis sp. nov., isolated from a sandy sediment of the Sea of Japan. Int. J. Syst. Evol. Microbiol. 60:317-320. [details] ...
Lineage: cellular organisms; Bacteria; Proteobacteria; Gammaproteobacteria; Alteromonadales; Alteromonadaceae; Marinobacter; unclassified ...
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On the basis of phenotypical characteristics and analysis of 16S rRNA sequence, a new species belonging to a new genus is described, and the name Marinobacter hydrocarbonoclasticus is proposed. This organism, isolated from Mediterranean seawater near a petroleum refinery, is a gram-negative, aerobic, rod-shaped bacterium. It grows at NaCl concentrations of 0.08 to 3.5 M and uses various hydrocarbons as the sole source of carbon and energy. Its DNA has a guanine-plus-cytosine content of 52.7 mol%. The 16S rRNA analysis shows a clear affiliation between M. hydrocarbonoclasticus and the gamma group of the phylum Proteobacteria. A close phylogenetic relationship appears among the species Marinomonas vaga, Oceanospirillum linum, Halomonas elongata, and Pseudomonas aeruginosa. Because of the impossibility of finding a single most closely related species, we suggest that this bacterium be assigned to a new genus, at least temporarily. The possibility of a revision of this status when new data appear is,
General Information: Marinobacter aquaeolei VT8, also known as Marinobacter hydrocarbonoclasticus VT8, is a moderately halophilic, hydrocarbon-degrading bacterium isolated from an oil well off the coast of Vietnam. Hydrocarbon-degrading marine bacterium. This organism is a moderately halophilic, hydrocarbon-degrading bacterium which has been isolated from a number of hydrocarbon polluted marine environments. Marinobacter hydrocarbonoclasticus is able to produce biofilms as well as survive in open seawater. ...
Catalyzes the conversion of dethiobiotin (DTB) to biotin by the insertion of a sulfur atom into dethiobiotin via a radical-based mechanism.
Lineage: cellular organisms; Bacteria; Proteobacteria; Gammaproteobacteria; Alteromonadales; Alteromonadaceae; Alteromonas; Alteromonas ...
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Marine bacterium Catenovulum agarivorans YM01(T) can produce highly thermostable agarases. The draft genome of YM01(T) is about 5.36 Mb and harbors approximately 4,913 genes, including 15 agarase (2 α-agarase and 13 β-agarase)-encoding genes, which will provide references to functional characterization of various agarases from marine bacteria.
ID A0A0D2AGV2_9EURO Unreviewed; 858 AA. AC A0A0D2AGV2; DT 29-APR-2015, integrated into UniProtKB/TrEMBL. DT 29-APR-2015, sequence version 1. DT 07-JUN-2017, entry version 10. DE RecName: Full=V-type proton ATPase subunit a {ECO:0000256,RuleBase:RU361189}; GN ORFNames=PV10_01843 {ECO:0000313,EMBL:KIV98163.1}; OS Exophiala mesophila. OC Eukaryota; Fungi; Dikarya; Ascomycota; Pezizomycotina; Eurotiomycetes; OC Chaetothyriomycetidae; Chaetothyriales; Herpotrichiellaceae; OC Exophiala. OX NCBI_TaxID=212818 {ECO:0000313,EMBL:KIV98163.1, ECO:0000313,Proteomes:UP000054302}; RN [1] {ECO:0000313,EMBL:KIV98163.1, ECO:0000313,Proteomes:UP000054302} RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. RC STRAIN=CBS 40295 {ECO:0000313,EMBL:KIV98163.1, RC ECO:0000313,Proteomes:UP000054302}; RG The Broad Institute Genomics Platform; RA Cuomo C., de Hoog S., Gorbushina A., Stielow B., Teixiera M., RA Abouelleil A., Chapman S.B., Priest M., Young S.K., Wortman J., RA Nusbaum C., Birren B.; RT The Genome Sequence of ...
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