Aequorivita sublithincola 9-3 is an obligate aerobe, chemoheterotroph, Gram-negative bacterium that was isolated from quartz stone sublith.
Gram-negative filament-shaped obligate aerobe chemoheterotroph genome sequence Bacteria| @ref 20215 |
|
|
| Domain Bacteria |
| Phylum Bacteroidota |
| Class Flavobacteriia |
| Order Flavobacteriales |
| Family Flavobacteriaceae |
| Genus Aequorivita |
| Species Aequorivita sublithincola |
| Full scientific name Aequorivita sublithincola Bowman and Nichols 2002 |
| @ref: | 66793 |
| multimedia content: | EM_DSM_14238_1.jpg |
| multimedia.multimedia content: | EM_DSM_14238_1.jpg |
| caption: | electron microscopic image |
| intellectual property rights: | © HZI/Manfred Rohde |
| manual_annotation: | 1 |
| @ref | Name | Growth | Medium link | Composition | |
|---|---|---|---|---|---|
| 5266 | BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514) | Medium recipe at MediaDive | Name: BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514) Composition: NaCl 19.45 g/l MgCl2 5.9 g/l Bacto peptone 5.0 g/l Na2SO4 3.24 g/l CaCl2 1.8 g/l Yeast extract 1.0 g/l KCl 0.55 g/l NaHCO3 0.16 g/l Fe(III) citrate 0.1 g/l KBr 0.08 g/l SrCl2 0.034 g/l H3BO3 0.022 g/l Na2HPO4 0.008 g/l Na-silicate 0.004 g/l NaF 0.0024 g/l (NH4)NO3 0.0016 g/l Distilled water | ||
| 42118 | MEDIUM 72- for trypto casein soja agar | Distilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g) | |||
| 123346 | CIP Medium 72 | Medium recipe at CIP |
| @ref | Ability | Type | PH | |
|---|---|---|---|---|
| 43341 | positive | optimum | 7-7.5 |
| 43341 | Typechemoheterotroph |
| @ref | Spore formation | Confidence | |
|---|---|---|---|
| 125439 | 99.739 |
| @ref | Chebi-ID | Metabolite | Utilization activity | Kind of utilization tested | |
|---|---|---|---|---|---|
| 43341 | casein | - | hydrolysis | ||
| 43341 | 62968 ChEBI | cellulose | - | degradation | |
| 43341 | 4767 ChEBI | elastin | - | hydrolysis | |
| 43341 | 4853 ChEBI | esculin | - | hydrolysis | |
| 123346 | 4853 ChEBI | esculin | - | hydrolysis | |
| 43341 | 5291 ChEBI | gelatin | + | hydrolysis | |
| 123346 | 606565 ChEBI | hippurate | - | hydrolysis | |
| 43341 | 17895 ChEBI | L-tyrosine | + | hydrolysis | |
| 123346 | 15792 ChEBI | malonate | - | assimilation | |
| 123346 | 17632 ChEBI | nitrate | - | reduction | |
| 123346 | 17632 ChEBI | nitrate | - | respiration | |
| 123346 | 16301 ChEBI | nitrite | - | reduction | |
| 43341 | 28017 ChEBI | starch | - | hydrolysis | |
| 43341 | 35020 ChEBI | tributyrin | - | hydrolysis | |
| 43341 | 27226 ChEBI | uric acid | - | degradation | |
| 43341 | 15318 ChEBI | xanthine | - | degradation | |
| 43341 | 37166 ChEBI | xylan | - | degradation |
| @ref | Value | Activity | Ec | |
|---|---|---|---|---|
| 43341 | 6-phospho-beta-galactosidase | - | 3.2.1.85 | |
| 68382 | acid phosphatase | + | 3.1.3.2 | from API zym |
| 123346 | alcohol dehydrogenase | - | 1.1.1.1 | |
| 43341 | alkaline phosphatase | + | 3.1.3.1 | |
| 68382 | alkaline phosphatase | + | 3.1.3.1 | from API zym |
| 43341 | alpha-arabinosidase | - | 3.2.1.55 | |
| 68382 | alpha-chymotrypsin | + | 3.4.21.1 | from API zym |
| 43341 | alpha-fucosidase | - | 3.2.1.51 | |
| 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 |
| 123346 | amylase | - | ||
| 43341 | arginine dihydrolase | - | 3.5.3.6 | |
| 43341 | beta-galactosidase | - | 3.2.1.23 | |
| 68382 | beta-galactosidase | - | 3.2.1.23 | from API zym |
| 123346 | beta-galactosidase | + | 3.2.1.23 | |
| 43341 | beta-glucosidase | - | 3.2.1.21 | |
| 68382 | beta-glucosidase | - | 3.2.1.21 | from API zym |
| 43341 | beta-glucuronidase | - | 3.2.1.31 | |
| 68382 | beta-glucuronidase | - | 3.2.1.31 | from API zym |
| 123346 | caseinase | - | 3.4.21.50 | |
| 123346 | catalase | + | 1.11.1.6 | |
| 68382 | cystine arylamidase | - | 3.4.11.3 | from API zym |
| 123346 | DNase | - | ||
| 43341 | esterase | - | ||
| 43341 | esterase | + | ||
| 68382 | esterase (C 4) | + | from API zym | |
| 68382 | esterase lipase (C 8) | + | from API zym | |
| 123346 | gamma-glutamyltransferase | + | 2.3.2.2 | |
| 123346 | gelatinase | +/- | ||
| 123346 | lecithinase | - | ||
| 68382 | leucine arylamidase | + | 3.4.11.1 | from API zym |
| 43341 | lipase | - | ||
| 123346 | lipase | - | ||
| 68382 | lipase (C 14) | - | from API zym | |
| 43341 | lysine decarboxylase | - | 4.1.1.18 | |
| 123346 | lysine decarboxylase | - | 4.1.1.18 | |
| 43341 | N-acetyl-beta-glucosaminidase | + | 3.2.1.52 | |
| 68382 | N-acetyl-beta-glucosaminidase | + | 3.2.1.52 | from API zym |
| 68382 | naphthol-AS-BI-phosphohydrolase | + | from API zym | |
| 43341 | ornithine decarboxylase | - | 4.1.1.17 | |
| 123346 | ornithine decarboxylase | - | 4.1.1.17 | |
| 123346 | oxidase | - | ||
| 123346 | phenylalanine ammonia-lyase | - | 4.3.1.24 | |
| 68382 | trypsin | + | 3.4.21.4 | from API zym |
| 123346 | tryptophan deaminase | - | ||
| 123346 | tween esterase | + | ||
| 123346 | urease | - | 3.5.1.5 | |
| 68382 | valine arylamidase | + | from API zym |
| @ref | pathway | enzyme coverage | annotated reactions | external links | |
|---|---|---|---|---|---|
| 66794 | sulfopterin metabolism | 100 | 4 of 4 | ||
| 66794 | CDP-diacylglycerol biosynthesis | 100 | 2 of 2 | ||
| 66794 | denitrification | 100 | 2 of 2 | ||
| 66794 | vitamin K metabolism | 100 | 5 of 5 | ||
| 66794 | UDP-GlcNAc biosynthesis | 100 | 3 of 3 | ||
| 66794 | cis-vaccenate biosynthesis | 100 | 2 of 2 | ||
| 66794 | palmitate biosynthesis | 100 | 22 of 22 | ||
| 66794 | ppGpp biosynthesis | 100 | 4 of 4 | ||
| 66794 | suberin monomers biosynthesis | 100 | 2 of 2 | ||
| 66794 | CMP-KDO biosynthesis | 100 | 4 of 4 | ||
| 66794 | coenzyme A metabolism | 100 | 4 of 4 | ||
| 66794 | acetate fermentation | 100 | 4 of 4 | ||
| 66794 | anapleurotic synthesis of oxalacetate | 100 | 1 of 1 | ||
| 66794 | folate polyglutamylation | 100 | 1 of 1 | ||
| 66794 | adipate degradation | 100 | 2 of 2 | ||
| 66794 | phenylacetate degradation (aerobic) | 100 | 5 of 5 | ||
| 66794 | methylglyoxal degradation | 100 | 5 of 5 | ||
| 66794 | NAD metabolism | 94.44 | 17 of 18 | ||
| 66794 | serine metabolism | 88.89 | 8 of 9 | ||
| 66794 | chorismate metabolism | 88.89 | 8 of 9 | ||
| 66794 | lipid A biosynthesis | 88.89 | 8 of 9 | ||
| 66794 | gluconeogenesis | 87.5 | 7 of 8 | ||
| 66794 | C4 and CAM-carbon fixation | 87.5 | 7 of 8 | ||
| 66794 | tetrahydrofolate metabolism | 85.71 | 12 of 14 | ||
| 66794 | phenylalanine metabolism | 84.62 | 11 of 13 | ||
| 66794 | tryptophan metabolism | 81.58 | 31 of 38 | ||
| 66794 | lipoate biosynthesis | 80 | 4 of 5 | ||
| 66794 | peptidoglycan biosynthesis | 80 | 12 of 15 | ||
| 66794 | photosynthesis | 78.57 | 11 of 14 | ||
| 66794 | CO2 fixation in Crenarchaeota | 77.78 | 7 of 9 | ||
| 66794 | aspartate and asparagine metabolism | 77.78 | 7 of 9 | ||
| 66794 | purine metabolism | 74.47 | 70 of 94 | ||
| 66794 | lipid metabolism | 74.19 | 23 of 31 | ||
| 66794 | glutamate and glutamine metabolism | 71.43 | 20 of 28 | ||
| 66794 | cardiolipin biosynthesis | 71.43 | 5 of 7 | ||
| 66794 | ubiquinone biosynthesis | 71.43 | 5 of 7 | ||
| 66794 | propionate fermentation | 70 | 7 of 10 | ||
| 66794 | leucine metabolism | 69.23 | 9 of 13 | ||
| 66794 | lysine metabolism | 69.05 | 29 of 42 | ||
| 66794 | pyrimidine metabolism | 68.89 | 31 of 45 | ||
| 66794 | formaldehyde oxidation | 66.67 | 2 of 3 | ||
| 66794 | L-lactaldehyde degradation | 66.67 | 2 of 3 | ||
| 66794 | acetyl CoA biosynthesis | 66.67 | 2 of 3 | ||
| 66794 | flavin biosynthesis | 66.67 | 10 of 15 | ||
| 66794 | octane oxidation | 66.67 | 2 of 3 | ||
| 66794 | acetoin degradation | 66.67 | 2 of 3 | ||
| 66794 | histidine metabolism | 65.52 | 19 of 29 | ||
| 66794 | methionine metabolism | 65.38 | 17 of 26 | ||
| 66794 | glycolysis | 64.71 | 11 of 17 | ||
| 66794 | heme metabolism | 64.29 | 9 of 14 | ||
| 66794 | glutathione metabolism | 64.29 | 9 of 14 | ||
| 66794 | citric acid cycle | 64.29 | 9 of 14 | ||
| 66794 | isoleucine metabolism | 62.5 | 5 of 8 | ||
| 66794 | 6-hydroxymethyl-dihydropterin diphosphate biosynthesis | 62.5 | 5 of 8 | ||
| 66794 | dTDPLrhamnose biosynthesis | 62.5 | 5 of 8 | ||
| 66794 | alanine metabolism | 62.07 | 18 of 29 | ||
| 66794 | non-pathway related | 60.53 | 23 of 38 | ||
| 66794 | arachidonate biosynthesis | 60 | 3 of 5 | ||
| 66794 | threonine metabolism | 60 | 6 of 10 | ||
| 66794 | glycine betaine biosynthesis | 60 | 3 of 5 | ||
| 66794 | reductive acetyl coenzyme A pathway | 57.14 | 4 of 7 | ||
| 66794 | tyrosine metabolism | 57.14 | 8 of 14 | ||
| 66794 | propanol degradation | 57.14 | 4 of 7 | ||
| 66794 | cysteine metabolism | 55.56 | 10 of 18 | ||
| 66794 | d-mannose degradation | 55.56 | 5 of 9 | ||
| 66794 | valine metabolism | 55.56 | 5 of 9 | ||
| 66794 | pentose phosphate pathway | 54.55 | 6 of 11 | ||
| 66794 | glycogen biosynthesis | 50 | 2 of 4 | ||
| 66794 | glycine metabolism | 50 | 5 of 10 | ||
| 66794 | kanosamine biosynthesis II | 50 | 1 of 2 | ||
| 66794 | Entner Doudoroff pathway | 50 | 5 of 10 | ||
| 66794 | ketogluconate metabolism | 50 | 4 of 8 | ||
| 66794 | ethanol fermentation | 50 | 1 of 2 | ||
| 66794 | phenylmercury acetate degradation | 50 | 1 of 2 | ||
| 66794 | cyclohexanol degradation | 50 | 2 of 4 | ||
| 66794 | quinate degradation | 50 | 1 of 2 | ||
| 66794 | vitamin B1 metabolism | 46.15 | 6 of 13 | ||
| 66794 | phenylpropanoid biosynthesis | 46.15 | 6 of 13 | ||
| 66794 | isoprenoid biosynthesis | 46.15 | 12 of 26 | ||
| 66794 | vitamin B6 metabolism | 45.45 | 5 of 11 | ||
| 66794 | degradation of sugar alcohols | 43.75 | 7 of 16 | ||
| 66794 | polyamine pathway | 43.48 | 10 of 23 | ||
| 66794 | mevalonate metabolism | 42.86 | 3 of 7 | ||
| 66794 | carotenoid biosynthesis | 40.91 | 9 of 22 | ||
| 66794 | oxidative phosphorylation | 40.66 | 37 of 91 | ||
| 66794 | phenol degradation | 40 | 8 of 20 | ||
| 66794 | myo-inositol biosynthesis | 40 | 4 of 10 | ||
| 66794 | arachidonic acid metabolism | 38.89 | 7 of 18 | ||
| 66794 | ascorbate metabolism | 36.36 | 8 of 22 | ||
| 66794 | proline metabolism | 36.36 | 4 of 11 | ||
| 66794 | pantothenate biosynthesis | 33.33 | 2 of 6 | ||
| 66794 | degradation of aromatic, nitrogen containing compounds | 33.33 | 4 of 12 | ||
| 66794 | selenocysteine biosynthesis | 33.33 | 2 of 6 | ||
| 66794 | glycolate and glyoxylate degradation | 33.33 | 2 of 6 | ||
| 66794 | 4-hydroxymandelate degradation | 33.33 | 3 of 9 | ||
| 66794 | (5R)-carbapenem carboxylate biosynthesis | 33.33 | 1 of 3 | ||
| 66794 | cyanate degradation | 33.33 | 1 of 3 | ||
| 66794 | allantoin degradation | 33.33 | 3 of 9 | ||
| 66794 | IAA biosynthesis | 33.33 | 1 of 3 | ||
| 66794 | enterobactin biosynthesis | 33.33 | 1 of 3 | ||
| 66794 | degradation of pentoses | 32.14 | 9 of 28 | ||
| 66794 | phosphatidylethanolamine bioynthesis | 30.77 | 4 of 13 | ||
| 66794 | coenzyme M biosynthesis | 30 | 3 of 10 | ||
| 66794 | arginine metabolism | 29.17 | 7 of 24 | ||
| 66794 | degradation of hexoses | 27.78 | 5 of 18 | ||
| 66794 | d-xylose degradation | 27.27 | 3 of 11 | ||
| 66794 | dolichyl-diphosphooligosaccharide biosynthesis | 27.27 | 3 of 11 | ||
| 66794 | carnitine metabolism | 25 | 2 of 8 | ||
| 66794 | lactate fermentation | 25 | 1 of 4 | ||
| 66794 | toluene degradation | 25 | 1 of 4 | ||
| 66794 | androgen and estrogen metabolism | 25 | 4 of 16 | ||
| 66794 | butanoate fermentation | 25 | 1 of 4 | ||
| 66794 | catecholamine biosynthesis | 25 | 1 of 4 | ||
| 66794 | biotin biosynthesis | 25 | 1 of 4 | ||
| 66794 | sulfate reduction | 23.08 | 3 of 13 | ||
| 66794 | urea cycle | 23.08 | 3 of 13 | ||
| 66794 | nitrate assimilation | 22.22 | 2 of 9 | ||
| 66794 | molybdenum cofactor biosynthesis | 22.22 | 2 of 9 |
| @ref | Sample type | Geographic location | Country | Country ISO 3 Code | Continent | Isolation date | Enrichment culture | Isolation procedure | |
|---|---|---|---|---|---|---|---|---|---|
| 5266 | quartz stone sublith | Vestfold Hills | Australia and Oceania | ||||||
| 43341 | quartz stone aublithic material | marine agar (Difco, Oxoid) | sublithic biomass is scraped , vortexed and then diluted in trypicase soy broth | ||||||
| 123346 | Quartz stone sublim | Vestfold hills | Antarctica | ATA | Antarctica | 1998 |
| @ref | Trait | Model | Prediction | Confidence in % | In training data |
|---|---|---|---|---|---|
| 125439 | oxygen_tolerance | BacteriaNetⓘ | obligate aerobe | 99.26 | no |
| 125439 | gram_stain | BacteriaNetⓘ | negative | 99.67 | no |
| 125439 | motility | BacteriaNetⓘ | no | 84.40 | no |
| 125439 | spore_formation | BacteriaNetⓘ | no | 99.74 | no |
| @ref | Trait | Model | Prediction | Confidence in % | In training data |
|---|---|---|---|---|---|
| 125438 | gram-positive | gram-positiveⓘ | no | 98.86 | yes |
| 125438 | anaerobic | anaerobicⓘ | no | 97.81 | yes |
| 125438 | aerobic | aerobicⓘ | yes | 86.34 | no |
| 125438 | spore-forming | spore-formingⓘ | no | 86.72 | no |
| 125438 | thermophilic | thermophileⓘ | no | 96.63 | yes |
| 125438 | flagellated | motile2+ⓘ | no | 91.50 | yes |
| Topic | Title | Authors | Journal | DOI | Year | |
|---|---|---|---|---|---|---|
| Enzymology | Carbohydrate-Active Enzymes of a Novel Halotolerant Alkalihalobacillus Species for Hydrolysis of Starch and Other Algal Polysaccharides. | Masasa M, Kushmaro A, Chernova H, Shashar N, Guttman L. | Microbiol Spectr | 10.1128/spectrum.01078-22 | 2022 | |
| Enzymology | In Situ Corn Fiber Conversion for Ethanol Improvement by the Addition of a Novel Lignocellulolytic Enzyme Cocktail. | Gao L, Zhang D, Wu X. | J Fungi (Basel) | 10.3390/jof8030221 | 2022 | |
| Genetics | Genome sequence of Talaromyces piceus 9-3 provides insights into lignocellulose degradation. | He R, Bai X, Cai P, Sun C, Zhang D, Chen S. | 3 Biotech | 10.1007/s13205-017-1001-5 | 2017 | |
| Genetics | Salinity and Time Can Alter Epibacterial Communities of an Invasive Seaweed. | Saha M, Ferguson RMW, Dove S, Kunzel S, Meichssner R, Neulinger SC, Petersen FO, Weinberger F. | Front Microbiol | 10.3389/fmicb.2019.02870 | 2019 | |
| Metabolism | [Biosynthesis of the subtilisin-like serine proteinase of Bacillus intermedius under salt stress conditions]. | Kaiumov AR, Balaban NP, Mardanova AM, Kostrov SV, Sharipova MR. | Mikrobiologiia | 10.1134/s0026261706050043 | 2006 | |
| Enzymology | Structural insights into the catalytic mechanism of a novel glycoside hydrolase family 113 beta-1,4-mannanase from Amphibacillus xylanus. | You X, Qin Z, Yan Q, Yang S, Li Y, Jiang Z. | J Biol Chem | 10.1074/jbc.ra118.002363 | 2018 | |
| Abundant Intergenic TAACTGA Direct Repeats and Putative Alternate RNA Polymerase beta' Subunits in Marine Beggiatoaceae Genomes: Possible Regulatory Roles and Origins. | MacGregor BJ. | Front Microbiol | 10.3389/fmicb.2015.01397 | 2015 | ||
| Genetics | Isolation by Miniaturized Culture Chip of an Antarctic bacterium Aequorivita sp. with antimicrobial and anthelmintic activity. | Palma Esposito F, Ingham CJ, Hurtado-Ortiz R, Bizet C, Tasdemir D, de Pascale D. | Biotechnol Rep (Amst) | 10.1016/j.btre.2018.e00281 | 2018 | |
| Metabolism | Novel m4C modification in type I restriction-modification systems. | Morgan RD, Luyten YA, Johnson SA, Clough EM, Clark TA, Roberts RJ. | Nucleic Acids Res | 10.1093/nar/gkw743 | 2016 | |
| Phylogeny | Genome-Based Taxonomic Classification of Bacteroidetes. | Hahnke RL, Meier-Kolthoff JP, Garcia-Lopez M, Mukherjee S, Huntemann M, Ivanova NN, Woyke T, Kyrpides NC, Klenk HP, Goker M. | Front Microbiol | 10.3389/fmicb.2016.02003 | 2016 | |
| Phylogeny | Aequorivita gen. nov., a member of the family Flavobacteriaceae isolated from terrestrial and marine Antarctic habitats. | Bowman JP, Nichols DS | Int J Syst Evol Microbiol | 10.1099/00207713-52-5-1533 | 2002 |
| #5266 | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 14238 |
| #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 ) |
| #42118 | ; Curators of the CIP; |
| #43341 | ; 4: 155 - 157 ISBN 978 ( DOI 10.1007/978-0-387-68572-4 ) |
| #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) . |
| #66793 | Mukherjee et al.: GEBA: 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life. 35: 676 - 683 2017 ( DOI 10.1038/nbt.3886 , PubMed 28604660 ) |
| #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. Nucleic Acids Res. 49: D498 - D508 2020 ( DOI 10.1093/nar/gkaa1025 , PubMed 33211880 ) |
| #68382 | Automatically annotated from API zym . |
| #123346 | Collection of Institut Pasteur ; Curators of the CIP; CIP 107454 |
| #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 ) |
| #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 . |
| #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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