{ "type": "genome", "identifier": "GCF_002723975.1", "organism": "Gluconobacter japonicus", "title": "Gluconobacter japonicus", "description": "na", "data type": "Genome sequencing and assembly", "organization": "National Institute of Technology and Evaluation", "publication": [ {} ], "properties": { "assembly_accession": "GCF_002723975.1", "bioproject": "PRJNA224116", "biosample": "SAMD00093681", "wgs_master": "BEWO00000000.1", "refseq_category": "na", "taxid": "376620", "species_taxid": "376620", "organism_name": "Gluconobacter japonicus", "infraspecific_name": "strain=NBRC 3271", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2017/10/24", "asm_name": "ASM272397v1", "asm_submitter": "National Institute of Technology and Evaluation", "gbrs_paired_asm": "GCA_002723975.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/002/723/975/GCF_002723975.1_ASM272397v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "3156896", "genome_size_ungapped": "3156896", "gc_percent": "56.000000", "replicon_count": "0", "scaffold_count": "75", "contig_count": "75", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_002723975.1-RS_2024_12_15", "annotation_date": "2024-12-15", "total_gene_count": "3012", "protein_coding_gene_count": "2890", "non_coding_gene_count": "53", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2017-10-24", "dateModified": "2017-10-24", "datePublished": "2017-10-24", "_annotation": { "sample_count": 1, "sample_organism": [ "Gluconobacter japonicus" ], "sample_taxid": [ "376620" ], "sample_host_organism": [ "Morella rubra" ], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "Japan:Hyogo, Nishinomiya" ], "sample_host_location_id": [], "data_size": "0.899 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": null, "max": null }, "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0, "genome_count": 1 }, "data_type": "G", "data_source": "RefSeq", "_dfast": { "Total Sequence Length (bp)": "3156896", "Number of Sequences": "75", "Longest Sequences (bp)": "284089", "N50 (bp)": "140254", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "56.1", "Number of CDSs": "2939", "Average Protein Length": "318.7", "Coding Ratio (%)": "89.0", "Number of rRNAs": "3", "Number of tRNAs": "46", "Number of CRISPRs": "3" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Gluconobacter japonicus", "strain": "strain=NBRC 3271", "accession": "GCA_002723975.1", "taxid": 376620, "species_taxid": 376620, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1011, "total_fragments": 1017, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Gluconobacter frateurii", "strain": "strain=NBRC 3264", "accession": "GCA_002723955.1", "taxid": 38308, "species_taxid": 38308, "relation_to_type": "suspected-type", "validated": true, "ani": 87.9739, "matched_fragments": 778, "total_fragments": 1017, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Gluconobacter thailandicus", "strain": "strain=F149-1", "accession": "GCA_000964465.1", "taxid": 257438, "species_taxid": 257438, "relation_to_type": "type", "validated": true, "ani": 86.8756, "matched_fragments": 789, "total_fragments": 1017, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Gluconobacter thailandicus", "strain": "strain=NBRC 100600", "accession": "GCA_007990185.1", "taxid": 257438, "species_taxid": 257438, "relation_to_type": "type", "validated": true, "ani": 86.8455, "matched_fragments": 789, "total_fragments": 1017, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Gluconobacter cerinus", "strain": "strain=NBRC 3267", "accession": "GCA_002723935.1", "taxid": 38307, "species_taxid": 38307, "relation_to_type": "type", "validated": true, "ani": 83.0656, "matched_fragments": 634, "total_fragments": 1017, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Gluconobacter aidae", "strain": "strain=AC10", "accession": "GCA_009547075.1", "taxid": 2662454, "species_taxid": 2662454, "relation_to_type": "type", "validated": true, "ani": 80.1702, "matched_fragments": 412, "total_fragments": 1017, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Gluconobacter potus", "strain": "strain=R-71646", "accession": "GCA_015244705.1", "taxid": 2724927, "species_taxid": 2724927, "relation_to_type": "type", "validated": true, "ani": 80.0405, "matched_fragments": 418, "total_fragments": 1017, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Gluconobacter cerevisiae", "strain": "strain=LMG 27748", "accession": "GCA_015244675.1", "taxid": 1379734, "species_taxid": 1379734, "relation_to_type": "type", "validated": true, "ani": 79.8986, "matched_fragments": 394, "total_fragments": 1017, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Gluconobacter cerevisiae", "strain": "strain=DSM 27644", "accession": "GCA_018811965.1", "taxid": 1379734, "species_taxid": 1379734, "relation_to_type": "type", "validated": true, "ani": 79.8122, "matched_fragments": 394, "total_fragments": 1017, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Gluconobacter kanchanaburiensis", "strain": "strain=NBRC 103587", "accession": "GCA_007988905.1", "taxid": 563199, "species_taxid": 563199, "relation_to_type": "type", "validated": true, "ani": 79.7169, "matched_fragments": 348, "total_fragments": 1017, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Gluconobacter morbifer", "strain": "strain=G707", "accession": "GCA_000234355.2", "taxid": 479935, "species_taxid": 479935, "relation_to_type": "type", "validated": true, "ani": 79.1564, "matched_fragments": 367, "total_fragments": 1017, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Acetobacter garciniae", "strain": "strain=TBRC 12339", "accession": "GCA_017377735.1", "taxid": 2817435, "species_taxid": 2817435, "relation_to_type": "type", "validated": true, "ani": 77.63, "matched_fragments": 90, "total_fragments": 1017, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Neokomagataea anthophila", "strain": "strain=TBRC 2177", "accession": "GCA_018122595.1", "taxid": 2826925, "species_taxid": 2826925, "relation_to_type": "type", "validated": true, "ani": 77.4616, "matched_fragments": 129, "total_fragments": 1017, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_002723975.1", "gtdb_species": "s__Gluconobacter_A japonicus", "ani": 100.0, "matched_fragments": 1011, "total_fragments": 1017, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconobacter_A", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "96.84", "min_intra_species_ani": "95.27", "mean_intra_species_af": "0.89", "min_intra_species_af": "0.85", "num_clustered_genomes": 9, "status": "conclusive" }, { "accession": "GCF_002723955.1", "gtdb_species": "s__Gluconobacter_A frateurii", "ani": 87.9739, "matched_fragments": 778, "total_fragments": 1017, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconobacter_A", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.06", "min_intra_species_ani": "97.06", "mean_intra_species_af": "0.93", "min_intra_species_af": "0.93", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_000964465.1", "gtdb_species": "s__Gluconobacter_A thailandicus", "ani": 86.8756, "matched_fragments": 789, "total_fragments": 1017, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconobacter_A", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.77", "min_intra_species_ani": "97.43", "mean_intra_species_af": "0.93", "min_intra_species_af": "0.88", "num_clustered_genomes": 11, "status": "-" }, { "accession": "GCF_014132155.1", "gtdb_species": "s__Gluconobacter_A sp014132155", "ani": 83.2579, "matched_fragments": 618, "total_fragments": 1017, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconobacter_A", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.46", "min_intra_species_ani": "96.68", "mean_intra_species_af": "0.90", "min_intra_species_af": "0.89", "num_clustered_genomes": 4, "status": "-" }, { "accession": "GCF_002723935.1", "gtdb_species": "s__Gluconobacter_A cerinus", "ani": 83.0591, "matched_fragments": 633, "total_fragments": 1017, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconobacter_A", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "96.40", "min_intra_species_ani": "95.61", "mean_intra_species_af": "0.88", "min_intra_species_af": "0.86", "num_clustered_genomes": 20, "status": "-" }, { "accession": "GCF_001580675.1", "gtdb_species": "s__Gluconobacter potus", "ani": 80.2738, "matched_fragments": 408, "total_fragments": 1017, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconobacter", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "96.92", "min_intra_species_ani": "96.89", "mean_intra_species_af": "0.82", "min_intra_species_af": "0.80", "num_clustered_genomes": 7, "status": "-" }, { "accession": "GCF_009547075.1", "gtdb_species": "s__Gluconobacter sp009547075", "ani": 80.1702, "matched_fragments": 412, "total_fragments": 1017, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconobacter", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "N/A", "min_intra_species_ani": "N/A", "mean_intra_species_af": "N/A", "min_intra_species_af": "N/A", "num_clustered_genomes": 1, "status": "-" }, { "accession": "GCF_015244675.1", "gtdb_species": "s__Gluconobacter cerevisiae", "ani": 79.8986, "matched_fragments": 394, "total_fragments": 1017, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconobacter", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.99", "min_intra_species_ani": "99.99", "mean_intra_species_af": "0.99", "min_intra_species_af": "0.99", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_007988905.1", "gtdb_species": "s__Gluconobacter kanchanaburiensis", "ani": 79.7322, "matched_fragments": 347, "total_fragments": 1017, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconobacter", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "100.00", "min_intra_species_ani": "100.00", "mean_intra_species_af": "1.00", "min_intra_species_af": "1.00", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_006538885.1", "gtdb_species": "s__Gluconobacter roseus", "ani": 79.6853, "matched_fragments": 402, "total_fragments": 1017, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconobacter", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.99", "min_intra_species_ani": "99.99", "mean_intra_species_af": "1.00", "min_intra_species_af": "1.00", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_000234355.1", "gtdb_species": "s__Gluconobacter_C morbifer", "ani": 79.1309, "matched_fragments": 369, "total_fragments": 1017, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconobacter_C", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "N/A", "min_intra_species_ani": "N/A", "mean_intra_species_af": "N/A", "min_intra_species_af": "N/A", "num_clustered_genomes": 1, "status": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": -0.097, "cell_length": 0.0, "doubling_h": -0.027, "growth_tmp": 27.381, "optimum_tmp": 25.0, "optimum_ph": 5.5, "genome_size": 3232432.333, "gc_content": 57.761, "coding_genes": 2938.4, "rRNA16S_genes": 4.75, "tRNA_genes": 56.643, "gram_stain": 0.0, "sporulation": 0.0, "motility": 1.0, "range_salinity": null, "facultative_respiration": 0.0, "anaerobic_respiration": 0.0, "aerobic_respiration": 1.0, "mesophilic_range_tmp": 1.0, "thermophilic_range_tmp": 0.0, "psychrophilic_range_tmp": 0.0, "bacillus_cell_shape": 1.0, "coccus_cell_shape": 0.0, "filament_cell_shape": 0.0, "coccobacillus_cell_shape": 0.0, "vibrio_cell_shape": 0.0, "spiral_cell_shape": 0.0 }, "_genome_taxon": [ "Gluconobacter", "japonicus" ], "quality": 4, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }