{ "type": "genome", "identifier": "GCF_006539925.1", "organism": "Glutamicibacter uratoxydans", "title": "Glutamicibacter uratoxydans", "description": "na", "data type": "Genome sequencing and assembly", "organization": "National Institute of Technology and Evaluation", "publication": [ {} ], "properties": { "assembly_accession": "GCF_006539925.1", "bioproject": "PRJNA224116", "biosample": "SAMD00097580", "wgs_master": "BJNY00000000.1", "refseq_category": "reference genome", "taxid": "43667", "species_taxid": "43667", "organism_name": "Glutamicibacter uratoxydans", "infraspecific_name": "strain=NBRC 15515", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2019/06/12", "asm_name": "ASM653992v1", "asm_submitter": "National Institute of Technology and Evaluation", "gbrs_paired_asm": "GCA_006539925.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/006/539/925/GCF_006539925.1_ASM653992v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "3786014", "genome_size_ungapped": "3786014", "gc_percent": "61.000000", "replicon_count": "0", "scaffold_count": "49", "contig_count": "49", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_006539925.1-RS_2024_12_09", "annotation_date": "2024-12-09", "total_gene_count": "3610", "protein_coding_gene_count": "3521", "non_coding_gene_count": "65", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2019-06-12", "dateModified": "2019-06-12", "datePublished": "2019-06-12", "_annotation": { "sample_count": 1, "sample_organism": [ "Glutamicibacter uratoxydans" ], "sample_taxid": [ "43667" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "missing" ], "sample_host_location_id": [], "data_size": "1.067 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)": "3786014", "Number of Sequences": "49", "Longest Sequences (bp)": "362529", "N50 (bp)": "175646", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "61.1", "Number of CDSs": "3532", "Average Protein Length": "313.1", "Coding Ratio (%)": "87.6", "Number of rRNAs": "3", "Number of tRNAs": "57", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Glutamicibacter uratoxydans", "strain": "strain=NBRC 15515", "accession": "GCA_006539925.1", "taxid": 43667, "species_taxid": 43667, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1238, "total_fragments": 1240, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Glutamicibacter protophormiae", "strain": "strain=JCM 1973", "accession": "GCA_014647495.1", "taxid": 37930, "species_taxid": 37930, "relation_to_type": "type", "validated": true, "ani": 83.6578, "matched_fragments": 733, "total_fragments": 1240, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Glutamicibacter protophormiae", "strain": "strain=DSM 20168", "accession": "GCA_017876615.1", "taxid": 37930, "species_taxid": 37930, "relation_to_type": "type", "validated": true, "ani": 83.6253, "matched_fragments": 748, "total_fragments": 1240, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Glutamicibacter nicotianae", "strain": "strain=NBRC 14234", "accession": "GCA_006539525.1", "taxid": 37929, "species_taxid": 37929, "relation_to_type": "type", "validated": true, "ani": 82.2737, "matched_fragments": 633, "total_fragments": 1240, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Glutamicibacter mysorens", "strain": "strain=NBRC 103060", "accession": "GCA_001552115.1", "taxid": 257984, "species_taxid": 257984, "relation_to_type": "type", "validated": true, "ani": 82.2699, "matched_fragments": 636, "total_fragments": 1240, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Glutamicibacter mysorens", "strain": "strain=DSM 12798", "accession": "GCA_002797775.1", "taxid": 257984, "species_taxid": 257984, "relation_to_type": "type", "validated": true, "ani": 82.2455, "matched_fragments": 628, "total_fragments": 1240, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Glutamicibacter halophytocola", "strain": "strain=KLBMP 5180", "accession": "GCA_001302565.1", "taxid": 1933880, "species_taxid": 1933880, "relation_to_type": "type", "validated": true, "ani": 81.3557, "matched_fragments": 589, "total_fragments": 1240, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Paeniglutamicibacter psychrophenolicus", "strain": "strain=DSM 15454", "accession": "GCA_017876575.1", "taxid": 257454, "species_taxid": 257454, "relation_to_type": "type", "validated": true, "ani": 79.5744, "matched_fragments": 470, "total_fragments": 1240, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Arthrobacter ipis", "strain": "strain=IA7", "accession": "GCA_014694315.1", "taxid": 2716202, "species_taxid": 2716202, "relation_to_type": "type", "validated": true, "ani": 78.1054, "matched_fragments": 232, "total_fragments": 1240, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Arthrobacter sunyaminii", "strain": "strain=zg-ZUI122", "accession": "GCA_017353495.1", "taxid": 2816859, "species_taxid": 2816859, "relation_to_type": "type", "validated": true, "ani": 77.9526, "matched_fragments": 213, "total_fragments": 1240, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Arthrobacter sunyaminii", "strain": "strain=zg-ZUI122", "accession": "GCA_018866305.1", "taxid": 2816859, "species_taxid": 2816859, "relation_to_type": "type", "validated": true, "ani": 77.9424, "matched_fragments": 212, "total_fragments": 1240, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Arthrobacter sedimenti", "strain": "strain=MIC A30", "accession": "GCA_011750795.2", "taxid": 2694931, "species_taxid": 2694931, "relation_to_type": "type", "validated": true, "ani": 77.2632, "matched_fragments": 205, "total_fragments": 1240, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Garicola koreensis", "strain": "strain=DSM 28238", "accession": "GCA_014195445.1", "taxid": 1262554, "species_taxid": 1262554, "relation_to_type": "type", "validated": true, "ani": 77.1507, "matched_fragments": 116, "total_fragments": 1240, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Georgenia yuyongxinii", "strain": "strain=Z443", "accession": "GCA_006352065.1", "taxid": 2589797, "species_taxid": 2589797, "relation_to_type": "type", "validated": true, "ani": 76.6559, "matched_fragments": 123, "total_fragments": 1240, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_006539925.1", "gtdb_species": "s__Glutamicibacter uratoxydans", "ani": 100.0, "matched_fragments": 1238, "total_fragments": 1240, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Glutamicibacter", "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": "conclusive" }, { "accession": "GCF_003309065.1", "gtdb_species": "s__Glutamicibacter soli", "ani": 83.7427, "matched_fragments": 766, "total_fragments": 1240, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Glutamicibacter", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.33", "min_intra_species_ani": "97.69", "mean_intra_species_af": "0.91", "min_intra_species_af": "0.87", "num_clustered_genomes": 6, "status": "-" }, { "accession": "GCF_014647495.1", "gtdb_species": "s__Glutamicibacter protophormiae", "ani": 83.6828, "matched_fragments": 731, "total_fragments": 1240, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Glutamicibacter", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.76", "min_intra_species_ani": "97.53", "mean_intra_species_af": "0.93", "min_intra_species_af": "0.87", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_006539525.1", "gtdb_species": "s__Glutamicibacter nicotianae", "ani": 82.2898, "matched_fragments": 631, "total_fragments": 1240, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Glutamicibacter", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.59", "min_intra_species_ani": "96.22", "mean_intra_species_af": "0.88", "min_intra_species_af": "0.85", "num_clustered_genomes": 10, "status": "-" }, { "accession": "GCF_002979865.1", "gtdb_species": "s__Glutamicibacter sp002979865", "ani": 81.573, "matched_fragments": 623, "total_fragments": 1240, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Glutamicibacter", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.88", "min_intra_species_ani": "98.56", "mean_intra_species_af": "0.94", "min_intra_species_af": "0.92", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_001302565.1", "gtdb_species": "s__Glutamicibacter halophytocola", "ani": 81.3443, "matched_fragments": 590, "total_fragments": 1240, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Glutamicibacter", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.28", "min_intra_species_ani": "98.01", "mean_intra_species_af": "0.91", "min_intra_species_af": "0.89", "num_clustered_genomes": 4, "status": "-" }, { "accession": "GCF_006094275.1", "gtdb_species": "s__Glutamicibacter creatinolyticus", "ani": 80.7025, "matched_fragments": 545, "total_fragments": 1240, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Glutamicibacter", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.17", "min_intra_species_ani": "97.78", "mean_intra_species_af": "0.92", "min_intra_species_af": "0.89", "num_clustered_genomes": 4, "status": "-" }, { "accession": "GCF_900094805.1", "gtdb_species": "s__Glutamicibacter sp900094805", "ani": 80.478, "matched_fragments": 433, "total_fragments": 1240, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Glutamicibacter", "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_003287975.1", "gtdb_species": "s__Paeniglutamicibacter sp003287975", "ani": 79.6945, "matched_fragments": 447, "total_fragments": 1240, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Paeniglutamicibacter", "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_017876575.1", "gtdb_species": "s__Paeniglutamicibacter psychrophenolicus", "ani": 79.6007, "matched_fragments": 468, "total_fragments": 1240, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Paeniglutamicibacter", "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_900010755.1", "gtdb_species": "s__Paeniglutamicibacter antarcticus_A", "ani": 79.1889, "matched_fragments": 379, "total_fragments": 1240, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Paeniglutamicibacter", "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_000348945.1", "gtdb_species": "s__Paeniglutamicibacter gangotriensis", "ani": 78.7783, "matched_fragments": 372, "total_fragments": 1240, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Paeniglutamicibacter", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.63", "min_intra_species_ani": "97.63", "mean_intra_species_af": "0.86", "min_intra_species_af": "0.86", "num_clustered_genomes": 2, "status": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": -0.097, "cell_length": 0.0, "doubling_h": null, "growth_tmp": 27.0, "optimum_tmp": 30.0, "optimum_ph": null, "genome_size": 3786014.0, "gc_content": 61.088, "coding_genes": 3485.625, "rRNA16S_genes": 6.0, "tRNA_genes": 64.5, "gram_stain": 1.0, "sporulation": 0.0, "motility": 0.0, "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": [ "Glutamicibacter", "uratoxydans" ], "quality": 4, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }