{ "type": "genome", "identifier": "GCF_011839805.1", "organism": "Kineococcus rubinsiae", "title": "Kineococcus rubinsiae", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Jet Propulsion Laboratory, California Institute of Technology", "publication": [ {} ], "properties": { "assembly_accession": "GCF_011839805.1", "bioproject": "PRJNA224116", "biosample": "SAMN12717667", "wgs_master": "VWPY00000000.1", "refseq_category": "reference genome", "taxid": "2609562", "species_taxid": "2609562", "organism_name": "Kineococcus rubinsiae", "infraspecific_name": "strain=B12", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2020/04/01", "asm_name": "ASM1183980v1", "asm_submitter": "Jet Propulsion Laboratory, California Institute of Technology", "gbrs_paired_asm": "GCA_011839805.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/011/839/805/GCF_011839805.1_ASM1183980v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "4880137", "genome_size_ungapped": "4880137", "gc_percent": "74.000000", "replicon_count": "0", "scaffold_count": "119", "contig_count": "119", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_011839805.1-RS_2024_09_03", "annotation_date": "2024-09-03", "total_gene_count": "4589", "protein_coding_gene_count": "4451", "non_coding_gene_count": "56", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2020-04-01", "dateModified": "2020-04-01", "datePublished": "2020-04-01", "_annotation": { "sample_count": 1, "sample_organism": [ "Kineococcus rubinsiae" ], "sample_taxid": [ "2609562" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "USA:California, Pasadena, NASA Jet Propulsion Laboratory" ], "sample_host_location_id": [], "data_size": "1.279 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": 204.0, "max": 204.0 }, "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0, "genome_count": 1 }, "data_type": "G", "data_source": "RefSeq", "_dfast": { "Total Sequence Length (bp)": "4880137", "Number of Sequences": "119", "Longest Sequences (bp)": "392027", "N50 (bp)": "66629", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "74.2", "Number of CDSs": "4501", "Average Protein Length": "320.7", "Coding Ratio (%)": "88.7", "Number of rRNAs": "5", "Number of tRNAs": "60", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Kineococcus rubinsiae", "strain": "strain=B12", "accession": "GCA_011839805.1", "taxid": 2609562, "species_taxid": 2609562, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1564, "total_fragments": 1567, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Kineococcus siccus", "strain": "strain=R8", "accession": "GCA_009906795.1", "taxid": 2696567, "species_taxid": 2696567, "relation_to_type": "type", "validated": true, "ani": 87.2809, "matched_fragments": 965, "total_fragments": 1567, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Kineococcus vitellinus", "strain": "strain=T13", "accession": "GCA_009906315.1", "taxid": 2696565, "species_taxid": 2696565, "relation_to_type": "type", "validated": true, "ani": 82.1048, "matched_fragments": 788, "total_fragments": 1567, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Kineococcus radiotolerans", "strain": "strain=SRS30216", "accession": "GCA_000017305.1", "taxid": 131568, "species_taxid": 131568, "relation_to_type": "type", "validated": true, "ani": 81.9007, "matched_fragments": 909, "total_fragments": 1567, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Kineococcus indalonis", "strain": "strain=T90", "accession": "GCA_009906395.1", "taxid": 2696566, "species_taxid": 2696566, "relation_to_type": "type", "validated": true, "ani": 81.6073, "matched_fragments": 676, "total_fragments": 1567, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Kineococcus aurantiacus", "strain": "strain=DSM 7487", "accession": "GCA_013409345.1", "taxid": 37633, "species_taxid": 37633, "relation_to_type": "type", "validated": true, "ani": 81.4729, "matched_fragments": 918, "total_fragments": 1567, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Kineococcus rhizosphaerae", "strain": "strain=DSM 19711", "accession": "GCA_003002055.1", "taxid": 559628, "species_taxid": 559628, "relation_to_type": "type", "validated": true, "ani": 81.2453, "matched_fragments": 929, "total_fragments": 1567, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Kineococcus xinjiangensis", "strain": "strain=DSM 22857", "accession": "GCA_002934625.1", "taxid": 512762, "species_taxid": 512762, "relation_to_type": "type", "validated": true, "ani": 79.6363, "matched_fragments": 729, "total_fragments": 1567, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Georgenia wutianyii", "strain": "strain=Z294", "accession": "GCA_006349365.1", "taxid": 2585135, "species_taxid": 2585135, "relation_to_type": "type", "validated": true, "ani": 77.011, "matched_fragments": 437, "total_fragments": 1567, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Motilibacter deserti", "strain": "strain=E257", "accession": "GCA_011250635.1", "taxid": 2714956, "species_taxid": 2714956, "relation_to_type": "type", "validated": true, "ani": 76.7252, "matched_fragments": 489, "total_fragments": 1567, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Occultella aeris", "strain": "strain=CIP 111667", "accession": "GCA_902703175.1", "taxid": 2761496, "species_taxid": 2761496, "relation_to_type": "type", "validated": true, "ani": 76.5004, "matched_fragments": 384, "total_fragments": 1567, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Occultella glacieicola", "strain": "strain=T3246-1", "accession": "GCA_004353825.1", "taxid": 2518684, "species_taxid": 2518684, "relation_to_type": "type", "validated": true, "ani": 76.4362, "matched_fragments": 385, "total_fragments": 1567, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Nonomuraea roseoviolacea subsp. carminata", "strain": "strain=DSM 44170", "accession": "GCA_024172185.1", "taxid": 160689, "species_taxid": 103837, "relation_to_type": "type", "validated": true, "ani": 75.9949, "matched_fragments": 599, "total_fragments": 1567, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_011839805.1", "gtdb_species": "s__Kineococcus rubinsiae", "ani": 100.0, "matched_fragments": 1564, "total_fragments": 1567, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Kineococcaceae;g__Kineococcus", "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_009906795.1", "gtdb_species": "s__Kineococcus siccus", "ani": 87.2772, "matched_fragments": 966, "total_fragments": 1567, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Kineococcaceae;g__Kineococcus", "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_009906315.1", "gtdb_species": "s__Kineococcus vitellinus", "ani": 82.2069, "matched_fragments": 776, "total_fragments": 1567, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Kineococcaceae;g__Kineococcus", "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_000017305.1", "gtdb_species": "s__Kineococcus radiotolerans", "ani": 81.927, "matched_fragments": 907, "total_fragments": 1567, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Kineococcaceae;g__Kineococcus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.46", "min_intra_species_ani": "98.46", "mean_intra_species_af": "0.90", "min_intra_species_af": "0.90", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_013409345.1", "gtdb_species": "s__Kineococcus aurantiacus", "ani": 81.4533, "matched_fragments": 920, "total_fragments": 1567, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Kineococcaceae;g__Kineococcus", "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_003002055.1", "gtdb_species": "s__Kineococcus rhizosphaerae", "ani": 81.2221, "matched_fragments": 932, "total_fragments": 1567, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Kineococcaceae;g__Kineococcus", "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_002934625.1", "gtdb_species": "s__Kineococcus xinjiangensis", "ani": 79.6274, "matched_fragments": 730, "total_fragments": 1567, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Kineococcaceae;g__Kineococcus", "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": 0.0, "cell_length": 0.0, "doubling_h": null, "growth_tmp": 29.2, "optimum_tmp": 31.433, "optimum_ph": 8.0, "genome_size": 5061461.866, "gc_content": 72.525, "coding_genes": 4618.0, "rRNA16S_genes": 4.0, "tRNA_genes": 49.0, "gram_stain": 1.0, "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": 0.0, "coccus_cell_shape": 1.0, "filament_cell_shape": 0.0, "coccobacillus_cell_shape": 0.0, "vibrio_cell_shape": 0.0, "spiral_cell_shape": 0.0 }, "_genome_taxon": [ "Kineococcus", "rubinsiae" ], "quality": 4, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }