{ "type": "genome", "identifier": "GCF_010725055.1", "organism": "Gelidibacter japonicus", "title": "Gelidibacter japonicus", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Numazu, Institute of Microbial Chemistry", "publication": [ {} ], "properties": { "assembly_accession": "GCF_010725055.1", "bioproject": "PRJNA224116", "biosample": "SAMD00166236", "wgs_master": "BJKB00000000.1", "refseq_category": "reference genome", "taxid": "1962232", "species_taxid": "1962232", "organism_name": "Gelidibacter japonicus", "infraspecific_name": "strain=Bio7-1", "isolate": "na", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2020/01/31", "asm_name": "ASM1072505v1", "asm_submitter": "Numazu, Institute of Microbial Chemistry", "gbrs_paired_asm": "GCA_010725055.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/010/725/055/GCF_010725055.1_ASM1072505v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "4669066", "genome_size_ungapped": "4668986", "gc_percent": "38.000000", "replicon_count": "0", "scaffold_count": "61", "contig_count": "61", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_010725055.1-RS_2024_08_26", "annotation_date": "2024-08-26", "total_gene_count": "3969", "protein_coding_gene_count": "3879", "non_coding_gene_count": "52", "pubmed_id": "31098768" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2020-01-31", "dateModified": "2020-01-31", "datePublished": "2020-01-31", "_annotation": { "sample_count": 1, "sample_organism": [ "Gelidibacter japonicus" ], "sample_taxid": [ "1962232" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "Japan:Hyogo" ], "sample_host_location_id": [], "data_size": "1.322 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)": "4669066", "Number of Sequences": "61", "Longest Sequences (bp)": "507395", "N50 (bp)": "196459", "Gap Ratio (%)": "0.001713", "GCcontent (%)": "38.0", "Number of CDSs": "3856", "Average Protein Length": "345.5", "Coding Ratio (%)": "85.6", "Number of rRNAs": "6", "Number of tRNAs": "39", "Number of CRISPRs": "1" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Gelidibacter japonicus", "strain": "strain=Bio7-1", "accession": "GCA_010725055.1", "taxid": 1962232, "species_taxid": 1962232, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1510, "total_fragments": 1526, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Gelidibacter pelagius", "strain": "strain=DF109", "accession": "GCA_017581925.1", "taxid": 2819985, "species_taxid": 2819985, "relation_to_type": "type", "validated": true, "ani": 86.5304, "matched_fragments": 1125, "total_fragments": 1526, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Gelidibacter maritimus", "strain": "strain=F6074", "accession": "GCA_014062315.1", "taxid": 2761487, "species_taxid": 2761487, "relation_to_type": "type", "validated": true, "ani": 84.3969, "matched_fragments": 1067, "total_fragments": 1526, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Gelidibacter gilvus", "strain": "strain=IC158", "accession": "GCA_004115975.1", "taxid": 59602, "species_taxid": 59602, "relation_to_type": "type", "validated": true, "ani": 83.6052, "matched_fragments": 1033, "total_fragments": 1526, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Gelidibacter mesophilus", "strain": "strain=DSM 14095", "accession": "GCA_000423005.1", "taxid": 169050, "species_taxid": 169050, "relation_to_type": "type", "validated": true, "ani": 80.67, "matched_fragments": 813, "total_fragments": 1526, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Gelidibacter algens", "strain": "strain=DSM 12408", "accession": "GCA_003259265.1", "taxid": 49280, "species_taxid": 49280, "relation_to_type": "type", "validated": true, "ani": 79.0602, "matched_fragments": 606, "total_fragments": 1526, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Hanstruepera flava", "strain": "strain=NBU2984", "accession": "GCA_023634025.1", "taxid": 2930218, "species_taxid": 2930218, "relation_to_type": "type", "validated": true, "ani": 76.9806, "matched_fragments": 125, "total_fragments": 1526, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Psychroserpens mesophilus", "strain": "strain=JCM 13413", "accession": "GCA_000826645.1", "taxid": 325473, "species_taxid": 325473, "relation_to_type": "type", "validated": true, "ani": 76.9155, "matched_fragments": 174, "total_fragments": 1526, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Aestuariivivens insulae", "strain": "strain=AH-MY3", "accession": "GCA_022662195.1", "taxid": 1621988, "species_taxid": 1621988, "relation_to_type": "type", "validated": true, "ani": 76.8184, "matched_fragments": 113, "total_fragments": 1526, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Aestuariivivens marinum", "strain": "strain=MT3-5-12", "accession": "GCA_022662175.1", "taxid": 2913555, "species_taxid": 2913555, "relation_to_type": "type", "validated": true, "ani": 76.8153, "matched_fragments": 110, "total_fragments": 1526, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Paucihalobacter ruber", "strain": "strain=CWB-1", "accession": "GCA_006494535.1", "taxid": 2567861, "species_taxid": 2567861, "relation_to_type": "type", "validated": true, "ani": 76.7778, "matched_fragments": 103, "total_fragments": 1526, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pontimicrobium aquaticum", "strain": "strain=CAU 1491", "accession": "GCA_005047595.1", "taxid": 2565367, "species_taxid": 2565367, "relation_to_type": "type", "validated": true, "ani": 76.6136, "matched_fragments": 117, "total_fragments": 1526, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Tenacibaculum aquimarinum", "strain": "strain=K20-16", "accession": "GCA_022478115.1", "taxid": 2910675, "species_taxid": 2910675, "relation_to_type": "type", "validated": true, "ani": 76.194, "matched_fragments": 52, "total_fragments": 1526, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_010725055.1", "gtdb_species": "s__Gelidibacter japonicus", "ani": 100.0, "matched_fragments": 1516, "total_fragments": 1526, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gelidibacter", "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_017581925.1", "gtdb_species": "s__Gelidibacter sp017581925", "ani": 86.5304, "matched_fragments": 1125, "total_fragments": 1526, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gelidibacter", "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_014062315.1", "gtdb_species": "s__Gelidibacter sp014062315", "ani": 84.3893, "matched_fragments": 1068, "total_fragments": 1526, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gelidibacter", "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_004115975.1", "gtdb_species": "s__Gelidibacter gilvus", "ani": 83.6202, "matched_fragments": 1031, "total_fragments": 1526, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gelidibacter", "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_000423005.1", "gtdb_species": "s__Gelidibacter mesophilus", "ani": 80.673, "matched_fragments": 811, "total_fragments": 1526, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gelidibacter", "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_001678675.1", "gtdb_species": "s__Gelidibacter algens", "ani": 79.0496, "matched_fragments": 601, "total_fragments": 1526, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gelidibacter", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.95", "min_intra_species_ani": "99.95", "mean_intra_species_af": "0.98", "min_intra_species_af": "0.98", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_004364975.1", "gtdb_species": "s__Gelidibacter sediminis", "ani": 78.7201, "matched_fragments": 518, "total_fragments": 1526, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gelidibacter", "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_000826645.1", "gtdb_species": "s__Psychroserpens mesophilus", "ani": 76.9155, "matched_fragments": 174, "total_fragments": 1526, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Psychroserpens", "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_006494535.1", "gtdb_species": "s__Paucihalobacter ruber", "ani": 76.7778, "matched_fragments": 103, "total_fragments": 1526, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Paucihalobacter", "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": "GCA_002441545.1", "gtdb_species": "s__Yeosuana sp002441545", "ani": 76.1949, "matched_fragments": 130, "total_fragments": 1526, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Yeosuana", "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": -0.302, "cell_length": 0.601, "doubling_h": null, "growth_tmp": 20.8, "optimum_tmp": 17.666, "optimum_ph": null, "genome_size": 4151575.0, "gc_content": null, "coding_genes": null, "rRNA16S_genes": null, "tRNA_genes": null, "gram_stain": 0.0, "sporulation": 0.0, "motility": 0.666, "range_salinity": null, "facultative_respiration": 0.0, "anaerobic_respiration": 0.0, "aerobic_respiration": 1.0, "mesophilic_range_tmp": null, "thermophilic_range_tmp": null, "psychrophilic_range_tmp": null, "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": [ "Gelidibacter", "japonicus" ], "quality": 4, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }