{ "type": "genome", "identifier": "GCF_900111355.1", "organism": "Isobaculum melis", "title": "Isobaculum melis", "description": "na", "data type": "Genome sequencing and assembly", "organization": "DOE - JOINT GENOME INSTITUTE", "publication": [ {} ], "properties": { "assembly_accession": "GCF_900111355.1", "bioproject": "PRJNA224116", "biosample": "SAMN04488559", "wgs_master": "FOHA00000000.1", "refseq_category": "reference genome", "taxid": "142588", "species_taxid": "142588", "organism_name": "Isobaculum melis", "infraspecific_name": "strain=DSM 13760", "isolate": "na", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2016/10/31", "asm_name": "IMG-taxon 2634166323 annotated assembly", "asm_submitter": "DOE - JOINT GENOME INSTITUTE", "gbrs_paired_asm": "GCA_900111355.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/900/111/355/GCF_900111355.1_IMG-taxon_2634166323_annotated_assembly", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "2821134", "genome_size_ungapped": "2820614", "gc_percent": "35.000000", "replicon_count": "0", "scaffold_count": "44", "contig_count": "44", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_900111355.1-RS_2024_05_03", "annotation_date": "2024-05-03", "total_gene_count": "2774", "protein_coding_gene_count": "2678", "non_coding_gene_count": "67", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2016-10-31", "dateModified": "2016-10-31", "datePublished": "2016-10-31", "_annotation": { "sample_count": 1, "sample_organism": [ "Isobaculum melis" ], "sample_taxid": [ "142588" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "missing" ], "sample_host_location_id": [], "data_size": "0.789 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": null, "max": null }, "completeness": 100.0, "contamination": 2.78, "strain_heterogeneity": 0.0, "genome_count": 1 }, "data_type": "G", "data_source": "RefSeq", "_dfast": { "Total Sequence Length (bp)": "2821134", "Number of Sequences": "44", "Longest Sequences (bp)": "374597", "N50 (bp)": "118318", "Gap Ratio (%)": "0.018432", "GCcontent (%)": "35.2", "Number of CDSs": "2697", "Average Protein Length": "302.6", "Coding Ratio (%)": "86.8", "Number of rRNAs": "5", "Number of tRNAs": "50", "Number of CRISPRs": "2" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Isobaculum melis", "strain": "strain=DSM 13760", "accession": "GCA_900111355.1", "taxid": 142588, "species_taxid": 142588, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 913, "total_fragments": 916, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Carnobacterium divergens", "strain": "strain=NCTC13772", "accession": "GCA_900446755.1", "taxid": 2748, "species_taxid": 2748, "relation_to_type": "type", "validated": true, "ani": 78.2194, "matched_fragments": 141, "total_fragments": 916, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Carnobacterium divergens", "strain": "strain=DSM 20623", "accession": "GCA_001437085.1", "taxid": 2748, "species_taxid": 2748, "relation_to_type": "type", "validated": true, "ani": 78.18, "matched_fragments": 137, "total_fragments": 916, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Carnobacterium divergens", "strain": "strain=66", "accession": "GCA_000744255.1", "taxid": 2748, "species_taxid": 2748, "relation_to_type": "type", "validated": true, "ani": 78.1595, "matched_fragments": 135, "total_fragments": 916, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Carnobacterium viridans", "strain": "strain=MPL-11", "accession": "GCA_900102725.1", "taxid": 174587, "species_taxid": 174587, "relation_to_type": "type", "validated": true, "ani": 77.5681, "matched_fragments": 72, "total_fragments": 916, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Carnobacterium jeotgali", "strain": "strain=MS3", "accession": "GCA_000745125.1", "taxid": 545534, "species_taxid": 545534, "relation_to_type": "type", "validated": true, "ani": 77.4577, "matched_fragments": 77, "total_fragments": 916, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Carnobacterium mobile", "strain": "strain=MT37L", "accession": "GCA_000744825.1", "taxid": 2750, "species_taxid": 2750, "relation_to_type": "type", "validated": true, "ani": 77.225, "matched_fragments": 71, "total_fragments": 916, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Vagococcus bubulae", "strain": "strain=SS1994", "accession": "GCA_003950315.1", "taxid": 1977868, "species_taxid": 1977868, "relation_to_type": "type", "validated": true, "ani": 77.056, "matched_fragments": 79, "total_fragments": 916, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Enterococcus saccharolyticus subsp. saccharolyticus", "strain": "strain=ATCC 43076", "accession": "GCA_000407005.1", "taxid": 1814218, "species_taxid": 41997, "relation_to_type": "type", "validated": true, "ani": 76.8188, "matched_fragments": 83, "total_fragments": 916, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Enterococcus pseudoavium", "strain": "strain=NBRC 100491", "accession": "GCA_001544295.1", "taxid": 44007, "species_taxid": 44007, "relation_to_type": "type", "validated": true, "ani": 76.8177, "matched_fragments": 59, "total_fragments": 916, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Enterococcus hermanniensis", "strain": "strain=DSM 17122", "accession": "GCA_001885945.1", "taxid": 249189, "species_taxid": 249189, "relation_to_type": "type", "validated": true, "ani": 76.757, "matched_fragments": 59, "total_fragments": 916, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Enterococcus saccharolyticus subsp. saccharolyticus", "strain": "strain=ATCC 43076", "accession": "GCA_000407285.1", "taxid": 1814218, "species_taxid": 41997, "relation_to_type": "type", "validated": true, "ani": 76.737, "matched_fragments": 79, "total_fragments": 916, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Enterococcus saccharolyticus", "strain": "strain=DSM 20726", "accession": "GCA_001886235.1", "taxid": 41997, "species_taxid": 41997, "relation_to_type": "type", "validated": true, "ani": 76.6563, "matched_fragments": 75, "total_fragments": 916, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 2.78, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_900111355.1", "gtdb_species": "s__Isobaculum melis", "ani": 100.0, "matched_fragments": 913, "total_fragments": 916, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Carnobacteriaceae;g__Isobaculum", "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_000744255.1", "gtdb_species": "s__Carnobacterium divergens", "ani": 78.1687, "matched_fragments": 134, "total_fragments": 916, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Carnobacteriaceae;g__Carnobacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.06", "min_intra_species_ani": "98.93", "mean_intra_species_af": "0.92", "min_intra_species_af": "0.90", "num_clustered_genomes": 24, "status": "-" }, { "accession": "GCF_900258435.1", "gtdb_species": "s__Carnobacterium divergens_A", "ani": 78.0146, "matched_fragments": 149, "total_fragments": 916, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Carnobacteriaceae;g__Carnobacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.21", "min_intra_species_ani": "98.87", "mean_intra_species_af": "0.95", "min_intra_species_af": "0.92", "num_clustered_genomes": 17, "status": "-" }, { "accession": "GCF_900102725.1", "gtdb_species": "s__Carnobacterium_A viridans", "ani": 77.5681, "matched_fragments": 72, "total_fragments": 916, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Carnobacteriaceae;g__Carnobacterium_A", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.44", "min_intra_species_ani": "98.44", "mean_intra_species_af": "0.88", "min_intra_species_af": "0.88", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_000745125.1", "gtdb_species": "s__Carnobacterium_A jeotgali", "ani": 77.4577, "matched_fragments": 77, "total_fragments": 916, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Carnobacteriaceae;g__Carnobacterium_A", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.33", "min_intra_species_ani": "98.67", "mean_intra_species_af": "0.94", "min_intra_species_af": "0.87", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_000746825.1", "gtdb_species": "s__Carnobacterium_A inhibens", "ani": 77.4179, "matched_fragments": 78, "total_fragments": 916, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Carnobacteriaceae;g__Carnobacterium_A", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.16", "min_intra_species_ani": "98.07", "mean_intra_species_af": "0.90", "min_intra_species_af": "0.88", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_000744285.1", "gtdb_species": "s__Carnobacterium_A pleistocenium", "ani": 77.3913, "matched_fragments": 75, "total_fragments": 916, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Carnobacteriaceae;g__Carnobacterium_A", "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_001730295.1", "gtdb_species": "s__Enterococcus plantarum", "ani": 77.3041, "matched_fragments": 102, "total_fragments": 916, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.57", "min_intra_species_ani": "98.46", "mean_intra_species_af": "0.89", "min_intra_species_af": "0.88", "num_clustered_genomes": 4, "status": "-" }, { "accession": "GCF_000744825.1", "gtdb_species": "s__Carnobacterium_A mobile", "ani": 77.2652, "matched_fragments": 70, "total_fragments": 916, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Carnobacteriaceae;g__Carnobacterium_A", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.99", "min_intra_species_ani": "97.99", "mean_intra_species_af": "0.87", "min_intra_species_af": "0.87", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_900115825.1", "gtdb_species": "s__Desemzia incerta", "ani": 77.2624, "matched_fragments": 50, "total_fragments": 916, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Carnobacteriaceae;g__Desemzia", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.61", "min_intra_species_ani": "97.61", "mean_intra_species_af": "0.88", "min_intra_species_af": "0.88", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_014397115.1", "gtdb_species": "s__Vagococcus carniphilus", "ani": 77.2105, "matched_fragments": 96, "total_fragments": 916, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Vagococcaceae;g__Vagococcus", "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_900163795.1", "gtdb_species": "s__Vagococcus fluvialis_A", "ani": 77.1709, "matched_fragments": 82, "total_fragments": 916, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Vagococcaceae;g__Vagococcus", "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_017316185.1", "gtdb_species": "s__Vagococcus sp017316185", "ani": 77.1391, "matched_fragments": 87, "total_fragments": 916, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Vagococcaceae;g__Vagococcus", "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_000195575.1", "gtdb_species": "s__Carnobacterium_A sp000195575", "ani": 77.1081, "matched_fragments": 70, "total_fragments": 916, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Carnobacteriaceae;g__Carnobacterium_A", "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_003950315.1", "gtdb_species": "s__Vagococcus bubulae", "ani": 77.056, "matched_fragments": 79, "total_fragments": 916, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Vagococcaceae;g__Vagococcus", "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_017316125.1", "gtdb_species": "s__Enterococcus_B sp017316125", "ani": 76.9757, "matched_fragments": 77, "total_fragments": 916, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_B", "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_013874835.1", "gtdb_species": "s__WM01 sp013874835", "ani": 76.9399, "matched_fragments": 55, "total_fragments": 916, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Aerococcaceae;g__WM01", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.19", "min_intra_species_ani": "98.77", "mean_intra_species_af": "0.92", "min_intra_species_af": "0.86", "num_clustered_genomes": 4, "status": "-" }, { "accession": "GCF_000407285.1", "gtdb_species": "s__Enterococcus_F saccharolyticus", "ani": 76.737, "matched_fragments": 79, "total_fragments": 916, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_F", "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": 3, "status": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": null, "cell_length": null, "doubling_h": null, "growth_tmp": 37.0, "optimum_tmp": null, "optimum_ph": null, "genome_size": 2821134.0, "gc_content": null, "coding_genes": null, "rRNA16S_genes": null, "tRNA_genes": null, "gram_stain": 1.0, "sporulation": null, "motility": null, "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": null, "coccus_cell_shape": null, "filament_cell_shape": null, "coccobacillus_cell_shape": null, "vibrio_cell_shape": null, "spiral_cell_shape": null }, "_genome_taxon": [ "Isobaculum", "melis" ], "quality": 4, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }