{ "type": "genome", "identifier": "GCF_023923085.1", "organism": "Companilactobacillus allii", "title": "Companilactobacillus allii", "description": "na", "data type": "Genome sequencing and assembly", "organization": "World institute of kimchi", "publication": [ {} ], "properties": { "assembly_accession": "GCF_023923085.1", "bioproject": "PRJNA224116", "biosample": "SAMN28187464", "wgs_master": "na", "refseq_category": "na", "taxid": "1847728", "species_taxid": "1847728", "organism_name": "Companilactobacillus allii", "infraspecific_name": "strain=WiKim39", "isolate": "na", "version_status": "latest", "assembly_level": "Complete Genome", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2022/06/27", "asm_name": "ASM2392308v1", "asm_submitter": "World institute of kimchi", "gbrs_paired_asm": "GCA_023923085.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/023/923/085/GCF_023923085.1_ASM2392308v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "2556534", "genome_size_ungapped": "2556534", "gc_percent": "35.500000", "replicon_count": "4", "scaffold_count": "4", "contig_count": "4", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_023923085.1-RS_2024_07_04", "annotation_date": "2024-07-04", "total_gene_count": "2586", "protein_coding_gene_count": "2489", "non_coding_gene_count": "74", "pubmed_id": "34829632" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2022-06-27", "dateModified": "2022-06-27", "datePublished": "2022-06-27", "_annotation": { "sample_count": 1, "sample_organism": [ "Companilactobacillus allii" ], "sample_taxid": [ "1847728" ], "sample_host_organism": [ "food" ], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "South Korea" ], "sample_host_location_id": [], "data_size": "0.717 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)": "2556534", "Number of Sequences": "4", "Longest Sequences (bp)": "2508658", "N50 (bp)": "2508658", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "35.4", "Number of CDSs": "2540", "Average Protein Length": "297.0", "Coding Ratio (%)": "88.5", "Number of rRNAs": "12", "Number of tRNAs": "58", "Number of CRISPRs": "2" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Companilactobacillus allii", "strain": "strain=WiKim39", "accession": "GCA_023923085.1", "taxid": 1847728, "species_taxid": 1847728, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 849, "total_fragments": 851, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Companilactobacillus allii", "strain": "strain=WiKim39", "accession": "GCA_001971585.1", "taxid": 1847728, "species_taxid": 1847728, "relation_to_type": "type", "validated": true, "ani": 99.9798, "matched_fragments": 843, "total_fragments": 851, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Companilactobacillus allii", "strain": "strain=JCM 31938", "accession": "GCA_003946005.1", "taxid": 1847728, "species_taxid": 1847728, "relation_to_type": "type", "validated": true, "ani": 99.9569, "matched_fragments": 829, "total_fragments": 851, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Companilactobacillus hulinensis", "strain": "strain=8-1(1)", "accession": "GCA_003946555.1", "taxid": 2486007, "species_taxid": 2486007, "relation_to_type": "type", "validated": true, "ani": 83.6435, "matched_fragments": 525, "total_fragments": 851, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Companilactobacillus nodensis", "strain": "strain=DSM 19682", "accession": "GCA_001435555.1", "taxid": 460870, "species_taxid": 460870, "relation_to_type": "type", "validated": true, "ani": 81.9624, "matched_fragments": 429, "total_fragments": 851, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Companilactobacillus jidongensis", "strain": "strain=204-8", "accession": "GCA_003946575.1", "taxid": 2486006, "species_taxid": 2486006, "relation_to_type": "type", "validated": true, "ani": 81.9028, "matched_fragments": 448, "total_fragments": 851, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Companilactobacillus insicii", "strain": "strain=DSM 29801", "accession": "GCA_003946015.1", "taxid": 1732567, "species_taxid": 1732567, "relation_to_type": "type", "validated": true, "ani": 81.4606, "matched_fragments": 415, "total_fragments": 851, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Companilactobacillus kimchii", "strain": "strain=DSM 13961", "accession": "GCA_009764365.1", "taxid": 2801452, "species_taxid": 2801452, "relation_to_type": "type", "validated": true, "ani": 79.6812, "matched_fragments": 277, "total_fragments": 851, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Companilactobacillus baiquanensis", "strain": "strain=184-8", "accession": "GCA_003946605.1", "taxid": 2486005, "species_taxid": 2486005, "relation_to_type": "type", "validated": true, "ani": 79.633, "matched_fragments": 287, "total_fragments": 851, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Companilactobacillus paralimentarius", "strain": "strain=DSM 13238", "accession": "GCA_009764345.1", "taxid": 83526, "species_taxid": 83526, "relation_to_type": "type", "validated": true, "ani": 79.4155, "matched_fragments": 264, "total_fragments": 851, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Companilactobacillus mishanensis", "strain": "strain=256-3", "accession": "GCA_003946505.1", "taxid": 2486008, "species_taxid": 2486008, "relation_to_type": "type", "validated": true, "ani": 79.1427, "matched_fragments": 202, "total_fragments": 851, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Companilactobacillus huachuanensis", "strain": "strain=395-6.2", "accession": "GCA_005404815.1", "taxid": 2559914, "species_taxid": 2559914, "relation_to_type": "type", "validated": true, "ani": 79.0961, "matched_fragments": 262, "total_fragments": 851, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_001971585.1", "gtdb_species": "s__Companilactobacillus allii", "ani": 99.9798, "matched_fragments": 843, "total_fragments": 851, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Companilactobacillus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "100.00", "min_intra_species_ani": "100.00", "mean_intra_species_af": "0.99", "min_intra_species_af": "0.99", "num_clustered_genomes": 2, "status": "conclusive" }, { "accession": "GCF_003946555.1", "gtdb_species": "s__Companilactobacillus hulinensis", "ani": 83.6664, "matched_fragments": 523, "total_fragments": 851, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Companilactobacillus", "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_000615905.1", "gtdb_species": "s__Companilactobacillus nodensis", "ani": 81.9011, "matched_fragments": 424, "total_fragments": 851, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Companilactobacillus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.98", "min_intra_species_ani": "99.98", "mean_intra_species_af": "1.00", "min_intra_species_af": "1.00", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_003946575.1", "gtdb_species": "s__Companilactobacillus jidongensis", "ani": 81.8923, "matched_fragments": 449, "total_fragments": 851, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Companilactobacillus", "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_003946015.1", "gtdb_species": "s__Companilactobacillus insicii", "ani": 81.4493, "matched_fragments": 416, "total_fragments": 851, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Companilactobacillus", "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_009764355.1", "gtdb_species": "s__Companilactobacillus paralimentarius_A", "ani": 79.686, "matched_fragments": 277, "total_fragments": 851, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Companilactobacillus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.92", "min_intra_species_ani": "99.92", "mean_intra_species_af": "1.00", "min_intra_species_af": "0.99", "num_clustered_genomes": 4, "status": "-" }, { "accession": "GCF_003946605.1", "gtdb_species": "s__Companilactobacillus baiquanensis", "ani": 79.6628, "matched_fragments": 285, "total_fragments": 851, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Companilactobacillus", "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_001434665.1", "gtdb_species": "s__Companilactobacillus tucceti", "ani": 79.5751, "matched_fragments": 291, "total_fragments": 851, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Companilactobacillus", "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_009600985.1", "gtdb_species": "s__Companilactobacillus halodurans", "ani": 79.2768, "matched_fragments": 244, "total_fragments": 851, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Companilactobacillus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.75", "min_intra_species_ani": "99.75", "mean_intra_species_af": "0.93", "min_intra_species_af": "0.93", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_005404815.1", "gtdb_species": "s__Companilactobacillus huachuanensis", "ani": 79.1381, "matched_fragments": 258, "total_fragments": 851, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Companilactobacillus", "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": null, "cell_length": null, "doubling_h": null, "growth_tmp": null, "optimum_tmp": null, "optimum_ph": null, "genome_size": null, "gc_content": null, "coding_genes": null, "rRNA16S_genes": null, "tRNA_genes": null, "gram_stain": null, "sporulation": null, "motility": null, "range_salinity": null, "facultative_respiration": null, "anaerobic_respiration": null, "aerobic_respiration": null, "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": [ "Companilactobacillus", "allii" ], "quality": 5, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }