{ "type": "genome", "identifier": "GCF_001433995.1", "organism": "Secundilactobacillus kimchicus JCM 15530", "title": "Secundilactobacillus kimchicus JCM 15530", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Shanghai Majorbio", "publication": [ {} ], "properties": { "assembly_accession": "GCF_001433995.1", "bioproject": "PRJNA224116", "biosample": "SAMN02369456", "wgs_master": "AZCX00000000.1", "refseq_category": "reference genome", "taxid": "1302272", "species_taxid": "528209", "organism_name": "Secundilactobacillus kimchicus JCM 15530", "infraspecific_name": "strain=JCM 15530", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2015/11/06", "asm_name": "ASM143399v1", "asm_submitter": "Shanghai Majorbio", "gbrs_paired_asm": "GCA_001433995.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/001/433/995/GCF_001433995.1_ASM143399v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "2593269", "genome_size_ungapped": "2593269", "gc_percent": "46.500000", "replicon_count": "0", "scaffold_count": "45", "contig_count": "45", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_001433995.1-RS_2024_03_28", "annotation_date": "2024-03-28", "total_gene_count": "2570", "protein_coding_gene_count": "2499", "non_coding_gene_count": "50", "pubmed_id": "26415554" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2015-11-06", "dateModified": "2015-11-06", "datePublished": "2015-11-06", "_annotation": { "sample_count": 1, "sample_organism": [ "Secundilactobacillus kimchicus JCM 15530" ], "sample_taxid": [ "1302272" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "South Korea" ], "sample_host_location_id": [], "data_size": "0.742 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)": "2593269", "Number of Sequences": "45", "Longest Sequences (bp)": "486001", "N50 (bp)": "292702", "Gap Ratio (%)": "0.000116", "GCcontent (%)": "46.6", "Number of CDSs": "2518", "Average Protein Length": "294.9", "Coding Ratio (%)": "85.9", "Number of rRNAs": "2", "Number of tRNAs": "43", "Number of CRISPRs": "4" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Secundilactobacillus kimchicus", "strain": "strain=JCM 15530", "accession": "GCA_001433995.1", "taxid": 528209, "species_taxid": 528209, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 847, "total_fragments": 848, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Secundilactobacillus odoratitofui", "strain": "strain=DSM 19909", "accession": "GCA_001434895.1", "taxid": 480930, "species_taxid": 480930, "relation_to_type": "type", "validated": true, "ani": 78.3409, "matched_fragments": 131, "total_fragments": 848, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Levilactobacillus fujinensis", "strain": "strain=218-6", "accession": "GCA_003946335.1", "taxid": 2486024, "species_taxid": 2486024, "relation_to_type": "type", "validated": true, "ani": 78.3166, "matched_fragments": 53, "total_fragments": 848, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Secundilactobacillus odoratitofui", "strain": "strain=JCM 15043", "accession": "GCA_001313185.1", "taxid": 480930, "species_taxid": 480930, "relation_to_type": "type", "validated": true, "ani": 78.2559, "matched_fragments": 129, "total_fragments": 848, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Secundilactobacillus similis", "strain": "strain=DSM 23365", "accession": "GCA_001436595.1", "taxid": 414682, "species_taxid": 414682, "relation_to_type": "type", "validated": true, "ani": 78.214, "matched_fragments": 132, "total_fragments": 848, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Secundilactobacillus similis", "strain": "strain=JCM 2765", "accession": "GCA_001311075.1", "taxid": 414682, "species_taxid": 414682, "relation_to_type": "type", "validated": true, "ani": 78.2036, "matched_fragments": 129, "total_fragments": 848, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Secundilactobacillus silagincola", "strain": "strain=IWT5", "accession": "GCA_002583405.1", "taxid": 1714681, "species_taxid": 1714681, "relation_to_type": "type", "validated": true, "ani": 78.1133, "matched_fragments": 103, "total_fragments": 848, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Secundilactobacillus silagei", "strain": "strain=DSM 27022", "accession": "GCA_004354595.1", "taxid": 1293415, "species_taxid": 1293415, "relation_to_type": "type", "validated": true, "ani": 78.0322, "matched_fragments": 113, "total_fragments": 848, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Secundilactobacillus hailunensis", "strain": "strain=887-11", "accession": "GCA_005405185.1", "taxid": 2559923, "species_taxid": 2559923, "relation_to_type": "type", "validated": true, "ani": 77.9792, "matched_fragments": 115, "total_fragments": 848, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Secundilactobacillus collinoides", "strain": "strain=JCM 1123", "accession": "GCA_001312845.1", "taxid": 33960, "species_taxid": 33960, "relation_to_type": "type", "validated": true, "ani": 77.9321, "matched_fragments": 117, "total_fragments": 848, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Secundilactobacillus silagei", "strain": "strain=IWT126", "accession": "GCA_002217945.1", "taxid": 1293415, "species_taxid": 1293415, "relation_to_type": "type", "validated": true, "ani": 77.8343, "matched_fragments": 113, "total_fragments": 848, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Levilactobacillus angrenensis", "strain": "strain=M1530-1", "accession": "GCA_003946085.1", "taxid": 2486020, "species_taxid": 2486020, "relation_to_type": "type", "validated": true, "ani": 77.7561, "matched_fragments": 59, "total_fragments": 848, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Secundilactobacillus angelensis", "strain": "strain=HBUAS51383", "accession": "GCA_012641075.1", "taxid": 2722706, "species_taxid": 2722706, "relation_to_type": "type", "validated": true, "ani": 77.7355, "matched_fragments": 119, "total_fragments": 848, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Levilactobacillus cerevisiae", "strain": "strain=DSM 100836", "accession": "GCA_003946245.1", "taxid": 1704076, "species_taxid": 1704076, "relation_to_type": "type", "validated": true, "ani": 77.6747, "matched_fragments": 58, "total_fragments": 848, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Lactiplantibacillus pentosus", "strain": "strain=DSM 20314", "accession": "GCA_003641185.1", "taxid": 1589, "species_taxid": 1589, "relation_to_type": "type", "validated": true, "ani": 77.5458, "matched_fragments": 58, "total_fragments": 848, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Lactiplantibacillus pentosus", "strain": "strain=ATCC 8041", "accession": "GCA_004354685.1", "taxid": 1589, "species_taxid": 1589, "relation_to_type": "type", "validated": true, "ani": 77.5377, "matched_fragments": 60, "total_fragments": 848, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Lactiplantibacillus pentosus", "strain": "strain=DSM 20314", "accession": "GCA_001433755.1", "taxid": 1589, "species_taxid": 1589, "relation_to_type": "type", "validated": true, "ani": 77.3994, "matched_fragments": 60, "total_fragments": 848, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_001433995.1", "gtdb_species": "s__Secundilactobacillus kimchicus", "ani": 100.0, "matched_fragments": 847, "total_fragments": 848, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Secundilactobacillus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.61", "min_intra_species_ani": "99.40", "mean_intra_species_af": "0.97", "min_intra_species_af": "0.95", "num_clustered_genomes": 3, "status": "conclusive" }, { "accession": "GCF_001434895.1", "gtdb_species": "s__Secundilactobacillus odoratitofui", "ani": 78.3622, "matched_fragments": 129, "total_fragments": 848, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Secundilactobacillus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.87", "min_intra_species_ani": "99.87", "mean_intra_species_af": "1.00", "min_intra_species_af": "1.00", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_003946335.1", "gtdb_species": "s__Levilactobacillus fujinensis", "ani": 78.3166, "matched_fragments": 53, "total_fragments": 848, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Levilactobacillus", "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_003946045.1", "gtdb_species": "s__Levilactobacillus mulengensis", "ani": 78.2134, "matched_fragments": 54, "total_fragments": 848, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Levilactobacillus", "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_001311075.1", "gtdb_species": "s__Secundilactobacillus similis", "ani": 78.2036, "matched_fragments": 129, "total_fragments": 848, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Secundilactobacillus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.93", "min_intra_species_ani": "99.93", "mean_intra_species_af": "0.98", "min_intra_species_af": "0.98", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_002583405.1", "gtdb_species": "s__Secundilactobacillus silagincola", "ani": 78.1133, "matched_fragments": 103, "total_fragments": 848, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Secundilactobacillus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.58", "min_intra_species_ani": "97.58", "mean_intra_species_af": "0.87", "min_intra_species_af": "0.87", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_001435095.1", "gtdb_species": "s__Levilactobacillus spicheri", "ani": 78.1051, "matched_fragments": 51, "total_fragments": 848, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Levilactobacillus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.77", "min_intra_species_ani": "97.54", "mean_intra_species_af": "0.95", "min_intra_species_af": "0.91", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_007115095.1", "gtdb_species": "s__Levilactobacillus enshiensis", "ani": 78.0356, "matched_fragments": 52, "total_fragments": 848, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Levilactobacillus", "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_001435975.1", "gtdb_species": "s__Secundilactobacillus collinoides", "ani": 77.9829, "matched_fragments": 118, "total_fragments": 848, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Secundilactobacillus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.82", "min_intra_species_ani": "99.79", "mean_intra_species_af": "0.97", "min_intra_species_af": "0.94", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_005405185.1", "gtdb_species": "s__Secundilactobacillus sp005405185", "ani": 77.9792, "matched_fragments": 115, "total_fragments": 848, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Secundilactobacillus", "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_001311135.1", "gtdb_species": "s__Secundilactobacillus paracollinoides", "ani": 77.9355, "matched_fragments": 114, "total_fragments": 848, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Secundilactobacillus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.57", "min_intra_species_ani": "99.45", "mean_intra_species_af": "0.95", "min_intra_species_af": "0.89", "num_clustered_genomes": 5, "status": "-" }, { "accession": "GCF_002217945.1", "gtdb_species": "s__Secundilactobacillus silagei", "ani": 77.8343, "matched_fragments": 113, "total_fragments": 848, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Secundilactobacillus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.92", "min_intra_species_ani": "99.86", "mean_intra_species_af": "1.00", "min_intra_species_af": "0.99", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_004745505.1", "gtdb_species": "s__Levilactobacillus suantsaiihabitans", "ani": 77.7864, "matched_fragments": 58, "total_fragments": 848, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Levilactobacillus", "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_003946085.1", "gtdb_species": "s__Levilactobacillus angrenensis", "ani": 77.7561, "matched_fragments": 59, "total_fragments": 848, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Levilactobacillus", "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_012641075.1", "gtdb_species": "s__Secundilactobacillus sp012641075", "ani": 77.7355, "matched_fragments": 119, "total_fragments": 848, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Secundilactobacillus", "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_003946245.1", "gtdb_species": "s__Levilactobacillus cerevisiae", "ani": 77.6747, "matched_fragments": 58, "total_fragments": 848, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Levilactobacillus", "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": [ "Secundilactobacillus", "kimchicus", "JCM", "15530" ], "quality": 3, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }