{ "type": "genome", "identifier": "GCF_016127255.1", "organism": "Leuconostoc pseudomesenteroides", "title": "Leuconostoc pseudomesenteroides", "description": "na", "data type": "Genome sequencing and assembly", "organization": "US Food and Drug Administration", "publication": [ {} ], "properties": { "assembly_accession": "GCF_016127255.1", "bioproject": "PRJNA224116", "biosample": "SAMN16357172", "wgs_master": "na", "refseq_category": "reference genome", "taxid": "33968", "species_taxid": "33968", "organism_name": "Leuconostoc pseudomesenteroides", "infraspecific_name": "strain=FDAARGOS_1003", "isolate": "na", "version_status": "latest", "assembly_level": "Complete Genome", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2020/12/20", "asm_name": "ASM1612725v1", "asm_submitter": "US Food and Drug Administration", "gbrs_paired_asm": "GCA_016127255.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/016/127/255/GCF_016127255.1_ASM1612725v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "2114657", "genome_size_ungapped": "2114657", "gc_percent": "39.000000", "replicon_count": "1", "scaffold_count": "1", "contig_count": "1", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_016127255.1-RS_2024_04_15", "annotation_date": "2024-04-15", "total_gene_count": "2129", "protein_coding_gene_count": "2027", "non_coding_gene_count": "84", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2020-12-20", "dateModified": "2020-12-20", "datePublished": "2020-12-20", "_annotation": { "sample_count": 1, "sample_organism": [ "Leuconostoc pseudomesenteroides" ], "sample_taxid": [ "33968" ], "sample_host_organism": [ "missing" ], "sample_host_organism_id": [], "sample_host_disease": [ "Unknown", "Unknown" ], "sample_host_disease_id": [], "sample_host_location": [ "Germany: Braunschweig" ], "sample_host_location_id": [], "data_size": "0.596 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)": "2114657", "Number of Sequences": "1", "Longest Sequences (bp)": "2114657", "N50 (bp)": "2114657", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "39.0", "Number of CDSs": "2059", "Average Protein Length": "303.9", "Coding Ratio (%)": "88.8", "Number of rRNAs": "11", "Number of tRNAs": "70", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Leuconostoc pseudomesenteroides", "strain": "strain=FDAARGOS_1003", "accession": "GCA_016127255.1", "taxid": 33968, "species_taxid": 33968, "relation_to_type": "suspected-type", "validated": true, "ani": 100.0, "matched_fragments": 698, "total_fragments": 704, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Leuconostoc pseudomesenteroides", "strain": "strain=NCDO 768", "accession": "GCA_012396745.1", "taxid": 33968, "species_taxid": 33968, "relation_to_type": "suspected-type", "validated": true, "ani": 99.984, "matched_fragments": 671, "total_fragments": 704, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Leuconostoc pseudomesenteroides", "strain": "strain=LMG 11482", "accession": "GCA_014634745.1", "taxid": 33968, "species_taxid": 33968, "relation_to_type": "suspected-type", "validated": true, "ani": 99.9657, "matched_fragments": 662, "total_fragments": 704, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Leuconostoc falkenbergense", "strain": "strain=LMG 10779", "accession": "GCA_014634805.1", "taxid": 2766470, "species_taxid": 2766470, "relation_to_type": "type", "validated": true, "ani": 92.4278, "matched_fragments": 518, "total_fragments": 704, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Leuconostoc suionicum", "strain": "strain=DSM 20241", "accession": "GCA_001891125.1", "taxid": 1511761, "species_taxid": 1511761, "relation_to_type": "type", "validated": true, "ani": 80.4196, "matched_fragments": 215, "total_fragments": 704, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Leuconostoc mesenteroides subsp. jonggajibkimchii", "strain": "strain=DRC1506", "accession": "GCA_001886915.1", "taxid": 2026657, "species_taxid": 1245, "relation_to_type": "type", "validated": true, "ani": 80.2195, "matched_fragments": 223, "total_fragments": 704, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Leuconostoc mesenteroides subsp. mesenteroides", "strain": "strain=NBRC 100496", "accession": "GCA_007990165.1", "taxid": 33967, "species_taxid": 1245, "relation_to_type": "type", "validated": true, "ani": 79.7073, "matched_fragments": 219, "total_fragments": 704, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Leuconostoc gelidum subsp. gasicomitatum", "strain": "strain=type strain: LMG 18811", "accession": "GCA_000196855.1", "taxid": 115778, "species_taxid": 1244, "relation_to_type": "type", "validated": true, "ani": 79.4911, "matched_fragments": 162, "total_fragments": 704, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Leuconostoc gelidum subsp. gelidum", "strain": "strain=KCTC 3527", "accession": "GCA_000166715.2", "taxid": 1607839, "species_taxid": 1244, "relation_to_type": "type", "validated": true, "ani": 79.0384, "matched_fragments": 160, "total_fragments": 704, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Leuconostoc gelidum subsp. gasicomitatum", "strain": "strain=NBRC 113245", "accession": "GCA_019655955.1", "taxid": 115778, "species_taxid": 1244, "relation_to_type": "type", "validated": true, "ani": 78.7388, "matched_fragments": 158, "total_fragments": 704, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_014634745.1", "gtdb_species": "s__Leuconostoc pseudomesenteroides", "ani": 99.9657, "matched_fragments": 662, "total_fragments": 704, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Leuconostoc", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.98", "min_intra_species_ani": "96.85", "mean_intra_species_af": "0.90", "min_intra_species_af": "0.84", "num_clustered_genomes": 11, "status": "conclusive" }, { "accession": "GCF_014634805.1", "gtdb_species": "s__Leuconostoc falkenbergense", "ani": 92.4279, "matched_fragments": 518, "total_fragments": 704, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Leuconostoc", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.11", "min_intra_species_ani": "96.75", "mean_intra_species_af": "0.91", "min_intra_species_af": "0.87", "num_clustered_genomes": 34, "status": "-" }, { "accession": "GCF_001891125.1", "gtdb_species": "s__Leuconostoc suionicum", "ani": 80.4945, "matched_fragments": 217, "total_fragments": 704, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Leuconostoc", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.16", "min_intra_species_ani": "97.05", "mean_intra_species_af": "0.94", "min_intra_species_af": "0.91", "num_clustered_genomes": 7, "status": "-" }, { "accession": "GCF_000014445.1", "gtdb_species": "s__Leuconostoc mesenteroides", "ani": 80.356, "matched_fragments": 231, "total_fragments": 704, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Leuconostoc", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.82", "min_intra_species_ani": "97.34", "mean_intra_species_af": "0.92", "min_intra_species_af": "0.82", "num_clustered_genomes": 89, "status": "-" }, { "accession": "GCF_009676745.1", "gtdb_species": "s__Leuconostoc mesenteroides_B", "ani": 80.2451, "matched_fragments": 225, "total_fragments": 704, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Leuconostoc", "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": "-" }, { "accession": "GCF_004354555.1", "gtdb_species": "s__Leuconostoc citreum", "ani": 79.5055, "matched_fragments": 155, "total_fragments": 704, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Leuconostoc", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.02", "min_intra_species_ani": "98.68", "mean_intra_species_af": "0.92", "min_intra_species_af": "0.88", "num_clustered_genomes": 33, "status": "-" }, { "accession": "GCF_012396485.1", "gtdb_species": "s__Leuconostoc holzapfelii", "ani": 79.1816, "matched_fragments": 154, "total_fragments": 704, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Leuconostoc", "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_001047135.2", "gtdb_species": "s__Fructobacillus tropaeoli", "ani": 79.0512, "matched_fragments": 50, "total_fragments": 704, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Fructobacillus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.33", "min_intra_species_ani": "96.88", "mean_intra_species_af": "0.89", "min_intra_species_af": "0.88", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCA_000166735.2", "gtdb_species": "s__Leuconostoc inhae", "ani": 79.0452, "matched_fragments": 144, "total_fragments": 704, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Leuconostoc", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.95", "min_intra_species_ani": "98.13", "mean_intra_species_af": "0.88", "min_intra_species_af": "0.76", "num_clustered_genomes": 13, "status": "-" }, { "accession": "GCF_000166715.1", "gtdb_species": "s__Leuconostoc gelidum", "ani": 79.0404, "matched_fragments": 159, "total_fragments": 704, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Leuconostoc", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.91", "min_intra_species_ani": "98.75", "mean_intra_species_af": "0.91", "min_intra_species_af": "0.89", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_016908715.1", "gtdb_species": "s__Leuconostoc rapi", "ani": 78.8758, "matched_fragments": 169, "total_fragments": 704, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Leuconostoc", "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_000165675.1", "gtdb_species": "s__Leuconostoc_B fallax", "ani": 78.415, "matched_fragments": 109, "total_fragments": 704, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Leuconostoc_B", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.89", "min_intra_species_ani": "99.83", "mean_intra_species_af": "0.97", "min_intra_species_af": "0.96", "num_clustered_genomes": 3, "status": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": -0.302, "cell_length": -0.155, "doubling_h": null, "growth_tmp": 32.0, "optimum_tmp": 23.75, "optimum_ph": 5.899, "genome_size": 2200218.667, "gc_content": 39.0, "coding_genes": 1785.127, "rRNA16S_genes": 4.0, "tRNA_genes": 67.495, "gram_stain": 1.0, "sporulation": 0.0, "motility": 0.0, "range_salinity": 0.0, "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": 0.0, "filament_cell_shape": 0.0, "coccobacillus_cell_shape": 0.0, "vibrio_cell_shape": 1.0, "spiral_cell_shape": 0.0 }, "_genome_taxon": [ "Leuconostoc", "pseudomesenteroides" ], "quality": 5, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }