{ "type": "genome", "identifier": "GCF_001434745.1", "organism": "Companilactobacillus alimentarius DSM 20249", "title": "Companilactobacillus alimentarius DSM 20249", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Shanghai Majorbio", "publication": [ {} ], "properties": { "assembly_accession": "GCF_001434745.1", "bioproject": "PRJNA224116", "biosample": "SAMN02369426", "wgs_master": "AZDQ00000000.1", "refseq_category": "na", "taxid": "1423720", "species_taxid": "1602", "organism_name": "Companilactobacillus alimentarius DSM 20249", "infraspecific_name": "strain=DSM 20249", "isolate": "na", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2015/11/06", "asm_name": "ASM143474v1", "asm_submitter": "Shanghai Majorbio", "gbrs_paired_asm": "GCA_001434745.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/001/434/745/GCF_001434745.1_ASM143474v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "2336325", "genome_size_ungapped": "2335968", "gc_percent": "35.500000", "replicon_count": "0", "scaffold_count": "46", "contig_count": "46", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_001434745.1-RS_2024_03_29", "annotation_date": "2024-03-29", "total_gene_count": "2294", "protein_coding_gene_count": "2211", "non_coding_gene_count": "58", "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": [ "Companilactobacillus alimentarius DSM 20249" ], "sample_taxid": [ "1423720" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "-" ], "sample_host_location_id": [], "data_size": "0.659 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)": "2336325", "Number of Sequences": "46", "Longest Sequences (bp)": "533142", "N50 (bp)": "213737", "Gap Ratio (%)": "0.015280", "GCcontent (%)": "35.4", "Number of CDSs": "2245", "Average Protein Length": "306.8", "Coding Ratio (%)": "88.4", "Number of rRNAs": "3", "Number of tRNAs": "50", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Companilactobacillus alimentarius", "strain": "strain=DSM 20249", "accession": "GCA_001434745.1", "taxid": 1602, "species_taxid": 1602, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 762, "total_fragments": 762, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Companilactobacillus alimentarius", "strain": "strain=DSM 20249", "accession": "GCA_002849895.1", "taxid": 1602, "species_taxid": 1602, "relation_to_type": "type", "validated": true, "ani": 99.9919, "matched_fragments": 762, "total_fragments": 762, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Companilactobacillus paralimentarius", "strain": "strain=JCM 10415", "accession": "GCA_000615725.1", "taxid": 83526, "species_taxid": 83526, "relation_to_type": "type", "validated": true, "ani": 83.1836, "matched_fragments": 465, "total_fragments": 762, "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": 83.1761, "matched_fragments": 485, "total_fragments": 762, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Companilactobacillus paralimentarius", "strain": "strain=DSM 13238", "accession": "GCA_001434985.1", "taxid": 83526, "species_taxid": 83526, "relation_to_type": "type", "validated": true, "ani": 83.151, "matched_fragments": 477, "total_fragments": 762, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Companilactobacillus bobalius", "strain": "strain=DSM 19674", "accession": "GCA_001434855.1", "taxid": 2801451, "species_taxid": 2801451, "relation_to_type": "type", "validated": true, "ani": 82.9355, "matched_fragments": 535, "total_fragments": 762, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Companilactobacillus kimchii", "strain": "strain=DSM 13961", "accession": "GCA_001435445.1", "taxid": 2801452, "species_taxid": 2801452, "relation_to_type": "type", "validated": true, "ani": 82.86, "matched_fragments": 521, "total_fragments": 762, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Companilactobacillus bobalius", "strain": "strain=203", "accession": "GCA_009764355.1", "taxid": 2801451, "species_taxid": 2801451, "relation_to_type": "type", "validated": true, "ani": 82.8419, "matched_fragments": 523, "total_fragments": 762, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Companilactobacillus kimchii", "strain": "strain=JCM 10707", "accession": "GCA_001311095.1", "taxid": 2801452, "species_taxid": 2801452, "relation_to_type": "type", "validated": true, "ani": 82.8339, "matched_fragments": 521, "total_fragments": 762, "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": 82.7993, "matched_fragments": 529, "total_fragments": 762, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Companilactobacillus suantsaicola", "strain": "strain=BCRC 81127", "accession": "GCA_004745525.1", "taxid": 2487723, "species_taxid": 2487723, "relation_to_type": "type", "validated": true, "ani": 82.4364, "matched_fragments": 475, "total_fragments": 762, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Companilactobacillus allii", "strain": "strain=WiKim39", "accession": "GCA_023923085.1", "taxid": 1847728, "species_taxid": 1847728, "relation_to_type": "type", "validated": true, "ani": 79.2875, "matched_fragments": 246, "total_fragments": 762, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_002849895.1", "gtdb_species": "s__Companilactobacillus alimentarius", "ani": 99.9919, "matched_fragments": 762, "total_fragments": 762, "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": "99.99", "mean_intra_species_af": "1.00", "min_intra_species_af": "1.00", "num_clustered_genomes": 3, "status": "conclusive" }, { "accession": "GCF_001434985.1", "gtdb_species": "s__Companilactobacillus paralimentarius", "ani": 83.1694, "matched_fragments": 476, "total_fragments": 762, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Companilactobacillus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.97", "min_intra_species_ani": "99.96", "mean_intra_species_af": "0.99", "min_intra_species_af": "0.99", "num_clustered_genomes": 4, "status": "-" }, { "accession": "GCF_009764355.1", "gtdb_species": "s__Companilactobacillus paralimentarius_A", "ani": 82.8854, "matched_fragments": 523, "total_fragments": 762, "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_001435445.1", "gtdb_species": "s__Companilactobacillus kimchii", "ani": 82.844, "matched_fragments": 522, "total_fragments": 762, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Companilactobacillus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.99", "min_intra_species_ani": "99.97", "mean_intra_species_af": "1.00", "min_intra_species_af": "1.00", "num_clustered_genomes": 5, "status": "-" }, { "accession": "GCA_019116025.1", "gtdb_species": "s__Companilactobacillus pullicola", "ani": 82.6049, "matched_fragments": 471, "total_fragments": 762, "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_004745525.1", "gtdb_species": "s__Companilactobacillus suantsaicola", "ani": 82.4364, "matched_fragments": 475, "total_fragments": 762, "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_002872255.1", "gtdb_species": "s__Companilactobacillus nuruki", "ani": 81.4794, "matched_fragments": 366, "total_fragments": 762, "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": 81.4382, "matched_fragments": 400, "total_fragments": 762, "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_003606365.2", "gtdb_species": "s__Companilactobacillus zhachilii", "ani": 81.2527, "matched_fragments": 383, "total_fragments": 762, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Companilactobacillus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.75", "min_intra_species_ani": "97.75", "mean_intra_species_af": "0.87", "min_intra_species_af": "0.87", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_001435815.1", "gtdb_species": "s__Companilactobacillus nantensis", "ani": 81.1496, "matched_fragments": 387, "total_fragments": 762, "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": "-" } ] }, "_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", "alimentarius", "DSM", "20249" ], "quality": 4, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }