{ "type": "genome", "identifier": "GCF_006539445.1", "organism": "Microbacterium lacticum", "title": "Microbacterium lacticum", "description": "na", "data type": "Genome sequencing and assembly", "organization": "National Institute of Technology and Evaluation", "publication": [ {} ], "properties": { "assembly_accession": "GCF_006539445.1", "bioproject": "PRJNA224116", "biosample": "SAMD00097244", "wgs_master": "BJNA00000000.1", "refseq_category": "na", "taxid": "33885", "species_taxid": "33885", "organism_name": "Microbacterium lacticum", "infraspecific_name": "strain=NBRC 14135", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2019/06/12", "asm_name": "ASM653944v1", "asm_submitter": "National Institute of Technology and Evaluation", "gbrs_paired_asm": "GCA_006539445.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/006/539/445/GCF_006539445.1_ASM653944v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "2882668", "genome_size_ungapped": "2882668", "gc_percent": "70.500000", "replicon_count": "0", "scaffold_count": "173", "contig_count": "173", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_006539445.1-RS_2024_09_09", "annotation_date": "2024-09-09", "total_gene_count": "2910", "protein_coding_gene_count": "2744", "non_coding_gene_count": "53", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2019-06-12", "dateModified": "2019-06-12", "datePublished": "2019-06-12", "_annotation": { "sample_count": 1, "sample_organism": [ "Microbacterium lacticum" ], "sample_taxid": [ "33885" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "missing" ], "sample_host_location_id": [], "data_size": "0.774 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)": "2882668", "Number of Sequences": "173", "Longest Sequences (bp)": "121347", "N50 (bp)": "45787", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "70.5", "Number of CDSs": "2724", "Average Protein Length": "309.6", "Coding Ratio (%)": "87.8", "Number of rRNAs": "3", "Number of tRNAs": "49", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Microbacterium lacticum", "strain": "strain=NBRC 14135", "accession": "GCA_006539445.1", "taxid": 33885, "species_taxid": 33885, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 880, "total_fragments": 883, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Microbacterium lacticum", "strain": "strain=DSM 20427", "accession": "GCA_006716815.1", "taxid": 33885, "species_taxid": 33885, "relation_to_type": "type", "validated": true, "ani": 99.9907, "matched_fragments": 878, "total_fragments": 883, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Microbacterium lacticum", "strain": "strain=JCM 1379", "accession": "GCA_014646835.1", "taxid": 33885, "species_taxid": 33885, "relation_to_type": "type", "validated": true, "ani": 99.988, "matched_fragments": 864, "total_fragments": 883, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Microbacterium paulum", "strain": "strain=2C", "accession": "GCA_015707995.1", "taxid": 2707006, "species_taxid": 2707006, "relation_to_type": "type", "validated": true, "ani": 88.6225, "matched_fragments": 663, "total_fragments": 883, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Microbacterium aurum", "strain": "strain=DSM 8600", "accession": "GCA_016907815.1", "taxid": 36805, "species_taxid": 36805, "relation_to_type": "type", "validated": true, "ani": 84.2704, "matched_fragments": 633, "total_fragments": 883, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Microbacterium dextranolyticum", "strain": "strain=DSM 8607", "accession": "GCA_016907295.1", "taxid": 36806, "species_taxid": 36806, "relation_to_type": "type", "validated": true, "ani": 83.885, "matched_fragments": 595, "total_fragments": 883, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Microbacterium hominis", "strain": "strain=LCDC 84-0209", "accession": "GCA_001553805.1", "taxid": 162426, "species_taxid": 162426, "relation_to_type": "type", "validated": true, "ani": 83.3657, "matched_fragments": 597, "total_fragments": 883, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Microbacterium telephonicum", "strain": "strain=S2T63", "accession": "GCA_003651225.1", "taxid": 1714841, "species_taxid": 1714841, "relation_to_type": "type", "validated": true, "ani": 82.7779, "matched_fragments": 605, "total_fragments": 883, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Microbacterium gallinarum", "strain": "strain=Sa1CUA4", "accession": "GCA_014837165.1", "taxid": 2762209, "species_taxid": 2762209, "relation_to_type": "type", "validated": true, "ani": 81.4302, "matched_fragments": 525, "total_fragments": 883, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Microbacterium cremeum", "strain": "strain=NY27", "accession": "GCA_015277855.1", "taxid": 2782169, "species_taxid": 2782169, "relation_to_type": "type", "validated": true, "ani": 81.4011, "matched_fragments": 518, "total_fragments": 883, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Microbacterium pullorum", "strain": "strain=Sa4CUA7", "accession": "GCA_014836535.1", "taxid": 2762236, "species_taxid": 2762236, "relation_to_type": "type", "validated": true, "ani": 81.2906, "matched_fragments": 522, "total_fragments": 883, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Microbacterium yannicii", "strain": "strain=DSM 23203", "accession": "GCA_024055635.1", "taxid": 671622, "species_taxid": 671622, "relation_to_type": "type", "validated": true, "ani": 80.9152, "matched_fragments": 520, "total_fragments": 883, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_006716815.1", "gtdb_species": "s__Microbacterium lacticum", "ani": 99.9907, "matched_fragments": 878, "total_fragments": 883, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.05", "min_intra_species_ani": "97.16", "mean_intra_species_af": "0.92", "min_intra_species_af": "0.78", "num_clustered_genomes": 4, "status": "conclusive" }, { "accession": "GCF_015707995.1", "gtdb_species": "s__Microbacterium sp015707995", "ani": 88.6734, "matched_fragments": 660, "total_fragments": 883, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium", "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_017305435.1", "gtdb_species": "s__Microbacterium sp017305435", "ani": 84.4731, "matched_fragments": 629, "total_fragments": 883, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium", "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_001898315.1", "gtdb_species": "s__Microbacterium sp001898315", "ani": 84.3235, "matched_fragments": 612, "total_fragments": 883, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.98", "min_intra_species_ani": "99.98", "mean_intra_species_af": "0.99", "min_intra_species_af": "0.99", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_016907815.1", "gtdb_species": "s__Microbacterium aurum", "ani": 84.2638, "matched_fragments": 634, "total_fragments": 883, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.09", "min_intra_species_ani": "96.17", "mean_intra_species_af": "0.91", "min_intra_species_af": "0.83", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCA_003248655.1", "gtdb_species": "s__Microbacterium sp003248655", "ani": 83.9912, "matched_fragments": 598, "total_fragments": 883, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium", "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_016907295.1", "gtdb_species": "s__Microbacterium dextranolyticum", "ani": 83.8803, "matched_fragments": 595, "total_fragments": 883, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium", "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_001724425.1", "gtdb_species": "s__Microbacterium sp001724425", "ani": 83.6761, "matched_fragments": 559, "total_fragments": 883, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.98", "min_intra_species_ani": "99.98", "mean_intra_species_af": "0.98", "min_intra_species_af": "0.98", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_018717645.1", "gtdb_species": "s__Microbacterium flavum", "ani": 83.5905, "matched_fragments": 644, "total_fragments": 883, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium", "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_001592125.1", "gtdb_species": "s__Microbacterium hominis", "ani": 83.4186, "matched_fragments": 585, "total_fragments": 883, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.96", "min_intra_species_ani": "98.42", "mean_intra_species_af": "0.92", "min_intra_species_af": "0.89", "num_clustered_genomes": 6, "status": "-" }, { "accession": "GCF_016807485.1", "gtdb_species": "s__Microbacterium sp016807485", "ani": 83.1949, "matched_fragments": 386, "total_fragments": 883, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium", "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_003651225.1", "gtdb_species": "s__Microbacterium telephonicum", "ani": 82.7679, "matched_fragments": 606, "total_fragments": 883, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium", "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_016907555.1", "gtdb_species": "s__Microbacterium laevaniformans", "ani": 82.6674, "matched_fragments": 590, "total_fragments": 883, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "96.33", "min_intra_species_ani": "96.04", "mean_intra_species_af": "0.85", "min_intra_species_af": "0.81", "num_clustered_genomes": 5, "status": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": -0.344, "cell_length": -0.025, "doubling_h": null, "growth_tmp": 29.0, "optimum_tmp": 30.0, "optimum_ph": 7.341, "genome_size": 2882668.0, "gc_content": 70.484, "coding_genes": 3206.916, "rRNA16S_genes": 1.75, "tRNA_genes": 50.166, "gram_stain": 1.0, "sporulation": 0.111, "motility": 0.289, "range_salinity": 1.0, "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": 0.977, "coccus_cell_shape": 0.022, "filament_cell_shape": 0.0, "coccobacillus_cell_shape": 0.0, "vibrio_cell_shape": 0.0, "spiral_cell_shape": 0.0 }, "_genome_taxon": [ "Microbacterium", "lacticum" ], "quality": 4, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }