{ "type": "genome", "identifier": "GCF_004135285.1", "organism": "Microbacterium protaetiae", "title": "Microbacterium protaetiae", "description": "na", "data type": "Genome sequencing and assembly", "organization": "National Institute of Agricultural Sciences", "publication": [ {} ], "properties": { "assembly_accession": "GCF_004135285.1", "bioproject": "PRJNA224116", "biosample": "SAMN10817558", "wgs_master": "na", "refseq_category": "reference genome", "taxid": "2509458", "species_taxid": "2509458", "organism_name": "Microbacterium protaetiae", "infraspecific_name": "strain=DFW100M-13", "isolate": "na", "version_status": "latest", "assembly_level": "Complete Genome", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2019/02/03", "asm_name": "ASM413528v1", "asm_submitter": "National Institute of Agricultural Sciences", "gbrs_paired_asm": "GCA_004135285.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/004/135/285/GCF_004135285.1_ASM413528v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "3790483", "genome_size_ungapped": "3790483", "gc_percent": "68.000000", "replicon_count": "1", "scaffold_count": "1", "contig_count": "1", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_004135285.1-RS_2024_04_08", "annotation_date": "2024-04-08", "total_gene_count": "3562", "protein_coding_gene_count": "3473", "non_coding_gene_count": "56", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2019-02-03", "dateModified": "2019-02-03", "datePublished": "2019-02-03", "_annotation": { "sample_count": 1, "sample_organism": [ "Microbacterium protaetiae" ], "sample_taxid": [ "2509458" ], "sample_host_organism": [ "Protaetia brevitarsis seulensis larva" ], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "South Korea: Wanju-gun" ], "sample_host_location_id": [], "data_size": "1.024 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)": "3790483", "Number of Sequences": "1", "Longest Sequences (bp)": "3790483", "N50 (bp)": "3790483", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "68.0", "Number of CDSs": "3567", "Average Protein Length": "321.2", "Coding Ratio (%)": "90.7", "Number of rRNAs": "6", "Number of tRNAs": "49", "Number of CRISPRs": "1" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Microbacterium protaetiae", "strain": "strain=DFW100M-13", "accession": "GCA_004135285.1", "taxid": 2509458, "species_taxid": 2509458, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1263, "total_fragments": 1263, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Microbacterium luticocti", "strain": "strain=DSM 19459", "accession": "GCA_000422405.1", "taxid": 451764, "species_taxid": 451764, "relation_to_type": "type", "validated": true, "ani": 82.0389, "matched_fragments": 650, "total_fragments": 1263, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Microbacterium thalassium", "strain": "strain=DSM 12511", "accession": "GCA_014208045.1", "taxid": 362649, "species_taxid": 362649, "relation_to_type": "type", "validated": true, "ani": 79.8015, "matched_fragments": 471, "total_fragments": 1263, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Microbacterium kyungheense", "strain": "strain=DSM 105492", "accession": "GCA_006783905.1", "taxid": 1263636, "species_taxid": 1263636, "relation_to_type": "type", "validated": true, "ani": 79.7844, "matched_fragments": 529, "total_fragments": 1263, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Microbacterium invictum", "strain": "strain=DSM 19600", "accession": "GCA_023155715.1", "taxid": 515415, "species_taxid": 515415, "relation_to_type": "type", "validated": true, "ani": 79.7724, "matched_fragments": 502, "total_fragments": 1263, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Microbacterium invictum", "strain": "strain=JCM 17023", "accession": "GCA_015278285.1", "taxid": 515415, "species_taxid": 515415, "relation_to_type": "type", "validated": true, "ani": 79.7241, "matched_fragments": 498, "total_fragments": 1263, "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": 79.6257, "matched_fragments": 466, "total_fragments": 1263, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Microbacterium helvum", "strain": "strain=NEAU-LLC", "accession": "GCA_014779795.1", "taxid": 2773713, "species_taxid": 2773713, "relation_to_type": "type", "validated": true, "ani": 79.5382, "matched_fragments": 567, "total_fragments": 1263, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Microbacterium atlanticum", "strain": "strain=WY121", "accession": "GCA_015277815.1", "taxid": 2782168, "species_taxid": 2782168, "relation_to_type": "type", "validated": true, "ani": 79.532, "matched_fragments": 496, "total_fragments": 1263, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Microbacterium ginsengisoli", "strain": "strain=DSM 18659", "accession": "GCA_000956535.1", "taxid": 400772, "species_taxid": 400772, "relation_to_type": "type", "validated": true, "ani": 79.5062, "matched_fragments": 412, "total_fragments": 1263, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Microbacterium flavescens", "strain": "strain=JCM 3877", "accession": "GCA_018588945.1", "taxid": 69366, "species_taxid": 69366, "relation_to_type": "type", "validated": true, "ani": 79.4428, "matched_fragments": 481, "total_fragments": 1263, "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": 79.432, "matched_fragments": 494, "total_fragments": 1263, "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": 79.421, "matched_fragments": 526, "total_fragments": 1263, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Microbacterium mangrovi", "strain": "strain=MUSC 115", "accession": "GCA_000802305.1", "taxid": 1348253, "species_taxid": 1348253, "relation_to_type": "type", "validated": true, "ani": 79.4144, "matched_fragments": 498, "total_fragments": 1263, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Microbacterium pseudoresistens", "strain": "strain=DSM 22185", "accession": "GCA_013409745.1", "taxid": 640634, "species_taxid": 640634, "relation_to_type": "type", "validated": true, "ani": 79.3813, "matched_fragments": 389, "total_fragments": 1263, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Microbacterium lushaniae", "strain": "strain=L-031", "accession": "GCA_008727775.1", "taxid": 2614639, "species_taxid": 2614639, "relation_to_type": "type", "validated": true, "ani": 79.3792, "matched_fragments": 428, "total_fragments": 1263, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Microbacterium ureisolvens", "strain": "strain=CFH S00084", "accession": "GCA_015278315.1", "taxid": 2781186, "species_taxid": 2781186, "relation_to_type": "type", "validated": true, "ani": 79.3339, "matched_fragments": 549, "total_fragments": 1263, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Microbacterium ulmi", "strain": "strain=JCM 14282", "accession": "GCA_013004565.1", "taxid": 179095, "species_taxid": 179095, "relation_to_type": "type", "validated": true, "ani": 79.273, "matched_fragments": 479, "total_fragments": 1263, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Microbacterium aerolatum", "strain": "strain=NBRC 103071", "accession": "GCA_007988825.1", "taxid": 153731, "species_taxid": 153731, "relation_to_type": "type", "validated": true, "ani": 79.2646, "matched_fragments": 409, "total_fragments": 1263, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Microbacterium aerolatum", "strain": "strain=CCM 4955", "accession": "GCA_014635005.1", "taxid": 153731, "species_taxid": 153731, "relation_to_type": "type", "validated": true, "ani": 79.2188, "matched_fragments": 414, "total_fragments": 1263, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Microbacterium azadirachtae", "strain": "strain=DSM 23848", "accession": "GCA_000956545.1", "taxid": 582680, "species_taxid": 582680, "relation_to_type": "type", "validated": true, "ani": 78.7664, "matched_fragments": 440, "total_fragments": 1263, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Microbacterium rhizomatis", "strain": "strain=JCM 30598", "accession": "GCA_008710745.1", "taxid": 1631477, "species_taxid": 1631477, "relation_to_type": "type", "validated": true, "ani": 78.7157, "matched_fragments": 443, "total_fragments": 1263, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Microbacterium marinilacus", "strain": "strain=YM11-607", "accession": "GCA_019753765.1", "taxid": 415209, "species_taxid": 415209, "relation_to_type": "type", "validated": true, "ani": 78.566, "matched_fragments": 420, "total_fragments": 1263, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Microbacterium album", "strain": "strain=CGMCC 1.15794", "accession": "GCA_014643695.1", "taxid": 2053191, "species_taxid": 2053191, "relation_to_type": "type", "validated": true, "ani": 78.5278, "matched_fragments": 369, "total_fragments": 1263, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_004135285.1", "gtdb_species": "s__Microbacterium protaetiae", "ani": 100.0, "matched_fragments": 1263, "total_fragments": 1263, "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": "conclusive" }, { "accession": "GCF_000422405.1", "gtdb_species": "s__Microbacterium luticocti", "ani": 82.0163, "matched_fragments": 652, "total_fragments": 1263, "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_009649635.1", "gtdb_species": "s__Microbacterium sp009649635", "ani": 81.1095, "matched_fragments": 597, "total_fragments": 1263, "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_006783905.1", "gtdb_species": "s__Microbacterium kyungheense", "ani": 79.7451, "matched_fragments": 534, "total_fragments": 1263, "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_014836535.1", "gtdb_species": "s__Microbacterium sp014836535", "ani": 79.6382, "matched_fragments": 465, "total_fragments": 1263, "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": 79.6094, "matched_fragments": 465, "total_fragments": 1263, "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_014779795.1", "gtdb_species": "s__Microbacterium helvum", "ani": 79.5299, "matched_fragments": 568, "total_fragments": 1263, "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_003075375.1", "gtdb_species": "s__Microbacterium testaceum_E", "ani": 79.5023, "matched_fragments": 406, "total_fragments": 1263, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "96.83", "min_intra_species_ani": "96.83", "mean_intra_species_af": "0.84", "min_intra_species_af": "0.84", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_000956535.1", "gtdb_species": "s__Microbacterium ginsengisoli", "ani": 79.4923, "matched_fragments": 413, "total_fragments": 1263, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.60", "min_intra_species_ani": "98.14", "mean_intra_species_af": "0.85", "min_intra_species_af": "0.83", "num_clustered_genomes": 9, "status": "-" }, { "accession": "GCF_010634855.1", "gtdb_species": "s__Microbacterium sp010634855", "ani": 79.484, "matched_fragments": 504, "total_fragments": 1263, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.26", "min_intra_species_ani": "99.26", "mean_intra_species_af": "0.95", "min_intra_species_af": "0.95", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_018588945.1", "gtdb_species": "s__Microbacterium flavescens", "ani": 79.453, "matched_fragments": 480, "total_fragments": 1263, "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_000802305.1", "gtdb_species": "s__Microbacterium mangrovi", "ani": 79.4148, "matched_fragments": 498, "total_fragments": 1263, "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_013409745.1", "gtdb_species": "s__Microbacterium pseudoresistens", "ani": 79.4053, "matched_fragments": 388, "total_fragments": 1263, "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_017831975.1", "gtdb_species": "s__Microbacterium terrae", "ani": 79.4019, "matched_fragments": 517, "total_fragments": 1263, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium", "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_009758255.1", "gtdb_species": "s__Microbacterium sp009758255", "ani": 79.3541, "matched_fragments": 443, "total_fragments": 1263, "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_015278315.1", "gtdb_species": "s__Microbacterium ureisolvens", "ani": 79.3408, "matched_fragments": 549, "total_fragments": 1263, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.97", "min_intra_species_ani": "99.97", "mean_intra_species_af": "1.00", "min_intra_species_af": "1.00", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_903645325.1", "gtdb_species": "s__Microbacterium sp903645325", "ani": 79.2639, "matched_fragments": 402, "total_fragments": 1263, "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_007988825.1", "gtdb_species": "s__Microbacterium aerolatum", "ani": 79.2531, "matched_fragments": 410, "total_fragments": 1263, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.99", "min_intra_species_ani": "99.99", "mean_intra_species_af": "1.00", "min_intra_species_af": "1.00", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCA_002837415.1", "gtdb_species": "s__Microbacterium sp002837415", "ani": 78.9742, "matched_fragments": 390, "total_fragments": 1263, "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_008710745.1", "gtdb_species": "s__Microbacterium rhizomatis", "ani": 78.6983, "matched_fragments": 445, "total_fragments": 1263, "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": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": -0.344, "cell_length": -0.025, "doubling_h": null, "growth_tmp": 28.643, "optimum_tmp": 29.019, "optimum_ph": 7.341, "genome_size": 3469503.118, "gc_content": 69.764, "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": 0.012, "anaerobic_respiration": 0.0, "aerobic_respiration": 0.987, "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", "protaetiae" ], "quality": 5, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }