{ "type": "genome", "identifier": "GCF_000422405.1", "organism": "Microbacterium luticocti DSM 19459", "title": "Microbacterium luticocti DSM 19459", "description": "na", "data type": "Genome sequencing and assembly", "organization": "DOE Joint Genome Institute", "publication": [ {} ], "properties": { "assembly_accession": "GCF_000422405.1", "bioproject": "PRJNA224116", "biosample": "SAMN02440801", "wgs_master": "AULS00000000.1", "refseq_category": "reference genome", "taxid": "1122239", "species_taxid": "451764", "organism_name": "Microbacterium luticocti DSM 19459", "infraspecific_name": "strain=DSM 19459", "isolate": "na", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2013/07/11", "asm_name": "ASM42240v1", "asm_submitter": "DOE Joint Genome Institute", "gbrs_paired_asm": "GCA_000422405.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/422/405/GCF_000422405.1_ASM42240v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "3115873", "genome_size_ungapped": "3113993", "gc_percent": "70.500000", "replicon_count": "0", "scaffold_count": "27", "contig_count": "32", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_000422405.1-RS_2024_05_02", "annotation_date": "2024-05-02", "total_gene_count": "2879", "protein_coding_gene_count": "2791", "non_coding_gene_count": "53", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2013-07-11", "dateModified": "2013-07-11", "datePublished": "2013-07-11", "_annotation": { "sample_count": 1, "sample_organism": [ "Microbacterium luticocti DSM 19459" ], "sample_taxid": [ "1122239" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "Portugal" ], "sample_host_location_id": [], "data_size": "0.832 MB", "sample_ph_range": { "min": 5597.0, "max": 5597.0 }, "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)": "3115873", "Number of Sequences": "27", "Longest Sequences (bp)": "580408", "N50 (bp)": "196367", "Gap Ratio (%)": "0.060336", "GCcontent (%)": "70.7", "Number of CDSs": "2831", "Average Protein Length": "332.6", "Coding Ratio (%)": "90.7", "Number of rRNAs": "2", "Number of tRNAs": "52", "Number of CRISPRs": "5" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Microbacterium luticocti", "strain": "strain=DSM 19459", "accession": "GCA_000422405.1", "taxid": 451764, "species_taxid": 451764, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1023, "total_fragments": 1026, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Microbacterium protaetiae", "strain": "strain=DFW100M-13", "accession": "GCA_004135285.1", "taxid": 2509458, "species_taxid": 2509458, "relation_to_type": "type", "validated": true, "ani": 82.2858, "matched_fragments": 632, "total_fragments": 1026, "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": 80.6316, "matched_fragments": 497, "total_fragments": 1026, "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": 80.5705, "matched_fragments": 505, "total_fragments": 1026, "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": 80.5358, "matched_fragments": 505, "total_fragments": 1026, "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": 80.4698, "matched_fragments": 510, "total_fragments": 1026, "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": 80.4663, "matched_fragments": 574, "total_fragments": 1026, "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": 80.4522, "matched_fragments": 503, "total_fragments": 1026, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Microbacterium hibisci", "strain": "strain=CCTCC AB 2016180", "accession": "GCA_015278255.1", "taxid": 2036000, "species_taxid": 2036000, "relation_to_type": "type", "validated": true, "ani": 80.4256, "matched_fragments": 527, "total_fragments": 1026, "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": 80.4166, "matched_fragments": 567, "total_fragments": 1026, "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": 80.396, "matched_fragments": 511, "total_fragments": 1026, "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": 80.377, "matched_fragments": 527, "total_fragments": 1026, "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": 80.2952, "matched_fragments": 544, "total_fragments": 1026, "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": 80.246, "matched_fragments": 532, "total_fragments": 1026, "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": 80.2331, "matched_fragments": 502, "total_fragments": 1026, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Microbacterium saccharophilum", "strain": "strain=NBRC 108778", "accession": "GCA_007992455.1", "taxid": 1213358, "species_taxid": 1213358, "relation_to_type": "type", "validated": true, "ani": 80.1209, "matched_fragments": 481, "total_fragments": 1026, "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": 80.0327, "matched_fragments": 546, "total_fragments": 1026, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Microbacterium sediminis", "strain": "strain=YLB-01", "accession": "GCA_001689915.1", "taxid": 904291, "species_taxid": 904291, "relation_to_type": "type", "validated": true, "ani": 79.8251, "matched_fragments": 427, "total_fragments": 1026, "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": 79.7722, "matched_fragments": 436, "total_fragments": 1026, "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": 79.648, "matched_fragments": 450, "total_fragments": 1026, "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": 79.4818, "matched_fragments": 429, "total_fragments": 1026, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Microbacterium gorillae", "strain": "strain=G3", "accession": "GCA_000826185.2", "taxid": 1231063, "species_taxid": 1231063, "relation_to_type": "type", "validated": true, "ani": 79.1646, "matched_fragments": 391, "total_fragments": 1026, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_000422405.1", "gtdb_species": "s__Microbacterium luticocti", "ani": 100.0, "matched_fragments": 1023, "total_fragments": 1026, "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_009649635.1", "gtdb_species": "s__Microbacterium sp009649635", "ani": 82.8342, "matched_fragments": 623, "total_fragments": 1026, "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_004135285.1", "gtdb_species": "s__Microbacterium protaetiae", "ani": 82.2681, "matched_fragments": 634, "total_fragments": 1026, "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_004010105.1", "gtdb_species": "s__Microbacterium sp004010105", "ani": 80.6316, "matched_fragments": 371, "total_fragments": 1026, "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": 80.6187, "matched_fragments": 499, "total_fragments": 1026, "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_014208045.1", "gtdb_species": "s__Microbacterium thalassium", "ani": 80.5951, "matched_fragments": 503, "total_fragments": 1026, "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_000380605.1", "gtdb_species": "s__Microbacterium sp000380605", "ani": 80.5659, "matched_fragments": 562, "total_fragments": 1026, "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_014197265.1", "gtdb_species": "s__Microbacterium invictum", "ani": 80.4892, "matched_fragments": 518, "total_fragments": 1026, "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": "1.00", "min_intra_species_af": "1.00", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_003651225.1", "gtdb_species": "s__Microbacterium telephonicum", "ani": 80.4873, "matched_fragments": 508, "total_fragments": 1026, "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_013282805.1", "gtdb_species": "s__Microbacterium hominis_B", "ani": 80.4365, "matched_fragments": 515, "total_fragments": 1026, "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": 80.431, "matched_fragments": 529, "total_fragments": 1026, "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_000802305.1", "gtdb_species": "s__Microbacterium mangrovi", "ani": 80.3165, "matched_fragments": 526, "total_fragments": 1026, "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_003386735.1", "gtdb_species": "s__Microbacterium trichothecenolyticum_A", "ani": 80.2666, "matched_fragments": 552, "total_fragments": 1026, "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_018588945.1", "gtdb_species": "s__Microbacterium flavescens", "ani": 80.2222, "matched_fragments": 504, "total_fragments": 1026, "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_001314225.1", "gtdb_species": "s__Microbacterium sp001314225", "ani": 80.1466, "matched_fragments": 499, "total_fragments": 1026, "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_001427525.1", "gtdb_species": "s__Microbacterium sp001427525", "ani": 80.0636, "matched_fragments": 511, "total_fragments": 1026, "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_005502885.1", "gtdb_species": "s__Microbacterium sp005502885", "ani": 79.9383, "matched_fragments": 495, "total_fragments": 1026, "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_001428485.1", "gtdb_species": "s__Microbacterium sp001428485", "ani": 79.9329, "matched_fragments": 500, "total_fragments": 1026, "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_002837415.1", "gtdb_species": "s__Microbacterium sp002837415", "ani": 79.8582, "matched_fragments": 423, "total_fragments": 1026, "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": 79.749, "matched_fragments": 438, "total_fragments": 1026, "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": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": -0.302, "cell_length": 0.204, "doubling_h": null, "growth_tmp": 28.0, "optimum_tmp": 36.0, "optimum_ph": 8.0, "genome_size": 3166379.0, "gc_content": 69.764, "coding_genes": 3206.916, "rRNA16S_genes": 1.75, "tRNA_genes": 50.166, "gram_stain": 1.0, "sporulation": 0.0, "motility": 1.0, "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": 1.0, "coccus_cell_shape": 0.0, "filament_cell_shape": 0.0, "coccobacillus_cell_shape": 0.0, "vibrio_cell_shape": 0.0, "spiral_cell_shape": 0.0 }, "_genome_taxon": [ "Microbacterium", "luticocti", "DSM", "19459" ], "quality": 4, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }