{ "type": "genome", "identifier": "GCF_000701445.1", "organism": "Brevundimonas bacteroides DSM 4726", "title": "Brevundimonas bacteroides DSM 4726", "description": "na", "data type": "Genome sequencing and assembly", "organization": "DOE Joint Genome Institute", "publication": [ {} ], "properties": { "assembly_accession": "GCF_000701445.1", "bioproject": "PRJNA224116", "biosample": "SAMN02841166", "wgs_master": "JNIX00000000.1", "refseq_category": "reference genome", "taxid": "1121124", "species_taxid": "74311", "organism_name": "Brevundimonas bacteroides DSM 4726", "infraspecific_name": "strain=DSM 4726", "isolate": "na", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2014/06/11", "asm_name": "ASM70144v1", "asm_submitter": "DOE Joint Genome Institute", "gbrs_paired_asm": "GCA_000701445.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/701/445/GCF_000701445.1_ASM70144v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "3220540", "genome_size_ungapped": "3220465", "gc_percent": "68.000000", "replicon_count": "0", "scaffold_count": "15", "contig_count": "16", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_000701445.1-RS_2024_12_01", "annotation_date": "2024-12-01", "total_gene_count": "3230", "protein_coding_gene_count": "3170", "non_coding_gene_count": "50", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2014-06-11", "dateModified": "2014-06-11", "datePublished": "2014-06-11", "_annotation": { "sample_count": 1, "sample_organism": [ "Brevundimonas bacteroides DSM 4726" ], "sample_taxid": [ "1121124" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "USA" ], "sample_host_location_id": [], "data_size": "0.879 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)": "3220540", "Number of Sequences": "15", "Longest Sequences (bp)": "495336", "N50 (bp)": "324476", "Gap Ratio (%)": "0.002329", "GCcontent (%)": "68.2", "Number of CDSs": "3198", "Average Protein Length": "307.9", "Coding Ratio (%)": "91.7", "Number of rRNAs": "3", "Number of tRNAs": "50", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Brevundimonas bacteroides", "strain": "strain=DSM 4726", "accession": "GCA_000701445.1", "taxid": 74311, "species_taxid": 74311, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1066, "total_fragments": 1069, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Brevundimonas subvibrioides", "strain": "strain=ATCC 15264", "accession": "GCA_000144605.1", "taxid": 74313, "species_taxid": 74313, "relation_to_type": "type", "validated": true, "ani": 82.8675, "matched_fragments": 684, "total_fragments": 1069, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Brevundimonas albigilva", "strain": "strain=KEME 9005-016", "accession": "GCA_023503965.1", "taxid": 1312364, "species_taxid": 1312364, "relation_to_type": "type", "validated": true, "ani": 81.6758, "matched_fragments": 588, "total_fragments": 1069, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Brevundimonas goettingensis", "strain": "strain=LVF2", "accession": "GCA_017487405.1", "taxid": 2774190, "species_taxid": 2774190, "relation_to_type": "type", "validated": true, "ani": 81.4304, "matched_fragments": 655, "total_fragments": 1069, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Brevundimonas lenta", "strain": "strain=DSM 23960", "accession": "GCA_014196335.1", "taxid": 424796, "species_taxid": 424796, "relation_to_type": "type", "validated": true, "ani": 81.3251, "matched_fragments": 576, "total_fragments": 1069, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Brevundimonas fluminis", "strain": "strain=LA-55", "accession": "GCA_003934285.1", "taxid": 2487274, "species_taxid": 2487274, "relation_to_type": "type", "validated": true, "ani": 81.2761, "matched_fragments": 569, "total_fragments": 1069, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Brevundimonas viscosa", "strain": "strain=CGMCC 1.10683", "accession": "GCA_900116065.1", "taxid": 871741, "species_taxid": 871741, "relation_to_type": "type", "validated": true, "ani": 81.2614, "matched_fragments": 583, "total_fragments": 1069, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Brevundimonas diminuta", "strain": "strain=ATCC 11568", "accession": "GCA_000204035.1", "taxid": 293, "species_taxid": 293, "relation_to_type": "type", "validated": true, "ani": 81.0889, "matched_fragments": 556, "total_fragments": 1069, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Brevundimonas diminuta", "strain": "strain=NCTC8545", "accession": "GCA_900445995.1", "taxid": 293, "species_taxid": 293, "relation_to_type": "type", "validated": true, "ani": 81.0625, "matched_fragments": 570, "total_fragments": 1069, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Brevundimonas basaltis", "strain": "strain=DSM 25335", "accession": "GCA_014202075.1", "taxid": 472166, "species_taxid": 472166, "relation_to_type": "type", "validated": true, "ani": 81.0151, "matched_fragments": 564, "total_fragments": 1069, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Brevundimonas alba", "strain": "strain=DSM 4736", "accession": "GCA_011927945.1", "taxid": 74314, "species_taxid": 74314, "relation_to_type": "type", "validated": true, "ani": 80.8976, "matched_fragments": 584, "total_fragments": 1069, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Brevundimonas guildfordensis", "strain": "strain=Sa3CVA3", "accession": "GCA_014836405.1", "taxid": 2762241, "species_taxid": 2762241, "relation_to_type": "type", "validated": true, "ani": 80.834, "matched_fragments": 541, "total_fragments": 1069, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Brevundimonas naejangsanensis", "strain": "strain=DSM 23858", "accession": "GCA_000421705.1", "taxid": 588932, "species_taxid": 588932, "relation_to_type": "type", "validated": true, "ani": 80.7077, "matched_fragments": 534, "total_fragments": 1069, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Brevundimonas vitisensis", "strain": "strain=GR-TSA-9", "accession": "GCA_016656965.1", "taxid": 2800818, "species_taxid": 2800818, "relation_to_type": "type", "validated": true, "ani": 80.6543, "matched_fragments": 515, "total_fragments": 1069, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Brevundimonas variabilis", "strain": "strain=DSM 4737", "accession": "GCA_014199945.1", "taxid": 74312, "species_taxid": 74312, "relation_to_type": "type", "validated": true, "ani": 80.1147, "matched_fragments": 529, "total_fragments": 1069, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Caulobacter rhizosphaerae", "strain": "strain=CGMCC 1.15915", "accession": "GCA_014645055.1", "taxid": 2010972, "species_taxid": 2010972, "relation_to_type": "type", "validated": true, "ani": 78.51, "matched_fragments": 393, "total_fragments": 1069, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Roseomonas haemaphysalidis", "strain": "strain=546", "accession": "GCA_017355405.1", "taxid": 2768162, "species_taxid": 2768162, "relation_to_type": "type", "validated": true, "ani": 76.1564, "matched_fragments": 159, "total_fragments": 1069, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_000701445.1", "gtdb_species": "s__Brevundimonas bacteroides", "ani": 100.0, "matched_fragments": 1066, "total_fragments": 1069, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas", "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_001295975.1", "gtdb_species": "s__Brevundimonas sp001295975", "ani": 88.7981, "matched_fragments": 752, "total_fragments": 1069, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas", "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_002280475.1", "gtdb_species": "s__Brevundimonas subvibrioides_C", "ani": 85.4891, "matched_fragments": 795, "total_fragments": 1069, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.76", "min_intra_species_ani": "99.76", "mean_intra_species_af": "0.91", "min_intra_species_af": "0.91", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_002002865.1", "gtdb_species": "s__Brevundimonas sp002002865", "ani": 82.4459, "matched_fragments": 688, "total_fragments": 1069, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas", "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_002280785.1", "gtdb_species": "s__Brevundimonas subvibrioides_B", "ani": 82.3716, "matched_fragments": 680, "total_fragments": 1069, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas", "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_017795885.1", "gtdb_species": "s__Brevundimonas sp017795885", "ani": 82.2405, "matched_fragments": 659, "total_fragments": 1069, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas", "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_018820205.1", "gtdb_species": "s__Brevundimonas sp018820205", "ani": 81.9274, "matched_fragments": 608, "total_fragments": 1069, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.87", "min_intra_species_ani": "99.87", "mean_intra_species_af": "0.87", "min_intra_species_af": "0.87", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCA_013912005.1", "gtdb_species": "s__Brevundimonas sp013912005", "ani": 81.4875, "matched_fragments": 574, "total_fragments": 1069, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas", "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_003934285.1", "gtdb_species": "s__Brevundimonas fluminis", "ani": 81.2868, "matched_fragments": 567, "total_fragments": 1069, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas", "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_900116065.1", "gtdb_species": "s__Brevundimonas viscosa", "ani": 81.2838, "matched_fragments": 581, "total_fragments": 1069, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas", "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_016183935.1", "gtdb_species": "s__Brevundimonas sp016183935", "ani": 81.2032, "matched_fragments": 567, "total_fragments": 1069, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas", "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_003627995.1", "gtdb_species": "s__Brevundimonas naejangsanensis_B", "ani": 81.189, "matched_fragments": 573, "total_fragments": 1069, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas", "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_002292165.1", "gtdb_species": "s__Brevundimonas sp002292165", "ani": 81.0315, "matched_fragments": 547, "total_fragments": 1069, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas", "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_003248925.1", "gtdb_species": "s__Brevundimonas sp003248925", "ani": 80.9777, "matched_fragments": 492, "total_fragments": 1069, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas", "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_003248455.1", "gtdb_species": "s__Brevundimonas sp003248455", "ani": 80.8581, "matched_fragments": 555, "total_fragments": 1069, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas", "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": -0.348, "cell_length": 0.266, "doubling_h": null, "growth_tmp": 30.0, "optimum_tmp": 28.178, "optimum_ph": 7.406, "genome_size": 3220540.0, "gc_content": 67.057, "coding_genes": 3106.166, "rRNA16S_genes": 2.0, "tRNA_genes": 49.0, "gram_stain": 0.0, "sporulation": 0.0, "motility": 1.0, "range_salinity": null, "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": [ "Brevundimonas", "bacteroides", "DSM", "4726" ], "quality": 5, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }