{ "type": "genome", "identifier": "GCF_000230695.2", "organism": "Rhodanobacter denitrificans", "title": "Rhodanobacter denitrificans", "description": "na", "data type": "Genome sequencing and assembly", "organization": "DOE Joint Genome Institute", "publication": [ {} ], "properties": { "assembly_accession": "GCF_000230695.2", "bioproject": "PRJNA224116", "biosample": "SAMN02232048", "wgs_master": "na", "refseq_category": "na", "taxid": "666685", "species_taxid": "666685", "organism_name": "Rhodanobacter denitrificans", "infraspecific_name": "strain=2APBS1", "isolate": "na", "version_status": "latest", "assembly_level": "Complete Genome", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2013/03/11", "asm_name": "ASM23069v3", "asm_submitter": "DOE Joint Genome Institute", "gbrs_paired_asm": "GCA_000230695.3", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/230/695/GCF_000230695.2_ASM23069v3", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "4225490", "genome_size_ungapped": "4225490", "gc_percent": "67.500000", "replicon_count": "1", "scaffold_count": "1", "contig_count": "1", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_000230695.2-RS_2024_05_05", "annotation_date": "2024-05-05", "total_gene_count": "3950", "protein_coding_gene_count": "3855", "non_coding_gene_count": "59", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2013-03-11", "dateModified": "2013-03-11", "datePublished": "2013-03-11", "_annotation": { "sample_count": 1, "sample_organism": [ "Rhodanobacter denitrificans" ], "sample_taxid": [ "666685" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "USA" ], "sample_host_location_id": [], "data_size": "1.146 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)": "4225490", "Number of Sequences": "1", "Longest Sequences (bp)": "4225490", "N50 (bp)": "4225490", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "67.5", "Number of CDSs": "3916", "Average Protein Length": "324.5", "Coding Ratio (%)": "90.2", "Number of rRNAs": "6", "Number of tRNAs": "59", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Rhodanobacter denitrificans", "strain": "strain=2APBS1", "accession": "GCA_000230695.3", "taxid": 666685, "species_taxid": 666685, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1403, "total_fragments": 1408, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Rhodanobacter thiooxydans", "strain": "strain=LCS2", "accession": "GCA_000264375.1", "taxid": 416169, "species_taxid": 416169, "relation_to_type": "type", "validated": true, "ani": 90.6149, "matched_fragments": 1026, "total_fragments": 1408, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rhodanobacter spathiphylli", "strain": "strain=B39", "accession": "GCA_000264295.1", "taxid": 347483, "species_taxid": 347483, "relation_to_type": "type", "validated": true, "ani": 86.9042, "matched_fragments": 887, "total_fragments": 1408, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rhodanobacter panaciterrae", "strain": "strain=KCTC 22232", "accession": "GCA_014651895.1", "taxid": 490572, "species_taxid": 490572, "relation_to_type": "type", "validated": true, "ani": 85.2912, "matched_fragments": 837, "total_fragments": 1408, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Fulvimonas soli", "strain": "strain=LMG 19981", "accession": "GCA_006352285.1", "taxid": 155197, "species_taxid": 155197, "relation_to_type": "type", "validated": true, "ani": 84.7932, "matched_fragments": 742, "total_fragments": 1408, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Fulvimonas soli", "strain": "strain=DSM 14263", "accession": "GCA_003148905.1", "taxid": 155197, "species_taxid": 155197, "relation_to_type": "type", "validated": true, "ani": 84.7384, "matched_fragments": 806, "total_fragments": 1408, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rhodanobacter fulvus", "strain": "strain=Jip2", "accession": "GCA_000264315.1", "taxid": 219571, "species_taxid": 219571, "relation_to_type": "type", "validated": true, "ani": 84.1855, "matched_fragments": 774, "total_fragments": 1408, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Frateuria flava", "strain": "strain=MAH-13", "accession": "GCA_017837635.1", "taxid": 2821489, "species_taxid": 2821489, "relation_to_type": "type", "validated": true, "ani": 82.7514, "matched_fragments": 762, "total_fragments": 1408, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Dyella amyloliquefaciens", "strain": "strain=DHC06", "accession": "GCA_004296575.1", "taxid": 1770545, "species_taxid": 1770545, "relation_to_type": "type", "validated": true, "ani": 81.2462, "matched_fragments": 710, "total_fragments": 1408, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Dyella telluris", "strain": "strain=G9", "accession": "GCA_014297575.1", "taxid": 2763498, "species_taxid": 2763498, "relation_to_type": "type", "validated": true, "ani": 81.1822, "matched_fragments": 703, "total_fragments": 1408, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Dyella japonica", "strain": "strain=DSM 16301", "accession": "GCA_001010355.1", "taxid": 231455, "species_taxid": 231455, "relation_to_type": "type", "validated": true, "ani": 81.1449, "matched_fragments": 596, "total_fragments": 1408, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Dyella acidiphila", "strain": "strain=7MK23", "accession": "GCA_014863405.1", "taxid": 2775866, "species_taxid": 2775866, "relation_to_type": "type", "validated": true, "ani": 80.8237, "matched_fragments": 663, "total_fragments": 1408, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Tahibacter caeni", "strain": "strain=BUT-6", "accession": "GCA_024609805.1", "taxid": 1453545, "species_taxid": 1453545, "relation_to_type": "type", "validated": true, "ani": 78.687, "matched_fragments": 478, "total_fragments": 1408, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_000230695.2", "gtdb_species": "s__Rhodanobacter denitrificans", "ani": 100.0, "matched_fragments": 1402, "total_fragments": 1408, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Rhodanobacter", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.49", "min_intra_species_ani": "98.47", "mean_intra_species_af": "0.91", "min_intra_species_af": "0.89", "num_clustered_genomes": 4, "status": "conclusive" }, { "accession": "GCF_018599185.1", "gtdb_species": "s__Rhodanobacter sp018599185", "ani": 90.8344, "matched_fragments": 1016, "total_fragments": 1408, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Rhodanobacter", "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_003069545.1", "gtdb_species": "s__Rhodanobacter thiooxydans_A", "ani": 90.833, "matched_fragments": 998, "total_fragments": 1408, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Rhodanobacter", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.26", "min_intra_species_ani": "98.26", "mean_intra_species_af": "0.94", "min_intra_species_af": "0.94", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_000264375.1", "gtdb_species": "s__Rhodanobacter thiooxydans", "ani": 90.6307, "matched_fragments": 1025, "total_fragments": 1408, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Rhodanobacter", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.24", "min_intra_species_ani": "99.24", "mean_intra_species_af": "0.91", "min_intra_species_af": "0.91", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_000427505.1", "gtdb_species": "s__Rhodanobacter sp000427505", "ani": 90.4955, "matched_fragments": 1012, "total_fragments": 1408, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Rhodanobacter", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.93", "min_intra_species_ani": "99.93", "mean_intra_species_af": "0.96", "min_intra_species_af": "0.96", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_001617365.1", "gtdb_species": "s__Rhodanobacter sp001617365", "ani": 90.3121, "matched_fragments": 967, "total_fragments": 1408, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Rhodanobacter", "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": "0.97", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_001428385.1", "gtdb_species": "s__Rhodanobacter sp001428385", "ani": 90.2727, "matched_fragments": 971, "total_fragments": 1408, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Rhodanobacter", "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_003335105.1", "gtdb_species": "s__Rhodanobacter denitrificans_A", "ani": 89.2906, "matched_fragments": 982, "total_fragments": 1408, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Rhodanobacter", "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_000264295.1", "gtdb_species": "s__Rhodanobacter spathiphylli", "ani": 86.9015, "matched_fragments": 887, "total_fragments": 1408, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Rhodanobacter", "ani_circumscription_radius": 95.107, "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_008329435.1", "gtdb_species": "s__Rhodanobacter sp008329435", "ani": 86.4541, "matched_fragments": 897, "total_fragments": 1408, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Rhodanobacter", "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_001898415.1", "gtdb_species": "s__Rhodanobacter sp001898415", "ani": 86.4203, "matched_fragments": 920, "total_fragments": 1408, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Rhodanobacter", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.06", "min_intra_species_ani": "98.37", "mean_intra_species_af": "0.88", "min_intra_species_af": "0.82", "num_clustered_genomes": 4, "status": "-" }, { "accession": "GCF_001428405.1", "gtdb_species": "s__Frateuria_A sp001428405", "ani": 85.0315, "matched_fragments": 843, "total_fragments": 1408, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Frateuria_A", "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": -0.268, "cell_length": 0.301, "doubling_h": null, "growth_tmp": 29.0, "optimum_tmp": 30.0, "optimum_ph": 6.5, "genome_size": 4454648.143, "gc_content": 67.635, "coding_genes": 3789.667, "rRNA16S_genes": 2.0, "tRNA_genes": 49.0, "gram_stain": 0.0, "sporulation": 0.0, "motility": 1.0, "range_salinity": null, "facultative_respiration": 1.0, "anaerobic_respiration": 0.0, "aerobic_respiration": 0.0, "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": [ "Rhodanobacter", "denitrificans" ], "quality": 5, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }