{ "type": "genome", "identifier": "GCF_003050705.1", "organism": "Sphingomonas aurantiaca", "title": "Sphingomonas aurantiaca", "description": "na", "data type": "Genome sequencing and assembly", "organization": "DOE Joint Genome Institute", "publication": [ {} ], "properties": { "assembly_accession": "GCF_003050705.1", "bioproject": "PRJNA224116", "biosample": "SAMN08777253", "wgs_master": "QAOG00000000.1", "refseq_category": "reference genome", "taxid": "185949", "species_taxid": "185949", "organism_name": "Sphingomonas aurantiaca", "infraspecific_name": "strain=MA101b", "isolate": "na", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2018/04/13", "asm_name": "ASM305070v1", "asm_submitter": "DOE Joint Genome Institute", "gbrs_paired_asm": "GCA_003050705.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/003/050/705/GCF_003050705.1_ASM305070v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "4411230", "genome_size_ungapped": "4410490", "gc_percent": "66.000000", "replicon_count": "0", "scaffold_count": "13", "contig_count": "13", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_003050705.1-RS_2024_04_22", "annotation_date": "2024-04-22", "total_gene_count": "4038", "protein_coding_gene_count": "3949", "non_coding_gene_count": "57", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2018-04-13", "dateModified": "2018-04-13", "datePublished": "2018-04-13", "_annotation": { "sample_count": 1, "sample_organism": [ "Sphingomonas aurantiaca" ], "sample_taxid": [ "185949" ], "sample_host_organism": [ "not applicable" ], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "Finland" ], "sample_host_location_id": [], "data_size": "1.207 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": null, "max": null }, "completeness": 95.83, "contamination": 0.0, "strain_heterogeneity": 0.0, "genome_count": 1 }, "data_type": "G", "data_source": "RefSeq", "_dfast": { "Total Sequence Length (bp)": "4411230", "Number of Sequences": "13", "Longest Sequences (bp)": "1169946", "N50 (bp)": "577097", "Gap Ratio (%)": "0.016775", "GCcontent (%)": "66.2", "Number of CDSs": "4015", "Average Protein Length": "325.6", "Coding Ratio (%)": "88.9", "Number of rRNAs": "4", "Number of tRNAs": "53", "Number of CRISPRs": "1" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Sphingomonas aurantiaca", "strain": "strain=MA101b", "accession": "GCA_003050705.1", "taxid": 185949, "species_taxid": 185949, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1463, "total_fragments": 1463, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Sphingomonas albertensis", "strain": "strain=DOAB 1063", "accession": "GCA_014358075.1", "taxid": 2762591, "species_taxid": 2762591, "relation_to_type": "type", "validated": true, "ani": 87.9695, "matched_fragments": 946, "total_fragments": 1463, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sphingomonas faeni", "strain": "strain=MA-olki", "accession": "GCA_003053745.1", "taxid": 185950, "species_taxid": 185950, "relation_to_type": "type", "validated": true, "ani": 87.5289, "matched_fragments": 985, "total_fragments": 1463, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sphingomonas aerolata", "strain": "strain=NW12", "accession": "GCA_003046295.1", "taxid": 185951, "species_taxid": 185951, "relation_to_type": "type", "validated": true, "ani": 85.7661, "matched_fragments": 870, "total_fragments": 1463, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sphingomonas ginsenosidivorax", "strain": "strain=KHI67", "accession": "GCA_007995065.1", "taxid": 862135, "species_taxid": 862135, "relation_to_type": "type", "validated": true, "ani": 84.1538, "matched_fragments": 820, "total_fragments": 1463, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sphingomonas hylomeconis", "strain": "strain=CCTCC AB 2013304", "accession": "GCA_025370105.1", "taxid": 1395958, "species_taxid": 1395958, "relation_to_type": "type", "validated": true, "ani": 80.5207, "matched_fragments": 644, "total_fragments": 1463, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sphingomonas folli", "strain": "strain=RHCKR7", "accession": "GCA_019429525.1", "taxid": 2862497, "species_taxid": 2862497, "relation_to_type": "type", "validated": true, "ani": 79.8687, "matched_fragments": 669, "total_fragments": 1463, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sphingomonas citricola", "strain": "strain=RHCKR47", "accession": "GCA_019429535.1", "taxid": 2862498, "species_taxid": 2862498, "relation_to_type": "type", "validated": true, "ani": 79.7811, "matched_fragments": 641, "total_fragments": 1463, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sphingomonas citri", "strain": "strain=RRHST34", "accession": "GCA_019429485.1", "taxid": 2862499, "species_taxid": 2862499, "relation_to_type": "type", "validated": true, "ani": 79.7717, "matched_fragments": 673, "total_fragments": 1463, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sphingomonas alpina", "strain": "strain=DSM 22537", "accession": "GCA_025370095.1", "taxid": 653931, "species_taxid": 653931, "relation_to_type": "type", "validated": true, "ani": 79.49, "matched_fragments": 584, "total_fragments": 1463, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sphingomonas corticis", "strain": "strain=36D10-4-7", "accession": "GCA_012035195.1", "taxid": 2722791, "species_taxid": 2722791, "relation_to_type": "type", "validated": true, "ani": 79.322, "matched_fragments": 607, "total_fragments": 1463, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Novosphingobium huizhouense", "strain": "strain=c7", "accession": "GCA_020179475.1", "taxid": 2866625, "species_taxid": 2866625, "relation_to_type": "type", "validated": true, "ani": 77.9946, "matched_fragments": 381, "total_fragments": 1463, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Novosphingobium malaysiense", "strain": "strain=MUSC 273", "accession": "GCA_000802225.1", "taxid": 1348853, "species_taxid": 1348853, "relation_to_type": "type", "validated": true, "ani": 77.5262, "matched_fragments": 238, "total_fragments": 1463, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mesorhizobium albiziae", "strain": "strain=DSM 21822", "accession": "GCA_900114255.1", "taxid": 335020, "species_taxid": 335020, "relation_to_type": "type", "validated": true, "ani": 76.0969, "matched_fragments": 127, "total_fragments": 1463, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mesorhizobium sanjuanii", "strain": "strain=BSA136", "accession": "GCA_002529485.1", "taxid": 2037900, "species_taxid": 2037900, "relation_to_type": "type", "validated": true, "ani": 75.9233, "matched_fragments": 146, "total_fragments": 1463, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 95.83, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_003050705.1", "gtdb_species": "s__Sphingomonas aurantiaca", "ani": 100.0, "matched_fragments": 1463, "total_fragments": 1463, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "96.29", "min_intra_species_ani": "95.02", "mean_intra_species_af": "0.87", "min_intra_species_af": "0.86", "num_clustered_genomes": 4, "status": "conclusive" }, { "accession": "GCF_001421805.1", "gtdb_species": "s__Sphingomonas sp001421805", "ani": 90.8332, "matched_fragments": 1009, "total_fragments": 1463, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.24", "min_intra_species_ani": "98.24", "mean_intra_species_af": "0.93", "min_intra_species_af": "0.93", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_013374115.1", "gtdb_species": "s__Sphingomonas sp013374115", "ani": 88.6422, "matched_fragments": 940, "total_fragments": 1463, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas", "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_004340945.1", "gtdb_species": "s__Sphingomonas sp004340945", "ani": 88.1926, "matched_fragments": 1053, "total_fragments": 1463, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "95.25", "min_intra_species_ani": "95.25", "mean_intra_species_af": "0.84", "min_intra_species_af": "0.84", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_004101245.1", "gtdb_species": "s__Sphingomonas sp004101245", "ani": 88.0054, "matched_fragments": 974, "total_fragments": 1463, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas", "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_014358075.1", "gtdb_species": "s__Sphingomonas albertensis", "ani": 87.9225, "matched_fragments": 950, "total_fragments": 1463, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas", "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_900115295.1", "gtdb_species": "s__Sphingomonas sp900115295", "ani": 87.649, "matched_fragments": 988, "total_fragments": 1463, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas", "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_003050745.1", "gtdb_species": "s__Sphingomonas sp003050745", "ani": 87.6436, "matched_fragments": 958, "total_fragments": 1463, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "95.19", "min_intra_species_ani": "95.12", "mean_intra_species_af": "0.89", "min_intra_species_af": "0.88", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_004795835.1", "gtdb_species": "s__Sphingomonas sp004795835", "ani": 87.4357, "matched_fragments": 949, "total_fragments": 1463, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas", "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_001421415.1", "gtdb_species": "s__Sphingomonas sp001421415", "ani": 87.4138, "matched_fragments": 965, "total_fragments": 1463, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas", "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_001422045.1", "gtdb_species": "s__Sphingomonas sp001422045", "ani": 87.4023, "matched_fragments": 949, "total_fragments": 1463, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas", "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_001421535.1", "gtdb_species": "s__Sphingomonas sp001421535", "ani": 85.8267, "matched_fragments": 890, "total_fragments": 1463, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas", "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_003046295.1", "gtdb_species": "s__Sphingomonas aerolata", "ani": 85.7663, "matched_fragments": 870, "total_fragments": 1463, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "96.52", "min_intra_species_ani": "96.36", "mean_intra_species_af": "0.90", "min_intra_species_af": "0.73", "num_clustered_genomes": 15, "status": "-" }, { "accession": "GCF_016743815.1", "gtdb_species": "s__Sphingomonas sp016743815", "ani": 79.4904, "matched_fragments": 578, "total_fragments": 1463, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas", "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_001314325.1", "gtdb_species": "s__Sphingopyxis macrogoltabida", "ani": 77.8305, "matched_fragments": 406, "total_fragments": 1463, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis", "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": -0.288, "cell_length": 0.14, "doubling_h": null, "growth_tmp": 24.0, "optimum_tmp": 28.407, "optimum_ph": 7.016, "genome_size": 4411230.0, "gc_content": 66.116, "coding_genes": 4592.69, "rRNA16S_genes": 2.285, "tRNA_genes": 51.0, "gram_stain": 0.0, "sporulation": 0.0, "motility": 0.586, "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": 0.98, "coccus_cell_shape": 0.0, "filament_cell_shape": 0.0, "coccobacillus_cell_shape": 0.0, "vibrio_cell_shape": 0.0, "spiral_cell_shape": 0.019 }, "_genome_taxon": [ "Sphingomonas", "aurantiaca" ], "quality": 5, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }