{ "type": "genome", "identifier": "GCA_022702005.1", "organism": "Sphingomonadaceae bacterium", "title": "Sphingomonadaceae bacterium", "description": "derived from metagenome; genus undefined", "data type": "Genome sequencing and assembly", "organization": "Iowa State University", "publication": [ {} ], "properties": { "assembly_accession": "GCA_022702005.1", "bioproject": "PRJNA800073", "biosample": "SAMN25223845", "wgs_master": "JAKONJ000000000.1", "refseq_category": "na", "taxid": "1930536", "species_taxid": "1930536", "organism_name": "Sphingomonadaceae bacterium", "infraspecific_name": "", "isolate": "M55", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2022/03/28", "asm_name": "ASM2270200v1", "submitter": "Iowa State University", "gbrs_paired_asm": "na", "paired_asm_comp": "na", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/022/702/005/GCA_022702005.1_ASM2270200v1", "excluded_from_refseq": "derived from metagenome; genus undefined", "relation_to_type_material": "", "asm_not_live_date": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2022-03-28", "dateModified": "2022-03-28", "datePublished": "2022-03-28", "_annotation": { "sample_count": 1, "sample_organism": [ "Sphingomonadaceae bacterium" ], "sample_taxid": [ "1930536" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "USA: Hickory Corners, Michigan" ], "sample_host_location_id": [], "data_size": "0.760 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": null, "max": null }, "completeness": 65.61, "contamination": 4.17, "strain_heterogeneity": 100.0, "genome_count": 1 }, "data_type": "MAG", "data_source": "INSDC", "_dfast": { "Total Sequence Length (bp)": "2745001", "Number of Sequences": "511", "Longest Sequences (bp)": "24526", "N50 (bp)": "5920", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "66.7", "Number of CDSs": "2088", "Average Protein Length": "296.1", "Coding Ratio (%)": "67.6", "Number of rRNAs": "0", "Number of tRNAs": "31", "Number of CRISPRs": "1" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Sphingomonas parapaucimobilis", "strain": "strain=NBRC 15100", "accession": "GCA_000787715.1", "taxid": 28213, "species_taxid": 28213, "relation_to_type": "type", "validated": true, "ani": 88.1899, "matched_fragments": 523, "total_fragments": 663, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sphingomonas yabuuchiae", "strain": "strain=DSM 14562", "accession": "GCA_014199595.1", "taxid": 172044, "species_taxid": 172044, "relation_to_type": "type", "validated": true, "ani": 88.0594, "matched_fragments": 544, "total_fragments": 663, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sphingomonas yabuuchiae", "strain": "strain=DSM 14562", "accession": "GCA_017052455.1", "taxid": 172044, "species_taxid": 172044, "relation_to_type": "type", "validated": true, "ani": 88.0478, "matched_fragments": 543, "total_fragments": 663, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sphingomonas sanguinis", "strain": "strain=NBRC 13937", "accession": "GCA_001591005.1", "taxid": 33051, "species_taxid": 33051, "relation_to_type": "suspected-type", "validated": true, "ani": 87.7983, "matched_fragments": 535, "total_fragments": 663, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sphingomonas pseudosanguinis", "strain": "strain=DSM 19512", "accession": "GCA_014196255.1", "taxid": 413712, "species_taxid": 413712, "relation_to_type": "type", "validated": true, "ani": 86.9488, "matched_fragments": 522, "total_fragments": 663, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sphingomonas pseudosanguinis", "strain": "strain=DSM 19512", "accession": "GCA_017052355.1", "taxid": 413712, "species_taxid": 413712, "relation_to_type": "type", "validated": true, "ani": 86.8902, "matched_fragments": 530, "total_fragments": 663, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sphingomonas carotinifaciens", "strain": "strain=DSM 27347", "accession": "GCA_009789535.1", "taxid": 1166323, "species_taxid": 1166323, "relation_to_type": "type", "validated": true, "ani": 81.1606, "matched_fragments": 412, "total_fragments": 663, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sphingomonas panni", "strain": "strain=DSM 15761", "accession": "GCA_022664435.1", "taxid": 237612, "species_taxid": 237612, "relation_to_type": "type", "validated": true, "ani": 79.3176, "matched_fragments": 324, "total_fragments": 663, "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": 79.1754, "matched_fragments": 334, "total_fragments": 663, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sphingomonas hankookensis", "strain": "strain=KCTC 22579", "accession": "GCA_022664465.1", "taxid": 563996, "species_taxid": 563996, "relation_to_type": "type", "validated": true, "ani": 79.1538, "matched_fragments": 325, "total_fragments": 663, "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": 79.0106, "matched_fragments": 342, "total_fragments": 663, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sphingomonas yunnanensis", "strain": "strain=YIM 3", "accession": "GCA_019898765.1", "taxid": 310400, "species_taxid": 310400, "relation_to_type": "type", "validated": true, "ani": 78.7475, "matched_fragments": 332, "total_fragments": 663, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 65.61, "contamination": 4.17, "strain_heterogeneity": 100.0 }, "gtdb_result": [ { "accession": "GCF_000787715.1", "gtdb_species": "s__Sphingomonas parapaucimobilis", "ani": 88.1899, "matched_fragments": 523, "total_fragments": 663, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.90", "min_intra_species_ani": "97.90", "mean_intra_species_af": "0.87", "min_intra_species_af": "0.87", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_014199595.1", "gtdb_species": "s__Sphingomonas yabuuchiae", "ani": 88.0845, "matched_fragments": 543, "total_fragments": 663, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.94", "min_intra_species_ani": "96.78", "mean_intra_species_af": "0.92", "min_intra_species_af": "0.88", "num_clustered_genomes": 4, "status": "-" }, { "accession": "GCF_001476905.1", "gtdb_species": "s__Sphingomonas sanguinis_B", "ani": 87.8834, "matched_fragments": 514, "total_fragments": 663, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "96.13", "min_intra_species_ani": "96.11", "mean_intra_species_af": "0.83", "min_intra_species_af": "0.82", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_001591005.1", "gtdb_species": "s__Sphingomonas sanguinis", "ani": 87.8693, "matched_fragments": 532, "total_fragments": 663, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.09", "min_intra_species_ani": "96.84", "mean_intra_species_af": "0.89", "min_intra_species_af": "0.83", "num_clustered_genomes": 8, "status": "-" }, { "accession": "GCF_001477495.1", "gtdb_species": "s__Sphingomonas yabuuchiae_A", "ani": 87.7787, "matched_fragments": 518, "total_fragments": 663, "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": "GCA_019112965.1", "gtdb_species": "s__Sphingomonas excrementigallinarum", "ani": 87.4863, "matched_fragments": 507, "total_fragments": 663, "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_014197135.1", "gtdb_species": "s__Sphingomonas zeae", "ani": 87.1684, "matched_fragments": 530, "total_fragments": 663, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas", "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_014196255.1", "gtdb_species": "s__Sphingomonas pseudosanguinis", "ani": 86.9095, "matched_fragments": 524, "total_fragments": 663, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas", "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": -0.295, "cell_length": 0.115, "doubling_h": 0.382, "growth_tmp": 28.085, "optimum_tmp": 28.28, "optimum_ph": 6.964, "genome_size": 4338904.594, "gc_content": 64.279, "coding_genes": 4285.982, "rRNA16S_genes": 2.113, "tRNA_genes": 51.225, "gram_stain": 0.008, "sporulation": 0.024, "motility": 0.504, "range_salinity": null, "facultative_respiration": 0.013, "anaerobic_respiration": 0.0, "aerobic_respiration": 0.986, "mesophilic_range_tmp": 0.964, "thermophilic_range_tmp": 0.0, "psychrophilic_range_tmp": 0.035, "bacillus_cell_shape": 0.983, "coccus_cell_shape": 0.0, "filament_cell_shape": 0.0, "coccobacillus_cell_shape": 0.008, "vibrio_cell_shape": 0.0, "spiral_cell_shape": 0.008 }, "_gtdb_taxon": [ "d__Bacteria", "p__Pseudomonadota", "c__Alphaproteobacteria", "o__Sphingomonadales", "f__Sphingomonadaceae", "g__Sphingomonas", "s__" ], "_genome_taxon": [ "Sphingomonadaceae", "bacterium", "d__Bacteria", "p__Pseudomonadota", "c__Alphaproteobacteria", "o__Sphingomonadales", "f__Sphingomonadaceae", "g__Sphingomonas", "s__", "Bacteria", "Pseudomonadota", "Alphaproteobacteria", "Sphingomonadales", "Sphingomonadaceae", "Sphingomonas", "s", "", "" ], "_meo": [ { "id": "MEO_0000379", "label": "leaf" }, { "id": "MEO_0000419", "label": "plant body associated" } ], "quality": 3, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }