{ "type": "genome", "identifier": "GCF_009789535.1", "organism": "Sphingomonas carotinifaciens", "title": "Sphingomonas carotinifaciens", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Ministry of Agriculture/Luzhou Branch of National Rice Improvement Center", "publication": [ {} ], "properties": { "assembly_accession": "GCF_009789535.1", "bioproject": "PRJNA224116", "biosample": "SAMN13567891", "wgs_master": "WSUT00000000.1", "refseq_category": "reference genome", "taxid": "1166323", "species_taxid": "1166323", "organism_name": "Sphingomonas carotinifaciens", "infraspecific_name": "strain=DSM 27347", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2019/12/21", "asm_name": "ASM978953v1", "asm_submitter": "Ministry of Agriculture/Luzhou Branch of National Rice Improvement Center", "gbrs_paired_asm": "GCA_009789535.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/009/789/535/GCF_009789535.1_ASM978953v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "4094655", "genome_size_ungapped": "4094655", "gc_percent": "67.000000", "replicon_count": "0", "scaffold_count": "7", "contig_count": "7", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_009789535.1-RS_2024_05_17", "annotation_date": "2024-05-17", "total_gene_count": "3852", "protein_coding_gene_count": "3733", "non_coding_gene_count": "73", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2019-12-21", "dateModified": "2019-12-21", "datePublished": "2019-12-21", "_annotation": { "sample_count": 1, "sample_organism": [ "Sphingomonas carotinifaciens" ], "sample_taxid": [ "1166323" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "none" ], "sample_host_location_id": [], "data_size": "1.114 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)": "4094655", "Number of Sequences": "7", "Longest Sequences (bp)": "3353608", "N50 (bp)": "3353608", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "66.9", "Number of CDSs": "3809", "Average Protein Length": "323.8", "Coding Ratio (%)": "90.4", "Number of rRNAs": "12", "Number of tRNAs": "61", "Number of CRISPRs": "1" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Sphingomonas carotinifaciens", "strain": "strain=DSM 27347", "accession": "GCA_009789535.1", "taxid": 1166323, "species_taxid": 1166323, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1358, "total_fragments": 1362, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Sphingomonas carotinifaciens", "strain": "strain=DSM 27347", "accession": "GCA_014197095.1", "taxid": 1166323, "species_taxid": 1166323, "relation_to_type": "type", "validated": true, "ani": 99.988, "matched_fragments": 1329, "total_fragments": 1362, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Sphingomonas pseudosanguinis", "strain": "strain=DSM 19512", "accession": "GCA_014196255.1", "taxid": 413712, "species_taxid": 413712, "relation_to_type": "type", "validated": true, "ani": 82.2604, "matched_fragments": 739, "total_fragments": 1362, "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": 82.23, "matched_fragments": 743, "total_fragments": 1362, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sphingomonas paucimobilis", "strain": "strain=NBRC 13935", "accession": "GCA_000739895.2", "taxid": 13689, "species_taxid": 13689, "relation_to_type": "type", "validated": true, "ani": 81.9697, "matched_fragments": 685, "total_fragments": 1362, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sphingomonas paucimobilis", "strain": "strain=FDAARGOS_908", "accession": "GCA_016027095.1", "taxid": 13689, "species_taxid": 13689, "relation_to_type": "type", "validated": true, "ani": 81.9542, "matched_fragments": 746, "total_fragments": 1362, "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": 81.9106, "matched_fragments": 702, "total_fragments": 1362, "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": 81.9005, "matched_fragments": 755, "total_fragments": 1362, "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": 81.8842, "matched_fragments": 754, "total_fragments": 1362, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sphingomonas zeae", "strain": "strain=DSM 100049", "accession": "GCA_014197135.1", "taxid": 1646122, "species_taxid": 1646122, "relation_to_type": "type", "validated": true, "ani": 81.7111, "matched_fragments": 723, "total_fragments": 1362, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sphingomonas zeae", "strain": "strain=DSM 100049", "accession": "GCA_013359795.1", "taxid": 1646122, "species_taxid": 1646122, "relation_to_type": "type", "validated": true, "ani": 81.6905, "matched_fragments": 719, "total_fragments": 1362, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sphingomonas metalli", "strain": "strain=CGMCC 1.15330", "accession": "GCA_014641735.1", "taxid": 1779358, "species_taxid": 1779358, "relation_to_type": "type", "validated": true, "ani": 81.4391, "matched_fragments": 655, "total_fragments": 1362, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sphingomonas rubra", "strain": "strain=CGMCC 1.9113", "accession": "GCA_900115745.1", "taxid": 634430, "species_taxid": 634430, "relation_to_type": "type", "validated": true, "ani": 81.2031, "matched_fragments": 639, "total_fragments": 1362, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sphingomonas melonis", "strain": "strain=DAPP-PG 224", "accession": "GCA_000379045.1", "taxid": 152682, "species_taxid": 152682, "relation_to_type": "type", "validated": true, "ani": 80.7952, "matched_fragments": 663, "total_fragments": 1362, "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": 80.151, "matched_fragments": 644, "total_fragments": 1362, "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": 80.0502, "matched_fragments": 607, "total_fragments": 1362, "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": 79.8918, "matched_fragments": 655, "total_fragments": 1362, "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": 79.7945, "matched_fragments": 619, "total_fragments": 1362, "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": 79.753, "matched_fragments": 606, "total_fragments": 1362, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_009789535.1", "gtdb_species": "s__Sphingomonas carotinifaciens", "ani": 100.0, "matched_fragments": 1358, "total_fragments": 1362, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.06", "min_intra_species_ani": "97.19", "mean_intra_species_af": "0.97", "min_intra_species_af": "0.90", "num_clustered_genomes": 4, "status": "conclusive" }, { "accession": "GCF_014196255.1", "gtdb_species": "s__Sphingomonas pseudosanguinis", "ani": 82.239, "matched_fragments": 742, "total_fragments": 1362, "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": "-" }, { "accession": "GCF_000787715.1", "gtdb_species": "s__Sphingomonas parapaucimobilis", "ani": 82.1438, "matched_fragments": 694, "total_fragments": 1362, "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_001476905.1", "gtdb_species": "s__Sphingomonas sanguinis_B", "ani": 82.0222, "matched_fragments": 663, "total_fragments": 1362, "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_001477495.1", "gtdb_species": "s__Sphingomonas yabuuchiae_A", "ani": 81.9945, "matched_fragments": 682, "total_fragments": 1362, "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_000739895.2", "gtdb_species": "s__Sphingomonas paucimobilis", "ani": 81.943, "matched_fragments": 689, "total_fragments": 1362, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.74", "min_intra_species_ani": "99.40", "mean_intra_species_af": "0.92", "min_intra_species_af": "0.87", "num_clustered_genomes": 13, "status": "-" }, { "accession": "GCF_001591005.1", "gtdb_species": "s__Sphingomonas sanguinis", "ani": 81.8861, "matched_fragments": 705, "total_fragments": 1362, "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": "GCA_019112965.1", "gtdb_species": "s__Sphingomonas excrementigallinarum", "ani": 81.8844, "matched_fragments": 652, "total_fragments": 1362, "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_014199595.1", "gtdb_species": "s__Sphingomonas yabuuchiae", "ani": 81.8818, "matched_fragments": 754, "total_fragments": 1362, "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_014197135.1", "gtdb_species": "s__Sphingomonas zeae", "ani": 81.6853, "matched_fragments": 726, "total_fragments": 1362, "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_014641735.1", "gtdb_species": "s__Sphingomonas metalli", "ani": 81.4451, "matched_fragments": 655, "total_fragments": 1362, "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_900115745.1", "gtdb_species": "s__Sphingomonas rubra", "ani": 81.2099, "matched_fragments": 638, "total_fragments": 1362, "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_003345355.1", "gtdb_species": "s__Sphingomonas sp003345355", "ani": 80.4589, "matched_fragments": 564, "total_fragments": 1362, "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_017304635.1", "gtdb_species": "s__Sphingomonas sp017304635", "ani": 79.5534, "matched_fragments": 487, "total_fragments": 1362, "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": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": -0.288, "cell_length": 0.14, "doubling_h": null, "growth_tmp": 28.338, "optimum_tmp": 28.407, "optimum_ph": 7.016, "genome_size": 4164406.103, "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", "carotinifaciens" ], "quality": 5, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }