{ "type": "genome", "identifier": "GCF_000373385.1", "organism": "Thiobacillus thioparus DSM 505", "title": "Thiobacillus thioparus DSM 505", "description": "na", "data type": "Genome sequencing and assembly", "organization": "DOE Joint Genome Institute", "publication": [ {} ], "properties": { "assembly_accession": "GCF_000373385.1", "bioproject": "PRJNA224116", "biosample": "SAMN02441034", "wgs_master": "ARDU00000000.1", "refseq_category": "reference genome", "taxid": "1123393", "species_taxid": "931", "organism_name": "Thiobacillus thioparus DSM 505", "infraspecific_name": "strain=DSM 505", "isolate": "na", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2013/04/23", "asm_name": "ASM37338v1", "asm_submitter": "DOE Joint Genome Institute", "gbrs_paired_asm": "GCA_000373385.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/373/385/GCF_000373385.1_ASM37338v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "3201518", "genome_size_ungapped": "3200073", "gc_percent": "62.500000", "replicon_count": "0", "scaffold_count": "18", "contig_count": "20", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_000373385.1-RS_2024_05_02", "annotation_date": "2024-05-02", "total_gene_count": "3206", "protein_coding_gene_count": "3129", "non_coding_gene_count": "55", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2013-04-23", "dateModified": "2013-04-23", "datePublished": "2013-04-23", "_annotation": { "sample_count": 1, "sample_organism": [ "Thiobacillus thioparus DSM 505" ], "sample_taxid": [ "1123393" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "Missing" ], "sample_host_location_id": [], "data_size": "0.894 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)": "3201518", "Number of Sequences": "18", "Longest Sequences (bp)": "1101984", "N50 (bp)": "286980", "Gap Ratio (%)": "0.045760", "GCcontent (%)": "62.3", "Number of CDSs": "3119", "Average Protein Length": "311.8", "Coding Ratio (%)": "91.1", "Number of rRNAs": "5", "Number of tRNAs": "44", "Number of CRISPRs": "2" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Thiobacillus thioparus", "strain": "strain=DSM 505", "accession": "GCA_000373385.1", "taxid": 931, "species_taxid": 931, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1056, "total_fragments": 1056, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Thiobacillus denitrificans", "strain": "strain=DSM 12475", "accession": "GCA_000376425.1", "taxid": 36861, "species_taxid": 36861, "relation_to_type": "type", "validated": true, "ani": 83.9493, "matched_fragments": 697, "total_fragments": 1056, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sulfuritortus calidifontis", "strain": "strain=J1A", "accession": "GCA_003967275.1", "taxid": 1914471, "species_taxid": 1914471, "relation_to_type": "type", "validated": true, "ani": 78.7489, "matched_fragments": 282, "total_fragments": 1056, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sulfuritortus calidifontis", "strain": "strain=DSM 103923", "accession": "GCA_004346085.1", "taxid": 1914471, "species_taxid": 1914471, "relation_to_type": "type", "validated": true, "ani": 78.6154, "matched_fragments": 290, "total_fragments": 1056, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Crenobacter luteus", "strain": "strain=DSM 27258", "accession": "GCA_004345725.1", "taxid": 1452487, "species_taxid": 1452487, "relation_to_type": "type", "validated": true, "ani": 77.9843, "matched_fragments": 193, "total_fragments": 1056, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sulfuriferula plumbiphila", "strain": "strain=Gro7", "accession": "GCA_009938015.1", "taxid": 171865, "species_taxid": 171865, "relation_to_type": "type", "validated": true, "ani": 77.9644, "matched_fragments": 221, "total_fragments": 1056, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sulfurimicrobium lacus", "strain": "strain=skT11", "accession": "GCA_011764585.1", "taxid": 2715678, "species_taxid": 2715678, "relation_to_type": "type", "validated": true, "ani": 77.9323, "matched_fragments": 246, "total_fragments": 1056, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sulfuriferula plumbiphila", "strain": "strain=NBRC 107929", "accession": "GCA_007992375.1", "taxid": 171865, "species_taxid": 171865, "relation_to_type": "type", "validated": true, "ani": 77.8879, "matched_fragments": 212, "total_fragments": 1056, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rhodocyclus purpureus", "strain": "strain=DSM 168", "accession": "GCA_016653115.1", "taxid": 1067, "species_taxid": 1067, "relation_to_type": "type", "validated": true, "ani": 77.7172, "matched_fragments": 188, "total_fragments": 1056, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Azonexus fungiphilus", "strain": "strain=DSM 23841", "accession": "GCA_003634965.1", "taxid": 146940, "species_taxid": 146940, "relation_to_type": "type", "validated": true, "ani": 77.6737, "matched_fragments": 181, "total_fragments": 1056, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Thauera linaloolentis", "strain": "strain=DSM 12138", "accession": "GCA_000621305.1", "taxid": 76112, "species_taxid": 76112, "relation_to_type": "type", "validated": true, "ani": 77.5658, "matched_fragments": 208, "total_fragments": 1056, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Thauera linaloolentis", "strain": "strain=47Lol = DSM 12138", "accession": "GCA_000310205.1", "taxid": 76112, "species_taxid": 76112, "relation_to_type": "type", "validated": true, "ani": 77.5565, "matched_fragments": 203, "total_fragments": 1056, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sulfuriferula multivorans", "strain": "strain=TTN", "accession": "GCA_003851125.1", "taxid": 1559896, "species_taxid": 1559896, "relation_to_type": "type", "validated": true, "ani": 77.501, "matched_fragments": 202, "total_fragments": 1056, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Cupriavidus cauae", "strain": "strain=MKL-01", "accession": "GCA_008632125.1", "taxid": 2608999, "species_taxid": 2608999, "relation_to_type": "type", "validated": true, "ani": 77.43, "matched_fragments": 208, "total_fragments": 1056, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Schlegelella thermodepolymerans", "strain": "strain=DSM 15344", "accession": "GCA_015476235.1", "taxid": 215580, "species_taxid": 215580, "relation_to_type": "type", "validated": true, "ani": 77.3118, "matched_fragments": 180, "total_fragments": 1056, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Cupriavidus neocaledonicus", "strain": "strain=STM6070", "accession": "GCA_000372525.1", "taxid": 1040979, "species_taxid": 1040979, "relation_to_type": "type", "validated": true, "ani": 77.2555, "matched_fragments": 227, "total_fragments": 1056, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Cupriavidus malaysiensis", "strain": "strain=USMAA1020", "accession": "GCA_001854325.1", "taxid": 367825, "species_taxid": 367825, "relation_to_type": "type", "validated": true, "ani": 77.1007, "matched_fragments": 218, "total_fragments": 1056, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Cupriavidus nantongensis", "strain": "strain=X1", "accession": "GCA_001598055.1", "taxid": 1796606, "species_taxid": 1796606, "relation_to_type": "type", "validated": true, "ani": 77.0933, "matched_fragments": 234, "total_fragments": 1056, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Cupriavidus pauculus", "strain": "strain=FDAARGOS_1472", "accession": "GCA_019931045.1", "taxid": 82633, "species_taxid": 82633, "relation_to_type": "type", "validated": true, "ani": 76.785, "matched_fragments": 151, "total_fragments": 1056, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Cupriavidus pauculus", "strain": "strain=CCUG 12507", "accession": "GCA_008801835.1", "taxid": 82633, "species_taxid": 82633, "relation_to_type": "type", "validated": true, "ani": 76.7593, "matched_fragments": 154, "total_fragments": 1056, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_000373385.1", "gtdb_species": "s__Thiobacillus thioparus", "ani": 100.0, "matched_fragments": 1056, "total_fragments": 1056, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Thiobacillaceae;g__Thiobacillus", "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": "GCA_002343685.1", "gtdb_species": "s__Thiobacillus denitrificans_A", "ani": 92.4474, "matched_fragments": 825, "total_fragments": 1056, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Thiobacillaceae;g__Thiobacillus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.48", "min_intra_species_ani": "97.29", "mean_intra_species_af": "0.88", "min_intra_species_af": "0.86", "num_clustered_genomes": 5, "status": "-" }, { "accession": "GCA_001899305.1", "gtdb_species": "s__Thiobacillus sp001899305", "ani": 92.3568, "matched_fragments": 914, "total_fragments": 1056, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Thiobacillaceae;g__Thiobacillus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.65", "min_intra_species_ani": "95.89", "mean_intra_species_af": "0.93", "min_intra_species_af": "0.87", "num_clustered_genomes": 5, "status": "-" }, { "accession": "GCA_016195805.1", "gtdb_species": "s__Thiobacillus sp016195805", "ani": 87.2141, "matched_fragments": 767, "total_fragments": 1056, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Thiobacillaceae;g__Thiobacillus", "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_001899765.1", "gtdb_species": "s__Thiobacillus sp001899765", "ani": 86.1875, "matched_fragments": 731, "total_fragments": 1056, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Thiobacillaceae;g__Thiobacillus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.02", "min_intra_species_ani": "98.01", "mean_intra_species_af": "0.93", "min_intra_species_af": "0.89", "num_clustered_genomes": 5, "status": "-" }, { "accession": "GCA_018820765.1", "gtdb_species": "s__Thiobacillus sp018820765", "ani": 84.6751, "matched_fragments": 688, "total_fragments": 1056, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Thiobacillaceae;g__Thiobacillus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.99", "min_intra_species_ani": "99.99", "mean_intra_species_af": "0.98", "min_intra_species_af": "0.97", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCA_018262815.1", "gtdb_species": "s__Thiobacillus sp018262815", "ani": 84.1703, "matched_fragments": 547, "total_fragments": 1056, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Thiobacillaceae;g__Thiobacillus", "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_000376425.1", "gtdb_species": "s__Thiobacillus denitrificans", "ani": 83.9492, "matched_fragments": 697, "total_fragments": 1056, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Thiobacillaceae;g__Thiobacillus", "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_003510325.1", "gtdb_species": "s__Thiobacillus sp003510325", "ani": 83.9067, "matched_fragments": 510, "total_fragments": 1056, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Thiobacillaceae;g__Thiobacillus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.33", "min_intra_species_ani": "99.33", "mean_intra_species_af": "0.73", "min_intra_species_af": "0.73", "num_clustered_genomes": 2, "status": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": -0.523, "cell_length": -0.155, "doubling_h": 1.144, "growth_tmp": 29.6, "optimum_tmp": 28.687, "optimum_ph": 7.4, "genome_size": 3201518.0, "gc_content": 66.1, "coding_genes": 2784.667, "rRNA16S_genes": 2.0, "tRNA_genes": 43.0, "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": [ "Thiobacillus", "thioparus", "DSM", "505" ], "quality": 5, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }