{ "type": "genome", "identifier": "GCF_000016545.1", "organism": "Caldicellulosiruptor saccharolyticus DSM 8903", "title": "Caldicellulosiruptor saccharolyticus DSM 8903", "description": "na", "data type": "Genome sequencing and assembly", "organization": "US DOE Joint Genome Institute", "publication": [ {} ], "properties": { "assembly_accession": "GCF_000016545.1", "bioproject": "PRJNA224116", "biosample": "SAMN00623033", "wgs_master": "na", "refseq_category": "reference genome", "taxid": "351627", "species_taxid": "44001", "organism_name": "Caldicellulosiruptor saccharolyticus DSM 8903", "infraspecific_name": "strain=DSM 8903", "isolate": "na", "version_status": "latest", "assembly_level": "Complete Genome", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2007/04/19", "asm_name": "ASM1654v1", "asm_submitter": "US DOE Joint Genome Institute", "gbrs_paired_asm": "GCA_000016545.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/016/545/GCF_000016545.1_ASM1654v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "2970275", "genome_size_ungapped": "2970275", "gc_percent": "35.500000", "replicon_count": "1", "scaffold_count": "1", "contig_count": "1", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_000016545.1-RS_2024_12_13", "annotation_date": "2024-12-13", "total_gene_count": "2934", "protein_coding_gene_count": "2749", "non_coding_gene_count": "59", "pubmed_id": "18776029" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2007-04-19", "dateModified": "2007-04-19", "datePublished": "2007-04-19", "_annotation": { "sample_count": 1, "sample_organism": [ "Caldicellulosiruptor saccharolyticus DSM 8903" ], "sample_taxid": [ "351627" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [], "sample_host_location_id": [], "data_size": "0.818 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)": "2970275", "Number of Sequences": "1", "Longest Sequences (bp)": "2970275", "N50 (bp)": "2970275", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "35.3", "Number of CDSs": "2875", "Average Protein Length": "302.9", "Coding Ratio (%)": "88.0", "Number of rRNAs": "9", "Number of tRNAs": "46", "Number of CRISPRs": "10" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Caldicellulosiruptor saccharolyticus", "strain": "strain=DSM 8903", "accession": "GCA_000016545.1", "taxid": 44001, "species_taxid": 44001, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 990, "total_fragments": 990, "ani_threshold": 95, "status": "inconclusive" }, { "organism_name": "Caldicellulosiruptor changbaiensis", "strain": "strain=CBS-Z", "accession": "GCA_003999255.1", "taxid": 1222016, "species_taxid": 1222016, "relation_to_type": "type", "validated": true, "ani": 95.2159, "matched_fragments": 766, "total_fragments": 990, "ani_threshold": 95, "status": "inconclusive" }, { "organism_name": "Caldicellulosiruptor naganoensis", "strain": "strain=NA10", "accession": "GCA_000955735.1", "taxid": 29324, "species_taxid": 29324, "relation_to_type": "type", "validated": true, "ani": 89.8163, "matched_fragments": 638, "total_fragments": 990, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Caldicellulosiruptor bescii", "strain": "strain=DSM 6725", "accession": "GCA_000022325.1", "taxid": 31899, "species_taxid": 31899, "relation_to_type": "type", "validated": true, "ani": 84.6176, "matched_fragments": 553, "total_fragments": 990, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Caldicellulosiruptor hydrothermalis", "strain": "strain=108", "accession": "GCA_000166355.1", "taxid": 413888, "species_taxid": 413888, "relation_to_type": "type", "validated": true, "ani": 84.1096, "matched_fragments": 524, "total_fragments": 990, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Caldicellulosiruptor kronotskyensis", "strain": "strain=2002", "accession": "GCA_000166775.1", "taxid": 413889, "species_taxid": 413889, "relation_to_type": "type", "validated": true, "ani": 83.9384, "matched_fragments": 538, "total_fragments": 990, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Caldicellulosiruptor acetigenus", "strain": "strain=DSM 7040", "accession": "GCA_000421725.1", "taxid": 301953, "species_taxid": 301953, "relation_to_type": "type", "validated": true, "ani": 82.4948, "matched_fragments": 490, "total_fragments": 990, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Caldicellulosiruptor obsidiansis", "strain": "strain=OB47", "accession": "GCA_000145215.1", "taxid": 717609, "species_taxid": 717609, "relation_to_type": "type", "validated": true, "ani": 82.2628, "matched_fragments": 496, "total_fragments": 990, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Caldicellulosiruptor owensensis", "strain": "strain=OL", "accession": "GCA_000166335.1", "taxid": 55205, "species_taxid": 55205, "relation_to_type": "type", "validated": true, "ani": 81.7843, "matched_fragments": 440, "total_fragments": 990, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_000016545.1", "gtdb_species": "s__Caldicellulosiruptor saccharolyticus", "ani": 100.0, "matched_fragments": 990, "total_fragments": 990, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Thermoanaerobacteria;o__Caldicellulosiruptorales;f__Caldicellulosiruptoraceae;g__Caldicellulosiruptor", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "96.00", "min_intra_species_ani": "95.22", "mean_intra_species_af": "0.88", "min_intra_species_af": "0.80", "num_clustered_genomes": 3, "status": "conclusive" }, { "accession": "GCF_000955735.1", "gtdb_species": "s__Caldicellulosiruptor naganoensis", "ani": 89.8187, "matched_fragments": 637, "total_fragments": 990, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Thermoanaerobacteria;o__Caldicellulosiruptorales;f__Caldicellulosiruptoraceae;g__Caldicellulosiruptor", "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_000955725.1", "gtdb_species": "s__Caldicellulosiruptor danielii", "ani": 84.7795, "matched_fragments": 575, "total_fragments": 990, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Thermoanaerobacteria;o__Caldicellulosiruptorales;f__Caldicellulosiruptoraceae;g__Caldicellulosiruptor", "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_000022325.1", "gtdb_species": "s__Caldicellulosiruptor bescii", "ani": 84.5916, "matched_fragments": 552, "total_fragments": 990, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Thermoanaerobacteria;o__Caldicellulosiruptorales;f__Caldicellulosiruptoraceae;g__Caldicellulosiruptor", "ani_circumscription_radius": 96.1491, "mean_intra_species_ani": "99.98", "min_intra_species_ani": "99.96", "mean_intra_species_af": "0.99", "min_intra_species_af": "0.98", "num_clustered_genomes": 23, "status": "-" }, { "accession": "GCF_017347585.1", "gtdb_species": "s__Caldicellulosiruptor sp017347585", "ani": 84.1543, "matched_fragments": 514, "total_fragments": 990, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Thermoanaerobacteria;o__Caldicellulosiruptorales;f__Caldicellulosiruptoraceae;g__Caldicellulosiruptor", "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_000166355.1", "gtdb_species": "s__Caldicellulosiruptor hydrothermalis", "ani": 84.0923, "matched_fragments": 525, "total_fragments": 990, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Thermoanaerobacteria;o__Caldicellulosiruptorales;f__Caldicellulosiruptoraceae;g__Caldicellulosiruptor", "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_000166775.1", "gtdb_species": "s__Caldicellulosiruptor kronotskyensis", "ani": 83.9584, "matched_fragments": 538, "total_fragments": 990, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Thermoanaerobacteria;o__Caldicellulosiruptorales;f__Caldicellulosiruptoraceae;g__Caldicellulosiruptor", "ani_circumscription_radius": 96.1491, "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_000955745.1", "gtdb_species": "s__Caldicellulosiruptor morganii", "ani": 83.3448, "matched_fragments": 554, "total_fragments": 990, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Thermoanaerobacteria;o__Caldicellulosiruptorales;f__Caldicellulosiruptoraceae;g__Caldicellulosiruptor", "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_000421725.1", "gtdb_species": "s__Caldicellulosiruptor acetigenus", "ani": 82.5224, "matched_fragments": 489, "total_fragments": 990, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Thermoanaerobacteria;o__Caldicellulosiruptorales;f__Caldicellulosiruptoraceae;g__Caldicellulosiruptor", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.40", "min_intra_species_ani": "97.22", "mean_intra_species_af": "0.81", "min_intra_species_af": "0.79", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_000145215.1", "gtdb_species": "s__Caldicellulosiruptor obsidiansis", "ani": 82.2404, "matched_fragments": 492, "total_fragments": 990, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Thermoanaerobacteria;o__Caldicellulosiruptorales;f__Caldicellulosiruptoraceae;g__Caldicellulosiruptor", "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_000166335.1", "gtdb_species": "s__Caldicellulosiruptor owensensis", "ani": 81.744, "matched_fragments": 439, "total_fragments": 990, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Thermoanaerobacteria;o__Caldicellulosiruptorales;f__Caldicellulosiruptoraceae;g__Caldicellulosiruptor", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "95.74", "min_intra_species_ani": "95.71", "mean_intra_species_af": "0.88", "min_intra_species_af": "0.85", "num_clustered_genomes": 3, "status": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": -0.398, "cell_length": 0.513, "doubling_h": 0.358, "growth_tmp": 68.0, "optimum_tmp": 74.5, "optimum_ph": 7.1, "genome_size": 2970274.0, "gc_content": 35.3, "coding_genes": 2647.0, "rRNA16S_genes": 3.0, "tRNA_genes": 46.0, "gram_stain": 1.0, "sporulation": 0.0, "motility": 0.25, "range_salinity": null, "facultative_respiration": 0.0, "anaerobic_respiration": 1.0, "aerobic_respiration": 0.0, "mesophilic_range_tmp": 0.0, "thermophilic_range_tmp": 1.0, "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": [ "Caldicellulosiruptor", "saccharolyticus", "DSM", "8903" ], "quality": 5, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }