{ "type": "genome", "identifier": "GCF_003097175.1", "organism": "Clostridium thermopalmarium DSM 5974", "title": "Clostridium thermopalmarium DSM 5974", "description": "na", "data type": "Genome sequencing and assembly", "organization": "DOE Joint Genome Institute", "publication": [ {} ], "properties": { "assembly_accession": "GCF_003097175.1", "bioproject": "PRJNA224116", "biosample": "SAMN07703233", "wgs_master": "QEQN00000000.1", "refseq_category": "na", "taxid": "1121340", "species_taxid": "29373", "organism_name": "Clostridium thermopalmarium DSM 5974", "infraspecific_name": "strain=DSM 5974", "isolate": "na", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2018/05/07", "asm_name": "ASM309717v1", "asm_submitter": "DOE Joint Genome Institute", "gbrs_paired_asm": "GCA_003097175.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/003/097/175/GCF_003097175.1_ASM309717v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "2814649", "genome_size_ungapped": "2814639", "gc_percent": "31.000000", "replicon_count": "0", "scaffold_count": "57", "contig_count": "57", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_003097175.1-RS_2024_04_12", "annotation_date": "2024-04-12", "total_gene_count": "2793", "protein_coding_gene_count": "2659", "non_coding_gene_count": "86", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2018-05-07", "dateModified": "2018-05-07", "datePublished": "2018-05-07", "_annotation": { "sample_count": 1, "sample_organism": [ "Clostridium thermopalmarium DSM 5974" ], "sample_taxid": [ "1121340" ], "sample_host_organism": [ "not applicable" ], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "Senegal: Casamance" ], "sample_host_location_id": [], "data_size": "0.777 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)": "2814649", "Number of Sequences": "57", "Longest Sequences (bp)": "196915", "N50 (bp)": "104894", "Gap Ratio (%)": "0.000355", "GCcontent (%)": "30.9", "Number of CDSs": "2686", "Average Protein Length": "302.7", "Coding Ratio (%)": "86.7", "Number of rRNAs": "9", "Number of tRNAs": "56", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Clostridium thermopalmarium", "strain": "strain=DSM 5974", "accession": "GCA_003097175.1", "taxid": 29373, "species_taxid": 29373, "relation_to_type": "suspected-type", "validated": true, "ani": 100.0, "matched_fragments": 905, "total_fragments": 909, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Clostridium thermopalmarium", "strain": "strain=DSM 5974", "accession": "GCA_002995795.1", "taxid": 29373, "species_taxid": 29373, "relation_to_type": "suspected-type", "validated": true, "ani": 99.9849, "matched_fragments": 889, "total_fragments": 909, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Clostridium massiliodielmoense", "strain": "strain=MT26", "accession": "GCA_900176615.1", "taxid": 1776385, "species_taxid": 1776385, "relation_to_type": "type", "validated": true, "ani": 78.3838, "matched_fragments": 265, "total_fragments": 909, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Clostridium homopropionicum", "strain": "strain=DSM 5847", "accession": "GCA_900113195.1", "taxid": 36844, "species_taxid": 36844, "relation_to_type": "type", "validated": true, "ani": 78.125, "matched_fragments": 260, "total_fragments": 909, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Clostridium homopropionicum", "strain": "strain=DSM 5847", "accession": "GCA_001263795.1", "taxid": 36844, "species_taxid": 36844, "relation_to_type": "type", "validated": true, "ani": 78.1005, "matched_fragments": 257, "total_fragments": 909, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Clostridium oryzae", "strain": "strain=DSM 28571", "accession": "GCA_002029235.1", "taxid": 1450648, "species_taxid": 1450648, "relation_to_type": "type", "validated": true, "ani": 77.2879, "matched_fragments": 82, "total_fragments": 909, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Clostridium drakei", "strain": "strain=SL1", "accession": "GCA_003096175.1", "taxid": 332101, "species_taxid": 332101, "relation_to_type": "type", "validated": true, "ani": 76.7657, "matched_fragments": 193, "total_fragments": 909, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Clostridium drakei", "strain": "strain=SL1", "accession": "GCA_000633595.2", "taxid": 332101, "species_taxid": 332101, "relation_to_type": "type", "validated": true, "ani": 76.7444, "matched_fragments": 179, "total_fragments": 909, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Clostridium faecium", "strain": "strain=N37", "accession": "GCA_014836835.1", "taxid": 2762223, "species_taxid": 2762223, "relation_to_type": "type", "validated": true, "ani": 76.5226, "matched_fragments": 136, "total_fragments": 909, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Clostridium cochlearium", "strain": "strain=NCTC13027", "accession": "GCA_900187165.1", "taxid": 1494, "species_taxid": 1494, "relation_to_type": "type", "validated": true, "ani": 76.3572, "matched_fragments": 128, "total_fragments": 909, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Clostridium thailandense", "strain": "strain=PL3", "accession": "GCA_019207025.1", "taxid": 2794346, "species_taxid": 2794346, "relation_to_type": "type", "validated": true, "ani": 76.3364, "matched_fragments": 133, "total_fragments": 909, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Clostridium mobile", "strain": "strain=MSJ-11", "accession": "GCA_018918285.1", "taxid": 2841512, "species_taxid": 2841512, "relation_to_type": "type", "validated": true, "ani": 76.3362, "matched_fragments": 124, "total_fragments": 909, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Clostridium rectalis", "strain": "strain=Marseille-P4200", "accession": "GCA_900626095.1", "taxid": 2040295, "species_taxid": 2040295, "relation_to_type": "type", "validated": true, "ani": 76.3239, "matched_fragments": 136, "total_fragments": 909, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Clostridium felsineum", "strain": "strain=DSM 793", "accession": "GCA_002006235.2", "taxid": 36839, "species_taxid": 36839, "relation_to_type": "type", "validated": true, "ani": 76.3086, "matched_fragments": 125, "total_fragments": 909, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Clostridium felsineum", "strain": "strain=DSM 7320", "accession": "GCA_002006215.2", "taxid": 36839, "species_taxid": 36839, "relation_to_type": "type", "validated": true, "ani": 76.2654, "matched_fragments": 119, "total_fragments": 909, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Clostridium felsineum", "strain": "strain=DSM 794", "accession": "GCA_002006355.2", "taxid": 36839, "species_taxid": 36839, "relation_to_type": "type", "validated": true, "ani": 76.2378, "matched_fragments": 111, "total_fragments": 909, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Clostridium collagenovorans", "strain": "strain=DSM 3089", "accession": "GCA_900130005.1", "taxid": 29357, "species_taxid": 29357, "relation_to_type": "type", "validated": true, "ani": 76.1548, "matched_fragments": 81, "total_fragments": 909, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Clostridium arbusti", "strain": "strain=SL206", "accession": "GCA_000246895.2", "taxid": 1137848, "species_taxid": 1137848, "relation_to_type": "type", "validated": true, "ani": 76.1526, "matched_fragments": 104, "total_fragments": 909, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Clostridium fungisolvens", "strain": "strain=TW1", "accession": "GCA_014193895.1", "taxid": 1604897, "species_taxid": 1604897, "relation_to_type": "type", "validated": true, "ani": 76.1229, "matched_fragments": 100, "total_fragments": 909, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sarcina ventriculi", "strain": "strain=NCTC12966", "accession": "GCA_900456775.1", "taxid": 1267, "species_taxid": 1267, "relation_to_type": "type", "validated": true, "ani": 75.9825, "matched_fragments": 104, "total_fragments": 909, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Clostridium akagii", "strain": "strain=DSM 12554", "accession": "GCA_000686725.1", "taxid": 91623, "species_taxid": 91623, "relation_to_type": "type", "validated": true, "ani": 75.8632, "matched_fragments": 98, "total_fragments": 909, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_002995795.1", "gtdb_species": "s__Clostridium_H thermopalmarium", "ani": 99.9849, "matched_fragments": 889, "total_fragments": 909, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_H", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.57", "min_intra_species_ani": "99.32", "mean_intra_species_af": "0.95", "min_intra_species_af": "0.92", "num_clustered_genomes": 4, "status": "conclusive" }, { "accession": "GCA_009738435.1", "gtdb_species": "s__Clostridium_H bovifaecis", "ani": 81.3873, "matched_fragments": 591, "total_fragments": 909, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_H", "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_003614235.1", "gtdb_species": "s__Clostridium_H haemolyticum", "ani": 78.4012, "matched_fragments": 265, "total_fragments": 909, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_H", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.44", "min_intra_species_ani": "97.38", "mean_intra_species_af": "0.90", "min_intra_species_af": "0.84", "num_clustered_genomes": 13, "status": "-" }, { "accession": "GCF_900176615.1", "gtdb_species": "s__Clostridium_H massiliodielmoense", "ani": 78.3838, "matched_fragments": 265, "total_fragments": 909, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_H", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.64", "min_intra_species_ani": "96.44", "mean_intra_species_af": "0.92", "min_intra_species_af": "0.87", "num_clustered_genomes": 5, "status": "-" }, { "accession": "GCF_000014125.1", "gtdb_species": "s__Clostridium_H novyi", "ani": 78.33, "matched_fragments": 278, "total_fragments": 909, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_H", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.92", "min_intra_species_ani": "96.35", "mean_intra_species_af": "0.94", "min_intra_species_af": "0.92", "num_clustered_genomes": 7, "status": "-" }, { "accession": "GCF_017100085.1", "gtdb_species": "s__Clostridium_H botulinum_A", "ani": 78.2719, "matched_fragments": 277, "total_fragments": 909, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_H", "ani_circumscription_radius": 95.0162, "mean_intra_species_ani": "99.30", "min_intra_species_ani": "99.03", "mean_intra_species_af": "0.94", "min_intra_species_af": "0.90", "num_clustered_genomes": 14, "status": "-" }, { "accession": "GCF_000204565.1", "gtdb_species": "s__Clostridium_H botulinum_B", "ani": 78.1172, "matched_fragments": 297, "total_fragments": 909, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_H", "ani_circumscription_radius": 95.0162, "mean_intra_species_ani": "99.87", "min_intra_species_ani": "99.52", "mean_intra_species_af": "0.98", "min_intra_species_af": "0.95", "num_clustered_genomes": 19, "status": "-" }, { "accession": "GCF_001263795.1", "gtdb_species": "s__Clostridium_H homopropionicum", "ani": 78.1016, "matched_fragments": 258, "total_fragments": 909, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_H", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "100.00", "min_intra_species_ani": "100.00", "mean_intra_species_af": "0.99", "min_intra_species_af": "0.99", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_000968375.1", "gtdb_species": "s__Clostridium_AM scatologenes", "ani": 76.7852, "matched_fragments": 185, "total_fragments": 909, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_AM", "ani_circumscription_radius": 96.092, "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_000633595.2", "gtdb_species": "s__Clostridium_AM drakei", "ani": 76.7571, "matched_fragments": 178, "total_fragments": 909, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_AM", "ani_circumscription_radius": 96.092, "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_000816675.1", "gtdb_species": "s__Clostridium_J argentinense", "ani": 76.1453, "matched_fragments": 139, "total_fragments": 909, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_J", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.28", "min_intra_species_ani": "97.50", "mean_intra_species_af": "0.97", "min_intra_species_af": "0.91", "num_clustered_genomes": 8, "status": "-" }, { "accession": "GCF_000612845.1", "gtdb_species": "s__Clostridium_J ihumii", "ani": 76.0998, "matched_fragments": 129, "total_fragments": 909, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_J", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "100.00", "min_intra_species_ani": "100.00", "mean_intra_species_af": "0.99", "min_intra_species_af": "0.99", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_002006345.1", "gtdb_species": "s__Clostridium puniceum", "ani": 76.0194, "matched_fragments": 121, "total_fragments": 909, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium", "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_004794105.1", "gtdb_species": "s__Clostridium sartagoforme_B", "ani": 75.935, "matched_fragments": 104, "total_fragments": 909, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.58", "min_intra_species_ani": "98.58", "mean_intra_species_af": "0.90", "min_intra_species_af": "0.90", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCA_002341865.1", "gtdb_species": "s__Clostridium_J sp002341865", "ani": 75.9162, "matched_fragments": 123, "total_fragments": 909, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_J", "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": -0.155, "cell_length": 0.301, "doubling_h": 0.353, "growth_tmp": 55.0, "optimum_tmp": 55.0, "optimum_ph": 6.947, "genome_size": 2814649.0, "gc_content": 29.49, "coding_genes": 3796.985, "rRNA16S_genes": 9.374, "tRNA_genes": 78.312, "gram_stain": 1.0, "sporulation": 1.0, "motility": 0.0, "range_salinity": 0.0, "facultative_respiration": 0.0, "anaerobic_respiration": 1.0, "aerobic_respiration": 0.0, "mesophilic_range_tmp": 0.944, "thermophilic_range_tmp": 0.055, "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": [ "Clostridium", "thermopalmarium", "DSM", "5974" ], "quality": 4, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }