{ "type": "genome", "identifier": "GCF_001047375.1", "organism": "Clostridium cylindrosporum DSM 605", "title": "Clostridium cylindrosporum DSM 605", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Goettingen Genomics Laboratory", "publication": [ {} ], "properties": { "assembly_accession": "GCF_001047375.1", "bioproject": "PRJNA224116", "biosample": "SAMN03794733", "wgs_master": "LFVU00000000.1", "refseq_category": "reference genome", "taxid": "1121307", "species_taxid": "1495", "organism_name": "Clostridium cylindrosporum DSM 605", "infraspecific_name": "strain=DSM 605", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2015/07/07", "asm_name": "ASM104737v1", "asm_submitter": "Goettingen Genomics Laboratory", "gbrs_paired_asm": "GCA_001047375.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/001/047/375/GCF_001047375.1_ASM104737v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "2735032", "genome_size_ungapped": "2735032", "gc_percent": "31.500000", "replicon_count": "0", "scaffold_count": "28", "contig_count": "28", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_001047375.1-RS_2024_04_12", "annotation_date": "2024-04-12", "total_gene_count": "2708", "protein_coding_gene_count": "2613", "non_coding_gene_count": "81", "pubmed_id": "26272578" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2015-07-07", "dateModified": "2015-07-07", "datePublished": "2015-07-07", "_annotation": { "sample_count": 1, "sample_organism": [ "Clostridium cylindrosporum DSM 605" ], "sample_taxid": [ "1121307" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "not collected" ], "sample_host_location_id": [], "data_size": "0.752 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)": "2735032", "Number of Sequences": "28", "Longest Sequences (bp)": "501278", "N50 (bp)": "302301", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "31.4", "Number of CDSs": "2647", "Average Protein Length": "299.3", "Coding Ratio (%)": "86.9", "Number of rRNAs": "6", "Number of tRNAs": "67", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Clostridium cylindrosporum", "strain": "strain=DSM 605", "accession": "GCA_001047375.1", "taxid": 1495, "species_taxid": 1495, "relation_to_type": "type", "validated": true, "ani": 99.9718, "matched_fragments": 901, "total_fragments": 902, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Clostridium niameyense", "strain": "strain=MT5", "accession": "GCA_001243045.1", "taxid": 1622073, "species_taxid": 1622073, "relation_to_type": "type", "validated": true, "ani": 76.2676, "matched_fragments": 60, "total_fragments": 902, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Clostridium paraputrificum", "strain": "strain=NCTC11833", "accession": "GCA_900447045.1", "taxid": 29363, "species_taxid": 29363, "relation_to_type": "type", "validated": true, "ani": 76.2293, "matched_fragments": 56, "total_fragments": 902, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Caloramator australicus", "strain": "strain=RC3", "accession": "GCA_000297115.1", "taxid": 515264, "species_taxid": 515264, "relation_to_type": "type", "validated": true, "ani": 75.9813, "matched_fragments": 53, "total_fragments": 902, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Clostridium perfringens", "strain": "strain=FDAARGOS_903", "accession": "GCA_016027375.1", "taxid": 1502, "species_taxid": 1502, "relation_to_type": "type", "validated": true, "ani": 75.9761, "matched_fragments": 71, "total_fragments": 902, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Clostridium magnum", "strain": "strain=DSM 2767", "accession": "GCA_001623875.1", "taxid": 33954, "species_taxid": 33954, "relation_to_type": "type", "validated": true, "ani": 75.969, "matched_fragments": 78, "total_fragments": 902, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Clostridium perfringens", "strain": "strain=ATCC 13124", "accession": "GCA_000013285.1", "taxid": 1502, "species_taxid": 1502, "relation_to_type": "type", "validated": true, "ani": 75.9376, "matched_fragments": 66, "total_fragments": 902, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Clostridium nigeriense", "strain": "strain=Marseille-P2414", "accession": "GCA_900086595.1", "taxid": 1805470, "species_taxid": 1805470, "relation_to_type": "type", "validated": true, "ani": 75.9212, "matched_fragments": 77, "total_fragments": 902, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Clostridium pasteurianum", "strain": "strain=ATCC 6013", "accession": "GCA_001856645.1", "taxid": 1501, "species_taxid": 1501, "relation_to_type": "type", "validated": true, "ani": 75.8795, "matched_fragments": 56, "total_fragments": 902, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Clostridium pasteurianum", "strain": "strain=DSM 525", "accession": "GCA_000807255.1", "taxid": 1501, "species_taxid": 1501, "relation_to_type": "type", "validated": true, "ani": 75.8348, "matched_fragments": 58, "total_fragments": 902, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Clostridium pasteurianum", "strain": "strain=DSM 525", "accession": "GCA_000330945.1", "taxid": 1501, "species_taxid": 1501, "relation_to_type": "type", "validated": true, "ani": 75.8183, "matched_fragments": 57, "total_fragments": 902, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Clostridium hydrogeniformans", "strain": "strain=DSM 21757", "accession": "GCA_000686705.1", "taxid": 349933, "species_taxid": 349933, "relation_to_type": "type", "validated": true, "ani": 75.7785, "matched_fragments": 81, "total_fragments": 902, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Clostridium magnum", "strain": "strain=DSM 2767", "accession": "GCA_900129955.1", "taxid": 33954, "species_taxid": 33954, "relation_to_type": "type", "validated": true, "ani": 75.5848, "matched_fragments": 75, "total_fragments": 902, "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": 75.5463, "matched_fragments": 57, "total_fragments": 902, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Clostridium lundense", "strain": "strain=DSM 17049", "accession": "GCA_000619945.1", "taxid": 319475, "species_taxid": 319475, "relation_to_type": "type", "validated": true, "ani": 75.5313, "matched_fragments": 65, "total_fragments": 902, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_001047375.1", "gtdb_species": "s__Clostridium_AB cylindrosporum", "ani": 100.0, "matched_fragments": 900, "total_fragments": 902, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Caloramatoraceae;g__Clostridium_AB", "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": "GCF_000430995.1", "gtdb_species": "s__Thermobrachium celere", "ani": 77.288, "matched_fragments": 68, "total_fragments": 902, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Caloramatoraceae;g__Thermobrachium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.16", "min_intra_species_ani": "98.16", "mean_intra_species_af": "0.91", "min_intra_species_af": "0.91", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_017100085.1", "gtdb_species": "s__Clostridium_H botulinum_A", "ani": 76.3899, "matched_fragments": 50, "total_fragments": 902, "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_016908015.1", "gtdb_species": "s__Clostridium_AK pascui", "ani": 76.3204, "matched_fragments": 52, "total_fragments": 902, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_AK", "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_001243045.1", "gtdb_species": "s__Clostridium_F niameyense", "ani": 76.2968, "matched_fragments": 59, "total_fragments": 902, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_F", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.56", "min_intra_species_ani": "99.11", "mean_intra_species_af": "0.96", "min_intra_species_af": "0.92", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_006016075.1", "gtdb_species": "s__Caloramator_B sp006016075", "ani": 76.2438, "matched_fragments": 63, "total_fragments": 902, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Caloramatoraceae;g__Caloramator_B", "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_900447045.1", "gtdb_species": "s__Clostridium paraputrificum", "ani": 76.2292, "matched_fragments": 56, "total_fragments": 902, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.58", "min_intra_species_ani": "95.42", "mean_intra_species_af": "0.89", "min_intra_species_af": "0.83", "num_clustered_genomes": 29, "status": "-" }, { "accession": "GCF_000297115.1", "gtdb_species": "s__Caloramator australicus", "ani": 75.9813, "matched_fragments": 53, "total_fragments": 902, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Caloramatoraceae;g__Caloramator", "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_000204565.1", "gtdb_species": "s__Clostridium_H botulinum_B", "ani": 75.9717, "matched_fragments": 54, "total_fragments": 902, "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_000013285.1", "gtdb_species": "s__Clostridium_P perfringens", "ani": 75.9376, "matched_fragments": 66, "total_fragments": 902, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_P", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.05", "min_intra_species_ani": "95.74", "mean_intra_species_af": "0.91", "min_intra_species_af": "0.81", "num_clustered_genomes": 315, "status": "-" }, { "accession": "GCF_000686705.1", "gtdb_species": "s__Clostridium_Z hydrogeniformans", "ani": 75.7628, "matched_fragments": 82, "total_fragments": 902, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_Z", "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": 75.6878, "matched_fragments": 79, "total_fragments": 902, "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": "GCF_000619945.1", "gtdb_species": "s__Clostridium_AO lundense", "ani": 75.5606, "matched_fragments": 63, "total_fragments": 902, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_AO", "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_000246895.1", "gtdb_species": "s__Clostridium_I arbusti", "ani": 75.5505, "matched_fragments": 57, "total_fragments": 902, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_I", "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": -0.097, "cell_length": 0.518, "doubling_h": 0.353, "growth_tmp": 37.0, "optimum_tmp": 42.5, "optimum_ph": 6.947, "genome_size": 2735032.0, "gc_content": 29.49, "coding_genes": 3796.985, "rRNA16S_genes": 9.374, "tRNA_genes": 78.312, "gram_stain": 1.0, "sporulation": 1.0, "motility": 1.0, "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", "cylindrosporum", "DSM", "605" ], "quality": 5, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }