{ "type": "genome", "identifier": "GCF_001856645.1", "organism": "Clostridium pasteurianum DSM 525 = ATCC 6013", "title": "Clostridium pasteurianum DSM 525 = ATCC 6013", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Papoutsakis Research Group", "publication": [ {} ], "properties": { "assembly_accession": "GCF_001856645.1", "bioproject": "PRJNA224116", "biosample": "SAMN04208873", "wgs_master": "na", "refseq_category": "reference genome", "taxid": "1262449", "species_taxid": "1501", "organism_name": "Clostridium pasteurianum DSM 525 = ATCC 6013", "infraspecific_name": "strain=ATCC 6013", "isolate": "na", "version_status": "latest", "assembly_level": "Complete Genome", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2016/10/31", "asm_name": "ASM185664v1", "asm_submitter": "Papoutsakis Research Group", "gbrs_paired_asm": "GCA_001856645.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/001/856/645/GCF_001856645.1_ASM185664v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "4352852", "genome_size_ungapped": "4352852", "gc_percent": "30.000000", "replicon_count": "1", "scaffold_count": "1", "contig_count": "1", "annotation_provider": "NCBI RefSeq", "annotation_name": "NCBI Prokaryotic Genome Annotation Pipeline (PGAP)", "annotation_date": "2024-03-04", "total_gene_count": "4112", "protein_coding_gene_count": "3934", "non_coding_gene_count": "116", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2016-10-31", "dateModified": "2016-10-31", "datePublished": "2016-10-31", "_annotation": { "sample_count": 1, "sample_organism": [ "Clostridium pasteurianum DSM 525 = ATCC 6013" ], "sample_taxid": [ "1262449" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "USA: Delaware" ], "sample_host_location_id": [], "data_size": "1.181 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)": "4352852", "Number of Sequences": "1", "Longest Sequences (bp)": "4352852", "N50 (bp)": "4352852", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "29.9", "Number of CDSs": "4023", "Average Protein Length": "297.6", "Coding Ratio (%)": "82.5", "Number of rRNAs": "30", "Number of tRNAs": "81", "Number of CRISPRs": "2" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Clostridium pasteurianum", "strain": "strain=ATCC 6013", "accession": "GCA_001856645.1", "taxid": 1501, "species_taxid": 1501, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1447, "total_fragments": 1450, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Clostridium pasteurianum", "strain": "strain=DSM 525", "accession": "GCA_000807255.1", "taxid": 1501, "species_taxid": 1501, "relation_to_type": "type", "validated": true, "ani": 99.9994, "matched_fragments": 1446, "total_fragments": 1450, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Clostridium pasteurianum", "strain": "strain=ATCC 6013", "accession": "GCA_000807175.1", "taxid": 1501, "species_taxid": 1501, "relation_to_type": "type", "validated": true, "ani": 99.9993, "matched_fragments": 1447, "total_fragments": 1450, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Clostridium pasteurianum", "strain": "strain=ATCC 6013", "accession": "GCA_000724205.3", "taxid": 1501, "species_taxid": 1501, "relation_to_type": "type", "validated": true, "ani": 99.9977, "matched_fragments": 1449, "total_fragments": 1450, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Clostridium pasteurianum", "strain": "strain=DSM 525", "accession": "GCA_000330945.1", "taxid": 1501, "species_taxid": 1501, "relation_to_type": "type", "validated": true, "ani": 99.978, "matched_fragments": 1400, "total_fragments": 1450, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Clostridium autoethanogenum", "strain": "strain=DSM 10061", "accession": "GCA_000484505.2", "taxid": 84023, "species_taxid": 84023, "relation_to_type": "suspected-type", "validated": true, "ani": 78.0524, "matched_fragments": 176, "total_fragments": 1450, "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": 77.933, "matched_fragments": 200, "total_fragments": 1450, "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": 77.6774, "matched_fragments": 203, "total_fragments": 1450, "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": 77.4028, "matched_fragments": 191, "total_fragments": 1450, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Defluviitalea phaphyphila", "strain": "strain=Alg1", "accession": "GCA_001466305.1", "taxid": 1473580, "species_taxid": 1473580, "relation_to_type": "type", "validated": true, "ani": 75.4573, "matched_fragments": 79, "total_fragments": 1450, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_000807255.1", "gtdb_species": "s__Clostridium_I pasteurianum", "ani": 99.9994, "matched_fragments": 1447, "total_fragments": 1450, "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": "99.98", "min_intra_species_ani": "99.90", "mean_intra_species_af": "1.00", "min_intra_species_af": "0.99", "num_clustered_genomes": 7, "status": "conclusive" }, { "accession": "GCF_000389635.1", "gtdb_species": "s__Clostridium_I pasteurianum_A", "ani": 82.672, "matched_fragments": 895, "total_fragments": 1450, "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": "-" }, { "accession": "GCF_000246895.1", "gtdb_species": "s__Clostridium_I arbusti", "ani": 81.6415, "matched_fragments": 767, "total_fragments": 1450, "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": "-" }, { "accession": "GCF_900176305.1", "gtdb_species": "s__Clostridium_I acidisoli", "ani": 78.0433, "matched_fragments": 305, "total_fragments": 1450, "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": "-" }, { "accession": "GCF_001038625.1", "gtdb_species": "s__Clostridium_AM carboxidivorans", "ani": 77.664, "matched_fragments": 249, "total_fragments": 1450, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_AM", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.97", "min_intra_species_ani": "99.96", "mean_intra_species_af": "1.00", "min_intra_species_af": "0.99", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_000686725.1", "gtdb_species": "s__Clostridium_I akagii", "ani": 77.4481, "matched_fragments": 269, "total_fragments": 1450, "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": "-" }, { "accession": "GCF_001705235.1", "gtdb_species": "s__Clostridium_S pasteurianum_A", "ani": 77.2763, "matched_fragments": 195, "total_fragments": 1450, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_S", "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_012926525.1", "gtdb_species": "s__Clostridium_AM sp012926525", "ani": 76.7502, "matched_fragments": 241, "total_fragments": 1450, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_AM", "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_017873215.1", "gtdb_species": "s__Clostridium_AO tetanomorphum", "ani": 76.3503, "matched_fragments": 172, "total_fragments": 1450, "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": "99.85", "min_intra_species_ani": "99.71", "mean_intra_species_af": "0.98", "min_intra_species_af": "0.97", "num_clustered_genomes": 5, "status": "-" }, { "accession": "GCF_001758365.1", "gtdb_species": "s__Clostridium_C acetireducens", "ani": 76.3133, "matched_fragments": 162, "total_fragments": 1450, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_C", "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": 76.2957, "matched_fragments": 146, "total_fragments": 1450, "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_007115085.1", "gtdb_species": "s__Clostridium sp007115085", "ani": 76.2244, "matched_fragments": 121, "total_fragments": 1450, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.42", "min_intra_species_ani": "99.42", "mean_intra_species_af": "0.90", "min_intra_species_af": "0.90", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCA_015058405.1", "gtdb_species": "s__Clostridium sp015058405", "ani": 75.377, "matched_fragments": 102, "total_fragments": 1450, "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": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": -0.302, "cell_length": 0.431, "doubling_h": 0.353, "growth_tmp": 36.0, "optimum_tmp": 30.8, "optimum_ph": 6.947, "genome_size": 4520248.864, "gc_content": 29.933, "coding_genes": 4052.7, "rRNA16S_genes": 9.6, "tRNA_genes": 79.0, "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": 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": [ "Clostridium", "pasteurianum", "DSM", "525", "=", "ATCC", "6013" ], "quality": 5, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }