{ "type": "genome", "identifier": "GCF_900111365.1", "organism": "Propionibacterium cyclohexanicum", "title": "Propionibacterium cyclohexanicum", "description": "na", "data type": "Genome sequencing and assembly", "organization": "DOE - JOINT GENOME INSTITUTE", "publication": [ {} ], "properties": { "assembly_accession": "GCF_900111365.1", "bioproject": "PRJNA224116", "biosample": "SAMN05443377", "wgs_master": "FOGZ00000000.1", "refseq_category": "reference genome", "taxid": "64702", "species_taxid": "64702", "organism_name": "Propionibacterium cyclohexanicum", "infraspecific_name": "strain=DSM 16859", "isolate": "na", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2016/10/31", "asm_name": "IMG-taxon 2675903216 annotated assembly", "asm_submitter": "DOE - JOINT GENOME INSTITUTE", "gbrs_paired_asm": "GCA_900111365.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/900/111/365/GCF_900111365.1_IMG-taxon_2675903216_annotated_assembly", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "2808950", "genome_size_ungapped": "2808867", "gc_percent": "67.000000", "replicon_count": "0", "scaffold_count": "58", "contig_count": "58", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_900111365.1-RS_2024_05_03", "annotation_date": "2024-05-03", "total_gene_count": "2551", "protein_coding_gene_count": "2465", "non_coding_gene_count": "51", "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": [ "Propionibacterium cyclohexanicum DSM 16859" ], "sample_taxid": [ "1122996" ], "sample_host_organism": [ "not applicable" ], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "Japan" ], "sample_host_location_id": [], "data_size": "0.776 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)": "2808950", "Number of Sequences": "58", "Longest Sequences (bp)": "261630", "N50 (bp)": "91355", "Gap Ratio (%)": "0.002955", "GCcontent (%)": "66.9", "Number of CDSs": "2539", "Average Protein Length": "328.3", "Coding Ratio (%)": "89.0", "Number of rRNAs": "3", "Number of tRNAs": "45", "Number of CRISPRs": "2" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Propionibacterium cyclohexanicum", "strain": "strain=DSM 16859", "accession": "GCA_900111365.1", "taxid": 64702, "species_taxid": 64702, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 906, "total_fragments": 907, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Propionibacterium acidifaciens", "strain": "strain=DSM 21887", "accession": "GCA_000426605.1", "taxid": 556499, "species_taxid": 556499, "relation_to_type": "type", "validated": true, "ani": 78.8961, "matched_fragments": 319, "total_fragments": 907, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Propionibacterium freudenreichii subsp. freudenreichii", "strain": "strain=DSM 20271", "accession": "GCA_000940845.1", "taxid": 66712, "species_taxid": 1744, "relation_to_type": "type", "validated": true, "ani": 78.5458, "matched_fragments": 336, "total_fragments": 907, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Propionibacterium australiense", "strain": "strain=NCTC13651", "accession": "GCA_900637915.1", "taxid": 119981, "species_taxid": 119981, "relation_to_type": "type", "validated": true, "ani": 78.4783, "matched_fragments": 299, "total_fragments": 907, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Propionibacterium australiense", "strain": "strain=NML98A072", "accession": "GCA_003666605.1", "taxid": 119981, "species_taxid": 119981, "relation_to_type": "type", "validated": true, "ani": 78.4596, "matched_fragments": 298, "total_fragments": 907, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Acidipropionibacterium jensenii", "strain": "strain=DSM 20535", "accession": "GCA_000425285.1", "taxid": 1749, "species_taxid": 1749, "relation_to_type": "type", "validated": true, "ani": 77.2394, "matched_fragments": 195, "total_fragments": 907, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Propioniciclava coleopterorum", "strain": "strain=HDW11", "accession": "GCA_011393335.1", "taxid": 2714937, "species_taxid": 2714937, "relation_to_type": "type", "validated": true, "ani": 76.8777, "matched_fragments": 190, "total_fragments": 907, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Desertihabitans brevis", "strain": "strain=16Sb5-5", "accession": "GCA_003327535.1", "taxid": 2268447, "species_taxid": 2268447, "relation_to_type": "type", "validated": true, "ani": 76.6638, "matched_fragments": 174, "total_fragments": 907, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Tessaracoccus lapidicaptus", "strain": "strain=IPBSL-7", "accession": "GCA_001693815.1", "taxid": 1427523, "species_taxid": 1427523, "relation_to_type": "type", "validated": true, "ani": 76.6489, "matched_fragments": 146, "total_fragments": 907, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Desertihabitans aurantiacus", "strain": "strain=CPCC 204711", "accession": "GCA_003344635.1", "taxid": 2282477, "species_taxid": 2282477, "relation_to_type": "type", "validated": true, "ani": 76.5353, "matched_fragments": 163, "total_fragments": 907, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Nocardioides baculatus", "strain": "strain=G10", "accession": "GCA_016735675.1", "taxid": 2801337, "species_taxid": 2801337, "relation_to_type": "type", "validated": true, "ani": 76.2873, "matched_fragments": 118, "total_fragments": 907, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Nocardioides carbamazepini", "strain": "strain=CBZ_1", "accession": "GCA_024614185.1", "taxid": 2854259, "species_taxid": 2854259, "relation_to_type": "type", "validated": true, "ani": 75.9857, "matched_fragments": 146, "total_fragments": 907, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Janibacter endophyticus", "strain": "strain=YIM B02568", "accession": "GCA_016888335.1", "taxid": 2806261, "species_taxid": 2806261, "relation_to_type": "type", "validated": true, "ani": 75.9059, "matched_fragments": 110, "total_fragments": 907, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Nocardiopsis valliformis", "strain": "strain=DSM 45023", "accession": "GCA_000340985.1", "taxid": 239974, "species_taxid": 239974, "relation_to_type": "type", "validated": true, "ani": 75.6226, "matched_fragments": 92, "total_fragments": 907, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Streptomyces coryli", "strain": "strain=A7024", "accession": "GCA_011044975.1", "taxid": 1128680, "species_taxid": 1128680, "relation_to_type": "type", "validated": true, "ani": 75.5246, "matched_fragments": 135, "total_fragments": 907, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Nonomuraea roseoviolacea subsp. carminata", "strain": "strain=DSM 44170", "accession": "GCA_024172185.1", "taxid": 160689, "species_taxid": 103837, "relation_to_type": "type", "validated": true, "ani": 75.5051, "matched_fragments": 152, "total_fragments": 907, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Nocardiopsis exhalans", "strain": "strain=JCM11759T", "accession": "GCA_024134545.1", "taxid": 163604, "species_taxid": 163604, "relation_to_type": "type", "validated": true, "ani": 75.419, "matched_fragments": 113, "total_fragments": 907, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_900111365.1", "gtdb_species": "s__Propionibacterium cyclohexanicum", "ani": 100.0, "matched_fragments": 906, "total_fragments": 907, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Propionibacterium", "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_000426605.1", "gtdb_species": "s__Propionibacterium acidifaciens", "ani": 78.8439, "matched_fragments": 323, "total_fragments": 907, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Propionibacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.24", "min_intra_species_ani": "99.02", "mean_intra_species_af": "0.93", "min_intra_species_af": "0.90", "num_clustered_genomes": 4, "status": "-" }, { "accession": "GCF_900289195.1", "gtdb_species": "s__Propionibacterium sp900289195", "ani": 78.5571, "matched_fragments": 270, "total_fragments": 907, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Propionibacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.03", "min_intra_species_ani": "99.03", "mean_intra_species_af": "0.94", "min_intra_species_af": "0.94", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_000940845.1", "gtdb_species": "s__Propionibacterium freudenreichii", "ani": 78.5442, "matched_fragments": 336, "total_fragments": 907, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Propionibacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.89", "min_intra_species_ani": "98.71", "mean_intra_species_af": "0.93", "min_intra_species_af": "0.90", "num_clustered_genomes": 43, "status": "-" }, { "accession": "GCF_003666605.1", "gtdb_species": "s__Propionibacterium australiense", "ani": 78.4676, "matched_fragments": 298, "total_fragments": 907, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Propionibacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.91", "min_intra_species_ani": "99.75", "mean_intra_species_af": "0.98", "min_intra_species_af": "0.97", "num_clustered_genomes": 4, "status": "-" }, { "accession": "GCF_000425285.1", "gtdb_species": "s__Acidipropionibacterium jensenii", "ani": 77.2541, "matched_fragments": 194, "total_fragments": 907, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Acidipropionibacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.58", "min_intra_species_ani": "97.66", "mean_intra_species_af": "0.92", "min_intra_species_af": "0.89", "num_clustered_genomes": 5, "status": "-" }, { "accession": "GCF_001693815.1", "gtdb_species": "s__Arachnia lapidicapta", "ani": 76.6489, "matched_fragments": 146, "total_fragments": 907, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Arachnia", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.86", "min_intra_species_ani": "97.76", "mean_intra_species_af": "0.95", "min_intra_species_af": "0.93", "num_clustered_genomes": 4, "status": "-" }, { "accession": "GCF_003344635.1", "gtdb_species": "s__Desertihabitans aurantiacus", "ani": 76.5228, "matched_fragments": 164, "total_fragments": 907, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Desertihabitans", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "95.17", "min_intra_species_ani": "95.17", "mean_intra_species_af": "0.87", "min_intra_species_af": "0.87", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCA_012517965.1", "gtdb_species": "s__Propioniciclava sp012517965", "ani": 76.4089, "matched_fragments": 133, "total_fragments": 907, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Propioniciclava", "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_012837465.1", "gtdb_species": "s__Arachnia sp012837465", "ani": 76.3971, "matched_fragments": 119, "total_fragments": 907, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Arachnia", "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_013778305.1", "gtdb_species": "s__Nocardioides sp013778305", "ani": 76.0959, "matched_fragments": 142, "total_fragments": 907, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides", "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_000426525.1", "gtdb_species": "s__Nocardioides alkalitolerans", "ani": 75.7987, "matched_fragments": 133, "total_fragments": 907, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides", "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_000340985.1", "gtdb_species": "s__Nocardiopsis valliformis", "ani": 75.6124, "matched_fragments": 93, "total_fragments": 907, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis", "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": 0.041, "cell_length": 0.176, "doubling_h": null, "growth_tmp": 37.0, "optimum_tmp": 35.0, "optimum_ph": 7.2, "genome_size": 2808950.0, "gc_content": 57.416, "coding_genes": 2891.269, "rRNA16S_genes": 2.0, "tRNA_genes": 44.0, "gram_stain": 1.0, "sporulation": 0.0, "motility": 0.0, "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": [ "Propionibacterium", "cyclohexanicum" ], "quality": 4, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }