{ "type": "genome", "identifier": "GCF_004000825.1", "organism": "Paenibacillus kobensis NBRC 15729", "title": "Paenibacillus kobensis NBRC 15729", "description": "na", "data type": "Genome sequencing and assembly", "organization": "National Institute of Technology and Evaluation", "publication": [ {} ], "properties": { "assembly_accession": "GCF_004000825.1", "bioproject": "PRJNA224116", "biosample": "SAMD00034168", "wgs_master": "BILZ00000000.1", "refseq_category": "reference genome", "taxid": "1220566", "species_taxid": "59841", "organism_name": "Paenibacillus kobensis NBRC 15729", "infraspecific_name": "strain=NBRC 15729", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2018/12/29", "asm_name": "ASM400082v1", "asm_submitter": "National Institute of Technology and Evaluation", "gbrs_paired_asm": "GCA_004000825.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/004/000/825/GCF_004000825.1_ASM400082v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "6469217", "genome_size_ungapped": "6469217", "gc_percent": "52.000000", "replicon_count": "0", "scaffold_count": "167", "contig_count": "167", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_004000825.1-RS_2024_12_09", "annotation_date": "2024-12-09", "total_gene_count": "5795", "protein_coding_gene_count": "5665", "non_coding_gene_count": "44", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2018-12-29", "dateModified": "2018-12-29", "datePublished": "2018-12-29", "_annotation": { "sample_count": 1, "sample_organism": [ "Paenibacillus kobensis NBRC 15729" ], "sample_taxid": [ "1220566" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "Japan:Hyogo, Kobe" ], "sample_host_location_id": [], "data_size": "1.845 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)": "6469217", "Number of Sequences": "167", "Longest Sequences (bp)": "397820", "N50 (bp)": "89259", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "52.2", "Number of CDSs": "5692", "Average Protein Length": "321.2", "Coding Ratio (%)": "84.8", "Number of rRNAs": "0", "Number of tRNAs": "40", "Number of CRISPRs": "2" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Paenibacillus kobensis", "strain": "strain=NBRC 15729", "accession": "GCA_004000825.1", "taxid": 59841, "species_taxid": 59841, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 2067, "total_fragments": 2076, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Paenibacillus xylaniclasticus", "strain": "strain=NBRC 106381", "accession": "GCA_004001065.1", "taxid": 588083, "species_taxid": 588083, "relation_to_type": "type", "validated": true, "ani": 81.9751, "matched_fragments": 904, "total_fragments": 2076, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Paenibacillus cellulosilyticus", "strain": "strain=CECT 5696", "accession": "GCA_003182255.1", "taxid": 375489, "species_taxid": 375489, "relation_to_type": "type", "validated": true, "ani": 79.7024, "matched_fragments": 670, "total_fragments": 2076, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Paenibacillus curdlanolyticus", "strain": "strain=YK9", "accession": "GCA_000179615.1", "taxid": 59840, "species_taxid": 59840, "relation_to_type": "type", "validated": true, "ani": 79.3449, "matched_fragments": 593, "total_fragments": 2076, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Paenibacillus glycanilyticus subsp. hiroshimensis", "strain": "strain=CCI5", "accession": "GCA_015473105.1", "taxid": 2805378, "species_taxid": 126569, "relation_to_type": "type", "validated": true, "ani": 77.9168, "matched_fragments": 254, "total_fragments": 2076, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Paenibacillus methanolicus", "strain": "strain=BL24", "accession": "GCA_008124765.1", "taxid": 582686, "species_taxid": 582686, "relation_to_type": "type", "validated": true, "ani": 77.7405, "matched_fragments": 318, "total_fragments": 2076, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Paenibacillus glycanilyticus", "strain": "strain=NBRC 16618", "accession": "GCA_004000805.1", "taxid": 126569, "species_taxid": 126569, "relation_to_type": "type", "validated": true, "ani": 77.6973, "matched_fragments": 262, "total_fragments": 2076, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Paenibacillus albus", "strain": "strain=18JY67-1", "accession": "GCA_003952225.1", "taxid": 2495582, "species_taxid": 2495582, "relation_to_type": "type", "validated": true, "ani": 77.5987, "matched_fragments": 231, "total_fragments": 2076, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Paenibacillus lycopersici", "strain": "strain=12200R-189", "accession": "GCA_010119935.1", "taxid": 2704462, "species_taxid": 2704462, "relation_to_type": "type", "validated": true, "ani": 77.5438, "matched_fragments": 318, "total_fragments": 2076, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Paenibacillus taihuensis", "strain": "strain=CGMCC 1.10966", "accession": "GCA_003386535.1", "taxid": 1156355, "species_taxid": 1156355, "relation_to_type": "type", "validated": true, "ani": 77.4632, "matched_fragments": 257, "total_fragments": 2076, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Paenibacillus artemisiicola", "strain": "strain=MWE-103", "accession": "GCA_017652985.1", "taxid": 1172618, "species_taxid": 1172618, "relation_to_type": "type", "validated": true, "ani": 77.4118, "matched_fragments": 289, "total_fragments": 2076, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Paenibacillus gorillae", "strain": "", "accession": "GCA_000513275.1", "taxid": 1243662, "species_taxid": 1243662, "relation_to_type": "type", "validated": true, "ani": 77.3848, "matched_fragments": 203, "total_fragments": 2076, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Paenibacillus glycinis", "strain": "strain=T1", "accession": "GCA_009909185.1", "taxid": 2697035, "species_taxid": 2697035, "relation_to_type": "type", "validated": true, "ani": 77.2728, "matched_fragments": 277, "total_fragments": 2076, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Paenibacillus darwinianus", "strain": "strain=Br", "accession": "GCA_000598065.1", "taxid": 1380763, "species_taxid": 1380763, "relation_to_type": "type", "validated": true, "ani": 77.2675, "matched_fragments": 150, "total_fragments": 2076, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Paenibacillus lignilyticus", "strain": "strain=DLE-14", "accession": "GCA_017942085.1", "taxid": 1172615, "species_taxid": 1172615, "relation_to_type": "type", "validated": true, "ani": 77.2434, "matched_fragments": 214, "total_fragments": 2076, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Paenibacillus pasadenensis", "strain": "strain=DSM 19293", "accession": "GCA_000422485.1", "taxid": 217090, "species_taxid": 217090, "relation_to_type": "type", "validated": true, "ani": 76.9952, "matched_fragments": 230, "total_fragments": 2076, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Paenibacillus alkaliterrae", "strain": "strain=DSM 17040", "accession": "GCA_021532375.1", "taxid": 320909, "species_taxid": 320909, "relation_to_type": "type", "validated": true, "ani": 76.8395, "matched_fragments": 169, "total_fragments": 2076, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Thermobacillus composti", "strain": "strain=KWC4", "accession": "GCA_000227705.3", "taxid": 377615, "species_taxid": 377615, "relation_to_type": "type", "validated": true, "ani": 76.4676, "matched_fragments": 168, "total_fragments": 2076, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Paenibacillus macerans", "strain": "strain=ATCC 8244", "accession": "GCA_000746875.1", "taxid": 44252, "species_taxid": 44252, "relation_to_type": "type", "validated": true, "ani": 76.2217, "matched_fragments": 129, "total_fragments": 2076, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_004000825.1", "gtdb_species": "s__Paenibacillus_T kobensis", "ani": 100.0, "matched_fragments": 2067, "total_fragments": 2076, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_T", "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_004001065.1", "gtdb_species": "s__Paenibacillus_T xylaniclasticus", "ani": 81.9671, "matched_fragments": 905, "total_fragments": 2076, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_T", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.97", "min_intra_species_ani": "99.97", "mean_intra_species_af": "0.98", "min_intra_species_af": "0.98", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_003182255.1", "gtdb_species": "s__Paenibacillus_T cellulosilyticus", "ani": 79.7097, "matched_fragments": 669, "total_fragments": 2076, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_T", "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_014779765.1", "gtdb_species": "s__Paenibacillus_T sp014779765", "ani": 79.6949, "matched_fragments": 689, "total_fragments": 2076, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_T", "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_000179615.1", "gtdb_species": "s__Paenibacillus_T curdlanolyticus", "ani": 79.3449, "matched_fragments": 593, "total_fragments": 2076, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_T", "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_009789195.1", "gtdb_species": "s__Paenibacillus_T sp009789195", "ani": 79.1607, "matched_fragments": 562, "total_fragments": 2076, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_T", "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_009737085.1", "gtdb_species": "s__Paenibacillus_C sp009737085", "ani": 77.8104, "matched_fragments": 260, "total_fragments": 2076, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_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_004342525.1", "gtdb_species": "s__Paenibacillus_Z sp004342525", "ani": 77.7458, "matched_fragments": 246, "total_fragments": 2076, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_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_003386535.1", "gtdb_species": "s__Paenibacillus_Z taihuensis", "ani": 77.4632, "matched_fragments": 257, "total_fragments": 2076, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_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_004345425.1", "gtdb_species": "s__Paenibacillus_C sp004345425", "ani": 77.3104, "matched_fragments": 263, "total_fragments": 2076, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_C", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.19", "min_intra_species_ani": "99.19", "mean_intra_species_af": "0.96", "min_intra_species_af": "0.96", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_000598065.1", "gtdb_species": "s__Paenibacillus_I darwinianus", "ani": 77.2677, "matched_fragments": 150, "total_fragments": 2076, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_I", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.89", "min_intra_species_ani": "99.87", "mean_intra_species_af": "0.94", "min_intra_species_af": "0.94", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_009909185.1", "gtdb_species": "s__Paenibacillus_Z glycinis", "ani": 77.2621, "matched_fragments": 278, "total_fragments": 2076, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_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": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": -0.187, "cell_length": 0.433, "doubling_h": 0.565, "growth_tmp": 30.0, "optimum_tmp": 30.0, "optimum_ph": 7.238, "genome_size": 6469217.0, "gc_content": 52.213, "coding_genes": 5381.029, "rRNA16S_genes": 10.237, "tRNA_genes": 93.313, "gram_stain": 1.0, "sporulation": 1.0, "motility": 1.0, "range_salinity": 0.0, "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": [ "Paenibacillus", "kobensis", "NBRC", "15729" ], "quality": 3, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }