{ "type": "genome", "identifier": "GCF_017874255.1", "organism": "Paenibacillus shirakamiensis", "title": "Paenibacillus shirakamiensis", "description": "na", "data type": "Genome sequencing and assembly", "organization": "DOE Joint Genome Institute", "publication": [ {} ], "properties": { "assembly_accession": "GCF_017874255.1", "bioproject": "PRJNA224116", "biosample": "SAMN18245315", "wgs_master": "JAGGLD000000000.1", "refseq_category": "reference genome", "taxid": "1265935", "species_taxid": "1265935", "organism_name": "Paenibacillus shirakamiensis", "infraspecific_name": "strain=DSM 26806", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2021/04/08", "asm_name": "ASM1787425v1", "asm_submitter": "DOE Joint Genome Institute", "gbrs_paired_asm": "GCA_017874255.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/017/874/255/GCF_017874255.1_ASM1787425v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "4087951", "genome_size_ungapped": "4087951", "gc_percent": "43.000000", "replicon_count": "0", "scaffold_count": "15", "contig_count": "15", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_017874255.1-RS_2024_04_30", "annotation_date": "2024-04-30", "total_gene_count": "3832", "protein_coding_gene_count": "3709", "non_coding_gene_count": "100", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2021-04-08", "dateModified": "2021-04-08", "datePublished": "2021-04-08", "_annotation": { "sample_count": 1, "sample_organism": [ "Paenibacillus shirakamiensis" ], "sample_taxid": [ "1265935" ], "sample_host_organism": [ "not applicable" ], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "missing" ], "sample_host_location_id": [], "data_size": "1.169 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)": "4087951", "Number of Sequences": "15", "Longest Sequences (bp)": "1535308", "N50 (bp)": "547010", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "42.9", "Number of CDSs": "3787", "Average Protein Length": "312.5", "Coding Ratio (%)": "86.8", "Number of rRNAs": "2", "Number of tRNAs": "79", "Number of CRISPRs": "3" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Paenibacillus shirakamiensis", "strain": "strain=DSM 26806", "accession": "GCA_017874255.1", "taxid": 1265935, "species_taxid": 1265935, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1356, "total_fragments": 1356, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Paenibacillus zeisoli", "strain": "strain=3-5-3", "accession": "GCA_003994465.1", "taxid": 2496267, "species_taxid": 2496267, "relation_to_type": "type", "validated": true, "ani": 78.4513, "matched_fragments": 242, "total_fragments": 1356, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Paenibacillus tuaregi", "strain": "strain=Marseille-P2472", "accession": "GCA_900086655.1", "taxid": 1816681, "species_taxid": 1816681, "relation_to_type": "type", "validated": true, "ani": 78.3297, "matched_fragments": 232, "total_fragments": 1356, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Paenibacillus bouchesdurhonensis", "strain": "strain=Marseille-P3071", "accession": "GCA_900155685.1", "taxid": 1870990, "species_taxid": 1870990, "relation_to_type": "type", "validated": true, "ani": 77.7974, "matched_fragments": 106, "total_fragments": 1356, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Paenibacillus massiliensis subsp. panacisoli", "strain": "strain=DSM 21345", "accession": "GCA_000426545.1", "taxid": 363858, "species_taxid": 225917, "relation_to_type": "type", "validated": true, "ani": 77.7137, "matched_fragments": 74, "total_fragments": 1356, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Paenibacillus sediminis", "strain": "strain=DSM 23491", "accession": "GCA_017873765.1", "taxid": 664909, "species_taxid": 664909, "relation_to_type": "type", "validated": true, "ani": 77.5577, "matched_fragments": 82, "total_fragments": 1356, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Paenibacillus segetis", "strain": "strain=CGMCC 1.12769", "accession": "GCA_014639155.1", "taxid": 1325360, "species_taxid": 1325360, "relation_to_type": "type", "validated": true, "ani": 77.542, "matched_fragments": 139, "total_fragments": 1356, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Paenibacillus physcomitrellae", "strain": "strain=XB", "accession": "GCA_002240225.1", "taxid": 1619311, "species_taxid": 1619311, "relation_to_type": "type", "validated": true, "ani": 77.5009, "matched_fragments": 105, "total_fragments": 1356, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Paenibacillus xylanilyticus", "strain": "strain=LMG 21957", "accession": "GCA_013359935.1", "taxid": 248903, "species_taxid": 248903, "relation_to_type": "type", "validated": true, "ani": 77.4969, "matched_fragments": 97, "total_fragments": 1356, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Paenibacillus tepidiphilus", "strain": "strain=SYSU G01001", "accession": "GCA_008635795.1", "taxid": 2608683, "species_taxid": 2608683, "relation_to_type": "type", "validated": true, "ani": 77.4469, "matched_fragments": 64, "total_fragments": 1356, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Paenibacillus aceti", "strain": "strain=L14", "accession": "GCA_003614185.1", "taxid": 1820010, "species_taxid": 1820010, "relation_to_type": "type", "validated": true, "ani": 77.4445, "matched_fragments": 95, "total_fragments": 1356, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Paenibacillus odorifer", "strain": "strain=DSM 15391", "accession": "GCA_000758725.1", "taxid": 189426, "species_taxid": 189426, "relation_to_type": "type", "validated": true, "ani": 77.3799, "matched_fragments": 93, "total_fragments": 1356, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Paenibacillus aceti", "strain": "strain=CGMCC 1.15420", "accession": "GCA_014642755.1", "taxid": 1820010, "species_taxid": 1820010, "relation_to_type": "type", "validated": true, "ani": 77.3627, "matched_fragments": 93, "total_fragments": 1356, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Paenibacillus marchantiophytorum", "strain": "strain=CGMCC 1.15043", "accession": "GCA_014640555.1", "taxid": 1619310, "species_taxid": 1619310, "relation_to_type": "type", "validated": true, "ani": 77.2682, "matched_fragments": 51, "total_fragments": 1356, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Paenibacillus rhizophilus", "strain": "strain=7197", "accession": "GCA_003854965.1", "taxid": 1850366, "species_taxid": 1850366, "relation_to_type": "type", "validated": true, "ani": 77.1645, "matched_fragments": 53, "total_fragments": 1356, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Paenibacillus massiliensis", "strain": "strain=DSM 16942", "accession": "GCA_000377505.1", "taxid": 225917, "species_taxid": 225917, "relation_to_type": "type", "validated": true, "ani": 77.1578, "matched_fragments": 81, "total_fragments": 1356, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Paenibacillus sinensis", "strain": "strain=HN-1", "accession": "GCA_019904155.1", "taxid": 2834413, "species_taxid": 2834413, "relation_to_type": "type", "validated": true, "ani": 77.1527, "matched_fragments": 62, "total_fragments": 1356, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Paenibacillus arenosi", "strain": "strain=CAU 1523", "accession": "GCA_014841135.1", "taxid": 2774142, "species_taxid": 2774142, "relation_to_type": "type", "validated": true, "ani": 77.1041, "matched_fragments": 51, "total_fragments": 1356, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Paenibacillus nuruki", "strain": "strain=TI45-13ar", "accession": "GCA_001721045.1", "taxid": 1886670, "species_taxid": 1886670, "relation_to_type": "type", "validated": true, "ani": 77.0405, "matched_fragments": 75, "total_fragments": 1356, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_017874255.1", "gtdb_species": "s__Paenibacillus_A shirakamiensis", "ani": 100.0, "matched_fragments": 1356, "total_fragments": 1356, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_A", "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_003994465.1", "gtdb_species": "s__Paenibacillus_A zeisoli", "ani": 78.4746, "matched_fragments": 242, "total_fragments": 1356, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_A", "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_900086655.1", "gtdb_species": "s__Paenibacillus_A tuaregi", "ani": 78.3292, "matched_fragments": 233, "total_fragments": 1356, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_A", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.53", "min_intra_species_ani": "97.06", "mean_intra_species_af": "0.96", "min_intra_species_af": "0.92", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_018614975.1", "gtdb_species": "s__Paenibacillus polymyxa_E", "ani": 77.9328, "matched_fragments": 107, "total_fragments": 1356, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus", "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_900155685.1", "gtdb_species": "s__Paenibacillus_A bouchesdurhonensis", "ani": 77.8103, "matched_fragments": 105, "total_fragments": 1356, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_A", "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_000426545.1", "gtdb_species": "s__Paenibacillus panacisoli", "ani": 77.727, "matched_fragments": 72, "total_fragments": 1356, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus", "ani_circumscription_radius": 96.1083, "mean_intra_species_ani": "98.22", "min_intra_species_ani": "98.22", "mean_intra_species_af": "0.93", "min_intra_species_af": "0.93", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_002968835.1", "gtdb_species": "s__Paenibacillus sp002968835", "ani": 77.6705, "matched_fragments": 95, "total_fragments": 1356, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus", "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_003268635.1", "gtdb_species": "s__Paenibacillus sp003268635", "ani": 77.6552, "matched_fragments": 99, "total_fragments": 1356, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus", "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_001955535.1", "gtdb_species": "s__Paenibacillus sp001955535", "ani": 77.6426, "matched_fragments": 84, "total_fragments": 1356, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.62", "min_intra_species_ani": "98.62", "mean_intra_species_af": "0.85", "min_intra_species_af": "0.85", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_001570725.1", "gtdb_species": "s__Paenibacillus amylolyticus_A", "ani": 77.6289, "matched_fragments": 108, "total_fragments": 1356, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.59", "min_intra_species_ani": "97.52", "mean_intra_species_af": "0.92", "min_intra_species_af": "0.91", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_002240225.1", "gtdb_species": "s__Paenibacillus_A physcomitrellae", "ani": 77.5417, "matched_fragments": 105, "total_fragments": 1356, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_A", "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_014639155.1", "gtdb_species": "s__Paenibacillus_A segetis", "ani": 77.5404, "matched_fragments": 137, "total_fragments": 1356, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_A", "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_013359935.1", "gtdb_species": "s__Paenibacillus xylanilyticus", "ani": 77.492, "matched_fragments": 97, "total_fragments": 1356, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus", "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_003614185.1", "gtdb_species": "s__Paenibacillus_A aceti", "ani": 77.3964, "matched_fragments": 97, "total_fragments": 1356, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_A", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.99", "min_intra_species_ani": "99.99", "mean_intra_species_af": "1.00", "min_intra_species_af": "1.00", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_000758725.1", "gtdb_species": "s__Paenibacillus odorifer", "ani": 77.3799, "matched_fragments": 93, "total_fragments": 1356, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.05", "min_intra_species_ani": "97.01", "mean_intra_species_af": "0.93", "min_intra_species_af": "0.91", "num_clustered_genomes": 32, "status": "-" }, { "accession": "GCF_012912005.1", "gtdb_species": "s__Paenibacillus sp012912005", "ani": 77.3741, "matched_fragments": 101, "total_fragments": 1356, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus", "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_007680605.1", "gtdb_species": "s__Paenibacillus xylanexedens_B", "ani": 77.3596, "matched_fragments": 89, "total_fragments": 1356, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.13", "min_intra_species_ani": "99.13", "mean_intra_species_af": "0.96", "min_intra_species_af": "0.96", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_016908805.1", "gtdb_species": "s__Paenibacillus_J nicotianae", "ani": 77.3334, "matched_fragments": 75, "total_fragments": 1356, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_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": "-" }, { "accession": "GCF_001955855.1", "gtdb_species": "s__Paenibacillus sp001955855", "ani": 77.2995, "matched_fragments": 112, "total_fragments": 1356, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus", "ani_circumscription_radius": 95.7262, "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_000377505.1", "gtdb_species": "s__Paenibacillus massiliensis", "ani": 77.1916, "matched_fragments": 82, "total_fragments": 1356, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus", "ani_circumscription_radius": 96.1083, "mean_intra_species_ani": "98.51", "min_intra_species_ani": "98.51", "mean_intra_species_af": "0.94", "min_intra_species_af": "0.94", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_003719335.1", "gtdb_species": "s__Paenibacillus amylolyticus_D", "ani": 77.1077, "matched_fragments": 93, "total_fragments": 1356, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus", "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_001721045.1", "gtdb_species": "s__Paenibacillus_J nuruki", "ani": 77.0405, "matched_fragments": 75, "total_fragments": 1356, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_J", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.40", "min_intra_species_ani": "98.40", "mean_intra_species_af": "0.93", "min_intra_species_af": "0.93", "num_clustered_genomes": 2, "status": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": -0.187, "cell_length": 0.433, "doubling_h": 0.565, "growth_tmp": 25.0, "optimum_tmp": 31.323, "optimum_ph": 7.238, "genome_size": 6197949.921, "gc_content": 50.283, "coding_genes": 5381.029, "rRNA16S_genes": 10.237, "tRNA_genes": 93.313, "gram_stain": 1.0, "sporulation": 1.0, "motility": 0.918, "range_salinity": 0.0, "facultative_respiration": 0.0, "anaerobic_respiration": 0.0, "aerobic_respiration": 1.0, "mesophilic_range_tmp": 0.9, "thermophilic_range_tmp": 0.033, "psychrophilic_range_tmp": 0.066, "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", "shirakamiensis" ], "quality": 4, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }