{ "type": "genome", "identifier": "GCF_002233675.1", "organism": "Paenibacillus herberti", "title": "Paenibacillus herberti", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Capital Normal University", "publication": [ {} ], "properties": { "assembly_accession": "GCF_002233675.1", "bioproject": "PRJNA224116", "biosample": "SAMN07356179", "wgs_master": "NMUQ00000000.1", "refseq_category": "reference genome", "taxid": "1619309", "species_taxid": "1619309", "organism_name": "Paenibacillus herberti", "infraspecific_name": "strain=R33", "isolate": "na", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2017/07/26", "asm_name": "ASM223367v1", "asm_submitter": "Capital Normal University", "gbrs_paired_asm": "GCA_002233675.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/002/233/675/GCF_002233675.1_ASM223367v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "5414232", "genome_size_ungapped": "5407973", "gc_percent": "51.000000", "replicon_count": "0", "scaffold_count": "17", "contig_count": "17", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_002233675.1-RS_2024_05_03", "annotation_date": "2024-05-03", "total_gene_count": "4901", "protein_coding_gene_count": "4727", "non_coding_gene_count": "90", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2017-07-26", "dateModified": "2017-07-26", "datePublished": "2017-07-26", "_annotation": { "sample_count": 1, "sample_organism": [ "Paenibacillus herberti" ], "sample_taxid": [ "1619309" ], "sample_host_organism": [ "Herbertus sendtneri" ], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "China: Bomi County, Tibet" ], "sample_host_location_id": [], "data_size": "1.537 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)": "5414232", "Number of Sequences": "17", "Longest Sequences (bp)": "2773355", "N50 (bp)": "2773355", "Gap Ratio (%)": "0.119611", "GCcontent (%)": "51.0", "Number of CDSs": "4897", "Average Protein Length": "313.7", "Coding Ratio (%)": "85.1", "Number of rRNAs": "13", "Number of tRNAs": "73", "Number of CRISPRs": "9" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Paenibacillus herberti", "strain": "strain=R33", "accession": "GCA_002233675.1", "taxid": 1619309, "species_taxid": 1619309, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1798, "total_fragments": 1800, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Paenibacillus albicereus", "strain": "strain=UniB2", "accession": "GCA_012676905.1", "taxid": 2726185, "species_taxid": 2726185, "relation_to_type": "type", "validated": true, "ani": 79.3505, "matched_fragments": 628, "total_fragments": 1800, "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": 79.1786, "matched_fragments": 654, "total_fragments": 1800, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Paenibacillus pasadenensis", "strain": "strain=NBRC 101214", "accession": "GCA_004001085.1", "taxid": 217090, "species_taxid": 217090, "relation_to_type": "type", "validated": true, "ani": 79.1717, "matched_fragments": 625, "total_fragments": 1800, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Paenibacillus castaneae", "strain": "strain=DSM 19417", "accession": "GCA_002884445.1", "taxid": 474957, "species_taxid": 474957, "relation_to_type": "type", "validated": true, "ani": 78.7835, "matched_fragments": 98, "total_fragments": 1800, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Paenibacillus humicus", "strain": "strain=NBRC 102415", "accession": "GCA_004000905.1", "taxid": 412861, "species_taxid": 412861, "relation_to_type": "type", "validated": true, "ani": 78.7688, "matched_fragments": 454, "total_fragments": 1800, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Paenibacillus castaneae", "strain": "strain=CECT 7279", "accession": "GCA_011761405.1", "taxid": 474957, "species_taxid": 474957, "relation_to_type": "type", "validated": true, "ani": 77.6195, "matched_fragments": 92, "total_fragments": 1800, "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": 77.2103, "matched_fragments": 94, "total_fragments": 1800, "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": 76.6849, "matched_fragments": 101, "total_fragments": 1800, "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": 76.6508, "matched_fragments": 171, "total_fragments": 1800, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Paenibacillus tarimensis", "strain": "strain=DSM 19409", "accession": "GCA_021532315.1", "taxid": 416012, "species_taxid": 416012, "relation_to_type": "type", "validated": true, "ani": 76.6337, "matched_fragments": 100, "total_fragments": 1800, "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": 76.5052, "matched_fragments": 77, "total_fragments": 1800, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Thermobacillus xylanilyticus", "strain": "strain=XE", "accession": "GCA_907165215.1", "taxid": 76633, "species_taxid": 76633, "relation_to_type": "type", "validated": true, "ani": 76.1637, "matched_fragments": 87, "total_fragments": 1800, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": 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"s__Paenibacillus_O sp012676905", "ani": 79.3487, "matched_fragments": 629, "total_fragments": 1800, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_O", "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_000422485.1", "gtdb_species": "s__Paenibacillus_O pasadenensis", "ani": 79.1715, "matched_fragments": 655, "total_fragments": 1800, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_O", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.23", "min_intra_species_ani": "98.68", "mean_intra_species_af": "0.94", "min_intra_species_af": "0.90", "num_clustered_genomes": 4, "status": "-" }, { "accession": "GCF_002884445.1", "gtdb_species": "s__Paenibacillus_C castaneae", "ani": 78.9556, "matched_fragments": 99, "total_fragments": 1800, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_C", "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_002243345.2", "gtdb_species": "s__Paenibacillus_O sp002243345", "ani": 78.92, "matched_fragments": 483, "total_fragments": 1800, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_O", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.98", "min_intra_species_ani": "99.98", "mean_intra_species_af": "0.98", "min_intra_species_af": "0.98", "num_clustered_genomes": 4, "status": "-" }, { "accession": "GCF_004000905.1", "gtdb_species": "s__Paenibacillus_O humicus", "ani": 78.7688, "matched_fragments": 454, 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"d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_D", "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_907165215.1", "gtdb_species": "s__Thermobacillus xylanilyticus", "ani": 76.1637, "matched_fragments": 87, "total_fragments": 1800, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Thermobacillus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.85", "min_intra_species_ani": "97.19", "mean_intra_species_af": "0.88", "min_intra_species_af": "0.86", "num_clustered_genomes": 4, "status": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": -0.187, "cell_length": 0.433, "doubling_h": 0.565, "growth_tmp": 30.106, "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": 0.347, "anaerobic_respiration": 0.007, "aerobic_respiration": 0.645, "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", "herberti" ], "quality": 5, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }