{ "type": "genome", "identifier": "GCF_000767615.3", "organism": "Pandoraea pnomenusa", "title": "Pandoraea pnomenusa", "description": "na", "data type": "Genome sequencing and assembly", "organization": "University of Malaya", "publication": [ {} ], "properties": { "assembly_accession": "GCF_000767615.3", "bioproject": "PRJNA224116", "biosample": "SAMN03078809", "wgs_master": "na", "refseq_category": "na", "taxid": "93220", "species_taxid": "93220", "organism_name": "Pandoraea pnomenusa", "infraspecific_name": "strain=DSM 16536", "isolate": "na", "version_status": "latest", "assembly_level": "Complete Genome", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2016/08/18", "asm_name": "ASM76761v3", "asm_submitter": "University of Malaya", "gbrs_paired_asm": "GCA_000767615.3", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/767/615/GCF_000767615.3_ASM76761v3", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "5389285", "genome_size_ungapped": "5389285", "gc_percent": "65.000000", "replicon_count": "1", "scaffold_count": "1", "contig_count": "1", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_000767615.3-RS_2024_08_23", "annotation_date": "2024-08-23", "total_gene_count": "4858", "protein_coding_gene_count": "4709", "non_coding_gene_count": "81", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2016-08-18", "dateModified": "2016-08-18", "datePublished": "2016-08-18", "_annotation": { "sample_count": 1, "sample_organism": [ "Pandoraea pnomenusa" ], "sample_taxid": [ "93220" ], "sample_host_organism": [ "Homo sapiens" ], "sample_host_organism_id": [], "sample_host_disease": [ "Cystic Fibrosis" ], "sample_host_disease_id": [], "sample_host_location": [ "United Kingdom" ], "sample_host_location_id": [], "data_size": "1.488 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)": "5389285", "Number of Sequences": "1", "Longest Sequences (bp)": "5389285", "N50 (bp)": "5389285", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "64.9", "Number of CDSs": "4857", "Average Protein Length": "323.5", "Coding Ratio (%)": "87.5", "Number of rRNAs": "12", "Number of tRNAs": "68", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Pandoraea pnomenusa", "strain": "strain=DSM 16536", "accession": "GCA_000767615.3", "taxid": 93220, "species_taxid": 93220, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1796, "total_fragments": 1796, "ani_threshold": 95, "status": "inconclusive" }, { "organism_name": "Pandoraea pnomenusa", "strain": "strain=NCTC13160", "accession": "GCA_900454355.1", "taxid": 93220, "species_taxid": 93220, "relation_to_type": "type", "validated": true, "ani": 99.9977, "matched_fragments": 1796, "total_fragments": 1796, "ani_threshold": 95, "status": "inconclusive" }, { "organism_name": "Pandoraea morbifera", "strain": "strain=LMG 31116", "accession": "GCA_902459575.1", "taxid": 2508300, "species_taxid": 2508300, "relation_to_type": "type", "validated": true, "ani": 95.1142, "matched_fragments": 1598, "total_fragments": 1796, "ani_threshold": 95, "status": "inconclusive" }, { "organism_name": "Pandoraea pulmonicola", "strain": "strain=NCTC13159", "accession": "GCA_900454575.1", "taxid": 93221, "species_taxid": 93221, "relation_to_type": "type", "validated": true, "ani": 85.2132, "matched_fragments": 1318, "total_fragments": 1796, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pandoraea nosoerga", "strain": "strain=LMG 31109", "accession": "GCA_902459585.1", "taxid": 2508296, "species_taxid": 2508296, "relation_to_type": "type", "validated": true, "ani": 85.1748, "matched_fragments": 1249, "total_fragments": 1796, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pandoraea bronchicola", "strain": "strain=LMG 20603", "accession": "GCA_902459805.1", "taxid": 2508287, "species_taxid": 2508287, "relation_to_type": "type", "validated": true, "ani": 85.1601, "matched_fragments": 1288, "total_fragments": 1796, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pandoraea pulmonicola", "strain": "strain=DSM 16583", "accession": "GCA_000815105.2", "taxid": 93221, "species_taxid": 93221, "relation_to_type": "type", "validated": true, "ani": 85.1409, "matched_fragments": 1319, "total_fragments": 1796, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pandoraea communis", "strain": "strain=LMG 31110", "accession": "GCA_902459745.1", "taxid": 2508297, "species_taxid": 2508297, "relation_to_type": "type", "validated": true, "ani": 84.8722, "matched_fragments": 1288, "total_fragments": 1796, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pandoraea capi", "strain": "strain=LMG 20602", "accession": "GCA_902459735.1", "taxid": 2508286, "species_taxid": 2508286, "relation_to_type": "type", "validated": true, "ani": 84.8695, "matched_fragments": 1337, "total_fragments": 1796, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pandoraea cepalis", "strain": "strain=LMG 31106", "accession": "GCA_902459665.1", "taxid": 2508294, "species_taxid": 2508294, "relation_to_type": "type", "validated": true, "ani": 84.7939, "matched_fragments": 1237, "total_fragments": 1796, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pandoraea horticolens", "strain": "strain=LMG 31112", "accession": "GCA_902459555.1", "taxid": 2508298, "species_taxid": 2508298, "relation_to_type": "type", "validated": true, "ani": 84.688, "matched_fragments": 1298, "total_fragments": 1796, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pandoraea anhela", "strain": "strain=LMG 31108", "accession": "GCA_902459655.1", "taxid": 2508295, "species_taxid": 2508295, "relation_to_type": "type", "validated": true, "ani": 84.5542, "matched_fragments": 1273, "total_fragments": 1796, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pandoraea captiosa", "strain": "strain=LMG 31118", "accession": "GCA_902459775.1", "taxid": 2508302, "species_taxid": 2508302, "relation_to_type": "type", "validated": true, "ani": 84.4269, "matched_fragments": 1332, "total_fragments": 1796, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Paraburkholderia pallida", "strain": "strain=7MH5", "accession": "GCA_004524855.1", "taxid": 2547399, "species_taxid": 2547399, "relation_to_type": "type", "validated": true, "ani": 78.6633, "matched_fragments": 637, "total_fragments": 1796, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Paraburkholderia podalyriae", "strain": "strain=WC7.3b", "accession": "GCA_014397785.1", "taxid": 1938811, "species_taxid": 1938811, "relation_to_type": "type", "validated": true, "ani": 78.3648, "matched_fragments": 508, "total_fragments": 1796, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Paraburkholderia saeva", "strain": "strain=LMG 31841", "accession": "GCA_907164555.1", "taxid": 2777537, "species_taxid": 2777537, "relation_to_type": "type", "validated": true, "ani": 78.29, "matched_fragments": 470, "total_fragments": 1796, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Paraburkholderia haematera", "strain": "strain=LMG 31837", "accession": "GCA_905220975.1", "taxid": 2793077, "species_taxid": 2793077, "relation_to_type": "type", "validated": true, "ani": 78.1398, "matched_fragments": 460, "total_fragments": 1796, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Paraburkholderia kirstenboschensis", "strain": "strain=KB15", "accession": "GCA_001636975.1", "taxid": 1245436, "species_taxid": 1245436, "relation_to_type": "type", "validated": true, "ani": 78.0295, "matched_fragments": 388, "total_fragments": 1796, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Aquabacterium commune", "strain": "strain=DSM 11901", "accession": "GCA_004362855.1", "taxid": 70586, "species_taxid": 70586, "relation_to_type": "type", "validated": true, "ani": 77.0794, "matched_fragments": 197, "total_fragments": 1796, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_000767615.3", "gtdb_species": "s__Pandoraea pnomenusa", "ani": 100.0, "matched_fragments": 1796, "total_fragments": 1796, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pandoraea", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.00", "min_intra_species_ani": "95.12", "mean_intra_species_af": "0.95", "min_intra_species_af": "0.92", "num_clustered_genomes": 14, "status": "conclusive" }, { "accession": "GCF_902459725.1", "gtdb_species": "s__Pandoraea eparura", "ani": 85.1851, "matched_fragments": 1218, "total_fragments": 1796, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pandoraea", "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_902459585.1", "gtdb_species": "s__Pandoraea nosoerga", "ani": 85.1648, "matched_fragments": 1250, "total_fragments": 1796, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pandoraea", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.66", "min_intra_species_ani": "99.29", "mean_intra_species_af": "0.94", "min_intra_species_af": "0.91", "num_clustered_genomes": 4, "status": "-" }, { "accession": "GCF_902459805.1", "gtdb_species": "s__Pandoraea bronchicola", "ani": 85.1638, "matched_fragments": 1288, "total_fragments": 1796, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pandoraea", "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_000815105.2", "gtdb_species": "s__Pandoraea pulmonicola", "ani": 85.1327, "matched_fragments": 1318, "total_fragments": 1796, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pandoraea", "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_902459565.1", "gtdb_species": "s__Pandoraea aquatica", "ani": 84.9588, "matched_fragments": 1330, "total_fragments": 1796, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pandoraea", "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_902459735.1", "gtdb_species": "s__Pandoraea capi", "ani": 84.8849, "matched_fragments": 1335, "total_fragments": 1796, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pandoraea", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "96.45", "min_intra_species_ani": "96.45", "mean_intra_species_af": "0.90", "min_intra_species_af": "0.90", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_902459745.1", "gtdb_species": "s__Pandoraea communis", "ani": 84.8502, "matched_fragments": 1291, "total_fragments": 1796, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pandoraea", "ani_circumscription_radius": 95.0166, "mean_intra_species_ani": "98.36", "min_intra_species_ani": "97.48", "mean_intra_species_af": "0.89", "min_intra_species_af": "0.87", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_902459665.1", "gtdb_species": "s__Pandoraea cepalis", "ani": 84.8088, "matched_fragments": 1235, "total_fragments": 1796, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pandoraea", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.00", "min_intra_species_ani": "95.81", "mean_intra_species_af": "0.88", "min_intra_species_af": "0.85", "num_clustered_genomes": 6, "status": "-" }, { "accession": "GCF_902459615.1", "gtdb_species": "s__Pandoraea commovens", "ani": 84.6999, "matched_fragments": 1339, "total_fragments": 1796, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pandoraea", "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_902459555.1", "gtdb_species": "s__Pandoraea horticolens", "ani": 84.6956, "matched_fragments": 1297, "total_fragments": 1796, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pandoraea", "ani_circumscription_radius": 95.0166, "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_000814845.2", "gtdb_species": "s__Pandoraea sputorum", "ani": 84.6627, "matched_fragments": 1337, "total_fragments": 1796, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pandoraea", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.03", "min_intra_species_ani": "97.40", "mean_intra_species_af": "0.96", "min_intra_species_af": "0.92", "num_clustered_genomes": 5, "status": "-" }, { "accession": "GCF_902459655.1", "gtdb_species": "s__Pandoraea anhela", "ani": 84.5718, "matched_fragments": 1271, "total_fragments": 1796, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pandoraea", "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_000934605.2", "gtdb_species": "s__Pandoraea vervacti", "ani": 84.5251, "matched_fragments": 1318, "total_fragments": 1796, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pandoraea", "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_902459775.1", "gtdb_species": "s__Pandoraea captiosa", "ani": 84.4288, "matched_fragments": 1333, "total_fragments": 1796, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pandoraea", "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_002179965.1", "gtdb_species": "s__Pandoraea sp002179965", "ani": 83.8173, "matched_fragments": 1277, "total_fragments": 1796, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pandoraea", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.74", "min_intra_species_ani": "98.74", "mean_intra_species_af": "0.95", "min_intra_species_af": "0.95", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_004216565.1", "gtdb_species": "s__Leptothrix mobilis", "ani": 77.0269, "matched_fragments": 225, "total_fragments": 1796, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Leptothrix", "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_903903975.1", "gtdb_species": "s__UBA4615 sp903903975", "ani": 76.3047, "matched_fragments": 130, "total_fragments": 1796, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__UBA4615", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.67", "min_intra_species_ani": "99.60", "mean_intra_species_af": "0.92", "min_intra_species_af": "0.90", "num_clustered_genomes": 5, "status": "-" }, { "accession": "GCA_016713435.1", "gtdb_species": "s__JADJOM01 sp016713435", "ani": 75.2774, "matched_fragments": 85, "total_fragments": 1796, "gtdb_taxonomy": "d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Gemmatimonadales;f__GWC2-71-9;g__JADJOM01", "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": -0.26, "cell_length": 0.29, "doubling_h": null, "growth_tmp": 37.0, "optimum_tmp": 30.0, "optimum_ph": 7.0, "genome_size": 5465249.778, "gc_content": 64.769, "coding_genes": 4636.6, "rRNA16S_genes": 4.0, "tRNA_genes": 67.5, "gram_stain": 0.0, "sporulation": 0.0, "motility": 1.0, "range_salinity": null, "facultative_respiration": 0.0, "anaerobic_respiration": 0.0, "aerobic_respiration": 1.0, "mesophilic_range_tmp": null, "thermophilic_range_tmp": null, "psychrophilic_range_tmp": null, "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": [ "Pandoraea", "pnomenusa" ], "quality": 5, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }