{ "type": "genome", "identifier": "GCA_002367775.1", "organism": "Pantoea sp. UBA3038", "title": "Pantoea sp. UBA3038", "description": "derived from metagenome", "data type": "Genome sequencing and assembly", "organization": "University of Queensland", "publication": [ {} ], "properties": { "assembly_accession": "GCA_002367775.1", "bioproject": "PRJNA348753", "biosample": "SAMN06454659", "wgs_master": "DFDB00000000.1", "refseq_category": "na", "taxid": "1947029", "species_taxid": "1947029", "organism_name": "Pantoea sp. UBA3038", "infraspecific_name": "", "isolate": "UBA3038", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2017/09/26", "asm_name": "ASM236777v1", "submitter": "University of Queensland", "gbrs_paired_asm": "na", "paired_asm_comp": "na", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/002/367/775/GCA_002367775.1_ASM236777v1", "excluded_from_refseq": "derived from metagenome", "relation_to_type_material": "", "asm_not_live_date": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2017-09-26", "dateModified": "2017-09-26", "datePublished": "2017-09-26", "_annotation": { "sample_count": 1, "sample_organism": [ "Pantoea sp. UBA3038" ], "sample_taxid": [ "1947029" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "USA:New York City" ], "sample_host_location_id": [], "data_size": "0.839 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": null, "max": null }, "completeness": 37.96, "contamination": 0.0, "strain_heterogeneity": 0.0, "genome_count": 1 }, "data_type": "MAG", "data_source": "INSDC", "_dfast": { "Total Sequence Length (bp)": "2961937", "Number of Sequences": "329", "Longest Sequences (bp)": "48357", "N50 (bp)": "12180", "Gap Ratio (%)": "0.197506", "GCcontent (%)": "56.6", "Number of CDSs": "2724", "Average Protein Length": "276.9", "Coding Ratio (%)": "76.4", "Number of rRNAs": "0", "Number of tRNAs": "25", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Pantoea eucrina", "strain": "strain=LMG 5346", "accession": "GCA_002095385.1", "taxid": 472693, "species_taxid": 472693, "relation_to_type": "type", "validated": true, "ani": 99.4232, "matched_fragments": 793, "total_fragments": 830, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Pantoea dispersa", "strain": "strain=DSM 30073", "accession": "GCA_014155765.1", "taxid": 59814, "species_taxid": 59814, "relation_to_type": "type", "validated": true, "ani": 82.5948, "matched_fragments": 648, "total_fragments": 830, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pantoea dispersa", "strain": "strain=CCUG 25232T", "accession": "GCA_008692915.1", "taxid": 59814, "species_taxid": 59814, "relation_to_type": "type", "validated": true, "ani": 82.5897, "matched_fragments": 650, "total_fragments": 830, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pantoea wallisii", "strain": "strain=LMG 26277", "accession": "GCA_002095485.1", "taxid": 1076551, "species_taxid": 1076551, "relation_to_type": "type", "validated": true, "ani": 82.2115, "matched_fragments": 619, "total_fragments": 830, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pantoea endophytica", "strain": "strain=596", "accession": "GCA_002858935.1", "taxid": 92488, "species_taxid": 92488, "relation_to_type": "type", "validated": true, "ani": 81.2329, "matched_fragments": 588, "total_fragments": 830, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pantoea septica", "strain": "strain=LMG 5345", "accession": "GCA_002095575.1", "taxid": 472695, "species_taxid": 472695, "relation_to_type": "type", "validated": true, "ani": 80.843, "matched_fragments": 583, "total_fragments": 830, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pantoea cypripedii", "strain": "strain=LMG 2657", "accession": "GCA_002095535.1", "taxid": 55209, "species_taxid": 55209, "relation_to_type": "type", "validated": true, "ani": 80.448, "matched_fragments": 542, "total_fragments": 830, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pantoea deleyi", "strain": "strain=LMG 24200", "accession": "GCA_002095375.1", "taxid": 470932, "species_taxid": 470932, "relation_to_type": "type", "validated": true, "ani": 80.29, "matched_fragments": 525, "total_fragments": 830, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "[Pantoea] beijingensis", "strain": "strain=JZB2120001", "accession": "GCA_022647505.1", "taxid": 1324864, "species_taxid": 1324864, "relation_to_type": "type", "validated": true, "ani": 77.8477, "matched_fragments": 234, "total_fragments": 830, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Citrobacter rodentium", "strain": "strain=DSM 16636", "accession": "GCA_021278985.1", "taxid": 67825, "species_taxid": 67825, "relation_to_type": "type", "validated": true, "ani": 77.6421, "matched_fragments": 270, "total_fragments": 830, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Enterobacter wuhouensis", "strain": "strain=WCHEW120002", "accession": "GCA_004331265.1", "taxid": 2529381, "species_taxid": 2529381, "relation_to_type": "type", "validated": true, "ani": 77.5927, "matched_fragments": 255, "total_fragments": 830, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Escherichia albertii", "strain": "strain=NBRC 107761", "accession": "GCA_000759775.1", "taxid": 208962, "species_taxid": 208962, "relation_to_type": "type", "validated": true, "ani": 77.206, "matched_fragments": 169, "total_fragments": 830, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Escherichia albertii", "strain": "strain=DSM 17582", "accession": "GCA_022833075.1", "taxid": 208962, "species_taxid": 208962, "relation_to_type": "type", "validated": true, "ani": 77.0904, "matched_fragments": 173, "total_fragments": 830, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 37.96, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_002095385.1", "gtdb_species": "s__Pantoea eucrina", "ani": 99.4232, "matched_fragments": 793, "total_fragments": 830, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pantoea", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.84", "min_intra_species_ani": "96.54", "mean_intra_species_af": "0.93", "min_intra_species_af": "0.90", "num_clustered_genomes": 17, "status": "conclusive" }, { "accession": "GCF_001691555.1", "gtdb_species": "s__Pantoea eucrina_A", "ani": 93.1844, "matched_fragments": 788, "total_fragments": 830, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pantoea", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.39", "min_intra_species_ani": "99.35", "mean_intra_species_af": "0.94", "min_intra_species_af": "0.93", "num_clustered_genomes": 4, "status": "-" }, { "accession": "GCF_014155765.1", "gtdb_species": "s__Pantoea dispersa", "ani": 82.5858, "matched_fragments": 649, "total_fragments": 830, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pantoea", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.93", "min_intra_species_ani": "96.36", "mean_intra_species_af": "0.92", "min_intra_species_af": "0.86", "num_clustered_genomes": 38, "status": "-" }, { "accession": "GCF_007833795.1", "gtdb_species": "s__Pantoea dispersa_B", "ani": 82.4538, "matched_fragments": 653, "total_fragments": 830, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pantoea", "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_002095485.1", "gtdb_species": "s__Pantoea wallisii", "ani": 82.2029, "matched_fragments": 620, "total_fragments": 830, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pantoea", "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_002858935.1", "gtdb_species": "s__Pantoea endophytica", "ani": 81.2213, "matched_fragments": 589, "total_fragments": 830, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pantoea", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.84", "min_intra_species_ani": "95.24", "mean_intra_species_af": "0.93", "min_intra_species_af": "0.88", "num_clustered_genomes": 7, "status": "-" }, { "accession": "GCF_000468095.1", "gtdb_species": "s__Pantoea sp000468095", "ani": 80.2968, "matched_fragments": 503, "total_fragments": 830, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pantoea", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.52", "min_intra_species_ani": "98.52", "mean_intra_species_af": "0.95", "min_intra_species_af": "0.95", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCA_013753875.1", "gtdb_species": "s__Pantoea persica", "ani": 79.8442, "matched_fragments": 415, "total_fragments": 830, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pantoea", "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_900604315.1", "gtdb_species": "s__Pantoea mediterraneensis", "ani": 79.7123, "matched_fragments": 476, "total_fragments": 830, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pantoea", "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": -0.021, "cell_length": 0.214, "doubling_h": null, "growth_tmp": 29.095, "optimum_tmp": 33.875, "optimum_ph": null, "genome_size": 4580554.261, "gc_content": 53.712, "coding_genes": 3801.881, "rRNA16S_genes": 6.428, "tRNA_genes": 74.931, "gram_stain": 0.047, "sporulation": 0.0, "motility": 0.944, "range_salinity": null, "facultative_respiration": 0.809, "anaerobic_respiration": 0.0, "aerobic_respiration": 0.19, "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 }, "_gtdb_taxon": [ "d__Bacteria", "p__Pseudomonadota", "c__Gammaproteobacteria", "o__Enterobacterales", "f__Enterobacteriaceae", "g__Pantoea", "s__Pantoea eucrina" ], "_genome_taxon": [ "Pantoea", "sp.", "UBA3038", "d__Bacteria", "p__Pseudomonadota", "c__Gammaproteobacteria", "o__Enterobacterales", "f__Enterobacteriaceae", "g__Pantoea", "s__Pantoea eucrina", "Bacteria", "Pseudomonadota", "Gammaproteobacteria", "Enterobacterales", "Enterobacteriaceae", "Pantoea", "Pantoea", "eucrina" ], "_meo": [ { "id": "MEO_0000419", "label": "plant body associated" } ], "quality": 2, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f" }