{ "type": "genome", "identifier": "GCF_000757405.2", "organism": "Pantoea stewartii subsp. indologenes", "title": "Pantoea stewartii subsp. indologenes", "description": "na", "data type": "Genome sequencing and assembly", "organization": "University of Pretoria", "publication": [ {} ], "properties": { "assembly_accession": "GCF_000757405.2", "bioproject": "PRJNA224116", "biosample": "SAMN02905159", "wgs_master": "JPKO00000000.1", "refseq_category": "na", "taxid": "66270", "species_taxid": "66269", "organism_name": "Pantoea stewartii subsp. indologenes", "infraspecific_name": "strain=LMG 2632", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Minor", "genome_rep": "Full", "seq_rel_date": "2014/09/23", "asm_name": "LMG2632assem4", "asm_submitter": "University of Pretoria", "gbrs_paired_asm": "GCA_000757405.2", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/757/405/GCF_000757405.2_LMG2632assem4", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "4681235", "genome_size_ungapped": "4681235", "gc_percent": "53.500000", "replicon_count": "1", "scaffold_count": "35", "contig_count": "35", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_000757405.2-RS_2024_10_23", "annotation_date": "2024-10-23", "total_gene_count": "4391", "protein_coding_gene_count": "4053", "non_coding_gene_count": "84", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2014-09-23", "dateModified": "2014-09-23", "datePublished": "2014-09-23", "_annotation": { "sample_count": 1, "sample_organism": [ "Pantoea stewartii subsp. indologenes" ], "sample_taxid": [ "66270" ], "sample_host_organism": [ "Setaria italica" ], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "India" ], "sample_host_location_id": [], "data_size": "1.331 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)": "4681235", "Number of Sequences": "35", "Longest Sequences (bp)": "594322", "N50 (bp)": "304929", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "53.7", "Number of CDSs": "4439", "Average Protein Length": "299.4", "Coding Ratio (%)": "85.2", "Number of rRNAs": "5", "Number of tRNAs": "65", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Pantoea stewartii subsp. indologenes", "strain": "strain=LMG 2632", "accession": "GCA_000757405.2", "taxid": 66270, "species_taxid": 66269, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1540, "total_fragments": 1542, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Pantoea stewartii subsp. stewartii", "strain": "strain=CCUG 26359", "accession": "GCA_008801695.1", "taxid": 66271, "species_taxid": 66269, "relation_to_type": "type", "validated": true, "ani": 98.7303, "matched_fragments": 1227, "total_fragments": 1542, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Pantoea allii", "strain": "strain=LMG 24248", "accession": "GCA_002307475.1", "taxid": 574096, "species_taxid": 574096, "relation_to_type": "type", "validated": true, "ani": 84.8663, "matched_fragments": 1248, "total_fragments": 1542, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pantoea ananatis", "strain": "strain=LMG 2665", "accession": "GCA_000710035.2", "taxid": 553, "species_taxid": 553, "relation_to_type": "type", "validated": true, "ani": 84.8657, "matched_fragments": 1232, "total_fragments": 1542, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pantoea ananatis", "strain": "strain=LMG 2665", "accession": "GCA_000661975.1", "taxid": 553, "species_taxid": 553, "relation_to_type": "type", "validated": true, "ani": 84.8378, "matched_fragments": 1244, "total_fragments": 1542, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pantoea allii", "strain": "strain=LMG 24248", "accession": "GCA_002095545.1", "taxid": 574096, "species_taxid": 574096, "relation_to_type": "type", "validated": true, "ani": 84.8368, "matched_fragments": 1214, "total_fragments": 1542, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pantoea deleyi", "strain": "strain=LMG24200", "accession": "GCA_022647325.1", "taxid": 470932, "species_taxid": 470932, "relation_to_type": "type", "validated": true, "ani": 81.1831, "matched_fragments": 843, "total_fragments": 1542, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Erwinia aphidicola", "strain": "strain=X001", "accession": "GCA_024169515.1", "taxid": 68334, "species_taxid": 68334, "relation_to_type": "type", "validated": true, "ani": 78.9294, "matched_fragments": 556, "total_fragments": 1542, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Enterobacter sichuanensis", "strain": "strain=WCHECL1597", "accession": "GCA_025002605.1", "taxid": 2071710, "species_taxid": 2071710, "relation_to_type": "type", "validated": true, "ani": 78.5189, "matched_fragments": 358, "total_fragments": 1542, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Enterobacter hormaechei", "strain": "strain=FDAARGOS 1433", "accession": "GCA_019048245.1", "taxid": 158836, "species_taxid": 158836, "relation_to_type": "suspected-type", "validated": true, "ani": 78.3629, "matched_fragments": 372, "total_fragments": 1542, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_008801695.1", "gtdb_species": "s__Pantoea stewartii", "ani": 98.714, "matched_fragments": 1228, "total_fragments": 1542, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pantoea", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.82", "min_intra_species_ani": "98.55", "mean_intra_species_af": "0.82", "min_intra_species_af": "0.77", "num_clustered_genomes": 34, "status": "conclusive" }, { "accession": "GCF_002307475.1", "gtdb_species": "s__Pantoea allii", "ani": 84.871, "matched_fragments": 1247, "total_fragments": 1542, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pantoea", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.91", "min_intra_species_ani": "98.49", "mean_intra_species_af": "0.92", "min_intra_species_af": "0.90", "num_clustered_genomes": 6, "status": "-" }, { "accession": "GCF_000710035.2", "gtdb_species": "s__Pantoea ananatis", "ani": 84.8657, "matched_fragments": 1232, "total_fragments": 1542, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pantoea", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.81", "min_intra_species_ani": "96.45", "mean_intra_species_af": "0.92", "min_intra_species_af": "0.81", "num_clustered_genomes": 152, "status": "-" }, { "accession": "GCA_002434205.1", "gtdb_species": "s__Pantoea sp002434205", "ani": 81.4305, "matched_fragments": 824, "total_fragments": 1542, "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_002095315.1", "gtdb_species": "s__Pantoea conspicua", "ani": 81.3957, "matched_fragments": 792, "total_fragments": 1542, "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": "GCA_002095305.1", "gtdb_species": "s__Pantoea brenneri", "ani": 81.2126, "matched_fragments": 807, "total_fragments": 1542, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pantoea", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.27", "min_intra_species_ani": "99.10", "mean_intra_species_af": "0.90", "min_intra_species_af": "0.85", "num_clustered_genomes": 24, "status": "-" }, { "accession": "GCF_006494415.1", "gtdb_species": "s__Pantoea deleyi", "ani": 81.1712, "matched_fragments": 835, "total_fragments": 1542, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pantoea", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.95", "min_intra_species_ani": "99.95", "mean_intra_species_af": "0.98", "min_intra_species_af": "0.98", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_004792415.1", "gtdb_species": "s__Pantoea vagans", "ani": 81.1583, "matched_fragments": 859, "total_fragments": 1542, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pantoea", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.00", "min_intra_species_ani": "95.86", "mean_intra_species_af": "0.91", "min_intra_species_af": "0.88", "num_clustered_genomes": 14, "status": "-" }, { "accession": "GCF_013415305.1", "gtdb_species": "s__Pantoea sp002419935", "ani": 81.0104, "matched_fragments": 798, "total_fragments": 1542, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pantoea", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.92", "min_intra_species_ani": "98.92", "mean_intra_species_af": "0.97", "min_intra_species_af": "0.97", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCA_018842655.1", "gtdb_species": "s__Pantoea sp018842655", "ani": 80.7666, "matched_fragments": 747, "total_fragments": 1542, "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_018842675.1", "gtdb_species": "s__Pantoea sp018842675", "ani": 80.5836, "matched_fragments": 745, "total_fragments": 1542, "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_002920175.1", "gtdb_species": "s__Pantoea sp002920175", "ani": 80.1684, "matched_fragments": 754, "total_fragments": 1542, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pantoea", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.09", "min_intra_species_ani": "99.09", "mean_intra_species_af": "0.94", "min_intra_species_af": "0.94", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_002858935.1", "gtdb_species": "s__Pantoea endophytica", "ani": 79.9236, "matched_fragments": 739, "total_fragments": 1542, "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": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": -0.021, "cell_length": 0.214, "doubling_h": null, "growth_tmp": 28.5, "optimum_tmp": 33.875, "optimum_ph": null, "genome_size": 4842889.231, "gc_content": 53.739, "coding_genes": 4912.5, "rRNA16S_genes": 7.0, "tRNA_genes": 73.0, "gram_stain": 0.0, "sporulation": 0.0, "motility": 1.0, "range_salinity": null, "facultative_respiration": 1.0, "anaerobic_respiration": 0.0, "aerobic_respiration": 0.0, "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": [ "Pantoea", "stewartii", "subsp.", "indologenes" ], "quality": 4, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }