{ "type": "genome", "identifier": "GCF_900103875.1", "organism": "Pseudomonas arsenicoxydans", "title": "Pseudomonas arsenicoxydans", "description": "na", "data type": "Genome sequencing and assembly", "organization": "DOE - JOINT GENOME INSTITUTE", "publication": [ {} ], "properties": { "assembly_accession": "GCF_900103875.1", "bioproject": "PRJNA224116", "biosample": "SAMN04489798", "wgs_master": "na", "refseq_category": "reference genome", "taxid": "702115", "species_taxid": "702115", "organism_name": "Pseudomonas arsenicoxydans", "infraspecific_name": "strain=CECT 7543", "isolate": "na", "version_status": "latest", "assembly_level": "Chromosome", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2016/10/20", "asm_name": "IMG-taxon 2636416065 annotated assembly", "asm_submitter": "DOE - JOINT GENOME INSTITUTE", "gbrs_paired_asm": "GCA_900103875.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/900/103/875/GCF_900103875.1_IMG-taxon_2636416065_annotated_assembly", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "6502978", "genome_size_ungapped": "6502878", "gc_percent": "58.500000", "replicon_count": "1", "scaffold_count": "1", "contig_count": "1", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_900103875.1-RS_2024_12_11", "annotation_date": "2024-12-11", "total_gene_count": "6043", "protein_coding_gene_count": "5809", "non_coding_gene_count": "87", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2016-10-20", "dateModified": "2016-10-20", "datePublished": "2016-10-20", "_annotation": { "sample_count": 1, "sample_organism": [ "Pseudomonas arsenicoxydans" ], "sample_taxid": [ "702115" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "missing" ], "sample_host_location_id": [], "data_size": "1.826 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)": "6502878", "Number of Sequences": "1", "Longest Sequences (bp)": "6502878", "N50 (bp)": "6502878", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "58.7", "Number of CDSs": "6023", "Average Protein Length": "315.6", "Coding Ratio (%)": "87.7", "Number of rRNAs": "16", "Number of tRNAs": "67", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Pseudomonas mandelii", "strain": "strain=LMG 21607", "accession": "GCA_900106065.1", "taxid": 75612, "species_taxid": 75612, "relation_to_type": "suspected-type", "validated": true, "ani": 89.4685, "matched_fragments": 1736, "total_fragments": 2167, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas mandelii", "strain": "strain=DSM 17967", "accession": "GCA_007858265.1", "taxid": 75612, "species_taxid": 75612, "relation_to_type": "suspected-type", "validated": true, "ani": 89.421, "matched_fragments": 1715, "total_fragments": 2167, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas mandelii", "strain": "strain=NBRC 103147", "accession": "GCA_002091695.1", "taxid": 75612, "species_taxid": 75612, "relation_to_type": "suspected-type", "validated": true, "ani": 89.4092, "matched_fragments": 1701, "total_fragments": 2167, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas lini", "strain": "strain=CCUG 51522", "accession": "GCA_008801525.1", "taxid": 163011, "species_taxid": 163011, "relation_to_type": "type", "validated": true, "ani": 87.8464, "matched_fragments": 1545, "total_fragments": 2167, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas lini", "strain": "strain=DSM 16768", "accession": "GCA_001042905.1", "taxid": 163011, "species_taxid": 163011, "relation_to_type": "type", "validated": true, "ani": 87.8381, "matched_fragments": 1546, "total_fragments": 2167, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas farris", "strain": "strain=SWRI79", "accession": "GCA_019145235.1", "taxid": 2841207, "species_taxid": 2841207, "relation_to_type": "type", "validated": true, "ani": 87.8057, "matched_fragments": 1554, "total_fragments": 2167, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas izuensis", "strain": "strain=IzPS43_3003", "accession": "GCA_009861505.1", "taxid": 2684212, "species_taxid": 2684212, "relation_to_type": "type", "validated": true, "ani": 86.5429, "matched_fragments": 1513, "total_fragments": 2167, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas laurylsulfativorans", "strain": "strain=AP3_22", "accession": "GCA_002906155.1", "taxid": 1943631, "species_taxid": 1943631, "relation_to_type": "type", "validated": true, "ani": 86.5016, "matched_fragments": 1469, "total_fragments": 2167, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas pharyngis", "strain": "strain=BML-PP036", "accession": "GCA_021602345.1", "taxid": 2892333, "species_taxid": 2892333, "relation_to_type": "type", "validated": true, "ani": 85.9133, "matched_fragments": 1487, "total_fragments": 2167, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas sputi", "strain": "strain=BML-PP014", "accession": "GCA_021603585.1", "taxid": 2892325, "species_taxid": 2892325, "relation_to_type": "type", "validated": true, "ani": 85.7841, "matched_fragments": 1491, "total_fragments": 2167, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas germanica", "strain": "strain=FIT28", "accession": "GCA_019614655.1", "taxid": 2815720, "species_taxid": 2815720, "relation_to_type": "type", "validated": true, "ani": 85.4183, "matched_fragments": 1488, "total_fragments": 2167, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas rhizophila", "strain": "strain=S211", "accession": "GCA_003033885.1", "taxid": 2045200, "species_taxid": 2045200, "relation_to_type": "type", "validated": true, "ani": 83.9329, "matched_fragments": 1270, "total_fragments": 2167, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_900103875.1", "gtdb_species": "s__Pseudomonas_E arsenicoxydans", "ani": 100.0, "matched_fragments": 2167, "total_fragments": 2167, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "96.47", "min_intra_species_ani": "96.47", "mean_intra_species_af": "0.86", "min_intra_species_af": "0.86", "num_clustered_genomes": 2, "status": "conclusive" }, { "accession": "GCF_003151075.1", "gtdb_species": "s__Pseudomonas_E sp003151075", "ani": 89.8568, "matched_fragments": 1737, "total_fragments": 2167, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E", "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_004310295.1", "gtdb_species": "s__Pseudomonas_E sp004310295", "ani": 89.6191, "matched_fragments": 1613, "total_fragments": 2167, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E", "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_900106065.1", "gtdb_species": "s__Pseudomonas_E mandelii", "ani": 89.4513, "matched_fragments": 1738, "total_fragments": 2167, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.92", "min_intra_species_ani": "98.70", "mean_intra_species_af": "0.92", "min_intra_species_af": "0.88", "num_clustered_genomes": 64, "status": "-" }, { "accession": "GCF_000968015.1", "gtdb_species": "s__Pseudomonas_E fluorescens_W", "ani": 88.8833, "matched_fragments": 1615, "total_fragments": 2167, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "96.19", "min_intra_species_ani": "96.19", "mean_intra_species_af": "0.86", "min_intra_species_af": "0.86", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_000282315.2", "gtdb_species": "s__Pseudomonas_E sp000282315", "ani": 88.8696, "matched_fragments": 1629, "total_fragments": 2167, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "96.54", "min_intra_species_ani": "96.05", "mean_intra_species_af": "0.87", "min_intra_species_af": "0.83", "num_clustered_genomes": 6, "status": "-" }, { "accession": "GCF_900187425.1", "gtdb_species": "s__Pseudomonas_E sp900187425", "ani": 88.8594, "matched_fragments": 1619, "total_fragments": 2167, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "95.77", "min_intra_species_ani": "95.75", "mean_intra_species_af": "0.84", "min_intra_species_af": "0.83", "num_clustered_genomes": 4, "status": "-" }, { "accession": "GCF_006438925.1", "gtdb_species": "s__Pseudomonas_E mandelii_C", "ani": 88.7677, "matched_fragments": 1663, "total_fragments": 2167, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.98", "min_intra_species_ani": "96.81", "mean_intra_species_af": "0.87", "min_intra_species_af": "0.83", "num_clustered_genomes": 4, "status": "-" }, { "accession": "GCF_018502625.1", "gtdb_species": "s__Pseudomonas_E fluorescens_BW", "ani": 88.4409, "matched_fragments": 1575, "total_fragments": 2167, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E", "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_001297125.1", "gtdb_species": "s__Pseudomonas_E sp001297125", "ani": 88.418, "matched_fragments": 1614, "total_fragments": 2167, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E", "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_000282415.1", "gtdb_species": "s__Pseudomonas_E sp000282415", "ani": 88.364, "matched_fragments": 1523, "total_fragments": 2167, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.45", "min_intra_species_ani": "97.21", "mean_intra_species_af": "0.89", "min_intra_species_af": "0.87", "num_clustered_genomes": 6, "status": "-" }, { "accession": "GCF_902498065.1", "gtdb_species": "s__Pseudomonas_E fluorescens_BJ", "ani": 88.263, "matched_fragments": 1586, "total_fragments": 2167, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.26", "min_intra_species_ani": "99.24", "mean_intra_species_af": "0.94", "min_intra_species_af": "0.93", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_008370045.1", "gtdb_species": "s__Pseudomonas_E sp008370045", "ani": 88.0115, "matched_fragments": 1655, "total_fragments": 2167, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E", "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_000282375.1", "gtdb_species": "s__Pseudomonas_E sp000282375", "ani": 87.9732, "matched_fragments": 1507, "total_fragments": 2167, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "96.36", "min_intra_species_ani": "96.36", "mean_intra_species_af": "0.86", "min_intra_species_af": "0.86", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_003732665.1", "gtdb_species": "s__Pseudomonas_E frederiksbergensis_G", "ani": 87.8563, "matched_fragments": 1634, "total_fragments": 2167, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E", "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_003732275.1", "gtdb_species": "s__Pseudomonas_E frederiksbergensis_H", "ani": 87.8383, "matched_fragments": 1555, "total_fragments": 2167, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E", "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_001042905.1", "gtdb_species": "s__Pseudomonas_E lini", "ani": 87.8316, "matched_fragments": 1546, "total_fragments": 2167, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.33", "min_intra_species_ani": "98.85", "mean_intra_species_af": "0.97", "min_intra_species_af": "0.92", "num_clustered_genomes": 6, "status": "-" }, { "accession": "GCF_002967995.1", "gtdb_species": "s__Pseudomonas_E frederiksbergensis_D", "ani": 87.7854, "matched_fragments": 1586, "total_fragments": 2167, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E", "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_001238485.1", "gtdb_species": "s__Pseudomonas_E syringae_E", "ani": 87.6768, "matched_fragments": 1504, "total_fragments": 2167, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "95.97", "min_intra_species_ani": "95.90", "mean_intra_species_af": "0.85", "min_intra_species_af": "0.84", "num_clustered_genomes": 15, "status": "-" }, { "accession": "GCF_000512695.2", "gtdb_species": "s__Pseudomonas_E sp000512695", "ani": 87.6738, "matched_fragments": 1423, "total_fragments": 2167, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E", "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_000282215.1", "gtdb_species": "s__Pseudomonas_E sp000282215", "ani": 87.5536, "matched_fragments": 1456, "total_fragments": 2167, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.42", "min_intra_species_ani": "97.42", "mean_intra_species_af": "0.82", "min_intra_species_af": "0.82", "num_clustered_genomes": 2, "status": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": -0.248, "cell_length": 0.186, "doubling_h": -0.025, "growth_tmp": 28.0, "optimum_tmp": 27.972, "optimum_ph": 7.258, "genome_size": 6502878.0, "gc_content": 60.938, "coding_genes": 5204.79, "rRNA16S_genes": 5.319, "tRNA_genes": 67.35, "gram_stain": 0.0, "sporulation": 0.013, "motility": 0.975, "range_salinity": 0.666, "facultative_respiration": 0.021, "anaerobic_respiration": 0.0, "aerobic_respiration": 0.978, "mesophilic_range_tmp": 0.926, "thermophilic_range_tmp": 0.0, "psychrophilic_range_tmp": 0.073, "bacillus_cell_shape": 0.988, "coccus_cell_shape": 0.011, "filament_cell_shape": 0.0, "coccobacillus_cell_shape": 0.0, "vibrio_cell_shape": 0.0, "spiral_cell_shape": 0.0 }, "_genome_taxon": [ "Pseudomonas", "arsenicoxydans" ], "quality": 5, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }