{ "type": "genome", "identifier": "GCF_000820515.1", "organism": "Pseudomonas batumici", "title": "Pseudomonas batumici", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Institute of Microbiology and Virology", "publication": [ {} ], "properties": { "assembly_accession": "GCF_000820515.1", "bioproject": "PRJNA224116", "biosample": "SAMN03273282", "wgs_master": "JXDG00000000.1", "refseq_category": "na", "taxid": "226910", "species_taxid": "226910", "organism_name": "Pseudomonas batumici", "infraspecific_name": "strain=UCM B-321", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2015/01/16", "asm_name": "ASM82051v1", "asm_submitter": "Institute of Microbiology and Virology", "gbrs_paired_asm": "GCA_000820515.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/820/515/GCF_000820515.1_ASM82051v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "6606796", "genome_size_ungapped": "6606796", "gc_percent": "62.000000", "replicon_count": "0", "scaffold_count": "126", "contig_count": "126", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_000820515.1-RS_2024_04_29", "annotation_date": "2024-04-29", "total_gene_count": "5978", "protein_coding_gene_count": "5788", "non_coding_gene_count": "63", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2015-01-16", "dateModified": "2015-01-16", "datePublished": "2015-01-16", "_annotation": { "sample_count": 1, "sample_organism": [ "Pseudomonas batumici" ], "sample_taxid": [ "226910" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "Georgia: Batumi, the Black Sea coast of the Caucasus" ], "sample_host_location_id": [], "data_size": "1.847 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)": "6606796", "Number of Sequences": "126", "Longest Sequences (bp)": "468112", "N50 (bp)": "133994", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "61.8", "Number of CDSs": "5791", "Average Protein Length": "327.4", "Coding Ratio (%)": "86.1", "Number of rRNAs": "3", "Number of tRNAs": "62", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Pseudomonas batumici", "strain": "strain=UCM B-321", "accession": "GCA_000820515.1", "taxid": 226910, "species_taxid": 226910, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 2125, "total_fragments": 2147, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Pseudomonas fuscovaginae", "strain": "strain=LMG 2158", "accession": "GCA_900108595.1", "taxid": 50340, "species_taxid": 50340, "relation_to_type": "suspected-type", "validated": true, "ani": 85.5104, "matched_fragments": 1333, "total_fragments": 2147, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas chlororaphis subsp. aureofaciens", "strain": "strain=DSM 6698", "accession": "GCA_003851905.1", "taxid": 587851, "species_taxid": 587753, "relation_to_type": "type", "validated": true, "ani": 84.886, "matched_fragments": 1266, "total_fragments": 2147, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas chlororaphis subsp. aureofaciens", "strain": "strain=LMG 1245", "accession": "GCA_001269575.1", "taxid": 587851, "species_taxid": 587753, "relation_to_type": "type", "validated": true, "ani": 84.8683, "matched_fragments": 1242, "total_fragments": 2147, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas chlororaphis subsp. aureofaciens", "strain": "strain=NBRC 3521", "accession": "GCA_000813225.1", "taxid": 587851, "species_taxid": 587753, "relation_to_type": "type", "validated": true, "ani": 84.8116, "matched_fragments": 1250, "total_fragments": 2147, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas agarici", "strain": "strain=IPO3740", "accession": "GCA_013385305.1", "taxid": 46677, "species_taxid": 46677, "relation_to_type": "type", "validated": true, "ani": 84.7962, "matched_fragments": 1102, "total_fragments": 2147, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas agarici", "strain": "strain=NCPPB 2289", "accession": "GCA_000280785.1", "taxid": 46677, "species_taxid": 46677, "relation_to_type": "type", "validated": true, "ani": 84.7705, "matched_fragments": 1104, "total_fragments": 2147, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas chlororaphis subsp. aurantiaca", "strain": "strain=DSM 19603", "accession": "GCA_003851835.1", "taxid": 86192, "species_taxid": 587753, "relation_to_type": "type", "validated": true, "ani": 84.7618, "matched_fragments": 1280, "total_fragments": 2147, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas agarici", "strain": "strain=LMG 2112", "accession": "GCA_900109755.1", "taxid": 46677, "species_taxid": 46677, "relation_to_type": "type", "validated": true, "ani": 84.7501, "matched_fragments": 1104, "total_fragments": 2147, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas protegens", "strain": "strain=CHA0", "accession": "GCA_000397205.1", "taxid": 380021, "species_taxid": 380021, "relation_to_type": "type", "validated": true, "ani": 84.3347, "matched_fragments": 1227, "total_fragments": 2147, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas protegens", "strain": "strain=CHA0", "accession": "GCA_900560965.1", "taxid": 380021, "species_taxid": 380021, "relation_to_type": "type", "validated": true, "ani": 84.3347, "matched_fragments": 1227, "total_fragments": 2147, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas kielensis", "strain": "strain=MBT-1", "accession": "GCA_014236655.1", "taxid": 2762577, "species_taxid": 2762577, "relation_to_type": "type", "validated": true, "ani": 84.1594, "matched_fragments": 1069, "total_fragments": 2147, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas gessardii", "strain": "strain=DSM 17152", "accession": "GCA_001983165.1", "taxid": 78544, "species_taxid": 78544, "relation_to_type": "type", "validated": true, "ani": 83.7828, "matched_fragments": 1082, "total_fragments": 2147, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas gessardii", "strain": "strain=DSM 17152", "accession": "GCA_009671285.1", "taxid": 78544, "species_taxid": 78544, "relation_to_type": "type", "validated": true, "ani": 83.7657, "matched_fragments": 1084, "total_fragments": 2147, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas gessardii", "strain": "", "accession": "GCA_900625085.1", "taxid": 78544, "species_taxid": 78544, "relation_to_type": "type", "validated": true, "ani": 83.7467, "matched_fragments": 1085, "total_fragments": 2147, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas zanjanensis", "strain": "strain=SWRI12", "accession": "GCA_014268745.2", "taxid": 2745496, "species_taxid": 2745496, "relation_to_type": "type", "validated": true, "ani": 83.6558, "matched_fragments": 1131, "total_fragments": 2147, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas brenneri", "strain": "strain=JCM 13307", "accession": "GCA_014646715.1", "taxid": 129817, "species_taxid": 129817, "relation_to_type": "type", "validated": true, "ani": 83.5911, "matched_fragments": 1085, "total_fragments": 2147, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas mediterranea", "strain": "strain=DSM 16733", "accession": "GCA_900106005.1", "taxid": 183795, "species_taxid": 183795, "relation_to_type": "type", "validated": true, "ani": 83.5041, "matched_fragments": 1147, "total_fragments": 2147, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas mediterranea", "strain": "strain=CFBP 5447", "accession": "GCA_000774145.1", "taxid": 183795, "species_taxid": 183795, "relation_to_type": "type", "validated": true, "ani": 83.4069, "matched_fragments": 1163, "total_fragments": 2147, "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": 83.194, "matched_fragments": 1143, "total_fragments": 2147, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas bharatica", "strain": "strain=CSV86", "accession": "GCA_000319305.2", "taxid": 2692112, "species_taxid": 2692112, "relation_to_type": "type", "validated": true, "ani": 82.6623, "matched_fragments": 976, "total_fragments": 2147, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas faucium", "strain": "strain=BML-PP048", "accession": "GCA_013373935.1", "taxid": 2740518, "species_taxid": 2740518, "relation_to_type": "type", "validated": true, "ani": 82.5627, "matched_fragments": 923, "total_fragments": 2147, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas faucium", "strain": "strain=BML-PP048", "accession": "GCA_021602585.1", "taxid": 2740518, "species_taxid": 2740518, "relation_to_type": "type", "validated": true, "ani": 82.5039, "matched_fragments": 971, "total_fragments": 2147, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas capeferrum", "strain": "strain=WCS358", "accession": "GCA_022548835.1", "taxid": 1495066, "species_taxid": 1495066, "relation_to_type": "type", "validated": true, "ani": 81.8088, "matched_fragments": 858, "total_fragments": 2147, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas lalucatii", "strain": "strain=R1b54", "accession": "GCA_018398425.1", "taxid": 1424203, "species_taxid": 1424203, "relation_to_type": "type", "validated": true, "ani": 81.385, "matched_fragments": 775, "total_fragments": 2147, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_000820515.1", "gtdb_species": "s__Pseudomonas_E batumici", "ani": 100.0, "matched_fragments": 2122, "total_fragments": 2147, "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": "conclusive" }, { "accession": "GCF_002814235.1", "gtdb_species": "s__Pseudomonas_E sp002814235", "ani": 90.8266, "matched_fragments": 1694, "total_fragments": 2147, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.25", "min_intra_species_ani": "95.56", "mean_intra_species_af": "0.91", "min_intra_species_af": "0.90", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_013385425.1", "gtdb_species": "s__Pseudomonas_E gingeri_D", "ani": 90.7864, "matched_fragments": 1689, "total_fragments": 2147, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.70", "min_intra_species_ani": "98.70", "mean_intra_species_af": "0.93", "min_intra_species_af": "0.93", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_004011535.1", "gtdb_species": "s__Pseudomonas_E asplenii_A", "ani": 90.7773, "matched_fragments": 1703, "total_fragments": 2147, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E", "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": 4, "status": "-" }, { "accession": "GCF_904067045.1", "gtdb_species": "s__Pseudomonas_E sp904067045", "ani": 90.557, "matched_fragments": 1574, "total_fragments": 2147, "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_013386165.1", "gtdb_species": "s__Pseudomonas_E gingeri_C", "ani": 90.1642, "matched_fragments": 1694, "total_fragments": 2147, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.61", "min_intra_species_ani": "98.31", "mean_intra_species_af": "0.93", "min_intra_species_af": "0.92", "num_clustered_genomes": 4, "status": "-" }, { "accession": "GCF_013386115.1", "gtdb_species": "s__Pseudomonas_E gingeri_B", "ani": 87.1769, "matched_fragments": 1482, "total_fragments": 2147, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.74", "min_intra_species_ani": "98.43", "mean_intra_species_af": "0.94", "min_intra_species_af": "0.92", "num_clustered_genomes": 9, "status": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": -0.248, "cell_length": 0.186, "doubling_h": -0.025, "growth_tmp": 28.767, "optimum_tmp": 27.972, "optimum_ph": 7.258, "genome_size": 6593132.0, "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", "batumici" ], "quality": 4, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }