{ "type": "genome", "identifier": "GCA_022705125.1", "organism": "Pseudomonadota bacterium", "title": "Pseudomonadota bacterium", "description": "derived from metagenome; genus undefined", "data type": "Genome sequencing and assembly", "organization": "University of Illinois at Urbana-Champaign", "publication": [ {} ], "properties": { "assembly_accession": "GCA_022705125.1", "bioproject": "PRJNA797469", "biosample": "SAMN25010683", "wgs_master": "JAKJFB000000000.1", "refseq_category": "na", "taxid": "1977087", "species_taxid": "1977087", "organism_name": "Pseudomonadota bacterium", "infraspecific_name": "", "isolate": "UR.bin41", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2022/03/28", "asm_name": "ASM2270512v1", "submitter": "University of Illinois at Urbana-Champaign", "gbrs_paired_asm": "na", "paired_asm_comp": "na", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/022/705/125/GCA_022705125.1_ASM2270512v1", "excluded_from_refseq": "derived from metagenome; genus undefined", "relation_to_type_material": "", "asm_not_live_date": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2022-03-28", "dateModified": "2022-03-28", "datePublished": "2022-03-28", "_annotation": { "sample_count": 1, "sample_organism": [ "Pseudomonadota bacterium" ], "sample_taxid": [ "1977087" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "USA: Urbana" ], "sample_host_location_id": [], "data_size": "1.086 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": null, "max": null }, "completeness": 41.67, "contamination": 0.0, "strain_heterogeneity": 0.0, "genome_count": 1 }, "data_type": "MAG", "data_source": "INSDC", "_dfast": { "Total Sequence Length (bp)": "3916540", "Number of Sequences": "949", "Longest Sequences (bp)": "42010", "N50 (bp)": "6464", "Gap Ratio (%)": "0.251957", "GCcontent (%)": "68.6", "Number of CDSs": "2958", "Average Protein Length": "297.8", "Coding Ratio (%)": "67.5", "Number of rRNAs": "0", "Number of tRNAs": "32", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Pseudomonas lalucatii", "strain": "strain=R1b54", "accession": "GCA_018398425.1", "taxid": 1424203, "species_taxid": 1424203, "relation_to_type": "type", "validated": true, "ani": 77.1943, "matched_fragments": 177, "total_fragments": 845, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Azotobacter chroococcum subsp. isscasi", "strain": "strain=P205", "accession": "GCA_004327895.1", "taxid": 2528971, "species_taxid": 353, "relation_to_type": "type", "validated": true, "ani": 77.0913, "matched_fragments": 154, "total_fragments": 845, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas thermotolerans", "strain": "strain=DSM 14292", "accession": "GCA_000364625.1", "taxid": 157784, "species_taxid": 157784, "relation_to_type": "type", "validated": true, "ani": 77.0688, "matched_fragments": 132, "total_fragments": 845, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Halomonas heilongjiangensis", "strain": "strain=9-2", "accession": "GCA_003202165.1", "taxid": 1387883, "species_taxid": 1387883, "relation_to_type": "type", "validated": true, "ani": 77.0397, "matched_fragments": 130, "total_fragments": 845, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas mangrovi", "strain": "strain=TC11", "accession": "GCA_003052585.1", "taxid": 2161748, "species_taxid": 2161748, "relation_to_type": "type", "validated": true, "ani": 76.9296, "matched_fragments": 124, "total_fragments": 845, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas hydrolytica", "strain": "strain=DSWY01", "accession": "GCA_021495345.2", "taxid": 2493633, "species_taxid": 2493633, "relation_to_type": "type", "validated": true, "ani": 76.8529, "matched_fragments": 148, "total_fragments": 845, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Halomonas shengliensis", "strain": "strain=CGMCC 1.6444", "accession": "GCA_900104135.1", "taxid": 419597, "species_taxid": 419597, "relation_to_type": "type", "validated": true, "ani": 76.7006, "matched_fragments": 135, "total_fragments": 845, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Halomonas aestuarii", "strain": "strain=Hb3", "accession": "GCA_001886615.1", "taxid": 1897729, "species_taxid": 1897729, "relation_to_type": "type", "validated": true, "ani": 76.6479, "matched_fragments": 130, "total_fragments": 845, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas mosselii", "strain": "strain=DSM 17497", "accession": "GCA_019823065.1", "taxid": 78327, "species_taxid": 78327, "relation_to_type": "type", "validated": true, "ani": 76.6458, "matched_fragments": 133, "total_fragments": 845, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas mosselii", "strain": "strain=DSM 17497", "accession": "GCA_000621225.1", "taxid": 78327, "species_taxid": 78327, "relation_to_type": "type", "validated": true, "ani": 76.6249, "matched_fragments": 134, "total_fragments": 845, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Thiohalobacter thiocyanaticus", "strain": "strain=Hrh1", "accession": "GCA_003932505.1", "taxid": 585455, "species_taxid": 585455, "relation_to_type": "type", "validated": true, "ani": 76.5636, "matched_fragments": 102, "total_fragments": 845, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Thioalkalivibrio sulfidiphilus", "strain": "strain=HL-EbGR7", "accession": "GCA_000021985.1", "taxid": 1033854, "species_taxid": 1033854, "relation_to_type": "type", "validated": true, "ani": 76.5588, "matched_fragments": 87, "total_fragments": 845, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Salinicola tamaricis", "strain": "strain=F01", "accession": "GCA_003006155.1", "taxid": 1771309, "species_taxid": 1771309, "relation_to_type": "type", "validated": true, "ani": 76.4711, "matched_fragments": 111, "total_fragments": 845, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Thioalbus denitrificans", "strain": "strain=DSM 26407", "accession": "GCA_003337735.1", "taxid": 547122, "species_taxid": 547122, "relation_to_type": "type", "validated": true, "ani": 76.4418, "matched_fragments": 125, "total_fragments": 845, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Halomonas ethanolica", "strain": "strain=MCCC 1A11081", "accession": "GCA_021404305.1", "taxid": 2733486, "species_taxid": 2733486, "relation_to_type": "type", "validated": true, "ani": 76.4069, "matched_fragments": 107, "total_fragments": 845, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Halomonas kenyensis", "strain": "strain=DSM 17331", "accession": "GCA_022341445.1", "taxid": 321266, "species_taxid": 321266, "relation_to_type": "type", "validated": true, "ani": 76.4036, "matched_fragments": 96, "total_fragments": 845, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas oryzihabitans", "strain": "strain=DSM 6835", "accession": "GCA_012986195.1", "taxid": 47885, "species_taxid": 47885, "relation_to_type": "suspected-type", "validated": true, "ani": 76.3412, "matched_fragments": 140, "total_fragments": 845, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas oryzihabitans", "strain": "strain=NBRC 102199", "accession": "GCA_000730625.1", "taxid": 47885, "species_taxid": 47885, "relation_to_type": "suspected-type", "validated": true, "ani": 76.3135, "matched_fragments": 141, "total_fragments": 845, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas rhizoryzae", "strain": "strain=RY24", "accession": "GCA_005250615.1", "taxid": 2571129, "species_taxid": 2571129, "relation_to_type": "type", "validated": true, "ani": 76.2488, "matched_fragments": 119, "total_fragments": 845, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudohaliea rubra", "strain": "strain=DSM 19751", "accession": "GCA_000764025.1", "taxid": 475795, "species_taxid": 475795, "relation_to_type": "type", "validated": true, "ani": 76.0889, "matched_fragments": 99, "total_fragments": 845, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Fulvimonas soli", "strain": "strain=LMG 19981", "accession": "GCA_006352285.1", "taxid": 155197, "species_taxid": 155197, "relation_to_type": "type", "validated": true, "ani": 75.9946, "matched_fragments": 190, "total_fragments": 845, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Fulvimonas soli", "strain": "strain=DSM 14263", "accession": "GCA_003148905.1", "taxid": 155197, "species_taxid": 155197, "relation_to_type": "type", "validated": true, "ani": 75.9335, "matched_fragments": 203, "total_fragments": 845, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 41.67, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCA_016718385.1", "gtdb_species": "s__UBA5518 sp016718385", "ani": 94.8703, "matched_fragments": 677, "total_fragments": 845, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__UBA5518;g__UBA5518", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.99", "min_intra_species_ani": "98.50", "mean_intra_species_af": "0.94", "min_intra_species_af": "0.92", "num_clustered_genomes": 5, "status": "-" }, { "accession": "GCA_018057015.1", "gtdb_species": "s__UBA5518 sp018057015", "ani": 87.8526, "matched_fragments": 466, "total_fragments": 845, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__UBA5518;g__UBA5518", "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_016705365.1", "gtdb_species": "s__UBA5518 sp002396625", "ani": 78.5031, "matched_fragments": 350, "total_fragments": 845, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__UBA5518;g__UBA5518", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.76", "min_intra_species_ani": "99.45", "mean_intra_species_af": "0.96", "min_intra_species_af": "0.89", "num_clustered_genomes": 14, "status": "-" }, { "accession": "GCA_903928015.1", "gtdb_species": "s__UBA5518 sp903928015", "ani": 78.4709, "matched_fragments": 258, "total_fragments": 845, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__UBA5518;g__UBA5518", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.79", "min_intra_species_ani": "99.63", "mean_intra_species_af": "0.93", "min_intra_species_af": "0.92", "num_clustered_genomes": 4, "status": "-" }, { "accession": "GCA_903921135.1", "gtdb_species": "s__UBA5518 sp903921135", "ani": 78.2004, "matched_fragments": 251, "total_fragments": 845, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__UBA5518;g__UBA5518", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.78", "min_intra_species_ani": "97.78", "mean_intra_species_af": "0.78", "min_intra_species_af": "0.78", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCA_903938575.1", "gtdb_species": "s__UBA5518 sp903938575", "ani": 78.1378, "matched_fragments": 226, "total_fragments": 845, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__UBA5518;g__UBA5518", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.92", "min_intra_species_ani": "98.84", "mean_intra_species_af": "0.83", "min_intra_species_af": "0.82", "num_clustered_genomes": 4, "status": "-" }, { "accession": "GCA_001577635.1", "gtdb_species": "s__Halomonas_C sp001577635", "ani": 76.9195, "matched_fragments": 122, "total_fragments": 845, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas_C", "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_002699145.1", "gtdb_species": "s__Halioglobus sp002699145", "ani": 76.7176, "matched_fragments": 174, "total_fragments": 845, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Halioglobus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.96", "min_intra_species_ani": "99.96", "mean_intra_species_af": "0.98", "min_intra_species_af": "0.98", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_007665395.1", "gtdb_species": "s__Pseudomonas_B psychrotolerans_C", "ani": 76.2632, "matched_fragments": 144, "total_fragments": 845, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_B", "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_001182895.1", "gtdb_species": "s__Frateuria_B defendens", "ani": 75.9898, "matched_fragments": 160, "total_fragments": 845, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Frateuria_B", "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_013362045.1", "gtdb_species": "s__Frateuria_A sp013362045", "ani": 75.94, "matched_fragments": 123, "total_fragments": 845, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Frateuria_A", "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": null, "cell_length": null, "doubling_h": null, "growth_tmp": null, "optimum_tmp": null, "optimum_ph": null, "genome_size": null, "gc_content": null, "coding_genes": null, "rRNA16S_genes": null, "tRNA_genes": null, "gram_stain": null, "sporulation": null, "motility": null, "range_salinity": null, "facultative_respiration": null, "anaerobic_respiration": null, "aerobic_respiration": null, "mesophilic_range_tmp": null, "thermophilic_range_tmp": null, "psychrophilic_range_tmp": null, "bacillus_cell_shape": null, "coccus_cell_shape": null, "filament_cell_shape": null, "coccobacillus_cell_shape": null, "vibrio_cell_shape": null, "spiral_cell_shape": null }, "_gtdb_taxon": [ "d__Bacteria", "p__Pseudomonadota", "c__Gammaproteobacteria", "o__Pseudomonadales", "f__UBA5518", "g__UBA5518", "s__UBA5518 sp022705125" ], "_genome_taxon": [ "Pseudomonadota", "bacterium", "d__Bacteria", "p__Pseudomonadota", "c__Gammaproteobacteria", "o__Pseudomonadales", "f__UBA5518", "g__UBA5518", "s__UBA5518 sp022705125", "Bacteria", "Pseudomonadota", "Gammaproteobacteria", "Pseudomonadales", "UBA5518", "UBA5518", "UBA5518", "sp022705125" ], "_meo": [ { "id": "MEO_0001192", "label": "anaerobic digester" } ], "quality": 2, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f" }