{ "type": "genome", "identifier": "GCA_004322295.1", "organism": "Porticoccaceae bacterium", "title": "Porticoccaceae bacterium", "description": "derived from metagenome; fragmented assembly; genus undefined", "data type": "Genome sequencing and assembly", "organization": "University of Oklahoma", "publication": [ {} ], "properties": { "assembly_accession": "GCA_004322295.1", "bioproject": "PRJNA514088", "biosample": "SAMN10720187", "wgs_master": "SCTH00000000.1", "refseq_category": "na", "taxid": "2026782", "species_taxid": "2026782", "organism_name": "Porticoccaceae bacterium", "infraspecific_name": "", "isolate": "FW300_bin.53", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2019/02/25", "asm_name": "ASM432229v1", "submitter": "University of Oklahoma", "gbrs_paired_asm": "na", "paired_asm_comp": "na", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/004/322/295/GCA_004322295.1_ASM432229v1", "excluded_from_refseq": "derived from metagenome; fragmented assembly; genus undefined", "relation_to_type_material": "", "asm_not_live_date": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2019-02-25", "dateModified": "2019-02-25", "datePublished": "2019-02-25", "_annotation": { "sample_count": 1, "sample_organism": [ "Porticoccaceae bacterium" ], "sample_taxid": [ "2026782" ], "sample_host_organism": [ "not applicable" ], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "USA: Tennessee" ], "sample_host_location_id": [], "data_size": "0.720 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": null, "max": null }, "completeness": 95.45, "contamination": 9.84, "strain_heterogeneity": 57.14, "genome_count": 1 }, "data_type": "MAG", "data_source": "INSDC", "_dfast": { "Total Sequence Length (bp)": "2550519", "Number of Sequences": "736", "Longest Sequences (bp)": "22435", "N50 (bp)": "4491", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "64.5", "Number of CDSs": "1696", "Average Protein Length": "291.0", "Coding Ratio (%)": "58.1", "Number of rRNAs": "1", "Number of tRNAs": "36", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Microbulbifer rhizosphaerae", "strain": "strain=CECT 8799", "accession": "GCA_014191725.1", "taxid": 1562603, "species_taxid": 1562603, "relation_to_type": "type", "validated": true, "ani": 77.0624, "matched_fragments": 55, "total_fragments": 457, "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": 76.7581, "matched_fragments": 52, "total_fragments": 457, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Alcanivorax gelatiniphagus", "strain": "strain=MEBiC 08158", "accession": "GCA_005938655.1", "taxid": 1194167, "species_taxid": 1194167, "relation_to_type": "type", "validated": true, "ani": 76.5691, "matched_fragments": 67, "total_fragments": 457, "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": 76.5572, "matched_fragments": 53, "total_fragments": 457, "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": 76.5553, "matched_fragments": 67, "total_fragments": 457, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Marinobacterium nitratireducens", "strain": "strain=CGMCC 1.7286", "accession": "GCA_014645375.1", "taxid": 518897, "species_taxid": 518897, "relation_to_type": "type", "validated": true, "ani": 76.5238, "matched_fragments": 51, "total_fragments": 457, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Halomonas sulfidoxydans", "strain": "strain=MCCC 1A11059", "accession": "GCA_017868775.1", "taxid": 2733484, "species_taxid": 2733484, "relation_to_type": "type", "validated": true, "ani": 76.5142, "matched_fragments": 60, "total_fragments": 457, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas yangonensis", "strain": "strain=MY50", "accession": "GCA_009932725.1", "taxid": 2579922, "species_taxid": 2579922, "relation_to_type": "type", "validated": true, "ani": 76.4875, "matched_fragments": 50, "total_fragments": 457, "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": 76.4313, "matched_fragments": 73, "total_fragments": 457, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas guguanensis", "strain": "strain=JCM 18416", "accession": "GCA_900104265.1", "taxid": 1198456, "species_taxid": 1198456, "relation_to_type": "type", "validated": true, "ani": 76.3258, "matched_fragments": 58, "total_fragments": 457, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas psychrotolerans", "strain": "strain=DSM 15758", "accession": "GCA_012985915.1", "taxid": 237610, "species_taxid": 237610, "relation_to_type": "suspected-type", "validated": true, "ani": 76.3228, "matched_fragments": 58, "total_fragments": 457, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas psychrotolerans", "strain": "strain=DSM 15758", "accession": "GCA_900102665.1", "taxid": 237610, "species_taxid": 237610, "relation_to_type": "suspected-type", "validated": true, "ani": 76.3155, "matched_fragments": 57, "total_fragments": 457, "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": 76.2514, "matched_fragments": 53, "total_fragments": 457, "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": 76.2173, "matched_fragments": 54, "total_fragments": 457, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas campi", "strain": "strain=S1-A32-2", "accession": "GCA_013200955.2", "taxid": 2731681, "species_taxid": 2731681, "relation_to_type": "type", "validated": true, "ani": 76.0989, "matched_fragments": 56, "total_fragments": 457, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas cavernae", "strain": "strain=K2W31S-8", "accession": "GCA_003595175.1", "taxid": 2320867, "species_taxid": 2320867, "relation_to_type": "type", "validated": true, "ani": 75.9249, "matched_fragments": 61, "total_fragments": 457, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 95.45, "contamination": 9.84, "strain_heterogeneity": 57.14 }, "gtdb_result": [ { "accession": "GCA_016191205.1", "gtdb_species": "s__JAGPUQ01 sp016191205", "ani": 97.908, "matched_fragments": 351, "total_fragments": 457, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__JAGPUQ01", "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": "GCA_016708925.1", "gtdb_species": "s__JAGPUQ01 sp016708925", "ani": 91.536, "matched_fragments": 402, "total_fragments": 457, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__JAGPUQ01", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.16", "min_intra_species_ani": "98.04", "mean_intra_species_af": "0.89", "min_intra_species_af": "0.89", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_004745945.1", "gtdb_species": "s__Halioglobus sp004745945", "ani": 76.6695, "matched_fragments": 75, "total_fragments": 457, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Halioglobus", "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_005938655.1", "gtdb_species": "s__Alcanivorax gelatiniphagus", "ani": 76.5691, "matched_fragments": 67, "total_fragments": 457, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__Alcanivorax", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.53", "min_intra_species_ani": "98.53", "mean_intra_species_af": "0.93", "min_intra_species_af": "0.93", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_017255185.1", "gtdb_species": "s__Parahaliea mediterranea_A", "ani": 76.492, "matched_fragments": 75, "total_fragments": 457, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Parahaliea", "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_005250615.1", "gtdb_species": "s__Pseudomonas_B rhizoryzae", "ani": 76.4821, "matched_fragments": 55, "total_fragments": 457, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_B", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.30", "min_intra_species_ani": "97.74", "mean_intra_species_af": "0.93", "min_intra_species_af": "0.89", "num_clustered_genomes": 15, "status": "-" }, { "accession": "GCF_018398425.1", "gtdb_species": "s__Pseudomonas_E lalucatii", "ani": 76.4313, "matched_fragments": 73, "total_fragments": 457, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.68", "min_intra_species_ani": "99.28", "mean_intra_species_af": "0.97", "min_intra_species_af": "0.92", "num_clustered_genomes": 4, "status": "-" }, { "accession": "GCF_900187975.1", "gtdb_species": "s__Pseudomonas delhiensis", "ani": 76.4289, "matched_fragments": 77, "total_fragments": 457, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas", "ani_circumscription_radius": 95.078, "mean_intra_species_ani": "98.79", "min_intra_species_ani": "97.59", "mean_intra_species_af": "0.94", "min_intra_species_af": "0.89", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_900112375.1", "gtdb_species": "s__Pseudomonas citronellolis", "ani": 76.4022, "matched_fragments": 82, "total_fragments": 457, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas", "ani_circumscription_radius": 95.078, "mean_intra_species_ani": "97.44", "min_intra_species_ani": "97.08", "mean_intra_species_af": "0.86", "min_intra_species_af": "0.82", "num_clustered_genomes": 26, "status": "-" }, { "accession": "GCF_000730625.1", "gtdb_species": "s__Pseudomonas_B oryzihabitans", "ani": 76.2173, "matched_fragments": 54, "total_fragments": 457, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_B", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.97", "min_intra_species_ani": "96.38", "mean_intra_species_af": "0.92", "min_intra_species_af": "0.87", "num_clustered_genomes": 28, "status": "-" }, { "accession": "GCF_000377945.1", "gtdb_species": "s__Thioalkalivibrio_A sulfidiphilus_A", "ani": 76.2038, "matched_fragments": 51, "total_fragments": 457, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Ectothiorhodospirales;f__Ectothiorhodospiraceae;g__Thioalkalivibrio_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": "-" }, { "accession": "GCF_006384975.1", "gtdb_species": "s__Pseudomonas_B psychrotolerans_B", "ani": 76.0559, "matched_fragments": 53, "total_fragments": 457, "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_001650425.1", "gtdb_species": "s__Pseudomonas_B oryzihabitans_B", "ani": 76.0252, "matched_fragments": 54, "total_fragments": 457, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_B", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.78", "min_intra_species_ani": "97.39", "mean_intra_species_af": "0.90", "min_intra_species_af": "0.88", "num_clustered_genomes": 6, "status": "-" }, { "accession": "GCF_001512295.1", "gtdb_species": "s__Pseudomonas_B sp001512295", "ani": 75.9535, "matched_fragments": 56, "total_fragments": 457, "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": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": -0.31, "cell_length": -0.31, "doubling_h": null, "growth_tmp": 25.0, "optimum_tmp": 22.5, "optimum_ph": 7.5, "genome_size": 2547762.0, "gc_content": null, "coding_genes": null, "rRNA16S_genes": null, "tRNA_genes": null, "gram_stain": 0.0, "sporulation": 0.0, "motility": 0.5, "range_salinity": null, "facultative_respiration": 0.0, "anaerobic_respiration": 0.0, "aerobic_respiration": 1.0, "mesophilic_range_tmp": null, "thermophilic_range_tmp": null, "psychrophilic_range_tmp": null, "bacillus_cell_shape": 0.5, "coccus_cell_shape": 0.5, "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__Pseudomonadales", "f__Porticoccaceae", "g__JAGPUQ01", "s__JAGPUQ01 sp016191205" ], "_genome_taxon": [ "Porticoccaceae", "bacterium", "d__Bacteria", "p__Pseudomonadota", "c__Gammaproteobacteria", "o__Pseudomonadales", "f__Porticoccaceae", "g__JAGPUQ01", "s__JAGPUQ01 sp016191205", "Bacteria", "Pseudomonadota", "Gammaproteobacteria", "Pseudomonadales", "Porticoccaceae", "JAGPUQ01", "JAGPUQ01", "sp016191205" ], "_meo": [ { "id": "MEO_0000366", "label": "ground water" } ], "quality": 3, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }