{ "type": "genome", "identifier": "GCF_000158475.2", "organism": "Oxalobacter paraformigenes", "title": "Oxalobacter paraformigenes", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Broad Institute", "publication": [ {} ], "properties": { "assembly_accession": "GCF_000158475.2", "bioproject": "PRJNA224116", "biosample": "SAMN02463716", "wgs_master": "ACDP00000000.2", "refseq_category": "reference genome", "taxid": "556268", "species_taxid": "556268", "organism_name": "Oxalobacter paraformigenes", "infraspecific_name": "strain=HOxBLS", "isolate": "na", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2013/09/30", "asm_name": "Oxal_for_HOxBLS_2_V2", "asm_submitter": "Broad Institute", "gbrs_paired_asm": "GCA_000158475.2", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/158/475/GCF_000158475.2_Oxal_for_HOxBLS_2_V2", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "2488386", "genome_size_ungapped": "2485686", "gc_percent": "52.500000", "replicon_count": "0", "scaffold_count": "2", "contig_count": "29", "annotation_provider": "NCBI RefSeq", "annotation_name": "NCBI Prokaryotic Genome Annotation Pipeline (PGAP)", "annotation_date": "2024-03-03", "total_gene_count": "2285", "protein_coding_gene_count": "2220", "non_coding_gene_count": "51", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2013-09-30", "dateModified": "2013-09-30", "datePublished": "2013-09-30", "_annotation": { "sample_count": 1, "sample_organism": [ "Oxalobacter paraformigenes" ], "sample_taxid": [ "556268" ], "sample_host_organism": [ "Homo sapiens" ], "sample_host_organism_id": [], "sample_host_disease": [], 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"ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Herbaspirillum huttiense subsp. putei", "strain": "strain=IAM 15032", "accession": "GCA_000478365.1", "taxid": 230311, "species_taxid": 863372, "relation_to_type": "type", "validated": true, "ani": 76.9083, "matched_fragments": 52, "total_fragments": 829, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Herbaspirillum aquaticum", "strain": "strain=IEH 4430", "accession": "GCA_002213425.1", "taxid": 568783, "species_taxid": 568783, "relation_to_type": "type", "validated": true, "ani": 76.8569, "matched_fragments": 53, "total_fragments": 829, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Collimonas fungivorans", "strain": "strain=Ter6", "accession": "GCA_001584145.1", "taxid": 158899, "species_taxid": 158899, "relation_to_type": "type", "validated": true, "ani": 76.8329, "matched_fragments": 55, "total_fragments": 829, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Collimonas pratensis", "strain": "strain=Ter91", "accession": "GCA_001584185.1", "taxid": 279113, "species_taxid": 279113, "relation_to_type": "type", "validated": true, "ani": 76.7525, "matched_fragments": 53, "total_fragments": 829, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Oxalicibacterium solurbis", "strain": "strain=CCM 7664", "accession": "GCA_014635845.1", "taxid": 69280, "species_taxid": 69280, "relation_to_type": "type", "validated": true, "ani": 76.4488, "matched_fragments": 64, "total_fragments": 829, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Noviherbaspirillum autotrophicum", "strain": "strain=TSA66", "accession": "GCA_000818395.1", "taxid": 709839, "species_taxid": 709839, "relation_to_type": "type", "validated": true, "ani": 76.4021, "matched_fragments": 50, "total_fragments": 829, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Herbaspirillum autotrophicum", "strain": "strain=IAM 14942", "accession": "GCA_001189915.1", "taxid": 180195, "species_taxid": 180195, "relation_to_type": "type", "validated": true, "ani": 76.3033, "matched_fragments": 63, "total_fragments": 829, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Collimonas humicola", "strain": "strain=RLT1W51", "accession": "GCA_018304945.1", "taxid": 2825886, "species_taxid": 2825886, "relation_to_type": "type", "validated": true, "ani": 76.2877, "matched_fragments": 62, "total_fragments": 829, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Janthinobacterium agaricidamnosum", "strain": "strain=NBRC 102515", "accession": "GCA_001571185.1", "taxid": 55508, "species_taxid": 55508, "relation_to_type": "type", "validated": true, "ani": 76.1366, "matched_fragments": 58, "total_fragments": 829, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, 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"s__Oxalobacter sp017524145", "ani": 76.0963, "matched_fragments": 66, "total_fragments": 829, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Oxalobacter", "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": -0.398, "cell_length": 0.079, "doubling_h": null, "growth_tmp": 29.5, "optimum_tmp": 37.0, "optimum_ph": null, "genome_size": 2463878.833, "gc_content": 50.375, "coding_genes": 2217.667, "rRNA16S_genes": 1.5, "tRNA_genes": 47.0, "gram_stain": 0.0, "sporulation": 0.0, "motility": null, "range_salinity": null, "facultative_respiration": 0.0, "anaerobic_respiration": 1.0, "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": [ "Oxalobacter", "paraformigenes" ], "quality": 5, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }