{ "type": "genome", "identifier": "GCF_000227685.2", "organism": "Thioalkalivibrio paradoxus ARh 1", "title": "Thioalkalivibrio paradoxus ARh 1", "description": "na", "data type": "Genome sequencing and assembly", "organization": "DOE Joint Genome Institute", "publication": [ {} ], "properties": { "assembly_accession": "GCF_000227685.2", "bioproject": "PRJNA224116", "biosample": "SAMN02256529", "wgs_master": "na", "refseq_category": "reference genome", "taxid": "713585", "species_taxid": "108010", "organism_name": "Thioalkalivibrio paradoxus ARh 1", "infraspecific_name": "strain=ARh 1", "isolate": "na", "version_status": "latest", "assembly_level": "Complete Genome", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2014/01/03", "asm_name": "ASM22768v3", "asm_submitter": "DOE Joint Genome Institute", "gbrs_paired_asm": "GCA_000227685.3", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/227/685/GCF_000227685.2_ASM22768v3", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "3756729", "genome_size_ungapped": "3756729", "gc_percent": "66.500000", "replicon_count": "1", "scaffold_count": "1", "contig_count": "1", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_000227685.2-RS_2024_12_13", "annotation_date": "2024-12-13", "total_gene_count": "3549", "protein_coding_gene_count": "3405", "non_coding_gene_count": "53", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2014-01-03", "dateModified": "2014-01-03", "datePublished": "2014-01-03", "_annotation": { "sample_count": 1, "sample_organism": [ "Thioalkalivibrio paradoxus ARh 1" ], "sample_taxid": [ "713585" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [ "None" ], "sample_host_disease_id": [], "sample_host_location": [ "Missing" ], "sample_host_location_id": [], "data_size": "1.029 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)": "3756729", "Number of Sequences": "1", "Longest Sequences (bp)": "3756729", "N50 (bp)": "3756729", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "66.5", "Number of CDSs": "3456", "Average Protein Length": "315.7", "Coding Ratio (%)": "87.1", "Number of rRNAs": "3", "Number of tRNAs": "47", "Number of CRISPRs": "8" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Thioalkalivibrio paradoxus", "strain": "strain=ARh 1", "accession": "GCA_000227685.3", "taxid": 108010, "species_taxid": 108010, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1252, "total_fragments": 1252, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Thioalkalivibrio nitratireducens", "strain": "strain=DSM 14787", "accession": "GCA_000321415.2", "taxid": 186931, "species_taxid": 186931, "relation_to_type": "type", "validated": true, "ani": 89.7657, "matched_fragments": 1005, "total_fragments": 1252, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Thioalkalivibrio thiocyanoxidans", "strain": "strain=ARh2", "accession": "GCA_000385215.1", "taxid": 152475, "species_taxid": 152475, "relation_to_type": "type", "validated": true, "ani": 78.8248, "matched_fragments": 314, "total_fragments": 1252, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Thioalkalivibrio versutus", "strain": "strain=AL 2", "accession": "GCA_001999325.1", "taxid": 106634, "species_taxid": 106634, "relation_to_type": "type", "validated": true, "ani": 78.7438, "matched_fragments": 317, "total_fragments": 1252, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Thioalkalivibrio halophilus", "strain": "strain=HL17", "accession": "GCA_001995255.1", "taxid": 252474, "species_taxid": 252474, "relation_to_type": "type", "validated": true, "ani": 78.6292, "matched_fragments": 314, "total_fragments": 1252, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Acidihalobacter aeolianus", "strain": "strain=V6", "accession": "GCA_001753165.1", "taxid": 2792603, "species_taxid": 2792603, "relation_to_type": "type", "validated": true, "ani": 77.4668, "matched_fragments": 133, "total_fragments": 1252, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Acidihalobacter prosperus", "strain": "strain=DSM 5130", "accession": "GCA_000754095.2", "taxid": 160660, "species_taxid": 160660, "relation_to_type": "type", "validated": true, "ani": 77.3323, "matched_fragments": 128, "total_fragments": 1252, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Allochromatium tepidum", "strain": "strain=NZ", "accession": "GCA_018409545.1", "taxid": 553982, "species_taxid": 553982, "relation_to_type": "type", "validated": true, "ani": 77.1963, "matched_fragments": 138, "total_fragments": 1252, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Methylonatrum kenyense", "strain": "strain=AMT 1", "accession": "GCA_023195885.1", "taxid": 455253, "species_taxid": 455253, "relation_to_type": "type", "validated": true, "ani": 77.1094, "matched_fragments": 119, "total_fragments": 1252, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Crenobacter cavernae", "strain": "strain=K1W11S-77", "accession": "GCA_003355495.1", "taxid": 2290923, "species_taxid": 2290923, "relation_to_type": "type", "validated": true, "ani": 76.682, "matched_fragments": 127, "total_fragments": 1252, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Luteimonas colneyensis", "strain": "strain=Sa2BVA3", "accession": "GCA_014836665.1", "taxid": 2762230, "species_taxid": 2762230, "relation_to_type": "type", "validated": true, "ani": 76.5845, "matched_fragments": 137, "total_fragments": 1252, "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": 76.3145, "matched_fragments": 138, "total_fragments": 1252, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Chromobacterium sphagni", "strain": "strain=IIBBL 14B-1", "accession": "GCA_001855555.1", "taxid": 1903179, "species_taxid": 1903179, "relation_to_type": "type", "validated": true, "ani": 76.2664, "matched_fragments": 106, "total_fragments": 1252, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas insulae", "strain": "strain=UL073", "accession": "GCA_016901015.1", "taxid": 2809017, "species_taxid": 2809017, "relation_to_type": "type", "validated": true, "ani": 76.1495, "matched_fragments": 133, "total_fragments": 1252, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Microbulbifer hainanensis", "strain": "strain=NBU-8HK146", "accession": "GCA_014904735.1", "taxid": 2735675, "species_taxid": 2735675, "relation_to_type": "type", "validated": true, "ani": 76.0203, "matched_fragments": 62, "total_fragments": 1252, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_000227685.2", "gtdb_species": "s__Thioalkalivibrio_B paradoxus", "ani": 100.0, "matched_fragments": 1252, "total_fragments": 1252, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Ectothiorhodospirales;f__Thioalkalivibrionaceae;g__Thioalkalivibrio_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": "conclusive" }, { "accession": "GCF_000321415.2", "gtdb_species": "s__Thioalkalivibrio_B nitratireducens", "ani": 89.7813, "matched_fragments": 1004, "total_fragments": 1252, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Ectothiorhodospirales;f__Thioalkalivibrionaceae;g__Thioalkalivibrio_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_003550945.1", "gtdb_species": "s__Thioalkalivibrio_B sp003550945", "ani": 80.5049, "matched_fragments": 312, "total_fragments": 1252, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Ectothiorhodospirales;f__Thioalkalivibrionaceae;g__Thioalkalivibrio_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_007692535.1", "gtdb_species": "s__Thioalkalivibrio_B sp007692535", "ani": 80.3393, "matched_fragments": 489, "total_fragments": 1252, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Ectothiorhodospirales;f__Thioalkalivibrionaceae;g__Thioalkalivibrio_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_007692435.1", "gtdb_species": "s__Thioalkalivibrio_B sp007692435", "ani": 80.1436, "matched_fragments": 446, "total_fragments": 1252, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Ectothiorhodospirales;f__Thioalkalivibrionaceae;g__Thioalkalivibrio_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_003563455.1", "gtdb_species": "s__Thioalkalivibrio_B sp003563455", "ani": 80.0834, "matched_fragments": 325, "total_fragments": 1252, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Ectothiorhodospirales;f__Thioalkalivibrionaceae;g__Thioalkalivibrio_B", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.96", "min_intra_species_ani": "98.96", "mean_intra_species_af": "0.85", "min_intra_species_af": "0.85", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCA_011389655.1", "gtdb_species": "s__Thioalkalivibrio_B sp011389655", "ani": 79.7968, "matched_fragments": 457, "total_fragments": 1252, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Ectothiorhodospirales;f__Thioalkalivibrionaceae;g__Thioalkalivibrio_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_003555285.1", "gtdb_species": "s__Thioalkalivibrio_B sp003555285", "ani": 79.7338, "matched_fragments": 407, "total_fragments": 1252, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Ectothiorhodospirales;f__Thioalkalivibrionaceae;g__Thioalkalivibrio_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_018224485.1", "gtdb_species": "s__Thioalkalivibrio_B sp018224485", "ani": 79.6963, "matched_fragments": 349, "total_fragments": 1252, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Ectothiorhodospirales;f__Thioalkalivibrionaceae;g__Thioalkalivibrio_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_011390565.1", "gtdb_species": "s__Thioalkalivibrio_B paradoxus_A", "ani": 79.6495, "matched_fragments": 440, "total_fragments": 1252, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Ectothiorhodospirales;f__Thioalkalivibrionaceae;g__Thioalkalivibrio_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_007133115.1", "gtdb_species": "s__Thioalkalivibrio_B sp007133115", "ani": 78.9312, "matched_fragments": 234, "total_fragments": 1252, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Ectothiorhodospirales;f__Thioalkalivibrionaceae;g__Thioalkalivibrio_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": -0.35, "cell_length": 0.458, "doubling_h": null, "growth_tmp": 30.0, "optimum_tmp": 35.0, "optimum_ph": 9.887, "genome_size": 3756729.333, "gc_content": 66.5, "coding_genes": 3327.0, "rRNA16S_genes": 1.0, "tRNA_genes": 44.0, "gram_stain": 0.0, "sporulation": 0.0, "motility": 1.0, "range_salinity": 1.0, "facultative_respiration": 1.0, "anaerobic_respiration": 0.0, "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": [ "Thioalkalivibrio", "paradoxus", "ARh", "1" ], "quality": 5, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }