{ "type": "genome", "identifier": "GCF_000021985.1", "organism": "Thioalkalivibrio sulfidiphilus HL-EbGr7", "title": "Thioalkalivibrio sulfidiphilus HL-EbGr7", "description": "na", "data type": "Genome sequencing and assembly", "organization": "US DOE Joint Genome Institute (JGI-PGF)", "publication": [ {} ], "properties": { "assembly_accession": "GCF_000021985.1", "bioproject": "PRJNA224116", "biosample": "SAMN00001443", "wgs_master": "na", "refseq_category": "reference genome", "taxid": "396588", "species_taxid": "1033854", "organism_name": "Thioalkalivibrio sulfidiphilus HL-EbGr7", "infraspecific_name": "strain=HL-EbGR7", "isolate": "na", "version_status": "latest", "assembly_level": "Complete Genome", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2009/01/13", "asm_name": "ASM2198v1", "asm_submitter": "US DOE Joint Genome Institute (JGI-PGF)", "gbrs_paired_asm": "GCA_000021985.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/021/985/GCF_000021985.1_ASM2198v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "3464554", "genome_size_ungapped": "3464554", "gc_percent": "65.000000", "replicon_count": "1", "scaffold_count": "1", "contig_count": "1", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_000021985.1-RS_2024_05_01", "annotation_date": "2024-05-01", "total_gene_count": "3383", "protein_coding_gene_count": "3284", "non_coding_gene_count": "52", "pubmed_id": "21475584" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2009-01-13", "dateModified": "2009-01-13", "datePublished": "2009-01-13", "_annotation": { "sample_count": 1, "sample_organism": [ "Thioalkalivibrio sulfidiphilus HL-EbGr7" ], "sample_taxid": [ "396588" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [], "sample_host_location_id": [], "data_size": "0.954 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)": "3464554", "Number of Sequences": "1", "Longest Sequences (bp)": "3464554", "N50 (bp)": "3464554", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "65.1", "Number of CDSs": "3348", "Average Protein Length": "303.7", "Coding Ratio (%)": "88.0", "Number of rRNAs": "3", "Number of tRNAs": "48", "Number of CRISPRs": "2" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Thioalkalivibrio sulfidiphilus", "strain": "strain=HL-EbGR7", "accession": "GCA_000021985.1", "taxid": 1033854, "species_taxid": 1033854, 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true, "ani": 79.2258, "matched_fragments": 345, "total_fragments": 1154, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Ectothiorhodospira magna", "strain": "strain=B7-7", "accession": "GCA_900110965.1", "taxid": 867345, "species_taxid": 867345, "relation_to_type": "type", "validated": true, "ani": 78.9393, "matched_fragments": 293, "total_fragments": 1154, "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": 78.8419, "matched_fragments": 362, "total_fragments": 1154, "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": 78.3838, "matched_fragments": 343, "total_fragments": 1154, "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": 78.3334, "matched_fragments": 274, "total_fragments": 1154, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Inmirania thermothiophila", "strain": "strain=DSM 100275", "accession": "GCA_003751635.1", "taxid": 1750597, "species_taxid": 1750597, "relation_to_type": "type", "validated": true, "ani": 78.0101, "matched_fragments": 285, "total_fragments": 1154, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas citronellolis", "strain": "strain=NBRC 103043", "accession": "GCA_002091555.1", "taxid": 53408, "species_taxid": 53408, "relation_to_type": "type", "validated": true, "ani": 77.0714, "matched_fragments": 308, "total_fragments": 1154, "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": 76.8595, "matched_fragments": 166, "total_fragments": 1154, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas aeruginosa", "strain": "strain=JCM 5962", "accession": "GCA_022496575.1", "taxid": 287, "species_taxid": 287, "relation_to_type": "type", "validated": true, "ani": 76.8028, "matched_fragments": 216, "total_fragments": 1154, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas aeruginosa", "strain": "strain=DSM 50071", "accession": "GCA_024169805.1", "taxid": 287, "species_taxid": 287, "relation_to_type": "type", "validated": true, "ani": 76.7147, "matched_fragments": 223, "total_fragments": 1154, "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": 76.6072, "matched_fragments": 115, "total_fragments": 1154, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_000021985.1", "gtdb_species": "s__Thioalkalivibrio_A sulfidiphilus", "ani": 100.0, "matched_fragments": 1154, "total_fragments": 1154, "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": "conclusive" }, { "accession": "GCF_000377945.1", "gtdb_species": "s__Thioalkalivibrio_A sulfidiphilus_A", "ani": 94.61, "matched_fragments": 852, "total_fragments": 1154, "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_000378965.1", "gtdb_species": "s__Thioalkalivibrio_A thiocyanodenitrificans", "ani": 82.4343, "matched_fragments": 631, "total_fragments": 1154, "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_002000365.1", 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"GCF_016584115.1", "gtdb_species": "s__Ectothiorhodospira mobilis", "ani": 80.4107, "matched_fragments": 418, "total_fragments": 1154, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Ectothiorhodospirales;f__Ectothiorhodospiraceae;g__Ectothiorhodospira", "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_016584105.1", "gtdb_species": "s__Ectothiorhodospira shaposhnikovii", "ani": 79.9186, "matched_fragments": 389, "total_fragments": 1154, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Ectothiorhodospirales;f__Ectothiorhodospiraceae;g__Ectothiorhodospira", "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": 0.74, "doubling_h": null, "growth_tmp": 29.555, "optimum_tmp": 35.0, "optimum_ph": 10.0, "genome_size": 3395964.833, "gc_content": 65.099, "coding_genes": 3258.0, "rRNA16S_genes": 1.0, "tRNA_genes": 44.0, "gram_stain": 0.0, "sporulation": 0.0, "motility": 1.0, "range_salinity": 1.0, "facultative_respiration": 0.0, "anaerobic_respiration": 0.0, "aerobic_respiration": 1.0, "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", "sulfidiphilus", "HL-EbGr7" ], "quality": 5, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }