{ "type": "genome", "identifier": "GCF_000297055.2", "organism": "Sulfuricella denitrificans skB26", "title": "Sulfuricella denitrificans skB26", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Institute of Low Temperature Science", "publication": [ {} ], "properties": { "assembly_accession": "GCF_000297055.2", "bioproject": "PRJNA224116", "biosample": "SAMD00061061", "wgs_master": "na", "refseq_category": "reference genome", "taxid": "1163617", "species_taxid": "649841", "organism_name": "Sulfuricella denitrificans skB26", "infraspecific_name": "strain=skB26", "isolate": "na", "version_status": "latest", "assembly_level": "Complete Genome", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2013/09/09", "asm_name": "ASM29705v2", "asm_submitter": "Institute of Low Temperature Science", "gbrs_paired_asm": "GCA_000297055.2", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/297/055/GCF_000297055.2_ASM29705v2", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "3217213", "genome_size_ungapped": "3217213", "gc_percent": "56.000000", "replicon_count": "2", "scaffold_count": "2", "contig_count": "2", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_000297055.2-RS_2024_12_13", "annotation_date": "2024-12-13", "total_gene_count": "3137", "protein_coding_gene_count": "3052", "non_coding_gene_count": "55", "pubmed_id": "22773644;25017294" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2013-09-09", "dateModified": "2013-09-09", "datePublished": "2013-09-09", "_annotation": { "sample_count": 1, "sample_organism": [ "Sulfuricella denitrificans skB26" ], "sample_taxid": [ "1163617" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [], "sample_host_location_id": [], "data_size": "0.912 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)": "3217213", "Number of Sequences": "2", "Longest Sequences (bp)": "3130594", "N50 (bp)": "3130594", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "56.1", "Number of CDSs": "3103", "Average Protein Length": "312.6", "Coding Ratio (%)": "90.4", "Number of rRNAs": "6", "Number of tRNAs": "47", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Sulfuricella denitrificans", "strain": "strain=skB26", "accession": "GCA_000297055.2", "taxid": 649841, "species_taxid": 649841, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1071, "total_fragments": 1071, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Sulfurimicrobium lacus", "strain": "strain=skT11", "accession": "GCA_011764585.1", "taxid": 2715678, "species_taxid": 2715678, "relation_to_type": "type", "validated": true, "ani": 79.0801, "matched_fragments": 367, "total_fragments": 1071, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sulfuriferula plumbiphila", "strain": "strain=Gro7", "accession": "GCA_009938015.1", "taxid": 171865, "species_taxid": 171865, "relation_to_type": "type", "validated": true, "ani": 78.1301, "matched_fragments": 144, "total_fragments": 1071, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sulfuriferula multivorans", "strain": "strain=TTN", "accession": "GCA_003851125.1", "taxid": 1559896, "species_taxid": 1559896, "relation_to_type": "type", "validated": true, "ani": 77.9287, "matched_fragments": 143, "total_fragments": 1071, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sulfuriferula plumbiphila", "strain": "strain=NBRC 107929", "accession": "GCA_007992375.1", "taxid": 171865, "species_taxid": 171865, "relation_to_type": "type", "validated": true, "ani": 77.8325, "matched_fragments": 140, "total_fragments": 1071, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Thiobacillus denitrificans", "strain": "strain=DSM 12475", "accession": "GCA_000376425.1", "taxid": 36861, "species_taxid": 36861, "relation_to_type": "type", "validated": true, "ani": 77.6921, "matched_fragments": 183, "total_fragments": 1071, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Thiobacillus thioparus", "strain": "strain=DSM 505", "accession": "GCA_000373385.1", "taxid": 931, "species_taxid": 931, "relation_to_type": "type", "validated": true, "ani": 77.3909, "matched_fragments": 145, "total_fragments": 1071, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Methylobacillus flagellatus", "strain": "strain=KT", "accession": "GCA_000013705.1", "taxid": 405, "species_taxid": 405, "relation_to_type": "type", "validated": true, "ani": 77.3252, "matched_fragments": 59, "total_fragments": 1071, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Cupriavidus nantongensis", "strain": "strain=X1", "accession": "GCA_001598055.1", "taxid": 1796606, "species_taxid": 1796606, "relation_to_type": "type", "validated": true, "ani": 77.256, "matched_fragments": 117, "total_fragments": 1071, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Cupriavidus taiwanensis", "strain": "strain=LMG 19424", "accession": "GCA_000069785.1", "taxid": 164546, "species_taxid": 164546, "relation_to_type": "suspected-type", "validated": true, "ani": 77.211, "matched_fragments": 116, "total_fragments": 1071, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Aquitalea aquatilis", "strain": "strain=THG-DN7.12", "accession": "GCA_005155025.1", "taxid": 1537400, "species_taxid": 1537400, "relation_to_type": "type", "validated": true, "ani": 76.9686, "matched_fragments": 77, "total_fragments": 1071, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Azoarcus rhizosphaerae", "strain": "strain=CC-YHH848", "accession": "GCA_004801305.1", "taxid": 2565932, "species_taxid": 2565932, "relation_to_type": "type", "validated": true, "ani": 76.9036, "matched_fragments": 131, "total_fragments": 1071, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Methylobacillus arboreus", "strain": "strain=VKM B-2590", "accession": "GCA_020532725.1", "taxid": 755170, "species_taxid": 755170, "relation_to_type": "type", "validated": true, "ani": 76.7175, "matched_fragments": 64, "total_fragments": 1071, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Burkholderia ubonensis subsp. mesacidophila", "strain": "strain=ATCC 31433", "accession": "GCA_002362295.1", "taxid": 265293, "species_taxid": 101571, "relation_to_type": "type", "validated": true, "ani": 76.7067, "matched_fragments": 76, "total_fragments": 1071, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Novimethylophilus kurashikiensis", "strain": "strain=La2-4", "accession": "GCA_003112435.1", "taxid": 1825523, "species_taxid": 1825523, "relation_to_type": "type", "validated": true, "ani": 76.6683, "matched_fragments": 91, "total_fragments": 1071, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Paludibacterium purpuratum", "strain": "strain=CECT 8976", "accession": "GCA_004363805.1", "taxid": 1144873, "species_taxid": 1144873, "relation_to_type": "type", "validated": true, "ani": 76.6118, "matched_fragments": 74, "total_fragments": 1071, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rivicola pingtungensis", "strain": "strain=DSM 29661", "accession": "GCA_003201855.1", "taxid": 1054498, "species_taxid": 1054498, "relation_to_type": "type", "validated": true, "ani": 76.4875, "matched_fragments": 88, "total_fragments": 1071, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Burkholderia glumae", "strain": "strain=LMG 2196", "accession": "GCA_902832765.1", "taxid": 337, "species_taxid": 337, "relation_to_type": "type", "validated": true, "ani": 76.4595, "matched_fragments": 88, "total_fragments": 1071, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas monteilii", "strain": "strain=DSM 14164", "accession": "GCA_000621245.1", "taxid": 76759, "species_taxid": 76759, "relation_to_type": "type", "validated": true, "ani": 75.3099, "matched_fragments": 56, "total_fragments": 1071, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_000297055.2", "gtdb_species": "s__Sulfuricella denitrificans", "ani": 100.0, "matched_fragments": 1070, "total_fragments": 1071, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Sulfuricellaceae;g__Sulfuricella", "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_018823025.1", "gtdb_species": "s__Sulfuricella sp018823025", "ani": 93.4821, "matched_fragments": 808, "total_fragments": 1071, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Sulfuricellaceae;g__Sulfuricella", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.85", "min_intra_species_ani": "99.85", "mean_intra_species_af": "0.92", "min_intra_species_af": "0.92", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_000971475.1", "gtdb_species": "s__Sulfuricella sp000971475", "ani": 90.1369, "matched_fragments": 827, "total_fragments": 1071, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Sulfuricellaceae;g__Sulfuricella", "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_002784065.1", "gtdb_species": "s__Sulfuricella sp002784065", "ani": 85.7042, "matched_fragments": 490, "total_fragments": 1071, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Sulfuricellaceae;g__Sulfuricella", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.65", "min_intra_species_ani": "99.21", "mean_intra_species_af": "0.84", "min_intra_species_af": "0.80", "num_clustered_genomes": 4, "status": "-" }, { "accession": "GCF_011764585.1", "gtdb_species": "s__Sulfurimicrobium lacus", "ani": 79.1051, "matched_fragments": 370, "total_fragments": 1071, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Sulfuricellaceae;g__Sulfurimicrobium", "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_003104895.1", "gtdb_species": "s__Sulfurimicrobium sp003104895", "ani": 78.1611, "matched_fragments": 263, "total_fragments": 1071, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Sulfuricellaceae;g__Sulfurimicrobium", "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_018336195.1", "gtdb_species": "s__JAGXQV01 sp018336195", "ani": 77.9153, "matched_fragments": 269, "total_fragments": 1071, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Sulfuricellaceae;g__JAGXQV01", "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_000013705.1", "gtdb_species": "s__Methylobacillus flagellatus", "ani": 77.3252, "matched_fragments": 59, "total_fragments": 1071, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Methylophilaceae;g__Methylobacillus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.96", "min_intra_species_ani": "97.96", "mean_intra_species_af": "0.89", "min_intra_species_af": "0.89", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCA_016218445.1", "gtdb_species": "s__CAITJF01 sp016218445", "ani": 77.17, "matched_fragments": 111, "total_fragments": 1071, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Gallionellaceae;g__CAITJF01", "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": -0.097, "doubling_h": null, "growth_tmp": 22.0, "optimum_tmp": 22.0, "optimum_ph": 7.75, "genome_size": 3222587.5, "gc_content": 56.116, "coding_genes": 3030.0, "rRNA16S_genes": 2.0, "tRNA_genes": 45.0, "gram_stain": 0.0, "sporulation": 0.0, "motility": 1.0, "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": 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": [ "Sulfuricella", "denitrificans", "skB26" ], "quality": 5, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }