{ "type": "genome", "identifier": "GCF_000759715.1", "organism": "Demequina mangrovi", "title": "Demequina mangrovi", "description": "na", "data type": "Genome sequencing and assembly", "organization": "National Institute of Technology and Evaluation Biological Resource Center", "publication": [ {} ], "properties": { "assembly_accession": "GCF_000759715.1", "bioproject": "PRJNA224116", "biosample": "SAMD00019178", "wgs_master": "BBLU00000000.1", "refseq_category": "na", "taxid": "1043493", "species_taxid": "1043493", "organism_name": "Demequina mangrovi", "infraspecific_name": "strain=NBRC 105856", "isolate": "na", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2014/09/23", "asm_name": "ASM75971v1", "asm_submitter": "National Institute of Technology and Evaluation Biological Resource Center", "gbrs_paired_asm": "GCA_000759715.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/759/715/GCF_000759715.1_ASM75971v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "2968736", "genome_size_ungapped": "2967880", "gc_percent": "72.000000", "replicon_count": "0", "scaffold_count": "33", "contig_count": "33", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_000759715.1-RS_2024_08_08", "annotation_date": "2024-08-08", "total_gene_count": "2815", "protein_coding_gene_count": "2744", "non_coding_gene_count": "53", "pubmed_id": "25377709" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2014-09-23", "dateModified": "2014-09-23", "datePublished": "2014-09-23", "_annotation": { "sample_count": 1, "sample_organism": [ "Demequina mangrovi" ], "sample_taxid": [ "1043493" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "Japan:Okinawa, Iriomote Island" ], "sample_host_location_id": [], "data_size": "0.784 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)": "2968736", "Number of Sequences": "33", "Longest Sequences (bp)": "421019", "N50 (bp)": "207197", "Gap Ratio (%)": "0.028834", "GCcontent (%)": "71.8", "Number of CDSs": "2767", "Average Protein Length": "328.9", "Coding Ratio (%)": "92.0", "Number of rRNAs": "2", "Number of tRNAs": "50", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Demequina mangrovi", "strain": "strain=NBRC 105856", "accession": "GCA_000759715.1", "taxid": 1043493, "species_taxid": 1043493, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 973, "total_fragments": 973, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Demequina mangrovi", "strain": "strain=DSM 24868", "accession": "GCA_900109245.1", "taxid": 1043493, "species_taxid": 1043493, "relation_to_type": "type", "validated": true, "ani": 99.9993, "matched_fragments": 972, "total_fragments": 973, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Demequina subtropica", "strain": "strain=NBRC 109396", "accession": "GCA_000971235.1", "taxid": 1638989, "species_taxid": 1638989, "relation_to_type": "type", "validated": true, "ani": 87.2198, "matched_fragments": 785, "total_fragments": 973, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Demequina iriomotensis", "strain": "strain=NBRC 109399", "accession": "GCA_000971395.1", "taxid": 1536641, "species_taxid": 1536641, "relation_to_type": "type", "validated": true, "ani": 86.7703, "matched_fragments": 762, "total_fragments": 973, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Demequina gelatinilytica", "strain": "strain=NBRC 109390", "accession": "GCA_000971115.1", "taxid": 1638980, "species_taxid": 1638980, "relation_to_type": "type", "validated": true, "ani": 86.7582, "matched_fragments": 778, "total_fragments": 973, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Demequina rhizosphaerae", "strain": "strain=NBRC 109397", "accession": "GCA_000971255.1", "taxid": 1638985, "species_taxid": 1638985, "relation_to_type": "type", "validated": true, "ani": 86.601, "matched_fragments": 753, "total_fragments": 973, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Demequina maris", "strain": "strain=NBRC 109392", "accession": "GCA_000971155.1", "taxid": 1638982, "species_taxid": 1638982, "relation_to_type": "type", "validated": true, "ani": 86.536, "matched_fragments": 732, "total_fragments": 973, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Demequina soli", "strain": "strain=NBRC 109394", "accession": "GCA_000971195.1", "taxid": 1638987, "species_taxid": 1638987, "relation_to_type": "type", "validated": true, "ani": 85.716, "matched_fragments": 680, "total_fragments": 973, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Cellulomonas palmilytica", "strain": "strain=EW123", "accession": "GCA_021590045.1", "taxid": 2608402, "species_taxid": 2608402, "relation_to_type": "type", "validated": true, "ani": 78.2937, "matched_fragments": 394, "total_fragments": 973, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Actinotalea solisilvae", "strain": "strain=KACC 19191", "accession": "GCA_016464425.1", "taxid": 2072922, "species_taxid": 2072922, "relation_to_type": "type", "validated": true, "ani": 78.1715, "matched_fragments": 404, "total_fragments": 973, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Oerskovia douganii", "strain": "strain=Sa1BUA8", "accession": "GCA_015142735.1", "taxid": 2762210, "species_taxid": 2762210, "relation_to_type": "type", "validated": true, "ani": 77.9645, "matched_fragments": 363, "total_fragments": 973, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Cellulomonas fulva", "strain": "strain=DKR-3", "accession": "GCA_018531375.1", "taxid": 2835530, "species_taxid": 2835530, "relation_to_type": "type", "validated": true, "ani": 77.9332, "matched_fragments": 392, "total_fragments": 973, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Arthrobacter sedimenti", "strain": "strain=MIC A30", "accession": "GCA_011750795.2", "taxid": 2694931, "species_taxid": 2694931, "relation_to_type": "type", "validated": true, "ani": 77.3289, "matched_fragments": 169, "total_fragments": 973, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_000759715.1", "gtdb_species": "s__Demequina mangrovi", "ani": 100.0, "matched_fragments": 973, "total_fragments": 973, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Demequinaceae;g__Demequina", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "100.00", "min_intra_species_ani": "100.00", "mean_intra_species_af": "1.00", "min_intra_species_af": "1.00", "num_clustered_genomes": 2, "status": "conclusive" }, { "accession": "GCF_000971235.1", "gtdb_species": "s__Demequina subtropica", "ani": 87.2198, "matched_fragments": 785, "total_fragments": 973, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Demequinaceae;g__Demequina", "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_000971115.1", "gtdb_species": "s__Demequina gelatinilytica", "ani": 86.7585, "matched_fragments": 778, "total_fragments": 973, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Demequinaceae;g__Demequina", "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_000971395.1", "gtdb_species": "s__Demequina iriomotensis", "ani": 86.7413, "matched_fragments": 763, "total_fragments": 973, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Demequinaceae;g__Demequina", "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_000971255.1", "gtdb_species": "s__Demequina rhizosphaerae", "ani": 86.6144, "matched_fragments": 751, "total_fragments": 973, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Demequinaceae;g__Demequina", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.98", "min_intra_species_ani": "97.96", "mean_intra_species_af": "0.93", "min_intra_species_af": "0.92", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_000971155.1", "gtdb_species": "s__Demequina maris", "ani": 86.5355, "matched_fragments": 732, "total_fragments": 973, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Demequinaceae;g__Demequina", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.20", "min_intra_species_ani": "96.53", "mean_intra_species_af": "0.93", "min_intra_species_af": "0.91", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_000971195.1", "gtdb_species": "s__Demequina soli", "ani": 85.6828, "matched_fragments": 682, "total_fragments": 973, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Demequinaceae;g__Demequina", "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": -0.331, "cell_length": 0.187, "doubling_h": 0.806, "growth_tmp": 26.75, "optimum_tmp": 27.937, "optimum_ph": 7.25, "genome_size": 2681769.125, "gc_content": 65.941, "coding_genes": null, "rRNA16S_genes": null, "tRNA_genes": null, "gram_stain": 1.0, "sporulation": 0.0, "motility": 0.0, "range_salinity": null, "facultative_respiration": 0.166, "anaerobic_respiration": 0.0, "aerobic_respiration": 0.833, "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": [ "Demequina", "mangrovi" ], "quality": 3, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }