{ "type": "genome", "identifier": "GCF_002797595.1", "organism": "Sediminihabitans luteus", "title": "Sediminihabitans luteus", "description": "na", "data type": "Genome sequencing and assembly", "organization": "DOE Joint Genome Institute", "publication": [ {} ], "properties": { "assembly_accession": "GCF_002797595.1", "bioproject": "PRJNA224116", "biosample": "SAMN07621134", "wgs_master": "PGFE00000000.1", "refseq_category": "na", "taxid": "1138585", "species_taxid": "1138585", "organism_name": "Sediminihabitans luteus", "infraspecific_name": "strain=DSM 25478", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2017/11/28", "asm_name": "ASM279759v1", "asm_submitter": "DOE Joint Genome Institute", "gbrs_paired_asm": "GCA_002797595.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/002/797/595/GCF_002797595.1_ASM279759v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "3421787", "genome_size_ungapped": "3421787", "gc_percent": "73.500000", "replicon_count": "0", "scaffold_count": "9", "contig_count": "9", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_002797595.1-RS_2024_04_27", "annotation_date": "2024-04-27", "total_gene_count": "3071", "protein_coding_gene_count": "2998", "non_coding_gene_count": "52", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2017-11-28", "dateModified": "2017-11-28", "datePublished": "2017-11-28", "_annotation": { "sample_count": 1, "sample_organism": [ "Sediminihabitans luteus" ], "sample_taxid": [ "1138585" ], "sample_host_organism": [ "not applicable" ], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "missing" ], "sample_host_location_id": [], "data_size": "0.884 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)": "3421787", "Number of Sequences": "9", "Longest Sequences (bp)": "1303450", "N50 (bp)": "817742", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "73.6", "Number of CDSs": "3039", "Average Protein Length": "344.3", "Coding Ratio (%)": "91.7", "Number of rRNAs": "3", "Number of tRNAs": "55", "Number of CRISPRs": "1" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Sediminihabitans luteus", "strain": "strain=DSM 25478", "accession": "GCA_002797595.1", "taxid": 1138585, "species_taxid": 1138585, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1135, "total_fragments": 1135, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Sediminihabitans luteus", "strain": "strain=NBRC 108568", "accession": "GCA_016863455.1", "taxid": 1138585, "species_taxid": 1138585, "relation_to_type": "type", "validated": true, "ani": 99.992, "matched_fragments": 1115, "total_fragments": 1135, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Cellulosimicrobium funkei", "strain": "strain=JCM 14302", "accession": "GCA_004519295.1", "taxid": 264251, "species_taxid": 264251, "relation_to_type": "suspected-type", "validated": true, "ani": 81.3812, "matched_fragments": 720, "total_fragments": 1135, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Cellulosimicrobium funkei", "strain": "strain=NBRC 104118", "accession": "GCA_001570825.1", "taxid": 264251, "species_taxid": 264251, "relation_to_type": "suspected-type", "validated": true, "ani": 81.3685, "matched_fragments": 694, "total_fragments": 1135, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Oerskovia turbata", "strain": "strain=JCM3160", "accession": "GCA_004121315.1", "taxid": 1713, "species_taxid": 1713, "relation_to_type": "type", "validated": true, "ani": 81.3453, "matched_fragments": 678, "total_fragments": 1135, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Oerskovia turbata", "strain": "strain=NRRL B-8019", "accession": "GCA_000718325.1", "taxid": 1713, "species_taxid": 1713, "relation_to_type": "type", "validated": true, "ani": 81.3281, "matched_fragments": 675, "total_fragments": 1135, "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": 81.2706, "matched_fragments": 683, "total_fragments": 1135, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Oerskovia rustica", "strain": "strain=Sa4CUA1", "accession": "GCA_014836555.1", "taxid": 2762237, "species_taxid": 2762237, "relation_to_type": "type", "validated": true, "ani": 81.2677, "matched_fragments": 691, "total_fragments": 1135, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Oerskovia merdavium", "strain": "strain=Sa2CUA9", "accession": "GCA_014836755.1", "taxid": 2762227, "species_taxid": 2762227, "relation_to_type": "type", "validated": true, "ani": 81.1268, "matched_fragments": 699, "total_fragments": 1135, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Oerskovia enterophila", "strain": "strain=DSM 43852", "accession": "GCA_001692445.1", "taxid": 43678, "species_taxid": 43678, "relation_to_type": "type", "validated": true, "ani": 81.0975, "matched_fragments": 682, "total_fragments": 1135, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Cellulosimicrobium arenosum", "strain": "strain=KCTC 49039", "accession": "GCA_014837295.1", "taxid": 2708133, "species_taxid": 2708133, "relation_to_type": "type", "validated": true, "ani": 80.5974, "matched_fragments": 663, "total_fragments": 1135, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Cellulomonas cellasea", "strain": "strain=NBRC 3753", "accession": "GCA_006538745.1", "taxid": 43670, "species_taxid": 43670, "relation_to_type": "type", "validated": true, "ani": 79.9118, "matched_fragments": 641, "total_fragments": 1135, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Cellulomonas fimi", "strain": "strain=ATCC 484", "accession": "GCA_000212695.1", "taxid": 1708, "species_taxid": 1708, "relation_to_type": "type", "validated": true, "ani": 79.9002, "matched_fragments": 607, "total_fragments": 1135, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Cellulomonas fimi", "strain": "strain=NCTC7547", "accession": "GCA_900637695.1", "taxid": 1708, "species_taxid": 1708, "relation_to_type": "type", "validated": true, "ani": 79.8442, "matched_fragments": 606, "total_fragments": 1135, "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": 79.7816, "matched_fragments": 621, "total_fragments": 1135, "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": 79.34, "matched_fragments": 599, "total_fragments": 1135, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_002797595.1", "gtdb_species": "s__Sediminihabitans luteus", "ani": 100.0, "matched_fragments": 1135, "total_fragments": 1135, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Sediminihabitans", "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_003752595.1", "gtdb_species": "s__Sediminihabitans sp003752595", "ani": 82.0009, "matched_fragments": 692, "total_fragments": 1135, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Sediminihabitans", "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_001722485.1", "gtdb_species": "s__Cellulosimicrobium cellulans_A", "ani": 81.608, "matched_fragments": 591, "total_fragments": 1135, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulosimicrobium", "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_010287905.1", "gtdb_species": "s__Cellulosimicrobium fucosivorans", "ani": 81.5841, "matched_fragments": 704, "total_fragments": 1135, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulosimicrobium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.84", "min_intra_species_ani": "98.55", "mean_intra_species_af": "0.94", "min_intra_species_af": "0.90", "num_clustered_genomes": 6, "status": "-" }, { "accession": "GCF_004519295.1", "gtdb_species": "s__Cellulosimicrobium funkei", "ani": 81.4058, "matched_fragments": 717, "total_fragments": 1135, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulosimicrobium", "ani_circumscription_radius": 96.0261, "mean_intra_species_ani": "98.03", "min_intra_species_ani": "96.84", "mean_intra_species_af": "0.93", "min_intra_species_af": "0.88", "num_clustered_genomes": 18, "status": "-" }, { "accession": "GCF_000718325.1", "gtdb_species": "s__Oerskovia turbata", "ani": 81.3684, "matched_fragments": 671, "total_fragments": 1135, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Oerskovia", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.78", "min_intra_species_ani": "99.34", "mean_intra_species_af": "0.96", "min_intra_species_af": "0.90", "num_clustered_genomes": 4, "status": "-" }, { "accession": "GCF_009708005.2", "gtdb_species": "s__Cellulosimicrobium sp009708005", "ani": 81.2729, "matched_fragments": 731, "total_fragments": 1135, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulosimicrobium", "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_006539945.1", "gtdb_species": "s__Cellulosimicrobium cellulans", "ani": 81.2707, "matched_fragments": 717, "total_fragments": 1135, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulosimicrobium", "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_001019615.1", "gtdb_species": "s__Cellulosimicrobium cellulans_E", "ani": 81.249, "matched_fragments": 736, "total_fragments": 1135, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulosimicrobium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.64", "min_intra_species_ani": "98.58", "mean_intra_species_af": "0.94", "min_intra_species_af": "0.93", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_015142735.1", "gtdb_species": "s__Oerskovia sp015142735", "ani": 81.2466, "matched_fragments": 686, "total_fragments": 1135, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Oerskovia", "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_005937995.2", "gtdb_species": "s__Oerskovia sp005937995", "ani": 81.2091, "matched_fragments": 695, "total_fragments": 1135, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Oerskovia", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "96.13", "min_intra_species_ani": "96.13", "mean_intra_species_af": "0.91", "min_intra_species_af": "0.91", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_016921195.1", "gtdb_species": "s__Cellulosimicrobium cellulans_F", "ani": 81.2024, "matched_fragments": 734, "total_fragments": 1135, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulosimicrobium", "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_016907755.1", "gtdb_species": "s__Cellulosimicrobium cellulans_D", "ani": 81.1858, "matched_fragments": 743, "total_fragments": 1135, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulosimicrobium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.18", "min_intra_species_ani": "99.18", "mean_intra_species_af": "0.97", "min_intra_species_af": "0.97", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_016907235.1", "gtdb_species": "s__Oerskovia jenensis", "ani": 81.1786, "matched_fragments": 711, "total_fragments": 1135, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Oerskovia", "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_014836755.1", "gtdb_species": "s__Oerskovia sp014836755", "ani": 81.1152, "matched_fragments": 699, "total_fragments": 1135, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Oerskovia", "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_001942335.1", "gtdb_species": "s__Cellulosimicrobium sp001942335", "ani": 81.1038, "matched_fragments": 678, "total_fragments": 1135, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulosimicrobium", "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_001692445.1", "gtdb_species": "s__Oerskovia enterophila", "ani": 81.1024, "matched_fragments": 682, "total_fragments": 1135, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Oerskovia", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.35", "min_intra_species_ani": "97.89", "mean_intra_species_af": "0.90", "min_intra_species_af": "0.89", "num_clustered_genomes": 4, "status": "-" }, { "accession": "GCF_000701465.1", "gtdb_species": "s__Paraoerskovia marina", "ani": 80.7664, "matched_fragments": 592, "total_fragments": 1135, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Paraoerskovia", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.25", "min_intra_species_ani": "98.25", "mean_intra_species_af": "0.95", "min_intra_species_af": "0.95", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_004306155.1", "gtdb_species": "s__Cellulomonas biazotea", "ani": 79.9638, "matched_fragments": 544, "total_fragments": 1135, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas", "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_900167525.1", "gtdb_species": "s__Isoptericola flava", "ani": 79.8808, "matched_fragments": 632, "total_fragments": 1135, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Isoptericola", "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_000212695.1", "gtdb_species": "s__Cellulomonas fimi", "ani": 79.859, "matched_fragments": 611, "total_fragments": 1135, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "100.00", "min_intra_species_ani": "99.99", "mean_intra_species_af": "1.00", "min_intra_species_af": "1.00", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_014635665.1", "gtdb_species": "s__Isoptericola cucumis", "ani": 79.7649, "matched_fragments": 626, "total_fragments": 1135, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Isoptericola", "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_003755175.1", "gtdb_species": "s__Cellulomonas sp003755175", "ani": 79.6546, "matched_fragments": 579, "total_fragments": 1135, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas", "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": null, "cell_length": null, "doubling_h": null, "growth_tmp": 28.0, "optimum_tmp": null, "optimum_ph": null, "genome_size": 3421787.0, "gc_content": null, "coding_genes": null, "rRNA16S_genes": null, "tRNA_genes": null, "gram_stain": null, "sporulation": null, "motility": null, "range_salinity": null, "facultative_respiration": null, "anaerobic_respiration": null, "aerobic_respiration": null, "mesophilic_range_tmp": null, "thermophilic_range_tmp": null, "psychrophilic_range_tmp": null, "bacillus_cell_shape": null, "coccus_cell_shape": null, "filament_cell_shape": null, "coccobacillus_cell_shape": null, "vibrio_cell_shape": null, "spiral_cell_shape": null }, "_genome_taxon": [ "Sediminihabitans", "luteus" ], "quality": 5, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }