{ "type": "genome", "identifier": "GCF_003344965.1", "organism": "Streptomyces paludis", "title": "Streptomyces paludis", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Hunan University of Science and Technology", "publication": [ {} ], "properties": { "assembly_accession": "GCF_003344965.1", "bioproject": "PRJNA224116", "biosample": "SAMN09699158", "wgs_master": "na", "refseq_category": "reference genome", "taxid": "2282738", "species_taxid": "2282738", "organism_name": "Streptomyces paludis", "infraspecific_name": "strain=GSSD-12", "isolate": "na", "version_status": "latest", "assembly_level": "Complete Genome", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2018/07/30", "asm_name": "ASM334496v1", "asm_submitter": "Hunan University of Science and Technology", "gbrs_paired_asm": "GCA_003344965.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/003/344/965/GCF_003344965.1_ASM334496v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "8454852", "genome_size_ungapped": "8454852", "gc_percent": "71.000000", "replicon_count": "1", "scaffold_count": "1", "contig_count": "1", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_003344965.1-RS_2024_12_11", "annotation_date": "2024-12-11", "total_gene_count": "7179", "protein_coding_gene_count": "6972", "non_coding_gene_count": "88", "pubmed_id": "31674894" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2018-07-30", "dateModified": "2018-07-30", "datePublished": "2018-07-30", "_annotation": { "sample_count": 1, "sample_organism": [ "Streptomyces paludis" ], "sample_taxid": [ "2282738" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "China: Hunan" ], "sample_host_location_id": [], "data_size": "2.267 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": null, "max": null }, "completeness": 100.0, "contamination": 1.04, "strain_heterogeneity": 0.0, "genome_count": 1 }, "data_type": "G", "data_source": "RefSeq", "_dfast": { "Total Sequence Length (bp)": "8454852", "Number of Sequences": "1", "Longest Sequences (bp)": "8454852", "N50 (bp)": "8454852", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "71.2", "Number of CDSs": "7321", "Average Protein Length": "343.1", "Coding Ratio (%)": "89.1", "Number of rRNAs": "18", "Number of tRNAs": "78", "Number of CRISPRs": "7" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Streptomyces paludis", "strain": "strain=GSSD-12", "accession": "GCA_003344965.1", "taxid": 2282738, "species_taxid": 2282738, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 2817, "total_fragments": 2818, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Streptomyces corynorhini", "strain": "strain=AC230", "accession": "GCA_003346515.1", "taxid": 2282652, "species_taxid": 2282652, "relation_to_type": "type", "validated": true, "ani": 87.4662, "matched_fragments": 1674, "total_fragments": 2818, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Streptomyces scopuliridis", "strain": "strain=RB72", "accession": "GCA_003073355.1", "taxid": 452529, "species_taxid": 452529, "relation_to_type": "type", "validated": true, "ani": 85.7272, "matched_fragments": 1495, "total_fragments": 2818, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Streptomyces scopuliridis", "strain": "strain=NRRL B-24574", "accession": "GCA_000718095.1", "taxid": 452529, "species_taxid": 452529, "relation_to_type": "type", "validated": true, "ani": 85.6186, "matched_fragments": 1624, "total_fragments": 2818, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Streptomyces lushanensis", "strain": "strain=NRRL B-24994", "accession": "GCA_001700515.1", "taxid": 1434255, "species_taxid": 1434255, "relation_to_type": "type", "validated": true, "ani": 84.7883, "matched_fragments": 1299, "total_fragments": 2818, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Streptomyces odonnellii", "strain": "strain=NRRL B-24891", "accession": "GCA_000981895.1", "taxid": 1417980, "species_taxid": 1417980, "relation_to_type": "type", "validated": true, "ani": 84.5294, "matched_fragments": 1372, "total_fragments": 2818, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Streptomyces liangshanensis", "strain": "strain=QMT-12", "accession": "GCA_011694815.1", "taxid": 2717324, "species_taxid": 2717324, "relation_to_type": "type", "validated": true, "ani": 83.9069, "matched_fragments": 1486, "total_fragments": 2818, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Streptomyces formicae", "strain": "strain=1H-GS9", "accession": "GCA_022647665.1", "taxid": 1616117, "species_taxid": 1616117, "relation_to_type": "type", "validated": true, "ani": 82.5521, "matched_fragments": 1343, "total_fragments": 2818, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Streptomyces rhizosphaericola", "strain": "strain=1AS2c", "accession": "GCA_004794175.1", "taxid": 2564098, "species_taxid": 2564098, "relation_to_type": "type", "validated": true, "ani": 82.4833, "matched_fragments": 1180, "total_fragments": 2818, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Streptomyces gelaticus", "strain": "strain=JCM 4376", "accession": "GCA_014649535.1", "taxid": 285446, "species_taxid": 285446, "relation_to_type": "type", "validated": true, "ani": 82.3041, "matched_fragments": 1331, "total_fragments": 2818, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Streptomyces melanogenes", "strain": "strain=JCM 4398", "accession": "GCA_014649795.1", "taxid": 67326, "species_taxid": 67326, "relation_to_type": "type", "validated": true, "ani": 81.9541, "matched_fragments": 1342, "total_fragments": 2818, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Streptomyces somaliensis", "strain": "strain=DSM 40738", "accession": "GCA_024349285.1", "taxid": 78355, "species_taxid": 78355, "relation_to_type": "type", "validated": true, "ani": 81.5674, "matched_fragments": 1002, "total_fragments": 2818, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Streptomyces aurantiacus", "strain": "strain=NRRL ISP-5412", "accession": "GCA_001418335.1", "taxid": 47760, "species_taxid": 47760, "relation_to_type": "type", "validated": true, "ani": 80.9333, "matched_fragments": 1241, "total_fragments": 2818, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Streptomyces caniscabiei", "strain": "strain=NE06-02D", "accession": "GCA_014930365.1", "taxid": 2746961, "species_taxid": 2746961, "relation_to_type": "type", "validated": true, "ani": 80.7903, "matched_fragments": 1390, "total_fragments": 2818, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 1.04, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_003344965.1", "gtdb_species": "s__Streptomyces paludis", "ani": 100.0, "matched_fragments": 2817, "total_fragments": 2818, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces", "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_003346515.1", "gtdb_species": "s__Streptomyces corynorhini", "ani": 87.4778, "matched_fragments": 1671, "total_fragments": 2818, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces", "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_000718095.1", "gtdb_species": "s__Streptomyces scopuliridis", "ani": 85.559, "matched_fragments": 1634, "total_fragments": 2818, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.98", "min_intra_species_ani": "99.98", "mean_intra_species_af": "0.99", "min_intra_species_af": "0.99", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_004151105.1", "gtdb_species": "s__Streptomyces sp004151105", "ani": 85.3603, "matched_fragments": 1615, "total_fragments": 2818, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces", "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_001700515.1", "gtdb_species": "s__Streptomyces lushanensis", "ani": 84.8095, "matched_fragments": 1296, "total_fragments": 2818, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces", "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_000981895.1", "gtdb_species": "s__Streptomyces odonnellii", "ani": 84.528, "matched_fragments": 1372, "total_fragments": 2818, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "95.86", "min_intra_species_ani": "95.86", "mean_intra_species_af": "0.85", "min_intra_species_af": "0.85", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_011694815.1", "gtdb_species": "s__Streptomyces liangshanensis", "ani": 83.8395, "matched_fragments": 1495, "total_fragments": 2818, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces", "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_010384365.1", "gtdb_species": "s__Streptomyces sp010384365", "ani": 82.9906, "matched_fragments": 1444, "total_fragments": 2818, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.09", "min_intra_species_ani": "98.09", "mean_intra_species_af": "0.85", "min_intra_species_af": "0.85", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_900119365.1", "gtdb_species": "s__Streptomyces atratus_B", "ani": 82.2807, "matched_fragments": 1349, "total_fragments": 2818, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces", "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_003846175.1", "gtdb_species": "s__Streptomyces sp003846175", "ani": 82.135, "matched_fragments": 1436, "total_fragments": 2818, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces", "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_014649795.1", "gtdb_species": "s__Streptomyces melanogenes", "ani": 81.9454, "matched_fragments": 1344, "total_fragments": 2818, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "95.19", "min_intra_species_ani": "95.19", "mean_intra_species_af": "0.83", "min_intra_species_af": "0.83", "num_clustered_genomes": 2, "status": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": -0.201, "cell_length": -0.05, "doubling_h": 0.103, "growth_tmp": 27.757, "optimum_tmp": 29.036, "optimum_ph": 7.341, "genome_size": 8292419.302, "gc_content": 71.543, "coding_genes": 7141.289, "rRNA16S_genes": 6.155, "tRNA_genes": 67.804, "gram_stain": 0.998, "sporulation": 0.958, "motility": 0.049, "range_salinity": 0.666, "facultative_respiration": 0.0, "anaerobic_respiration": 0.005, "aerobic_respiration": 0.994, "mesophilic_range_tmp": 0.98, "thermophilic_range_tmp": 0.019, "psychrophilic_range_tmp": 0.0, "bacillus_cell_shape": 0.208, "coccus_cell_shape": 0.032, "filament_cell_shape": 0.582, "coccobacillus_cell_shape": 0.098, "vibrio_cell_shape": 0.0, "spiral_cell_shape": 0.076 }, "_genome_taxon": [ "Streptomyces", "paludis" ], "quality": 5, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }