{ "type": "genome", "identifier": "GCF_004331735.1", "organism": "Pedobacter psychrodurus", "title": "Pedobacter psychrodurus", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Kyonggi University", "publication": [ {} ], "properties": { "assembly_accession": "GCF_004331735.1", "bioproject": "PRJNA224116", "biosample": "SAMN11032503", "wgs_master": "SJSO00000000.1", "refseq_category": "reference genome", "taxid": "2530456", "species_taxid": "2530456", "organism_name": "Pedobacter psychrodurus", "infraspecific_name": "strain=RP-3-21", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2019/03/06", "asm_name": "ASM433173v1", "asm_submitter": "Kyonggi University", "gbrs_paired_asm": "GCA_004331735.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/004/331/735/GCF_004331735.1_ASM433173v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "6094659", "genome_size_ungapped": "6094659", "gc_percent": "38.000000", "replicon_count": "0", "scaffold_count": "58", "contig_count": "58", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_004331735.1-RS_2024_10_23", "annotation_date": "2024-10-23", "total_gene_count": "5061", "protein_coding_gene_count": "4965", "non_coding_gene_count": "55", "pubmed_id": "32160145" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2019-03-06", "dateModified": "2019-03-06", "datePublished": "2019-03-06", "_annotation": { "sample_count": 1, "sample_organism": [ "Pedobacter psychrodurus" ], "sample_taxid": [ "2530456" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "Canada: Cambridge Bay, NU" ], "sample_host_location_id": [], "data_size": "1.722 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)": "6094659", "Number of Sequences": "58", "Longest Sequences (bp)": "424833", "N50 (bp)": "231308", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "38.2", "Number of CDSs": "4873", "Average Protein Length": "351.3", "Coding Ratio (%)": "84.3", "Number of rRNAs": "4", "Number of tRNAs": "47", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Pedobacter psychrodurus", "strain": "strain=RP-3-21", "accession": "GCA_004331735.1", "taxid": 2530456, "species_taxid": 2530456, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 2001, "total_fragments": 2003, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Pedobacter kyonggii", "strain": "strain=K-4-11-1", "accession": "GCA_004310665.1", "taxid": 1926871, "species_taxid": 1926871, "relation_to_type": "type", "validated": true, "ani": 89.1663, "matched_fragments": 1391, "total_fragments": 2003, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pedobacter ginsenosidimutans", "strain": "strain=KACC 14530", "accession": "GCA_001442625.1", "taxid": 687842, "species_taxid": 687842, "relation_to_type": "type", "validated": true, "ani": 89.0688, "matched_fragments": 1413, "total_fragments": 2003, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pedobacter borealis", "strain": "strain=DSM 19626", "accession": "GCA_000708285.2", "taxid": 475254, "species_taxid": 475254, "relation_to_type": "type", "validated": true, "ani": 88.9604, "matched_fragments": 1212, "total_fragments": 2003, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pedobacter alluvionis", "strain": "strain=DSM 19624", "accession": "GCA_004402005.1", "taxid": 475253, "species_taxid": 475253, "relation_to_type": "type", "validated": true, "ani": 86.0038, "matched_fragments": 1251, "total_fragments": 2003, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pedobacter alluvionis", "strain": "strain=DSM 19624", "accession": "GCA_003664035.1", "taxid": 475253, "species_taxid": 475253, "relation_to_type": "type", "validated": true, "ani": 86.0033, "matched_fragments": 1268, "total_fragments": 2003, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pedobacter miscanthi", "strain": "strain=RS10", "accession": "GCA_003315595.1", "taxid": 2259170, "species_taxid": 2259170, "relation_to_type": "type", "validated": true, "ani": 82.7517, "matched_fragments": 1172, "total_fragments": 2003, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pedobacter ghigonis", "strain": "strain=Marseille-Q2390", "accession": "GCA_903166585.1", "taxid": 2730403, "species_taxid": 2730403, "relation_to_type": "type", "validated": true, "ani": 81.4739, "matched_fragments": 1080, "total_fragments": 2003, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pedobacter fastidiosus", "strain": "strain=CCM 8938", "accession": "GCA_014306625.1", "taxid": 2765361, "species_taxid": 2765361, "relation_to_type": "type", "validated": true, "ani": 80.4934, "matched_fragments": 780, "total_fragments": 2003, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pedobacter mucosus", "strain": "strain=Q8-18", "accession": "GCA_022200785.1", "taxid": 2895286, "species_taxid": 2895286, "relation_to_type": "type", "validated": true, "ani": 79.4329, "matched_fragments": 626, "total_fragments": 2003, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_004331735.1", "gtdb_species": "s__Pedobacter sp004331735", "ani": 100.0, "matched_fragments": 2001, "total_fragments": 2003, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter", "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_004310665.1", "gtdb_species": "s__Pedobacter kyonggii", "ani": 89.1769, "matched_fragments": 1390, "total_fragments": 2003, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter", "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_001442625.1", "gtdb_species": "s__Pedobacter ginsenosidimutans", "ani": 89.0895, "matched_fragments": 1411, "total_fragments": 2003, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter", "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_002151545.1", "gtdb_species": "s__Pedobacter sp002151545", "ani": 89.01, "matched_fragments": 1432, "total_fragments": 2003, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter", "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_000708285.2", "gtdb_species": "s__Pedobacter borealis", "ani": 88.9366, "matched_fragments": 1214, "total_fragments": 2003, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter", "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_018613605.1", "gtdb_species": "s__Pedobacter sp018613605", "ani": 88.7714, "matched_fragments": 1403, "total_fragments": 2003, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "100.00", "min_intra_species_ani": "100.00", "mean_intra_species_af": "0.95", "min_intra_species_af": "0.95", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_003054145.1", "gtdb_species": "s__Pedobacter sp003054145", "ani": 88.6167, "matched_fragments": 1410, "total_fragments": 2003, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter", "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_003387415.1", "gtdb_species": "s__Pedobacter sp003387415", "ani": 88.534, "matched_fragments": 1352, "total_fragments": 2003, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter", "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_014692875.1", "gtdb_species": "s__Pedobacter sp011759615", "ani": 87.5392, "matched_fragments": 1367, "total_fragments": 2003, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.16", "min_intra_species_ani": "98.15", "mean_intra_species_af": "0.91", "min_intra_species_af": "0.91", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_014205835.1", "gtdb_species": "s__Pedobacter sp014205835", "ani": 87.153, "matched_fragments": 1334, "total_fragments": 2003, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter", "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_003664035.1", "gtdb_species": "s__Pedobacter alluvionis", "ani": 85.9909, "matched_fragments": 1269, "total_fragments": 2003, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter", "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": "-" }, { "accession": "GCF_004342125.1", "gtdb_species": "s__Pedobacter sp004342125", "ani": 85.891, "matched_fragments": 1254, "total_fragments": 2003, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "95.29", "min_intra_species_ani": "95.29", "mean_intra_species_af": "0.84", "min_intra_species_af": "0.84", "num_clustered_genomes": 2, "status": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": -0.28, "cell_length": 0.284, "doubling_h": null, "growth_tmp": 24.703, "optimum_tmp": 25.616, "optimum_ph": 7.026, "genome_size": 5519163.389, "gc_content": 42.651, "coding_genes": 4725.333, "rRNA16S_genes": 4.333, "tRNA_genes": 57.25, "gram_stain": 0.0, "sporulation": 0.0, "motility": 0.281, "range_salinity": null, "facultative_respiration": 0.031, "anaerobic_respiration": 0.0, "aerobic_respiration": 0.968, "mesophilic_range_tmp": 0.5, "thermophilic_range_tmp": 0.0, "psychrophilic_range_tmp": 0.5, "bacillus_cell_shape": 0.939, "coccus_cell_shape": 0.06, "filament_cell_shape": 0.0, "coccobacillus_cell_shape": 0.0, "vibrio_cell_shape": 0.0, "spiral_cell_shape": 0.0 }, "_genome_taxon": [ "Pedobacter", "psychrodurus" ], "quality": 4, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }