{ "type": "genome", "identifier": "GCF_011290685.1", "organism": "Cyclobacterium plantarum", "title": "Cyclobacterium plantarum", "description": "na", "data type": "Genome sequencing and assembly", "organization": "University of Sevilla, Spain", "publication": [ {} ], "properties": { "assembly_accession": "GCF_011290685.1", "bioproject": "PRJNA224116", "biosample": "SAMN14331233", "wgs_master": "JAANYN000000000.1", "refseq_category": "reference genome", "taxid": "2716263", "species_taxid": "2716263", "organism_name": "Cyclobacterium plantarum", "infraspecific_name": "strain=GBPx2", "isolate": "na", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2020/03/15", "asm_name": "ASM1129068v1", "asm_submitter": "University of Sevilla, Spain", "gbrs_paired_asm": "GCA_011290685.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/011/290/685/GCF_011290685.1_ASM1129068v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "6169285", "genome_size_ungapped": "6168707", "gc_percent": "43.000000", "replicon_count": "0", "scaffold_count": "37", "contig_count": "37", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_011290685.1-RS_2024_10_23", "annotation_date": "2024-10-23", "total_gene_count": "4957", "protein_coding_gene_count": "4882", "non_coding_gene_count": "50", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2020-03-15", "dateModified": "2020-03-15", "datePublished": "2020-03-15", "_annotation": { "sample_count": 1, "sample_organism": [ "Cyclobacterium plantarum" ], "sample_taxid": [ "2716263" ], "sample_host_organism": [ "plant" ], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "Iran: Gomishan wetland" ], "sample_host_location_id": [], "data_size": "1.742 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": null, "max": null }, "completeness": 100.0, "contamination": 4.17, "strain_heterogeneity": 0.0, "genome_count": 1 }, "data_type": "G", "data_source": "RefSeq", "_dfast": { "Total Sequence Length (bp)": "6169285", "Number of Sequences": "37", "Longest Sequences (bp)": "1009915", "N50 (bp)": "547880", "Gap Ratio (%)": "0.009369", "GCcontent (%)": "43.0", "Number of CDSs": "4838", "Average Protein Length": "368.4", "Coding Ratio (%)": "86.7", "Number of rRNAs": "3", "Number of tRNAs": "41", "Number of CRISPRs": "1" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Cyclobacterium plantarum", "strain": "strain=GBPx2", "accession": "GCA_011290685.1", "taxid": 2716263, "species_taxid": 2716263, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 2041, "total_fragments": 2042, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Cyclobacterium lianum", "strain": "strain=CGMCC 1.6102", "accession": "GCA_900143075.1", "taxid": 388280, "species_taxid": 388280, "relation_to_type": "type", "validated": true, "ani": 81.5911, "matched_fragments": 1125, "total_fragments": 2042, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Cyclobacterium salsum", "strain": "strain=SYSU L10167", "accession": "GCA_010119245.1", "taxid": 2666329, "species_taxid": 2666329, "relation_to_type": "type", "validated": true, "ani": 80.3526, "matched_fragments": 758, "total_fragments": 2042, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Cyclobacterium roseum", "strain": "strain=SYSU L10180", "accession": "GCA_010119225.1", "taxid": 2666137, "species_taxid": 2666137, "relation_to_type": "type", "validated": true, "ani": 80.0746, "matched_fragments": 735, "total_fragments": 2042, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Cyclobacterium jeungdonense", "strain": "strain=KCTC 23150", "accession": "GCA_010994275.1", "taxid": 708087, "species_taxid": 708087, "relation_to_type": "type", "validated": true, "ani": 80.0503, "matched_fragments": 772, "total_fragments": 2042, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Cyclobacterium xiamenense", "strain": "strain=CGMCC 1.12432", "accession": "GCA_009467825.1", "taxid": 1297121, "species_taxid": 1297121, "relation_to_type": "type", "validated": true, "ani": 79.1762, "matched_fragments": 573, "total_fragments": 2042, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Cyclobacterium qasimii", "strain": "strain=NBRC 106168", "accession": "GCA_007991695.1", "taxid": 1350429, "species_taxid": 1350429, "relation_to_type": "type", "validated": true, "ani": 77.3624, "matched_fragments": 319, "total_fragments": 2042, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Cyclobacterium qasimii", "strain": "strain=M12-11B", "accession": "GCA_000427295.1", "taxid": 1350429, "species_taxid": 1350429, "relation_to_type": "type", "validated": true, "ani": 77.3599, "matched_fragments": 306, "total_fragments": 2042, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Echinicola marina", "strain": "strain=SCS 3-6", "accession": "GCA_020463795.1", "taxid": 2859768, "species_taxid": 2859768, "relation_to_type": "type", "validated": true, "ani": 77.0472, "matched_fragments": 103, "total_fragments": 2042, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Lunatibacter salilacus", "strain": "strain=CUG 91308", "accession": "GCA_009797935.1", "taxid": 2483804, "species_taxid": 2483804, "relation_to_type": "type", "validated": true, "ani": 76.7913, "matched_fragments": 182, "total_fragments": 2042, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Echinicola vietnamensis", "strain": "strain=DSM 17526", "accession": "GCA_000325705.1", "taxid": 390884, "species_taxid": 390884, "relation_to_type": "type", "validated": true, "ani": 76.7268, "matched_fragments": 90, "total_fragments": 2042, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Cecembia calidifontis", "strain": "strain=DSM 21411", "accession": "GCA_004216715.1", "taxid": 1187080, "species_taxid": 1187080, "relation_to_type": "type", "validated": true, "ani": 76.3754, "matched_fragments": 88, "total_fragments": 2042, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Lunatimonas lonarensis", "strain": "strain=AK24", "accession": "GCA_000390185.1", "taxid": 1232681, "species_taxid": 1232681, "relation_to_type": "type", "validated": true, "ani": 76.2949, "matched_fragments": 122, "total_fragments": 2042, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Algoriphagus antarcticus", "strain": "strain=DSM 15986", "accession": "GCA_003387655.1", "taxid": 238540, "species_taxid": 238540, "relation_to_type": "type", "validated": true, "ani": 76.1831, "matched_fragments": 54, "total_fragments": 2042, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Belliella kenyensis", "strain": "strain=DSM 46651", "accession": "GCA_022549675.1", "taxid": 1472724, "species_taxid": 1472724, "relation_to_type": "type", "validated": true, "ani": 76.1803, "matched_fragments": 67, "total_fragments": 2042, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Algoriphagus antarcticus", "strain": "strain=DSM 15986", "accession": "GCA_002150685.1", "taxid": 238540, "species_taxid": 238540, "relation_to_type": "type", "validated": true, "ani": 75.8523, "matched_fragments": 51, "total_fragments": 2042, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 4.17, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_011290685.1", "gtdb_species": "s__Cyclobacterium plantarum", "ani": 100.0, "matched_fragments": 2041, "total_fragments": 2042, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Cyclobacterium", "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_014762705.1", "gtdb_species": "s__Cyclobacterium sp014762705", "ani": 94.0976, "matched_fragments": 1658, "total_fragments": 2042, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Cyclobacterium", "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_010993705.1", "gtdb_species": "s__Cyclobacterium sp010993705", "ani": 82.5504, "matched_fragments": 1411, "total_fragments": 2042, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Cyclobacterium", "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_900143075.1", "gtdb_species": "s__Cyclobacterium lianum", "ani": 81.5842, "matched_fragments": 1126, "total_fragments": 2042, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Cyclobacterium", "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_010119245.1", "gtdb_species": "s__Cyclobacterium sp010119245", "ani": 80.358, "matched_fragments": 756, "total_fragments": 2042, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Cyclobacterium", "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_010119225.1", "gtdb_species": "s__Cyclobacterium sp010119225", "ani": 80.0721, "matched_fragments": 734, "total_fragments": 2042, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Cyclobacterium", "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_010994275.1", "gtdb_species": "s__Cyclobacterium jeungdonense", "ani": 80.0611, "matched_fragments": 770, "total_fragments": 2042, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Cyclobacterium", "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_009467825.1", "gtdb_species": "s__Cyclobacterium xiamenense", "ani": 79.1839, "matched_fragments": 572, "total_fragments": 2042, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Cyclobacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.69", "min_intra_species_ani": "97.69", "mean_intra_species_af": "0.89", "min_intra_species_af": "0.89", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_000427295.1", "gtdb_species": "s__Cyclobacterium qasimii", "ani": 77.3599, "matched_fragments": 306, "total_fragments": 2042, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Cyclobacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.96", "min_intra_species_ani": "99.96", "mean_intra_species_af": "0.99", "min_intra_species_af": "0.99", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_002150685.1", "gtdb_species": "s__Algoriphagus antarcticus", "ani": 75.8523, "matched_fragments": 51, "total_fragments": 2042, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus", "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": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": -0.437, "cell_length": -0.013, "doubling_h": null, "growth_tmp": 24.333, "optimum_tmp": 25.666, "optimum_ph": 7.5, "genome_size": 5929341.875, "gc_content": 38.202, "coding_genes": 4875.833, "rRNA16S_genes": 3.5, "tRNA_genes": 39.0, "gram_stain": 0.0, "sporulation": 0.0, "motility": 0.0, "range_salinity": null, "facultative_respiration": 0.0, "anaerobic_respiration": 0.0, "aerobic_respiration": 1.0, "mesophilic_range_tmp": 1.0, "thermophilic_range_tmp": 0.0, "psychrophilic_range_tmp": 0.0, "bacillus_cell_shape": 0.0, "coccus_cell_shape": 0.0, "filament_cell_shape": 0.0, "coccobacillus_cell_shape": 0.0, "vibrio_cell_shape": 0.0, "spiral_cell_shape": 1.0 }, "_genome_taxon": [ "Cyclobacterium", "plantarum" ], "quality": 4, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }