{ "type": "genome", "identifier": "GCF_002557795.1", "organism": "Chitinophaga caeni", "title": "Chitinophaga caeni", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences", "publication": [ {} ], "properties": { "assembly_accession": "GCF_002557795.1", "bioproject": "PRJNA224116", "biosample": "SAMN07665588", "wgs_master": "na", "refseq_category": "reference genome", "taxid": "2029983", "species_taxid": "2029983", "organism_name": "Chitinophaga caeni", "infraspecific_name": "strain=13", "isolate": "na", "version_status": "latest", "assembly_level": "Complete Genome", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2017/10/16", "asm_name": "ASM255779v1", "asm_submitter": "Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences", "gbrs_paired_asm": "GCA_002557795.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/002/557/795/GCF_002557795.1_ASM255779v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "5279921", "genome_size_ungapped": "5279921", "gc_percent": "42.500000", "replicon_count": "1", "scaffold_count": "1", "contig_count": "1", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_002557795.1-RS_2024_10_22", "annotation_date": "2024-10-22", "total_gene_count": "4368", "protein_coding_gene_count": "4267", "non_coding_gene_count": "77", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2017-10-16", "dateModified": "2017-10-16", "datePublished": "2017-10-16", "_annotation": { "sample_count": 1, "sample_organism": [ "Chitinophaga caeni" ], "sample_taxid": [ "2029983" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "China:Beijing" ], "sample_host_location_id": [], "data_size": "1.490 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)": "5279921", "Number of Sequences": "1", "Longest Sequences (bp)": "5279921", "N50 (bp)": "5279921", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "42.5", "Number of CDSs": "4272", "Average Protein Length": "352.2", "Coding Ratio (%)": "85.5", "Number of rRNAs": "12", "Number of tRNAs": "61", "Number of CRISPRs": "1" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Chitinophaga caeni", "strain": "strain=13", "accession": "GCA_002557795.1", "taxid": 2029983, "species_taxid": 2029983, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1759, "total_fragments": 1759, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Chitinophaga skermanii", "strain": "strain=DSM 23857", "accession": "GCA_003259335.1", "taxid": 331697, "species_taxid": 331697, "relation_to_type": "type", "validated": true, "ani": 78.4391, "matched_fragments": 318, "total_fragments": 1759, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Chitinophaga oryzae", "strain": "strain=1303", "accession": "GCA_012516375.2", "taxid": 2725414, "species_taxid": 2725414, "relation_to_type": "type", "validated": true, "ani": 77.9043, "matched_fragments": 124, "total_fragments": 1759, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Chitinophaga fulva", "strain": "strain=G-6-1-13", "accession": "GCA_012927205.1", "taxid": 2728842, "species_taxid": 2728842, "relation_to_type": "type", "validated": true, "ani": 77.7128, "matched_fragments": 118, "total_fragments": 1759, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Chitinophaga silvatica", "strain": "strain=GDMCC 1.1288", "accession": "GCA_003419895.1", "taxid": 2282649, "species_taxid": 2282649, "relation_to_type": "type", "validated": true, "ani": 77.3906, "matched_fragments": 118, "total_fragments": 1759, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Chitinophaga varians", "strain": "strain=KACC 19415", "accession": "GCA_014529945.1", "taxid": 2202339, "species_taxid": 2202339, "relation_to_type": "type", "validated": true, "ani": 77.3206, "matched_fragments": 111, "total_fragments": 1759, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Chitinophaga terrae (ex Kim and Jung 2007)", "strain": "strain=DSM 23920", "accession": "GCA_900107795.1", "taxid": 408074, "species_taxid": 408074, "relation_to_type": "type", "validated": true, "ani": 77.2266, "matched_fragments": 153, "total_fragments": 1759, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Chitinophaga niabensis", "strain": "strain=DSM 24787", "accession": "GCA_900129465.1", "taxid": 536979, "species_taxid": 536979, "relation_to_type": "type", "validated": true, "ani": 77.1983, "matched_fragments": 132, "total_fragments": 1759, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Chitinophaga agri", "strain": "strain=H33E-04", "accession": "GCA_010093065.1", "taxid": 2703787, "species_taxid": 2703787, "relation_to_type": "type", "validated": true, "ani": 77.1416, "matched_fragments": 120, "total_fragments": 1759, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Chitinophaga eiseniae", "strain": "strain=DSM 22224", "accession": "GCA_900167135.1", "taxid": 634771, "species_taxid": 634771, "relation_to_type": "type", "validated": true, "ani": 77.131, "matched_fragments": 129, "total_fragments": 1759, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Chitinophaga jiangningensis", "strain": "strain=DSM 27406", "accession": "GCA_900142605.1", "taxid": 1419482, "species_taxid": 1419482, "relation_to_type": "type", "validated": true, "ani": 76.9872, "matched_fragments": 134, "total_fragments": 1759, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Chitinophaga qingshengii", "strain": "strain=JCM 30026", "accession": "GCA_014529935.1", "taxid": 1569794, "species_taxid": 1569794, "relation_to_type": "type", "validated": true, "ani": 76.9295, "matched_fragments": 139, "total_fragments": 1759, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Chitinophaga alhagiae", "strain": "strain=T22", "accession": "GCA_003177275.1", "taxid": 2203219, "species_taxid": 2203219, "relation_to_type": "suspected-type", "validated": true, "ani": 76.9291, "matched_fragments": 75, "total_fragments": 1759, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Chitinophaga flava", "strain": "strain=GDMCC 1.1325", "accession": "GCA_003308995.1", "taxid": 2259036, "species_taxid": 2259036, "relation_to_type": "type", "validated": true, "ani": 76.9153, "matched_fragments": 136, "total_fragments": 1759, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Chitinophaga agrisoli", "strain": "strain=BN140078", "accession": "GCA_008386695.1", "taxid": 2607653, "species_taxid": 2607653, "relation_to_type": "type", "validated": true, "ani": 76.9065, "matched_fragments": 116, "total_fragments": 1759, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Chitinophaga deserti", "strain": "strain=XJ-2", "accession": "GCA_003149455.1", "taxid": 2164099, "species_taxid": 2164099, "relation_to_type": "type", "validated": true, "ani": 76.7482, "matched_fragments": 135, "total_fragments": 1759, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Chitinophaga sancti", "strain": "strain=DSM 784", "accession": "GCA_900119105.1", "taxid": 1004, "species_taxid": 1004, "relation_to_type": "type", "validated": true, "ani": 76.6564, "matched_fragments": 104, "total_fragments": 1759, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_002557795.1", "gtdb_species": "s__Chitinophaga caeni", "ani": 100.0, "matched_fragments": 1759, "total_fragments": 1759, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Chitinophaga", "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_003259335.1", "gtdb_species": "s__Chitinophaga skermanii", "ani": 78.4474, "matched_fragments": 318, "total_fragments": 1759, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Chitinophaga", "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_012516355.1", "gtdb_species": "s__Chitinophaga sp012516355", "ani": 77.8294, "matched_fragments": 122, "total_fragments": 1759, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Chitinophaga", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.48", "min_intra_species_ani": "99.48", "mean_intra_species_af": "0.97", "min_intra_species_af": "0.97", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_902167325.1", "gtdb_species": "s__Chitinophaga pinensis_A", "ani": 77.7365, "matched_fragments": 114, "total_fragments": 1759, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Chitinophaga", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.49", "min_intra_species_ani": "99.49", "mean_intra_species_af": "0.97", "min_intra_species_af": "0.97", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCA_001870995.2", "gtdb_species": "s__Chitinophaga sp001870995", "ani": 77.6052, "matched_fragments": 132, "total_fragments": 1759, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Chitinophaga", "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_018255755.1", "gtdb_species": "s__Chitinophaga sp018255755", "ani": 77.5308, "matched_fragments": 149, "total_fragments": 1759, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Chitinophaga", "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_003419895.1", "gtdb_species": "s__Chitinophaga sp003419895", "ani": 77.4203, "matched_fragments": 116, "total_fragments": 1759, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Chitinophaga", "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_007829335.1", "gtdb_species": "s__Chitinophaga polysaccharea_B", "ani": 77.3365, "matched_fragments": 125, "total_fragments": 1759, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Chitinophaga", "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_014529945.1", "gtdb_species": "s__Chitinophaga varians", "ani": 77.3257, "matched_fragments": 110, "total_fragments": 1759, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Chitinophaga", "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_900107795.1", "gtdb_species": "s__Chitinophaga terrae", "ani": 77.2495, "matched_fragments": 153, "total_fragments": 1759, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Chitinophaga", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.99", "min_intra_species_ani": "99.99", "mean_intra_species_af": "1.00", "min_intra_species_af": "1.00", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_009647655.1", "gtdb_species": "s__Chitinophaga sp009647655", "ani": 77.2285, "matched_fragments": 134, "total_fragments": 1759, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Chitinophaga", "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_019219075.1", "gtdb_species": "s__Chitinophaga sp019219075", "ani": 77.2094, "matched_fragments": 135, "total_fragments": 1759, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Chitinophaga", "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_900129465.1", "gtdb_species": "s__Chitinophaga niabensis", "ani": 77.1879, "matched_fragments": 131, "total_fragments": 1759, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Chitinophaga", "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_900167135.1", "gtdb_species": "s__Chitinophaga eiseniae", "ani": 77.131, "matched_fragments": 129, "total_fragments": 1759, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Chitinophaga", "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_003014755.1", "gtdb_species": "s__Chitinophaga niastensis", "ani": 76.9635, "matched_fragments": 120, "total_fragments": 1759, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Chitinophaga", "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_014529935.1", "gtdb_species": "s__Chitinophaga qingshengii", "ani": 76.9472, "matched_fragments": 138, "total_fragments": 1759, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Chitinophaga", "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_003308995.1", "gtdb_species": "s__Chitinophaga flava", "ani": 76.9308, "matched_fragments": 135, "total_fragments": 1759, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Chitinophaga", "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_008386695.1", "gtdb_species": "s__Chitinophaga agrisoli", "ani": 76.9041, "matched_fragments": 115, "total_fragments": 1759, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Chitinophaga", "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_009758205.1", "gtdb_species": "s__Chitinophaga sp009758205", "ani": 76.7221, "matched_fragments": 107, "total_fragments": 1759, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Chitinophaga", "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_900119105.1", "gtdb_species": "s__Chitinophaga sancti", "ani": 76.6551, "matched_fragments": 103, "total_fragments": 1759, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Chitinophaga", "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": -0.308, "cell_length": 0.473, "doubling_h": null, "growth_tmp": 28.733, "optimum_tmp": 26.937, "optimum_ph": 7.0, "genome_size": 7579043.287, "gc_content": 45.2, "coding_genes": 7126.333, "rRNA16S_genes": 6.0, "tRNA_genes": 72.0, "gram_stain": 0.0, "sporulation": 0.0, "motility": 0.181, "range_salinity": null, "facultative_respiration": 0.058, "anaerobic_respiration": 0.0, "aerobic_respiration": 0.941, "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": [ "Chitinophaga", "caeni" ], "quality": 5, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }