{ "type": "genome", "identifier": "GCF_004152845.1", "organism": "Sphingobium fuliginis", "title": "Sphingobium fuliginis", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Guangdong Microbial Culture Collection Center (GDMCC), Guangdong Institute of Microbiology", "publication": [ {} ], "properties": { "assembly_accession": "GCF_004152845.1", "bioproject": "PRJNA224116", "biosample": "SAMN10868459", "wgs_master": "SEON00000000.1", "refseq_category": "na", "taxid": "336203", "species_taxid": "336203", "organism_name": "Sphingobium fuliginis", "infraspecific_name": "strain=DSM 18781", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2019/02/10", "asm_name": "ASM415284v1", "asm_submitter": "Guangdong Microbial Culture Collection Center (GDMCC), Guangdong Institute of Microbiology", "gbrs_paired_asm": "GCA_004152845.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/004/152/845/GCF_004152845.1_ASM415284v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "4595643", "genome_size_ungapped": "4595643", "gc_percent": "65.000000", "replicon_count": "0", "scaffold_count": "21", "contig_count": "21", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_004152845.1-RS_2024_04_08", "annotation_date": "2024-04-08", "total_gene_count": "4341", "protein_coding_gene_count": "4239", "non_coding_gene_count": "58", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2019-02-10", "dateModified": "2019-02-10", "datePublished": "2019-02-10", "_annotation": { "sample_count": 1, "sample_organism": [ "Sphingobium fuliginis" ], "sample_taxid": [ "336203" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "India: Panki, Kanpur" ], "sample_host_location_id": [], "data_size": "1.264 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)": "4595643", "Number of Sequences": "21", "Longest Sequences (bp)": "980512", "N50 (bp)": "446120", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "64.9", "Number of CDSs": "4282", "Average Protein Length": "322.7", "Coding Ratio (%)": "90.2", "Number of rRNAs": "3", "Number of tRNAs": "53", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Sphingobium fuliginis", "strain": "strain=DSM 18781", "accession": "GCA_004152845.1", "taxid": 336203, "species_taxid": 336203, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1519, "total_fragments": 1520, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Sphingobium fuliginis", "strain": "strain=CCM 7327", "accession": "GCA_014636045.1", "taxid": 336203, "species_taxid": 336203, "relation_to_type": "type", "validated": true, "ani": 99.9958, "matched_fragments": 1509, "total_fragments": 1520, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Sphingobium indicum", "strain": "strain=B90A", "accession": "GCA_000264945.2", "taxid": 332055, "species_taxid": 332055, "relation_to_type": "type", "validated": true, "ani": 91.6759, "matched_fragments": 948, "total_fragments": 1520, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sphingobium chlorophenolicum", "strain": "strain=NBRC 16172", "accession": "GCA_001598515.1", "taxid": 46429, "species_taxid": 46429, "relation_to_type": "type", "validated": true, "ani": 88.2043, "matched_fragments": 878, "total_fragments": 1520, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sphingobium chlorophenolicum", "strain": "strain=NBRC 16172", "accession": "GCA_000722875.1", "taxid": 46429, "species_taxid": 46429, "relation_to_type": "type", "validated": true, "ani": 88.0466, "matched_fragments": 953, "total_fragments": 1520, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sphingobium chungbukense", "strain": "strain=DJ77", "accession": "GCA_001005725.1", "taxid": 56193, "species_taxid": 56193, "relation_to_type": "type", "validated": true, "ani": 86.93, "matched_fragments": 1030, "total_fragments": 1520, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sphingobium estronivorans", "strain": "strain=AXB", "accession": "GCA_008692605.1", "taxid": 1577690, "species_taxid": 1577690, "relation_to_type": "type", "validated": true, "ani": 86.4898, "matched_fragments": 819, "total_fragments": 1520, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sphingobium quisquiliarum", "strain": "strain=P25", "accession": "GCA_000445065.1", "taxid": 538379, "species_taxid": 538379, "relation_to_type": "type", "validated": true, "ani": 83.775, "matched_fragments": 724, "total_fragments": 1520, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sphingomonas changnyeongensis", "strain": "strain=C33", "accession": "GCA_009913435.1", "taxid": 2698679, "species_taxid": 2698679, "relation_to_type": "type", "validated": true, "ani": 78.4423, "matched_fragments": 382, "total_fragments": 1520, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sphingomonas aracearum", "strain": "strain=WZY 27", "accession": "GCA_003345355.1", "taxid": 2283317, "species_taxid": 2283317, "relation_to_type": "type", "validated": true, "ani": 78.2933, "matched_fragments": 385, "total_fragments": 1520, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sphingomonas cavernae", "strain": "strain=K2R01-6", "accession": "GCA_003590775.1", "taxid": 2320861, "species_taxid": 2320861, "relation_to_type": "type", "validated": true, "ani": 78.1413, "matched_fragments": 372, "total_fragments": 1520, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rhizorhabdus phycosphaerae", "strain": "strain=MK52", "accession": "GCA_011044255.1", "taxid": 2711156, "species_taxid": 2711156, "relation_to_type": "type", "validated": true, "ani": 78.0893, "matched_fragments": 366, "total_fragments": 1520, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sphingomonas profundi", "strain": "strain=LMO-1", "accession": "GCA_009739515.1", "taxid": 2681549, "species_taxid": 2681549, "relation_to_type": "type", "validated": true, "ani": 77.88, "matched_fragments": 429, "total_fragments": 1520, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_004152845.1", "gtdb_species": "s__Sphingobium fuliginis", "ani": 100.0, "matched_fragments": 1519, "total_fragments": 1520, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.53", "min_intra_species_ani": "97.80", "mean_intra_species_af": "0.87", "min_intra_species_af": "0.78", "num_clustered_genomes": 14, "status": "conclusive" }, { "accession": "GCA_000264945.2", "gtdb_species": "s__Sphingobium indicum", "ani": 91.6898, "matched_fragments": 947, "total_fragments": 1520, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.64", "min_intra_species_ani": "97.75", "mean_intra_species_af": "0.82", "min_intra_species_af": "0.64", "num_clustered_genomes": 8, "status": "-" }, { "accession": "GCF_013375535.1", "gtdb_species": "s__Sphingobium sp013375535", "ani": 89.1989, "matched_fragments": 990, "total_fragments": 1520, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium", "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_004361945.1", "gtdb_species": "s__Sphingobium barthaii_A", "ani": 88.5211, "matched_fragments": 1021, "total_fragments": 1520, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium", "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_000722875.1", "gtdb_species": "s__Sphingobium chlorophenolicum", "ani": 88.0504, "matched_fragments": 953, "total_fragments": 1520, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.94", "min_intra_species_ani": "95.89", "mean_intra_species_af": "0.87", "min_intra_species_af": "0.76", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_001005725.1", "gtdb_species": "s__Sphingobium chungbukense", "ani": 86.9462, "matched_fragments": 1028, "total_fragments": 1520, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.77", "min_intra_species_ani": "97.77", "mean_intra_species_af": "0.72", "min_intra_species_af": "0.72", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_008692605.1", "gtdb_species": "s__Sphingobium estronivorans", "ani": 86.4705, "matched_fragments": 820, "total_fragments": 1520, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium", "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_013375555.1", "gtdb_species": "s__Sphingobium sp013375555", "ani": 86.1249, "matched_fragments": 867, "total_fragments": 1520, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium", "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_014873695.1", "gtdb_species": "s__Sphingobium sp014873695", "ani": 85.628, "matched_fragments": 951, "total_fragments": 1520, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium", "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_000412635.1", "gtdb_species": "s__Sphingobium bisphenolivorans", "ani": 83.8346, "matched_fragments": 810, "total_fragments": 1520, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium", "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": -0.278, "cell_length": 0.094, "doubling_h": null, "growth_tmp": 29.0, "optimum_tmp": 28.868, "optimum_ph": 7.125, "genome_size": 5565812.0, "gc_content": 64.099, "coding_genes": 4211.023, "rRNA16S_genes": 2.333, "tRNA_genes": 53.785, "gram_stain": 0.0, "sporulation": 0.0, "motility": 0.347, "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": 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": [ "Sphingobium", "fuliginis" ], "quality": 5, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }