{ "type": "genome", "identifier": "GCF_004122095.1", "organism": "Pseudoxanthomonas composti", "title": "Pseudoxanthomonas composti", "description": "na", "data type": "Genome sequencing and assembly", "organization": "School of Environment", "publication": [ {} ], "properties": { "assembly_accession": "GCF_004122095.1", "bioproject": "PRJNA224116", "biosample": "SAMN10712917", "wgs_master": "SAWZ00000000.1", "refseq_category": "reference genome", "taxid": "2137479", "species_taxid": "2137479", "organism_name": "Pseudoxanthomonas composti", "infraspecific_name": "strain=GSS15", "isolate": "na", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2019/01/30", "asm_name": "ASM412209v1", "asm_submitter": "School of Environment", "gbrs_paired_asm": "GCA_004122095.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/004/122/095/GCF_004122095.1_ASM412209v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "4340104", "genome_size_ungapped": "4340084", "gc_percent": "68.000000", "replicon_count": "0", "scaffold_count": "25", "contig_count": "25", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_004122095.1-RS_2024_05_06", "annotation_date": "2024-05-06", "total_gene_count": "3741", "protein_coding_gene_count": "3644", "non_coding_gene_count": "60", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2019-01-30", "dateModified": "2019-01-30", "datePublished": "2019-01-30", "_annotation": { "sample_count": 1, "sample_organism": [ "Pseudoxanthomonas composti" ], "sample_taxid": [ "2137479" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "China:Guangzhou" ], "sample_host_location_id": [], "data_size": "1.174 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)": "4340104", "Number of Sequences": "25", "Longest Sequences (bp)": "803374", "N50 (bp)": "409705", "Gap Ratio (%)": "0.000461", "GCcontent (%)": "68.2", "Number of CDSs": "3718", "Average Protein Length": "341.3", "Coding Ratio (%)": "87.7", "Number of rRNAs": "2", "Number of tRNAs": "54", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Pseudoxanthomonas composti", "strain": "strain=GSS15", "accession": "GCA_004122095.1", "taxid": 2137479, "species_taxid": 2137479, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1433, "total_fragments": 1433, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Pseudoxanthomonas winnipegensis", "strain": "strain=NML 130738", "accession": "GCA_004283755.1", "taxid": 2480810, "species_taxid": 2480810, "relation_to_type": "type", "validated": true, "ani": 84.0759, "matched_fragments": 955, "total_fragments": 1433, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudoxanthomonas spadix", "strain": "strain=DSM 18855", "accession": "GCA_003703395.1", "taxid": 415229, "species_taxid": 415229, "relation_to_type": "type", "validated": true, "ani": 82.9522, "matched_fragments": 720, "total_fragments": 1433, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Xanthomonas indica", "strain": "strain=PPL560", "accession": "GCA_022669045.1", "taxid": 2912242, "species_taxid": 2912242, "relation_to_type": "type", "validated": true, "ani": 82.1397, "matched_fragments": 867, "total_fragments": 1433, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudoxanthomonas taiwanensis", "strain": "strain=DSM 22914", "accession": "GCA_010093135.1", "taxid": 176598, "species_taxid": 176598, "relation_to_type": "type", "validated": true, "ani": 81.8669, "matched_fragments": 648, "total_fragments": 1433, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudoxanthomonas jiangsuensis", "strain": "strain=DSM 22398", "accession": "GCA_010093185.1", "taxid": 619688, "species_taxid": 619688, "relation_to_type": "type", "validated": true, "ani": 81.8599, "matched_fragments": 703, "total_fragments": 1433, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Stenotrophomonas acidaminiphila", "strain": "strain=DSM 13117", "accession": "GCA_024221815.1", "taxid": 128780, "species_taxid": 128780, "relation_to_type": "type", "validated": true, "ani": 81.7628, "matched_fragments": 734, "total_fragments": 1433, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudoxanthomonas japonensis", "strain": "strain=DSM 17109", "accession": "GCA_010093445.1", "taxid": 69284, "species_taxid": 69284, "relation_to_type": "type", "validated": true, "ani": 81.5034, "matched_fragments": 695, "total_fragments": 1433, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudoxanthomonas beigongshangi", "strain": "strain=REN9", "accession": "GCA_016820515.1", "taxid": 2782537, "species_taxid": 2782537, "relation_to_type": "type", "validated": true, "ani": 81.4578, "matched_fragments": 704, "total_fragments": 1433, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudoxanthomonas helianthi", "strain": "strain=110414", "accession": "GCA_017939625.1", "taxid": 1453541, "species_taxid": 1453541, "relation_to_type": "type", "validated": true, "ani": 81.1897, "matched_fragments": 621, "total_fragments": 1433, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Xanthomonas cassavae", "strain": "strain=NCPPB 101", "accession": "GCA_020783895.1", "taxid": 56450, "species_taxid": 56450, "relation_to_type": "type", "validated": true, "ani": 80.7643, "matched_fragments": 745, "total_fragments": 1433, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Luteimonas aquatica", "strain": "strain=RIB1-20", "accession": "GCA_022662575.1", "taxid": 450364, "species_taxid": 450364, "relation_to_type": "type", "validated": true, "ani": 80.7204, "matched_fragments": 663, "total_fragments": 1433, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Xanthomonas cucurbitae", "strain": "strain=CFBP2542", "accession": "GCA_002939885.1", "taxid": 56453, "species_taxid": 56453, "relation_to_type": "type", "validated": true, "ani": 80.7178, "matched_fragments": 721, "total_fragments": 1433, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Lysobacter silvisoli", "strain": "strain=zong2l5", "accession": "GCA_003382365.1", "taxid": 2293254, "species_taxid": 2293254, "relation_to_type": "type", "validated": true, "ani": 80.6196, "matched_fragments": 695, "total_fragments": 1433, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudoxanthomonas indica", "strain": "strain=CCM 7430", "accession": "GCA_014635165.1", "taxid": 428993, "species_taxid": 428993, "relation_to_type": "type", "validated": true, "ani": 80.5632, "matched_fragments": 674, "total_fragments": 1433, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Thermomonas haemolytica", "strain": "strain=LMG 19653", "accession": "GCA_006352395.1", "taxid": 141949, "species_taxid": 141949, "relation_to_type": "type", "validated": true, "ani": 80.4145, "matched_fragments": 505, "total_fragments": 1433, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Luteimonas padinae", "strain": "strain=KCTC 52403", "accession": "GCA_014652935.1", "taxid": 1714359, "species_taxid": 1714359, "relation_to_type": "type", "validated": true, "ani": 80.3467, "matched_fragments": 551, "total_fragments": 1433, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Luteimonas arsenica", "strain": "strain=26-35", "accession": "GCA_004352825.1", "taxid": 1586242, "species_taxid": 1586242, "relation_to_type": "type", "validated": true, "ani": 80.3212, "matched_fragments": 550, "total_fragments": 1433, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Luteimonas colneyensis", "strain": "strain=Sa2BVA3", "accession": "GCA_014836665.1", "taxid": 2762230, "species_taxid": 2762230, "relation_to_type": "type", "validated": true, "ani": 80.2042, "matched_fragments": 557, "total_fragments": 1433, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Xanthomonas citri", "strain": "strain=ICMP5732", "accession": "GCA_021474205.1", "taxid": 346, "species_taxid": 346, "relation_to_type": "pathovar", "validated": true, "ani": 80.1362, "matched_fragments": 730, "total_fragments": 1433, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Luteimonas salinisoli", "strain": "strain=SJ-92", "accession": "GCA_013425525.1", "taxid": 2752307, "species_taxid": 2752307, "relation_to_type": "type", "validated": true, "ani": 79.9562, "matched_fragments": 594, "total_fragments": 1433, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Lysobacter antibioticus", "strain": "strain=ATCC 29479", "accession": "GCA_001442535.1", "taxid": 84531, "species_taxid": 84531, "relation_to_type": "type", "validated": true, "ani": 79.4692, "matched_fragments": 616, "total_fragments": 1433, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Lysobacter capsici", "strain": "strain=VKM B-2533", "accession": "GCA_014779555.2", "taxid": 435897, "species_taxid": 435897, "relation_to_type": "type", "validated": true, "ani": 79.3935, "matched_fragments": 671, "total_fragments": 1433, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_004122095.1", "gtdb_species": "s__Pseudoxanthomonas_A composti", "ani": 100.0, "matched_fragments": 1433, "total_fragments": 1433, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudoxanthomonas_A", "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_004284655.1", "gtdb_species": "s__Pseudoxanthomonas_A spadix_A", "ani": 84.1042, "matched_fragments": 945, "total_fragments": 1433, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudoxanthomonas_A", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.46", "min_intra_species_ani": "98.41", "mean_intra_species_af": "0.91", "min_intra_species_af": "0.91", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_004284195.1", "gtdb_species": "s__Pseudoxanthomonas_A sp004284195", "ani": 84.0815, "matched_fragments": 957, "total_fragments": 1433, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudoxanthomonas_A", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.94", "min_intra_species_ani": "97.04", "mean_intra_species_af": "0.92", "min_intra_species_af": "0.87", "num_clustered_genomes": 11, "status": "-" }, { "accession": "GCF_003703395.1", "gtdb_species": "s__Pseudoxanthomonas_A spadix", "ani": 82.9685, "matched_fragments": 718, "total_fragments": 1433, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudoxanthomonas_A", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.25", "min_intra_species_ani": "98.51", "mean_intra_species_af": "0.95", "min_intra_species_af": "0.90", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_900109775.1", "gtdb_species": "s__Pseudoxanthomonas_A sp900109775", "ani": 82.9615, "matched_fragments": 915, "total_fragments": 1433, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudoxanthomonas_A", "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_004216795.1", "gtdb_species": "s__Stenotrophomonas_A sp004216795", "ani": 82.0318, "matched_fragments": 777, "total_fragments": 1433, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas_A", "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_001431645.1", "gtdb_species": "s__Stenotrophomonas_A panacihumi", "ani": 81.9851, "matched_fragments": 750, "total_fragments": 1433, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas_A", "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_010093185.1", "gtdb_species": "s__Pseudoxanthomonas jiangsuensis", "ani": 81.8521, "matched_fragments": 704, "total_fragments": 1433, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudoxanthomonas", "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_000513955.1", "gtdb_species": "s__Pseudoxanthomonas suwonensis_C", "ani": 81.7589, "matched_fragments": 676, "total_fragments": 1433, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudoxanthomonas", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.37", "min_intra_species_ani": "96.94", "mean_intra_species_af": "0.95", "min_intra_species_af": "0.91", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_017939625.1", "gtdb_species": "s__Pseudoxanthomonas_A helianthi", "ani": 81.168, "matched_fragments": 623, "total_fragments": 1433, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudoxanthomonas_A", "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_002939785.1", "gtdb_species": "s__Xanthomonas codiaei", "ani": 80.946, "matched_fragments": 784, "total_fragments": 1433, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas", "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_002939885.1", "gtdb_species": "s__Xanthomonas cucurbitae", "ani": 80.7462, "matched_fragments": 718, "total_fragments": 1433, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.30", "min_intra_species_ani": "99.30", "mean_intra_species_af": "0.96", "min_intra_species_af": "0.96", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_014652935.1", "gtdb_species": "s__Luteimonas padinae", "ani": 80.3579, "matched_fragments": 550, "total_fragments": 1433, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas", "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_017305095.1", "gtdb_species": "s__Thermomonas sp017305095", "ani": 80.2885, "matched_fragments": 511, "total_fragments": 1433, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Thermomonas", "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_004352825.1", "gtdb_species": "s__Luteimonas arsenica", "ani": 80.2709, "matched_fragments": 554, "total_fragments": 1433, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas", "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_014836665.1", "gtdb_species": "s__Luteimonas sp014836665", "ani": 80.1939, "matched_fragments": 558, "total_fragments": 1433, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas", "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": -0.365, "cell_length": 0.003, "doubling_h": 0.294, "growth_tmp": 31.833, "optimum_tmp": 31.704, "optimum_ph": 7.425, "genome_size": 3611866.173, "gc_content": 68.223, "coding_genes": 3072.5, "rRNA16S_genes": 1.25, "tRNA_genes": 49.5, "gram_stain": 0.071, "sporulation": 0.0, "motility": 0.545, "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": [ "Pseudoxanthomonas", "composti" ], "quality": 4, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }