{ "type": "genome", "identifier": "GCF_030160115.1", "organism": "Devosia nitrariae", "title": "Devosia nitrariae", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Institution of Microbiology, Chinese Academy of Science(WDCM)", "publication": [ {} ], "properties": { "assembly_accession": "GCF_030160115.1", "bioproject": "PRJNA224116", "biosample": "SAMD00235834", "wgs_master": "BSNS00000000.1", "refseq_category": "reference genome", "taxid": "2071872", "species_taxid": "2071872", "organism_name": "Devosia nitrariae", "infraspecific_name": "strain=NBRC 112416", "isolate": "na", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2023/02/15", "asm_name": "ASM3016011v1", "asm_submitter": "Institution of Microbiology, Chinese Academy of Science(WDCM)", "gbrs_paired_asm": "GCA_030160115.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/030/160/115/GCF_030160115.1_ASM3016011v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "5544318", "genome_size_ungapped": "5544276", "gc_percent": "64.000000", "replicon_count": "0", "scaffold_count": "35", "contig_count": "35", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_030160115.1-RS_2024_06_02", "annotation_date": "2024-06-02", "total_gene_count": "5477", "protein_coding_gene_count": "5358", "non_coding_gene_count": "53", "pubmed_id": "30832757" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2023-02-15", "dateModified": "2023-02-15", "datePublished": "2023-02-15", "_annotation": { "sample_count": 1, "sample_organism": [ "Devosia nitrariae" ], "sample_taxid": [ "2071872" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "not applicable" ], "sample_host_location_id": [], "data_size": "1.545 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)": "5544318", "Number of Sequences": "35", "Longest Sequences (bp)": "826863", "N50 (bp)": "487617", "Gap Ratio (%)": "0.000758", "GCcontent (%)": "63.8", "Number of CDSs": "5460", "Average Protein Length": "300.9", "Coding Ratio (%)": "88.9", "Number of rRNAs": "3", "Number of tRNAs": "50", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Devosia geojensis", "strain": "strain=BD-c194", "accession": "GCA_000969415.1", "taxid": 443610, "species_taxid": 443610, "relation_to_type": "type", "validated": true, "ani": 83.1285, "matched_fragments": 991, "total_fragments": 1830, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Devosia salina", "strain": "strain=SCS-3", "accession": "GCA_019504385.1", "taxid": 2860336, "species_taxid": 2860336, "relation_to_type": "type", "validated": true, "ani": 78.6835, "matched_fragments": 528, "total_fragments": 1830, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Devosia ginsengisoli", "strain": "strain=Gsoil 520", "accession": "GCA_007859655.1", "taxid": 400770, "species_taxid": 400770, "relation_to_type": "type", "validated": true, "ani": 78.5918, "matched_fragments": 573, "total_fragments": 1830, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Devosia elaeis", "strain": "strain=S37", "accession": "GCA_001650025.1", "taxid": 1770058, "species_taxid": 1770058, "relation_to_type": "type", "validated": true, "ani": 78.5491, "matched_fragments": 528, "total_fragments": 1830, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Youhaiella tibetensis", "strain": "strain=fig4", "accession": "GCA_008000755.1", "taxid": 1447062, "species_taxid": 1447062, "relation_to_type": "type", "validated": true, "ani": 78.5098, "matched_fragments": 512, "total_fragments": 1830, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Youhaiella tibetensis", "strain": "strain=CGMCC 1.12719", "accession": "GCA_014638565.1", "taxid": 1447062, "species_taxid": 1447062, "relation_to_type": "type", "validated": true, "ani": 78.4731, "matched_fragments": 503, "total_fragments": 1830, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Devosia oryziradicis", "strain": "strain=G19", "accession": "GCA_016698645.1", "taxid": 2801335, "species_taxid": 2801335, "relation_to_type": "type", "validated": true, "ani": 78.3951, "matched_fragments": 512, "total_fragments": 1830, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Devosia beringensis", "strain": "strain=S02", "accession": "GCA_014926585.1", "taxid": 2657486, "species_taxid": 2657486, "relation_to_type": "type", "validated": true, "ani": 78.3112, "matched_fragments": 529, "total_fragments": 1830, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Devosia enhydra", "strain": "strain=ATCC 23634", "accession": "GCA_900119845.1", "taxid": 665118, "species_taxid": 665118, "relation_to_type": "type", "validated": true, "ani": 78.2255, "matched_fragments": 435, "total_fragments": 1830, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Devosia indica", "strain": "strain=IO390501", "accession": "GCA_003056405.1", "taxid": 2079253, "species_taxid": 2079253, "relation_to_type": "type", "validated": true, "ani": 78.1964, "matched_fragments": 445, "total_fragments": 1830, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Devosia chinhatensis", "strain": "strain=IPL18", "accession": "GCA_000969445.1", "taxid": 429727, "species_taxid": 429727, "relation_to_type": "type", "validated": true, "ani": 78.1659, "matched_fragments": 412, "total_fragments": 1830, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Devosia insulae", "strain": "strain=DS-56", "accession": "GCA_000970465.2", "taxid": 408174, "species_taxid": 408174, "relation_to_type": "type", "validated": true, "ani": 78.0647, "matched_fragments": 531, "total_fragments": 1830, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Devosia faecipullorum", "strain": "strain=CC-YST696", "accession": "GCA_015158295.1", "taxid": 2755039, "species_taxid": 2755039, "relation_to_type": "type", "validated": true, "ani": 78.0342, "matched_fragments": 403, "total_fragments": 1830, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Devosia riboflavina", "strain": "strain=IFO13584", "accession": "GCA_000743575.1", "taxid": 46914, "species_taxid": 46914, "relation_to_type": "type", "validated": true, "ani": 77.8893, "matched_fragments": 492, "total_fragments": 1830, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Devosia rhizoryzae", "strain": "strain=LEGU1", "accession": "GCA_016698665.1", "taxid": 2774137, "species_taxid": 2774137, "relation_to_type": "type", "validated": true, "ani": 77.8641, "matched_fragments": 399, "total_fragments": 1830, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Devosia psychrophila", "strain": "strain=Cr7-05", "accession": "GCA_000971275.1", "taxid": 728005, "species_taxid": 728005, "relation_to_type": "type", "validated": true, "ani": 77.7304, "matched_fragments": 458, "total_fragments": 1830, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Devosia crocina", "strain": "strain=IPL20", "accession": "GCA_900116545.1", "taxid": 429728, "species_taxid": 429728, "relation_to_type": "type", "validated": true, "ani": 77.6689, "matched_fragments": 373, "total_fragments": 1830, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Devosia psychrophila", "strain": "strain=CGMCC 1.10210", "accession": "GCA_900112505.1", "taxid": 728005, "species_taxid": 728005, "relation_to_type": "type", "validated": true, "ani": 77.6592, "matched_fragments": 478, "total_fragments": 1830, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Ancylobacter dichloromethanicus", "strain": "strain=VKM B-2484", "accession": "GCA_018390645.1", "taxid": 518825, "species_taxid": 518825, "relation_to_type": "type", "validated": true, "ani": 76.5947, "matched_fragments": 230, "total_fragments": 1830, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Methylobacterium terricola", "strain": "strain=17Sr1-39", "accession": "GCA_006151805.1", "taxid": 2583531, "species_taxid": 2583531, "relation_to_type": "type", "validated": true, "ani": 76.3217, "matched_fragments": 245, "total_fragments": 1830, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_000969415.1", "gtdb_species": "s__Devosia geojensis", "ani": 83.1593, "matched_fragments": 988, "total_fragments": 1830, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia", "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_001426345.1", "gtdb_species": "s__Devosia sp001426345", "ani": 78.6869, "matched_fragments": 543, "total_fragments": 1830, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia", "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_001650025.1", "gtdb_species": "s__Devosia elaeis", "ani": 78.5572, "matched_fragments": 527, "total_fragments": 1830, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia", "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_018828145.1", "gtdb_species": "s__Devosia sp018828145", "ani": 78.5197, "matched_fragments": 572, "total_fragments": 1830, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.99", "min_intra_species_ani": "99.98", "mean_intra_species_af": "0.99", "min_intra_species_af": "0.98", "num_clustered_genomes": 4, "status": "-" }, { "accession": "GCF_008000755.1", "gtdb_species": "s__Youhaiella tibetensis", "ani": 78.4872, "matched_fragments": 512, "total_fragments": 1830, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Youhaiella", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.26", "min_intra_species_ani": "98.52", "mean_intra_species_af": "0.98", "min_intra_species_af": "0.97", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_016698645.1", "gtdb_species": "s__Devosia sp016698645", "ani": 78.403, "matched_fragments": 511, "total_fragments": 1830, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia", "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_017307495.1", "gtdb_species": "s__Devosia_A sp017307495", "ani": 78.3589, "matched_fragments": 474, "total_fragments": 1830, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia_A", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.70", "min_intra_species_ani": "98.70", "mean_intra_species_af": "0.95", "min_intra_species_af": "0.95", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_001402915.1", "gtdb_species": "s__Devosia_A sp001402915", "ani": 78.2526, "matched_fragments": 513, "total_fragments": 1830, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia_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": "GCA_001899075.1", "gtdb_species": "s__Devosia_A sp001899075", "ani": 78.2523, "matched_fragments": 496, "total_fragments": 1830, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia_A", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "100.00", "min_intra_species_ani": "100.00", "mean_intra_species_af": "0.99", "min_intra_species_af": "0.99", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_900128975.1", "gtdb_species": "s__Devosia limi", "ani": 78.2501, "matched_fragments": 525, "total_fragments": 1830, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.98", "min_intra_species_ani": "99.98", "mean_intra_species_af": "0.97", "min_intra_species_af": "0.97", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_003056405.1", "gtdb_species": "s__Devosia indica", "ani": 78.2073, "matched_fragments": 443, "total_fragments": 1830, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia", "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_900110945.1", "gtdb_species": "s__Devosia sp900110945", "ani": 78.2048, "matched_fragments": 513, "total_fragments": 1830, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia", "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_005222805.1", "gtdb_species": "s__Devosia sp005222805", "ani": 78.173, "matched_fragments": 526, "total_fragments": 1830, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia", "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_016801025.1", "gtdb_species": "s__Paradevosia shaoguanensis", "ani": 78.1365, "matched_fragments": 514, "total_fragments": 1830, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Paradevosia", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.16", "min_intra_species_ani": "97.13", "mean_intra_species_af": "0.92", "min_intra_species_af": "0.92", "num_clustered_genomes": 4, "status": "-" }, { "accession": "GCF_001425235.1", "gtdb_species": "s__Devosia_A sp001425235", "ani": 78.1089, "matched_fragments": 566, "total_fragments": 1830, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia_A", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.96", "min_intra_species_ani": "97.96", "mean_intra_species_af": "0.95", "min_intra_species_af": "0.95", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCA_001899085.1", "gtdb_species": "s__Devosia_A sp001899085", "ani": 78.0932, "matched_fragments": 537, "total_fragments": 1830, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia_A", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.98", "min_intra_species_ani": "99.97", "mean_intra_species_af": "0.99", "min_intra_species_af": "0.99", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_015158295.1", "gtdb_species": "s__Devosia sp015158295", "ani": 78.0345, "matched_fragments": 399, "total_fragments": 1830, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia", "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_015234425.1", "gtdb_species": "s__Devosia sp015234425", "ani": 78.0165, "matched_fragments": 439, "total_fragments": 1830, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia", "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_001425445.1", "gtdb_species": "s__Devosia sp001425445", "ani": 77.78, "matched_fragments": 409, "total_fragments": 1830, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "96.74", "min_intra_species_ani": "96.74", "mean_intra_species_af": "0.91", "min_intra_species_af": "0.91", "num_clustered_genomes": 2, "status": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": -0.26, "cell_length": 0.157, "doubling_h": null, "growth_tmp": 26.73, "optimum_tmp": 27.125, "optimum_ph": 7.393, "genome_size": 4123393.25, "gc_content": null, "coding_genes": null, "rRNA16S_genes": null, "tRNA_genes": null, "gram_stain": 0.0, "sporulation": 0.0, "motility": 0.909, "range_salinity": null, "facultative_respiration": 0.0, "anaerobic_respiration": 0.0, "aerobic_respiration": 1.0, "mesophilic_range_tmp": null, "thermophilic_range_tmp": null, "psychrophilic_range_tmp": null, "bacillus_cell_shape": 0.909, "coccus_cell_shape": 0.0, "filament_cell_shape": 0.0, "coccobacillus_cell_shape": 0.09, "vibrio_cell_shape": 0.0, "spiral_cell_shape": 0.0 }, "_genome_taxon": [ "Devosia", "nitrariae" ], "quality": 4, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }