{ "type": "genome", "identifier": "GCF_001314325.1", "organism": "Sphingopyxis macrogoltabida", "title": "Sphingopyxis macrogoltabida", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Tohoku university", "publication": [ {} ], "properties": { "assembly_accession": "GCF_001314325.1", "bioproject": "PRJNA224116", "biosample": "SAMN03031197", "wgs_master": "na", "refseq_category": "reference genome", "taxid": "33050", "species_taxid": "33050", "organism_name": "Sphingopyxis macrogoltabida", "infraspecific_name": "strain=203", "isolate": "na", "version_status": "latest", "assembly_level": "Complete Genome", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2015/10/14", "asm_name": "ASM131432v1", "asm_submitter": "Tohoku university", "gbrs_paired_asm": "GCA_001314325.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/001/314/325/GCF_001314325.1_ASM131432v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "5748623", "genome_size_ungapped": "5748623", "gc_percent": "65.000000", "replicon_count": "3", "scaffold_count": "3", "contig_count": "3", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_001314325.1-RS_2024_12_09", "annotation_date": "2024-12-09", "total_gene_count": "5640", "protein_coding_gene_count": "5507", "non_coding_gene_count": "63", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2015-10-14", "dateModified": "2015-10-14", "datePublished": "2015-10-14", "_annotation": { "sample_count": 1, "sample_organism": [ "Sphingopyxis macrogoltabida" ], "sample_taxid": [ "33050" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "Japan" ], "sample_host_location_id": [], "data_size": "1.574 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": null, "max": null }, "completeness": 95.83, "contamination": 0.0, "strain_heterogeneity": 0.0, "genome_count": 1 }, "data_type": "G", "data_source": "RefSeq", "_dfast": { "Total Sequence Length (bp)": "5748623", "Number of Sequences": "3", "Longest Sequences (bp)": "5174928", "N50 (bp)": "5174928", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "64.9", "Number of CDSs": "5601", "Average Protein Length": "312.4", "Coding Ratio (%)": "91.3", "Number of rRNAs": "3", "Number of tRNAs": "62", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Sphingopyxis macrogoltabida", "strain": "strain=203", "accession": "GCA_001314325.1", "taxid": 33050, "species_taxid": 33050, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1914, "total_fragments": 1914, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Sphingopyxis panaciterrae", "strain": "strain=DSM 27164", "accession": "GCA_011762125.1", "taxid": 363841, "species_taxid": 363841, "relation_to_type": "type", "validated": true, "ani": 86.9091, "matched_fragments": 1090, "total_fragments": 1914, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sphingopyxis italica", "strain": "strain=DSM 25229", "accession": "GCA_011926545.1", "taxid": 1129133, "species_taxid": 1129133, "relation_to_type": "type", "validated": true, "ani": 86.1224, "matched_fragments": 951, "total_fragments": 1914, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sphingopyxis fribergensis", "strain": "strain=Kp5.2", "accession": "GCA_000803645.1", "taxid": 1515612, "species_taxid": 1515612, "relation_to_type": "type", "validated": true, "ani": 85.5617, "matched_fragments": 1005, "total_fragments": 1914, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sphingopyxis soli", "strain": "strain=BL03", "accession": "GCA_018682675.1", "taxid": 592051, "species_taxid": 592051, "relation_to_type": "type", "validated": true, "ani": 85.0206, "matched_fragments": 848, "total_fragments": 1914, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sphingopyxis microcysteis", "strain": "strain=Z10-6", "accession": "GCA_012274265.1", "taxid": 2484145, "species_taxid": 2484145, "relation_to_type": "type", "validated": true, "ani": 84.4478, "matched_fragments": 840, "total_fragments": 1914, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sphingopyxis panaciterrulae", "strain": "strain=DSM 27163", "accession": "GCA_014199295.1", "taxid": 462372, "species_taxid": 462372, "relation_to_type": "type", "validated": true, "ani": 84.2787, "matched_fragments": 915, "total_fragments": 1914, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sphingopyxis alaskensis", "strain": "strain=RB2256", "accession": "GCA_000013985.1", "taxid": 117207, "species_taxid": 117207, "relation_to_type": "type", "validated": true, "ani": 84.217, "matched_fragments": 839, "total_fragments": 1914, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sphingopyxis granuli", "strain": "strain=NBRC 100800", "accession": "GCA_001591045.1", "taxid": 267128, "species_taxid": 267128, "relation_to_type": "type", "validated": true, "ani": 84.1303, "matched_fragments": 819, "total_fragments": 1914, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sphingopyxis solisilvae", "strain": "strain=R366", "accession": "GCA_015475875.1", "taxid": 1886788, "species_taxid": 1886788, "relation_to_type": "type", "validated": true, "ani": 84.1301, "matched_fragments": 804, "total_fragments": 1914, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sphingopyxis indica", "strain": "strain=DS15", "accession": "GCA_900188185.1", "taxid": 436663, "species_taxid": 436663, "relation_to_type": "type", "validated": true, "ani": 84.0895, "matched_fragments": 875, "total_fragments": 1914, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sphingopyxis terrae subsp. ummariensis", "strain": "strain=UI2", "accession": "GCA_900177755.1", "taxid": 429001, "species_taxid": 33052, "relation_to_type": "type", "validated": true, "ani": 83.9457, "matched_fragments": 827, "total_fragments": 1914, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sphingopyxis witflariensis", "strain": "strain=DSM 14551", "accession": "GCA_002205635.1", "taxid": 173675, "species_taxid": 173675, "relation_to_type": "type", "validated": true, "ani": 83.9025, "matched_fragments": 917, "total_fragments": 1914, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sphingopyxis bauzanensis", "strain": "strain=CGMCC 1.8959", "accession": "GCA_014645635.1", "taxid": 651663, "species_taxid": 651663, "relation_to_type": "type", "validated": true, "ani": 83.8363, "matched_fragments": 890, "total_fragments": 1914, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sphingopyxis terrae subsp. ummariensis", "strain": "strain=DSM 24316", "accession": "GCA_002374275.1", "taxid": 429001, "species_taxid": 33052, "relation_to_type": "type", "validated": true, "ani": 83.8322, "matched_fragments": 832, "total_fragments": 1914, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sphingopyxis bauzanensis", "strain": "strain=DSM 22271", "accession": "GCA_002205675.1", "taxid": 651663, "species_taxid": 651663, "relation_to_type": "type", "validated": true, "ani": 83.8186, "matched_fragments": 888, "total_fragments": 1914, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sphingomonas citricola", "strain": "strain=RHCKR47", "accession": "GCA_019429535.1", "taxid": 2862498, "species_taxid": 2862498, "relation_to_type": "type", "validated": true, "ani": 77.8847, "matched_fragments": 383, "total_fragments": 1914, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sphingomonas segetis", "strain": "strain=YJ09", "accession": "GCA_009720245.1", "taxid": 1104779, "species_taxid": 1104779, "relation_to_type": "type", "validated": true, "ani": 77.8678, "matched_fragments": 206, "total_fragments": 1914, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Alteriqipengyuania abyssalis", "strain": "strain=NZ-12B", "accession": "GCA_019857185.1", "taxid": 2860200, "species_taxid": 2860200, "relation_to_type": "type", "validated": true, "ani": 77.7247, "matched_fragments": 312, "total_fragments": 1914, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Qipengyuania gelatinilytica", "strain": "strain=1NDH1", "accession": "GCA_019711315.1", "taxid": 2867231, "species_taxid": 2867231, "relation_to_type": "type", "validated": true, "ani": 77.6465, "matched_fragments": 259, "total_fragments": 1914, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Qipengyuania flava", "strain": "strain=DSM 16421", "accession": "GCA_011762005.1", "taxid": 192812, "species_taxid": 192812, "relation_to_type": "type", "validated": true, "ani": 77.5547, "matched_fragments": 285, "total_fragments": 1914, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sphingomonas corticis", "strain": "strain=36D10-4-7", "accession": "GCA_012035195.1", "taxid": 2722791, "species_taxid": 2722791, "relation_to_type": "type", "validated": true, "ani": 77.5195, "matched_fragments": 414, "total_fragments": 1914, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Croceicoccus ponticola", "strain": "strain=GM-16", "accession": "GCA_004004515.1", "taxid": 2217664, "species_taxid": 2217664, "relation_to_type": "type", "validated": true, "ani": 77.497, "matched_fragments": 237, "total_fragments": 1914, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 95.83, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_001314325.1", "gtdb_species": "s__Sphingopyxis macrogoltabida", "ani": 100.0, "matched_fragments": 1914, "total_fragments": 1914, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis", "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": "conclusive" }, { "accession": "GCF_001307295.1", "gtdb_species": "s__Sphingopyxis macrogoltabida_B", "ani": 93.9491, "matched_fragments": 1307, "total_fragments": 1914, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "N/A", "min_intra_species_ani": "N/A", 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"mean_intra_species_af": "0.88", "min_intra_species_af": "0.88", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_000756385.1", "gtdb_species": "s__Sphingopyxis sp000756385", "ani": 85.7586, "matched_fragments": 948, "total_fragments": 1914, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis", "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_004795895.1", "gtdb_species": "s__Sphingopyxis sp004795895", "ani": 85.6352, "matched_fragments": 990, "total_fragments": 1914, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis", "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_900078365.1", "gtdb_species": "s__Sphingopyxis sp900078365", "ani": 85.5683, "matched_fragments": 910, "total_fragments": 1914, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis", "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_000756375.1", "gtdb_species": "s__Sphingopyxis sp000756375", "ani": 85.4796, "matched_fragments": 923, "total_fragments": 1914, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis", "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_013821905.1", "gtdb_species": "s__Sphingopyxis sp013821905", "ani": 85.4164, "matched_fragments": 718, "total_fragments": 1914, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis", "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_001468285.1", "gtdb_species": "s__Sphingopyxis sp001468285", "ani": 85.3676, "matched_fragments": 1005, "total_fragments": 1914, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.98", "min_intra_species_ani": "99.98", "mean_intra_species_af": "0.98", 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"N/A", "num_clustered_genomes": 1, "status": "-" }, { "accession": "GCA_017745175.1", "gtdb_species": "s__Sphingopyxis sp017745175", "ani": 85.0052, "matched_fragments": 866, "total_fragments": 1914, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis", "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_001047015.1", "gtdb_species": "s__Sphingopyxis sp001047015", "ani": 84.9427, "matched_fragments": 982, "total_fragments": 1914, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis", "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", 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