{ "type": "genome", "identifier": "GCF_014237875.1", "organism": "Parasphingopyxis marina", "title": "Parasphingopyxis marina", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Chungbuk national university", "publication": [ {} ], "properties": { "assembly_accession": "GCF_014237875.1", "bioproject": "PRJNA224116", "biosample": "SAMN15768573", "wgs_master": "JACJVJ000000000.1", "refseq_category": "reference genome", "taxid": "2761622", "species_taxid": "2761622", "organism_name": "Parasphingopyxis marina", "infraspecific_name": "strain=GrpM-11", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2020/08/18", "asm_name": "ASM1423787v1", "asm_submitter": "Chungbuk national university", "gbrs_paired_asm": "GCA_014237875.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/014/237/875/GCF_014237875.1_ASM1423787v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "3306929", "genome_size_ungapped": "3306929", "gc_percent": "63.500000", "replicon_count": "0", "scaffold_count": "5", "contig_count": "5", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_014237875.1-RS_2024_12_11", "annotation_date": "2024-12-11", "total_gene_count": "3279", "protein_coding_gene_count": "3214", "non_coding_gene_count": "54", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2020-08-18", "dateModified": "2020-08-18", "datePublished": "2020-08-18", "_annotation": { "sample_count": 1, "sample_organism": [ "Parasphingopyxis marina" ], "sample_taxid": [ "2761622" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "South Korea:East Sea" ], "sample_host_location_id": [], "data_size": "0.909 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)": "3306929", "Number of Sequences": "5", "Longest Sequences (bp)": "1744606", "N50 (bp)": "1744606", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "63.7", "Number of CDSs": "3228", "Average Protein Length": "315.6", "Coding Ratio (%)": "92.4", "Number of rRNAs": "3", "Number of tRNAs": "51", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Parasphingopyxis marina", "strain": "strain=GrpM-11", "accession": "GCA_014237875.1", "taxid": 2761622, "species_taxid": 2761622, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1099, "total_fragments": 1099, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Parasphingopyxis algicola", "strain": "strain=JCM 31719", "accession": "GCA_013378075.1", "taxid": 2026624, "species_taxid": 2026624, "relation_to_type": "type", "validated": true, "ani": 80.9826, "matched_fragments": 646, "total_fragments": 1099, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Parasphingopyxis lamellibrachiae", "strain": "strain=DSM 26725", "accession": "GCA_003385775.1", "taxid": 680125, "species_taxid": 680125, "relation_to_type": "type", "validated": true, "ani": 79.178, "matched_fragments": 547, "total_fragments": 1099, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sphingosinithalassobacter tenebrarum", "strain": "strain=zrk23", "accession": "GCA_011057975.1", "taxid": 2711215, "species_taxid": 2711215, "relation_to_type": "type", "validated": true, "ani": 78.2044, "matched_fragments": 328, "total_fragments": 1099, "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": 78.2001, "matched_fragments": 332, "total_fragments": 1099, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sphingomonas gilva", "strain": "strain=ZDH117", "accession": "GCA_003515075.1", "taxid": 2305907, "species_taxid": 2305907, "relation_to_type": "type", "validated": true, "ani": 78.0882, "matched_fragments": 366, "total_fragments": 1099, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sphingosinicella ginsenosidimutans", "strain": "strain=BS-11", "accession": "GCA_007995055.1", "taxid": 1176539, "species_taxid": 1176539, "relation_to_type": "type", "validated": true, "ani": 78.0858, "matched_fragments": 328, "total_fragments": 1099, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sphingomonas laterariae", "strain": "strain=LNB2", "accession": "GCA_900188165.1", "taxid": 861865, "species_taxid": 861865, "relation_to_type": "type", "validated": true, "ani": 78.0271, "matched_fragments": 338, "total_fragments": 1099, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sphingomonas fennica", "strain": "strain=K101", "accession": "GCA_003034225.1", "taxid": 114404, "species_taxid": 114404, "relation_to_type": "type", "validated": true, "ani": 78.0026, "matched_fragments": 327, "total_fragments": 1099, "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": 77.8623, "matched_fragments": 343, "total_fragments": 1099, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sphingomonas flavalba", "strain": "strain=ZLT-5", "accession": "GCA_004796535.1", "taxid": 2559804, "species_taxid": 2559804, "relation_to_type": "type", "validated": true, "ani": 77.84, "matched_fragments": 308, "total_fragments": 1099, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sphingomonas alpina", "strain": "strain=DSM 22537", "accession": "GCA_025370095.1", "taxid": 653931, "species_taxid": 653931, "relation_to_type": "type", "validated": true, "ani": 77.8303, "matched_fragments": 309, "total_fragments": 1099, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sphingobium amiense", "strain": "strain=DSM 16289", "accession": "GCA_003967075.1", "taxid": 135719, "species_taxid": 135719, "relation_to_type": "type", "validated": true, "ani": 77.7401, "matched_fragments": 260, "total_fragments": 1099, "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": 77.7164, "matched_fragments": 309, "total_fragments": 1099, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sphingomonas morindae", "strain": "strain=NBD5", "accession": "GCA_023822065.1", "taxid": 1541170, "species_taxid": 1541170, "relation_to_type": "type", "validated": true, "ani": 77.7017, "matched_fragments": 310, "total_fragments": 1099, "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": 77.6914, "matched_fragments": 322, "total_fragments": 1099, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sphingomonas formosensis", "strain": "strain=CC-Nfb-2", "accession": "GCA_009755815.1", "taxid": 861534, "species_taxid": 861534, "relation_to_type": "type", "validated": true, "ani": 77.621, "matched_fragments": 334, "total_fragments": 1099, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sphingomonas jatrophae", "strain": "strain=S5-249", "accession": "GCA_900113315.1", "taxid": 1166337, "species_taxid": 1166337, "relation_to_type": "type", "validated": true, "ani": 77.5677, "matched_fragments": 274, "total_fragments": 1099, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sphingomonas echinoides", "strain": "strain=ATCC 14820", "accession": "GCA_000241465.1", "taxid": 59803, "species_taxid": 59803, "relation_to_type": "type", "validated": true, "ani": 77.5545, "matched_fragments": 281, "total_fragments": 1099, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sphingomonas psychrolutea", "strain": "strain=CGMCC 1.10106", "accession": "GCA_014636175.1", "taxid": 1259676, "species_taxid": 1259676, "relation_to_type": "type", "validated": true, "ani": 77.5318, "matched_fragments": 258, "total_fragments": 1099, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sphingomonas dokdonensis", "strain": "strain=DSM 21029", "accession": "GCA_002197685.1", "taxid": 344880, "species_taxid": 344880, "relation_to_type": "type", "validated": true, "ani": 77.4264, "matched_fragments": 247, "total_fragments": 1099, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Novosphingobium kunmingense", "strain": "strain=CGMCC 1.12274", "accession": "GCA_002813245.1", "taxid": 1211806, "species_taxid": 1211806, "relation_to_type": "type", "validated": true, "ani": 77.3873, "matched_fragments": 216, "total_fragments": 1099, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sphingobium cupriresistens", "strain": "strain=CCTCC AB 2011146", "accession": "GCA_004152865.1", "taxid": 1132417, "species_taxid": 1132417, "relation_to_type": "type", "validated": true, "ani": 77.3478, "matched_fragments": 272, "total_fragments": 1099, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sphingobium limneticum", "strain": "strain=DSM 25076", "accession": "GCA_008710155.1", "taxid": 1007511, "species_taxid": 1007511, "relation_to_type": "type", "validated": true, "ani": 77.1926, "matched_fragments": 264, "total_fragments": 1099, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Camelimonas lactis", "strain": "strain=DSM 22958", "accession": "GCA_004342915.1", "taxid": 659006, "species_taxid": 659006, "relation_to_type": "type", "validated": true, "ani": 75.3876, "matched_fragments": 74, "total_fragments": 1099, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_014237875.1", "gtdb_species": "s__Parasphingopyxis sp014237875", "ani": 100.0, "matched_fragments": 1099, "total_fragments": 1099, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Parasphingopyxis", "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_013378075.1", "gtdb_species": "s__Parasphingopyxis algicola", "ani": 81.0058, "matched_fragments": 643, "total_fragments": 1099, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Parasphingopyxis", "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_013001755.1", "gtdb_species": "s__Parasphingopyxis sp013001755", "ani": 79.8286, "matched_fragments": 427, "total_fragments": 1099, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Parasphingopyxis", "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_003385775.1", "gtdb_species": "s__Parasphingopyxis lamellibrachiae", "ani": 79.1648, "matched_fragments": 548, "total_fragments": 1099, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Parasphingopyxis", "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_905479515.1", "gtdb_species": "s__Parasphingopyxis sp905479515", "ani": 79.0518, "matched_fragments": 295, "total_fragments": 1099, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Parasphingopyxis", "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_013378055.1", "gtdb_species": "s__Parasphingopyxis sp013378055", "ani": 78.3269, "matched_fragments": 409, "total_fragments": 1099, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Parasphingopyxis", "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_900177405.1", "gtdb_species": "s__Allosphingosinicella indica", "ani": 78.0834, "matched_fragments": 312, "total_fragments": 1099, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Allosphingosinicella", "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_000016765.1", "gtdb_species": "s__Rhizorhabdus wittichii", "ani": 77.9921, "matched_fragments": 385, "total_fragments": 1099, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Rhizorhabdus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.56", "min_intra_species_ani": "98.46", "mean_intra_species_af": "0.83", "min_intra_species_af": "0.82", "num_clustered_genomes": 5, "status": "-" }, { "accession": "GCF_001429065.1", "gtdb_species": "s__Rhizorhabdus sp001429065", "ani": 77.8021, "matched_fragments": 329, "total_fragments": 1099, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Rhizorhabdus", "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_013409985.1", "gtdb_species": "s__Sphingomonas melonis_A", "ani": 77.7933, "matched_fragments": 314, "total_fragments": 1099, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas", "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_009739515.1", "gtdb_species": "s__Sphingomonas_G sp009739515", "ani": 77.6688, "matched_fragments": 313, "total_fragments": 1099, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas_G", "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_000241465.1", "gtdb_species": "s__Sphingomonas echinoides", "ani": 77.5545, "matched_fragments": 281, "total_fragments": 1099, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "96.65", "min_intra_species_ani": "96.65", "mean_intra_species_af": "0.85", "min_intra_species_af": "0.85", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_001650725.1", "gtdb_species": "s__Sphingobium sp001650725", "ani": 77.4816, "matched_fragments": 290, "total_fragments": 1099, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.12", "min_intra_species_ani": "99.12", "mean_intra_species_af": "0.95", "min_intra_species_af": "0.95", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_002813245.1", "gtdb_species": "s__Novosphingobium kunmingense", "ani": 77.3873, "matched_fragments": 216, "total_fragments": 1099, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium", "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_900111125.1", "gtdb_species": "s__Sphingobium sp900111125", "ani": 77.3769, "matched_fragments": 272, "total_fragments": 1099, "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": -0.26, "cell_length": 0.176, "doubling_h": null, "growth_tmp": 28.0, "optimum_tmp": 29.0, "optimum_ph": 7.0, "genome_size": null, "gc_content": null, "coding_genes": null, "rRNA16S_genes": null, "tRNA_genes": null, "gram_stain": null, "sporulation": 0.0, "motility": 1.0, "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": 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": [ "Parasphingopyxis", "marina" ], "quality": 5, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }