{ "type": "genome", "identifier": "GCA_018433945.1", "organism": "Proteiniphilum sp.", "title": "Proteiniphilum sp.", "description": "derived from metagenome", "data type": "Genome sequencing and assembly", "organization": "University of California, Berkeley", "publication": [ {} ], "properties": { "assembly_accession": "GCA_018433945.1", "bioproject": "PRJNA655520", "biosample": "SAMN16056145", "wgs_master": "JAHDQF000000000.1", "refseq_category": "na", "taxid": "1926877", "species_taxid": "1926877", "organism_name": "Proteiniphilum sp.", "infraspecific_name": "", "isolate": "SM3-B12.2", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2021/05/21", "asm_name": "SM3", "submitter": "University of California, Berkeley", "gbrs_paired_asm": "GCF_018433945.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/018/433/945/GCA_018433945.1_SM3", "excluded_from_refseq": "derived from metagenome", "relation_to_type_material": "", "asm_not_live_date": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2021-05-21", "dateModified": "2021-05-21", "datePublished": "2021-05-21", "_annotation": { "sample_count": 1, "sample_organism": [ "Proteiniphilum sp." ], "sample_taxid": [ "1926877" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "USA: San Mateo, CA" ], "sample_host_location_id": [], "data_size": "0.664 MB", "sample_ph_range": { "min": 7.0, "max": 7.0 }, "sample_temperature_range": { "min": null, "max": null }, "completeness": 95.83, "contamination": 2.08, "strain_heterogeneity": 100.0, "genome_count": 1 }, "data_type": "MAG", "data_source": "INSDC", "_dfast": { "Total Sequence Length (bp)": "2313649", "Number of Sequences": "92", "Longest Sequences (bp)": "119930", "N50 (bp)": "41579", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "49.5", "Number of CDSs": "1917", "Average Protein Length": "343.0", "Coding Ratio (%)": "85.3", "Number of rRNAs": "4", "Number of tRNAs": "46", "Number of CRISPRs": "1" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Seramator thermalis", "strain": "strain=SYSU GA16112", "accession": "GCA_004138125.1", "taxid": 2496270, "species_taxid": 2496270, "relation_to_type": "type", "validated": true, "ani": 78.259, "matched_fragments": 54, "total_fragments": 725, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Petrimonas mucosa", "strain": "strain=ING2-E5A", "accession": "GCA_900095795.1", "taxid": 1642646, "species_taxid": 1642646, "relation_to_type": "type", "validated": true, "ani": 77.8147, "matched_fragments": 135, "total_fragments": 725, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Proteiniphilum acetatigenes", "strain": "strain=DSM 18083", "accession": "GCA_000380985.1", "taxid": 294710, "species_taxid": 294710, "relation_to_type": "type", "validated": true, "ani": 77.6379, "matched_fragments": 154, "total_fragments": 725, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Proteiniphilum saccharofermentans", "strain": "strain=M3/6", "accession": "GCA_900095135.1", "taxid": 1642647, "species_taxid": 1642647, "relation_to_type": "type", "validated": true, "ani": 77.3289, "matched_fragments": 159, "total_fragments": 725, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 95.83, "contamination": 2.08, "strain_heterogeneity": 100.0 }, "gtdb_result": [ { "accession": "GCA_018433945.1", "gtdb_species": "s__Proteiniphilum sp018433945", "ani": 100.0, "matched_fragments": 720, "total_fragments": 725, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Dysgonomonadaceae;g__Proteiniphilum", "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": "GCA_003517675.1", "gtdb_species": "s__Proteiniphilum sp003517675", "ani": 93.7663, "matched_fragments": 373, "total_fragments": 725, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Dysgonomonadaceae;g__Proteiniphilum", "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_011620695.1", "gtdb_species": "s__Proteiniphilum sp011620695", "ani": 93.5956, "matched_fragments": 402, "total_fragments": 725, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Dysgonomonadaceae;g__Proteiniphilum", "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_016916535.1", "gtdb_species": "s__Proteiniphilum sp016916535", "ani": 81.4149, "matched_fragments": 467, "total_fragments": 725, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Dysgonomonadaceae;g__Proteiniphilum", "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_012837345.1", "gtdb_species": "s__Proteiniphilum sp012837345", "ani": 81.3787, "matched_fragments": 396, "total_fragments": 725, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Dysgonomonadaceae;g__Proteiniphilum", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.09", "min_intra_species_ani": "98.76", "mean_intra_species_af": "0.86", "min_intra_species_af": "0.84", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCA_016839025.1", "gtdb_species": "s__Proteiniphilum sp016839025", "ani": 80.9548, "matched_fragments": 389, "total_fragments": 725, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Dysgonomonadaceae;g__Proteiniphilum", "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_012799155.1", "gtdb_species": "s__Proteiniphilum sp012799155", "ani": 80.4219, "matched_fragments": 262, "total_fragments": 725, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Dysgonomonadaceae;g__Proteiniphilum", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.74", "min_intra_species_ani": "98.58", "mean_intra_species_af": "0.95", "min_intra_species_af": "0.92", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCA_002408485.1", "gtdb_species": "s__Proteiniphilum sp002408485", "ani": 78.4986, "matched_fragments": 250, "total_fragments": 725, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Dysgonomonadaceae;g__Proteiniphilum", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.68", "min_intra_species_ani": "99.43", "mean_intra_species_af": "0.85", "min_intra_species_af": "0.77", "num_clustered_genomes": 12, "status": "-" }, { "accession": "GCA_002398565.1", "gtdb_species": "s__Proteiniphilum sp002398565", "ani": 77.9016, "matched_fragments": 231, "total_fragments": 725, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Dysgonomonadaceae;g__Proteiniphilum", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.17", "min_intra_species_ani": "99.05", "mean_intra_species_af": "0.83", "min_intra_species_af": "0.81", "num_clustered_genomes": 4, "status": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": -0.171, "cell_length": 0.295, "doubling_h": null, "growth_tmp": 37.0, "optimum_tmp": 35.5, "optimum_ph": 7.8, "genome_size": 4595827.5, "gc_content": 43.6, "coding_genes": 3375.0, "rRNA16S_genes": 2.0, "tRNA_genes": 48.0, "gram_stain": 0.0, "sporulation": 0.0, "motility": 1.0, "range_salinity": null, "facultative_respiration": 0.0, "anaerobic_respiration": 1.0, "aerobic_respiration": 0.0, "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 }, "_gtdb_taxon": [ "d__Bacteria", "p__Bacteroidota", "c__Bacteroidia", "o__Bacteroidales", "f__Dysgonomonadaceae", "g__Proteiniphilum", "s__Proteiniphilum sp018433945" ], "_genome_taxon": [ "Proteiniphilum", "sp.", "d__Bacteria", "p__Bacteroidota", "c__Bacteroidia", "o__Bacteroidales", "f__Dysgonomonadaceae", "g__Proteiniphilum", "s__Proteiniphilum sp018433945", "Bacteria", "Bacteroidota", "Bacteroidia", "Bacteroidales", "Dysgonomonadaceae", "Proteiniphilum", "Proteiniphilum", "sp018433945" ], "_meo": [ { "id": "MEO_0000035", "label": "waste water" }, { "id": "MEO_0000014", "label": "activated sludge" } ], "quality": 4, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }