{ "type": "genome", "identifier": "GCF_016583625.1", "organism": "Halorhodospira abdelmalekii", "title": "Halorhodospira abdelmalekii", "description": "na", "data type": "Genome sequencing and assembly", "organization": "GEOMAR Helmholtz Centre for Ocean Research Kiel", "publication": [ {} ], "properties": { "assembly_accession": "GCF_016583625.1", "bioproject": "PRJNA224116", "biosample": "SAMN07535005", "wgs_master": "NRRN00000000.1", "refseq_category": "reference genome", "taxid": "421629", "species_taxid": "421629", "organism_name": "Halorhodospira abdelmalekii", "infraspecific_name": "strain=DSM 2110", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2021/01/08", "asm_name": "ASM1658362v1", "asm_submitter": "GEOMAR Helmholtz Centre for Ocean Research Kiel", "gbrs_paired_asm": "GCA_016583625.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/016/583/625/GCF_016583625.1_ASM1658362v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "3090835", "genome_size_ungapped": "3090835", "gc_percent": "63.000000", "replicon_count": "0", "scaffold_count": "158", "contig_count": "158", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_016583625.1-RS_2024_03_28", "annotation_date": "2024-03-28", "total_gene_count": "2788", "protein_coding_gene_count": "2652", "non_coding_gene_count": "53", "pubmed_id": "33375353" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2021-01-08", "dateModified": "2021-01-08", "datePublished": "2021-01-08", "_annotation": { "sample_count": 1, "sample_organism": [ "Halorhodospira abdelmalekii" ], "sample_taxid": [ "421629" ], "sample_host_organism": [ "not applicable" ], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "Egypt: Wadi Natrun" ], "sample_host_location_id": [], "data_size": "0.871 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)": "3090835", "Number of Sequences": "158", "Longest Sequences (bp)": "133097", "N50 (bp)": "52165", "Gap Ratio (%)": "0.000291", "GCcontent (%)": "62.9", "Number of CDSs": "2641", "Average Protein Length": "333.6", "Coding Ratio (%)": "85.5", "Number of rRNAs": "4", "Number of tRNAs": "47", "Number of CRISPRs": "5" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Halorhodospira abdelmalekii", "strain": "strain=DSM 2110", "accession": "GCA_016583625.1", "taxid": 421629, "species_taxid": 421629, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 945, "total_fragments": 955, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Halorhodospira halochloris", "strain": "strain=DSM 1059", "accession": "GCA_002356555.2", "taxid": 1052, "species_taxid": 1052, "relation_to_type": "type", "validated": true, "ani": 78.1847, "matched_fragments": 189, "total_fragments": 955, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Halorhodospira halochloris", "strain": "strain=DSM 1059", "accession": "GCA_016583605.1", "taxid": 1052, "species_taxid": 1052, "relation_to_type": "type", "validated": true, "ani": 78.0654, "matched_fragments": 190, "total_fragments": 955, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Halorhodospira neutriphila", "strain": "strain=DSM 15116", "accession": "GCA_016584055.1", "taxid": 168379, "species_taxid": 168379, "relation_to_type": "type", "validated": true, "ani": 78.0569, "matched_fragments": 220, "total_fragments": 955, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Halorhodospira halophila", "strain": "strain=SL1", "accession": "GCA_000015585.1", "taxid": 1053, "species_taxid": 1053, "relation_to_type": "suspected-type", "validated": true, "ani": 77.676, "matched_fragments": 257, "total_fragments": 955, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Allochromatium tepidum", "strain": "strain=NZ", "accession": "GCA_018409545.1", "taxid": 553982, "species_taxid": 553982, "relation_to_type": "type", "validated": true, "ani": 76.609, "matched_fragments": 64, "total_fragments": 955, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Inmirania thermothiophila", "strain": "strain=DSM 100275", "accession": "GCA_003751635.1", "taxid": 1750597, "species_taxid": 1750597, "relation_to_type": "type", "validated": true, "ani": 76.3837, "matched_fragments": 76, "total_fragments": 955, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Spiribacter aquaticus", "strain": "strain=SP30", "accession": "GCA_007625215.1", "taxid": 1935996, "species_taxid": 1935996, "relation_to_type": "type", "validated": true, "ani": 76.2292, "matched_fragments": 57, "total_fragments": 955, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Spiribacter vilamensis", "strain": "strain=DSM 21056", "accession": "GCA_004217415.1", "taxid": 531306, "species_taxid": 531306, "relation_to_type": "type", "validated": true, "ani": 76.2136, "matched_fragments": 55, "total_fragments": 955, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Spiribacter vilamensis", "strain": "strain=DSM 21056", "accession": "GCA_007625165.1", "taxid": 531306, "species_taxid": 531306, "relation_to_type": "type", "validated": true, "ani": 76.1798, "matched_fragments": 56, "total_fragments": 955, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Halomonas lactosivorans", "strain": "strain=KCTC 52281", "accession": "GCA_003254665.1", "taxid": 2185141, "species_taxid": 2185141, "relation_to_type": "type", "validated": true, "ani": 76.0447, "matched_fragments": 64, "total_fragments": 955, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sulfurivermis fontis", "strain": "strain=JG42", "accession": "GCA_004001245.1", "taxid": 1972068, "species_taxid": 1972068, "relation_to_type": "type", "validated": true, "ani": 76.0002, "matched_fragments": 54, "total_fragments": 955, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas lalucatii", "strain": "strain=R1b54", "accession": "GCA_018398425.1", "taxid": 1424203, "species_taxid": 1424203, "relation_to_type": "type", "validated": true, "ani": 75.8525, "matched_fragments": 66, "total_fragments": 955, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Metallibacterium scheffleri", "strain": "strain=DSM 24874", "accession": "GCA_004798955.1", "taxid": 993689, "species_taxid": 993689, "relation_to_type": "type", "validated": true, "ani": 75.791, "matched_fragments": 51, "total_fragments": 955, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Metallibacterium scheffleri", "strain": "strain=DKE6", "accession": "GCA_002077135.1", "taxid": 993689, "species_taxid": 993689, "relation_to_type": "type", "validated": true, "ani": 75.7655, "matched_fragments": 52, "total_fragments": 955, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas aromaticivorans", "strain": "strain=MAP12", "accession": "GCA_019097855.1", "taxid": 2849492, "species_taxid": 2849492, "relation_to_type": "type", "validated": true, "ani": 75.6859, "matched_fragments": 62, "total_fragments": 955, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_016583625.1", "gtdb_species": "s__Halorhodospira abdelmalekii", "ani": 100.0, "matched_fragments": 945, "total_fragments": 955, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrococcales;f__Halorhodospiraceae;g__Halorhodospira", "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_016653405.1", "gtdb_species": "s__Halorhodospira halophila_A", "ani": 78.4067, "matched_fragments": 255, "total_fragments": 955, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrococcales;f__Halorhodospiraceae;g__Halorhodospira", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.67", "min_intra_species_ani": "98.67", "mean_intra_species_af": "0.87", "min_intra_species_af": "0.87", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_016584055.1", "gtdb_species": "s__Halorhodospira neutriphila", "ani": 78.073, "matched_fragments": 219, "total_fragments": 955, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrococcales;f__Halorhodospiraceae;g__Halorhodospira", "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_000015585.1", "gtdb_species": "s__Halorhodospira halophila", "ani": 77.676, "matched_fragments": 257, "total_fragments": 955, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrococcales;f__Halorhodospiraceae;g__Halorhodospira", "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": "-" }, { "accession": "GCA_003552625.1", "gtdb_species": "s__Halorhodospira sp003552625", "ani": 77.542, "matched_fragments": 172, "total_fragments": 955, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrococcales;f__Halorhodospiraceae;g__Halorhodospira", "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_003552345.1", "gtdb_species": "s__Halorhodospira sp003552345", "ani": 77.3551, "matched_fragments": 177, "total_fragments": 955, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrococcales;f__Halorhodospiraceae;g__Halorhodospira", "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_007121755.1", "gtdb_species": "s__SKYL01 sp007121755", "ani": 76.577, "matched_fragments": 99, "total_fragments": 955, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrococcales;f__Halorhodospiraceae;g__SKYL01", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.19", "min_intra_species_ani": "99.19", "mean_intra_species_af": "0.80", "min_intra_species_af": "0.80", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCA_007127935.1", "gtdb_species": "s__SKYL01 sp007127935", "ani": 76.4232, "matched_fragments": 96, "total_fragments": 955, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrococcales;f__Halorhodospiraceae;g__SKYL01", "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_004217415.1", "gtdb_species": "s__Spiribacter vilamensis", "ani": 76.2136, "matched_fragments": 55, "total_fragments": 955, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrococcales;f__Nitrococcaceae;g__Spiribacter", "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": "GCA_002840095.1", "gtdb_species": "s__Sulfurivermis sp002840095", "ani": 76.0083, "matched_fragments": 54, "total_fragments": 955, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiohalomonadales;f__Thiohalomonadaceae;g__Sulfurivermis", "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_011390365.1", "gtdb_species": "s__SLIM01 sp011390365", "ani": 75.7124, "matched_fragments": 50, "total_fragments": 955, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Sedimenticolaceae;g__SLIM01", "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_003062205.1", "gtdb_species": "s__Sedimenticola_A endophacoides", "ani": 75.573, "matched_fragments": 50, "total_fragments": 955, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Sedimenticolaceae;g__Sedimenticola_A", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.88", "min_intra_species_ani": "99.76", "mean_intra_species_af": "0.97", "min_intra_species_af": "0.95", "num_clustered_genomes": 6, "status": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": -0.046, "cell_length": 0.602, "doubling_h": null, "growth_tmp": 30.0, "optimum_tmp": 45.0, "optimum_ph": null, "genome_size": 3303740.5, "gc_content": 59.5, "coding_genes": 2728.0, "rRNA16S_genes": null, "tRNA_genes": 46.0, "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 }, "_genome_taxon": [ "Halorhodospira", "abdelmalekii" ], "quality": 4, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }