##gff-version 3 ##sequence-region NZ_DS995531 1 15370 # conversion-by bp_genbank2gff3.pl # organism Phocaeicola dorei DSM 17855 # Note Phocaeicola dorei DSM 17855 Scfld3, whole genome shotgun sequence. # date 06-OCT-2022 NZ_DS995531 GenBank region 1 15370 . + 1 ID=NZ_DS995531;Dbxref=BioProject:PRJNA224116,taxon:483217;Name=NZ_DS995531;Note=Phocaeicola dorei DSM 17855 Scfld3%2C whole genome shotgun sequence.,REFSEQ INFORMATION: The reference sequence is identical to DS995531.1. Bacteroides dorei (GenBank Accession Number for 16S rDNA gene: AB242142) is a member of the Bacteroidetes division of the domain bacteria and has been isolated from human feces. The sequenced strain was obtained from Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSMZ)(DSM 17855). This is a Newbler assembly (http://www.454.com/enabling-technology/the-software.asp) consisting of one full plate of a Roche 454 FLX fragment library and one full plate of a Roche 454 FLX paired end library run with a Q20 coverage of 38.4X. This sequenced strain is part of a comprehensive,sequence-based survey of members of the normal human gut microbiota. A joint effort of the WU-GSC and the Center for Genome Sciences at Washington University School of Medicine,the purpose of this survey is to provide the general scientific community with a broad view of the gene content of 100 representatives of the major divisions represented in the intestine's microbial community. This information should provide a frame of reference for analyzing metagenomic studies of the human gut microbiome. Further details of this effort are described in a white paper entitled 'Extending Our View of Self: the Human Gut Microbiome Initiative (HGMI)' (http://www.genome.gov/Pages/Research/Sequencing/SeqProposals/HGMIS eq.pdf). These studies are supported by National Human Genome Research Institute. For answers to your questions regarding this assembly or project,or any other GSC genome project,please visit our Genome Groups web page (http://genome.wustl.edu/genome_group_index.cgi) and email the designated contact person. Bacteroides dorei (GenBank Accession Number for 16S rDNA gene: AB242142) is a member of the Bacteroidetes division of the domain bacteria and has been isolated from human feces. The sequenced strain was obtained from Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSMZ) (DSM 17855). This is a Newbler assembly (http://www.454.com/enabling-technology/the-software.asp) consisting of one full plate of a Roche 454 FLX fragment library and one full plate of a Roche 454 FLX paired end library run with a Q20 coverage of 38.4X. This sequenced strain is part of a comprehensive,sequence-based survey of members of the normal human gut microbiota. A joint effort of the WU-GSC and the Center for Genome Sciences at Washington University School of Medicine,the purpose of this survey is to provide the general scientific community with a broad view of the gene content of 100 representatives of the major divisions represented in the intestine's microbial community. This information should provide a frame of reference for analyzing metagenomic studies of the human gut microbiome. Further details of this effort are described in a white paper entitled 'Extending Our View of Self: the Human Gut Microbiome Initiative (HGMI)' (http://www.genome.gov/Pages/Research/Sequencing/SeqProposals/HGMIS eq.pdf). These studies are supported by National Human Genome Research Institute. Coding sequences were predicted using GeneMark v3.3 and Glimmer2 v2.13. Intergenic regions not spanned by GeneMark and Glimmer2 were blasted against NCBI's non-redundant (NR) database and predictions generated based on protein alignments. tRNA genes were determined using tRNAscan-SE 1.23 and non-coding RNA genes by RNAmmer-1.2 and Rfam v8.0. Gene names are generated at the contig level and may not necessarily reflect any known order or orientation between contigs. For answers to your questions regarding this assembly or project,or any other GSC genome project,please visit our Genome Groups web page (http://genome.wustl.edu/genome_group_index.cgi) and email the designated contact person. Annotation was added to the contigs in November 2008. This is a reference genome for the Human Microbiome Project. This project is co-owned with the Human Microbiome Project DACC. The annotation was added by the NCBI Prokaryotic Genome Annotation Pipeline (PGAP). Information about PGAP can be found here: https://www.ncbi.nlm.nih.gov/genome/annotation_prok/ \n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 10/05/2022 08:53:52\nAnnotation Pipeline :: NCBI Prokaryotic Genome\nAnnotation Pipeline (PGAP)\nAnnotation Method :: Best-placed reference protein\nset,GeneMarkS-2+\nAnnotation Software revision :: 6.3\nFeatures Annotated :: Gene,CDS,rRNA,tRNA,ncRNA,\nrepeat_region\nGenes (total) :: 4,532\nCDSs (total) :: 4,459\nGenes (coding) :: 4,340\nCDSs (with protein) :: 4,340\nGenes (RNA) :: 73\nrRNAs :: 2,1,1 (5S,16S,23S)\ncomplete rRNAs :: 2,1,1 (5S,16S,23S)\ntRNAs :: 67\nncRNAs :: 2\nPseudo Genes (total) :: 119\nCDSs (without protein) :: 119\nPseudo Genes (ambiguous residues) :: 0 of 119\nPseudo Genes (frameshifted) :: 41 of 119\nPseudo Genes (incomplete) :: 79 of 119\nPseudo Genes (internal stop) :: 27 of 119\nPseudo Genes (multiple problems) :: 23 of 119\nCRISPR Arrays :: 1\n##Genome-Annotation-Data-END##;comment1=REFSEQ INFORMATION: The reference sequence is identical to DS995531.1. Bacteroides dorei (GenBank Accession Number for 16S rDNA gene: AB242142) is a member of the Bacteroidetes division of the domain bacteria and has been isolated from human feces. The sequenced strain was obtained from Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSMZ)(DSM 17855). This is a Newbler assembly (http://www.454.com/enabling-technology/the-software.asp) consisting of one full plate of a Roche 454 FLX fragment library and one full plate of a Roche 454 FLX paired end library run with a Q20 coverage of 38.4X. This sequenced strain is part of a comprehensive%2Csequence-based survey of members of the normal human gut microbiota. A joint effort of the WU-GSC and the Center for Genome Sciences at Washington University School of Medicine%2C the purpose of this survey is to provide the general scientific community with a broad view of the gene content of 100 representatives of the major divisions represented in the intestine's microbial community. This information should provide a frame of reference for analyzing metagenomic studies of the human gut microbiome. Further details of this effort are described in a white paper entitled 'Extending Our View of Self: the Human Gut Microbiome Initiative (HGMI)' (http://www.genome.gov/Pages/Research/Sequencing/SeqProposals/HGMIS eq.pdf). These studies are supported by National Human Genome Research Institute. For answers to your questions regarding this assembly or project%2C or any other GSC genome project%2C please visit our Genome Groups web page (http://genome.wustl.edu/genome_group_index.cgi) and email the designated contact person. Bacteroides dorei (GenBank Accession Number for 16S rDNA gene: AB242142) is a member of the Bacteroidetes division of the domain bacteria and has been isolated from human feces. The sequenced strain was obtained from Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSMZ) (DSM 17855). This is a Newbler assembly (http://www.454.com/enabling-technology/the-software.asp) consisting of one full plate of a Roche 454 FLX fragment library and one full plate of a Roche 454 FLX paired end library run with a Q20 coverage of 38.4X. This sequenced strain is part of a comprehensive%2C sequence-based survey of members of the normal human gut microbiota. A joint effort of the WU-GSC and the Center for Genome Sciences at Washington University School of Medicine%2C the purpose of this survey is to provide the general scientific community with a broad view of the gene content of 100 representatives of the major divisions represented in the intestine's microbial community. This information should provide a frame of reference for analyzing metagenomic studies of the human gut microbiome. Further details of this effort are described in a white paper entitled 'Extending Our View of Self: the Human Gut Microbiome Initiative (HGMI)' (http://www.genome.gov/Pages/Research/Sequencing/SeqProposals/HGMIS eq.pdf). These studies are supported by National Human Genome Research Institute. Coding sequences were predicted using GeneMark v3.3 and Glimmer2 v2.13. Intergenic regions not spanned by GeneMark and Glimmer2 were blasted against NCBI's non-redundant (NR) database and predictions generated based on protein alignments. tRNA genes were determined using tRNAscan-SE 1.23 and non-coding RNA genes by RNAmmer-1.2 and Rfam v8.0. Gene names are generated at the contig level and may not necessarily reflect any known order or orientation between contigs. For answers to your questions regarding this assembly or project%2C or any other GSC genome project%2C please visit our Genome Groups web page (http://genome.wustl.edu/genome_group_index.cgi) and email the designated contact person. Annotation was added to the contigs in November 2008. This is a reference genome for the Human Microbiome Project. This project is co-owned with the Human Microbiome Project DACC. The annotation was added by the NCBI Prokaryotic Genome Annotation Pipeline (PGAP). Information about PGAP can be found here: https://www.ncbi.nlm.nih.gov/genome/annotation_prok/ \n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 10/05/2022 08:53:52\nAnnotation Pipeline :: NCBI Prokaryotic Genome\nAnnotation Pipeline (PGAP)\nAnnotation Method :: Best-placed reference protein\nset%3B GeneMarkS-2+\nAnnotation Software revision :: 6.3\nFeatures Annotated :: Gene%3B CDS%3B rRNA%3B tRNA%3B ncRNA%3B\nrepeat_region\nGenes (total) :: 4%2C532\nCDSs (total) :: 4%2C459\nGenes (coding) :: 4%2C340\nCDSs (with protein) :: 4%2C340\nGenes (RNA) :: 73\nrRNAs :: 2%2C 1%2C 1 (5S%2C 16S%2C 23S)\ncomplete rRNAs :: 2%2C 1%2C 1 (5S%2C 16S%2C 23S)\ntRNAs :: 67\nncRNAs :: 2\nPseudo Genes (total) :: 119\nCDSs (without protein) :: 119\nPseudo Genes (ambiguous residues) :: 0 of 119\nPseudo Genes (frameshifted) :: 41 of 119\nPseudo Genes (incomplete) :: 79 of 119\nPseudo Genes (internal stop) :: 27 of 119\nPseudo Genes (multiple problems) :: 23 of 119\nCRISPR Arrays :: 1\n##Genome-Annotation-Data-END##;date=06-OCT-2022;host=Homo sapiens;isolation_source=biological product [ENVO:02000043];mol_type=genomic DNA;organism=Phocaeicola dorei DSM 17855;strain=DSM 17855;submitter_seqid=Scfld3;type_material=type strain of Bacteroides dorei NZ_DS995531 GenBank gene 1 3924 . - 1 ID=BACDOR_RS18975;Name=BACDOR_RS18975;old_locus_tag=BACDOR_00577 NZ_DS995531 GenBank mRNA 1 3924 . - 1 ID=BACDOR_RS18975.t01;Parent=BACDOR_RS18975 NZ_DS995531 GenBank CDS 1 3924 . - 1 ID=BACDOR_RS18975;Parent=BACDOR_RS18975.t01;gO_process=GO:0000160 - phosphorelay signal transduction system [Evidence IEA];Name=BACDOR_RS18975;Note=Derived by automated computational analysis using gene prediction method: Protein Homology.;codon_start=1;inference=COORDINATES: similar to AA sequence:RefSeq:WP_009038898.1;old_locus_tag=BACDOR_00577;product=two-component regulator propeller domain-containing protein;protein_id=WP_032935600.1;transl_table=11;translation=length.1307 NZ_DS995531 GenBank exon 1 3924 . - 1 Parent=BACDOR_RS18975.t01 NZ_DS995531 GenBank gene 4237 5433 . + 1 ID=BACDOR_RS18965;Name=BACDOR_RS18965;old_locus_tag=BACDOR_00578 NZ_DS995531 GenBank mRNA 4237 5433 . + 1 ID=BACDOR_RS18965.t01;Parent=BACDOR_RS18965 NZ_DS995531 GenBank CDS 4237 5433 . + 1 ID=BACDOR_RS18965;Parent=BACDOR_RS18965.t01;Name=BACDOR_RS18965;Note=Derived by automated computational analysis using gene prediction method: Protein Homology.;codon_start=1;inference=COORDINATES: similar to AA sequence:RefSeq:WP_007568643.1;old_locus_tag=BACDOR_00578;product=beta-mannosidase;protein_id=WP_227235709.1;transl_table=11;translation=length.398 NZ_DS995531 GenBank exon 4237 5433 . + 1 Parent=BACDOR_RS18965.t01 NZ_DS995531 GenBank gene 5505 6734 . + 1 ID=BACDOR_RS18960;Name=BACDOR_RS18960;old_locus_tag=BACDOR_00580 NZ_DS995531 GenBank mRNA 5505 6734 . + 1 ID=BACDOR_RS18960.t01;Parent=BACDOR_RS18960 NZ_DS995531 GenBank CDS 5505 6734 . + 1 ID=BACDOR_RS18960;Parent=BACDOR_RS18960.t01;Name=BACDOR_RS18960;Note=Derived by automated computational analysis using gene prediction method: Protein Homology.;codon_start=1;inference=COORDINATES: similar to AA sequence:RefSeq:WP_018710037.1;old_locus_tag=BACDOR_00580;product=acetylxylan esterase;protein_id=WP_235778214.1;transl_table=11;translation=length.409 NZ_DS995531 GenBank exon 5505 6734 . + 1 Parent=BACDOR_RS18960.t01 NZ_DS995531 GenBank gene 6769 10020 . + 1 ID=BACDOR_RS18955;Name=BACDOR_RS18955;old_locus_tag=BACDOR_00581 NZ_DS995531 GenBank mRNA 6769 10020 . + 1 ID=BACDOR_RS18955.t01;Parent=BACDOR_RS18955 NZ_DS995531 GenBank CDS 6769 10020 . + 1 ID=BACDOR_RS18955;Parent=BACDOR_RS18955.t01;Name=BACDOR_RS18955;Note=Derived by automated computational analysis using gene prediction method: Protein Homology.;codon_start=1;inference=COORDINATES: similar to AA sequence:RefSeq:WP_004324119.1;old_locus_tag=BACDOR_00581;product=TonB-dependent receptor;protein_id=WP_007831881.1;transl_table=11;translation=length.1083 NZ_DS995531 GenBank exon 6769 10020 . + 1 Parent=BACDOR_RS18955.t01 NZ_DS995531 GenBank gene 10066 11850 . + 1 ID=BACDOR_RS18950;Name=BACDOR_RS18950;old_locus_tag=BACDOR_00582 NZ_DS995531 GenBank mRNA 10066 11850 . + 1 ID=BACDOR_RS18950.t01;Parent=BACDOR_RS18950 NZ_DS995531 GenBank CDS 10066 11850 . + 1 ID=BACDOR_RS18950;Parent=BACDOR_RS18950.t01;Name=BACDOR_RS18950;Note=Derived by automated computational analysis using gene prediction method: Protein Homology.;codon_start=1;inference=COORDINATES: similar to AA sequence:RefSeq:WP_009038900.1;old_locus_tag=BACDOR_00582;product=RagB/SusD family nutrient uptake outer membrane protein;protein_id=WP_007831882.1;transl_table=11;translation=length.594 NZ_DS995531 GenBank exon 10066 11850 . + 1 Parent=BACDOR_RS18950.t01 NZ_DS995531 GenBank gene 11896 13068 . + 1 ID=BACDOR_RS18945;Name=BACDOR_RS18945;old_locus_tag=BACDOR_00583 NZ_DS995531 GenBank mRNA 11896 13068 . + 1 ID=BACDOR_RS18945.t01;Parent=BACDOR_RS18945 NZ_DS995531 GenBank CDS 11896 13068 . + 1 ID=BACDOR_RS18945;Parent=BACDOR_RS18945.t01;Name=BACDOR_RS18945;Note=Derived by automated computational analysis using gene prediction method: Protein Homology.;codon_start=1;inference=COORDINATES: similar to AA sequence:RefSeq:WP_004324115.1;old_locus_tag=BACDOR_00583;product=glycan-binding surface protein;protein_id=WP_007831884.1;transl_table=11;translation=length.390 NZ_DS995531 GenBank exon 11896 13068 . + 1 Parent=BACDOR_RS18945.t01 NZ_DS995531 GenBank gene 13072 14172 . + 1 ID=BACDOR_RS18940;Name=BACDOR_RS18940;old_locus_tag=BACDOR_00584 NZ_DS995531 GenBank mRNA 13072 14172 . + 1 ID=BACDOR_RS18940.t01;Parent=BACDOR_RS18940 NZ_DS995531 GenBank CDS 13072 14172 . + 1 ID=BACDOR_RS18940;Parent=BACDOR_RS18940.t01;Name=BACDOR_RS18940;Note=Derived by automated computational analysis using gene prediction method: Protein Homology.;codon_start=1;inference=COORDINATES: similar to AA sequence:RefSeq:WP_007564370.1;old_locus_tag=BACDOR_00584;product=glycosyl hydrolase;protein_id=WP_007831886.1;transl_table=11;translation=length.366 NZ_DS995531 GenBank exon 13072 14172 . + 1 Parent=BACDOR_RS18940.t01 NZ_DS995531 GenBank gene 14198 15370 . + 1 ID=BACDOR_RS18935;Name=BACDOR_RS18935;old_locus_tag=BACDOR_00585 NZ_DS995531 GenBank mRNA 14198 15370 . + 1 ID=BACDOR_RS18935.t01;Parent=BACDOR_RS18935 NZ_DS995531 GenBank CDS 14198 15370 . + 1 ID=BACDOR_RS18935;Parent=BACDOR_RS18935.t01;Name=BACDOR_RS18935;Note=Derived by automated computational analysis using gene prediction method: Protein Homology.;codon_start=1;inference=COORDINATES: similar to AA sequence:RefSeq:WP_005785018.1;old_locus_tag=BACDOR_00585;product=glycosidase;protein_id=WP_007831887.1;transl_table=11;translation=length.390 NZ_DS995531 GenBank exon 14198 15370 . + 1 Parent=BACDOR_RS18935.t01