##gff-version 3 ##sequence-region NZ_DS990123 1 15684 # conversion-by bp_genbank2gff3.pl # organism Phocaeicola plebeius DSM 17135 # Note Phocaeicola plebeius DSM 17135 Scfld_02_6, whole genome shotgun sequence. # date 06-OCT-2022 NZ_DS990123 GenBank region 1 15684 . + 1 ID=NZ_DS990123;Dbxref=BioProject:PRJNA224116,taxon:484018;Name=NZ_DS990123;Note=Phocaeicola plebeius DSM 17135 Scfld_02_6%2C whole genome shotgun sequence.,REFSEQ INFORMATION: The reference sequence is identical to DS990123.1. On Mar 3,2009 this sequence version replaced NW_002063606.1. Bacteroides plebeius (GenBank Accession Number for 16S rDNA gene: AB200217) 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 17135). We have collected 7.9X coverage in plasmid end reads and 454 reads. We have performed one round of automated sequence improvement (pre-finishing),along with manual improvement that includes breaking apart any mis-assembly,and making manual joins where possible. Manual edits also are made where the consensus appears to be incorrect. All low quality data on the ends of contigs is removed. Contigs are ordered and oriented where possible. Sequencing/Assembly: The genomic DNA was purified from liquid culture derived from a single bacterial colony. A hybrid sequencing strategy that utilized reads from both 454 GS-20 and ABI 3730xl sequencers was devised and implemented to generate the draft genome sequences. 454 reads were assembled using Newbler (454 Life Sciences) into 454 de novo contigs. These de novo contigs were converted in silico to 800 base paired reads ('superreads') with 400 base overlaps with neighboring superreads. Finally,PCAP (Huang,et al,Genome Research,13:2164,(2003)) was used to assemble the super-reads and the conventional 3730xl capillary reads. 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 plebeius (GenBank Accession Number for 16S rDNA gene: AB200217) 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 17135). We have collected 7.9X coverage in plasmid end reads and 454 reads. We have performed one round of automated sequence improvement(pre-finishing),along with manual improvement that includes breaking apart any mis-assembly,and making manual joins where possible. Manual edits also are made where the consensus appears to be incorrect. All low quality data on the ends of contigs is removed. Contigs are ordered and oriented where possible. Sequencing/Assembly: The genomic DNA was purified from liquid culture derived from a single bacterial colony. A hybrid sequencing strategy that utilized reads from both 454 GS-20 and ABI 3730xlsequencers was devised and implemented to generate the draft genome sequences. 454 reads were assembled using Newbler (454 Life Sciences) into 454 de novo contigs. These de novo contigs were converted in silico to 800 base paired reads ('superreads') with 400 base overlaps with neighboring superreads. Finally,PCAP (Huang,et al,Genome Research,13:2164,(2003)) was used to assemble the super-reads and the conventional 3730xl capillary reads. 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 September 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 09:16:28\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) :: 3,688\nCDSs (total) :: 3,591\nGenes (coding) :: 3,539\nCDSs (with protein) :: 3,539\nGenes (RNA) :: 97\nrRNAs :: 6,5,6 (5S,16S,23S)\ncomplete rRNAs :: 6 (5S)\npartial rRNAs :: 5,6 (16S,23S)\ntRNAs :: 78\nncRNAs :: 2\nPseudo Genes (total) :: 52\nCDSs (without protein) :: 52\nPseudo Genes (ambiguous residues) :: 0 of 52\nPseudo Genes (frameshifted) :: 15 of 52\nPseudo Genes (incomplete) :: 43 of 52\nPseudo Genes (internal stop) :: 4 of 52\nPseudo Genes (multiple problems) :: 8 of 52\nCRISPR Arrays :: 1\n##Genome-Annotation-Data-END##;comment1=REFSEQ INFORMATION: The reference sequence is identical to DS990123.1. On Mar 3%2C 2009 this sequence version replaced NW_002063606.1. Bacteroides plebeius (GenBank Accession Number for 16S rDNA gene: AB200217) 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 17135). We have collected 7.9X coverage in plasmid end reads and 454 reads. We have performed one round of automated sequence improvement (pre-finishing)%2C along with manual improvement that includes breaking apart any mis-assembly%2C and making manual joins where possible. Manual edits also are made where the consensus appears to be incorrect. All low quality data on the ends of contigs is removed. Contigs are ordered and oriented where possible. Sequencing/Assembly: The genomic DNA was purified from liquid culture derived from a single bacterial colony. A hybrid sequencing strategy that utilized reads from both 454 GS-20 and ABI 3730xl sequencers was devised and implemented to generate the draft genome sequences. 454 reads were assembled using Newbler (454 Life Sciences) into 454 de novo contigs. These de novo contigs were converted in silico to 800 base paired reads ('superreads') with 400 base overlaps with neighboring superreads. Finally%2C PCAP (Huang%2C et al%2C Genome Research%2C 13:2164%2C (2003)) was used to assemble the super-reads and the conventional 3730xl capillary reads. 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. 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 plebeius (GenBank Accession Number for 16S rDNA gene: AB200217) 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 17135). We have collected 7.9X coverage in plasmid end reads and 454 reads. We have performed one round of automated sequence improvement(pre-finishing)%2C along with manual improvement that includes breaking apart any mis-assembly%2C and making manual joins where possible. Manual edits also are made where the consensus appears to be incorrect. All low quality data on the ends of contigs is removed. Contigs are ordered and oriented where possible. Sequencing/Assembly: The genomic DNA was purified from liquid culture derived from a single bacterial colony. A hybrid sequencing strategy that utilized reads from both 454 GS-20 and ABI 3730xlsequencers was devised and implemented to generate the draft genome sequences. 454 reads were assembled using Newbler (454 Life Sciences) into 454 de novo contigs. These de novo contigs were converted in silico to 800 base paired reads ('superreads') with 400 base overlaps with neighboring superreads. Finally%2C PCAP (Huang%2C et al%2C Genome Research%2C 13:2164%2C (2003)) was used to assemble the super-reads and the conventional 3730xl capillary reads. 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 September 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 09:16:28\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) :: 3%2C688\nCDSs (total) :: 3%2C591\nGenes (coding) :: 3%2C539\nCDSs (with protein) :: 3%2C539\nGenes (RNA) :: 97\nrRNAs :: 6%2C 5%2C 6 (5S%2C 16S%2C 23S)\ncomplete rRNAs :: 6 (5S)\npartial rRNAs :: 5%2C 6 (16S%2C 23S)\ntRNAs :: 78\nncRNAs :: 2\nPseudo Genes (total) :: 52\nCDSs (without protein) :: 52\nPseudo Genes (ambiguous residues) :: 0 of 52\nPseudo Genes (frameshifted) :: 15 of 52\nPseudo Genes (incomplete) :: 43 of 52\nPseudo Genes (internal stop) :: 4 of 52\nPseudo Genes (multiple problems) :: 8 of 52\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 plebeius DSM 17135;strain=DSM 17135;type_material=type strain of Bacteroides plebeius NZ_DS990123 GenBank gene 1 2028 . - 1 ID=BACPLE_RS05590;Name=BACPLE_RS05590;old_locus_tag=BACPLE_00332 NZ_DS990123 GenBank mRNA 1 2028 . - 1 ID=BACPLE_RS05590.t01;Parent=BACPLE_RS05590 NZ_DS990123 GenBank CDS 1 2028 . - 1 ID=BACPLE_RS05590;Parent=BACPLE_RS05590.t01;Name=BACPLE_RS05590;Note=Derived by automated computational analysis using gene prediction method: Protein Homology.;codon_start=1;inference=COORDINATES: similar to AA sequence:RefSeq:WP_007660088.1;old_locus_tag=BACPLE_00332;product=RagB/SusD family nutrient uptake outer membrane protein;protein_id=WP_007559719.1;transl_table=11;translation=length.675 NZ_DS990123 GenBank exon 1 2028 . - 1 Parent=BACPLE_RS05590.t01 NZ_DS990123 GenBank gene 2045 5347 . - 1 ID=BACPLE_RS05595;Name=BACPLE_RS05595;old_locus_tag=BACPLE_00333 NZ_DS990123 GenBank mRNA 2045 5347 . - 1 ID=BACPLE_RS05595.t01;Parent=BACPLE_RS05595 NZ_DS990123 GenBank CDS 2045 5347 . - 1 ID=BACPLE_RS05595;Parent=BACPLE_RS05595.t01;Name=BACPLE_RS05595;Note=Derived by automated computational analysis using gene prediction method: Protein Homology.;codon_start=1;inference=COORDINATES: similar to AA sequence:RefSeq:WP_005840711.1;old_locus_tag=BACPLE_00333;product=TonB-dependent receptor;protein_id=WP_007559720.1;transl_table=11;translation=length.1100 NZ_DS990123 GenBank exon 2045 5347 . - 1 Parent=BACPLE_RS05595.t01 NZ_DS990123 GenBank gene 5669 9697 . + 1 ID=BACPLE_RS05600;Name=BACPLE_RS05600;old_locus_tag=BACPLE_00334 NZ_DS990123 GenBank mRNA 5669 9697 . + 1 ID=BACPLE_RS05600.t01;Parent=BACPLE_RS05600 NZ_DS990123 GenBank CDS 5669 9697 . + 1 ID=BACPLE_RS05600;Parent=BACPLE_RS05600.t01;gO_process=GO:0000160 - phosphorelay signal transduction system [Evidence IEA];Name=BACPLE_RS05600;Note=Derived by automated computational analysis using gene prediction method: Protein Homology.;codon_start=1;inference=COORDINATES: similar to AA sequence:RefSeq:WP_007660937.1;old_locus_tag=BACPLE_00334;product=two-component regulator propeller domain-containing protein;protein_id=WP_040312477.1;transl_table=11;translation=length.1342 NZ_DS990123 GenBank exon 5669 9697 . + 1 Parent=BACPLE_RS05600.t01 NZ_DS990123 GenBank gene 9768 10919 . - 1 ID=BACPLE_RS05605;Name=BACPLE_RS05605;old_locus_tag=BACPLE_00335 NZ_DS990123 GenBank mRNA 9768 10919 . - 1 ID=BACPLE_RS05605.t01;Parent=BACPLE_RS05605 NZ_DS990123 GenBank CDS 9768 10919 . - 1 ID=BACPLE_RS05605;Parent=BACPLE_RS05605.t01;Name=BACPLE_RS05605;Note=Derived by automated computational analysis using gene prediction method: Protein Homology.;codon_start=1;inference=COORDINATES: similar to AA sequence:RefSeq:WP_011966837.1;old_locus_tag=BACPLE_00335;product=glycoside hydrolase family 43 protein;protein_id=WP_007559722.1;transl_table=11;translation=length.383 NZ_DS990123 GenBank exon 9768 10919 . - 1 Parent=BACPLE_RS05605.t01 NZ_DS990123 GenBank gene 10960 11952 . - 1 ID=BACPLE_RS05610;Name=BACPLE_RS05610;old_locus_tag=BACPLE_00336 NZ_DS990123 GenBank mRNA 10960 11952 . - 1 ID=BACPLE_RS05610.t01;Parent=BACPLE_RS05610 NZ_DS990123 GenBank CDS 10960 11952 . - 1 ID=BACPLE_RS05610;Parent=BACPLE_RS05610.t01;Name=BACPLE_RS05610;Note=Derived by automated computational analysis using gene prediction method: Protein Homology.;codon_start=1;inference=COORDINATES: similar to AA sequence:RefSeq:WP_008619024.1;old_locus_tag=BACPLE_00336;product=glycoside hydrolase family 43 protein;protein_id=WP_007559723.1;transl_table=11;translation=length.330 NZ_DS990123 GenBank exon 10960 11952 . - 1 Parent=BACPLE_RS05610.t01 NZ_DS990123 GenBank gene 12082 13278 . - 1 ID=BACPLE_RS19680;Name=BACPLE_RS19680 NZ_DS990123 GenBank mRNA 12082 13278 . - 1 ID=BACPLE_RS19680.t01;Parent=BACPLE_RS19680 NZ_DS990123 GenBank CDS 12082 13278 . - 1 ID=BACPLE_RS19680;Parent=BACPLE_RS19680.t01;Name=BACPLE_RS19680;Note=Derived by automated computational analysis using gene prediction method: Protein Homology.;codon_start=1;inference=COORDINATES: similar to AA sequence:RefSeq:WP_004373664.1;product=DUF2264 domain-containing protein;protein_id=WP_235777910.1;transl_table=11;translation=length.398 NZ_DS990123 GenBank exon 12082 13278 . - 1 Parent=BACPLE_RS19680.t01 NZ_DS990123 GenBank pseudogenic_exon 13288 14295 . - 1 ID=BACPLE_RS19685;Name=BACPLE_RS19685;Note=incomplete%3B partial in the middle of a contig%3B missing C-terminus%3B Derived by automated computational analysis using gene prediction method: Protein Homology.;codon_start=1;inference=COORDINATES: protein motif:HMM:NF019113.2;product=glycoside hydrolase family 88 protein;pseudo=_no_value;transl_table=11 NZ_DS990123 GenBank pseudogene 13288 14295 . - 1 ID=BACPLE_RS19685.pseudogene;Alias=BACPLE_RS19685;Name=BACPLE_RS19685;pseudo=_no_value NZ_DS990123 GenBank gene 14407 15684 . - 1 ID=BACPLE_RS05620;Name=BACPLE_RS05620;old_locus_tag=BACPLE_00338 NZ_DS990123 GenBank mRNA 14407 15684 . - 1 ID=BACPLE_RS05620.t01;Parent=BACPLE_RS05620 NZ_DS990123 GenBank CDS 14407 15684 . - 1 ID=BACPLE_RS05620;Parent=BACPLE_RS05620.t01;Name=BACPLE_RS05620;Note=Derived by automated computational analysis using gene prediction method: Protein Homology.;codon_start=1;inference=COORDINATES: similar to AA sequence:RefSeq:WP_009039811.1;old_locus_tag=BACPLE_00338;product=BNR repeat-containing protein;protein_id=WP_007559725.1;transl_table=11;translation=length.425 NZ_DS990123 GenBank exon 14407 15684 . - 1 Parent=BACPLE_RS05620.t01