##gff-version 3
##sequence-region NZ_DS264579 1 9403
# conversion-by bp_genbank2gff3.pl
# organism Bacteroides ovatus ATCC 8483
# Note Bacteroides ovatus ATCC 8483 Scfld0226, whole genome shotgun sequence.
# date 25-NOV-2019
NZ_DS264579	GenBank	region	1	9403	.	+	1	ID=NZ_DS264579;Dbxref=BioProject:PRJNA224116,ATCC:8483,taxon:411476;Name=NZ_DS264579;Note=Bacteroides ovatus ATCC 8483 Scfld0226%2C whole genome shotgun sequence.,REFSEQ INFORMATION: The reference sequence was derived from DS264579. Bacteroides ovatus (GenBank Accession Number for 16S rDNA gene: X83952) is a member of the division Bacteroidetes. In one comprehensive 16S rDNA sequence-based enumeration of the colonic microbiota of three healthy adult humans,it represents,on average,0.034%25 of all 16S rDNA sequences and 0.071%25 of the sequences in its division (Eckburg et. al. (2005)). The sequenced strain was obtained from ATCC (ATCC 8483T). We have collected 6.9X coverage in plasmid end reads and 454 reads. We will be performing one round of automated sequence improvement (pre-finishing). 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 ovatus (GenBank Accession Number for 16S rDNA gene: X83952) is a member of the division Bacteroidetes. In one comprehensive 16S rDNA sequence-based enumeration of the colonic microbiota of three healthy adult humans,it represents,on average,0.034%25 of all 16S rDNA sequences and 0.071%25 of the sequences in its division (Eckburg et. al. (2005)). The sequenced strain was obtained from ATCC (ATCC 8483T). We have collected 6.9X coverage in plasmid end reads and 454 reads. We will be performing one round of automated sequence improvement (pre-finishing). 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. Coding sequences were predicted using GeneMark v3.3 and Glimmer2 v2.13. Intergenic regions notspanned by GeneMark and Glimmer2 were blasted against NCBI'snon-redundant (NR) database and predictions generated based on proteinalignments. RNA genes were determined using tRNAscan-SE 1.23 or Rfamv8.0. Gene names are generated at the contig level and may notnecessarily reflect any known order or orientation betweencontigs. 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 August 2007,and the CDS comments were updated in January 2008. This is a reference genome for the Human Microbiome Project. This project is co-owned with the Human Microbiome Project DACC. Product names were updated in August 2012. 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/ ##Genome-Annotation-Data-START## Annotation Provider :: NCBI RefSeq Annotation Date :: 11/25/2019 16:35:53 Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline (PGAP) Annotation Method :: Best-placed reference protein set,GeneMarkS-2+ Annotation Software revision :: 4.10 Features Annotated :: Gene,CDS,rRNA,tRNA,ncRNA,repeat_region Genes (total) :: 4,931 CDSs (total) :: 4,837 Genes (coding) :: 4,690 CDSs (with protein) :: 4,690 Genes (RNA) :: 94 rRNAs :: 4,4,6 (5S,16S,23S) complete rRNAs :: 4,3,5 (5S,16S,23S) partial rRNAs :: 1,1 (16S,23S) tRNAs :: 78 ncRNAs :: 2 Pseudo Genes (total) :: 149 CDSs (without protein) :: 147 Pseudo Genes (ambiguous residues) :: 1 of 149 Pseudo Genes (frameshifted) :: 75 of 149 Pseudo Genes (incomplete) :: 69 of 149 Pseudo Genes (internal stop) :: 17 of 149 Pseudo Genes (multiple problems) :: 14 of 149 ##Genome-Annotation-Data-END## ,type strain of Bacteroides ovatus ATCC 8483;comment1=REFSEQ INFORMATION: The reference sequence was derived from DS264579. Bacteroides ovatus (GenBank Accession Number for 16S rDNA gene: X83952) is a member of the division Bacteroidetes. In one comprehensive 16S rDNA sequence-based enumeration of the colonic microbiota of three healthy adult humans%2C it represents%2C on average%2C 0.034%25 of all 16S rDNA sequences and 0.071%25 of the sequences in its division (Eckburg et. al. (2005)). The sequenced strain was obtained from ATCC (ATCC 8483T). We have collected 6.9X coverage in plasmid end reads and 454 reads. We will be performing one round of automated sequence improvement (pre-finishing). 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 ovatus (GenBank Accession Number for 16S rDNA gene: X83952) is a member of the division Bacteroidetes. In one comprehensive 16S rDNA sequence-based enumeration of the colonic microbiota of three healthy adult humans%2C it represents%2C on average%2C 0.034%25 of all 16S rDNA sequences and 0.071%25 of the sequences in its division (Eckburg et. al. (2005)). The sequenced strain was obtained from ATCC (ATCC 8483T). We have collected 6.9X coverage in plasmid end reads and 454 reads. We will be performing one round of automated sequence improvement (pre-finishing). 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. Coding sequences were predicted using GeneMark v3.3 and Glimmer2 v2.13. Intergenic regions notspanned by GeneMark and Glimmer2 were blasted against NCBI'snon-redundant (NR) database and predictions generated based on proteinalignments. RNA genes were determined using tRNAscan-SE 1.23 or Rfamv8.0. Gene names are generated at the contig level and may notnecessarily reflect any known order or orientation betweencontigs. 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 August 2007%2C and the CDS comments were updated in January 2008. This is a reference genome for the Human Microbiome Project. This project is co-owned with the Human Microbiome Project DACC. Product names were updated in August 2012. 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/ ##Genome-Annotation-Data-START## Annotation Provider :: NCBI RefSeq Annotation Date :: 11/25/2019 16:35:53 Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline (PGAP) Annotation Method :: Best-placed reference protein set%3B GeneMarkS-2+ Annotation Software revision :: 4.10 Features Annotated :: Gene%3B CDS%3B rRNA%3B tRNA%3B ncRNA%3B repeat_region Genes (total) :: 4%2C931 CDSs (total) :: 4%2C837 Genes (coding) :: 4%2C690 CDSs (with protein) :: 4%2C690 Genes (RNA) :: 94 rRNAs :: 4%2C 4%2C 6 (5S%2C 16S%2C 23S) complete rRNAs :: 4%2C 3%2C 5 (5S%2C 16S%2C 23S) partial rRNAs :: 1%2C 1 (16S%2C 23S) tRNAs :: 78 ncRNAs :: 2 Pseudo Genes (total) :: 149 CDSs (without protein) :: 147 Pseudo Genes (ambiguous residues) :: 1 of 149 Pseudo Genes (frameshifted) :: 75 of 149 Pseudo Genes (incomplete) :: 69 of 149 Pseudo Genes (internal stop) :: 17 of 149 Pseudo Genes (multiple problems) :: 14 of 149 ##Genome-Annotation-Data-END## ;date=25-NOV-2019;host=Homo sapiens;isolation_source=biological product [ENVO:02000043];mol_type=genomic DNA;organism=Bacteroides ovatus ATCC 8483;strain=ATCC 8483;type_material=type strain of Bacteroides ovatus
NZ_DS264579	GenBank	gene	1	816	.	+	1	ID=BACOVA_RS11930;Name=BACOVA_RS11930;old_locus_tag=BACOVA_02741
NZ_DS264579	GenBank	mRNA	1	816	.	+	1	ID=BACOVA_RS11930.t01;Parent=BACOVA_RS11930
NZ_DS264579	GenBank	CDS	1	816	.	+	1	ID=BACOVA_RS11930.p01;Parent=BACOVA_RS11930.t01;Name=BACOVA_RS11930;Note=Derived by automated computational analysis using gene prediction method: Protein Homology.;codon_start=1;inference=COORDINATES: similar to AA sequence:RefSeq:WP_004298557.1;old_locus_tag=BACOVA_02741;product=glycoside hydrolase family 16 protein;protein_id=WP_004298557.1;transl_table=11;translation=length.271
NZ_DS264579	GenBank	exon	1	816	.	+	1	Parent=BACOVA_RS11930.t01
NZ_DS264579	GenBank	gene	837	4025	.	+	1	ID=BACOVA_RS11935;Name=BACOVA_RS11935;old_locus_tag=BACOVA_02742
NZ_DS264579	GenBank	mRNA	837	4025	.	+	1	ID=BACOVA_RS11935.t01;Parent=BACOVA_RS11935
NZ_DS264579	GenBank	CDS	837	4025	.	+	1	ID=BACOVA_RS11935.p01;Parent=BACOVA_RS11935.t01;Name=BACOVA_RS11935;Note=Derived by automated computational analysis using gene prediction method: Protein Homology.;codon_start=1;inference=COORDINATES: similar to AA sequence:RefSeq:WP_004298558.1;old_locus_tag=BACOVA_02742;product=SusC/RagA family TonB-linked outer membrane protein;protein_id=WP_004298558.1;transl_table=11;translation=length.1062
NZ_DS264579	GenBank	exon	837	4025	.	+	1	Parent=BACOVA_RS11935.t01
NZ_DS264579	GenBank	gene	4037	5713	.	+	1	ID=BACOVA_RS11940;Name=BACOVA_RS11940;old_locus_tag=BACOVA_02743
NZ_DS264579	GenBank	mRNA	4037	5713	.	+	1	ID=BACOVA_RS11940.t01;Parent=BACOVA_RS11940
NZ_DS264579	GenBank	CDS	4037	5713	.	+	1	ID=BACOVA_RS11940.p01;Parent=BACOVA_RS11940.t01;Name=BACOVA_RS11940;Note=Derived by automated computational analysis using gene prediction method: Protein Homology.;codon_start=1;inference=COORDINATES: similar to AA sequence:RefSeq:WP_004302737.1;old_locus_tag=BACOVA_02743;product=SusD/RagB family nutrient-binding outer membrane lipoprotein;protein_id=WP_004298559.1;transl_table=11;translation=length.558
NZ_DS264579	GenBank	exon	4037	5713	.	+	1	Parent=BACOVA_RS11940.t01
NZ_DS264579	GenBank	gene	5734	6996	.	+	1	ID=BACOVA_RS11945;Name=BACOVA_RS11945;old_locus_tag=BACOVA_02744
NZ_DS264579	GenBank	mRNA	5734	6996	.	+	1	ID=BACOVA_RS11945.t01;Parent=BACOVA_RS11945
NZ_DS264579	GenBank	CDS	5734	6996	.	+	1	ID=BACOVA_RS11945.p01;Parent=BACOVA_RS11945.t01;Name=BACOVA_RS11945;Note=Derived by automated computational analysis using gene prediction method: Protein Homology.;codon_start=1;inference=COORDINATES: similar to AA sequence:RefSeq:WP_004298560.1;old_locus_tag=BACOVA_02744;product=hypothetical protein;protein_id=WP_004298560.1;transl_table=11;translation=length.420
NZ_DS264579	GenBank	exon	5734	6996	.	+	1	Parent=BACOVA_RS11945.t01
NZ_DS264579	GenBank	gene	7109	9403	.	+	1	ID=BACOVA_RS11950;Name=BACOVA_RS11950;old_locus_tag=BACOVA_02745
NZ_DS264579	GenBank	mRNA	7109	9403	.	+	1	ID=BACOVA_RS11950.t01;Parent=BACOVA_RS11950
NZ_DS264579	GenBank	CDS	7109	9403	.	+	1	ID=BACOVA_RS11950.p01;Parent=BACOVA_RS11950.t01;Name=BACOVA_RS11950;Note=Derived by automated computational analysis using gene prediction method: Protein Homology.;codon_start=1;inference=COORDINATES: similar to AA sequence:RefSeq:WP_004298561.1;old_locus_tag=BACOVA_02745;product=beta-glucosidase;protein_id=WP_004298561.1;transl_table=11;translation=length.764
NZ_DS264579	GenBank	exon	7109	9403	.	+	1	Parent=BACOVA_RS11950.t01