##gff-version 3
##sequence-region NZ_DS264584 1 16470
# conversion-by bp_genbank2gff3.pl
# organism Bacteroides ovatus ATCC 8483
# Note Bacteroides ovatus ATCC 8483 Scfld0231, whole genome shotgun sequence.
# date 25-NOV-2019
NZ_DS264584	GenBank	region	1	16470	.	+	1	ID=NZ_DS264584;Dbxref=BioProject:PRJNA224116,ATCC:8483,taxon:411476;Name=NZ_DS264584;Note=Bacteroides ovatus ATCC 8483 Scfld0231%2C whole genome shotgun sequence.,REFSEQ INFORMATION: The reference sequence was derived from DS264584. 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 DS264584. 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_DS264584	GenBank	gene	1	2448	.	-	1	ID=BACOVA_RS23965;Name=BACOVA_RS23965;old_locus_tag=BACOVA_05487
NZ_DS264584	GenBank	mRNA	1	2448	.	-	1	ID=BACOVA_RS23965.t01;Parent=BACOVA_RS23965
NZ_DS264584	GenBank	CDS	1	2448	.	-	1	ID=BACOVA_RS23965.p01;Parent=BACOVA_RS23965.t01;Name=BACOVA_RS23965;Note=Derived by automated computational analysis using gene prediction method: Protein Homology.;codon_start=1;inference=COORDINATES: similar to AA sequence:RefSeq:NP_813578.1;old_locus_tag=BACOVA_05487;product=glycoside hydrolase family 2 protein;protein_id=WP_004302201.1;transl_table=11;translation=length.815
NZ_DS264584	GenBank	exon	1	2448	.	-	1	Parent=BACOVA_RS23965.t01
NZ_DS264584	GenBank	gene	2514	3599	.	-	1	ID=BACOVA_RS23970;Name=BACOVA_RS23970;old_locus_tag=BACOVA_05488
NZ_DS264584	GenBank	mRNA	2514	3599	.	-	1	ID=BACOVA_RS23970.t01;Parent=BACOVA_RS23970
NZ_DS264584	GenBank	CDS	2514	3599	.	-	1	ID=BACOVA_RS23970.p01;Parent=BACOVA_RS23970.t01;Name=BACOVA_RS23970;Note=Derived by automated computational analysis using gene prediction method: Protein Homology.;codon_start=1;inference=COORDINATES: similar to AA sequence:RefSeq:WP_004325364.1;old_locus_tag=BACOVA_05488;product=arabinogalactan endo-1%2C4-beta-galactosidase;protein_id=WP_052588049.1;transl_table=11;translation=length.361
NZ_DS264584	GenBank	exon	2514	3599	.	-	1	Parent=BACOVA_RS23970.t01
NZ_DS264584	GenBank	gene	3645	5399	.	-	1	ID=BACOVA_RS23975;Name=BACOVA_RS23975;old_locus_tag=BACOVA_05489
NZ_DS264584	GenBank	mRNA	3645	5399	.	-	1	ID=BACOVA_RS23975.t01;Parent=BACOVA_RS23975
NZ_DS264584	GenBank	CDS	3645	5399	.	-	1	ID=BACOVA_RS23975.p01;Parent=BACOVA_RS23975.t01;Name=BACOVA_RS23975;Note=Derived by automated computational analysis using gene prediction method: Protein Homology.;codon_start=1;inference=COORDINATES: similar to AA sequence:RefSeq:WP_004312460.1;old_locus_tag=BACOVA_05489;product=DUF5114 domain-containing protein;protein_id=WP_004302203.1;transl_table=11;translation=length.584
NZ_DS264584	GenBank	exon	3645	5399	.	-	1	Parent=BACOVA_RS23975.t01
NZ_DS264584	GenBank	gene	5423	7003	.	-	1	ID=BACOVA_RS23980;Name=BACOVA_RS23980;old_locus_tag=BACOVA_05490
NZ_DS264584	GenBank	mRNA	5423	7003	.	-	1	ID=BACOVA_RS23980.t01;Parent=BACOVA_RS23980
NZ_DS264584	GenBank	CDS	5423	7003	.	-	1	ID=BACOVA_RS23980.p01;Parent=BACOVA_RS23980.t01;Name=BACOVA_RS23980;Note=Derived by automated computational analysis using gene prediction method: Protein Homology.;codon_start=1;inference=COORDINATES: similar to AA sequence:RefSeq:WP_004305745.1;old_locus_tag=BACOVA_05490;product=RagB/SusD family nutrient uptake outer membrane protein;protein_id=WP_004302204.1;transl_table=11;translation=length.526
NZ_DS264584	GenBank	exon	5423	7003	.	-	1	Parent=BACOVA_RS23980.t01
NZ_DS264584	GenBank	gene	7022	9997	.	-	1	ID=BACOVA_RS23985;Name=BACOVA_RS23985;old_locus_tag=BACOVA_05491
NZ_DS264584	GenBank	mRNA	7022	9997	.	-	1	ID=BACOVA_RS23985.t01;Parent=BACOVA_RS23985
NZ_DS264584	GenBank	CDS	7022	9997	.	-	1	ID=BACOVA_RS23985.p01;Parent=BACOVA_RS23985.t01;Name=BACOVA_RS23985;Note=Derived by automated computational analysis using gene prediction method: Protein Homology.;codon_start=1;inference=COORDINATES: similar to AA sequence:RefSeq:WP_004312459.1;old_locus_tag=BACOVA_05491;product=TonB-dependent receptor;protein_id=WP_004302205.1;transl_table=11;translation=length.991
NZ_DS264584	GenBank	exon	7022	9997	.	-	1	Parent=BACOVA_RS23985.t01
NZ_DS264584	GenBank	gene	10221	12830	.	-	1	ID=BACOVA_RS23990;Name=BACOVA_RS23990;old_locus_tag=BACOVA_05493
NZ_DS264584	GenBank	mRNA	10221	12830	.	-	1	ID=BACOVA_RS23990.t01;Parent=BACOVA_RS23990
NZ_DS264584	GenBank	CDS	10221	12830	.	-	1	ID=BACOVA_RS23990.p01;Parent=BACOVA_RS23990.t01;Name=BACOVA_RS23990;Note=Derived by automated computational analysis using gene prediction method: Protein Homology.;codon_start=1;inference=COORDINATES: similar to AA sequence:RefSeq:WP_008651432.1;old_locus_tag=BACOVA_05493;product=cellulase family glycosylhydrolase;protein_id=WP_004302207.1;transl_table=11;translation=length.869
NZ_DS264584	GenBank	exon	10221	12830	.	-	1	Parent=BACOVA_RS23990.t01
NZ_DS264584	GenBank	gene	12946	16470	.	-	1	ID=BACOVA_RS23995;Name=BACOVA_RS23995;old_locus_tag=BACOVA_05495
NZ_DS264584	GenBank	mRNA	12946	16470	.	-	1	ID=BACOVA_RS23995.t01;Parent=BACOVA_RS23995
NZ_DS264584	GenBank	CDS	12946	16470	.	-	1	ID=BACOVA_RS23995.p01;Parent=BACOVA_RS23995.t01;Name=BACOVA_RS23995;Note=Derived by automated computational analysis using gene prediction method: Protein Homology.;codon_start=1;inference=COORDINATES: similar to AA sequence:RefSeq:WP_008651436.1;old_locus_tag=BACOVA_05495;product=helix-turn-helix domain-containing protein;protein_id=WP_004302208.1;transl_table=11;translation=length.1174
NZ_DS264584	GenBank	exon	12946	16470	.	-	1	Parent=BACOVA_RS23995.t01