##gff-version 3
##sequence-region AAXF02000045 1 20376
# conversion-by bp_genbank2gff3.pl
# organism Bacteroides ovatus ATCC 8483
# Note Bacteroides ovatus ATCC 8483 B_ovatus-MSIQ_Cont463, whole genome shotgun sequence.
# date 04-AUG-2012
AAXF02000045	GenBank	region	1	20376	.	+	1	ID=AAXF02000045;Dbxref=BioProject:PRJNA18191,ATCC:8483,taxon:411476;Name=AAXF02000045;Note=Bacteroides ovatus ATCC 8483 B_ovatus-MSIQ_Cont463%2C whole genome shotgun sequence.,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. ;comment1=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. ;date=04-AUG-2012;mol_type=genomic DNA;organism=Bacteroides ovatus ATCC 8483;strain=ATCC 8483;type_material=type strain of Bacteroides ovatus
AAXF02000045	GenBank	gene	1	1875	.	+	1	ID=BACOVA_01792;Name=BACOVA_01792
AAXF02000045	GenBank	mRNA	1	1875	.	+	1	ID=BACOVA_01792.t01;Parent=BACOVA_01792
AAXF02000045	GenBank	CDS	1	1875	.	+	1	ID=BACOVA_01792.p01;Parent=BACOVA_01792.t01;Dbxref=InterPro:IPR001100,InterPro:IPR013027;Name=BACOVA_01792;Note=KEGG: lsl:LSL_1326 0.0075 frdA%3B fumarate reductase flavoprotein subunit K00238%3B COG: NOG04720 non supervised orthologous group;codon_start=1;inference=protein motif:FPrintScan:IPR001100,protein motif:FPrintScan:IPR013027,protein motif:HMMPfam:IPR013027,similar to AA sequence:REFSEQ:NP_809347.1;product=hypothetical protein;protein_id=EDO12649.1;transl_table=11;translation=length.624
AAXF02000045	GenBank	exon	1	1875	.	+	1	Parent=BACOVA_01792.t01
AAXF02000045	GenBank	gene	1920	3017	.	+	1	ID=BACOVA_01793;Name=BACOVA_01793
AAXF02000045	GenBank	mRNA	1920	3017	.	+	1	ID=BACOVA_01793.t01;Parent=BACOVA_01793
AAXF02000045	GenBank	CDS	1920	3017	.	+	1	ID=BACOVA_01793.p01;Parent=BACOVA_01793.t01;Dbxref=InterPro:IPR006311;Name=BACOVA_01793;codon_start=1;inference=protein motif:HMMTigr:IPR006311,similar to AA sequence:REFSEQ:NP_809348.1;product=hypothetical protein;protein_id=EDO12650.1;transl_table=11;translation=length.365
AAXF02000045	GenBank	exon	1920	3017	.	+	1	Parent=BACOVA_01793.t01
AAXF02000045	GenBank	gene	3023	4426	.	+	1	ID=BACOVA_01794;Name=BACOVA_01794
AAXF02000045	GenBank	mRNA	3023	4426	.	+	1	ID=BACOVA_01794.t01;Parent=BACOVA_01794
AAXF02000045	GenBank	CDS	3023	4426	.	+	1	ID=BACOVA_01794.p01;Parent=BACOVA_01794.t01;Dbxref=InterPro:IPR003663,InterPro:IPR005828,InterPro:IPR005829;Name=BACOVA_01794;Note=KEGG: cal:orf19.3526 2.5e-48 ITR2%3B myo-inositol transporter K08140%3B COG: COG0477 Permeases of the major facilitator superfamily%3B Psort location: CytoplasmicMembrane%2C score:10.00;codon_start=1;inference=protein motif:FPrintScan:IPR003663,protein motif:HMMPfam:IPR005828,protein motif:HMMTigr:IPR003663,protein motif:ScanRegExp:IPR005829,similar to AA sequence:REFSEQ:NP_809349.1;product=sugar transporter family protein;protein_id=EDO12651.1;transl_table=11;translation=length.467
AAXF02000045	GenBank	exon	3023	4426	.	+	1	Parent=BACOVA_01794.t01
AAXF02000045	GenBank	gene	4467	5630	.	+	1	ID=BACOVA_01795;Name=BACOVA_01795
AAXF02000045	GenBank	mRNA	4467	5630	.	+	1	ID=BACOVA_01795.t01;Parent=BACOVA_01795
AAXF02000045	GenBank	CDS	4467	5630	.	+	1	ID=BACOVA_01795.p01;Parent=BACOVA_01795.t01;Dbxref=InterPro:IPR008928,InterPro:IPR010819,InterPro:IPR013330;Name=BACOVA_01795;Note=KEGG: bth:BT0453 1.1e-205 N-acylglucosamine 2-epimerase K01787%3B COG: COG2942 N-acyl-D-glucosamine 2-epimerase;codon_start=1;inference=protein motif:Gene3D:IPR013330,protein motif:HMMPfam:IPR010819,protein motif:superfamily:IPR008928,similar to AA sequence:REFSEQ:NP_809366.1;product=hypothetical protein;protein_id=EDO12652.1;transl_table=11;translation=length.387
AAXF02000045	GenBank	exon	4467	5630	.	+	1	Parent=BACOVA_01795.t01
AAXF02000045	GenBank	gene	5683	8907	.	+	1	ID=BACOVA_01796;Name=BACOVA_01796
AAXF02000045	GenBank	mRNA	5683	8907	.	+	1	ID=BACOVA_01796.t01;Parent=BACOVA_01796
AAXF02000045	GenBank	CDS	5683	8907	.	+	1	ID=BACOVA_01796.p01;Parent=BACOVA_01796.t01;Dbxref=InterPro:IPR000531,InterPro:IPR008969,InterPro:IPR012910;Name=BACOVA_01796;codon_start=1;inference=protein motif:HMMPfam:IPR000531,protein motif:HMMPfam:IPR012910,protein motif:superfamily:IPR008969;product=hypothetical protein;protein_id=EDO12653.1;transl_table=11;translation=length.1074
AAXF02000045	GenBank	exon	5683	8907	.	+	1	Parent=BACOVA_01796.t01
AAXF02000045	GenBank	gene	8926	10587	.	+	1	ID=BACOVA_01797;Name=BACOVA_01797
AAXF02000045	GenBank	mRNA	8926	10587	.	+	1	ID=BACOVA_01797.t01;Parent=BACOVA_01797
AAXF02000045	GenBank	CDS	8926	10587	.	+	1	ID=BACOVA_01797.p01;Parent=BACOVA_01797.t01;Dbxref=InterPro:IPR012944;Name=BACOVA_01797;Note=COG: NOG37591 non supervised orthologous group;codon_start=1;inference=protein motif:HMMPfam:IPR012944,similar to AA sequence:INSD:AAO75558.1;product=hypothetical protein;protein_id=EDO12654.1;transl_table=11;translation=length.553
AAXF02000045	GenBank	exon	8926	10587	.	+	1	Parent=BACOVA_01797.t01
AAXF02000045	GenBank	gene	10606	12303	.	+	1	ID=BACOVA_01798;Name=BACOVA_01798
AAXF02000045	GenBank	mRNA	10606	12303	.	+	1	ID=BACOVA_01798.t01;Parent=BACOVA_01798
AAXF02000045	GenBank	CDS	10606	12303	.	+	1	ID=BACOVA_01798.p01;Parent=BACOVA_01798.t01;Dbxref=InterPro:IPR011050;Name=BACOVA_01798;Note=COG: COG2931 RTX toxins and related Ca2+-binding proteins;codon_start=1;inference=protein motif:superfamily:IPR011050,similar to AA sequence:REFSEQ:NP_809363.1;product=hypothetical protein;protein_id=EDO12655.1;transl_table=11;translation=length.565
AAXF02000045	GenBank	exon	10606	12303	.	+	1	Parent=BACOVA_01798.t01
AAXF02000045	GenBank	gene	12394	13392	.	+	1	ID=BACOVA_01799;Name=BACOVA_01799
AAXF02000045	GenBank	mRNA	12394	13392	.	+	1	ID=BACOVA_01799.t01;Parent=BACOVA_01799
AAXF02000045	GenBank	CDS	12394	13392	.	+	1	ID=BACOVA_01799.p01;Parent=BACOVA_01799.t01;Name=BACOVA_01799;Note=COG: COG4632 Exopolysaccharide biosynthesis protein related to N-acetylglucosamine-1-phosphodiester alpha-N-acetylglucosaminidase;codon_start=1;inference=similar to AA sequence:REFSEQ:NP_812505.1;product=hypothetical protein;protein_id=EDO12656.1;transl_table=11;translation=length.332
AAXF02000045	GenBank	exon	12394	13392	.	+	1	Parent=BACOVA_01799.t01
AAXF02000045	GenBank	gene	13446	14849	.	+	1	ID=BACOVA_01800;Name=BACOVA_01800
AAXF02000045	GenBank	mRNA	13446	14849	.	+	1	ID=BACOVA_01800.t01;Parent=BACOVA_01800
AAXF02000045	GenBank	CDS	13446	14849	.	+	1	ID=BACOVA_01800.p01;Parent=BACOVA_01800.t01;Dbxref=InterPro:IPR003790;Name=BACOVA_01800;Note=COG: COG1649 Uncharacterized protein conserved in bacteria;codon_start=1;inference=protein motif:HMMPfam:IPR003790,similar to AA sequence:INSD:AAO75556.1;product=hypothetical protein;protein_id=EDO12657.1;transl_table=11;translation=length.467
AAXF02000045	GenBank	exon	13446	14849	.	+	1	Parent=BACOVA_01800.t01
AAXF02000045	GenBank	gene	14872	16305	.	+	1	ID=BACOVA_01801;Name=BACOVA_01801
AAXF02000045	GenBank	mRNA	14872	16305	.	+	1	ID=BACOVA_01801.t01;Parent=BACOVA_01801
AAXF02000045	GenBank	CDS	14872	16305	.	+	1	ID=BACOVA_01801.p01;Parent=BACOVA_01801.t01;Dbxref=InterPro:IPR004843;Name=BACOVA_01801;Note=KEGG: lpl:lp_3251 0.00041 3'%2C5'-cyclic-nucleotide phosphodiesterase K01120%3B COG: NOG12131 non supervised orthologous group;codon_start=1;inference=protein motif:HMMPfam:IPR004843,similar to AA sequence:REFSEQ:NP_809361.1;product=hypothetical protein;protein_id=EDO12658.1;transl_table=11;translation=length.477
AAXF02000045	GenBank	exon	14872	16305	.	+	1	Parent=BACOVA_01801.t01
AAXF02000045	GenBank	gene	16274	18967	.	+	1	ID=BACOVA_01802;Name=BACOVA_01802
AAXF02000045	GenBank	mRNA	16274	18967	.	+	1	ID=BACOVA_01802.t01;Parent=BACOVA_01802
AAXF02000045	GenBank	CDS	16274	18967	.	+	1	ID=BACOVA_01802.p01;Parent=BACOVA_01802.t01;Dbxref=InterPro:IPR003790,InterPro:IPR005181,InterPro:IPR013781;Name=BACOVA_01802;Note=KEGG: aba:Acid345_1697 4.3e-61 sialate O-acetylesterase%3B COG: COG1649 Uncharacterized protein conserved in bacteria;codon_start=1;inference=protein motif:Gene3D:IPR013781,protein motif:HMMPfam:IPR003790,protein motif:HMMPfam:IPR005181;product=hypothetical protein;protein_id=EDO12659.1;transl_table=11;translation=length.897
AAXF02000045	GenBank	exon	16274	18967	.	+	1	Parent=BACOVA_01802.t01
AAXF02000045	GenBank	gene	18964	20376	.	+	1	ID=BACOVA_01803;Name=BACOVA_01803
AAXF02000045	GenBank	mRNA	18964	20376	.	+	1	ID=BACOVA_01803.t01;Parent=BACOVA_01803
AAXF02000045	GenBank	CDS	18964	20376	.	+	1	ID=BACOVA_01803.p01;Parent=BACOVA_01803.t01;Name=BACOVA_01803;Note=COG: COG4299 Uncharacterized conserved protein%3B Psort location: CytoplasmicMembrane%2C score:10.00;codon_start=1;inference=similar to AA sequence:REFSEQ:NP_809359.1;product=hypothetical protein;protein_id=EDO12660.1;transl_table=11;translation=length.470
AAXF02000045	GenBank	exon	18964	20376	.	+	1	Parent=BACOVA_01803.t01