##gff-version 3
##sequence-region AAXF02000045 1 19315
# 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	19315	.	+	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	1251	.	-	1	ID=BACOVA_01807;Name=BACOVA_01807
AAXF02000045	GenBank	mRNA	1	1251	.	-	1	ID=BACOVA_01807.t01;Parent=BACOVA_01807
AAXF02000045	GenBank	CDS	1	1251	.	-	1	ID=BACOVA_01807.p01;Parent=BACOVA_01807.t01;Name=BACOVA_01807;Note=KEGG: mmu:27426 0.00020 Nagpa%3B N-acetylglucosamine-1-phosphodiester alpha-N-acetylglucosaminidase K01125%3B 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=EDO12664.1;transl_table=11;translation=length.416
AAXF02000045	GenBank	exon	1	1251	.	-	1	Parent=BACOVA_01807.t01
AAXF02000045	GenBank	gene	1271	3601	.	-	1	ID=BACOVA_01808;Name=BACOVA_01808
AAXF02000045	GenBank	mRNA	1271	3601	.	-	1	ID=BACOVA_01808.t01;Parent=BACOVA_01808
AAXF02000045	GenBank	CDS	1271	3601	.	-	1	ID=BACOVA_01808.p01;Parent=BACOVA_01808.t01;Dbxref=InterPro:IPR005181;Name=BACOVA_01808;Note=KEGG: sus:Acid_3201 5.0e-66 sialate O-acetylesterase%3B COG: COG1649 Uncharacterized protein conserved in bacteria;codon_start=1;inference=protein motif:HMMPfam:IPR005181,similar to AA sequence:INSD:AAO75554.1;product=hypothetical protein;protein_id=EDO12665.1;transl_table=11;translation=length.776
AAXF02000045	GenBank	exon	1271	3601	.	-	1	Parent=BACOVA_01808.t01
AAXF02000045	GenBank	gene	3609	5012	.	-	1	ID=BACOVA_01809;Name=BACOVA_01809
AAXF02000045	GenBank	mRNA	3609	5012	.	-	1	ID=BACOVA_01809.t01;Parent=BACOVA_01809
AAXF02000045	GenBank	CDS	3609	5012	.	-	1	ID=BACOVA_01809.p01;Parent=BACOVA_01809.t01;Name=BACOVA_01809;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=EDO12666.1;transl_table=11;translation=length.467
AAXF02000045	GenBank	exon	3609	5012	.	-	1	Parent=BACOVA_01809.t01
AAXF02000045	GenBank	gene	5041	5925	.	-	1	ID=BACOVA_01810;Name=BACOVA_01810
AAXF02000045	GenBank	mRNA	5041	5925	.	-	1	ID=BACOVA_01810.t01;Parent=BACOVA_01810
AAXF02000045	GenBank	CDS	5041	5925	.	-	1	ID=BACOVA_01810.p01;Parent=BACOVA_01810.t01;Name=BACOVA_01810;codon_start=1;product=hypothetical protein;protein_id=EDO12667.1;transl_table=11;translation=length.294
AAXF02000045	GenBank	exon	5041	5925	.	-	1	Parent=BACOVA_01810.t01
AAXF02000045	GenBank	gene	5966	6841	.	-	1	ID=BACOVA_01811;Name=BACOVA_01811
AAXF02000045	GenBank	mRNA	5966	6841	.	-	1	ID=BACOVA_01811.t01;Parent=BACOVA_01811
AAXF02000045	GenBank	CDS	5966	6841	.	-	1	ID=BACOVA_01811.p01;Parent=BACOVA_01811.t01;Name=BACOVA_01811;codon_start=1;product=hypothetical protein;protein_id=EDO12668.1;transl_table=11;translation=length.291
AAXF02000045	GenBank	exon	5966	6841	.	-	1	Parent=BACOVA_01811.t01
AAXF02000045	GenBank	gene	6899	8692	.	-	1	ID=BACOVA_01812;Name=BACOVA_01812
AAXF02000045	GenBank	mRNA	6899	8692	.	-	1	ID=BACOVA_01812.t01;Parent=BACOVA_01812
AAXF02000045	GenBank	CDS	6899	8692	.	-	1	ID=BACOVA_01812.p01;Parent=BACOVA_01812.t01;Name=BACOVA_01812;codon_start=1;product=hypothetical protein;protein_id=EDO12669.1;transl_table=11;translation=length.597
AAXF02000045	GenBank	exon	6899	8692	.	-	1	Parent=BACOVA_01812.t01
AAXF02000045	GenBank	gene	8716	10725	.	-	1	ID=BACOVA_01813;Name=BACOVA_01813
AAXF02000045	GenBank	mRNA	8716	10725	.	-	1	ID=BACOVA_01813.t01;Parent=BACOVA_01813
AAXF02000045	GenBank	CDS	8716	10725	.	-	1	ID=BACOVA_01813.p01;Parent=BACOVA_01813.t01;Dbxref=InterPro:IPR002345,InterPro:IPR003790;Name=BACOVA_01813;Note=COG: COG1649 Uncharacterized protein conserved in bacteria;codon_start=1;inference=protein motif:HMMPfam:IPR003790,protein motif:ScanRegExp:IPR002345,similar to AA sequence:REFSEQ:ZP_01355434.1;product=hypothetical protein;protein_id=EDO12670.1;transl_table=11;translation=length.669
AAXF02000045	GenBank	exon	8716	10725	.	-	1	Parent=BACOVA_01813.t01
AAXF02000045	GenBank	gene	10743	12629	.	-	1	ID=BACOVA_01814;Name=BACOVA_01814
AAXF02000045	GenBank	mRNA	10743	12629	.	-	1	ID=BACOVA_01814.t01;Parent=BACOVA_01814
AAXF02000045	GenBank	CDS	10743	12629	.	-	1	ID=BACOVA_01814.p01;Parent=BACOVA_01814.t01;Dbxref=InterPro:IPR012944;Name=BACOVA_01814;Note=COG: NOG28830 non supervised orthologous group;codon_start=1;inference=protein motif:HMMPfam:IPR012944,similar to AA sequence:REFSEQ:YP_210284.1;product=SusD family protein;protein_id=EDO12671.1;transl_table=11;translation=length.628
AAXF02000045	GenBank	exon	10743	12629	.	-	1	Parent=BACOVA_01814.t01
AAXF02000045	GenBank	gene	12643	15732	.	-	1	ID=BACOVA_01815;Name=BACOVA_01815
AAXF02000045	GenBank	mRNA	12643	15732	.	-	1	ID=BACOVA_01815.t01;Parent=BACOVA_01815
AAXF02000045	GenBank	CDS	12643	15732	.	-	1	ID=BACOVA_01815.p01;Parent=BACOVA_01815.t01;Dbxref=InterPro:IPR000531,InterPro:IPR008969,InterPro:IPR012910;Name=BACOVA_01815;Note=Psort location: OuterMembrane%2C score:9.52;codon_start=1;inference=protein motif:HMMPfam:IPR000531,protein motif:HMMPfam:IPR012910,protein motif:superfamily:IPR008969,similar to AA sequence:REFSEQ:YP_098346.1;product=TonB-linked outer membrane protein%2C SusC/RagA family;protein_id=EDO12672.1;transl_table=11;translation=length.1029
AAXF02000045	GenBank	exon	12643	15732	.	-	1	Parent=BACOVA_01815.t01
AAXF02000045	GenBank	gene	15690	16955	.	-	1	ID=BACOVA_01816;Name=BACOVA_01816
AAXF02000045	GenBank	mRNA	15690	16955	.	-	1	ID=BACOVA_01816.t01;Parent=BACOVA_01816
AAXF02000045	GenBank	CDS	15690	16955	.	-	1	ID=BACOVA_01816.p01;Parent=BACOVA_01816.t01;Dbxref=InterPro:IPR008928,InterPro:IPR010819,InterPro:IPR013330;eC_number=5.1.3.8;Name=BACOVA_01816;Note=KEGG: bth:BT0453 2.7e-209 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=N-acylglucosamine 2-epimerase;protein_id=EDO12673.1;transl_table=11;translation=length.421
AAXF02000045	GenBank	exon	15690	16955	.	-	1	Parent=BACOVA_01816.t01
AAXF02000045	GenBank	gene	17000	17848	.	-	1	ID=BACOVA_01817;Name=BACOVA_01817
AAXF02000045	GenBank	mRNA	17000	17848	.	-	1	ID=BACOVA_01817.t01;Parent=BACOVA_01817
AAXF02000045	GenBank	CDS	17000	17848	.	-	1	ID=BACOVA_01817.p01;Parent=BACOVA_01817.t01;Dbxref=InterPro:IPR005829,InterPro:IPR011701;Name=BACOVA_01817;Note=KEGG: cal:orf19.3526 3.6e-27 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:HMMPfam:IPR011701,protein motif:ScanRegExp:IPR005829,similar to AA sequence:REFSEQ:NP_809349.1;product=putative arabinose-proton symporter;protein_id=EDO12674.1;transl_table=11;translation=length.282
AAXF02000045	GenBank	exon	17000	17848	.	-	1	Parent=BACOVA_01817.t01
AAXF02000045	GenBank	gene	17940	18401	.	-	1	ID=BACOVA_01818;Name=BACOVA_01818
AAXF02000045	GenBank	mRNA	17940	18401	.	-	1	ID=BACOVA_01818.t01;Parent=BACOVA_01818
AAXF02000045	GenBank	CDS	17940	18401	.	-	1	ID=BACOVA_01818.p01;Parent=BACOVA_01818.t01;Dbxref=InterPro:IPR005828,InterPro:IPR005829;Name=BACOVA_01818;Note=KEGG: cal:orf19.7094 2.0e-16 SNF32%3B glucose sensor or transporter protein K01804%3B COG: COG0477 Permeases of the major facilitator superfamily%3B Psort location: CytoplasmicMembrane%2C score:10.00;codon_start=1;inference=protein motif:HMMPfam:IPR005828,protein motif:ScanRegExp:IPR005829,similar to AA sequence:REFSEQ:NP_809349.1;product=sugar transporter family protein;protein_id=EDO12675.1;transl_table=11;translation=length.153
AAXF02000045	GenBank	exon	17940	18401	.	-	1	Parent=BACOVA_01818.t01
AAXF02000045	GenBank	gene	18407	19315	.	-	1	ID=BACOVA_01819;Name=BACOVA_01819
AAXF02000045	GenBank	mRNA	18407	19315	.	-	1	ID=BACOVA_01819.t01;Parent=BACOVA_01819
AAXF02000045	GenBank	CDS	18407	19315	.	-	1	ID=BACOVA_01819.p01;Parent=BACOVA_01819.t01;Name=BACOVA_01819;Note=Psort location: Cytoplasmic%2C score:8.96;codon_start=1;inference=similar to AA sequence:REFSEQ:NP_809348.1;product=hypothetical protein;protein_id=EDO12676.1;transl_table=11;translation=length.302
AAXF02000045	GenBank	exon	18407	19315	.	-	1	Parent=BACOVA_01819.t01