##gff-version 3
##sequence-region AAXF02000047 1 14774
# conversion-by bp_genbank2gff3.pl
# organism Bacteroides ovatus ATCC 8483
# Note Bacteroides ovatus ATCC 8483 B_ovatus-MSIQ_Cont517, whole genome shotgun sequence.
# date 04-AUG-2012
AAXF02000047	GenBank	region	1	14774	.	+	1	ID=AAXF02000047;Dbxref=BioProject:PRJNA18191,ATCC:8483,taxon:411476;Name=AAXF02000047;Note=Bacteroides ovatus ATCC 8483 B_ovatus-MSIQ_Cont517%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
AAXF02000047	GenBank	gene	1	2871	.	+	1	ID=BACOVA_02051;Name=BACOVA_02051
AAXF02000047	GenBank	mRNA	1	2871	.	+	1	ID=BACOVA_02051.t01;Parent=BACOVA_02051
AAXF02000047	GenBank	CDS	1	2871	.	+	1	ID=BACOVA_02051.p01;Parent=BACOVA_02051.t01;Dbxref=InterPro:IPR000531,InterPro:IPR008969,InterPro:IPR012910;Name=BACOVA_02051;Note=COG: NOG06412 non supervised orthologous group%3B Psort location: OuterMembrane%2C score:9.49;codon_start=1;inference=protein motif:HMMPfam:IPR000531,protein motif:HMMPfam:IPR012910,protein motif:superfamily:IPR008969,similar to AA sequence:INSD:AAO78058.1;product=TonB-linked outer membrane protein%2C SusC/RagA family;protein_id=EDO12162.1;transl_table=11;translation=length.956
AAXF02000047	GenBank	exon	1	2871	.	+	1	Parent=BACOVA_02051.t01
AAXF02000047	GenBank	gene	2887	4416	.	+	1	ID=BACOVA_02052;Name=BACOVA_02052
AAXF02000047	GenBank	mRNA	2887	4416	.	+	1	ID=BACOVA_02052.t01;Parent=BACOVA_02052
AAXF02000047	GenBank	CDS	2887	4416	.	+	1	ID=BACOVA_02052.p01;Parent=BACOVA_02052.t01;Dbxref=InterPro:IPR012944;Name=BACOVA_02052;Note=COG: NOG26547 non supervised orthologous group%3B Psort location: OuterMembrane%2C score:9.52;codon_start=1;inference=protein motif:HMMPfam:IPR012944,similar to AA sequence:REFSEQ:ZP_01719514.1;product=SusD family protein;protein_id=EDO12163.1;transl_table=11;translation=length.509
AAXF02000047	GenBank	exon	2887	4416	.	+	1	Parent=BACOVA_02052.t01
AAXF02000047	GenBank	gene	4476	6440	.	+	1	ID=BACOVA_02053;Name=BACOVA_02053
AAXF02000047	GenBank	mRNA	4476	6440	.	+	1	ID=BACOVA_02053.t01;Parent=BACOVA_02053
AAXF02000047	GenBank	CDS	4476	6440	.	+	1	ID=BACOVA_02053.p01;Parent=BACOVA_02053.t01;Dbxref=InterPro:IPR008009;Name=BACOVA_02053;Note=COG: NOG08360 non supervised orthologous group;codon_start=1;inference=protein motif:HMMPfam:IPR008009,similar to AA sequence:REFSEQ:ZP_01122507.1;product=hypothetical protein;protein_id=EDO12164.1;transl_table=11;translation=length.654
AAXF02000047	GenBank	exon	4476	6440	.	+	1	Parent=BACOVA_02053.t01
AAXF02000047	GenBank	gene	6453	8060	.	+	1	ID=BACOVA_02054;Name=BACOVA_02054
AAXF02000047	GenBank	mRNA	6453	8060	.	+	1	ID=BACOVA_02054.t01;Parent=BACOVA_02054
AAXF02000047	GenBank	CDS	6453	8060	.	+	1	ID=BACOVA_02054.p01;Parent=BACOVA_02054.t01;Dbxref=InterPro:IPR005502;Name=BACOVA_02054;Note=KEGG: mst:Msp_0683 0.0010 hypothetical protein K00788%3B COG: NOG08360 non supervised orthologous group;codon_start=1;inference=protein motif:HMMPfam:IPR005502,similar to AA sequence:INSD:EDJ82860.1;product=hypothetical protein;protein_id=EDO12165.1;transl_table=11;translation=length.535
AAXF02000047	GenBank	exon	6453	8060	.	+	1	Parent=BACOVA_02054.t01
AAXF02000047	GenBank	gene	8067	9614	.	+	1	ID=BACOVA_02055;Name=BACOVA_02055
AAXF02000047	GenBank	mRNA	8067	9614	.	+	1	ID=BACOVA_02055.t01;Parent=BACOVA_02055
AAXF02000047	GenBank	CDS	8067	9614	.	+	1	ID=BACOVA_02055.p01;Parent=BACOVA_02055.t01;Name=BACOVA_02055;Note=COG: NOG08360 non supervised orthologous group;codon_start=1;inference=similar to AA sequence:INSD:EDJ82860.1;product=hypothetical protein;protein_id=EDO12166.1;transl_table=11;translation=length.515
AAXF02000047	GenBank	exon	8067	9614	.	+	1	Parent=BACOVA_02055.t01
AAXF02000047	GenBank	gene	9627	11225	.	+	1	ID=BACOVA_02056;Name=BACOVA_02056
AAXF02000047	GenBank	mRNA	9627	11225	.	+	1	ID=BACOVA_02056.t01;Parent=BACOVA_02056
AAXF02000047	GenBank	CDS	9627	11225	.	+	1	ID=BACOVA_02056.p01;Parent=BACOVA_02056.t01;Dbxref=InterPro:IPR000801;Name=BACOVA_02056;Note=KEGG: pgi:PG0425 4.7e-23 esterase%2C putative K03929%3B COG: COG0627 Predicted esterase%3B Psort location: OuterMembrane%2C score:9.52;codon_start=1;inference=protein motif:HMMPfam:IPR000801,similar to AA sequence:REFSEQ:ZP_01104988.1;product=putative esterase;protein_id=EDO12167.1;transl_table=11;translation=length.532
AAXF02000047	GenBank	exon	9627	11225	.	+	1	Parent=BACOVA_02056.t01
AAXF02000047	GenBank	gene	11227	12747	.	+	1	ID=BACOVA_02057;Name=BACOVA_02057
AAXF02000047	GenBank	mRNA	11227	12747	.	+	1	ID=BACOVA_02057.t01;Parent=BACOVA_02057
AAXF02000047	GenBank	CDS	11227	12747	.	+	1	ID=BACOVA_02057.p01;Parent=BACOVA_02057.t01;Dbxref=InterPro:IPR000801;Name=BACOVA_02057;Note=KEGG: pgi:PG0425 4.9e-28 esterase%2C putative K03929%3B COG: COG0627 Predicted esterase;codon_start=1;inference=protein motif:HMMPfam:IPR000801,similar to AA sequence:REFSEQ:ZP_01104988.1;product=putative esterase;protein_id=EDO12168.1;transl_table=11;translation=length.506
AAXF02000047	GenBank	exon	11227	12747	.	+	1	Parent=BACOVA_02057.t01
AAXF02000047	GenBank	gene	12817	13773	.	+	1	ID=BACOVA_02058;Name=BACOVA_02058
AAXF02000047	GenBank	mRNA	12817	13773	.	+	1	ID=BACOVA_02058.t01;Parent=BACOVA_02058
AAXF02000047	GenBank	CDS	12817	13773	.	+	1	ID=BACOVA_02058.p01;Parent=BACOVA_02058.t01;Dbxref=InterPro:IPR010651;Name=BACOVA_02058;Note=COG: NOG04879 non supervised orthologous group%3B Psort location: CytoplasmicMembrane%2C score:10.00;codon_start=1;inference=protein motif:HMMPfam:IPR010651,similar to AA sequence:REFSEQ:NP_811721.1;product=fatty acid elongase 3-ketoacyl-CoA synthase 1;protein_id=EDO12169.1;transl_table=11;translation=length.318
AAXF02000047	GenBank	exon	12817	13773	.	+	1	Parent=BACOVA_02058.t01
AAXF02000047	GenBank	gene	13797	14774	.	+	1	ID=BACOVA_02059;Name=BACOVA_02059
AAXF02000047	GenBank	mRNA	13797	14774	.	+	1	ID=BACOVA_02059.t01;Parent=BACOVA_02059
AAXF02000047	GenBank	CDS	13797	14774	.	+	1	ID=BACOVA_02059.p01;Parent=BACOVA_02059.t01;Dbxref=InterPro:IPR003961,InterPro:IPR008957,InterPro:IPR011050;Name=BACOVA_02059;Note=KEGG bcl:ABC0646 0.0016 chitinase K01183;codon_start=1;inference=protein motif:Gene3D:IPR008957,protein motif:HMMPfam:IPR003961,protein motif:HMMSmart:IPR003961,protein motif:superfamily:IPR008957,protein motif:superfamily:IPR011050;product=fibronectin type III domain protein;protein_id=EDO12170.1;transl_table=11;translation=length.325
AAXF02000047	GenBank	exon	13797	14774	.	+	1	Parent=BACOVA_02059.t01