##gff-version 3
##sequence-region AAXF02000051 1 14216
# conversion-by bp_genbank2gff3.pl
# organism Bacteroides ovatus ATCC 8483
# Note Bacteroides ovatus ATCC 8483 B_ovatus-MSIQ_Cont521, whole genome shotgun sequence.
# date 04-AUG-2012
AAXF02000051	GenBank	region	1	14216	.	+	1	ID=AAXF02000051;Dbxref=BioProject:PRJNA18191,ATCC:8483,taxon:411476;Name=AAXF02000051;Note=Bacteroides ovatus ATCC 8483 B_ovatus-MSIQ_Cont521%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
AAXF02000051	GenBank	gene	1	2277	.	-	1	ID=BACOVA_03514;Name=BACOVA_03514
AAXF02000051	GenBank	mRNA	1	2277	.	-	1	ID=BACOVA_03514.t01;Parent=BACOVA_03514
AAXF02000051	GenBank	CDS	1	2277	.	-	1	ID=BACOVA_03514.p01;Parent=BACOVA_03514.t01;Dbxref=InterPro:IPR006047,InterPro:IPR006589,InterPro:IPR013781,InterPro:IPR013784;Name=BACOVA_03514;Note=KEGG: rba:RB548 2.4e-31 glgB%3B 1%2C4-alpha-glucan branching enzyme K00700%3B COG: COG0296 1%2C4-alpha-glucan branching enzyme;codon_start=1;inference=protein motif:Gene3D:IPR013781,protein motif:HMMPfam:IPR006047,protein motif:HMMSmart:IPR006589,protein motif:superfamily:IPR013784,similar to AA sequence:INSD:BAD50048.1;product=alpha amylase%2C catalytic domain protein;protein_id=EDO10881.1;transl_table=11;translation=length.758
AAXF02000051	GenBank	exon	1	2277	.	-	1	Parent=BACOVA_03514.t01
AAXF02000051	GenBank	gene	2441	3904	.	-	1	ID=BACOVA_03515;Name=BACOVA_03515
AAXF02000051	GenBank	mRNA	2441	3904	.	-	1	ID=BACOVA_03515.t01;Parent=BACOVA_03515
AAXF02000051	GenBank	CDS	2441	3904	.	-	1	ID=BACOVA_03515.p01;Parent=BACOVA_03515.t01;Dbxref=InterPro:IPR013784;Name=BACOVA_03515;codon_start=1;inference=protein motif:superfamily:IPR013784,similar to AA sequence:REFSEQ:NP_812610.1;product=hypothetical protein;protein_id=EDO10882.1;transl_table=11;translation=length.487
AAXF02000051	GenBank	exon	2441	3904	.	-	1	Parent=BACOVA_03515.t01
AAXF02000051	GenBank	gene	3948	5120	.	-	1	ID=BACOVA_03516;Name=BACOVA_03516
AAXF02000051	GenBank	mRNA	3948	5120	.	-	1	ID=BACOVA_03516.t01;Parent=BACOVA_03516
AAXF02000051	GenBank	CDS	3948	5120	.	-	1	ID=BACOVA_03516.p01;Parent=BACOVA_03516.t01;Name=BACOVA_03516;codon_start=1;inference=similar to AA sequence:REFSEQ:NP_812611.1;product=hypothetical protein;protein_id=EDO10883.1;transl_table=11;translation=length.390
AAXF02000051	GenBank	exon	3948	5120	.	-	1	Parent=BACOVA_03516.t01
AAXF02000051	GenBank	gene	5156	6766	.	-	1	ID=BACOVA_03517;Name=BACOVA_03517
AAXF02000051	GenBank	mRNA	5156	6766	.	-	1	ID=BACOVA_03517.t01;Parent=BACOVA_03517
AAXF02000051	GenBank	CDS	5156	6766	.	-	1	ID=BACOVA_03517.p01;Parent=BACOVA_03517.t01;Dbxref=InterPro:IPR012944;Name=BACOVA_03517;Note=COG: NOG27599 non supervised orthologous group;codon_start=1;inference=protein motif:HMMPfam:IPR012944,similar to AA sequence:INSD:AAB42172.1;product=SusD family protein;protein_id=EDO10884.1;transl_table=11;translation=length.536
AAXF02000051	GenBank	exon	5156	6766	.	-	1	Parent=BACOVA_03517.t01
AAXF02000051	GenBank	gene	6796	9843	.	-	1	ID=BACOVA_03518;Name=BACOVA_03518
AAXF02000051	GenBank	mRNA	6796	9843	.	-	1	ID=BACOVA_03518.t01;Parent=BACOVA_03518
AAXF02000051	GenBank	CDS	6796	9843	.	-	1	ID=BACOVA_03518.p01;Parent=BACOVA_03518.t01;Dbxref=InterPro:IPR000531,InterPro:IPR000627,InterPro:IPR008969,InterPro:IPR012910;Name=BACOVA_03518;Note=KEGG: shn:Shewana3_3063 7.1e-06 phosphatidylglycerophosphatase K01094%3B COG: NOG06412 non supervised orthologous group;codon_start=1;inference=protein motif:HMMPfam:IPR000531,protein motif:HMMPfam:IPR012910,protein motif:superfamily:IPR000627,protein motif:superfamily:IPR008969;product=TonB-linked outer membrane protein%2C SusC/RagA family;protein_id=EDO10885.1;transl_table=11;translation=length.1015
AAXF02000051	GenBank	exon	6796	9843	.	-	1	Parent=BACOVA_03518.t01
AAXF02000051	GenBank	gene	9949	12165	.	-	1	ID=BACOVA_03519;Name=BACOVA_03519
AAXF02000051	GenBank	mRNA	9949	12165	.	-	1	ID=BACOVA_03519.t01;Parent=BACOVA_03519
AAXF02000051	GenBank	CDS	9949	12165	.	-	1	ID=BACOVA_03519.p01;Parent=BACOVA_03519.t01;Dbxref=InterPro:IPR012338;Name=BACOVA_03519;Note=KEGG: pha:PSHAa2848 2.7e-129 alpha-glucosidase K01187%3B COG: NOG06228 non supervised orthologous group;codon_start=1;inference=protein motif:superfamily:IPR012338;product=hypothetical protein;protein_id=EDO10886.1;transl_table=11;translation=length.738
AAXF02000051	GenBank	exon	9949	12165	.	-	1	Parent=BACOVA_03519.t01
AAXF02000051	GenBank	gene	12363	14216	.	-	1	ID=BACOVA_03520;Name=BACOVA_03520
AAXF02000051	GenBank	mRNA	12363	14216	.	-	1	ID=BACOVA_03520.t01;Parent=BACOVA_03520
AAXF02000051	GenBank	CDS	12363	14216	.	-	1	ID=BACOVA_03520.p01;Parent=BACOVA_03520.t01;Dbxref=InterPro:IPR006047,InterPro:IPR006589,InterPro:IPR013780,InterPro:IPR013781;Name=BACOVA_03520;Note=KEGG: sru:SRU_2409 3.5e-129 glycosyl hydrolase%2C family 13%2C putative K00701%3B COG: COG0366 Glycosidases;codon_start=1;inference=protein motif:Gene3D:IPR013780,protein motif:Gene3D:IPR013781,protein motif:HMMPfam:IPR006047,protein motif:HMMSmart:IPR006589;product=alpha amylase%2C catalytic domain protein;protein_id=EDO10887.1;transl_table=11;translation=length.617
AAXF02000051	GenBank	exon	12363	14216	.	-	1	Parent=BACOVA_03520.t01