##gff-version 3
##sequence-region AAXF02000034 1 8973
# conversion-by bp_genbank2gff3.pl
# organism Bacteroides ovatus ATCC 8483
# Note Bacteroides ovatus ATCC 8483 B_ovatus-MSIQ_Cont531, whole genome shotgun sequence.
# date 04-AUG-2012
AAXF02000034	GenBank	region	1	8973	.	+	1	ID=AAXF02000034;Dbxref=BioProject:PRJNA18191,ATCC:8483,taxon:411476;Name=AAXF02000034;Note=Bacteroides ovatus ATCC 8483 B_ovatus-MSIQ_Cont531%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
AAXF02000034	GenBank	gene	1	1731	.	-	1	ID=BACOVA_00557;Name=BACOVA_00557
AAXF02000034	GenBank	mRNA	1	1731	.	-	1	ID=BACOVA_00557.t01;Parent=BACOVA_00557
AAXF02000034	GenBank	CDS	1	1731	.	-	1	ID=BACOVA_00557.p01;Parent=BACOVA_00557.t01;Dbxref=InterPro:IPR012944;Name=BACOVA_00557;Note=COG: NOG26547 non supervised orthologous group;codon_start=1;inference=protein motif:HMMPfam:IPR012944,similar to AA sequence:INSD:AAO75591.1;product=SusD family protein;protein_id=EDO13793.1;transl_table=11;translation=length.576
AAXF02000034	GenBank	exon	1	1731	.	-	1	Parent=BACOVA_00557.t01
AAXF02000034	GenBank	gene	1731	4475	.	-	1	ID=BACOVA_00558;Name=BACOVA_00558
AAXF02000034	GenBank	mRNA	1731	4475	.	-	1	ID=BACOVA_00558.t01;Parent=BACOVA_00558
AAXF02000034	GenBank	CDS	1731	4475	.	-	1	ID=BACOVA_00558.p01;Parent=BACOVA_00558.t01;Dbxref=InterPro:IPR000531,InterPro:IPR012910;Name=BACOVA_00558;Note=COG: NOG26198 non supervised orthologous group%3B Psort location: OuterMembrane%2C score:9.49;codon_start=1;inference=protein motif:HMMPfam:IPR000531,protein motif:HMMPfam:IPR012910;product=TonB-linked outer membrane protein%2C SusC/RagA family;protein_id=EDO13794.1;transl_table=11;translation=length.914
AAXF02000034	GenBank	exon	1731	4475	.	-	1	Parent=BACOVA_00558.t01
AAXF02000034	GenBank	gene	4574	6649	.	-	1	ID=BACOVA_00559;Name=BACOVA_00559
AAXF02000034	GenBank	mRNA	4574	6649	.	-	1	ID=BACOVA_00559.t01;Parent=BACOVA_00559
AAXF02000034	GenBank	CDS	4574	6649	.	-	1	ID=BACOVA_00559.p01;Parent=BACOVA_00559.t01;Dbxref=InterPro:IPR001540,InterPro:IPR008979,InterPro:IPR013781;Name=BACOVA_00559;Note=KEGG: bth:BT0460 0. beta-hexosaminidase precursor K01207%3B COG: COG3525 N-acetyl-beta-hexosaminidase%3B Psort location: Periplasmic%2C score:9.44;codon_start=1;inference=protein motif:Gene3D:IPR013781,protein motif:HMMPfam:IPR001540,protein motif:superfamily:IPR008979;product=glycosyl hydrolase family 20%2C catalytic domain protein;protein_id=EDO13795.1;transl_table=11;translation=length.691
AAXF02000034	GenBank	exon	4574	6649	.	-	1	Parent=BACOVA_00559.t01
AAXF02000034	GenBank	gene	6649	8973	.	-	1	ID=BACOVA_00560;Name=BACOVA_00560
AAXF02000034	GenBank	mRNA	6649	8973	.	-	1	ID=BACOVA_00560.t01;Parent=BACOVA_00560
AAXF02000034	GenBank	CDS	6649	8973	.	-	1	ID=BACOVA_00560.p01;Parent=BACOVA_00560.t01;Dbxref=InterPro:IPR000421,InterPro:IPR001540,InterPro:IPR008979,InterPro:IPR013781;Name=BACOVA_00560;Note=KEGG: bth:BT0459 0. beta-hexosaminidase precursor K01207%3B COG: COG3525 N-acetyl-beta-hexosaminidase%3B Psort location: Periplasmic%2C score:9.76;codon_start=1;inference=protein motif:Gene3D:IPR013781,protein motif:HMMPfam:IPR000421,protein motif:HMMPfam:IPR001540,protein motif:superfamily:IPR008979;product=glycosyl hydrolase family 20%2C catalytic domain protein;protein_id=EDO13796.1;transl_table=11;translation=length.774
AAXF02000034	GenBank	exon	6649	8973	.	-	1	Parent=BACOVA_00560.t01