##gff-version 3
##sequence-region AAXF02000053 1 16169
# conversion-by bp_genbank2gff3.pl
# organism Bacteroides ovatus ATCC 8483
# Note Bacteroides ovatus ATCC 8483 B_ovatus-MSIQ_Cont571, whole genome shotgun sequence.
# date 04-AUG-2012
AAXF02000053	GenBank	region	1	16169	.	+	1	ID=AAXF02000053;Dbxref=BioProject:PRJNA18191,ATCC:8483,taxon:411476;Name=AAXF02000053;Note=Bacteroides ovatus ATCC 8483 B_ovatus-MSIQ_Cont571%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
AAXF02000053	GenBank	gene	1	105	.	-	1	ID=BACOVA_04497;Name=BACOVA_04497
AAXF02000053	GenBank	mRNA	1	105	.	-	1	ID=BACOVA_04497.t01;Parent=BACOVA_04497
AAXF02000053	GenBank	CDS	1	105	.	-	1	ID=BACOVA_04497.p01;Parent=BACOVA_04497.t01;Name=BACOVA_04497;codon_start=1;product=hypothetical protein;protein_id=EDO10116.1;transl_table=11;translation=length.34
AAXF02000053	GenBank	exon	1	105	.	-	1	Parent=BACOVA_04497.t01
AAXF02000053	GenBank	gene	339	1226	.	-	1	ID=BACOVA_04498;Name=BACOVA_04498
AAXF02000053	GenBank	mRNA	339	1226	.	-	1	ID=BACOVA_04498.t01;Parent=BACOVA_04498
AAXF02000053	GenBank	CDS	339	1226	.	-	1	ID=BACOVA_04498.p01;Parent=BACOVA_04498.t01;Dbxref=InterPro:IPR002173,InterPro:IPR011611;Name=BACOVA_04498;Note=KEGG: bth:BT1757 2.2e-150 fructokinase K00847%3B COG: COG0524 Sugar kinases%2C ribokinase family%3B Psort location: Cytoplasmic%2C score:8.96;codon_start=1;inference=protein motif:HMMPfam:IPR011611,protein motif:ScanRegExp:IPR002173,similar to AA sequence:INSD:AAO76864.1;product=kinase%2C PfkB family;protein_id=EDO10117.1;transl_table=11;translation=length.295
AAXF02000053	GenBank	exon	339	1226	.	-	1	Parent=BACOVA_04498.t01
AAXF02000053	GenBank	gene	1262	2428	.	-	1	ID=BACOVA_04500;Name=BACOVA_04500
AAXF02000053	GenBank	mRNA	1262	2428	.	-	1	ID=BACOVA_04500.t01;Parent=BACOVA_04500
AAXF02000053	GenBank	CDS	1262	2428	.	-	1	ID=BACOVA_04500.p01;Parent=BACOVA_04500.t01;Dbxref=InterPro:IPR011701;Name=BACOVA_04500;Note=COG: COG0738 Fucose permease%3B Psort location: CytoplasmicMembrane%2C score:10.00;codon_start=1;inference=protein motif:HMMPfam:IPR011701,similar to AA sequence:REFSEQ:NP_810671.1;product=transporter%2C major facilitator family protein;protein_id=EDO10119.1;transl_table=11;translation=length.388
AAXF02000053	GenBank	exon	1262	2428	.	-	1	Parent=BACOVA_04500.t01
AAXF02000053	GenBank	gene	2428	2541	.	+	1	ID=BACOVA_04499;Name=BACOVA_04499
AAXF02000053	GenBank	mRNA	2428	2541	.	+	1	ID=BACOVA_04499.t01;Parent=BACOVA_04499
AAXF02000053	GenBank	CDS	2428	2541	.	+	1	ID=BACOVA_04499.p01;Parent=BACOVA_04499.t01;Name=BACOVA_04499;codon_start=1;product=hypothetical protein;protein_id=EDO10118.1;transl_table=11;translation=length.37
AAXF02000053	GenBank	exon	2428	2541	.	+	1	Parent=BACOVA_04499.t01
AAXF02000053	GenBank	gene	2988	4835	.	-	1	ID=BACOVA_04501;Name=BACOVA_04501
AAXF02000053	GenBank	mRNA	2988	4835	.	-	1	ID=BACOVA_04501.t01;Parent=BACOVA_04501
AAXF02000053	GenBank	CDS	2988	4835	.	-	1	ID=BACOVA_04501.p01;Parent=BACOVA_04501.t01;Dbxref=InterPro:IPR001362,InterPro:IPR011040,InterPro:IPR013148,InterPro:IPR013189;Name=BACOVA_04501;Note=KEGG: bth:BT1759 5.6e-280 levanase precursor (2%2C6-beta-D-fructofuranosidase) K01238%3B COG: COG1621 Beta-fructosidases (levanase/invertase);codon_start=1;inference=protein motif:HMMPfam:IPR013148,protein motif:HMMPfam:IPR013189,protein motif:HMMSmart:IPR001362,protein motif:ScanRegExp:IPR001362,protein motif:superfamily:IPR011040,similar to AA sequence:REFSEQ:NP_810672.1;product=glycosyl hydrolase family 32;protein_id=EDO10120.1;transl_table=11;translation=length.615
AAXF02000053	GenBank	exon	2988	4835	.	-	1	Parent=BACOVA_04501.t01
AAXF02000053	GenBank	gene	4961	6913	.	-	1	ID=BACOVA_04502;Name=BACOVA_04502
AAXF02000053	GenBank	mRNA	4961	6913	.	-	1	ID=BACOVA_04502.t01;Parent=BACOVA_04502
AAXF02000053	GenBank	CDS	4961	6913	.	-	1	ID=BACOVA_04502.p01;Parent=BACOVA_04502.t01;Dbxref=InterPro:IPR011050,InterPro:IPR012334;Name=BACOVA_04502;Note=KEGG nca:Noca_0068 0.00041 inulin fructotransferase (DFA-I-forming);codon_start=1;inference=protein motif:Gene3D:IPR012334,protein motif:superfamily:IPR011050,similar to AA sequence:INSD:AAG09641.1;product=hypothetical protein;protein_id=EDO10121.1;transl_table=11;translation=length.650
AAXF02000053	GenBank	exon	4961	6913	.	-	1	Parent=BACOVA_04502.t01
AAXF02000053	GenBank	gene	6951	8081	.	-	1	ID=BACOVA_04503;Name=BACOVA_04503
AAXF02000053	GenBank	mRNA	6951	8081	.	-	1	ID=BACOVA_04503.t01;Parent=BACOVA_04503
AAXF02000053	GenBank	CDS	6951	8081	.	-	1	ID=BACOVA_04503.p01;Parent=BACOVA_04503.t01;Dbxref=InterPro:IPR011050,InterPro:IPR012334;Name=BACOVA_04503;Note=KEGG: art:Arth_0051 6.5e-09 inulin fructotransferase (DFA-I-forming)%3B COG: NOG23229 non supervised orthologous group;codon_start=1;inference=protein motif:Gene3D:IPR012334,protein motif:superfamily:IPR011050,similar to AA sequence:INSD:BAA18967.1;product=hypothetical protein;protein_id=EDO10122.1;transl_table=11;translation=length.376
AAXF02000053	GenBank	exon	6951	8081	.	-	1	Parent=BACOVA_04503.t01
AAXF02000053	GenBank	gene	8104	9861	.	-	1	ID=BACOVA_04504;Name=BACOVA_04504
AAXF02000053	GenBank	mRNA	8104	9861	.	-	1	ID=BACOVA_04504.t01;Parent=BACOVA_04504
AAXF02000053	GenBank	CDS	8104	9861	.	-	1	ID=BACOVA_04504.p01;Parent=BACOVA_04504.t01;Dbxref=InterPro:IPR012944;Name=BACOVA_04504;Note=COG: NOG27574 non supervised orthologous group;codon_start=1;inference=protein motif:HMMPfam:IPR012944,similar to AA sequence:REFSEQ:YP_860092.1;product=SusD family protein;protein_id=EDO10123.1;transl_table=11;translation=length.585
AAXF02000053	GenBank	exon	8104	9861	.	-	1	Parent=BACOVA_04504.t01
AAXF02000053	GenBank	gene	9886	12969	.	-	1	ID=BACOVA_04505;Name=BACOVA_04505
AAXF02000053	GenBank	mRNA	9886	12969	.	-	1	ID=BACOVA_04505.t01;Parent=BACOVA_04505
AAXF02000053	GenBank	CDS	9886	12969	.	-	1	ID=BACOVA_04505.p01;Parent=BACOVA_04505.t01;Dbxref=InterPro:IPR000531,InterPro:IPR002048,InterPro:IPR008969,InterPro:IPR012910;Name=BACOVA_04505;Note=COG: NOG24971 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:ScanRegExp:IPR002048,protein motif:superfamily:IPR008969,similar to AA sequence:REFSEQ:YP_101798.1;product=TonB-linked outer membrane protein%2C SusC/RagA family;protein_id=EDO10124.1;transl_table=11;translation=length.1027
AAXF02000053	GenBank	exon	9886	12969	.	-	1	Parent=BACOVA_04505.t01
AAXF02000053	GenBank	gene	13246	14118	.	+	1	ID=BACOVA_04506;Name=BACOVA_04506
AAXF02000053	GenBank	mRNA	13246	14118	.	+	1	ID=BACOVA_04506.t01;Parent=BACOVA_04506
AAXF02000053	GenBank	CDS	13246	14118	.	+	1	ID=BACOVA_04506.p01;Parent=BACOVA_04506.t01;Dbxref=InterPro:IPR008183,InterPro:IPR011013;Name=BACOVA_04506;Note=KEGG: ldb:Ldb1268 3.5e-42 putative mutarotase K01785%3B COG: COG2017 Galactose mutarotase and related enzymes;codon_start=1;inference=protein motif:HMMPfam:IPR008183,protein motif:superfamily:IPR011013,similar to AA sequence:REFSEQ:NP_810677.1;product=aldose 1-epimerase;protein_id=EDO10125.1;transl_table=11;translation=length.290
AAXF02000053	GenBank	exon	13246	14118	.	+	1	Parent=BACOVA_04506.t01
AAXF02000053	GenBank	gene	14289	16169	.	-	1	ID=BACOVA_04507;Name=BACOVA_04507
AAXF02000053	GenBank	mRNA	14289	16169	.	-	1	ID=BACOVA_04507.t01;Parent=BACOVA_04507
AAXF02000053	GenBank	CDS	14289	16169	.	-	1	ID=BACOVA_04507.p01;Parent=BACOVA_04507.t01;Dbxref=InterPro:IPR001362,InterPro:IPR011040,InterPro:IPR013148,InterPro:IPR013189;Name=BACOVA_04507;Note=KEGG: bth:BT1765 0. levanase precursor (2%2C6-beta-D-fructofuranosidase) K01238%3B COG: COG1621 Beta-fructosidases (levanase/invertase)%3B Psort location: Cytoplasmic%2C score:9.26;codon_start=1;inference=protein motif:HMMPfam:IPR013148,protein motif:HMMPfam:IPR013189,protein motif:HMMSmart:IPR001362,protein motif:superfamily:IPR011040;product=glycosyl hydrolase family 32;protein_id=EDO10126.1;transl_table=11;translation=length.626
AAXF02000053	GenBank	exon	14289	16169	.	-	1	Parent=BACOVA_04507.t01