##gff-version 3
##sequence-region AAXF02000049 1 18777
# conversion-by bp_genbank2gff3.pl
# organism Bacteroides ovatus ATCC 8483
# Note Bacteroides ovatus ATCC 8483 B_ovatus-MSIQ_Cont503, whole genome shotgun sequence.
# date 04-AUG-2012
AAXF02000049	GenBank	region	1	18777	.	+	1	ID=AAXF02000049;Dbxref=BioProject:PRJNA18191,ATCC:8483,taxon:411476;Name=AAXF02000049;Note=Bacteroides ovatus ATCC 8483 B_ovatus-MSIQ_Cont503%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
AAXF02000049	GenBank	gene	1	984	.	+	1	ID=BACOVA_02626;Name=BACOVA_02626
AAXF02000049	GenBank	mRNA	1	984	.	+	1	ID=BACOVA_02626.t01;Parent=BACOVA_02626
AAXF02000049	GenBank	CDS	1	984	.	+	1	ID=BACOVA_02626.p01;Parent=BACOVA_02626.t01;Dbxref=InterPro:IPR001547,InterPro:IPR005829,InterPro:IPR013781;Name=BACOVA_02626;Note=KEGG: chu:CHU_2103 1.4e-70 cel%3B endoglucanase%2C glycoside hydrolase family 5 protein K01179%3B COG: COG2730 Endoglucanase;codon_start=1;inference=protein motif:Gene3D:IPR013781,protein motif:HMMPfam:IPR001547,protein motif:ScanRegExp:IPR005829,similar to AA sequence:INSD:CAJ19149.1;product=cellulase (glycosyl hydrolase family 5);protein_id=EDO11417.1;transl_table=11;translation=length.327
AAXF02000049	GenBank	exon	1	984	.	+	1	Parent=BACOVA_02626.t01
AAXF02000049	GenBank	gene	1104	4355	.	+	1	ID=BACOVA_02627;Name=BACOVA_02627
AAXF02000049	GenBank	mRNA	1104	4355	.	+	1	ID=BACOVA_02627.t01;Parent=BACOVA_02627
AAXF02000049	GenBank	CDS	1104	4355	.	+	1	ID=BACOVA_02627.p01;Parent=BACOVA_02627.t01;Dbxref=InterPro:IPR000531,InterPro:IPR001005,InterPro:IPR008969,InterPro:IPR012910;Name=BACOVA_02627;Note=COG: NOG26669 non supervised orthologous group;codon_start=1;inference=protein motif:HMMPfam:IPR000531,protein motif:HMMPfam:IPR012910,protein motif:ScanRegExp:IPR001005,protein motif:superfamily:IPR008969,similar to AA sequence:REFSEQ:YP_210458.1;product=TonB-linked outer membrane protein%2C SusC/RagA family;protein_id=EDO11418.1;transl_table=11;translation=length.1083
AAXF02000049	GenBank	exon	1104	4355	.	+	1	Parent=BACOVA_02627.t01
AAXF02000049	GenBank	gene	4365	6131	.	+	1	ID=BACOVA_02628;Name=BACOVA_02628
AAXF02000049	GenBank	mRNA	4365	6131	.	+	1	ID=BACOVA_02628.t01;Parent=BACOVA_02628
AAXF02000049	GenBank	CDS	4365	6131	.	+	1	ID=BACOVA_02628.p01;Parent=BACOVA_02628.t01;Dbxref=InterPro:IPR012944;Name=BACOVA_02628;Note=COG: NOG31573 non supervised orthologous group;codon_start=1;inference=protein motif:HMMPfam:IPR012944,similar to AA sequence:INSD:BAD47585.1;product=SusD family protein;protein_id=EDO11419.1;transl_table=11;translation=length.588
AAXF02000049	GenBank	exon	4365	6131	.	+	1	Parent=BACOVA_02628.t01
AAXF02000049	GenBank	gene	6161	7333	.	+	1	ID=BACOVA_02629;Name=BACOVA_02629
AAXF02000049	GenBank	mRNA	6161	7333	.	+	1	ID=BACOVA_02629.t01;Parent=BACOVA_02629
AAXF02000049	GenBank	CDS	6161	7333	.	+	1	ID=BACOVA_02629.p01;Parent=BACOVA_02629.t01;Name=BACOVA_02629;codon_start=1;inference=similar to AA sequence:INSD:BAD47586.1;product=hypothetical protein;protein_id=EDO11420.1;transl_table=11;translation=length.390
AAXF02000049	GenBank	exon	6161	7333	.	+	1	Parent=BACOVA_02629.t01
AAXF02000049	GenBank	gene	7393	8478	.	+	1	ID=BACOVA_02630;Name=BACOVA_02630
AAXF02000049	GenBank	mRNA	7393	8478	.	+	1	ID=BACOVA_02630.t01;Parent=BACOVA_02630
AAXF02000049	GenBank	CDS	7393	8478	.	+	1	ID=BACOVA_02630.p01;Parent=BACOVA_02630.t01;Dbxref=InterPro:IPR001547,InterPro:IPR013781;Name=BACOVA_02630;Note=KEGG: xcb:XC_0028 3.3e-53 cellulase K01179%3B COG: COG2730 Endoglucanase;codon_start=1;inference=protein motif:Gene3D:IPR013781,protein motif:HMMPfam:IPR001547,similar to AA sequence:INSD:ABP79150.1;product=cellulase (glycosyl hydrolase family 5);protein_id=EDO11421.1;transl_table=11;translation=length.361
AAXF02000049	GenBank	exon	7393	8478	.	+	1	Parent=BACOVA_02630.t01
AAXF02000049	GenBank	gene	8545	11067	.	+	1	ID=BACOVA_02631;Name=BACOVA_02631
AAXF02000049	GenBank	mRNA	8545	11067	.	+	1	ID=BACOVA_02631.t01;Parent=BACOVA_02631
AAXF02000049	GenBank	CDS	8545	11067	.	+	1	ID=BACOVA_02631.p01;Parent=BACOVA_02631.t01;Dbxref=InterPro:IPR006101,InterPro:IPR006102,InterPro:IPR006103,InterPro:IPR006104,InterPro:IPR008979,InterPro:IPR013781,InterPro:IPR013812;Name=BACOVA_02631;Note=KEGG: bfr:BF1733 7.9e-68 beta-mannosidase K01192%3B COG: COG3250 Beta-galactosidase/beta-glucuronidase;codon_start=1;inference=protein motif:FPrintScan:IPR006101,protein motif:Gene3D:IPR013781,protein motif:Gene3D:IPR013812,protein motif:HMMPfam:IPR006103,protein motif:HMMPfam:IPR006104,protein motif:ScanRegExp:IPR006101,protein motif:superfamily:IPR006102,protein motif:superfamily:IPR008979,similar to AA sequence:INSD:BAC56899.2;product=glycosyl hydrolase family 2%2C sugar binding domain protein;protein_id=EDO11422.1;transl_table=11;translation=length.840
AAXF02000049	GenBank	exon	8545	11067	.	+	1	Parent=BACOVA_02631.t01
AAXF02000049	GenBank	gene	11078	12118	.	+	1	ID=BACOVA_02632;Name=BACOVA_02632
AAXF02000049	GenBank	mRNA	11078	12118	.	+	1	ID=BACOVA_02632.t01;Parent=BACOVA_02632
AAXF02000049	GenBank	CDS	11078	12118	.	+	1	ID=BACOVA_02632.p01;Parent=BACOVA_02632.t01;Dbxref=InterPro:IPR001547,InterPro:IPR013781;Name=BACOVA_02632;Note=KEGG: xoo:XOO0281 8.1e-59 egl%3B cellulase K01179%3B COG: COG2730 Endoglucanase;codon_start=1;inference=protein motif:Gene3D:IPR013781,protein motif:HMMPfam:IPR001547,similar to AA sequence:INSD:ABP79150.1;product=cellulase (glycosyl hydrolase family 5);protein_id=EDO11423.1;transl_table=11;translation=length.346
AAXF02000049	GenBank	exon	11078	12118	.	+	1	Parent=BACOVA_02632.t01
AAXF02000049	GenBank	gene	12159	13484	.	+	1	ID=BACOVA_02633;Name=BACOVA_02633
AAXF02000049	GenBank	mRNA	12159	13484	.	+	1	ID=BACOVA_02633.t01;Parent=BACOVA_02633
AAXF02000049	GenBank	CDS	12159	13484	.	+	1	ID=BACOVA_02633.p01;Parent=BACOVA_02633.t01;Dbxref=InterPro:IPR013781;Name=BACOVA_02633;Note=COG: NOG16715 non supervised orthologous group;codon_start=1;inference=protein motif:Gene3D:IPR013781,similar to AA sequence:INSD:ABQ90194.1;product=hypothetical protein;protein_id=EDO11424.1;transl_table=11;translation=length.441
AAXF02000049	GenBank	exon	12159	13484	.	+	1	Parent=BACOVA_02633.t01
AAXF02000049	GenBank	gene	13511	14680	.	+	1	ID=BACOVA_02634;Name=BACOVA_02634
AAXF02000049	GenBank	mRNA	13511	14680	.	+	1	ID=BACOVA_02634.t01;Parent=BACOVA_02634
AAXF02000049	GenBank	CDS	13511	14680	.	+	1	ID=BACOVA_02634.p01;Parent=BACOVA_02634.t01;Dbxref=InterPro:IPR007184;Name=BACOVA_02634;Note=COG: COG2152 Predicted glycosylase%3B Psort location: Cytoplasmic%2C score:8.96;codon_start=1;inference=protein motif:HMMPfam:IPR007184,protein motif:HMMPIR:IPR007184,similar to AA sequence:INSD:BAD47598.1;product=hypothetical protein;protein_id=EDO11425.1;transl_table=11;translation=length.389
AAXF02000049	GenBank	exon	13511	14680	.	+	1	Parent=BACOVA_02634.t01
AAXF02000049	GenBank	gene	14691	16085	.	+	1	ID=BACOVA_02635;Name=BACOVA_02635
AAXF02000049	GenBank	mRNA	14691	16085	.	+	1	ID=BACOVA_02635.t01;Parent=BACOVA_02635
AAXF02000049	GenBank	CDS	14691	16085	.	+	1	ID=BACOVA_02635.p01;Parent=BACOVA_02635.t01;Dbxref=InterPro:IPR001927,InterPro:IPR011701;Name=BACOVA_02635;Note=KEGG: eci:UTI89_C4210 6.2e-68 yicJ%3B hypothetical symporter YicJ K03292%3B COG: COG2211 Na+/melibiose symporter and related transporters%3B Psort location: CytoplasmicMembrane%2C score:10.00;codon_start=1;inference=protein motif:HMMPfam:IPR011701,protein motif:HMMTigr:IPR001927,similar to AA sequence:REFSEQ:YP_001197272.1;product=transporter%2C major facilitator family protein;protein_id=EDO11426.1;transl_table=11;translation=length.464
AAXF02000049	GenBank	exon	14691	16085	.	+	1	Parent=BACOVA_02635.t01
AAXF02000049	GenBank	gene	16030	18777	.	+	1	ID=BACOVA_02636;Name=BACOVA_02636
AAXF02000049	GenBank	mRNA	16030	18777	.	+	1	ID=BACOVA_02636.t01;Parent=BACOVA_02636
AAXF02000049	GenBank	CDS	16030	18777	.	+	1	ID=BACOVA_02636.p01;Parent=BACOVA_02636.t01;Dbxref=InterPro:IPR008902,InterPro:IPR008928,InterPro:IPR008957,InterPro:IPR008979,InterPro:IPR013737;Name=BACOVA_02636;Note=KEGG: bcz:BCZK2019 1.4e-107 ramA%3B alfa-L-rhamnosidase%3B COG: NOG04002 non supervised orthologous group;codon_start=1;inference=protein motif:HMMPfam:IPR008902,protein motif:HMMPfam:IPR013737,protein motif:HMMPIR:IPR008902,protein motif:superfamily:IPR008928,protein motif:superfamily:IPR008957,protein motif:superfamily:IPR008979,similar to AA sequence:INSD:AAO77631.1;product=Alpha-L-rhamnosidase N-terminal domain protein;protein_id=EDO11427.1;transl_table=11;translation=length.915
AAXF02000049	GenBank	exon	16030	18777	.	+	1	Parent=BACOVA_02636.t01