##gff-version 3
##sequence-region AAXF02000052 1 25263
# conversion-by bp_genbank2gff3.pl
# organism Bacteroides ovatus ATCC 8483
# Note Bacteroides ovatus ATCC 8483 B_ovatus-MSIQ_Cont580, whole genome shotgun sequence.
# date 04-AUG-2012
AAXF02000052	GenBank	region	1	25263	.	+	1	ID=AAXF02000052;Dbxref=BioProject:PRJNA18191,ATCC:8483,taxon:411476;Name=AAXF02000052;Note=Bacteroides ovatus ATCC 8483 B_ovatus-MSIQ_Cont580%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
AAXF02000052	GenBank	gene	1	162	.	-	1	ID=BACOVA_04094;Name=BACOVA_04094
AAXF02000052	GenBank	mRNA	1	162	.	-	1	ID=BACOVA_04094.t01;Parent=BACOVA_04094
AAXF02000052	GenBank	CDS	1	162	.	-	1	ID=BACOVA_04094.p01;Parent=BACOVA_04094.t01;Dbxref=InterPro:IPR008979;Name=BACOVA_04094;codon_start=1;inference=protein motif:superfamily:IPR008979;product=hypothetical protein;protein_id=EDO10645.1;transl_table=11;translation=length.53
AAXF02000052	GenBank	exon	1	162	.	-	1	Parent=BACOVA_04094.t01
AAXF02000052	GenBank	gene	150	950	.	-	1	ID=BACOVA_04095;Name=BACOVA_04095
AAXF02000052	GenBank	mRNA	150	950	.	-	1	ID=BACOVA_04095.t01;Parent=BACOVA_04095
AAXF02000052	GenBank	CDS	150	950	.	-	1	ID=BACOVA_04095.p01;Parent=BACOVA_04095.t01;Dbxref=InterPro:IPR000421,InterPro:IPR008979;Name=BACOVA_04095;codon_start=1;inference=protein motif:HMMPfam:IPR000421,protein motif:superfamily:IPR008979,similar to AA sequence:REFSEQ:NP_809963.1;product=hypothetical protein;protein_id=EDO10646.1;transl_table=11;translation=length.266
AAXF02000052	GenBank	exon	150	950	.	-	1	Parent=BACOVA_04095.t01
AAXF02000052	GenBank	gene	974	2173	.	-	1	ID=BACOVA_04096;Name=BACOVA_04096
AAXF02000052	GenBank	mRNA	974	2173	.	-	1	ID=BACOVA_04096.t01;Parent=BACOVA_04096
AAXF02000052	GenBank	CDS	974	2173	.	-	1	ID=BACOVA_04096.p01;Parent=BACOVA_04096.t01;Dbxref=InterPro:IPR008985,InterPro:IPR013320,InterPro:IPR013728;Name=BACOVA_04096;Note=COG: NOG29908 non supervised orthologous group;codon_start=1;inference=protein motif:Gene3D:IPR013320,protein motif:HMMPfam:IPR013728,protein motif:superfamily:IPR008985,similar to AA sequence:REFSEQ:NP_809962.1;product=hypothetical protein;protein_id=EDO10647.1;transl_table=11;translation=length.399
AAXF02000052	GenBank	exon	974	2173	.	-	1	Parent=BACOVA_04096.t01
AAXF02000052	GenBank	gene	2182	3321	.	-	1	ID=BACOVA_04097;Name=BACOVA_04097
AAXF02000052	GenBank	mRNA	2182	3321	.	-	1	ID=BACOVA_04097.t01;Parent=BACOVA_04097
AAXF02000052	GenBank	CDS	2182	3321	.	-	1	ID=BACOVA_04097.p01;Parent=BACOVA_04097.t01;Dbxref=InterPro:IPR001579,InterPro:IPR013781;Name=BACOVA_04097;Note=KEGG: spi:MGAS10750_Spy1599 1.6e-05 endoS%3B endo-beta-N-acetylglucosaminidase F2 precursor K01227%3B COG: NOG25511 non supervised orthologous group%3B Psort location: Extracellular%2C score:9.72;codon_start=1;inference=protein motif:Gene3D:IPR013781,protein motif:ScanRegExp:IPR001579,similar to AA sequence:REFSEQ:NP_809961.1;product=hypothetical protein;protein_id=EDO10648.1;transl_table=11;translation=length.379
AAXF02000052	GenBank	exon	2182	3321	.	-	1	Parent=BACOVA_04097.t01
AAXF02000052	GenBank	gene	3349	4899	.	-	1	ID=BACOVA_04098;Name=BACOVA_04098
AAXF02000052	GenBank	mRNA	3349	4899	.	-	1	ID=BACOVA_04098.t01;Parent=BACOVA_04098
AAXF02000052	GenBank	CDS	3349	4899	.	-	1	ID=BACOVA_04098.p01;Parent=BACOVA_04098.t01;Name=BACOVA_04098;Note=COG: NOG26077 non supervised orthologous group;codon_start=1;inference=similar to AA sequence:REFSEQ:NP_809960.1;product=hypothetical protein;protein_id=EDO10649.1;transl_table=11;translation=length.516
AAXF02000052	GenBank	exon	3349	4899	.	-	1	Parent=BACOVA_04098.t01
AAXF02000052	GenBank	gene	4917	8219	.	-	1	ID=BACOVA_04099;Name=BACOVA_04099
AAXF02000052	GenBank	mRNA	4917	8219	.	-	1	ID=BACOVA_04099.t01;Parent=BACOVA_04099
AAXF02000052	GenBank	CDS	4917	8219	.	-	1	ID=BACOVA_04099.p01;Parent=BACOVA_04099.t01;Dbxref=InterPro:IPR000531,InterPro:IPR008969,InterPro:IPR011662,InterPro:IPR012910;Name=BACOVA_04099;Note=COG: NOG26295 non supervised orthologous group;codon_start=1;inference=protein motif:HMMPfam:IPR000531,protein motif:HMMPfam:IPR011662,protein motif:HMMPfam:IPR012910,protein motif:superfamily:IPR008969;product=TonB-linked outer membrane protein%2C SusC/RagA family;protein_id=EDO10650.1;transl_table=11;translation=length.1100
AAXF02000052	GenBank	exon	4917	8219	.	-	1	Parent=BACOVA_04099.t01
AAXF02000052	GenBank	gene	8598	9833	.	+	1	ID=BACOVA_04100;Name=BACOVA_04100
AAXF02000052	GenBank	mRNA	8598	9833	.	+	1	ID=BACOVA_04100.t01;Parent=BACOVA_04100
AAXF02000052	GenBank	CDS	8598	9833	.	+	1	ID=BACOVA_04100.p01;Parent=BACOVA_04100.t01;Dbxref=InterPro:IPR002104,InterPro:IPR010998,InterPro:IPR011010,InterPro:IPR013762;Name=BACOVA_04100;Note=COG: NOG27661 non supervised orthologous group;codon_start=1;inference=protein motif:Gene3D:IPR013762,protein motif:HMMPfam:IPR002104,protein motif:superfamily:IPR010998,protein motif:superfamily:IPR011010,similar to AA sequence:INSD:AAO76148.1;product=site-specific recombinase%2C phage integrase family;protein_id=EDO10651.1;transl_table=11;translation=length.411
AAXF02000052	GenBank	exon	8598	9833	.	+	1	Parent=BACOVA_04100.t01
AAXF02000052	GenBank	gene	9951	10142	.	+	1	ID=BACOVA_04101;Name=BACOVA_04101
AAXF02000052	GenBank	mRNA	9951	10142	.	+	1	ID=BACOVA_04101.t01;Parent=BACOVA_04101
AAXF02000052	GenBank	CDS	9951	10142	.	+	1	ID=BACOVA_04101.p01;Parent=BACOVA_04101.t01;Name=BACOVA_04101;codon_start=1;product=hypothetical protein;protein_id=EDO10652.1;transl_table=11;translation=length.63
AAXF02000052	GenBank	exon	9951	10142	.	+	1	Parent=BACOVA_04101.t01
AAXF02000052	GenBank	gene	10221	10373	.	+	1	ID=BACOVA_04102;Name=BACOVA_04102
AAXF02000052	GenBank	mRNA	10221	10373	.	+	1	ID=BACOVA_04102.t01;Parent=BACOVA_04102
AAXF02000052	GenBank	CDS	10221	10373	.	+	1	ID=BACOVA_04102.p01;Parent=BACOVA_04102.t01;Name=BACOVA_04102;codon_start=1;product=hypothetical protein;protein_id=EDO10653.1;transl_table=11;translation=length.50
AAXF02000052	GenBank	exon	10221	10373	.	+	1	Parent=BACOVA_04102.t01
AAXF02000052	GenBank	gene	10460	13288	.	+	1	ID=BACOVA_04103;Name=BACOVA_04103
AAXF02000052	GenBank	mRNA	10460	13288	.	+	1	ID=BACOVA_04103.t01;Parent=BACOVA_04103
AAXF02000052	GenBank	CDS	10460	13288	.	+	1	ID=BACOVA_04103.p01;Parent=BACOVA_04103.t01;Dbxref=InterPro:IPR000531,InterPro:IPR012910;Name=BACOVA_04103;Note=COG: NOG26295 non supervised orthologous group%3B Psort location: OuterMembrane%2C score:10.00;codon_start=1;inference=protein motif:HMMPfam:IPR000531,protein motif:HMMPfam:IPR012910,similar to AA sequence:INSD:BAD48075.1;product=TonB-linked outer membrane protein%2C SusC/RagA family;protein_id=EDO10654.1;transl_table=11;translation=length.942
AAXF02000052	GenBank	exon	10460	13288	.	+	1	Parent=BACOVA_04103.t01
AAXF02000052	GenBank	gene	13307	14884	.	+	1	ID=BACOVA_04104;Name=BACOVA_04104
AAXF02000052	GenBank	mRNA	13307	14884	.	+	1	ID=BACOVA_04104.t01;Parent=BACOVA_04104
AAXF02000052	GenBank	CDS	13307	14884	.	+	1	ID=BACOVA_04104.p01;Parent=BACOVA_04104.t01;Name=BACOVA_04104;Note=COG: NOG26077 non supervised orthologous group;codon_start=1;inference=similar to AA sequence:REFSEQ:YP_210973.1;product=hypothetical protein;protein_id=EDO10655.1;transl_table=11;translation=length.525
AAXF02000052	GenBank	exon	13307	14884	.	+	1	Parent=BACOVA_04104.t01
AAXF02000052	GenBank	gene	14917	15981	.	+	1	ID=BACOVA_04105;Name=BACOVA_04105
AAXF02000052	GenBank	mRNA	14917	15981	.	+	1	ID=BACOVA_04105.t01;Parent=BACOVA_04105
AAXF02000052	GenBank	CDS	14917	15981	.	+	1	ID=BACOVA_04105.p01;Parent=BACOVA_04105.t01;Dbxref=InterPro:IPR001579,InterPro:IPR013781;Name=BACOVA_04105;Note=KEGG: spz:M5005_Spy_1540 1.0e-09 endoS%3B endo-beta-N-acetylglucosaminidase F2 precursor K01227%3B COG: NOG25511 non supervised orthologous group;codon_start=1;inference=protein motif:Gene3D:IPR013781,protein motif:ScanRegExp:IPR001579,similar to AA sequence:REFSEQ:YP_098611.1;product=hypothetical protein;protein_id=EDO10656.1;transl_table=11;translation=length.354
AAXF02000052	GenBank	exon	14917	15981	.	+	1	Parent=BACOVA_04105.t01
AAXF02000052	GenBank	gene	16004	17215	.	+	1	ID=BACOVA_04106;Name=BACOVA_04106
AAXF02000052	GenBank	mRNA	16004	17215	.	+	1	ID=BACOVA_04106.t01;Parent=BACOVA_04106
AAXF02000052	GenBank	CDS	16004	17215	.	+	1	ID=BACOVA_04106.p01;Parent=BACOVA_04106.t01;Dbxref=InterPro:IPR000530,InterPro:IPR008985,InterPro:IPR013320,InterPro:IPR013728;Name=BACOVA_04106;Note=COG: NOG29908 non supervised orthologous group;codon_start=1;inference=protein motif:Gene3D:IPR013320,protein motif:HMMPfam:IPR013728,protein motif:ScanRegExp:IPR000530,protein motif:superfamily:IPR008985,similar to AA sequence:INSD:BAD48078.1;product=hypothetical protein;protein_id=EDO10657.1;transl_table=11;translation=length.403
AAXF02000052	GenBank	exon	16004	17215	.	+	1	Parent=BACOVA_04106.t01
AAXF02000052	GenBank	gene	17239	18204	.	+	1	ID=BACOVA_04107;Name=BACOVA_04107
AAXF02000052	GenBank	mRNA	17239	18204	.	+	1	ID=BACOVA_04107.t01;Parent=BACOVA_04107
AAXF02000052	GenBank	CDS	17239	18204	.	+	1	ID=BACOVA_04107.p01;Parent=BACOVA_04107.t01;Dbxref=InterPro:IPR000421,InterPro:IPR008979,InterPro:IPR013728;Name=BACOVA_04107;Note=KEGG cpe:CPE1364 6.1e-06 beta-N-acetylhexosaminidase K01207;codon_start=1;inference=protein motif:HMMPfam:IPR000421,protein motif:HMMPfam:IPR013728,protein motif:superfamily:IPR008979,similar to AA sequence:INSD:BAD48079.1;product=F5/8 type C domain protein;protein_id=EDO10658.1;transl_table=11;translation=length.321
AAXF02000052	GenBank	exon	17239	18204	.	+	1	Parent=BACOVA_04107.t01
AAXF02000052	GenBank	gene	18408	20570	.	+	1	ID=BACOVA_04108;Name=BACOVA_04108
AAXF02000052	GenBank	mRNA	18408	20570	.	+	1	ID=BACOVA_04108.t01;Parent=BACOVA_04108
AAXF02000052	GenBank	CDS	18408	20570	.	+	1	ID=BACOVA_04108.p01;Parent=BACOVA_04108.t01;Dbxref=InterPro:IPR000421,InterPro:IPR008979;Name=BACOVA_04108;Note=KEGG: bfs:BF1811 4.3e-14 nahB%3B beta-N-acetylhexosaminidase K01207%3B COG: COG3525 N-acetyl-beta-hexosaminidase;codon_start=1;inference=protein motif:HMMPfam:IPR000421,protein motif:superfamily:IPR008979;product=F5/8 type C domain protein;protein_id=EDO10659.1;transl_table=11;translation=length.720
AAXF02000052	GenBank	exon	18408	20570	.	+	1	Parent=BACOVA_04108.t01
AAXF02000052	GenBank	gene	20669	21997	.	+	1	ID=BACOVA_04109;Name=BACOVA_04109
AAXF02000052	GenBank	mRNA	20669	21997	.	+	1	ID=BACOVA_04109.t01;Parent=BACOVA_04109
AAXF02000052	GenBank	CDS	20669	21997	.	+	1	ID=BACOVA_04109.p01;Parent=BACOVA_04109.t01;Dbxref=InterPro:IPR011701;Name=BACOVA_04109;Note=KEGG: eci:UTI89_C0457 4.4e-19 ampG%3B AmpG muropeptide MFS transporter K08218%3B COG: COG0477 Permeases of the major facilitator superfamily%3B Psort location: CytoplasmicMembrane%2C score:10.00;codon_start=1;inference=protein motif:HMMPfam:IPR011701,similar to AA sequence:REFSEQ:NP_809947.1;product=hypothetical protein;protein_id=EDO10660.1;transl_table=11;translation=length.442
AAXF02000052	GenBank	exon	20669	21997	.	+	1	Parent=BACOVA_04109.t01
AAXF02000052	GenBank	gene	21975	22982	.	+	1	ID=BACOVA_04110;Name=BACOVA_04110
AAXF02000052	GenBank	mRNA	21975	22982	.	+	1	ID=BACOVA_04110.t01;Parent=BACOVA_04110
AAXF02000052	GenBank	CDS	21975	22982	.	+	1	ID=BACOVA_04110.p01;Parent=BACOVA_04110.t01;Dbxref=InterPro:IPR007184;Name=BACOVA_04110;Note=COG: COG2152 Predicted glycosylase;codon_start=1;inference=protein motif:HMMPfam:IPR007184,protein motif:HMMPIR:IPR007184,similar to AA sequence:REFSEQ:NP_809946.1;product=hypothetical protein;protein_id=EDO10661.1;transl_table=11;translation=length.335
AAXF02000052	GenBank	exon	21975	22982	.	+	1	Parent=BACOVA_04110.t01
AAXF02000052	GenBank	gene	22990	25263	.	+	1	ID=BACOVA_04111;Name=BACOVA_04111
AAXF02000052	GenBank	mRNA	22990	25263	.	+	1	ID=BACOVA_04111.t01;Parent=BACOVA_04111
AAXF02000052	GenBank	CDS	22990	25263	.	+	1	ID=BACOVA_04111.p01;Parent=BACOVA_04111.t01;Dbxref=InterPro:IPR005887,InterPro:IPR012939;Name=BACOVA_04111;Note=COG: COG3537 Putative alpha-1%2C2-mannosidase;codon_start=1;inference=protein motif:HMMPfam:IPR012939,protein motif:HMMTigr:IPR005887;product=putative alpha-1%2C2-mannosidase;protein_id=EDO10662.1;transl_table=11;translation=length.757
AAXF02000052	GenBank	exon	22990	25263	.	+	1	Parent=BACOVA_04111.t01