##gff-version 3
##sequence-region AAXF02000047 1 19005
# conversion-by bp_genbank2gff3.pl
# organism Bacteroides ovatus ATCC 8483
# Note Bacteroides ovatus ATCC 8483 B_ovatus-MSIQ_Cont517, whole genome shotgun sequence.
# date 04-AUG-2012
AAXF02000047	GenBank	region	1	19005	.	+	1	ID=AAXF02000047;Dbxref=BioProject:PRJNA18191,ATCC:8483,taxon:411476;Name=AAXF02000047;Note=Bacteroides ovatus ATCC 8483 B_ovatus-MSIQ_Cont517%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
AAXF02000047	GenBank	gene	1	201	.	-	1	ID=BACOVA_02087;Name=BACOVA_02087
AAXF02000047	GenBank	mRNA	1	201	.	-	1	ID=BACOVA_02087.t01;Parent=BACOVA_02087
AAXF02000047	GenBank	CDS	1	201	.	-	1	ID=BACOVA_02087.p01;Parent=BACOVA_02087.t01;Name=BACOVA_02087;codon_start=1;product=hypothetical protein;protein_id=EDO12197.1;transl_table=11;translation=length.66
AAXF02000047	GenBank	exon	1	201	.	-	1	Parent=BACOVA_02087.t01
AAXF02000047	GenBank	gene	174	1364	.	-	1	ID=BACOVA_02088;Name=BACOVA_02088
AAXF02000047	GenBank	mRNA	174	1364	.	-	1	ID=BACOVA_02088.t01;Parent=BACOVA_02088
AAXF02000047	GenBank	CDS	174	1364	.	-	1	ID=BACOVA_02088.p01;Parent=BACOVA_02088.t01;Dbxref=InterPro:IPR008928,InterPro:IPR010819,InterPro:IPR013330;eC_number=5.1.3.8;Name=BACOVA_02088;Note=KEGG: syn:slr1975 5.6e-20 renin-binding protein K01787%3B COG: COG2942 N-acyl-D-glucosamine 2-epimerase%3B Psort location: Cytoplasmic%2C score:8.96;codon_start=1;inference=protein motif:Gene3D:IPR013330,protein motif:HMMPfam:IPR010819,protein motif:superfamily:IPR008928,similar to AA sequence:REFSEQ:YP_098134.1;product=N-acylglucosamine 2-epimerase;protein_id=EDO12198.1;transl_table=11;translation=length.396
AAXF02000047	GenBank	exon	174	1364	.	-	1	Parent=BACOVA_02088.t01
AAXF02000047	GenBank	gene	1377	2750	.	-	1	ID=BACOVA_02089;Name=BACOVA_02089
AAXF02000047	GenBank	mRNA	1377	2750	.	-	1	ID=BACOVA_02089.t01;Parent=BACOVA_02089
AAXF02000047	GenBank	CDS	1377	2750	.	-	1	ID=BACOVA_02089.p01;Parent=BACOVA_02089.t01;Dbxref=InterPro:IPR001927,InterPro:IPR011701;Name=BACOVA_02089;Note=KEGG: eci:UTI89_C4210 2.1e-74 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:INSD:CAH06519.1;product=transporter%2C major facilitator family protein;protein_id=EDO12199.1;transl_table=11;translation=length.457
AAXF02000047	GenBank	exon	1377	2750	.	-	1	Parent=BACOVA_02089.t01
AAXF02000047	GenBank	gene	2780	3997	.	-	1	ID=BACOVA_02090;Name=BACOVA_02090
AAXF02000047	GenBank	mRNA	2780	3997	.	-	1	ID=BACOVA_02090.t01;Parent=BACOVA_02090
AAXF02000047	GenBank	CDS	2780	3997	.	-	1	ID=BACOVA_02090.p01;Parent=BACOVA_02090.t01;Dbxref=InterPro:IPR007184;Name=BACOVA_02090;Note=COG: COG2152 Predicted glycosylase;codon_start=1;inference=protein motif:HMMPfam:IPR007184,protein motif:HMMPIR:IPR007184,similar to AA sequence:INSD:CAH06518.1;product=hypothetical protein;protein_id=EDO12200.1;transl_table=11;translation=length.405
AAXF02000047	GenBank	exon	2780	3997	.	-	1	Parent=BACOVA_02090.t01
AAXF02000047	GenBank	gene	3994	6204	.	-	1	ID=BACOVA_02091;Name=BACOVA_02091
AAXF02000047	GenBank	mRNA	3994	6204	.	-	1	ID=BACOVA_02091.t01;Parent=BACOVA_02091
AAXF02000047	GenBank	CDS	3994	6204	.	-	1	ID=BACOVA_02091.p01;Parent=BACOVA_02091.t01;Dbxref=InterPro:IPR000111,InterPro:IPR002252;Name=BACOVA_02091;Note=KEGG: bfr:BF0550 7.0e-163 alpha-galactosidase K07407%3B COG: COG3345 Alpha-galactosidase;codon_start=1;inference=protein motif:FPrintScan:IPR002252,protein motif:HMMPfam:IPR000111,similar to AA sequence:INSD:BAD47299.1;product=alpha-galactosidase;protein_id=EDO12201.1;transl_table=11;translation=length.736
AAXF02000047	GenBank	exon	3994	6204	.	-	1	Parent=BACOVA_02091.t01
AAXF02000047	GenBank	gene	6211	7311	.	-	1	ID=BACOVA_02092;Name=BACOVA_02092
AAXF02000047	GenBank	mRNA	6211	7311	.	-	1	ID=BACOVA_02092.t01;Parent=BACOVA_02092
AAXF02000047	GenBank	CDS	6211	7311	.	-	1	ID=BACOVA_02092.p01;Parent=BACOVA_02092.t01;Dbxref=InterPro:IPR000805;Name=BACOVA_02092;Note=KEGG: bfs:BF0771 1.7e-129 manA%3B putative mannosidase K01218%3B COG: COG4124 Beta-mannanase;codon_start=1;inference=protein motif:FPrintScan:IPR000805,protein motif:HMMPfam:IPR000805,similar to AA sequence:REFSEQ:YP_210469.1;product=glycosyl hydrolase family 26;protein_id=EDO12202.1;transl_table=11;translation=length.366
AAXF02000047	GenBank	exon	6211	7311	.	-	1	Parent=BACOVA_02092.t01
AAXF02000047	GenBank	gene	7329	8411	.	-	1	ID=BACOVA_02093;Name=BACOVA_02093
AAXF02000047	GenBank	mRNA	7329	8411	.	-	1	ID=BACOVA_02093.t01;Parent=BACOVA_02093
AAXF02000047	GenBank	CDS	7329	8411	.	-	1	ID=BACOVA_02093.p01;Parent=BACOVA_02093.t01;Dbxref=InterPro:IPR000805;Name=BACOVA_02093;Note=KEGG: sde:Sde_3691 3.3e-46 mannan endo-1%2C4-beta-mannosidase K01218%3B COG: COG4124 Beta-mannanase;codon_start=1;inference=protein motif:FPrintScan:IPR000805,protein motif:HMMPfam:IPR000805,similar to AA sequence:INSD:AAB20175.1;product=glycosyl hydrolase family 26;protein_id=EDO12203.1;transl_table=11;translation=length.360
AAXF02000047	GenBank	exon	7329	8411	.	-	1	Parent=BACOVA_02093.t01
AAXF02000047	GenBank	gene	8431	9564	.	-	1	ID=BACOVA_02094;Name=BACOVA_02094
AAXF02000047	GenBank	mRNA	8431	9564	.	-	1	ID=BACOVA_02094.t01;Parent=BACOVA_02094
AAXF02000047	GenBank	CDS	8431	9564	.	-	1	ID=BACOVA_02094.p01;Parent=BACOVA_02094.t01;Name=BACOVA_02094;codon_start=1;inference=similar to AA sequence:INSD:BAD47586.1;product=hypothetical protein;protein_id=EDO12204.1;transl_table=11;translation=length.377
AAXF02000047	GenBank	exon	8431	9564	.	-	1	Parent=BACOVA_02094.t01
AAXF02000047	GenBank	gene	9657	11468	.	-	1	ID=BACOVA_02095;Name=BACOVA_02095
AAXF02000047	GenBank	mRNA	9657	11468	.	-	1	ID=BACOVA_02095.t01;Parent=BACOVA_02095
AAXF02000047	GenBank	CDS	9657	11468	.	-	1	ID=BACOVA_02095.p01;Parent=BACOVA_02095.t01;Dbxref=InterPro:IPR012944;Name=BACOVA_02095;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=EDO12205.1;transl_table=11;translation=length.603
AAXF02000047	GenBank	exon	9657	11468	.	-	1	Parent=BACOVA_02095.t01
AAXF02000047	GenBank	gene	11495	14743	.	-	1	ID=BACOVA_02096;Name=BACOVA_02096
AAXF02000047	GenBank	mRNA	11495	14743	.	-	1	ID=BACOVA_02096.t01;Parent=BACOVA_02096
AAXF02000047	GenBank	CDS	11495	14743	.	-	1	ID=BACOVA_02096.p01;Parent=BACOVA_02096.t01;Dbxref=InterPro:IPR000531,InterPro:IPR008969,InterPro:IPR012910;Name=BACOVA_02096;Note=COG: NOG26669 non supervised orthologous group;codon_start=1;inference=protein motif:HMMPfam:IPR000531,protein motif:HMMPfam:IPR012910,protein motif:superfamily:IPR008969;product=TonB-linked outer membrane protein%2C SusC/RagA family;protein_id=EDO12206.1;transl_table=11;translation=length.1082
AAXF02000047	GenBank	exon	11495	14743	.	-	1	Parent=BACOVA_02096.t01
AAXF02000047	GenBank	gene	15076	19005	.	+	1	ID=BACOVA_02097;Name=BACOVA_02097
AAXF02000047	GenBank	mRNA	15076	19005	.	+	1	ID=BACOVA_02097.t01;Parent=BACOVA_02097
AAXF02000047	GenBank	CDS	15076	19005	.	+	1	ID=BACOVA_02097.p01;Parent=BACOVA_02097.t01;Dbxref=InterPro:IPR000005,InterPro:IPR001789,InterPro:IPR003594,InterPro:IPR003661,InterPro:IPR004358,InterPro:IPR009057,InterPro:IPR009082,InterPro:IPR011006,InterPro:IPR011123,InterPro:IPR012287;Name=BACOVA_02097;Note=KEGG: ana:all4963 1.6e-47 cyaC%3B adenylate cyclase carring two-component hybrid sensor and regulator domains%3B COG: COG0642 Signal transduction histidine kinase%3B Psort location: CytoplasmicMembrane%2C score:9.82;codon_start=1;inference=protein motif:BlastProDom:IPR001789,protein motif:FPrintScan:IPR004358,protein motif:Gene3D:IPR003594,protein motif:Gene3D:IPR012287,protein motif:HMMPfam:IPR000005,protein motif:HMMPfam:IPR001789,protein motif:HMMPfam:IPR003594,protein motif:HMMPfam:IPR003661,protein motif:HMMPfam:IPR011123,protein motif:HMMSmart:IPR000005,protein motif:HMMSmart:IPR001789,protein motif:HMMSmart:IPR003594,protein motif:HMMSmart:IPR003661,protein motif:ScanRegExp:IPR000005,protein motif:superfamily:IPR003594,protein motif:superfamily:IPR009057,protein motif:superfamily:IPR009082,protein motif:superfamily:IPR011006,similar to AA sequence:REFSEQ:NP_811772.1;product=response regulator receiver domain protein;protein_id=EDO12207.1;transl_table=11;translation=length.1309
AAXF02000047	GenBank	exon	15076	19005	.	+	1	Parent=BACOVA_02097.t01
AAXF02000047	GenBank	gene	18979	19005	.	-	1	ID=BACOVA_02098;Name=BACOVA_02098
AAXF02000047	GenBank	mRNA	18979	19005	.	-	1	ID=BACOVA_02098.t01;Parent=BACOVA_02098
AAXF02000047	GenBank	CDS	18979	19005	.	-	1	ID=BACOVA_02098.p01;Parent=BACOVA_02098.t01;Name=BACOVA_02098;codon_start=1;product=hypothetical protein;protein_id=EDO12208.1;transl_table=11;translation=length.36
AAXF02000047	GenBank	exon	18979	19005	.	-	1	Parent=BACOVA_02098.t01