##gff-version 3
##sequence-region DS264579 1 13993
# conversion-by bp_genbank2gff3.pl
# organism Bacteroides ovatus ATCC 8483
# Note Bacteroides ovatus ATCC 8483 Scfld0226 genomic scaffold, whole genome shotgun sequence.
# date 25-MAY-2007
DS264579	GenBank	region	1	13993	.	+	1	ID=DS264579;Dbxref=BioProject:PRJNA18191,ATCC:8483,taxon:411476;Name=DS264579;Note=Bacteroides ovatus ATCC 8483 Scfld0226 genomic scaffold%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 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. ;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 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. ;date=25-MAY-2007;mol_type=genomic DNA;organism=Bacteroides ovatus ATCC 8483;strain=ATCC 8483;type_material=type strain of Bacteroides ovatus
DS264579	GenBank	gene	1	3972	.	+	1	ID=BACOVA_02740;Name=BACOVA_02740
DS264579	GenBank	mRNA	1	3972	.	+	1	ID=BACOVA_02740.t01;Parent=BACOVA_02740
DS264579	GenBank	CDS	1	3972	.	+	1	ID=BACOVA_02740.p01;Parent=BACOVA_02740.t01;Dbxref=InterPro:IPR000005,InterPro:IPR001789,InterPro:IPR003594,InterPro:IPR003661,InterPro:IPR004358,InterPro:IPR009057,InterPro:IPR009082,InterPro:IPR011006,InterPro:IPR011047,InterPro:IPR011110,InterPro:IPR011123,InterPro:IPR012287;Name=BACOVA_02740;Note=KEGG: ana:all4963 4.5e-43 cyaC%3B adenylate cyclase carring two-component hybrid sensor and regulator domains%3B COG: COG3437 Response regulator containing a CheY-like receiver domain and an HD-GYP domain%3B Psort location: CytoplasmicMembrane%2C score:10.00;codon_start=1;inference=protein motif:BlastProDom:IPR001789,protein motif:FPrintScan:IPR000005,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:IPR011110,protein motif:HMMPfam:IPR011123,protein motif:HMMSmart:IPR000005,protein motif:HMMSmart:IPR001789,protein motif:HMMSmart:IPR003594,protein motif:HMMSmart:IPR003661,protein motif:superfamily:IPR003594,protein motif:superfamily:IPR009057,protein motif:superfamily:IPR009082,protein motif:superfamily:IPR011006,protein motif:superfamily:IPR011047,similar to AA sequence:REFSEQ:NP_810647.1;product=response regulator receiver domain protein;protein_id=EDO11531.1;transl_table=11;translation=length.1323
DS264579	GenBank	exon	1	3972	.	+	1	Parent=BACOVA_02740.t01
DS264579	GenBank	gene	4591	5406	.	+	1	ID=BACOVA_02741;Name=BACOVA_02741
DS264579	GenBank	mRNA	4591	5406	.	+	1	ID=BACOVA_02741.t01;Parent=BACOVA_02741
DS264579	GenBank	CDS	4591	5406	.	+	1	ID=BACOVA_02741.p01;Parent=BACOVA_02741.t01;Dbxref=InterPro:IPR000757,InterPro:IPR008985,InterPro:IPR013320;Name=BACOVA_02741;Note=KEGG: saz:Sama_1396 1.9e-24 glucan endo-1%2C3-beta-D-glucosidase K01199%3B COG: COG3291 FOG: PKD repeat%3B Psort location: Extracellular%2C score:9.71;codon_start=1;inference=protein motif:Gene3D:IPR013320,protein motif:HMMPfam:IPR000757,protein motif:superfamily:IPR008985,similar to AA sequence:INSD:BAE48357.1;product=glycosyl hydrolase family 16;protein_id=EDO11532.1;transl_table=11;translation=length.271
DS264579	GenBank	exon	4591	5406	.	+	1	Parent=BACOVA_02741.t01
DS264579	GenBank	gene	5427	8615	.	+	1	ID=BACOVA_02742;Name=BACOVA_02742
DS264579	GenBank	mRNA	5427	8615	.	+	1	ID=BACOVA_02742.t01;Parent=BACOVA_02742
DS264579	GenBank	CDS	5427	8615	.	+	1	ID=BACOVA_02742.p01;Parent=BACOVA_02742.t01;Dbxref=InterPro:IPR000531,InterPro:IPR008969,InterPro:IPR012910;Name=BACOVA_02742;Note=COG: NOG25259 non supervised orthologous group%3B Psort location: OuterMembrane%2C score:10.00;codon_start=1;inference=protein motif:HMMPfam:IPR000531,protein motif:HMMPfam:IPR012910,protein motif:superfamily:IPR008969,similar to AA sequence:REFSEQ:YP_001196880.1;product=TonB-linked outer membrane protein%2C SusC/RagA family;protein_id=EDO11533.1;transl_table=11;translation=length.1062
DS264579	GenBank	exon	5427	8615	.	+	1	Parent=BACOVA_02742.t01
DS264579	GenBank	gene	8627	10303	.	+	1	ID=BACOVA_02743;Name=BACOVA_02743
DS264579	GenBank	mRNA	8627	10303	.	+	1	ID=BACOVA_02743.t01;Parent=BACOVA_02743
DS264579	GenBank	CDS	8627	10303	.	+	1	ID=BACOVA_02743.p01;Parent=BACOVA_02743.t01;Name=BACOVA_02743;Note=COG: NOG26077 non supervised orthologous group;codon_start=1;inference=similar to AA sequence:REFSEQ:YP_001196879.1;product=hypothetical protein;protein_id=EDO11534.1;transl_table=11;translation=length.558
DS264579	GenBank	exon	8627	10303	.	+	1	Parent=BACOVA_02743.t01
DS264579	GenBank	gene	10324	11586	.	+	1	ID=BACOVA_02744;Name=BACOVA_02744
DS264579	GenBank	mRNA	10324	11586	.	+	1	ID=BACOVA_02744.t01;Parent=BACOVA_02744
DS264579	GenBank	CDS	10324	11586	.	+	1	ID=BACOVA_02744.p01;Parent=BACOVA_02744.t01;Name=BACOVA_02744;Note=COG: COG3210 Large exoproteins involved in heme utilization or adhesion;codon_start=1;product=hypothetical protein;protein_id=EDO11535.1;transl_table=11;translation=length.420
DS264579	GenBank	exon	10324	11586	.	+	1	Parent=BACOVA_02744.t01
DS264579	GenBank	gene	11699	13993	.	+	1	ID=BACOVA_02745;Name=BACOVA_02745
DS264579	GenBank	mRNA	11699	13993	.	+	1	ID=BACOVA_02745.t01;Parent=BACOVA_02745
DS264579	GenBank	CDS	11699	13993	.	+	1	ID=BACOVA_02745.p01;Parent=BACOVA_02745.t01;Dbxref=InterPro:IPR001764,InterPro:IPR002772,InterPro:IPR008958;Name=BACOVA_02745;Note=KEGG: chu:CHU_2268 6.0e-157 bglX%3B b-glucosidase%2C glycoside hydrolase family 3 protein K05349%3B COG: COG1472 Beta-glucosidase-related glycosidases%3B Psort location: Periplasmic%2C score:9.76;codon_start=1;inference=protein motif:FPrintScan:IPR001764,protein motif:HMMPfam:IPR001764,protein motif:HMMPfam:IPR002772,protein motif:superfamily:IPR008958,similar to AA sequence:REFSEQ:YP_001193915.1;product=glycosyl hydrolase family 3 N-terminal domain protein;protein_id=EDO11536.1;transl_table=11;translation=length.764
DS264579	GenBank	exon	11699	13993	.	+	1	Parent=BACOVA_02745.t01