##gff-version 3
##sequence-region DS264579 1 27767
# 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	27767	.	+	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	2244	.	-	1	ID=BACOVA_02644;Name=BACOVA_02644
DS264579	GenBank	mRNA	1	2244	.	-	1	ID=BACOVA_02644.t01;Parent=BACOVA_02644
DS264579	GenBank	CDS	1	2244	.	-	1	ID=BACOVA_02644.p01;Parent=BACOVA_02644.t01;Dbxref=InterPro:IPR001764,InterPro:IPR002772;Name=BACOVA_02644;Note=KEGG: bth:BT3314 8.5e-222 thermostable beta-glucosidase B K05349%3B COG: COG1472 Beta-glucosidase-related glycosidases%3B Psort location: Periplasmic%2C score:9.44;codon_start=1;inference=protein motif:HMMPfam:IPR001764,protein motif:HMMPfam:IPR002772,protein motif:ScanRegExp:IPR001764,similar to AA sequence:INSD:EAM62862.1;product=glycosyl hydrolase family 3 N-terminal domain protein;protein_id=EDO11435.1;transl_table=11;translation=length.747
DS264579	GenBank	exon	1	2244	.	-	1	Parent=BACOVA_02644.t01
DS264579	GenBank	gene	2252	4807	.	-	1	ID=BACOVA_02645;Name=BACOVA_02645
DS264579	GenBank	mRNA	2252	4807	.	-	1	ID=BACOVA_02645.t01;Parent=BACOVA_02645
DS264579	GenBank	CDS	2252	4807	.	-	1	ID=BACOVA_02645.p01;Parent=BACOVA_02645.t01;Dbxref=InterPro:IPR006101,InterPro:IPR006102,InterPro:IPR006103,InterPro:IPR006104,InterPro:IPR008964,InterPro:IPR008979,InterPro:IPR013781,InterPro:IPR013812;Name=BACOVA_02645;Note=KEGG: xcb:XC_4208 3.0e-152 beta-galactosidase K01190%3B COG: COG3250 Beta-galactosidase/beta-glucuronidase;codon_start=1;inference=protein motif:Gene3D:IPR013781,protein motif:Gene3D:IPR013812,protein motif:HMMPfam:IPR006102,protein motif:HMMPfam:IPR006103,protein motif:HMMPfam:IPR006104,protein motif:ScanRegExp:IPR006101,protein motif:superfamily:IPR006102,protein motif:superfamily:IPR008964,protein motif:superfamily:IPR008979,similar to AA sequence:REFSEQ:YP_001193132.1;product=glycosyl hydrolase family 2%2C sugar binding domain protein;protein_id=EDO11436.1;transl_table=11;translation=length.851
DS264579	GenBank	exon	2252	4807	.	-	1	Parent=BACOVA_02645.t01
DS264579	GenBank	gene	4827	7691	.	-	1	ID=BACOVA_02646;Name=BACOVA_02646
DS264579	GenBank	mRNA	4827	7691	.	-	1	ID=BACOVA_02646.t01;Parent=BACOVA_02646
DS264579	GenBank	CDS	4827	7691	.	-	1	ID=BACOVA_02646.p01;Parent=BACOVA_02646.t01;Dbxref=InterPro:IPR000322;eC_number=3.2.1.-;Name=BACOVA_02646;Note=KEGG: aba:Acid345_0898 8.8e-155 alpha-glucosidase K01187%3B COG: COG1501 Alpha-glucosidases%2C family 31 of glycosyl hydrolases;codon_start=1;inference=protein motif:HMMPfam:IPR000322,similar to AA sequence:REFSEQ:NP_637122.2;product=glycosyl hydrolase%2C family 31;protein_id=EDO11437.1;transl_table=11;translation=length.954
DS264579	GenBank	exon	4827	7691	.	-	1	Parent=BACOVA_02646.t01
DS264579	GenBank	gene	7834	11874	.	-	1	ID=BACOVA_02648;Name=BACOVA_02648
DS264579	GenBank	mRNA	7834	11874	.	-	1	ID=BACOVA_02648.t01;Parent=BACOVA_02648
DS264579	GenBank	CDS	7834	11874	.	-	1	ID=BACOVA_02648.p01;Parent=BACOVA_02648.t01;Dbxref=InterPro:IPR000005,InterPro:IPR001789,InterPro:IPR002052,InterPro:IPR003594,InterPro:IPR003661,InterPro:IPR008957,InterPro:IPR009057,InterPro:IPR009082,InterPro:IPR011006,InterPro:IPR011046,InterPro:IPR011110,InterPro:IPR011123,InterPro:IPR012287;Name=BACOVA_02648;Note=KEGG: ava:Ava_2239 7.2e-52 adenylate/guanylate cyclase K01768%3B COG: COG0642 Signal transduction histidine kinase%3B Psort location: CytoplasmicMembrane%2C score:9.97;codon_start=1;inference=protein motif:BlastProDom:IPR001789,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:ScanRegExp:IPR000005,protein motif:ScanRegExp:IPR002052,protein motif:superfamily:IPR003594,protein motif:superfamily:IPR008957,protein motif:superfamily:IPR009057,protein motif:superfamily:IPR009082,protein motif:superfamily:IPR011006,protein motif:superfamily:IPR011046,similar to AA sequence:INSD:ABQ06873.1;product=ATPase/histidine kinase/DNA gyrase B/HSP90 domain protein;protein_id=EDO11439.1;transl_table=11;translation=length.1346
DS264579	GenBank	exon	7834	11874	.	-	1	Parent=BACOVA_02648.t01
DS264579	GenBank	gene	11814	11954	.	+	1	ID=BACOVA_02647;Name=BACOVA_02647
DS264579	GenBank	mRNA	11814	11954	.	+	1	ID=BACOVA_02647.t01;Parent=BACOVA_02647
DS264579	GenBank	CDS	11814	11954	.	+	1	ID=BACOVA_02647.p01;Parent=BACOVA_02647.t01;Name=BACOVA_02647;codon_start=1;product=hypothetical protein;protein_id=EDO11438.1;transl_table=11;translation=length.46
DS264579	GenBank	exon	11814	11954	.	+	1	Parent=BACOVA_02647.t01
DS264579	GenBank	gene	11939	13702	.	-	1	ID=BACOVA_02649;Name=BACOVA_02649
DS264579	GenBank	mRNA	11939	13702	.	-	1	ID=BACOVA_02649.t01;Parent=BACOVA_02649
DS264579	GenBank	CDS	11939	13702	.	-	1	ID=BACOVA_02649.p01;Parent=BACOVA_02649.t01;Dbxref=InterPro:IPR001701,InterPro:IPR004197,InterPro:IPR008928,InterPro:IPR012343,InterPro:IPR013783;Name=BACOVA_02649;Note=KEGG: xcv:XCV2704 7.1e-115 egl4%3B cellulase precursor K01179%3B COG: NOG07884 non supervised orthologous group;codon_start=1;inference=protein motif:Gene3D:IPR012343,protein motif:Gene3D:IPR013783,protein motif:HMMPanther:IPR001701,protein motif:HMMPfam:IPR001701,protein motif:HMMPfam:IPR004197,protein motif:ScanRegExp:IPR001701,protein motif:superfamily:IPR008928,similar to AA sequence:REFSEQ:YP_677892.1;product=N-terminal ig-like domain of cellulase;protein_id=EDO11440.1;transl_table=11;translation=length.587
DS264579	GenBank	exon	11939	13702	.	-	1	Parent=BACOVA_02649.t01
DS264579	GenBank	gene	13769	15238	.	-	1	ID=BACOVA_02650;Name=BACOVA_02650
DS264579	GenBank	mRNA	13769	15238	.	-	1	ID=BACOVA_02650.t01;Parent=BACOVA_02650
DS264579	GenBank	CDS	13769	15238	.	-	1	ID=BACOVA_02650.p01;Parent=BACOVA_02650.t01;Name=BACOVA_02650;Note=COG: COG3209 Rhs family protein;codon_start=1;product=IPT/TIG domain protein;protein_id=EDO11441.1;transl_table=11;translation=length.489
DS264579	GenBank	exon	13769	15238	.	-	1	Parent=BACOVA_02650.t01
DS264579	GenBank	gene	15252	16892	.	-	1	ID=BACOVA_02651;Name=BACOVA_02651
DS264579	GenBank	mRNA	15252	16892	.	-	1	ID=BACOVA_02651.t01;Parent=BACOVA_02651
DS264579	GenBank	CDS	15252	16892	.	-	1	ID=BACOVA_02651.p01;Parent=BACOVA_02651.t01;Dbxref=InterPro:IPR012944;Name=BACOVA_02651;codon_start=1;inference=protein motif:HMMPfam:IPR012944,similar to AA sequence:INSD:ABQ06875.1;product=SusD family protein;protein_id=EDO11442.1;transl_table=11;translation=length.546
DS264579	GenBank	exon	15252	16892	.	-	1	Parent=BACOVA_02651.t01
DS264579	GenBank	gene	16904	20077	.	-	1	ID=BACOVA_02652;Name=BACOVA_02652
DS264579	GenBank	mRNA	16904	20077	.	-	1	ID=BACOVA_02652.t01;Parent=BACOVA_02652
DS264579	GenBank	CDS	16904	20077	.	-	1	ID=BACOVA_02652.p01;Parent=BACOVA_02652.t01;Dbxref=InterPro:IPR000531,InterPro:IPR008969,InterPro:IPR012910;Name=BACOVA_02652;Note=COG: NOG06407 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:superfamily:IPR008969,similar to AA sequence:INSD:AAO78196.1;product=TonB-linked outer membrane protein%2C SusC/RagA family;protein_id=EDO11443.1;transl_table=11;translation=length.1057
DS264579	GenBank	exon	16904	20077	.	-	1	Parent=BACOVA_02652.t01
DS264579	GenBank	gene	20103	21611	.	-	1	ID=BACOVA_02653;Name=BACOVA_02653
DS264579	GenBank	mRNA	20103	21611	.	-	1	ID=BACOVA_02653.t01;Parent=BACOVA_02653
DS264579	GenBank	CDS	20103	21611	.	-	1	ID=BACOVA_02653.p01;Parent=BACOVA_02653.t01;Dbxref=InterPro:IPR001547,InterPro:IPR013781;Name=BACOVA_02653;Note=KEGG: sde:Sde_2636 1.6e-69 DNA mismatch repair protein K01179%3B COG: COG2730 Endoglucanase;codon_start=1;inference=protein motif:Gene3D:IPR013781,protein motif:HMMPfam:IPR001547,similar to AA sequence:REFSEQ:YP_001193127.1;product=cellulase (glycosyl hydrolase family 5);protein_id=EDO11444.1;transl_table=11;translation=length.502
DS264579	GenBank	exon	20103	21611	.	-	1	Parent=BACOVA_02653.t01
DS264579	GenBank	gene	21784	23364	.	-	1	ID=BACOVA_02654;Name=BACOVA_02654
DS264579	GenBank	mRNA	21784	23364	.	-	1	ID=BACOVA_02654.t01;Parent=BACOVA_02654
DS264579	GenBank	CDS	21784	23364	.	-	1	ID=BACOVA_02654.p01;Parent=BACOVA_02654.t01;Dbxref=InterPro:IPR006710;Name=BACOVA_02654;Note=KEGG: bcl:ABC1148 3.5e-106 xylosidase/arabinosidase K01198:K01209%3B COG: COG3507 Beta-xylosidase%3B Psort location: OuterMembrane%2C score:9.49;codon_start=1;inference=protein motif:HMMPanther:IPR006710,protein motif:HMMPfam:IPR006710,similar to AA sequence:INSD:ABC75004.1;product=glycosyl hydrolase%2C family 43;protein_id=EDO11445.1;transl_table=11;translation=length.526
DS264579	GenBank	exon	21784	23364	.	-	1	Parent=BACOVA_02654.t01
DS264579	GenBank	gene	23382	23486	.	-	1	ID=BACOVA_02655;Name=BACOVA_02655
DS264579	GenBank	mRNA	23382	23486	.	-	1	ID=BACOVA_02655.t01;Parent=BACOVA_02655
DS264579	GenBank	CDS	23382	23486	.	-	1	ID=BACOVA_02655.p01;Parent=BACOVA_02655.t01;Name=BACOVA_02655;codon_start=1;product=hypothetical protein;protein_id=EDO11446.1;transl_table=11;translation=length.34
DS264579	GenBank	exon	23382	23486	.	-	1	Parent=BACOVA_02655.t01
DS264579	GenBank	gene	23533	24993	.	-	1	ID=BACOVA_02656;Name=BACOVA_02656
DS264579	GenBank	mRNA	23533	24993	.	-	1	ID=BACOVA_02656.t01;Parent=BACOVA_02656
DS264579	GenBank	CDS	23533	24993	.	-	1	ID=BACOVA_02656.p01;Parent=BACOVA_02656.t01;Dbxref=InterPro:IPR006710;Name=BACOVA_02656;Note=KEGG: oih:OB2087 4.8e-100 arabinofuranosidase K01198:K01209%3B COG: COG3507 Beta-xylosidase;codon_start=1;inference=protein motif:HMMPanther:IPR006710,protein motif:HMMPfam:IPR006710,similar to AA sequence:INSD:CAI78695.1;product=glycosyl hydrolase%2C family 43;protein_id=EDO11447.1;transl_table=11;translation=length.486
DS264579	GenBank	exon	23533	24993	.	-	1	Parent=BACOVA_02656.t01
DS264579	GenBank	gene	25001	25222	.	+	1	ID=BACOVA_02657;Name=BACOVA_02657
DS264579	GenBank	mRNA	25001	25222	.	+	1	ID=BACOVA_02657.t01;Parent=BACOVA_02657
DS264579	GenBank	CDS	25001	25222	.	+	1	ID=BACOVA_02657.p01;Parent=BACOVA_02657.t01;Name=BACOVA_02657;Note=Psort location: Cytoplasmic%2C score:8.96;codon_start=1;product=hypothetical protein;protein_id=EDO11448.1;transl_table=11;translation=length.73
DS264579	GenBank	exon	25001	25222	.	+	1	Parent=BACOVA_02657.t01
DS264579	GenBank	gene	25067	25195	.	-	1	ID=BACOVA_02658;Name=BACOVA_02658
DS264579	GenBank	mRNA	25067	25195	.	-	1	ID=BACOVA_02658.t01;Parent=BACOVA_02658
DS264579	GenBank	CDS	25067	25195	.	-	1	ID=BACOVA_02658.p01;Parent=BACOVA_02658.t01;Name=BACOVA_02658;codon_start=1;product=hypothetical protein;protein_id=EDO11449.1;transl_table=11;translation=length.42
DS264579	GenBank	exon	25067	25195	.	-	1	Parent=BACOVA_02658.t01
DS264579	GenBank	gene	25407	27767	.	+	1	ID=BACOVA_02659;Name=BACOVA_02659
DS264579	GenBank	mRNA	25407	27767	.	+	1	ID=BACOVA_02659.t01;Parent=BACOVA_02659
DS264579	GenBank	CDS	25407	27767	.	+	1	ID=BACOVA_02659.p01;Parent=BACOVA_02659.t01;Dbxref=InterPro:IPR001764,InterPro:IPR002772;Name=BACOVA_02659;Note=KEGG: chu:CHU_3577 1.5e-151 bglX%3B b-glucosidase%2C glycoside hydrolase family 3 protein K01188%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,similar to AA sequence:REFSEQ:YP_001193915.1;product=glycosyl hydrolase family 3 N-terminal domain protein;protein_id=EDO11450.1;transl_table=11;translation=length.786
DS264579	GenBank	exon	25407	27767	.	+	1	Parent=BACOVA_02659.t01