##gff-version 3
##sequence-region DS264583 1 20932
# conversion-by bp_genbank2gff3.pl
# organism Bacteroides ovatus ATCC 8483
# Note Bacteroides ovatus ATCC 8483 Scfld0230 genomic scaffold, whole genome shotgun sequence.
# date 25-MAY-2007
DS264583	GenBank	region	1	20932	.	+	1	ID=DS264583;Dbxref=BioProject:PRJNA18191,ATCC:8483,taxon:411476;Name=DS264583;Note=Bacteroides ovatus ATCC 8483 Scfld0230 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
DS264583	GenBank	gene	1	19	.	+	1	ID=BACOVA_04384;Name=BACOVA_04384
DS264583	GenBank	mRNA	1	19	.	+	1	ID=BACOVA_04384.t01;Parent=BACOVA_04384
DS264583	GenBank	CDS	1	19	.	+	1	ID=BACOVA_04384.p01;Parent=BACOVA_04384.t01;Name=BACOVA_04384;codon_start=3;product=hypothetical protein;protein_id=EDO10004.1;transl_table=11;translation=length.44
DS264583	GenBank	exon	1	19	.	+	1	Parent=BACOVA_04384.t01
DS264583	GenBank	gene	1	2136	.	-	1	ID=BACOVA_04385;Name=BACOVA_04385
DS264583	GenBank	mRNA	1	2136	.	-	1	ID=BACOVA_04385.t01;Parent=BACOVA_04385
DS264583	GenBank	CDS	1	2136	.	-	1	ID=BACOVA_04385.p01;Parent=BACOVA_04385.t01;Dbxref=InterPro:IPR005154,InterPro:IPR011099,InterPro:IPR011100;Name=BACOVA_04385;Note=KEGG: xcc:XCC4102 5.8e-191 aguA%3B alpha-glucuronidase K01235%3B COG: COG3661 Alpha-glucuronidase;codon_start=1;inference=protein motif:HMMPfam:IPR005154,protein motif:HMMPfam:IPR011099,protein motif:HMMPfam:IPR011100,similar to AA sequence:INSD:ABQ05025.1;product=glycosyl hydrolase family 67 middle domain protein;protein_id=EDO10005.1;transl_table=11;translation=length.711
DS264583	GenBank	exon	1	2136	.	-	1	Parent=BACOVA_04385.t01
DS264583	GenBank	gene	2302	3279	.	-	1	ID=BACOVA_04386;Name=BACOVA_04386
DS264583	GenBank	mRNA	2302	3279	.	-	1	ID=BACOVA_04386.t01;Parent=BACOVA_04386
DS264583	GenBank	CDS	2302	3279	.	-	1	ID=BACOVA_04386.p01;Parent=BACOVA_04386.t01;Dbxref=InterPro:IPR006710;Name=BACOVA_04386;Note=KEGG: sde:Sde_0822 1.8e-109 alpha-L-arabinofuranosidase K01209%3B COG: NOG06229 non supervised orthologous group;codon_start=1;inference=protein motif:HMMPanther:IPR006710,protein motif:HMMPfam:IPR006710,similar to AA sequence:SwissProt:P49943;product=glycosyl hydrolase%2C family 43;protein_id=EDO10006.1;transl_table=11;translation=length.325
DS264583	GenBank	exon	2302	3279	.	-	1	Parent=BACOVA_04386.t01
DS264583	GenBank	gene	3306	4436	.	-	1	ID=BACOVA_04387;Name=BACOVA_04387
DS264583	GenBank	mRNA	3306	4436	.	-	1	ID=BACOVA_04387.t01;Parent=BACOVA_04387
DS264583	GenBank	CDS	3306	4436	.	-	1	ID=BACOVA_04387.p01;Parent=BACOVA_04387.t01;Dbxref=InterPro:IPR001000,InterPro:IPR013781;Name=BACOVA_04387;Note=KEGG: sus:Acid_2681 1.1e-88 endo-1%2C4-beta-xylanase K01181%3B COG: COG3693 Beta-1%2C4-xylanase;codon_start=1;inference=protein motif:Gene3D:IPR013781,protein motif:HMMPfam:IPR001000,protein motif:HMMSmart:IPR001000,protein motif:ScanRegExp:IPR001000,similar to AA sequence:SwissProt:P49942;product=glycosyl hydrolase family 10;protein_id=EDO10007.1;transl_table=11;translation=length.376
DS264583	GenBank	exon	3306	4436	.	-	1	Parent=BACOVA_04387.t01
DS264583	GenBank	gene	4476	5891	.	-	1	ID=BACOVA_04388;Name=gph;locus_tag=BACOVA_04388
DS264583	GenBank	mRNA	4476	5891	.	-	1	ID=BACOVA_04388.t01;Parent=BACOVA_04388
DS264583	GenBank	CDS	4476	5891	.	-	1	ID=BACOVA_04388.p01;Parent=BACOVA_04388.t01;Dbxref=InterPro:IPR001927,InterPro:IPR011701;Name=gph;Note=KEGG: eci:UTI89_C4210 2.5e-48 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:AAB08022.1;locus_tag=BACOVA_04388;product=glycoside/pentoside/hexuronide transporter;protein_id=EDO10008.1;transl_table=11;translation=length.471
DS264583	GenBank	exon	4476	5891	.	-	1	Parent=BACOVA_04388.t01
DS264583	GenBank	gene	5908	7686	.	-	1	ID=BACOVA_04389;Name=BACOVA_04389
DS264583	GenBank	mRNA	5908	7686	.	-	1	ID=BACOVA_04389.t01;Parent=BACOVA_04389
DS264583	GenBank	CDS	5908	7686	.	-	1	ID=BACOVA_04389.p01;Parent=BACOVA_04389.t01;Dbxref=InterPro:IPR005181,InterPro:IPR006104,InterPro:IPR008979;Name=BACOVA_04389;Note=KEGG: xac:XAC1771 2.0e-78 sialic acid-specific 9-O-acetylesterase%3B COG: NOG04984 non supervised orthologous group;codon_start=1;inference=protein motif:HMMPfam:IPR005181,protein motif:HMMPfam:IPR006104,protein motif:superfamily:IPR008979,similar to AA sequence:INSD:BAD80890.1;product=glycosyl hydrolase family 2%2C sugar binding domain protein;protein_id=EDO10009.1;transl_table=11;translation=length.592
DS264583	GenBank	exon	5908	7686	.	-	1	Parent=BACOVA_04389.t01
DS264583	GenBank	gene	7899	10121	.	-	1	ID=BACOVA_04390;Name=BACOVA_04390
DS264583	GenBank	mRNA	7899	10121	.	-	1	ID=BACOVA_04390.t01;Parent=BACOVA_04390
DS264583	GenBank	CDS	7899	10121	.	-	1	ID=BACOVA_04390.p01;Parent=BACOVA_04390.t01;Dbxref=InterPro:IPR000015,InterPro:IPR001000,InterPro:IPR003305,InterPro:IPR008979,InterPro:IPR013781;Name=BACOVA_04390;Note=KEGG: bha:BH2120 3.2e-28 alkaline xylanase A (1%2C4-beta-D-xylan xylanohydrolase) K01181%3B COG: COG3693 Beta-1%2C4-xylanase%3B Psort location: OuterMembrane%2C score:9.97;codon_start=1;inference=protein motif:Gene3D:IPR013781,protein motif:HMMPfam:IPR001000,protein motif:HMMPfam:IPR003305,protein motif:HMMSmart:IPR001000,protein motif:ScanRegExp:IPR000015,protein motif:ScanRegExp:IPR001000,protein motif:superfamily:IPR008979,similar to AA sequence:INSD:CAB01855.1;product=glycosyl hydrolase family 10;protein_id=EDO10010.1;transl_table=11;translation=length.740
DS264583	GenBank	exon	7899	10121	.	-	1	Parent=BACOVA_04390.t01
DS264583	GenBank	gene	10146	11549	.	-	1	ID=BACOVA_04391;Name=BACOVA_04391
DS264583	GenBank	mRNA	10146	11549	.	-	1	ID=BACOVA_04391.t01;Parent=BACOVA_04391
DS264583	GenBank	CDS	10146	11549	.	-	1	ID=BACOVA_04391.p01;Parent=BACOVA_04391.t01;Name=BACOVA_04391;codon_start=1;inference=similar to AA sequence:REFSEQ:YP_001197267.1;product=hypothetical protein;protein_id=EDO10011.1;transl_table=11;translation=length.467
DS264583	GenBank	exon	10146	11549	.	-	1	Parent=BACOVA_04391.t01
DS264583	GenBank	gene	11564	13210	.	-	1	ID=BACOVA_04392;Name=BACOVA_04392
DS264583	GenBank	mRNA	11564	13210	.	-	1	ID=BACOVA_04392.t01;Parent=BACOVA_04392
DS264583	GenBank	CDS	11564	13210	.	-	1	ID=BACOVA_04392.p01;Parent=BACOVA_04392.t01;Dbxref=InterPro:IPR012944;Name=BACOVA_04392;Note=COG: NOG28394 non supervised orthologous group%3B Psort location: OuterMembrane%2C score:9.52;codon_start=1;inference=protein motif:HMMPfam:IPR012944,similar to AA sequence:INSD:ABQ07949.1;product=SusD family protein;protein_id=EDO10012.1;transl_table=11;translation=length.548
DS264583	GenBank	exon	11564	13210	.	-	1	Parent=BACOVA_04392.t01
DS264583	GenBank	gene	13230	16403	.	-	1	ID=BACOVA_04393;Name=BACOVA_04393
DS264583	GenBank	mRNA	13230	16403	.	-	1	ID=BACOVA_04393.t01;Parent=BACOVA_04393
DS264583	GenBank	CDS	13230	16403	.	-	1	ID=BACOVA_04393.p01;Parent=BACOVA_04393.t01;Dbxref=InterPro:IPR000531,InterPro:IPR008969,InterPro:IPR012910;Name=BACOVA_04393;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:REFSEQ:YP_001197269.1;product=TonB-linked outer membrane protein%2C SusC/RagA family;protein_id=EDO10013.1;transl_table=11;translation=length.1057
DS264583	GenBank	exon	13230	16403	.	-	1	Parent=BACOVA_04393.t01
DS264583	GenBank	gene	16799	20932	.	+	1	ID=BACOVA_04394;Name=BACOVA_04394
DS264583	GenBank	mRNA	16799	20932	.	+	1	ID=BACOVA_04394.t01;Parent=BACOVA_04394
DS264583	GenBank	CDS	16799	20932	.	+	1	ID=BACOVA_04394.p01;Parent=BACOVA_04394.t01;Dbxref=InterPro:IPR000005,InterPro:IPR001789,InterPro:IPR003594,InterPro:IPR003661,InterPro:IPR008957,InterPro:IPR009057,InterPro:IPR009082,InterPro:IPR011006,InterPro:IPR011110,InterPro:IPR011123,InterPro:IPR012287;Name=BACOVA_04394;Note=KEGG: ava:Ava_2239 2.1e-59 adenylate/guanylate cyclase K01768%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: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:superfamily:IPR003594,protein motif:superfamily:IPR008957,protein motif:superfamily:IPR009057,protein motif:superfamily:IPR009082,protein motif:superfamily:IPR011006,similar to AA sequence:REFSEQ:YP_861734.1;product=response regulator receiver domain protein;protein_id=EDO10014.1;transl_table=11;translation=length.1377
DS264583	GenBank	exon	16799	20932	.	+	1	Parent=BACOVA_04394.t01