##gff-version 3
##sequence-region AAXF02000054 1 22324
# conversion-by bp_genbank2gff3.pl
# organism Bacteroides ovatus ATCC 8483
# Note Bacteroides ovatus ATCC 8483 B_ovatus-MSIQ_Cont457, whole genome shotgun sequence.
# date 04-AUG-2012
AAXF02000054	GenBank	region	1	22324	.	+	1	ID=AAXF02000054;Dbxref=BioProject:PRJNA18191,ATCC:8483,taxon:411476;Name=AAXF02000054;Note=Bacteroides ovatus ATCC 8483 B_ovatus-MSIQ_Cont457%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
AAXF02000054	GenBank	gene	1	1503	.	-	1	ID=BACOVA_04799;Name=BACOVA_04799
AAXF02000054	GenBank	mRNA	1	1503	.	-	1	ID=BACOVA_04799.t01;Parent=BACOVA_04799
AAXF02000054	GenBank	CDS	1	1503	.	-	1	ID=BACOVA_04799.p01;Parent=BACOVA_04799.t01;Dbxref=InterPro:IPR000276;Name=BACOVA_04799;Note=COG: COG2931 RTX toxins and related Ca2+-binding proteins%3B Psort location: OuterMembrane%2C score:9.49;codon_start=1;inference=protein motif:ScanRegExp:IPR000276;product=hypothetical protein;protein_id=EDO08942.1;transl_table=11;translation=length.500
AAXF02000054	GenBank	exon	1	1503	.	-	1	Parent=BACOVA_04799.t01
AAXF02000054	GenBank	gene	1536	2960	.	-	1	ID=BACOVA_04800;Name=BACOVA_04800
AAXF02000054	GenBank	mRNA	1536	2960	.	-	1	ID=BACOVA_04800.t01;Parent=BACOVA_04800
AAXF02000054	GenBank	CDS	1536	2960	.	-	1	ID=BACOVA_04800.p01;Parent=BACOVA_04800.t01;Dbxref=InterPro:IPR001223,InterPro:IPR013781;Name=BACOVA_04800;Note=KEGG: pac:PPA0990 4.7e-18 endo-beta-N-acetylglucosaminidase H K01227%3B COG: NOG09344 non supervised orthologous group%3B Psort location: Extracellular%2C score:9.45;codon_start=1;inference=protein motif:Gene3D:IPR013781,protein motif:HMMPfam:IPR001223,similar to AA sequence:REFSEQ:NP_812898.1;product=putative endo-beta-N-acetylglucosaminidase H;protein_id=EDO08943.1;transl_table=11;translation=length.474
AAXF02000054	GenBank	exon	1536	2960	.	-	1	Parent=BACOVA_04800.t01
AAXF02000054	GenBank	gene	2986	4152	.	-	1	ID=BACOVA_04801;Name=BACOVA_04801
AAXF02000054	GenBank	mRNA	2986	4152	.	-	1	ID=BACOVA_04801.t01;Parent=BACOVA_04801
AAXF02000054	GenBank	CDS	2986	4152	.	-	1	ID=BACOVA_04801.p01;Parent=BACOVA_04801.t01;Dbxref=InterPro:IPR001759,InterPro:IPR008985,InterPro:IPR013320,InterPro:IPR013728;Name=BACOVA_04801;codon_start=1;inference=protein motif:BlastProDom:IPR001759,protein motif:Gene3D:IPR013320,protein motif:HMMPfam:IPR013728,protein motif:superfamily:IPR008985,similar to AA sequence:REFSEQ:NP_812897.1;product=hypothetical protein;protein_id=EDO08944.1;transl_table=11;translation=length.388
AAXF02000054	GenBank	exon	2986	4152	.	-	1	Parent=BACOVA_04801.t01
AAXF02000054	GenBank	gene	4164	5249	.	-	1	ID=BACOVA_04802;Name=BACOVA_04802
AAXF02000054	GenBank	mRNA	4164	5249	.	-	1	ID=BACOVA_04802.t01;Parent=BACOVA_04802
AAXF02000054	GenBank	CDS	4164	5249	.	-	1	ID=BACOVA_04802.p01;Parent=BACOVA_04802.t01;Name=BACOVA_04802;codon_start=1;inference=similar to AA sequence:REFSEQ:NP_812896.1;product=hypothetical protein;protein_id=EDO08945.1;transl_table=11;translation=length.361
AAXF02000054	GenBank	exon	4164	5249	.	-	1	Parent=BACOVA_04802.t01
AAXF02000054	GenBank	gene	5349	6971	.	-	1	ID=BACOVA_04803;Name=BACOVA_04803
AAXF02000054	GenBank	mRNA	5349	6971	.	-	1	ID=BACOVA_04803.t01;Parent=BACOVA_04803
AAXF02000054	GenBank	CDS	5349	6971	.	-	1	ID=BACOVA_04803.p01;Parent=BACOVA_04803.t01;Name=BACOVA_04803;Note=COG: NOG11943 non supervised orthologous group;codon_start=1;inference=similar to AA sequence:REFSEQ:NP_810194.1;product=hypothetical protein;protein_id=EDO08946.1;transl_table=11;translation=length.540
AAXF02000054	GenBank	exon	5349	6971	.	-	1	Parent=BACOVA_04803.t01
AAXF02000054	GenBank	gene	6983	10309	.	-	1	ID=BACOVA_04804;Name=BACOVA_04804
AAXF02000054	GenBank	mRNA	6983	10309	.	-	1	ID=BACOVA_04804.t01;Parent=BACOVA_04804
AAXF02000054	GenBank	CDS	6983	10309	.	-	1	ID=BACOVA_04804.p01;Parent=BACOVA_04804.t01;Dbxref=InterPro:IPR000531,InterPro:IPR008969,InterPro:IPR011662,InterPro:IPR012910;Name=BACOVA_04804;Note=COG: NOG26295 non supervised orthologous group%3B Psort location: OuterMembrane%2C score:9.52;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=EDO08947.1;transl_table=11;translation=length.1108
AAXF02000054	GenBank	exon	6983	10309	.	-	1	Parent=BACOVA_04804.t01
AAXF02000054	GenBank	gene	10546	11616	.	+	1	ID=BACOVA_04805;Name=BACOVA_04805
AAXF02000054	GenBank	mRNA	10546	11616	.	+	1	ID=BACOVA_04805.t01;Parent=BACOVA_04805
AAXF02000054	GenBank	CDS	10546	11616	.	+	1	ID=BACOVA_04805.p01;Parent=BACOVA_04805.t01;Name=BACOVA_04805;Note=COG: NOG25511 non supervised orthologous group;codon_start=1;inference=similar to AA sequence:REFSEQ:NP_812896.1;product=hypothetical protein;protein_id=EDO08948.1;transl_table=11;translation=length.356
AAXF02000054	GenBank	exon	10546	11616	.	+	1	Parent=BACOVA_04805.t01
AAXF02000054	GenBank	gene	11626	12786	.	+	1	ID=BACOVA_04806;Name=BACOVA_04806
AAXF02000054	GenBank	mRNA	11626	12786	.	+	1	ID=BACOVA_04806.t01;Parent=BACOVA_04806
AAXF02000054	GenBank	CDS	11626	12786	.	+	1	ID=BACOVA_04806.p01;Parent=BACOVA_04806.t01;Dbxref=InterPro:IPR008985,InterPro:IPR013320,InterPro:IPR013728;Name=BACOVA_04806;codon_start=1;inference=protein motif:Gene3D:IPR013320,protein motif:HMMPfam:IPR013728,protein motif:superfamily:IPR008985,similar to AA sequence:REFSEQ:NP_812897.1;product=hypothetical protein;protein_id=EDO08949.1;transl_table=11;translation=length.386
AAXF02000054	GenBank	exon	11626	12786	.	+	1	Parent=BACOVA_04806.t01
AAXF02000054	GenBank	gene	12813	14240	.	+	1	ID=BACOVA_04807;Name=BACOVA_04807
AAXF02000054	GenBank	mRNA	12813	14240	.	+	1	ID=BACOVA_04807.t01;Parent=BACOVA_04807
AAXF02000054	GenBank	CDS	12813	14240	.	+	1	ID=BACOVA_04807.p01;Parent=BACOVA_04807.t01;Dbxref=InterPro:IPR013728,InterPro:IPR013781;Name=BACOVA_04807;Note=KEGG: pac:PPA0990 3.2e-10 endo-beta-N-acetylglucosaminidase H K01227%3B COG: NOG09344 non supervised orthologous group%3B Psort location: Extracellular%2C score:9.71;codon_start=1;inference=protein motif:Gene3D:IPR013781,protein motif:HMMPfam:IPR013728,similar to AA sequence:REFSEQ:NP_812898.1;product=putative endo-beta-N-acetylglucosaminidase F1;protein_id=EDO08950.1;transl_table=11;translation=length.475
AAXF02000054	GenBank	exon	12813	14240	.	+	1	Parent=BACOVA_04807.t01
AAXF02000054	GenBank	gene	14261	15568	.	+	1	ID=BACOVA_04808;Name=BACOVA_04808
AAXF02000054	GenBank	mRNA	14261	15568	.	+	1	ID=BACOVA_04808.t01;Parent=BACOVA_04808
AAXF02000054	GenBank	CDS	14261	15568	.	+	1	ID=BACOVA_04808.p01;Parent=BACOVA_04808.t01;Dbxref=InterPro:IPR000421,InterPro:IPR008979;Name=BACOVA_04808;Note=Psort location: OuterMembrane%2C score:9.52;codon_start=1;inference=protein motif:HMMPfam:IPR000421,protein motif:superfamily:IPR008979,similar to AA sequence:REFSEQ:NP_812899.1;product=F5/8 type C domain protein;protein_id=EDO08951.1;transl_table=11;translation=length.435
AAXF02000054	GenBank	exon	14261	15568	.	+	1	Parent=BACOVA_04808.t01
AAXF02000054	GenBank	gene	16589	18859	.	-	1	ID=BACOVA_04809;Name=BACOVA_04809
AAXF02000054	GenBank	mRNA	16589	18859	.	-	1	ID=BACOVA_04809.t01;Parent=BACOVA_04809
AAXF02000054	GenBank	CDS	16589	18859	.	-	1	ID=BACOVA_04809.p01;Parent=BACOVA_04809.t01;Dbxref=InterPro:IPR005887,InterPro:IPR008928,InterPro:IPR012939;Name=BACOVA_04809;Note=COG: COG3537 Putative alpha-1%2C2-mannosidase;codon_start=1;inference=protein motif:HMMPfam:IPR012939,protein motif:HMMTigr:IPR005887,protein motif:superfamily:IPR008928;product=putative alpha-1%2C2-mannosidase;protein_id=EDO08952.1;transl_table=11;translation=length.756
AAXF02000054	GenBank	exon	16589	18859	.	-	1	Parent=BACOVA_04809.t01
AAXF02000054	GenBank	gene	18966	21272	.	-	1	ID=BACOVA_04810;Name=BACOVA_04810
AAXF02000054	GenBank	mRNA	18966	21272	.	-	1	ID=BACOVA_04810.t01;Parent=BACOVA_04810
AAXF02000054	GenBank	CDS	18966	21272	.	-	1	ID=BACOVA_04810.p01;Parent=BACOVA_04810.t01;Dbxref=InterPro:IPR005887,InterPro:IPR008972,InterPro:IPR012939;Name=BACOVA_04810;Note=COG: COG3537 Putative alpha-1%2C2-mannosidase;codon_start=1;inference=protein motif:HMMPfam:IPR012939,protein motif:HMMTigr:IPR005887,protein motif:superfamily:IPR008972;product=putative alpha-1%2C2-mannosidase;protein_id=EDO08953.1;transl_table=11;translation=length.768
AAXF02000054	GenBank	exon	18966	21272	.	-	1	Parent=BACOVA_04810.t01
AAXF02000054	GenBank	gene	21317	22324	.	-	1	ID=BACOVA_04811;Name=BACOVA_04811
AAXF02000054	GenBank	mRNA	21317	22324	.	-	1	ID=BACOVA_04811.t01;Parent=BACOVA_04811
AAXF02000054	GenBank	CDS	21317	22324	.	-	1	ID=BACOVA_04811.p01;Parent=BACOVA_04811.t01;Dbxref=InterPro:IPR006860,InterPro:IPR012373;Name=BACOVA_04811;Note=COG: COG3712 Fe2+-dicitrate sensor%2C membrane component;codon_start=1;inference=protein motif:HMMPfam:IPR006860,protein motif:HMMPIR:IPR012373,similar to AA sequence:REFSEQ:NP_812903.1;product=sigma factor regulatory protein%2C FecR/PupR family;protein_id=EDO08954.1;transl_table=11;translation=length.335
AAXF02000054	GenBank	exon	21317	22324	.	-	1	Parent=BACOVA_04811.t01