##gff-version 3
##sequence-region AAXF02000047 1 22100
# 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	22100	.	+	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	1896	.	+	1	ID=BACOVA_02085;Name=BACOVA_02085
AAXF02000047	GenBank	mRNA	1	1896	.	+	1	ID=BACOVA_02085.t01;Parent=BACOVA_02085
AAXF02000047	GenBank	CDS	1	1896	.	+	1	ID=BACOVA_02085.p01;Parent=BACOVA_02085.t01;Dbxref=InterPro:IPR002880,InterPro:IPR009014;Name=BACOVA_02085;Note=KEGG: bth:BT2836 0. korA%3B 2-oxoglutarate synthase subunit korA K00174%3B COG: COG1014 Pyruvate:ferredoxin oxidoreductase and related 2-oxoacid:ferredoxin oxidoreductases%2C gamma subunit;codon_start=1;inference=protein motif:Gene3D:IPR009014,protein motif:HMMPfam:IPR002880,protein motif:superfamily:IPR009014;product=2-oxoacid:acceptor oxidoreductase%2C alpha subunit;protein_id=EDO12195.1;transl_table=11;translation=length.631
AAXF02000047	GenBank	exon	1	1896	.	+	1	Parent=BACOVA_02085.t01
AAXF02000047	GenBank	gene	1900	2910	.	+	1	ID=BACOVA_02086;Name=BACOVA_02086
AAXF02000047	GenBank	mRNA	1900	2910	.	+	1	ID=BACOVA_02086.t01;Parent=BACOVA_02086
AAXF02000047	GenBank	CDS	1900	2910	.	+	1	ID=BACOVA_02086.p01;Parent=BACOVA_02086.t01;Dbxref=InterPro:IPR011766;Name=BACOVA_02086;Note=KEGG: bth:BT2837 1.0e-177 korB%3B 2-oxoglutarate synthase subunit korB K00175%3B COG: COG1013 Pyruvate:ferredoxin oxidoreductase and related 2-oxoacid:ferredoxin oxidoreductases%2C beta subunit%3B Psort location: Cytoplasmic%2C score:8.96;codon_start=1;inference=protein motif:HMMPfam:IPR011766,similar to AA sequence:REFSEQ:NP_811749.1;product=thiamine pyrophosphate enzyme%2C C-terminal TPP binding domain protein;protein_id=EDO12196.1;transl_table=11;translation=length.336
AAXF02000047	GenBank	exon	1900	2910	.	+	1	Parent=BACOVA_02086.t01
AAXF02000047	GenBank	gene	3012	3212	.	-	1	ID=BACOVA_02087;Name=BACOVA_02087
AAXF02000047	GenBank	mRNA	3012	3212	.	-	1	ID=BACOVA_02087.t01;Parent=BACOVA_02087
AAXF02000047	GenBank	CDS	3012	3212	.	-	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	3012	3212	.	-	1	Parent=BACOVA_02087.t01
AAXF02000047	GenBank	gene	3185	4375	.	-	1	ID=BACOVA_02088;Name=BACOVA_02088
AAXF02000047	GenBank	mRNA	3185	4375	.	-	1	ID=BACOVA_02088.t01;Parent=BACOVA_02088
AAXF02000047	GenBank	CDS	3185	4375	.	-	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	3185	4375	.	-	1	Parent=BACOVA_02088.t01
AAXF02000047	GenBank	gene	4388	5761	.	-	1	ID=BACOVA_02089;Name=BACOVA_02089
AAXF02000047	GenBank	mRNA	4388	5761	.	-	1	ID=BACOVA_02089.t01;Parent=BACOVA_02089
AAXF02000047	GenBank	CDS	4388	5761	.	-	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	4388	5761	.	-	1	Parent=BACOVA_02089.t01
AAXF02000047	GenBank	gene	5791	7008	.	-	1	ID=BACOVA_02090;Name=BACOVA_02090
AAXF02000047	GenBank	mRNA	5791	7008	.	-	1	ID=BACOVA_02090.t01;Parent=BACOVA_02090
AAXF02000047	GenBank	CDS	5791	7008	.	-	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	5791	7008	.	-	1	Parent=BACOVA_02090.t01
AAXF02000047	GenBank	gene	7005	9215	.	-	1	ID=BACOVA_02091;Name=BACOVA_02091
AAXF02000047	GenBank	mRNA	7005	9215	.	-	1	ID=BACOVA_02091.t01;Parent=BACOVA_02091
AAXF02000047	GenBank	CDS	7005	9215	.	-	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	7005	9215	.	-	1	Parent=BACOVA_02091.t01
AAXF02000047	GenBank	gene	9222	10322	.	-	1	ID=BACOVA_02092;Name=BACOVA_02092
AAXF02000047	GenBank	mRNA	9222	10322	.	-	1	ID=BACOVA_02092.t01;Parent=BACOVA_02092
AAXF02000047	GenBank	CDS	9222	10322	.	-	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	9222	10322	.	-	1	Parent=BACOVA_02092.t01
AAXF02000047	GenBank	gene	10340	11422	.	-	1	ID=BACOVA_02093;Name=BACOVA_02093
AAXF02000047	GenBank	mRNA	10340	11422	.	-	1	ID=BACOVA_02093.t01;Parent=BACOVA_02093
AAXF02000047	GenBank	CDS	10340	11422	.	-	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	10340	11422	.	-	1	Parent=BACOVA_02093.t01
AAXF02000047	GenBank	gene	11442	12575	.	-	1	ID=BACOVA_02094;Name=BACOVA_02094
AAXF02000047	GenBank	mRNA	11442	12575	.	-	1	ID=BACOVA_02094.t01;Parent=BACOVA_02094
AAXF02000047	GenBank	CDS	11442	12575	.	-	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	11442	12575	.	-	1	Parent=BACOVA_02094.t01
AAXF02000047	GenBank	gene	12668	14479	.	-	1	ID=BACOVA_02095;Name=BACOVA_02095
AAXF02000047	GenBank	mRNA	12668	14479	.	-	1	ID=BACOVA_02095.t01;Parent=BACOVA_02095
AAXF02000047	GenBank	CDS	12668	14479	.	-	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	12668	14479	.	-	1	Parent=BACOVA_02095.t01
AAXF02000047	GenBank	gene	14506	17754	.	-	1	ID=BACOVA_02096;Name=BACOVA_02096
AAXF02000047	GenBank	mRNA	14506	17754	.	-	1	ID=BACOVA_02096.t01;Parent=BACOVA_02096
AAXF02000047	GenBank	CDS	14506	17754	.	-	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	14506	17754	.	-	1	Parent=BACOVA_02096.t01
AAXF02000047	GenBank	gene	18087	22016	.	+	1	ID=BACOVA_02097;Name=BACOVA_02097
AAXF02000047	GenBank	mRNA	18087	22016	.	+	1	ID=BACOVA_02097.t01;Parent=BACOVA_02097
AAXF02000047	GenBank	CDS	18087	22016	.	+	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	18087	22016	.	+	1	Parent=BACOVA_02097.t01
AAXF02000047	GenBank	gene	21990	22100	.	-	1	ID=BACOVA_02098;Name=BACOVA_02098
AAXF02000047	GenBank	mRNA	21990	22100	.	-	1	ID=BACOVA_02098.t01;Parent=BACOVA_02098
AAXF02000047	GenBank	CDS	21990	22100	.	-	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	21990	22100	.	-	1	Parent=BACOVA_02098.t01