##gff-version 3
##sequence-region NZ_DS362241 1 14533
# conversion-by bp_genbank2gff3.pl
# organism Bacteroides uniformis ATCC 8492
# Note Bacteroides uniformis ATCC 8492 Scfld_3.0.1_24, whole genome shotgun sequence.
# date 06-APR-2020
NZ_DS362241	GenBank	region	1	14533	.	+	1	ID=NZ_DS362241;Dbxref=BioProject:PRJNA224116,ATCC:8492,taxon:411479;Name=NZ_DS362241;Note=Bacteroides uniformis ATCC 8492 Scfld_3.0.1_24%2C whole genome shotgun sequence.,REFSEQ INFORMATION: The reference sequence was derived from DS362241. Bacteroides uniformis (GenBank Accession Number for 16S rDNA gene: L16486) 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,0.718%25 of all 16S rDNA sequences and 1.506%25 of the sequences in its division (Eckburg et. al. (2005)). The sequenced strain was obtained from ATCC (ATCC 8492). We have collected 8.1X 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. Bacteroides uniformis (GenBank Accession Number for 16S rDNA gene: L16486) 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,0.718%25 of all 16S rDNA sequences and 1.506%25 of the sequences in its division (Eckburg et. al. (2005)). The sequenced strain was obtained from ATCC (ATCC 8492). We have collected 8.1X 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. 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. The annotation was added by the NCBI Prokaryotic Genome Annotation Pipeline (PGAP). Information about PGAP can be found here: https://www.ncbi.nlm.nih.gov/genome/annotation_prok/ ##Genome-Annotation-Data-START## Annotation Provider :: NCBI RefSeq Annotation Date :: 04/04/2020 12:47:04 Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline (PGAP) Annotation Method :: Best-placed reference protein set,GeneMarkS-2+ Annotation Software revision :: 4.11 Features Annotated :: Gene,CDS,rRNA,tRNA,ncRNA,repeat_region Genes (total) :: 3,910 CDSs (total) :: 3,841 Genes (coding) :: 3,701 CDSs (with protein) :: 3,701 Genes (RNA) :: 69 rRNAs :: 4,4,3 (5S,16S,23S) complete rRNAs :: 4,4,1 (5S,16S,23S) partial rRNAs :: 2 (23S) tRNAs :: 56 ncRNAs :: 2 Pseudo Genes (total) :: 140 CDSs (without protein) :: 140 Pseudo Genes (ambiguous residues) :: 0 of 140 Pseudo Genes (frameshifted) :: 86 of 140 Pseudo Genes (incomplete) :: 65 of 140 Pseudo Genes (internal stop) :: 23 of 140 Pseudo Genes (multiple problems) :: 30 of 140 ##Genome-Annotation-Data-END## ;comment1=REFSEQ INFORMATION: The reference sequence was derived from DS362241. Bacteroides uniformis (GenBank Accession Number for 16S rDNA gene: L16486) 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 0.718%25 of all 16S rDNA sequences and 1.506%25 of the sequences in its division (Eckburg et. al. (2005)). The sequenced strain was obtained from ATCC (ATCC 8492). We have collected 8.1X coverage in plasmid end reads and 454 reads. We will be performing one round of automated sequence improvement (pre-finishing)%3B 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. Bacteroides uniformis (GenBank Accession Number for 16S rDNA gene: L16486) 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 0.718%25 of all 16S rDNA sequences and 1.506%25 of the sequences in its division (Eckburg et. al. (2005)). The sequenced strain was obtained from ATCC (ATCC 8492). We have collected 8.1X coverage in plasmid end reads and 454 reads. We will be performing one round of automated sequence improvement (pre-finishing)%3B 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. 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. The annotation was added by the NCBI Prokaryotic Genome Annotation Pipeline (PGAP). Information about PGAP can be found here: https://www.ncbi.nlm.nih.gov/genome/annotation_prok/ ##Genome-Annotation-Data-START## Annotation Provider :: NCBI RefSeq Annotation Date :: 04/04/2020 12:47:04 Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline (PGAP) Annotation Method :: Best-placed reference protein set%3B GeneMarkS-2+ Annotation Software revision :: 4.11 Features Annotated :: Gene%3B CDS%3B rRNA%3B tRNA%3B ncRNA%3B repeat_region Genes (total) :: 3%2C910 CDSs (total) :: 3%2C841 Genes (coding) :: 3%2C701 CDSs (with protein) :: 3%2C701 Genes (RNA) :: 69 rRNAs :: 4%2C 4%2C 3 (5S%2C 16S%2C 23S) complete rRNAs :: 4%2C 4%2C 1 (5S%2C 16S%2C 23S) partial rRNAs :: 2 (23S) tRNAs :: 56 ncRNAs :: 2 Pseudo Genes (total) :: 140 CDSs (without protein) :: 140 Pseudo Genes (ambiguous residues) :: 0 of 140 Pseudo Genes (frameshifted) :: 86 of 140 Pseudo Genes (incomplete) :: 65 of 140 Pseudo Genes (internal stop) :: 23 of 140 Pseudo Genes (multiple problems) :: 30 of 140 ##Genome-Annotation-Data-END## ;date=06-APR-2020;host=Homo sapiens;isolation_source=biological product [ENVO:02000043];mol_type=genomic DNA;organism=Bacteroides uniformis ATCC 8492;strain=ATCC 8492;type_material=type strain of Bacteroides uniformis
NZ_DS362241	GenBank	gene	1	2253	.	-	1	ID=BACUNI_RS07655;Name=bglX;locus_tag=BACUNI_RS07655;old_locus_tag=BACUNI_01484
NZ_DS362241	GenBank	mRNA	1	2253	.	-	1	ID=BACUNI_RS07655.t01;Parent=BACUNI_RS07655
NZ_DS362241	GenBank	CDS	1	2253	.	-	1	ID=BACUNI_RS07655.p01;Parent=BACUNI_RS07655.t01;eC_number=3.2.1.21;Name=bglX;Note=Derived by automated computational analysis using gene prediction method: Protein Homology.;codon_start=1;inference=COORDINATES: similar to AA sequence:RefSeq:WP_002562026.1;locus_tag=BACUNI_RS07655;old_locus_tag=BACUNI_01484;product=beta-glucosidase BglX;protein_id=WP_005826828.1;transl_table=11;translation=length.750
NZ_DS362241	GenBank	exon	1	2253	.	-	1	Parent=BACUNI_RS07655.t01
NZ_DS362241	GenBank	gene	2256	3545	.	-	1	ID=BACUNI_RS07660;Name=BACUNI_RS07660;old_locus_tag=BACUNI_01485
NZ_DS362241	GenBank	mRNA	2256	3545	.	-	1	ID=BACUNI_RS07660.t01;Parent=BACUNI_RS07660
NZ_DS362241	GenBank	CDS	2256	3545	.	-	1	ID=BACUNI_RS07660.p01;Parent=BACUNI_RS07660.t01;Name=BACUNI_RS07660;Note=Derived by automated computational analysis using gene prediction method: Protein Homology.;codon_start=1;inference=COORDINATES: similar to AA sequence:RefSeq:WP_005826831.1;old_locus_tag=BACUNI_01485;product=hypothetical protein;protein_id=WP_005826831.1;transl_table=11;translation=length.429
NZ_DS362241	GenBank	exon	2256	3545	.	-	1	Parent=BACUNI_RS07660.t01
NZ_DS362241	GenBank	gene	3634	4995	.	-	1	ID=BACUNI_RS07665;Name=BACUNI_RS07665;old_locus_tag=BACUNI_01486
NZ_DS362241	GenBank	mRNA	3634	4995	.	-	1	ID=BACUNI_RS07665.t01;Parent=BACUNI_RS07665
NZ_DS362241	GenBank	CDS	3634	4995	.	-	1	ID=BACUNI_RS07665.p01;Parent=BACUNI_RS07665.t01;Name=BACUNI_RS07665;Note=Derived by automated computational analysis using gene prediction method: Protein Homology.;codon_start=1;inference=COORDINATES: similar to AA sequence:RefSeq:WP_005826833.1;old_locus_tag=BACUNI_01486;product=family 16 glycosylhydrolase;protein_id=WP_005826833.1;transl_table=11;translation=length.453
NZ_DS362241	GenBank	exon	3634	4995	.	-	1	Parent=BACUNI_RS07665.t01
NZ_DS362241	GenBank	gene	5134	6507	.	-	1	ID=BACUNI_RS07670;Name=BACUNI_RS07670;old_locus_tag=BACUNI_01487
NZ_DS362241	GenBank	mRNA	5134	6507	.	-	1	ID=BACUNI_RS07670.t01;Parent=BACUNI_RS07670
NZ_DS362241	GenBank	CDS	5134	6507	.	-	1	ID=BACUNI_RS07670.p01;Parent=BACUNI_RS07670.t01;Name=BACUNI_RS07670;Note=Derived by automated computational analysis using gene prediction method: Protein Homology.;codon_start=1;inference=COORDINATES: similar to AA sequence:RefSeq:WP_005826835.1;old_locus_tag=BACUNI_01487;product=hypothetical protein;protein_id=WP_005826835.1;transl_table=11;translation=length.457
NZ_DS362241	GenBank	exon	5134	6507	.	-	1	Parent=BACUNI_RS07670.t01
NZ_DS362241	GenBank	gene	6539	8128	.	-	1	ID=BACUNI_RS07675;Name=BACUNI_RS07675;old_locus_tag=BACUNI_01488
NZ_DS362241	GenBank	mRNA	6539	8128	.	-	1	ID=BACUNI_RS07675.t01;Parent=BACUNI_RS07675
NZ_DS362241	GenBank	CDS	6539	8128	.	-	1	ID=BACUNI_RS07675.p01;Parent=BACUNI_RS07675.t01;Name=BACUNI_RS07675;Note=Derived by automated computational analysis using gene prediction method: Protein Homology.;codon_start=1;inference=COORDINATES: similar to AA sequence:RefSeq:WP_005826837.1;old_locus_tag=BACUNI_01488;product=RagB/SusD family nutrient uptake outer membrane protein;protein_id=WP_005826837.1;transl_table=11;translation=length.529
NZ_DS362241	GenBank	exon	6539	8128	.	-	1	Parent=BACUNI_RS07675.t01
NZ_DS362241	GenBank	gene	8147	11350	.	-	1	ID=BACUNI_RS07680;Name=BACUNI_RS07680;old_locus_tag=BACUNI_01489
NZ_DS362241	GenBank	mRNA	8147	11350	.	-	1	ID=BACUNI_RS07680.t01;Parent=BACUNI_RS07680
NZ_DS362241	GenBank	CDS	8147	11350	.	-	1	ID=BACUNI_RS07680.p01;Parent=BACUNI_RS07680.t01;Name=BACUNI_RS07680;Note=Derived by automated computational analysis using gene prediction method: Protein Homology.;codon_start=1;inference=COORDINATES: similar to AA sequence:RefSeq:WP_005826839.1;old_locus_tag=BACUNI_01489;product=TonB-dependent receptor;protein_id=WP_005826839.1;transl_table=11;translation=length.1067
NZ_DS362241	GenBank	exon	8147	11350	.	-	1	Parent=BACUNI_RS07680.t01
NZ_DS362241	GenBank	gene	11642	14533	.	-	1	ID=BACUNI_RS07685;Name=BACUNI_RS07685;old_locus_tag=BACUNI_01490
NZ_DS362241	GenBank	mRNA	11642	14533	.	-	1	ID=BACUNI_RS07685.t01;Parent=BACUNI_RS07685
NZ_DS362241	GenBank	CDS	11642	14533	.	-	1	ID=BACUNI_RS07685.p01;Parent=BACUNI_RS07685.t01;Name=BACUNI_RS07685;Note=Derived by automated computational analysis using gene prediction method: Protein Homology.;codon_start=1;inference=COORDINATES: similar to AA sequence:RefSeq:WP_009036780.1;old_locus_tag=BACUNI_01490;product=transcriptional regulator;protein_id=WP_005826840.1;transl_table=11;translation=length.963
NZ_DS362241	GenBank	exon	11642	14533	.	-	1	Parent=BACUNI_RS07685.t01