##gff-version 3 ##sequence-region NZ_EQ973490 1 23343 # conversion-by bp_genbank2gff3.pl # organism Bacteroides cellulosilyticus DSM 14838 # Note Bacteroides cellulosilyticus DSM 14838 Scfld4, whole genome shotgun sequence. # date 10-MAY-2022 NZ_EQ973490 GenBank region 1 23343 . + 1 ID=NZ_EQ973490;Dbxref=BioProject:PRJNA224116,taxon:537012;Name=NZ_EQ973490;Note=Bacteroides cellulosilyticus DSM 14838 Scfld4%2C whole genome shotgun sequence.,REFSEQ INFORMATION: The reference sequence is identical to EQ973490.1. Bacteroides cellulosilyticus (GenBank Accession Number for 16S rDNA gene: AJ583243) is a member of the Bacteroidetes division of the domain bacteria and has been isolated from human feces. The sequenced strain was obtained from Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSMZ) (DSM 14838). This is a Newbler assembly (http://www.454.com/enabling-technology/the-software.asp) comprised of one full plate FLX PE 454 Data with a Q20 coverage of 16.3X. 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 cellulosilyticus (GenBank Accession Number for 16S rDNA gene: AJ583243) is a member of the Bacteroidetes division of the domain bacteria and has been isolated from human feces. The sequenced strain was obtained from Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSMZ) (DSM 14838). This is a Newbler assembly (http://www.454.com/enabling-technology/the-software.asp) comprised of one full plate FLX PE 454 Data with a Q20 coverage of 16.3X. 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 not spanned by GeneMark and Glimmer2 were blasted against NCBI's non-redundant (NR) database and predictions generated based on protein alignments. tRNA genes were determined using tRNAscan-SE 1.23 and non-coding RNA genes by RNAmmer-1.2 and Rfam v8.0. Gene names are generated at the contig level and may not necessarily reflect any known order or orientation between contigs. 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 March 2009 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 June 2013. 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/ \n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 05/05/2022 02:16:44\nAnnotation Pipeline :: NCBI Prokaryotic Genome\nAnnotation Pipeline (PGAP)\nAnnotation Method :: Best-placed reference protein\nset,GeneMarkS-2+\nAnnotation Software revision :: 6.1\nFeatures Annotated :: Gene,CDS,rRNA,tRNA,ncRNA,\nrepeat_region\nGenes (total) :: 5,175\nCDSs (total) :: 5,120\nGenes (coding) :: 4,851\nCDSs (with protein) :: 4,851\nGenes (RNA) :: 55\nrRNAs :: 1,1,1 (5S,16S,23S)\ncomplete rRNAs :: 1,1,1 (5S,16S,23S)\ntRNAs :: 50\nncRNAs :: 2\nPseudo Genes (total) :: 270\nCDSs (without protein) :: 269\nPseudo Genes (ambiguous residues) :: 0 of 270\nPseudo Genes (frameshifted) :: 97 of 270\nPseudo Genes (incomplete) :: 176 of 270\nPseudo Genes (internal stop) :: 16 of 270\nPseudo Genes (multiple problems) :: 15 of 270\nCRISPR Arrays :: 1\n##Genome-Annotation-Data-END##;comment1=REFSEQ INFORMATION: The reference sequence is identical to EQ973490.1. Bacteroides cellulosilyticus (GenBank Accession Number for 16S rDNA gene: AJ583243) is a member of the Bacteroidetes division of the domain bacteria and has been isolated from human feces. The sequenced strain was obtained from Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSMZ) (DSM 14838). This is a Newbler assembly (http://www.454.com/enabling-technology/the-software.asp) comprised of one full plate FLX PE 454 Data with a Q20 coverage of 16.3X. 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 cellulosilyticus (GenBank Accession Number for 16S rDNA gene: AJ583243) is a member of the Bacteroidetes division of the domain bacteria and has been isolated from human feces. The sequenced strain was obtained from Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSMZ) (DSM 14838). This is a Newbler assembly (http://www.454.com/enabling-technology/the-software.asp) comprised of one full plate FLX PE 454 Data with a Q20 coverage of 16.3X. 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 not spanned by GeneMark and Glimmer2 were blasted against NCBI's non-redundant (NR) database and predictions generated based on protein alignments. tRNA genes were determined using tRNAscan-SE 1.23 and non-coding RNA genes by RNAmmer-1.2 and Rfam v8.0. Gene names are generated at the contig level and may not necessarily reflect any known order or orientation between contigs. 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 March 2009 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 June 2013. 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/ \n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 05/05/2022 02:16:44\nAnnotation Pipeline :: NCBI Prokaryotic Genome\nAnnotation Pipeline (PGAP)\nAnnotation Method :: Best-placed reference protein\nset%3B GeneMarkS-2+\nAnnotation Software revision :: 6.1\nFeatures Annotated :: Gene%3B CDS%3B rRNA%3B tRNA%3B ncRNA%3B\nrepeat_region\nGenes (total) :: 5%2C175\nCDSs (total) :: 5%2C120\nGenes (coding) :: 4%2C851\nCDSs (with protein) :: 4%2C851\nGenes (RNA) :: 55\nrRNAs :: 1%2C 1%2C 1 (5S%2C 16S%2C 23S)\ncomplete rRNAs :: 1%2C 1%2C 1 (5S%2C 16S%2C 23S)\ntRNAs :: 50\nncRNAs :: 2\nPseudo Genes (total) :: 270\nCDSs (without protein) :: 269\nPseudo Genes (ambiguous residues) :: 0 of 270\nPseudo Genes (frameshifted) :: 97 of 270\nPseudo Genes (incomplete) :: 176 of 270\nPseudo Genes (internal stop) :: 16 of 270\nPseudo Genes (multiple problems) :: 15 of 270\nCRISPR Arrays :: 1\n##Genome-Annotation-Data-END##;culture_collection=DSM:14838;date=10-MAY-2022;host=Homo sapiens;isolation_source=biological product [ENVO:02000043];mol_type=genomic DNA;organism=Bacteroides cellulosilyticus DSM 14838;strain=DSM 14838;submitter_seqid=Scfld4;type_material=type strain of Bacteroides cellulosilyticus NZ_EQ973490 GenBank gene 1 4095 . - 1 ID=BACCELL_RS09475;Name=BACCELL_RS09475;old_locus_tag=BACCELL_02140 NZ_EQ973490 GenBank mRNA 1 4095 . - 1 ID=BACCELL_RS09475.t01;Parent=BACCELL_RS09475 NZ_EQ973490 GenBank CDS 1 4095 . - 1 ID=BACCELL_RS09475;Parent=BACCELL_RS09475.t01;gO_process=GO:0000160 - phosphorelay signal transduction system [Evidence IEA];Name=BACCELL_RS09475;Note=Derived by automated computational analysis using gene prediction method: Protein Homology.;codon_start=1;inference=COORDINATES: similar to AA sequence:RefSeq:WP_007661009.1;old_locus_tag=BACCELL_02140;product=two-component regulator propeller domain-containing protein;protein_id=WP_149949311.1;transl_table=11;translation=length.1364 NZ_EQ973490 GenBank exon 1 4095 . - 1 Parent=BACCELL_RS09475.t01 NZ_EQ973490 GenBank gene 4115 5446 . - 1 ID=BACCELL_RS09480;Name=BACCELL_RS09480;old_locus_tag=BACCELL_02141 NZ_EQ973490 GenBank mRNA 4115 5446 . - 1 ID=BACCELL_RS09480.t01;Parent=BACCELL_RS09480 NZ_EQ973490 GenBank CDS 4115 5446 . - 1 ID=BACCELL_RS09480;Parent=BACCELL_RS09480.t01;gO_process=GO:0005975 - carbohydrate metabolic process [Evidence IEA];Name=BACCELL_RS09480;Note=Derived by automated computational analysis using gene prediction method: Protein Homology.;codon_start=1;inference=COORDINATES: similar to AA sequence:RefSeq:WP_007661008.1;old_locus_tag=BACCELL_02141;product=family 43 glycosylhydrolase;protein_id=WP_007211515.1;transl_table=11;translation=length.443 NZ_EQ973490 GenBank exon 4115 5446 . - 1 Parent=BACCELL_RS09480.t01 NZ_EQ973490 GenBank gene 5623 8280 . - 1 ID=BACCELL_RS09485;Name=BACCELL_RS09485;old_locus_tag=BACCELL_02142 NZ_EQ973490 GenBank mRNA 5623 8280 . - 1 ID=BACCELL_RS09485.t01;Parent=BACCELL_RS09485 NZ_EQ973490 GenBank CDS 5623 8280 . - 1 ID=BACCELL_RS09485;Parent=BACCELL_RS09485.t01;gO_process=GO:0005975 - carbohydrate metabolic process [Evidence IEA];Name=BACCELL_RS09485;Note=Derived by automated computational analysis using gene prediction method: Protein Homology.;codon_start=1;inference=COORDINATES: similar to AA sequence:RefSeq:WP_007411427.1;old_locus_tag=BACCELL_02142;product=glycoside hydrolase family 3 C-terminal domain-containing protein;protein_id=WP_007211516.1;transl_table=11;translation=length.885 NZ_EQ973490 GenBank exon 5623 8280 . - 1 Parent=BACCELL_RS09485.t01 NZ_EQ973490 GenBank gene 8329 9387 . - 1 ID=BACCELL_RS09490;Name=BACCELL_RS09490;old_locus_tag=BACCELL_02143 NZ_EQ973490 GenBank mRNA 8329 9387 . - 1 ID=BACCELL_RS09490.t01;Parent=BACCELL_RS09490 NZ_EQ973490 GenBank CDS 8329 9387 . - 1 ID=BACCELL_RS09490;Parent=BACCELL_RS09490.t01;Name=BACCELL_RS09490;Note=Derived by automated computational analysis using gene prediction method: Protein Homology.;codon_start=1;inference=COORDINATES: similar to AA sequence:RefSeq:WP_007661006.1;old_locus_tag=BACCELL_02143;product=glycoside hydrolase family 43 protein;protein_id=WP_007211517.1;transl_table=11;translation=length.352 NZ_EQ973490 GenBank exon 8329 9387 . - 1 Parent=BACCELL_RS09490.t01 NZ_EQ973490 GenBank gene 9434 10588 . - 1 ID=BACCELL_RS09495;Name=BACCELL_RS09495;old_locus_tag=BACCELL_02144 NZ_EQ973490 GenBank mRNA 9434 10588 . - 1 ID=BACCELL_RS09495.t01;Parent=BACCELL_RS09495 NZ_EQ973490 GenBank CDS 9434 10588 . - 1 ID=BACCELL_RS09495;Parent=BACCELL_RS09495.t01;Name=BACCELL_RS09495;Note=Derived by automated computational analysis using gene prediction method: Protein Homology.;codon_start=1;inference=COORDINATES: similar to AA sequence:RefSeq:WP_007216414.1;old_locus_tag=BACCELL_02144;product=alpha/beta hydrolase-fold protein;protein_id=WP_007211518.1;transl_table=11;translation=length.384 NZ_EQ973490 GenBank exon 9434 10588 . - 1 Parent=BACCELL_RS09495.t01 NZ_EQ973490 GenBank gene 10596 11762 . - 1 ID=BACCELL_RS09500;Name=BACCELL_RS09500;old_locus_tag=BACCELL_02145 NZ_EQ973490 GenBank mRNA 10596 11762 . - 1 ID=BACCELL_RS09500.t01;Parent=BACCELL_RS09500 NZ_EQ973490 GenBank CDS 10596 11762 . - 1 ID=BACCELL_RS09500;Parent=BACCELL_RS09500.t01;Name=BACCELL_RS09500;Note=Derived by automated computational analysis using gene prediction method: Protein Homology.;codon_start=1;inference=COORDINATES: similar to AA sequence:RefSeq:WP_008626297.1;old_locus_tag=BACCELL_02145;product=alpha/beta hydrolase-fold protein;protein_id=WP_052309546.1;transl_table=11;translation=length.388 NZ_EQ973490 GenBank exon 10596 11762 . - 1 Parent=BACCELL_RS09500.t01 NZ_EQ973490 GenBank gene 11999 14503 . - 1 ID=BACCELL_RS09510;Name=BACCELL_RS09510;old_locus_tag=BACCELL_02147 NZ_EQ973490 GenBank mRNA 11999 14503 . - 1 ID=BACCELL_RS09510.t01;Parent=BACCELL_RS09510 NZ_EQ973490 GenBank CDS 11999 14503 . - 1 ID=BACCELL_RS09510;Parent=BACCELL_RS09510.t01;gO_process=GO:0005975 - carbohydrate metabolic process [Evidence IEA];Name=BACCELL_RS09510;Note=Derived by automated computational analysis using gene prediction method: Protein Homology.;codon_start=1;inference=COORDINATES: protein motif:HMM:NF012961.2;old_locus_tag=BACCELL_02147;product=glycoside hydrolase family 9 protein;protein_id=WP_081450809.1;transl_table=11;translation=length.834 NZ_EQ973490 GenBank exon 11999 14503 . - 1 Parent=BACCELL_RS09510.t01 NZ_EQ973490 GenBank gene 14832 16566 . - 1 ID=BACCELL_RS09515;Name=BACCELL_RS09515;old_locus_tag=BACCELL_02148 NZ_EQ973490 GenBank mRNA 14832 16566 . - 1 ID=BACCELL_RS09515.t01;Parent=BACCELL_RS09515 NZ_EQ973490 GenBank CDS 14832 16566 . - 1 ID=BACCELL_RS09515;Parent=BACCELL_RS09515.t01;Name=BACCELL_RS09515;Note=Derived by automated computational analysis using gene prediction method: Protein Homology.;codon_start=1;inference=COORDINATES: similar to AA sequence:RefSeq:WP_004292104.1;old_locus_tag=BACCELL_02148;product=RagB/SusD family nutrient uptake outer membrane protein;protein_id=WP_007211522.1;transl_table=11;translation=length.578 NZ_EQ973490 GenBank exon 14832 16566 . - 1 Parent=BACCELL_RS09515.t01 NZ_EQ973490 GenBank pseudogenic_exon 16590 17151 . - 1 ID=BACCELL_RS27335;Name=BACCELL_RS27335;Note=incomplete%3B too short partial abutting assembly gap%3B missing N-terminus%3B Derived by automated computational analysis using gene prediction method: Protein Homology.;codon_start=2;inference=COORDINATES: similar to AA sequence:RefSeq:WP_017141023.1;old_locus_tag=BACCELL_02149;product=SusC/RagA family TonB-linked outer membrane protein;pseudo=_no_value;transl_table=11 NZ_EQ973490 GenBank pseudogene 16590 17151 . - 1 ID=BACCELL_RS27335.pseudogene;Alias=BACCELL_RS27335;Name=BACCELL_RS27335;old_locus_tag=BACCELL_02149;pseudo=_no_value NZ_EQ973490 GenBank gene 17172 19741 . - 1 ID=BACCELL_RS09520;Name=BACCELL_RS09520;old_locus_tag=BACCELL_02150 NZ_EQ973490 GenBank mRNA 17172 19741 . - 1 ID=BACCELL_RS09520.t01;Parent=BACCELL_RS09520 NZ_EQ973490 GenBank CDS 17172 19741 . - 1 ID=BACCELL_RS09520;Parent=BACCELL_RS09520.t01;gO_component=GO:0045203 - integral component of cell outer membrane [Evidence IEA];gO_function=GO:0022857 - transmembrane transporter activity [Evidence IEA];gO_process=GO:0071702 - organic substance transport [Evidence IEA];Name=BACCELL_RS09520;Note=Derived by automated computational analysis using gene prediction method: Protein Homology.;codon_start=1;inference=COORDINATES: similar to AA sequence:RefSeq:WP_007216410.1;old_locus_tag=BACCELL_02150;product=SusC/RagA family TonB-linked outer membrane protein;protein_id=WP_007211524.1;transl_table=11;translation=length.856 NZ_EQ973490 GenBank exon 17172 19741 . - 1 Parent=BACCELL_RS09520.t01 NZ_EQ973490 GenBank gene 20005 21456 . - 1 ID=BACCELL_RS09525;Name=BACCELL_RS09525;old_locus_tag=BACCELL_02152 NZ_EQ973490 GenBank mRNA 20005 21456 . - 1 ID=BACCELL_RS09525.t01;Parent=BACCELL_RS09525 NZ_EQ973490 GenBank CDS 20005 21456 . - 1 ID=BACCELL_RS09525;Parent=BACCELL_RS09525.t01;gO_process=GO:0005975 - carbohydrate metabolic process [Evidence IEA];Name=BACCELL_RS09525;Note=Derived by automated computational analysis using gene prediction method: Protein Homology.;codon_start=1;inference=COORDINATES: similar to AA sequence:RefSeq:WP_004292093.1;old_locus_tag=BACCELL_02152;product=family 43 glycosylhydrolase;protein_id=WP_044153754.1;transl_table=11;translation=length.483 NZ_EQ973490 GenBank exon 20005 21456 . - 1 Parent=BACCELL_RS09525.t01 NZ_EQ973490 GenBank gene 21459 22157 . - 1 ID=BACCELL_RS09530;Name=BACCELL_RS09530;old_locus_tag=BACCELL_02153 NZ_EQ973490 GenBank mRNA 21459 22157 . - 1 ID=BACCELL_RS09530.t01;Parent=BACCELL_RS09530 NZ_EQ973490 GenBank CDS 21459 22157 . - 1 ID=BACCELL_RS09530;Parent=BACCELL_RS09530.t01;Name=BACCELL_RS09530;Note=Derived by automated computational analysis using gene prediction method: Protein Homology.;codon_start=1;inference=COORDINATES: similar to AA sequence:RefSeq:WP_004292094.1;old_locus_tag=BACCELL_02153;product=hypothetical protein;protein_id=WP_007211527.1;transl_table=11;translation=length.232 NZ_EQ973490 GenBank exon 21459 22157 . - 1 Parent=BACCELL_RS09530.t01 NZ_EQ973490 GenBank gene 22186 23343 . - 1 ID=BACCELL_RS09535;Name=BACCELL_RS09535;old_locus_tag=BACCELL_02154 NZ_EQ973490 GenBank mRNA 22186 23343 . - 1 ID=BACCELL_RS09535.t01;Parent=BACCELL_RS09535 NZ_EQ973490 GenBank CDS 22186 23343 . - 1 ID=BACCELL_RS09535;Parent=BACCELL_RS09535.t01;Name=BACCELL_RS09535;Note=Derived by automated computational analysis using gene prediction method: Protein Homology.;codon_start=1;inference=COORDINATES: similar to AA sequence:RefSeq:WP_007216407.1;old_locus_tag=BACCELL_02154;product=alpha/beta hydrolase-fold protein;protein_id=WP_044153756.1;transl_table=11;translation=length.385 NZ_EQ973490 GenBank exon 22186 23343 . - 1 Parent=BACCELL_RS09535.t01