##gff-version 3 ##sequence-region NZ_ACFY01000084 1 16455 # conversion-by bp_genbank2gff3.pl # organism Roseburia inulinivorans DSM 16841 # Note Roseburia inulinivorans DSM 16841 R_inulinivorans-1.0.1_Cont419.1, whole genome shotgun sequence. # date 31-JUL-2020 NZ_ACFY01000084 GenBank region 1 16455 . + 1 ID=NZ_ACFY01000084;Dbxref=BioProject:PRJNA224116,taxon:622312;Name=NZ_ACFY01000084;Note=Roseburia inulinivorans DSM 16841 R_inulinivorans-1.0.1_Cont419.1%2C whole genome shotgun sequence.,REFSEQ INFORMATION: The reference sequence was derived from ACFY01000084. 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/ Roseburia inulinivorans (GenBank Accession Number for 16S rDNA gene: AJ270473) is a member of the Firmicutes division of the domain bacteria and has been isolated from human feces. The sequenced strain,A2-194,was obtained from the Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSMZ) (DSM 16841). This is a Newbler assembly (http://www.454.com/enabling-technology/the-software.asp) comprised of 1/4 plate of XLR fragment 454 DATA with a Q20 coverage of 15.8X. 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. 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. \n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 04/08/2020 14:18:27\nAnnotation Pipeline :: NCBI Prokaryotic Genome\nAnnotation Pipeline (PGAP)\nAnnotation Method :: Best-placed reference protein\nset,GeneMarkS-2+\nAnnotation Software revision :: 4.11\nFeatures Annotated :: Gene,CDS,rRNA,tRNA,ncRNA,\nrepeat_region\nGenes (total) :: 3,990\nCDSs (total) :: 3,924\nGenes (coding) :: 3,520\nCDSs (with protein) :: 3,520\nGenes (RNA) :: 66\nrRNAs :: 1,4,3 (5S,16S,23S)\ncomplete rRNAs :: 1 (5S)\npartial rRNAs :: 4,3 (16S,23S)\ntRNAs :: 54\nncRNAs :: 4\nPseudo Genes (total) :: 404\nCDSs (without protein) :: 404\nPseudo Genes (ambiguous residues) :: 0 of 404\nPseudo Genes (frameshifted) :: 271 of 404\nPseudo Genes (incomplete) :: 133 of 404\nPseudo Genes (internal stop) :: 30 of 404\nPseudo Genes (multiple problems) :: 27 of 404\nCRISPR Arrays :: 2\n##Genome-Annotation-Data-END##;comment1=REFSEQ INFORMATION: The reference sequence was derived from ACFY01000084. 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/ Roseburia inulinivorans (GenBank Accession Number for 16S rDNA gene: AJ270473) is a member of the Firmicutes division of the domain bacteria and has been isolated from human feces. The sequenced strain%2C A2-194%2C was obtained from the Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSMZ) (DSM 16841). This is a Newbler assembly (http://www.454.com/enabling-technology/the-software.asp) comprised of 1/4 plate of XLR fragment 454 DATA with a Q20 coverage of 15.8X. 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. 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. \n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 04/08/2020 14:18:27\nAnnotation Pipeline :: NCBI Prokaryotic Genome\nAnnotation Pipeline (PGAP)\nAnnotation Method :: Best-placed reference protein\nset%3B GeneMarkS-2+\nAnnotation Software revision :: 4.11\nFeatures Annotated :: Gene%3B CDS%3B rRNA%3B tRNA%3B ncRNA%3B\nrepeat_region\nGenes (total) :: 3%2C990\nCDSs (total) :: 3%2C924\nGenes (coding) :: 3%2C520\nCDSs (with protein) :: 3%2C520\nGenes (RNA) :: 66\nrRNAs :: 1%2C 4%2C 3 (5S%2C 16S%2C 23S)\ncomplete rRNAs :: 1 (5S)\npartial rRNAs :: 4%2C 3 (16S%2C 23S)\ntRNAs :: 54\nncRNAs :: 4\nPseudo Genes (total) :: 404\nCDSs (without protein) :: 404\nPseudo Genes (ambiguous residues) :: 0 of 404\nPseudo Genes (frameshifted) :: 271 of 404\nPseudo Genes (incomplete) :: 133 of 404\nPseudo Genes (internal stop) :: 30 of 404\nPseudo Genes (multiple problems) :: 27 of 404\nCRISPR Arrays :: 2\n##Genome-Annotation-Data-END##;culture_collection=DSM:16841;date=31-JUL-2020;host=Homo sapiens;isolation_source=biological product [ENVO:02000043];mol_type=genomic DNA;organism=Roseburia inulinivorans DSM 16841;strain=DSM 16841;submitter_seqid=R_inulinivorans-1.0.1_Cont419.1;type_material=type strain of Roseburia inulinivorans NZ_ACFY01000084 GenBank gene 1 2169 . - 1 ID=ROSEINA2194_RS08245;Name=gnpA;locus_tag=ROSEINA2194_RS08245;old_locus_tag=ROSEINA2194_01886 NZ_ACFY01000084 GenBank mRNA 1 2169 . - 1 ID=ROSEINA2194_RS08245.t01;Parent=ROSEINA2194_RS08245 NZ_ACFY01000084 GenBank CDS 1 2169 . - 1 ID=ROSEINA2194_RS08245.p01;Parent=ROSEINA2194_RS08245.t01;eC_number=2.4.1.211;Name=gnpA;Note=Derived by automated computational analysis using gene prediction method: Protein Homology.;codon_start=1;inference=COORDINATES: similar to AA sequence:RefSeq:WP_014078991.1;locus_tag=ROSEINA2194_RS08245;old_locus_tag=ROSEINA2194_01886;product=1%2C3-beta-galactosyl-N-acetylhexosamine phosphorylase;protein_id=WP_007885595.1;transl_table=11;translation=length.722 NZ_ACFY01000084 GenBank exon 1 2169 . - 1 Parent=ROSEINA2194_RS08245.t01 NZ_ACFY01000084 GenBank gene 2181 3353 . - 1 ID=ROSEINA2194_RS08250;Name=ROSEINA2194_RS08250;old_locus_tag=ROSEINA2194_01887 NZ_ACFY01000084 GenBank mRNA 2181 3353 . - 1 ID=ROSEINA2194_RS08250.t01;Parent=ROSEINA2194_RS08250 NZ_ACFY01000084 GenBank CDS 2181 3353 . - 1 ID=ROSEINA2194_RS08250.p01;Parent=ROSEINA2194_RS08250.t01;Name=ROSEINA2194_RS08250;Note=Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.;codon_start=1;inference=COORDINATES: ab initio prediction:GeneMarkS-2+;old_locus_tag=ROSEINA2194_01887;product=hypothetical protein;protein_id=WP_044927509.1;transl_table=11;translation=length.390 NZ_ACFY01000084 GenBank exon 2181 3353 . - 1 Parent=ROSEINA2194_RS08250.t01 NZ_ACFY01000084 GenBank gene 3319 3492 . - 1 ID=ROSEINA2194_RS21035;Name=ROSEINA2194_RS21035;old_locus_tag=ROSEINA2194_01888 NZ_ACFY01000084 GenBank mRNA 3319 3492 . - 1 ID=ROSEINA2194_RS21035.t01;Parent=ROSEINA2194_RS21035 NZ_ACFY01000084 GenBank CDS 3319 3492 . - 1 ID=ROSEINA2194_RS21035.p01;Parent=ROSEINA2194_RS21035.t01;Name=ROSEINA2194_RS21035;Note=Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.;codon_start=1;inference=COORDINATES: ab initio prediction:GeneMarkS-2+;old_locus_tag=ROSEINA2194_01888;product=hypothetical protein;protein_id=WP_007885600.1;transl_table=11;translation=length.57 NZ_ACFY01000084 GenBank exon 3319 3492 . - 1 Parent=ROSEINA2194_RS21035.t01 NZ_ACFY01000084 GenBank gene 3563 4405 . - 1 ID=ROSEINA2194_RS08255;Name=ROSEINA2194_RS08255;old_locus_tag=ROSEINA2194_01889 NZ_ACFY01000084 GenBank mRNA 3563 4405 . - 1 ID=ROSEINA2194_RS08255.t01;Parent=ROSEINA2194_RS08255 NZ_ACFY01000084 GenBank CDS 3563 4405 . - 1 ID=ROSEINA2194_RS08255.p01;Parent=ROSEINA2194_RS08255.t01;Name=ROSEINA2194_RS08255;Note=Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.;codon_start=1;inference=COORDINATES: ab initio prediction:GeneMarkS-2+;old_locus_tag=ROSEINA2194_01889;product=glycoside hydrolase N-terminal domain-containing protein;protein_id=WP_007885603.1;transl_table=11;translation=length.280 NZ_ACFY01000084 GenBank exon 3563 4405 . - 1 Parent=ROSEINA2194_RS08255.t01 NZ_ACFY01000084 GenBank pseudogenic_exon 4438 5855 . - 1 ID=ROSEINA2194_RS21040;Name=ROSEINA2194_RS21040;Note=frameshifted%3B Derived by automated computational analysis using gene prediction method: Protein Homology.;codon_start=1;inference=COORDINATES: similar to AA sequence:RefSeq:WP_015736742.1;product=alpha-L-fucosidase;pseudo=_no_value;transl_table=11 NZ_ACFY01000084 GenBank pseudogene 4438 5855 . - 1 ID=ROSEINA2194_RS21040.pseudogene;Alias=ROSEINA2194_RS21040;Name=ROSEINA2194_RS21040;pseudo=_no_value NZ_ACFY01000084 GenBank gene 5903 6694 . - 1 ID=ROSEINA2194_RS08265;Name=ROSEINA2194_RS08265;old_locus_tag=ROSEINA2194_01892 NZ_ACFY01000084 GenBank mRNA 5903 6694 . - 1 ID=ROSEINA2194_RS08265.t01;Parent=ROSEINA2194_RS08265 NZ_ACFY01000084 GenBank CDS 5903 6694 . - 1 ID=ROSEINA2194_RS08265.p01;Parent=ROSEINA2194_RS08265.t01;Name=ROSEINA2194_RS08265;Note=Derived by automated computational analysis using gene prediction method: Protein Homology.;codon_start=1;inference=COORDINATES: similar to AA sequence:RefSeq:WP_008706708.1;old_locus_tag=ROSEINA2194_01892;product=carbohydrate ABC transporter permease;protein_id=WP_156337721.1;transl_table=11;translation=length.263 NZ_ACFY01000084 GenBank exon 5903 6694 . - 1 Parent=ROSEINA2194_RS08265.t01 NZ_ACFY01000084 GenBank gene 6773 7672 . - 1 ID=ROSEINA2194_RS08270;Name=ROSEINA2194_RS08270;old_locus_tag=ROSEINA2194_01893 NZ_ACFY01000084 GenBank mRNA 6773 7672 . - 1 ID=ROSEINA2194_RS08270.t01;Parent=ROSEINA2194_RS08270 NZ_ACFY01000084 GenBank CDS 6773 7672 . - 1 ID=ROSEINA2194_RS08270.p01;Parent=ROSEINA2194_RS08270.t01;Name=ROSEINA2194_RS08270;Note=Derived by automated computational analysis using gene prediction method: Protein Homology.;codon_start=1;inference=COORDINATES: similar to AA sequence:RefSeq:WP_009003154.1;old_locus_tag=ROSEINA2194_01893;product=sugar ABC transporter permease;protein_id=WP_081453893.1;transl_table=11;translation=length.299 NZ_ACFY01000084 GenBank exon 6773 7672 . - 1 Parent=ROSEINA2194_RS08270.t01 NZ_ACFY01000084 GenBank gene 7766 9178 . - 1 ID=ROSEINA2194_RS08275;Name=ROSEINA2194_RS08275;old_locus_tag=ROSEINA2194_01895 NZ_ACFY01000084 GenBank mRNA 7766 9178 . - 1 ID=ROSEINA2194_RS08275.t01;Parent=ROSEINA2194_RS08275 NZ_ACFY01000084 GenBank CDS 7766 9178 . - 1 ID=ROSEINA2194_RS08275.p01;Parent=ROSEINA2194_RS08275.t01;Name=ROSEINA2194_RS08275;Note=Derived by automated computational analysis using gene prediction method: Protein Homology.;codon_start=1;inference=COORDINATES: similar to AA sequence:RefSeq:WP_009003153.1;old_locus_tag=ROSEINA2194_01895;product=carbohydrate ABC transporter substrate-binding protein;protein_id=WP_007885619.1;transl_table=11;translation=length.470 NZ_ACFY01000084 GenBank exon 7766 9178 . - 1 Parent=ROSEINA2194_RS08275.t01 NZ_ACFY01000084 GenBank gene 9370 11160 . + 1 ID=ROSEINA2194_RS08280;Name=ROSEINA2194_RS08280;old_locus_tag=ROSEINA2194_01896 NZ_ACFY01000084 GenBank mRNA 9370 11160 . + 1 ID=ROSEINA2194_RS08280.t01;Parent=ROSEINA2194_RS08280 NZ_ACFY01000084 GenBank CDS 9370 11160 . + 1 ID=ROSEINA2194_RS08280.p01;Parent=ROSEINA2194_RS08280.t01;Name=ROSEINA2194_RS08280;Note=Derived by automated computational analysis using gene prediction method: Protein Homology.;codon_start=1;inference=COORDINATES: protein motif:HMM:NF012876.1%2CHMM:NF014567.1%2CHMM:NF018305.1;old_locus_tag=ROSEINA2194_01896;product=histidine kinase;protein_id=WP_007885620.1;transl_table=11;translation=length.596 NZ_ACFY01000084 GenBank exon 9370 11160 . + 1 Parent=ROSEINA2194_RS08280.t01 NZ_ACFY01000084 GenBank gene 11162 12757 . + 1 ID=ROSEINA2194_RS08285;Name=ROSEINA2194_RS08285;old_locus_tag=ROSEINA2194_01897 NZ_ACFY01000084 GenBank mRNA 11162 12757 . + 1 ID=ROSEINA2194_RS08285.t01;Parent=ROSEINA2194_RS08285 NZ_ACFY01000084 GenBank CDS 11162 12757 . + 1 ID=ROSEINA2194_RS08285.p01;Parent=ROSEINA2194_RS08285.t01;Name=ROSEINA2194_RS08285;Note=Derived by automated computational analysis using gene prediction method: Protein Homology.;codon_start=1;inference=COORDINATES: protein motif:HMM:NF012301.1%2CHMM:NF024242.1;old_locus_tag=ROSEINA2194_01897;product=response regulator;protein_id=WP_007885621.1;transl_table=11;translation=length.531 NZ_ACFY01000084 GenBank exon 11162 12757 . + 1 Parent=ROSEINA2194_RS08285.t01 NZ_ACFY01000084 GenBank gene 12838 15399 . - 1 ID=ROSEINA2194_RS19690;Name=ROSEINA2194_RS19690;old_locus_tag=ROSEINA2194_01898 NZ_ACFY01000084 GenBank mRNA 12838 15399 . - 1 ID=ROSEINA2194_RS19690.t01;Parent=ROSEINA2194_RS19690 NZ_ACFY01000084 GenBank CDS 12838 15399 . - 1 ID=ROSEINA2194_RS19690.p01;Parent=ROSEINA2194_RS19690.t01;Name=ROSEINA2194_RS19690;Note=Derived by automated computational analysis using gene prediction method: Protein Homology.;codon_start=1;inference=COORDINATES: protein motif:HMM:NF012956.1;old_locus_tag=ROSEINA2194_01898;product=discoidin domain-containing protein;protein_id=WP_007885622.1;transl_table=11;translation=length.853 NZ_ACFY01000084 GenBank exon 12838 15399 . - 1 Parent=ROSEINA2194_RS19690.t01 NZ_ACFY01000084 GenBank gene 15433 16455 . - 1 ID=ROSEINA2194_RS08295;Name=ROSEINA2194_RS08295;old_locus_tag=ROSEINA2194_01899 NZ_ACFY01000084 GenBank mRNA 15433 16455 . - 1 ID=ROSEINA2194_RS08295.t01;Parent=ROSEINA2194_RS08295 NZ_ACFY01000084 GenBank CDS 15433 16455 . - 1 ID=ROSEINA2194_RS08295.p01;Parent=ROSEINA2194_RS08295.t01;Name=ROSEINA2194_RS08295;Note=Derived by automated computational analysis using gene prediction method: Protein Homology.;codon_start=1;inference=COORDINATES: protein motif:HMM:NF024545.1;old_locus_tag=ROSEINA2194_01899;product=peptidyl-prolyl cis-trans isomerase;protein_id=WP_007885623.1;transl_table=11;translation=length.340 NZ_ACFY01000084 GenBank exon 15433 16455 . - 1 Parent=ROSEINA2194_RS08295.t01