##gff-version 3 ##sequence-region NZ_DS499729 1 8289 # conversion-by bp_genbank2gff3.pl # organism Anaerostipes caccae L1-92 # Note Anaerostipes caccae L1-92 strain DSM 14662 Scfld_03_10, whole genome shotgun sequence. # date 25-APR-2021 NZ_DS499729 GenBank region 1 8289 . + 1 ID=NZ_DS499729;Dbxref=BioProject:PRJNA224116,taxon:411490;Name=NZ_DS499729;Note=Anaerostipes caccae L1-92 strain DSM 14662 Scfld_03_10%2C whole genome shotgun sequence.,REFSEQ INFORMATION: The reference sequence is identical to DS499729.1. Anaerostipes caccae (GenBank Accession Number: AJ270487) is a member of the division Firmicutes. It is an acetate-converting butyrate-producing colon bacteria that is involved in metabolic cross-feeding with Bifidobacterium species (Falony et. al. (2006),Belenguer et. al. (2006)). The sequenced strain was obtained from Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSMZ) (DSM 14662). We have collected 9.8X coverage in plasmid end reads (pOTW13 and pJAZZ vectors) and 454 reads. We have performed one round of automated sequence improvement(pre-finishing),along with manual improvement that includes breaking apart any mis-assembly,and making manual joins where possible. Manual edits also are made where the consensus appears to be incorrect. All low quality data on the ends of contigs is removed. Contigs are ordered and oriented where possible. 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. Anaerostipes caccae (GenBank Accession Number: AJ270487) is a member of the division Firmicutes. It is an acetate-converting butyrate-producing colon bacteria that is involved in metabolic cross-feeding with Bifidobacterium species (Falony et. al. (2006),Belenguer et. al. (2006)). The sequenced strain was obtained from Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSMZ) (DSM 14662). We have collected 9.8X coverage in plasmid end reads (pOTW13 and pJAZZ vectors) and 454 reads. We have performed one round of automated sequence improvement(pre-finishing),along with manual improvement that includes breaking apart any mis-assembly,and making manual joins where possible. Manual edits also are made where the consensus appears to be incorrect. All low quality data on the ends of contigs is removed. Contigs are ordered and oriented where possible. 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. 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. 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 February 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/ \n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 04/25/2021 09:13:49\nAnnotation Pipeline :: NCBI Prokaryotic Genome\nAnnotation Pipeline (PGAP)\nAnnotation Method :: Best-placed reference protein\nset,GeneMarkS-2+\nAnnotation Software revision :: 5.1\nFeatures Annotated :: Gene,CDS,rRNA,tRNA,ncRNA,\nrepeat_region\nGenes (total) :: 3,533\nCDSs (total) :: 3,441\nGenes (coding) :: 3,342\nCDSs (with protein) :: 3,342\nGenes (RNA) :: 92\nrRNAs :: 5,6,7 (5S,16S,23S)\ncomplete rRNAs :: 5,4,4 (5S,16S,23S)\npartial rRNAs :: 2,3 (16S,23S)\ntRNAs :: 70\nncRNAs :: 4\nPseudo Genes (total) :: 99\nCDSs (without protein) :: 99\nPseudo Genes (ambiguous residues) :: 0 of 99\nPseudo Genes (frameshifted) :: 72 of 99\nPseudo Genes (incomplete) :: 23 of 99\nPseudo Genes (internal stop) :: 12 of 99\nPseudo Genes (multiple problems) :: 8 of 99\nCRISPR Arrays :: 7\n##Genome-Annotation-Data-END##;comment1=REFSEQ INFORMATION: The reference sequence is identical to DS499729.1. Anaerostipes caccae (GenBank Accession Number: AJ270487) is a member of the division Firmicutes. It is an acetate-converting butyrate-producing colon bacteria that is involved in metabolic cross-feeding with Bifidobacterium species (Falony et. al. (2006)%2C Belenguer et. al. (2006)). The sequenced strain was obtained from Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSMZ) (DSM 14662). We have collected 9.8X coverage in plasmid end reads (pOTW13 and pJAZZ vectors) and 454 reads. We have performed one round of automated sequence improvement(pre-finishing)%2C along with manual improvement that includes breaking apart any mis-assembly%2C and making manual joins where possible. Manual edits also are made where the consensus appears to be incorrect. All low quality data on the ends of contigs is removed. Contigs are ordered and oriented where possible. 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. Anaerostipes caccae (GenBank Accession Number: AJ270487) is a member of the division Firmicutes. It is an acetate-converting butyrate-producing colon bacteria that is involved in metabolic cross-feeding with Bifidobacterium species (Falony et. al. (2006)%2C Belenguer et. al. (2006)). The sequenced strain was obtained from Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSMZ) (DSM 14662). We have collected 9.8X coverage in plasmid end reads (pOTW13 and pJAZZ vectors) and 454 reads. We have performed one round of automated sequence improvement(pre-finishing)%2C along with manual improvement that includes breaking apart any mis-assembly%2C and making manual joins where possible. Manual edits also are made where the consensus appears to be incorrect. All low quality data on the ends of contigs is removed. Contigs are ordered and oriented where possible. 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. 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. 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 February 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/ \n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 04/25/2021 09:13:49\nAnnotation Pipeline :: NCBI Prokaryotic Genome\nAnnotation Pipeline (PGAP)\nAnnotation Method :: Best-placed reference protein\nset%3B GeneMarkS-2+\nAnnotation Software revision :: 5.1\nFeatures Annotated :: Gene%3B CDS%3B rRNA%3B tRNA%3B ncRNA%3B\nrepeat_region\nGenes (total) :: 3%2C533\nCDSs (total) :: 3%2C441\nGenes (coding) :: 3%2C342\nCDSs (with protein) :: 3%2C342\nGenes (RNA) :: 92\nrRNAs :: 5%2C 6%2C 7 (5S%2C 16S%2C 23S)\ncomplete rRNAs :: 5%2C 4%2C 4 (5S%2C 16S%2C 23S)\npartial rRNAs :: 2%2C 3 (16S%2C 23S)\ntRNAs :: 70\nncRNAs :: 4\nPseudo Genes (total) :: 99\nCDSs (without protein) :: 99\nPseudo Genes (ambiguous residues) :: 0 of 99\nPseudo Genes (frameshifted) :: 72 of 99\nPseudo Genes (incomplete) :: 23 of 99\nPseudo Genes (internal stop) :: 12 of 99\nPseudo Genes (multiple problems) :: 8 of 99\nCRISPR Arrays :: 7\n##Genome-Annotation-Data-END##;date=25-APR-2021;host=Homo sapiens;isolation_source=biological product [ENVO:02000043];mol_type=genomic DNA;organism=Anaerostipes caccae L1-92;strain=DSM 14662;type_material=type strain of Anaerostipes caccae NZ_DS499729 GenBank gene 1 8 . - 1 ID=ANACAC_RS03030;Name=ANACAC_RS03030;old_locus_tag=ANACAC_00492 NZ_DS499729 GenBank mRNA 1 8 . - 1 ID=ANACAC_RS03030;Parent=ANACAC_RS03030 NZ_DS499729 GenBank CDS 1 8 . - 1 ID=ANACAC_RS03030;Parent=ANACAC_RS03030;Name=ANACAC_RS03030;Note=Derived by automated computational analysis using gene prediction method: Protein Homology.;codon_start=1;inference=COORDINATES: similar to AA sequence:RefSeq:WP_006566000.1;old_locus_tag=ANACAC_00492;product=DUF1700 domain-containing protein;protein_id=WP_006566000.1;transl_table=11;translation=length.203 NZ_DS499729 GenBank exon 1 8 . - 1 Parent=ANACAC_RS03030 NZ_DS499729 GenBank gene 1 318 . - 1 ID=ANACAC_RS03035;Name=ANACAC_RS03035;old_locus_tag=ANACAC_00493 NZ_DS499729 GenBank mRNA 1 318 . - 1 ID=ANACAC_RS03035;Parent=ANACAC_RS03035 NZ_DS499729 GenBank CDS 1 318 . - 1 ID=ANACAC_RS03035;Parent=ANACAC_RS03035;Name=ANACAC_RS03035;Note=Derived by automated computational analysis using gene prediction method: Protein Homology.;codon_start=1;inference=COORDINATES: similar to AA sequence:RefSeq:WP_006566001.1;old_locus_tag=ANACAC_00493;product=PadR family transcriptional regulator;protein_id=WP_006566001.1;transl_table=11;translation=length.105 NZ_DS499729 GenBank exon 1 318 . - 1 Parent=ANACAC_RS03035 NZ_DS499729 GenBank gene 477 1448 . - 1 ID=ANACAC_RS03040;Name=ANACAC_RS03040;old_locus_tag=ANACAC_00494 NZ_DS499729 GenBank mRNA 477 1448 . - 1 ID=ANACAC_RS03040;Parent=ANACAC_RS03040 NZ_DS499729 GenBank CDS 477 1448 . - 1 ID=ANACAC_RS03040;Parent=ANACAC_RS03040;Name=ANACAC_RS03040;Note=Derived by automated computational analysis using gene prediction method: Protein Homology.;codon_start=1;inference=COORDINATES: similar to AA sequence:RefSeq:WP_008394375.1;old_locus_tag=ANACAC_00494;product=carbohydrate kinase;protein_id=WP_006566002.1;transl_table=11;translation=length.323 NZ_DS499729 GenBank exon 477 1448 . - 1 Parent=ANACAC_RS03040 NZ_DS499729 GenBank gene 1445 2908 . - 1 ID=ANACAC_RS03045;Name=ANACAC_RS03045;old_locus_tag=ANACAC_00495 NZ_DS499729 GenBank mRNA 1445 2908 . - 1 ID=ANACAC_RS03045;Parent=ANACAC_RS03045 NZ_DS499729 GenBank CDS 1445 2908 . - 1 ID=ANACAC_RS03045;Parent=ANACAC_RS03045;Name=ANACAC_RS03045;Note=Derived by automated computational analysis using gene prediction method: Protein Homology.;codon_start=1;inference=COORDINATES: similar to AA sequence:RefSeq:WP_006566003.1;old_locus_tag=ANACAC_00495;product=glycoside hydrolase family 32 protein;protein_id=WP_006566003.1;transl_table=11;translation=length.487 NZ_DS499729 GenBank exon 1445 2908 . - 1 Parent=ANACAC_RS03045 NZ_DS499729 GenBank gene 2919 4832 . - 1 ID=ANACAC_RS03050;Name=ANACAC_RS03050;old_locus_tag=ANACAC_00496 NZ_DS499729 GenBank mRNA 2919 4832 . - 1 ID=ANACAC_RS03050;Parent=ANACAC_RS03050 NZ_DS499729 GenBank CDS 2919 4832 . - 1 ID=ANACAC_RS03050;Parent=ANACAC_RS03050;eC_number=2.7.1.211;Name=ANACAC_RS03050;Note=Derived by automated computational analysis using gene prediction method: Protein Homology.;codon_start=1;inference=COORDINATES: similar to AA sequence:RefSeq:WP_009288910.1;old_locus_tag=ANACAC_00496;product=sucrose-specific PTS transporter subunit IIBC;protein_id=WP_006566004.1;transl_table=11;translation=length.637 NZ_DS499729 GenBank exon 2919 4832 . - 1 Parent=ANACAC_RS03050 NZ_DS499729 GenBank gene 5003 6037 . - 1 ID=ANACAC_RS03055;Name=ANACAC_RS03055;old_locus_tag=ANACAC_00497 NZ_DS499729 GenBank mRNA 5003 6037 . - 1 ID=ANACAC_RS03055;Parent=ANACAC_RS03055 NZ_DS499729 GenBank CDS 5003 6037 . - 1 ID=ANACAC_RS03055;Parent=ANACAC_RS03055;Name=ANACAC_RS03055;Note=Derived by automated computational analysis using gene prediction method: Protein Homology.;codon_start=1;inference=COORDINATES: similar to AA sequence:RefSeq:WP_006566005.1;old_locus_tag=ANACAC_00497;product=hypothetical protein;protein_id=WP_006566005.1;transl_table=11;translation=length.344 NZ_DS499729 GenBank exon 5003 6037 . - 1 Parent=ANACAC_RS03055 NZ_DS499729 GenBank gene 6034 6588 . - 1 ID=ANACAC_RS03060;Name=ANACAC_RS03060;old_locus_tag=ANACAC_00498 NZ_DS499729 GenBank mRNA 6034 6588 . - 1 ID=ANACAC_RS03060;Parent=ANACAC_RS03060 NZ_DS499729 GenBank CDS 6034 6588 . - 1 ID=ANACAC_RS03060;Parent=ANACAC_RS03060;Name=ANACAC_RS03060;Note=Derived by automated computational analysis using gene prediction method: Protein Homology.;codon_start=1;inference=COORDINATES: similar to AA sequence:RefSeq:WP_009288911.1;old_locus_tag=ANACAC_00498;product=sigma-70 family RNA polymerase sigma factor;protein_id=WP_039946252.1;transl_table=11;translation=length.184 NZ_DS499729 GenBank exon 6034 6588 . - 1 Parent=ANACAC_RS03060 NZ_DS499729 GenBank gene 6716 7705 . - 1 ID=ANACAC_RS03065;Name=ANACAC_RS03065;old_locus_tag=ANACAC_00499 NZ_DS499729 GenBank mRNA 6716 7705 . - 1 ID=ANACAC_RS03065;Parent=ANACAC_RS03065 NZ_DS499729 GenBank CDS 6716 7705 . - 1 ID=ANACAC_RS03065;Parent=ANACAC_RS03065;Name=ANACAC_RS03065;Note=Derived by automated computational analysis using gene prediction method: Protein Homology.;codon_start=1;inference=COORDINATES: similar to AA sequence:RefSeq:WP_007713560.1;old_locus_tag=ANACAC_00499;product=LacI family DNA-binding transcriptional regulator;protein_id=WP_182483054.1;transl_table=11;translation=length.329 NZ_DS499729 GenBank exon 6716 7705 . - 1 Parent=ANACAC_RS03065 NZ_DS499729 GenBank gene 7846 8289 . + 1 ID=ANACAC_RS03070;Name=ANACAC_RS03070;old_locus_tag=ANACAC_00500 NZ_DS499729 GenBank mRNA 7846 8289 . + 1 ID=ANACAC_RS03070;Parent=ANACAC_RS03070 NZ_DS499729 GenBank CDS 7846 8289 . + 1 ID=ANACAC_RS03070;Parent=ANACAC_RS03070;Name=ANACAC_RS03070;Note=Derived by automated computational analysis using gene prediction method: Protein Homology.;codon_start=1;inference=COORDINATES: similar to AA sequence:RefSeq:WP_009288913.1;old_locus_tag=ANACAC_00500;product=MarR family transcriptional regulator;protein_id=WP_006566008.1;transl_table=11;translation=length.147 NZ_DS499729 GenBank exon 7846 8289 . + 1 Parent=ANACAC_RS03070 NZ_DS499729 GenBank gene 8286 8289 . + 1 ID=ANACAC_RS03075;Name=ANACAC_RS03075;old_locus_tag=ANACAC_00501 NZ_DS499729 GenBank mRNA 8286 8289 . + 1 ID=ANACAC_RS03075;Parent=ANACAC_RS03075 NZ_DS499729 GenBank CDS 8286 8289 . + 1 ID=ANACAC_RS03075;Parent=ANACAC_RS03075;Name=ANACAC_RS03075;Note=Derived by automated computational analysis using gene prediction method: Protein Homology.;codon_start=1;inference=COORDINATES: similar to AA sequence:RefSeq:WP_009288914.1;old_locus_tag=ANACAC_00501;product=flavodoxin;protein_id=WP_006566009.1;transl_table=11;translation=length.182 NZ_DS499729 GenBank exon 8286 8289 . + 1 Parent=ANACAC_RS03075