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Sequence Set Browser

 

NZ_ABAX00000000.3 Anaerostipes caccae DSM 14662

Master
# of Scaffolds/Chrs: 26
BioProject: PRJNA224116
BioSample: SAMN00627053
Assembly: GCF_000154305.1
Keywords: WGS
Annotation: Scaffolds
Organism: Anaerostipes caccae DSM 14662show lineagehide lineage
Biosource:
/mol_type = genomic
/strain = DSM 14662
WGS: ABAX03000001:ABAX03000065
Reference:
Draft genome sequence of Anaerostipes caccae (DSM 14662) : Unpublished – show 7 authorshide authors
Sudarsanam,P., Ley,R., Guruge,J., Turnbaugh,P.J., Mahowald,M., Liep,D., Gordon,J.
Submission:
Submitted (22-MAY-2007) Genome Sequencing Center, Washington University School of Medicine, 4444 Forest Park, St. Louis, MO 63108, USA – show 7 authorshide authors
Fulton,L., Clifton,S., Fulton,B., Xu,J., Minx,P., Mardis,E.R., Wilson,R.K.
Submission:
Submitted (07-NOV-2007) Genome Sequencing Center, Washington University School of Medicine, 4444 Forest Park, St. Louis, MO 63108, USA – show 12 authorshide authors
Fulton,L., Clifton,S., Fulton,B., Xu,J., Minx,P., Pepin,K.H., Johnson,M., Thiruvilangam,P., Bhonagiri,V., Nash,W.E., Mardis,E.R., Wilson,R.K.

On Nov 21, 2007 this sequence version replaced gi:149118174.

The Anaerostipes caccae DSM 14662 whole genome shotgun (WGS) project has the project accession NZ_ABAX00000000. This version of the project (03) has the accession number NZ_ABAX03000000, and consists of sequences NZ_DS499719-NZ_DS499744.

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/HGMISeq.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.

##Genome-Annotation-Data-START##
Annotation Provider : NCBI
Annotation Date : 04/14/2017 18:14:53
Annotation Pipeline : NCBI Prokaryotic Genome Annotation Pipeline
Annotation Method : Best-placed reference protein set; GeneMarkS+
Annotation Software revision : 4.1
Features Annotated : Gene; CDS; rRNA; tRNA; ncRNA; repeat_region
Genes (total) : 3,546
CDS (total) : 3,455
Genes (coding) : 3,363
CDS (coding) : 3,363
Genes (RNA) : 91
rRNAs : 5, 4, 8 ( 5S, 16S, 23S )
complete rRNAs : 5, 4, 4 ( 5S, 16S, 23S )
partial rRNAs : 4 ( 23S )
tRNAs : 70
ncRNAs : 4
Pseudo Genes (total) : 92
Pseudo Genes (ambiguous residues) : 0 of 92
Pseudo Genes (frameshifted) : 60 of 92
Pseudo Genes (incomplete) : 21 of 92
Pseudo Genes (internal stop) : 18 of 92
Pseudo Genes (multiple problems) : 7 of 92
CRISPR Arrays : 7
##Genome-Annotation-Data-END##