##gff-version 3
##sequence-region NZ_GG692727 1 9529
# conversion-by bp_genbank2gff3.pl
# organism Roseburia intestinalis L1-82
# Note Roseburia intestinalis L1-82 Scfld14, whole genome shotgun sequence.
# date 20-DEC-2019
NZ_GG692727	GenBank	region	1	9529	.	+	1	ID=NZ_GG692727;Dbxref=BioProject:PRJNA224116,taxon:536231;Name=NZ_GG692727;Note=Roseburia intestinalis L1-82 Scfld14%2C whole genome shotgun sequence.,REFSEQ INFORMATION: The reference sequence was derived from GG692727. Roseburia intestinalis L1-82 (GenBank Accession Number for 16S rDNA gene: AJ312385 is a member of the division Firmicutes in the domain bacteria and has been isolated from human feces. The sequenced strain was obtained from the laboratory of Prof. Harry Flint,Rowett Research Institute,Aberdeen,Scotland,UK (H.Flint@rowett.ac.uk). 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. This work was supported by the National Human Genome Research Institute and the NIH Roadmap Human Microbiome Project [http://nihroadmap.nih.gov/hmp/]. This is a reference genome for the Human Microbiome Project. This project is co-owned with the Human Microbiome Project DACC. Genome Coverage: 15.8X Sequencing Technology: 454. Roseburia intestinalis L1-82 (GenBank Accession Number for 16S rDNA gene: AJ312385) is a member of the division Firmicutes in the domain bacteria and has been isolated from human feces. The sequenced strain was obtained from the laboratory of Prof. Harry Flint,Rowett Research Institute,Aberdeen,Scotland,UK (H.Flint@rowett.ac.uk). 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. This work was supported by the National Human Genome Research Institute and the NIH Roadmap Human Microbiome Project [http://nihroadmap.nih.gov/hmp/]. 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 is a reference genome for the Human Microbiome Project. This project is co-owned with the Human Microbiome Project DACC. Genome Coverage: 15.8X Sequencing Technology: 454 Annotation was added to the contigs in August 2009. 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/ ##Genome-Annotation-Data-START## Annotation Provider :: NCBI RefSeq Annotation Date :: 12/17/2019 04:46:02 Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline (PGAP) Annotation Method :: Best-placed reference protein set,GeneMarkS-2+ Annotation Software revision :: 4.10 Features Annotated :: Gene,CDS,rRNA,tRNA,ncRNA,repeat_region Genes (total) :: 4,283 CDSs (total) :: 4,204 Genes (coding) :: 3,739 CDSs (with protein) :: 3,739 Genes (RNA) :: 79 rRNAs :: 4,2,9 (5S,16S,23S) complete rRNAs :: 4,1,1 (5S,16S,23S) partial rRNAs :: 1,8 (16S,23S) tRNAs :: 60 ncRNAs :: 4 Pseudo Genes (total) :: 467 CDSs (without protein) :: 465 Pseudo Genes (ambiguous residues) :: 39 of 467 Pseudo Genes (frameshifted) :: 133 of 467 Pseudo Genes (incomplete) :: 320 of 467 Pseudo Genes (internal stop) :: 22 of 467 Pseudo Genes (multiple problems) :: 46 of 467 CRISPR Arrays :: 3 ##Genome-Annotation-Data-END## ;comment1=REFSEQ INFORMATION: The reference sequence was derived from GG692727. Roseburia intestinalis L1-82 (GenBank Accession Number for 16S rDNA gene: AJ312385 is a member of the division Firmicutes in the domain bacteria and has been isolated from human feces. The sequenced strain was obtained from the laboratory of Prof. Harry Flint%2C Rowett Research Institute%2C Aberdeen%2C Scotland%2C UK (H.Flint@rowett.ac.uk). 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. This work was supported by the National Human Genome Research Institute and the NIH Roadmap Human Microbiome Project [http://nihroadmap.nih.gov/hmp/]. This is a reference genome for the Human Microbiome Project. This project is co-owned with the Human Microbiome Project DACC. Genome Coverage: 15.8X Sequencing Technology: 454. Roseburia intestinalis L1-82 (GenBank Accession Number for 16S rDNA gene: AJ312385) is a member of the division Firmicutes in the domain bacteria and has been isolated from human feces. The sequenced strain was obtained from the laboratory of Prof. Harry Flint%2C Rowett Research Institute%2C Aberdeen%2C Scotland%2C UK (H.Flint@rowett.ac.uk). 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. This work was supported by the National Human Genome Research Institute and the NIH Roadmap Human Microbiome Project [http://nihroadmap.nih.gov/hmp/]. 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 is a reference genome for the Human Microbiome Project. This project is co-owned with the Human Microbiome Project DACC. Genome Coverage: 15.8X Sequencing Technology: 454 Annotation was added to the contigs in August 2009. 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/ ##Genome-Annotation-Data-START## Annotation Provider :: NCBI RefSeq Annotation Date :: 12/17/2019 04:46:02 Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline (PGAP) Annotation Method :: Best-placed reference protein set%3B GeneMarkS-2+ Annotation Software revision :: 4.10 Features Annotated :: Gene%3B CDS%3B rRNA%3B tRNA%3B ncRNA%3B repeat_region Genes (total) :: 4%2C283 CDSs (total) :: 4%2C204 Genes (coding) :: 3%2C739 CDSs (with protein) :: 3%2C739 Genes (RNA) :: 79 rRNAs :: 4%2C 2%2C 9 (5S%2C 16S%2C 23S) complete rRNAs :: 4%2C 1%2C 1 (5S%2C 16S%2C 23S) partial rRNAs :: 1%2C 8 (16S%2C 23S) tRNAs :: 60 ncRNAs :: 4 Pseudo Genes (total) :: 467 CDSs (without protein) :: 465 Pseudo Genes (ambiguous residues) :: 39 of 467 Pseudo Genes (frameshifted) :: 133 of 467 Pseudo Genes (incomplete) :: 320 of 467 Pseudo Genes (internal stop) :: 22 of 467 Pseudo Genes (multiple problems) :: 46 of 467 CRISPR Arrays :: 3 ##Genome-Annotation-Data-END## ;date=20-DEC-2019;host=Homo sapiens;isolation_source=biological product [ENVO:02000043];mol_type=genomic DNA;organism=Roseburia intestinalis L1-82;strain=L1-82;submitter_seqid=Scfld14;type_material=type strain of Roseburia intestinalis
NZ_GG692727	GenBank	gene	1	3927	.	-	1	ID=ROSINTL182_RS11930;Dbxref=GeneID:43319281;Name=ROSINTL182_RS11930;old_locus_tag=ROSINTL182_07683
NZ_GG692727	GenBank	mRNA	1	3927	.	-	1	ID=ROSINTL182_RS11930.t01;Parent=ROSINTL182_RS11930
NZ_GG692727	GenBank	CDS	1	3927	.	-	1	ID=ROSINTL182_RS11930.p01;Parent=ROSINTL182_RS11930.t01;Dbxref=GeneID:43319281;Name=ROSINTL182_RS11930;Note=Derived by automated computational analysis using gene prediction method: Protein Homology.;codon_start=1;inference=COORDINATES: similar to AA sequence:RefSeq:WP_015522404.1;old_locus_tag=ROSINTL182_07683;product=beta-mannanase;protein_id=WP_044999186.1;transl_table=11;translation=length.1308
NZ_GG692727	GenBank	exon	1	3927	.	-	1	Parent=ROSINTL182_RS11930.t01
NZ_GG692727	GenBank	gene	4120	6924	.	-	1	ID=ROSINTL182_RS11935;Dbxref=GeneID:43319282;Name=ROSINTL182_RS11935;old_locus_tag=ROSINTL182_07684
NZ_GG692727	GenBank	mRNA	4120	6924	.	-	1	ID=ROSINTL182_RS11935.t01;Parent=ROSINTL182_RS11935
NZ_GG692727	GenBank	CDS	4120	6924	.	-	1	ID=ROSINTL182_RS11935.p01;Parent=ROSINTL182_RS11935.t01;Dbxref=GeneID:43319282;Name=ROSINTL182_RS11935;Note=Derived by automated computational analysis using gene prediction method: Protein Homology.;codon_start=1;inference=COORDINATES: similar to AA sequence:RefSeq:WP_015559372.1;old_locus_tag=ROSINTL182_07684;product=beta-glucosidase;protein_id=WP_006857766.1;transl_table=11;translation=length.934
NZ_GG692727	GenBank	exon	4120	6924	.	-	1	Parent=ROSINTL182_RS11935.t01
NZ_GG692727	GenBank	gene	7112	9529	.	-	1	ID=ROSINTL182_RS11940;Dbxref=GeneID:43319283;Name=ROSINTL182_RS11940;old_locus_tag=ROSINTL182_07685
NZ_GG692727	GenBank	mRNA	7112	9529	.	-	1	ID=ROSINTL182_RS11940.t01;Parent=ROSINTL182_RS11940
NZ_GG692727	GenBank	CDS	7112	9529	.	-	1	ID=ROSINTL182_RS11940.p01;Parent=ROSINTL182_RS11940.t01;Dbxref=GeneID:43319283;Name=ROSINTL182_RS11940;Note=Derived by automated computational analysis using gene prediction method: Protein Homology.;codon_start=1;inference=COORDINATES: similar to AA sequence:RefSeq:WP_006857767.1;old_locus_tag=ROSINTL182_07685;product=beta-glucosidase;protein_id=WP_006857767.1;transl_table=11;translation=length.805
NZ_GG692727	GenBank	exon	7112	9529	.	-	1	Parent=ROSINTL182_RS11940.t01