##gff-version 3
##sequence-region NC_012914 1 12493
# conversion-by bp_genbank2gff3.pl
# organism Paenibacillus sp. JDR-2
# Note Paenibacillus sp. JDR-2, complete sequence.
# date 25-SEP-2019
NC_012914	GenBank	region	1	12493	.	+	1	ID=NC_012914;Dbxref=BioProject:PRJNA224116,taxon:324057;Name=NC_012914;Note=Paenibacillus sp. JDR-2%2C complete sequence.,REFSEQ INFORMATION: The reference sequence was derived from CP001656. URL -- http://www.jgi.doe.gov JGI Project ID: 4043135 Source DNA and bacteria available from James Preston (jpreston@ufl.edu) Contacts: James Preston (jpreston@ufl.edu) David Bruce (microbe@cuba.jgi-psf.org) Annotation done by JGI-ORNL and JGI-PGF Finishing done by JGI-LANL Finished microbial genomes have been curated to close all gaps with greater than 98%25 coverage of at least two independent clones. Each base pair has a minimum q (quality) value of 30 and the total error rate is less than one per 50000. The JGI and collaborators endorse the principles for the distribution and use of large scale sequencing data adopted by the larger genome sequencing community and urge users of this data to follow them. it is our intention to publish the work of this project in a timely fashion and we welcome collaborative interaction on the project and analysis. (http://www.genome.gov/page.cfm?pageID%3D10506376). 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 :: 09/25/2019 01:21:26 Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline (PGAP) Annotation Method :: Best-placed reference protein set,GeneMarkS-2+ Annotation Software revision :: 4.9 Features Annotated :: Gene,CDS,rRNA,tRNA,ncRNA,repeat_region Genes (total) :: 6,343 CDSs (total) :: 6,217 Genes (coding) :: 6,122 CDSs (with protein) :: 6,122 Genes (RNA) :: 126 rRNAs :: 11,12,12 (5S,16S,23S) complete rRNAs :: 11,12,12 (5S,16S,23S) tRNAs :: 87 ncRNAs :: 4 Pseudo Genes (total) :: 95 CDSs (without protein) :: 95 Pseudo Genes (ambiguous residues) :: 0 of 95 Pseudo Genes (frameshifted) :: 35 of 95 Pseudo Genes (incomplete) :: 62 of 95 Pseudo Genes (internal stop) :: 6 of 95 Pseudo Genes (multiple problems) :: 8 of 95 ##Genome-Annotation-Data-END## ##Metadata-START## Organism Display Name :: Paenibacillus sp. JDR-2 GOLD Stamp ID :: Gi02023 Greengenes ID :: 270979 Isolation Site :: Sweet gum stem wood buried in surface soil Oxygen Requirement :: Aerobe Cell Shape :: Rod-shaped Sporulation :: Sporulating Temperature Range :: Mesophile Temperature Optimum :: 30 C Gram Staining :: gram+ Biotic Relationship :: Free living Diseases :: None Habitat :: Host,Wood Phenotypes :: Methylglucuronoxylan utilization ##Metadata-END## COMPLETENESS: full length. ;comment1=REFSEQ INFORMATION: The reference sequence was derived from CP001656. URL -- http://www.jgi.doe.gov JGI Project ID: 4043135 Source DNA and bacteria available from James Preston (jpreston@ufl.edu) Contacts: James Preston (jpreston@ufl.edu) David Bruce (microbe@cuba.jgi-psf.org) Annotation done by JGI-ORNL and JGI-PGF Finishing done by JGI-LANL Finished microbial genomes have been curated to close all gaps with greater than 98%25 coverage of at least two independent clones. Each base pair has a minimum q (quality) value of 30 and the total error rate is less than one per 50000. The JGI and collaborators endorse the principles for the distribution and use of large scale sequencing data adopted by the larger genome sequencing community and urge users of this data to follow them. it is our intention to publish the work of this project in a timely fashion and we welcome collaborative interaction on the project and analysis. (http://www.genome.gov/page.cfm?pageID%3D10506376). 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 :: 09/25/2019 01:21:26 Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline (PGAP) Annotation Method :: Best-placed reference protein set%3B GeneMarkS-2+ Annotation Software revision :: 4.9 Features Annotated :: Gene%3B CDS%3B rRNA%3B tRNA%3B ncRNA%3B repeat_region Genes (total) :: 6%2C343 CDSs (total) :: 6%2C217 Genes (coding) :: 6%2C122 CDSs (with protein) :: 6%2C122 Genes (RNA) :: 126 rRNAs :: 11%2C 12%2C 12 (5S%2C 16S%2C 23S) complete rRNAs :: 11%2C 12%2C 12 (5S%2C 16S%2C 23S) tRNAs :: 87 ncRNAs :: 4 Pseudo Genes (total) :: 95 CDSs (without protein) :: 95 Pseudo Genes (ambiguous residues) :: 0 of 95 Pseudo Genes (frameshifted) :: 35 of 95 Pseudo Genes (incomplete) :: 62 of 95 Pseudo Genes (internal stop) :: 6 of 95 Pseudo Genes (multiple problems) :: 8 of 95 ##Genome-Annotation-Data-END## ##Metadata-START## Organism Display Name :: Paenibacillus sp. JDR-2 GOLD Stamp ID :: Gi02023 Greengenes ID :: 270979 Isolation Site :: Sweet gum stem wood buried in surface soil Oxygen Requirement :: Aerobe Cell Shape :: Rod-shaped Sporulation :: Sporulating Temperature Range :: Mesophile Temperature Optimum :: 30 C Gram Staining :: gram+ Biotic Relationship :: Free living Diseases :: None Habitat :: Host%2C Wood Phenotypes :: Methylglucuronoxylan utilization ##Metadata-END## COMPLETENESS: full length. ;date=25-SEP-2019;mol_type=genomic DNA;organism=Paenibacillus sp. JDR-2;strain=JDR-2
NC_012914	GenBank	gene	1	1629	.	-	1	ID=PJDR2_RS04870;Name=PJDR2_RS04870;old_locus_tag=Pjdr2_0947
NC_012914	GenBank	mRNA	1	1629	.	-	1	ID=PJDR2_RS04870.t01;Parent=PJDR2_RS04870
NC_012914	GenBank	CDS	1	1629	.	-	1	ID=PJDR2_RS04870.p01;Parent=PJDR2_RS04870.t01;Name=PJDR2_RS04870;Note=Derived by automated computational analysis using gene prediction method: Protein Homology.;codon_start=1;inference=COORDINATES: similar to AA sequence:RefSeq:WP_017688357.1;old_locus_tag=Pjdr2_0947;product=response regulator;protein_id=WP_015842573.1;transl_table=11;translation=length.542
NC_012914	GenBank	exon	1	1629	.	-	1	Parent=PJDR2_RS04870.t01
NC_012914	GenBank	gene	1640	3352	.	-	1	ID=PJDR2_RS04875;Name=PJDR2_RS04875;old_locus_tag=Pjdr2_0948
NC_012914	GenBank	mRNA	1640	3352	.	-	1	ID=PJDR2_RS04875.t01;Parent=PJDR2_RS04875
NC_012914	GenBank	CDS	1640	3352	.	-	1	ID=PJDR2_RS04875.p01;Parent=PJDR2_RS04875.t01;Name=PJDR2_RS04875;Note=Derived by automated computational analysis using gene prediction method: Protein Homology.;codon_start=1;inference=COORDINATES: similar to AA sequence:RefSeq:WP_017688356.1;old_locus_tag=Pjdr2_0948;product=sensor histidine kinase;protein_id=WP_015842574.1;transl_table=11;translation=length.570
NC_012914	GenBank	exon	1640	3352	.	-	1	Parent=PJDR2_RS04875.t01
NC_012914	GenBank	gene	3488	4456	.	+	1	ID=PJDR2_RS04880;Name=PJDR2_RS04880;old_locus_tag=Pjdr2_0949
NC_012914	GenBank	mRNA	3488	4456	.	+	1	ID=PJDR2_RS04880.t01;Parent=PJDR2_RS04880
NC_012914	GenBank	CDS	3488	4456	.	+	1	ID=PJDR2_RS04880.p01;Parent=PJDR2_RS04880.t01;Name=PJDR2_RS04880;Note=Derived by automated computational analysis using gene prediction method: Protein Homology.;codon_start=1;inference=COORDINATES: similar to AA sequence:RefSeq:WP_020617044.1;old_locus_tag=Pjdr2_0949;product=ABC transporter permease subunit;protein_id=WP_150106437.1;transl_table=11;translation=length.322
NC_012914	GenBank	exon	3488	4456	.	+	1	Parent=PJDR2_RS04880.t01
NC_012914	GenBank	gene	4470	5348	.	+	1	ID=PJDR2_RS04885;Name=PJDR2_RS04885;old_locus_tag=Pjdr2_0950
NC_012914	GenBank	mRNA	4470	5348	.	+	1	ID=PJDR2_RS04885.t01;Parent=PJDR2_RS04885
NC_012914	GenBank	CDS	4470	5348	.	+	1	ID=PJDR2_RS04885.p01;Parent=PJDR2_RS04885.t01;Name=PJDR2_RS04885;Note=Derived by automated computational analysis using gene prediction method: Protein Homology.;codon_start=1;inference=COORDINATES: similar to AA sequence:RefSeq:WP_006040641.1;old_locus_tag=Pjdr2_0950;product=carbohydrate ABC transporter permease;protein_id=WP_015842576.1;transl_table=11;translation=length.292
NC_012914	GenBank	exon	4470	5348	.	+	1	Parent=PJDR2_RS04885.t01
NC_012914	GenBank	gene	5412	9713	.	+	1	ID=PJDR2_RS04890;Name=PJDR2_RS04890;old_locus_tag=Pjdr2_0951
NC_012914	GenBank	mRNA	5412	9713	.	+	1	ID=PJDR2_RS04890.t01;Parent=PJDR2_RS04890
NC_012914	GenBank	CDS	5412	9713	.	+	1	ID=PJDR2_RS04890.p01;Parent=PJDR2_RS04890.t01;Name=PJDR2_RS04890;Note=Derived by automated computational analysis using gene prediction method: Protein Homology.;codon_start=1;inference=COORDINATES: similar to AA sequence:RefSeq:WP_006040642.1;old_locus_tag=Pjdr2_0951;product=family 16 glycosylhydrolase;protein_id=WP_015842577.1;transl_table=11;translation=length.1433
NC_012914	GenBank	exon	5412	9713	.	+	1	Parent=PJDR2_RS04890.t01
NC_012914	GenBank	gene	9807	10520	.	+	1	ID=PJDR2_RS04895;Name=PJDR2_RS04895;old_locus_tag=Pjdr2_0952
NC_012914	GenBank	mRNA	9807	10520	.	+	1	ID=PJDR2_RS04895.t01;Parent=PJDR2_RS04895
NC_012914	GenBank	CDS	9807	10520	.	+	1	ID=PJDR2_RS04895.p01;Parent=PJDR2_RS04895.t01;Name=PJDR2_RS04895;Note=Derived by automated computational analysis using gene prediction method: Protein Homology.;codon_start=1;inference=COORDINATES: similar to AA sequence:RefSeq:WP_015842578.1;old_locus_tag=Pjdr2_0952;product=family 16 glycosylhydrolase;protein_id=WP_015842578.1;transl_table=11;translation=length.237
NC_012914	GenBank	exon	9807	10520	.	+	1	Parent=PJDR2_RS04895.t01
NC_012914	GenBank	gene	10769	12493	.	+	1	ID=PJDR2_RS04900;Name=PJDR2_RS04900;old_locus_tag=Pjdr2_0953
NC_012914	GenBank	mRNA	10769	12493	.	+	1	ID=PJDR2_RS04900.t01;Parent=PJDR2_RS04900
NC_012914	GenBank	CDS	10769	12493	.	+	1	ID=PJDR2_RS04900.p01;Parent=PJDR2_RS04900.t01;Name=PJDR2_RS04900;Note=Derived by automated computational analysis using gene prediction method: Protein Homology.;codon_start=1;inference=COORDINATES: similar to AA sequence:RefSeq:WP_006039961.1;old_locus_tag=Pjdr2_0953;product=extracellular solute-binding protein;protein_id=WP_015842579.1;transl_table=11;translation=length.574
NC_012914	GenBank	exon	10769	12493	.	+	1	Parent=PJDR2_RS04900.t01