##gff-version 3
##sequence-region NC_013132 1 11166
# conversion-by bp_genbank2gff3.pl
# organism Chitinophaga pinensis DSM 2588
# Note Chitinophaga pinensis DSM 2588, complete genome.
# date 26-AUG-2019
NC_013132	GenBank	region	1	11166	.	+	1	ID=NC_013132;Dbxref=BioProject:PRJNA224116,taxon:485918;Name=NC_013132;Note=Chitinophaga pinensis DSM 2588%2C complete genome.,REFSEQ INFORMATION: The reference sequence was derived from CP001699. URL -- http://www.jgi.doe.gov JGI Project ID: 4082984 Source DNA and organism available from Hans-Peter Klenk at the German Collection of Microorganisms and Cell Cultures (DSMZ) (hans-peter.klenk@dsmz.de) Contacts: Jonathan A. Eisen (jaeisen@ucdavis.edu) David Bruce (microbe@cuba.jgi-psf.org) Whole genome sequencing and draft assembly at JGI-PGF Finishing done by JGI-LANL Annotation by JGI-ORNL and JGI-PGF 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 :: 08/26/2019 00:28:39 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) :: 7,171 CDSs (total) :: 7,077 Genes (coding) :: 7,009 CDSs (with protein) :: 7,009 Genes (RNA) :: 94 rRNAs :: 6,6,6 (5S,16S,23S) complete rRNAs :: 6,6,6 (5S,16S,23S) tRNAs :: 73 ncRNAs :: 3 Pseudo Genes (total) :: 68 CDSs (without protein) :: 68 Pseudo Genes (ambiguous residues) :: 0 of 68 Pseudo Genes (frameshifted) :: 19 of 68 Pseudo Genes (incomplete) :: 47 of 68 Pseudo Genes (internal stop) :: 11 of 68 Pseudo Genes (multiple problems) :: 8 of 68 ##Genome-Annotation-Data-END## ##Metadata-START## Organism Display Name :: Chitinophaga pinensis UQM 2034,DSM 2588 Culture Collection ID :: DSM 2588,ATCC 43595,LMG 13176,UQM 2034 GOLD Stamp ID :: Gi02244 Funding Program :: DOE-GEBA 2007 Gene Calling Method :: Prodigal Isolation Site :: Pine litter in Australia Isolation Country :: Australia Oxygen Requirement :: Aerobe Cell Shape :: Rod-shaped Motility :: Motile Sporulation :: Nonsporulating Temperature Range :: Mesophile Temperature Optimum :: 23 - 24C pH :: 7 Gram Staining :: gram- Biotic Relationship :: Free living Diseases :: None Phenotypes :: Biomass degrader,Chitin degradation Energy Source :: Chemoorganotroph ##Metadata-END## COMPLETENESS: full length. ,type strain of Chitinophaga pinensis;comment1=REFSEQ INFORMATION: The reference sequence was derived from CP001699. URL -- http://www.jgi.doe.gov JGI Project ID: 4082984 Source DNA and organism available from Hans-Peter Klenk at the German Collection of Microorganisms and Cell Cultures (DSMZ) (hans-peter.klenk@dsmz.de) Contacts: Jonathan A. Eisen (jaeisen@ucdavis.edu) David Bruce (microbe@cuba.jgi-psf.org) Whole genome sequencing and draft assembly at JGI-PGF Finishing done by JGI-LANL Annotation by JGI-ORNL and JGI-PGF 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 :: 08/26/2019 00:28:39 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) :: 7%2C171 CDSs (total) :: 7%2C077 Genes (coding) :: 7%2C009 CDSs (with protein) :: 7%2C009 Genes (RNA) :: 94 rRNAs :: 6%2C 6%2C 6 (5S%2C 16S%2C 23S) complete rRNAs :: 6%2C 6%2C 6 (5S%2C 16S%2C 23S) tRNAs :: 73 ncRNAs :: 3 Pseudo Genes (total) :: 68 CDSs (without protein) :: 68 Pseudo Genes (ambiguous residues) :: 0 of 68 Pseudo Genes (frameshifted) :: 19 of 68 Pseudo Genes (incomplete) :: 47 of 68 Pseudo Genes (internal stop) :: 11 of 68 Pseudo Genes (multiple problems) :: 8 of 68 ##Genome-Annotation-Data-END## ##Metadata-START## Organism Display Name :: Chitinophaga pinensis UQM 2034%2C DSM 2588 Culture Collection ID :: DSM 2588%2C ATCC 43595%2C LMG 13176%2C UQM 2034 GOLD Stamp ID :: Gi02244 Funding Program :: DOE-GEBA 2007 Gene Calling Method :: Prodigal Isolation Site :: Pine litter in Australia Isolation Country :: Australia Oxygen Requirement :: Aerobe Cell Shape :: Rod-shaped Motility :: Motile Sporulation :: Nonsporulating Temperature Range :: Mesophile Temperature Optimum :: 23 - 24C pH :: 7 Gram Staining :: gram- Biotic Relationship :: Free living Diseases :: None Phenotypes :: Biomass degrader%2C Chitin degradation Energy Source :: Chemoorganotroph ##Metadata-END## COMPLETENESS: full length. ;date=26-AUG-2019;mol_type=genomic DNA;organism=Chitinophaga pinensis DSM 2588;strain=DSM 2588;type_material=type strain of Chitinophaga pinensis
NC_013132	GenBank	gene	1	2856	.	+	1	ID=CPIN_RS27450;Name=CPIN_RS27450;old_locus_tag=Cpin_5548
NC_013132	GenBank	mRNA	1	2856	.	+	1	ID=CPIN_RS27450.t01;Parent=CPIN_RS27450
NC_013132	GenBank	CDS	1	2856	.	+	1	ID=CPIN_RS27450.p01;Parent=CPIN_RS27450.t01;Name=CPIN_RS27450;Note=Derived by automated computational analysis using gene prediction method: Protein Homology.;codon_start=1;inference=COORDINATES: similar to AA sequence:RefSeq:WP_015267782.1;old_locus_tag=Cpin_5548;product=DUF5110 domain-containing protein;protein_id=WP_012793142.1;transl_table=11;translation=length.951
NC_013132	GenBank	exon	1	2856	.	+	1	Parent=CPIN_RS27450.t01
NC_013132	GenBank	gene	2967	6077	.	+	1	ID=CPIN_RS27455;Name=CPIN_RS27455;old_locus_tag=Cpin_5549
NC_013132	GenBank	mRNA	2967	6077	.	+	1	ID=CPIN_RS27455.t01;Parent=CPIN_RS27455
NC_013132	GenBank	CDS	2967	6077	.	+	1	ID=CPIN_RS27455.p01;Parent=CPIN_RS27455.t01;Name=CPIN_RS27455;Note=Derived by automated computational analysis using gene prediction method: Protein Homology.;codon_start=1;inference=COORDINATES: protein motif:HMM:TIGR04056.1;old_locus_tag=Cpin_5549;product=TonB-dependent receptor;protein_id=WP_012793143.1;transl_table=11;translation=length.1036
NC_013132	GenBank	exon	2967	6077	.	+	1	Parent=CPIN_RS27455.t01
NC_013132	GenBank	gene	6096	7658	.	+	1	ID=CPIN_RS27460;Name=CPIN_RS27460;old_locus_tag=Cpin_5550
NC_013132	GenBank	mRNA	6096	7658	.	+	1	ID=CPIN_RS27460.t01;Parent=CPIN_RS27460
NC_013132	GenBank	CDS	6096	7658	.	+	1	ID=CPIN_RS27460.p01;Parent=CPIN_RS27460.t01;Name=CPIN_RS27460;Note=Derived by automated computational analysis using gene prediction method: Protein Homology.;codon_start=1;inference=COORDINATES: similar to AA sequence:RefSeq:WP_008465421.1;old_locus_tag=Cpin_5550;product=RagB/SusD family nutrient uptake outer membrane protein;protein_id=WP_012793144.1;transl_table=11;translation=length.520
NC_013132	GenBank	exon	6096	7658	.	+	1	Parent=CPIN_RS27460.t01
NC_013132	GenBank	gene	7688	8452	.	+	1	ID=CPIN_RS37120;Name=CPIN_RS37120;old_locus_tag=Cpin_5551
NC_013132	GenBank	mRNA	7688	8452	.	+	1	ID=CPIN_RS37120.t01;Parent=CPIN_RS37120
NC_013132	GenBank	CDS	7688	8452	.	+	1	ID=CPIN_RS37120.p01;Parent=CPIN_RS37120.t01;Name=CPIN_RS37120;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=Cpin_5551;product=hypothetical protein;protein_id=WP_012793145.1;transl_table=11;translation=length.254
NC_013132	GenBank	exon	7688	8452	.	+	1	Parent=CPIN_RS37120.t01
NC_013132	GenBank	gene	8670	9062	.	-	1	ID=CPIN_RS27470;Name=CPIN_RS27470;old_locus_tag=Cpin_5552
NC_013132	GenBank	mRNA	8670	9062	.	-	1	ID=CPIN_RS27470.t01;Parent=CPIN_RS27470
NC_013132	GenBank	CDS	8670	9062	.	-	1	ID=CPIN_RS27470.p01;Parent=CPIN_RS27470.t01;Name=CPIN_RS27470;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=Cpin_5552;product=hypothetical protein;protein_id=WP_012793146.1;transl_table=11;translation=length.130
NC_013132	GenBank	exon	8670	9062	.	-	1	Parent=CPIN_RS27470.t01
NC_013132	GenBank	gene	9163	11166	.	-	1	ID=CPIN_RS37125;Name=CPIN_RS37125;old_locus_tag=Cpin_5553
NC_013132	GenBank	mRNA	9163	11166	.	-	1	ID=CPIN_RS37125.t01;Parent=CPIN_RS37125
NC_013132	GenBank	CDS	9163	11166	.	-	1	ID=CPIN_RS37125.p01;Parent=CPIN_RS37125.t01;Name=CPIN_RS37125;Note=Derived by automated computational analysis using gene prediction method: Protein Homology.;codon_start=1;inference=COORDINATES: protein motif:HMM:PF02839.12%2CHMM:TIGR04183.1,COORDINATES: similar to AA sequence:RefSeq:WP_009087829.1;old_locus_tag=Cpin_5553;product=T9SS type A sorting domain-containing protein;protein_id=WP_148230654.1;transl_table=11;translation=length.667
NC_013132	GenBank	exon	9163	11166	.	-	1	Parent=CPIN_RS37125.t01