##gff-version 3
##sequence-region NC_013132 1 18398
# 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	18398	.	+	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	4089	.	+	1	ID=CPIN_RS36525;Name=CPIN_RS36525;old_locus_tag=Cpin_2184
NC_013132	GenBank	mRNA	1	4089	.	+	1	ID=CPIN_RS36525;Parent=CPIN_RS36525
NC_013132	GenBank	CDS	1	4089	.	+	1	ID=CPIN_RS36525;Parent=CPIN_RS36525;Name=CPIN_RS36525;Note=Derived by automated computational analysis using gene prediction method: Protein Homology.;codon_start=1;inference=COORDINATES: protein motif:HMM:PF00704.26;old_locus_tag=Cpin_2184;product=chitinase;protein_id=WP_012789852.1;transl_table=11;translation=length.1362
NC_013132	GenBank	exon	1	4089	.	+	1	Parent=CPIN_RS36525
NC_013132	GenBank	gene	4292	5740	.	+	1	ID=CPIN_RS10950;Name=CPIN_RS10950;old_locus_tag=Cpin_2185
NC_013132	GenBank	mRNA	4292	5740	.	+	1	ID=CPIN_RS10950;Parent=CPIN_RS10950
NC_013132	GenBank	CDS	4292	5740	.	+	1	ID=CPIN_RS10950;Parent=CPIN_RS10950;Name=CPIN_RS10950;Note=Derived by automated computational analysis using gene prediction method: Protein Homology.;codon_start=1;inference=COORDINATES: similar to AA sequence:RefSeq:WP_014216792.1;old_locus_tag=Cpin_2185;product=T9SS type A sorting domain-containing protein;protein_id=WP_148230751.1;transl_table=11;translation=length.482
NC_013132	GenBank	exon	4292	5740	.	+	1	Parent=CPIN_RS10950
NC_013132	GenBank	gene	5910	7520	.	+	1	ID=CPIN_RS10955;Name=CPIN_RS10955;old_locus_tag=Cpin_2186
NC_013132	GenBank	mRNA	5910	7520	.	+	1	ID=CPIN_RS10955;Parent=CPIN_RS10955
NC_013132	GenBank	CDS	5910	7520	.	+	1	ID=CPIN_RS10955;Parent=CPIN_RS10955;Name=CPIN_RS10955;Note=Derived by automated computational analysis using gene prediction method: Protein Homology.;codon_start=1;inference=COORDINATES: similar to AA sequence:RefSeq:WP_014217069.1;old_locus_tag=Cpin_2186;product=carbohydrate-binding protein;protein_id=WP_012789854.1;transl_table=11;translation=length.536
NC_013132	GenBank	exon	5910	7520	.	+	1	Parent=CPIN_RS10955
NC_013132	GenBank	gene	7604	8770	.	+	1	ID=CPIN_RS10960;Name=CPIN_RS10960;old_locus_tag=Cpin_2187
NC_013132	GenBank	mRNA	7604	8770	.	+	1	ID=CPIN_RS10960;Parent=CPIN_RS10960
NC_013132	GenBank	CDS	7604	8770	.	+	1	ID=CPIN_RS10960;Parent=CPIN_RS10960;Name=CPIN_RS10960;Note=Derived by automated computational analysis using gene prediction method: Protein Homology.;codon_start=1;inference=COORDINATES: similar to AA sequence:RefSeq:WP_009577602.1;old_locus_tag=Cpin_2187;product=carbohydrate-binding protein;protein_id=WP_044218343.1;transl_table=11;translation=length.388
NC_013132	GenBank	exon	7604	8770	.	+	1	Parent=CPIN_RS10960
NC_013132	GenBank	gene	8812	10890	.	+	1	ID=CPIN_RS36530;Name=CPIN_RS36530;old_locus_tag=Cpin_2188
NC_013132	GenBank	mRNA	8812	10890	.	+	1	ID=CPIN_RS36530;Parent=CPIN_RS36530
NC_013132	GenBank	CDS	8812	10890	.	+	1	ID=CPIN_RS36530;Parent=CPIN_RS36530;Name=CPIN_RS36530;Note=Derived by automated computational analysis using gene prediction method: Protein Homology.;codon_start=1;inference=COORDINATES: protein motif:HMM:PF04151.13%2CHMM:TIGR04183.1;old_locus_tag=Cpin_2188;product=T9SS type A sorting domain-containing protein;protein_id=WP_012789856.1;transl_table=11;translation=length.692
NC_013132	GenBank	exon	8812	10890	.	+	1	Parent=CPIN_RS36530
NC_013132	GenBank	gene	11178	11762	.	+	1	ID=CPIN_RS10975;Name=CPIN_RS10975;old_locus_tag=Cpin_2189
NC_013132	GenBank	mRNA	11178	11762	.	+	1	ID=CPIN_RS10975;Parent=CPIN_RS10975
NC_013132	GenBank	CDS	11178	11762	.	+	1	ID=CPIN_RS10975;Parent=CPIN_RS10975;Name=CPIN_RS10975;Note=Derived by automated computational analysis using gene prediction method: Protein Homology.;codon_start=1;inference=COORDINATES: similar to AA sequence:RefSeq:WP_014219044.1;old_locus_tag=Cpin_2189;product=sigma-70 family RNA polymerase sigma factor;protein_id=WP_012789857.1;transl_table=11;translation=length.194
NC_013132	GenBank	exon	11178	11762	.	+	1	Parent=CPIN_RS10975
NC_013132	GenBank	gene	11961	12968	.	+	1	ID=CPIN_RS10980;Name=CPIN_RS10980;old_locus_tag=Cpin_2190
NC_013132	GenBank	mRNA	11961	12968	.	+	1	ID=CPIN_RS10980;Parent=CPIN_RS10980
NC_013132	GenBank	CDS	11961	12968	.	+	1	ID=CPIN_RS10980;Parent=CPIN_RS10980;Name=CPIN_RS10980;Note=Derived by automated computational analysis using gene prediction method: Protein Homology.;codon_start=1;inference=COORDINATES: protein motif:HMM:PF04773.11;old_locus_tag=Cpin_2190;product=DUF4974 domain-containing protein;protein_id=WP_012789858.1;transl_table=11;translation=length.335
NC_013132	GenBank	exon	11961	12968	.	+	1	Parent=CPIN_RS10980
NC_013132	GenBank	gene	13273	16932	.	+	1	ID=CPIN_RS10985;Name=CPIN_RS10985;old_locus_tag=Cpin_2191
NC_013132	GenBank	mRNA	13273	16932	.	+	1	ID=CPIN_RS10985;Parent=CPIN_RS10985
NC_013132	GenBank	CDS	13273	16932	.	+	1	ID=CPIN_RS10985;Parent=CPIN_RS10985;Name=CPIN_RS10985;Note=Derived by automated computational analysis using gene prediction method: Protein Homology.;codon_start=1;inference=COORDINATES: similar to AA sequence:RefSeq:WP_014220129.1;old_locus_tag=Cpin_2191;product=SusC/RagA family TonB-linked outer membrane protein;protein_id=WP_012789859.1;transl_table=11;translation=length.1219
NC_013132	GenBank	exon	13273	16932	.	+	1	Parent=CPIN_RS10985
NC_013132	GenBank	gene	16944	18398	.	+	1	ID=CPIN_RS10990;Name=CPIN_RS10990;old_locus_tag=Cpin_2192
NC_013132	GenBank	mRNA	16944	18398	.	+	1	ID=CPIN_RS10990;Parent=CPIN_RS10990
NC_013132	GenBank	CDS	16944	18398	.	+	1	ID=CPIN_RS10990;Parent=CPIN_RS10990;Name=CPIN_RS10990;Note=Derived by automated computational analysis using gene prediction method: Protein Homology.;codon_start=1;inference=COORDINATES: similar to AA sequence:RefSeq:WP_016194536.1;old_locus_tag=Cpin_2192;product=RagB/SusD family nutrient uptake outer membrane protein;protein_id=WP_012789860.1;transl_table=11;translation=length.484
NC_013132	GenBank	exon	16944	18398	.	+	1	Parent=CPIN_RS10990