##gff-version 3
##sequence-region NC_013132 1 20512
# 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	20512	.	+	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	972	.	-	1	ID=CPIN_RS33320;Name=CPIN_RS33320;old_locus_tag=Cpin_6730
NC_013132	GenBank	mRNA	1	972	.	-	1	ID=CPIN_RS33320.t01;Parent=CPIN_RS33320
NC_013132	GenBank	CDS	1	972	.	-	1	ID=CPIN_RS33320.p01;Parent=CPIN_RS33320.t01;Name=CPIN_RS33320;Note=Derived by automated computational analysis using gene prediction method: Protein Homology.;codon_start=1;inference=COORDINATES: similar to AA sequence:RefSeq:WP_015332438.1;old_locus_tag=Cpin_6730;product=family 43 glycosylhydrolase;protein_id=WP_012794294.1;transl_table=11;translation=length.323
NC_013132	GenBank	exon	1	972	.	-	1	Parent=CPIN_RS33320.t01
NC_013132	GenBank	gene	1168	1845	.	+	1	ID=CPIN_RS33325;Name=CPIN_RS33325;old_locus_tag=Cpin_6731
NC_013132	GenBank	mRNA	1168	1845	.	+	1	ID=CPIN_RS33325.t01;Parent=CPIN_RS33325
NC_013132	GenBank	CDS	1168	1845	.	+	1	ID=CPIN_RS33325.p01;Parent=CPIN_RS33325.t01;Name=CPIN_RS33325;Note=Derived by automated computational analysis using gene prediction method: Protein Homology.;codon_start=1;inference=COORDINATES: protein motif:HMM:PF07638.9;old_locus_tag=Cpin_6731;product=sigma-70 family RNA polymerase sigma factor;protein_id=WP_083781182.1;transl_table=11;translation=length.225
NC_013132	GenBank	exon	1168	1845	.	+	1	Parent=CPIN_RS33325.t01
NC_013132	GenBank	gene	2001	3185	.	+	1	ID=CPIN_RS33330;Name=CPIN_RS33330
NC_013132	GenBank	mRNA	2001	3185	.	+	1	ID=CPIN_RS33330.t01;Parent=CPIN_RS33330
NC_013132	GenBank	CDS	2001	3185	.	+	1	ID=CPIN_RS33330.p01;Parent=CPIN_RS33330.t01;Name=CPIN_RS33330;Note=Derived by automated computational analysis using gene prediction method: Protein Homology.;codon_start=1;inference=COORDINATES: protein motif:HMM:PF04773.11;product=FecR family protein;protein_id=WP_012794296.1;transl_table=11;translation=length.394
NC_013132	GenBank	exon	2001	3185	.	+	1	Parent=CPIN_RS33330.t01
NC_013132	GenBank	gene	3381	6746	.	+	1	ID=CPIN_RS33335;Name=CPIN_RS33335;old_locus_tag=Cpin_6733
NC_013132	GenBank	mRNA	3381	6746	.	+	1	ID=CPIN_RS33335.t01;Parent=CPIN_RS33335
NC_013132	GenBank	CDS	3381	6746	.	+	1	ID=CPIN_RS33335.p01;Parent=CPIN_RS33335.t01;Name=CPIN_RS33335;Note=Derived by automated computational analysis using gene prediction method: Protein Homology.;codon_start=1;inference=COORDINATES: protein motif:HMM:PF07660.12;old_locus_tag=Cpin_6733;product=SusC/RagA family TonB-linked outer membrane protein;protein_id=WP_148230690.1;transl_table=11;translation=length.1121
NC_013132	GenBank	exon	3381	6746	.	+	1	Parent=CPIN_RS33335.t01
NC_013132	GenBank	gene	6765	8405	.	+	1	ID=CPIN_RS33340;Name=CPIN_RS33340;old_locus_tag=Cpin_6734
NC_013132	GenBank	mRNA	6765	8405	.	+	1	ID=CPIN_RS33340.t01;Parent=CPIN_RS33340
NC_013132	GenBank	CDS	6765	8405	.	+	1	ID=CPIN_RS33340.p01;Parent=CPIN_RS33340.t01;Name=CPIN_RS33340;Note=Derived by automated computational analysis using gene prediction method: Protein Homology.;codon_start=1;inference=COORDINATES: similar to AA sequence:RefSeq:WP_003000101.1;old_locus_tag=Cpin_6734;product=SusD/RagB family nutrient-binding outer membrane lipoprotein;protein_id=WP_044220307.1;transl_table=11;translation=length.546
NC_013132	GenBank	exon	6765	8405	.	+	1	Parent=CPIN_RS33340.t01
NC_013132	GenBank	gene	8569	10026	.	-	1	ID=CPIN_RS33345;Name=CPIN_RS33345;old_locus_tag=Cpin_6735
NC_013132	GenBank	mRNA	8569	10026	.	-	1	ID=CPIN_RS33345.t01;Parent=CPIN_RS33345
NC_013132	GenBank	CDS	8569	10026	.	-	1	ID=CPIN_RS33345.p01;Parent=CPIN_RS33345.t01;Name=CPIN_RS33345;Note=Derived by automated computational analysis using gene prediction method: Protein Homology.;codon_start=1;inference=COORDINATES: similar to AA sequence:RefSeq:WP_010601754.1;old_locus_tag=Cpin_6735;product=glycoside hydrolase family 30 protein;protein_id=WP_012794299.1;transl_table=11;translation=length.485
NC_013132	GenBank	exon	8569	10026	.	-	1	Parent=CPIN_RS33345.t01
NC_013132	GenBank	gene	10049	11452	.	-	1	ID=CPIN_RS33350;Name=CPIN_RS33350;old_locus_tag=Cpin_6736
NC_013132	GenBank	mRNA	10049	11452	.	-	1	ID=CPIN_RS33350.t01;Parent=CPIN_RS33350
NC_013132	GenBank	CDS	10049	11452	.	-	1	ID=CPIN_RS33350.p01;Parent=CPIN_RS33350.t01;Name=CPIN_RS33350;Note=Derived by automated computational analysis using gene prediction method: Protein Homology.;codon_start=1;inference=COORDINATES: similar to AA sequence:RefSeq:WP_015027989.1;old_locus_tag=Cpin_6736;product=glucosylceramidase;protein_id=WP_148230854.1;transl_table=11;translation=length.467
NC_013132	GenBank	exon	10049	11452	.	-	1	Parent=CPIN_RS33350.t01
NC_013132	GenBank	gene	11503	12363	.	-	1	ID=CPIN_RS33355;Name=CPIN_RS33355;old_locus_tag=Cpin_6737
NC_013132	GenBank	mRNA	11503	12363	.	-	1	ID=CPIN_RS33355.t01;Parent=CPIN_RS33355
NC_013132	GenBank	CDS	11503	12363	.	-	1	ID=CPIN_RS33355.p01;Parent=CPIN_RS33355.t01;Name=CPIN_RS33355;Note=Derived by automated computational analysis using gene prediction method: Protein Homology.;codon_start=1;inference=COORDINATES: similar to AA sequence:RefSeq:WP_015265672.1;old_locus_tag=Cpin_6737;product=glycoside hydrolase family 16 protein;protein_id=WP_012794301.1;transl_table=11;translation=length.286
NC_013132	GenBank	exon	11503	12363	.	-	1	Parent=CPIN_RS33355.t01
NC_013132	GenBank	gene	12541	13398	.	-	1	ID=CPIN_RS33360;Name=CPIN_RS33360;old_locus_tag=Cpin_6738
NC_013132	GenBank	mRNA	12541	13398	.	-	1	ID=CPIN_RS33360.t01;Parent=CPIN_RS33360
NC_013132	GenBank	CDS	12541	13398	.	-	1	ID=CPIN_RS33360.p01;Parent=CPIN_RS33360.t01;Name=CPIN_RS33360;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_6738;product=hypothetical protein;protein_id=WP_012794302.1;transl_table=11;translation=length.285
NC_013132	GenBank	exon	12541	13398	.	-	1	Parent=CPIN_RS33360.t01
NC_013132	GenBank	gene	13443	14984	.	-	1	ID=CPIN_RS33365;Name=CPIN_RS33365;old_locus_tag=Cpin_6739
NC_013132	GenBank	mRNA	13443	14984	.	-	1	ID=CPIN_RS33365.t01;Parent=CPIN_RS33365
NC_013132	GenBank	CDS	13443	14984	.	-	1	ID=CPIN_RS33365.p01;Parent=CPIN_RS33365.t01;Name=CPIN_RS33365;Note=Derived by automated computational analysis using gene prediction method: Protein Homology.;codon_start=1;inference=COORDINATES: similar to AA sequence:RefSeq:WP_018472771.1;old_locus_tag=Cpin_6739;product=RagB/SusD family nutrient uptake outer membrane protein;protein_id=WP_012794303.1;transl_table=11;translation=length.513
NC_013132	GenBank	exon	13443	14984	.	-	1	Parent=CPIN_RS33365.t01
NC_013132	GenBank	gene	15006	18356	.	-	1	ID=CPIN_RS33370;Name=CPIN_RS33370;old_locus_tag=Cpin_6740
NC_013132	GenBank	mRNA	15006	18356	.	-	1	ID=CPIN_RS33370.t01;Parent=CPIN_RS33370
NC_013132	GenBank	CDS	15006	18356	.	-	1	ID=CPIN_RS33370.p01;Parent=CPIN_RS33370.t01;Name=CPIN_RS33370;Note=Derived by automated computational analysis using gene prediction method: Protein Homology.;codon_start=1;inference=COORDINATES: similar to AA sequence:RefSeq:WP_018472772.1;old_locus_tag=Cpin_6740;product=TonB-dependent receptor;protein_id=WP_012794304.1;transl_table=11;translation=length.1116
NC_013132	GenBank	exon	15006	18356	.	-	1	Parent=CPIN_RS33370.t01
NC_013132	GenBank	gene	18648	19838	.	-	1	ID=CPIN_RS33375;Name=CPIN_RS33375;old_locus_tag=Cpin_6741
NC_013132	GenBank	mRNA	18648	19838	.	-	1	ID=CPIN_RS33375.t01;Parent=CPIN_RS33375
NC_013132	GenBank	CDS	18648	19838	.	-	1	ID=CPIN_RS33375.p01;Parent=CPIN_RS33375.t01;Name=CPIN_RS33375;Note=Derived by automated computational analysis using gene prediction method: Protein Homology.;codon_start=1;inference=COORDINATES: protein motif:HMM:PF16344.3;old_locus_tag=Cpin_6741;product=DUF4974 domain-containing protein;protein_id=WP_012794305.1;transl_table=11;translation=length.396
NC_013132	GenBank	exon	18648	19838	.	-	1	Parent=CPIN_RS33375.t01
NC_013132	GenBank	gene	19922	20512	.	-	1	ID=CPIN_RS33380;Name=CPIN_RS33380;old_locus_tag=Cpin_6742
NC_013132	GenBank	mRNA	19922	20512	.	-	1	ID=CPIN_RS33380.t01;Parent=CPIN_RS33380
NC_013132	GenBank	CDS	19922	20512	.	-	1	ID=CPIN_RS33380.p01;Parent=CPIN_RS33380.t01;Name=CPIN_RS33380;Note=Derived by automated computational analysis using gene prediction method: Protein Homology.;codon_start=1;inference=COORDINATES: protein motif:HMM:PF07638.9;old_locus_tag=Cpin_6742;product=RNA polymerase sigma-70 factor;protein_id=WP_012794306.1;transl_table=11;translation=length.196
NC_013132	GenBank	exon	19922	20512	.	-	1	Parent=CPIN_RS33380.t01