##gff-version 3
##sequence-region NC_013132 1 7872
# 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	7872	.	+	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	1035	.	-	1	ID=CPIN_RS35530;Name=CPIN_RS35530;old_locus_tag=Cpin_7180
NC_013132	GenBank	mRNA	1	1035	.	-	1	ID=CPIN_RS35530.t01;Parent=CPIN_RS35530
NC_013132	GenBank	CDS	1	1035	.	-	1	ID=CPIN_RS35530.p01;Parent=CPIN_RS35530.t01;Name=CPIN_RS35530;Note=Derived by automated computational analysis using gene prediction method: Protein Homology.;codon_start=1;inference=COORDINATES: similar to AA sequence:RefSeq:WP_013667530.1;old_locus_tag=Cpin_7180;product=exo-alpha-sialidase;protein_id=WP_063715272.1;transl_table=11;translation=length.344
NC_013132	GenBank	exon	1	1035	.	-	1	Parent=CPIN_RS35530.t01
NC_013132	GenBank	gene	1142	2773	.	-	1	ID=CPIN_RS35535;Name=CPIN_RS35535;old_locus_tag=Cpin_7181
NC_013132	GenBank	mRNA	1142	2773	.	-	1	ID=CPIN_RS35535.t01;Parent=CPIN_RS35535
NC_013132	GenBank	CDS	1142	2773	.	-	1	ID=CPIN_RS35535.p01;Parent=CPIN_RS35535.t01;Name=CPIN_RS35535;Note=Derived by automated computational analysis using gene prediction method: Protein Homology.;codon_start=1;inference=COORDINATES: protein motif:HMM:PF12741.5;old_locus_tag=Cpin_7181;product=SusD/RagB family nutrient-binding outer membrane lipoprotein;protein_id=WP_052306944.1;transl_table=11;translation=length.543
NC_013132	GenBank	exon	1142	2773	.	-	1	Parent=CPIN_RS35535.t01
NC_013132	GenBank	gene	2803	6429	.	-	1	ID=CPIN_RS35540;Name=CPIN_RS35540;old_locus_tag=Cpin_7182
NC_013132	GenBank	mRNA	2803	6429	.	-	1	ID=CPIN_RS35540.t01;Parent=CPIN_RS35540
NC_013132	GenBank	CDS	2803	6429	.	-	1	ID=CPIN_RS35540.p01;Parent=CPIN_RS35540.t01;Name=CPIN_RS35540;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_7182;product=SusC/RagA family TonB-linked outer membrane protein;protein_id=WP_148230703.1;transl_table=11;translation=length.1208
NC_013132	GenBank	exon	2803	6429	.	-	1	Parent=CPIN_RS35540.t01
NC_013132	GenBank	gene	6742	7872	.	-	1	ID=CPIN_RS37360;Name=CPIN_RS37360;old_locus_tag=Cpin_7183
NC_013132	GenBank	mRNA	6742	7872	.	-	1	ID=CPIN_RS37360.t01;Parent=CPIN_RS37360
NC_013132	GenBank	CDS	6742	7872	.	-	1	ID=CPIN_RS37360.p01;Parent=CPIN_RS37360.t01;Name=CPIN_RS37360;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_7183;product=DUF4974 domain-containing protein;protein_id=WP_012794746.1;transl_table=11;translation=length.376
NC_013132	GenBank	exon	6742	7872	.	-	1	Parent=CPIN_RS37360.t01