##gff-version 3
##sequence-region NC_013132 1 21188
# 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	21188	.	+	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	1230	.	-	1	ID=CPIN_RS25335;Name=CPIN_RS25335;old_locus_tag=Cpin_5109
NC_013132	GenBank	mRNA	1	1230	.	-	1	ID=CPIN_RS25335;Parent=CPIN_RS25335
NC_013132	GenBank	CDS	1	1230	.	-	1	ID=CPIN_RS25335;Parent=CPIN_RS25335;Name=CPIN_RS25335;Note=Derived by automated computational analysis using gene prediction method: Protein Homology.;codon_start=1;inference=COORDINATES: similar to AA sequence:RefSeq:WP_014216967.1;old_locus_tag=Cpin_5109;product=family 16 glycosylhydrolase;protein_id=WP_012792709.1;transl_table=11;translation=length.409
NC_013132	GenBank	exon	1	1230	.	-	1	Parent=CPIN_RS25335
NC_013132	GenBank	gene	1512	4412	.	+	1	ID=CPIN_RS25340;Name=CPIN_RS25340;old_locus_tag=Cpin_5110
NC_013132	GenBank	mRNA	1512	4412	.	+	1	ID=CPIN_RS25340;Parent=CPIN_RS25340
NC_013132	GenBank	CDS	1512	4412	.	+	1	ID=CPIN_RS25340;Parent=CPIN_RS25340;Name=CPIN_RS25340;Note=Derived by automated computational analysis using gene prediction method: Protein Homology.;codon_start=1;inference=COORDINATES: protein motif:HMM:PF00196.17%2CHMM:PF07495.11;old_locus_tag=Cpin_5110;product=two component regulator three Y domain-containing protein;protein_id=WP_012792710.1;transl_table=11;translation=length.966
NC_013132	GenBank	exon	1512	4412	.	+	1	Parent=CPIN_RS25340
NC_013132	GenBank	gene	4428	5072	.	+	1	ID=CPIN_RS25345;Name=CPIN_RS25345;old_locus_tag=Cpin_5111
NC_013132	GenBank	mRNA	4428	5072	.	+	1	ID=CPIN_RS25345;Parent=CPIN_RS25345
NC_013132	GenBank	CDS	4428	5072	.	+	1	ID=CPIN_RS25345;Parent=CPIN_RS25345;Name=CPIN_RS25345;Note=Derived by automated computational analysis using gene prediction method: Protein Homology.;codon_start=1;inference=COORDINATES: protein motif:HMM:TIGR02937.1;old_locus_tag=Cpin_5111;product=sigma-70 family RNA polymerase sigma factor;protein_id=WP_012792711.1;transl_table=11;translation=length.214
NC_013132	GenBank	exon	4428	5072	.	+	1	Parent=CPIN_RS25345
NC_013132	GenBank	gene	5139	6365	.	+	1	ID=CPIN_RS25350;Name=CPIN_RS25350
NC_013132	GenBank	mRNA	5139	6365	.	+	1	ID=CPIN_RS25350;Parent=CPIN_RS25350
NC_013132	GenBank	CDS	5139	6365	.	+	1	ID=CPIN_RS25350;Parent=CPIN_RS25350;Name=CPIN_RS25350;Note=Derived by automated computational analysis using gene prediction method: Protein Homology.;codon_start=1;inference=COORDINATES: protein motif:HMM:PF04773.11;product=DUF4974 domain-containing protein;protein_id=WP_083781147.1;transl_table=11;translation=length.408
NC_013132	GenBank	exon	5139	6365	.	+	1	Parent=CPIN_RS25350
NC_013132	GenBank	gene	6600	9908	.	+	1	ID=CPIN_RS25355;Name=CPIN_RS25355;old_locus_tag=Cpin_5113
NC_013132	GenBank	mRNA	6600	9908	.	+	1	ID=CPIN_RS25355;Parent=CPIN_RS25355
NC_013132	GenBank	CDS	6600	9908	.	+	1	ID=CPIN_RS25355;Parent=CPIN_RS25355;Name=CPIN_RS25355;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_5113;product=SusC/RagA family TonB-linked outer membrane protein;protein_id=WP_012792713.1;transl_table=11;translation=length.1102
NC_013132	GenBank	exon	6600	9908	.	+	1	Parent=CPIN_RS25355
NC_013132	GenBank	gene	9920	11362	.	+	1	ID=CPIN_RS25360;Name=CPIN_RS25360;old_locus_tag=Cpin_5114
NC_013132	GenBank	mRNA	9920	11362	.	+	1	ID=CPIN_RS25360;Parent=CPIN_RS25360
NC_013132	GenBank	CDS	9920	11362	.	+	1	ID=CPIN_RS25360;Parent=CPIN_RS25360;Name=CPIN_RS25360;Note=Derived by automated computational analysis using gene prediction method: Protein Homology.;codon_start=1;inference=COORDINATES: protein motif:HMM:PF14322.4;old_locus_tag=Cpin_5114;product=RagB/SusD family nutrient uptake outer membrane protein;protein_id=WP_012792714.1;transl_table=11;translation=length.480
NC_013132	GenBank	exon	9920	11362	.	+	1	Parent=CPIN_RS25360
NC_013132	GenBank	gene	11437	13977	.	+	1	ID=CPIN_RS25365;Name=CPIN_RS25365;old_locus_tag=Cpin_5115
NC_013132	GenBank	mRNA	11437	13977	.	+	1	ID=CPIN_RS25365;Parent=CPIN_RS25365
NC_013132	GenBank	CDS	11437	13977	.	+	1	ID=CPIN_RS25365;Parent=CPIN_RS25365;Name=CPIN_RS25365;Note=Derived by automated computational analysis using gene prediction method: Protein Homology.;codon_start=1;inference=COORDINATES: similar to AA sequence:RefSeq:WP_014221315.1;old_locus_tag=Cpin_5115;product=zinc-dependent metalloprotease;protein_id=WP_012792715.1;transl_table=11;translation=length.846
NC_013132	GenBank	exon	11437	13977	.	+	1	Parent=CPIN_RS25365
NC_013132	GenBank	gene	14311	17490	.	+	1	ID=CPIN_RS37445;Name=CPIN_RS37445;old_locus_tag=Cpin_5116
NC_013132	GenBank	mRNA	14311	17490	.	+	1	ID=CPIN_RS37445;Parent=CPIN_RS37445
NC_013132	GenBank	CDS	14311	17490	.	+	1	ID=CPIN_RS37445;Parent=CPIN_RS37445;Name=CPIN_RS37445;Note=Derived by automated computational analysis using gene prediction method: Protein Homology.;codon_start=1;inference=COORDINATES: protein motif:HMM:TIGR04183.1,COORDINATES: similar to AA sequence:RefSeq:WP_005989889.1;old_locus_tag=Cpin_5116;product=family 16 glycosylhydrolase;protein_id=WP_012792716.1;transl_table=11;translation=length.1059
NC_013132	GenBank	exon	14311	17490	.	+	1	Parent=CPIN_RS37445
NC_013132	GenBank	gene	17790	21188	.	+	1	ID=CPIN_RS37015;Name=CPIN_RS37015;old_locus_tag=Cpin_5117
NC_013132	GenBank	mRNA	17790	21188	.	+	1	ID=CPIN_RS37015;Parent=CPIN_RS37015
NC_013132	GenBank	CDS	17790	21188	.	+	1	ID=CPIN_RS37015;Parent=CPIN_RS37015;Name=CPIN_RS37015;Note=Derived by automated computational analysis using gene prediction method: Protein Homology.;codon_start=1;inference=COORDINATES: protein motif:HMM:PF03422.13%2CHMM:PF07995.9%2CHMM:TIGR04183.1;old_locus_tag=Cpin_5117;product=carbohydrate-binding protein;protein_id=WP_012792717.1;transl_table=11;translation=length.1132
NC_013132	GenBank	exon	17790	21188	.	+	1	Parent=CPIN_RS37015