##gff-version 3
##sequence-region NC_013132 1 24473
# 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	24473	.	+	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	2325	.	-	1	ID=CPIN_RS25225;Name=CPIN_RS25225;old_locus_tag=Cpin_5087
NC_013132	GenBank	mRNA	1	2325	.	-	1	ID=CPIN_RS25225.t01;Parent=CPIN_RS25225
NC_013132	GenBank	CDS	1	2325	.	-	1	ID=CPIN_RS25225.p01;Parent=CPIN_RS25225.t01;Name=CPIN_RS25225;Note=Derived by automated computational analysis using gene prediction method: Protein Homology.;codon_start=1;inference=COORDINATES: similar to AA sequence:RefSeq:WP_014680589.1;old_locus_tag=Cpin_5087;product=glycoside hydrolase family 65 protein;protein_id=WP_012792687.1;transl_table=11;translation=length.774
NC_013132	GenBank	exon	1	2325	.	-	1	Parent=CPIN_RS25225.t01
NC_013132	GenBank	gene	2370	3029	.	-	1	ID=CPIN_RS25230;Name=pgmB;locus_tag=CPIN_RS25230;old_locus_tag=Cpin_5088
NC_013132	GenBank	mRNA	2370	3029	.	-	1	ID=CPIN_RS25230.t01;Parent=CPIN_RS25230
NC_013132	GenBank	CDS	2370	3029	.	-	1	ID=CPIN_RS25230.p01;Parent=CPIN_RS25230.t01;eC_number=5.4.2.6;Name=pgmB;Note=Derived by automated computational analysis using gene prediction method: Protein Homology.;codon_start=1;inference=COORDINATES: similar to AA sequence:RefSeq:WP_014312712.1;locus_tag=CPIN_RS25230;old_locus_tag=Cpin_5088;product=beta-phosphoglucomutase;protein_id=WP_012792688.1;transl_table=11;translation=length.219
NC_013132	GenBank	exon	2370	3029	.	-	1	Parent=CPIN_RS25230.t01
NC_013132	GenBank	gene	3059	4918	.	-	1	ID=CPIN_RS25235;Name=CPIN_RS25235;old_locus_tag=Cpin_5089
NC_013132	GenBank	mRNA	3059	4918	.	-	1	ID=CPIN_RS25235.t01;Parent=CPIN_RS25235
NC_013132	GenBank	CDS	3059	4918	.	-	1	ID=CPIN_RS25235.p01;Parent=CPIN_RS25235.t01;Name=CPIN_RS25235;Note=Derived by automated computational analysis using gene prediction method: Protein Homology.;codon_start=1;inference=COORDINATES: similar to AA sequence:RefSeq:WP_016196628.1;old_locus_tag=Cpin_5089;product=glycoside hydrolase family 13 protein;protein_id=WP_012792689.1;transl_table=11;translation=length.619
NC_013132	GenBank	exon	3059	4918	.	-	1	Parent=CPIN_RS25235.t01
NC_013132	GenBank	gene	4987	6024	.	-	1	ID=CPIN_RS25240;Name=CPIN_RS25240;old_locus_tag=Cpin_5090
NC_013132	GenBank	mRNA	4987	6024	.	-	1	ID=CPIN_RS25240.t01;Parent=CPIN_RS25240
NC_013132	GenBank	CDS	4987	6024	.	-	1	ID=CPIN_RS25240.p01;Parent=CPIN_RS25240.t01;Name=CPIN_RS25240;Note=Derived by automated computational analysis using gene prediction method: Protein Homology.;codon_start=1;inference=COORDINATES: protein motif:HMM:PF14292.4;old_locus_tag=Cpin_5090;product=hypothetical protein;protein_id=WP_012792690.1;transl_table=11;translation=length.345
NC_013132	GenBank	exon	4987	6024	.	-	1	Parent=CPIN_RS25240.t01
NC_013132	GenBank	gene	6067	7659	.	-	1	ID=CPIN_RS25245;Name=CPIN_RS25245;old_locus_tag=Cpin_5091
NC_013132	GenBank	mRNA	6067	7659	.	-	1	ID=CPIN_RS25245.t01;Parent=CPIN_RS25245
NC_013132	GenBank	CDS	6067	7659	.	-	1	ID=CPIN_RS25245.p01;Parent=CPIN_RS25245.t01;Name=CPIN_RS25245;Note=Derived by automated computational analysis using gene prediction method: Protein Homology.;codon_start=1;inference=COORDINATES: similar to AA sequence:RefSeq:WP_018478677.1;old_locus_tag=Cpin_5091;product=RagB/SusD family nutrient uptake outer membrane protein;protein_id=WP_012792691.1;transl_table=11;translation=length.530
NC_013132	GenBank	exon	6067	7659	.	-	1	Parent=CPIN_RS25245.t01
NC_013132	GenBank	gene	7679	10645	.	-	1	ID=CPIN_RS25250;Name=CPIN_RS25250;old_locus_tag=Cpin_5092
NC_013132	GenBank	mRNA	7679	10645	.	-	1	ID=CPIN_RS25250.t01;Parent=CPIN_RS25250
NC_013132	GenBank	CDS	7679	10645	.	-	1	ID=CPIN_RS25250.p01;Parent=CPIN_RS25250.t01;Name=CPIN_RS25250;Note=Derived by automated computational analysis using gene prediction method: Protein Homology.;codon_start=1;inference=COORDINATES: similar to AA sequence:RefSeq:WP_008512511.1;old_locus_tag=Cpin_5092;product=TonB-dependent receptor;protein_id=WP_012792692.1;transl_table=11;translation=length.988
NC_013132	GenBank	exon	7679	10645	.	-	1	Parent=CPIN_RS25250.t01
NC_013132	GenBank	gene	11070	12101	.	-	1	ID=CPIN_RS25255;Name=CPIN_RS25255;old_locus_tag=Cpin_5093
NC_013132	GenBank	mRNA	11070	12101	.	-	1	ID=CPIN_RS25255.t01;Parent=CPIN_RS25255
NC_013132	GenBank	CDS	11070	12101	.	-	1	ID=CPIN_RS25255.p01;Parent=CPIN_RS25255.t01;Name=CPIN_RS25255;Note=Derived by automated computational analysis using gene prediction method: Protein Homology.;codon_start=1;inference=COORDINATES: similar to AA sequence:RefSeq:WP_016196623.1;old_locus_tag=Cpin_5093;product=LacI family transcriptional regulator;protein_id=WP_012792693.1;transl_table=11;translation=length.343
NC_013132	GenBank	exon	11070	12101	.	-	1	Parent=CPIN_RS25255.t01
NC_013132	GenBank	gene	12420	24473	.	+	1	ID=CPIN_RS38720;Name=CPIN_RS38720;old_locus_tag=Cpin_5094
NC_013132	GenBank	mRNA	12420	24473	.	+	1	ID=CPIN_RS38720.t01;Parent=CPIN_RS38720
NC_013132	GenBank	CDS	12420	24473	.	+	1	ID=CPIN_RS38720.p01;Parent=CPIN_RS38720.t01;Name=CPIN_RS38720;Note=Derived by automated computational analysis using gene prediction method: Protein Homology.;codon_start=1;inference=COORDINATES: protein motif:HMM:PF00754.23%2CHMM:PF01345.16%2CHMM:PF03160.12;old_locus_tag=Cpin_5094;product=DUF11 domain-containing protein;protein_id=WP_148230638.1;transl_table=11;translation=length.4017
NC_013132	GenBank	exon	12420	24473	.	+	1	Parent=CPIN_RS38720.t01