##gff-version 3
##sequence-region NC_008526 1 16592
# conversion-by bp_genbank2gff3.pl
# organism Lactobacillus paracasei ATCC 334
# Note Lactobacillus paracasei ATCC 334, complete sequence.
# date 10-MAR-2020
NC_008526	GenBank	region	1	16592	.	+	1	ID=NC_008526;Dbxref=BioProject:PRJNA224116,ATCC:334,taxon:321967;Name=NC_008526;Note=Lactobacillus paracasei ATCC 334%2C complete sequence.,REFSEQ INFORMATION: The reference sequence was derived from CP000423. URL -- http://www.jgi.doe.gov JGI Project ID: 2662185 Source DNA and bacteria available from Jeffery R. Broadbent (broadbnt@cc.usu.edu) Bacteria also available from ATCC: ATCC 334 Contacts: Jeffery R. Broadbent (broadbnt@cc.usu.edu) Paul Richardson (microbes@cuba.jgi-psf.org) Annotation done by Kira Makarova and Eugene Koonin Finishing done by Fidelity Systems Inc. (Gaithersburg) http://www.fidelitysystems.com Project Information available at: http://genome.jgi-psf.org/mic_home.html 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. (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 :: 03/10/2020 07:18:09 Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline (PGAP) Annotation Method :: Best-placed reference protein set,GeneMarkS-2+ Annotation Software revision :: 4.11 Features Annotated :: Gene,CDS,rRNA,tRNA,ncRNA,repeat_region Genes (total) :: 2,874 CDSs (total) :: 2,797 Genes (coding) :: 2,630 CDSs (with protein) :: 2,630 Genes (RNA) :: 77 rRNAs :: 5,5,5 (5S,16S,23S) complete rRNAs :: 5,5,5 (5S,16S,23S) tRNAs :: 59 ncRNAs :: 3 Pseudo Genes (total) :: 167 CDSs (without protein) :: 167 Pseudo Genes (ambiguous residues) :: 0 of 167 Pseudo Genes (frameshifted) :: 77 of 167 Pseudo Genes (incomplete) :: 78 of 167 Pseudo Genes (internal stop) :: 25 of 167 Pseudo Genes (multiple problems) :: 13 of 167 CRISPR Arrays :: 1 ##Genome-Annotation-Data-END## COMPLETENESS: full length. ;comment1=REFSEQ INFORMATION: The reference sequence was derived from CP000423. URL -- http://www.jgi.doe.gov JGI Project ID: 2662185 Source DNA and bacteria available from Jeffery R. Broadbent (broadbnt@cc.usu.edu) Bacteria also available from ATCC: ATCC 334 Contacts: Jeffery R. Broadbent (broadbnt@cc.usu.edu) Paul Richardson (microbes@cuba.jgi-psf.org) Annotation done by Kira Makarova and Eugene Koonin Finishing done by Fidelity Systems Inc. (Gaithersburg) http://www.fidelitysystems.com Project Information available at: http://genome.jgi-psf.org/mic_home.html 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. (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 :: 03/10/2020 07:18:09 Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline (PGAP) Annotation Method :: Best-placed reference protein set%3B GeneMarkS-2+ Annotation Software revision :: 4.11 Features Annotated :: Gene%3B CDS%3B rRNA%3B tRNA%3B ncRNA%3B repeat_region Genes (total) :: 2%2C874 CDSs (total) :: 2%2C797 Genes (coding) :: 2%2C630 CDSs (with protein) :: 2%2C630 Genes (RNA) :: 77 rRNAs :: 5%2C 5%2C 5 (5S%2C 16S%2C 23S) complete rRNAs :: 5%2C 5%2C 5 (5S%2C 16S%2C 23S) tRNAs :: 59 ncRNAs :: 3 Pseudo Genes (total) :: 167 CDSs (without protein) :: 167 Pseudo Genes (ambiguous residues) :: 0 of 167 Pseudo Genes (frameshifted) :: 77 of 167 Pseudo Genes (incomplete) :: 78 of 167 Pseudo Genes (internal stop) :: 25 of 167 Pseudo Genes (multiple problems) :: 13 of 167 CRISPR Arrays :: 1 ##Genome-Annotation-Data-END## COMPLETENESS: full length. ;date=10-MAR-2020;mol_type=genomic DNA;organism=Lactobacillus paracasei ATCC 334;strain=ATCC 334
NC_008526	GenBank	gene	1	984	.	-	1	ID=LSEI_RS12770;Name=LSEI_RS12770;old_locus_tag=LSEI_2661
NC_008526	GenBank	mRNA	1	984	.	-	1	ID=LSEI_RS12770.t01;Parent=LSEI_RS12770
NC_008526	GenBank	CDS	1	984	.	-	1	ID=LSEI_RS12770.p01;Parent=LSEI_RS12770.t01;Name=LSEI_RS12770;Note=Derived by automated computational analysis using gene prediction method: Protein Homology.;codon_start=1;inference=COORDINATES: similar to AA sequence:RefSeq:WP_003596390.1;old_locus_tag=LSEI_2661;product=hypothetical protein;protein_id=WP_003596390.1;transl_table=11;translation=length.327
NC_008526	GenBank	exon	1	984	.	-	1	Parent=LSEI_RS12770.t01
NC_008526	GenBank	gene	1054	2979	.	-	1	ID=LSEI_RS12775;Name=LSEI_RS12775;old_locus_tag=LSEI_2662
NC_008526	GenBank	mRNA	1054	2979	.	-	1	ID=LSEI_RS12775.t01;Parent=LSEI_RS12775
NC_008526	GenBank	CDS	1054	2979	.	-	1	ID=LSEI_RS12775.p01;Parent=LSEI_RS12775.t01;Name=LSEI_RS12775;Note=Derived by automated computational analysis using gene prediction method: Protein Homology.;codon_start=1;inference=COORDINATES: similar to AA sequence:RefSeq:WP_012492080.1;old_locus_tag=LSEI_2662;product=alginate lyase family protein;protein_id=WP_011674964.1;transl_table=11;translation=length.641
NC_008526	GenBank	exon	1054	2979	.	-	1	Parent=LSEI_RS12775.t01
NC_008526	GenBank	gene	2918	3265	.	-	1	ID=LSEI_RS12780;Name=LSEI_RS12780;old_locus_tag=LSEI_2663
NC_008526	GenBank	mRNA	2918	3265	.	-	1	ID=LSEI_RS12780.t01;Parent=LSEI_RS12780
NC_008526	GenBank	CDS	2918	3265	.	-	1	ID=LSEI_RS12780.p01;Parent=LSEI_RS12780.t01;Name=LSEI_RS12780;Note=Derived by automated computational analysis using gene prediction method: Protein Homology.;codon_start=1;inference=COORDINATES: similar to AA sequence:RefSeq:WP_003662554.1;old_locus_tag=LSEI_2663;product=preprotein translocase subunit YajC;protein_id=WP_011674965.1;transl_table=11;translation=length.115
NC_008526	GenBank	exon	2918	3265	.	-	1	Parent=LSEI_RS12780.t01
NC_008526	GenBank	gene	3265	3735	.	-	1	ID=LSEI_RS12785;Name=LSEI_RS12785;old_locus_tag=LSEI_2664
NC_008526	GenBank	mRNA	3265	3735	.	-	1	ID=LSEI_RS12785.t01;Parent=LSEI_RS12785
NC_008526	GenBank	CDS	3265	3735	.	-	1	ID=LSEI_RS12785.p01;Parent=LSEI_RS12785.t01;eC_number=2.7.1.69;Name=LSEI_RS12785;Note=Derived by automated computational analysis using gene prediction method: Protein Homology.;codon_start=1;inference=COORDINATES: similar to AA sequence:RefSeq:WP_003567928.1;old_locus_tag=LSEI_2664;product=PTS fructose transporter subunit IIA;protein_id=WP_003596394.1;transl_table=11;translation=length.156
NC_008526	GenBank	exon	3265	3735	.	-	1	Parent=LSEI_RS12785.t01
NC_008526	GenBank	gene	3855	4670	.	-	1	ID=LSEI_RS12790;Name=LSEI_RS12790;old_locus_tag=LSEI_2665
NC_008526	GenBank	mRNA	3855	4670	.	-	1	ID=LSEI_RS12790.t01;Parent=LSEI_RS12790
NC_008526	GenBank	CDS	3855	4670	.	-	1	ID=LSEI_RS12790.p01;Parent=LSEI_RS12790.t01;Name=LSEI_RS12790;Note=Derived by automated computational analysis using gene prediction method: Protein Homology.;codon_start=1;inference=COORDINATES: similar to AA sequence:RefSeq:WP_019898856.1;old_locus_tag=LSEI_2665;product=PTS system mannose/fructose/sorbose family transporter subunit IID;protein_id=WP_003567930.1;transl_table=11;translation=length.271
NC_008526	GenBank	exon	3855	4670	.	-	1	Parent=LSEI_RS12790.t01
NC_008526	GenBank	gene	4660	5472	.	-	1	ID=LSEI_RS12795;Name=LSEI_RS12795;old_locus_tag=LSEI_2666
NC_008526	GenBank	mRNA	4660	5472	.	-	1	ID=LSEI_RS12795.t01;Parent=LSEI_RS12795
NC_008526	GenBank	CDS	4660	5472	.	-	1	ID=LSEI_RS12795.p01;Parent=LSEI_RS12795.t01;Name=LSEI_RS12795;Note=Derived by automated computational analysis using gene prediction method: Protein Homology.;codon_start=1;inference=COORDINATES: similar to AA sequence:RefSeq:WP_016364848.1;old_locus_tag=LSEI_2666;product=PTS sugar transporter subunit IIC;protein_id=WP_003577476.1;transl_table=11;translation=length.270
NC_008526	GenBank	exon	4660	5472	.	-	1	Parent=LSEI_RS12795.t01
NC_008526	GenBank	gene	5625	6125	.	-	1	ID=LSEI_RS12800;Name=LSEI_RS12800;old_locus_tag=LSEI_2667
NC_008526	GenBank	mRNA	5625	6125	.	-	1	ID=LSEI_RS12800.t01;Parent=LSEI_RS12800
NC_008526	GenBank	CDS	5625	6125	.	-	1	ID=LSEI_RS12800.p01;Parent=LSEI_RS12800.t01;Name=LSEI_RS12800;Note=Derived by automated computational analysis using gene prediction method: Protein Homology.;codon_start=1;inference=COORDINATES: similar to AA sequence:RefSeq:WP_005690843.1;old_locus_tag=LSEI_2667;product=PTS sugar transporter subunit IIB;protein_id=WP_003658805.1;transl_table=11;translation=length.166
NC_008526	GenBank	exon	5625	6125	.	-	1	Parent=LSEI_RS12800.t01
NC_008526	GenBank	gene	6225	7403	.	-	1	ID=LSEI_RS12805;Name=LSEI_RS12805;old_locus_tag=LSEI_2668
NC_008526	GenBank	mRNA	6225	7403	.	-	1	ID=LSEI_RS12805.t01;Parent=LSEI_RS12805
NC_008526	GenBank	CDS	6225	7403	.	-	1	ID=LSEI_RS12805.p01;Parent=LSEI_RS12805.t01;eC_number=3.2.1.-;Name=LSEI_RS12805;Note=Derived by automated computational analysis using gene prediction method: Protein Homology.;codon_start=1;inference=COORDINATES: similar to AA sequence:RefSeq:WP_003589148.1;old_locus_tag=LSEI_2668;product=glucuronyl hydrolase;protein_id=WP_003596395.1;transl_table=11;translation=length.392
NC_008526	GenBank	exon	6225	7403	.	-	1	Parent=LSEI_RS12805.t01
NC_008526	GenBank	gene	7400	8230	.	-	1	ID=LSEI_RS12810;Name=LSEI_RS12810;old_locus_tag=LSEI_2669
NC_008526	GenBank	mRNA	7400	8230	.	-	1	ID=LSEI_RS12810.t01;Parent=LSEI_RS12810
NC_008526	GenBank	CDS	7400	8230	.	-	1	ID=LSEI_RS12810.p01;Parent=LSEI_RS12810.t01;Name=LSEI_RS12810;Note=Derived by automated computational analysis using gene prediction method: Protein Homology.;codon_start=1;inference=COORDINATES: similar to AA sequence:RefSeq:WP_019887695.1;old_locus_tag=LSEI_2669;product=hypothetical protein;protein_id=WP_011674966.1;transl_table=11;translation=length.276
NC_008526	GenBank	exon	7400	8230	.	-	1	Parent=LSEI_RS12810.t01
NC_008526	GenBank	gene	8445	9212	.	+	1	ID=LSEI_RS12815;Name=LSEI_RS12815;old_locus_tag=LSEI_2670
NC_008526	GenBank	mRNA	8445	9212	.	+	1	ID=LSEI_RS12815.t01;Parent=LSEI_RS12815
NC_008526	GenBank	CDS	8445	9212	.	+	1	ID=LSEI_RS12815.p01;Parent=LSEI_RS12815.t01;Name=LSEI_RS12815;Note=Derived by automated computational analysis using gene prediction method: Protein Homology.;codon_start=1;inference=COORDINATES: similar to AA sequence:RefSeq:WP_003662537.1;old_locus_tag=LSEI_2670;product=IclR family transcriptional regulator;protein_id=WP_003567939.1;transl_table=11;translation=length.255
NC_008526	GenBank	exon	8445	9212	.	+	1	Parent=LSEI_RS12815.t01
NC_008526	GenBank	gene	9486	10319	.	+	1	ID=LSEI_RS12820;Name=kduI;locus_tag=LSEI_RS12820;old_locus_tag=LSEI_2671
NC_008526	GenBank	mRNA	9486	10319	.	+	1	ID=LSEI_RS12820.t01;Parent=LSEI_RS12820
NC_008526	GenBank	CDS	9486	10319	.	+	1	ID=LSEI_RS12820.p01;Parent=LSEI_RS12820.t01;eC_number=5.3.1.17;Name=kduI;Note=Derived by automated computational analysis using gene prediction method: Protein Homology.;codon_start=1;inference=COORDINATES: similar to AA sequence:RefSeq:WP_005712253.1;locus_tag=LSEI_RS12820;old_locus_tag=LSEI_2671;product=5-dehydro-4-deoxy-D-glucuronate isomerase;protein_id=WP_032784565.1;transl_table=11;translation=length.277
NC_008526	GenBank	exon	9486	10319	.	+	1	Parent=LSEI_RS12820.t01
NC_008526	GenBank	gene	10354	11178	.	+	1	ID=LSEI_RS12825;Name=kduD;locus_tag=LSEI_RS12825;old_locus_tag=LSEI_2672
NC_008526	GenBank	mRNA	10354	11178	.	+	1	ID=LSEI_RS12825.t01;Parent=LSEI_RS12825
NC_008526	GenBank	CDS	10354	11178	.	+	1	ID=LSEI_RS12825.p01;Parent=LSEI_RS12825.t01;eC_number=1.1.1.127;Name=kduD;Note=Derived by automated computational analysis using gene prediction method: Protein Homology.;codon_start=1;inference=COORDINATES: similar to AA sequence:RefSeq:WP_019887699.1;locus_tag=LSEI_RS12825;old_locus_tag=LSEI_2672;product=2-dehydro-3-deoxy-D-gluconate 5-dehydrogenase KduD;protein_id=WP_011674968.1;transl_table=11;translation=length.274
NC_008526	GenBank	exon	10354	11178	.	+	1	Parent=LSEI_RS12825.t01
NC_008526	GenBank	pseudogenic_exon	11289	11927	.	+	1	ID=LSEI_RS12830;Name=eda;Note=incomplete%3B partial in the middle of a contig%3B missing C-terminus%3B Derived by automated computational analysis using gene prediction method: Protein Homology.;codon_start=1;inference=COORDINATES: similar to AA sequence:RefSeq:WP_005687550.1;locus_tag=LSEI_RS12830;product=bifunctional 4-hydroxy-2-oxoglutarate aldolase/2-dehydro-3-deoxy-phosphogluconate aldolase;pseudo=_no_value;transl_table=11
NC_008526	GenBank	pseudogene	11289	11927	.	+	1	ID=LSEI_RS12830.pseudogene;Alias=LSEI_RS12830;Name=eda;locus_tag=LSEI_RS12830;pseudo=_no_value
NC_008526	GenBank	gene	11946	12965	.	+	1	ID=LSEI_RS12835;Name=LSEI_RS12835
NC_008526	GenBank	mRNA	11946	12965	.	+	1	ID=LSEI_RS12835.t01;Parent=LSEI_RS12835
NC_008526	GenBank	CDS	11946	12965	.	+	1	ID=LSEI_RS12835.p01;Parent=LSEI_RS12835.t01;Name=LSEI_RS12835;Note=Derived by automated computational analysis using gene prediction method: Protein Homology.;codon_start=1;inference=COORDINATES: similar to AA sequence:RefSeq:WP_003596400.1;product=sugar kinase;protein_id=WP_003596400.1;transl_table=11;translation=length.339
NC_008526	GenBank	exon	11946	12965	.	+	1	Parent=LSEI_RS12835.t01
NC_008526	GenBank	gene	13068	13712	.	-	1	ID=LSEI_RS12840;Name=LSEI_RS12840;old_locus_tag=LSEI_2674
NC_008526	GenBank	mRNA	13068	13712	.	-	1	ID=LSEI_RS12840.t01;Parent=LSEI_RS12840
NC_008526	GenBank	CDS	13068	13712	.	-	1	ID=LSEI_RS12840.p01;Parent=LSEI_RS12840.t01;Name=LSEI_RS12840;Note=Derived by automated computational analysis using gene prediction method: Protein Homology.;codon_start=1;inference=COORDINATES: similar to AA sequence:RefSeq:WP_003567949.1;old_locus_tag=LSEI_2674;product=DNA alkylation repair protein;protein_id=WP_003596401.1;transl_table=11;translation=length.214
NC_008526	GenBank	exon	13068	13712	.	-	1	Parent=LSEI_RS12840.t01
NC_008526	GenBank	gene	13781	14470	.	-	1	ID=LSEI_RS12845;Name=rpiA;locus_tag=LSEI_RS12845;old_locus_tag=LSEI_2675
NC_008526	GenBank	mRNA	13781	14470	.	-	1	ID=LSEI_RS12845.t01;Parent=LSEI_RS12845
NC_008526	GenBank	CDS	13781	14470	.	-	1	ID=LSEI_RS12845.p01;Parent=LSEI_RS12845.t01;eC_number=5.3.1.6;Name=rpiA;Note=Derived by automated computational analysis using gene prediction method: Protein Homology.;codon_start=1;inference=COORDINATES: similar to AA sequence:RefSeq:WP_016388769.1;locus_tag=LSEI_RS12845;old_locus_tag=LSEI_2675;product=ribose-5-phosphate isomerase RpiA;protein_id=WP_003567951.1;transl_table=11;translation=length.229
NC_008526	GenBank	exon	13781	14470	.	-	1	Parent=LSEI_RS12845.t01
NC_008526	GenBank	gene	14628	16592	.	-	1	ID=LSEI_RS12850;Name=LSEI_RS12850;old_locus_tag=LSEI_2676
NC_008526	GenBank	mRNA	14628	16592	.	-	1	ID=LSEI_RS12850.t01;Parent=LSEI_RS12850
NC_008526	GenBank	CDS	14628	16592	.	-	1	ID=LSEI_RS12850.p01;Parent=LSEI_RS12850.t01;Name=LSEI_RS12850;Note=Derived by automated computational analysis using gene prediction method: Protein Homology.;codon_start=1;inference=COORDINATES: similar to AA sequence:RefSeq:WP_016388770.1;old_locus_tag=LSEI_2676;product=membrane protein;protein_id=WP_011674970.1;transl_table=11;translation=length.654
NC_008526	GenBank	exon	14628	16592	.	-	1	Parent=LSEI_RS12850.t01