##gff-version 3
##sequence-region NC_012028 1 20976
# conversion-by bp_genbank2gff3.pl
# organism Halorubrum lacusprofundi ATCC 49239
# Note Halorubrum lacusprofundi ATCC 49239 chromosome 2, complete sequence.
# date 18-NOV-2019
NC_012028	GenBank	chromosome	1	20976	.	+	1	ID=NC_012028;Alias=2;Dbxref=BioProject:PRJNA224116,taxon:416348;Name=NC_012028;Note=Halorubrum lacusprofundi ATCC 49239 chromosome 2%2C complete sequence.,REFSEQ INFORMATION: The reference sequence was derived from CP001366. URL -- http://www.jgi.doe.gov JGI Project ID: 4001421 Source DNA available from Ricardo Cavicchioli (r.cavicchioli@unsw.edu.au) Archaea available from ATCC: ATCC 49239 Contacts: Ricardo Cavicchioli (r.cavicchioli@unsw.edu.au) Shiladitya DasSarma (dassarma@umbi.umd.edu) David Bruce (microbe@cuba.jgi-psf.org) Annotation done by JGI-ORNL and JGI-PGF Finishing done by JGI-LANL Finished microbial genomes have been curated to close all gaps with greater than 98%25 coverage of at least two independent clones. Each base pair has a minimum q (quality) value of 30 and the total error rate is less than one per 50000. 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 :: 11/18/2019 03:50:09 Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline (PGAP) Annotation Method :: Best-placed reference protein set,GeneMarkS-2+ Annotation Software revision :: 4.10 Features Annotated :: Gene,CDS,rRNA,tRNA,ncRNA,repeat_region Genes (total) :: 3,640 CDSs (total) :: 3,578 Genes (coding) :: 3,414 CDSs (with protein) :: 3,414 Genes (RNA) :: 62 rRNAs :: 3,3,3 (5S,16S,23S) complete rRNAs :: 3,3,3 (5S,16S,23S) tRNAs :: 51 ncRNAs :: 2 Pseudo Genes (total) :: 164 CDSs (without protein) :: 164 Pseudo Genes (ambiguous residues) :: 0 of 164 Pseudo Genes (frameshifted) :: 44 of 164 Pseudo Genes (incomplete) :: 124 of 164 Pseudo Genes (internal stop) :: 27 of 164 Pseudo Genes (multiple problems) :: 27 of 164 CRISPR Arrays :: 2 ##Genome-Annotation-Data-END## COMPLETENESS: full length. ;chromosome=2;comment1=REFSEQ INFORMATION: The reference sequence was derived from CP001366. URL -- http://www.jgi.doe.gov JGI Project ID: 4001421 Source DNA available from Ricardo Cavicchioli (r.cavicchioli@unsw.edu.au) Archaea available from ATCC: ATCC 49239 Contacts: Ricardo Cavicchioli (r.cavicchioli@unsw.edu.au) Shiladitya DasSarma (dassarma@umbi.umd.edu) David Bruce (microbe@cuba.jgi-psf.org) Annotation done by JGI-ORNL and JGI-PGF Finishing done by JGI-LANL Finished microbial genomes have been curated to close all gaps with greater than 98%25 coverage of at least two independent clones. Each base pair has a minimum q (quality) value of 30 and the total error rate is less than one per 50000. 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 :: 11/18/2019 03:50:09 Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline (PGAP) Annotation Method :: Best-placed reference protein set%3B GeneMarkS-2+ Annotation Software revision :: 4.10 Features Annotated :: Gene%3B CDS%3B rRNA%3B tRNA%3B ncRNA%3B repeat_region Genes (total) :: 3%2C640 CDSs (total) :: 3%2C578 Genes (coding) :: 3%2C414 CDSs (with protein) :: 3%2C414 Genes (RNA) :: 62 rRNAs :: 3%2C 3%2C 3 (5S%2C 16S%2C 23S) complete rRNAs :: 3%2C 3%2C 3 (5S%2C 16S%2C 23S) tRNAs :: 51 ncRNAs :: 2 Pseudo Genes (total) :: 164 CDSs (without protein) :: 164 Pseudo Genes (ambiguous residues) :: 0 of 164 Pseudo Genes (frameshifted) :: 44 of 164 Pseudo Genes (incomplete) :: 124 of 164 Pseudo Genes (internal stop) :: 27 of 164 Pseudo Genes (multiple problems) :: 27 of 164 CRISPR Arrays :: 2 ##Genome-Annotation-Data-END## COMPLETENESS: full length. ;culture_collection=ATCC:49239;date=18-NOV-2019;mol_type=genomic DNA;organism=Halorubrum lacusprofundi ATCC 49239;strain=ATCC 49239;type_material=type strain of Halorubrum lacusprofundi
NC_012028	GenBank	gene	1	1167	.	+	1	ID=HLAC_RS14125;Dbxref=GeneID:7399093;Name=HLAC_RS14125;old_locus_tag=Hlac_2855
NC_012028	GenBank	mRNA	1	1167	.	+	1	ID=HLAC_RS14125.t01;Parent=HLAC_RS14125
NC_012028	GenBank	CDS	1	1167	.	+	1	ID=HLAC_RS14125.p01;Parent=HLAC_RS14125.t01;Dbxref=GeneID:7399093;Name=HLAC_RS14125;Note=Derived by automated computational analysis using gene prediction method: Protein Homology.;codon_start=1;inference=COORDINATES: similar to AA sequence:RefSeq:WP_014053295.1;old_locus_tag=Hlac_2855;product=ISH3-like element ISHla1 family transposase;protein_id=WP_009486633.1;transl_table=11;translation=length.388
NC_012028	GenBank	exon	1	1167	.	+	1	Parent=HLAC_RS14125.t01
NC_012028	GenBank	pseudogenic_exon	1282	1362	.	-	1	ID=HLAC_RS18870;Dbxref=GeneID:42369488;Name=HLAC_RS18870;Note=incomplete%3B partial in the middle of a contig%3B missing N-terminus%3B Derived by automated computational analysis using gene prediction method: Protein Homology.;codon_start=1;inference=COORDINATES: similar to AA sequence:RefSeq:WP_009486645.1;product=TATA box-binding protein;pseudo=_no_value;transl_table=11
NC_012028	GenBank	pseudogene	1282	1362	.	-	1	ID=HLAC_RS18870.pseudogene;Alias=HLAC_RS18870;Dbxref=GeneID:42369488;Name=HLAC_RS18870;pseudo=_no_value
NC_012028	GenBank	gene	2965	4137	.	+	1	ID=HLAC_RS14135;Dbxref=GeneID:7398871;Name=HLAC_RS14135;old_locus_tag=Hlac_2857
NC_012028	GenBank	mRNA	2965	4137	.	+	1	ID=HLAC_RS14135.t01;Parent=HLAC_RS14135
NC_012028	GenBank	CDS	2965	4137	.	+	1	ID=HLAC_RS14135.p01;Parent=HLAC_RS14135.t01;Dbxref=GeneID:7398871;Name=HLAC_RS14135;Note=Derived by automated computational analysis using gene prediction method: Protein Homology.;codon_start=1;inference=COORDINATES: similar to AA sequence:RefSeq:WP_012659234.1;old_locus_tag=Hlac_2857;product=ISH3-like element ISHla8 family transposase;protein_id=WP_012659234.1;transl_table=11;translation=length.390
NC_012028	GenBank	exon	2965	4137	.	+	1	Parent=HLAC_RS14135.t01
NC_012028	GenBank	gene	5030	5668	.	-	1	ID=HLAC_RS14140;Dbxref=GeneID:7399096;Name=eda;locus_tag=HLAC_RS14140;old_locus_tag=Hlac_2860
NC_012028	GenBank	mRNA	5030	5668	.	-	1	ID=HLAC_RS14140.t01;Parent=HLAC_RS14140
NC_012028	GenBank	CDS	5030	5668	.	-	1	ID=HLAC_RS14140.p01;Parent=HLAC_RS14140.t01;Dbxref=GeneID:7399096;Name=eda;Note=Derived by automated computational analysis using gene prediction method: Protein Homology.;codon_start=1;inference=COORDINATES: similar to AA sequence:RefSeq:WP_012659236.1;locus_tag=HLAC_RS14140;old_locus_tag=Hlac_2860;product=bifunctional 4-hydroxy-2-oxoglutarate aldolase/2-dehydro-3-deoxy-phosphogluconate aldolase;protein_id=WP_012659236.1;transl_table=11;translation=length.212
NC_012028	GenBank	exon	5030	5668	.	-	1	Parent=HLAC_RS14140.t01
NC_012028	GenBank	gene	5729	6475	.	-	1	ID=HLAC_RS14145;Dbxref=GeneID:7399097;Name=HLAC_RS14145;old_locus_tag=Hlac_2861
NC_012028	GenBank	mRNA	5729	6475	.	-	1	ID=HLAC_RS14145.t01;Parent=HLAC_RS14145
NC_012028	GenBank	CDS	5729	6475	.	-	1	ID=HLAC_RS14145.p01;Parent=HLAC_RS14145.t01;Dbxref=GeneID:7399097;Name=HLAC_RS14145;Note=Derived by automated computational analysis using gene prediction method: Protein Homology.;codon_start=1;inference=COORDINATES: similar to AA sequence:RefSeq:WP_008440863.1;old_locus_tag=Hlac_2861;product=IclR family transcriptional regulator;protein_id=WP_012659237.1;transl_table=11;translation=length.248
NC_012028	GenBank	exon	5729	6475	.	-	1	Parent=HLAC_RS14145.t01
NC_012028	GenBank	gene	6800	8158	.	+	1	ID=HLAC_RS14150;Dbxref=GeneID:7399098;Name=HLAC_RS14150;old_locus_tag=Hlac_2862
NC_012028	GenBank	mRNA	6800	8158	.	+	1	ID=HLAC_RS14150.t01;Parent=HLAC_RS14150
NC_012028	GenBank	CDS	6800	8158	.	+	1	ID=HLAC_RS14150.p01;Parent=HLAC_RS14150.t01;Dbxref=GeneID:7399098;Name=HLAC_RS14150;Note=Derived by automated computational analysis using gene prediction method: Protein Homology.;codon_start=1;inference=COORDINATES: similar to AA sequence:RefSeq:WP_007997751.1;old_locus_tag=Hlac_2862;product=extracellular solute-binding protein;protein_id=WP_049933796.1;transl_table=11;translation=length.452
NC_012028	GenBank	exon	6800	8158	.	+	1	Parent=HLAC_RS14150.t01
NC_012028	GenBank	gene	8177	9247	.	+	1	ID=HLAC_RS14155;Dbxref=GeneID:7399099;Name=HLAC_RS14155;old_locus_tag=Hlac_2863
NC_012028	GenBank	mRNA	8177	9247	.	+	1	ID=HLAC_RS14155.t01;Parent=HLAC_RS14155
NC_012028	GenBank	CDS	8177	9247	.	+	1	ID=HLAC_RS14155.p01;Parent=HLAC_RS14155.t01;Dbxref=GeneID:7399099;Name=HLAC_RS14155;Note=Derived by automated computational analysis using gene prediction method: Protein Homology.;codon_start=1;inference=COORDINATES: similar to AA sequence:RefSeq:WP_008440855.1;old_locus_tag=Hlac_2863;product=sugar ABC transporter permease;protein_id=WP_012659239.1;transl_table=11;translation=length.356
NC_012028	GenBank	exon	8177	9247	.	+	1	Parent=HLAC_RS14155.t01
NC_012028	GenBank	gene	9247	10083	.	+	1	ID=HLAC_RS14160;Dbxref=GeneID:7399100;Name=HLAC_RS14160;old_locus_tag=Hlac_2864
NC_012028	GenBank	mRNA	9247	10083	.	+	1	ID=HLAC_RS14160.t01;Parent=HLAC_RS14160
NC_012028	GenBank	CDS	9247	10083	.	+	1	ID=HLAC_RS14160.p01;Parent=HLAC_RS14160.t01;Dbxref=GeneID:7399100;Name=HLAC_RS14160;Note=Derived by automated computational analysis using gene prediction method: Protein Homology.;codon_start=1;inference=COORDINATES: similar to AA sequence:RefSeq:WP_007997753.1;old_locus_tag=Hlac_2864;product=carbohydrate ABC transporter permease;protein_id=WP_012659240.1;transl_table=11;translation=length.278
NC_012028	GenBank	exon	9247	10083	.	+	1	Parent=HLAC_RS14160.t01
NC_012028	GenBank	gene	10086	11207	.	+	1	ID=HLAC_RS14165;Dbxref=GeneID:7399101;Name=HLAC_RS14165;old_locus_tag=Hlac_2865
NC_012028	GenBank	mRNA	10086	11207	.	+	1	ID=HLAC_RS14165.t01;Parent=HLAC_RS14165
NC_012028	GenBank	CDS	10086	11207	.	+	1	ID=HLAC_RS14165.p01;Parent=HLAC_RS14165.t01;Dbxref=GeneID:7399101;Name=HLAC_RS14165;Note=Derived by automated computational analysis using gene prediction method: Protein Homology.;codon_start=1;inference=COORDINATES: similar to AA sequence:RefSeq:WP_008848339.1;old_locus_tag=Hlac_2865;product=ABC transporter ATP-binding protein;protein_id=WP_012659241.1;transl_table=11;translation=length.373
NC_012028	GenBank	exon	10086	11207	.	+	1	Parent=HLAC_RS14165.t01
NC_012028	GenBank	gene	11214	12362	.	+	1	ID=HLAC_RS14170;Dbxref=GeneID:7399102;Name=dgoD;locus_tag=HLAC_RS14170;old_locus_tag=Hlac_2866
NC_012028	GenBank	mRNA	11214	12362	.	+	1	ID=HLAC_RS14170.t01;Parent=HLAC_RS14170
NC_012028	GenBank	CDS	11214	12362	.	+	1	ID=HLAC_RS14170.p01;Parent=HLAC_RS14170.t01;Dbxref=GeneID:7399102;eC_number=4.2.1.6;Name=dgoD;Note=Derived by automated computational analysis using gene prediction method: Protein Homology.;codon_start=1;inference=COORDINATES: similar to AA sequence:RefSeq:WP_007997758.1;locus_tag=HLAC_RS14170;old_locus_tag=Hlac_2866;product=galactonate dehydratase;protein_id=WP_012659242.1;transl_table=11;translation=length.382
NC_012028	GenBank	exon	11214	12362	.	+	1	Parent=HLAC_RS14170.t01
NC_012028	GenBank	gene	12403	13257	.	+	1	ID=HLAC_RS14175;Dbxref=GeneID:7399103;Name=HLAC_RS14175;old_locus_tag=Hlac_2867
NC_012028	GenBank	mRNA	12403	13257	.	+	1	ID=HLAC_RS14175.t01;Parent=HLAC_RS14175
NC_012028	GenBank	CDS	12403	13257	.	+	1	ID=HLAC_RS14175.p01;Parent=HLAC_RS14175.t01;Dbxref=GeneID:7399103;Name=HLAC_RS14175;Note=Derived by automated computational analysis using gene prediction method: Protein Homology.;codon_start=1;inference=COORDINATES: similar to AA sequence:RefSeq:WP_006630851.1;old_locus_tag=Hlac_2867;product=SDR family oxidoreductase;protein_id=WP_049933798.1;transl_table=11;translation=length.284
NC_012028	GenBank	exon	12403	13257	.	+	1	Parent=HLAC_RS14175.t01
NC_012028	GenBank	gene	13305	15407	.	-	1	ID=HLAC_RS14180;Dbxref=GeneID:7399104;Name=HLAC_RS14180;old_locus_tag=Hlac_2868
NC_012028	GenBank	mRNA	13305	15407	.	-	1	ID=HLAC_RS14180.t01;Parent=HLAC_RS14180
NC_012028	GenBank	CDS	13305	15407	.	-	1	ID=HLAC_RS14180.p01;Parent=HLAC_RS14180.t01;Dbxref=GeneID:7399104;Name=HLAC_RS14180;Note=Derived by automated computational analysis using gene prediction method: Protein Homology.;codon_start=1;inference=COORDINATES: similar to AA sequence:RefSeq:WP_006630850.1;old_locus_tag=Hlac_2868;product=beta-galactosidase;protein_id=WP_012659244.1;transl_table=11;translation=length.700
NC_012028	GenBank	exon	13305	15407	.	-	1	Parent=HLAC_RS14180.t01
NC_012028	GenBank	gene	15537	17576	.	+	1	ID=HLAC_RS14185;Dbxref=GeneID:7399105;Name=HLAC_RS14185;old_locus_tag=Hlac_2869
NC_012028	GenBank	mRNA	15537	17576	.	+	1	ID=HLAC_RS14185.t01;Parent=HLAC_RS14185
NC_012028	GenBank	CDS	15537	17576	.	+	1	ID=HLAC_RS14185.p01;Parent=HLAC_RS14185.t01;Dbxref=GeneID:7399105;Name=HLAC_RS14185;Note=Derived by automated computational analysis using gene prediction method: Protein Homology.;codon_start=1;inference=COORDINATES: similar to AA sequence:RefSeq:WP_008848343.1;old_locus_tag=Hlac_2869;product=alpha-galactosidase;protein_id=WP_012659245.1;transl_table=11;translation=length.679
NC_012028	GenBank	exon	15537	17576	.	+	1	Parent=HLAC_RS14185.t01
NC_012028	GenBank	gene	17707	18663	.	+	1	ID=HLAC_RS14190;Dbxref=GeneID:7399106;Name=HLAC_RS14190;old_locus_tag=Hlac_2870
NC_012028	GenBank	mRNA	17707	18663	.	+	1	ID=HLAC_RS14190.t01;Parent=HLAC_RS14190
NC_012028	GenBank	CDS	17707	18663	.	+	1	ID=HLAC_RS14190.p01;Parent=HLAC_RS14190.t01;Dbxref=GeneID:7399106;Name=HLAC_RS14190;Note=Derived by automated computational analysis using gene prediction method: Protein Homology.;codon_start=1;inference=COORDINATES: similar to AA sequence:RefSeq:WP_008440848.1;old_locus_tag=Hlac_2870;product=sugar kinase;protein_id=WP_012659246.1;transl_table=11;translation=length.318
NC_012028	GenBank	exon	17707	18663	.	+	1	Parent=HLAC_RS14190.t01
NC_012028	GenBank	gene	19274	19705	.	+	1	ID=HLAC_RS14195;Dbxref=GeneID:7399107;Name=HLAC_RS14195;old_locus_tag=Hlac_2871
NC_012028	GenBank	mRNA	19274	19705	.	+	1	ID=HLAC_RS14195.t01;Parent=HLAC_RS14195
NC_012028	GenBank	CDS	19274	19705	.	+	1	ID=HLAC_RS14195.p01;Parent=HLAC_RS14195.t01;Dbxref=GeneID:7399107;Name=HLAC_RS14195;Note=Derived by automated computational analysis using gene prediction method: Protein Homology.;codon_start=1;inference=COORDINATES: similar to AA sequence:RefSeq:WP_012659247.1;old_locus_tag=Hlac_2871;product=IS200/IS605-like element ISHla17 family transposase;protein_id=WP_012659247.1;transl_table=11;translation=length.143
NC_012028	GenBank	exon	19274	19705	.	+	1	Parent=HLAC_RS14195.t01
NC_012028	GenBank	gene	19702	20976	.	+	1	ID=HLAC_RS14200;Dbxref=GeneID:7399108;Name=HLAC_RS14200;old_locus_tag=Hlac_2872
NC_012028	GenBank	mRNA	19702	20976	.	+	1	ID=HLAC_RS14200.t01;Parent=HLAC_RS14200
NC_012028	GenBank	CDS	19702	20976	.	+	1	ID=HLAC_RS14200.p01;Parent=HLAC_RS14200.t01;Dbxref=GeneID:7399108;Name=HLAC_RS14200;Note=Derived by automated computational analysis using gene prediction method: Protein Homology.;codon_start=1;inference=COORDINATES: similar to AA sequence:RefSeq:WP_006054393.1;old_locus_tag=Hlac_2872;product=transposase;protein_id=WP_012659248.1;transl_table=11;translation=length.424
NC_012028	GenBank	exon	19702	20976	.	+	1	Parent=HLAC_RS14200.t01