##gff-version 3
##sequence-region NC_013515 1 18331
# conversion-by bp_genbank2gff3.pl
# organism Streptobacillus moniliformis DSM 12112
# Note Streptobacillus moniliformis DSM 12112, complete genome.
# date 25-AUG-2019
NC_013515	GenBank	region	1	18331	.	+	1	ID=NC_013515;Dbxref=BioProject:PRJNA224116,taxon:519441;Name=NC_013515;Note=Streptobacillus moniliformis DSM 12112%2C complete genome.,REFSEQ INFORMATION: The reference sequence was derived from CP001779. URL -- http://www.jgi.doe.gov JGI Project ID: 4083288 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/ ##Metadata-START## Organism Display Name :: Streptobacillus moniliformis 9901,DSM 12112 Culture Collection ID :: DSM 12112,ATCC 14647 GOLD Stamp ID :: Gi02312 Funding Program :: DOE-GEBA 2007 Number of Reads :: 22979 Sanger,326576 pyrosequence Assembly Method :: Newbler version 1.1.02.15,Phrap Sequencing Depth :: 11.5x Sanger,24.9x pyrosequence Gene Calling Method :: Prodigal 1.4,GenePRIMP Isolation Site :: Patient with rat-bite fever in France Isolation Country :: France Host Name :: Homo sapiens Host Health :: Patient with rat-bite fever Oxygen Requirement :: Facultative Cell Shape :: Rod-shaped Motility :: Nonmotile Sporulation :: Nonsporulating Temperature Range :: Mesophile Temperature Optimum :: 37C Gram Staining :: gram- Biotic Relationship :: Free living Diseases :: Endocarditis,Haverhill fever,Rat-bite fever Habitat :: Host Phenotypes :: Pathogen ##Metadata-END## ##Genome-Annotation-Data-START## Annotation Provider :: NCBI RefSeq Annotation Date :: 08/25/2019 19:15:01 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) :: 1,543 CDSs (total) :: 1,485 Genes (coding) :: 1,426 CDSs (with protein) :: 1,426 Genes (RNA) :: 58 rRNAs :: 6,5,5 (5S,16S,23S) complete rRNAs :: 6,5,5 (5S,16S,23S) tRNAs :: 39 ncRNAs :: 3 Pseudo Genes (total) :: 59 CDSs (without protein) :: 59 Pseudo Genes (ambiguous residues) :: 0 of 59 Pseudo Genes (frameshifted) :: 33 of 59 Pseudo Genes (incomplete) :: 21 of 59 Pseudo Genes (internal stop) :: 18 of 59 Pseudo Genes (multiple problems) :: 11 of 59 CRISPR Arrays :: 1 ##Genome-Annotation-Data-END## COMPLETENESS: full length. ;comment1=REFSEQ INFORMATION: The reference sequence was derived from CP001779. URL -- http://www.jgi.doe.gov JGI Project ID: 4083288 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/ ##Metadata-START## Organism Display Name :: Streptobacillus moniliformis 9901%2C DSM 12112 Culture Collection ID :: DSM 12112%2C ATCC 14647 GOLD Stamp ID :: Gi02312 Funding Program :: DOE-GEBA 2007 Number of Reads :: 22979 Sanger%2C 326576 pyrosequence Assembly Method :: Newbler version 1.1.02.15%2C Phrap Sequencing Depth :: 11.5x Sanger%3B 24.9x pyrosequence Gene Calling Method :: Prodigal 1.4%2C GenePRIMP Isolation Site :: Patient with rat-bite fever in France Isolation Country :: France Host Name :: Homo sapiens Host Health :: Patient with rat-bite fever Oxygen Requirement :: Facultative Cell Shape :: Rod-shaped Motility :: Nonmotile Sporulation :: Nonsporulating Temperature Range :: Mesophile Temperature Optimum :: 37C Gram Staining :: gram- Biotic Relationship :: Free living Diseases :: Endocarditis%2C Haverhill fever%2C Rat-bite fever Habitat :: Host Phenotypes :: Pathogen ##Metadata-END## ##Genome-Annotation-Data-START## Annotation Provider :: NCBI RefSeq Annotation Date :: 08/25/2019 19:15:01 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) :: 1%2C543 CDSs (total) :: 1%2C485 Genes (coding) :: 1%2C426 CDSs (with protein) :: 1%2C426 Genes (RNA) :: 58 rRNAs :: 6%2C 5%2C 5 (5S%2C 16S%2C 23S) complete rRNAs :: 6%2C 5%2C 5 (5S%2C 16S%2C 23S) tRNAs :: 39 ncRNAs :: 3 Pseudo Genes (total) :: 59 CDSs (without protein) :: 59 Pseudo Genes (ambiguous residues) :: 0 of 59 Pseudo Genes (frameshifted) :: 33 of 59 Pseudo Genes (incomplete) :: 21 of 59 Pseudo Genes (internal stop) :: 18 of 59 Pseudo Genes (multiple problems) :: 11 of 59 CRISPR Arrays :: 1 ##Genome-Annotation-Data-END## COMPLETENESS: full length. ;culture_collection=DSM:12112;date=25-AUG-2019;mol_type=genomic DNA;organism=Streptobacillus moniliformis DSM 12112;strain=DSM 12112;type_material=type strain of Streptobacillus moniliformis
NC_013515	GenBank	gene	1	4	.	+	1	ID=SMON_RS00570;Dbxref=GeneID:29673064;Name=SMON_RS00570;old_locus_tag=Smon_0114
NC_013515	GenBank	mRNA	1	4	.	+	1	ID=SMON_RS00570.t01;Parent=SMON_RS00570
NC_013515	GenBank	CDS	1	4	.	+	1	ID=SMON_RS00570.p01;Parent=SMON_RS00570.t01;Dbxref=GeneID:29673064;Name=SMON_RS00570;Note=Derived by automated computational analysis using gene prediction method: Protein Homology.;codon_start=3;inference=COORDINATES: protein motif:HMM:PF00356.19;old_locus_tag=Smon_0114;product=LacI family transcriptional regulator;protein_id=WP_012858165.1;transl_table=11;translation=length.341
NC_013515	GenBank	exon	1	4	.	+	1	Parent=SMON_RS00570.t01
NC_013515	GenBank	gene	1	942	.	+	1	ID=SMON_RS00575;Dbxref=GeneID:29673226;Name=SMON_RS00575;old_locus_tag=Smon_0115
NC_013515	GenBank	mRNA	1	942	.	+	1	ID=SMON_RS00575.t01;Parent=SMON_RS00575
NC_013515	GenBank	CDS	1	942	.	+	1	ID=SMON_RS00575.p01;Parent=SMON_RS00575.t01;Dbxref=GeneID:29673226;Name=SMON_RS00575;Note=Derived by automated computational analysis using gene prediction method: Protein Homology.;codon_start=1;inference=COORDINATES: similar to AA sequence:RefSeq:WP_004826906.1;old_locus_tag=Smon_0115;product=sugar kinase;protein_id=WP_012858166.1;transl_table=11;translation=length.313
NC_013515	GenBank	exon	1	942	.	+	1	Parent=SMON_RS00575.t01
NC_013515	GenBank	gene	953	1600	.	+	1	ID=SMON_RS00580;Dbxref=GeneID:29674289;Name=eda;locus_tag=SMON_RS00580;old_locus_tag=Smon_0116
NC_013515	GenBank	mRNA	953	1600	.	+	1	ID=SMON_RS00580.t01;Parent=SMON_RS00580
NC_013515	GenBank	CDS	953	1600	.	+	1	ID=SMON_RS00580.p01;Parent=SMON_RS00580.t01;Dbxref=GeneID:29674289;eC_number=4.1.2.14,4.1.3.16;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_013711688.1;locus_tag=SMON_RS00580;old_locus_tag=Smon_0116;product=bifunctional 4-hydroxy-2-oxoglutarate aldolase/2-dehydro-3-deoxy-phosphogluconate aldolase;protein_id=WP_041794192.1;transl_table=11;translation=length.215
NC_013515	GenBank	exon	953	1600	.	+	1	Parent=SMON_RS00580.t01
NC_013515	GenBank	gene	1649	3505	.	+	1	ID=SMON_RS00585;Dbxref=GeneID:29673833;Name=SMON_RS00585;old_locus_tag=Smon_0117
NC_013515	GenBank	mRNA	1649	3505	.	+	1	ID=SMON_RS00585.t01;Parent=SMON_RS00585
NC_013515	GenBank	CDS	1649	3505	.	+	1	ID=SMON_RS00585.p01;Parent=SMON_RS00585.t01;Dbxref=GeneID:29673833;eC_number=4.2.2.1;Name=SMON_RS00585;Note=Derived by automated computational analysis using gene prediction method: Protein Homology.;codon_start=1;inference=COORDINATES: protein motif:HMM:PF08124.9;old_locus_tag=Smon_0117;product=hyaluronate lyase;protein_id=WP_012858168.1;transl_table=11;translation=length.618
NC_013515	GenBank	exon	1649	3505	.	+	1	Parent=SMON_RS00585.t01
NC_013515	GenBank	gene	3519	4268	.	+	1	ID=SMON_RS00590;Dbxref=GeneID:29673502;Name=kduD;locus_tag=SMON_RS00590;old_locus_tag=Smon_0118
NC_013515	GenBank	mRNA	3519	4268	.	+	1	ID=SMON_RS00590.t01;Parent=SMON_RS00590
NC_013515	GenBank	CDS	3519	4268	.	+	1	ID=SMON_RS00590.p01;Parent=SMON_RS00590.t01;Dbxref=GeneID:29673502;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_011967797.1;locus_tag=SMON_RS00590;old_locus_tag=Smon_0118;product=2-dehydro-3-deoxy-D-gluconate 5-dehydrogenase KduD;protein_id=WP_041794195.1;transl_table=11;translation=length.249
NC_013515	GenBank	exon	3519	4268	.	+	1	Parent=SMON_RS00590.t01
NC_013515	GenBank	gene	4287	5123	.	+	1	ID=SMON_RS00595;Dbxref=GeneID:29673971;Name=kduI;locus_tag=SMON_RS00595;old_locus_tag=Smon_0119
NC_013515	GenBank	mRNA	4287	5123	.	+	1	ID=SMON_RS00595.t01;Parent=SMON_RS00595
NC_013515	GenBank	CDS	4287	5123	.	+	1	ID=SMON_RS00595.p01;Parent=SMON_RS00595.t01;Dbxref=GeneID:29673971;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_005883583.1;locus_tag=SMON_RS00595;old_locus_tag=Smon_0119;product=5-dehydro-4-deoxy-D-glucuronate isomerase;protein_id=WP_012858170.1;transl_table=11;translation=length.278
NC_013515	GenBank	exon	4287	5123	.	+	1	Parent=SMON_RS00595.t01
NC_013515	GenBank	gene	5134	6234	.	+	1	ID=SMON_RS00600;Dbxref=GeneID:29673413;Name=ugpC;locus_tag=SMON_RS00600;old_locus_tag=Smon_0120
NC_013515	GenBank	mRNA	5134	6234	.	+	1	ID=SMON_RS00600.t01;Parent=SMON_RS00600
NC_013515	GenBank	CDS	5134	6234	.	+	1	ID=SMON_RS00600.p01;Parent=SMON_RS00600.t01;Dbxref=GeneID:29673413;Name=ugpC;Note=Derived by automated computational analysis using gene prediction method: Protein Homology.;codon_start=1;inference=COORDINATES: similar to AA sequence:RefSeq:WP_006807764.1;locus_tag=SMON_RS00600;old_locus_tag=Smon_0120;product=sn-glycerol-3-phosphate ABC transporter ATP-binding protein UgpC;protein_id=WP_012858171.1;transl_table=11;translation=length.366
NC_013515	GenBank	exon	5134	6234	.	+	1	Parent=SMON_RS00600.t01
NC_013515	GenBank	gene	6244	7140	.	+	1	ID=SMON_RS00605;Dbxref=GeneID:29673539;Name=SMON_RS00605;old_locus_tag=Smon_0121
NC_013515	GenBank	mRNA	6244	7140	.	+	1	ID=SMON_RS00605.t01;Parent=SMON_RS00605
NC_013515	GenBank	CDS	6244	7140	.	+	1	ID=SMON_RS00605.p01;Parent=SMON_RS00605.t01;Dbxref=GeneID:29673539;Name=SMON_RS00605;Note=Derived by automated computational analysis using gene prediction method: Protein Homology.;codon_start=1;inference=COORDINATES: similar to AA sequence:RefSeq:WP_005883586.1;old_locus_tag=Smon_0121;product=sugar ABC transporter permease;protein_id=WP_012858172.1;transl_table=11;translation=length.298
NC_013515	GenBank	exon	6244	7140	.	+	1	Parent=SMON_RS00605.t01
NC_013515	GenBank	gene	7150	8028	.	+	1	ID=SMON_RS00610;Dbxref=GeneID:29673869;Name=SMON_RS00610;old_locus_tag=Smon_0122
NC_013515	GenBank	mRNA	7150	8028	.	+	1	ID=SMON_RS00610.t01;Parent=SMON_RS00610
NC_013515	GenBank	CDS	7150	8028	.	+	1	ID=SMON_RS00610.p01;Parent=SMON_RS00610.t01;Dbxref=GeneID:29673869;Name=SMON_RS00610;Note=Derived by automated computational analysis using gene prediction method: Protein Homology.;codon_start=1;inference=COORDINATES: similar to AA sequence:RefSeq:WP_006807262.1;old_locus_tag=Smon_0122;product=carbohydrate ABC transporter permease;protein_id=WP_012858173.1;transl_table=11;translation=length.292
NC_013515	GenBank	exon	7150	8028	.	+	1	Parent=SMON_RS00610.t01
NC_013515	GenBank	gene	8055	9572	.	+	1	ID=SMON_RS00615;Dbxref=GeneID:29674010;Name=SMON_RS00615;old_locus_tag=Smon_0123
NC_013515	GenBank	mRNA	8055	9572	.	+	1	ID=SMON_RS00615.t01;Parent=SMON_RS00615
NC_013515	GenBank	CDS	8055	9572	.	+	1	ID=SMON_RS00615.p01;Parent=SMON_RS00615.t01;Dbxref=GeneID:29674010;Name=SMON_RS00615;Note=Derived by automated computational analysis using gene prediction method: Protein Homology.;codon_start=1;inference=COORDINATES: similar to AA sequence:RefSeq:WP_005883590.1;old_locus_tag=Smon_0123;product=extracellular solute-binding protein;protein_id=WP_012858174.1;transl_table=11;translation=length.505
NC_013515	GenBank	exon	8055	9572	.	+	1	Parent=SMON_RS00615.t01
NC_013515	GenBank	gene	9617	11413	.	+	1	ID=SMON_RS00620;Dbxref=GeneID:29673353;Name=SMON_RS00620;old_locus_tag=Smon_0124
NC_013515	GenBank	mRNA	9617	11413	.	+	1	ID=SMON_RS00620.t01;Parent=SMON_RS00620
NC_013515	GenBank	CDS	9617	11413	.	+	1	ID=SMON_RS00620.p01;Parent=SMON_RS00620.t01;Dbxref=GeneID:29673353;Name=SMON_RS00620;Note=Derived by automated computational analysis using gene prediction method: Protein Homology.;codon_start=1;inference=COORDINATES: protein motif:HMM:PF16889.3;old_locus_tag=Smon_0124;product=hypothetical protein;protein_id=WP_041793794.1;transl_table=11;translation=length.598
NC_013515	GenBank	exon	9617	11413	.	+	1	Parent=SMON_RS00620.t01
NC_013515	GenBank	gene	11410	13629	.	+	1	ID=SMON_RS00625;Dbxref=GeneID:29672896;Name=SMON_RS00625;old_locus_tag=Smon_0125
NC_013515	GenBank	mRNA	11410	13629	.	+	1	ID=SMON_RS00625.t01;Parent=SMON_RS00625
NC_013515	GenBank	CDS	11410	13629	.	+	1	ID=SMON_RS00625.p01;Parent=SMON_RS00625.t01;Dbxref=GeneID:29672896;Name=SMON_RS00625;Note=Derived by automated computational analysis using gene prediction method: Protein Homology.;codon_start=1;inference=COORDINATES: protein motif:HMM:PF02278.16%2CHMM:PF08124.9;old_locus_tag=Smon_0125;product=polysaccharide lyase 8 family protein;protein_id=WP_012858176.1;transl_table=11;translation=length.739
NC_013515	GenBank	exon	11410	13629	.	+	1	Parent=SMON_RS00625.t01
NC_013515	GenBank	gene	13642	15045	.	+	1	ID=SMON_RS00630;Dbxref=GeneID:29673582;Name=SMON_RS00630;old_locus_tag=Smon_0126
NC_013515	GenBank	mRNA	13642	15045	.	+	1	ID=SMON_RS00630.t01;Parent=SMON_RS00630
NC_013515	GenBank	CDS	13642	15045	.	+	1	ID=SMON_RS00630.p01;Parent=SMON_RS00630.t01;Dbxref=GeneID:29673582;Name=SMON_RS00630;Note=Derived by automated computational analysis using gene prediction method: Protein Homology.;codon_start=1;inference=COORDINATES: similar to AA sequence:RefSeq:WP_006807765.1;old_locus_tag=Smon_0126;product=sulfatase;protein_id=WP_012858177.1;transl_table=11;translation=length.467
NC_013515	GenBank	exon	13642	15045	.	+	1	Parent=SMON_RS00630.t01
NC_013515	GenBank	gene	15059	16243	.	+	1	ID=SMON_RS00635;Dbxref=GeneID:29672968;Name=SMON_RS00635;old_locus_tag=Smon_0127
NC_013515	GenBank	mRNA	15059	16243	.	+	1	ID=SMON_RS00635.t01;Parent=SMON_RS00635
NC_013515	GenBank	CDS	15059	16243	.	+	1	ID=SMON_RS00635.p01;Parent=SMON_RS00635.t01;Dbxref=GeneID:29672968;Name=SMON_RS00635;Note=Derived by automated computational analysis using gene prediction method: Protein Homology.;codon_start=1;inference=COORDINATES: similar to AA sequence:RefSeq:WP_006807772.1;old_locus_tag=Smon_0127;product=glucuronyl hydrolase;protein_id=WP_012858178.1;transl_table=11;translation=length.394
NC_013515	GenBank	exon	15059	16243	.	+	1	Parent=SMON_RS00635.t01
NC_013515	GenBank	gene	16253	18331	.	+	1	ID=SMON_RS00640;Dbxref=GeneID:29673838;Name=SMON_RS00640;old_locus_tag=Smon_0128
NC_013515	GenBank	mRNA	16253	18331	.	+	1	ID=SMON_RS00640.t01;Parent=SMON_RS00640
NC_013515	GenBank	CDS	16253	18331	.	+	1	ID=SMON_RS00640.p01;Parent=SMON_RS00640.t01;Dbxref=GeneID:29673838;Name=SMON_RS00640;Note=Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.;codon_start=1;inference=COORDINATES: ab initio prediction:GeneMarkS-2+;old_locus_tag=Smon_0128;product=hypothetical protein;protein_id=WP_012858179.1;transl_table=11;translation=length.692
NC_013515	GenBank	exon	16253	18331	.	+	1	Parent=SMON_RS00640.t01