##gff-version 3 ##sequence-region CP001807 1 31440 # conversion-by bp_genbank2gff3.pl # organism Rhodothermus marinus DSM 4252 # Note Rhodothermus marinus DSM 4252, complete genome. # date 11-DEC-2013 CP001807 GenBank region 1 31440 . + 1 ID=CP001807;Dbxref=BioProject:PRJNA29281,taxon:518766;Name=CP001807;Note=Rhodothermus marinus DSM 4252%2C complete genome.,URL -- http://www.jgi.doe.gov JGI Project ID: 4083220 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). \n##Metadata-START##\nOrganism Display Name :: Rhodothermus marinus R-10,DSM 4252\nCulture Collection ID :: DSM 4252,ATCC 43812\nGOLD Stamp ID :: Gi02303\nFunding Program :: DOE-GEBA 2007\nAssembly Method :: Newbler version 1.1.02.15,Phrap\nSequencing Depth :: 8.8x Sanger,23.8x 454\nGene Calling Method :: Prodigal 1.4,GenePRIMP\nIsolation Site :: Submarine alkaline hot spring at Reykjanes\nin Iceland\nCollection Date :: 1988\nIsolation Country :: Iceland\nLatitude :: 63.88\nLongitude :: -22.5\nDepth :: 2-3 meters\nOxygen Requirement :: Aerobe\nCell Shape :: Rod-shaped\nMotility :: Nonmotile\nSporulation :: Nonsporulating\nTemperature Range :: Thermophile\nTemperature Optimum :: 65C\nSalinity :: Halophile\npH :: 7\nGram Staining :: gram-\nBiotic Relationship :: Free living\nDiseases :: None\nHabitat :: Hot spring,Marine\nEnergy Source :: Heterotroph\n##Metadata-END##;comment1=URL -- http://www.jgi.doe.gov JGI Project ID: 4083220 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). \n##Metadata-START##\nOrganism Display Name :: Rhodothermus marinus R-10%2C DSM 4252\nCulture Collection ID :: DSM 4252%2C ATCC 43812\nGOLD Stamp ID :: Gi02303\nFunding Program :: DOE-GEBA 2007\nAssembly Method :: Newbler version 1.1.02.15%2C Phrap\nSequencing Depth :: 8.8x Sanger%3B 23.8x 454\nGene Calling Method :: Prodigal 1.4%2C GenePRIMP\nIsolation Site :: Submarine alkaline hot spring at Reykjanes\nin Iceland\nCollection Date :: 1988\nIsolation Country :: Iceland\nLatitude :: 63.88\nLongitude :: -22.5\nDepth :: 2-3 meters\nOxygen Requirement :: Aerobe\nCell Shape :: Rod-shaped\nMotility :: Nonmotile\nSporulation :: Nonsporulating\nTemperature Range :: Thermophile\nTemperature Optimum :: 65C\nSalinity :: Halophile\npH :: 7\nGram Staining :: gram-\nBiotic Relationship :: Free living\nDiseases :: None\nHabitat :: Hot spring%2C Marine\nEnergy Source :: Heterotroph\n##Metadata-END##;date=11-DEC-2013;mol_type=genomic DNA;organism=Rhodothermus marinus DSM 4252;strain=DSM 4252;type_material=type strain of Rhodothermus marinus CP001807 GenBank gene 1 1050 . + 1 ID=Rmar_1067;Name=Rmar_1067 CP001807 GenBank mRNA 1 1050 . + 1 ID=Rmar_1067.t01;Parent=Rmar_1067 CP001807 GenBank CDS 1 1050 . + 1 ID=Rmar_1067.p01;Parent=Rmar_1067.t01;Dbxref=InterPro:IPR000843,InterPro:IPR001761;Name=Rmar_1067;Note=PFAM: periplasmic binding protein/LacI transcriptional regulator%3B regulatory protein LacI%3B SMART: regulatory protein LacI%3B KEGG: vsp:VS_1088 HTH-type transcriptional repressor PurR;codon_start=1;inference=protein motif:PFAM:PF00532;product=transcriptional regulator%2C LacI family;protein_id=ACY47959.1;transl_table=11;translation=length.349 CP001807 GenBank exon 1 1050 . + 1 Parent=Rmar_1067.t01 CP001807 GenBank gene 1477 3870 . + 1 ID=Rmar_1068;Name=Rmar_1068 CP001807 GenBank mRNA 1477 3870 . + 1 ID=Rmar_1068.t01;Parent=Rmar_1068 CP001807 GenBank signal_peptide 1477 1608 . + 1 Parent=Rmar_1068;Name=Rmar_1068;Note=Signal predicted by SignalP 3.0 HMM (Signal peptide probability 0.955) with cleavage site probability 0.881 at residue 44 CP001807 GenBank CDS 1477 3870 . + 1 ID=Rmar_1068.p01;Parent=Rmar_1068.t01;Dbxref=InterPro:IPR005084,InterPro:IPR006584,InterPro:IPR006710;Name=Rmar_1068;Note=PFAM: glycoside hydrolase family 43%3B Carbohydrate binding family 6%3B SMART: cellulose binding type IV%3B KEGG: scl:sce3304 putative xylosidase/arabinosidase;codon_start=1;inference=protein motif:PFAM:PF04616;product=glycoside hydrolase family 43;protein_id=ACY47960.1;transl_table=11;translation=length.797 CP001807 GenBank exon 1477 3870 . + 1 Parent=Rmar_1068.t01 CP001807 GenBank gene 4026 7019 . + 1 ID=Rmar_1069;Name=Rmar_1069 CP001807 GenBank mRNA 4026 7019 . + 1 ID=Rmar_1069.t01;Parent=Rmar_1069 CP001807 GenBank signal_peptide 4026 4136 . + 1 Parent=Rmar_1069;Name=Rmar_1069;Note=Signal predicted by SignalP 3.0 HMM (Signal peptide probability 0.989) with cleavage site probability 0.883 at residue 37 CP001807 GenBank CDS 4026 7019 . + 1 ID=Rmar_1069.p01;Parent=Rmar_1069.t01;Dbxref=InterPro:IPR001000,InterPro:IPR003305;Name=Rmar_1069;Note=PFAM: glycoside hydrolase family 10%3B Carbohydrate- binding CenC domain protein%3B SMART: glycoside hydrolase family 10%3B KEGG: xca:xccb100_4330 exported endo-1%2C4-beta- xylanase;codon_start=1;inference=protein motif:PFAM:PF00331;product=glycoside hydrolase family 10;protein_id=ACY47961.1;transl_table=11;translation=length.997 CP001807 GenBank exon 4026 7019 . + 1 Parent=Rmar_1069.t01 CP001807 GenBank gene 7065 10040 . + 1 ID=Rmar_1070;Name=Rmar_1070 CP001807 GenBank mRNA 7065 10040 . + 1 ID=Rmar_1070.t01;Parent=Rmar_1070 CP001807 GenBank signal_peptide 7065 7142 . + 1 Parent=Rmar_1070;Name=Rmar_1070;Note=Signal predicted by SignalP 3.0 HMM (Signal peptide probability 0.862) with cleavage site probability 0.548 at residue 26 CP001807 GenBank CDS 7065 10040 . + 1 ID=Rmar_1070.p01;Parent=Rmar_1070.t01;Dbxref=InterPro:IPR000531,InterPro:IPR010104,InterPro:IPR012910;Name=Rmar_1070;Note=TIGRFAM: TonB-dependent receptor%3B PFAM: TonB-dependent receptor plug%3B TonB-dependent receptor%3B KEGG: amc:MADE_02398 putative TonB-dependent receptor;codon_start=1;inference=protein motif:TFAM:TIGR01782;product=TonB-dependent receptor;protein_id=ACY47962.1;transl_table=11;translation=length.991 CP001807 GenBank exon 7065 10040 . + 1 Parent=Rmar_1070.t01 CP001807 GenBank gene 10073 12079 . + 1 ID=Rmar_1071;Name=Rmar_1071 CP001807 GenBank mRNA 10073 12079 . + 1 ID=Rmar_1071.t01;Parent=Rmar_1071 CP001807 GenBank signal_peptide 10073 10135 . + 1 Parent=Rmar_1071;Name=Rmar_1071;Note=Signal predicted by SignalP 3.0 HMM (Signal peptide probability 1.000) with cleavage site probability 0.992 at residue 21 CP001807 GenBank CDS 10073 12079 . + 1 ID=Rmar_1071.p01;Parent=Rmar_1071.t01;Name=Rmar_1071;codon_start=1;inference=ab initio prediction:Prodigal:1.4;product=hypothetical protein;protein_id=ACY47963.1;transl_table=11;translation=length.668 CP001807 GenBank exon 10073 12079 . + 1 Parent=Rmar_1071.t01 CP001807 GenBank gene 12183 13955 . + 1 ID=Rmar_1072;Name=Rmar_1072 CP001807 GenBank mRNA 12183 13955 . + 1 ID=Rmar_1072.t01;Parent=Rmar_1072 CP001807 GenBank signal_peptide 12183 12275 . + 1 Parent=Rmar_1072;Name=Rmar_1072;Note=Signal predicted by SignalP 3.0 HMM (Signal peptide probability 0.935) with cleavage site probability 0.934 at residue 31 CP001807 GenBank CDS 12183 13955 . + 1 ID=Rmar_1072.p01;Parent=Rmar_1072.t01;Name=Rmar_1072;Note=KEGG: mxa:MXAN_0469 putative foldase protein PrsA;codon_start=1;inference=ab initio prediction:Prodigal:1.4;product=hypothetical protein;protein_id=ACY47964.1;transl_table=11;translation=length.590 CP001807 GenBank exon 12183 13955 . + 1 Parent=Rmar_1072.t01 CP001807 GenBank gene 13978 15684 . + 1 ID=Rmar_1073;Name=Rmar_1073 CP001807 GenBank mRNA 13978 15684 . + 1 ID=Rmar_1073.t01;Parent=Rmar_1073 CP001807 GenBank signal_peptide 13978 14046 . + 1 Parent=Rmar_1073;Name=Rmar_1073;Note=Signal predicted by SignalP 3.0 HMM (Signal peptide probability 1.000) with cleavage site probability 0.997 at residue 23 CP001807 GenBank CDS 13978 15684 . + 1 ID=Rmar_1073.p01;Parent=Rmar_1073.t01;Name=Rmar_1073;Note=KEGG: mrd:Mrad2831_3094 glucose/sorbosone dehydrogenase-like protein;codon_start=1;inference=ab initio prediction:Prodigal:1.4;product=hypothetical protein;protein_id=ACY47965.1;transl_table=11;translation=length.568 CP001807 GenBank exon 13978 15684 . + 1 Parent=Rmar_1073.t01 CP001807 GenBank gene 15960 17456 . + 1 ID=Rmar_1074;Name=Rmar_1074 CP001807 GenBank mRNA 15960 17456 . + 1 ID=Rmar_1074.t01;Parent=Rmar_1074 CP001807 GenBank CDS 15960 17456 . + 1 ID=Rmar_1074.p01;Parent=Rmar_1074.t01;Dbxref=InterPro:IPR001000;Name=Rmar_1074;Note=PFAM: glycoside hydrolase family 10%3B SMART: glycoside hydrolase family 10%3B KEGG: sus:Acid_2816 glycoside hydrolase family protein;codon_start=1;inference=protein motif:PFAM:PF00331;product=glycoside hydrolase family 10;protein_id=ACY47966.1;transl_table=11;translation=length.498 CP001807 GenBank exon 15960 17456 . + 1 Parent=Rmar_1074.t01 CP001807 GenBank gene 17497 18060 . + 1 ID=Rmar_1075;Name=Rmar_1075 CP001807 GenBank mRNA 17497 18060 . + 1 ID=Rmar_1075.t01;Parent=Rmar_1075 CP001807 GenBank CDS 17497 18060 . + 1 ID=Rmar_1075.p01;Parent=Rmar_1075.t01;Dbxref=InterPro:IPR007627,InterPro:IPR007630,InterPro:IPR013249,InterPro:IPR014284,InterPro:IPR014327;Name=Rmar_1075;Note=TIGRFAM: RNA polymerase sigma-70 factor%3B RNA polymerase sigma factor%2C sigma-70 family%3B PFAM: Sigma-70 region 4 type 2%3B sigma-70 region 2 domain protein%3B sigma-70 region 4 domain protein%3B KEGG: acp:A2cp1_0252 RNA polymerase%2C sigma-24 subunit%2C ECF subfamily;codon_start=1;inference=protein motif:TFAM:TIGR02985;product=RNA polymerase%2C sigma-24 subunit%2C ECF subfamily;protein_id=ACY47967.1;transl_table=11;translation=length.187 CP001807 GenBank exon 17497 18060 . + 1 Parent=Rmar_1075.t01 CP001807 GenBank gene 18136 19179 . + 1 ID=Rmar_1076;Name=Rmar_1076 CP001807 GenBank mRNA 18136 19179 . + 1 ID=Rmar_1076.t01;Parent=Rmar_1076 CP001807 GenBank CDS 18136 19179 . + 1 ID=Rmar_1076.p01;Parent=Rmar_1076.t01;Dbxref=InterPro:IPR006860;Name=Rmar_1076;Note=PFAM: FecR protein%3B KEGG: smt:Smal_2017 anti-FecI sigma factor%2C FecR;codon_start=1;inference=protein motif:PFAM:PF04773;product=anti-FecI sigma factor%2C FecR;protein_id=ACY47968.1;transl_table=11;translation=length.347 CP001807 GenBank exon 18136 19179 . + 1 Parent=Rmar_1076.t01 CP001807 GenBank gene 19251 22694 . + 1 ID=Rmar_1077;Name=Rmar_1077 CP001807 GenBank mRNA 19251 22694 . + 1 ID=Rmar_1077.t01;Parent=Rmar_1077 CP001807 GenBank signal_peptide 19251 19355 . + 1 Parent=Rmar_1077;Name=Rmar_1077;Note=Signal predicted by SignalP 3.0 HMM (Signal peptide probability 1.000) with cleavage site probability 1.000 at residue 35 CP001807 GenBank CDS 19251 22694 . + 1 ID=Rmar_1077.p01;Parent=Rmar_1077.t01;Dbxref=InterPro:IPR000531,InterPro:IPR012910;Name=Rmar_1077;Note=PFAM: TonB-dependent receptor plug%3B TonB-dependent receptor%3B KEGG: mxa:MXAN_4746 TonB-dependent receptor;codon_start=1;inference=protein motif:PFAM:PF07715;product=TonB-dependent receptor plug;protein_id=ACY47969.1;transl_table=11;translation=length.1147 CP001807 GenBank exon 19251 22694 . + 1 Parent=Rmar_1077.t01 CP001807 GenBank gene 22741 24270 . + 1 ID=Rmar_1078;Name=Rmar_1078 CP001807 GenBank mRNA 22741 24270 . + 1 ID=Rmar_1078.t01;Parent=Rmar_1078 CP001807 GenBank signal_peptide 22741 22830 . + 1 Parent=Rmar_1078;Name=Rmar_1078;Note=Signal predicted by SignalP 3.0 HMM (Signal peptide probability 0.853) with cleavage site probability 0.543 at residue 30 CP001807 GenBank CDS 22741 24270 . + 1 ID=Rmar_1078.p01;Parent=Rmar_1078.t01;Dbxref=InterPro:IPR012944;Name=Rmar_1078;Note=PFAM: RagB/SusD domain protein;codon_start=1;inference=protein motif:PFAM:PF07980;product=RagB/SusD domain protein;protein_id=ACY47970.1;transl_table=11;translation=length.509 CP001807 GenBank exon 22741 24270 . + 1 Parent=Rmar_1078.t01 CP001807 GenBank gene 24404 26584 . + 1 ID=Rmar_1079;Name=Rmar_1079 CP001807 GenBank mRNA 24404 26584 . + 1 ID=Rmar_1079.t01;Parent=Rmar_1079 CP001807 GenBank signal_peptide 24404 24475 . + 1 Parent=Rmar_1079;Name=Rmar_1079;Note=Signal predicted by SignalP 3.0 HMM (Signal peptide probability 0.998) with cleavage site probability 0.998 at residue 24 CP001807 GenBank CDS 24404 26584 . + 1 ID=Rmar_1079.p01;Parent=Rmar_1079.t01;Dbxref=InterPro:IPR005154,InterPro:IPR011099,InterPro:IPR011100,InterPro:IPR016160;eC_number=3.2.1.139;Name=Rmar_1079;Note=PFAM: Glycosyl hydrolase 67 middle domain protein%3B glycosyl hydrolase 67 C-teriminal domain protein%3B glycoside hydrolase family 67%3B KEGG: xca:xccb100_4307 exported alpha-glucuronidase;codon_start=1;inference=protein motif:PRIAM:3.2.1.139;product=Alpha-glucuronidase;protein_id=ACY47971.1;transl_table=11;translation=length.726 CP001807 GenBank exon 24404 26584 . + 1 Parent=Rmar_1079.t01 CP001807 GenBank gene 26648 29026 . + 1 ID=Rmar_1080;Name=Rmar_1080 CP001807 GenBank mRNA 26648 29026 . + 1 ID=Rmar_1080.t01;Parent=Rmar_1080 CP001807 GenBank signal_peptide 26648 26704 . + 1 Parent=Rmar_1080;Name=Rmar_1080;Note=Signal predicted by SignalP 3.0 HMM (Signal peptide probability 1.000) with cleavage site probability 1.000 at residue 19 CP001807 GenBank CDS 26648 29026 . + 1 ID=Rmar_1080.p01;Parent=Rmar_1080.t01;Dbxref=InterPro:IPR001764,InterPro:IPR002772;Name=Rmar_1080;Note=PFAM: glycoside hydrolase family 3 domain protein%3B KEGG: sus:Acid_2679 glycoside hydrolase family 3 protein;codon_start=1;inference=protein motif:PFAM:PF01915;product=glycoside hydrolase family 3 domain protein;protein_id=ACY47972.1;transl_table=11;translation=length.792 CP001807 GenBank exon 26648 29026 . + 1 Parent=Rmar_1080.t01 CP001807 GenBank gene 29086 31440 . + 1 ID=Rmar_1081;Name=Rmar_1081 CP001807 GenBank mRNA 29086 31440 . + 1 ID=Rmar_1081.t01;Parent=Rmar_1081 CP001807 GenBank CDS 29086 31440 . + 1 ID=Rmar_1081.p01;Parent=Rmar_1081.t01;Dbxref=InterPro:IPR001764,InterPro:IPR002772;Name=Rmar_1081;Note=PFAM: glycoside hydrolase family 3 domain protein%3B KEGG: sus:Acid_2679 glycoside hydrolase family 3 protein;codon_start=1;inference=protein motif:PFAM:PF01915;product=glycoside hydrolase family 3 domain protein;protein_id=ACY47973.1;transl_table=11;translation=length.784 CP001807 GenBank exon 29086 31440 . + 1 Parent=Rmar_1081.t01