Deinococcus proteolyticus MRP plasmid pDEIPR03, complete sequence.
Bacteria; Deinococcota; Deinococci; Deinococcales; Deinococcaceae; Deinococcus.
Complete genome sequence of the orange-red pigmented, radioresistant Deinococcus proteolyticus type strain (MRP(T))
Submitted (18-FEB-2011) US DOE Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598-1698, USA
REFSEQ INFORMATION: The reference sequence is identical to\nCP002539.1.\nURL -- http://www.jgi.doe.gov\nJGI Project ID: 4087341\nSource DNA and organism available from Hans-Peter Klenk at the\nGerman Collection of Microorganisms and Cell Cultures (DSMZ)\n(hans-peter.klenk@dsmz.de)\nContacts: Jonathan A. Eisen (jaeisen@ucdavis.edu)\n David Bruce (microbe@cuba.jgi-psf.org)\nWhole genome sequencing and draft assembly at JGI-PGF\nFinishing done by JGI-LANL\nAnnotation by JGI-ORNL and JGI-PGF\nThe JGI and collaborators endorse the principles for the\ndistribution and use of large scale sequencing data adopted by the\nlarger genome sequencing community and urge users of this data to\nfollow them. It is our intention to publish the work of this\nproject in a timely fashion and we welcome collaborative\ninteraction on the project and analysis.\n(http://www.genome.gov/page.cfm?pageID=10506376).\nThe annotation was added by the NCBI Prokaryotic Genome Annotation\nPipeline (PGAP). Information about PGAP can be found here:\nhttps://www.ncbi.nlm.nih.gov/genome/annotation_prok/\n\n##MIGS-Data-START##\ninvestigation_type :: bacteria_archaea\nproject_name :: Deinococcus proteolyticus MRP, DSM 20540\ncollection_date :: Missing\nlat_lon :: Missing\ndepth :: Missing\nalt_elev :: Missing\ncountry :: Missing\nenvironment :: Soil\nnum_replicons :: 5\nref_biomaterial :: DSM 20540, ATCC 35074, CCM 2703\nbiotic_relationship :: Free living\ntrophic_level :: Missing\nrel_to_oxygen :: Aerobe\nisol_growth_condt :: Missing\nsequencing_meth :: WGS\nassembly :: Newbler v. 2.3 (pre-release)\nfinishing_strategy :: Finished\nGOLD Stamp ID :: Gi04185\nType Strain :: Yes\nFunding Program :: DOE-GEBA 2007\nGene Calling Method :: Prodigal 1.4, GenePRIMP\nIsolation Site :: Faeces of Lama glama\nIsolation Comments :: isolated by M. Kobatake MRP\nHost Name :: Lama glama\nCell Shape :: Coccus-shaped\nMotility :: Nonmotile\nTemperature Range :: Mesophile\nGram Staining :: Gram+\nPhenotypes :: Radiation resistant\n##MIGS-Data-END##\n\n##Genome-Assembly-Data-START##\nFinishing Goal :: Finished\nCurrent Finishing Status :: Finished\nAssembly Method :: Newbler v. 2.3\nGenome Coverage :: 30x\nSequencing Technology :: 454-Titanium, Illumina\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 05/02/2023 02:11:33\nAnnotation Pipeline :: NCBI Prokaryotic Genome\n Annotation Pipeline (PGAP)\nAnnotation Method :: Best-placed reference protein\n set; GeneMarkS-2+\nAnnotation Software revision :: 6.5\nFeatures Annotated :: Gene; CDS; rRNA; tRNA; ncRNA\nGenes (total) :: 2,790\nCDSs (total) :: 2,732\nGenes (coding) :: 2,688\nCDSs (with protein) :: 2,688\nGenes (RNA) :: 58\nrRNAs :: 3, 3, 3 (5S, 16S, 23S)\ncomplete rRNAs :: 3, 3, 3 (5S, 16S, 23S)\ntRNAs :: 46\nncRNAs :: 3\nPseudo Genes (total) :: 44\nCDSs (without protein) :: 44\nPseudo Genes (ambiguous residues) :: 0 of 44\nPseudo Genes (frameshifted) :: 17 of 44\nPseudo Genes (incomplete) :: 28 of 44\nPseudo Genes (internal stop) :: 4 of 44\nPseudo Genes (multiple problems) :: 4 of 44\nCRISPR Arrays :: 3\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.
type strain of Deinococcus proteolyticus
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: similar to AA sequence:RefSeq:WP_017871875.1
GO:0017168 - 5-oxoprolinase (ATP-hydrolyzing) activity [Evidence IEA]; GO:0005524 - ATP binding [Evidence IEA]; GO:0016810 - hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds [Evidence IEA]
GO:0005975 - carbohydrate metabolic process [Evidence IEA]
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_017871876.1
COORDINATES: similar to AA sequence:RefSeq:WP_009497548.1
COORDINATES: similar to AA sequence:RefSeq:WP_011529506.1
GO:0016829 - lyase activity [Evidence IEA]; GO:0046872 - metal ion binding [Evidence IEA]
COORDINATES: protein motif:HMM:NF021637.2
COORDINATES: similar to AA sequence:RefSeq:WP_015248603.1
GO:0005524 - ATP binding [Evidence IEA]; GO:0008887 - glycerate kinase activity [Evidence IEA]
COORDINATES: protein motif:HMM:TIGR00229.1
COORDINATES: similar to AA sequence:RefSeq:WP_003440186.1
GO:0046873 - metal ion transmembrane transporter activity [Evidence IEA]
GO:0030001 - metal ion transport [Evidence IEA]
COORDINATES: protein motif:HMM:TIGR00254.1
GO:0005886 - plasma membrane [Evidence IEA]
GO:0005525 - GTP binding [Evidence IEA]; GO:0046872 - metal ion binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_019586765.1
GO:0003684 - damaged DNA binding [Evidence IEA]; GO:0003887 - DNA-directed DNA polymerase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_008904226.1
COORDINATES: protein motif:HMM:NF024854.2
GO:0003700 - DNA-binding transcription factor activity [Evidence IEA]
GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_015235638.1
COORDINATES: similar to AA sequence:RefSeq:WP_012693946.1
COORDINATES: similar to AA sequence:RefSeq:WP_019400964.1
COORDINATES: similar to AA sequence:RefSeq:WP_017769953.1
COORDINATES: similar to AA sequence:RefSeq:WP_011530385.1
GO:0010181 - FMN binding [Evidence IEA]; GO:0016491 - oxidoreductase activity [Evidence IEA]
LLM class flavin-dependent oxidoreductase
COORDINATES: protein motif:HMM:NF019310.2
COORDINATES: similar to AA sequence:RefSeq:WP_012683676.1
GO:0010181 - FMN binding [Evidence IEA]; GO:0052873 - FMN reductase (NADPH) activity [Evidence IEA]; GO:0008752 - FMN reductase activity [Evidence IEA]; GO:0016491 - oxidoreductase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_003045636.1
GO:0016787 - hydrolase activity [Evidence IEA]; GO:0046872 - metal ion binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_019584775.1
GO:0008080 - N-acetyltransferase activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF013053.2
COORDINATES: similar to AA sequence:RefSeq:WP_017655676.1
COORDINATES: similar to AA sequence:RefSeq:WP_017869487.1
COORDINATES: protein motif:HMM:NF012772.2
COORDINATES: similar to AA sequence:RefSeq:WP_010889502.1
GO:0071949 - FAD binding [Evidence IEA]; GO:0020037 - heme binding [Evidence IEA]; GO:0008941 - nitric oxide dioxygenase activity [Evidence IEA]; GO:0019825 - oxygen binding [Evidence IEA]
GO:0051409 - response to nitrosative stress [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_014650502.1
GO:0022857 - transmembrane transporter activity [Evidence IEA]
GO:0071705 - nitrogen compound transport [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_013616032.1
COORDINATES: protein motif:HMM:TIGR00180.1
ParB/RepB/Spo0J family partition protein
COORDINATES: similar to AA sequence:RefSeq:WP_076612365.1
GO:0004803 - transposase activity [Evidence IEA]
programmed frameshift; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: protein motif:HMM:NF025167.2
COORDINATES: similar to AA sequence:RefSeq:WP_012693966.1
GO:0008381 - mechanosensitive monoatomic ion channel activity [Evidence IEA]
mechanosensitive ion channel family protein
COORDINATES: similar to AA sequence:RefSeq:WP_017871750.1
COORDINATES: similar to AA sequence:RefSeq:WP_018465948.1
GO:0055085 - transmembrane transport [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_019955929.1
GO:0004617 - phosphoglycerate dehydrogenase activity [Evidence IEA]
GO:0006564 - L-serine biosynthetic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_008027203.1
GO:0004648 - O-phospho-L-serine:2-oxoglutarate aminotransferase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_013385585.1
GO:0036424 - L-phosphoserine phosphatase activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF037660.2
COORDINATES: similar to AA sequence:RefSeq:WP_014695806.1
GO:0003676 - nucleic acid binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011525937.1
CRISPR-associated helicase/endonuclease Cas3
COORDINATES: similar to AA sequence:RefSeq:WP_011525936.1
GO:0003674 - molecular_function [Evidence IEA]
GO:0043571 - maintenance of CRISPR repeat elements [Evidence IEA]
type I-E CRISPR-associated protein Cse1/CasA
COORDINATES: similar to AA sequence:RefSeq:WP_076611089.1
COORDINATES: protein motif:HMM:NF021030.2
incomplete; partial in the middle of a contig; missing C-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_011525935.1
type I-E CRISPR-associated protein Cse2/CasB
COORDINATES: protein motif:HMM:NF020902.2
type I-E CRISPR-associated protein Cas7/Cse4/CasC
COORDINATES: similar to AA sequence:RefSeq:WP_013614122.1
COORDINATES: similar to AA sequence:RefSeq:WP_011525934.1
incomplete; partial in the middle of a contig; missing N-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_011525933.1
type I-E CRISPR-associated protein Cas5/CasD
COORDINATES: similar to AA sequence:RefSeq:WP_013015256.1
type I-E CRISPR-associated protein Cas6/Cse3/CasE
COORDINATES: similar to AA sequence:RefSeq:WP_019586904.1
GO:0004520 - endodeoxyribonuclease activity [Evidence IEA]; GO:0046872 - metal ion binding [Evidence IEA]; GO:0003676 - nucleic acid binding [Evidence IEA]
GO:0051607 - defense response to virus [Evidence IEA]; GO:0043571 - maintenance of CRISPR repeat elements [Evidence IEA]
type I-E CRISPR-associated endonuclease Cas1e
COORDINATES: similar to AA sequence:RefSeq:WP_011525929.1
GO:0004521 - endoribonuclease activity [Evidence IEA]
type I-E CRISPR-associated endoribonuclease Cas2e
COORDINATES: nucleotide motif:Rfam:14.4:RF01051
cyclic di-GMP riboswitch class I; Derived by automated computational analysis using gene prediction method: cmsearch.
COORDINATES: protein motif:HMM:TIGR00350.1
COORDINATES: protein motif:HMM:NF014051.2
COORDINATES: protein motif:HMM:NF024831.2
COORDINATES: protein motif:HMM:NF016800.2
COORDINATES: protein motif:HMM:NF025072.2
COORDINATES: protein motif:HMM:NF012744.2
COORDINATES: similar to AA sequence:RefSeq:WP_013014393.1
GO:0003978 - UDP-glucose 4-epimerase activity [Evidence IEA]
GO:0006012 - galactose metabolic process [Evidence IEA]
COORDINATES: protein motif:HMM:NF013793.2
COORDINATES: protein motif:HMM:TIGR03025.1
GO:0016740 - transferase activity [Evidence IEA]
GO:0006486 - protein glycosylation [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_019008790.1
GO:0016491 - oxidoreductase activity [Evidence IEA]; GO:0016651 - oxidoreductase activity, acting on NAD(P)H [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_019586174.1
GO:0140359 - ABC-type transporter activity [Evidence IEA]; GO:0005524 - ATP binding [Evidence IEA]; GO:0016887 - ATP hydrolysis activity [Evidence IEA]; GO:0042626 - ATPase-coupled transmembrane transporter activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_013014667.1
GO:0140359 - ABC-type transporter activity [Evidence IEA]; GO:0042626 - ATPase-coupled transmembrane transporter activity [Evidence IEA]
GO:0006826 - iron ion transport [Evidence IEA]
COORDINATES: protein motif:HMM:NF013648.2
ABC transporter substrate-binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_018466258.1
COORDINATES: protein motif:HMM:NF018677.2
COORDINATES: similar to AA sequence:RefSeq:WP_012694343.1
COORDINATES: similar to AA sequence:RefSeq:WP_019586179.1
COORDINATES: similar to AA sequence:RefSeq:WP_012692778.1
GO:0008410 - CoA-transferase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_017869493.1
GO:0043546 - molybdopterin cofactor binding [Evidence IEA]
xanthine dehydrogenase family protein molybdopterin-binding subunit
COORDINATES: similar to AA sequence:RefSeq:WP_010889495.1
xanthine dehydrogenase family protein subunit M
COORDINATES: similar to AA sequence:RefSeq:WP_017273324.1
aldehyde dehydrogenase iron-sulfur subunit
COORDINATES: similar to AA sequence:RefSeq:WP_015231620.1
COORDINATES: similar to AA sequence:RefSeq:WP_017871850.1
COORDINATES: similar to AA sequence:RefSeq:WP_014685865.1
GO:0051539 - 4 iron, 4 sulfur cluster binding [Evidence IEA]
GO:0006777 - Mo-molybdopterin cofactor biosynthetic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_013557248.1
GO:0051073 - adenosylcobinamide-GDP ribazoletransferase activity [Evidence IEA]; GO:0008818 - cobalamin 5'-phosphate synthase activity [Evidence IEA]
GO:0009236 - cobalamin biosynthetic process [Evidence IEA]
adenosylcobinamide-GDP ribazoletransferase
COORDINATES: similar to AA sequence:RefSeq:WP_011525708.1
GO:0008939 - nicotinate-nucleotide-dimethylbenzimidazole phosphoribosyltransferase activity [Evidence IEA]
nicotinate-nucleotide--dimethylbenzimidazole phosphoribosyltransferase
COORDINATES: similar to AA sequence:RefSeq:WP_017869446.1
GO:0043752 - adenosylcobinamide kinase activity [Evidence IEA]; GO:0000166 - nucleotide binding [Evidence IEA]
bifunctional adenosylcobinamide kinase/adenosylcobinamide-phosphate guanylyltransferase
COORDINATES: similar to AA sequence:RefSeq:WP_010883988.1
GO:0042242 - cobyrinic acid a,c-diamide synthase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_015236086.1
GO:0008817 - corrinoid adenosyltransferase activity [Evidence IEA]
cob(I)yrinic acid a,c-diamide adenosyltransferase
COORDINATES: similar to AA sequence:RefSeq:WP_015236085.1
COORDINATES: nucleotide motif:Rfam:14.4:RF00174
cobalamin riboswitch; Derived by automated computational analysis using gene prediction method: cmsearch.
COORDINATES: similar to AA sequence:RefSeq:WP_013557749.1
COORDINATES: similar to AA sequence:RefSeq:WP_020670363.1
COORDINATES: similar to AA sequence:RefSeq:WP_009548606.1
GO:0055052 - ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing [Evidence IEA]; GO:0009897 - external side of plasma membrane [Evidence IEA]; GO:0030288 - outer membrane-bounded periplasmic space [Evidence IEA]
GO:0015412 - ABC-type molybdate transporter activity [Evidence IEA]; GO:0030973 - molybdate ion binding [Evidence IEA]
GO:0015689 - molybdate ion transport [Evidence IEA]
molybdate ABC transporter substrate-binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_005013281.1
GO:0055052 - ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing [Evidence IEA]; GO:0005886 - plasma membrane [Evidence IEA]
GO:0015412 - ABC-type molybdate transporter activity [Evidence IEA]
molybdate ABC transporter permease subunit
COORDINATES: similar to AA sequence:RefSeq:WP_005796661.1
ATP-binding cassette domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_013557638.1
GO:0005524 - ATP binding [Evidence IEA]; GO:0004797 - thymidine kinase activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF017870.2
COORDINATES: similar to AA sequence:RefSeq:WP_006758964.1
5-carboxymethyl-2-hydroxymuconate Delta-isomerase
COORDINATES: similar to AA sequence:RefSeq:WP_013623235.1
GO:0003824 - catalytic activity [Evidence IEA]
fumarylacetoacetate hydrolase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_012695132.1
GO:0008687 - 3,4-dihydroxyphenylacetate 2,3-dioxygenase activity [Evidence IEA]
3,4-dihydroxyphenylacetate 2,3-dioxygenase
COORDINATES: similar to AA sequence:RefSeq:WP_017869506.1
4-hydroxyphenylacetate 3-monooxygenase, oxygenase component
COORDINATES: similar to AA sequence:RefSeq:WP_011440457.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0004519 - endonuclease activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_019586247.1
GO:0016491 - oxidoreductase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_017869510.1
GO:0018480 - 5-carboxymethyl-2-hydroxymuconic-semialdehyde dehydrogenase activity [Evidence IEA]
GO:1901023 - 4-hydroxyphenylacetate catabolic process [Evidence IEA]
5-carboxymethyl-2-hydroxymuconate semialdehyde dehydrogenase
COORDINATES: similar to AA sequence:RefSeq:WP_006213468.1
GO:0047470 - (1,4)-alpha-D-glucan 1-alpha-D-glucosylmutase activity [Evidence IEA]
GO:0005992 - trehalose biosynthetic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_017872053.1
GO:0030612 - arsenate reductase (thioredoxin) activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011526016.1
GO:0015105 - arsenite transmembrane transporter activity [Evidence IEA]
GO:0046685 - response to arsenic-containing substance [Evidence IEA]
frameshifted; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_017869751.1
GO:0046872 - metal ion binding [Evidence IEA]; GO:0042578 - phosphoric ester hydrolase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_017872051.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0003700 - DNA-binding transcription factor activity [Evidence IEA]
metalloregulator ArsR/SmtB family transcription factor
COORDINATES: protein motif:HMM:NF012301.2
GO:0000160 - phosphorelay signal transduction system [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_019585522.1