Deinococcus proteolyticus MRP plasmid pDEIPR04, 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\nCP002540.1.\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_013615989.1
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_009180746.1
COORDINATES: similar to AA sequence:RefSeq:WP_011146601.1
type II toxin-antitoxin system PemK/MazF family toxin
COORDINATES: similar to AA sequence:RefSeq:WP_013615946.1
GO:0005524 - ATP binding [Evidence IEA]; GO:0008233 - peptidase activity [Evidence IEA]
cysteine peptidase family C39 domain-containing protein
COORDINATES: protein motif:HMM:TIGR02293.1
COORDINATES: protein motif:HMM:NF020387.2
COORDINATES: similar to AA sequence:RefSeq:WP_013615945.1
COORDINATES: similar to AA sequence:RefSeq:WP_013615944.1
COORDINATES: similar to AA sequence:RefSeq:WP_086558286.1
incomplete; partial in the middle of a contig; missing C-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: protein motif:HMM:NF021537.2
predicted Zn-dependent protease with a strongly conserved HExxH motif; Derived by automated computational analysis using gene prediction method: Protein Homology.
DUF2268 domain-containing putative Zn-dependent protease
COORDINATES: protein motif:HMM:NF024248.2
helix-turn-helix domain-containing protein
COORDINATES: protein motif:HMM:NF012235.2
COORDINATES: protein motif:HMM:NF024803.2
GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_013616020.1
GO:0015074 - DNA integration [Evidence IEA]
DDE-type integrase/transposase/recombinase
COORDINATES: protein motif:HMM:NF013677.2
GO:0003677 - DNA binding [Evidence IEA]; GO:0004803 - transposase activity [Evidence IEA]
GO:0006313 - transposition, DNA-mediated [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_017870386.1
nuclease-related domain-containing DEAD/DEAH box helicase
COORDINATES: similar to AA sequence:RefSeq:WP_014685618.1
GO:0055052 - ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing [Evidence IEA]
GO:0140359 - ABC-type transporter activity [Evidence IEA]; GO:0042626 - ATPase-coupled transmembrane transporter activity [Evidence IEA]
ABC transporter substrate-binding protein
COORDINATES: protein motif:HMM:NF024252.2
helix-turn-helix transcriptional regulator
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: similar to AA sequence:RefSeq:WP_013615974.1
putative UvrD/rep helicase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_001549957.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0000150 - DNA strand exchange activity [Evidence IEA]
GO:0006310 - DNA recombination [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_018385313.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0003700 - DNA-binding transcription factor activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_019928389.1
COORDINATES: similar to AA sequence:RefSeq:WP_017870462.1
GO:0010181 - FMN binding [Evidence IEA]; GO:0004733 - pyridoxamine-phosphate oxidase activity [Evidence IEA]
GO:0008615 - pyridoxine biosynthetic process [Evidence IEA]
COORDINATES: protein motif:HMM:NF025079.2
COORDINATES: protein motif:HMM:NF033527.1
COORDINATES: similar to AA sequence:RefSeq:WP_009764920.1
COORDINATES: similar to AA sequence:RefSeq:WP_010886790.1
COORDINATES: similar to AA sequence:RefSeq:WP_013616005.1
integrase core domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_017872031.1
COORDINATES: protein motif:HMM:NF015658.2
COORDINATES: similar to AA sequence:RefSeq:WP_013616025.1
GO:0000160 - phosphorelay signal transduction system [Evidence IEA]; GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_013616026.1
GO:0005524 - ATP binding [Evidence IEA]; GO:0000156 - phosphorelay response regulator activity [Evidence IEA]; GO:0004673 - protein histidine kinase activity [Evidence IEA]
GO:0007165 - signal transduction [Evidence IEA]
HAMP domain-containing sensor histidine kinase
COORDINATES: similar to AA sequence:RefSeq:WP_013616027.1
COORDINATES: similar to AA sequence:RefSeq:WP_012173261.1
COORDINATES: similar to AA sequence:RefSeq:WP_002707056.1
frameshifted; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_017871113.1
COORDINATES: similar to AA sequence:RefSeq:WP_076612277.1
COORDINATES: similar to AA sequence:RefSeq:WP_076612299.1
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_012694762.1
COORDINATES: protein motif:HMM:TIGR00180.1
GO:0007059 - chromosome segregation [Evidence IEA]; GO:0000910 - cytokinesis [Evidence IEA]
ParB/RepB/Spo0J family partition protein
COORDINATES: similar to AA sequence:RefSeq:WP_013623169.1
COORDINATES: similar to AA sequence:RefSeq:WP_019009217.1
COORDINATES: similar to AA sequence:RefSeq:WP_013558293.1
GO:0005524 - ATP binding [Evidence IEA]; GO:0003677 - DNA binding [Evidence IEA]; GO:0016787 - hydrolase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_013614240.1
COORDINATES: similar to AA sequence:RefSeq:WP_012695243.1
COORDINATES: similar to AA sequence:RefSeq:WP_013156685.1
COORDINATES: protein motif:HMM:NF025056.2
GO:0003953 - NAD+ nucleosidase activity [Evidence IEA]; GO:0005515 - protein binding [Evidence IEA]
toll/interleukin-1 receptor domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_012814599.1
COORDINATES: protein motif:HMM:NF021873.2
COORDINATES: protein motif:HMM:NF015340.2
phage antirepressor KilAC domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_013616019.1
COORDINATES: similar to AA sequence:RefSeq:WP_017300409.1
GO:0016301 - kinase activity [Evidence IEA]
type II toxin-antitoxin system death-on-curing family toxin
COORDINATES: similar to AA sequence:RefSeq:WP_014686953.1
AbrB/MazE/SpoVT family DNA-binding domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_012275131.1
COORDINATES: similar to AA sequence:RefSeq:WP_012695078.1
frameshifted; 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_010884088.1
COORDINATES: similar to AA sequence:RefSeq:WP_006592278.1
GO:0004222 - metalloendopeptidase activity [Evidence IEA]
GO:0071586 - CAAX-box protein processing [Evidence IEA]
CPBP family intramembrane metalloprotease
COORDINATES: similar to AA sequence:RefSeq:WP_012639711.1
COORDINATES: similar to AA sequence:RefSeq:WP_013615942.1
COORDINATES: protein motif:HMM:NF033516.0
COORDINATES: similar to AA sequence:RefSeq:WP_006470258.1
GO:0015036 - disulfide oxidoreductase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011529241.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0046872 - metal ion binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_019010851.1
COORDINATES: protein motif:HMM:NF012655.2
TetR/AcrR family transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_011313787.1
GO:0005524 - ATP binding [Evidence IEA]; GO:0022857 - transmembrane transporter activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011061468.1
COORDINATES: similar to AA sequence:RefSeq:WP_016705144.1
GO:0005524 - ATP binding [Evidence IEA]; GO:0016887 - ATP hydrolysis activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_017904449.1
GO:0050660 - flavin adenine dinucleotide binding [Evidence IEA]; GO:0016491 - oxidoreductase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_020086315.1
carboxymuconolactone decarboxylase family protein