Deinococcus aetherius strain ST0316 plasmid pDAETH-3, complete sequence.
Bacteria; Deinococcota; Deinococci; Deinococcales; Deinococcaceae; Deinococcus.
Complete Genome Sequence of the Radioresistant Bacterium Deinococcus aetherius ST0316, Isolated from the Air Dust collected in Lower Stratosphere above Japan
Submitted (29-JUL-2022) Contact:Katsuya Satoh National Institutes for Quantum Science and Technology, Department of Radiation-Applied Biology Research, Takasaki Advanced Radiation Research Institute, Quantum Beam Science Research Directorate; Watanuki 1233, Takasaki 370-1292, Japan
REFSEQ INFORMATION: The reference sequence is identical to\nAP026563.1.\nAnnotated by DFAST https://dfast.ddbj.nig.ac.jp/\n\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##Genome-Assembly-Data-START##\nAssembly Method :: Unicycler v. 0.4.7\nGenome Coverage :: 648x\nSequencing Technology :: Nanopore GridION X5; DNBSEQ-G400\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 11/07/2022 17:37:47\nAnnotation Pipeline :: NCBI Prokaryotic Genome\n Annotation Pipeline (PGAP)\nAnnotation Method :: Best-placed reference protein\n set; GeneMarkS-2+\nAnnotation Software revision :: 6.3\nFeatures Annotated :: Gene; CDS; rRNA; tRNA; ncRNA;\n repeat_region\nGenes (total) :: 4,905\nCDSs (total) :: 4,832\nGenes (coding) :: 4,720\nCDSs (with protein) :: 4,720\nGenes (RNA) :: 73\nrRNAs :: 4, 4, 4 (5S, 16S, 23S)\ncomplete rRNAs :: 4, 4, 4 (5S, 16S, 23S)\ntRNAs :: 58\nncRNAs :: 3\nPseudo Genes (total) :: 112\nCDSs (without protein) :: 112\nPseudo Genes (ambiguous residues) :: 0 of 112\nPseudo Genes (frameshifted) :: 39 of 112\nPseudo Genes (incomplete) :: 80 of 112\nPseudo Genes (internal stop) :: 18 of 112\nPseudo Genes (multiple problems) :: 23 of 112\nCRISPR Arrays :: 7\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: similar to AA sequence:RefSeq:WP_014684199.1
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: protein motif:HMM:NF012706.2
ABC transporter substrate-binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_014682860.1
COORDINATES: protein motif:HMM:NF018691.2
type II toxin-antitoxin system prevent-host-death family antitoxin
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_014682863.1
COORDINATES: similar to AA sequence:RefSeq:WP_014682864.1
COORDINATES: protein motif:HMM:NF012234.2
GO:0005524 - ATP binding [Evidence IEA]; GO:0016887 - ATP hydrolysis activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_014682869.1
COORDINATES: similar to AA sequence:RefSeq:WP_013615826.1
COORDINATES: similar to AA sequence:RefSeq:WP_027480237.1
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_014682978.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0003917 - DNA topoisomerase type I (single strand cut, ATP-independent) activity [Evidence IEA]
GO:0006260 - DNA replication [Evidence IEA]; GO:0006265 - DNA topological change [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_006725532.1
COORDINATES: similar to AA sequence:RefSeq:WP_011142675.1
Lrp/AsnC family transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_012843438.1
GO:0004073 - aspartate-semialdehyde dehydrogenase activity [Evidence IEA]
GO:0009089 - lysine biosynthetic process via diaminopimelate [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_013703673.1
COORDINATES: similar to AA sequence:RefSeq:WP_012407620.1
GO:0004803 - transposase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_010884084.1
COORDINATES: similar to AA sequence:RefSeq:WP_019010866.1
COORDINATES: similar to AA sequence:RefSeq:WP_017596188.1
ankyrin repeat domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_012113579.1
COORDINATES: similar to AA sequence:RefSeq:WP_006219359.1
GO:0000160 - phosphorelay signal transduction system [Evidence IEA]
COORDINATES: protein motif:HMM:NF014567.2
COORDINATES: protein motif:HMM:NF033542.1
COORDINATES: similar to AA sequence:RefSeq:WP_013615832.1
COORDINATES: similar to AA sequence:RefSeq:WP_014682720.1
COORDINATES: similar to AA sequence:RefSeq:WP_014682724.1
COORDINATES: similar to AA sequence:RefSeq:WP_013615839.1
COORDINATES: similar to AA sequence:RefSeq:WP_011525852.1
COORDINATES: protein motif:HMM:NF025056.2
toll/interleukin-1 receptor domain-containing protein
COORDINATES: protein motif:HMM:NF024642.2
COORDINATES: similar to AA sequence:RefSeq:WP_012694843.1
bifunctional UDP-sugar hydrolase/5'-nucleotidase
COORDINATES: protein motif:HMM:NF015658.2
COORDINATES: similar to AA sequence:RefSeq:WP_015235526.1
COORDINATES: similar to AA sequence:RefSeq:WP_019588013.1
COORDINATES: protein motif:HMM:NF020123.2
COORDINATES: similar to AA sequence:RefSeq:WP_019012463.1
COORDINATES: protein motif:HMM:NF017539.2
COORDINATES: protein motif:HMM:NF013700.2
peptidoglycan DD-metalloendopeptidase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_014685564.1
COORDINATES: similar to AA sequence:RefSeq:WP_019009387.1
GO:0016410 - N-acyltransferase activity [Evidence IEA]
GO:0042158 - lipoprotein biosynthetic process [Evidence IEA]; GO:0006497 - protein lipidation [Evidence IEA]
COORDINATES: protein motif:HMM:NF020419.2
nucleotidyl transferase AbiEii/AbiGii toxin family protein
COORDINATES: protein motif:HMM:NF013703.2
GO:0015297 - antiporter activity [Evidence IEA]; GO:0042910 - xenobiotic transmembrane transporter activity [Evidence IEA]
GO:0055085 - transmembrane transport [Evidence IEA]
COORDINATES: protein motif:HMM:NF024975.2
COORDINATES: protein motif:HMM:NF013752.2
GO:0003677 - DNA binding [Evidence IEA]; GO:0004803 - transposase activity [Evidence IEA]
GO:0006313 - transposition, DNA-mediated [Evidence IEA]
COORDINATES: protein motif:HMM:NF024736.2
COORDINATES: protein motif:HMM:NF033545.0
COORDINATES: protein motif:HMM:NF024954.2
helix-turn-helix domain-containing protein
COORDINATES: protein motif:HMM:NF012981.2
GO:0016301 - kinase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011526016.1
frameshifted; Derived by automated computational analysis using gene prediction method: Protein Homology.
arsenical efflux pump membrane protein ArsB
COORDINATES: similar to AA sequence:RefSeq:WP_017291687.1
iron export ABC transporter permease subunit FetB
COORDINATES: similar to AA sequence:RefSeq:WP_013339155.1
ATP-binding cassette domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_019587700.1
COORDINATES: similar to AA sequence:RefSeq:WP_011525867.1
GO:0016682 - oxidoreductase activity, acting on diphenols and related substances as donors, oxygen as acceptor [Evidence IEA]
cytochrome d ubiquinol oxidase subunit II
COORDINATES: similar to AA sequence:RefSeq:WP_011525866.1
COORDINATES: similar to AA sequence:RefSeq:WP_011525865.1
COORDINATES: similar to AA sequence:RefSeq:WP_014695590.1
COORDINATES: similar to AA sequence:RefSeq:WP_015236769.1
COORDINATES: similar to AA sequence:RefSeq:WP_019584875.1
heparan-alpha-glucosaminide N-acetyltransferase domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_019011818.1
COORDINATES: protein motif:HMM:NF013117.2
mechanosensitive ion channel family protein
COORDINATES: protein motif:HMM:NF018648.2
GO:0006885 - regulation of pH [Evidence IEA]; GO:0006814 - sodium ion transport [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_014684151.1
COORDINATES: similar to AA sequence:RefSeq:WP_010883958.1
COORDINATES: similar to AA sequence:RefSeq:WP_010883957.1
HAMP domain-containing sensor histidine kinase
COORDINATES: similar to AA sequence:RefSeq:WP_013157372.1
COORDINATES: similar to AA sequence:RefSeq:WP_017869474.1
GO:0004096 - catalase activity [Evidence IEA]; GO:0020037 - heme binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_017869475.1
COORDINATES: similar to AA sequence:RefSeq:WP_011525787.1
COORDINATES: similar to AA sequence:RefSeq:WP_011525786.1
polysaccharide deacetylase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_011525785.1
COORDINATES: protein motif:HMM:NF024898.2
GO:0008080 - N-acetyltransferase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_019010008.1
GO:0003700 - DNA-binding transcription factor activity [Evidence IEA]
GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
metalloregulator ArsR/SmtB family transcription factor
COORDINATES: similar to AA sequence:RefSeq:WP_011525804.1
COORDINATES: similar to AA sequence:RefSeq:WP_012695081.1
GO:0015267 - channel activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_019012132.1
MarR family winged helix-turn-helix transcriptional regulator
COORDINATES: protein motif:HMM:NF040501.1
arsenic resistance N-acetyltransferase ArsN2
COORDINATES: similar to AA sequence:RefSeq:WP_019009354.1
GO:0022857 - transmembrane transporter activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF012311.2
GO:0008236 - serine-type peptidase activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF012455.2
COORDINATES: similar to AA sequence:RefSeq:WP_019832118.1
GO:0016491 - oxidoreductase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_013556076.1
GO:0004553 - hydrolase activity, hydrolyzing O-glycosyl compounds [Evidence IEA]
GO:0005975 - carbohydrate metabolic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_018620892.1
COORDINATES: similar to AA sequence:RefSeq:WP_018614038.1
COORDINATES: similar to AA sequence:RefSeq:WP_019586219.1
COORDINATES: similar to AA sequence:RefSeq:WP_015929418.1
COORDINATES: protein motif:HMM:NF012698.2
winged helix-turn-helix domain-containing protein
COORDINATES: protein motif:HMM:NF013718.2
COORDINATES: similar to AA sequence:RefSeq:WP_020629218.1
COORDINATES: protein motif:HMM:NF021466.2
COORDINATES: similar to AA sequence:RefSeq:WP_011526079.1
COORDINATES: similar to AA sequence:RefSeq:WP_019011805.1
COORDINATES: similar to AA sequence:RefSeq:WP_019011804.1
COORDINATES: similar to AA sequence:RefSeq:WP_019011803.1
COORDINATES: similar to AA sequence:RefSeq:WP_011525822.1
COORDINATES: similar to AA sequence:RefSeq:WP_018465956.1
COORDINATES: similar to AA sequence:RefSeq:WP_019011819.1
COORDINATES: protein motif:HMM:NF024245.2
helix-hairpin-helix domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_003347562.1
COORDINATES: similar to AA sequence:RefSeq:WP_011806420.1
COORDINATES: similar to AA sequence:RefSeq:WP_019009308.1
COORDINATES: similar to AA sequence:RefSeq:WP_011529250.1
COORDINATES: similar to AA sequence:RefSeq:WP_011529365.1
cation diffusion facilitator family transporter
COORDINATES: similar to AA sequence:RefSeq:WP_011525983.1
COORDINATES: similar to AA sequence:RefSeq:WP_019008660.1
COORDINATES: similar to AA sequence:RefSeq:WP_013616039.1
COORDINATES: similar to AA sequence:RefSeq:WP_013616025.1
COORDINATES: similar to AA sequence:RefSeq:WP_019009313.1
COORDINATES: similar to AA sequence:RefSeq:WP_013556344.1
GO:0008961 - phosphatidylglycerol-prolipoprotein diacylglyceryl transferase activity [Evidence IEA]
GO:0009249 - protein lipoylation [Evidence IEA]
prolipoprotein diacylglyceryl transferase
COORDINATES: similar to AA sequence:RefSeq:WP_019009383.1
COORDINATES: similar to AA sequence:RefSeq:WP_019011636.1
COORDINATES: protein motif:HMM:NF012955.2
COORDINATES: similar to AA sequence:RefSeq:WP_019009418.1
COORDINATES: similar to AA sequence:RefSeq:WP_011530226.1
COORDINATES: protein motif:HMM:NF036520.2
TetR/AcrR family transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_019009369.1
COORDINATES: similar to AA sequence:RefSeq:WP_012694743.1
COORDINATES: similar to AA sequence:RefSeq:WP_017870256.1
heavy-metal-associated domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_019009395.1
metal-sensitive transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_011526003.1
COORDINATES: similar to AA sequence:RefSeq:WP_017870508.1
COORDINATES: similar to AA sequence:RefSeq:WP_011525996.1
COORDINATES: similar to AA sequence:RefSeq:WP_019009411.1
four-helix bundle copper-binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_018466271.1
GO:0033573 - high-affinity iron permease complex [Evidence IEA]; GO:0016020 - membrane [Evidence IEA]
GO:0005381 - iron ion transmembrane transporter activity [Evidence IEA]
GO:0034755 - iron ion transmembrane transport [Evidence IEA]
COORDINATES: protein motif:HMM:NF020932.2
COORDINATES: similar to AA sequence:RefSeq:WP_013555492.1
incomplete; partial in the middle of a contig; missing N-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: protein motif:HMM:NF019310.2
COORDINATES: protein motif:HMM:NF013933.2
GO:0006865 - amino acid transport [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011531383.1
metal-dependent transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_019585839.1
COORDINATES: protein motif:HMM:NF021255.2
COORDINATES: protein motif:HMM:NF020387.2
COORDINATES: similar to AA sequence:RefSeq:WP_011526021.1
COORDINATES: protein motif:HMM:NF024602.2
COORDINATES: similar to AA sequence:RefSeq:WP_019587942.1
COORDINATES: protein motif:HMM:NF024491.2
COORDINATES: similar to AA sequence:RefSeq:WP_019007993.1
COORDINATES: similar to AA sequence:RefSeq:WP_011530380.1
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_011530381.1
COORDINATES: protein motif:HMM:NF024834.2
COORDINATES: similar to AA sequence:RefSeq:WP_019009386.1
COORDINATES: protein motif:HMM:NF018745.2
COORDINATES: similar to AA sequence:RefSeq:WP_019009334.1
COORDINATES: similar to AA sequence:RefSeq:WP_014431889.1
COORDINATES: protein motif:HMM:NF024751.2
COORDINATES: protein motif:HMM:NF013842.2
COORDINATES: similar to AA sequence:RefSeq:WP_076612053.1
incomplete; partial in the middle of a contig; missing N-terminus and C-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_019585799.1
COORDINATES: similar to AA sequence:RefSeq:WP_013703700.1
COORDINATES: similar to AA sequence:RefSeq:WP_019585813.1
COORDINATES: similar to AA sequence:RefSeq:WP_019008669.1
COORDINATES: similar to AA sequence:RefSeq:WP_019009310.1
COORDINATES: similar to AA sequence:RefSeq:WP_019010206.1
COORDINATES: similar to AA sequence:RefSeq:WP_014682920.1
COORDINATES: similar to AA sequence:RefSeq:WP_014682893.1
COORDINATES: similar to AA sequence:RefSeq:WP_019009314.1
COORDINATES: similar to AA sequence:RefSeq:WP_019009329.1
GO:0042625 - ATPase-coupled ion transmembrane transporter activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_019009390.1
COORDINATES: similar to AA sequence:RefSeq:WP_010659232.1
COORDINATES: similar to AA sequence:RefSeq:WP_011525988.1
COORDINATES: similar to AA sequence:RefSeq:WP_019585844.1
GO:0004252 - serine-type endopeptidase activity [Evidence IEA]
GO:0009306 - protein secretion [Evidence IEA]; GO:0006465 - signal peptide processing [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_076611840.1
programmed frameshift; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_013614657.1
COORDINATES: protein motif:HMM:NF033550.5
COORDINATES: similar to AA sequence:RefSeq:WP_019585640.1
COORDINATES: similar to AA sequence:RefSeq:WP_017964028.1
COORDINATES: similar to AA sequence:RefSeq:WP_014764334.1
COORDINATES: similar to AA sequence:RefSeq:WP_015716394.1
COORDINATES: similar to AA sequence:RefSeq:WP_019012034.1
COORDINATES: similar to AA sequence:RefSeq:WP_014457489.1
COORDINATES: similar to AA sequence:RefSeq:WP_019586571.1
LysM peptidoglycan-binding domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_011525778.1
COORDINATES: protein motif:HMM:NF017416.2
COORDINATES: similar to AA sequence:RefSeq:WP_012173259.1
COORDINATES: protein motif:HMM:NF024880.2
GO:0008168 - methyltransferase activity [Evidence IEA]
methyltransferase domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_015231625.1
sulfite exporter TauE/SafE family protein
COORDINATES: similar to AA sequence:RefSeq:WP_015231624.1
COORDINATES: protein motif:HMM:NF033580.1
COORDINATES: similar to AA sequence:RefSeq:WP_011526061.1
COORDINATES: similar to AA sequence:RefSeq:WP_012694567.1
GO:0003676 - nucleic acid binding [Evidence IEA]; GO:0004523 - RNA-DNA hybrid ribonuclease activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_012173413.1
COORDINATES: protein motif:HMM:NF014626.2
COORDINATES: protein motif:HMM:NF012798.2
GO:0015074 - DNA integration [Evidence IEA]; GO:0006310 - DNA recombination [Evidence IEA]
COORDINATES: protein motif:HMM:NF020897.2
COORDINATES: similar to AA sequence:RefSeq:WP_016330239.1
DUF2227 family putative metal-binding protein
COORDINATES: protein motif:HMM:NF017009.2
COORDINATES: protein motif:HMM:NF024919.2
COORDINATES: protein motif:HMM:NF025063.2
GO:0015074 - DNA integration [Evidence IEA]
integrase core domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_011727847.1
COORDINATES: protein motif:HMM:NF033516.0
COORDINATES: protein motif:HMM:NF013677.2
COORDINATES: similar to AA sequence:RefSeq:WP_013615954.1
COORDINATES: protein motif:HMM:NF021637.2
COORDINATES: similar to AA sequence:RefSeq:WP_013615966.1
COORDINATES: similar to AA sequence:RefSeq:WP_013615970.1
COORDINATES: protein motif:HMM:NF014581.2
type IV secretory system conjugative DNA transfer family protein
COORDINATES: similar to AA sequence:RefSeq:WP_014682753.1
COORDINATES: similar to AA sequence:RefSeq:WP_014686594.1
GO:0003697 - single-stranded DNA binding [Evidence IEA]
GO:0006310 - DNA recombination [Evidence IEA]; GO:0006281 - DNA repair [Evidence IEA]; GO:0006260 - DNA replication [Evidence IEA]; GO:0006351 - DNA-templated transcription [Evidence IEA]
COORDINATES: protein motif:HMM:NF020265.2
COORDINATES: similar to AA sequence:RefSeq:WP_012558362.1
COORDINATES: similar to AA sequence:RefSeq:WP_014682821.1
COORDINATES: protein motif:HMM:NF025642.2