Deinococcus radiophilus strain ATCC 27603 plasmid pRadio3, complete sequence.
Bacteria; Deinococcus-Thermus; Deinococci; Deinococcales; Deinococcaceae; Deinococcus.
Single Nanopore flow cell sequencing of Deinococcus radiophilus hints at prophage related plasmids: An amateur research perspective
Submitted (04-NOV-2021) Research, Binomica Labs, 4301 22nd St 3FL Studio 342, Long Island City, NY 11101, USA
REFSEQ INFORMATION: The reference sequence is identical to\nCP086384.1.\nBacteria and source DNA available from ATCC 27603 - Carolina\nBiological Supply.\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 Date :: 11-SEP-2020\nAssembly Method :: Trycycler v. 0.3.2\nGenome Representation :: Full\nExpected Final Version :: No\nGenome Coverage :: 800.0x\nSequencing Technology :: Oxford Nanopore MinION\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 12/06/2022 04:26:03\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\nGenes (total) :: 2,840\nCDSs (total) :: 2,779\nGenes (coding) :: 2,720\nCDSs (with protein) :: 2,720\nGenes (RNA) :: 61\nrRNAs :: 3, 3, 3 (5S, 16S, 23S)\ncomplete rRNAs :: 3, 3, 3 (5S, 16S, 23S)\ntRNAs :: 49\nncRNAs :: 3\nPseudo Genes (total) :: 59\nCDSs (without protein) :: 59\nPseudo Genes (ambiguous residues) :: 0 of 59\nPseudo Genes (frameshifted) :: 28 of 59\nPseudo Genes (incomplete) :: 30 of 59\nPseudo Genes (internal stop) :: 12 of 59\nPseudo Genes (multiple problems) :: 10 of 59\nCRISPR Arrays :: 2\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.
COORDINATES: similar to AA sequence:RefSeq:WP_018054521.1
GO:0019812 - type I site-specific deoxyribonuclease complex [Evidence IEA]
GO:0009035 - type I site-specific deoxyribonuclease activity [Evidence IEA]
GO:0009307 - DNA restriction-modification system [Evidence IEA]
Derived by automated computational analysis using gene prediction method: Protein Homology.
HsdR family type I site-specific deoxyribonuclease
COORDINATES: similar to AA sequence:RefSeq:WP_007363018.1
putative DNA binding domain-containing protein
COORDINATES: protein motif:HMM:TIGR02607.1
COORDINATES: similar to AA sequence:RefSeq:WP_006424271.1
type II toxin-antitoxin system RelE/ParE family toxin
COORDINATES: similar to AA sequence:RefSeq:WP_019927710.1
COORDINATES: similar to AA sequence:RefSeq:WP_006889350.1
GO:0006304 - DNA modification [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_012638343.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0008170 - N-methyltransferase activity [Evidence IEA]
GO:0006306 - DNA methylation [Evidence IEA]
class I SAM-dependent DNA methyltransferase
COORDINATES: protein motif:HMM:NF024420.2
COORDINATES: protein motif:HMM:NF018933.2
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: protein motif:HMM:NF021637.2
COORDINATES: protein motif:HMM:NF040044.1
COORDINATES: similar to AA sequence:RefSeq:WP_010474779.1
COORDINATES: similar to AA sequence:RefSeq:WP_013615909.1
COORDINATES: similar to AA sequence:RefSeq:WP_019585218.1
COORDINATES: similar to AA sequence:RefSeq:WP_076612299.1
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_019008660.1
COORDINATES: similar to AA sequence:RefSeq:WP_004095157.1
COORDINATES: similar to AA sequence:RefSeq:WP_014695541.1
COORDINATES: similar to AA sequence:RefSeq:WP_010889330.1
metalloregulator ArsR/SmtB family transcription factor
COORDINATES: similar to AA sequence:RefSeq:WP_019009310.1
COORDINATES: similar to AA sequence:RefSeq:WP_013615355.1
cation diffusion facilitator family transporter
COORDINATES: similar to AA sequence:RefSeq:WP_019009334.1
COORDINATES: protein motif:HMM:NF016107.2
isoprenylcysteine carboxylmethyltransferase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_010889332.1
GO:0042625 - ATPase-coupled ion transmembrane transporter activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_013615894.1
COORDINATES: protein motif:HMM:NF024975.2
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_011525626.1
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_076612364.1
COORDINATES: protein motif:HMM:NF024980.2
winged helix-turn-helix domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_010886790.1
COORDINATES: similar to AA sequence:RefSeq:WP_013615904.1
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:NF017832.2
COORDINATES: protein motif:HMM:NF020387.2
COORDINATES: similar to AA sequence:RefSeq:WP_013615891.1
COORDINATES: similar to AA sequence:RefSeq:WP_013615890.1
COORDINATES: similar to AA sequence:RefSeq:WP_013615889.1
COORDINATES: similar to AA sequence:RefSeq:WP_013615876.1
COORDINATES: similar to AA sequence:RefSeq:WP_013615875.1
COORDINATES: similar to AA sequence:RefSeq:WP_013615874.1
COORDINATES: similar to AA sequence:RefSeq:WP_013615873.1
COORDINATES: similar to AA sequence:RefSeq:WP_013615871.1
COORDINATES: similar to AA sequence:RefSeq:WP_013615870.1
COORDINATES: similar to AA sequence:RefSeq:WP_013615869.1
COORDINATES: similar to AA sequence:RefSeq:WP_013615865.1
COORDINATES: similar to AA sequence:RefSeq:WP_013615990.1
COORDINATES: similar to AA sequence:RefSeq:WP_009629570.1
type II toxin-antitoxin system PemK/MazF family toxin
COORDINATES: similar to AA sequence:RefSeq:WP_013616020.1
GO:0015074 - DNA integration [Evidence IEA]
integrase core domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_013615937.1
COORDINATES: similar to AA sequence:RefSeq:WP_013615936.1
COORDINATES: similar to AA sequence:RefSeq:WP_009764920.1
COORDINATES: similar to AA sequence:RefSeq:WP_015147274.1
GO:0016301 - kinase activity [Evidence IEA]
type II toxin-antitoxin system death-on-curing family toxin
COORDINATES: protein motif:HMM:NF014871.2
GO:0016787 - hydrolase activity [Evidence IEA]
GO:0009166 - nucleotide catabolic process [Evidence IEA]
5'-nucleotidase C-terminal domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_017871895.1
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_013615768.1
GO:0016787 - hydrolase activity [Evidence IEA]; GO:0046872 - metal ion binding [Evidence IEA]; GO:0003676 - nucleic acid binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_019008488.1
COORDINATES: protein motif:HMM:NF040426.1
COORDINATES: similar to AA sequence:RefSeq:WP_013616034.1
COORDINATES: similar to AA sequence:RefSeq:WP_019586172.1
COORDINATES: protein motif:HMM:NF024787.2
COORDINATES: similar to AA sequence:RefSeq:WP_013614240.1
frameshifted; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_013616040.1
COORDINATES: similar to AA sequence:RefSeq:WP_012695243.1
COORDINATES: similar to AA sequence:RefSeq:WP_013616025.1
COORDINATES: protein motif:HMM:NF015658.2
frameshifted; internal stop; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: protein motif:HMM:NF012789.2
COORDINATES: similar to AA sequence:RefSeq:WP_018054520.1
SprT family zinc-dependent metalloprotease