Deinococcus radiophilus strain ATCC 27603 plasmid pRadio4, 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\nCP086383.1.\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: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: similar to AA sequence:RefSeq:WP_011583147.1
Derived by automated computational analysis using gene prediction method: Protein Homology.
type II toxin-antitoxin system RelE/ParE family toxin
COORDINATES: similar to AA sequence:RefSeq:WP_013952323.1
COORDINATES: similar to AA sequence:RefSeq:WP_017878030.1
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_013616058.1
AbrB/MazE/SpoVT family DNA-binding domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_013616059.1
COORDINATES: similar to AA sequence:RefSeq:WP_012695021.1
GO:0004803 - transposase activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF015076.2
COORDINATES: similar to AA sequence:RefSeq:WP_015078774.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0008170 - N-methyltransferase activity [Evidence IEA]
GO:0006306 - DNA methylation [Evidence IEA]
COORDINATES: protein motif:HMM:NF025056.2
toll/interleukin-1 receptor domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_012173261.1
COORDINATES: similar to AA sequence:RefSeq:WP_010886790.1
frameshifted; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_013613827.1
COORDINATES: similar to AA sequence:RefSeq:WP_014935016.1
COORDINATES: protein motif:HMM:NF021431.2
type II toxin-antitoxin system HigB family toxin
COORDINATES: protein motif:HMM:NF013540.2
helix-turn-helix domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_015231498.1
COORDINATES: similar to AA sequence:RefSeq:WP_017871100.1
COORDINATES: similar to AA sequence:RefSeq:WP_013623029.1
incomplete; partial in the middle of a contig; missing N-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.