Deinococcus ficus strain CC-FR2-10 plasmid pDFI3, complete sequence.
Bacteria; Deinococcota; Deinococci; Deinococcales; Deinococcaceae; Deinococcus.
The complete genome sequence of Deinococcus ficus isolated from the rhizosphere of the Ficus religiosa L. in Taiwan
Submitted (01-MAY-2017) Institute of Molecular and Genomic Medicine, National Health Research Institutes, 35, Keyan Road, Zhunan Town, Miaoli County 350, Taiwan
REFSEQ INFORMATION: The reference sequence is identical to\nCP021084.1.\nBacteria and source DNA available from Lab. of Soil Environmental\nMicrobiology and Biochemistry.\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 :: Newbler v. MAR-2006\nAssembly Name :: DFI1.0\nLong Assembly Name :: Deinococcus ficus CC-FR2-10 1.0\nGenome Coverage :: 18x\nSequencing Technology :: Sanger\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 03/25/2023 00:26:31\nAnnotation Pipeline :: NCBI Prokaryotic Genome\n Annotation Pipeline (PGAP)\nAnnotation Method :: Best-placed reference protein\n set; GeneMarkS-2+\nAnnotation Software revision :: 6.4\nFeatures Annotated :: Gene; CDS; rRNA; tRNA; ncRNA\nGenes (total) :: 4,050\nCDSs (total) :: 3,979\nGenes (coding) :: 3,952\nCDSs (with protein) :: 3,952\nGenes (RNA) :: 71\nrRNAs :: 3, 3, 3 (5S, 16S, 23S)\ncomplete rRNAs :: 3, 3, 3 (5S, 16S, 23S)\ntRNAs :: 59\nncRNAs :: 3\nPseudo Genes (total) :: 27\nCDSs (without protein) :: 27\nPseudo Genes (ambiguous residues) :: 0 of 27\nPseudo Genes (frameshifted) :: 5 of 27\nPseudo Genes (incomplete) :: 22 of 27\nPseudo Genes (internal stop) :: 2 of 27\nPseudo Genes (multiple problems) :: 2 of 27\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_015234887.1
Derived by automated computational analysis using gene prediction method: Protein Homology.
ABC transporter substrate-binding protein
COORDINATES: protein motif:HMM:NF024748.2
COORDINATES: protein motif:HMM:NF024579.2
COORDINATES: protein motif:HMM:NF022649.2
tellurite-like stress resistance cysteine protease StiP
COORDINATES: similar to AA sequence:RefSeq:WP_014774885.1
COORDINATES: similar to AA sequence:RefSeq:WP_011530619.1
COORDINATES: protein motif:HMM:NF013884.2
COORDINATES: protein motif:HMM:NF012451.2
COORDINATES: similar to AA sequence:RefSeq:WP_015236035.1
COORDINATES: protein motif:HMM:NF020795.2
COORDINATES: protein motif:HMM:NF012772.2
COORDINATES: similar to AA sequence:RefSeq:WP_011531305.1
COORDINATES: similar to AA sequence:RefSeq:WP_011529594.1
COORDINATES: similar to AA sequence:RefSeq:WP_005061662.1
COORDINATES: protein motif:HMM:NF021503.2
DUF2227 family putative metal-binding protein
COORDINATES: protein motif:HMM:NF013793.2
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_014686684.1
GO:0004803 - transposase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_015237040.1
internal stop; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_015235757.1
GO:0005524 - ATP binding [Evidence IEA]; GO:0004748 - ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor [Evidence IEA]
GO:0006260 - DNA replication [Evidence IEA]
ribonucleotide reductase N-terminal alpha domain-containing protein
COORDINATES: protein motif:HMM:NF024642.2
COORDINATES: protein motif:HMM:NF013835.2
COORDINATES: protein motif:HMM:NF016724.2
COORDINATES: protein motif:HMM:NF021637.2
COORDINATES: similar to AA sequence:RefSeq:WP_076612365.1
programmed frameshift; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_012695205.1
COORDINATES: protein motif:HMM:NF012493.2
COORDINATES: similar to AA sequence:RefSeq:WP_012173348.1
COORDINATES: similar to AA sequence:RefSeq:WP_012693258.1
COORDINATES: similar to AA sequence:RefSeq:WP_012693257.1
branched-chain amino acid ABC transporter permease
COORDINATES: similar to AA sequence:RefSeq:WP_012693256.1
COORDINATES: similar to AA sequence:RefSeq:WP_012693255.1
COORDINATES: similar to AA sequence:RefSeq:WP_015234747.1
COORDINATES: protein motif:HMM:NF014759.2
GO:0003824 - catalytic activity [Evidence IEA]; GO:0003677 - DNA binding [Evidence IEA]
5'-3' exonuclease H3TH domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_019586139.1
COORDINATES: protein motif:HMM:NF012234.2
GO:0005524 - ATP binding [Evidence IEA]; GO:0016887 - ATP hydrolysis activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF019997.2
COORDINATES: protein motif:HMM:NF012876.2
GO:0007165 - signal transduction [Evidence IEA]
COORDINATES: protein motif:HMM:NF022337.2
COORDINATES: protein motif:HMM:TIGR03741.1
COORDINATES: protein motif:HMM:TIGR03738.1
COORDINATES: protein motif:HMM:TIGR03737.1
COORDINATES: protein motif:HMM:TIGR03736.1
COORDINATES: protein motif:HMM:NF024158.2
COORDINATES: protein motif:HMM:TIGR01051.1
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: protein motif:HMM:NF024853.2
COORDINATES: protein motif:HMM:NF012613.2
S-layer homology domain-containing protein
COORDINATES: protein motif:HMM:NF017009.2
COORDINATES: protein motif:HMM:NF020811.2
COORDINATES: protein motif:HMM:NF020302.2
COORDINATES: similar to AA sequence:RefSeq:WP_012173391.1
COORDINATES: protein motif:HMM:NF014581.2
type IV secretory system conjugative DNA transfer family protein
COORDINATES: protein motif:HMM:NF013618.2
lytic transglycosylase domain-containing protein
COORDINATES: protein motif:HMM:NF014626.2
GO:0003697 - single-stranded DNA binding [Evidence IEA]
GO:0006974 - cellular response to DNA damage stimulus [Evidence IEA]; GO:0018142 - protein-DNA covalent cross-linking [Evidence IEA]
SOS response-associated peptidase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_013556893.1
COORDINATES: similar to AA sequence:RefSeq:WP_017412000.1
COORDINATES: similar to AA sequence:RefSeq:WP_019011199.1
COORDINATES: similar to AA sequence:RefSeq:WP_012173379.1
COORDINATES: protein motif:HMM:TIGR00621.2
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:NF024991.2
COORDINATES: similar to AA sequence:RefSeq:WP_019008025.1
ADP-ribosylglycohydrolase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_017301342.1
COORDINATES: protein motif:HMM:NF025918.2
COORDINATES: protein motif:HMM:NF012933.2
GO:0003677 - DNA binding [Evidence IEA]; GO:0008168 - methyltransferase activity [Evidence IEA]; GO:0008270 - zinc ion binding [Evidence IEA]
GO:0006281 - DNA repair [Evidence IEA]; GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
Ada metal-binding domain-containing protein
COORDINATES: protein motif:HMM:NF025091.2
isocitrate lyase/phosphoenolpyruvate mutase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_013615788.1
COORDINATES: similar to AA sequence:RefSeq:WP_019587783.1
COORDINATES: similar to AA sequence:RefSeq:WP_016329705.1
COORDINATES: similar to AA sequence:RefSeq:WP_020576137.1
COORDINATES: protein motif:HMM:NF023580.2
COORDINATES: similar to AA sequence:RefSeq:WP_012694753.1
COORDINATES: similar to AA sequence:RefSeq:WP_019010430.1
GO:0009360 - DNA polymerase III complex [Evidence IEA]
GO:0003887 - DNA-directed DNA polymerase activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF017870.2
COORDINATES: similar to AA sequence:RefSeq:WP_014650593.1
COORDINATES: similar to AA sequence:RefSeq:WP_015235547.1
GO:0003684 - damaged DNA binding [Evidence IEA]; GO:0003887 - DNA-directed DNA polymerase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_012694654.1
COORDINATES: similar to AA sequence:RefSeq:WP_019008533.1
GO:0003678 - DNA helicase activity [Evidence IEA]
GO:0006310 - DNA recombination [Evidence IEA]
COORDINATES: protein motif:HMM:NF015531.2
GO:0008236 - serine-type peptidase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_017871193.1
COORDINATES: similar to AA sequence:RefSeq:WP_017870136.1
COORDINATES: similar to AA sequence:RefSeq:WP_014683829.1
COORDINATES: protein motif:HMM:NF012301.2
GO:0000160 - phosphorelay signal transduction system [Evidence IEA]
COORDINATES: protein motif:HMM:NF024621.2
COORDINATES: protein motif:HMM:NF016932.2
COORDINATES: similar to AA sequence:RefSeq:WP_014370561.1
COORDINATES: protein motif:HMM:NF024850.2
branched-chain amino acid ABC transporter substrate-binding protein
COORDINATES: protein motif:HMM:NF022643.2
COORDINATES: similar to AA sequence:RefSeq:WP_012695246.1
COORDINATES: similar to AA sequence:RefSeq:WP_017870434.1
GO:0004252 - serine-type endopeptidase activity [Evidence IEA]
GO:0009306 - protein secretion [Evidence IEA]; GO:0006465 - signal peptide processing [Evidence IEA]
COORDINATES: protein motif:HMM:TIGR00254.1
COORDINATES: similar to AA sequence:RefSeq:WP_012694809.1
COORDINATES: similar to AA sequence:RefSeq:WP_012694808.1
COORDINATES: similar to AA sequence:RefSeq:WP_012694807.1
COORDINATES: protein motif:HMM:NF005932.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0003911 - DNA ligase (NAD+) activity [Evidence IEA]
GO:0006281 - DNA repair [Evidence IEA]; GO:0006260 - DNA replication [Evidence IEA]
COORDINATES: protein motif:HMM:NF019310.2
COORDINATES: protein motif:HMM:NF025056.2
toll/interleukin-1 receptor domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_017871658.1
helix-turn-helix transcriptional regulator
COORDINATES: protein motif:HMM:NF024977.2
COORDINATES: protein motif:HMM:NF025690.2
COORDINATES: similar to AA sequence:RefSeq:WP_011529838.1
BMP family ABC transporter substrate-binding protein
COORDINATES: protein motif:HMM:NF015692.2
COORDINATES: protein motif:HMM:NF024880.2
COORDINATES: protein motif:HMM:NF014832.2
GO:0016746 - acyltransferase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_019012503.1
Derived by automated computational analysis using gene prediction method: tRNAscan-SE.
COORDINATES: similar to AA sequence:RefSeq:WP_012694773.1
COORDINATES: similar to AA sequence:RefSeq:WP_012694772.1
COORDINATES: similar to AA sequence:RefSeq:WP_012694771.1
COORDINATES: similar to AA sequence:RefSeq:WP_017870827.1