Deinococcus ficus strain CC-FR2-10 plasmid pDFI4, complete sequence.
type: Entry
definition: Deinococcus ficus strain CC-FR2-10 plasmid pDFI4, complete sequence.
sequence version: NZ_CP021085.1
sequence date: 2023-03-25
sequence: sequence
division: CON
label: NZ_CP021085.1
type: RefSeq
SIO_000068: refseq
dblink: PRJNA224116
dblink: SAMN06314862
keyword: RefSeq
source: Deinococcus ficus
organism: Deinococcus ficus
taxonomy: Bacteria; Deinococcota; Deinococci; Deinococcales; Deinococcaceae; Deinococcus.
reference: 1
reference: 2
comment: REFSEQ INFORMATION: The reference sequence is identical to\nCP021085.1.\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.

sequence
subclass of: SO_0000155
sequence length: 5785
topology: circular
so has quality: SO_0000988
location: 1..5785
location: region:1-5785:1
RO_0002162: 317577

NZ_CP021085
type: RefSeq
SIO_000068: refseq

PRJNA224116
type: BioProject
SIO_000068: bioproject

SAMN06314862
type: BioSample
SIO_000068: biosample

1
title: The complete genome sequence of Deinococcus ficus isolated from the rhizosphere of the Ficus religiosa L. in Taiwan
author: Wu, K.-M.
author: Liao, T.-L.
author: Liu, Y.-M.
author: Young, C.-C.
author: Tsai, S.-F.
journal: Unpublished

2
title: Direct Submission
author: Wu, K.-M.
author: Liao, T.-L.
author: Liu, Y.-M.
author: Young, C.-C.
author: Tsai, S.-F.
journal: Submitted (01-MAY-2017) Institute of Molecular and Genomic Medicine, National Health Research Institutes, 35, Keyan Road, Zhunan Town, Miaoli County 350, Taiwan

position:1:1
position: 1
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:5785:1
position: 5785
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

feature:1-5785:1:source
so part of: sequence
organism: Deinococcus ficus
mol type: genomic DNA
strain: CC-FR2-10
isolation source: rhizosphere
host: Ficus religiosa L.
type material: type strain of Deinococcus ficus
plasmid: pDFI4
country: Taiwan: Taichung
lat lon: 24.121298 N 120.675666 E
collection date: 2005-03-09
collected by: Wei-An Lai
identified by: Wei-Shuo Huang

317577
type: Taxonomy
SIO_000068: taxonomy

DFI_RS19975
type: Gene
subclass of: SO_0000704
RO_0002162: 317577
locus tag: DFI_RS19975
old locus tag: DFI_19985
so part of: sequence
location: complement(8..199)
location: region:8-199:-1
so has part: feature:8-199:-1:exon
subclass of: SO_0000010

position:8:-1
position: 8
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:199:-1
position: 199
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:8-199:-1:exon

DFI_RS19975
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 317577
locus tag: DFI_RS19975
old locus tag: DFI_19985
inference: COORDINATES: ab initio prediction:GeneMarkS-2+
note: Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
codon start: 1
transl table: 11
product: hypothetical protein
translation: MNPAELVGVDRAELLRTVDDMAELPLFQHRPELRRPRLLALLDDDALRVLVAELVAEFRAALR
SIO_010081: DFI_RS19975
subclass of: SO_0000673
so part of: DFI_RS19975
location: complement(8..199)
location: region:8-199:-1
so has part: feature:8-199:-1:exon

WP_027464334.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:8-199:-1:exon

DFI_RS19980
type: Gene
subclass of: SO_0000704
RO_0002162: 317577
locus tag: DFI_RS19980
old locus tag: DFI_19990
so part of: sequence
location: complement(196..348)
location: region:196-348:-1
so has part: feature:196-348:-1:exon
subclass of: SO_0000010

position:196:-1
position: 196
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:348:-1
position: 348
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:196-348:-1:exon

DFI_RS19980
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 317577
locus tag: DFI_RS19980
old locus tag: DFI_19990
inference: COORDINATES: protein motif:HMM:NF024139.2
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: helix-turn-helix domain-containing protein
translation: MPSYTDIQTAARYYALTPKTLRKLARHGDVPAVKIGSRWRFLLPALDGAA
SIO_010081: DFI_RS19980
subclass of: SO_0000673
so part of: DFI_RS19980
location: complement(196..348)
location: region:196-348:-1
so has part: feature:196-348:-1:exon

WP_081426045.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:196-348:-1:exon

DFI_RS19985
type: Gene
subclass of: SO_0000704
RO_0002162: 317577
locus tag: DFI_RS19985
old locus tag: DFI_19995
so part of: sequence
location: 1034..1177
location: region:1034-1177:1
so has part: feature:1034-1177:1:exon
subclass of: SO_0000010

position:1034:1
position: 1034
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:1177:1
position: 1177
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:1034-1177:1:exon

DFI_RS19985
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 317577
locus tag: DFI_RS19985
old locus tag: DFI_19995
inference: COORDINATES: ab initio prediction:GeneMarkS-2+
note: Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
codon start: 1
transl table: 11
product: hypothetical protein
translation: MAERLLAQGHTLTRMADGADYNTEAGEVMSWRTVEALLKRGVVVALV
SIO_010081: DFI_RS19985
subclass of: SO_0000673
so part of: DFI_RS19985
location: 1034..1177
location: region:1034-1177:1
so has part: feature:1034-1177:1:exon

WP_162899094.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:1034-1177:1:exon

DFI_RS20505
type: Gene
subclass of: SO_0000704
RO_0002162: 317577
locus tag: DFI_RS20505
so part of: sequence
location: 1505..2341
location: region:1505-2341:1
so has part: feature:1505-2341:1:exon
subclass of: SO_0000010

position:1505:1
position: 1505
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:2341:1
position: 2341
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:1505-2341:1:exon

DFI_RS20505
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 317577
locus tag: DFI_RS20505
inference: COORDINATES: ab initio prediction:GeneMarkS-2+
note: Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
codon start: 1
transl table: 11
product: hypothetical protein
translation: MPNADTVRQGVRLSRGAALLFDELHRLACHVAQVRAYTVAPGQVVYHLPAVIVAALVGYSERHLYRLADELRAAGLLDERGHVATVGHMRRYDGTLWAVSMKSGAAPRLRWQDFQHDWRPDFAADLHGESGAWHEVQSVMSEPLAFQEKQERLGDLAKSWAAATRTPKSPVEGGSDMTPERALGVIAADLPALLHLHPRQRHREVSRLAADLAATLQEPERRKQWARAMYRALAEEHEQRAGLTYFTAQLYRLAADLREGAPWRKAGAVLTARLNGVS
SIO_010081: DFI_RS20505
subclass of: SO_0000673
so part of: DFI_RS20505
location: 1505..2341
location: region:1505-2341:1
so has part: feature:1505-2341:1:exon

WP_162899095.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:1505-2341:1:exon

DFI_RS20510
type: Gene
subclass of: SO_0000704
RO_0002162: 317577
locus tag: DFI_RS20510
so part of: sequence
location: complement(2353..3399)
location: region:2353-3399:-1
so has part: feature:2353-3399:-1:exon
subclass of: SO_0000010

position:2353:-1
position: 2353
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:3399:-1
position: 3399
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:2353-3399:-1:exon

DFI_RS20510
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 317577
locus tag: DFI_RS20510
inference: COORDINATES: ab initio prediction:GeneMarkS-2+
note: Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
codon start: 1
transl table: 11
product: hypothetical protein
translation: MRKILIACTLLLGTASGLSQQQREQHINQVFSAAGISLINCPSSSTPNITMFCGQTSMSDTLVRQSWDLYSDWSSKVTNTAKHKTAWSLSDTGKAYSATFSLSDGDFYVVTTSSGSAPSFVIVSWLNISQQASTSSSSVTQSSSQASSQTDKPKSKCDPRVTRTASVSGTSWVHGSWLEPAVFPKPSQEFKLGGPSQDYSIVCPTFRADFSNSTGEYTFKGSSFNDIVLYSGVSYYDNVTSIDFYDSSESGDDLRLVGLTYNKRTKKFELSTENPSAFINLPIGYRVNNGTLKPLYFEGKIYPIDLPADAKILEVYASPSKNTGWQYLKIDFSNNSVTLKRSYPFPSN
SIO_010081: DFI_RS20510
subclass of: SO_0000673
so part of: DFI_RS20510
location: complement(2353..3399)
location: region:2353-3399:-1
so has part: feature:2353-3399:-1:exon

WP_155864624.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:2353-3399:-1:exon

DFI_RS20000
type: Gene
subclass of: SO_0000704
RO_0002162: 317577
locus tag: DFI_RS20000
old locus tag: DFI_20010
so part of: sequence
location: complement(3773..4819)
location: region:3773-4819:-1
so has part: feature:3773-4819:-1:exon
subclass of: SO_0000010

position:3773:-1
position: 3773
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:4819:-1
position: 4819
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:3773-4819:-1:exon

DFI_RS20000
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 317577
locus tag: DFI_RS20000
old locus tag: DFI_20010
inference: COORDINATES: protein motif:HMM:NF022021.2
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: P63C domain-containing protein
translation: MDEEFTLQRQGGIARAKKLSSEERSEISRKAADTRWAKAEAEGKILPRATHSGELQIGGLSIKCAVLQDGTRVITETAFMKALGVYYSGWLSTRREESDSGEKVPNYISHKALIPYISDHLNPEDYDSVWYRSEKGTKSRGIRAEIIPKICEIWMDARNAGVLTGETAKAIAARAEIMLRALARVGITALVDEATGYQEIRDRQALQALLDQYLRKEFATWAKRFPDEFYHEIYRLRGWTLQDFHKRPGIVGKYTTDIVYERMAPELVEELEKKNPSLSPGYRRQKHHQWLTEDVGHPALSKHIDNVIVLMRASDNWDMFKRLLDRSLPKRTAANTFIMPGLFDDIEY
SIO_010081: DFI_RS20000
subclass of: SO_0000673
so part of: DFI_RS20000
location: complement(3773..4819)
location: region:3773-4819:-1
so has part: feature:3773-4819:-1:exon

WP_162145447.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:3773-4819:-1:exon

DFI_RS20005
type: Gene
subclass of: SO_0000704
RO_0002162: 317577
locus tag: DFI_RS20005
old locus tag: DFI_20015
so part of: sequence
location: complement(5068..5754)
location: region:5068-5754:-1
so has part: feature:5068-5754:-1:exon
subclass of: SO_0000010

position:5068:-1
position: 5068
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:5754:-1
position: 5754
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:5068-5754:-1:exon

DFI_RS20005
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 317577
locus tag: DFI_RS20005
old locus tag: DFI_20015
inference: COORDINATES: ab initio prediction:GeneMarkS-2+
note: Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
codon start: 1
transl table: 11
product: hypothetical protein
translation: MDDTHSLPPNWERENDGPDAPEDLTDWPAELIEAFPATHDRCLEKSGHLHDTITDSTHLRQRRSKPFMTAFERLAEIVDGPLIFATVNLPDFAGRPLYSKTTINAARRRAKGIIQASGGPGVWKLERGLAGGYHLHLVLAGGGDVSDLDDWREVDDLDGLAKYLSKPADARACKSRPRLQDLTADLRRRQLAASEEFLTTRRPGQRYTFHGQVGLGVNTLRLAAPTSD
SIO_010081: DFI_RS20005
subclass of: SO_0000673
so part of: DFI_RS20005
location: complement(5068..5754)
location: region:5068-5754:-1
so has part: feature:5068-5754:-1:exon

WP_118376078.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:5068-5754:-1:exon