Dickeya fangzhongdai strain DSM 101947 plasmid pJS5, complete sequence.
type: Entry
definition: Dickeya fangzhongdai strain DSM 101947 plasmid pJS5, complete sequence.
sequence version: NZ_CP025004.1
sequence date: 2023-04-23
sequence: sequence
division: CON
label: NZ_CP025004.1
type: RefSeq
SIO_000068: refseq
dblink: PRJNA224116
dblink: SAMN08038254
keyword: RefSeq
source: Dickeya fangzhongdai
organism: Dickeya fangzhongdai
taxonomy: Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales; Pectobacteriaceae; Dickeya.
reference: 1
reference: 2
comment: REFSEQ INFORMATION: The reference sequence is identical to\nCP025004.1.\nBacteria and source DNA available from Department of Plant\nPathology, Nanjing Agricultural University, 1 Weigang, Nanjing,\nJiangsu 210095, China.\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-NOV-2014\nAssembly Method :: GS De Novo Assembler v. Jan-2015\nGenome Representation :: Full\nExpected Final Version :: Yes\nGenome Coverage :: 100.0x\nSequencing Technology :: Illumina HiSeq\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 04/23/2023 02:59:04\nAnnotation Pipeline :: NCBI Prokaryotic Genome\n Annotation Pipeline (PGAP)\nAnnotation Method :: Best-placed reference protein\n set; GeneMarkS-2+\nAnnotation Software revision :: 6.5\nFeatures Annotated :: Gene; CDS; rRNA; tRNA; ncRNA\nGenes (total) :: 4,452\nCDSs (total) :: 4,348\nGenes (coding) :: 4,286\nCDSs (with protein) :: 4,286\nGenes (RNA) :: 104\nrRNAs :: 8, 7, 7 (5S, 16S, 23S)\ncomplete rRNAs :: 8, 7, 7 (5S, 16S, 23S)\ntRNAs :: 75\nncRNAs :: 7\nPseudo Genes (total) :: 62\nCDSs (without protein) :: 62\nPseudo Genes (ambiguous residues) :: 0 of 62\nPseudo Genes (frameshifted) :: 24 of 62\nPseudo Genes (incomplete) :: 49 of 62\nPseudo Genes (internal stop) :: 8 of 62\nPseudo Genes (multiple problems) :: 17 of 62\nCRISPR Arrays :: 4\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.

sequence
subclass of: SO_0000155
sequence length: 5284
topology: circular
so has quality: SO_0000988
location: 1..5284
location: region:1-5284:1
RO_0002162: 1778540

NZ_CP025004
type: RefSeq
SIO_000068: refseq

PRJNA224116
type: BioProject
SIO_000068: bioproject

SAMN08038254
type: BioSample
SIO_000068: biosample

1
title: Genome Sequence of a Type Strain of Dickeya fangzhongdai Causing Bleeding Canker of Pear Tree Trunks
author: Tian, Y.
author: Hu, B.
author: Zhao, Y.
journal: Unpublished

2
title: Direct Submission
author: Tian, Y.
author: Hu, B.
author: Zhao, Y.
journal: Submitted (17-NOV-2017) Department of Plant Pathology,Nanjing Agricultural University, Nanjing Agricultural University, No.1 Weigang, Nanjing, Jiangsu 210095, China

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

position:5284:1
position: 5284
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

feature:1-5284:1:source
so part of: sequence
organism: Dickeya fangzhongdai
mol type: genomic DNA
strain: DSM 101947
host: Pyrus pyrifolia
culture collection: DSM:101947
type material: type strain of Dickeya fangzhongdai
plasmid: pJS5
country: China:Jiangshan,Zhejiang
lat lon: 28.30 N 118.22 E
altitude: 96 m
collection date: 2009-08-08
collected by: Yanli Tian
identified by: Yanli Tian et al.

1778540
type: Taxonomy
SIO_000068: taxonomy

CVE23_RS22540
type: Gene
subclass of: SO_0000704
RO_0002162: 1778540
locus tag: CVE23_RS22540
old locus tag: CVE23_22540
so part of: sequence
location: complement(join(5211..5284,1..163))
location: region:1-5284:-1
so has part: feature:1-163:-1:exon
so has part: feature:5211-5284:-1:exon
subclass of: SO_0000010

66567102
type: Gene
SIO_000068: ncbigene

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

position:5284:-1
position: 5284
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:1-163:-1:exon

position:163:-1
position: 163
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 2
SIO_000628: feature:5211-5284:-1:exon

position:5211:-1
position: 5211
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

CVE23_RS22540
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 1778540
locus tag: CVE23_RS22540
old locus tag: CVE23_22540
inference: COORDINATES: similar to AA sequence:RefSeq:WP_010566328.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: hypothetical protein
translation: MAKGAQAISKEINELMRKNGNECITLKWEQFYEICERERLAEVVMERVSESLKKNDLHIIYGNNVIIVRDFCWKPVSL
SIO_010081: CVE23_RS22540
subclass of: SO_0000673
so part of: CVE23_RS22540
location: complement(join(5211..5284,1..163))
location: region:1-5284:-1
so has part: feature:1-163:-1:exon
so has part: feature:5211-5284:-1:exon

WP_023135788.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:1-163:-1:exon

urn:…
SIO_000300: 2
SIO_000628: feature:5211-5284:-1:exon

CVE23_RS22830
type: Gene
subclass of: SO_0000704
RO_0002162: 1778540
locus tag: CVE23_RS22830
so part of: sequence
location: complement(325..552)
location: region:325-552:-1
so has part: feature:325-552:-1:exon
subclass of: SO_0000010

66567147
type: Gene
SIO_000068: ncbigene

position:325:-1
position: 325
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:552:-1
position: 552
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:325-552:-1:exon

CVE23_RS22830
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 1778540
locus tag: CVE23_RS22830
inference: COORDINATES: protein motif:HMM:NF016769.2
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: MbeD family mobilization/exclusion protein
translation: MEKQLLSALESLQTSYEQQQQAWQASYSSLQHMFETTSQALERSDRVCQHLSSQVNNLRDQVENLSCNVSRLMRS
SIO_010081: CVE23_RS22830
subclass of: SO_0000673
so part of: CVE23_RS22830
location: complement(325..552)
location: region:325-552:-1
so has part: feature:325-552:-1:exon

WP_244183538.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:325-552:-1:exon

CVE23_RS22835
type: Gene
subclass of: SO_0000704
RO_0002162: 1778540
locus tag: CVE23_RS22835
so part of: sequence
location: complement(622..1107)
location: region:622-1107:-1
so has part: feature:622-1107:-1:exon
subclass of: SO_0000010

66567148
type: Gene
SIO_000068: ncbigene

position:622:-1
position: 622
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:1107:-1
position: 1107
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:622-1107:-1:exon

CVE23_RS22835
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 1778540
locus tag: CVE23_RS22835
inference: COORDINATES: protein motif:HMM:NF016710.2
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: MbeB family mobilization protein
translation: MSEILNLAKGFEEKSKQQAQDTEQSVKREFGRLEMSIGAELQSSSQSISNAIREQNGRLTGMIRASVSTAMAWIFTSFALLIGILGGIIWFQGTIITSRLSEMDSYSQQLASLKAKSGAGVTIYSDDSRRNTYLVVLPKQAHGVETYTSQAGNTVVKYTAK
SIO_010081: CVE23_RS22835
subclass of: SO_0000673
so part of: CVE23_RS22835
location: complement(622..1107)
location: region:622-1107:-1
so has part: feature:622-1107:-1:exon

WP_145958446.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:622-1107:-1:exon

CVE23_RS23145
type: Gene
subclass of: SO_0000704
RO_0002162: 1778540
locus tag: CVE23_RS23145
pseudo: true
so part of: sequence
location: complement(<1154..1576)
location: region:1154-1576:-1
so has part: feature:1154-1576:-1:exon
subclass of: SO_0000010

71691466
type: Gene
SIO_000068: ncbigene

position:1154:-1
position: 1154
reference: sequence
type: ReverseStrandPosition
type: FuzzyPosition

position:1576:-1
position: 1576
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:1154-1576:-1:exon

CVE23_RS23145
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 1778540
locus tag: CVE23_RS23145
inference: COORDINATES: protein motif:HMM:NF015397.2
note: incomplete; partial in the middle of a contig; missing C-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
pseudo: true
codon start: 1
transl table: 11
product: relaxase/mobilization nuclease domain-containing protein
SIO_010081: CVE23_RS23145
subclass of: SO_0000673
so part of: CVE23_RS23145
location: complement(<1154..1576)
location: region:1154-1576:-1
so has part: feature:1154-1576:-1:exon

urn:…
SIO_000300: 1
SIO_000628: feature:1154-1576:-1:exon

CVE23_RS22550
type: Gene
subclass of: SO_0000704
RO_0002162: 1778540
gene: mobC
locus tag: CVE23_RS22550
old locus tag: CVE23_22550
so part of: sequence
location: complement(1785..2111)
location: region:1785-2111:-1
so has part: feature:1785-2111:-1:exon
subclass of: SO_0000010

66567103
type: Gene
SIO_000068: ncbigene

position:1785:-1
position: 1785
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:2111:-1
position: 2111
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:1785-2111:-1:exon

CVE23_RS22550
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 1778540
gene: mobC
locus tag: CVE23_RS22550
old locus tag: CVE23_22550
inference: COORDINATES: similar to AA sequence:RefSeq:WP_006674374.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: plasmid mobilization relaxosome protein MobC
translation: MEKRTKEIKIRLTETEHQRLLERCDRTYLAEWLRHLGLGEHTSRKRRVPSVAPELLRQVSGIGNNLNQIARRLNQSDSLTPSERVSLLAVLNSLDRQLGDLLEQNRDR
SIO_010081: CVE23_RS22550
subclass of: SO_0000673
so part of: CVE23_RS22550
location: complement(1785..2111)
location: region:1785-2111:-1
so has part: feature:1785-2111:-1:exon

WP_100850519.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:1785-2111:-1:exon

CVE23_RS22555
type: Gene
subclass of: SO_0000704
RO_0002162: 1778540
locus tag: CVE23_RS22555
old locus tag: CVE23_22555
so part of: sequence
location: complement(2352..3497)
location: region:2352-3497:-1
so has part: feature:2352-3497:-1:exon
subclass of: SO_0000010

66567104
type: Gene
SIO_000068: ncbigene

position:2352:-1
position: 2352
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:3497:-1
position: 3497
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:2352-3497:-1:exon

CVE23_RS22555
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 1778540
locus tag: CVE23_RS22555
old locus tag: CVE23_22555
inference: COORDINATES: similar to AA sequence:RefSeq:WP_006674372.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: DUF4868 domain-containing protein
translation: MAEEKLDLSELHHDAQKASELSSYYSHFDTKVEDFDLHVYFNFRHKIKGGDGKYRYEYRVAKIDDTTVLKESIKDNVITKTLNDLSSGGVAVSDIKQLSDRASTISFLEDAKSYKDEQMSFLTGIIFDKGFGGDGDIPVVNFEKFDKISKVDSIVFVLRKGDKCITIYKKQYPIQNLTKQKNHYFSYSKDTLSKIDTDMISIDGKASIVFVKGTAYIYDQDVFEKFFGYKKWIKKVAGEFVSEMKQKFSSIVDFGKVTDRLEKESADADAFSRKLARIYNNKDLRASFNTVTPEKISDFLVGNEYFARLLKYKSAEEPLEVSTHDQQEAFILIVSEGVLRSLITGFDYLSPAAKRKIATGQTAQKPSSVVTSIPSSASDAA
SIO_010081: CVE23_RS22555
subclass of: SO_0000673
so part of: CVE23_RS22555
location: complement(2352..3497)
location: region:2352-3497:-1
so has part: feature:2352-3497:-1:exon

WP_100850520.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:2352-3497:-1:exon

CVE23_RS22560
type: Gene
subclass of: SO_0000704
RO_0002162: 1778540
gene: kwaA
locus tag: CVE23_RS22560
old locus tag: CVE23_22560
so part of: sequence
location: complement(3490..4146)
location: region:3490-4146:-1
so has part: feature:3490-4146:-1:exon
subclass of: SO_0000010

66567105
type: Gene
SIO_000068: ncbigene

position:3490:-1
position: 3490
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:4146:-1
position: 4146
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:3490-4146:-1:exon

CVE23_RS22560
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 1778540
gene: kwaA
locus tag: CVE23_RS22560
old locus tag: CVE23_22560
inference: COORDINATES: protein motif:HMM:NF041622.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: anti-phage protein KwaA
translation: MKVKMYVLSLFFLFIPIIFYFSGIDDVWNVFSKANGFCDGVSNRIVCITGNMGNQLSLSVSRLCVCIFLVFLCGYTYWWYKRQLSFLDRGITSAEVVVVGCEKESTEYLSFLSTYIMPLVFTDLTKPSNVFNFIFILVIVGFLHIKTRRIHSNPTLSLFGVSAYKIDYIIRVDGQDSDITKGLIVLSKDEISVKSVIRIIKKEDYITFAKYIRNDSNG
SIO_010081: CVE23_RS22560
subclass of: SO_0000673
so part of: CVE23_RS22560
location: complement(3490..4146)
location: region:3490-4146:-1
so has part: feature:3490-4146:-1:exon

WP_145958447.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:3490-4146:-1:exon

CVE23_RS22565
type: Gene
subclass of: SO_0000704
RO_0002162: 1778540
locus tag: CVE23_RS22565
old locus tag: CVE23_22565
so part of: sequence
location: complement(4136..5032)
location: region:4136-5032:-1
so has part: feature:4136-5032:-1:exon
subclass of: SO_0000010

66567106
type: Gene
SIO_000068: ncbigene

position:4136:-1
position: 4136
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:5032:-1
position: 5032
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:4136-5032:-1:exon

CVE23_RS22565
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 1778540
locus tag: CVE23_RS22565
old locus tag: CVE23_22565
inference: COORDINATES: similar to AA sequence:RefSeq:WP_006674370.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: replication initiation protein
translation: MSNAALELFNERLPHKPYFSDDLHFGVRIAGKERAILAKYIQFNQPHAMFWLGFDVDRAGAAIDWSDRNAPAPTLTITNPENGHAHLLYALKTSIRTAPDGKMKPLRYAAAVENALRKKLEADAGYSGLICKNPNHGHWKIAVWQPELYSLDWLADFLDLNAANDKEIVADYGLGRNCTLFDKTRKWAYRAIRQGWPEYGQWMLACVERATAYNMQFSAPLDEKEVISIAKSISKWTYSKFTQQSFDEYVKKTHSAECQSIRGRKSSGGGRPKIRSEEWVSLGISRATWYRMHYKNES
SIO_010081: CVE23_RS22565
subclass of: SO_0000673
so part of: CVE23_RS22565
location: complement(4136..5032)
location: region:4136-5032:-1
so has part: feature:4136-5032:-1:exon

WP_100850522.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:4136-5032:-1:exon