Photobacterium toruni strain WD2103 plasmid unnamed3, complete sequence.
type: Entry
definition: Photobacterium toruni strain WD2103 plasmid unnamed3, complete sequence.
sequence version: NZ_CP101698.1
sequence date: 2022-08-02
sequence: sequence
division: CON
label: NZ_CP101698.1
type: RefSeq
SIO_000068: refseq
dblink: PRJNA224116
dblink: SAMN29720330
keyword: RefSeq
source: Photobacterium toruni
organism: Photobacterium toruni
taxonomy: Bacteria; Pseudomonadota; Gammaproteobacteria; Vibrionales; Vibrionaceae; Photobacterium.
reference: 1
reference: 2
comment: REFSEQ INFORMATION: The reference sequence is identical to\nCP101698.1.\nBacteria and source DNA available from Department of Aqualife\nMedicine, Chonnam National University, Yeosu, Republic of\nKorea-59626.\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 :: 25-MAR-2021\nAssembly Method :: Unicycler v. V0.4.8\nGenome Representation :: Full\nExpected Final Version :: Yes\nGenome Coverage :: 100.0x\nSequencing Technology :: Illumina MiSeq; Oxford Nanopore MinION\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 07/31/2022 10:22:48\nAnnotation Pipeline :: NCBI Prokaryotic Genome\n Annotation Pipeline (PGAP)\nAnnotation Method :: Best-placed reference protein\n set; GeneMarkS-2+\nAnnotation Software revision :: 6.2\nFeatures Annotated :: Gene; CDS; rRNA; tRNA; ncRNA;\n repeat_region\nGenes (total) :: 4,319\nCDSs (total) :: 4,037\nGenes (coding) :: 3,963\nCDSs (with protein) :: 3,963\nGenes (RNA) :: 282\nrRNAs :: 22, 20, 20 (5S, 16S, 23S)\ncomplete rRNAs :: 22, 20, 20 (5S, 16S, 23S)\ntRNAs :: 216\nncRNAs :: 4\nPseudo Genes (total) :: 74\nCDSs (without protein) :: 74\nPseudo Genes (ambiguous residues) :: 0 of 74\nPseudo Genes (frameshifted) :: 18 of 74\nPseudo Genes (incomplete) :: 51 of 74\nPseudo Genes (internal stop) :: 22 of 74\nPseudo Genes (multiple problems) :: 14 of 74\nCRISPR Arrays :: 3\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.

sequence
subclass of: SO_0000155
sequence length: 10791
topology: circular
so has quality: SO_0000988
location: 1..10791
location: region:1-10791:1
RO_0002162: 1935446

NZ_CP101698
type: RefSeq
SIO_000068: refseq

PRJNA224116
type: BioProject
SIO_000068: bioproject

SAMN29720330
type: BioSample
SIO_000068: biosample

1
title: Photobacterium toruni isolated from olive flounder(Paralichthys olivaceus) in Korea: pathogenicity and completed genome sequences
author: Kwon, Y.H.
author: Kole, S.
author: Jung, S.J.
journal: Unpublished

2
title: Direct Submission
author: Kwon, Y.H.
author: Kole, S.
author: Jung, S.J.
journal: Submitted (21-JUL-2022) Department of Aqualife Medical Sciences, Chonnam National University, 50, Daehak-ro, Yeosu-si, Yeosu 59626, South Korea

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

position:10791:1
position: 10791
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

feature:1-10791:1:source
so part of: sequence
organism: Photobacterium toruni
mol type: genomic DNA
strain: WD2103
isolation source: Estuarine water
host: Paralichthys olivaceus
plasmid: unnamed3
country: South Korea: Wando
lat lon: 34.316667 N 126.75 E
collection date: 2021-03-25

1935446
type: Taxonomy
SIO_000068: taxonomy

NM620_RS21520
type: Gene
subclass of: SO_0000704
RO_0002162: 1935446
locus tag: NM620_RS21520
so part of: sequence
location: complement(1..249)
location: region:1-249:-1
so has part: feature:1-249:-1:exon
subclass of: SO_0000010

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

position:249:-1
position: 249
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:1-249:-1:exon

NM620_RS21520
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 1935446
locus tag: NM620_RS21520
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: MKSLEELIKIKAYCKKKQARFQEGSPEYIRQATHITSLEKQIEEEKQIEDQRGGWSHWDEVSDGDGDGYLGDGVYASNYDPN
SIO_010081: NM620_RS21520
subclass of: SO_0000673
so part of: NM620_RS21520
location: complement(1..249)
location: region:1-249:-1
so has part: feature:1-249:-1:exon

WP_256385192.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:1-249:-1:exon

NM620_RS21525
type: Gene
subclass of: SO_0000704
RO_0002162: 1935446
locus tag: NM620_RS21525
so part of: sequence
location: complement(335..757)
location: region:335-757:-1
so has part: feature:335-757:-1:exon
subclass of: SO_0000010

position:335:-1
position: 335
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:757:-1
position: 757
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:335-757:-1:exon

NM620_RS21525
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 1935446
locus tag: NM620_RS21525
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: MNKKTLAENIGIDTTNGYDTRCWDFETENAIIFLIARDELDTENGFSELMYDVCEDSQGGRKKRCALRQQNVLKVMLGKKRGYVLVRSKKLLEDDRDNHKWSLSNGYKVHPVTALSMIMRDKCGWVTTDTDTLLDIHDIK
SIO_010081: NM620_RS21525
subclass of: SO_0000673
so part of: NM620_RS21525
location: complement(335..757)
location: region:335-757:-1
so has part: feature:335-757:-1:exon

WP_256385193.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:335-757:-1:exon

NM620_RS21530
type: Gene
subclass of: SO_0000704
RO_0002162: 1935446
locus tag: NM620_RS21530
so part of: sequence
location: complement(987..1466)
location: region:987-1466:-1
so has part: feature:987-1466:-1:exon
subclass of: SO_0000010

position:987:-1
position: 987
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:1466:-1
position: 1466
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:987-1466:-1:exon

NM620_RS21530
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 1935446
locus tag: NM620_RS21530
inference: COORDINATES: similar to AA sequence:RefSeq:WP_017042795.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: hypothetical protein
translation: MELKKLNTSFYTENPTVENALDYYSNDGLWDLSKVRGHGVVNITVNNLMFAIPVRSNVLHSASYILLKNTQKRWIKGMGLDYSKALLIRKPEYITGDNFILKDKGAGKKLVGKEQHVTDQFEAYVNKYISAVKKNDLNVLSDKRYEETTLINYHADLGI
SIO_010081: NM620_RS21530
subclass of: SO_0000673
so part of: NM620_RS21530
location: complement(987..1466)
location: region:987-1466:-1
so has part: feature:987-1466:-1:exon

WP_256385194.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:987-1466:-1:exon

NM620_RS21535
type: Gene
subclass of: SO_0000704
RO_0002162: 1935446
locus tag: NM620_RS21535
so part of: sequence
location: 3303..4193
location: region:3303-4193:1
so has part: feature:3303-4193:1:exon
subclass of: SO_0000010

position:3303:1
position: 3303
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:4193:1
position: 4193
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:3303-4193:1:exon

NM620_RS21535
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 1935446
locus tag: NM620_RS21535
inference: COORDINATES: similar to AA sequence:RefSeq:WP_005398372.1
GO function: GO:0003677 - DNA binding [Evidence IEA]
GO process: GO:0015074 - DNA integration [Evidence IEA]
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: site-specific integrase
translation: MTRGHFASATKQSASVMKELQGSVLKSVGTVRNYEQSLKTCCEHLKSEHLGALRDITKEMAENYLSERALSVSQSTIDRDRLALQCMMQNVTHQLSPNERLKTIKSTKETLLKSRGYTPKQVELITEHQTEKYVFVTQLCYESGLRAHELYTLRPTSEIKPSPREVHENKFSYLAGKTKSYTVNGKGGLIREVQIPIALANQLETYRLKNPITIVDRKVNYQSHYAIPGGLKFSNAFSKNSTRTLGYSHGAHGLRHSYAQNRYQQLSNHYQRNTVMKIISQELGHFREDITAVYLR
SIO_010081: NM620_RS21535
subclass of: SO_0000673
so part of: NM620_RS21535
location: 3303..4193
location: region:3303-4193:1
so has part: feature:3303-4193:1:exon

WP_256385195.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:3303-4193:1:exon

NM620_RS21540
type: Gene
subclass of: SO_0000704
RO_0002162: 1935446
locus tag: NM620_RS21540
so part of: sequence
location: 4716..5669
location: region:4716-5669:1
so has part: feature:4716-5669:1:exon
subclass of: SO_0000010

position:4716:1
position: 4716
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:5669:1
position: 5669
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:4716-5669:1:exon

NM620_RS21540
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 1935446
locus tag: NM620_RS21540
inference: COORDINATES: protein motif:HMM:NF013235.2
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: replication initiation protein
translation: MKQLDKFREPIAVFPERLTASEQDVFALALCEISKSVAYNQIAKKNGSDQKEIPYIFEFSEKILIDLFQCSKDNLRKTLEPAARSLLNANVGYSNKHEFDYFSPLVRVRYVVGDKFIIEMAKSISELIAENIQSGFSEMDLKLFVSLSGRYHRRILKILSQWKTVPNKTIRFTIDEFRNAIGVPDDKYKRFQHLKSICMEEPFKDIINKSNGVWTATDKNGAGFELDKVGRSYKYITFKMKYNAVKSEKISINSNVDNIKIIFDLINIFSVNKKIYKSLSETAISRDMLSYFISNASINNEYIKVLPVAAELLNLPD
SIO_010081: NM620_RS21540
subclass of: SO_0000673
so part of: NM620_RS21540
location: 4716..5669
location: region:4716-5669:1
so has part: feature:4716-5669:1:exon

WP_256385196.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:4716-5669:1:exon

NM620_RS21545
type: Gene
subclass of: SO_0000704
RO_0002162: 1935446
locus tag: NM620_RS21545
so part of: sequence
location: complement(5826..6278)
location: region:5826-6278:-1
so has part: feature:5826-6278:-1:exon
subclass of: SO_0000010

position:5826:-1
position: 5826
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:6278:-1
position: 6278
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:5826-6278:-1:exon

NM620_RS21545
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 1935446
locus tag: NM620_RS21545
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: MQNKKKANETTTSVRKDMRIDKDLLAKIDAVRGDVPFAAWVKRSIKMRLDGLNNPPPVESVPVVISADKKNKKEPKVTVKTATVRTTNEIRAEKTRQLLFSAISSLSCTEKSKIINARYPKNQCRKAIGEVVSKDSIAKYWGEIEIALGC
SIO_010081: NM620_RS21545
subclass of: SO_0000673
so part of: NM620_RS21545
location: complement(5826..6278)
location: region:5826-6278:-1
so has part: feature:5826-6278:-1:exon

WP_256385187.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:5826-6278:-1:exon

NM620_RS21550
type: Gene
subclass of: SO_0000704
RO_0002162: 1935446
locus tag: NM620_RS21550
so part of: sequence
location: complement(6936..7403)
location: region:6936-7403:-1
so has part: feature:6936-7403:-1:exon
subclass of: SO_0000010

position:6936:-1
position: 6936
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:7403:-1
position: 7403
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:6936-7403:-1:exon

NM620_RS21550
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 1935446
locus tag: NM620_RS21550
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: MSDDIIFAGLFGMLSTLIGAGVTYALSFSRDQRALKQELKIMYSALIADLKAMNVGFERSDEYLPRFSSLNVFMIKGGYQLAPSEVVLCLESISHDLSRIEDISKSDHAFNVAVASTGQVGLVYNNRSNLRERAELIAAVKQQIPNLVDKLEQYT
SIO_010081: NM620_RS21550
subclass of: SO_0000673
so part of: NM620_RS21550
location: complement(6936..7403)
location: region:6936-7403:-1
so has part: feature:6936-7403:-1:exon

WP_256385188.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:6936-7403:-1:exon

NM620_RS21555
type: Gene
subclass of: SO_0000704
RO_0002162: 1935446
locus tag: NM620_RS21555
so part of: sequence
location: 7916..8416
location: region:7916-8416:1
so has part: feature:7916-8416:1:exon
subclass of: SO_0000010

position:7916:1
position: 7916
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:8416:1
position: 8416
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:7916-8416:1:exon

NM620_RS21555
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 1935446
locus tag: NM620_RS21555
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: MNSDKALEEAFHYFTKKVNDNEDYKTSPWNEGFFTYLFTKKQQNILKRICLKEGWELPENYGITIKGEFILHVLNSRKKKDQTTMYECAEILSASFSSKSEISINIGYEEQAVVLNSVKKINVQKNTYYASAFFSVGEKLESKTAYHTNYTKLKRILDDRKKCIGS
SIO_010081: NM620_RS21555
subclass of: SO_0000673
so part of: NM620_RS21555
location: 7916..8416
location: region:7916-8416:1
so has part: feature:7916-8416:1:exon

WP_256385189.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:7916-8416:1:exon

NM620_RS21560
type: Gene
subclass of: SO_0000704
RO_0002162: 1935446
locus tag: NM620_RS21560
so part of: sequence
location: complement(9275..9535)
location: region:9275-9535:-1
so has part: feature:9275-9535:-1:exon
subclass of: SO_0000010

position:9275:-1
position: 9275
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:9535:-1
position: 9535
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:9275-9535:-1:exon

NM620_RS21560
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 1935446
locus tag: NM620_RS21560
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: MKRKAKAVCHPIPWTIGTLIVVEPYRVDGELPFFEQQIERWRLPADAKRIFGFELCDRDTEKYQQRIRELLALNEVVLLQIERIPR
SIO_010081: NM620_RS21560
subclass of: SO_0000673
so part of: NM620_RS21560
location: complement(9275..9535)
location: region:9275-9535:-1
so has part: feature:9275-9535:-1:exon

WP_256385190.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:9275-9535:-1:exon

NM620_RS21565
type: Gene
subclass of: SO_0000704
RO_0002162: 1935446
locus tag: NM620_RS21565
so part of: sequence
location: complement(10302..10715)
location: region:10302-10715:-1
so has part: feature:10302-10715:-1:exon
subclass of: SO_0000010

position:10302:-1
position: 10302
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:10715:-1
position: 10715
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:10302-10715:-1:exon

NM620_RS21565
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 1935446
locus tag: NM620_RS21565
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: MKLVNYLVMIVLFGLSGCDSDEQYISYENINTSVLKSSNFSRYIVETCVDIYREKQNKKFNPRYAVTEVVQTGHNNIVEIKMNEVRYVQGSRQEKNLFLYCSRFDRNNTDSILSHRYLDTFIKYFNEKQYITYRIEF
SIO_010081: NM620_RS21565
subclass of: SO_0000673
so part of: NM620_RS21565
location: complement(10302..10715)
location: region:10302-10715:-1
so has part: feature:10302-10715:-1:exon

WP_256385191.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:10302-10715:-1:exon