Xenorhabdus doucetiae strain FRM16 plasmid XD_p, complete sequence.
type: Entry
definition: Xenorhabdus doucetiae strain FRM16 plasmid XD_p, complete sequence.
sequence version: NZ_FO704549.1
sequence date: 2022-12-24
sequence: sequence
division: CON
label: NZ_FO704549.1
type: RefSeq
SIO_000068: refseq
dblink: PRJNA224116
dblink: SAMEA3283113
keyword: RefSeq
keyword: complete genome
source: Xenorhabdus doucetiae
organism: Xenorhabdus doucetiae
taxonomy: Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales; Morganellaceae; Xenorhabdus.
reference: 1
comment: REFSEQ INFORMATION: The reference sequence is identical to\nFO704549.1.\nAnnotation results relative to BLAST similarities, COG\nassignations, enzymatic function prediction (PRIAM software), TMHMM\nand SignalP predictions, and synteny conservation (Syntonizer\nsoftware) are available in the MicroScope annotation system\nhttp://www.genoscope.cns.fr/agc/microscope.\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-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 12/24/2022 02:31:33\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) :: 3,735\nCDSs (total) :: 3,633\nGenes (coding) :: 3,514\nCDSs (with protein) :: 3,514\nGenes (RNA) :: 102\nrRNAs :: 8, 7, 7 (5S, 16S, 23S)\ncomplete rRNAs :: 8, 7, 7 (5S, 16S, 23S)\ntRNAs :: 76\nncRNAs :: 4\nPseudo Genes (total) :: 119\nCDSs (without protein) :: 119\nPseudo Genes (ambiguous residues) :: 0 of 119\nPseudo Genes (frameshifted) :: 53 of 119\nPseudo Genes (incomplete) :: 73 of 119\nPseudo Genes (internal stop) :: 28 of 119\nPseudo Genes (multiple problems) :: 32 of 119\nCRISPR Arrays :: 3\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.

sequence
subclass of: SO_0000155
sequence length: 8449
topology: circular
so has quality: SO_0000988
location: 1..8449
location: region:1-8449:1
RO_0002162: 351671

NZ_FO704549
type: RefSeq
SIO_000068: refseq

PRJNA224116
type: BioProject
SIO_000068: bioproject

SAMEA3283113
type: BioSample
SIO_000068: biosample

1
title: Direct Submission
author: Genoscope -, C.E.A.
journal: Submitted (16-JUL-2013) Genoscope - CEA (Commissariat a l'energie atomique et aux energies alternatives) : BP 191 91006 EVRY cedex - FRANCE (E-mail : seqref@genoscope.cns.fr - Web : www.genoscope.cns.fr)

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

position:8449:1
position: 8449
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

feature:1-8449:1:source
so part of: sequence
organism: Xenorhabdus doucetiae
mol type: genomic DNA
strain: FRM16
type material: type strain of Xenorhabdus doucetiae
plasmid: XD_p

351671
type: Taxonomy
SIO_000068: taxonomy

XDD1_RS18345
type: Gene
subclass of: SO_0000704
RO_0002162: 351671
locus tag: XDD1_RS18345
so part of: sequence
location: complement(join(8206..8449,1..236))
location: region:1-8449:-1
so has part: feature:1-236:-1:exon
so has part: feature:8206-8449:-1:exon
subclass of: SO_0000010

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

position:8449:-1
position: 8449
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:1-236:-1:exon

position:236:-1
position: 236
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 2
SIO_000628: feature:8206-8449:-1:exon

position:8206:-1
position: 8206
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

XDD1_RS18345
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 351671
locus tag: XDD1_RS18345
inference: COORDINATES: similar to AA sequence:RefSeq:WP_004243590.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: Hcp family type VI secretion system effector
translation: MANIIYLKLQGSKQGLISSGCSTMESIGNKFQKGHEDEILVNELSSNLSMHQNVNFQPIDIRKPIDKSSPLLSQALTSNEILTCEFFFYRTSMNGGLELYYKVKLTEASLVNINFFCPNSITHNDAQPEESLSIKFKSITWEHVTAGTSSYSIWDERVY
SIO_010081: XDD1_RS18345
subclass of: SO_0000673
so part of: XDD1_RS18345
location: complement(join(8206..8449,1..236))
location: region:1-8449:-1
so has part: feature:1-236:-1:exon
so has part: feature:8206-8449:-1:exon

WP_052705612.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:1-236:-1:exon

urn:…
SIO_000300: 2
SIO_000628: feature:8206-8449:-1:exon

XDD1_RS00010
type: Gene
subclass of: SO_0000704
RO_0002162: 351671
locus tag: XDD1_RS00010
old locus tag: XDD1_p0001
so part of: sequence
location: complement(594..884)
location: region:594-884:-1
so has part: feature:594-884:-1:exon
subclass of: SO_0000010

position:594:-1
position: 594
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:884:-1
position: 884
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:594-884:-1:exon

XDD1_RS00010
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 351671
locus tag: XDD1_RS00010
old locus tag: XDD1_p0001
inference: COORDINATES: similar to AA sequence:RefSeq:WP_010848993.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: helix-turn-helix transcriptional regulator
translation: MNTKDWHPADIVAALHKQGTTVAALSRESGLSSSTLANALKRAWPKGEWIIARRLNMHPAQIWPSRYFDLRGRMTERKPRNTPNWDELVSKDGYDV
SIO_010081: XDD1_RS00010
subclass of: SO_0000673
so part of: XDD1_RS00010
location: complement(594..884)
location: region:594-884:-1
so has part: feature:594-884:-1:exon

WP_045967623.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:594-884:-1:exon

XDD1_RS00015
type: Gene
subclass of: SO_0000704
RO_0002162: 351671
locus tag: XDD1_RS00015
old locus tag: XDD1_p0002
so part of: sequence
location: 1326..1592
location: region:1326-1592:1
so has part: feature:1326-1592:1:exon
subclass of: SO_0000010

position:1326:1
position: 1326
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:1592:1
position: 1592
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:1326-1592:1:exon

XDD1_RS00015
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 351671
locus tag: XDD1_RS00015
old locus tag: XDD1_p0002
inference: COORDINATES: similar to AA sequence:RefSeq:WP_000072676.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: hypothetical protein
translation: MSNTTHYENANFLRELAESLPRIMPNANAARKAELLQRLANEELAQAEYEERVRAKVAAARADSRPGMTTEQLRQQLQRRYQELRDAV
SIO_010081: XDD1_RS00015
subclass of: SO_0000673
so part of: XDD1_RS00015
location: 1326..1592
location: region:1326-1592:1
so has part: feature:1326-1592:1:exon

WP_045967626.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:1326-1592:1:exon

XDD1_RS00020
type: Gene
subclass of: SO_0000704
RO_0002162: 351671
locus tag: XDD1_RS00020
old locus tag: XDD1_p0003
so part of: sequence
location: 1582..1881
location: region:1582-1881:1
so has part: feature:1582-1881:1:exon
subclass of: SO_0000010

position:1582:1
position: 1582
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:1881:1
position: 1881
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:1582-1881:1:exon

XDD1_RS00020
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 351671
locus tag: XDD1_RS00020
old locus tag: XDD1_p0003
inference: COORDINATES: similar to AA sequence:RefSeq:WP_010848995.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: type II toxin-antitoxin system RelE/ParE family toxin
translation: MPYDLEWKQGAIEDVTALFDYIAENSSLWDARDVTERILNATDKLAEFPRLYEVDTRYGEDVRRISLVGQHVLYEVDDQAKQIRVLAVVGQRQNPRSIR
SIO_010081: XDD1_RS00020
subclass of: SO_0000673
so part of: XDD1_RS00020
location: 1582..1881
location: region:1582-1881:1
so has part: feature:1582-1881:1:exon

WP_045967628.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:1582-1881:1:exon

XDD1_RS00025
type: Gene
subclass of: SO_0000704
RO_0002162: 351671
locus tag: XDD1_RS00025
old locus tag: XDD1_p0004
so part of: sequence
location: 2421..2645
location: region:2421-2645:1
so has part: feature:2421-2645:1:exon
subclass of: SO_0000010

position:2421:1
position: 2421
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:2645:1
position: 2645
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:2421-2645:1:exon

XDD1_RS00025
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 351671
locus tag: XDD1_RS00025
old locus tag: XDD1_p0004
inference: COORDINATES: similar to AA sequence:RefSeq:WP_010848996.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: hypothetical protein
translation: MPQFNAGKELAALREQTRIIRKRRYRKSRLDRHAGELLQLYREGASAAELQRWLRAKRIRVVLSTVTRWLARNG
SIO_010081: XDD1_RS00025
subclass of: SO_0000673
so part of: XDD1_RS00025
location: 2421..2645
location: region:2421-2645:1
so has part: feature:2421-2645:1:exon

WP_045967630.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:2421-2645:1:exon

XDD1_RS00030
type: Gene
subclass of: SO_0000704
RO_0002162: 351671
locus tag: XDD1_RS00030
old locus tag: XDD1_p0005
so part of: sequence
location: 2638..3522
location: region:2638-3522:1
so has part: feature:2638-3522:1:exon
subclass of: SO_0000010

position:2638:1
position: 2638
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:3522:1
position: 3522
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:2638-3522:1:exon

XDD1_RS00030
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 351671
locus tag: XDD1_RS00030
old locus tag: XDD1_p0005
inference: COORDINATES: similar to AA sequence:RefSeq:WP_016947203.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: integrase
translation: MAKFASPAKQAASVMKAMQGSALRSVGTVRNYEQALTRVAEWVKSSRACSDLRKLTPATAIDYLETRGEAVGQKTLDMERQAIQAMMHHVTGALPHGQTLPVIHSESPQVLTGRAYTPAQVALIASAQTAKNALATELAYAAGLRAHELHTLAPVRECPANERPATETKWNGRDGQLYTVQGKGGLVREVLIPHHLAKRLETLRRPEPRTVTDRGINYLSRYEIGAGKAWTNSFSAAASRVLGWSAGAHGVRHAYAQERMSELQRQGLVREDALTTVSQEMGHFRPEITETYLR
SIO_010081: XDD1_RS00030
subclass of: SO_0000673
so part of: XDD1_RS00030
location: 2638..3522
location: region:2638-3522:1
so has part: feature:2638-3522:1:exon

WP_045967632.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:2638-3522:1:exon

XDD1_RS00035
type: Gene
subclass of: SO_0000704
RO_0002162: 351671
locus tag: XDD1_RS00035
old locus tag: XDD1_p0006
so part of: sequence
location: 3519..4121
location: region:3519-4121:1
so has part: feature:3519-4121:1:exon
subclass of: SO_0000010

position:3519:1
position: 3519
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:4121:1
position: 4121
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:3519-4121:1:exon

XDD1_RS00035
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 351671
locus tag: XDD1_RS00035
old locus tag: XDD1_p0006
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: MKWRVMTGLAFLLVLSVVSFGVYAGMNDLIVGILTENDRLRVIAQGFAVVIHFWPVALAGAVLGGVLTLMVCAPAFSTAQDADHENQRRYYRQQAEAAEHRAESAEKVAHQRLQAQLQAAEKWEREASDALDRARQLQQDVAAKVRNIVAETERQRAAAAQEVEQSHTKAEDAERRRRNAAATAERLRRKQKQERQDRDL
SIO_010081: XDD1_RS00035
subclass of: SO_0000673
so part of: XDD1_RS00035
location: 3519..4121
location: region:3519-4121:1
so has part: feature:3519-4121:1:exon

WP_045967634.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:3519-4121:1:exon

XDD1_RS00040
type: Gene
subclass of: SO_0000704
RO_0002162: 351671
locus tag: XDD1_RS00040
old locus tag: XDD1_p0007
so part of: sequence
location: complement(4218..4577)
location: region:4218-4577:-1
so has part: feature:4218-4577:-1:exon
subclass of: SO_0000010

position:4218:-1
position: 4218
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:4577:-1
position: 4577
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:4218-4577:-1:exon

XDD1_RS00040
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 351671
locus tag: XDD1_RS00040
old locus tag: XDD1_p0007
inference: COORDINATES: protein motif:HMM:NF016255.2
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: ProQ/FINO family protein
translation: MATQEEKKQAAREARALLEGFWPTLFCYRVPRPLKVGVLDELILDAKARGLPFDKKILRKALDNYTVRYRYQKALAKGGKRYGLDGKADGVVTDEQQAYAKGLIIQRDAKAVLTKNLKK
SIO_010081: XDD1_RS00040
subclass of: SO_0000673
so part of: XDD1_RS00040
location: complement(4218..4577)
location: region:4218-4577:-1
so has part: feature:4218-4577:-1:exon

WP_052705613.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:4218-4577:-1:exon

XDD1_RS00045
type: Gene
subclass of: SO_0000704
RO_0002162: 351671
locus tag: XDD1_RS00045
old locus tag: XDD1_p0008
so part of: sequence
location: complement(4815..5117)
location: region:4815-5117:-1
so has part: feature:4815-5117:-1:exon
subclass of: SO_0000010

position:4815:-1
position: 4815
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:5117:-1
position: 5117
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:4815-5117:-1:exon

XDD1_RS00045
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 351671
locus tag: XDD1_RS00045
old locus tag: XDD1_p0008
inference: COORDINATES: similar to AA sequence:RefSeq:WP_010617912.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: BrnA antitoxin family protein
translation: MSMVRYKRNELPPLSEKQKAELRKLSDKPDSDIDYSDIAPLDTAFWKNATQGQFYRPVKTQTSVRIDADVLAWLKETGKGYQTRLNAILREAMLRDLHRK
SIO_010081: XDD1_RS00045
subclass of: SO_0000673
so part of: XDD1_RS00045
location: complement(4815..5117)
location: region:4815-5117:-1
so has part: feature:4815-5117:-1:exon

WP_045967636.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:4815-5117:-1:exon

XDD1_RS00050
type: Gene
subclass of: SO_0000704
RO_0002162: 351671
locus tag: XDD1_RS00050
old locus tag: XDD1_p0009
so part of: sequence
location: complement(5098..5397)
location: region:5098-5397:-1
so has part: feature:5098-5397:-1:exon
subclass of: SO_0000010

position:5098:-1
position: 5098
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:5397:-1
position: 5397
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:5098-5397:-1:exon

XDD1_RS00050
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 351671
locus tag: XDD1_RS00050
old locus tag: XDD1_p0009
inference: COORDINATES: similar to AA sequence:RefSeq:WP_010849001.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: BrnT family toxin
translation: MKPEIEFEWDTVKAASNFRKHGVRFEAASRVFDDPFHLTVQDRFENGEYRWQTIGTVENCVLVLVAHTTRFEDGTEIIRIISARKAERHERKRYEHGEI
SIO_010081: XDD1_RS00050
subclass of: SO_0000673
so part of: XDD1_RS00050
location: complement(5098..5397)
location: region:5098-5397:-1
so has part: feature:5098-5397:-1:exon

WP_045967644.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:5098-5397:-1:exon

XDD1_RS18350
type: Gene
subclass of: SO_0000704
RO_0002162: 351671
locus tag: XDD1_RS18350
old locus tag: XDD1_p0011
so part of: sequence
location: 6525..6890
location: region:6525-6890:1
so has part: feature:6525-6890:1:exon
subclass of: SO_0000010

position:6525:1
position: 6525
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:6890:1
position: 6890
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:6525-6890:1:exon

XDD1_RS18350
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 351671
locus tag: XDD1_RS18350
old locus tag: XDD1_p0011
inference: COORDINATES: protein motif:HMM:NF017454.2
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: type VI secretion system tube protein Hcp
translation: MQYTTYMEITGAEQGLLSENCSNNDTHKHKIQVNSLELSKGIEGLSYIEKIVLEKNVDGSSPLLFNAIDKNESLELKIFQCVDNKITHEFKFKNAFIERINTHFSEESKTSPYEKIEIKIA
SIO_010081: XDD1_RS18350
subclass of: SO_0000673
so part of: XDD1_RS18350
location: 6525..6890
location: region:6525-6890:1
so has part: feature:6525-6890:1:exon

WP_052705614.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:6525-6890:1:exon

XDD1_RS00060
type: Gene
subclass of: SO_0000704
RO_0002162: 351671
locus tag: XDD1_RS00060
old locus tag: XDD1_p0012
so part of: sequence
location: complement(7286..8206)
location: region:7286-8206:-1
so has part: feature:7286-8206:-1:exon
subclass of: SO_0000010

position:7286:-1
position: 7286
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:7286-8206:-1:exon

XDD1_RS00060
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 351671
locus tag: XDD1_RS00060
old locus tag: XDD1_p0012
inference: COORDINATES: protein motif:HMM:NF025354.2
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: DUF4225 domain-containing protein
translation: MIIPTMRYFDYYGDELIKVSKYSAAYLLDNVESKKQYLYEISQVVRLIRRDYQIALYNYNQRRHEYLADMKRCIAEIRRELDAETYGYEQGRRKDRKTYLNTQEYSGKGFLYYGKNGLKVIGGIVQFGAGIMAFSTRGGWVRGMESKGMGVLAIATGVGDAVEGASNIMYEWTDGYINPSNPTKFLTEKGFSFFGADEGTGELAYDIVNFGIGIYFGFTAFAKYDPSKRIINLPVEKKSGLEKVPLLHRLFAEKGGVRLFRHMENDYKRKMFTSGKAVLTYKASNTAIKAYLLLDKYLFNEENENN
SIO_010081: XDD1_RS00060
subclass of: SO_0000673
so part of: XDD1_RS00060
location: complement(7286..8206)
location: region:7286-8206:-1
so has part: feature:7286-8206:-1:exon

WP_045967638.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:7286-8206:-1:exon