Yersinia enterocolitica strain NW56 plasmid unnamed1.
type: Entry
definition: Yersinia enterocolitica strain NW56 plasmid unnamed1.
sequence version: NZ_CP107103.1
sequence date: 2022-12-29
sequence: sequence
division: CON
label: NZ_CP107103.1
type: RefSeq
SIO_000068: refseq
dblink: PRJNA224116
dblink: SAMN30737596
keyword: RefSeq
source: Yersinia enterocolitica
organism: Yersinia enterocolitica
taxonomy: Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales; Yersiniaceae; Yersinia.
reference: 1
reference: 2
comment: REFSEQ INFORMATION: The reference sequence is identical to\nCP107103.1.\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 :: 2022\nAssembly Method :: SPAdes v. Version 3.15.3\nGenome Representation :: Full\nExpected Final Version :: Yes\nGenome Coverage :: 173x\nSequencing Technology :: Illumina HiSeq\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 10/21/2022 10:20:33\nAnnotation Pipeline :: NCBI Prokaryotic Genome\n Annotation Pipeline (PGAP)\nAnnotation Method :: Best-placed reference protein\n set; GeneMarkS-2+\nAnnotation Software revision :: 6.3\nFeatures Annotated :: Gene; CDS; rRNA; tRNA; ncRNA;\n repeat_region\nGenes (total) :: 4,113\nCDSs (total) :: 4,043\nGenes (coding) :: 3,996\nCDSs (with protein) :: 3,996\nGenes (RNA) :: 70\nrRNAs :: 1 (5S)\ncomplete rRNAs :: 1 (5S)\ntRNAs :: 59\nncRNAs :: 10\nPseudo Genes (total) :: 47\nCDSs (without protein) :: 47\nPseudo Genes (ambiguous residues) :: 0 of 47\nPseudo Genes (frameshifted) :: 17 of 47\nPseudo Genes (incomplete) :: 29 of 47\nPseudo Genes (internal stop) :: 11 of 47\nPseudo Genes (multiple problems) :: 8 of 47\nCRISPR Arrays :: 1\n##Genome-Annotation-Data-END##

sequence
subclass of: SO_0000155
sequence length: 5350
topology: linear
so has quality: SO_0000987
location: 1..5350
location: region:1-5350:1
RO_0002162: 630

NZ_CP107103
type: RefSeq
SIO_000068: refseq

PRJNA224116
type: BioProject
SIO_000068: bioproject

SAMN30737596
type: BioSample
SIO_000068: biosample

1
title: GDARD project (Project number: P10000158)
author: Matle, I.
journal: Unpublished

2
title: Direct Submission
author: Matle, I.
journal: Submitted (26-SEP-2022) Bioinformatics, University of Pretoria, 202 Lunnon road, Pretoria, Gauteng 0083, South Africa

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

position:5350:1
position: 5350
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

feature:1-5350:1:source
so part of: sequence
organism: Yersinia enterocolitica
mol type: genomic DNA
strain: NW56
isolation source: Rustenburg
plasmid: unnamed1
country: South Africa
lat lon: 25.6544 S 27.2559 E
collection date: 2021
collected by: ARC-Onderstepoort Veterinary Research

630
type: Taxonomy
SIO_000068: taxonomy

N4222_RS20495
type: Gene
subclass of: SO_0000704
RO_0002162: 630
locus tag: N4222_RS20495
old locus tag: N4222_20495
so part of: sequence
location: <1..509
location: region:1-509:1
so has part: feature:1-509:1:exon
subclass of: SO_0000010

77330239
type: Gene
SIO_000068: ncbigene

position:509:1
position: 509
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:1-509:1:exon

N4222_RS20495
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 630
locus tag: N4222_RS20495
old locus tag: N4222_20495
inference: COORDINATES: protein motif:HMM:NF017524.2
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 3
transl table: 11
product: MobC family plasmid mobilization relaxosome protein
translation: FFAATTESDILQYTLSQYTQRPLYEVPSVTGSGGSPPPETPGIHCESFALWVRIFLSGVRMQKRTREIKIRLTDSEHQRLIDRCDRTHLAEWLRQLGLGEHTARKRRLPDVAPELLRQVSGIGNNLNQIARRLNQLDGLTPTERVSLLAVLNSLDRNLGELLEQHRDH
SIO_010081: N4222_RS20495
subclass of: SO_0000673
so part of: N4222_RS20495
location: <1..509
location: region:1-509:1
so has part: feature:1-509:1:exon

WP_263699614.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:1-509:1:exon

N4222_RS20500
type: Gene
subclass of: SO_0000704
RO_0002162: 630
locus tag: N4222_RS20500
old locus tag: N4222_20500
pseudo: true
so part of: sequence
location: 718..>1137
location: region:718-1137:1
so has part: feature:718-1137:1:exon
subclass of: SO_0000010

77330240
type: Gene
SIO_000068: ncbigene

position:718:1
position: 718
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:1137:1
position: 1137
reference: sequence
type: ForwardStrandPosition
type: FuzzyPosition

urn:…
SIO_000300: 1
SIO_000628: feature:718-1137:1:exon

N4222_RS20500
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 630
locus tag: N4222_RS20500
old locus tag: N4222_20500
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: N4222_RS20500
subclass of: SO_0000673
so part of: N4222_RS20500
location: 718..>1137
location: region:718-1137:1
so has part: feature:718-1137:1:exon

urn:…
SIO_000300: 1
SIO_000628: feature:718-1137:1:exon

N4222_RS20505
type: Gene
subclass of: SO_0000704
RO_0002162: 630
locus tag: N4222_RS20505
old locus tag: N4222_20505
so part of: sequence
location: 1187..1672
location: region:1187-1672:1
so has part: feature:1187-1672:1:exon
subclass of: SO_0000010

77330241
type: Gene
SIO_000068: ncbigene

position:1187:1
position: 1187
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:1672:1
position: 1672
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:1187-1672:1:exon

N4222_RS20505
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 630
locus tag: N4222_RS20505
old locus tag: N4222_20505
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: MSEILNLAKGFEEKSKQQAQDTEQSVKREFERLETSISEDLKSSSQSISNAIHEQNGRLTGMIRATATTVLIWIVVCSALLIGILSGIIWLQGQIISSRLSDIDGYSQQLTSLKAKSGAGVTIYSDDSQKNGYLVVLPVKAHGVESYTSTAGNTVVKYTAK
SIO_010081: N4222_RS20505
subclass of: SO_0000673
so part of: N4222_RS20505
location: 1187..1672
location: region:1187-1672:1
so has part: feature:1187-1672:1:exon

WP_145595267.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:1187-1672:1:exon

N4222_RS20510
type: Gene
subclass of: SO_0000704
RO_0002162: 630
locus tag: N4222_RS20510
old locus tag: N4222_20510
so part of: sequence
location: 1742..1969
location: region:1742-1969:1
so has part: feature:1742-1969:1:exon
subclass of: SO_0000010

77330242
type: Gene
SIO_000068: ncbigene

position:1742:1
position: 1742
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:1969:1
position: 1969
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:1742-1969:1:exon

N4222_RS20510
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 630
locus tag: N4222_RS20510
old locus tag: N4222_20510
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: MEKQLLSALESLQASYEQQHQAWQESYSSLQHMFETTSQALNRSDRACQHLSNQVNSLRGQVENLSDNVSRLMRS
SIO_010081: N4222_RS20510
subclass of: SO_0000673
so part of: N4222_RS20510
location: 1742..1969
location: region:1742-1969:1
so has part: feature:1742-1969:1:exon

WP_241652297.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:1742-1969:1:exon

N4222_RS20515
type: Gene
subclass of: SO_0000704
RO_0002162: 630
locus tag: N4222_RS20515
old locus tag: N4222_20515
so part of: sequence
location: 2118..2450
location: region:2118-2450:1
so has part: feature:2118-2450:1:exon
subclass of: SO_0000010

77330243
type: Gene
SIO_000068: ncbigene

position:2118:1
position: 2118
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:2450:1
position: 2450
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:2118-2450:1:exon

N4222_RS20515
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 630
locus tag: N4222_RS20515
old locus tag: N4222_20515
inference: COORDINATES: similar to AA sequence:RefSeq:WP_015873600.1
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: MSHAIEFIETPMFTRQIKQIATDDELKELQKTLIESPDKGDLIRQTGGLRKIRMATGTQGKSGSVRVIYFLATDEIIYLVMAYPKSTKDSLTDAEKSDLKKLTKLLKDEV
SIO_010081: N4222_RS20515
subclass of: SO_0000673
so part of: N4222_RS20515
location: 2118..2450
location: region:2118-2450:1
so has part: feature:2118-2450:1:exon

WP_050152597.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:2118-2450:1:exon

N4222_RS20520
type: Gene
subclass of: SO_0000704
RO_0002162: 630
locus tag: N4222_RS20520
old locus tag: N4222_20520
so part of: sequence
location: 2452..2736
location: region:2452-2736:1
so has part: feature:2452-2736:1:exon
subclass of: SO_0000010

77330244
type: Gene
SIO_000068: ncbigene

position:2452:1
position: 2452
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:2736:1
position: 2736
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:2452-2736:1:exon

N4222_RS20520
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 630
locus tag: N4222_RS20520
old locus tag: N4222_20520
inference: COORDINATES: similar to AA sequence:RefSeq:WP_000007431.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: NadS family protein
translation: MSFFDELKASLEEAVEIKNGVKAPARVTRYELADVKALRTQLNVTQDEMAKVLGTSLDTIKSWETGRRNPTGLAAKVLATIQANPKFFQELASH
SIO_010081: N4222_RS20520
subclass of: SO_0000673
so part of: N4222_RS20520
location: 2452..2736
location: region:2452-2736:1
so has part: feature:2452-2736:1:exon

WP_050152599.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:2452-2736:1:exon

N4222_RS20525
type: Gene
subclass of: SO_0000704
RO_0002162: 630
locus tag: N4222_RS20525
old locus tag: N4222_20525
so part of: sequence
location: 2928..3824
location: region:2928-3824:1
so has part: feature:2928-3824:1:exon
subclass of: SO_0000010

77330245
type: Gene
SIO_000068: ncbigene

position:2928:1
position: 2928
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:3824:1
position: 3824
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:2928-3824:1:exon

N4222_RS20525
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 630
locus tag: N4222_RS20525
old locus tag: N4222_20525
inference: COORDINATES: similar to AA sequence:RefSeq:WP_019725130.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: replication initiation protein
translation: MTNPALDLFNDRLPNKPYFSDDLHFGVRIAGKERAILAKYIQFNQPHAMFWLGFDVDRLGAAIDWSDRNAPAPTLTITNPENGHAHLLYALKTSIRTAPDGKMKPLKYAAAVENALRKKLDADVGYSGLICKNPNHGHWKIAVWQPELYTLDWLADSLDLNAANDKEIVADYGLGRNCTLFDKTRKWAYRAIRQGWPEYEQWLKACYERANAYNLQFPACLDEREVMTVAKSVAKWTSNKFSSDHFERFVEITHSSDIQSIRGKKSGVSRRKGSIEEKKPWVEMGISRRKYFYIKKSK
SIO_010081: N4222_RS20525
subclass of: SO_0000673
so part of: N4222_RS20525
location: 2928..3824
location: region:2928-3824:1
so has part: feature:2928-3824:1:exon

WP_050296665.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:2928-3824:1:exon

N4222_RS20530
type: Gene
subclass of: SO_0000704
RO_0002162: 630
locus tag: N4222_RS20530
old locus tag: N4222_20530
so part of: sequence
location: 3834..4541
location: region:3834-4541:1
so has part: feature:3834-4541:1:exon
subclass of: SO_0000010

77330246
type: Gene
SIO_000068: ncbigene

position:3834:1
position: 3834
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:4541:1
position: 4541
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:3834-4541:1:exon

N4222_RS20530
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 630
locus tag: N4222_RS20530
old locus tag: N4222_20530
inference: COORDINATES: similar to AA sequence:RefSeq:WP_001258875.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: hypothetical protein
translation: MKTFVTLWTIAFLAFVGVMCTVDISNYIPSVYTVFSKNRPLVTGVLSILLISVFIWLMVSLYLLKKYSVKVEKLSLGGISILFNESSTLYKKSIKNHLDSKRAIFKVRKNVDAFDEVISSYYQTYQFIRDEMKILNPKKDREIYDFSNEMLMVLNKFLTNYQNNYKRWYKYISDKDEVNDRATGDVMRFHSTGINKIQMQYYDYDRILKGFKDVNRFFINDVKPKFGINTDKWNW
SIO_010081: N4222_RS20530
subclass of: SO_0000673
so part of: N4222_RS20530
location: 3834..4541
location: region:3834-4541:1
so has part: feature:3834-4541:1:exon

WP_050152589.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:3834-4541:1:exon

N4222_RS20535
type: Gene
subclass of: SO_0000704
RO_0002162: 630
locus tag: N4222_RS20535
old locus tag: N4222_20535
so part of: sequence
location: complement(4574..5188)
location: region:4574-5188:-1
so has part: feature:4574-5188:-1:exon
subclass of: SO_0000010

77330247
type: Gene
SIO_000068: ncbigene

position:4574:-1
position: 4574
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:5188:-1
position: 5188
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:4574-5188:-1:exon

N4222_RS20535
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 630
locus tag: N4222_RS20535
old locus tag: N4222_20535
inference: COORDINATES: similar to AA sequence:RefSeq:WP_000160640.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: TIR domain-containing protein
translation: MGKHKVFISYHHANDQDYKNALETMNDEHEIFVNRSVSLGDIDEDEEPQTIREIIRDKYLRDTTVLILLVGTETKNRKHVDWEVFSSMRDSTINKKSGILVVNLPSTNTTYIRSTHGSDEKSEIHPTVSDWVSIDKRSTFEERFPYMPARIIDNFMKTGSYISVVNWSQIDENPEALRNLIDMTYDDREKATYDMSREMRMRNG
SIO_010081: N4222_RS20535
subclass of: SO_0000673
so part of: N4222_RS20535
location: complement(4574..5188)
location: region:4574-5188:-1
so has part: feature:4574-5188:-1:exon

WP_050152591.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:4574-5188:-1:exon