Yersinia enterocolitica strain NW56 plasmid unnamed2.
type: Entry
definition: Yersinia enterocolitica strain NW56 plasmid unnamed2.
sequence version: NZ_CP107104.1
sequence date: 2022-12-29
sequence: sequence
division: CON
label: NZ_CP107104.1
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\nCP107104.1.\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: 3300
topology: linear
so has quality: SO_0000987
location: 1..3300
location: region:1-3300:1
RO_0002162: 630

NZ_CP107104
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journal: Unpublished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

position:3300:1
position: 3300
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

feature:1-3300:1:source
so part of: sequence
organism: Yersinia enterocolitica
mol type: genomic DNA
strain: NW56
isolation source: Rustenburg
plasmid: unnamed2
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_RS20540
type: Gene
subclass of: SO_0000704
RO_0002162: 630
locus tag: N4222_RS20540
old locus tag: N4222_20540
so part of: sequence
location: complement(31..354)
location: region:31-354:-1
so has part: feature:31-354:-1:exon
subclass of: SO_0000010

77330248
type: Gene
SIO_000068: ncbigene

position:31:-1
position: 31
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:354:-1
position: 354
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:31-354:-1:exon

N4222_RS20540
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 630
locus tag: N4222_RS20540
old locus tag: N4222_20540
inference: COORDINATES: similar to AA sequence:RefSeq:WP_000957083.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: MobC family plasmid mobilization relaxosome protein
translation: MLTMWVTEDEHRRLLERCEGKQLAAWMRQTCLDEKPARAGKLPSISPALLRQLAGMGNNLNQIARQVNAGGGSGHDRVQIVAALMAIDAGLERLRHAVLEKGADDDR
SIO_010081: N4222_RS20540
subclass of: SO_0000673
so part of: N4222_RS20540
location: complement(31..354)
location: region:31-354:-1
so has part: feature:31-354:-1:exon

WP_004193914.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:31-354:-1:exon

N4222_RS20545
type: Gene
subclass of: SO_0000704
RO_0002162: 630
locus tag: N4222_RS20545
old locus tag: N4222_20545
so part of: sequence
location: 993..1163
location: region:993-1163:1
so has part: feature:993-1163:1:exon
subclass of: SO_0000010

77330249
type: Gene
SIO_000068: ncbigene

position:993:1
position: 993
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:1163:1
position: 1163
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:993-1163:1:exon

N4222_RS20545
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 630
locus tag: N4222_RS20545
old locus tag: N4222_20545
inference: COORDINATES: similar to AA sequence:RefSeq:WP_005761324.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: hypothetical protein
translation: MHEPPVQSDYHARSGNYQLESNPERHDKSPVAVAIGNWVHGAEIVENAYRVLEVKA
SIO_010081: N4222_RS20545
subclass of: SO_0000673
so part of: N4222_RS20545
location: 993..1163
location: region:993-1163:1
so has part: feature:993-1163:1:exon

WP_004193911.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:993-1163:1:exon

N4222_RS20550
type: Gene
subclass of: SO_0000704
RO_0002162: 630
locus tag: N4222_RS20550
old locus tag: N4222_20550
so part of: sequence
location: complement(1372..1704)
location: region:1372-1704:-1
so has part: feature:1372-1704:-1:exon
subclass of: SO_0000010

77330250
type: Gene
SIO_000068: ncbigene

position:1372:-1
position: 1372
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:1704:-1
position: 1704
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:1372-1704:-1:exon

N4222_RS20550
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 630
locus tag: N4222_RS20550
old locus tag: N4222_20550
inference: COORDINATES: similar to AA sequence:RefSeq:WP_001070439.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: EmrE family multidrug efflux SMR transporter
translation: MNTYIFLGGAIVAEVIGTTFMKYSEGFTRLWPSVGTAISYCAAFYLLSQTLENIPTGIAYAIWSGAGIVLISLAGWLVSGQKLDWPAIAGMFLICVGVLVINIFSKSSAH
SIO_010081: N4222_RS20550
subclass of: SO_0000673
so part of: N4222_RS20550
location: complement(1372..1704)
location: region:1372-1704:-1
so has part: feature:1372-1704:-1:exon

WP_001099531.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:1372-1704:-1:exon

N4222_RS20555
type: Gene
subclass of: SO_0000704
RO_0002162: 630
locus tag: N4222_RS20555
old locus tag: N4222_20555
so part of: sequence
location: complement(1872..2087)
location: region:1872-2087:-1
so has part: feature:1872-2087:-1:exon
subclass of: SO_0000010

77330251
type: Gene
SIO_000068: ncbigene

position:1872:-1
position: 1872
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:2087:-1
position: 2087
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:1872-2087:-1:exon

N4222_RS20555
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 630
locus tag: N4222_RS20555
old locus tag: N4222_20555
inference: COORDINATES: similar to AA sequence:RefSeq:WP_000137421.1
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: MTELEKQLLSALEQLQQDYSKRLDEWENAFAEWRTMSGLIQRENAALNERVTVLSRQVQSLSEQLRRLSKG
SIO_010081: N4222_RS20555
subclass of: SO_0000673
so part of: N4222_RS20555
location: complement(1872..2087)
location: region:1872-2087:-1
so has part: feature:1872-2087:-1:exon

WP_024195375.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:1872-2087:-1:exon

N4222_RS20560
type: Gene
subclass of: SO_0000704
RO_0002162: 630
locus tag: N4222_RS20560
old locus tag: N4222_20560
so part of: sequence
location: complement(2091..2576)
location: region:2091-2576:-1
so has part: feature:2091-2576:-1:exon
subclass of: SO_0000010

77330252
type: Gene
SIO_000068: ncbigene

position:2091:-1
position: 2091
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:2576:-1
position: 2576
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:2091-2576:-1:exon

N4222_RS20560
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 630
locus tag: N4222_RS20560
old locus tag: N4222_20560
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: MNSLLTLAKDLEQKSKAQQQTTGEMLKAAFSEHEKSVRAELSESEKRISAAILDHDRKLSSAMSQRTKGMLRMVSQTWLTIVLVSALLIASSAGILWWQGQQILENYTTIREQKSTQAMLSERNSGVQLSTCGEQRRRCVRVNPEAGQFGEDSSWMILAGK
SIO_010081: N4222_RS20560
subclass of: SO_0000673
so part of: N4222_RS20560
location: complement(2091..2576)
location: region:2091-2576:-1
so has part: feature:2091-2576:-1:exon

WP_025367738.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:2091-2576:-1:exon

N4222_RS20565
type: Gene
subclass of: SO_0000704
RO_0002162: 630
locus tag: N4222_RS20565
old locus tag: N4222_20565
pseudo: true
so part of: sequence
location: complement(<2611..3045)
location: region:2611-3045:-1
so has part: feature:2611-3045:-1:exon
subclass of: SO_0000010

77330253
type: Gene
SIO_000068: ncbigene

position:2611:-1
position: 2611
reference: sequence
type: ReverseStrandPosition
type: FuzzyPosition

position:3045:-1
position: 3045
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:2611-3045:-1:exon

N4222_RS20565
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 630
locus tag: N4222_RS20565
old locus tag: N4222_20565
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_RS20565
subclass of: SO_0000673
so part of: N4222_RS20565
location: complement(<2611..3045)
location: region:2611-3045:-1
so has part: feature:2611-3045:-1:exon

urn:…
SIO_000300: 1
SIO_000628: feature:2611-3045:-1:exon