Yersinia rochesterensis strain ATCC BAA-2637 plasmid pUnnamed2.
type: Entry
definition: Yersinia rochesterensis strain ATCC BAA-2637 plasmid pUnnamed2.
sequence version: NZ_CP032484.1
sequence date: 2023-07-04
sequence: sequence
division: CON
label: NZ_CP032484.1
type: RefSeq
SIO_000068: refseq
dblink: PRJNA224116
dblink: SAMN09765716
keyword: RefSeq
source: Yersinia rochesterensis
organism: Yersinia rochesterensis
taxonomy: Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales; Yersiniaceae; Yersinia.
reference: 1
references: 33406034
reference: 2
references: 31135335
reference: 3
comment: REFSEQ INFORMATION: The reference sequence is identical to\nCP032484.1.\nGenome assembly not circularized.\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 Method :: SPAdes v. JAN-2014\nGenome Representation :: Full\nExpected Final Version :: Yes\nGenome Coverage :: 200.0x\nSequencing Technology :: Illumina MiSeq\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 04/28/2023 02:57:36\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) :: 4,024\nCDSs (total) :: 3,899\nGenes (coding) :: 3,821\nCDSs (with protein) :: 3,821\nGenes (RNA) :: 125\nrRNAs :: 8, 7, 7 (5S, 16S, 23S)\ncomplete rRNAs :: 8, 7, 7 (5S, 16S, 23S)\ntRNAs :: 80\nncRNAs :: 23\nPseudo Genes (total) :: 78\nCDSs (without protein) :: 78\nPseudo Genes (ambiguous residues) :: 0 of 78\nPseudo Genes (frameshifted) :: 31 of 78\nPseudo Genes (incomplete) :: 61 of 78\nPseudo Genes (internal stop) :: 17 of 78\nPseudo Genes (multiple problems) :: 25 of 78\nCRISPR Arrays :: 1\n##Genome-Annotation-Data-END##

sequence
subclass of: SO_0000155
sequence length: 4160
topology: circular
so has quality: SO_0000988
location: 1..4160
location: region:1-4160:1
RO_0002162: 1604335

NZ_CP032484
type: RefSeq
SIO_000068: refseq

PRJNA224116
type: BioProject
SIO_000068: bioproject

SAMN09765716
type: BioSample
SIO_000068: biosample

1
title: Yersinia occitanica is a later heterotypic synonym of Yersinia kristensenii subsp. rochesterensis and elevation of Yersinia kristensenii subsp. rochesterensis to species status
author: Nguyen, S.V.
author: Cunningham, S.A.
author: Jeraldo, P.
author: Tran, A.
author: Patel, R.
journal: Int J Syst Evol Microbiol 71 (2) (2021)
pubmed: 33406034

33406034
type: PubMed
SIO_000068: pubmed

2
title: Yersinia kristensenii subsp. rochesterensis subsp. nov., isolated from human feces
author: Cunningham, S.A.
author: Jeraldo, P.
author: Patel, R.
journal: Int J Syst Evol Microbiol
volume: 69
issue: 8
pages: 2292-2298
year: 2019
pubmed: 31135335

31135335
type: PubMed
SIO_000068: pubmed

3
title: Direct Submission
author: Cunningham, S.A.
author: Jeraldo, P.
author: Patel, R.
journal: Submitted (19-SEP-2018) Laboratory Medicine and Pathology, Division of Clinical Microbiology, Mayo Clinic, 200 First Street SW, Rochester, MN 55905, USA

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

position:4160:1
position: 4160
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

feature:1-4160:1:source
so part of: sequence
organism: Yersinia rochesterensis
mol type: genomic DNA
strain: ATCC BAA-2637
isolation source: feces
host: Homo sapiens
culture collection: ATCC:BAA-2637
type material: type strain of Yersinia kristensenii subsp. rochesterensis
plasmid: pUnnamed2
country: USA: Rochester, MN
lat lon: 44.1242 N 92.2746 W
collection date: 2011-01
collected by: Mayo Clinic

1604335
type: Taxonomy
SIO_000068: taxonomy

DXZ79_RS21090
type: Gene
subclass of: SO_0000704
RO_0002162: 1604335
locus tag: DXZ79_RS21090
pseudo: true
so part of: sequence
location: complement(<63..128)
location: region:63-128:-1
so has part: feature:63-128:-1:exon
subclass of: SO_0000010

82553204
type: Gene
SIO_000068: ncbigene

position:63:-1
position: 63
reference: sequence
type: ReverseStrandPosition
type: FuzzyPosition

position:128:-1
position: 128
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:63-128:-1:exon

DXZ79_RS21090
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 1604335
locus tag: DXZ79_RS21090
inference: COORDINATES: protein motif:HMM:NF016710.2
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: MbeB family mobilization protein
SIO_010081: DXZ79_RS21090
subclass of: SO_0000673
so part of: DXZ79_RS21090
location: complement(<63..128)
location: region:63-128:-1
so has part: feature:63-128:-1:exon

urn:…
SIO_000300: 1
SIO_000628: feature:63-128:-1:exon

DXZ79_RS21095
type: Gene
subclass of: SO_0000704
RO_0002162: 1604335
locus tag: DXZ79_RS21095
pseudo: true
so part of: sequence
location: complement(<163..597)
location: region:163-597:-1
so has part: feature:163-597:-1:exon
subclass of: SO_0000010

82553205
type: Gene
SIO_000068: ncbigene

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

position:597:-1
position: 597
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:163-597:-1:exon

DXZ79_RS21095
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 1604335
locus tag: DXZ79_RS21095
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: DXZ79_RS21095
subclass of: SO_0000673
so part of: DXZ79_RS21095
location: complement(<163..597)
location: region:163-597:-1
so has part: feature:163-597:-1:exon

urn:…
SIO_000300: 1
SIO_000628: feature:163-597:-1:exon

DXZ79_RS20595
type: Gene
subclass of: SO_0000704
RO_0002162: 1604335
locus tag: DXZ79_RS20595
old locus tag: DXZ79_20580
so part of: sequence
location: complement(806..1129)
location: region:806-1129:-1
so has part: feature:806-1129:-1:exon
subclass of: SO_0000010

82553120
type: Gene
SIO_000068: ncbigene

position:806:-1
position: 806
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:1129:-1
position: 1129
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:806-1129:-1:exon

DXZ79_RS20595
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 1604335
locus tag: DXZ79_RS20595
old locus tag: DXZ79_20580
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: MLTMWVTEDEHRRLLERCDGKQLAAWMRQTCLDEKPARAGKLPSISPALLRQLAGMGNNLNQIARQVNAGGGSGHDRVQVVAALMAIDAGLERLRHAVLEKGADDDR
SIO_010081: DXZ79_RS20595
subclass of: SO_0000673
so part of: DXZ79_RS20595
location: complement(806..1129)
location: region:806-1129:-1
so has part: feature:806-1129:-1:exon

WP_001445156.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:806-1129:-1:exon

DXZ79_RS20610
type: Gene
subclass of: SO_0000704
RO_0002162: 1604335
locus tag: DXZ79_RS20610
old locus tag: DXZ79_20595
so part of: sequence
location: complement(2201..2566)
location: region:2201-2566:-1
so has part: feature:2201-2566:-1:exon
subclass of: SO_0000010

82553121
type: Gene
SIO_000068: ncbigene

position:2201:-1
position: 2201
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:2566:-1
position: 2566
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:2201-2566:-1:exon

DXZ79_RS20610
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 1604335
locus tag: DXZ79_RS20610
old locus tag: DXZ79_20595
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: MKHLIKMRSAYTAFFLLTSYAASAEVISGPFKDKAECAAFATLAGYDNRISSAQKWGMYESSLRSFDEMRPNLRGTVRFISEYNYEMNVAAIRATDMVIAIKGKRESAAVKLWNQNACSSK
SIO_010081: DXZ79_RS20610
subclass of: SO_0000673
so part of: DXZ79_RS20610
location: complement(2201..2566)
location: region:2201-2566:-1
so has part: feature:2201-2566:-1:exon

WP_120011661.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:2201-2566:-1:exon

DXZ79_RS20615
type: Gene
subclass of: SO_0000704
RO_0002162: 1604335
locus tag: DXZ79_RS20615
old locus tag: DXZ79_20600
so part of: sequence
location: complement(2803..3327)
location: region:2803-3327:-1
so has part: feature:2803-3327:-1:exon
subclass of: SO_0000010

82553122
type: Gene
SIO_000068: ncbigene

position:2803:-1
position: 2803
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:3327:-1
position: 3327
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:2803-3327:-1:exon

DXZ79_RS20615
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 1604335
locus tag: DXZ79_RS20615
old locus tag: DXZ79_20600
inference: COORDINATES: similar to AA sequence:RefSeq:WP_016246513.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: hypothetical protein
translation: MKCSWACSVVLALSFTVAAAEKNDNVTSTKPSSERDLYLTCKGYQVKGASVINVEKPSYLEGTGEQVEFAIIAPTSGTTDGLKVFFDSWGFSSFGLIESHVMHESWSLVHVGGRASVKGDKIDYSFFDNQPQDGVSYKPKTRVFLYSCLNSDKRPSWVERIYTRTGIFRGRVED
SIO_010081: DXZ79_RS20615
subclass of: SO_0000673
so part of: DXZ79_RS20615
location: complement(2803..3327)
location: region:2803-3327:-1
so has part: feature:2803-3327:-1:exon

WP_120011662.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:2803-3327:-1:exon

DXZ79_RS20765
type: Gene
subclass of: SO_0000704
RO_0002162: 1604335
locus tag: DXZ79_RS20765
so part of: sequence
location: complement(3475..3684)
location: region:3475-3684:-1
so has part: feature:3475-3684:-1:exon
subclass of: SO_0000010

82553145
type: Gene
SIO_000068: ncbigene

position:3475:-1
position: 3475
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:3684:-1
position: 3684
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:3475-3684:-1:exon

DXZ79_RS20765
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 1604335
locus tag: DXZ79_RS20765
inference: COORDINATES: similar to AA sequence:RefSeq:WP_014538403.1
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: MTELEKQLLSALEQLQQDYSKRLDEWENAFAEWRTMSGLMQRENAALSEHVTDLSRQVQSLSEQLRRLS
SIO_010081: DXZ79_RS20765
subclass of: SO_0000673
so part of: DXZ79_RS20765
location: complement(3475..3684)
location: region:3475-3684:-1
so has part: feature:3475-3684:-1:exon

WP_162928793.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:3475-3684:-1:exon

DXZ79_RS20770
type: Gene
subclass of: SO_0000704
RO_0002162: 1604335
locus tag: DXZ79_RS20770
so part of: sequence
location: complement(3691..>4060)
location: region:3691-4060:-1
so has part: feature:3691-4060:-1:exon
subclass of: SO_0000010

82553146
type: Gene
SIO_000068: ncbigene

position:3691:-1
position: 3691
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:4060:-1
position: 4060
reference: sequence
type: ReverseStrandPosition
type: FuzzyPosition

urn:…
SIO_000300: 1
SIO_000628: feature:3691-4060:-1:exon

DXZ79_RS20770
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 1604335
locus tag: DXZ79_RS20770
inference: COORDINATES: similar to AA sequence:RefSeq:WP_001086853.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 2
transl table: 11
product: mobilization protein
translation: SAKRISAAMLDHDRTLSSAMSQRTKGMVRMVSQTWLTIVLVSVLLTASGAGILWWQGQQILDNYMSIREQQDALEKLNVKTWGVSFQSDSNGQFLVLPKGVKAETSWTVENGKRNAVKLVRE
SIO_010081: DXZ79_RS20770
subclass of: SO_0000673
so part of: DXZ79_RS20770
location: complement(3691..>4060)
location: region:3691-4060:-1
so has part: feature:3691-4060:-1:exon

WP_244942329.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:3691-4060:-1:exon