Yersinia rochesterensis strain ATCC BAA-2637 plasmid pUnnamed1.
type: Entry
definition: Yersinia rochesterensis strain ATCC BAA-2637 plasmid pUnnamed1.
sequence version: NZ_CP032483.1
sequence date: 2023-07-04
sequence: sequence
division: CON
label: NZ_CP032483.1
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\nCP032483.1.\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: 6670
topology: circular
so has quality: SO_0000988
location: 1..6670
location: region:1-6670:1
RO_0002162: 1604335

NZ_CP032483
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:6670:1
position: 6670
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

feature:1-6670:1: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: pUnnamed1
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_RS21085
type: Gene
subclass of: SO_0000704
RO_0002162: 1604335
locus tag: DXZ79_RS21085
pseudo: true
so part of: sequence
location: complement(<551..961)
location: region:551-961:-1
so has part: feature:551-961:-1:exon
subclass of: SO_0000010

82553203
type: Gene
SIO_000068: ncbigene

position:551:-1
position: 551
reference: sequence
type: ReverseStrandPosition
type: FuzzyPosition

position:961:-1
position: 961
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:551-961:-1:exon

DXZ79_RS21085
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 1604335
locus tag: DXZ79_RS21085
inference: COORDINATES: protein motif:HMM:NF013890.2
GO function: GO:0052689 - carboxylic ester hydrolase activity [Evidence IEA]
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: lipase family protein
SIO_010081: DXZ79_RS21085
subclass of: SO_0000673
so part of: DXZ79_RS21085
location: complement(<551..961)
location: region:551-961:-1
so has part: feature:551-961:-1:exon

urn:…
SIO_000300: 1
SIO_000628: feature:551-961:-1:exon

DXZ79_RS20560
type: Gene
subclass of: SO_0000704
RO_0002162: 1604335
locus tag: DXZ79_RS20560
old locus tag: DXZ79_20545
so part of: sequence
location: 2109..2282
location: region:2109-2282:1
so has part: feature:2109-2282:1:exon
subclass of: SO_0000010

82553116
type: Gene
SIO_000068: ncbigene

position:2109:1
position: 2109
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:2282:1
position: 2282
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:2109-2282:1:exon

DXZ79_RS20560
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 1604335
locus tag: DXZ79_RS20560
old locus tag: DXZ79_20545
inference: COORDINATES: similar to AA sequence:RefSeq:WP_002353195.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: ribbon-helix-helix domain-containing protein
translation: MAEPFLKNRTRFTSSLDNKLIQPFNELSKDTRIPKSRLLDEAIADLLKKHGSSKNTQ
SIO_010081: DXZ79_RS20560
subclass of: SO_0000673
so part of: DXZ79_RS20560
location: 2109..2282
location: region:2109-2282:1
so has part: feature:2109-2282:1:exon

WP_120011656.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:2109-2282:1:exon

DXZ79_RS20570
type: Gene
subclass of: SO_0000704
RO_0002162: 1604335
locus tag: DXZ79_RS20570
old locus tag: DXZ79_20555
so part of: sequence
location: 4299..4757
location: region:4299-4757:1
so has part: feature:4299-4757:1:exon
subclass of: SO_0000010

82553117
type: Gene
SIO_000068: ncbigene

position:4299:1
position: 4299
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:4757:1
position: 4757
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:4299-4757:1:exon

DXZ79_RS20570
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 1604335
locus tag: DXZ79_RS20570
old locus tag: DXZ79_20555
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: MAENLNLSDSAKAVGLSRKTLYTHIKEGKVSVTRYEGKRCIAVSELLRVYGNIDISAIQRVNTRLQPEKATSLRKKDTEVILSRLQEIQEDNNILRKEMQLLRETTQQLLTDQEQRRKEAENAVATRKENEALLLELENLKKRGWWRRILGR
SIO_010081: DXZ79_RS20570
subclass of: SO_0000673
so part of: DXZ79_RS20570
location: 4299..4757
location: region:4299-4757:1
so has part: feature:4299-4757:1:exon

WP_120011658.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:4299-4757:1:exon

DXZ79_RS20580
type: Gene
subclass of: SO_0000704
RO_0002162: 1604335
locus tag: DXZ79_RS20580
old locus tag: DXZ79_20565
so part of: sequence
location: complement(5578..6354)
location: region:5578-6354:-1
so has part: feature:5578-6354:-1:exon
subclass of: SO_0000010

82553118
type: Gene
SIO_000068: ncbigene

position:5578:-1
position: 5578
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:6354:-1
position: 6354
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:5578-6354:-1:exon

DXZ79_RS20580
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 1604335
locus tag: DXZ79_RS20580
old locus tag: DXZ79_20565
inference: COORDINATES: similar to AA sequence:RefSeq:WP_001010176.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: hypothetical protein
translation: MNFLSKTAVVVSAVTLLFGCDNRPDKTLSPPTGAKWVDVTFRVPEGITLQPAELLYRSSQCKSVRYNSSNEPHDVPGYNDIEQPFGASDGDNVRRLRVAVDGGGPCQWELNSLMVSFRIADDVPLVKGKEVIDTSYIFDFGDYGLSDGYGTGRARAFSGEILELETDFFPMTYISHMLNKTTLKLFGGDTNSEKWSRRYQLKSTEFIIIEPMFHAKKNVSIEADKKRGVGMVVTYPGGDEEHVRNVNPDYQRLLLLLK
SIO_010081: DXZ79_RS20580
subclass of: SO_0000673
so part of: DXZ79_RS20580
location: complement(5578..6354)
location: region:5578-6354:-1
so has part: feature:5578-6354:-1:exon

WP_120011659.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:5578-6354:-1:exon

DXZ79_RS20585
type: Gene
subclass of: SO_0000704
RO_0002162: 1604335
locus tag: DXZ79_RS20585
old locus tag: DXZ79_20570
pseudo: true
so part of: sequence
location: complement(6338..>6570)
location: region:6338-6570:-1
so has part: feature:6338-6570:-1:exon
subclass of: SO_0000010

82553119
type: Gene
SIO_000068: ncbigene

position:6338:-1
position: 6338
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:6570:-1
position: 6570
reference: sequence
type: ReverseStrandPosition
type: FuzzyPosition

urn:…
SIO_000300: 1
SIO_000628: feature:6338-6570:-1:exon

DXZ79_RS20585
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 1604335
locus tag: DXZ79_RS20585
old locus tag: DXZ79_20570
inference: COORDINATES: similar to AA sequence:RefSeq:WP_016536385.1
note: incomplete; too short partial abutting assembly gap; missing N-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
pseudo: true
codon start: 3
transl table: 11
product: lipase family protein
SIO_010081: DXZ79_RS20585
subclass of: SO_0000673
so part of: DXZ79_RS20585
location: complement(6338..>6570)
location: region:6338-6570:-1
so has part: feature:6338-6570:-1:exon

urn:…
SIO_000300: 1
SIO_000628: feature:6338-6570:-1:exon