Yersinia pestis A1122 plasmid unnamed2, complete sequence.
type: Entry
definition: Yersinia pestis A1122 plasmid unnamed2, complete sequence.
sequence version: NC_017170.1
sequence date: 2023-04-07
sequence: sequence
division: CON
label: NC_017170.1
type: RefSeq
SIO_000068: refseq
dblink: PRJNA224116
dblink: SAMN02603531
keyword: RefSeq
source: Yersinia pestis A1122
organism: Yersinia pestis A1122
taxonomy: Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales; Yersiniaceae; Yersinia.
reference: 1
reference: 2
comment: REFSEQ INFORMATION: The reference sequence is identical to\nCP002958.1.\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-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 04/07/2023 01:20:55\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) :: 4,234\nCDSs (total) :: 4,138\nGenes (coding) :: 3,973\nCDSs (with protein) :: 3,973\nGenes (RNA) :: 96\nrRNAs :: 6, 6, 6 (5S, 16S, 23S)\ncomplete rRNAs :: 6, 6, 6 (5S, 16S, 23S)\ntRNAs :: 68\nncRNAs :: 10\nPseudo Genes (total) :: 165\nCDSs (without protein) :: 165\nPseudo Genes (ambiguous residues) :: 0 of 165\nPseudo Genes (frameshifted) :: 72 of 165\nPseudo Genes (incomplete) :: 108 of 165\nPseudo Genes (internal stop) :: 24 of 165\nPseudo Genes (multiple problems) :: 31 of 165\nCRISPR Arrays :: 3\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.

sequence
subclass of: SO_0000155
sequence length: 8431
topology: circular
so has quality: SO_0000988
location: 1..8431
location: region:1-8431:1
RO_0002162: 1035377

NC_017170
type: RefSeq
SIO_000068: refseq

PRJNA224116
type: BioProject
SIO_000068: bioproject

SAMN02603531
type: BioSample
SIO_000068: biosample

1
title: Finished sequence of Yersinia pestis A1122
author: Doggett, N.
author: Munk, A.C.
author: Bruce, D.C.
author: Detter, J.C.
author: Johnson, S.L.
author: Han, C.
journal: Unpublished

2
title: Direct Submission
author: Doggett, N.
author: Munk, A.C.
author: Bruce, D.C.
author: Detter, J.C.
author: Johnson, S.L.
author: Han, C.
journal: Submitted (14-JUL-2011) Genome Sciences Group, Los Alamos National Laboratory, P.O. Box 1663, Los Alamos, NM 87545, USA

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

position:8431:1
position: 8431
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

feature:1-8431:1:source
so part of: sequence
organism: Yersinia pestis A1122
mol type: genomic DNA
strain: A1122
plasmid: unnamed2

1035377
type: Taxonomy
SIO_000068: taxonomy

A1122_RS21705
type: Gene
subclass of: SO_0000704
RO_0002162: 1035377
locus tag: A1122_RS21705
old locus tag: A1122_21762
so part of: sequence
location: 253..648
location: region:253-648:1
so has part: feature:253-648:1:exon
subclass of: SO_0000010

57977663
type: Gene
SIO_000068: ncbigene

position:253:1
position: 253
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:648:1
position: 648
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:253-648:1:exon

A1122_RS21705
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 1035377
locus tag: A1122_RS21705
old locus tag: A1122_21762
inference: COORDINATES: similar to AA sequence:RefSeq:WP_002218512.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: pesticin immunity protein
translation: MFLSSSGLAEKNTYTAKDILQNLELNTFGNSLSHGIYGKQTTFKQTEFTNIKSNTKKHIALINKDNSWMISLKILGIKRDEYTVCFEDFSLIRPPTYVAIHPLLIKKVKSGNFIVVKEIKKSIPGCTVYYH
SIO_010081: A1122_RS21705
subclass of: SO_0000673
so part of: A1122_RS21705
location: 253..648
location: region:253-648:1
so has part: feature:253-648:1:exon

WP_223661135.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:253-648:1:exon

A1122_RS21710
type: Gene
subclass of: SO_0000704
RO_0002162: 1035377
gene: pst
locus tag: A1122_RS21710
old locus tag: A1122_21767
so part of: sequence
location: complement(683..1756)
location: region:683-1756:-1
so has part: feature:683-1756:-1:exon
subclass of: SO_0000010

57977664
type: Gene
SIO_000068: ncbigene

position:683:-1
position: 683
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:1756:-1
position: 1756
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:683-1756:-1:exon

A1122_RS21710
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 1035377
gene: pst
locus tag: A1122_RS21710
old locus tag: A1122_21767
EC number: 3.2.1.17
inference: COORDINATES: similar to AA sequence:RefSeq:WP_001285181.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: pesticin
translation: MSDTMVVNGSGGVPAFLFSGSTLSSYRPNFEANSITIALPHYVDLPGRSNFKLMYIMGFPIDTEMEKDSEYSNKIRQESKISKTEGTVSYEQKITVETGQEKDGVKVYRVMVLEGTIAESIEHLDKKENEDILNNNRNRIVLADNTVINFDNISQLKEFLRRSVNIVDHDIFSSNGFEGFNPTSHFPSNPSSDYFNSTGVTFGSGVDLGQRSKQDLLNDGVPQYIADRLDGYYMLRGKEAYDKVRTAPLTLSDNEAHLLSNIYIDKFSHKIEGLFNDANIGLRFSDLPLRTRTALVSIGYQKGFKLSRTAPTVWNKVIAKDWNGLVNAFNNIVDGMSDRRKREGALVQKDIDSGLLK
SIO_010081: A1122_RS21710
subclass of: SO_0000673
so part of: A1122_RS21710
location: complement(683..1756)
location: region:683-1756:-1
so has part: feature:683-1756:-1:exon

WP_002218509.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:683-1756:-1:exon

A1122_RS21715
type: Gene
subclass of: SO_0000704
RO_0002162: 1035377
locus tag: A1122_RS21715
old locus tag: A1122_21772
so part of: sequence
location: 1985..2290
location: region:1985-2290:1
so has part: feature:1985-2290:1:exon
subclass of: SO_0000010

57977665
type: Gene
SIO_000068: ncbigene

position:1985:1
position: 1985
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:2290:1
position: 2290
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:1985-2290:1:exon

A1122_RS21715
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 1035377
locus tag: A1122_RS21715
old locus tag: A1122_21772
inference: COORDINATES: similar to AA sequence:RefSeq:WP_002221218.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: hypothetical protein
translation: MSKTKSGRHRLSKTDKRLLAALVVAGYEERTARDLIQKHVYTLTQADLRHLVSEISNGVGQSQAYDAIYQARRIRLARKYLSGKKPEGVEPREGQEREDLP
SIO_010081: A1122_RS21715
subclass of: SO_0000673
so part of: A1122_RS21715
location: 1985..2290
location: region:1985-2290:1
so has part: feature:1985-2290:1:exon

WP_002221218.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:1985-2290:1:exon

A1122_RS21720
type: Gene
subclass of: SO_0000704
RO_0002162: 1035377
gene: pla
locus tag: A1122_RS21720
old locus tag: A1122_21777
so part of: sequence
location: 2533..3471
location: region:2533-3471:1
so has part: feature:2533-3471:1:exon
subclass of: SO_0000010

57977666
type: Gene
SIO_000068: ncbigene

position:2533:1
position: 2533
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:3471:1
position: 3471
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:2533-3471:1:exon

A1122_RS21720
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 1035377
gene: pla
locus tag: A1122_RS21720
old locus tag: A1122_21777
inference: COORDINATES: similar to AA sequence:RefSeq:WP_002231174.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: omptin family plasminogen activator Pla
translation: MKKSSIVATIITILSGSANAASSQLIPNISPDSFTVAASTGMLSGKSHEMLYDAETGRKISQLDWKIKNVAILKGDISWDPYSFLTLNARGWTSLASGSGNMDDYDWMNENQSEWTDHSSHPATNVNHANEYDLNVKGWLLQDENYKAGITAGYQETRFSWTATGGSYSYNNGAYTGNFPKGVRVIGYNQRFSMPYIGLAGQYRINDFELNALFKFSDWVRAHDNDEHYMRDLTFREKTSGSRYYGTVINAGYYVTPNAKVFAEFTYSKYDEGKGGTQTIDKNSGDSVSIGGDAAGISNKNYTVTAGLQYRF
SIO_010081: A1122_RS21720
subclass of: SO_0000673
so part of: A1122_RS21720
location: 2533..3471
location: region:2533-3471:1
so has part: feature:2533-3471:1:exon

WP_002218234.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:2533-3471:1:exon

A1122_RS21725
type: Gene
subclass of: SO_0000704
RO_0002162: 1035377
locus tag: A1122_RS21725
old locus tag: A1122_21782
so part of: sequence
location: complement(3658..3957)
location: region:3658-3957:-1
so has part: feature:3658-3957:-1:exon
subclass of: SO_0000010

57977667
type: Gene
SIO_000068: ncbigene

position:3658:-1
position: 3658
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:3957:-1
position: 3957
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:3658-3957:-1:exon

A1122_RS21725
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 1035377
locus tag: A1122_RS21725
old locus tag: A1122_21782
inference: COORDINATES: similar to AA sequence:RefSeq:WP_002218230.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: XRE family transcriptional regulator
translation: MRTLDEVIASRSPESQTRIKEMADEMILEVGLQMMREELQLSQKQVAEAMGISQPAVTKLEQRGNDLKLATLKRYVEAMGGKLSLDVELPTGRRVAFHV
SIO_010081: A1122_RS21725
subclass of: SO_0000673
so part of: A1122_RS21725
location: complement(3658..3957)
location: region:3658-3957:-1
so has part: feature:3658-3957:-1:exon

WP_002213446.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:3658-3957:-1:exon

A1122_RS21730
type: Gene
subclass of: SO_0000704
RO_0002162: 1035377
locus tag: A1122_RS21730
old locus tag: A1122_21787
so part of: sequence
location: complement(3957..4298)
location: region:3957-4298:-1
so has part: feature:3957-4298:-1:exon
subclass of: SO_0000010

57977668
type: Gene
SIO_000068: ncbigene

position:4298:-1
position: 4298
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:3957-4298:-1:exon

A1122_RS21730
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 1035377
locus tag: A1122_RS21730
old locus tag: A1122_21787
inference: COORDINATES: similar to AA sequence:RefSeq:WP_002225538.1
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: MVLFSQRFDDWLNEQEDALQEKVLADLKKLQVYGPELPRPYADTVKGSRYKNMKELRVQFSGRPIRAFYAFDPIRRAIVLCAGDKSNDKRFYEKLVRIAEDEFTAHLNTLESK
SIO_010081: A1122_RS21730
subclass of: SO_0000673
so part of: A1122_RS21730
location: complement(3957..4298)
location: region:3957-4298:-1
so has part: feature:3957-4298:-1:exon

WP_002225538.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:3957-4298:-1:exon

A1122_RS21740
type: Gene
subclass of: SO_0000704
RO_0002162: 1035377
gene: istA
locus tag: A1122_RS21740
old locus tag: A1122_21802
so part of: sequence
location: 5567..6589
location: region:5567-6589:1
so has part: feature:5567-6589:1:exon
subclass of: SO_0000010

57977669
type: Gene
SIO_000068: ncbigene

position:5567:1
position: 5567
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:6589:1
position: 6589
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:5567-6589:1:exon

A1122_RS21740
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 1035377
gene: istA
locus tag: A1122_RS21740
old locus tag: A1122_21802
inference: COORDINATES: similar to AA sequence:RefSeq:WP_000627495.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: IS21-like element IS100 family transposase
translation: MVTFETVMEIKILHKQGMSSRAIARELGISRNTVKRYLQAKSEPPKYTPRPAVASLLDEYRDYIRQRIADAHPYKIPATVIAREIRDQGYRGGMTILRAFIRSLSVPQEQEPAVRFETEPGRQMQVDWGTMRNGRSPLHVFVAVLGYSRMLYIEFTDNMRYDTLETCHRNAFRFFGGVPREVLYDNMKTVVLQRDAYQTGQHRFHPSLWQFGKEMGFSPRLCRPFRAQTKGKVERMVQYTRNSFYIPLMTRLRPMGITVDVETANRHGLRWLHDVANQRKHETIQARPCDRWLEEQQSMLALPPEKKEYDVHLDENLVNFDKHPLHHPLSIYDSFCRGVA
SIO_010081: A1122_RS21740
subclass of: SO_0000673
so part of: A1122_RS21740
location: 5567..6589
location: region:5567-6589:1
so has part: feature:5567-6589:1:exon

WP_000255944.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:5567-6589:1:exon

A1122_RS21745
type: Gene
subclass of: SO_0000704
RO_0002162: 1035377
gene: istB
locus tag: A1122_RS21745
old locus tag: A1122_21807
so part of: sequence
location: 6586..7368
location: region:6586-7368:1
so has part: feature:6586-7368:1:exon
subclass of: SO_0000010

57977670
type: Gene
SIO_000068: ncbigene

position:6586:1
position: 6586
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:7368:1
position: 7368
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:6586-7368:1:exon

A1122_RS21745
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 1035377
gene: istB
locus tag: A1122_RS21745
old locus tag: A1122_21807
inference: COORDINATES: similar to AA sequence:RefSeq:NP_858162.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: IS21-like element IS100kyp family helper ATPase IstB
translation: MMMELQHQRLMALAGQLQLESLISAAPALSQQAVDQEWSYMDFLEHLLHEEKLARHQRKQAMYTRMAAFPAVKTFEEYDFTFATGAPQKQLQSLRSLSFIERNENIVLLGPSGVGKTHLAIAMGYEAVRAGIKVRFTTAADLLLQLSTAQRQGRYKTTLQRGVMAPRLLIIDEIGYLPFSQEEAKLFFQVIAKRYEKSAMILTSNLPFGQWDQTFAGDAALTSAMLDRILHHSHVVQIKGESYRLRQKRKAGVIAEANPE
SIO_010081: A1122_RS21745
subclass of: SO_0000673
so part of: A1122_RS21745
location: 6586..7368
location: region:6586-7368:1
so has part: feature:6586-7368:1:exon

WP_001317493.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:6586-7368:1:exon