Pectobacterium parvum strain FN20211 plasmid unnamed2, complete sequence.
type: Entry
definition: Pectobacterium parvum strain FN20211 plasmid unnamed2, complete sequence.
sequence version: NZ_CP087394.1
sequence date: 2023-06-02
sequence: sequence
division: CON
label: NZ_CP087394.1
type: RefSeq
SIO_000068: refseq
dblink: PRJNA224116
dblink: SAMN23227730
keyword: RefSeq
source: Pectobacterium parvum
organism: Pectobacterium parvum
taxonomy: Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales; Pectobacteriaceae; Pectobacterium.
reference: 1
references: 35491949
reference: 2
comment: REFSEQ INFORMATION: The reference sequence is identical to\nCP087394.1.\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 :: 15-NOV-2021\nAssembly Method :: HGAP v. OCT-2020\nGenome Representation :: Full\nExpected Final Version :: Yes\nGenome Coverage :: 750.0x\nSequencing Technology :: Illumina NovaSeq; Oxford Nanopore\n PromethION\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 06/02/2023 00:23:34\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) :: 4,271\nCDSs (total) :: 4,166\nGenes (coding) :: 4,002\nCDSs (with protein) :: 4,002\nGenes (RNA) :: 105\nrRNAs :: 8, 7, 7 (5S, 16S, 23S)\ncomplete rRNAs :: 8, 7, 7 (5S, 16S, 23S)\ntRNAs :: 77\nncRNAs :: 6\nPseudo Genes (total) :: 164\nCDSs (without protein) :: 164\nPseudo Genes (ambiguous residues) :: 0 of 164\nPseudo Genes (frameshifted) :: 75 of 164\nPseudo Genes (incomplete) :: 106 of 164\nPseudo Genes (internal stop) :: 51 of 164\nPseudo Genes (multiple problems) :: 60 of 164\nCRISPR Arrays :: 1\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.

sequence
subclass of: SO_0000155
sequence length: 5731
topology: circular
so has quality: SO_0000988
location: 1..5731
location: region:1-5731:1
RO_0002162: 2778550

NZ_CP087394
type: RefSeq
SIO_000068: refseq

PRJNA224116
type: BioProject
SIO_000068: bioproject

SAMN23227730
type: BioSample
SIO_000068: biosample

1
title: High-Quality Complete Genome Resource of Pectobacterium parvum Isolate FN20211 Causing Aerial Stem Rot of Potato
author: Wang, J.
author: Han, W.
author: Pirhonen, M.
author: Pan, Y.
author: Zhang, D.
author: Zhao, D.
author: Li, Q.
author: Cheng, J.
author: Yang, Z.
author: Zhu, J.
journal: Mol Plant Microbe Interact
volume: 35
issue: 6
pages: 488-491
year: 2022
pubmed: 35491949

35491949
type: PubMed
SIO_000068: pubmed

2
title: Direct Submission
author: Wang, J.
journal: Submitted (17-NOV-2021) Plant Pathology, Hebei Agricultural University, Lekai South Street 2596, Baoding, Hebei 071001, China

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

position:5731:1
position: 5731
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

feature:1-5731:1:source
so part of: sequence
organism: Pectobacterium parvum
mol type: genomic DNA
strain: FN20211
isolation source: potato plant
host: Solanum tuberosum
plasmid: unnamed2
country: China:Fengning
lat lon: 41.12 N 116.38 E
collection date: 2020-07

2778550
type: Taxonomy
SIO_000068: taxonomy

LOZ86_RS21280
type: Gene
subclass of: SO_0000704
RO_0002162: 2778550
locus tag: LOZ86_RS21280
old locus tag: LOZ86_21280
so part of: sequence
location: 1..204
location: region:1-204:1
so has part: feature:1-204:1:exon
subclass of: SO_0000010

position:204:1
position: 204
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:1-204:1:exon

LOZ86_RS21280
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 2778550
locus tag: LOZ86_RS21280
old locus tag: LOZ86_21280
inference: COORDINATES: similar to AA sequence:RefSeq:WP_000427298.1
GO function: GO:0003676 - nucleic acid binding [Evidence IEA]
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: cold shock domain-containing protein
translation: MDHGFVNFFDSVKGYGFIRREQGRDVMFRSDDIPNENYTVDIPKGTKVQFNTVKTAKGLKAIDILFI
SIO_010081: LOZ86_RS21280
subclass of: SO_0000673
so part of: LOZ86_RS21280
location: 1..204
location: region:1-204:1
so has part: feature:1-204:1:exon

WP_224452644.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:1-204:1:exon

LOZ86_RS21285
type: Gene
subclass of: SO_0000704
RO_0002162: 2778550
locus tag: LOZ86_RS21285
old locus tag: LOZ86_21285
so part of: sequence
location: complement(193..1083)
location: region:193-1083:-1
so has part: feature:193-1083:-1:exon
subclass of: SO_0000010

position:193:-1
position: 193
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:1083:-1
position: 1083
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:193-1083:-1:exon

LOZ86_RS21285
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 2778550
locus tag: LOZ86_RS21285
old locus tag: LOZ86_21285
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: MTNPALDLFNDRLPNKPYFSDDLHFGVRIAGKERAILAKYIQFNQPHAMFWLGFDVDRLGAAIDWSDRNAPAPTLTITNPENGHAHLLYALKTSIRTAPDGKMKPLKYAAAVENALRKKLDADVGYSGLICKNPNHGYWKIAVWQPELYTLDWLADSLDLNAANDKEIVTDYGLGRNCTLFDKTRKWAYRAIRQGWPEYEQWLQACYERAIAYNLQFPFPLDESEVKGISNSIAKWTIKNFSEYSFDDFVKKTHAPEIQSLRGKKSKGGGRPSLGEPWIIMCVSRRTYFRMKSSDK
SIO_010081: LOZ86_RS21285
subclass of: SO_0000673
so part of: LOZ86_RS21285
location: complement(193..1083)
location: region:193-1083:-1
so has part: feature:193-1083:-1:exon

WP_230243184.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:193-1083:-1:exon

LOZ86_RS21290
type: Gene
subclass of: SO_0000704
RO_0002162: 2778550
gene: nadS
locus tag: LOZ86_RS21290
old locus tag: LOZ86_21290
so part of: sequence
location: complement(1278..1562)
location: region:1278-1562:-1
so has part: feature:1278-1562:-1:exon
subclass of: SO_0000010

position:1278:-1
position: 1278
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:1562:-1
position: 1562
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:1278-1562:-1:exon

LOZ86_RS21290
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 2778550
gene: nadS
locus tag: LOZ86_RS21290
old locus tag: LOZ86_21290
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: MSFFDELKASLEEAVEIKHGVKAPARVTRYELADVKALRAQLNVTQDEMAKVLGTSLDTIKSWETGRRNPTGLAAKVLATIQANPKFFQELASH
SIO_010081: LOZ86_RS21290
subclass of: SO_0000673
so part of: LOZ86_RS21290
location: complement(1278..1562)
location: region:1278-1562:-1
so has part: feature:1278-1562:-1:exon

WP_015060318.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:1278-1562:-1:exon

LOZ86_RS21295
type: Gene
subclass of: SO_0000704
RO_0002162: 2778550
locus tag: LOZ86_RS21295
old locus tag: LOZ86_21295
so part of: sequence
location: complement(1564..1896)
location: region:1564-1896:-1
so has part: feature:1564-1896:-1:exon
subclass of: SO_0000010

position:1564:-1
position: 1564
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:1896:-1
position: 1896
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:1564-1896:-1:exon

LOZ86_RS21295
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 2778550
locus tag: LOZ86_RS21295
old locus tag: LOZ86_21295
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: MSHAIEFIETPMFTRQIKQIATDDELKELQKLLIESPDKGDLIRQTGGLRKIRMATGTQGKSGSARVIYFLATEEIIYLVMAYPKSTKDSLTDAEKSDLKKLTKLLKDEV
SIO_010081: LOZ86_RS21295
subclass of: SO_0000673
so part of: LOZ86_RS21295
location: complement(1564..1896)
location: region:1564-1896:-1
so has part: feature:1564-1896:-1:exon

WP_116362726.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:1564-1896:-1:exon

LOZ86_RS21300
type: Gene
subclass of: SO_0000704
RO_0002162: 2778550
locus tag: LOZ86_RS21300
old locus tag: LOZ86_21300
so part of: sequence
location: complement(2044..2280)
location: region:2044-2280:-1
so has part: feature:2044-2280:-1:exon
subclass of: SO_0000010

position:2044:-1
position: 2044
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:2280:-1
position: 2280
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:2044-2280:-1:exon

LOZ86_RS21300
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 2778550
locus tag: LOZ86_RS21300
old locus tag: LOZ86_21300
inference: COORDINATES: similar to AA sequence:RefSeq:WP_006674368.1
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: MTEMEKQLLSALESLQASYEQQHQAWQESYSSLQHMFETTSQALSRSDRACQHLSNQVNSLRGQVESLSDNLSRLMRS
SIO_010081: LOZ86_RS21300
subclass of: SO_0000673
so part of: LOZ86_RS21300
location: complement(2044..2280)
location: region:2044-2280:-1
so has part: feature:2044-2280:-1:exon

WP_147306335.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:2044-2280:-1:exon

LOZ86_RS21305
type: Gene
subclass of: SO_0000704
RO_0002162: 2778550
locus tag: LOZ86_RS21305
old locus tag: LOZ86_21305
so part of: sequence
location: complement(2341..2826)
location: region:2341-2826:-1
so has part: feature:2341-2826:-1:exon
subclass of: SO_0000010

position:2341:-1
position: 2341
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:2826:-1
position: 2826
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:2341-2826:-1:exon

LOZ86_RS21305
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 2778550
locus tag: LOZ86_RS21305
old locus tag: LOZ86_21305
function: plasmid mobilisation
inference: COORDINATES: similar to AA sequence:RefSeq:WP_006674366.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: MbeB family mobilization protein
translation: MSEILNLAKGFEEKSKQQAQDTEQSVKREFGRLETSISAELQSSSQSISNAIREQNGRLTGMIRATVTTALIWIVVCAALLIGILSGIIWLQGQIISSRLSDIDGYSQQLASLKAKSGAGVTIYSDDSQKNGYLVVLPVKAHGVESYTSTAGNTVVKYTAK
SIO_010081: LOZ86_RS21305
subclass of: SO_0000673
so part of: LOZ86_RS21305
location: complement(2341..2826)
location: region:2341-2826:-1
so has part: feature:2341-2826:-1:exon

WP_015060315.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:2341-2826:-1:exon

LOZ86_RS21310
type: Gene
subclass of: SO_0000704
RO_0002162: 2778550
locus tag: LOZ86_RS21310
old locus tag: LOZ86_21310
pseudo: true
so part of: sequence
location: complement(<2876..3295)
location: region:2876-3295:-1
so has part: feature:2876-3295:-1:exon
subclass of: SO_0000010

position:2876:-1
position: 2876
reference: sequence
type: ReverseStrandPosition
type: FuzzyPosition

position:3295:-1
position: 3295
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:2876-3295:-1:exon

LOZ86_RS21310
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 2778550
locus tag: LOZ86_RS21310
old locus tag: LOZ86_21310
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: LOZ86_RS21310
subclass of: SO_0000673
so part of: LOZ86_RS21310
location: complement(<2876..3295)
location: region:2876-3295:-1
so has part: feature:2876-3295:-1:exon

urn:…
SIO_000300: 1
SIO_000628: feature:2876-3295:-1:exon

LOZ86_RS21315
type: Gene
subclass of: SO_0000704
RO_0002162: 2778550
gene: mobC
locus tag: LOZ86_RS21315
old locus tag: LOZ86_21315
so part of: sequence
location: complement(3504..3830)
location: region:3504-3830:-1
so has part: feature:3504-3830:-1:exon
subclass of: SO_0000010

position:3504:-1
position: 3504
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:3830:-1
position: 3830
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:3504-3830:-1:exon

LOZ86_RS21315
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 2778550
gene: mobC
locus tag: LOZ86_RS21315
old locus tag: LOZ86_21315
inference: COORDINATES: similar to AA sequence:RefSeq:WP_006674374.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: plasmid mobilization relaxosome protein MobC
translation: MEKRTREIKIRLTDSEHQRLIDRCDRTHLAEWLRQLGLGEHTARKRRLPDVAPELLRQVSGIGNNLNQIARRLNQLDGLTPTERVSLLAVLNSLDRNLGELLEQHRDH
SIO_010081: LOZ86_RS21315
subclass of: SO_0000673
so part of: LOZ86_RS21315
location: complement(3504..3830)
location: region:3504-3830:-1
so has part: feature:3504-3830:-1:exon

WP_116362722.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:3504-3830:-1:exon

LOZ86_RS21320
type: Gene
subclass of: SO_0000704
RO_0002162: 2778550
locus tag: LOZ86_RS21320
old locus tag: LOZ86_21320
so part of: sequence
location: 4586..5728
location: region:4586-5728:1
so has part: feature:4586-5728:1:exon
subclass of: SO_0000010

position:4586:1
position: 4586
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:5728:1
position: 5728
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:4586-5728:1:exon

LOZ86_RS21320
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 2778550
locus tag: LOZ86_RS21320
old locus tag: LOZ86_21320
EC number: 2.7.7.49
inference: COORDINATES: similar to AA sequence:RefSeq:WP_005761319.1
GO function: GO:0003964 - RNA-directed DNA polymerase activity [Evidence IEA]
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: reverse transcriptase family protein
translation: MMKPLFNGTQLASQDSLAAMLGVTTERLNKIVLSIPKSYKSFNIETGKNKKIRTLFEPKKGLKHIQKKINKEIFENVNYPNYLHGGLKERDYVSNAGTHAGKKTIISLDIENFYPSISKRDILNIFKNMMRFSPSISETLTELVTLDGKLPQGACCSSYIANLIFFNDEHNIVRKINNMGMNYTRLLDDVTISSDKKLSKEEETKAITTVVGMINRHRLSLNDAKTVIEKSDHPNSKLHVTGFWVKHKTPKINKENRRYIRYLVFICEKESAVDRTSTEYHTLWNKASGKVAQMSRVGHEQSVELREKLGKILPLYDEFKIRKIVFLANNYIKNFSLPLSEEQVSKVNKIIYDVGIVGRSNKKLSNELRKKLRSILPKDA
SIO_010081: LOZ86_RS21320
subclass of: SO_0000673
so part of: LOZ86_RS21320
location: 4586..5728
location: region:4586-5728:1
so has part: feature:4586-5728:1:exon

WP_230243183.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:4586-5728:1:exon