Weissella confusa strain VTT E-133279 plasmid pWconfE3279-1, complete sequence.
type: Entry
definition: Weissella confusa strain VTT E-133279 plasmid pWconfE3279-1, complete sequence.
sequence version: NZ_CP027564.1
sequence date: 2023-03-25
sequence: sequence
division: CON
label: NZ_CP027564.1
type: RefSeq
SIO_000068: refseq
dblink: PRJNA224116
dblink: SAMN08627292
keyword: RefSeq
source: Weissella confusa
organism: Weissella confusa
taxonomy: Bacteria; Bacillota; Bacilli; Lactobacillales; Lactobacillaceae; Weissella.
reference: 1
reference: 2
comment: REFSEQ INFORMATION: The reference sequence is identical to\nCP027564.1.\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 Method :: Celera Assembler v. 3.9.0\nGenome Representation :: Full\nExpected Final Version :: Yes\nGenome Coverage :: 15x\nSequencing Technology :: PacBio\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 03/24/2023 23:47:23\nAnnotation Pipeline :: NCBI Prokaryotic Genome\n Annotation Pipeline (PGAP)\nAnnotation Method :: Best-placed reference protein\n set; GeneMarkS-2+\nAnnotation Software revision :: 6.4\nFeatures Annotated :: Gene; CDS; rRNA; tRNA; ncRNA\nGenes (total) :: 2,101\nCDSs (total) :: 1,985\nGenes (coding) :: 1,974\nCDSs (with protein) :: 1,974\nGenes (RNA) :: 116\nrRNAs :: 10, 9, 9 (5S, 16S, 23S)\ncomplete rRNAs :: 10, 9, 9 (5S, 16S, 23S)\ntRNAs :: 85\nncRNAs :: 3\nPseudo Genes (total) :: 11\nCDSs (without protein) :: 11\nPseudo Genes (ambiguous residues) :: 0 of 11\nPseudo Genes (frameshifted) :: 3 of 11\nPseudo Genes (incomplete) :: 3 of 11\nPseudo Genes (internal stop) :: 5 of 11\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.

sequence
subclass of: SO_0000155
sequence length: 4613
topology: circular
so has quality: SO_0000988
location: 1..4613
location: region:1-4613:1
RO_0002162: 1583

NZ_CP027564
type: RefSeq
SIO_000068: refseq

PRJNA224116
type: BioProject
SIO_000068: bioproject

SAMN08627292
type: BioSample
SIO_000068: biosample

1
title: Genome sequencing of Weissella confusa isolates
author: Kajala, I.
author: Baruah, R.
author: Bergsveinson, J.
author: Juvonen, R.
author: Ziola, B.
journal: Unpublished

2
title: Direct Submission
author: Kajala, I.
author: Bergsveinson, J.
author: Ziola, B.
journal: Submitted (06-MAR-2018) Department of Pathology and Laboratory Medicine, University of Saskatchewan, Svinhufvudintie 9 C 44, Helsinki 00570, Finland

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

position:4613:1
position: 4613
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

feature:1-4613:1:source
so part of: sequence
organism: Weissella confusa
mol type: genomic DNA
strain: VTT E-133279
isolation source: cabbage
plasmid: pWconfE3279-1
country: India
collection date: 2013-01

1583
type: Taxonomy
SIO_000068: taxonomy

C6P13_RS10305
type: Gene
subclass of: SO_0000704
RO_0002162: 1583
locus tag: C6P13_RS10305
old locus tag: C6P13_10325
so part of: sequence
location: 986..1255
location: region:986-1255:1
so has part: feature:986-1255:1:exon
subclass of: SO_0000010

39752194
type: Gene
SIO_000068: ncbigene

position:986:1
position: 986
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:1255:1
position: 1255
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:986-1255:1:exon

C6P13_RS10305
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 1583
locus tag: C6P13_RS10305
old locus tag: C6P13_10325
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: MNELGNELQFVQLDADWGGLAEKVLVKQGMSVEEYLTAALKRVYVSDELPFESELSYDEEIDYQNKNGIDLTQDQKLADWWADTAEDYE
SIO_010081: C6P13_RS10305
subclass of: SO_0000673
so part of: C6P13_RS10305
location: 986..1255
location: region:986-1255:1
so has part: feature:986-1255:1:exon

WP_135388825.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:986-1255:1:exon

C6P13_RS10310
type: Gene
subclass of: SO_0000704
RO_0002162: 1583
locus tag: C6P13_RS10310
old locus tag: C6P13_10330
so part of: sequence
location: 1312..1794
location: region:1312-1794:1
so has part: feature:1312-1794:1:exon
subclass of: SO_0000010

39752192
type: Gene
SIO_000068: ncbigene

position:1312:1
position: 1312
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:1794:1
position: 1794
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:1312-1794:1:exon

C6P13_RS10310
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 1583
locus tag: C6P13_RS10310
old locus tag: C6P13_10330
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: MTEHLYKSVKALADELGVSRTTLYKRAKLNGIELNGIYTSQQIEQLKTVQPKMDTEQKTEHFAEPNEHKDEHVFQSEIQRLSSQLTVKDEQIAELNQQLKQAQKLADQAQQLQLKAQLQLEAEQQKVLALETELQQEEVVSEASANGAENKKGFWRRIFG
SIO_010081: C6P13_RS10310
subclass of: SO_0000673
so part of: C6P13_RS10310
location: 1312..1794
location: region:1312-1794:1
so has part: feature:1312-1794:1:exon

WP_135388823.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:1312-1794:1:exon

C6P13_RS10315
type: Gene
subclass of: SO_0000704
RO_0002162: 1583
locus tag: C6P13_RS10315
old locus tag: C6P13_10335
so part of: sequence
location: 2573..2818
location: region:2573-2818:1
so has part: feature:2573-2818:1:exon
subclass of: SO_0000010

39752189
type: Gene
SIO_000068: ncbigene

position:2573:1
position: 2573
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:2818:1
position: 2818
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:2573-2818:1:exon

C6P13_RS10315
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 1583
locus tag: C6P13_RS10315
old locus tag: C6P13_10335
inference: COORDINATES: similar to AA sequence:RefSeq:WP_010001715.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: GlsB/YeaQ/YmgE family stress response membrane protein
translation: MIWSLIVGAVIGAVAGALTNRGESMGWISNILAGLIGSSIGQGILGHWGPSLAGMAIFPSIIGAVILVLIVSAIFGIKAKK
SIO_010081: C6P13_RS10315
subclass of: SO_0000673
so part of: C6P13_RS10315
location: 2573..2818
location: region:2573-2818:1
so has part: feature:2573-2818:1:exon

WP_010370253.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:2573-2818:1:exon

C6P13_RS10320
type: Gene
subclass of: SO_0000704
RO_0002162: 1583
gene: amaP
locus tag: C6P13_RS10320
old locus tag: C6P13_10340
so part of: sequence
location: 2846..3400
location: region:2846-3400:1
so has part: feature:2846-3400:1:exon
subclass of: SO_0000010

39752193
type: Gene
SIO_000068: ncbigene

position:2846:1
position: 2846
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:3400:1
position: 3400
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:2846-3400:1:exon

C6P13_RS10320
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 1583
gene: amaP
locus tag: C6P13_RS10320
old locus tag: C6P13_10340
inference: COORDINATES: protein motif:HMM:NF033218.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: alkaline shock response membrane anchor protein AmaP
translation: MKRLYKVLLVIILLIYLISISTIIWPDIITKILSFLDHINLHSSLSEQMLLRYNELFILGLTSVILIVVIALPRQRKSILLINSGKGTLSLGNEGISSFIETQLSGEGLSNIQVNIKNTKHIKRFNVTADSEYKKSIISDLPRVEKNLTDSLRNLLSGVDKSPIRVNIKVNQSNKRNNKASRVI
SIO_010081: C6P13_RS10320
subclass of: SO_0000673
so part of: C6P13_RS10320
location: 2846..3400
location: region:2846-3400:1
so has part: feature:2846-3400:1:exon

WP_135388821.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:2846-3400:1:exon

C6P13_RS10325
type: Gene
subclass of: SO_0000704
RO_0002162: 1583
locus tag: C6P13_RS10325
old locus tag: C6P13_10345
so part of: sequence
location: 3420..3614
location: region:3420-3614:1
so has part: feature:3420-3614:1:exon
subclass of: SO_0000010

39752191
type: Gene
SIO_000068: ncbigene

position:3420:1
position: 3420
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:3614:1
position: 3614
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:3420-3614:1:exon

C6P13_RS10325
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 1583
locus tag: C6P13_RS10325
old locus tag: C6P13_10345
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: MDRKQTVVFLSSLIGFVITILLIQFGFIKTILVVFITVMFGLLGLLFDNNRIQLSKLLHDIFNK
SIO_010081: C6P13_RS10325
subclass of: SO_0000673
so part of: C6P13_RS10325
location: 3420..3614
location: region:3420-3614:1
so has part: feature:3420-3614:1:exon

WP_135388819.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:3420-3614:1:exon

C6P13_RS10330
type: Gene
subclass of: SO_0000704
RO_0002162: 1583
locus tag: C6P13_RS10330
old locus tag: C6P13_10350
so part of: sequence
location: 3631..4137
location: region:3631-4137:1
so has part: feature:3631-4137:1:exon
subclass of: SO_0000010

39752190
type: Gene
SIO_000068: ncbigene

position:3631:1
position: 3631
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:4137:1
position: 4137
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:3631-4137:1:exon

C6P13_RS10330
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 1583
locus tag: C6P13_RS10330
old locus tag: C6P13_10350
inference: COORDINATES: similar to AA sequence:RefSeq:WP_010370260.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: Asp23/Gls24 family envelope stress response protein
translation: MTTENKTVTQETVATKGQLTFDDKVIQKIVGYAIENVSGLLGVDGGFVANIKNKIVNSDNPTDGINVEVGKEQVAVDLNIVMEFGHNAHDVYKEISKVVAKQIEEATSLTLVELNVKVIDIQTKSEFEESQVTIQDRVTDAGKSVQDKATAGIDKVKSVTDSDDARVQ
SIO_010081: C6P13_RS10330
subclass of: SO_0000673
so part of: C6P13_RS10330
location: 3631..4137
location: region:3631-4137:1
so has part: feature:3631-4137:1:exon

WP_135388817.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:3631-4137:1:exon

C6P13_RS10595
type: Gene
subclass of: SO_0000704
RO_0002162: 1583
locus tag: C6P13_RS10595
so part of: sequence
location: 4178..4312
location: region:4178-4312:1
so has part: feature:4178-4312:1:exon
subclass of: SO_0000010

79383333
type: Gene
SIO_000068: ncbigene

position:4178:1
position: 4178
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:4312:1
position: 4312
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:4178-4312:1:exon

C6P13_RS10595
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 1583
locus tag: C6P13_RS10595
inference: COORDINATES: similar to AA sequence:RefSeq:WP_004905998.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: hypothetical protein
translation: MVNTILKVAAVTSLVLGGIVVAATVFTAKEIDKAGDKLADKLYN
SIO_010081: C6P13_RS10595
subclass of: SO_0000673
so part of: C6P13_RS10595
location: 4178..4312
location: region:4178-4312:1
so has part: feature:4178-4312:1:exon

WP_257193950.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:4178-4312:1:exon