Pediococcus damnosus strain TMW 2.1536 plasmid pL21536-1, complete sequence.
type: Entry
definition: Pediococcus damnosus strain TMW 2.1536 plasmid pL21536-1, complete sequence.
sequence version: NZ_CP012295.1
sequence date: 2023-03-13
sequence: sequence
division: CON
label: NZ_CP012295.1
type: RefSeq
SIO_000068: refseq
dblink: PRJNA224116
dblink: SAMN03876485
keyword: RefSeq
source: Pediococcus damnosus
organism: Pediococcus damnosus
taxonomy: Bacteria; Bacillota; Bacilli; Lactobacillales; Lactobacillaceae; Pediococcus.
reference: 1
references: 27028007
reference: 2
comment: REFSEQ INFORMATION: The reference sequence is identical to\nCP012295.1.\nBacteria available from Technische Mikrobiologie Weihenstephan\n(Technische Universitaet Muenchen).\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. 1\nAssembly Name :: Pda21536-1\nLong Assembly Name :: Pediococus damnosus TMW2.1536 1\nGenome Coverage :: 137\nSequencing Technology :: PacBio\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 03/12/2023 23:41:38\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) :: 2,081\nCDSs (total) :: 2,004\nGenes (coding) :: 1,968\nCDSs (with protein) :: 1,968\nGenes (RNA) :: 77\nrRNAs :: 4, 4, 4 (5S, 16S, 23S)\ncomplete rRNAs :: 4, 4, 4 (5S, 16S, 23S)\ntRNAs :: 62\nncRNAs :: 3\nPseudo Genes (total) :: 36\nCDSs (without protein) :: 36\nPseudo Genes (ambiguous residues) :: 0 of 36\nPseudo Genes (frameshifted) :: 17 of 36\nPseudo Genes (incomplete) :: 12 of 36\nPseudo Genes (internal stop) :: 8 of 36\nPseudo Genes (multiple problems) :: 1 of 36\nCRISPR Arrays :: 1\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.

sequence
subclass of: SO_0000155
sequence length: 7678
topology: circular
so has quality: SO_0000988
location: 1..7678
location: region:1-7678:1
RO_0002162: 51663

NZ_CP012295
type: RefSeq
SIO_000068: refseq

PRJNA224116
type: BioProject
SIO_000068: bioproject

SAMN03876485
type: BioSample
SIO_000068: biosample

1
title: The Identification of Novel Diagnostic Marker Genes for the Detection of Beer Spoiling Pediococcus damnosus Strains Using the BlAst Diagnostic Gene findEr
author: Behr, J.
author: Geissler, A.J.
author: Schmid, J.
author: Zehe, A.
author: Vogel, R.F.
journal: PLoS One 11 (3), e0152747 (2016)
pubmed: 27028007
comments: Publication Status: Online-Only

27028007
type: PubMed
SIO_000068: pubmed

2
title: Direct Submission
author: Behr, J.
author: Geissler, A.J.
author: Vogel, R.F.
journal: Submitted (04-AUG-2015) Technische Mikrobiologie, Technische Universitaet Muenchen, Gregor-Mendel-Stra##e 4, Freising, Bavaria 85354, Germany

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

position:7678:1
position: 7678
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

feature:1-7678:1:source
so part of: sequence
organism: Pediococcus damnosus
mol type: genomic DNA
strain: TMW 2.1536
isolation source: winery environment
plasmid: pL21536-1
country: Germany

51663
type: Taxonomy
SIO_000068: taxonomy

ADU73_RS09980
type: Gene
subclass of: SO_0000704
RO_0002162: 51663
locus tag: ADU73_RS09980
old locus tag: ADU73_2080
so part of: sequence
location: 214..789
location: region:214-789:1
so has part: feature:214-789:1:exon
subclass of: SO_0000010

57277394
type: Gene
SIO_000068: ncbigene

position:214:1
position: 214
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:789:1
position: 789
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:214-789:1:exon

ADU73_RS09980
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 51663
locus tag: ADU73_RS09980
old locus tag: ADU73_2080
inference: COORDINATES: similar to AA sequence:RefSeq:WP_010620856.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: DUF536 domain-containing protein
translation: MKLLGKTIRQLSEEFKLSKQAINQRINSINGFRSKHTYKVKNHLEIDNQGVKMLANFDKQKRQERQPNRQAENDKDKNIDQILLKQLDVKDQQIANLQQALDQQQKLQIATVAENHRLKEHVQKLSGLFESSSATHQQQLNDKDDTLTNSSNTSHIKDKNDNQNENKVAEYGNRQKKTFKNNTNNSWWHFW
SIO_010081: ADU73_RS09980
subclass of: SO_0000673
so part of: ADU73_RS09980
location: 214..789
location: region:214-789:1
so has part: feature:214-789:1:exon

WP_223876556.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:214-789:1:exon

ADU73_RS09985
type: Gene
subclass of: SO_0000704
RO_0002162: 51663
locus tag: ADU73_RS09985
old locus tag: ADU73_2081
pseudo: true
so part of: sequence
location: complement(<960..1127)
location: region:960-1127:-1
so has part: feature:960-1127:-1:exon
subclass of: SO_0000010

57277395
type: Gene
SIO_000068: ncbigene

position:960:-1
position: 960
reference: sequence
type: ReverseStrandPosition
type: FuzzyPosition

position:1127:-1
position: 1127
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:960-1127:-1:exon

ADU73_RS09985
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 51663
locus tag: ADU73_RS09985
old locus tag: ADU73_2081
inference: COORDINATES: similar to AA sequence:RefSeq:WP_003672587.1
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: recombinase family protein
SIO_010081: ADU73_RS09985
subclass of: SO_0000673
so part of: ADU73_RS09985
location: complement(<960..1127)
location: region:960-1127:-1
so has part: feature:960-1127:-1:exon

urn:…
SIO_000300: 1
SIO_000628: feature:960-1127:-1:exon

ADU73_RS09990
type: Gene
subclass of: SO_0000704
RO_0002162: 51663
locus tag: ADU73_RS09990
old locus tag: ADU73_2082
so part of: sequence
location: complement(1271..1654)
location: region:1271-1654:-1
so has part: feature:1271-1654:-1:exon
subclass of: SO_0000010

57277396
type: Gene
SIO_000068: ncbigene

position:1271:-1
position: 1271
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:1654:-1
position: 1654
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:1271-1654:-1:exon

ADU73_RS09990
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 51663
locus tag: ADU73_RS09990
old locus tag: ADU73_2082
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: MIGIADSDSDSYNASDLGIEPFKIEPISIVGIKRDLILSGKSIDEYYQHYFSALSQEPVSEEMMTMLKGIKSYTYNGFPVLSIKIDNTGKPEPYNGKYYRREGTNTVELNVPDLISLTQNLQKHMDD
SIO_010081: ADU73_RS09990
subclass of: SO_0000673
so part of: ADU73_RS09990
location: complement(1271..1654)
location: region:1271-1654:-1
so has part: feature:1271-1654:-1:exon

WP_062913473.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:1271-1654:-1:exon

ADU73_RS09995
type: Gene
subclass of: SO_0000704
RO_0002162: 51663
locus tag: ADU73_RS09995
old locus tag: ADU73_2083
so part of: sequence
location: complement(1938..2858)
location: region:1938-2858:-1
so has part: feature:1938-2858:-1:exon
subclass of: SO_0000010

57277397
type: Gene
SIO_000068: ncbigene

position:1938:-1
position: 1938
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:2858:-1
position: 2858
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:1938-2858:-1:exon

ADU73_RS09995
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 51663
locus tag: ADU73_RS09995
old locus tag: ADU73_2083
inference: COORDINATES: similar to AA sequence:RefSeq:WP_003574021.1
GO function: GO:0004803 - transposase activity [Evidence IEA]
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: IS30 family transposase
translation: MAIITLIERSQIELMQHHTIQYIAATLGRSRISIRHELHRCPEGDYSAIIAQDHADTCRHRCGRHSILTPKLKRMVTERLTLGWSPEMVGYAVHCAPHTIYHWIYQRQVDFQPSQLFDHGKRHKRRQDLRSRYNQAVGTSIEIRSESANRRTEKGHLEMDTVRGGRGSKAAVLTIVDRVTRLMATTKLENLSQNAVLKGFARLMVDFPGPVRSVTVDHGKEFSCDQALTKRYRIPVYFCHAYHPNERGTNERFNRELRYYFPKGTQFDQVSEANIQRATALINNKPRKCLRWQTPVQAVSKPLSRW
SIO_010081: ADU73_RS09995
subclass of: SO_0000673
so part of: ADU73_RS09995
location: complement(1938..2858)
location: region:1938-2858:-1
so has part: feature:1938-2858:-1:exon

WP_096836077.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:1938-2858:-1:exon

ADU73_RS10000
type: Gene
subclass of: SO_0000704
RO_0002162: 51663
locus tag: ADU73_RS10000
old locus tag: ADU73_2084
so part of: sequence
location: complement(3281..4060)
location: region:3281-4060:-1
so has part: feature:3281-4060:-1:exon
subclass of: SO_0000010

57277398
type: Gene
SIO_000068: ncbigene

position:3281:-1
position: 3281
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

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

urn:…
SIO_000300: 1
SIO_000628: feature:3281-4060:-1:exon

ADU73_RS10000
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 51663
locus tag: ADU73_RS10000
old locus tag: ADU73_2084
inference: COORDINATES: similar to AA sequence:RefSeq:WP_003563261.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: alpha/beta hydrolase
translation: MSEYITVKDGTRISYDVHGEGSPVLLIHGVTDCKETYDTDLPFLTKNHRVYRYDLRGHGASDHPKHPFTLENHIEDALAVISKLNLHNFVLYGGSLGSYIAEAVATKIPQDLSGLILNVSAAHNPASALADTAKNDNIPLDKVERRDYWIRHLTIDKDNIKQLTDSGFQKNSLSPEDEDRALRSITAFDFRNELPKITCPTLITSGLYDPVNGPSKGIEIQKYIPNACFVVFKSGHLQRLEMPTAYHHVVDDFIETVAR
SIO_010081: ADU73_RS10000
subclass of: SO_0000673
so part of: ADU73_RS10000
location: complement(3281..4060)
location: region:3281-4060:-1
so has part: feature:3281-4060:-1:exon

WP_062913474.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:3281-4060:-1:exon

ADU73_RS10375
type: Gene
subclass of: SO_0000704
RO_0002162: 51663
locus tag: ADU73_RS10375
old locus tag: ADU73_2085
pseudo: true
so part of: sequence
location: complement(<4302..4448)
location: region:4302-4448:-1
so has part: feature:4302-4448:-1:exon
subclass of: SO_0000010

57277465
type: Gene
SIO_000068: ncbigene

position:4302:-1
position: 4302
reference: sequence
type: ReverseStrandPosition
type: FuzzyPosition

position:4448:-1
position: 4448
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:4302-4448:-1:exon

ADU73_RS10375
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 51663
locus tag: ADU73_RS10375
old locus tag: ADU73_2085
inference: COORDINATES: similar to AA sequence:RefSeq:WP_016511122.1
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: MobA/MobL family protein
SIO_010081: ADU73_RS10375
subclass of: SO_0000673
so part of: ADU73_RS10375
location: complement(<4302..4448)
location: region:4302-4448:-1
so has part: feature:4302-4448:-1:exon

urn:…
SIO_000300: 1
SIO_000628: feature:4302-4448:-1:exon

ADU73_RS10005
type: Gene
subclass of: SO_0000704
RO_0002162: 51663
locus tag: ADU73_RS10005
old locus tag: ADU73_2086
so part of: sequence
location: 4830..5042
location: region:4830-5042:1
so has part: feature:4830-5042:1:exon
subclass of: SO_0000010

57277399
type: Gene
SIO_000068: ncbigene

position:4830:1
position: 4830
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:5042:1
position: 5042
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:4830-5042:1:exon

ADU73_RS10005
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 51663
locus tag: ADU73_RS10005
old locus tag: ADU73_2086
inference: COORDINATES: similar to AA sequence:RefSeq:WP_010620841.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: hypothetical protein
translation: MLGVIKMDEKKVLKPIDEMLADPWQVDIQELFEAFVNEPGEIKRNLYDSLDTYILQKRQEDISNRPDSVI
SIO_010081: ADU73_RS10005
subclass of: SO_0000673
so part of: ADU73_RS10005
location: 4830..5042
location: region:4830-5042:1
so has part: feature:4830-5042:1:exon

WP_062913475.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:4830-5042:1:exon

ADU73_RS10010
type: Gene
subclass of: SO_0000704
RO_0002162: 51663
locus tag: ADU73_RS10010
old locus tag: ADU73_2087
so part of: sequence
location: 5752..6687
location: region:5752-6687:1
so has part: feature:5752-6687:1:exon
subclass of: SO_0000010

57277400
type: Gene
SIO_000068: ncbigene

position:5752:1
position: 5752
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:6687:1
position: 6687
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:5752-6687:1:exon

ADU73_RS10010
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 51663
locus tag: ADU73_RS10010
old locus tag: ADU73_2087
inference: COORDINATES: similar to AA sequence:RefSeq:WP_010625604.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: replication initiation protein
translation: MSNELVKYDPELNTIPLRRFTPVEMNLFFSVVSRMRDKGDDTVRFTFDQLKELSAYKPTANNRFIDDIQSTYQKILGLRFGSRSKDGLDREMFVMFTRFEIKGSADVPYVDIQIYPKALKLLNNLESWVRYALTEFRDLKSSYAKTTFRILKQFRTTGYAYFSKNDFFELLDIPQSYWSKPANVESRVIRPIKEELTPLFRGLTIRKKYGKGRGKPVIGYTFTWKPERKDANDFSQGKFQDERQKLFNIQNNGELTEQEKWRATDKVKGLPLGSTEKQILAERQIEHDKTIRDQTRQEMLAELRKGFGNHA
SIO_010081: ADU73_RS10010
subclass of: SO_0000673
so part of: ADU73_RS10010
location: 5752..6687
location: region:5752-6687:1
so has part: feature:5752-6687:1:exon

WP_057802899.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:5752-6687:1:exon

ADU73_RS10380
type: Gene
subclass of: SO_0000704
RO_0002162: 51663
locus tag: ADU73_RS10380
so part of: sequence
location: 6797..7584
location: region:6797-7584:1
so has part: feature:6797-7584:1:exon
subclass of: SO_0000010

57277466
type: Gene
SIO_000068: ncbigene

position:6797:1
position: 6797
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:7584:1
position: 7584
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:6797-7584:1:exon

ADU73_RS10380
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 51663
locus tag: ADU73_RS10380
inference: COORDINATES: similar to AA sequence:RefSeq:WP_013727908.1
ribosomal slippage: true
GO function: GO:0004803 - transposase activity [Evidence IEA]
note: programmed frameshift; Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: IS5 family transposase
translation: MKNYPSNITRQQFELIRPALENFRKRTKPRKYDLYEVFCAVLYVLKTGCQWRQVPGDFPEWRSVYNYYKIWSTKAEPTADSLLEQVFKKIVIARRTYQGRSALTSFIIVDAQSVKNTATAENKGYDAGKKISGIKRHLAVDINGFPQAIHMTRANVSDRDGASAMIALHAMHLRQVQNVLVDGGYSGVNFQLDVASNLNATVQVAKRNELHRFEVMPQRWVVERSFSWLENCRRLWKNCERQLTTSLQMVVLAFLALLLKRF
SIO_010081: ADU73_RS10380
subclass of: SO_0000673
so part of: ADU73_RS10380
location: join(6797..7055,7055..7584)
location: region:6797-7584:1
so has part: feature:6797-7055:1:exon
so has part: feature:7055-7584:1:exon

WP_080487858.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:6797-7055:1:exon

position:7055:1
position: 7055
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 2
SIO_000628: feature:7055-7584:1:exon