Enterococcus durans strain BDGP3 plasmid pEdBDGP3A, complete sequence.
type: Entry
definition: Enterococcus durans strain BDGP3 plasmid pEdBDGP3A, complete sequence.
sequence version: NZ_CP022931.1
sequence date: 2022-12-30
sequence: sequence
division: CON
label: NZ_CP022931.1
type: RefSeq
SIO_000068: refseq
dblink: PRJNA224116
dblink: SAMN07510606
keyword: RefSeq
source: Enterococcus durans
organism: Enterococcus durans
taxonomy: Bacteria; Bacillota; Bacilli; Lactobacillales; Enterococcaceae; Enterococcus.
reference: 1
reference: 2
comment: REFSEQ INFORMATION: The reference sequence is identical to\nCP022931.1.\n\nAnnotation modified by submitter.\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 :: 11-SEP-2015\nAssembly Method :: Celera Assembler v. 2015-09-11\nGenome Representation :: Full\nExpected Final Version :: Yes\nGenome Coverage :: 150.0x\nSequencing Technology :: PacBio\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 12/30/2022 04:31:52\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) :: 2,816\nCDSs (total) :: 2,725\nGenes (coding) :: 2,683\nCDSs (with protein) :: 2,683\nGenes (RNA) :: 91\nrRNAs :: 6, 6, 6 (5S, 16S, 23S)\ncomplete rRNAs :: 6, 6, 6 (5S, 16S, 23S)\ntRNAs :: 69\nncRNAs :: 4\nPseudo Genes (total) :: 42\nCDSs (without protein) :: 42\nPseudo Genes (ambiguous residues) :: 0 of 42\nPseudo Genes (frameshifted) :: 26 of 42\nPseudo Genes (incomplete) :: 16 of 42\nPseudo Genes (internal stop) :: 10 of 42\nPseudo Genes (multiple problems) :: 9 of 42\nCRISPR Arrays :: 1\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.

sequence
subclass of: SO_0000155
sequence length: 5594
topology: circular
so has quality: SO_0000988
location: 1..5594
location: region:1-5594:1
RO_0002162: 53345

NZ_CP022931
type: RefSeq
SIO_000068: refseq

PRJNA224116
type: BioProject
SIO_000068: bioproject

SAMN07510606
type: BioSample
SIO_000068: biosample

1
title: Complete Genome Sequence of Enterococcus durans Oregon-R-modENCODE strain BDGP3, a lactic acid bacterium found in the Drosophila melanogaster gut
author: Wan, K.H.
author: Yu, C.
author: Park, S.
author: Hammonds, A.S.
author: Booth, B.W.
author: Celniker, S.E.
journal: Unpublished

2
title: Direct Submission
author: Wan, K.H.
author: Yu, C.
author: Park, S.
author: Hammonds, A.S.
author: Booth, B.W.
author: Celniker, S.E.
journal: Submitted (15-AUG-2017) BDGP, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA

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

position:5594:1
position: 5594
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

feature:1-5594:1:source
so part of: sequence
organism: Enterococcus durans
mol type: genomic DNA
strain: BDGP3
host: Drosophila melanogaster Oregon-R modENCODE
plasmid: pEdBDGP3A
country: USA:94710
collection date: 2015-04-06

53345
type: Taxonomy
SIO_000068: taxonomy

CJZ72_RS14315
type: Gene
subclass of: SO_0000704
RO_0002162: 53345
locus tag: CJZ72_RS14315
old locus tag: CJZ72_14305
so part of: sequence
location: complement(1..642)
location: region:1-642:-1
so has part: feature:1-642:-1:exon
subclass of: SO_0000010

56744507
type: Gene
SIO_000068: ncbigene

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

position:642:-1
position: 642
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:1-642:-1:exon

CJZ72_RS14315
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 53345
locus tag: CJZ72_RS14315
old locus tag: CJZ72_14305
inference: COORDINATES: similar to AA sequence:RefSeq:WP_015081747.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: hypothetical protein
translation: MSENLKTIKELADELGVSKNKIHYQVSKISSEYVVRNNGMKLLTAIAVKQIKENLGVELNSRSNSELDTDKHQEKTNITTNMNIEGVELNSSLNDYLNSLKHQIEYLESQNINKDEQIKSLVESQKQTQKLLDQQQRLALQDKKLLEEYKSENDSLKALKMPSKDIKKEKVDNQPQEEIENLRNEHTIFQEQLKEKVMIEKKEASKKWWQLWK
SIO_010081: CJZ72_RS14315
subclass of: SO_0000673
so part of: CJZ72_RS14315
location: complement(1..642)
location: region:1-642:-1
so has part: feature:1-642:-1:exon

WP_015065195.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:1-642:-1:exon

CJZ72_RS14320
type: Gene
subclass of: SO_0000704
RO_0002162: 53345
locus tag: CJZ72_RS14320
old locus tag: CJZ72_14310
pseudo: true
so part of: sequence
location: complement(635..1833)
location: region:635-1833:-1
so has part: feature:635-1833:-1:exon
subclass of: SO_0000010

56744508
type: Gene
SIO_000068: ncbigene

position:635:-1
position: 635
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:1833:-1
position: 1833
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:635-1833:-1:exon

CJZ72_RS14320
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 53345
locus tag: CJZ72_RS14320
old locus tag: CJZ72_14310
inference: COORDINATES: similar to AA sequence:RefSeq:WP_002339159.1
GO function: GO:0003887 - DNA-directed DNA polymerase activity [Evidence IEA]
GO process: GO:0006270 - DNA replication initiation [Evidence IEA]
note: frameshifted; Derived by automated computational analysis using gene prediction method: Protein Homology.
pseudo: true
codon start: 1
transl table: 11
product: RepB family plasmid replication initiator protein
SIO_010081: CJZ72_RS14320
subclass of: SO_0000673
so part of: CJZ72_RS14320
location: complement(635..1833)
location: region:635-1833:-1
so has part: feature:635-1833:-1:exon

urn:…
SIO_000300: 1
SIO_000628: feature:635-1833:-1:exon

CJZ72_RS14980
type: Gene
subclass of: SO_0000704
RO_0002162: 53345
locus tag: CJZ72_RS14980
so part of: sequence
location: 2668..2871
location: region:2668-2871:1
so has part: feature:2668-2871:1:exon
subclass of: SO_0000010

77383738
type: Gene
SIO_000068: ncbigene

position:2668:1
position: 2668
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:2871:1
position: 2871
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:2668-2871:1:exon

CJZ72_RS14980
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 53345
locus tag: CJZ72_RS14980
inference: COORDINATES: protein motif:HMM:NF020567.2
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: hypothetical protein
translation: MSKAKPERSKQHDIRLQKNFEIEIINEFQSAIHSKMLNYVLNNELDKSDSTKPTSKFIKTIIKHEPN
SIO_010081: CJZ72_RS14980
subclass of: SO_0000673
so part of: CJZ72_RS14980
location: 2668..2871
location: region:2668-2871:1
so has part: feature:2668-2871:1:exon

WP_269768799.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:2668-2871:1:exon

CJZ72_RS14985
type: Gene
subclass of: SO_0000704
RO_0002162: 53345
locus tag: CJZ72_RS14985
so part of: sequence
location: 2858..2965
location: region:2858-2965:1
so has part: feature:2858-2965:1:exon
subclass of: SO_0000010

77383739
type: Gene
SIO_000068: ncbigene

position:2858:1
position: 2858
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:2965:1
position: 2965
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:2858-2965:1:exon

CJZ72_RS14985
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 53345
locus tag: CJZ72_RS14985
inference: COORDINATES: protein motif:HMM:NF020567.2
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: hypothetical protein
translation: MNQINLFELSLEELEAYHDYLRTIKKYADNITRTA
SIO_010081: CJZ72_RS14985
subclass of: SO_0000673
so part of: CJZ72_RS14985
location: 2858..2965
location: region:2858-2965:1
so has part: feature:2858-2965:1:exon

WP_269768798.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:2858-2965:1:exon

CJZ72_RS14330
type: Gene
subclass of: SO_0000704
RO_0002162: 53345
locus tag: CJZ72_RS14330
old locus tag: CJZ72_14320
so part of: sequence
location: complement(3802..4083)
location: region:3802-4083:-1
so has part: feature:3802-4083:-1:exon
subclass of: SO_0000010

56744510
type: Gene
SIO_000068: ncbigene

position:3802:-1
position: 3802
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:4083:-1
position: 4083
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:3802-4083:-1:exon

CJZ72_RS14330
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 53345
locus tag: CJZ72_RS14330
old locus tag: CJZ72_14320
inference: COORDINATES: protein motif:HMM:NF013540.2
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: helix-turn-helix transcriptional regulator
translation: MTTRTNPYDPKNSNLIKIGSNLKRLRNKKKLSIETFSEKVSLSSKSISNYERGLNLISIESIIRIHESGLFEEYNLLDLFQILIIDVFDSSEK
SIO_010081: CJZ72_RS14330
subclass of: SO_0000673
so part of: CJZ72_RS14330
location: complement(3802..4083)
location: region:3802-4083:-1
so has part: feature:3802-4083:-1:exon

WP_015065197.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:3802-4083:-1:exon

CJZ72_RS14335
type: Gene
subclass of: SO_0000704
RO_0002162: 53345
locus tag: CJZ72_RS14335
old locus tag: CJZ72_14325
so part of: sequence
location: 4170..5396
location: region:4170-5396:1
so has part: feature:4170-5396:1:exon
subclass of: SO_0000010

56744511
type: Gene
SIO_000068: ncbigene

position:4170:1
position: 4170
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:5396:1
position: 5396
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:4170-5396:1:exon

CJZ72_RS14335
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 53345
locus tag: CJZ72_RS14335
old locus tag: CJZ72_14325
inference: COORDINATES: similar to AA sequence:RefSeq:WP_002830882.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: AIPR family protein
translation: MKNEKKFKYVRQVKMDSPYPKDKLTVHHLWVDVNELPTGIPTEVNPRNINTKTKVYRKIVDGLTESDNSFFINNRGILIAAKSVSVNAIDKVLSLDLGDDSVQSKSLYGVLDGGHTYHAVLQNRKNVPEGTTQYIHLEIVTEISNIDDLAAARNTSVQVSDKAIAELAEKFGFVKESIKDENYANQVSYRENETDKRLDSVDFVRLMYAFNIFKFKDIESVSNTQPISAYSGKANVLKDYLENYDRKVDGKIEKNNDNPYLKIAPLLPKITELYDTIEKEMPTAYLESISNGKFGRTKGVDVKSTAKTKFSNEKIDYQISQGLIFPIISAFRALLVEKENTLEWVIDPIEVWNETRSKLVNNTIEMSRQLGNNPQSAGKSSTLWSQNFDAVNTAKLQIQLRKLQEKQN
SIO_010081: CJZ72_RS14335
subclass of: SO_0000673
so part of: CJZ72_RS14335
location: 4170..5396
location: region:4170-5396:1
so has part: feature:4170-5396:1:exon

WP_015065196.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:4170-5396:1:exon

CJZ72_RS14340
type: Gene
subclass of: SO_0000704
RO_0002162: 53345
locus tag: CJZ72_RS14340
old locus tag: CJZ72_14330
pseudo: true
so part of: sequence
location: 5502..>5585
location: region:5502-5585:1
so has part: feature:5502-5585:1:exon
subclass of: SO_0000010

56744512
type: Gene
SIO_000068: ncbigene

position:5502:1
position: 5502
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:5585:1
position: 5585
reference: sequence
type: ForwardStrandPosition
type: FuzzyPosition

urn:…
SIO_000300: 1
SIO_000628: feature:5502-5585:1:exon

CJZ72_RS14340
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 53345
locus tag: CJZ72_RS14340
old locus tag: CJZ72_14330
inference: COORDINATES: similar to AA sequence:RefSeq:WP_016632525.1
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: type II toxin-antitoxin system prevent-host-death family antitoxin
SIO_010081: CJZ72_RS14340
subclass of: SO_0000673
so part of: CJZ72_RS14340
location: 5502..>5585
location: region:5502-5585:1
so has part: feature:5502-5585:1:exon

urn:…
SIO_000300: 1
SIO_000628: feature:5502-5585:1:exon