Lactococcus allomyrinae strain 1JSPR-7 plasmid unnamed2, complete sequence.
type: Entry
definition: Lactococcus allomyrinae strain 1JSPR-7 plasmid unnamed2, complete sequence.
sequence version: NZ_CP032629.1
sequence date: 2023-03-21
sequence: sequence
division: CON
label: NZ_CP032629.1
type: RefSeq
SIO_000068: refseq
dblink: PRJNA224116
dblink: SAMN10141031
keyword: RefSeq
source: Lactococcus allomyrinae
organism: Lactococcus allomyrinae
taxonomy: Bacteria; Bacillota; Bacilli; Lactobacillales; Streptococcaceae; Lactococcus.
reference: 1
reference: 2
comment: REFSEQ INFORMATION: The reference sequence is identical to\nCP032629.1.\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 :: AUG-2018\nAssembly Method :: RS HGAP Assembly v. 3.0\nGenome Representation :: Full\nExpected Final Version :: Yes\nGenome Coverage :: 254.0x\nSequencing Technology :: PacBio RSII\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 03/21/2023 02:12:17\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) :: 2,681\nCDSs (total) :: 2,592\nGenes (coding) :: 2,529\nCDSs (with protein) :: 2,529\nGenes (RNA) :: 89\nrRNAs :: 7, 6, 6 (5S, 16S, 23S)\ncomplete rRNAs :: 7, 6, 6 (5S, 16S, 23S)\ntRNAs :: 66\nncRNAs :: 4\nPseudo Genes (total) :: 63\nCDSs (without protein) :: 63\nPseudo Genes (ambiguous residues) :: 0 of 63\nPseudo Genes (frameshifted) :: 53 of 63\nPseudo Genes (incomplete) :: 12 of 63\nPseudo Genes (internal stop) :: 3 of 63\nPseudo Genes (multiple problems) :: 5 of 63\nCRISPR Arrays :: 1\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.

sequence
subclass of: SO_0000155
sequence length: 8331
topology: circular
so has quality: SO_0000988
location: 1..8331
location: region:1-8331:1
RO_0002162: 2419773

NZ_CP032629
type: RefSeq
SIO_000068: refseq

PRJNA224116
type: BioProject
SIO_000068: bioproject

SAMN10141031
type: BioSample
SIO_000068: biosample

1
title: Genome sequencing of strain 1JSPR-7
author: Heo, J.
author: Kim, S.-J.
author: Kwon, S.-W.
journal: Unpublished

2
title: Direct Submission
author: Heo, J.
author: Kim, S.-J.
author: Kwon, S.-W.
journal: Submitted (28-SEP-2018) Agricultural Mircrobiology Division, National Institute of Agricultural Sciences, 166 Nongsaengmyeong-ro, Iseo-myeon, Wanju-gun, Jeollabuk-do 55365, Korea, Republic of

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

position:8331:1
position: 8331
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

feature:1-8331:1:source
so part of: sequence
organism: Lactococcus allomyrinae
mol type: genomic DNA
strain: 1JSPR-7
isolation source: gut of larva
host: Trypoxylus dichotomus
culture collection: KACC:19319
type material: type strain of Lactococcus allomyrinae
plasmid: unnamed2
country: South Korea: Jeonju
collection date: 2017-05
collected by: Soo-Jin Kim, Soon-Wo Kwon
identified by: Soo-Jin Kim, Jun Heo, Soon-Wo Kwon

2419773
type: Taxonomy
SIO_000068: taxonomy

D7I46_RS13110
type: Gene
subclass of: SO_0000704
RO_0002162: 2419773
locus tag: D7I46_RS13110
old locus tag: D7I46_13110
so part of: sequence
location: join(8085..8331,1..992)
location: region:1-8331:1
so has part: feature:8085-8331:1:exon
so has part: feature:1-992:1:exon
subclass of: SO_0000010

urn:…
SIO_000300: 1
SIO_000628: feature:8085-8331:1:exon

position:8085:1
position: 8085
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 2
SIO_000628: feature:1-992:1:exon

position:992:1
position: 992
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

D7I46_RS13110
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 2419773
locus tag: D7I46_RS13110
old locus tag: D7I46_13110
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: MLIATISILIVAFILIILPPTRYVALISVLSLFSALLSQKVRETIKECFMTLKIETEGLLNNGIYLKEVQPSLEQKHIFVRLPKVTVKTDIEDNVREIAITISPYNQEKLSKLDLSSVFQGFIQQQAQSNRDSSQMVYKLLNIDSDYFYKFSNLKQLFQFQKNYDSEIPLDKYNSIPVLSHKIIVARSGNGKSFLLLYLISFLALSQKNILLIADYKQSDVFIACRDNLGLSSVSSKEDILQMVEDTYLEMLDRQKAFNDYEGNKLGLTMDKLGYEPLFLVIDELASFTAALDKKELEQFNFHFKQIMLLGRALSVFCLITMQQFNVKNLGGSSELKEQFGDQILLGNNDSQTIQNLYGSNELPNFQMEKGNGFLQNDSNLQPVLFRSPFLEPSFFKHLEKLNLKLQTKKES
SIO_010081: D7I46_RS13110
subclass of: SO_0000673
so part of: D7I46_RS13110
location: join(8085..8331,1..992)
location: region:1-8331:1
so has part: feature:8085-8331:1:exon
so has part: feature:1-992:1:exon

WP_162930952.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:8085-8331:1:exon

urn:…
SIO_000300: 2
SIO_000628: feature:1-992:1:exon

D7I46_RS13115
type: Gene
subclass of: SO_0000704
RO_0002162: 2419773
locus tag: D7I46_RS13115
old locus tag: D7I46_13115
so part of: sequence
location: complement(1209..2162)
location: region:1209-2162:-1
so has part: feature:1209-2162:-1:exon
subclass of: SO_0000010

position:1209:-1
position: 1209
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:2162:-1
position: 2162
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:1209-2162:-1:exon

D7I46_RS13115
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 2419773
locus tag: D7I46_RS13115
old locus tag: D7I46_13115
inference: COORDINATES: similar to AA sequence:RefSeq:WP_009247766.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: DNA cytosine methyltransferase
translation: MLKIASFFAGVGGIDLGFENAGFKTIYANEFDNYAADTFELNFDVKVDRRDINDVQADEIPDFDIMLAGFPCQAFSIAGYRQGFNDEQGRGNLFFELVRILEAKKPRVAFFENVKNLVSHDNGNTFRVICSELERLGYKYLFQVFNASEYGNIPQNRERIYIVAFKNKEDYANFELPKSIPLKTTIHDVIDFSKKQDDKFYYTSEKNKFFDELKENMTNHDTTYQWRRVYVRENKSNLVPTLTANMGTGGHNVPLILTYSGDIRKLTPRECFNVQGFPREYKLPNQSNGRLYKQAGNSVVVPVIERIAKNLADTIVE
SIO_010081: D7I46_RS13115
subclass of: SO_0000673
so part of: D7I46_RS13115
location: complement(1209..2162)
location: region:1209-2162:-1
so has part: feature:1209-2162:-1:exon

WP_120773438.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:1209-2162:-1:exon

D7I46_RS13120
type: Gene
subclass of: SO_0000704
RO_0002162: 2419773
locus tag: D7I46_RS13120
old locus tag: D7I46_13120
so part of: sequence
location: complement(2268..2810)
location: region:2268-2810:-1
so has part: feature:2268-2810:-1:exon
subclass of: SO_0000010

position:2268:-1
position: 2268
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:2810:-1
position: 2810
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:2268-2810:-1:exon

D7I46_RS13120
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 2419773
locus tag: D7I46_RS13120
old locus tag: D7I46_13120
EC number: 3.1.21.-
inference: COORDINATES: protein motif:HMM:NF021052.2
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: Bsp6I family type II restriction endonuclease
translation: MAYKKFGYIEIDDARIDATCDAYFKWKDLNTYIKNTSSRGMNMPDAISEPMGCYCLGYLWNRGSEVGDATDPITNKKIEFKATSKFEGDLSSFGPKTVFDNLVFLRFYLDENKLYIYDLNINSEEFGKYPANKTQTIQEQKAAGRRPHVSLQSLFVDAKNLQPDIIFDIRRCRIIEDNRH
SIO_010081: D7I46_RS13120
subclass of: SO_0000673
so part of: D7I46_RS13120
location: complement(2268..2810)
location: region:2268-2810:-1
so has part: feature:2268-2810:-1:exon

WP_162930951.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:2268-2810:-1:exon

D7I46_RS13125
type: Gene
subclass of: SO_0000704
RO_0002162: 2419773
locus tag: D7I46_RS13125
old locus tag: D7I46_13125
so part of: sequence
location: complement(2896..4245)
location: region:2896-4245:-1
so has part: feature:2896-4245:-1:exon
subclass of: SO_0000010

position:2896:-1
position: 2896
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:4245:-1
position: 4245
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:2896-4245:-1:exon

D7I46_RS13125
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 2419773
locus tag: D7I46_RS13125
old locus tag: D7I46_13125
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: MNELTTIDTLDVTQLPKKKLLDYFALTISQEQPAINARNTVNQNWEDMTNNSESPKYKEIKAMFNILPDKSLEELITIRDTFIKNDTEKLNEINKEIQQYLENIKTQESEYREQRRNLTVDSLTKHLNFKSKGELEKVFVGKKNMKISFWVYITLAITLGIFLYLFPENGLLYIGKSRVSKFGPVDINYTRIFLYSFISLFVWPILFKIGKIILWKLKLSKGNSIQEFIKQIPLDLAKVNYSIKNGKPSYCRNSKNYDYPNSLNYSVTLNVEEYKNNLERAKILKEHISIWKDKGEEFLVSVKNLTSEFKKSSMLEKSNTRLGKAMPEQWTKNKSEGMIETSLIFSSLISSGRADTWKEAANLAIEDKFKQAVLKELGDTRQSMIDTMIKTGERIRESISEEIYQMANNVSSSIEAEGIRNQLAMNNVNSSLDRIEIINSAILIDSLIR
SIO_010081: D7I46_RS13125
subclass of: SO_0000673
so part of: D7I46_RS13125
location: complement(2896..4245)
location: region:2896-4245:-1
so has part: feature:2896-4245:-1:exon

WP_120773440.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:2896-4245:-1:exon

D7I46_RS13130
type: Gene
subclass of: SO_0000704
RO_0002162: 2419773
locus tag: D7I46_RS13130
old locus tag: D7I46_13130
so part of: sequence
location: complement(4266..4667)
location: region:4266-4667:-1
so has part: feature:4266-4667:-1:exon
subclass of: SO_0000010

position:4266:-1
position: 4266
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:4667:-1
position: 4667
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:4266-4667:-1:exon

D7I46_RS13130
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 2419773
locus tag: D7I46_RS13130
old locus tag: D7I46_13130
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: MVKKTIKQLADELNVSKDKVKYQVRKLPSELTTKENGITYIKNTGIEIIKENIQGKIPNEKTSELPNNYLVDQLDFFQKELEKKNTQIDHLQQLLENQQILTKQTLDEKKQLELEFSELKKEEPKSWFRRIFG
SIO_010081: D7I46_RS13130
subclass of: SO_0000673
so part of: D7I46_RS13130
location: complement(4266..4667)
location: region:4266-4667:-1
so has part: feature:4266-4667:-1:exon

WP_120773441.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:4266-4667:-1:exon

D7I46_RS13135
type: Gene
subclass of: SO_0000704
RO_0002162: 2419773
locus tag: D7I46_RS13135
old locus tag: D7I46_13135
so part of: sequence
location: complement(4661..5593)
location: region:4661-5593:-1
so has part: feature:4661-5593:-1:exon
subclass of: SO_0000010

position:4661:-1
position: 4661
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:5593:-1
position: 5593
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:4661-5593:-1:exon

D7I46_RS13135
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 2419773
locus tag: D7I46_RS13135
old locus tag: D7I46_13135
inference: COORDINATES: similar to AA sequence:RefSeq:WP_016526795.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: replication initiation protein
translation: MANEIIKYDSELNTIPLKQFTPVEMNLFFSIISRMRDKKDETVVFSFEQLKELSDYKPTANKRFIDDLRKTYLKLLSLQFGSTSKSGLSFQAFNMFNKFAINGDIEEPYVEIQMNEMAIPLLNNLETWVRYSLAEFRELQSSYSKTMFRLLKQYRTTGWAEFSKANFFELLDIPKSYLNKSENVDLRVLKPIKEELTPLFRGLKISKKYGKGRGKPVIAYRFSWKPEKNDSDDFSKGEREDIRQKLFNIEHNGELSESEKLRAKDRILGLKLGQSEEDKKAQLLAEKQEEEDKQLKENILSDFLSRSNKW
SIO_010081: D7I46_RS13135
subclass of: SO_0000673
so part of: D7I46_RS13135
location: complement(4661..5593)
location: region:4661-5593:-1
so has part: feature:4661-5593:-1:exon

WP_120773442.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:4661-5593:-1:exon

D7I46_RS13140
type: Gene
subclass of: SO_0000704
RO_0002162: 2419773
locus tag: D7I46_RS13140
old locus tag: D7I46_13140
so part of: sequence
location: 6029..7402
location: region:6029-7402:1
so has part: feature:6029-7402:1:exon
subclass of: SO_0000010

position:6029:1
position: 6029
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:7402:1
position: 7402
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:6029-7402:1:exon

D7I46_RS13140
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 2419773
locus tag: D7I46_RS13140
old locus tag: D7I46_13140
inference: COORDINATES: protein motif:HMM:NF013105.2
GO component: GO:0005727 - extrachromosomal circular DNA [Evidence IEA]
GO function: GO:0003677 - DNA binding [Evidence IEA]; GO:0003916 - DNA topoisomerase activity [Evidence IEA]
GO process: GO:0006260 - DNA replication [Evidence IEA]
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: Rep family protein
translation: MPTNNLKRYRTFNGMINYDYFRKNENGKIENTLSETDFKELVISKIAKENSIDWFCLVAHNRDILDEESGTLKPHHIHFVLRFENARTINSVLNSLSKVKISERNISAAQSVASSLLYLTHTTPQAIKEKKTRYEVSELSIFAENHFLNQSEKELWYRNKISGSLGQISKKFDETPLIIDIYKEIQQGFIPTDNNLLNLIKSYRSLYQLSEEEILVFVRKNRKQFQMDRESYIQDYVRTKKSQGKVHNLFYINGSGGIGKSIFSKSLSEKLISLKYSTQDKQDLLFESSSSGKNSDLLNQYELQPISIFDDLNINSFSNTQHFLKLFEKNIVPLIQSRYQNKYFLSEYSFITKSEPIKTFISSIYRLNGVHSEINLKQQILRRFSLIIEIETDKLILKEIKRKPNTTEFEIVISEVIQFDNLTFIELFSSYDTDNTQFKKLHKQREKIIEKIVNEYL
SIO_010081: D7I46_RS13140
subclass of: SO_0000673
so part of: D7I46_RS13140
location: 6029..7402
location: region:6029-7402:1
so has part: feature:6029-7402:1:exon

WP_120773443.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:6029-7402:1:exon

D7I46_RS13145
type: Gene
subclass of: SO_0000704
RO_0002162: 2419773
locus tag: D7I46_RS13145
old locus tag: D7I46_13145
so part of: sequence
location: 7506..7691
location: region:7506-7691:1
so has part: feature:7506-7691:1:exon
subclass of: SO_0000010

position:7506:1
position: 7506
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:7691:1
position: 7691
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:7506-7691:1:exon

D7I46_RS13145
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 2419773
locus tag: D7I46_RS13145
old locus tag: D7I46_13145
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: MKNKNIIKLESNLDSTRFLLAKLAKEKAITFEEYNRLLDSTLPIQNVIIALKEENGGKDNA
SIO_010081: D7I46_RS13145
subclass of: SO_0000673
so part of: D7I46_RS13145
location: 7506..7691
location: region:7506-7691:1
so has part: feature:7506-7691:1:exon

WP_120773444.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:7506-7691:1:exon

D7I46_RS13150
type: Gene
subclass of: SO_0000704
RO_0002162: 2419773
locus tag: D7I46_RS13150
old locus tag: D7I46_13150
so part of: sequence
location: 7684..8043
location: region:7684-8043:1
so has part: feature:7684-8043:1:exon
subclass of: SO_0000010

position:7684:1
position: 7684
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:8043:1
position: 8043
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:7684-8043:1:exon

D7I46_RS13150
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 2419773
locus tag: D7I46_RS13150
old locus tag: D7I46_13150
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: MLKDLNKYNQFQVDKFLQDFGGIIFLNAEENYLYIDGKKSETVQGSKVEVILRGSEGVNEFEKLSIKFESIPVSEFEKVKKMTPIKLQGATGTLWGNGAFKNNLSIKAEGFTVLSKDNQ
SIO_010081: D7I46_RS13150
subclass of: SO_0000673
so part of: D7I46_RS13150
location: 7684..8043
location: region:7684-8043:1
so has part: feature:7684-8043:1:exon

WP_120773445.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:7684-8043:1:exon