Lactobacillus amylovorus GRL1118 plasmid p1, complete sequence.
type: Entry
definition: Lactobacillus amylovorus GRL1118 plasmid p1, complete sequence.
sequence version: NC_017471.1
sequence date: 2023-04-09
sequence: sequence
division: CON
label: NC_017471.1
type: RefSeq
SIO_000068: refseq
dblink: PRJNA224116
dblink: SAMN02603307
keyword: RefSeq
source: Lactobacillus amylovorus GRL1118
organism: Lactobacillus amylovorus GRL1118
taxonomy: Bacteria; Bacillota; Bacilli; Lactobacillales; Lactobacillaceae; Lactobacillus.
reference: 1
comment: REFSEQ INFORMATION: The reference sequence is identical to\nCP002610.1.\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-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 04/09/2023 01:16:33\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) :: 2,015\nCDSs (total) :: 1,938\nGenes (coding) :: 1,834\nCDSs (with protein) :: 1,834\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) :: 104\nCDSs (without protein) :: 104\nPseudo Genes (ambiguous residues) :: 0 of 104\nPseudo Genes (frameshifted) :: 56 of 104\nPseudo Genes (incomplete) :: 47 of 104\nPseudo Genes (internal stop) :: 32 of 104\nPseudo Genes (multiple problems) :: 27 of 104\nCRISPR Arrays :: 3\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.

sequence
subclass of: SO_0000155
sequence length: 4541
topology: circular
so has quality: SO_0000988
location: 1..4541
location: region:1-4541:1
RO_0002162: 695562

NC_017471
type: RefSeq
SIO_000068: refseq

PRJNA224116
type: BioProject
SIO_000068: bioproject

SAMN02603307
type: BioSample
SIO_000068: biosample

1
title: Direct Submission
author: Kant, R.
author: Paulin, L.
author: Alatalo, E.
author: de Vos, W.M.
author: Palva, A.
journal: Submitted (25-MAR-2011) Department of Veterinary Biosciences, Faculty of Veterinary Medicine, University of Helsinki, Finland

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

position:4541:1
position: 4541
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

feature:1-4541:1:source
so part of: sequence
organism: Lactobacillus amylovorus GRL1118
mol type: genomic DNA
strain: GRL1118
isolation source: ileum
host: pig
plasmid: p1

695562
type: Taxonomy
SIO_000068: taxonomy

LAB52_RS09505
type: Gene
subclass of: SO_0000704
RO_0002162: 695562
locus tag: LAB52_RS09505
old locus tag: LAB52_09863
so part of: sequence
location: join(4190..4541,1..818)
location: region:1-4541:1
so has part: feature:4190-4541:1:exon
so has part: feature:1-818:1:exon
subclass of: SO_0000010

66524640
type: Gene
SIO_000068: ncbigene

urn:…
SIO_000300: 1
SIO_000628: feature:4190-4541:1:exon

position:4190:1
position: 4190
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 2
SIO_000628: feature:1-818:1:exon

position:818:1
position: 818
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

LAB52_RS09505
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 695562
locus tag: LAB52_RS09505
old locus tag: LAB52_09863
inference: COORDINATES: similar to AA sequence:RefSeq:WP_014563300.1
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: IS256 family transposase
translation: MNDFTKNMAQALFNQDKINDLLRKELQQAVNDLLEAELTAFLGYDPYARAGWNTGNSRNGAYFRKVDTQFGEIEIQVPRDRNGMFHQHTLPDYKQHSDVLESMIIKLYSKGVTTREIADLIEKMYGSHYSPAQVSNISKQMIPKVEAYHQRKFSDKFFCVYLDATYIPLRRITFDREAVYIAIGIKPNGHKEVIDYRIAPSENVENWTEMLQDMKSRGLELFLSDGVVGMKTVLEQTYPKAHFQRCLVHVMRNICAKVRVDDRETIMNEFKQIHTQSNKEMAVQVLHEFYQNWEKAYKNVVRDLRQVEPDLLTFYNYPPAIRASIYSTNMIESFNNRLKRKTKPKTEFPTEQSLDTFIGVQAMDYNDRYFNRIHKGFGQVRDTLESYFD
SIO_010081: LAB52_RS09505
subclass of: SO_0000673
so part of: LAB52_RS09505
location: join(4190..4541,1..818)
location: region:1-4541:1
so has part: feature:4190-4541:1:exon
so has part: feature:1-818:1:exon

WP_014566277.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:4190-4541:1:exon

urn:…
SIO_000300: 2
SIO_000628: feature:1-818:1:exon

LAB52_RS09510
type: Gene
subclass of: SO_0000704
RO_0002162: 695562
locus tag: LAB52_RS09510
old locus tag: LAB52_09838
so part of: sequence
location: complement(1285..2103)
location: region:1285-2103:-1
so has part: feature:1285-2103:-1:exon
subclass of: SO_0000010

66524641
type: Gene
SIO_000068: ncbigene

position:1285:-1
position: 1285
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:2103:-1
position: 2103
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:1285-2103:-1:exon

LAB52_RS09510
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 695562
locus tag: LAB52_RS09510
old locus tag: LAB52_09838
inference: COORDINATES: similar to AA sequence:RefSeq:WP_007125785.1
GO function: GO:0004222 - metalloendopeptidase activity [Evidence IEA]
GO process: GO:0071586 - CAAX-box protein processing [Evidence IEA]
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: type II CAAX endopeptidase family protein
translation: MKTSKAILGSILAIVSLVVASFISQSIIMLLKKCRIGYVVPILIGAILYAVIAYLLVKLIADRYLKVSLPRLGIPKFKISLKWILIAILLPLAVTAVFLVMNGKIVDANSSDMENIVFNIFYASLAAGFVEELIFRGVILNVLSIRWNYLVGVLIPSVIFGLLHIVSRNLSFMSIIQLIIAGTLVGVMFSLIEMSEHYIWNSAVVHAIWNLITSAIFAVAVSPQKDALYSYVISSKNALLTGGGFGMESSLIAIIGYLIVALIAYKIFAKNK
SIO_010081: LAB52_RS09510
subclass of: SO_0000673
so part of: LAB52_RS09510
location: complement(1285..2103)
location: region:1285-2103:-1
so has part: feature:1285-2103:-1:exon

WP_014566272.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:1285-2103:-1:exon

LAB52_RS10230
type: Gene
subclass of: SO_0000704
RO_0002162: 695562
locus tag: LAB52_RS10230
pseudo: true
so part of: sequence
location: <2771..3079
location: region:2771-3079:1
so has part: feature:2771-3079:1:exon
subclass of: SO_0000010

66524739
type: Gene
SIO_000068: ncbigene

position:2771:1
position: 2771
reference: sequence
type: ForwardStrandPosition
type: FuzzyPosition

position:3079:1
position: 3079
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:2771-3079:1:exon

LAB52_RS10230
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 695562
locus tag: LAB52_RS10230
inference: COORDINATES: similar to AA sequence:RefSeq:WP_014563300.1
GO function: GO:0003677 - DNA binding [Evidence IEA]; GO:0004803 - transposase activity [Evidence IEA]
GO process: GO:0006313 - transposition, DNA-mediated [Evidence IEA]
note: frameshifted; incomplete; partial in the middle of a contig; missing N-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
pseudo: true
codon start: 1
transl table: 11
product: transposase
SIO_010081: LAB52_RS10230
subclass of: SO_0000673
so part of: LAB52_RS10230
location: <2771..3079
location: region:2771-3079:1
so has part: feature:2771-3079:1:exon

urn:…
SIO_000300: 1
SIO_000628: feature:2771-3079:1:exon

LAB52_RS09520
type: Gene
subclass of: SO_0000704
RO_0002162: 695562
locus tag: LAB52_RS09520
old locus tag: LAB52_09853
so part of: sequence
location: 3198..3560
location: region:3198-3560:1
so has part: feature:3198-3560:1:exon
subclass of: SO_0000010

66524642
type: Gene
SIO_000068: ncbigene

position:3198:1
position: 3198
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:3560:1
position: 3560
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:3198-3560:1:exon

LAB52_RS09520
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 695562
locus tag: LAB52_RS09520
old locus tag: LAB52_09853
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: DNA-entry nuclease
translation: MEAQSIGDNSVHFNVFIFNVQPGVKLNYKDGTSRVVNTTTHKKATDIGVKKNKVQRIKKTRTVHHVRGTVSTAKHRVVGNKKSKIYHVMNGANYHISKANAVYFPSEAAAKAAGYRKSLR
SIO_010081: LAB52_RS09520
subclass of: SO_0000673
so part of: LAB52_RS09520
location: 3198..3560
location: region:3198-3560:1
so has part: feature:3198-3560:1:exon

WP_014566275.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:3198-3560:1:exon

LAB52_RS09525
type: Gene
subclass of: SO_0000704
RO_0002162: 695562
locus tag: LAB52_RS09525
old locus tag: LAB52_09858
so part of: sequence
location: complement(3613..3963)
location: region:3613-3963:-1
so has part: feature:3613-3963:-1:exon
subclass of: SO_0000010

66524643
type: Gene
SIO_000068: ncbigene

position:3613:-1
position: 3613
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:3963:-1
position: 3963
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:3613-3963:-1:exon

LAB52_RS09525
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 695562
locus tag: LAB52_RS09525
old locus tag: LAB52_09858
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: MNTNEFKLKLTSRAAQESVSSLIEMNNMVGYVTHVDDSARDEKFYDTVKKAYYFAAQTELDFENIDKKIHDALLILLMEAKVAYDYFCKGCEDSEVVRLLGFTNHYATAKLQLLKN
SIO_010081: LAB52_RS09525
subclass of: SO_0000673
so part of: LAB52_RS09525
location: complement(3613..3963)
location: region:3613-3963:-1
so has part: feature:3613-3963:-1:exon

WP_014566276.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:3613-3963:-1:exon