Vagococcus fluvialis strain 36B2 plasmid p36B2_p4, complete sequence.
type: Entry
definition: Vagococcus fluvialis strain 36B2 plasmid p36B2_p4, complete sequence.
sequence version: NZ_CP081465.1
sequence date: 2022-11-02
sequence: sequence
division: CON
label: NZ_CP081465.1
type: RefSeq
SIO_000068: refseq
dblink: PRJNA224116
dblink: SAMN20834666
keyword: RefSeq
source: Vagococcus fluvialis
organism: Vagococcus fluvialis
taxonomy: Bacteria; Bacillota; Bacilli; Lactobacillales; Enterococcaceae; Vagococcus.
reference: 1
reference: 2
comment: REFSEQ INFORMATION: The reference sequence is identical to\nCP081465.1.\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 :: Unicycler v. MAR-2021\nGenome Representation :: Full\nExpected Final Version :: Yes\nGenome Coverage :: 278x\nSequencing Technology :: Illumina NovaSeq; Oxford Nanopore MinION\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 11/02/2022 04:19:51\nAnnotation Pipeline :: NCBI Prokaryotic Genome\n Annotation Pipeline (PGAP)\nAnnotation Method :: Best-placed reference protein\n set; GeneMarkS-2+\nAnnotation Software revision :: 6.3\nFeatures Annotated :: Gene; CDS; rRNA; tRNA; ncRNA;\n repeat_region\nGenes (total) :: 2,945\nCDSs (total) :: 2,841\nGenes (coding) :: 2,813\nCDSs (with protein) :: 2,813\nGenes (RNA) :: 104\nrRNAs :: 7, 7, 7 (5S, 16S, 23S)\ncomplete rRNAs :: 7, 7, 7 (5S, 16S, 23S)\ntRNAs :: 79\nncRNAs :: 4\nPseudo Genes (total) :: 28\nCDSs (without protein) :: 28\nPseudo Genes (ambiguous residues) :: 0 of 28\nPseudo Genes (frameshifted) :: 10 of 28\nPseudo Genes (incomplete) :: 19 of 28\nPseudo Genes (internal stop) :: 5 of 28\nPseudo Genes (multiple problems) :: 5 of 28\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.

sequence
subclass of: SO_0000155
sequence length: 4500
topology: circular
so has quality: SO_0000988
location: 1..4500
location: region:1-4500:1
RO_0002162: 2738

NZ_CP081465
type: RefSeq
SIO_000068: refseq

PRJNA224116
type: BioProject
SIO_000068: bioproject

SAMN20834666
type: BioSample
SIO_000068: biosample

1
title: High-quality genome assembly reveals abundance of mobile genetic elements in sponge-isolated Vagococcus fluvialis strains
author: Rodriguez Jimenez, A.
author: Guiglielmoni, N.
author: Goetghebuer, L.
author: Dechamps, E.
author: George, I.F.
author: Flot, J.-F.
journal: Unpublished

2
title: Direct Submission
author: Rodriguez Jimenez, A.
author: Guiglielmoni, N.
author: Goetghebuer, L.
author: Dechamps, E.
author: George, I.F.
author: Flot, J.-F.
journal: Submitted (17-AUG-2021) Ecology of Aquatic Systems, Universite Libre de Bruxelles, Boulevard du Triomphe, Brussels 1050, Belgium

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

position:4500:1
position: 4500
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

feature:1-4500:1:source
so part of: sequence
organism: Vagococcus fluvialis
mol type: genomic DNA
strain: 36B2
isolation source: marine sponge
host: Halichondria panicea
plasmid: p36B2_p4
country: France: Wimereux
collection date: 2013-10-20

2738
type: Taxonomy
SIO_000068: taxonomy

K5K99_RS14715
type: Gene
subclass of: SO_0000704
RO_0002162: 2738
locus tag: K5K99_RS14715
old locus tag: K5K99_14680
so part of: sequence
location: 57..491
location: region:57-491:1
so has part: feature:57-491:1:exon
subclass of: SO_0000010

69882613
type: Gene
SIO_000068: ncbigene

position:57:1
position: 57
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:491:1
position: 491
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:57-491:1:exon

K5K99_RS14715
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 2738
locus tag: K5K99_RS14715
old locus tag: K5K99_14680
inference: COORDINATES: protein motif:HMM:NF024139.2
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: helix-turn-helix domain-containing protein
translation: MISVTEIAEKLQISKMMVYRFINNNEIKHSAKDGRTFLYDMTAFQTIKEGLKDKSVISPDNNIEITENKNAEEPLQINDNDVIIEIMKSEIEIKNKQIDELTEMNKALNVTLQQQQQLLLYEQQKNTKLLEENIENKRWWQWWK
SIO_010081: K5K99_RS14715
subclass of: SO_0000673
so part of: K5K99_RS14715
location: 57..491
location: region:57-491:1
so has part: feature:57-491:1:exon

WP_219930772.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:57-491:1:exon

K5K99_RS14720
type: Gene
subclass of: SO_0000704
RO_0002162: 2738
locus tag: K5K99_RS14720
old locus tag: K5K99_14685
so part of: sequence
location: 1046..1972
location: region:1046-1972:1
so has part: feature:1046-1972:1:exon
subclass of: SO_0000010

69882614
type: Gene
SIO_000068: ncbigene

position:1046:1
position: 1046
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:1972:1
position: 1972
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:1046-1972:1:exon

K5K99_RS14720
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 2738
locus tag: K5K99_RS14720
old locus tag: K5K99_14685
inference: COORDINATES: similar to AA sequence:RefSeq:WP_002296860.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: replication initiation protein
translation: MSNEIIKYHTELNTIPLRKFTPVEMNLFFSIVSRMRDKGTQKIQFTFDQLKDLSDYKATANVRFIDDLETTYDKLMDLRFGRRSADGLERERFVMFNEFQIKGKADVPYAEIQIHEKALPLLNNLDEWVRYSLQQFTELQSSYSKTMFRLLKQFRTTGYAYFSKEDFFELLDIPKSYWNKPANIDSRILKPIKEELTPLFRGLTIKKKHGKGRGKPVIGYQFYFKAEAKNADDFSKGERENLRIKMFNIEHNGELSQEEKWVAKDKVLGLKIGTHEADYYSQQQKESDKIEEEKLRKDLLKELQNGFK
SIO_010081: K5K99_RS14720
subclass of: SO_0000673
so part of: K5K99_RS14720
location: 1046..1972
location: region:1046-1972:1
so has part: feature:1046-1972:1:exon

WP_219930773.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:1046-1972:1:exon

K5K99_RS14725
type: Gene
subclass of: SO_0000704
RO_0002162: 2738
locus tag: K5K99_RS14725
old locus tag: K5K99_14690
so part of: sequence
location: 2473..2628
location: region:2473-2628:1
so has part: feature:2473-2628:1:exon
subclass of: SO_0000010

69882615
type: Gene
SIO_000068: ncbigene

position:2473:1
position: 2473
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:2628:1
position: 2628
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:2473-2628:1:exon

K5K99_RS14725
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 2738
locus tag: K5K99_RS14725
old locus tag: K5K99_14690
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: MTLSLIENLNLLEKEIQKKKQGQPTHLNKFSIDVIENEKDKPTLPTDETLN
SIO_010081: K5K99_RS14725
subclass of: SO_0000673
so part of: K5K99_RS14725
location: 2473..2628
location: region:2473-2628:1
so has part: feature:2473-2628:1:exon

WP_219930770.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:2473-2628:1:exon

K5K99_RS14730
type: Gene
subclass of: SO_0000704
RO_0002162: 2738
locus tag: K5K99_RS14730
old locus tag: K5K99_14695
so part of: sequence
location: complement(3266..3613)
location: region:3266-3613:-1
so has part: feature:3266-3613:-1:exon
subclass of: SO_0000010

69882616
type: Gene
SIO_000068: ncbigene

position:3266:-1
position: 3266
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

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

urn:…
SIO_000300: 1
SIO_000628: feature:3266-3613:-1:exon

K5K99_RS14730
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 2738
locus tag: K5K99_RS14730
old locus tag: K5K99_14695
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: MIDSKEDNINEDEYEKEIRKESKRLANEVFLDLKKYEDIRLSNGNKHVFCMDYILDRYQDLSDISFDNNFNNFCNNLLEEFQNNNYVIKDFHIDYVEEKGFFKKYKIAKLRIIYA
SIO_010081: K5K99_RS14730
subclass of: SO_0000673
so part of: K5K99_RS14730
location: complement(3266..3613)
location: region:3266-3613:-1
so has part: feature:3266-3613:-1:exon

WP_227259548.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:3266-3613:-1:exon

K5K99_RS14735
type: Gene
subclass of: SO_0000704
RO_0002162: 2738
locus tag: K5K99_RS14735
old locus tag: K5K99_14700
so part of: sequence
location: complement(3789..4202)
location: region:3789-4202:-1
so has part: feature:3789-4202:-1:exon
subclass of: SO_0000010

69882617
type: Gene
SIO_000068: ncbigene

position:3789:-1
position: 3789
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:4202:-1
position: 4202
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:3789-4202:-1:exon

K5K99_RS14735
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 2738
locus tag: K5K99_RS14735
old locus tag: K5K99_14700
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: MTIGEKIKSLRQSKDLTQSGLGELLNVSSQAVSNWERGKGYPDISNVIQISELFQVSLDILIKEDIDFKAALIEDKAEKQVDIFFSSLAFIISLVIFIFSIYFLYKKGLEIQLIFGLVVGILGMVDFGKKIKNRIKK
SIO_010081: K5K99_RS14735
subclass of: SO_0000673
so part of: K5K99_RS14735
location: complement(3789..4202)
location: region:3789-4202:-1
so has part: feature:3789-4202:-1:exon

WP_219930771.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:3789-4202:-1:exon