Vibrio aquimaris strain THAF100 plasmid pTHAF100_c, complete sequence.
type: Entry
definition: Vibrio aquimaris strain THAF100 plasmid pTHAF100_c, complete sequence.
sequence version: NZ_CP045353.1
sequence date: 2023-05-06
sequence: sequence
division: CON
label: NZ_CP045353.1
type: RefSeq
SIO_000068: refseq
dblink: PRJNA224116
dblink: SAMN11996127
keyword: RefSeq
source: Vibrio aquimaris
organism: Vibrio aquimaris
taxonomy: Bacteria; Pseudomonadota; Gammaproteobacteria; Vibrionales; Vibrionaceae; Vibrio.
reference: 1
reference: 2
comment: REFSEQ INFORMATION: The reference sequence is identical to\nCP045353.1.\nAnnotated using prokka v1.11 from http://www.vicbioinformatics.com.\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. 0.4.6\nGenome Representation :: Full\nExpected Final Version :: Yes\nGenome Coverage :: 121.9x\nSequencing Technology :: Illumina MiSeq, Oxford Nanopore GridION\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 05/06/2023 02:41:20\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) :: 4,126\nCDSs (total) :: 3,989\nGenes (coding) :: 3,908\nCDSs (with protein) :: 3,908\nGenes (RNA) :: 137\nrRNAs :: 10, 9, 9 (5S, 16S, 23S)\ncomplete rRNAs :: 10, 9, 9 (5S, 16S, 23S)\ntRNAs :: 105\nncRNAs :: 4\nPseudo Genes (total) :: 81\nCDSs (without protein) :: 81\nPseudo Genes (ambiguous residues) :: 0 of 81\nPseudo Genes (frameshifted) :: 23 of 81\nPseudo Genes (incomplete) :: 59 of 81\nPseudo Genes (internal stop) :: 21 of 81\nPseudo Genes (multiple problems) :: 19 of 81\nCRISPR Arrays :: 1\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.

sequence
subclass of: SO_0000155
sequence length: 4831
topology: circular
so has quality: SO_0000988
location: 1..4831
location: region:1-4831:1
RO_0002162: 2587862

NZ_CP045353
type: RefSeq
SIO_000068: refseq

PRJNA224116
type: BioProject
SIO_000068: bioproject

SAMN11996127
type: BioSample
SIO_000068: biosample

1
title: Complete genome sequence of Vibrio sp. strain THAF100, isolated from non-filtered water from the water column of tank 6 of a marine aquarium containing stony-coral fragments. Water maintained at 26 degree C
author: Ruckert, C.
author: Franco, A.
author: Kalinowski, J.
author: Glaeser, S.
journal: Unpublished

2
title: Direct Submission
author: Ruckert, C.
author: Franco, A.
author: Kalinowski, J.
author: Glaeser, S.
journal: Submitted (08-OCT-2019) CeBiTec, Uni Bielefeld, Sequenz 1, Bielefeld 33615, Germany

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

position:4831:1
position: 4831
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

feature:1-4831:1:source
so part of: sequence
organism: Vibrio aquimaris
mol type: genomic DNA
strain: THAF100
isolation source: Non-filtered water from the water column of tank 6 of a marine aquarium containing stony-coral fragments. Water maintained at 26 degree C
type material: type strain of Vibrio aquimaris
plasmid: pTHAF100_c
country: Germany: Animal Facility, Justus-Liebig-University, Giessen
lat lon: 50.5686 N 8.6717 E
collection date: 2016-08-30

2587862
type: Taxonomy
SIO_000068: taxonomy

FIV01_RS20660
type: Gene
subclass of: SO_0000704
RO_0002162: 2587862
locus tag: FIV01_RS20660
so part of: sequence
location: join(4087..4831,1..23)
location: region:1-4831:1
so has part: feature:4087-4831:1:exon
so has part: feature:1-23:1:exon
subclass of: SO_0000010

urn:…
SIO_000300: 1
SIO_000628: feature:4087-4831:1:exon

position:4087:1
position: 4087
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 2
SIO_000628: feature:1-23:1:exon

position:23:1
position: 23
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

FIV01_RS20660
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 2587862
locus tag: FIV01_RS20660
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: MSSKTILDDWDIDSDYFTQVVRDNPSLRGMILGYIAERKLKDIFISSGKTTNHRKEDDHDRTKKGDLTLDYKGHEIVLEVKSLQTNKIKIQAPDGSWMPMIVKKNVGRKPSNGFNKNGTPKAGQIIYNYVPNPDFLALSDEYRLNANYMGAFQCDASDRRKIELDNGKVVNTTLLKVGEFDVIAAGIFSFRNKWEFGFALNGDLPRSNQYGDNSSHLIASLVQITYPLESPFVSDPFEIFDKVIAQRESLLLDEN
SIO_010081: FIV01_RS20660
subclass of: SO_0000673
so part of: FIV01_RS20660
location: join(4087..4831,1..23)
location: region:1-4831:1
so has part: feature:4087-4831:1:exon
so has part: feature:1-23:1:exon

WP_172971900.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:4087-4831:1:exon

urn:…
SIO_000300: 2
SIO_000628: feature:1-23:1:exon

FIV01_RS20535
type: Gene
subclass of: SO_0000704
RO_0002162: 2587862
locus tag: FIV01_RS20535
old locus tag: FIV01_20830
so part of: sequence
location: complement(3..734)
location: region:3-734:-1
so has part: feature:3-734:-1:exon
subclass of: SO_0000010

position:3:-1
position: 3
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:734:-1
position: 734
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:3-734:-1:exon

FIV01_RS20535
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 2587862
locus tag: FIV01_RS20535
old locus tag: FIV01_20830
inference: COORDINATES: similar to AA sequence:RefSeq:WP_011958749.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: site-specific DNA-methyltransferase
translation: MTLQNIESSLSLQEKTIKKRTQGGIATSNLIMSAYTDGNENVFPYVLDLHVPKGSKVADVTWGRGVFWKKVPKEDYDVTGTDISMGVDCRDLPYEDGSLDCVVLDPPYMEGFYRKNNAHKAGAGSHKGLAQAYSNGDEVNSDTQNTGTKKWHAAVTDMYFKASAEAYRVLRKKGILIVKCQDEVSAGKQWFTHVEIINELESMGYYSKDLFVVVRQNKPAVSRLKNQVHARKNHSYFLVFIKK
SIO_010081: FIV01_RS20535
subclass of: SO_0000673
so part of: FIV01_RS20535
location: complement(3..734)
location: region:3-734:-1
so has part: feature:3-734:-1:exon

WP_172971898.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:3-734:-1:exon

FIV01_RS20540
type: Gene
subclass of: SO_0000704
RO_0002162: 2587862
locus tag: FIV01_RS20540
old locus tag: FIV01_20835
so part of: sequence
location: 1277..1639
location: region:1277-1639:1
so has part: feature:1277-1639:1:exon
subclass of: SO_0000010

position:1277:1
position: 1277
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:1639:1
position: 1639
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:1277-1639:1:exon

FIV01_RS20540
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 2587862
locus tag: FIV01_RS20540
old locus tag: FIV01_20835
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: MRNDVFYKTPFVLFLVLVLGSSAILAFDYLGDYVEKASAFISSVITFLVISELLARSKGMSLFSREKIKIIAFLYVFWLLFEQGYPLYIYRDQTLPEGYLFTMYLQLAFNAFVAKVLIND
SIO_010081: FIV01_RS20540
subclass of: SO_0000673
so part of: FIV01_RS20540
location: 1277..1639
location: region:1277-1639:1
so has part: feature:1277-1639:1:exon

WP_152432867.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:1277-1639:1:exon

FIV01_RS20545
type: Gene
subclass of: SO_0000704
RO_0002162: 2587862
locus tag: FIV01_RS20545
old locus tag: FIV01_20840
so part of: sequence
location: 1632..1958
location: region:1632-1958:1
so has part: feature:1632-1958:1:exon
subclass of: SO_0000010

position:1632:1
position: 1632
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:1958:1
position: 1958
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:1632-1958:1:exon

FIV01_RS20545
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 2587862
locus tag: FIV01_RS20545
old locus tag: FIV01_20840
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: MIDFKSISGQLSKASPAYSLIVAMYKQLDARSKANNIYAELVPAMHDLLQAGYSYESPEIQAMVNVLRELPAWGVKRTNFEKNFLRDEQGLRKLPKDPTRLNGMGYWH
SIO_010081: FIV01_RS20545
subclass of: SO_0000673
so part of: FIV01_RS20545
location: 1632..1958
location: region:1632-1958:1
so has part: feature:1632-1958:1:exon

WP_152432868.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:1632-1958:1:exon

FIV01_RS20550
type: Gene
subclass of: SO_0000704
RO_0002162: 2587862
locus tag: FIV01_RS20550
old locus tag: FIV01_20845
so part of: sequence
location: 2514..2702
location: region:2514-2702:1
so has part: feature:2514-2702:1:exon
subclass of: SO_0000010

position:2514:1
position: 2514
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:2702:1
position: 2702
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:2514-2702:1:exon

FIV01_RS20550
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 2587862
locus tag: FIV01_RS20550
old locus tag: FIV01_20845
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: MSKLHPSQLVQILVLLERQSSTELRRIECRYYDVPRYRNSLEREGLIKGFLVESIVPHDIRG
SIO_010081: FIV01_RS20550
subclass of: SO_0000673
so part of: FIV01_RS20550
location: 2514..2702
location: region:2514-2702:1
so has part: feature:2514-2702:1:exon

WP_152432869.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:2514-2702:1:exon

FIV01_RS20665
type: Gene
subclass of: SO_0000704
RO_0002162: 2587862
locus tag: FIV01_RS20665
old locus tag: FIV01_20850
so part of: sequence
location: complement(2703..2888)
location: region:2703-2888:-1
so has part: feature:2703-2888:-1:exon
subclass of: SO_0000010

position:2703:-1
position: 2703
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:2888:-1
position: 2888
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:2703-2888:-1:exon

FIV01_RS20665
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 2587862
locus tag: FIV01_RS20665
old locus tag: FIV01_20850
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: MPGKISEAIFLGVVMRQAPDRLKLELRSQRGAFSINTKADIRRRAGSPQKLKERKLGTESK
SIO_010081: FIV01_RS20665
subclass of: SO_0000673
so part of: FIV01_RS20665
location: complement(2703..2888)
location: region:2703-2888:-1
so has part: feature:2703-2888:-1:exon

WP_172971899.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:2703-2888:-1:exon

FIV01_RS20555
type: Gene
subclass of: SO_0000704
RO_0002162: 2587862
locus tag: FIV01_RS20555
old locus tag: FIV01_20855
so part of: sequence
location: 3846..4097
location: region:3846-4097:1
so has part: feature:3846-4097:1:exon
subclass of: SO_0000010

position:3846:1
position: 3846
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:4097:1
position: 4097
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:3846-4097:1:exon

FIV01_RS20555
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 2587862
locus tag: FIV01_RS20555
old locus tag: FIV01_20855
inference: COORDINATES: similar to AA sequence:RefSeq:WP_017716966.1
GO function: GO:0003677 - DNA binding [Evidence IEA]
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: MTSSVFSKKYEIFRLLLVSARKDLGVTQKVLAEQLNKPQSFVSKYESGERRLDLIEFLDVAAALQFDACQFIKKLEGKSKGEQ
SIO_010081: FIV01_RS20555
subclass of: SO_0000673
so part of: FIV01_RS20555
location: 3846..4097
location: region:3846-4097:1
so has part: feature:3846-4097:1:exon

WP_152432870.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:3846-4097:1:exon