Haloferax volcanii DS2 plasmid pHV2, complete sequence.
type: Entry
definition: Haloferax volcanii DS2 plasmid pHV2, complete sequence.
sequence version: NC_013965.1
sequence date: 2023-03-12
sequence: sequence
division: CON
label: NC_013965.1
type: RefSeq
SIO_000068: refseq
dblink: PRJNA224116
dblink: SAMN02604027
keyword: RefSeq
source: Haloferax volcanii DS2
organism: Haloferax volcanii DS2
taxonomy: Archaea; Euryarchaeota; Stenosarchaea group; Halobacteria; Haloferacales; Haloferacaceae; Haloferax.
reference: 1
references: 20333302
reference: 2
reference: 3
reference: 4
reference: 5
comment: REFSEQ INFORMATION: The reference sequence is identical to\nCP001954.1.\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 :: 03/12/2023 12:20:58\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) :: 4,067\nCDSs (total) :: 4,006\nGenes (coding) :: 3,921\nCDSs (with protein) :: 3,921\nGenes (RNA) :: 61\nrRNAs :: 2, 2, 2 (5S, 16S, 23S)\ncomplete rRNAs :: 2, 2, 2 (5S, 16S, 23S)\ntRNAs :: 53\nncRNAs :: 2\nPseudo Genes (total) :: 85\nCDSs (without protein) :: 85\nPseudo Genes (ambiguous residues) :: 0 of 85\nPseudo Genes (frameshifted) :: 42 of 85\nPseudo Genes (incomplete) :: 44 of 85\nPseudo Genes (internal stop) :: 21 of 85\nPseudo Genes (multiple problems) :: 18 of 85\nCRISPR Arrays :: 3\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.

sequence
subclass of: SO_0000155
sequence length: 6359
topology: circular
so has quality: SO_0000988
location: 1..6359
location: region:1-6359:1
RO_0002162: 309800

NC_013965
type: RefSeq
SIO_000068: refseq

PRJNA224116
type: BioProject
SIO_000068: bioproject

SAMN02604027
type: BioSample
SIO_000068: biosample

1
title: The complete genome sequence of Haloferax volcanii DS2, a model archaeon
author: Hartman, A.L.
author: Norais, C.
author: Badger, J.H.
author: Delmas, S.
author: Haldenby, S.
author: Madupu, R.
author: Robinson, J.
author: Khouri, H.
author: Ren, Q.
author: Lowe, T.M.
author: Maupin-Furlow, J.
author: Pohlschroder, M.
author: Daniels, C.
author: Pfeiffer, F.
author: Allers, T.
author: Eisen, J.A.
journal: PLoS One 5 (3), e9605 (2010)
pubmed: 20333302
comments: Publication Status: Online-Only

20333302
type: PubMed
SIO_000068: pubmed

2
title: Direct Submission
author: Pfeiffer, F.
journal: Submitted (04-JUN-2021) Computational Biology Group, Max-Planck Institute of Biochemistry, Am Klopferspitz 18, Martinsreid D-82152, Germany
comments: Protein update by submitter

3
title: Direct Submission
author: Pfeiffer, F.
journal: Submitted (14-MAY-2020) Computational Biology Group, Max-Planck Institute of Biochemistry, Am Klopferspitz 18, Martinsreid D-82152, Germany
comments: Protein update by submitter

4
title: Direct Submission
author: Pfeiffer, F.
journal: Submitted (15-SEP-2016) Computational Biology Group, Max-Planck Institute of Biochemistry, Am Klopferspitz 18, Martinsreid D-82152, Germany
comments: Protein update by submitter

5
title: Direct Submission
author: Madupu, R.M.
author: Hartman, A.L.
author: Norais, C.
author: Badger, J.A.
author: Delma, S.
author: Haldenby, S.
author: Khouri, H.
author: Ren, Q.
author: Lowe, T.
author: Robinson, J.
author: Furlow, J.M.
author: Pohlschroder, M.
author: Pfeiffer, T.
author: Allers, T.
author: Daniels, C.
author: Eisen, J.A.
journal: Submitted (04-FEB-2010) J. Craig Venter Institute, 9704 Medical Center Drive, Rockville, MD 20850, USA

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

position:6359:1
position: 6359
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

feature:1-6359:1:source
so part of: sequence
organism: Haloferax volcanii DS2
mol type: genomic DNA
strain: DS2
type material: type strain of Haloferax volcanii
plasmid: pHV2
note: type strain of Haloferax volcanii

309800
type: Taxonomy
SIO_000068: taxonomy

HVO_RS01845
type: Gene
subclass of: SO_0000704
RO_0002162: 309800
locus tag: HVO_RS01845
old locus tag: HVO_D0001
so part of: sequence
location: complement(join(6038..6359,1..284))
location: region:1-6359:-1
so has part: feature:1-284:-1:exon
so has part: feature:6038-6359:-1:exon
subclass of: SO_0000010

25143369
type: Gene
SIO_000068: ncbigene

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

position:6359:-1
position: 6359
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:1-284:-1:exon

position:284:-1
position: 284
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 2
SIO_000628: feature:6038-6359:-1:exon

position:6038:-1
position: 6038
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

HVO_RS01845
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 309800
locus tag: HVO_RS01845
old locus tag: HVO_D0001
inference: COORDINATES: similar to AA sequence:RefSeq:WP_006655017.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: hypothetical protein
translation: MSLDERARGILSPADRRYLQKPKEYSKQAGYERRRAIVERLHEALHDMPLLVSELDEDLRTEAFEDGDLDGKEHTLNVLSWSFALLYLGITDTVEPSDLAKDAFEGIAASGVRQAYLQRGYSVEEVEVEVNVKRGEPLDELREREPDELSYPEVNQLLESGELSHLTGEEQMARIKEAWESGNTDKVGAFPNLELRDNADE
SIO_010081: HVO_RS01845
subclass of: SO_0000673
so part of: HVO_RS01845
location: complement(join(6038..6359,1..284))
location: region:1-6359:-1
so has part: feature:1-284:-1:exon
so has part: feature:6038-6359:-1:exon

WP_006655017.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:1-284:-1:exon

urn:…
SIO_000300: 2
SIO_000628: feature:6038-6359:-1:exon

HVO_RS20735
type: Gene
subclass of: SO_0000704
RO_0002162: 309800
locus tag: HVO_RS20735
old locus tag: HVO_D0002
so part of: sequence
location: 347..490
location: region:347-490:1
so has part: feature:347-490:1:exon
subclass of: SO_0000010

55575130
type: Gene
SIO_000068: ncbigene

position:347:1
position: 347
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:490:1
position: 490
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:347-490:1:exon

HVO_RS20735
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 309800
locus tag: HVO_RS20735
old locus tag: HVO_D0002
inference: COORDINATES: similar to AA sequence:RefSeq:WP_006655018.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: hypothetical protein
translation: MSATDTRIPVSKDVRRDLRVLKAREGRRSYDETIAVVLDAYLSEKVD
SIO_010081: HVO_RS20735
subclass of: SO_0000673
so part of: HVO_RS20735
location: 347..490
location: region:347-490:1
so has part: feature:347-490:1:exon

WP_006655018.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:347-490:1:exon

HVO_RS01850
type: Gene
subclass of: SO_0000704
RO_0002162: 309800
locus tag: HVO_RS01850
old locus tag: HVO_D0003
so part of: sequence
location: 702..3347
location: region:702-3347:1
so has part: feature:702-3347:1:exon
subclass of: SO_0000010

8919381
type: Gene
SIO_000068: ncbigene

position:702:1
position: 702
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:3347:1
position: 3347
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:702-3347:1:exon

HVO_RS01850
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 309800
locus tag: HVO_RS01850
old locus tag: HVO_D0003
inference: COORDINATES: similar to AA sequence:RefSeq:WP_006655019.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: transcriptional regulator
translation: MYDTDDTTAHEPTEKRSLRFATDLEADVSLTDWTALRVHRVIFDETESQFALLEALQTAADGVDILEFEHRLSSCGFDVDGSVVKLARRAVAGERRALWDLIRYARRLGHDEMGQPQSALEDALAFTRLLGYSNPQQTIAIGLNAAFRETRRDQADEIIEYVLTLSESVDVVLGGSEIDRVYLHNYYGDILPSSVTNPCNDTRNDYSITTLVDVVGTDGLAVEILRTVGETESGHMAYSALQSAFSQYDRTTVSRRLNEKLIEYGLCEKYGARGNLRIEILDKGALYLEELAKEKERQKALQDYVTNTPKPNHNTRVITDRPRGGREDDHRPTAEGEASTTPDGRVRLPRYHGVDYLSYAETVSAAKTPPKKGVSVTNYPVEPKSDRGEAGWGYLEDENTLVVSAEYDSAMSHVVMIARALLDPKTFDQVLTEDRLAELDGLIEDGTYVRGSRNLGWLADSVDSAGEYVDVLEDARDELLDMTRSLAHEDYECETSEYLSRITKTAMGLAGTAFHVLDLLDIDVVWEARLPDYNRHPERYGEDNAELLATTLAKNAPIAATYGNHVVRRLLFEDRDEKRRQSFDPVVDASNPYANLIASISVVGDFGNRADHVAGVIEDRLSNPGEIHEDAPEIALKVPVVVEHGPSTVARVTRAMCRAKGLDATRDAIRLFSGFARTPYDVAHAIGRGLSQEATPREIRSSEVRLSLASLPSKRLLEDATPTVRAMISTLLATNLSLSKTELAEKAGISTQSVRNHLPTLVAMGLVDETEGQCRLNLSFTDEQERHKRILPSFMLTESFTRDVLFETLEALDELTEEVIEIWVQCGPNGLPDIDRLHTMYDWVDWVRPLLSSLTEERDETVQTLSIGPEIAQQPLTEAGS
SIO_010081: HVO_RS01850
subclass of: SO_0000673
so part of: HVO_RS01850
location: 702..3347
location: region:702-3347:1
so has part: feature:702-3347:1:exon

WP_006655019.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:702-3347:1:exon

HVO_RS01855
type: Gene
subclass of: SO_0000704
RO_0002162: 309800
locus tag: HVO_RS01855
old locus tag: HVO_D0004A
so part of: sequence
location: complement(4457..4684)
location: region:4457-4684:-1
so has part: feature:4457-4684:-1:exon
subclass of: SO_0000010

25143370
type: Gene
SIO_000068: ncbigene

position:4457:-1
position: 4457
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:4684:-1
position: 4684
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:4457-4684:-1:exon

HVO_RS01855
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 309800
locus tag: HVO_RS01855
old locus tag: HVO_D0004A
inference: COORDINATES: similar to AA sequence:RefSeq:WP_004050879.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: hypothetical protein
translation: MSTNETRSQDSTAIIIAGDDAEVIDDTPDWEGPFTEYDRYGEPTGHNYVRCPVCGAEVLDGETSTASHRPACRYE
SIO_010081: HVO_RS01855
subclass of: SO_0000673
so part of: HVO_RS01855
location: complement(4457..4684)
location: region:4457-4684:-1
so has part: feature:4457-4684:-1:exon

WP_004050879.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:4457-4684:-1:exon

HVO_RS01860
type: Gene
subclass of: SO_0000704
RO_0002162: 309800
locus tag: HVO_RS01860
old locus tag: HVO_D0005
so part of: sequence
location: 4859..5476
location: region:4859-5476:1
so has part: feature:4859-5476:1:exon
subclass of: SO_0000010

8919384
type: Gene
SIO_000068: ncbigene

position:4859:1
position: 4859
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:5476:1
position: 5476
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:4859-5476:1:exon

HVO_RS01860
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 309800
locus tag: HVO_RS01860
old locus tag: HVO_D0005
inference: COORDINATES: similar to AA sequence:RefSeq:WP_004050876.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: hypothetical protein
translation: MPREHGDSGTFVETVSLEDVLGVFDVVDGPVILSADVADELDCSRETARRKLQALYERGDLERRKVSRRVVYWEADVTAETMGYDETARDAPQDAGDSIEGTRTSTASSAAESTIDIDAILSDIEVPGFGEKAEARKTAVRAVLEYLVDHKEAESKTLKEIAWEADSETYANARSLWSNAVVKALHQIPEVSSAGERQSGWSIDE
SIO_010081: HVO_RS01860
subclass of: SO_0000673
so part of: HVO_RS01860
location: 4859..5476
location: region:4859-5476:1
so has part: feature:4859-5476:1:exon

WP_004050876.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:4859-5476:1:exon

HVO_RS01865
type: Gene
subclass of: SO_0000704
RO_0002162: 309800
locus tag: HVO_RS01865
old locus tag: HVO_D0006
so part of: sequence
location: 5469..5891
location: region:5469-5891:1
so has part: feature:5469-5891:1:exon
subclass of: SO_0000010

8919382
type: Gene
SIO_000068: ncbigene

position:5469:1
position: 5469
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:5891:1
position: 5891
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:5469-5891:1:exon

HVO_RS01865
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 309800
locus tag: HVO_RS01865
old locus tag: HVO_D0006
inference: COORDINATES: similar to AA sequence:RefSeq:WP_004050867.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: hypothetical protein
translation: MSDDGDDVDPTNPRPKGHYGRFRDSPWYYVNDELAQTFILGPATDAEPGDDWILSFTGEGATETDRERVCVRLTPRALHELYIETKDLSPDARQAGHTAECDLCGESVPLEKAVPNKREEPVHKRCYVDAYGGPVWMEDY
SIO_010081: HVO_RS01865
subclass of: SO_0000673
so part of: HVO_RS01865
location: 5469..5891
location: region:5469-5891:1
so has part: feature:5469-5891:1:exon

WP_004050867.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:5469-5891:1:exon