Arsenophonus nasoniae strain FIN plasmid pArsFIN18, complete sequence.
type: Entry
definition: Arsenophonus nasoniae strain FIN plasmid pArsFIN18, complete sequence.
sequence version: NZ_CP038630.1
sequence date: 2023-03-25
sequence: sequence
division: CON
label: NZ_CP038630.1
type: RefSeq
SIO_000068: refseq
dblink: PRJNA224116
dblink: SAMN11265189
keyword: RefSeq
source: Arsenophonus nasoniae (son-killer infecting Nasonia vitripennis)
organism: Arsenophonus nasoniae
taxonomy: Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales; Morganellaceae; Arsenophonus.
reference: 1
reference: 2
comment: REFSEQ INFORMATION: The reference sequence is identical to\nCP038630.1.\nAnnotated using prokka 1.12-beta from\nhttps://github.com/tseemann/prokka.\nBacteria and source DNA available from Prof Greg Hurst, Institute\nof Integrative Biology, University of Liverpool.\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 :: 2018\nAssembly Method :: Unicycler v. 0.4.5\nGenome Representation :: Full\nExpected Final Version :: Yes\nGenome Coverage :: 169.0x\nSequencing Technology :: Oxford Nanopore MiniION; PacBio RSII;\n Illumina MiSeq\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 03/25/2023 01:21:09\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) :: 5,421\nCDSs (total) :: 5,317\nGenes (coding) :: 4,929\nCDSs (with protein) :: 4,929\nGenes (RNA) :: 104\nrRNAs :: 8, 7, 7 (5S, 16S, 23S)\ncomplete rRNAs :: 8, 7, 7 (5S, 16S, 23S)\ntRNAs :: 70\nncRNAs :: 12\nPseudo Genes (total) :: 388\nCDSs (without protein) :: 388\nPseudo Genes (ambiguous residues) :: 0 of 388\nPseudo Genes (frameshifted) :: 199 of 388\nPseudo Genes (incomplete) :: 170 of 388\nPseudo Genes (internal stop) :: 85 of 388\nPseudo Genes (multiple problems) :: 61 of 388\nCRISPR Arrays :: 1\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.

sequence
subclass of: SO_0000155
sequence length: 7173
topology: circular
so has quality: SO_0000988
location: 1..7173
location: region:1-7173:1
RO_0002162: 638

NZ_CP038630
type: RefSeq
SIO_000068: refseq

PRJNA224116
type: BioProject
SIO_000068: bioproject

SAMN11265189
type: BioSample
SIO_000068: biosample

1
title: Long-read sequencing reveals hyperdense prophage content in a complex bacterial symbiont genome
author: Frost, C.L.
author: Siozios, S.
author: Nadal-Jimenez, P.
author: Brockhurst, M.A.
author: King, K.C.
author: Darby, A.C.
author: Hurst, G.D.D.
journal: Unpublished

2
title: Direct Submission
author: Siozios, S.
author: Darby, A.C.
author: Hurst, G.D.D.
journal: Submitted (29-MAR-2019) Evolution, Ecology and Behaviour, University of Liverpool, Crown Street, Biosciences building, Liverpool L69 7ZB, United Kingdom

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

position:7173:1
position: 7173
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

feature:1-7173:1:source
so part of: sequence
organism: Arsenophonus nasoniae
mol type: genomic DNA
strain: FIN
isolation source: whole insect
host: Nasonia vitripennis
plasmid: pArsFIN18
country: Finland
collection date: 2013

638
type: Taxonomy
SIO_000068: taxonomy

ArsFIN_RS26095
type: Gene
subclass of: SO_0000704
RO_0002162: 638
locus tag: ArsFIN_RS26095
so part of: sequence
location: join(7120..7173,1..201)
location: region:1-7173:1
so has part: feature:7120-7173:1:exon
so has part: feature:1-201:1:exon
subclass of: SO_0000010

urn:…
SIO_000300: 1
SIO_000628: feature:7120-7173:1:exon

position:7120:1
position: 7120
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 2
SIO_000628: feature:1-201:1:exon

position:201:1
position: 201
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

ArsFIN_RS26095
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 638
locus tag: ArsFIN_RS26095
inference: COORDINATES: similar to AA sequence:RefSeq:WP_006703980.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: transcriptional regulator
translation: MRMFDVKQVEQFSNVFPELTTKEQLETAMLFSLGLSKKEIASARNVAYRTVEHSLEDIKTRYDLYSLNDMLSIFQVRLSFLAVL
SIO_010081: ArsFIN_RS26095
subclass of: SO_0000673
so part of: ArsFIN_RS26095
location: join(7120..7173,1..201)
location: region:1-7173:1
so has part: feature:7120-7173:1:exon
so has part: feature:1-201:1:exon

WP_135678710.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:7120-7173:1:exon

urn:…
SIO_000300: 2
SIO_000628: feature:1-201:1:exon

ArsFIN_RS26100
type: Gene
subclass of: SO_0000704
RO_0002162: 638
locus tag: ArsFIN_RS26100
old locus tag: ArsFIN_56450
so part of: sequence
location: complement(961..1683)
location: region:961-1683:-1
so has part: feature:961-1683:-1:exon
subclass of: SO_0000010

position:961:-1
position: 961
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:1683:-1
position: 1683
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:961-1683:-1:exon

ArsFIN_RS26100
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 638
locus tag: ArsFIN_RS26100
old locus tag: ArsFIN_56450
inference: COORDINATES: similar to AA sequence:RefSeq:WP_011145287.1
GO process: GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: PAS and helix-turn-helix domain-containing protein
translation: MKSKCMKFSINKDLDVHSNSFDAFISYMEHSNDFWVIKDHESRFVYANKTMIYYSGLPKGFNIEGLLDSECPAPWSEFEDVIQANDKNVMENKKTIPVLNTFVYGGRDKIVQPFMVEVTPLIKDGKSIGVVARGKKLEIFSMYHLENNKLPDSLSFGKSTDLFTDREFDVVFFALQSLSAKEIARRLNISPGTVENYLHSIYEKTGVSALNQLIEYCRNNGYDKYAPNKFINPNPYIPLA
SIO_010081: ArsFIN_RS26100
subclass of: SO_0000673
so part of: ArsFIN_RS26100
location: complement(961..1683)
location: region:961-1683:-1
so has part: feature:961-1683:-1:exon

WP_135679381.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:961-1683:-1:exon

ArsFIN_RS26105
type: Gene
subclass of: SO_0000704
RO_0002162: 638
locus tag: ArsFIN_RS26105
old locus tag: ArsFIN_56460
so part of: sequence
location: 2308..3336
location: region:2308-3336:1
so has part: feature:2308-3336:1:exon
subclass of: SO_0000010

position:2308:1
position: 2308
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:3336:1
position: 3336
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:2308-3336:1:exon

ArsFIN_RS26105
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 638
locus tag: ArsFIN_RS26105
old locus tag: ArsFIN_56460
inference: COORDINATES: protein motif:HMM:NF013603.2
GO function: GO:0003677 - DNA binding [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: protein rep
translation: MSNFIVGSAYSICESFNTVNTKNKSSDIALSEMSPKDAKFDKMKAASELLSEVLLGTDFDKWSVRINTCADILKYYPHIDKETGEFFIKLIEVYFCHCRHCPVCDGRRSLRHMAMFKKSLPNILNEYPKSRWVFMTLTVPNIPVESLRDELGLMSKGWKRFVKRKEFKQVKGWIRKTEVTCEGKRKNYAHPHFHCLLMVAPSWFDGKHYTKQSRWSEIWGECMKLDTVPIVDVRAVKGTPDIAAVEVLKAFNYSVKPETLVNNREWMLEYFNQVHYLKFIASGGVLKNVFKSTEPETDDSLIHVDGESESSEDEAKVRVAFNWRTHDKQYRRFRKGDSGFAS
SIO_010081: ArsFIN_RS26105
subclass of: SO_0000673
so part of: ArsFIN_RS26105
location: 2308..3336
location: region:2308-3336:1
so has part: feature:2308-3336:1:exon

WP_135679383.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:2308-3336:1:exon

ArsFIN_RS26110
type: Gene
subclass of: SO_0000704
RO_0002162: 638
locus tag: ArsFIN_RS26110
old locus tag: ArsFIN_56480
so part of: sequence
location: complement(5075..5332)
location: region:5075-5332:-1
so has part: feature:5075-5332:-1:exon
subclass of: SO_0000010

position:5075:-1
position: 5075
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:5332:-1
position: 5332
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:5075-5332:-1:exon

ArsFIN_RS26110
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 638
locus tag: ArsFIN_RS26110
old locus tag: ArsFIN_56480
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: MYEIDLSKNEGKNKSQTGIMSTMKGSTVNNEERFIKFKEPNLNINVNVNVNVDGSFGAKDLISIVKDFTNEYINNISKITSSVIE
SIO_010081: ArsFIN_RS26110
subclass of: SO_0000673
so part of: ArsFIN_RS26110
location: complement(5075..5332)
location: region:5075-5332:-1
so has part: feature:5075-5332:-1:exon

WP_135679385.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:5075-5332:-1:exon

ArsFIN_RS26115
type: Gene
subclass of: SO_0000704
RO_0002162: 638
locus tag: ArsFIN_RS26115
old locus tag: ArsFIN_56490
so part of: sequence
location: 5709..6653
location: region:5709-6653:1
so has part: feature:5709-6653:1:exon
subclass of: SO_0000010

position:5709:1
position: 5709
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:6653:1
position: 6653
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:5709-6653:1:exon

ArsFIN_RS26115
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 638
locus tag: ArsFIN_RS26115
old locus tag: ArsFIN_56490
inference: COORDINATES: similar to AA sequence:RefSeq:WP_011279251.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: Rpn family recombination-promoting nuclease/putative transposase
translation: MTKKFTPTPHDAVFKQFLSEKETAKDFFDIWLPDEIKALCDLDSLKVESGSFVDSEMKNYQSDILYSVSTTKGSGYIYVLIEHQSTPDKLIAWRLMRYSLAAMQKHLEAGNKQLPLVFPILFYCGEQSPHPYSTHWLDCFEDRKLAESIYINPFKLADVTTLDDGEIMQHKRIALLELLQKHIRRRDMTELLDSIVKLLSYNYYTDNQVITMFNYLIQEGNAKKPMEFITEIAKQSEKHEGALMTIAQQIEEIGIQKGLQKGLQRGKIEGIQEGMQQERIKLAKQFLANGVDRNTVKISTGLSDEELDKLQNKI
SIO_010081: ArsFIN_RS26115
subclass of: SO_0000673
so part of: ArsFIN_RS26115
location: 5709..6653
location: region:5709-6653:1
so has part: feature:5709-6653:1:exon

WP_135679387.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:5709-6653:1:exon