Arsenophonus nasoniae strain FIN plasmid pArsFIN16, complete sequence.
type: Entry
definition: Arsenophonus nasoniae strain FIN plasmid pArsFIN16, complete sequence.
sequence version: NZ_CP038628.1
sequence date: 2023-03-25
sequence: sequence
division: CON
label: NZ_CP038628.1
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\nCP038628.1.\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: 8312
topology: linear
so has quality: SO_0000987
location: 1..8312
location: region:1-8312:1
RO_0002162: 638

NZ_CP038628
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:8312:1
position: 8312
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

feature:1-8312:1:source
so part of: sequence
organism: Arsenophonus nasoniae
mol type: genomic DNA
strain: FIN
isolation source: whole insect
host: Nasonia vitripennis
plasmid: pArsFIN16
country: Finland
collection date: 2013

638
type: Taxonomy
SIO_000068: taxonomy

ArsFIN_RS26050
type: Gene
subclass of: SO_0000704
RO_0002162: 638
locus tag: ArsFIN_RS26050
old locus tag: ArsFIN_56340
so part of: sequence
location: 245..1810
location: region:245-1810:1
so has part: feature:245-1810:1:exon
subclass of: SO_0000010

position:245:1
position: 245
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:1810:1
position: 1810
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:245-1810:1:exon

ArsFIN_RS26050
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 638
locus tag: ArsFIN_RS26050
old locus tag: ArsFIN_56340
inference: COORDINATES: protein motif:HMM:NF027994.2
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: protelomerase family protein
translation: MTKVRDKTKKVIEKAEIYKKSITSEIDSKKVRQSVYDIYANYVKRDFGLKENTALIEGKKIKTWYFLPDSEYSSGELSASRIASLLIKYRRALKSLGAINKKFIPSLNAAKKALIKAGVEQSIIYGLKPSLKIKTLEERIALLKRKYPRGSASGKGEMVRQALTSIKMYHPSYYRLAGAVSYVKSITNEQQKIRLKARHDEKIKINPHFLLNKAKFILDNPNSTWVQLTVALCAVTGRRPTEIMKTAKFRVDDKTPDNYIRFSGILKSRDRKFEEDFGEWNIPIFHDVNKIIKALRRLRFELKKQEKKSHESGGKGNYWTGGYLHYINQEGKNIVASIFDPKYTNDVDHNMAINQQYNGVLNNELRKWFESGDIEIKSLRAIYTKMVWEREKDTSSETYDSMTTRILCYSKDSISEAVKHYAAIELSEKTEKIETTTGTVKNYIPSEELMAKLEKANAIIEQRSARAPTLKTIHEWAKNKANLGLTLNELTPTYIRRYCRVGGKTINANTAKLYLNVIDNI
SIO_010081: ArsFIN_RS26050
subclass of: SO_0000673
so part of: ArsFIN_RS26050
location: 245..1810
location: region:245-1810:1
so has part: feature:245-1810:1:exon

WP_026824072.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:245-1810:1:exon

ArsFIN_RS26055
type: Gene
subclass of: SO_0000704
RO_0002162: 638
locus tag: ArsFIN_RS26055
old locus tag: ArsFIN_56350
so part of: sequence
location: 2325..3233
location: region:2325-3233:1
so has part: feature:2325-3233:1:exon
subclass of: SO_0000010

position:2325:1
position: 2325
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:3233:1
position: 3233
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:2325-3233:1:exon

ArsFIN_RS26055
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 638
locus tag: ArsFIN_RS26055
old locus tag: ArsFIN_56350
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: MTKKFTPTPHDAVFKQFLSEKETAKDFFDIWLPDEIKALCDLDSLKMESGSFIDSEMKNYQSDILYSVSTTKGSGYIYVLIEHQSTPDKLIAWRLMRYSLAAMQKHLEDGNKQLPLVFPILFYCGEQSPHPYSTHWLDCFEDRKLAESIYNNPFKLADVTTLDDGEIMQHKRIALLELLQKHIRRRDMTELLDSIVKLLSYNYYTDNQVITMFNYLIQEGNAQRPMEFITNIAKQAEKHEGALMTIAQQIEEIGIQKGIQQGIQKTKIELAKQFLANGVDRNTVKISTGLSDEELNKFENQS
SIO_010081: ArsFIN_RS26055
subclass of: SO_0000673
so part of: ArsFIN_RS26055
location: 2325..3233
location: region:2325-3233:1
so has part: feature:2325-3233:1:exon

WP_135679369.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:2325-3233:1:exon

ArsFIN_RS26060
type: Gene
subclass of: SO_0000704
RO_0002162: 638
locus tag: ArsFIN_RS26060
old locus tag: ArsFIN_56370
so part of: sequence
location: 3706..3984
location: region:3706-3984:1
so has part: feature:3706-3984:1:exon
subclass of: SO_0000010

position:3706:1
position: 3706
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:3984:1
position: 3984
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:3706-3984:1:exon

ArsFIN_RS26060
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 638
locus tag: ArsFIN_RS26060
old locus tag: ArsFIN_56370
inference: COORDINATES: similar to AA sequence:RefSeq:WP_006704778.1
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: MRTFDLTNVTELHDVFPELTPAQFETAILFCLGLSQGEIAHLRSVSYPAINQTLEDIKVKLNFYSLNNLLAMFQVRLFIFVLEKCKVEYRKD
SIO_010081: ArsFIN_RS26060
subclass of: SO_0000673
so part of: ArsFIN_RS26060
location: 3706..3984
location: region:3706-3984:1
so has part: feature:3706-3984:1:exon

WP_026824102.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:3706-3984:1:exon

ArsFIN_RS26065
type: Gene
subclass of: SO_0000704
RO_0002162: 638
locus tag: ArsFIN_RS26065
old locus tag: ArsFIN_56380
so part of: sequence
location: complement(5138..6988)
location: region:5138-6988:-1
so has part: feature:5138-6988:-1:exon
subclass of: SO_0000010

position:5138:-1
position: 5138
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:6988:-1
position: 6988
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:5138-6988:-1:exon

ArsFIN_RS26065
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 638
locus tag: ArsFIN_RS26065
old locus tag: ArsFIN_56380
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: MDLSTQSEVIESIEENRATLDNTSNIIELEKEKSKPRKNKEKSKEKPFRELGYDSGVYYLISKEQLQVLPFKARDLKESNLLQLAPLSWWRKNYPQYNDNGDAKKAPDWIQAADDIMRRCAKAGVYSCEAVRGLGFWKDGNRIIHHRGNALEDLVNRKIISMLDPSLRGVYQRATAKEKYSNECATDEQIALFLAAINRIYWKDEAHSQLFLGWLVLALFCGLLDWRPHIWVTGEHGAGKSDTVLEAVRIALGAKNYISAKGSTTEAGLRQRLKHNAIPAVVDESEPNTTKDRLRLDSLLTLARNASSDDEATAIKGTVSGEAHSYRIRCMFCFASINPYIKELADQSRISILEIVKKPQTTESKADFQFIKKSFLELEKAGFSTLLNNLMISRLSTLENNIKVFVEAAGDILGSARDGKQYGTLLAGYATFIESEPVDIETAKSYVSNLKLTEVVEENRDTKATGWDECWVKMCAVMLVFRDSRSRVTVGEGYEMLRTKNIEELARIVGYEHSGTGKVAKEQMEKAARQGQLEIERALRRLGIIYQEGTVSLYGCVGEGLYIANSSEEMSKALAGTPFQNWKQHSSRVGEAVRKPIFIEGQARRVIFILRDLINQ
SIO_010081: ArsFIN_RS26065
subclass of: SO_0000673
so part of: ArsFIN_RS26065
location: complement(5138..6988)
location: region:5138-6988:-1
so has part: feature:5138-6988:-1:exon

WP_135679371.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:5138-6988:-1:exon

ArsFIN_RS26070
type: Gene
subclass of: SO_0000704
RO_0002162: 638
locus tag: ArsFIN_RS26070
old locus tag: ArsFIN_56390
so part of: sequence
location: complement(6992..7213)
location: region:6992-7213:-1
so has part: feature:6992-7213:-1:exon
subclass of: SO_0000010

position:6992:-1
position: 6992
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:7213:-1
position: 7213
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:6992-7213:-1:exon

ArsFIN_RS26070
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 638
locus tag: ArsFIN_RS26070
old locus tag: ArsFIN_56390
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: MKSINKDTPQFTLPSMITTDVAITLSGKSKALFYYAKRFDPTFPQGVLMQHNGRSRVMYPTAEICQYFQKVEA
SIO_010081: ArsFIN_RS26070
subclass of: SO_0000673
so part of: ArsFIN_RS26070
location: complement(6992..7213)
location: region:6992-7213:-1
so has part: feature:6992-7213:-1:exon

WP_026824027.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:6992-7213:-1:exon