Paracoccus stylophorae strain LMG25392 plasmid p7412, complete sequence.
type: Entry
definition: Paracoccus stylophorae strain LMG25392 plasmid p7412, complete sequence.
sequence version: NZ_CP067135.1
sequence date: 2023-02-10
sequence: sequence
division: CON
label: NZ_CP067135.1
type: RefSeq
SIO_000068: refseq
dblink: PRJNA224116
dblink: SAMN17208933
keyword: RefSeq
source: Paracoccus stylophorae
organism: Paracoccus stylophorae
taxonomy: Bacteria; Pseudomonadota; Alphaproteobacteria; Rhodobacterales; Paracoccaceae; Paracoccus.
reference: 1
reference: 2
comment: REFSEQ INFORMATION: The reference sequence is identical to\nCP067135.1.\nBacteria and source DNA available from Prof. Dr. Thorsten\nBrinkhoff, ICMB, University Oldenburg.\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 :: 08-OCT-2020\nAssembly Method :: Unicycler v. 0.4.8\nGenome Representation :: Full\nExpected Final Version :: Yes\nGenome Coverage :: 179.0x\nSequencing Technology :: Illumina MiSeq; Oxford Nanopore MinION\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 02/09/2023 15:59:04\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) :: 3,579\nCDSs (total) :: 3,522\nGenes (coding) :: 3,481\nCDSs (with protein) :: 3,481\nGenes (RNA) :: 57\nrRNAs :: 2, 2, 2 (5S, 16S, 23S)\ncomplete rRNAs :: 2, 2, 2 (5S, 16S, 23S)\ntRNAs :: 47\nncRNAs :: 4\nPseudo Genes (total) :: 41\nCDSs (without protein) :: 41\nPseudo Genes (ambiguous residues) :: 0 of 41\nPseudo Genes (frameshifted) :: 13 of 41\nPseudo Genes (incomplete) :: 30 of 41\nPseudo Genes (internal stop) :: 5 of 41\nPseudo Genes (multiple problems) :: 6 of 41\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.

sequence
subclass of: SO_0000155
sequence length: 7412
topology: circular
so has quality: SO_0000988
location: 1..7412
location: region:1-7412:1
RO_0002162: 659350

NZ_CP067135
type: RefSeq
SIO_000068: refseq

PRJNA224116
type: BioProject
SIO_000068: bioproject

SAMN17208933
type: BioSample
SIO_000068: biosample

1
title: Biogeographic distribution of Paracoccus
author: Hollensteiner, J.
author: Leineberger, J.
author: Brinkhoff, T.
author: Daniel, R.
journal: Unpublished

2
title: Direct Submission
author: Hollensteiner, J.
author: Leineberger, J.
author: Brinkhoff, T.
author: Daniel, R.
journal: Submitted (05-JAN-2021) Genomic and Applied Microbiology & Goettingen Genomics Laboratory, Georg-August-University Goettingen, Grisebachstr. 8, Goettingen, Lower Saxony 37077, Germany

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

position:7412:1
position: 7412
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

feature:1-7412:1:source
so part of: sequence
organism: Paracoccus stylophorae
mol type: genomic DNA
strain: LMG25392
isolation source: isolated from the reef-building coral Stylophora pistillata
type material: type strain of Paracoccus stylophorae
plasmid: p7412
country: China:Taiwan

659350
type: Taxonomy
SIO_000068: taxonomy

JHW45_RS17865
type: Gene
subclass of: SO_0000704
RO_0002162: 659350
locus tag: JHW45_RS17865
old locus tag: JHW45_17780
so part of: sequence
location: complement(join(7387..7412,1..937))
location: region:1-7412:-1
so has part: feature:1-937:-1:exon
so has part: feature:7387-7412:-1:exon
subclass of: SO_0000010

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

position:7412:-1
position: 7412
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:1-937:-1:exon

position:937:-1
position: 937
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 2
SIO_000628: feature:7387-7412:-1:exon

position:7387:-1
position: 7387
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

JHW45_RS17865
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 659350
locus tag: JHW45_RS17865
old locus tag: JHW45_17780
EC number: 2.4.-.-
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: glycosyltransferase family A protein
translation: MMTSPQTVSVIMPARNAERTIEKSVASVLAQRGLGELIVVDDGSTDRTRDVLDRISDRRIRIIQGPGAGIARALNAGLFEARFAYVARCDSDDLYPADRLARQSTWLDANPEFIGISGGFVTIDEAGKKLASLVSDGEAREVTNDLREGNVLTSLCTWLIRRNSICSIGGVRPWFETAEDVDLQFRLAGIGRIWHDPEPTYFYRLHHQSITHTRQSARLHFFDDMAVKFNHQRMTHGRDDLDIGAAPAVPEFSDCNNMKHTVLRRQVVGHLTAQAWRDFHGGRKLDGIAGLCSAIRRHPTSLACWRGLAVMILRAAQSKK
SIO_010081: JHW45_RS17865
subclass of: SO_0000673
so part of: JHW45_RS17865
location: complement(join(7387..7412,1..937))
location: region:1-7412:-1
so has part: feature:1-937:-1:exon
so has part: feature:7387-7412:-1:exon

WP_272860660.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:1-937:-1:exon

urn:…
SIO_000300: 2
SIO_000628: feature:7387-7412:-1:exon

JHW45_RS17870
type: Gene
subclass of: SO_0000704
RO_0002162: 659350
locus tag: JHW45_RS17870
old locus tag: JHW45_17785
so part of: sequence
location: complement(1157..2152)
location: region:1157-2152:-1
so has part: feature:1157-2152:-1:exon
subclass of: SO_0000010

position:1157:-1
position: 1157
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:2152:-1
position: 2152
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:1157-2152:-1:exon

JHW45_RS17870
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 659350
locus tag: JHW45_RS17870
old locus tag: JHW45_17785
inference: COORDINATES: similar to AA sequence:RefSeq:WP_004213426.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: replication initiation protein
translation: MAADRAADQTKTVLPAELARGIYMRNAPSLQALKLMHLMIGTAGGRMAEDTLHQIRLSDIRKIEGMKNHDRASLTPLFEELRGAVLTHDDPEKMRVTIGGLLDEAVIDYRHELTGDILVSWAFGRSFRRMAEESNHWAILDRQTVFHLGSKYSVLLFQHIASLVNLDRISAKTFTIPELRAVFGIAEGKVKRFADLKKDVLTPALLEINQLSRLTLTATPNKVGRSVVSVTIAWEKKTDPHAAKRELSGSKIGRRARRNGTAETVAAVFPETGGITYSPRWVELKRAAGCNVDNGKIATDFRRFLAERGIARDAGNIEKLFSDYCEKIGKV
SIO_010081: JHW45_RS17870
subclass of: SO_0000673
so part of: JHW45_RS17870
location: complement(1157..2152)
location: region:1157-2152:-1
so has part: feature:1157-2152:-1:exon

WP_272860661.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:1157-2152:-1:exon

JHW45_RS17875
type: Gene
subclass of: SO_0000704
RO_0002162: 659350
locus tag: JHW45_RS17875
pseudo: true
so part of: sequence
location: 2428..2690
location: region:2428-2690:1
so has part: feature:2428-2690:1:exon
subclass of: SO_0000010

position:2428:1
position: 2428
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:2690:1
position: 2690
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:2428-2690:1:exon

JHW45_RS17875
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 659350
locus tag: JHW45_RS17875
inference: COORDINATES: similar to AA sequence:RefSeq:WP_005990482.1
note: frameshifted; Derived by automated computational analysis using gene prediction method: Protein Homology.
pseudo: true
codon start: 1
transl table: 11
product: BrnT family toxin
SIO_010081: JHW45_RS17875
subclass of: SO_0000673
so part of: JHW45_RS17875
location: 2428..2690
location: region:2428-2690:1
so has part: feature:2428-2690:1:exon

urn:…
SIO_000300: 1
SIO_000628: feature:2428-2690:1:exon

JHW45_RS17880
type: Gene
subclass of: SO_0000704
RO_0002162: 659350
locus tag: JHW45_RS17880
old locus tag: JHW45_17790
so part of: sequence
location: complement(2874..3086)
location: region:2874-3086:-1
so has part: feature:2874-3086:-1:exon
subclass of: SO_0000010

position:2874:-1
position: 2874
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:3086:-1
position: 3086
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:2874-3086:-1:exon

JHW45_RS17880
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 659350
locus tag: JHW45_RS17880
old locus tag: JHW45_17790
inference: COORDINATES: protein motif:HMM:NF020835.2
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: plasmid partition protein ParG
translation: MALSAKRPSRGDEARKRILHDVTEASGKKKRLNAEIEEALYRRIKMKAVEEGRSISDITRDLWSEYLSNE
SIO_010081: JHW45_RS17880
subclass of: SO_0000673
so part of: JHW45_RS17880
location: complement(2874..3086)
location: region:2874-3086:-1
so has part: feature:2874-3086:-1:exon

WP_272860662.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:2874-3086:-1:exon

JHW45_RS17885
type: Gene
subclass of: SO_0000704
RO_0002162: 659350
locus tag: JHW45_RS17885
old locus tag: JHW45_17795
so part of: sequence
location: complement(3086..3736)
location: region:3086-3736:-1
so has part: feature:3086-3736:-1:exon
subclass of: SO_0000010

position:3736:-1
position: 3736
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:3086-3736:-1:exon

JHW45_RS17885
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 659350
locus tag: JHW45_RS17885
old locus tag: JHW45_17795
inference: COORDINATES: similar to AA sequence:RefSeq:WP_009503747.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: ParA family partition ATPase
translation: MSIISVLNPKGGSGKTTISTNLARSLHEQGHSVLIVDSDPQGSARDWHAASEENPIELVALDRPNNIKTLTSMATNYDYVVIDGAAKLEDMIAACIKVSDFVLIPVQPSPYDIWAASDLVEFIKARQEVTDGSPRAGFVISRVVEGTRLGNDVRAALDDYALPVCDTTIVQRQVYPQTASEGLSVFDADNTKARAETTALSDEILVMLAAAAREVA
SIO_010081: JHW45_RS17885
subclass of: SO_0000673
so part of: JHW45_RS17885
location: complement(3086..3736)
location: region:3086-3736:-1
so has part: feature:3086-3736:-1:exon

WP_272860663.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:3086-3736:-1:exon

JHW45_RS17890
type: Gene
subclass of: SO_0000704
RO_0002162: 659350
locus tag: JHW45_RS17890
old locus tag: JHW45_17800
so part of: sequence
location: complement(3852..4925)
location: region:3852-4925:-1
so has part: feature:3852-4925:-1:exon
subclass of: SO_0000010

position:3852:-1
position: 3852
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:4925:-1
position: 4925
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:3852-4925:-1:exon

JHW45_RS17890
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 659350
locus tag: JHW45_RS17890
old locus tag: JHW45_17800
EC number: 2.4.-.-
inference: COORDINATES: protein motif:HMM:NF024831.2
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: glycosyltransferase family 4 protein
translation: MARITFILPNLSFAGGIRVIGKYSLELARLGHQVSVVARKPRPPRLQDLLRGRTQPDISFEVIETYFSGVEKNFSLVPSNRPLRSSDLPDADFLIATWWETLEWVSAMPPSKGRVVHFMQGYEMFPWAPANRVAATYEMDTRKIAVSAWVKQQVFKNHGCLSEAVIHNAVDTDHFSFRLERNNLVFTMGFVYASEAIKNSRLAFDLQDTLATRGFPCELLAFHNSPMPAELKERPGLRTYHRPPQELIPSLYQQCDLWLFLSLEEGFGLPIIEALSCGTPVLATRAGAAPELIRSGENGYLCAPTAEAFADAAERFAALGTSERLMFAERARETVAGWTWRDCAQRLIEVLEHQSSA
SIO_010081: JHW45_RS17890
subclass of: SO_0000673
so part of: JHW45_RS17890
location: complement(3852..4925)
location: region:3852-4925:-1
so has part: feature:3852-4925:-1:exon

WP_272860659.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:3852-4925:-1:exon

JHW45_RS17895
type: Gene
subclass of: SO_0000704
RO_0002162: 659350
locus tag: JHW45_RS17895
old locus tag: JHW45_17805
so part of: sequence
location: 5899..7260
location: region:5899-7260:1
so has part: feature:5899-7260:1:exon
subclass of: SO_0000010

position:5899:1
position: 5899
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:7260:1
position: 7260
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:5899-7260:1:exon

JHW45_RS17895
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 659350
locus tag: JHW45_RS17895
old locus tag: JHW45_17805
inference: COORDINATES: protein motif:HMM:NF024832.2
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: oligosaccharide flippase family protein
translation: MIVFQYPYDRLKSLFQGDGSRARSMRATMLMAGAFGASKVMQLGSNLVLTRILFPEAFGLMTLVFVFIGALQLLSDVGVQPSIIRSARGDAPEFLQTAWTVMVVRGVWITGLAFVLAWPYARLYDQDILFPLICIAALSTVIHGFSSIGRNIRERDIVLGRVVLLDLLGQGAAISLTVLFAWLTQSVWGLAIGSVAGAIVTTALSHVLMPSSNNRFRWDRDVLSEIMVFGRWILLGTLLTYMGGEGIRAVNGYLVDIDTLAFLYMASMIGGVPGQLTSRILSGVAFPMLSRIVRERPDDLKLAVRKIRTLQIVFSLPLFFLLAMTAQPLIDFLYDTRYAPAGTFLAVLALNGAVAALPAAYLNALLSLGESRIHALLMGVASTLKIAGTICGFYLGGPVGMVLGVGLAELGVFCLSFAFARQRGFDSLQLDLACLLVLSGAYAYILPTINWAI
SIO_010081: JHW45_RS17895
subclass of: SO_0000673
so part of: JHW45_RS17895
location: 5899..7260
location: region:5899-7260:1
so has part: feature:5899-7260:1:exon

WP_272860664.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:5899-7260:1:exon