Paracoccus fistulariae strain KCTC 22803 plasmid p5041, complete sequence.
type: Entry
definition: Paracoccus fistulariae strain KCTC 22803 plasmid p5041, complete sequence.
sequence version: NZ_CP067139.1
sequence date: 2023-02-10
sequence: sequence
division: CON
label: NZ_CP067139.1
type: RefSeq
SIO_000068: refseq
dblink: PRJNA224116
dblink: SAMN17209169
keyword: RefSeq
source: Paracoccus fistulariae
organism: Paracoccus fistulariae
taxonomy: Bacteria; Pseudomonadota; Alphaproteobacteria; Rhodobacterales; Paracoccaceae; Paracoccus.
reference: 1
reference: 2
comment: REFSEQ INFORMATION: The reference sequence is identical to\nCP067139.1.\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 :: 11-OCT-2020\nAssembly Method :: Unicycler v. 0.4.8\nGenome Representation :: Full\nExpected Final Version :: Yes\nGenome Coverage :: 450.0x\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 16:22:47\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) :: 3,689\nCDSs (total) :: 3,633\nGenes (coding) :: 3,574\nCDSs (with protein) :: 3,574\nGenes (RNA) :: 56\nrRNAs :: 2, 2, 2 (5S, 16S, 23S)\ncomplete rRNAs :: 2, 2, 2 (5S, 16S, 23S)\ntRNAs :: 47\nncRNAs :: 3\nPseudo Genes (total) :: 59\nCDSs (without protein) :: 59\nPseudo Genes (ambiguous residues) :: 0 of 59\nPseudo Genes (frameshifted) :: 19 of 59\nPseudo Genes (incomplete) :: 47 of 59\nPseudo Genes (internal stop) :: 12 of 59\nPseudo Genes (multiple problems) :: 17 of 59\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.

sequence
subclass of: SO_0000155
sequence length: 5041
topology: circular
so has quality: SO_0000988
location: 1..5041
location: region:1-5041:1
RO_0002162: 658446

NZ_CP067139
type: RefSeq
SIO_000068: refseq

PRJNA224116
type: BioProject
SIO_000068: bioproject

SAMN17209169
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:5041:1
position: 5041
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

feature:1-5041:1:source
so part of: sequence
organism: Paracoccus fistulariae
mol type: genomic DNA
strain: KCTC 22803
isolation source: isolated from bluespotted cornetfish
culture collection: KCTC:22803
type material: type strain of Paracoccus fistulariae
plasmid: p5041
country: South Korea:South Sea
collection date: 2008

658446
type: Taxonomy
SIO_000068: taxonomy

JHX87_RS18420
type: Gene
subclass of: SO_0000704
RO_0002162: 658446
locus tag: JHX87_RS18420
so part of: sequence
location: join(4871..5041,1..1056)
location: region:1-5041:1
so has part: feature:4871-5041:1:exon
so has part: feature:1-1056:1:exon
subclass of: SO_0000010

urn:…
SIO_000300: 1
SIO_000628: feature:4871-5041:1:exon

position:4871:1
position: 4871
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 2
SIO_000628: feature:1-1056:1:exon

position:1056:1
position: 1056
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

JHX87_RS18420
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 658446
locus tag: JHX87_RS18420
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: Hint domain-containing protein
translation: MTVTNLISDNVQTNKFNYCIGTSTMPTSDTFNVIYLGNLPIIDPIEGGRLTDYDAENANALVGQTFDSLTKASVQTFSPVNFSSDDGSRLPTRNQTYNQDNSRGNDIFNITDVDGNAVQHTFDAIVQYSATITYANGTTVPVTLNVMQSTTGETWIAPPSLYSPDAVQLGADPIQSIQLTGVISNRSSGLYFEREVVDIVTVPCFAAGTMIRTPAGDVAIETLRVGELVMTLDGGPQPVRWIGSRKLTVADLEERPNLRPIRIKAGVLGKGVPTTDLVVSPQHRILVRSKIAQRLFGVDEVLVAVKQLLLIDGIDVVANQDGIEYFHFLFDNHQVVISNGAETESLYTGPEALKSVGPVAQEEIFAIFPELRGRDPRALPEGARMLISGGQGRKLAQRHAQNHKLLVS
SIO_010081: JHX87_RS18420
subclass of: SO_0000673
so part of: JHX87_RS18420
location: join(4871..5041,1..1056)
location: region:1-5041:1
so has part: feature:4871-5041:1:exon
so has part: feature:1-1056:1:exon

WP_272833971.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:4871-5041:1:exon

urn:…
SIO_000300: 2
SIO_000628: feature:1-1056:1:exon

JHX87_RS18425
type: Gene
subclass of: SO_0000704
RO_0002162: 658446
locus tag: JHX87_RS18425
old locus tag: JHX87_18410
so part of: sequence
location: complement(1343..1738)
location: region:1343-1738:-1
so has part: feature:1343-1738:-1:exon
subclass of: SO_0000010

position:1343:-1
position: 1343
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:1738:-1
position: 1738
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:1343-1738:-1:exon

JHX87_RS18425
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 658446
locus tag: JHX87_RS18425
old locus tag: JHX87_18410
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: MKYTAGQAAKATGVATATITRALKAGKISGKKDENGSWMIDPSELHRIFPPISQRTPESPSIKQDETPPIAPERGIGSMALEREVQTLRDALNDAREDRDKWRNMAERLSLAPPSPQIAPPRGWWPWRRRS
SIO_010081: JHX87_RS18425
subclass of: SO_0000673
so part of: JHX87_RS18425
location: complement(1343..1738)
location: region:1343-1738:-1
so has part: feature:1343-1738:-1:exon

WP_271886955.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:1343-1738:-1:exon

JHX87_RS18430
type: Gene
subclass of: SO_0000704
RO_0002162: 658446
locus tag: JHX87_RS18430
old locus tag: JHX87_18415
so part of: sequence
location: complement(1835..2374)
location: region:1835-2374:-1
so has part: feature:1835-2374:-1:exon
subclass of: SO_0000010

position:1835:-1
position: 1835
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:2374:-1
position: 2374
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:1835-2374:-1:exon

JHX87_RS18430
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 658446
locus tag: JHX87_RS18430
old locus tag: JHX87_18415
inference: COORDINATES: similar to AA sequence:RefSeq:WP_006926035.1
GO process: GO:0006260 - DNA replication [Evidence IEA]; GO:0006276 - plasmid maintenance [Evidence IEA]
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: replication/maintenance protein RepL
translation: MTSEINLRKLEYSPSDNPFVQGAEIVTRYKTVRTRTSPRELMDPETGEVVGQSIIHVIEEKDEQHFVKVFADGVKAAFDLTRTGARVFQAVLMEYQKAKMTGGFSDTIRLVWFDDGLNGHSIGMSDRTFHNGLKELIGKGFLKPRMPGEFWVNPALFFKGDRVAFLREYRRRPAIAAPE
SIO_010081: JHX87_RS18430
subclass of: SO_0000673
so part of: JHX87_RS18430
location: complement(1835..2374)
location: region:1835-2374:-1
so has part: feature:1835-2374:-1:exon

WP_271886956.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:1835-2374:-1:exon

JHX87_RS18435
type: Gene
subclass of: SO_0000704
RO_0002162: 658446
locus tag: JHX87_RS18435
old locus tag: JHX87_18420
so part of: sequence
location: complement(2912..3964)
location: region:2912-3964:-1
so has part: feature:2912-3964:-1:exon
subclass of: SO_0000010

position:2912:-1
position: 2912
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:3964:-1
position: 3964
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:2912-3964:-1:exon

JHX87_RS18435
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 658446
locus tag: JHX87_RS18435
old locus tag: JHX87_18420
inference: COORDINATES: protein motif:HMM:NF015354.2
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: MobA/MobL family protein
translation: MAIYHLSHRTVGRTTHAAGTAGAHVGYITRATACRAVIAQHIPEAAPGSKGGAARAWLDAQELADRKNARVIDKLEIALPIELDQAQRIEAVRVFVRDLAGGRSVPFFAAIHDKAGTKDEANPHAHVVIRDRDPATGKGRVIGMSEKGSTERAREVWEQVCNQALRNAGHSARVDRRSLVDQGITDRAPPGHEGPRARQIEAKGRPSEKLVRIREARKAPPKLHSALVRAAEREREAGWHVRATPTPEAATARAEALLIDRLRRMAERIWSDQRDKQTAKRTFRQKVAGDVGSRVFPDAVTRHFEDISTIVFRRKRKQLMPLRDIAASSGSQQMAQPLQPDQRSKFRPSF
SIO_010081: JHX87_RS18435
subclass of: SO_0000673
so part of: JHX87_RS18435
location: complement(2912..3964)
location: region:2912-3964:-1
so has part: feature:2912-3964:-1:exon

WP_271886952.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:2912-3964:-1:exon

JHX87_RS18440
type: Gene
subclass of: SO_0000704
RO_0002162: 658446
locus tag: JHX87_RS18440
old locus tag: JHX87_18425
so part of: sequence
location: 4274..4537
location: region:4274-4537:1
so has part: feature:4274-4537:1:exon
subclass of: SO_0000010

position:4274:1
position: 4274
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:4537:1
position: 4537
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:4274-4537:1:exon

JHX87_RS18440
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 658446
locus tag: JHX87_RS18440
old locus tag: JHX87_18425
inference: COORDINATES: similar to AA sequence:RefSeq:WP_011390988.1
GO process: GO:0051983 - regulation of chromosome segregation [Evidence IEA]
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: type II toxin-antitoxin system ParD family antitoxin
translation: MGAVERMTITMPAELANTLRQTVACGEYASTSEVVREALRDWTRNRDAERRELEVLRAAIKAGLDSGPGIPADQVFAELRARYAAKS
SIO_010081: JHX87_RS18440
subclass of: SO_0000673
so part of: JHX87_RS18440
location: 4274..4537
location: region:4274-4537:1
so has part: feature:4274-4537:1:exon

WP_271886953.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:4274-4537:1:exon

JHX87_RS18445
type: Gene
subclass of: SO_0000704
RO_0002162: 658446
locus tag: JHX87_RS18445
old locus tag: JHX87_18430
so part of: sequence
location: 4541..4831
location: region:4541-4831:1
so has part: feature:4541-4831:1:exon
subclass of: SO_0000010

position:4541:1
position: 4541
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

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

urn:…
SIO_000300: 1
SIO_000628: feature:4541-4831:1:exon

JHX87_RS18445
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 658446
locus tag: JHX87_RS18445
old locus tag: JHX87_18430
inference: COORDINATES: similar to AA sequence:RefSeq:WP_011390987.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: type II toxin-antitoxin system RelE/ParE family toxin
translation: MAQLIILPAAKADLIEIGDFIAQDNPARALSFVAEIEAKMLQAAERPESFPARDEVHEELRSVRHGRYLIFFLDAGNEVRIVRVLHGARDLPRVLG
SIO_010081: JHX87_RS18445
subclass of: SO_0000673
so part of: JHX87_RS18445
location: 4541..4831
location: region:4541-4831:1
so has part: feature:4541-4831:1:exon

WP_271886954.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:4541-4831:1:exon