Paracoccus marcusii strain CP157 plasmid pCP157_13, complete sequence.
type: Entry
definition: Paracoccus marcusii strain CP157 plasmid pCP157_13, complete sequence.
sequence version: NZ_CP065905.1
sequence date: 2023-03-25
sequence: sequence
division: CON
label: NZ_CP065905.1
type: RefSeq
SIO_000068: refseq
dblink: PRJNA224116
dblink: SAMN16776174
keyword: RefSeq
source: Paracoccus marcusii
organism: Paracoccus marcusii
taxonomy: Bacteria; Pseudomonadota; Alphaproteobacteria; Rhodobacterales; Paracoccaceae; Paracoccus.
reference: 1
reference: 2
comment: REFSEQ INFORMATION: The reference sequence is identical to\nCP065905.1.\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/\nThis genome has a base modification file available.\n\n##Genome-Assembly-Data-START##\nAssembly Method :: HGAP SMRTPortal v. 2.3.0\nGenome Coverage :: 65x\nSequencing Technology :: PacBio; Illumina MiSeq\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 03/25/2023 06:10:02\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) :: 4,059\nCDSs (total) :: 3,997\nGenes (coding) :: 3,913\nCDSs (with protein) :: 3,913\nGenes (RNA) :: 62\nrRNAs :: 3, 3, 3 (5S, 16S, 23S)\ncomplete rRNAs :: 3, 3, 3 (5S, 16S, 23S)\ntRNAs :: 50\nncRNAs :: 3\nPseudo Genes (total) :: 84\nCDSs (without protein) :: 84\nPseudo Genes (ambiguous residues) :: 0 of 84\nPseudo Genes (frameshifted) :: 47 of 84\nPseudo Genes (incomplete) :: 43 of 84\nPseudo Genes (internal stop) :: 20 of 84\nPseudo Genes (multiple problems) :: 23 of 84\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.

sequence
subclass of: SO_0000155
sequence length: 8491
topology: circular
so has quality: SO_0000988
location: 1..8491
location: region:1-8491:1
RO_0002162: 59779

NZ_CP065905
type: RefSeq
SIO_000068: refseq

PRJNA224116
type: BioProject
SIO_000068: bioproject

SAMN16776174
type: BioSample
SIO_000068: biosample

1
title: High Potential for Secondary Metabolite Production of Paracoccus marcusii CP157, Isolated From the Crustacean Cancer pagurus
author: Leinberger, J.
author: Holste, J.
author: Bunk, B.
author: Freese, H.M.
author: Sproeer, C.
author: Dlugosch, L.
author: Kueck, A.-C.
author: Schulz, S.
author: Brinkhoff, T.
journal: Front Microbiol 12 (2021)

2
title: Direct Submission
author: Leinberger, J.
author: Brinkhoff, T.
author: Bunk, B.
author: Freese, H.M.
journal: Submitted (10-DEC-2020) Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Carl-von-Ossietzky Strasse 9-11, Oldenburg 26129, Germany

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

position:8491:1
position: 8491
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

feature:1-8491:1:source
so part of: sequence
organism: Paracoccus marcusii
mol type: genomic DNA
strain: CP157
isolation source: carapace
host: Cancer pagurus
plasmid: pCP157_13
country: Germany: Helgoland
lat lon: 54.12 N 7.53 E
collection date: 2014-10-15

59779
type: Taxonomy
SIO_000068: taxonomy

CP157_RS19905
type: Gene
subclass of: SO_0000704
RO_0002162: 59779
locus tag: CP157_RS19905
old locus tag: CP157_03999
so part of: sequence
location: 1..558
location: region:1-558:1
so has part: feature:1-558:1:exon
subclass of: SO_0000010

position:558:1
position: 558
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:1-558:1:exon

CP157_RS19905
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 59779
locus tag: CP157_RS19905
old locus tag: CP157_03999
inference: COORDINATES: similar to AA sequence:RefSeq:WP_011930888.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: helix-turn-helix domain-containing protein
translation: MSRQTGQGLPEAKARGTWVQTERAAHEAWAALIDENPSAARLMNLLVARMGDHNAVVASQKTLGEMMGKSRDTVKRAVATLRDKNWIEVRQIGDRGTVCAYIINDRIAWTGKRDGIRYSLFSARVIVSDEEQPDRAMLDFQEPLRQLPSLFSGERQLPSGDGLPPVSQPFFNGMEPDLPSTQAED
SIO_010081: CP157_RS19905
subclass of: SO_0000673
so part of: CP157_RS19905
location: 1..558
location: region:1-558:1
so has part: feature:1-558:1:exon

WP_217847077.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:1-558:1:exon

CP157_RS19910
type: Gene
subclass of: SO_0000704
RO_0002162: 59779
locus tag: CP157_RS19910
so part of: sequence
location: 620..1066
location: region:620-1066:1
so has part: feature:620-1066:1:exon
subclass of: SO_0000010

position:620:1
position: 620
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:1066:1
position: 1066
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:620-1066:1:exon

CP157_RS19910
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 59779
locus tag: CP157_RS19910
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: MASLTLSQAAKASGKSKSTLSRAIKMGRLSATRLDDGNFSIDPAELFRAYPATSSHPYDEHPIEQGATPIPAELHSRISMLELLLEKEREAVAREREISAREREISADLKEDRDRWRQQATSLLADLRPQLTEPTSPARRRAWWPFNR
SIO_010081: CP157_RS19910
subclass of: SO_0000673
so part of: CP157_RS19910
location: 620..1066
location: region:620-1066:1
so has part: feature:620-1066:1:exon

WP_217847078.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:620-1066:1:exon

CP157_RS19915
type: Gene
subclass of: SO_0000704
RO_0002162: 59779
locus tag: CP157_RS19915
old locus tag: CP157_04000
so part of: sequence
location: complement(1294..2787)
location: region:1294-2787:-1
so has part: feature:1294-2787:-1:exon
subclass of: SO_0000010

position:1294:-1
position: 1294
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:2787:-1
position: 2787
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:1294-2787:-1:exon

CP157_RS19915
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 59779
locus tag: CP157_RS19915
old locus tag: CP157_04000
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: MNGFLDQFTKNVLIALRNTQRRLHLRFPNIFPDDSESRKFFKEHDAKENIISQVPLDEDLRQSAIWGVELYGPKEISALYEGLEKLGWAGSRFGLPDTDCLEWVRRARQYGHTGKRNLSIVYRHKEKGPGRDYFAPMPDICNYLLVSITQITPSLTAVHVYFVLNDEATKLYESILNEDRKTYYQKVRGRKGYLIPGVLNQKRDLIEQARLKRAHIASGWFSQHLPGLFSGGPLIDELPTGELILMDNYAALKDPGENKFSKTKWPDVLGIDQWLDGWINPTYEGYGLIIDSRHNLKKYHCTVTLRTSSVPDDYYLFRNGRNRGVYDAIVYQDLGGVAVHLATSSYIKEIGRRIRETREVVSQVSNNRLTLIDTLDQLETFYRDTIGDPAIVEELSKLGKHDFEFDCTKFVTQNLIRGEKVELPTALYKLTKRISENVHADGRSARQLFQEFSSTLSTRESIRTQQRMERLTIVAIVIACISLVVAAIGVYVSGTGK
SIO_010081: CP157_RS19915
subclass of: SO_0000673
so part of: CP157_RS19915
location: complement(1294..2787)
location: region:1294-2787:-1
so has part: feature:1294-2787:-1:exon

WP_217847079.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:1294-2787:-1:exon

CP157_RS19920
type: Gene
subclass of: SO_0000704
RO_0002162: 59779
locus tag: CP157_RS19920
old locus tag: CP157_04001
so part of: sequence
location: complement(2972..3265)
location: region:2972-3265:-1
so has part: feature:2972-3265:-1:exon
subclass of: SO_0000010

position:2972:-1
position: 2972
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:3265:-1
position: 3265
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:2972-3265:-1:exon

CP157_RS19920
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 59779
locus tag: CP157_RS19920
old locus tag: CP157_04001
inference: COORDINATES: similar to AA sequence:RefSeq:WP_017664490.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: HU family DNA-binding protein
translation: MIRSELLAKLRQAHPHLSSLAVETALDTILDEIAETLSQDHRVELRGFGSFFSKVRVARTGRNPRTGEAVDVPPKRHMHFRASRQLLERLNRPTTRG
SIO_010081: CP157_RS19920
subclass of: SO_0000673
so part of: CP157_RS19920
location: complement(2972..3265)
location: region:2972-3265:-1
so has part: feature:2972-3265:-1:exon

WP_217847080.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:2972-3265:-1:exon

CP157_RS19925
type: Gene
subclass of: SO_0000704
RO_0002162: 59779
locus tag: CP157_RS19925
old locus tag: CP157_04002
so part of: sequence
location: 3536..3850
location: region:3536-3850:1
so has part: feature:3536-3850:1:exon
subclass of: SO_0000010

position:3536:1
position: 3536
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:3850:1
position: 3850
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:3536-3850:1:exon

CP157_RS19925
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 59779
locus tag: CP157_RS19925
old locus tag: CP157_04002
inference: COORDINATES: similar to AA sequence:RefSeq:WP_011331338.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: H-NS histone family protein
translation: MSDLDFETMSLDELKRLRKELDKAIAHYDDRRKAEARRDLEEKAREYGFSLSELTDAKTTKRATPAPKYRNPGNPEQTWSGRGRQPVWFREAIVAGTEPDDLKI
SIO_010081: CP157_RS19925
subclass of: SO_0000673
so part of: CP157_RS19925
location: 3536..3850
location: region:3536-3850:1
so has part: feature:3536-3850:1:exon

WP_217847081.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:3536-3850:1:exon

CP157_RS19930
type: Gene
subclass of: SO_0000704
RO_0002162: 59779
locus tag: CP157_RS19930
old locus tag: CP157_04003
so part of: sequence
location: complement(4020..5378)
location: region:4020-5378:-1
so has part: feature:4020-5378:-1:exon
subclass of: SO_0000010

position:4020:-1
position: 4020
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:5378:-1
position: 5378
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:4020-5378:-1:exon

CP157_RS19930
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 59779
locus tag: CP157_RS19930
old locus tag: CP157_04003
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: MVKSSGLRDMEGMLSSVSDPAIEDYLQEAFTCYGTGAYRACIVLTFIATFEDLRSKVRAHSSLSREARDISKDIDLLANSQKPFENTMVERLQSSKLISALQGQKLKQIIDHRNKAAHPSGHHASAEEARFVYTECISLFLSQPVVNPGLLADELIERMKDGNFFPASSVEKNMPVFTDEMNRIDEKLYSKVFSRLAELIKSENEQERVNSRYFIAIAAGLKQQKIRDAIRGSIIEKKTTDKAYSQTICEIISADGNSIDSVSEGCLRRVIALILLDAKSIKVEPPQTRLRHPVRVLNGIITSEQKESFLKNGSEYIDYVIDAYLLQPILIRIIKKDDILKEKLLSKIIRRAESDDFEDANSFSISLPDIDSDFAKTFNEESSFKVICGVLHAAEIGAFRAKDVRASSFRDCPEIKNKSAIFINNNELEAKIILKDMKVNLEYDKVKLILNS
SIO_010081: CP157_RS19930
subclass of: SO_0000673
so part of: CP157_RS19930
location: complement(4020..5378)
location: region:4020-5378:-1
so has part: feature:4020-5378:-1:exon

WP_217847082.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:4020-5378:-1:exon

CP157_RS19935
type: Gene
subclass of: SO_0000704
RO_0002162: 59779
locus tag: CP157_RS19935
old locus tag: CP157_04004
so part of: sequence
location: 5707..6000
location: region:5707-6000:1
so has part: feature:5707-6000:1:exon
subclass of: SO_0000010

position:5707:1
position: 5707
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:6000:1
position: 6000
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:5707-6000:1:exon

CP157_RS19935
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 59779
locus tag: CP157_RS19935
old locus tag: CP157_04004
inference: COORDINATES: similar to AA sequence:RefSeq:WP_009812250.1
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: type II toxin-antitoxin system RelB/DinJ family antitoxin
translation: MPAQTSMLHVRVDDQLKAQATAALSGVGLTLSDAVRILLTRVAAEGGLPAGLTVDPAAYDTWFRTKVQEALADPRPATPHAQVMQEARALIDGKRRA
SIO_010081: CP157_RS19935
subclass of: SO_0000673
so part of: CP157_RS19935
location: 5707..6000
location: region:5707-6000:1
so has part: feature:5707-6000:1:exon

WP_217847073.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:5707-6000:1:exon

CP157_RS19940
type: Gene
subclass of: SO_0000704
RO_0002162: 59779
locus tag: CP157_RS19940
old locus tag: CP157_04005
so part of: sequence
location: 5993..6268
location: region:5993-6268:1
so has part: feature:5993-6268:1:exon
subclass of: SO_0000010

position:5993:1
position: 5993
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:6268:1
position: 6268
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:5993-6268:1:exon

CP157_RS19940
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 59779
locus tag: CP157_RS19940
old locus tag: CP157_04005
inference: COORDINATES: similar to AA sequence:RefSeq:WP_009812249.1
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: MPELEWKAAAVADLMAIVDYISDDNPNAALALMEGIQSKVAQLPAHPKRCRPGRVEGTRELVVRPNYIVVYAETAAAVTVLRVLHAAQMWP
SIO_010081: CP157_RS19940
subclass of: SO_0000673
so part of: CP157_RS19940
location: 5993..6268
location: region:5993-6268:1
so has part: feature:5993-6268:1:exon

WP_217847074.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:5993-6268:1:exon

CP157_RS19945
type: Gene
subclass of: SO_0000704
RO_0002162: 59779
locus tag: CP157_RS19945
old locus tag: CP157_04006
so part of: sequence
location: complement(6294..6455)
location: region:6294-6455:-1
so has part: feature:6294-6455:-1:exon
subclass of: SO_0000010

position:6294:-1
position: 6294
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:6455:-1
position: 6455
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:6294-6455:-1:exon

CP157_RS19945
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 59779
locus tag: CP157_RS19945
old locus tag: CP157_04006
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: MASRDPDHKKPVDEQADLTIAQKIEALQDRVRKMGPASDSSNDKAFMDEAWGE
SIO_010081: CP157_RS19945
subclass of: SO_0000673
so part of: CP157_RS19945
location: complement(6294..6455)
location: region:6294-6455:-1
so has part: feature:6294-6455:-1:exon

WP_217847075.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:6294-6455:-1:exon

CP157_RS19950
type: Gene
subclass of: SO_0000704
RO_0002162: 59779
gene: mobV
locus tag: CP157_RS19950
old locus tag: CP157_04007
so part of: sequence
location: 6730..8007
location: region:6730-8007:1
so has part: feature:6730-8007:1:exon
subclass of: SO_0000010

position:6730:1
position: 6730
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:8007:1
position: 8007
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:6730-8007:1:exon

CP157_RS19950
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 59779
gene: mobV
locus tag: CP157_RS19950
old locus tag: CP157_04007
inference: COORDINATES: protein motif:HMM:NF013258.2
GO function: GO:0003677 - DNA binding [Evidence IEA]
GO process: GO:0006310 - DNA recombination [Evidence IEA]
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: MobV family relaxase
translation: MSDVVTDFSKGMQLRSGSRPPRSFAILRVGKIKTKGHLGAALGHNYRERDTPNADQSRMAENLVLKGPGTAQGVMEAWDARAPEKIRKNAVHALEYFVGGSPEKVHAMGRDEQNNYFRRALDWLKDRHGAENVLSAVVHRDETTPHMQVLVIPLDARGKLNARELVGGKDKLRQMQTDFARDVGQPFGLERGQERSRATHQTIQEYYGRASTPVEADFSLPERRRGAVMGLGGESDREWQERASRAATERLAHLTAHLTEASGTLRREMEATEAVLGQTQTELARERAVSEAANKLVLTALQIPQIEGVTEDDKQDLLRDMARFHNRHASHFSDMQAQATKAALNHTGIAVIELKDGSYALPWRDFDAVGGPRLAGTDRQEVDAILNGLCQAERSRQHATEAMQEHEARKTRERERGQDSGSDWG
SIO_010081: CP157_RS19950
subclass of: SO_0000673
so part of: CP157_RS19950
location: 6730..8007
location: region:6730-8007:1
so has part: feature:6730-8007:1:exon

WP_217847076.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:6730-8007:1:exon