Paracoccus marcusii strain CP157 plasmid pCP157_16, complete sequence.
type: Entry
definition: Paracoccus marcusii strain CP157 plasmid pCP157_16, complete sequence.
sequence version: NZ_CP065908.1
sequence date: 2023-03-25
sequence: sequence
division: CON
label: NZ_CP065908.1
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\nCP065908.1.\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: 6378
topology: circular
so has quality: SO_0000988
location: 1..6378
location: region:1-6378:1
RO_0002162: 59779

NZ_CP065908
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:6378:1
position: 6378
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

feature:1-6378:1:source
so part of: sequence
organism: Paracoccus marcusii
mol type: genomic DNA
strain: CP157
isolation source: carapace
host: Cancer pagurus
plasmid: pCP157_16
country: Germany: Helgoland
lat lon: 54.12 N 7.53 E
collection date: 2014-10-15

59779
type: Taxonomy
SIO_000068: taxonomy

CP157_RS20060
type: Gene
subclass of: SO_0000704
RO_0002162: 59779
locus tag: CP157_RS20060
old locus tag: CP157_04028
so part of: sequence
location: 1..549
location: region:1-549:1
so has part: feature:1-549:1:exon
subclass of: SO_0000010

position:549:1
position: 549
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:1-549:1:exon

CP157_RS20060
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 59779
locus tag: CP157_RS20060
old locus tag: CP157_04028
inference: COORDINATES: similar to AA sequence:RefSeq:WP_011251600.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: hypothetical protein
translation: MSNLQALEKAPKGQWVQTERKAHEAWAKLIRKSPLAAQIMHVLTARVDTHNAVVISQKNLARLVEGSERGVRDALKLLTTDNWLEIRQIGGRGTVNAHIINDRVAWSGKRDGIRYSLFSAAVILSDDEQPDADHLDNQEPLRRLPSAFAGEQQLPSGDGLPPVSQPFFDGLEPDLPTKLEEK
SIO_010081: CP157_RS20060
subclass of: SO_0000673
so part of: CP157_RS20060
location: 1..549
location: region:1-549:1
so has part: feature:1-549:1:exon

WP_245008590.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:1-549:1:exon

CP157_RS20065
type: Gene
subclass of: SO_0000704
RO_0002162: 59779
locus tag: CP157_RS20065
so part of: sequence
location: 611..1006
location: region:611-1006:1
so has part: feature:611-1006:1:exon
subclass of: SO_0000010

position:611:1
position: 611
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:1006:1
position: 1006
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:611-1006:1:exon

CP157_RS20065
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 59779
locus tag: CP157_RS20065
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: MTGLTLSQAAKALGKSKSTLNRAIKTGRLSATRNEDGTFSINPAELYRAFPEPSENARQERPREQDRTVVPDDYGSRISLLQQLLEREREAVADLKEERDRWRQQATSLLANQEATPSTQPIEKRRRWWPF
SIO_010081: CP157_RS20065
subclass of: SO_0000673
so part of: CP157_RS20065
location: 611..1006
location: region:611-1006:1
so has part: feature:611-1006:1:exon

WP_217847099.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:611-1006:1:exon

CP157_RS20070
type: Gene
subclass of: SO_0000704
RO_0002162: 59779
locus tag: CP157_RS20070
so part of: sequence
location: 1164..1520
location: region:1164-1520:1
so has part: feature:1164-1520:1:exon
subclass of: SO_0000010

position:1164:1
position: 1164
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:1520:1
position: 1520
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:1164-1520:1:exon

CP157_RS20070
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 59779
locus tag: CP157_RS20070
inference: COORDINATES: protein motif:HMM:NF012772.2
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: EAL domain-containing protein
translation: MGKNKFWQKSFNASDIAFILKKIKSQRHVSDDGKVSFSGSWGFEGLFSIVSSAIPESEITEAAKSRVVAEGVETHEALESLIGLGCDEAQGYFFSRPIIAEQIHRWQQARDETVRSAA
SIO_010081: CP157_RS20070
subclass of: SO_0000673
so part of: CP157_RS20070
location: 1164..1520
location: region:1164-1520:1
so has part: feature:1164-1520:1:exon

WP_217847100.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:1164-1520:1:exon

CP157_RS20075
type: Gene
subclass of: SO_0000704
RO_0002162: 59779
locus tag: CP157_RS20075
old locus tag: CP157_04029
so part of: sequence
location: 1681..2859
location: region:1681-2859:1
so has part: feature:1681-2859:1:exon
subclass of: SO_0000010

position:1681:1
position: 1681
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:2859:1
position: 2859
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:1681-2859:1:exon

CP157_RS20075
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 59779
locus tag: CP157_RS20075
old locus tag: CP157_04029
EC number: 1.1.1.-
inference: COORDINATES: similar to AA sequence:RefSeq:WP_018250476.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: zinc-dependent alcohol dehydrogenase
translation: MRALCWHGKGDVRVDTVADPEIKHPRDAIIKVTACAICGSDLHLLDGYQPTMESGDILGHENMGEVVALGSEVTNLKIGDRVVVPFTISCGECWFCKKGLFSACCTTNPNAEVAIKAMGHSPAGLFGFSHMLGGYCGGQAEYLRVPMADFGPIKVPDNVTDEQALFLSDIFPTGYMAAENANIEEGDTVAIWGCGPVGQFAIRSALMLGAGRVIAIDEVPERLAMAEAGGAETINFAEVDNVYDELQFRTKGRGPDSCIDAVGAEAAGHGSVDAVLDKAKATVGLATDRIHVLREAIMSCRMGGTVSIPGVYVGMGDKVPLGAMMNKGLTIKTGQTHVQAYTAPLMARIEAGEIDPSFVITHPASLEDAPEMYKKFRDKEDGAIKVVMRPHG
SIO_010081: CP157_RS20075
subclass of: SO_0000673
so part of: CP157_RS20075
location: 1681..2859
location: region:1681-2859:1
so has part: feature:1681-2859:1:exon

WP_217847101.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:1681-2859:1:exon

CP157_RS20080
type: Gene
subclass of: SO_0000704
RO_0002162: 59779
locus tag: CP157_RS20080
old locus tag: CP157_04030
so part of: sequence
location: complement(3261..4289)
location: region:3261-4289:-1
so has part: feature:3261-4289:-1:exon
subclass of: SO_0000010

position:3261:-1
position: 3261
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:4289:-1
position: 4289
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:3261-4289:-1:exon

CP157_RS20080
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 59779
locus tag: CP157_RS20080
old locus tag: CP157_04030
inference: COORDINATES: similar to AA sequence:RefSeq:WP_009867760.1
GO function: GO:0004803 - transposase activity [Evidence IEA]
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: IS110 family transposase
translation: MSIVIVGIDLGKNSCSIVGLDSLGTVVVRRRLRRDSVIAFASKLPACIMAMEACCGVHHMGRSLAALGHEVRLMSPEYVRPYVKAQKNDDRDAEAIAEAATRPTMRFVELKSEEQLDVQTLHRVRDRLVGERTSLTNQIRSLLLERGHVVAQGHARLRHLLADLLDPATCSLSARMAFLLGDMRTRWDELDRRIAAFDAEFSAMARTDERARRLTSIPGIGALNATALVAAVGNAATFTKGRDLAAWLGLVPRQATTGGKPKLLGITKRGSRYLRKMLIQGARSAMPTLAKANTVIGAWLRALLVRTHPNIAVVALAAKMARTVWALLRHGRNYEAVPQAAG
SIO_010081: CP157_RS20080
subclass of: SO_0000673
so part of: CP157_RS20080
location: complement(3261..4289)
location: region:3261-4289:-1
so has part: feature:3261-4289:-1:exon

WP_217847096.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:3261-4289:-1:exon

CP157_RS20085
type: Gene
subclass of: SO_0000704
RO_0002162: 59779
gene: mobV
locus tag: CP157_RS20085
old locus tag: CP157_04031
so part of: sequence
location: 4629..5906
location: region:4629-5906:1
so has part: feature:4629-5906:1:exon
subclass of: SO_0000010

position:4629:1
position: 4629
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:5906:1
position: 5906
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:4629-5906:1:exon

CP157_RS20085
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 59779
gene: mobV
locus tag: CP157_RS20085
old locus tag: CP157_04031
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: MSDVVTDFSKGMHVRSGSRPPRSFAILRVGKIKTKGHLGAALGHNYRERDTPNADQTRMAENLVLKGPGTAQGVMEAWDARAPEKIRKNAVHALEYFVGGSPEKVHAMGRDEQNNYFRRALDWLKDRHGAENVLSAVVHRDETTPHMQVLVIPLDARGKLNARELVGGKDKLRQMQTDFARDVGQPFGLERGQERSRATHQTIQEYYGRASTPVEADFSLPERRRGAVMGLGGESDREWQERALRAASERLAHLTAHLTEASGTLRREMEATEVVLGQTQTELARERAVSEAANKLVLTALQIPQIEGVTEDDKQDLLRDMARFHNRHASHFSDMQAKATKAALNHTGIAVIELKDGSYALPWRDFDAVGGQRLAGTDRQATDAILNGLRQAERSRQQATEAMQEHEARKAREQERGQDSGSDWG
SIO_010081: CP157_RS20085
subclass of: SO_0000673
so part of: CP157_RS20085
location: 4629..5906
location: region:4629-5906:1
so has part: feature:4629-5906:1:exon

WP_217847097.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:4629-5906:1:exon