Paracoccus marcusii strain CP157 plasmid pCP157_18, complete sequence.
type: Entry
definition: Paracoccus marcusii strain CP157 plasmid pCP157_18, complete sequence.
sequence version: NZ_CP065910.1
sequence date: 2023-03-25
sequence: sequence
division: CON
label: NZ_CP065910.1
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\nCP065910.1.\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: 4977
topology: circular
so has quality: SO_0000988
location: 1..4977
location: region:1-4977:1
RO_0002162: 59779

NZ_CP065910
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:4977:1
position: 4977
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

feature:1-4977:1:source
so part of: sequence
organism: Paracoccus marcusii
mol type: genomic DNA
strain: CP157
isolation source: carapace
host: Cancer pagurus
plasmid: pCP157_18
country: Germany: Helgoland
lat lon: 54.12 N 7.53 E
collection date: 2014-10-15

59779
type: Taxonomy
SIO_000068: taxonomy

CP157_RS20115
type: Gene
subclass of: SO_0000704
RO_0002162: 59779
locus tag: CP157_RS20115
old locus tag: CP157_04037
so part of: sequence
location: 1..735
location: region:1-735:1
so has part: feature:1-735:1:exon
subclass of: SO_0000010

position:735:1
position: 735
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:1-735:1:exon

CP157_RS20115
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 59779
locus tag: CP157_RS20115
old locus tag: CP157_04037
inference: COORDINATES: similar to AA sequence:RefSeq:WP_013635166.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: hypothetical protein
translation: MGRISLHELRRMGVSTEDIEAAKVTQLAQRRTGAPVQSIGVIVGVAEQRQRTNPNSPTDLTARALHKRGAYDQAALLLDQQALRESSPERAAMAREAALAAKELSASNQLEFDFFGGGNVSIAFQYQDAVTERLFAAAKTPAQAFHAQAVLWQITRNLGWQSYECTKTAADLCEVMRTDKGDMARALDLLEQVGAIRRVKRGRVKIITVTPEGAFRGNVHNHAQAVERYKLDVIDGGKTEQTPK
SIO_010081: CP157_RS20115
subclass of: SO_0000673
so part of: CP157_RS20115
location: 1..735
location: region:1-735:1
so has part: feature:1-735:1:exon

WP_217847109.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:1-735:1:exon

CP157_RS20120
type: Gene
subclass of: SO_0000704
RO_0002162: 59779
locus tag: CP157_RS20120
old locus tag: CP157_04038
so part of: sequence
location: 806..1198
location: region:806-1198:1
so has part: feature:806-1198:1:exon
subclass of: SO_0000010

position:806:1
position: 806
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:1198:1
position: 1198
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:806-1198:1:exon

CP157_RS20120
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 59779
locus tag: CP157_RS20120
old locus tag: CP157_04038
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: MALTLNQAAKICSRSKSTLLDAIRSGRMSAPKDDRGRYVIDPAELHRAFPFQSQNQSLDQSSEPQPTSAENQPEPADLASKREIELLREMLGKAEANADHWRALAERQQALLEDKRPKEPRSLLQRLFGR
SIO_010081: CP157_RS20120
subclass of: SO_0000673
so part of: CP157_RS20120
location: 806..1198
location: region:806-1198:1
so has part: feature:806-1198:1:exon

WP_217847110.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:806-1198:1:exon

CP157_RS20125
type: Gene
subclass of: SO_0000704
RO_0002162: 59779
locus tag: CP157_RS20125
old locus tag: CP157_04039
so part of: sequence
location: complement(1365..2216)
location: region:1365-2216:-1
so has part: feature:1365-2216:-1:exon
subclass of: SO_0000010

position:1365:-1
position: 1365
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:2216:-1
position: 2216
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:1365-2216:-1:exon

CP157_RS20125
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 59779
locus tag: CP157_RS20125
old locus tag: CP157_04039
inference: COORDINATES: similar to AA sequence:RefSeq:WP_007803328.1
GO component: GO:0016020 - membrane [Evidence IEA]
GO function: GO:0015562 - efflux transmembrane transporter activity [Evidence IEA]; GO:0008324 - monoatomic cation transmembrane transporter activity [Evidence IEA]
GO process: GO:0006812 - monoatomic cation transport [Evidence IEA]
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: cation diffusion facilitator family transporter
translation: MSRADNTTLPTTSLPIRMRVHGMDCAKDAAEIERAARSAGVAEGDVKVSAATHVMTLRIAEDDLPKVRPALDATGYGFELIKSGDTSSDPAYKDPSYRRALWIVVALNLGYGVVEMFGGFLSGSQALKADALDFLGDGAITFLGLLAIGWSLTWRARSAMIQGVFLGLLGLGVVGSTLWRVLNQTTPEAGLMGAFAVGALIVNILAVLPLLKHRKGDANMRAVWLFSRNDAFGNLAVVIAAGLVAWLGSAWPDLIVAFAIAGLFLHSSWMIIRDARSDLSETE
SIO_010081: CP157_RS20125
subclass of: SO_0000673
so part of: CP157_RS20125
location: complement(1365..2216)
location: region:1365-2216:-1
so has part: feature:1365-2216:-1:exon

WP_217847111.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:1365-2216:-1:exon

CP157_RS20130
type: Gene
subclass of: SO_0000704
RO_0002162: 59779
locus tag: CP157_RS20130
so part of: sequence
location: 2280..2630
location: region:2280-2630:1
so has part: feature:2280-2630:1:exon
subclass of: SO_0000010

position:2280:1
position: 2280
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:2630:1
position: 2630
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:2280-2630:1:exon

CP157_RS20130
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 59779
locus tag: CP157_RS20130
inference: COORDINATES: similar to AA sequence:RefSeq:WP_014132722.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: metalloregulator ArsR/SmtB family transcription factor
translation: MTAQNIQDDLSAPDTLELRAKLFRGLSDPSRLTILDALLSDERSVQEIVTQTGLGQPNVSNHLRCLLDCGLVSRRNEGRFVRYRLADRRIADLIRDADQLLASTAVGVDACRSYTD
SIO_010081: CP157_RS20130
subclass of: SO_0000673
so part of: CP157_RS20130
location: 2280..2630
location: region:2280-2630:1
so has part: feature:2280-2630:1:exon

WP_099909049.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:2280-2630:1:exon

CP157_RS20420
type: Gene
subclass of: SO_0000704
RO_0002162: 59779
locus tag: CP157_RS20420
so part of: sequence
location: complement(2821..3090)
location: region:2821-3090:-1
so has part: feature:2821-3090:-1:exon
subclass of: SO_0000010

position:2821:-1
position: 2821
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:3090:-1
position: 3090
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:2821-3090:-1:exon

CP157_RS20420
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 59779
locus tag: CP157_RS20420
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: MNQLTPFERALLAQFETLVSTSETSLEASEATSKQLQTLSETVRKRLDKIEQKQSEIERFQAQLLRSFNTQTEQTMNLVRQVNALLEEE
SIO_010081: CP157_RS20420
subclass of: SO_0000673
so part of: CP157_RS20420
location: complement(2821..3090)
location: region:2821-3090:-1
so has part: feature:2821-3090:-1:exon

WP_245008592.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:2821-3090:-1:exon

CP157_RS20425
type: Gene
subclass of: SO_0000704
RO_0002162: 59779
locus tag: CP157_RS20425
so part of: sequence
location: complement(3094..3501)
location: region:3094-3501:-1
so has part: feature:3094-3501:-1:exon
subclass of: SO_0000010

position:3094:-1
position: 3094
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:3501:-1
position: 3501
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:3094-3501:-1:exon

CP157_RS20425
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 59779
locus tag: CP157_RS20425
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: MTESLTARLQQRLSSQTSEIEALTSAELTRLASSLRQQSEAALRTMRSDIQDTSTMMADELEIMRWTARWWWVALIVTWLVIAGLSVWHWMSPAPDPFPIFKTGGESYLMLPDGTEPMICQGEQPFLCLKLPNGM
SIO_010081: CP157_RS20425
subclass of: SO_0000673
so part of: CP157_RS20425
location: complement(3094..3501)
location: region:3094-3501:-1
so has part: feature:3094-3501:-1:exon

WP_245008593.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:3094-3501:-1:exon

CP157_RS20140
type: Gene
subclass of: SO_0000704
RO_0002162: 59779
gene: mobC
locus tag: CP157_RS20140
old locus tag: CP157_04042
so part of: sequence
location: complement(4221..4541)
location: region:4221-4541:-1
so has part: feature:4221-4541:-1:exon
subclass of: SO_0000010

position:4221:-1
position: 4221
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:4541:-1
position: 4541
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:4221-4541:-1:exon

CP157_RS20140
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 59779
gene: mobC
locus tag: CP157_RS20140
old locus tag: CP157_04042
inference: COORDINATES: protein motif:HMM:NF017524.2
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: plasmid mobilization relaxosome protein MobC
translation: MRIEIRTTPEEKRRWQEIAENKGVSLSELVRSALGGQRLRKRREPPRVDPDLLRELARMGNNLNQLARAANRRQPVPAAALLVRLIEIDRELSALRAAHERPADAD
SIO_010081: CP157_RS20140
subclass of: SO_0000673
so part of: CP157_RS20140
location: complement(4221..4541)
location: region:4221-4541:-1
so has part: feature:4221-4541:-1:exon

WP_217847108.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:4221-4541:-1:exon