Paracoccus marcusii strain CP157 plasmid pCP157_19, complete sequence.
type: Entry
definition: Paracoccus marcusii strain CP157 plasmid pCP157_19, complete sequence.
sequence version: NZ_CP065911.1
sequence date: 2023-03-25
sequence: sequence
division: CON
label: NZ_CP065911.1
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\nCP065911.1.\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: 4405
topology: circular
so has quality: SO_0000988
location: 1..4405
location: region:1-4405:1
RO_0002162: 59779

NZ_CP065911
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:4405:1
position: 4405
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

feature:1-4405:1:source
so part of: sequence
organism: Paracoccus marcusii
mol type: genomic DNA
strain: CP157
isolation source: carapace
host: Cancer pagurus
plasmid: pCP157_19
country: Germany: Helgoland
lat lon: 54.12 N 7.53 E
collection date: 2014-10-15

59779
type: Taxonomy
SIO_000068: taxonomy

CP157_RS20145
type: Gene
subclass of: SO_0000704
RO_0002162: 59779
locus tag: CP157_RS20145
old locus tag: CP157_04043
so part of: sequence
location: 1..723
location: region:1-723:1
so has part: feature:1-723:1:exon
subclass of: SO_0000010

position:723:1
position: 723
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:1-723:1:exon

CP157_RS20145
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 59779
locus tag: CP157_RS20145
old locus tag: CP157_04043
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: MSRIPIYELRRMGVSQEDIEIAQQTQEAQRRTGSPVQSIGVIVGAVQQRARHNPNPPVNLSDRAMRKRGTYDQAALLADQAALQEKSPERAMMARQASQTLKELSAAQQLEYDFFGGNVSIAFQYQDAVTERLFEAAKTPAQAKEALSILWTICRHLGWQTYECTKTAADLCELTRTKAPNMADALKLLEQVGAIQRVKRGRTKIITVTPEGAFRGNIKNHAQAVERYKLDVIDGGKSEN
SIO_010081: CP157_RS20145
subclass of: SO_0000673
so part of: CP157_RS20145
location: 1..723
location: region:1-723:1
so has part: feature:1-723:1:exon

WP_217847113.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:1-723:1:exon

CP157_RS20150
type: Gene
subclass of: SO_0000704
RO_0002162: 59779
locus tag: CP157_RS20150
so part of: sequence
location: complement(971..1728)
location: region:971-1728:-1
so has part: feature:971-1728:-1:exon
subclass of: SO_0000010

position:971:-1
position: 971
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:1728:-1
position: 1728
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:971-1728:-1:exon

CP157_RS20150
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 59779
locus tag: CP157_RS20150
inference: COORDINATES: similar to AA sequence:RefSeq:WP_076611905.1
ribosomal slippage: true
GO function: GO:0004803 - transposase activity [Evidence IEA]
note: programmed frameshift; Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: IS5 family transposase
translation: MSDLFWLTDAQMARLAPFFPKSHGKPRVDDRRVLSGIIFIIRNGLRWRDAPAAYGPHKTLYSRWRRWSGKGIFARMMAGLAAEHGEENTVMIDATYLKAHRTATSMAGQKGGRGRLIGRTKGGMNTKLHAICDSQGRPLDLFITAGQVSDYIGARALLSGLPNVRWLLGDRGYDADWLREALQDKGIRACIPGRKQRKMPVKYDKRRYKRRNRIEIMFGRIKDWRRVATRYDRCPKVFLSAIALAALVIYWL
SIO_010081: CP157_RS20150
subclass of: SO_0000673
so part of: CP157_RS20150
location: complement(join(971..1407,1407..1728))
location: region:971-1728:-1
so has part: feature:1407-1728:-1:exon
so has part: feature:971-1407:-1:exon

WP_217847034.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:1407-1728:-1:exon

position:1407:-1
position: 1407
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 2
SIO_000628: feature:971-1407:-1:exon

CP157_RS20430
type: Gene
subclass of: SO_0000704
RO_0002162: 59779
locus tag: CP157_RS20430
so part of: sequence
location: complement(2190..2459)
location: region:2190-2459:-1
so has part: feature:2190-2459:-1:exon
subclass of: SO_0000010

position:2190:-1
position: 2190
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:2459:-1
position: 2459
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:2190-2459:-1:exon

CP157_RS20430
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 59779
locus tag: CP157_RS20430
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: MNQLTAFERALLAQFETLVSTSETSLEASEATSKQLRTLSETVRNRLDSIERKQREIEHFQTQLLESLNTHNKQTASLVQQVNALLKER
SIO_010081: CP157_RS20430
subclass of: SO_0000673
so part of: CP157_RS20430
location: complement(2190..2459)
location: region:2190-2459:-1
so has part: feature:2190-2459:-1:exon

WP_245008595.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:2190-2459:-1:exon

CP157_RS20435
type: Gene
subclass of: SO_0000704
RO_0002162: 59779
locus tag: CP157_RS20435
so part of: sequence
location: complement(2463..2870)
location: region:2463-2870:-1
so has part: feature:2463-2870:-1:exon
subclass of: SO_0000010

position:2463:-1
position: 2463
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:2870:-1
position: 2870
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:2463-2870:-1:exon

CP157_RS20435
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 59779
locus tag: CP157_RS20435
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: MTESLTARLQQRLSSQTAEIEALTSAELTRLASSLRQQSEAALRTMQNDIQGTSLMMADELEIVRWTARWWWVALIVTWLAIAGLSVWHWMSPAPDQFPIFRNGGQSYLMLPEGTEPMICQGEQPFLCLKLPNGS
SIO_010081: CP157_RS20435
subclass of: SO_0000673
so part of: CP157_RS20435
location: complement(2463..2870)
location: region:2463-2870:-1
so has part: feature:2463-2870:-1:exon

WP_245008594.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:2463-2870:-1:exon

CP157_RS20160
type: Gene
subclass of: SO_0000704
RO_0002162: 59779
gene: mobC
locus tag: CP157_RS20160
old locus tag: CP157_04049
so part of: sequence
location: complement(3590..3910)
location: region:3590-3910:-1
so has part: feature:3590-3910:-1:exon
subclass of: SO_0000010

position:3590:-1
position: 3590
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:3910:-1
position: 3910
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:3590-3910:-1:exon

CP157_RS20160
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 59779
gene: mobC
locus tag: CP157_RS20160
old locus tag: CP157_04049
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: MRIEIRTTPEEKRRWQEIAENKGVSLSELVRSALGGQRLRKRREPPRVDPDLLRELARMGNNLNQLARGANRRQPVQAAALLVRLIEIDRELSALRAAHERPADAD
SIO_010081: CP157_RS20160
subclass of: SO_0000673
so part of: CP157_RS20160
location: complement(3590..3910)
location: region:3590-3910:-1
so has part: feature:3590-3910:-1:exon

WP_217847112.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:3590-3910:-1:exon