Paracoccus marcusii strain CP157 plasmid pCP157_12, complete sequence.
type: Entry
definition: Paracoccus marcusii strain CP157 plasmid pCP157_12, complete sequence.
sequence version: NZ_CP065904.1
sequence date: 2023-03-25
sequence: sequence
division: CON
label: NZ_CP065904.1
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\nCP065904.1.\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: 8745
topology: circular
so has quality: SO_0000988
location: 1..8745
location: region:1-8745:1
RO_0002162: 59779

NZ_CP065904
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:8745:1
position: 8745
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

feature:1-8745:1:source
so part of: sequence
organism: Paracoccus marcusii
mol type: genomic DNA
strain: CP157
isolation source: carapace
host: Cancer pagurus
plasmid: pCP157_12
country: Germany: Helgoland
lat lon: 54.12 N 7.53 E
collection date: 2014-10-15

59779
type: Taxonomy
SIO_000068: taxonomy

CP157_RS19860
type: Gene
subclass of: SO_0000704
RO_0002162: 59779
locus tag: CP157_RS19860
old locus tag: CP157_03991
so part of: sequence
location: 1..750
location: region:1-750:1
so has part: feature:1-750:1:exon
subclass of: SO_0000010

position:750:1
position: 750
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:1-750:1:exon

CP157_RS19860
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 59779
locus tag: CP157_RS19860
old locus tag: CP157_03991
inference: COORDINATES: protein motif:HMM:NF013235.2
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: replication initiation protein
translation: MARPRKDTPAIKLPVGGNVTMHNTLISASHGLNLGEKRLVAMAVAKLSPKAVALPGKPVRISAVDFAKQFGLDTTTAYEQLRDAQENLFNRYIRHIEHYGPNGQKTEVIKMRWITSISYKNGDGEVALAFAPEIAQFLVQLKKHFTSYQLSKAAALRSTYSWRLFENLERFRETGIWEVDMDRFHAIMETPKSYRRNFNDARRFVIDPALAELAAKTNITAEVEPIRRGRKIDRLRFTFENASQMKLAL
SIO_010081: CP157_RS19860
subclass of: SO_0000673
so part of: CP157_RS19860
location: 1..750
location: region:1-750:1
so has part: feature:1-750:1:exon

WP_217847070.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:1-750:1:exon

CP157_RS19865
type: Gene
subclass of: SO_0000704
RO_0002162: 59779
locus tag: CP157_RS19865
old locus tag: CP157_03992
so part of: sequence
location: 849..1292
location: region:849-1292:1
so has part: feature:849-1292:1:exon
subclass of: SO_0000010

position:849:1
position: 849
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:1292:1
position: 1292
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:849-1292:1:exon

CP157_RS19865
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 59779
locus tag: CP157_RS19865
old locus tag: CP157_03992
inference: COORDINATES: similar to AA sequence:RefSeq:WP_013221954.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: hypothetical protein
translation: MAYTLGEAAKASGKSKATISKAIKSGRLSAVKQETGVFRIEAAELHRVYPKTVDGNQDRTLQTVTQTPENTPSVRELQARLEAAQERLTDRDAVIADLRDDRDRWRQQATALLADQRPVPQPVIQPAPQPDQPVVQPPKGFWKRLFG
SIO_010081: CP157_RS19865
subclass of: SO_0000673
so part of: CP157_RS19865
location: 849..1292
location: region:849-1292:1
so has part: feature:849-1292:1:exon

WP_217847071.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:849-1292:1:exon

CP157_RS19870
type: Gene
subclass of: SO_0000704
RO_0002162: 59779
locus tag: CP157_RS19870
old locus tag: CP157_03993
so part of: sequence
location: complement(1296..4379)
location: region:1296-4379:-1
so has part: feature:1296-4379:-1:exon
subclass of: SO_0000010

position:1296:-1
position: 1296
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:4379:-1
position: 4379
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:1296-4379:-1:exon

CP157_RS19870
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 59779
locus tag: CP157_RS19870
old locus tag: CP157_03993
inference: COORDINATES: similar to AA sequence:RefSeq:WP_005863412.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: class I SAM-dependent DNA methyltransferase
translation: MLRARNQADGYARAVAREDGWPPFLLIVDVGHVIEVYADFSGQGQGYTQFPDGNRYRIALDDLRDEKTRTRLHDIWTDPHSLDPSRVSAQVTRQVAGHLAELGRSFEAQGHAPEVVARFLMRALFTMFAEDVRLIPEGAFTKLLKDRSGHPEHAAPMLENLWATMNTGGFSPALSCDLKRFNGGLFREATALPLSELQLGLLIQAASHNWREVEPAIFGTLLERALDTRQRHKLGAHYTPRAYVERLVNPTVIEPLRAEWRDVQAAAVTLAAQDKLTEARATVRDFHQRLCEIRVLDPACGSGNFLYVALELMKRLEGEVIALLRELGEDQGALALAGHTVDPHQFLGIEVNPWAAAVAELVLWIGYLQWHFRTHGEASPSEPVLRDFRNIENRDAVLACDGTRPRLDGEGRPVTRWDGVSTVYHMVTGEQVPDPAARVAVLDYLKPRPAKWPQAEFIIGNPPFIGASRMREILGDGYAEALRAAYPKMPESADFVMFWWDKAALAVRASKARRLGFITTNSLRQTFNRQVLEPHLADPKKPLSLTFAIPDHPWVDAGDGAAVRIAMTVAAPGSVPGRLFTVTDERRGEREAEGRPVTLSGQIGKVYGNLRVGADVAGARALRANERLAYRGMQLIGSGFIVTPTEAQALGLGTVPGLEAHIRTYRNGRDLTATPRGVMVIDLFGLSEGEARNNFPNVYQHVMDNVKPERDQNNRDSYKRNWWIHGEPRRDLRPALEGLRRYIATVETAKHRFFQFLDAATLPDNMLIAIGLDDAAALAVLSSRIHVAWALAAGGRLGYGNDPRYNKSRCFDPFSFPDASEAQKTRLRALGEELDAHRKAQQAAHPRLTLTTIYNVLEKLRAGERIEGRDRETYDAGLVGILRNIHDRIDAAVAEAYGWPEGLDDEAILTCLVDLNRARAAEEAQGLVRWLRPEYQNPAGRAAAAKGQQAELDVGAVPDAADKALWPKALPEQIAAVRAVLSDMGEATPEQIARQFKRGRAASVKPLLETLSALGQARLIDGGRFAA
SIO_010081: CP157_RS19870
subclass of: SO_0000673
so part of: CP157_RS19870
location: complement(1296..4379)
location: region:1296-4379:-1
so has part: feature:1296-4379:-1:exon

WP_245008589.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:1296-4379:-1:exon

CP157_RS20415
type: Gene
subclass of: SO_0000704
RO_0002162: 59779
locus tag: CP157_RS20415
so part of: sequence
location: 4413..4754
location: region:4413-4754:1
so has part: feature:4413-4754:1:exon
subclass of: SO_0000010

position:4413:1
position: 4413
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:4754:1
position: 4754
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:4413-4754:1:exon

CP157_RS20415
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 59779
locus tag: CP157_RS20415
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: MPLALHSGGGGKQIKLVFIRRRDRALFGLHDEGAAPVKVDETARLRAGVDEGHRPFEAVIVILCVGRRGLGRWHFQKLGQLNGELLEIGPLAATRCLPASDEIINVQNQSRLF
SIO_010081: CP157_RS20415
subclass of: SO_0000673
so part of: CP157_RS20415
location: 4413..4754
location: region:4413-4754:1
so has part: feature:4413-4754:1:exon

WP_245008588.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:4413-4754:1:exon

CP157_RS19875
type: Gene
subclass of: SO_0000704
RO_0002162: 59779
locus tag: CP157_RS19875
old locus tag: CP157_03994
so part of: sequence
location: 5143..5427
location: region:5143-5427:1
so has part: feature:5143-5427:1:exon
subclass of: SO_0000010

position:5143:1
position: 5143
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:5427:1
position: 5427
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:5143-5427:1:exon

CP157_RS19875
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 59779
locus tag: CP157_RS19875
old locus tag: CP157_03994
inference: COORDINATES: similar to AA sequence:RefSeq:WP_007396255.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: BrnT family toxin
translation: MKIAGFDWDTGNWPKCGKHGLSRAEIEEVFARTPAVLADPFPEEARMRAIGTTAAGRHVFVVFQLREIDGQTKLRPISARYMHQKEIAHYERPS
SIO_010081: CP157_RS19875
subclass of: SO_0000673
so part of: CP157_RS19875
location: 5143..5427
location: region:5143-5427:1
so has part: feature:5143-5427:1:exon

WP_217847064.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:5143-5427:1:exon

CP157_RS19880
type: Gene
subclass of: SO_0000704
RO_0002162: 59779
locus tag: CP157_RS19880
old locus tag: CP157_03995
so part of: sequence
location: 5411..5674
location: region:5411-5674:1
so has part: feature:5411-5674:1:exon
subclass of: SO_0000010

position:5411:1
position: 5411
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:5674:1
position: 5674
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:5411-5674:1:exon

CP157_RS19880
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 59779
locus tag: CP157_RS19880
old locus tag: CP157_03995
inference: COORDINATES: similar to AA sequence:RefSeq:WP_010511277.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: BrnA antitoxin family protein
translation: MNAHPKPLPPLTSDAEAEDFVEMADLSEYDLSGFTPMRFEIEPKAASLNMRLPASLLDAVKAKAKASGIPYTRYVRMLLETDVARPK
SIO_010081: CP157_RS19880
subclass of: SO_0000673
so part of: CP157_RS19880
location: 5411..5674
location: region:5411-5674:1
so has part: feature:5411-5674:1:exon

WP_217847065.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:5411-5674:1:exon

CP157_RS19885
type: Gene
subclass of: SO_0000704
RO_0002162: 59779
locus tag: CP157_RS19885
old locus tag: CP157_03996
so part of: sequence
location: 5749..6240
location: region:5749-6240:1
so has part: feature:5749-6240:1:exon
subclass of: SO_0000010

position:5749:1
position: 5749
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:6240:1
position: 6240
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:5749-6240:1:exon

CP157_RS19885
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 59779
locus tag: CP157_RS19885
old locus tag: CP157_03996
inference: COORDINATES: protein motif:HMM:NF024812.2
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: GNAT family N-acetyltransferase
translation: MFTYRSLTAADAQGWREIFITGVKNFPTGFLMTPAEVDDLTMERCQTILDAGGTRGIFEGELLAGFCGYRQFQPIRIRHRGEIGPFFVMENFHGSGAAQALMAGVVEEAKGAGVEQLELSVAQRNHRAIAFYERQGFVRYGAHPDAVRDEEADGSGFLYRRLL
SIO_010081: CP157_RS19885
subclass of: SO_0000673
so part of: CP157_RS19885
location: 5749..6240
location: region:5749-6240:1
so has part: feature:5749-6240:1:exon

WP_217847066.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:5749-6240:1:exon

CP157_RS19890
type: Gene
subclass of: SO_0000704
RO_0002162: 59779
locus tag: CP157_RS19890
so part of: sequence
location: complement(6427..7032)
location: region:6427-7032:-1
so has part: feature:6427-7032:-1:exon
subclass of: SO_0000010

position:6427:-1
position: 6427
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:7032:-1
position: 7032
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:6427-7032:-1:exon

CP157_RS19890
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 59779
locus tag: CP157_RS19890
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: MPRISHHISRKAATTLLHSARTAAATGRPFTVAVSIGTFLLNIPETEVSEKFRKMRRLRFVRWSTYVPKSGSGAVRNSRPADTWQIEAPNGFHHIHWMLHVRPENRTEFEKKLEKWVKDMAGLKPADPLPPNSLCVYDVHNPEGKKLYMAKGIDPFYASIFKIRPVDCGIVYGVRGGTARSLGPSVWKPIKKAYKASKPPK
SIO_010081: CP157_RS19890
subclass of: SO_0000673
so part of: CP157_RS19890
location: complement(6427..7032)
location: region:6427-7032:-1
so has part: feature:6427-7032:-1:exon

WP_217847067.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:6427-7032:-1:exon

CP157_RS19895
type: Gene
subclass of: SO_0000704
RO_0002162: 59779
locus tag: CP157_RS19895
old locus tag: CP157_03997
so part of: sequence
location: 7773..7991
location: region:7773-7991:1
so has part: feature:7773-7991:1:exon
subclass of: SO_0000010

position:7773:1
position: 7773
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:7991:1
position: 7991
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:7773-7991:1:exon

CP157_RS19895
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 59779
locus tag: CP157_RS19895
old locus tag: CP157_03997
inference: COORDINATES: similar to AA sequence:RefSeq:WP_015497693.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: antitoxin MazE family protein
translation: MPTPVSERVQKRRAALRAAGLRPVQIWVPDTRRPGFAAECRRQAALVAEADRTDTDMQNFMDAALTDLDDWQ
SIO_010081: CP157_RS19895
subclass of: SO_0000673
so part of: CP157_RS19895
location: 7773..7991
location: region:7773-7991:1
so has part: feature:7773-7991:1:exon

WP_217847068.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:7773-7991:1:exon

CP157_RS19900
type: Gene
subclass of: SO_0000704
RO_0002162: 59779
locus tag: CP157_RS19900
old locus tag: CP157_03998
so part of: sequence
location: 7988..8314
location: region:7988-8314:1
so has part: feature:7988-8314:1:exon
subclass of: SO_0000010

position:7988:1
position: 7988
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:8314:1
position: 8314
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:7988-8314:1:exon

CP157_RS19900
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 59779
locus tag: CP157_RS19900
old locus tag: CP157_03998
EC number: 3.1.-.-
inference: COORDINATES: similar to AA sequence:RefSeq:WP_015497694.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: type II toxin-antitoxin system PemK/MazF family toxin
translation: MKRGDLVTVALQGDYGKPRPALVIQSDQFSGTASVVVLPVTSTLVDAPLLRLTVEPEAGNGLRTTSQIMLDKPMTVKADKIGPAFGSLDDVAMVSISRSLALFLGLAG
SIO_010081: CP157_RS19900
subclass of: SO_0000673
so part of: CP157_RS19900
location: 7988..8314
location: region:7988-8314:1
so has part: feature:7988-8314:1:exon

WP_217847069.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:7988-8314:1:exon