Paracoccus marcusii strain CP157 plasmid pCP157_14, complete sequence.
type: Entry
definition: Paracoccus marcusii strain CP157 plasmid pCP157_14, complete sequence.
sequence version: NZ_CP065906.1
sequence date: 2023-03-25
sequence: sequence
division: CON
label: NZ_CP065906.1
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\nCP065906.1.\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: 8099
topology: circular
so has quality: SO_0000988
location: 1..8099
location: region:1-8099:1
RO_0002162: 59779

NZ_CP065906
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:8099:1
position: 8099
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

feature:1-8099:1:source
so part of: sequence
organism: Paracoccus marcusii
mol type: genomic DNA
strain: CP157
isolation source: carapace
host: Cancer pagurus
plasmid: pCP157_14
country: Germany: Helgoland
lat lon: 54.12 N 7.53 E
collection date: 2014-10-15

59779
type: Taxonomy
SIO_000068: taxonomy

CP157_RS19955
type: Gene
subclass of: SO_0000704
RO_0002162: 59779
locus tag: CP157_RS19955
old locus tag: CP157_04008
so part of: sequence
location: 79..576
location: region:79-576:1
so has part: feature:79-576:1:exon
subclass of: SO_0000010

position:79:1
position: 79
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:576:1
position: 576
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:79-576:1:exon

CP157_RS19955
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 59779
locus tag: CP157_RS19955
old locus tag: CP157_04008
inference: COORDINATES: similar to AA sequence:RefSeq:WP_010337276.1
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: MNLIAKSPVGAQIMHALTARLGDHNAVVISQVALAKIIGRSERAVRTALSVLKADNWIEVRQLGNAATVNAYIVNDRVAWTGKRDGIRYSLFSAAVVVSEEEQPDRDSLGQQAALRRIPDLLPGEMQLPSGEGLPPVSQPILEGMEPDLPARQRSYDPQTGKRLD
SIO_010081: CP157_RS19955
subclass of: SO_0000673
so part of: CP157_RS19955
location: 79..576
location: region:79-576:1
so has part: feature:79-576:1:exon

WP_217847086.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:79-576:1:exon

CP157_RS19960
type: Gene
subclass of: SO_0000704
RO_0002162: 59779
locus tag: CP157_RS19960
so part of: sequence
location: complement(579..827)
location: region:579-827:-1
so has part: feature:579-827:-1:exon
subclass of: SO_0000010

position:579:-1
position: 579
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:827:-1
position: 827
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:579-827:-1:exon

CP157_RS19960
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 59779
locus tag: CP157_RS19960
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: MSGAELRVNHLEELLEAERAAREDLKQALQARVDDLQTTVLDLRKRLDQAEEEKMRLLPPPGDGERETRSRPRGLWARLTGG
SIO_010081: CP157_RS19960
subclass of: SO_0000673
so part of: CP157_RS19960
location: complement(579..827)
location: region:579-827:-1
so has part: feature:579-827:-1:exon

WP_217847087.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:579-827:-1:exon

CP157_RS19965
type: Gene
subclass of: SO_0000704
RO_0002162: 59779
locus tag: CP157_RS19965
old locus tag: CP157_04010
so part of: sequence
location: 1388..1636
location: region:1388-1636:1
so has part: feature:1388-1636:1:exon
subclass of: SO_0000010

position:1388:1
position: 1388
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:1636:1
position: 1636
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:1388-1636:1:exon

CP157_RS19965
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 59779
locus tag: CP157_RS19965
old locus tag: CP157_04010
inference: COORDINATES: similar to AA sequence:RefSeq:WP_012760089.1
GO process: GO:0051983 - regulation of chromosome segregation [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 ParD family antitoxin
translation: MPRTTSVSLGEHFTGFISAQVDAGRYGSASDVVRAGLRLLEEHEAKVKALQDALIAGEQSGEPRPFDFDSFKARKRAEFEAG
SIO_010081: CP157_RS19965
subclass of: SO_0000673
so part of: CP157_RS19965
location: 1388..1636
location: region:1388-1636:1
so has part: feature:1388-1636:1:exon

WP_066613603.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:1388-1636:1:exon

CP157_RS19970
type: Gene
subclass of: SO_0000704
RO_0002162: 59779
locus tag: CP157_RS19970
old locus tag: CP157_04011
so part of: sequence
location: 1633..1920
location: region:1633-1920:1
so has part: feature:1633-1920:1:exon
subclass of: SO_0000010

position:1633:1
position: 1633
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:1920:1
position: 1920
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:1633-1920:1:exon

CP157_RS19970
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 59779
locus tag: CP157_RS19970
old locus tag: CP157_04011
inference: COORDINATES: similar to AA sequence:RefSeq:WP_012559995.1
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: MKPLAFSPAAEADIDGIWDYSAQTWGPDQADRYTDEIRDACLALAHDRKQGRPVDVRPGYLRLSTGSHVIYYRNRGDRLDVIRVLHNRMDADRHL
SIO_010081: CP157_RS19970
subclass of: SO_0000673
so part of: CP157_RS19970
location: 1633..1920
location: region:1633-1920:1
so has part: feature:1633-1920:1:exon

WP_066613605.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:1633-1920:1:exon

CP157_RS19975
type: Gene
subclass of: SO_0000704
RO_0002162: 59779
locus tag: CP157_RS19975
old locus tag: CP157_04012
so part of: sequence
location: 2010..2231
location: region:2010-2231:1
so has part: feature:2010-2231:1:exon
subclass of: SO_0000010

position:2010:1
position: 2010
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:2231:1
position: 2231
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:2010-2231:1:exon

CP157_RS19975
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 59779
locus tag: CP157_RS19975
old locus tag: CP157_04012
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: MSWHGVLLSALLVLAGGPAIANQPSAPPLEPFALCPPVVREFLEAVGLSPELPDYARPMVVIDTQGHPFDCLP
SIO_010081: CP157_RS19975
subclass of: SO_0000673
so part of: CP157_RS19975
location: 2010..2231
location: region:2010-2231:1
so has part: feature:2010-2231:1:exon

WP_148663113.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:2010-2231:1:exon

CP157_RS19980
type: Gene
subclass of: SO_0000704
RO_0002162: 59779
locus tag: CP157_RS19980
old locus tag: CP157_04013
so part of: sequence
location: 2292..2483
location: region:2292-2483:1
so has part: feature:2292-2483:1:exon
subclass of: SO_0000010

position:2292:1
position: 2292
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:2483:1
position: 2483
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:2292-2483:1:exon

CP157_RS19980
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 59779
locus tag: CP157_RS19980
old locus tag: CP157_04013
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: MAQNQEAGSVCRIGEARLQETSFIGLILSYDLARTNSPTCLHQARQDLDVLQERSLGKAPTQP
SIO_010081: CP157_RS19980
subclass of: SO_0000673
so part of: CP157_RS19980
location: 2292..2483
location: region:2292-2483:1
so has part: feature:2292-2483:1:exon

WP_217847088.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:2292-2483:1:exon

CP157_RS19985
type: Gene
subclass of: SO_0000704
RO_0002162: 59779
locus tag: CP157_RS19985
old locus tag: CP157_04014
so part of: sequence
location: complement(2674..2970)
location: region:2674-2970:-1
so has part: feature:2674-2970:-1:exon
subclass of: SO_0000010

position:2674:-1
position: 2674
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:2970:-1
position: 2970
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:2674-2970:-1:exon

CP157_RS19985
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 59779
locus tag: CP157_RS19985
old locus tag: CP157_04014
inference: COORDINATES: similar to AA sequence:RefSeq:WP_010188704.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: hypothetical protein
translation: MAVLEATFETRREAEMSIERLVQEFGLDRKAIEIVADGALNSAGEDTSGGDNAADTPTPSEREDAALNDRIKVSVTVDDEAEAERVRNAFSEFGGDRS
SIO_010081: CP157_RS19985
subclass of: SO_0000673
so part of: CP157_RS19985
location: complement(2674..2970)
location: region:2674-2970:-1
so has part: feature:2674-2970:-1:exon

WP_217847089.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:2674-2970:-1:exon

CP157_RS19990
type: Gene
subclass of: SO_0000704
RO_0002162: 59779
locus tag: CP157_RS19990
old locus tag: CP157_04015
so part of: sequence
location: 3416..4663
location: region:3416-4663:1
so has part: feature:3416-4663:1:exon
subclass of: SO_0000010

position:3416:1
position: 3416
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:4663:1
position: 4663
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:3416-4663:1:exon

CP157_RS19990
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 59779
locus tag: CP157_RS19990
old locus tag: CP157_04015
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: MTGSFMFLIDFPEMRARIESIPAGFLPLPSLSETIRSKLIIKASKETILTAQTQGEFFIYRVPIIINGTETFNLITAFRDDYENPLTIFTPIIEENDLIYNIRSVICSKEFDVHFFDEHARERVAYTVKNVDFEHAKKTFAVAPASLQATTAKESYQATVNWFGLRTPEDDANSLRIPLEEKLYNDNFSIIDLGDAHTNRLYFPKPSGLVREIAGPESEEDIAQCFSRSFKNGMIFIGPMKKNNKELADIVVVEENNVILVQAKDSPNNEAMLSRSIERKSRASRALAEKGFSQVKGAIRSVQTDGLKIENEFVRINMHPENINLYAILVIKERFPDSYRWYYEKSSEITRDKGVMTVLLSYRQLHEITHHMESGKDFIGAITQMYFQGSLDSQFPELNFPKKQRIAHYTLRGND
SIO_010081: CP157_RS19990
subclass of: SO_0000673
so part of: CP157_RS19990
location: 3416..4663
location: region:3416-4663:1
so has part: feature:3416-4663:1:exon

WP_217847090.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:3416-4663:1:exon

CP157_RS19995
type: Gene
subclass of: SO_0000704
RO_0002162: 59779
locus tag: CP157_RS19995
old locus tag: CP157_04016
so part of: sequence
location: 4787..5542
location: region:4787-5542:1
so has part: feature:4787-5542:1:exon
subclass of: SO_0000010

position:4787:1
position: 4787
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:5542:1
position: 5542
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:4787-5542:1:exon

CP157_RS19995
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 59779
locus tag: CP157_RS19995
old locus tag: CP157_04016
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: MPDFVDKFGTALAYFSLKIRETANIKHSGAKGSERELDVAAFIDDLLPMNYTAKKGEIVDLLGQKSPQMDVIIFDALKNFSFYSGESVVLPAEACLASVEIKSKINSTEIKTSQEASRKLKSLKPWKRQLGSSSQQLQESSGPRSARYLHSLFAYDTDIADANWAKSELTRIENHANGPADQSIDFLYVLNRGLIDTRSRSFIPEDEKTGQALVSFWFSLYNFIDRENRRRERAPYFSYANDLKRFWTKID
SIO_010081: CP157_RS19995
subclass of: SO_0000673
so part of: CP157_RS19995
location: 4787..5542
location: region:4787-5542:1
so has part: feature:4787-5542:1:exon

WP_217847083.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:4787-5542:1:exon

CP157_RS20000
type: Gene
subclass of: SO_0000704
RO_0002162: 59779
gene: mobV
locus tag: CP157_RS20000
old locus tag: CP157_04018
so part of: sequence
location: 6328..7167
location: region:6328-7167:1
so has part: feature:6328-7167:1:exon
subclass of: SO_0000010

position:6328:1
position: 6328
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:7167:1
position: 7167
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:6328-7167:1:exon

CP157_RS20000
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 59779
gene: mobV
locus tag: CP157_RS20000
old locus tag: CP157_04018
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: MSDVVTDFSKGMQVRSGSRPPRSFAILRVGKIKTKGHLGAALGHNYRERDTPNADQSRMAENLVLKGPGTAQGVMEAWDARAPEKIRKNAVHALEYFVGGSPEKVHAMGRDEQNNYFRSALDWLKDRHGAENVLSAVVHRDETTPHMQVLVIPLDARGKLNARELVGGKDKLRQMQTDFARDVGQPFGLERGQERSRATHQTIQEYYGRASTPVEADFSLPERRKGAVRGLGGESDREWQERASRAATERLAHLTAHLTEASGTLRREMEATEAVLGQT
SIO_010081: CP157_RS20000
subclass of: SO_0000673
so part of: CP157_RS20000
location: 6328..7167
location: region:6328-7167:1
so has part: feature:6328-7167:1:exon

WP_217847084.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:6328-7167:1:exon

CP157_RS20005
type: Gene
subclass of: SO_0000704
RO_0002162: 59779
locus tag: CP157_RS20005
old locus tag: CP157_04019
so part of: sequence
location: 7288..7539
location: region:7288-7539:1
so has part: feature:7288-7539:1:exon
subclass of: SO_0000010

position:7288:1
position: 7288
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:7539:1
position: 7539
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:7288-7539:1:exon

CP157_RS20005
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 59779
locus tag: CP157_RS20005
old locus tag: CP157_04019
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: MARFHNRHASHFSDMQAQATKAALNHTGIAVIELKDGSYALPWRDFDAVGGQRLAGTDRQDADAILNGLRQAERSRQQATEAM
SIO_010081: CP157_RS20005
subclass of: SO_0000673
so part of: CP157_RS20005
location: 7288..7539
location: region:7288-7539:1
so has part: feature:7288-7539:1:exon

WP_217847085.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:7288-7539:1:exon