Paracoccus marcusii strain CP157 plasmid pCP157_17, complete sequence.
type: Entry
definition: Paracoccus marcusii strain CP157 plasmid pCP157_17, complete sequence.
sequence version: NZ_CP065909.1
sequence date: 2023-03-25
sequence: sequence
division: CON
label: NZ_CP065909.1
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\nCP065909.1.\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: 6050
topology: circular
so has quality: SO_0000988
location: 1..6050
location: region:1-6050:1
RO_0002162: 59779

NZ_CP065909
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:6050:1
position: 6050
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

feature:1-6050:1:source
so part of: sequence
organism: Paracoccus marcusii
mol type: genomic DNA
strain: CP157
isolation source: carapace
host: Cancer pagurus
plasmid: pCP157_17
country: Germany: Helgoland
lat lon: 54.12 N 7.53 E
collection date: 2014-10-15

59779
type: Taxonomy
SIO_000068: taxonomy

CP157_RS20090
type: Gene
subclass of: SO_0000704
RO_0002162: 59779
locus tag: CP157_RS20090
old locus tag: CP157_04032
so part of: sequence
location: join(5889..6050,1..972)
location: region:1-6050:1
so has part: feature:5889-6050:1:exon
so has part: feature:1-972:1:exon
subclass of: SO_0000010

urn:…
SIO_000300: 1
SIO_000628: feature:5889-6050:1:exon

position:5889:1
position: 5889
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 2
SIO_000628: feature:1-972:1:exon

position:972:1
position: 972
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

CP157_RS20090
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 59779
locus tag: CP157_RS20090
old locus tag: CP157_04032
inference: COORDINATES: ab initio prediction:GeneMarkS-2+
GO function: GO:0003677 - DNA binding [Evidence IEA]
GO process: GO:0006260 - DNA replication [Evidence IEA]
note: Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
codon start: 1
transl table: 11
product: protein rep
translation: MRAWEEARGDLDAIDELPGRGVTMCGWTQIAGMETDLMRQPAPDGHHAYLTGLQMCGLRWVCPICTARKAMQDRQFVNDGLAAARRRGLFPVMITLTTRHHAGEAAEDVLRGIMQAEQKLKRLKVWTRLKDVSVGYVRVLEWTYGEHGHHPHFHTILLVRAESEDDAIAQAETLRGAYMRQLEKAGRDGKSPAAWEHSFHIQGAAAAEGYITKWGAAEELTGSLAKDGGRDSLTPWQLLRLARISPARGGRTADQERARYASIWWQVITATKGKAQLYKSQGWTDLVEAWRAEQPETDPVPEPELVRHLGQREKRAEASAGWLAARDRTITLREAAESATDLDAARAAVALALVAGMTDGDIIRAMRDDDDPGPLLE
SIO_010081: CP157_RS20090
subclass of: SO_0000673
so part of: CP157_RS20090
location: join(5889..6050,1..972)
location: region:1-6050:1
so has part: feature:5889-6050:1:exon
so has part: feature:1-972:1:exon

WP_217847104.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:5889-6050:1:exon

urn:…
SIO_000300: 2
SIO_000628: feature:1-972:1:exon

CP157_RS20095
type: Gene
subclass of: SO_0000704
RO_0002162: 59779
locus tag: CP157_RS20095
old locus tag: CP157_04033
so part of: sequence
location: 1106..2260
location: region:1106-2260:1
so has part: feature:1106-2260:1:exon
subclass of: SO_0000010

position:1106:1
position: 1106
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:2260:1
position: 2260
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:1106-2260:1:exon

CP157_RS20095
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 59779
locus tag: CP157_RS20095
old locus tag: CP157_04033
inference: COORDINATES: similar to AA sequence:RefSeq:WP_011731971.1
GO function: GO:0009007 - site-specific DNA-methyltransferase (adenine-specific) activity [Evidence IEA]
GO process: GO:0032775 - DNA methylation on adenine [Evidence IEA]
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: DNA adenine methylase
translation: MNQLFTPDPHRQEDLFGGDYIAEDSDYLSEQLITYIGNKRRLIPMIEQSLRLAMREVAGPNPSFADVFAGTGVVSRMARAYAKTLYVNDFEEYSSFSNTVYQTNRCDIPSQEVEIWRKNVNEAGEIGARRGIISEFYAPADECNITAQDRVFYTKRNAAFIDSARAAIDEAPEHIRPYLLAPLIQRASVHVNTSGVFKGFYKNKDGVGQFGGTMRNALQRIRAHIDVPFPVLSRFKRESFVTRKEATDFVSEMPDVDVAYFDPPYNQHPYGSNYFMLNLILRNERPEEISRVSGIPKQWQRSPYNIRAEAGPALASITSSCPAKILLVSYNSEGFISPEEMMSILEPLGEVEVFDQKYSTFRGCRNLSGRSAHVTEMLFKVKRT
SIO_010081: CP157_RS20095
subclass of: SO_0000673
so part of: CP157_RS20095
location: 1106..2260
location: region:1106-2260:1
so has part: feature:1106-2260:1:exon

WP_245008591.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:1106-2260:1:exon

CP157_RS20100
type: Gene
subclass of: SO_0000704
RO_0002162: 59779
locus tag: CP157_RS20100
old locus tag: CP157_04034
so part of: sequence
location: 2260..2976
location: region:2260-2976:1
so has part: feature:2260-2976:1:exon
subclass of: SO_0000010

position:2976:1
position: 2976
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:2260-2976:1:exon

CP157_RS20100
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 59779
locus tag: CP157_RS20100
old locus tag: CP157_04034
inference: COORDINATES: protein motif:HMM:NF014959.2
GO function: GO:0003677 - DNA binding [Evidence IEA]; GO:0000287 - magnesium ion binding [Evidence IEA]; GO:0009036 - type II site-specific deoxyribonuclease activity [Evidence IEA]
GO process: GO:0009307 - DNA restriction-modification system [Evidence IEA]
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: EcoRI family type II restriction endonuclease
translation: MARKGDLRIQRKGTVINVTSSRQEKALSNAMQRVSNEIGRKFPGIVQKFEGDWKLKDIVEKLSAIYPDVDFTYHFETSGMRPDGGILSIVDDRGQAHPILITEKKNQGTNDLRALEGKTKQAKGNAIERLGKNVIGFRAAFKPESIFPFICFGDGCDFSDDSSILDRVSTIAQFGALNVEHLHKQADGDFDRGTFYFRVAEWTEEEMYERSLSVAEKSVFYYFSKHGKAAFIKDGPAV
SIO_010081: CP157_RS20100
subclass of: SO_0000673
so part of: CP157_RS20100
location: 2260..2976
location: region:2260-2976:1
so has part: feature:2260-2976:1:exon

WP_217847105.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:2260-2976:1:exon

CP157_RS20105
type: Gene
subclass of: SO_0000704
RO_0002162: 59779
locus tag: CP157_RS20105
old locus tag: CP157_04035
so part of: sequence
location: 3844..4716
location: region:3844-4716:1
so has part: feature:3844-4716:1:exon
subclass of: SO_0000010

position:3844:1
position: 3844
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:4716:1
position: 4716
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:3844-4716:1:exon

CP157_RS20105
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 59779
locus tag: CP157_RS20105
old locus tag: CP157_04035
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: MDLTTKDGGKLLADVSASSWHATKAALAWGAARAWRDEMRAADRAQRAGDMASSATHVERAIRAARVMVRIDRAERPEPTKKRATKRASLPKAGGWQGRIFDAATPAQRPAVALLWATGCRPAEVETGVDVLRDDRGQLVVRISGAKVHDGHGAGQPMRFLLIDESTDAGRALAGILGSAKKVTIQRAATRLNKDFAAIREKVGGKASPYSMRHQVSAELKATFGPNGAETVAAAMGHRTTRSQSRYGAVAQAKGGGAIKAAKATHQVKETRPARRPSAPEKAAPEGPGL
SIO_010081: CP157_RS20105
subclass of: SO_0000673
so part of: CP157_RS20105
location: 3844..4716
location: region:3844-4716:1
so has part: feature:3844-4716:1:exon

WP_217847102.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:3844-4716:1:exon

CP157_RS20110
type: Gene
subclass of: SO_0000704
RO_0002162: 59779
locus tag: CP157_RS20110
old locus tag: CP157_04036
so part of: sequence
location: complement(4675..5070)
location: region:4675-5070:-1
so has part: feature:4675-5070:-1:exon
subclass of: SO_0000010

position:4675:-1
position: 4675
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:5070:-1
position: 5070
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:4675-5070:-1:exon

CP157_RS20110
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 59779
locus tag: CP157_RS20110
old locus tag: CP157_04036
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: MTGIWLTYADAAALLGIKLDSVKRRARARQWNRRTKNDGIVEVCIPEDALPDLRPDNPLNIPDAIRPNDPPLNALRDRAEAAEKEAAAQAARAAALADQVADLRIERDRLLTIIERHTLQTRPFWSRLFRR
SIO_010081: CP157_RS20110
subclass of: SO_0000673
so part of: CP157_RS20110
location: complement(4675..5070)
location: region:4675-5070:-1
so has part: feature:4675-5070:-1:exon

WP_217847103.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:4675-5070:-1:exon