Paracoccus marcusii strain CP157 plasmid pCP157_15, complete sequence.
type: Entry
definition: Paracoccus marcusii strain CP157 plasmid pCP157_15, complete sequence.
sequence version: NZ_CP065907.1
sequence date: 2023-03-25
sequence: sequence
division: CON
label: NZ_CP065907.1
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\nCP065907.1.\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: 6778
topology: circular
so has quality: SO_0000988
location: 1..6778
location: region:1-6778:1
RO_0002162: 59779

NZ_CP065907
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:6778:1
position: 6778
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

feature:1-6778:1:source
so part of: sequence
organism: Paracoccus marcusii
mol type: genomic DNA
strain: CP157
isolation source: carapace
host: Cancer pagurus
plasmid: pCP157_15
country: Germany: Helgoland
lat lon: 54.12 N 7.53 E
collection date: 2014-10-15

59779
type: Taxonomy
SIO_000068: taxonomy

CP157_RS20010
type: Gene
subclass of: SO_0000704
RO_0002162: 59779
locus tag: CP157_RS20010
old locus tag: CP157_04020
so part of: sequence
location: 1..573
location: region:1-573:1
so has part: feature:1-573:1:exon
subclass of: SO_0000010

position:573:1
position: 573
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:1-573:1:exon

CP157_RS20010
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 59779
locus tag: CP157_RS20010
old locus tag: CP157_04020
inference: COORDINATES: similar to AA sequence:RefSeq:WP_013641249.1
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: MPNDDQPNSLPVKKQRGTWVQTERAAHEAWAMFLGLPGSLNASRVLHLLIARVEDHNAVVMSQKTMAGLLSVDMRTVRRAVAMLKEHRWIETRQIGDRGTVNAYIINDRVAWSGPREGIRYSLFTANVVISDAEQPDSNTLDHQEPLRKLPSLYPGEQQLPSGDGLPPESQPSLEGMEFDLPATVKRNTP
SIO_010081: CP157_RS20010
subclass of: SO_0000673
so part of: CP157_RS20010
location: 1..573
location: region:1-573:1
so has part: feature:1-573:1:exon

WP_217847093.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:1-573:1:exon

CP157_RS20015
type: Gene
subclass of: SO_0000704
RO_0002162: 59779
locus tag: CP157_RS20015
so part of: sequence
location: 650..1054
location: region:650-1054:1
so has part: feature:650-1054:1:exon
subclass of: SO_0000010

position:650:1
position: 650
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:1054:1
position: 1054
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:650-1054:1:exon

CP157_RS20015
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 59779
locus tag: CP157_RS20015
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: MKYTAGQAAKAVGVSKATITRALQNGKISGSKDDNGAWSIDPAELHRVFPPVAHALPATQTVKQFATPEKVNETGVLERENQMLREALIEVRQERDRWHQIAERLSIAPPAPVPIQQKVAEGFWSRLFRKSNGT
SIO_010081: CP157_RS20015
subclass of: SO_0000673
so part of: CP157_RS20015
location: 650..1054
location: region:650-1054:1
so has part: feature:650-1054:1:exon

WP_217847094.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:650-1054:1:exon

CP157_RS20020
type: Gene
subclass of: SO_0000704
RO_0002162: 59779
locus tag: CP157_RS20020
old locus tag: CP157_04021
so part of: sequence
location: 1463..1705
location: region:1463-1705:1
so has part: feature:1463-1705:1:exon
subclass of: SO_0000010

position:1463:1
position: 1463
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:1705:1
position: 1705
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:1463-1705:1:exon

CP157_RS20020
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 59779
locus tag: CP157_RS20020
old locus tag: CP157_04021
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: MSKQQKAILAVLEQKKDAGEFVVTGAIIDALGLKRAPNVYSSVSRAISRLCSRGLVVVYQPSINRQGKGFGYGLPGQDLR
SIO_010081: CP157_RS20020
subclass of: SO_0000673
so part of: CP157_RS20020
location: 1463..1705
location: region:1463-1705:1
so has part: feature:1463-1705:1:exon

WP_143079952.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:1463-1705:1:exon

CP157_RS20025
type: Gene
subclass of: SO_0000704
RO_0002162: 59779
gene: mobQ
locus tag: CP157_RS20025
old locus tag: CP157_04022
so part of: sequence
location: complement(1780..2877)
location: region:1780-2877:-1
so has part: feature:1780-2877:-1:exon
subclass of: SO_0000010

position:1780:-1
position: 1780
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:2877:-1
position: 2877
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:1780-2877:-1:exon

CP157_RS20025
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 59779
gene: mobQ
locus tag: CP157_RS20025
old locus tag: CP157_04022
inference: COORDINATES: protein motif:HMM:NF041496.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: MobQ family relaxase
translation: MAIYHLRATMISRSAGRSATAAAAYRSAELIVDQRTGLSFDYRARGGVDHVETLAPADAPSWVQDRAALWNAVELAETRKNSQVAREVRVALPCELDAPQRLQLVRDFCRREFVDRGMVADIALHAPGREGDERNHHAHILLTTREIGPEGFTTKNRDWNAKELLEGWREAWARDTNHALERCGAETRVDHRTLEVQRVEAEERAQEARERGDEAEALRETVRAVSLDRQPLPQLSAGAWQLKERGIEVAAVQVWREIKEQAVEVARVAQELAEKGRAWLERVAERAAEQVRDVVERVAPADAWGEFFAAAAPGASAAAEGLARDLEVERRLEAQREAAEREARERVQEQERRAHERDDGHDHGW
SIO_010081: CP157_RS20025
subclass of: SO_0000673
so part of: CP157_RS20025
location: complement(1780..2877)
location: region:1780-2877:-1
so has part: feature:1780-2877:-1:exon

WP_217847095.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:1780-2877:-1:exon

CP157_RS20030
type: Gene
subclass of: SO_0000704
RO_0002162: 59779
locus tag: CP157_RS20030
old locus tag: CP157_04023
so part of: sequence
location: 3036..3287
location: region:3036-3287:1
so has part: feature:3036-3287:1:exon
subclass of: SO_0000010

position:3036:1
position: 3036
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:3287:1
position: 3287
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:3036-3287:1:exon

CP157_RS20030
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 59779
locus tag: CP157_RS20030
old locus tag: CP157_04023
inference: COORDINATES: similar to AA sequence:RefSeq:WP_009824546.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: hypothetical protein
translation: MPRTIDQQIAEAQAKLNRLKTRQKASDTRRKIIVGAIVTTEALKDPKIARWMAATLRKNATREVDQKEIAGLLVELDAKAGTA
SIO_010081: CP157_RS20030
subclass of: SO_0000673
so part of: CP157_RS20030
location: 3036..3287
location: region:3036-3287:1
so has part: feature:3036-3287:1:exon

WP_217847055.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:3036-3287:1:exon

CP157_RS20035
type: Gene
subclass of: SO_0000704
RO_0002162: 59779
locus tag: CP157_RS20035
old locus tag: CP157_04024
so part of: sequence
location: 3284..3844
location: region:3284-3844:1
so has part: feature:3284-3844:1:exon
subclass of: SO_0000010

position:3284:1
position: 3284
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

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

urn:…
SIO_000300: 1
SIO_000628: feature:3284-3844:1:exon

CP157_RS20035
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 59779
locus tag: CP157_RS20035
old locus tag: CP157_04024
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: MSAAAKSPAELIADLTDQVRLLRQDVGNLTATATTKAEAARLRASVQKITIDALEQNRQIASTAAEMSRRMHRDSVTAAQEAAEQAVRGLEREIQAAANHMRLEAVRGRKEALYNFGGGLAVFGGLLALGGVLGIVALLLIQGRGDARAFGKYPLTYCTAAGGQVASTSDGSRFCGIWIDPPKQTD
SIO_010081: CP157_RS20035
subclass of: SO_0000673
so part of: CP157_RS20035
location: 3284..3844
location: region:3284-3844:1
so has part: feature:3284-3844:1:exon

WP_071471166.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:3284-3844:1:exon

CP157_RS20040
type: Gene
subclass of: SO_0000704
RO_0002162: 59779
locus tag: CP157_RS20040
so part of: sequence
location: 4221..4508
location: region:4221-4508:1
so has part: feature:4221-4508:1:exon
subclass of: SO_0000010

position:4221:1
position: 4221
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:4508:1
position: 4508
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:4221-4508:1:exon

CP157_RS20040
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 59779
locus tag: CP157_RS20040
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: MENTMRIISIHAINYVVDNNTLWNNDDWANIRSRIFACQQRTAQAIQQLEIAHNALNECNLRLLKAKVVLHEVNALMPSSPSKDAYWSGSYAALK
SIO_010081: CP157_RS20040
subclass of: SO_0000673
so part of: CP157_RS20040
location: 4221..4508
location: region:4221-4508:1
so has part: feature:4221-4508:1:exon

WP_143079953.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:4221-4508:1:exon

CP157_RS20045
type: Gene
subclass of: SO_0000704
RO_0002162: 59779
locus tag: CP157_RS20045
so part of: sequence
location: 4730..5487
location: region:4730-5487:1
so has part: feature:4730-5487:1:exon
subclass of: SO_0000010

position:4730:1
position: 4730
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:5487:1
position: 5487
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:4730-5487:1:exon

CP157_RS20045
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 59779
locus tag: CP157_RS20045
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_RS20045
subclass of: SO_0000673
so part of: CP157_RS20045
location: join(4730..5051,5051..5487)
location: region:4730-5487:1
so has part: feature:4730-5051:1:exon
so has part: feature:5051-5487:1:exon

WP_217847034.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:4730-5051:1:exon

position:5051:1
position: 5051
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 2
SIO_000628: feature:5051-5487:1:exon

CP157_RS20050
type: Gene
subclass of: SO_0000704
RO_0002162: 59779
locus tag: CP157_RS20050
so part of: sequence
location: complement(5475..5891)
location: region:5475-5891:-1
so has part: feature:5475-5891:-1:exon
subclass of: SO_0000010

position:5475:-1
position: 5475
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:5891:-1
position: 5891
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:5475-5891:-1:exon

CP157_RS20050
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 59779
locus tag: CP157_RS20050
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: MLRPKDKISCPLLYRWSAPLRSRLFAGNAVLYWRFDRQVSQYDASKYQKGQTSRRLYGKKKSLFTEEYKNYEKIMDNYNDHLKVVSNAVSKKQLEVAFRHFFGLEPPEITSEAEYDAAKALYAAMDASMPPRVRIHNQ
SIO_010081: CP157_RS20050
subclass of: SO_0000673
so part of: CP157_RS20050
location: complement(5475..5891)
location: region:5475-5891:-1
so has part: feature:5475-5891:-1:exon

WP_217847091.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:5475-5891:-1:exon

CP157_RS20055
type: Gene
subclass of: SO_0000704
RO_0002162: 59779
locus tag: CP157_RS20055
old locus tag: CP157_04027
so part of: sequence
location: 5903..6223
location: region:5903-6223:1
so has part: feature:5903-6223:1:exon
subclass of: SO_0000010

position:5903:1
position: 5903
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:6223:1
position: 6223
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:5903-6223:1:exon

CP157_RS20055
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 59779
locus tag: CP157_RS20055
old locus tag: CP157_04027
inference: COORDINATES: protein motif:HMM:NF012442.2
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: HU family DNA-binding protein
translation: MFYHEEGISMLRSQLIAKLVETHSHLPRPVVEAALNAILNAITTGLAHGHRVELRKFGNFTSKVQEARMASDPRTGEAVSVERKRILRFRAGGHILERLNRPTTLG
SIO_010081: CP157_RS20055
subclass of: SO_0000673
so part of: CP157_RS20055
location: 5903..6223
location: region:5903-6223:1
so has part: feature:5903-6223:1:exon

WP_217847092.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:5903-6223:1:exon