Polaromonas naphthalenivorans CJ2 plasmid pPNAP08, complete sequence.
type: Entry
definition: Polaromonas naphthalenivorans CJ2 plasmid pPNAP08, complete sequence.
sequence version: NC_008764.1
sequence date: 2022-12-28
sequence: sequence
division: CON
label: NC_008764.1
type: RefSeq
SIO_000068: refseq
dblink: PRJNA224116
dblink: SAMN02598302
keyword: RefSeq
source: Polaromonas naphthalenivorans CJ2
organism: Polaromonas naphthalenivorans CJ2
taxonomy: Bacteria; Pseudomonadota; Betaproteobacteria; Burkholderiales; Comamonadaceae; Polaromonas.
reference: 1
reference: 2
comment: REFSEQ INFORMATION: The reference sequence is identical to\nCP000537.1.\nURL -- http://www.jgi.doe.gov\nJGI Project ID: 4000361\nSource DNA and bacteria available from Eugene L. Madsen\n(elm3@cornell.edu)\nContacts: Eugene L. Madsen (elm3@cornell.edu)\n Paul Richardson (microbes@cuba.jgi-psf.org)\nQuality assurance done by JGI-Stanford\nAnnotation done by JGI-ORNL and JGI-PGF\nFinishing done by JGI-LANL\nFinished microbial genomes have been curated to close all gaps with\ngreater than 98% coverage of at least two independent clones. Each\nbase pair has a minimum q (quality) value of 30 and the total error\nrate is less than one per 50000.\nThe JGI and collaborators endorse the principles for the\ndistribution and use of large scale sequencing data adopted by the\nlarger genome sequencing community and urge users of this data to\nfollow them. It is our intention to publish the work of this\nproject in a timely fashion and we welcome collaborative\ninteraction on the project and analysis.\n(http://www.genome.gov/page.cfm?pageID=10506376).\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/\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 12/28/2022 02:04:21\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) :: 5,174\nCDSs (total) :: 5,114\nGenes (coding) :: 4,993\nCDSs (with protein) :: 4,993\nGenes (RNA) :: 60\nrRNAs :: 2, 2, 2 (5S, 16S, 23S)\ncomplete rRNAs :: 2, 2, 2 (5S, 16S, 23S)\ntRNAs :: 51\nncRNAs :: 3\nPseudo Genes (total) :: 121\nCDSs (without protein) :: 121\nPseudo Genes (ambiguous residues) :: 0 of 121\nPseudo Genes (frameshifted) :: 42 of 121\nPseudo Genes (incomplete) :: 93 of 121\nPse…

sequence
subclass of: SO_0000155
sequence length: 6459
topology: circular
so has quality: SO_0000988
location: 1..6459
location: region:1-6459:1
RO_0002162: 365044

NC_008764
type: RefSeq
SIO_000068: refseq

PRJNA224116
type: BioProject
SIO_000068: bioproject

SAMN02598302
type: BioSample
SIO_000068: biosample

1
title: Complete sequence of plasmid pPNAP08 of Polaromonas naphthalenivorans CJ2
author: Copeland, A.
author: Lucas, S.
author: Lapidus, A.
author: Barry, K.
author: Detter, J.C.
author: Glavina del Rio, T.
author: Hammon, N.
author: Israni, S.
author: Dalin, E.
author: Tice, H.
author: Pitluck, S.
author: Sims, D.R.
author: Brettin, T.
author: Bruce, D.
author: Han, C.
author: Tapia, R.
author: Brainard, J.
author: Schmutz, J.
author: Larimer, F.
author: Land, M.
author: Hauser, L.
author: Kyrpides, N.
author: Kim, E.
author: Madsen, E.L.
author: Richardson, P.
journal: Unpublished

2
title: Direct Submission
author: Copeland, A.
author: Lucas, S.
author: Lapidus, A.
author: Barry, K.
author: Detter, J.C.
author: Glavina del Rio, T.
author: Hammon, N.
author: Israni, S.
author: Dalin, E.
author: Tice, H.
author: Pitluck, S.
author: Sims, D.R.
author: Brettin, T.
author: Bruce, D.
author: Han, C.
author: Tapia, R.
author: Brainard, J.
author: Schmutz, J.
author: Larimer, F.
author: Land, M.
author: Hauser, L.
author: Kyrpides, N.
author: Kim, E.
author: Madsen, E.L.
author: Richardson, P.
journal: Submitted (21-DEC-2006) US DOE Joint Genome Institute, 2800 Mitchell Drive B100, Walnut Creek, CA 94598-1698, USA

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

position:6459:1
position: 6459
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

feature:1-6459:1:source
so part of: sequence
organism: Polaromonas naphthalenivorans CJ2
mol type: genomic DNA
strain: CJ2
type material: type strain of Polaromonas naphthalenivorans
plasmid: pPNAP08

365044
type: Taxonomy
SIO_000068: taxonomy

PNAP_RS27500
type: Gene
subclass of: SO_0000704
RO_0002162: 365044
gene: repC
locus tag: PNAP_RS27500
old locus tag: Pnap_5004
so part of: sequence
location: complement(89..922)
location: region:89-922:-1
so has part: feature:89-922:-1:exon
subclass of: SO_0000010

position:89:-1
position: 89
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:922:-1
position: 922
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:89-922:-1:exon

PNAP_RS27500
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 365044
gene: repC
locus tag: PNAP_RS27500
old locus tag: Pnap_5004
inference: COORDINATES: similar to AA sequence:RefSeq:WP_000240538.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: replication protein C, IncQ-type
translation: MKPKQNLDHIRHEPGHVLAPGLFRSLKKGDYKRLKLDIAYEFGKGERLEFKGAEPLGVPELRILQGLIGMAGPNGLLLTPEPKTESGQQLRLLLETKFDAIETNALVVKGSYRALAKTIGYADIENTKNIQESIERLWGVSVIARKGGKHMGFRLLSEYASDDADGRLYVALNPVLARAILGEAQHCRISLDEVRALKTDPARLMHQRLCGWIDIGKSGKTTIETLCGYIWLDEATPEAMKKRKQAVRRALKEMEALGWKVTEYINGKFEITRPEIG
SIO_010081: PNAP_RS27500
subclass of: SO_0000673
so part of: PNAP_RS27500
location: complement(89..922)
location: region:89-922:-1
so has part: feature:89-922:-1:exon

WP_011798618.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:89-922:-1:exon

PNAP_RS27505
type: Gene
subclass of: SO_0000704
RO_0002162: 365044
locus tag: PNAP_RS27505
old locus tag: Pnap_5005
so part of: sequence
location: complement(912..1793)
location: region:912-1793:-1
so has part: feature:912-1793:-1:exon
subclass of: SO_0000010

position:912:-1
position: 912
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:1793:-1
position: 1793
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:912-1793:-1:exon

PNAP_RS27505
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 365044
locus tag: PNAP_RS27505
old locus tag: Pnap_5005
inference: COORDINATES: similar to AA sequence:RefSeq:WP_001162384.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: helicase RepA family protein
translation: MTQPNFNCKERERVMTIDILHAFEHQPPPLDFVLPGLLAGTVGSLVSPGGAGKSMLAMELAILVTCGQDIAGITDGKKYPCGDVAFLAAEDPAVAIQQRLYALGKQIPDPDIRMHVAERLAIEPLLGKQPDIANPEWAAYIKAMAEGKRLMFLDTLRRFHSKEENDSGQMAEVLGRMEAITAATGCAIVFLHHSSKAAAMNGQGDQQQASRGSSVLVDNIRWQMFLAGMNAAEAKKFGVDEELKGYWVRDGVSKQNYGPPYGERWLRRGEGGVLVQGKLEAKPPAKKGGRNEA
SIO_010081: PNAP_RS27505
subclass of: SO_0000673
so part of: PNAP_RS27505
location: complement(912..1793)
location: region:912-1793:-1
so has part: feature:912-1793:-1:exon

WP_269667388.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:912-1793:-1:exon

PNAP_RS24785
type: Gene
subclass of: SO_0000704
RO_0002162: 365044
locus tag: PNAP_RS24785
so part of: sequence
location: complement(1831..2022)
location: region:1831-2022:-1
so has part: feature:1831-2022:-1:exon
subclass of: SO_0000010

position:1831:-1
position: 1831
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:2022:-1
position: 2022
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:1831-2022:-1:exon

PNAP_RS24785
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 365044
locus tag: PNAP_RS24785
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: MITDAQILEFVEAFAGEESTLLTPMPEWWKDLSAEQQDQVMERAGRVTAGRLQAAIDRCNDKE
SIO_010081: PNAP_RS24785
subclass of: SO_0000673
so part of: PNAP_RS24785
location: complement(1831..2022)
location: region:1831-2022:-1
so has part: feature:1831-2022:-1:exon

WP_041377848.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:1831-2022:-1:exon

PNAP_RS26645
type: Gene
subclass of: SO_0000704
RO_0002162: 365044
locus tag: PNAP_RS26645
old locus tag: Pnap_5006
so part of: sequence
location: complement(2033..4519)
location: region:2033-4519:-1
so has part: feature:2033-4519:-1:exon
subclass of: SO_0000010

position:2033:-1
position: 2033
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:4519:-1
position: 4519
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:2033-4519:-1:exon

PNAP_RS26645
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 365044
locus tag: PNAP_RS26645
old locus tag: Pnap_5006
inference: COORDINATES: protein motif:HMM:NF015397.2
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: toprim domain-containing protein
translation: MHIKFLPHGTGVGQDAIDYLLGEEDHKGEIRASVEVWRGNPQLTGKLIDSLKTVHRYTSGVINFSPEDAPTDEEIGIVLDEFERTAFSGLERDQYDFCAVVHRESNGGIHIHTIIPRVELTTGKAMNIAPPGWEYTFDPLRDAFNHEKGWARPDDPSRARLVQQGKAKPEWKSGADKKIVVTDYLTKLVANNVVTDRQGVLKALGELGEITRTTDKSVSIKLEGTNKAIKLQGLLYASDFSPRTIRKVAEEAASRPAGRGRPDEAAARAARQELENAVQRRAGYNRERYPAPRPRTDLSAPSDAAAAPLDAALADPGQRLPGVVDDGQRQPVELVDGQPGTTESDELRADPATADGSVLQESSRAEAVQISEPVSEQVKIKKAAYGTVFEPGFKQFAERPSVEPAAGIGGLPDVSSLLVATQWPGASKFLSGAARHNLVRHGGPGAGSVRWERGSDRPTEGEGGTINDRARKIADEAIDQAKRAARATAGALGRCADAAGRAIDAIGRACRKADAAAPVIKANMDAELDRFKSDISLSDYAQAEFGYELVKKESSASSKVLKVGGDKIIVTRQKDGHDVYFSTGDASDCGSIVDFLQNRKRVNLGEVRKELRQWLPSSKKPSVKRPQRPPERAVATSKDRTEVLRQWATMKPYSASYLTDERRLDPQIIEAFGVRQDSHGNACIAHRDASGVLGWESKNKGFTGFAAGGTRNVSFTRLNDGPITRLVLTEAAIDAMSFAQLRHEPGTAYMSTGGTQLSQAQREQIAQIMGKYAVPVVLAMDKDEAGEKMAREIAAMAPESVQTLREVPEGAKDWNEALQAKQRAMPKP
SIO_010081: PNAP_RS26645
subclass of: SO_0000673
so part of: PNAP_RS26645
location: complement(2033..4519)
location: region:2033-4519:-1
so has part: feature:2033-4519:-1:exon

WP_011798620.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:2033-4519:-1:exon

PNAP_RS26650
type: Gene
subclass of: SO_0000704
RO_0002162: 365044
locus tag: PNAP_RS26650
old locus tag: Pnap_5007
so part of: sequence
location: complement(4522..4845)
location: region:4522-4845:-1
so has part: feature:4522-4845:-1:exon
subclass of: SO_0000010

position:4522:-1
position: 4522
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:4845:-1
position: 4845
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:4522-4845:-1:exon

PNAP_RS26650
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 365044
locus tag: PNAP_RS26650
old locus tag: Pnap_5007
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: MobC family plasmid mobilization relaxosome protein
translation: MPASLVARFAERAREQGVTLSDVLRAHLTVDEAKPLGKAVPRKRAGLAKVSGADPKLLRQLVGMGNNLNQIAKLANIASKTAQPMAMVELLITLKGIEKSLEKLSES
SIO_010081: PNAP_RS26650
subclass of: SO_0000673
so part of: PNAP_RS26650
location: complement(4522..4845)
location: region:4522-4845:-1
so has part: feature:4522-4845:-1:exon

WP_232290881.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:4522-4845:-1:exon

PNAP_RS24805
type: Gene
subclass of: SO_0000704
RO_0002162: 365044
locus tag: PNAP_RS24805
old locus tag: Pnap_5008
so part of: sequence
location: complement(5172..5627)
location: region:5172-5627:-1
so has part: feature:5172-5627:-1:exon
subclass of: SO_0000010

position:5172:-1
position: 5172
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:5627:-1
position: 5627
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:5172-5627:-1:exon

PNAP_RS24805
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 365044
locus tag: PNAP_RS24805
old locus tag: Pnap_5008
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: MYIREQGKKVQLLRSPYDPEKKRCVQKLAHSFPRSYSYSSTELDTYLSAEQIADLSDDEKKELTEWLTVRSDKNLAESRKSSITMTPYYADQLADNISSDVVDLSEKQADKIWDAMDKLAKAMRKAGYKKPAVKAAPGAQAGSADQPSLTL
SIO_010081: PNAP_RS24805
subclass of: SO_0000673
so part of: PNAP_RS24805
location: complement(5172..5627)
location: region:5172-5627:-1
so has part: feature:5172-5627:-1:exon

WP_011798622.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:5172-5627:-1:exon