Polaromonas naphthalenivorans CJ2 plasmid pPNAP02, complete sequence.
Bacteria; Pseudomonadota; Betaproteobacteria; Burkholderiales; Comamonadaceae; Polaromonas.
Complete sequence of plasmid pPNAP02 of Polaromonas naphthalenivorans CJ2
Submitted (21-DEC-2006) US DOE Joint Genome Institute, 2800 Mitchell Drive B100, Walnut Creek, CA 94598-1698, USA
REFSEQ INFORMATION: The reference sequence is identical to\nCP000531.1.\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\nPseudo Genes (internal stop) :: 16 of 121\nPseudo Genes (multiple problems) :: 27 of 121\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.
type strain of Polaromonas naphthalenivorans
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: similar to AA sequence:RefSeq:WP_011806698.1
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_020561570.1
COORDINATES: similar to AA sequence:RefSeq:WP_020561569.1
COORDINATES: similar to AA sequence:RefSeq:WP_020561568.1
COORDINATES: similar to AA sequence:RefSeq:WP_011798488.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0004803 - transposase activity [Evidence IEA]
GO:0006313 - transposition, DNA-mediated [Evidence IEA]
COORDINATES: protein motif:HMM:NF017528.2
TnpB, as the term is used for proteins encoded by IS66 family insertion elements, is considered an accessory protein, since TnpC, encoded by a neighboring gene, is a DDE family transposase; Derived by automated computational analysis using gene prediction method: Protein Homology.
IS66 family insertion sequence element accessory protein TnpB
COORDINATES: similar to AA sequence:RefSeq:WP_009238807.1
GO:0004803 - transposase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_008906819.1
frameshifted; internal stop; incomplete; partial in the middle of a contig; missing N-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_003436530.1
incomplete; partial in the middle of a contig; missing N-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_004687407.1
type II toxin-antitoxin system RelB/DinJ family antitoxin
COORDINATES: similar to AA sequence:RefSeq:WP_006175622.1
COORDINATES: similar to AA sequence:RefSeq:WP_004687408.1
COORDINATES: similar to AA sequence:RefSeq:WP_006164860.1
COORDINATES: similar to AA sequence:RefSeq:WP_013006590.1
COORDINATES: protein motif:HMM:NF016167.2
COORDINATES: similar to AA sequence:RefSeq:WP_011798484.1
GO:0007059 - chromosome segregation [Evidence IEA]; GO:0000910 - cytokinesis [Evidence IEA]
ParB/RepB/Spo0J family partition protein
COORDINATES: similar to AA sequence:RefSeq:WP_011485900.1
COORDINATES: protein motif:HMM:NF014273.2
COORDINATES: similar to AA sequence:RefSeq:WP_011486347.1
COORDINATES: similar to AA sequence:RefSeq:WP_011798477.1
GO:0015074 - DNA integration [Evidence IEA]; GO:0006310 - DNA recombination [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_004152391.1
frameshifted; incomplete; partial in the middle of a contig; missing N-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: protein motif:HMM:NF014567.2
HAMP domain-containing sensor histidine kinase
COORDINATES: similar to AA sequence:RefSeq:WP_006482428.1
incomplete; partial in the middle of a contig; missing N-terminus and C-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_020230161.1
GO:0005886 - plasma membrane [Evidence IEA]
GO:0008509 - monoatomic anion transmembrane transporter activity [Evidence IEA]
GO:0006820 - monoatomic anion transport [Evidence IEA]
frameshifted; Derived by automated computational analysis using gene prediction method: Protein Homology.
DASS family sodium-coupled anion symporter
COORDINATES: similar to AA sequence:RefSeq:WP_009549395.1
COORDINATES: protein motif:HMM:NF024751.2
COORDINATES: similar to AA sequence:RefSeq:WP_011798261.1
COORDINATES: similar to AA sequence:RefSeq:WP_012535823.1
winged helix-turn-helix domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_011515952.1
COORDINATES: similar to AA sequence:RefSeq:WP_011798493.1
COORDINATES: similar to AA sequence:RefSeq:WP_011798151.1
heavy-metal-associated domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_004635170.1
GO:0005575 - cellular_component [Evidence IEA]
GO:0008976 - polyphosphate kinase activity [Evidence IEA]
GO:0006793 - phosphorus metabolic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011463450.1
COORDINATES: similar to AA sequence:RefSeq:WP_004635142.1
GO:0042625 - ATPase-coupled ion transmembrane transporter activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_006911955.1
COORDINATES: similar to AA sequence:RefSeq:WP_008177412.1
COORDINATES: similar to AA sequence:RefSeq:WP_017941549.1
COORDINATES: similar to AA sequence:RefSeq:WP_008305101.1
COORDINATES: similar to AA sequence:RefSeq:WP_009205543.1
N-acetylglutaminylglutamine amidotransferase
COORDINATES: similar to AA sequence:RefSeq:WP_018973938.1
GO:0004801 - transaldolase activity [Evidence IEA]
GO:0006098 - pentose-phosphate shunt [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_007512236.1
GO:0004614 - phosphoglucomutase activity [Evidence IEA]
GO:0005975 - carbohydrate metabolic process [Evidence IEA]
phosphoglucomutase (alpha-D-glucose-1,6-bisphosphate-dependent)
COORDINATES: similar to AA sequence:RefSeq:WP_011474223.1
COORDINATES: similar to AA sequence:RefSeq:WP_010406928.1
COORDINATES: similar to AA sequence:RefSeq:WP_015449178.1
GO:0004802 - transketolase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_007177359.1
COORDINATES: similar to AA sequence:RefSeq:WP_011984916.1
GO:0004616 - phosphogluconate dehydrogenase (decarboxylating) activity [Evidence IEA]
decarboxylating 6-phosphogluconate dehydrogenase
COORDINATES: similar to AA sequence:RefSeq:WP_020468665.1
COORDINATES: similar to AA sequence:RefSeq:WP_019898539.1
COORDINATES: similar to AA sequence:RefSeq:WP_076611276.1
programmed frameshift; Derived by automated computational analysis using gene prediction method: Protein Homology.
IS630-like element ISPna1 family transposase
COORDINATES: protein motif:HMM:NF024491.2
phospholipase D-like domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_009048717.1
frameshifted; incomplete; partial in the middle of a contig; missing N-terminus and C-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_011484396.1
COORDINATES: similar to AA sequence:RefSeq:WP_011484395.1
GO:0015562 - efflux transmembrane transporter activity [Evidence IEA]
GO:0055085 - transmembrane transport [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011484394.1
GO:0005215 - transporter activity [Evidence IEA]
efflux RND transporter periplasmic adaptor subunit
COORDINATES: similar to AA sequence:RefSeq:WP_016451576.1
COORDINATES: similar to AA sequence:RefSeq:WP_011800657.1
COORDINATES: similar to AA sequence:RefSeq:WP_011798155.1
COORDINATES: similar to AA sequence:RefSeq:WP_011800659.1
COORDINATES: protein motif:HMM:NF019351.2
GO:0005507 - copper ion binding [Evidence IEA]; GO:0016491 - oxidoreductase activity [Evidence IEA]
multicopper oxidase domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_011798153.1
COORDINATES: similar to AA sequence:RefSeq:WP_011805873.1
isoprenylcysteine carboxylmethyltransferase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_013722308.1
heavy metal-associated domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_011482129.1
COORDINATES: similar to AA sequence:RefSeq:WP_018606493.1
COORDINATES: similar to AA sequence:RefSeq:WP_013722681.1
COORDINATES: similar to AA sequence:RefSeq:WP_011160100.1
GO:0004318 - enoyl-[acyl-carrier-protein] reductase (NADH) activity [Evidence IEA]
GO:0006633 - fatty acid biosynthetic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_006975426.1
GO:0008776 - acetate kinase activity [Evidence IEA]
GO:0006083 - acetate metabolic process [Evidence IEA]; GO:0006113 - fermentation [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011875655.1
COORDINATES: similar to AA sequence:RefSeq:WP_013722682.1
GO:0022857 - transmembrane transporter activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_007883227.1
internal stop; incomplete; partial in the middle of a contig; missing C-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
helix-turn-helix domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_011801904.1
COORDINATES: similar to AA sequence:RefSeq:WP_011801902.1
COORDINATES: protein motif:HMM:NF015658.2
COORDINATES: similar to AA sequence:RefSeq:WP_011798177.1
COORDINATES: similar to AA sequence:RefSeq:WP_008647609.1
COORDINATES: similar to AA sequence:RefSeq:WP_011798174.1
COORDINATES: similar to AA sequence:RefSeq:WP_011798173.1
COORDINATES: similar to AA sequence:RefSeq:WP_011798205.1
COORDINATES: similar to AA sequence:RefSeq:WP_008905318.1
COORDINATES: similar to AA sequence:RefSeq:WP_020795058.1
COORDINATES: similar to AA sequence:RefSeq:WP_007181564.1
COORDINATES: similar to AA sequence:RefSeq:WP_011875669.1
COORDINATES: similar to AA sequence:RefSeq:WP_005329307.1
COORDINATES: similar to AA sequence:RefSeq:WP_013722304.1
COORDINATES: similar to AA sequence:RefSeq:WP_008648201.1
COORDINATES: similar to AA sequence:RefSeq:WP_007862435.1
COORDINATES: similar to AA sequence:RefSeq:WP_011484389.1
COORDINATES: similar to AA sequence:RefSeq:WP_007828403.1
COORDINATES: similar to AA sequence:RefSeq:WP_011484386.1
COORDINATES: similar to AA sequence:RefSeq:WP_008904060.1
COORDINATES: similar to AA sequence:RefSeq:WP_011484384.1
COORDINATES: similar to AA sequence:RefSeq:WP_002943396.1
GO:0046872 - metal ion binding [Evidence IEA]
CopK family periplasmic copper-binding protein
COORDINATES: protein motif:HMM:TIGR01386.1
GO:0000155 - phosphorelay sensor kinase activity [Evidence IEA]; GO:0004673 - protein histidine kinase activity [Evidence IEA]; GO:0016772 - transferase activity, transferring phosphorus-containing groups [Evidence IEA]
GO:0000160 - phosphorelay signal transduction system [Evidence IEA]; GO:0016310 - phosphorylation [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_016498180.1
GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
heavy metal response regulator transcription factor
COORDINATES: protein motif:HMM:NF025045.2
COORDINATES: protein motif:HMM:NF023036.2
COORDINATES: similar to AA sequence:RefSeq:WP_007187102.1
four-helix bundle copper-binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_012241400.1
COORDINATES: similar to AA sequence:RefSeq:WP_009241683.1
COORDINATES: similar to AA sequence:RefSeq:WP_011798134.1
COORDINATES: similar to AA sequence:RefSeq:WP_004355838.1
COORDINATES: similar to AA sequence:RefSeq:WP_020229697.1
COORDINATES: similar to AA sequence:RefSeq:WP_003821159.1
HlyD family efflux transporter periplasmic adaptor subunit
COORDINATES: similar to AA sequence:RefSeq:WP_004248730.1
COORDINATES: similar to AA sequence:RefSeq:WP_018992685.1
COORDINATES: similar to AA sequence:RefSeq:WP_011798079.1
COORDINATES: similar to AA sequence:RefSeq:WP_018913937.1
nucleotidyl transferase AbiEii/AbiGii toxin family protein
COORDINATES: similar to AA sequence:RefSeq:WP_010105866.1
AbiEi antitoxin N-terminal domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_012746179.1
COORDINATES: similar to AA sequence:RefSeq:WP_011798509.1
Derived by automated computational analysis using gene prediction method: tRNAscan-SE.
COORDINATES: similar to AA sequence:RefSeq:WP_011798510.1
COORDINATES: similar to AA sequence:RefSeq:WP_011798511.1
GO:0005515 - protein binding [Evidence IEA]
GO:0006749 - glutathione metabolic process [Evidence IEA]
glutathione-dependent disulfide-bond oxidoreductase
COORDINATES: similar to AA sequence:RefSeq:WP_010463583.1
COORDINATES: similar to AA sequence:RefSeq:WP_007871869.1
COORDINATES: similar to AA sequence:RefSeq:WP_005780908.1
COORDINATES: similar to AA sequence:RefSeq:WP_014895645.1
COORDINATES: similar to AA sequence:RefSeq:WP_011094409.1
phosphoadenosine phosphosulfate reductase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_005763366.1
COORDINATES: similar to AA sequence:RefSeq:WP_019396320.1
GO:0005524 - ATP binding [Evidence IEA]; GO:0003677 - DNA binding [Evidence IEA]; GO:0000166 - nucleotide binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_005780901.1
COORDINATES: similar to AA sequence:RefSeq:WP_007835846.1
COORDINATES: similar to AA sequence:RefSeq:WP_011486155.1
COORDINATES: similar to AA sequence:RefSeq:WP_011486154.1
type II toxin-antitoxin system Phd/YefM family antitoxin
COORDINATES: similar to AA sequence:RefSeq:WP_013722504.1
COORDINATES: similar to AA sequence:RefSeq:WP_008375825.1
incomplete; partial in the middle of a contig; missing C-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_076612272.1
frameshifted; incomplete; partial in the middle of a contig; missing C-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: protein motif:HMM:NF012234.2
GO:0005524 - ATP binding [Evidence IEA]; GO:0016887 - ATP hydrolysis activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_010431411.1
4Fe-4S single cluster domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_019082290.1
COORDINATES: protein motif:HMM:NF025022.2
COORDINATES: protein motif:HMM:NF024487.2
GO:0004386 - helicase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_018312317.1