Polaromonas naphthalenivorans CJ2 plasmid pPNAP01, complete sequence.
Bacteria; Pseudomonadota; Betaproteobacteria; Burkholderiales; Comamonadaceae; Polaromonas.
Complete sequence of plasmid pPNAP01 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\nCP000530.1.\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+
GO:0008236 - serine-type peptidase activity [Evidence IEA]
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: similar to AA sequence:RefSeq:WP_019897068.1
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_014834018.1
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_011797795.1
GO:0004803 - transposase activity [Evidence IEA]
IS5-like element ISPna4 family transposase
COORDINATES: similar to AA sequence:RefSeq:WP_003801709.1
GO:0016787 - hydrolase activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF024491.2
phospholipase D-like domain-containing protein
COORDINATES: protein motif:HMM:NF019421.2
COORDINATES: protein motif:HMM:NF024949.2
helix-turn-helix domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_076611276.1
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: protein motif:HMM:NF019228.2
internal stop; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: protein motif:HMM:NF018644.2
COORDINATES: similar to AA sequence:RefSeq:WP_011494289.1
COORDINATES: similar to AA sequence:RefSeq:WP_011494290.1
type II toxin-antitoxin system RelE/ParE family toxin
COORDINATES: similar to AA sequence:RefSeq:WP_003296374.1
COORDINATES: protein motif:HMM:NF025713.2
COORDINATES: similar to AA sequence:RefSeq:WP_009520510.1
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:NF015857.2
COORDINATES: similar to AA sequence:RefSeq:WP_011797807.1
2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoate hydrolase
COORDINATES: similar to AA sequence:RefSeq:WP_003450974.1
GO:0008701 - 4-hydroxy-2-oxovalerate aldolase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011797809.1
GO:0008774 - acetaldehyde dehydrogenase (acetylating) activity [Evidence IEA]
acetaldehyde dehydrogenase (acetylating)
COORDINATES: similar to AA sequence:RefSeq:WP_020206177.1
COORDINATES: similar to AA sequence:RefSeq:WP_003450988.1
GO:0005515 - protein binding [Evidence IEA]
GO:0006749 - glutathione metabolic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_014160695.1
COORDINATES: similar to AA sequence:RefSeq:WP_015014865.1
cis-2,3-dihydrobiphenyl-2,3-diol dehydrogenase
COORDINATES: similar to AA sequence:RefSeq:WP_011797814.1
GO:0016491 - oxidoreductase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011797815.1
non-heme iron oxygenase ferredoxin subunit
COORDINATES: similar to AA sequence:RefSeq:WP_003451002.1
COORDINATES: similar to AA sequence:RefSeq:WP_019752919.1
aromatic-ring-hydroxylating dioxygenase subunit beta
COORDINATES: similar to AA sequence:RefSeq:WP_011797818.1
GO:0051537 - 2 iron, 2 sulfur cluster binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_014160689.1
COORDINATES: similar to AA sequence:RefSeq:WP_008251010.1
COORDINATES: similar to AA sequence:RefSeq:WP_007967235.1
COORDINATES: similar to AA sequence:RefSeq:WP_015912905.1
COORDINATES: similar to AA sequence:RefSeq:WP_008643221.1
ParB/RepB/Spo0J family partition protein
COORDINATES: similar to AA sequence:RefSeq:WP_012747205.1
COORDINATES: similar to AA sequence:RefSeq:WP_009518863.1
helix-turn-helix transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_003160616.1
COORDINATES: similar to AA sequence:RefSeq:WP_006414895.1
COORDINATES: similar to AA sequence:RefSeq:WP_011657225.1
COORDINATES: similar to AA sequence:RefSeq:WP_015014850.1
COORDINATES: similar to AA sequence:RefSeq:WP_009518857.1
COORDINATES: similar to AA sequence:RefSeq:WP_009518856.1
COORDINATES: similar to AA sequence:RefSeq:WP_007967250.1
COORDINATES: similar to AA sequence:RefSeq:WP_008786728.1
COORDINATES: similar to AA sequence:RefSeq:WP_006406703.1
relaxase/mobilization nuclease and DUF3363 domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_011486378.1
TetR/AcrR family transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_011801898.1
COORDINATES: similar to AA sequence:RefSeq:WP_007182752.1
COORDINATES: similar to AA sequence:RefSeq:WP_007182751.1
COORDINATES: similar to AA sequence:RefSeq:WP_007182750.1
COORDINATES: similar to AA sequence:RefSeq:WP_007182749.1
UDP-N-acetylglucosamine--LPS N-acetylglucosamine transferase
COORDINATES: similar to AA sequence:RefSeq:WP_011486384.1
GO:0006629 - lipid metabolic process [Evidence IEA]
patatin-like phospholipase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_007182747.1
GO:0008299 - isoprenoid biosynthetic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011486386.1
GO:0005215 - transporter activity [Evidence IEA]
efflux RND transporter periplasmic adaptor subunit
COORDINATES: similar to AA sequence:RefSeq:WP_011486387.1
COORDINATES: similar to AA sequence:RefSeq:WP_011797840.1
COORDINATES: similar to AA sequence:RefSeq:WP_012702119.1
COORDINATES: protein motif:HMM:NF024039.2
COORDINATES: similar to AA sequence:RefSeq:WP_008247232.1
COORDINATES: similar to AA sequence:RefSeq:WP_008247230.1
GO:0050660 - flavin adenine dinucleotide binding [Evidence IEA]; GO:0016614 - oxidoreductase activity, acting on CH-OH group of donors [Evidence IEA]
GMC family oxidoreductase N-terminal domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_013067270.1
COORDINATES: similar to AA sequence:RefSeq:WP_015499361.1
COORDINATES: similar to AA sequence:RefSeq:WP_011486313.1
COORDINATES: similar to AA sequence:RefSeq:WP_012584383.1
COORDINATES: similar to AA sequence:RefSeq:WP_012479472.1
COORDINATES: similar to AA sequence:RefSeq:WP_020230333.1
COORDINATES: similar to AA sequence:RefSeq:WP_007704373.1
COORDINATES: similar to AA sequence:RefSeq:WP_011793886.1
COORDINATES: similar to AA sequence:RefSeq:WP_018076602.1
COORDINATES: similar to AA sequence:RefSeq:WP_015014586.1
VirB3 family type IV secretion system protein
COORDINATES: similar to AA sequence:RefSeq:WP_008642621.1
COORDINATES: similar to AA sequence:RefSeq:WP_006414869.1
GO:0009291 - unidirectional conjugation [Evidence IEA]
P-type conjugative transfer protein TrbJ
COORDINATES: similar to AA sequence:RefSeq:WP_003056122.1
P-type conjugative transfer protein TrbL
COORDINATES: similar to AA sequence:RefSeq:WP_003056121.1
COORDINATES: similar to AA sequence:RefSeq:WP_020831658.1
P-type conjugative transfer protein TrbG
COORDINATES: similar to AA sequence:RefSeq:WP_006412605.1
COORDINATES: similar to AA sequence:RefSeq:WP_017679342.1
COORDINATES: similar to AA sequence:RefSeq:WP_009733794.1
COORDINATES: protein motif:HMM:NF013658.2
phosphoadenosine phosphosulfate reductase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_011798509.1
COORDINATES: similar to AA sequence:RefSeq:WP_086558010.1
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:NF019976.2
nuclease-related domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_011811417.1
COORDINATES: protein motif:HMM:NF016820.2
COORDINATES: similar to AA sequence:RefSeq:WP_011811414.1
COORDINATES: protein motif:HMM:NF016491.2
GO:0030255 - protein secretion by the type IV secretion system [Evidence IEA]
COORDINATES: protein motif:HMM:NF022136.2
toxin co-regulated pilus biosynthesis Q family protein
COORDINATES: protein motif:HMM:NF012652.2
COORDINATES: protein motif:HMM:NF016238.2
COORDINATES: protein motif:HMM:NF015487.2
TrbG/VirB9 family P-type conjugative transfer protein
COORDINATES: protein motif:HMM:NF015688.2
COORDINATES: protein motif:HMM:NF024642.2
COORDINATES: protein motif:HMM:NF013618.2
lytic transglycosylase domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_011486345.1
COORDINATES: similar to AA sequence:RefSeq:WP_011798435.1
COORDINATES: similar to AA sequence:RefSeq:WP_011799710.1
COORDINATES: similar to AA sequence:RefSeq:WP_012211057.1
COORDINATES: similar to AA sequence:RefSeq:WP_006749798.1
COORDINATES: protein motif:HMM:NF024975.2
COORDINATES: protein motif:HMM:NF033580.1
COORDINATES: protein motif:HMM:NF024736.2
COORDINATES: similar to AA sequence:RefSeq:WP_011798216.1
COORDINATES: similar to AA sequence:RefSeq:WP_004360021.1
GO:0005524 - ATP binding [Evidence IEA]; GO:0008134 - transcription factor binding [Evidence IEA]
GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
sigma 54-interacting transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_020655819.1
COORDINATES: similar to AA sequence:RefSeq:WP_015903370.1
COORDINATES: protein motif:HMM:NF018884.2
PP2C family serine/threonine-protein phosphatase
COORDINATES: protein motif:HMM:NF012298.2
GO:0004672 - protein kinase activity [Evidence IEA]
GO:0006468 - protein phosphorylation [Evidence IEA]
COORDINATES: protein motif:HMM:NF024486.2
COORDINATES: protein motif:HMM:NF019348.2
GO:0005524 - ATP binding [Evidence IEA]; GO:0016887 - ATP hydrolysis activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_012247247.1
GO:0005524 - ATP binding [Evidence IEA]; GO:0140658 - ATP-dependent chromatin remodeler activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF026949.2
COORDINATES: similar to AA sequence:RefSeq:WP_018907395.1
COORDINATES: protein motif:HMM:NF033916.0
COORDINATES: similar to AA sequence:RefSeq:WP_011798350.1
COORDINATES: similar to AA sequence:RefSeq:WP_011485838.1
COORDINATES: protein motif:HMM:NF019844.2
COORDINATES: similar to AA sequence:RefSeq:WP_013088143.1
COORDINATES: similar to AA sequence:RefSeq:WP_013088142.1
COORDINATES: similar to AA sequence:RefSeq:WP_019751263.1
COORDINATES: similar to AA sequence:RefSeq:WP_011481311.1
programmed frameshift; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_006416079.1
COORDINATES: similar to AA sequence:RefSeq:WP_000766277.1
COORDINATES: similar to AA sequence:RefSeq:WP_002730574.1
GO:0005524 - ATP binding [Evidence IEA]; GO:0003676 - nucleic acid binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_015434801.1
COORDINATES: similar to AA sequence:RefSeq:WP_015434800.1
COORDINATES: similar to AA sequence:RefSeq:WP_015434799.1
COORDINATES: protein motif:HMM:NF024573.2
COORDINATES: similar to AA sequence:RefSeq:WP_015434796.1
BREX-2 system adenine-specific DNA-methyltransferase PglX
COORDINATES: similar to AA sequence:RefSeq:WP_012273663.1
COORDINATES: similar to AA sequence:RefSeq:WP_015434795.1
BREX system serine/threonine kinase PglW
COORDINATES: similar to AA sequence:RefSeq:WP_018275679.1
COORDINATES: similar to AA sequence:RefSeq:WP_005768213.1
COORDINATES: similar to AA sequence:RefSeq:WP_011482869.1
COORDINATES: similar to AA sequence:RefSeq:WP_011235906.1
COORDINATES: protein motif:HMM:NF022224.2
COORDINATES: protein motif:HMM:TIGR03734.1
COORDINATES: protein motif:HMM:TIGR03741.1
COORDINATES: similar to AA sequence:RefSeq:WP_018004047.1
COORDINATES: protein motif:HMM:TIGR03742.1
COORDINATES: protein motif:HMM:TIGR03737.1
COORDINATES: protein motif:HMM:TIGR03735.1
COORDINATES: similar to AA sequence:RefSeq:WP_011485923.1
COORDINATES: protein motif:HMM:NF014442.2
GO:0003677 - DNA binding [Evidence IEA]; GO:0008170 - N-methyltransferase activity [Evidence IEA]
GO:0006306 - DNA methylation [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011811393.1
COORDINATES: similar to AA sequence:RefSeq:WP_011811391.1
COORDINATES: protein motif:HMM:NF014786.2
COORDINATES: protein motif:HMM:NF039495.1
COORDINATES: protein motif:HMM:NF018050.2
COORDINATES: similar to AA sequence:RefSeq:WP_011481442.1
COORDINATES: protein motif:HMM:NF012624.2
COORDINATES: protein motif:HMM:NF012789.2
COORDINATES: similar to AA sequence:RefSeq:WP_012745542.1
GO:0003697 - single-stranded DNA binding [Evidence IEA]
GO:0006310 - DNA recombination [Evidence IEA]; GO:0006281 - DNA repair [Evidence IEA]; GO:0006260 - DNA replication [Evidence IEA]; GO:0006351 - DNA-templated transcription [Evidence IEA]
COORDINATES: protein motif:HMM:NF024755.2
COORDINATES: protein motif:HMM:NF017124.2
GO:0045893 - positive regulation of DNA-templated transcription [Evidence IEA]; GO:1902208 - regulation of bacterial-type flagellum assembly [Evidence IEA]
COORDINATES: protein motif:HMM:NF019153.2
COORDINATES: similar to AA sequence:RefSeq:WP_011811451.1
GO:0003674 - molecular_function [Evidence IEA]
GO:0015074 - DNA integration [Evidence IEA]
Members of this protein family are the putative conjugative coupling factor, TraD, as the term is used for the SXT and TOL plasmid systems; Derived by automated computational analysis using gene prediction method: Protein Homology.
conjugative transfer system coupling protein TraD
COORDINATES: similar to AA sequence:RefSeq:WP_011798054.1
COORDINATES: protein motif:HMM:NF025706.2
COORDINATES: protein motif:HMM:NF020384.2
COORDINATES: similar to AA sequence:RefSeq:WP_012607034.1
frameshifted; internal stop; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: protein motif:HMM:TIGR02532.1
prepilin-type N-terminal cleavage/methylation domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_015038930.1
COORDINATES: similar to AA sequence:RefSeq:WP_019937306.1
COORDINATES: similar to AA sequence:RefSeq:WP_011798356.1
COORDINATES: protein motif:HMM:NF016408.2
COORDINATES: protein motif:HMM:NF037161.2
COORDINATES: protein motif:HMM:NF024243.2
COORDINATES: protein motif:HMM:NF019945.2
COORDINATES: similar to AA sequence:RefSeq:WP_017172476.1
COORDINATES: similar to AA sequence:RefSeq:WP_011485874.1
COORDINATES: similar to AA sequence:RefSeq:WP_003458619.1
COORDINATES: similar to AA sequence:RefSeq:WP_011484928.1
COORDINATES: similar to AA sequence:RefSeq:WP_010792116.1
COORDINATES: similar to AA sequence:RefSeq:WP_019486743.1
COORDINATES: similar to AA sequence:RefSeq:WP_019486742.1
GO:0008641 - ubiquitin-like modifier activating enzyme activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_019486741.1
COORDINATES: similar to AA sequence:RefSeq:WP_076612088.1
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_007588917.1
COORDINATES: similar to AA sequence:RefSeq:WP_076612154.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0004803 - transposase activity [Evidence IEA]
GO:0006313 - transposition, DNA-mediated [Evidence IEA]
COORDINATES: protein motif:HMM:NF023168.2
COORDINATES: protein motif:HMM:NF012722.2
histidine kinase dimerization/phospho-acceptor domain-containing protein
COORDINATES: protein motif:HMM:NF014567.2
COORDINATES: protein motif:HMM:NF023227.2
COORDINATES: similar to AA sequence:RefSeq:WP_014194265.1
nucleotidyl transferase AbiEii/AbiGii toxin family protein
COORDINATES: similar to AA sequence:RefSeq:WP_009548458.1
type IV toxin-antitoxin system AbiEi family antitoxin domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_011800042.1
GO:0016787 - hydrolase activity [Evidence IEA]; GO:0046872 - metal ion binding [Evidence IEA]; GO:0003676 - nucleic acid binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_008954510.1
GO:0004518 - nuclease activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF016370.2
COORDINATES: similar to AA sequence:RefSeq:WP_004760980.1
COORDINATES: similar to AA sequence:RefSeq:WP_011493156.1
COORDINATES: similar to AA sequence:RefSeq:WP_011493155.1
COORDINATES: similar to AA sequence:RefSeq:WP_005401577.1
COORDINATES: similar to AA sequence:RefSeq:WP_011800044.1
COORDINATES: similar to AA sequence:RefSeq:WP_011798584.1
COORDINATES: similar to AA sequence:RefSeq:WP_004215715.1
COORDINATES: protein motif:HMM:NF020452.2
GO:0000166 - nucleotide binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_009885214.1
COORDINATES: similar to AA sequence:RefSeq:WP_018003928.1
COORDINATES: protein motif:HMM:NF024867.2
COORDINATES: similar to AA sequence:RefSeq:WP_014657486.1
COORDINATES: similar to AA sequence:RefSeq:WP_013393191.1
COORDINATES: similar to AA sequence:RefSeq:WP_005372623.1
COORDINATES: protein motif:HMM:NF018714.2
COORDINATES: protein motif:HMM:NF024589.2
COORDINATES: similar to AA sequence:RefSeq:WP_011458570.1
COORDINATES: similar to AA sequence:RefSeq:WP_011797986.1
COORDINATES: similar to AA sequence:RefSeq:WP_005325951.1
COORDINATES: similar to AA sequence:RefSeq:WP_013516288.1
COORDINATES: similar to AA sequence:RefSeq:WP_011458605.1
COORDINATES: similar to AA sequence:RefSeq:WP_011486226.1
COORDINATES: similar to AA sequence:RefSeq:WP_013570250.1
COORDINATES: similar to AA sequence:RefSeq:WP_011486213.1
COORDINATES: similar to AA sequence:RefSeq:WP_007852765.1
COORDINATES: similar to AA sequence:RefSeq:WP_015866567.1
COORDINATES: similar to AA sequence:RefSeq:WP_017452657.1
COORDINATES: similar to AA sequence:RefSeq:WP_011798123.1
COORDINATES: similar to AA sequence:RefSeq:WP_011798082.1
IS5-like element ISPna5 family transposase
COORDINATES: similar to AA sequence:RefSeq:WP_019364429.1
COORDINATES: protein motif:HMM:NF024758.2