Polaromonas naphthalenivorans CJ2 plasmid pPNAP04, complete sequence.
Bacteria; Pseudomonadota; Betaproteobacteria; Burkholderiales; Comamonadaceae; Polaromonas.
Complete sequence of plasmid pPNAP04 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\nCP000533.1.\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: similar to AA sequence:RefSeq:WP_011484716.1
GO:0008660 - 1-aminocyclopropane-1-carboxylate deaminase activity [Evidence IEA]
GO:0042217 - 1-aminocyclopropane-1-carboxylate catabolic process [Evidence IEA]
Derived by automated computational analysis using gene prediction method: Protein Homology.
1-aminocyclopropane-1-carboxylate deaminase
COORDINATES: similar to AA sequence:RefSeq:WP_011484715.1
tripartite tricarboxylate transporter substrate binding protein
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: similar to AA sequence:RefSeq:WP_006579842.1
GO:0003700 - DNA-binding transcription factor activity [Evidence IEA]
GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011798407.1
GO:0008721 - D-serine ammonia-lyase activity [Evidence IEA]; GO:0030170 - pyridoxal phosphate binding [Evidence IEA]
GO:0046416 - D-amino acid metabolic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_013543319.1
COORDINATES: similar to AA sequence:RefSeq:WP_005017435.1
frameshifted; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_019447192.1
COORDINATES: similar to AA sequence:RefSeq:WP_013034160.1
type II toxin-antitoxin system RelE/ParE family toxin
COORDINATES: similar to AA sequence:RefSeq:WP_018283732.1
COORDINATES: similar to AA sequence:RefSeq:WP_076612180.1
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_003054420.1
COORDINATES: similar to AA sequence:RefSeq:WP_018906996.1
COORDINATES: similar to AA sequence:RefSeq:WP_018906997.1
COORDINATES: similar to AA sequence:RefSeq:WP_012247277.1
COORDINATES: similar to AA sequence:RefSeq:WP_006157068.1
COORDINATES: similar to AA sequence:RefSeq:WP_013953748.1
GO:0051537 - 2 iron, 2 sulfur cluster binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_017404446.1
COORDINATES: similar to AA sequence:RefSeq:WP_012355561.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0004803 - transposase activity [Evidence IEA]
GO:0006313 - transposition, DNA-mediated [Evidence IEA]
frameshifted; 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_076611837.1
IS701-like element ISPna6 family transposase
COORDINATES: similar to AA sequence:RefSeq:WP_011796883.1
GO:0004514 - nicotinate-nucleotide diphosphorylase (carboxylating) activity [Evidence IEA]
GO:0019363 - pyridine nucleotide biosynthetic process [Evidence IEA]
carboxylating nicotinate-nucleotide diphosphorylase
COORDINATES: similar to AA sequence:RefSeq:WP_010894925.1
type II toxin-antitoxin system MqsR family toxin
COORDINATES: similar to AA sequence:RefSeq:WP_004090697.1
type II toxin-antitoxin system MqsA family antitoxin
COORDINATES: similar to AA sequence:RefSeq:WP_017172610.1
GO:0005524 - ATP binding [Evidence IEA]; GO:0003676 - nucleic acid binding [Evidence IEA]
COORDINATES: protein motif:HMM:NF028103.2
DNA-primase RepB domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_006484960.1
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_004272601.1
COORDINATES: similar to AA sequence:RefSeq:WP_011798486.1
GO:0004803 - transposase activity [Evidence IEA]
COORDINATES: nucleotide motif:Rfam:14.4:RF01725
SAM-I-IV-variant riboswitch; SAM riboswitches modulate the expression of downstream genes in response to levels of S-adenosylmethionine; Derived by automated computational analysis using gene prediction method: cmsearch.
COORDINATES: similar to AA sequence:RefSeq:WP_011799848.1
frameshifted; incomplete; partial in the middle of a contig; missing C-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_011235908.1
COORDINATES: similar to AA sequence:RefSeq:WP_020158543.1
COORDINATES: similar to AA sequence:RefSeq:WP_008650706.1
COORDINATES: similar to AA sequence:RefSeq:WP_076611876.1
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_011001645.1
COORDINATES: similar to AA sequence:RefSeq:WP_011798435.1
IS5-like element ISPna3 family transposase
COORDINATES: similar to AA sequence:RefSeq:WP_012218039.1
COORDINATES: similar to AA sequence:RefSeq:WP_076611498.1
COORDINATES: similar to AA sequence:RefSeq:WP_017879231.1
COORDINATES: similar to AA sequence:RefSeq:WP_018604805.1
COORDINATES: similar to AA sequence:RefSeq:WP_017879230.1
COORDINATES: similar to AA sequence:RefSeq:WP_017879228.1
COORDINATES: similar to AA sequence:RefSeq:WP_017876786.1
COORDINATES: similar to AA sequence:RefSeq:WP_005663482.1
phosphoribosyltransferase domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_017876788.1
COORDINATES: similar to AA sequence:RefSeq:WP_017876789.1
COORDINATES: similar to AA sequence:RefSeq:WP_011254701.1
HpcH/HpaI aldolase/citrate lyase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_017876791.1
COORDINATES: similar to AA sequence:RefSeq:WP_007043106.1
COORDINATES: similar to AA sequence:RefSeq:WP_014779253.1
PP2C family serine/threonine-protein phosphatase
COORDINATES: similar to AA sequence:RefSeq:WP_001253653.1
TerY-C metal binding domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_014779255.1
COORDINATES: similar to AA sequence:RefSeq:WP_016540375.1
COORDINATES: similar to AA sequence:RefSeq:WP_015731191.1
COORDINATES: similar to AA sequence:RefSeq:WP_020583056.1
COORDINATES: similar to AA sequence:RefSeq:WP_010451562.1
COORDINATES: similar to AA sequence:RefSeq:WP_020583053.1
COORDINATES: similar to AA sequence:RefSeq:WP_008346350.1
COORDINATES: similar to AA sequence:RefSeq:WP_003078963.1
COORDINATES: protein motif:HMM:NF033580.1
COORDINATES: protein motif:HMM:NF024736.2
COORDINATES: similar to AA sequence:RefSeq:WP_008063804.1
COORDINATES: similar to AA sequence:RefSeq:WP_020204185.1
COORDINATES: protein motif:HMM:NF022182.2
COORDINATES: similar to AA sequence:RefSeq:WP_011798469.1
COORDINATES: similar to AA sequence:RefSeq:WP_011798468.1
COORDINATES: similar to AA sequence:RefSeq:WP_017285749.1
ADP-ribosylglycohydrolase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_004513537.1
GO:0016787 - hydrolase activity [Evidence IEA]
YqiA/YcfP family alpha/beta fold hydrolase
COORDINATES: protein motif:HMM:NF017437.2
COORDINATES: protein motif:HMM:NF020859.2
Mu transposase C-terminal domain-containing protein
COORDINATES: protein motif:HMM:NF012870.2
GO:0015074 - DNA integration [Evidence IEA]
DDE-type integrase/transposase/recombinase
COORDINATES: similar to AA sequence:RefSeq:WP_004337858.1
COORDINATES: similar to AA sequence:RefSeq:WP_011798216.1
GO:0015074 - DNA integration [Evidence IEA]; GO:0006310 - DNA recombination [Evidence IEA]
COORDINATES: protein motif:HMM:TIGR00180.1
GO:0007059 - chromosome segregation [Evidence IEA]; GO:0000910 - cytokinesis [Evidence IEA]
ParB/RepB/Spo0J family partition protein
COORDINATES: similar to AA sequence:RefSeq:WP_012406360.1
COORDINATES: protein motif:HMM:NF013235.2
COORDINATES: similar to AA sequence:RefSeq:WP_010458977.1
helix-turn-helix transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_006157828.1
COORDINATES: similar to AA sequence:RefSeq:WP_011798221.1
COORDINATES: similar to AA sequence:RefSeq:WP_017669295.1
COORDINATES: similar to AA sequence:RefSeq:WP_018912884.1
GO:0003849 - 3-deoxy-7-phosphoheptulonate synthase activity [Evidence IEA]
GO:0009423 - chorismate biosynthetic process [Evidence IEA]
COORDINATES: protein motif:HMM:NF017496.2
COORDINATES: similar to AA sequence:RefSeq:WP_011798490.1
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_017685557.1
COORDINATES: similar to AA sequence:RefSeq:WP_011798239.1
COORDINATES: similar to AA sequence:RefSeq:WP_020652834.1
COORDINATES: similar to AA sequence:RefSeq:WP_076612075.1
COORDINATES: similar to AA sequence:RefSeq:WP_011798207.1
COORDINATES: similar to AA sequence:RefSeq:WP_011295755.1
COORDINATES: protein motif:HMM:NF013014.2
COORDINATES: similar to AA sequence:RefSeq:WP_011799886.1
COORDINATES: similar to AA sequence:RefSeq:WP_011799887.1
COORDINATES: similar to AA sequence:RefSeq:WP_007874614.1
COORDINATES: similar to AA sequence:RefSeq:WP_019652715.1
COORDINATES: similar to AA sequence:RefSeq:WP_011798315.1
COORDINATES: protein motif:HMM:NF019604.2
COORDINATES: similar to AA sequence:RefSeq:WP_011798502.1
COORDINATES: similar to AA sequence:RefSeq:WP_014403018.1
frameshifted; internal stop; 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_076611276.1
programmed frameshift; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_007221374.1
COORDINATES: similar to AA sequence:RefSeq:WP_015451776.1
nuclear transport factor 2 family protein
COORDINATES: similar to AA sequence:RefSeq:WP_007579901.1
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_011798118.1
COORDINATES: similar to AA sequence:RefSeq:WP_011798117.1
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_006475990.1
COORDINATES: similar to AA sequence:RefSeq:WP_011798289.1
COORDINATES: similar to AA sequence:RefSeq:WP_008348329.1
COORDINATES: similar to AA sequence:RefSeq:WP_019186257.1
COORDINATES: similar to AA sequence:RefSeq:WP_018988699.1
COORDINATES: similar to AA sequence:RefSeq:WP_011800013.1
COORDINATES: similar to AA sequence:RefSeq:WP_008328818.1
COORDINATES: protein motif:HMM:NF013757.2
COORDINATES: similar to AA sequence:RefSeq:WP_020748615.1
carbon-nitrogen hydrolase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_006390788.1
ABC transporter substrate-binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_019575330.1
branched-chain amino acid ABC transporter permease
COORDINATES: similar to AA sequence:RefSeq:WP_010465654.1
COORDINATES: similar to AA sequence:RefSeq:WP_015014407.1
COORDINATES: similar to AA sequence:RefSeq:WP_008905665.1
COORDINATES: protein motif:HMM:NF024751.2
COORDINATES: similar to AA sequence:RefSeq:WP_011805887.1
winged helix-turn-helix domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_009491816.1
COORDINATES: similar to AA sequence:RefSeq:WP_011798261.1
COORDINATES: similar to AA sequence:RefSeq:WP_018574624.1
COORDINATES: similar to AA sequence:RefSeq:WP_011617570.1
PLP-dependent aminotransferase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_011829634.1
FMN-binding negative transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_011112293.1
COORDINATES: similar to AA sequence:RefSeq:WP_007863219.1
GO:0016491 - oxidoreductase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_020228336.1
winged helix-turn-helix transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_011798536.1
Lrp/AsnC family transcriptional regulator