Polaromonas naphthalenivorans CJ2 plasmid pPNAP03, complete sequence.
Bacteria; Pseudomonadota; Betaproteobacteria; Burkholderiales; Comamonadaceae; Polaromonas.
Complete sequence of plasmid pPNAP03 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\nCP000532.1.\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: protein motif:HMM:NF021508.2
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_016516133.1
COORDINATES: similar to AA sequence:RefSeq:WP_011463173.1
GO:0036211 - protein modification process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_015865805.1
COORDINATES: protein motif:HMM:NF024736.2
COORDINATES: protein motif:HMM:NF033580.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0004803 - transposase activity [Evidence IEA]
GO:0006313 - transposition, DNA-mediated [Evidence IEA]
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_013690437.1
COORDINATES: similar to AA sequence:RefSeq:WP_011798261.1
GO:0004803 - transposase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_013104709.1
GO:0003700 - DNA-binding transcription factor activity [Evidence IEA]
GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
COORDINATES: protein motif:HMM:NF024872.2
COORDINATES: similar to AA sequence:RefSeq:WP_019920524.1
frameshifted; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_009548459.1
COORDINATES: similar to AA sequence:RefSeq:WP_018418976.1
COORDINATES: similar to AA sequence:RefSeq:WP_018417869.1
GO:0016787 - hydrolase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011798282.1
COORDINATES: similar to AA sequence:RefSeq:WP_015635235.1
DNA alkylation repair enzyme-like protein
COORDINATES: similar to AA sequence:RefSeq:WP_018313615.1
helix-turn-helix domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_019654949.1
COORDINATES: similar to AA sequence:RefSeq:WP_007528244.1
COORDINATES: similar to AA sequence:RefSeq:WP_008046117.1
COORDINATES: similar to AA sequence:RefSeq:WP_019898216.1
COORDINATES: similar to AA sequence:RefSeq:WP_009517095.1
COORDINATES: similar to AA sequence:RefSeq:WP_011482512.1
type II toxin-antitoxin system HipA family toxin YjjJ
COORDINATES: similar to AA sequence:RefSeq:WP_002708622.1
COORDINATES: similar to AA sequence:RefSeq:WP_005220755.1
frameshifted; internal stop; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_013104996.1
COORDINATES: similar to AA sequence:RefSeq:WP_019398473.1
GO:0015562 - efflux transmembrane transporter activity [Evidence IEA]; GO:0008324 - monoatomic cation transmembrane transporter activity [Evidence IEA]
GO:0006812 - monoatomic cation transport [Evidence IEA]
cation diffusion facilitator family transporter
COORDINATES: similar to AA sequence:RefSeq:WP_003262851.1
COORDINATES: similar to AA sequence:RefSeq:WP_011801009.1
COORDINATES: similar to AA sequence:RefSeq:WP_011458667.1
COORDINATES: similar to AA sequence:RefSeq:WP_011483551.1
COORDINATES: similar to AA sequence:RefSeq:WP_012507766.1
COORDINATES: similar to AA sequence:RefSeq:WP_011300583.1
COORDINATES: similar to AA sequence:RefSeq:WP_011300582.1
COORDINATES: protein motif:HMM:NF023903.2
COORDINATES: similar to AA sequence:RefSeq:WP_011463511.1
GO:0004519 - endonuclease activity [Evidence IEA]; GO:0003676 - nucleic acid binding [Evidence IEA]
HNH endonuclease domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_011463512.1
COORDINATES: similar to AA sequence:RefSeq:WP_007865194.1
COORDINATES: similar to AA sequence:RefSeq:WP_011465382.1
COORDINATES: similar to AA sequence:RefSeq:WP_007857712.1
GO:0009318 - exodeoxyribonuclease VII complex [Evidence IEA]
GO:0008855 - exodeoxyribonuclease VII activity [Evidence IEA]
GO:0006308 - DNA catabolic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_007857711.1
COORDINATES: similar to AA sequence:RefSeq:WP_011798500.1
GO:0003697 - single-stranded DNA binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_012345151.1
COORDINATES: similar to AA sequence:RefSeq:WP_007586745.1
COORDINATES: similar to AA sequence:RefSeq:WP_011463063.1
COORDINATES: similar to AA sequence:RefSeq:WP_011802861.1
COORDINATES: similar to AA sequence:RefSeq:WP_011548443.1
GO:0003700 - DNA-binding transcription factor activity [Evidence IEA]; GO:0097351 - toxin sequestering activity [Evidence IEA]
GO:0001558 - regulation of cell growth [Evidence IEA]
type II toxin-antitoxin system PrlF family antitoxin
COORDINATES: similar to AA sequence:RefSeq:WP_012316909.1
COORDINATES: similar to AA sequence:RefSeq:WP_020183294.1
COORDINATES: similar to AA sequence:RefSeq:WP_017509747.1
COORDINATES: similar to AA sequence:RefSeq:WP_020071128.1
COORDINATES: similar to AA sequence:RefSeq:WP_011793696.1
GO:0051782 - negative regulation of cell division [Evidence IEA]; GO:0009432 - SOS response [Evidence IEA]
translesion DNA synthesis-associated protein ImuA
COORDINATES: similar to AA sequence:RefSeq:WP_019702945.1
COORDINATES: similar to AA sequence:RefSeq:WP_019702946.1
GO:0008408 - 3'-5' exonuclease activity [Evidence IEA]; GO:0003887 - DNA-directed DNA polymerase activity [Evidence IEA]
GO:0006260 - DNA replication [Evidence IEA]
COORDINATES: protein motif:HMM:NF024830.2
COORDINATES: similar to AA sequence:RefSeq:WP_011486036.1
GO:0016787 - hydrolase activity [Evidence IEA]; GO:0046872 - metal ion binding [Evidence IEA]; GO:0003676 - nucleic acid binding [Evidence IEA]
internal stop; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_017455068.1
COORDINATES: similar to AA sequence:RefSeq:WP_007852771.1
COORDINATES: similar to AA sequence:RefSeq:WP_009685257.1
COORDINATES: similar to AA sequence:RefSeq:WP_011831930.1
GO:0003676 - nucleic acid binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011347054.1
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_008111680.1
COORDINATES: similar to AA sequence:RefSeq:WP_008111678.1
COORDINATES: protein motif:HMM:NF024491.2
phospholipase D-like domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_011791644.1
class I SAM-dependent DNA methyltransferase
COORDINATES: protein motif:HMM:NF019421.2
type II toxin-antitoxin system HipA family toxin
COORDINATES: protein motif:HMM:NF024949.2
COORDINATES: protein motif:HMM:NF039631.1
COORDINATES: similar to AA sequence:RefSeq:WP_018578482.1
COORDINATES: protein motif:HMM:NF022607.2
COORDINATES: protein motif:HMM:NF037510.2
GO:0003677 - DNA binding [Evidence IEA]; GO:0004519 - endonuclease activity [Evidence IEA]
GO:0006304 - DNA modification [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_013539120.1
COORDINATES: similar to AA sequence:RefSeq:WP_011614292.1
COORDINATES: similar to AA sequence:RefSeq:WP_013539123.1
COORDINATES: similar to AA sequence:RefSeq:WP_011798082.1
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_012354632.1
COORDINATES: similar to AA sequence:RefSeq:WP_019576709.1
COORDINATES: protein motif:HMM:NF014273.2
ParB/RepB/Spo0J family partition protein
COORDINATES: protein motif:HMM:NF024975.2
COORDINATES: protein motif:HMM:NF024999.2
COORDINATES: protein motif:HMM:NF013235.2
COORDINATES: protein motif:HMM:NF012798.2
GO:0015074 - DNA integration [Evidence IEA]; GO:0006310 - DNA recombination [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011236894.1
Derived by automated computational analysis using gene prediction method: tRNAscan-SE.
COORDINATES: similar to AA sequence:RefSeq:WP_005671502.1
COORDINATES: similar to AA sequence:RefSeq:WP_011798377.1
COORDINATES: protein motif:HMM:NF018983.2
GO:0016977 - chitosanase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_019923460.1
COORDINATES: similar to AA sequence:RefSeq:WP_000597179.1
GO:0019867 - outer membrane [Evidence IEA]
glycine zipper 2TM domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_011463722.1
methyltransferase domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_012070465.1
COORDINATES: similar to AA sequence:RefSeq:WP_011051225.1
COORDINATES: similar to AA sequence:RefSeq:WP_015463133.1
COORDINATES: similar to AA sequence:RefSeq:WP_015603553.1
COORDINATES: protein motif:HMM:NF012789.2
COORDINATES: similar to AA sequence:RefSeq:WP_013516329.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0003916 - DNA topoisomerase activity [Evidence IEA]
GO:0006265 - DNA topological change [Evidence IEA]
topoisomerase DNA-binding C4 zinc finger domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_018915113.1
COORDINATES: similar to AA sequence:RefSeq:WP_015866043.1
GO:0032784 - regulation of DNA-templated transcription elongation [Evidence IEA]