Cupriavidus pauculus strain BHJ32i plasmid p2, complete sequence.
Bacteria; Pseudomonadota; Betaproteobacteria; Burkholderiales; Burkholderiaceae; Cupriavidus.
Prevalence and functional effects of a genomic island for insect symbiosis within Burkholderiaceae
Submitted (22-SEP-2021) Biology Department, University of Texas at Arlington, 501 S. Nedderman Dr., Arlington, TX 76019, USA
REFSEQ INFORMATION: The reference sequence is identical to\nCP084282.1.\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-Assembly-Data-START##\nAssembly Date :: 2020\nAssembly Method :: SPAdes v. 3.13.0; Unicycler v. 2.4.8-beta\nAssembly Name :: BHJ32i\nGenome Representation :: Full\nExpected Final Version :: Yes\nGenome Coverage :: 60x\nSequencing Technology :: Illumina HiSeq; Oxford Nanopore MinION\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 04/27/2023 06:36:08\nAnnotation Pipeline :: NCBI Prokaryotic Genome\n Annotation Pipeline (PGAP)\nAnnotation Method :: Best-placed reference protein\n set; GeneMarkS-2+\nAnnotation Software revision :: 6.5\nFeatures Annotated :: Gene; CDS; rRNA; tRNA; ncRNA\nGenes (total) :: 5,604\nCDSs (total) :: 5,526\nGenes (coding) :: 5,468\nCDSs (with protein) :: 5,468\nGenes (RNA) :: 78\nrRNAs :: 4, 4, 4 (5S, 16S, 23S)\ncomplete rRNAs :: 4, 4, 4 (5S, 16S, 23S)\ntRNAs :: 62\nncRNAs :: 4\nPseudo Genes (total) :: 58\nCDSs (without protein) :: 58\nPseudo Genes (ambiguous residues) :: 0 of 58\nPseudo Genes (frameshifted) :: 18 of 58\nPseudo Genes (incomplete) :: 45 of 58\nPseudo Genes (internal stop) :: 4 of 58\nPseudo Genes (multiple problems) :: 7 of 58\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.
COORDINATES: similar to AA sequence:RefSeq:WP_008648656.1
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_008648655.1
COORDINATES: similar to AA sequence:RefSeq:WP_008648653.1
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_008645421.1
COORDINATES: similar to AA sequence:RefSeq:WP_008645423.1
GO:0030261 - chromosome condensation [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_008648650.1
COORDINATES: similar to AA sequence:RefSeq:WP_011239921.1
COORDINATES: similar to AA sequence:RefSeq:WP_008649398.1
COORDINATES: similar to AA sequence:RefSeq:WP_008649399.1
COORDINATES: similar to AA sequence:RefSeq:WP_008649401.1
COORDINATES: similar to AA sequence:RefSeq:WP_011514906.1
GO:0003896 - DNA primase activity [Evidence IEA]; GO:0004386 - helicase activity [Evidence IEA]; GO:0008270 - zinc ion binding [Evidence IEA]
primase-helicase zinc-binding domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_008649404.1
COORDINATES: similar to AA sequence:RefSeq:WP_011514907.1
COORDINATES: similar to AA sequence:RefSeq:WP_008649407.1
COORDINATES: similar to AA sequence:RefSeq:WP_008649408.1
COORDINATES: similar to AA sequence:RefSeq:WP_008649410.1
COORDINATES: similar to AA sequence:RefSeq:WP_011239915.1
GO:0045893 - positive regulation of DNA-templated transcription [Evidence IEA]; GO:1902208 - regulation of bacterial-type flagellum assembly [Evidence IEA]
COORDINATES: protein motif:HMM:NF024788.2
PLDc N-terminal domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_008649420.1
COORDINATES: similar to AA sequence:RefSeq:WP_008649422.1
COORDINATES: similar to AA sequence:RefSeq:WP_008649424.1
COORDINATES: similar to AA sequence:RefSeq:WP_008649426.1
COORDINATES: similar to AA sequence:RefSeq:WP_008649429.1
toxin corregulated pilus biosynthesis protein E
COORDINATES: similar to AA sequence:RefSeq:WP_008649434.1
COORDINATES: similar to AA sequence:RefSeq:WP_008649435.1
COORDINATES: similar to AA sequence:RefSeq:WP_008649437.1
COORDINATES: similar to AA sequence:RefSeq:WP_008649439.1
COORDINATES: similar to AA sequence:RefSeq:WP_011239906.1
COORDINATES: similar to AA sequence:RefSeq:WP_008649443.1
toxin co-regulated pilus biosynthesis Q family protein
COORDINATES: similar to AA sequence:RefSeq:WP_008649444.1
lytic transglycosylase domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_008649445.1
TrbG/VirB9 family P-type conjugative transfer protein
COORDINATES: similar to AA sequence:RefSeq:WP_008649449.1
transglycosylase SLT domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_008649450.1
COORDINATES: similar to AA sequence:RefSeq:WP_008649451.1
COORDINATES: similar to AA sequence:RefSeq:WP_008649452.1
COORDINATES: similar to AA sequence:RefSeq:WP_011239902.1
COORDINATES: similar to AA sequence:RefSeq:WP_008649454.1
COORDINATES: similar to AA sequence:RefSeq:WP_008645668.1
COORDINATES: similar to AA sequence:RefSeq:WP_012354573.1
VirB4 family type IV secretion system protein
COORDINATES: similar to AA sequence:RefSeq:WP_008649459.1
COORDINATES: similar to AA sequence:RefSeq:WP_008649461.1
COORDINATES: similar to AA sequence:RefSeq:WP_008649463.1
COORDINATES: similar to AA sequence:RefSeq:WP_012354577.1
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_008649465.1
COORDINATES: similar to AA sequence:RefSeq:WP_018003854.1
COORDINATES: similar to AA sequence:RefSeq:WP_008649469.1
COORDINATES: similar to AA sequence:RefSeq:WP_012354581.1
COORDINATES: similar to AA sequence:RefSeq:WP_008645686.1
GO:0005524 - ATP binding [Evidence IEA]; GO:0016887 - ATP hydrolysis activity [Evidence IEA]; GO:0003677 - DNA binding [Evidence IEA]; GO:0004386 - helicase activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF016724.2
COORDINATES: protein motif:HMM:NF022633.2
COORDINATES: protein motif:HMM:NF018714.2
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: similar to AA sequence:RefSeq:WP_017183617.1
COORDINATES: similar to AA sequence:RefSeq:WP_008645706.1
COORDINATES: similar to AA sequence:RefSeq:WP_001280608.1
COORDINATES: protein motif:HMM:NF019371.2
COORDINATES: similar to AA sequence:RefSeq:WP_013818664.1
COORDINATES: protein motif:HMM:NF020442.2
COORDINATES: similar to AA sequence:RefSeq:WP_008650706.1
GO:0004803 - transposase activity [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_011154075.1
frameshifted; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_019104956.1
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_006764054.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0004803 - transposase activity [Evidence IEA]
GO:0006313 - transposition, DNA-mediated [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_006482547.1
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_000624623.1
COORDINATES: protein motif:HMM:NF013677.2
COORDINATES: protein motif:HMM:NF020387.2
COORDINATES: similar to AA sequence:RefSeq:WP_016424094.1
COORDINATES: similar to AA sequence:RefSeq:WP_011545416.1
COORDINATES: similar to AA sequence:RefSeq:WP_006160862.1
GO:0003697 - single-stranded DNA binding [Evidence IEA]
GO:0006974 - cellular response to DNA damage stimulus [Evidence IEA]; GO:0018142 - protein-DNA covalent cross-linking [Evidence IEA]
SOS response-associated peptidase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_012354474.1
COORDINATES: similar to AA sequence:RefSeq:WP_012354475.1
COORDINATES: similar to AA sequence:RefSeq:WP_018310027.1
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_011831409.1
GO:0006303 - double-strand break repair via nonhomologous end joining [Evidence IEA]
COORDINATES: protein motif:HMM:NF024824.2
COORDINATES: similar to AA sequence:RefSeq:WP_018006585.1
GO:0045027 - DNA end binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_018310023.1
COORDINATES: protein motif:HMM:NF023168.2
COORDINATES: similar to AA sequence:RefSeq:WP_014834018.1
COORDINATES: similar to AA sequence:RefSeq:WP_000147566.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0000150 - DNA strand exchange activity [Evidence IEA]
GO:0006310 - DNA recombination [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_008652068.1
COORDINATES: similar to AA sequence:RefSeq:WP_003132004.1
COORDINATES: similar to AA sequence:RefSeq:WP_001277466.1
GO:0045892 - negative regulation of DNA-templated transcription [Evidence IEA]; GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_013722692.1
GO:0016152 - mercury (II) reductase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:YP_005229640.1
GO:0045340 - mercury ion binding [Evidence IEA]
mercury resistance system periplasmic binding protein MerP
COORDINATES: similar to AA sequence:RefSeq:YP_005229639.1
COORDINATES: similar to AA sequence:RefSeq:YP_005229638.1
mercury resistance transcriptional regulator MerR
COORDINATES: similar to AA sequence:RefSeq:WP_008647962.1
COORDINATES: similar to AA sequence:RefSeq:WP_013954374.1
GO:0015074 - DNA integration [Evidence IEA]; GO:0006310 - DNA recombination [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011514871.1
COORDINATES: similar to AA sequence:RefSeq:WP_011519964.1
COORDINATES: similar to AA sequence:RefSeq:WP_011514872.1
COORDINATES: similar to AA sequence:RefSeq:WP_011239980.1
COORDINATES: similar to AA sequence:RefSeq:WP_011514873.1
COORDINATES: similar to AA sequence:RefSeq:WP_011514874.1
COORDINATES: similar to AA sequence:RefSeq:WP_011239977.1
GO:0022857 - transmembrane transporter activity [Evidence IEA]
GO:0055085 - transmembrane transport [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011514875.1
COORDINATES: similar to AA sequence:RefSeq:WP_019719540.1
COORDINATES: similar to AA sequence:RefSeq:WP_011239976.1
COORDINATES: similar to AA sequence:RefSeq:WP_011239975.1
rhodanese family chromate resistance protein ChrE
COORDINATES: similar to AA sequence:RefSeq:WP_011239974.1
COORDINATES: similar to AA sequence:RefSeq:WP_011514877.1
COORDINATES: similar to AA sequence:RefSeq:WP_011514878.1
COORDINATES: similar to AA sequence:RefSeq:WP_008344511.1
COORDINATES: similar to AA sequence:RefSeq:WP_017022281.1
COORDINATES: similar to AA sequence:RefSeq:WP_011239971.1
cobalt/nickel resistance anti-sigma factor CnrY
COORDINATES: similar to AA sequence:RefSeq:WP_011239970.1
COORDINATES: similar to AA sequence:RefSeq:WP_011239969.1
COORDINATES: similar to AA sequence:RefSeq:WP_011239968.1
nickel efflux RND transporter outer membrane subunit CnrC
COORDINATES: similar to AA sequence:RefSeq:WP_011239967.1
nickel efflux RND transporter periplasmic adaptor subunit CnrB
COORDINATES: similar to AA sequence:RefSeq:WP_011239966.1
nickel efflux RND transporter permease subunit CnrA
COORDINATES: similar to AA sequence:RefSeq:WP_011239965.1
COORDINATES: similar to AA sequence:RefSeq:WP_012406449.1
COORDINATES: protein motif:HMM:NF023173.2
COORDINATES: similar to AA sequence:RefSeq:WP_013954376.1
GO:0003824 - catalytic activity [Evidence IEA]
phosphoadenosine phosphosulfate reductase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_011239962.1
COORDINATES: similar to AA sequence:RefSeq:WP_008645363.1
COORDINATES: similar to AA sequence:RefSeq:WP_011514882.1
COORDINATES: similar to AA sequence:RefSeq:WP_011239960.1
COORDINATES: similar to AA sequence:RefSeq:WP_011514934.1
COORDINATES: similar to AA sequence:RefSeq:WP_018310419.1
COORDINATES: similar to AA sequence:RefSeq:WP_018310420.1
COORDINATES: similar to AA sequence:RefSeq:WP_011239957.1
COORDINATES: similar to AA sequence:RefSeq:WP_018004032.1
COORDINATES: similar to AA sequence:RefSeq:WP_008645377.1
COORDINATES: similar to AA sequence:RefSeq:WP_011239954.1
COORDINATES: similar to AA sequence:RefSeq:WP_011239953.1
COORDINATES: similar to AA sequence:RefSeq:WP_011239952.1
COORDINATES: similar to AA sequence:RefSeq:WP_011239951.1
COORDINATES: similar to AA sequence:RefSeq:WP_018004039.1
COORDINATES: similar to AA sequence:RefSeq:WP_011239949.1
COORDINATES: protein motif:HMM:NF022728.2
COORDINATES: similar to AA sequence:RefSeq:WP_008645390.1
COORDINATES: similar to AA sequence:RefSeq:WP_018004043.1
COORDINATES: similar to AA sequence:RefSeq:WP_011239945.1
COORDINATES: similar to AA sequence:RefSeq:WP_011239944.1
COORDINATES: similar to AA sequence:RefSeq:WP_012217989.1
COORDINATES: similar to AA sequence:RefSeq:WP_008645397.1
COORDINATES: similar to AA sequence:RefSeq:WP_008645398.1
COORDINATES: similar to AA sequence:RefSeq:WP_013954436.1
COORDINATES: similar to AA sequence:RefSeq:WP_008645404.1
GO:0005524 - ATP binding [Evidence IEA]; GO:0140658 - ATP-dependent chromatin remodeler activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_008645405.1
COORDINATES: similar to AA sequence:RefSeq:WP_012354522.1
COORDINATES: similar to AA sequence:RefSeq:WP_008645408.1
COORDINATES: similar to AA sequence:RefSeq:WP_008645409.1
COORDINATES: similar to AA sequence:RefSeq:WP_008645410.1
COORDINATES: similar to AA sequence:RefSeq:WP_011239938.1
COORDINATES: similar to AA sequence:RefSeq:WP_011239937.1
GO:0005524 - ATP binding [Evidence IEA]; GO:0016787 - hydrolase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011239936.1
COORDINATES: similar to AA sequence:RefSeq:WP_011239935.1
COORDINATES: similar to AA sequence:RefSeq:WP_012354532.1
COORDINATES: similar to AA sequence:RefSeq:WP_018004058.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0008170 - N-methyltransferase activity [Evidence IEA]
GO:0009307 - DNA restriction-modification system [Evidence IEA]