Cupriavidus pauculus strain BHJ32i plasmid p1, 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\nCP084281.1.\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_000439570.1
GO:0018738 - S-formylglutathione hydrolase activity [Evidence IEA]
GO:0046292 - formaldehyde metabolic process [Evidence IEA]
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_003291555.1
COORDINATES: similar to AA sequence:RefSeq:WP_009639360.1
COORDINATES: similar to AA sequence:RefSeq:WP_000842106.1
GO:0004024 - alcohol dehydrogenase activity, zinc-dependent [Evidence IEA]; GO:0051903 - S-(hydroxymethyl)glutathione dehydrogenase activity [Evidence IEA]
GO:0006113 - fermentation [Evidence IEA]; GO:0009404 - toxin metabolic process [Evidence IEA]
S-(hydroxymethyl)glutathione dehydrogenase/class III alcohol dehydrogenase
COORDINATES: similar to AA sequence:RefSeq:WP_017384071.1
formaldehyde-responsive transcriptional repressor FrmR
COORDINATES: similar to AA sequence:RefSeq:WP_076612410.1
GO:0004803 - transposase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_086558120.1
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_011804189.1
COORDINATES: protein motif:HMM:NF013858.2
GO:0016151 - nickel cation binding [Evidence IEA]
GO:0006807 - nitrogen compound metabolic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_005753676.1
COORDINATES: similar to AA sequence:RefSeq:WP_008058657.1
COORDINATES: similar to AA sequence:RefSeq:WP_020165098.1
transporter substrate-binding domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_006470598.1
ABC transporter substrate-binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_018410287.1
GO:0055052 - ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing [Evidence IEA]; GO:0030288 - outer membrane-bounded periplasmic space [Evidence IEA]
GO:0033221 - ATPase-coupled urea transmembrane transporter activity [Evidence IEA]; GO:0033219 - urea binding [Evidence IEA]
GO:0015840 - urea transport [Evidence IEA]
urea ABC transporter substrate-binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_019918875.1
GO:0055052 - ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing [Evidence IEA]; GO:0009898 - cytoplasmic side of plasma membrane [Evidence IEA]
GO:0005524 - ATP binding [Evidence IEA]; GO:0033221 - ATPase-coupled urea transmembrane transporter activity [Evidence IEA]
urea ABC transporter ATP-binding subunit UrtE
COORDINATES: similar to AA sequence:RefSeq:WP_016450222.1
urea ABC transporter ATP-binding protein UrtD
COORDINATES: similar to AA sequence:RefSeq:WP_007866234.1
GO:0055052 - ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing [Evidence IEA]; GO:0005886 - plasma membrane [Evidence IEA]
GO:0033221 - ATPase-coupled urea transmembrane transporter activity [Evidence IEA]
urea ABC transporter permease subunit UrtC
COORDINATES: similar to AA sequence:RefSeq:WP_007860428.1
urea ABC transporter permease subunit UrtB
COORDINATES: similar to AA sequence:RefSeq:WP_076611536.1
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_016495557.1
IS21-like element ISAav1 family helper ATPase IstB
COORDINATES: similar to AA sequence:RefSeq:WP_076612028.1
IS21-like element ISAav1 family transposase
COORDINATES: similar to AA sequence:RefSeq:WP_018003845.1
COORDINATES: similar to AA sequence:RefSeq:WP_018006585.1
GO:0045027 - DNA end binding [Evidence IEA]
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_011831409.1
COORDINATES: similar to AA sequence:RefSeq:WP_011876306.1
GO:0004519 - endonuclease activity [Evidence IEA]
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_012354475.1
COORDINATES: similar to AA sequence:RefSeq:WP_012354474.1
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: similar to AA sequence:RefSeq:WP_011519294.1
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_011514926.1
COORDINATES: similar to AA sequence:RefSeq:WP_011514921.1
COORDINATES: similar to AA sequence:RefSeq:WP_011514920.1
COORDINATES: similar to AA sequence:RefSeq:WP_011514855.1
COORDINATES: protein motif:HMM:NF024783.2
COORDINATES: similar to AA sequence:RefSeq:WP_008645706.1
COORDINATES: protein motif:HMM:NF012610.2
GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
helix-turn-helix domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_008645691.1
GO:0007059 - chromosome segregation [Evidence IEA]; GO:0000910 - cytokinesis [Evidence IEA]
ParB/RepB/Spo0J family partition protein
COORDINATES: similar to AA sequence:RefSeq:WP_008645689.1
COORDINATES: protein motif:HMM:NF016724.2
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: similar to AA sequence:RefSeq:WP_020203522.1
COORDINATES: similar to AA sequence:RefSeq:WP_012354580.1
COORDINATES: similar to AA sequence:RefSeq:WP_012354578.1
COORDINATES: similar to AA sequence:RefSeq:WP_006757255.1
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.; 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_012354576.1
COORDINATES: protein motif:HMM:NF016491.2
GO:0030255 - protein secretion by the type IV secretion system [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_008649459.1
COORDINATES: similar to AA sequence:RefSeq:WP_012354573.1
COORDINATES: similar to AA sequence:RefSeq:WP_008645668.1
VirB3 family type IV secretion system protein
COORDINATES: similar to AA sequence:RefSeq:WP_012354571.1
COORDINATES: similar to AA sequence:RefSeq:WP_011875532.1
COORDINATES: similar to AA sequence:RefSeq:WP_012435626.1
COORDINATES: similar to AA sequence:RefSeq:WP_008649451.1
TrbG/VirB9 family P-type conjugative transfer protein
COORDINATES: similar to AA sequence:RefSeq:WP_020203508.1
COORDINATES: similar to AA sequence:RefSeq:WP_012354566.1
transglycosylase SLT domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_011239903.1
COORDINATES: similar to AA sequence:RefSeq:WP_011239904.1
lytic transglycosylase domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_011514910.1
toxin co-regulated pilus biosynthesis Q family protein
COORDINATES: similar to AA sequence:RefSeq:WP_011239906.1
COORDINATES: similar to AA sequence:RefSeq:WP_011239907.1
COORDINATES: similar to AA sequence:RefSeq:WP_011239908.1
COORDINATES: similar to AA sequence:RefSeq:WP_011239909.1
COORDINATES: similar to AA sequence:RefSeq:WP_008649429.1
Toxin corregulated pilus biosynthesis protein E
COORDINATES: similar to AA sequence:RefSeq:WP_008649426.1
COORDINATES: similar to AA sequence:RefSeq:WP_011239912.1
shufflon system plasmid conjugative transfer pilus tip adhesin PilV
COORDINATES: similar to AA sequence:RefSeq:WP_011239913.1
COORDINATES: similar to AA sequence:RefSeq:WP_008649420.1
COORDINATES: similar to AA sequence:RefSeq:WP_011514909.1
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: similar to AA sequence:RefSeq:WP_020206972.1
COORDINATES: similar to AA sequence:RefSeq:WP_008649407.1
COORDINATES: similar to AA sequence:RefSeq:WP_012354546.1
COORDINATES: similar to AA sequence:RefSeq:WP_008649404.1
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: 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_012354543.1
COORDINATES: similar to AA sequence:RefSeq:WP_008649398.1
COORDINATES: similar to AA sequence:RefSeq:WP_012354539.1
COORDINATES: similar to AA sequence:RefSeq:WP_076612204.1
COORDINATES: similar to AA sequence:RefSeq:WP_011802320.1
3,4-dehydroadipyl-CoA semialdehyde dehydrogenase
COORDINATES: similar to AA sequence:RefSeq:WP_012356426.1
COORDINATES: similar to AA sequence:RefSeq:WP_018008453.1
helix-turn-helix transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_018308957.1
GO:0016830 - carbon-carbon lyase activity [Evidence IEA]
GO:0010128 - benzoate catabolic process via CoA ligation [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_013953515.1
GO:0051213 - dioxygenase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_018008456.1
COORDINATES: similar to AA sequence:RefSeq:WP_011482566.1
GO:0003824 - catalytic activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_012348664.1
GO:0016491 - oxidoreductase activity [Evidence IEA]; GO:0016616 - oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor [Evidence IEA]
GO:0006631 - fatty acid metabolic process [Evidence IEA]
3-hydroxyacyl-CoA dehydrogenase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_018988725.1
enoyl-CoA hydratase/isomerase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_007858520.1
COORDINATES: protein motif:HMM:NF024212.2
GO:0003700 - DNA-binding transcription factor activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF013757.2
GO:0003677 - DNA binding [Evidence IEA]; GO:0003700 - DNA-binding transcription factor activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF015366.2
GO:0042597 - periplasmic space [Evidence IEA]
tripartite tricarboxylate transporter substrate binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_011617444.1
COORDINATES: similar to AA sequence:RefSeq:WP_011493916.1
class I adenylate-forming enzyme family protein
COORDINATES: similar to AA sequence:RefSeq:WP_017998918.1
GO:0016740 - transferase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_006164482.1
GO:0009279 - cell outer membrane [Evidence IEA]
GO:0015288 - porin activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_020229130.1
COORDINATES: similar to AA sequence:RefSeq:WP_020202289.1
GO:0016747 - acyltransferase activity, transferring groups other than amino-acyl groups [Evidence IEA]
COORDINATES: protein motif:HMM:NF024950.2
COORDINATES: similar to AA sequence:RefSeq:WP_012337317.1
GO:0016627 - oxidoreductase activity, acting on the CH-CH group of donors [Evidence IEA]
COORDINATES: protein motif:HMM:NF014790.2
GO:0050660 - flavin adenine dinucleotide binding [Evidence IEA]; GO:0016491 - oxidoreductase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_016492752.1
MaoC/PaaZ C-terminal domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_013520089.1
COORDINATES: similar to AA sequence:RefSeq:WP_011000525.1
COORDINATES: similar to AA sequence:RefSeq:WP_008648650.1
COORDINATES: similar to AA sequence:RefSeq:WP_008648651.1
GO:0030261 - chromosome condensation [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_008645421.1
COORDINATES: similar to AA sequence:RefSeq:WP_008648653.1
COORDINATES: similar to AA sequence:RefSeq:WP_008648655.1
COORDINATES: similar to AA sequence:RefSeq:WP_008648656.1
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]
COORDINATES: similar to AA sequence:RefSeq:WP_012354532.1
COORDINATES: similar to AA sequence:RefSeq:WP_011239935.1
COORDINATES: similar to AA sequence:RefSeq:WP_012354529.1
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_011239938.1
COORDINATES: similar to AA sequence:RefSeq:WP_008645410.1
COORDINATES: similar to AA sequence:RefSeq:WP_008645409.1
COORDINATES: similar to AA sequence:RefSeq:WP_008645408.1
COORDINATES: similar to AA sequence:RefSeq:WP_008645407.1
COORDINATES: similar to AA sequence:RefSeq:WP_012354522.1
COORDINATES: similar to AA sequence:RefSeq:WP_008645405.1
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_008645403.1
COORDINATES: similar to AA sequence:RefSeq:WP_008645401.1
GO:0042546 - cell wall biogenesis [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_008645398.1
COORDINATES: similar to AA sequence:RefSeq:WP_008645397.1
COORDINATES: similar to AA sequence:RefSeq:WP_008645396.1
COORDINATES: similar to AA sequence:RefSeq:WP_011239944.1
COORDINATES: similar to AA sequence:RefSeq:WP_011239945.1
COORDINATES: similar to AA sequence:RefSeq:WP_018004043.1
COORDINATES: similar to AA sequence:RefSeq:WP_008645390.1
COORDINATES: similar to AA sequence:RefSeq:WP_011239949.1
COORDINATES: similar to AA sequence:RefSeq:WP_018004040.1
COORDINATES: similar to AA sequence:RefSeq:WP_013954392.1
COORDINATES: similar to AA sequence:RefSeq:WP_011239951.1
COORDINATES: similar to AA sequence:RefSeq:WP_011239952.1
COORDINATES: similar to AA sequence:RefSeq:WP_011239953.1
COORDINATES: similar to AA sequence:RefSeq:WP_020201331.1
COORDINATES: similar to AA sequence:RefSeq:WP_011239955.1
COORDINATES: similar to AA sequence:RefSeq:WP_020201328.1
COORDINATES: similar to AA sequence:RefSeq:WP_018310419.1
COORDINATES: similar to AA sequence:RefSeq:WP_011514934.1
COORDINATES: similar to AA sequence:RefSeq:WP_011239960.1
COORDINATES: similar to AA sequence:RefSeq:WP_011514882.1
COORDINATES: similar to AA sequence:RefSeq:WP_008645363.1
COORDINATES: similar to AA sequence:RefSeq:WP_011519964.1
COORDINATES: similar to AA sequence:RefSeq:WP_021138877.1
Tn3-like element IS1071 family transposase
COORDINATES: similar to AA sequence:RefSeq:WP_016486902.1
GO:0006260 - DNA replication [Evidence IEA]
replication-associated recombination protein A
COORDINATES: similar to AA sequence:RefSeq:WP_006402502.1