Paraburkholderia acidisoli strain DHF22 plasmid p1, complete sequence.
Bacteria; Proteobacteria; Betaproteobacteria; Burkholderiales; Burkholderiaceae; Paraburkholderia.
Paraburkholderia acidiphila 7Q-K02 sp. nov and Paraburkholderia acidisoli DHF22 sp. nov., two strains isolated from forest soil
Submitted (15-DEC-2019) School of Life Sciences, Sun Yat-sen University, No.135,Xinggang West Road, Guangzhou, Guangdong 510275, China
REFSEQ INFORMATION: The reference sequence is identical to\nCP046917.1.\nBacteria and source DNA available from State Key Laboratory of\nBiocontrol, School of Life Sciences, Sun Yat-sen University.\naddress:135 Xingang Road, W., Guangzhou 510275, P. R. China.\n\nAssembly not circularized.\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 :: 15-FEB-2019\nAssembly Method :: canu v. 1.7.11\nAssembly Name :: SYSU_PbDHF22_1.7.11\nGenome Representation :: Full\nExpected Final Version :: Yes\nGenome Coverage :: 272.0x\nSequencing Technology :: Oxford Nanopore GridION\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 12/08/2022 06:27:45\nAnnotation Pipeline :: NCBI Prokaryotic Genome\n Annotation Pipeline (PGAP)\nAnnotation Method :: Best-placed reference protein\n set; GeneMarkS-2+\nAnnotation Software revision :: 6.3\nFeatures Annotated :: Gene; CDS; rRNA; tRNA; ncRNA\nGenes (total) :: 7,109\nCDSs (total) :: 7,017\nGenes (coding) :: 6,923\nCDSs (with protein) :: 6,923\nGenes (RNA) :: 92\nrRNAs :: 6, 6, 6 (5S, 16S, 23S)\ncomplete rRNAs :: 6, 6, 6 (5S, 16S, 23S)\ntRNAs :: 70\nncRNAs :: 4\nPseudo Genes (total) :: 94\nCDSs (without protein) :: 94\nPseudo Genes (ambiguous residues) :: 0 of 94\nPseudo Genes (frameshifted) :: 26 of 94\nPseudo Genes (incomplete) :: 75 of 94\nPseudo Genes (internal stop) :: 2 of 94\nPseudo Genes (multiple problems) :: 8 of 94\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.
type strain of Paraburkholderia acidisoli
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: similar to AA sequence:RefSeq:WP_007589672.1
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_018435616.1
COORDINATES: similar to AA sequence:RefSeq:WP_012206033.1
COORDINATES: protein motif:HMM:NF012301.2
GO:0000160 - phosphorelay signal transduction system [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_006403941.1
COORDINATES: similar to AA sequence:RefSeq:WP_012211067.1
COORDINATES: similar to AA sequence:RefSeq:WP_012211068.1
COORDINATES: similar to AA sequence:RefSeq:WP_006493623.1
GO:0051782 - negative regulation of cell division [Evidence IEA]; GO:0009432 - SOS response [Evidence IEA]
translesion DNA synthesis-associated protein ImuA
COORDINATES: protein motif:HMM:NF012789.2
COORDINATES: similar to AA sequence:RefSeq:WP_004552328.1
COORDINATES: similar to AA sequence:RefSeq:WP_007182758.1
COORDINATES: similar to AA sequence:RefSeq:WP_011493226.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0016151 - nickel cation binding [Evidence IEA]
GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]; GO:0010045 - response to nickel cation [Evidence IEA]
nickel-responsive transcriptional regulator NikR
COORDINATES: similar to AA sequence:RefSeq:WP_011493225.1
HoxN/HupN/NixA family nickel/cobalt transporter
COORDINATES: similar to AA sequence:RefSeq:WP_008643867.1
COORDINATES: similar to AA sequence:RefSeq:WP_012336949.1
COORDINATES: similar to AA sequence:RefSeq:WP_013958806.1
PDDEXK nuclease domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_010111305.1
GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
frameshifted; Derived by automated computational analysis using gene prediction method: Protein Homology.
H-NS family nucleoid-associated regulatory protein
COORDINATES: similar to AA sequence:RefSeq:WP_007731387.1
GO:0015074 - DNA integration [Evidence IEA]; GO:0006310 - DNA recombination [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_020204770.1
COORDINATES: similar to AA sequence:RefSeq:WP_006752809.1
ParB/RepB/Spo0J family partition protein
COORDINATES: similar to AA sequence:RefSeq:WP_011875475.1
COORDINATES: protein motif:HMM:NF013793.2
COORDINATES: similar to AA sequence:RefSeq:WP_008343080.1
COORDINATES: similar to AA sequence:RefSeq:WP_007182593.1
TrbG/VirB9 family P-type conjugative transfer protein
COORDINATES: similar to AA sequence:RefSeq:WP_012217948.1
COORDINATES: similar to AA sequence:RefSeq:WP_007588639.1
transglycosylase SLT domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_006759128.1
COORDINATES: similar to AA sequence:RefSeq:WP_012367225.1
lytic transglycosylase domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_012217952.1
toxin co-regulated pilus biosynthesis Q family protein
COORDINATES: similar to AA sequence:RefSeq:WP_011875484.1
COORDINATES: similar to AA sequence:RefSeq:WP_013094404.1
COORDINATES: similar to AA sequence:RefSeq:WP_006760238.1
type II secretion system F family protein
COORDINATES: similar to AA sequence:RefSeq:WP_008343102.1
COORDINATES: similar to AA sequence:RefSeq:WP_012217959.1
COORDINATES: similar to AA sequence:RefSeq:WP_018432861.1
COORDINATES: similar to AA sequence:RefSeq:WP_012367213.1
COORDINATES: similar to AA sequence:RefSeq:WP_012367212.1
COORDINATES: similar to AA sequence:RefSeq:WP_012217965.1
GO:0045893 - positive regulation of DNA-templated transcription [Evidence IEA]; GO:1902208 - regulation of bacterial-type flagellum assembly [Evidence IEA]
COORDINATES: protein motif:HMM:NF019976.2
nuclease-related domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_018432869.1
COORDINATES: similar to AA sequence:RefSeq:WP_013094391.1
COORDINATES: similar to AA sequence:RefSeq:WP_018432872.1
COORDINATES: similar to AA sequence:RefSeq:WP_018432873.1
COORDINATES: similar to AA sequence:RefSeq:WP_012367202.1
COORDINATES: similar to AA sequence:RefSeq:WP_013094383.1
COORDINATES: similar to AA sequence:RefSeq:WP_006761115.1
COORDINATES: similar to AA sequence:RefSeq:WP_013094774.1
Lar family restriction alleviation protein
COORDINATES: protein motif:HMM:NF019146.2
COORDINATES: protein motif:HMM:NF018381.2
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_012217986.1
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_008343161.1
COORDINATES: similar to AA sequence:RefSeq:WP_012217988.1
COORDINATES: similar to AA sequence:RefSeq:WP_012217989.1
COORDINATES: similar to AA sequence:RefSeq:WP_008343166.1
COORDINATES: protein motif:HMM:TIGR03742.1
COORDINATES: similar to AA sequence:RefSeq:WP_007582512.1
COORDINATES: similar to AA sequence:RefSeq:WP_013700021.1
COORDINATES: similar to AA sequence:RefSeq:WP_011875520.1
COORDINATES: protein motif:HMM:NF013632.2
COORDINATES: similar to AA sequence:RefSeq:WP_012431294.1
COORDINATES: similar to AA sequence:RefSeq:WP_013094752.1
COORDINATES: similar to AA sequence:RefSeq:WP_012367179.1
COORDINATES: similar to AA sequence:RefSeq:WP_018432914.1
COORDINATES: similar to AA sequence:RefSeq:WP_013700031.1
COORDINATES: similar to AA sequence:RefSeq:WP_013700032.1
COORDINATES: similar to AA sequence:RefSeq:WP_012435702.1
COORDINATES: similar to AA sequence:RefSeq:WP_012435703.1
COORDINATES: similar to AA sequence:RefSeq:WP_004627028.1
COORDINATES: similar to AA sequence:RefSeq:WP_011875532.1
COORDINATES: similar to AA sequence:RefSeq:WP_018432931.1
COORDINATES: similar to AA sequence:RefSeq:WP_012367167.1
VirB3 family type IV secretion system protein
COORDINATES: similar to AA sequence:RefSeq:WP_018432933.1
COORDINATES: similar to AA sequence:RefSeq:WP_013094734.1
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_012218010.1
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; Derived by automated computational analysis using gene prediction method: Protein Homology.
conjugative transfer system coupling protein TraD
COORDINATES: similar to AA sequence:RefSeq:WP_013700044.1
COORDINATES: similar to AA sequence:RefSeq:WP_012218013.1
COORDINATES: similar to AA sequence:RefSeq:WP_013094728.1
COORDINATES: similar to AA sequence:RefSeq:WP_007585065.1
COORDINATES: similar to AA sequence:RefSeq:WP_011875543.1
COORDINATES: similar to AA sequence:RefSeq:WP_013229000.1
mandelate racemase/muconate lactonizing enzyme family protein
COORDINATES: similar to AA sequence:RefSeq:WP_013229001.1
COORDINATES: protein motif:HMM:NF015431.2
COORDINATES: protein motif:HMM:NF024996.2
COORDINATES: similar to AA sequence:RefSeq:WP_020071151.1
COORDINATES: similar to AA sequence:RefSeq:WP_018432948.1
COORDINATES: similar to AA sequence:RefSeq:WP_008343241.1
COORDINATES: similar to AA sequence:RefSeq:WP_012367422.1
COORDINATES: similar to AA sequence:RefSeq:WP_012367421.1
COORDINATES: similar to AA sequence:RefSeq:WP_006757243.1
COORDINATES: similar to AA sequence:RefSeq:WP_012367419.1
COORDINATES: similar to AA sequence:RefSeq:WP_007182569.1
COORDINATES: similar to AA sequence:RefSeq:WP_012367417.1
COORDINATES: similar to AA sequence:RefSeq:WP_007747323.1
GO:0005515 - protein binding [Evidence IEA]
SET domain-containing protein-lysine N-methyltransferase
COORDINATES: similar to AA sequence:RefSeq:WP_019367495.1
COORDINATES: protein motif:HMM:NF014567.2
COORDINATES: similar to AA sequence:RefSeq:WP_007732193.1
COORDINATES: similar to AA sequence:RefSeq:WP_076611281.1
GO:0004803 - transposase activity [Evidence IEA]
programmed frameshift; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_003230776.1
COORDINATES: similar to AA sequence:RefSeq:WP_011204862.1
COORDINATES: similar to AA sequence:RefSeq:WP_004548071.1
GO:0004129 - cytochrome-c oxidase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_014972080.1
COORDINATES: similar to AA sequence:RefSeq:WP_014253181.1
frameshifted; incomplete; partial in the middle of a contig; missing N-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_013590592.1
COORDINATES: similar to AA sequence:RefSeq:WP_013338243.1
COORDINATES: similar to AA sequence:RefSeq:WP_018423525.1
COORDINATES: similar to AA sequence:RefSeq:WP_011488027.1
COORDINATES: similar to AA sequence:RefSeq:WP_013690745.1
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_013092796.1
COORDINATES: protein motif:HMM:NF025774.2
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_004573923.1
glutathione-independent formaldehyde dehydrogenase
COORDINATES: similar to AA sequence:RefSeq:WP_006049350.1
phosphatidylserine decarboxylase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_011493261.1
COORDINATES: similar to AA sequence:RefSeq:WP_007576399.1
COORDINATES: protein motif:HMM:NF018604.2
COORDINATES: similar to AA sequence:RefSeq:WP_015072857.1
COORDINATES: similar to AA sequence:RefSeq:WP_010160673.1
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_020721678.1
COORDINATES: protein motif:HMM:NF019016.2
COORDINATES: similar to AA sequence:RefSeq:WP_017483907.1
COORDINATES: protein motif:HMM:NF024176.2
pyridoxamine 5'-phosphate oxidase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_020070492.1
COORDINATES: similar to AA sequence:RefSeq:WP_006049886.1
gluconate 2-dehydrogenase subunit 3 family protein
COORDINATES: similar to AA sequence:RefSeq:WP_014972134.1
COORDINATES: similar to AA sequence:RefSeq:WP_006049884.1
COORDINATES: similar to AA sequence:RefSeq:WP_020070488.1
GO:0000287 - magnesium ion binding [Evidence IEA]; GO:0030976 - thiamine pyrophosphate binding [Evidence IEA]
thiamine pyrophosphate-requiring protein
COORDINATES: similar to AA sequence:RefSeq:WP_017774177.1
COORDINATES: similar to AA sequence:RefSeq:WP_015875546.1
GO:0016491 - oxidoreductase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_015875534.1
COORDINATES: similar to AA sequence:RefSeq:WP_013690744.1
COORDINATES: similar to AA sequence:RefSeq:WP_013091705.1
COORDINATES: similar to AA sequence:RefSeq:WP_009771020.1
COORDINATES: similar to AA sequence:RefSeq:WP_007730200.1
GO:0016787 - hydrolase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011876278.1
COORDINATES: similar to AA sequence:RefSeq:WP_011300541.1
GO:0006303 - double-strand break repair via nonhomologous end joining [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_012404455.1
GO:0045027 - DNA end binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_012404456.1