Paraburkholderia aromaticivorans strain BN5 plasmid pBN3, complete sequence.
Bacteria; Pseudomonadota; Betaproteobacteria; Burkholderiales; Burkholderiaceae; Paraburkholderia.
Identification and genetic characteristics of simultaneous BTEX- and naphthalene-degrading Paraburkholderia sp. BN5 isolated from petroleum-contaminated soil
Submitted (16-AUG-2017) Life Science, Chung-Ang University, 84 HeukSeok-Ro, Dongjak-Gu, Seoul 06974, Korea, Republic of
REFSEQ INFORMATION: The reference sequence is identical to\nCP022993.1.\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 Method :: HGAP v. 3.0\nGenome Representation :: Full\nExpected Final Version :: Yes\nGenome Coverage :: 97.0x\nSequencing Technology :: PacBio\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 04/23/2023 04:56:50\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) :: 8,144\nCDSs (total) :: 8,058\nGenes (coding) :: 7,860\nCDSs (with protein) :: 7,860\nGenes (RNA) :: 86\nrRNAs :: 6, 6, 6 (5S, 16S, 23S)\ncomplete rRNAs :: 6, 6, 6 (5S, 16S, 23S)\ntRNAs :: 64\nncRNAs :: 4\nPseudo Genes (total) :: 198\nCDSs (without protein) :: 198\nPseudo Genes (ambiguous residues) :: 0 of 198\nPseudo Genes (frameshifted) :: 61 of 198\nPseudo Genes (incomplete) :: 157 of 198\nPseudo Genes (internal stop) :: 29 of 198\nPseudo Genes (multiple problems) :: 38 of 198\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.
type strain of Paraburkholderia aromaticivorans
COORDINATES: similar to AA sequence:RefSeq:WP_013094666.1
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: similar to AA sequence:RefSeq:WP_012464973.1
COORDINATES: similar to AA sequence:RefSeq:WP_008581439.1
GO:0004803 - transposase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_004303614.1
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_006965453.1
GO:0015074 - DNA integration [Evidence IEA]; GO:0006310 - DNA recombination [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_012428382.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0004803 - transposase activity [Evidence IEA]
GO:0006313 - transposition, DNA-mediated [Evidence IEA]
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_008344269.1
COORDINATES: similar to AA sequence:RefSeq:WP_008840512.1
COORDINATES: similar to AA sequence:RefSeq:WP_013836959.1
COORDINATES: protein motif:HMM:NF012798.2
COORDINATES: similar to AA sequence:RefSeq:WP_011694462.1
COORDINATES: protein motif:HMM:NF013828.2
COORDINATES: similar to AA sequence:RefSeq:WP_011875612.1
COORDINATES: similar to AA sequence:RefSeq:WP_018310013.1
Tn3 family transposase post-transcriptional regulator TnpC
COORDINATES: similar to AA sequence:RefSeq:WP_007578106.1
COORDINATES: similar to AA sequence:RefSeq:WP_007180429.1
COORDINATES: similar to AA sequence:RefSeq:WP_012405793.1
COORDINATES: similar to AA sequence:RefSeq:WP_018240406.1
COORDINATES: similar to AA sequence:RefSeq:WP_018420598.1
GO:0003964 - RNA-directed DNA polymerase activity [Evidence IEA]
GO:0000373 - Group II intron splicing [Evidence IEA]
group II intron reverse transcriptase/maturase
COORDINATES: similar to AA sequence:RefSeq:WP_013105992.1
COORDINATES: similar to AA sequence:RefSeq:WP_018432897.1
COORDINATES: similar to AA sequence:RefSeq:WP_012406119.1
COORDINATES: similar to AA sequence:RefSeq:WP_013651029.1
COORDINATES: similar to AA sequence:RefSeq:WP_011694206.1
GO:0009279 - cell outer membrane [Evidence IEA]
GO:0015288 - porin activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_018420374.1
COORDINATES: protein motif:HMM:NF019349.2
GO:0003700 - DNA-binding transcription factor activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011805220.1
COORDINATES: similar to AA sequence:RefSeq:WP_000125551.1
incomplete; partial in the middle of a contig; missing C-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
reverse transcriptase N-terminal domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_011024495.1
COORDINATES: similar to AA sequence:RefSeq:WP_013168925.1
GO:0010181 - FMN binding [Evidence IEA]; GO:0016491 - oxidoreductase activity [Evidence IEA]
This protein belongs to a clade of FMN-dependent monooxygenases, within a broader family of flavin-dependent oxidoreductases, the luciferase-like monooxygenase (LMM) family, some of whose members use coenzyme F420 rather than FMN; Derived by automated computational analysis using gene prediction method: Protein Homology.
LLM class flavin-dependent oxidoreductase
COORDINATES: protein motif:HMM:NF013275.2
ABC transporter substrate-binding protein
COORDINATES: protein motif:HMM:NF014684.2
GO:0140359 - ABC-type transporter activity [Evidence IEA]; GO:0042626 - ATPase-coupled transmembrane transporter activity [Evidence IEA]
GO:0015803 - branched-chain amino acid transport [Evidence IEA]
branched-chain amino acid ABC transporter permease
COORDINATES: similar to AA sequence:RefSeq:WP_014743847.1
COORDINATES: protein motif:HMM:NF012235.2
GO:0140359 - ABC-type transporter activity [Evidence IEA]; GO:0005524 - ATP binding [Evidence IEA]; GO:0016887 - ATP hydrolysis activity [Evidence IEA]; GO:0042626 - ATPase-coupled transmembrane transporter activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_004158264.1
COORDINATES: protein motif:HMM:NF013228.2
GO:0016787 - hydrolase activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF013088.2
COORDINATES: similar to AA sequence:RefSeq:WP_015918284.1
COORDINATES: similar to AA sequence:RefSeq:WP_007578716.1
COORDINATES: similar to AA sequence:RefSeq:WP_010097922.1
GO:0005524 - ATP binding [Evidence IEA]; GO:0003677 - DNA binding [Evidence IEA]; GO:0016787 - hydrolase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_006762299.1
COORDINATES: similar to AA sequence:RefSeq:WP_015006034.1
acetyl-CoA hydrolase/transferase C-terminal domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_012494366.1
COORDINATES: similar to AA sequence:RefSeq:WP_013503797.1
COORDINATES: similar to AA sequence:RefSeq:WP_011617414.1
COORDINATES: similar to AA sequence:RefSeq:WP_012356301.1
COORDINATES: similar to AA sequence:RefSeq:WP_011156221.1
2-hydroxycyclohexanecarboxyl-CoA dehydrogenase
COORDINATES: similar to AA sequence:RefSeq:WP_006156050.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0003700 - DNA-binding transcription factor activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_012508667.1
COORDINATES: similar to AA sequence:RefSeq:WP_011486384.1
GO:0006629 - lipid metabolic process [Evidence IEA]
patatin-like phospholipase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_011270718.1
COORDINATES: similar to AA sequence:RefSeq:WP_017775761.1
COORDINATES: similar to AA sequence:RefSeq:WP_011658824.1
GO:0032559 - adenyl ribonucleotide binding [Evidence IEA]
frameshifted; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_007587220.1
COORDINATES: similar to AA sequence:RefSeq:WP_018420534.1
COORDINATES: protein motif:HMM:NF024935.2
COORDINATES: similar to AA sequence:RefSeq:WP_076611295.1
GO:0015074 - DNA integration [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_020656898.1
GO:0016831 - carboxy-lyase activity [Evidence IEA]; GO:0106141 - flavin prenyltransferase activity [Evidence IEA]; GO:0010181 - FMN binding [Evidence IEA]
COORDINATES: protein motif:HMM:NF013714.2
GO:0050660 - flavin adenine dinucleotide binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_020161841.1
non-oxidative hydroxyarylic acid decarboxylases subunit D
COORDINATES: similar to AA sequence:RefSeq:WP_015005303.1
GO:0016831 - carboxy-lyase activity [Evidence IEA]
non-oxidative hydroxyarylic acid decarboxylases subunit C
COORDINATES: similar to AA sequence:RefSeq:WP_015005300.1
GO:0016491 - oxidoreductase activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF012264.2
GO:0009055 - electron transfer activity [Evidence IEA]; GO:0020037 - heme binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_015005305.1
COORDINATES: protein motif:HMM:NF014950.2
GO:0043565 - sequence-specific DNA binding [Evidence IEA]
helix-turn-helix domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_004195141.1
COORDINATES: similar to AA sequence:RefSeq:WP_076611930.1
COORDINATES: similar to AA sequence:RefSeq:WP_006051364.1
COORDINATES: similar to AA sequence:RefSeq:WP_076611361.1
integrase core domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_010919707.1
CaiB/BaiF CoA-transferase family protein
COORDINATES: protein motif:HMM:NF019958.2
GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
TetR/AcrR family transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_006413931.1
COORDINATES: protein motif:HMM:NF019604.2
COORDINATES: similar to AA sequence:RefSeq:WP_011501940.1
COORDINATES: similar to AA sequence:RefSeq:WP_014160654.1
non-heme iron oxygenase ferredoxin subunit
COORDINATES: protein motif:HMM:TIGR02286.1
GO:0010124 - phenylacetate catabolic process [Evidence IEA]
hydroxyphenylacetyl-CoA thioesterase PaaI
COORDINATES: similar to AA sequence:RefSeq:WP_014160652.1
COORDINATES: protein motif:HMM:NF013920.2
COORDINATES: similar to AA sequence:RefSeq:WP_011291915.1
COORDINATES: similar to AA sequence:RefSeq:WP_008344854.1
COORDINATES: similar to AA sequence:RefSeq:WP_014161605.1
GO:0006725 - cellular aromatic compound metabolic process [Evidence IEA]
aromatic-ring-hydroxylating dioxygenase subunit beta
COORDINATES: similar to AA sequence:RefSeq:WP_015006995.1
GO:0051537 - 2 iron, 2 sulfur cluster binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_076611088.1
COORDINATES: similar to AA sequence:RefSeq:WP_006046728.1
GO:0003860 - 3-hydroxyisobutyryl-CoA hydrolase activity [Evidence IEA]
enoyl-CoA hydratase/isomerase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_012428288.1
COORDINATES: similar to AA sequence:RefSeq:WP_012428289.1
COORDINATES: similar to AA sequence:RefSeq:WP_012406685.1
COORDINATES: similar to AA sequence:RefSeq:WP_012406686.1
COORDINATES: similar to AA sequence:RefSeq:WP_013700280.1
COORDINATES: similar to AA sequence:RefSeq:WP_013700281.1
COORDINATES: protein motif:HMM:TIGR00180.1
GO:0007059 - chromosome segregation [Evidence IEA]; GO:0000910 - cytokinesis [Evidence IEA]
ParB/RepB/Spo0J family partition protein
COORDINATES: protein motif:HMM:NF013793.2
COORDINATES: similar to AA sequence:RefSeq:WP_007182594.1
COORDINATES: similar to AA sequence:RefSeq:WP_018432848.1
TrbG/VirB9 family P-type conjugative transfer protein
COORDINATES: similar to AA sequence:RefSeq:WP_007182592.1
COORDINATES: similar to AA sequence:RefSeq:WP_007588639.1
transglycosylase SLT domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_013094410.1
COORDINATES: similar to AA sequence:RefSeq:WP_006417168.1
lytic transglycosylase domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_011875483.1
COORDINATES: similar to AA sequence:RefSeq:WP_018432854.1
COORDINATES: similar to AA sequence:RefSeq:WP_013094406.1
COORDINATES: similar to AA sequence:RefSeq:WP_013094405.1
COORDINATES: similar to AA sequence:RefSeq:WP_013094404.1
COORDINATES: similar to AA sequence:RefSeq:WP_007182758.1
GO:0005524 - ATP binding [Evidence IEA]; GO:0016787 - hydrolase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_020071169.1
COORDINATES: similar to AA sequence:RefSeq:WP_020071170.1
COORDINATES: similar to AA sequence:RefSeq:WP_020071171.1
COORDINATES: similar to AA sequence:RefSeq:WP_020071172.1
COORDINATES: similar to AA sequence:RefSeq:WP_020071173.1
GO:0005515 - protein binding [Evidence IEA]; GO:0016279 - protein-lysine N-methyltransferase activity [Evidence IEA]; GO:1904047 - S-adenosyl-L-methionine binding [Evidence IEA]
COORDINATES: protein motif:HMM:NF013964.2
GO:0004519 - endonuclease activity [Evidence IEA]
HNH endonuclease signature motif containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_015877482.1
COORDINATES: similar to AA sequence:RefSeq:WP_012406666.1
COORDINATES: similar to AA sequence:RefSeq:WP_020071177.1
GO:0006303 - double-strand break repair via nonhomologous end joining [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_010049652.1
COORDINATES: similar to AA sequence:RefSeq:WP_020066447.1
COORDINATES: protein motif:HMM:NF024820.2
COORDINATES: protein motif:HMM:NF024803.2
COORDINATES: similar to AA sequence:RefSeq:WP_013093213.1
GO:0045027 - DNA end binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_014194251.1
COORDINATES: similar to AA sequence:RefSeq:WP_014617575.1
COORDINATES: similar to AA sequence:RefSeq:WP_012427687.1
COORDINATES: similar to AA sequence:RefSeq:WP_013094685.1
COORDINATES: similar to AA sequence:RefSeq:WP_003269575.1
type II toxin-antitoxin system HigB family toxin
COORDINATES: similar to AA sequence:RefSeq:WP_019447838.1
type IV secretory system conjugative DNA transfer family protein
COORDINATES: similar to AA sequence:RefSeq:WP_014900315.1
COORDINATES: similar to AA sequence:RefSeq:WP_013094676.1