Paraburkholderia aromaticivorans strain BN5 plasmid pBN4, 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\nCP022994.1.\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_008344230.1
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_007183078.1
COORDINATES: similar to AA sequence:RefSeq:WP_011875748.1
COORDINATES: similar to AA sequence:RefSeq:WP_011875745.1
COORDINATES: similar to AA sequence:RefSeq:WP_011798656.1
GO:0003886 - DNA (cytosine-5-)-methyltransferase activity [Evidence IEA]; GO:0008168 - methyltransferase activity [Evidence IEA]; GO:1904047 - S-adenosyl-L-methionine binding [Evidence IEA]
GO:0006304 - DNA modification [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_008344239.1
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: similar to AA sequence:RefSeq:WP_007183087.1
COORDINATES: similar to AA sequence:RefSeq:WP_008344241.1
COORDINATES: similar to AA sequence:RefSeq:WP_005918230.1
COORDINATES: similar to AA sequence:RefSeq:WP_007183091.1
COORDINATES: similar to AA sequence:RefSeq:WP_008344246.1
COORDINATES: similar to AA sequence:RefSeq:WP_008344250.1
COORDINATES: similar to AA sequence:RefSeq:WP_011875715.1
COORDINATES: similar to AA sequence:RefSeq:WP_007183096.1
COORDINATES: similar to AA sequence:RefSeq:WP_011875711.1
COORDINATES: similar to AA sequence:RefSeq:WP_017461384.1
DotH/IcmK family type IV secretion protein
COORDINATES: similar to AA sequence:RefSeq:WP_008344316.1
COORDINATES: similar to AA sequence:RefSeq:WP_008344318.1
COORDINATES: similar to AA sequence:RefSeq:WP_007183101.1
COORDINATES: similar to AA sequence:RefSeq:WP_008344322.1
COORDINATES: similar to AA sequence:RefSeq:WP_007183103.1
COORDINATES: similar to AA sequence:RefSeq:WP_008344326.1
COORDINATES: similar to AA sequence:RefSeq:WP_008344329.1
COORDINATES: similar to AA sequence:RefSeq:WP_008344331.1
COORDINATES: similar to AA sequence:RefSeq:WP_007183107.1
COORDINATES: similar to AA sequence:RefSeq:WP_005933813.1
COORDINATES: similar to AA sequence:RefSeq:WP_007183109.1
COORDINATES: similar to AA sequence:RefSeq:WP_007183110.1
COORDINATES: similar to AA sequence:RefSeq:WP_011875696.1
COORDINATES: similar to AA sequence:RefSeq:WP_007183112.1
COORDINATES: similar to AA sequence:RefSeq:WP_008344343.1
COORDINATES: similar to AA sequence:RefSeq:WP_008344345.1
COORDINATES: similar to AA sequence:RefSeq:WP_007180429.1
COORDINATES: similar to AA sequence:RefSeq:WP_004152392.1
GO:0004803 - transposase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_018311698.1
COORDINATES: similar to AA sequence:RefSeq:WP_007180433.1
COORDINATES: similar to AA sequence:RefSeq:WP_008346670.1
GO:0004328 - formamidase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011927261.1
COORDINATES: protein motif:HMM:NF024996.2
GO:0009279 - cell outer membrane [Evidence IEA]
GO:0015288 - porin activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_004446571.1
COORDINATES: similar to AA sequence:RefSeq:WP_018420974.1
GO:0022857 - transmembrane transporter activity [Evidence IEA]
GO:0055085 - transmembrane transport [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_012205469.1
GO:0004040 - amidase activity [Evidence IEA]
GO:0006807 - nitrogen compound metabolic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_019653498.1
COORDINATES: protein motif:HMM:NF012321.2
COORDINATES: similar to AA sequence:RefSeq:WP_020165098.1
transporter substrate-binding domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_018420969.1
COORDINATES: similar to AA sequence:RefSeq:WP_016454627.1
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_010112033.1
COORDINATES: similar to AA sequence:RefSeq:WP_012339827.1
COORDINATES: similar to AA sequence:RefSeq:WP_010112035.1
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]
GO:0015840 - urea transport [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_011875583.1
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_013698628.1
urea ABC transporter permease subunit UrtB
COORDINATES: similar to AA sequence:RefSeq:WP_011547489.1
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]
urea ABC transporter substrate-binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_013698630.1
GO:0000160 - phosphorelay signal transduction system [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_017235678.1
COORDINATES: similar to AA sequence:RefSeq:WP_076612008.1
frameshifted; internal stop; 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_047389784.1
COORDINATES: similar to AA sequence:RefSeq:WP_007182568.1
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_011059703.1
COORDINATES: similar to AA sequence:RefSeq:WP_013541066.1
COORDINATES: similar to AA sequence:RefSeq:WP_017773426.1
COORDINATES: similar to AA sequence:RefSeq:WP_020071095.1
SDR family NAD(P)-dependent oxidoreductase
COORDINATES: similar to AA sequence:RefSeq:WP_013341056.1
COORDINATES: similar to AA sequence:RefSeq:WP_020071093.1
COORDINATES: similar to AA sequence:RefSeq:WP_018420495.1
GO:0005525 - GTP binding [Evidence IEA]; GO:0003924 - GTPase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_013341053.1
COORDINATES: similar to AA sequence:RefSeq:WP_017773420.1
COORDINATES: protein motif:HMM:NF024883.2
COORDINATES: similar to AA sequence:RefSeq:WP_005894177.1
COORDINATES: similar to AA sequence:RefSeq:WP_007733287.1
GO:0001216 - DNA-binding transcription activator activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF023898.2
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_020653145.1
DDE-type integrase/transposase/recombinase
COORDINATES: similar to AA sequence:RefSeq:WP_012406666.1
COORDINATES: similar to AA sequence:RefSeq:WP_012430942.1
COORDINATES: similar to AA sequence:RefSeq:WP_015877482.1
COORDINATES: similar to AA sequence:RefSeq:WP_011875602.1
COORDINATES: similar to AA sequence:RefSeq:WP_013699878.1
COORDINATES: similar to AA sequence:RefSeq:WP_076611361.1
programmed frameshift; Derived by automated computational analysis using gene prediction method: Protein Homology.
IS3-like element ISBxe1 family transposase
COORDINATES: similar to AA sequence:RefSeq:WP_009770542.1
COORDINATES: similar to AA sequence:RefSeq:WP_014194242.1
COORDINATES: similar to AA sequence:RefSeq:WP_008343270.1
GO:0003824 - catalytic activity [Evidence IEA]
phosphoadenosine phosphosulfate reductase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_007585033.1
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_012406426.1
COORDINATES: similar to AA sequence:RefSeq:WP_007182923.1
COORDINATES: similar to AA sequence:RefSeq:WP_011545436.1
COORDINATES: similar to AA sequence:RefSeq:WP_018420717.1
COORDINATES: similar to AA sequence:RefSeq:WP_012337163.1
COORDINATES: similar to AA sequence:RefSeq:WP_013026614.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0003700 - DNA-binding transcription factor activity [Evidence IEA]
GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_003811956.1
efflux transporter outer membrane subunit
COORDINATES: similar to AA sequence:RefSeq:WP_013742122.1
GO:0015562 - efflux transmembrane transporter activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_020293054.1
GO:0005215 - transporter activity [Evidence IEA]
efflux RND transporter periplasmic adaptor subunit
COORDINATES: similar to AA sequence:RefSeq:WP_007178901.1
GO:0000160 - phosphorelay signal transduction system [Evidence IEA]; GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011711650.1
COORDINATES: similar to AA sequence:RefSeq:WP_018004567.1
COORDINATES: similar to AA sequence:RefSeq:WP_011486259.1
COORDINATES: similar to AA sequence:RefSeq:WP_011875691.1
COORDINATES: similar to AA sequence:RefSeq:WP_011875690.1
COORDINATES: similar to AA sequence:RefSeq:WP_007183045.1
COORDINATES: similar to AA sequence:RefSeq:WP_011875688.1
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_003425687.1
COORDINATES: similar to AA sequence:RefSeq:WP_008344166.1
COORDINATES: similar to AA sequence:RefSeq:WP_011875783.1
COORDINATES: similar to AA sequence:RefSeq:WP_007183049.1
COORDINATES: similar to AA sequence:RefSeq:WP_008344171.1
COORDINATES: similar to AA sequence:RefSeq:WP_008344173.1
GO:0008657 - DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) inhibitor activity [Evidence IEA]; GO:0042803 - protein homodimerization activity [Evidence IEA]
GO:0030541 - plasmid partitioning [Evidence IEA]; GO:0051290 - protein heterotetramerization [Evidence IEA]; GO:0009432 - SOS response [Evidence IEA]
type II toxin-antitoxin system RelE/ParE family toxin
COORDINATES: similar to AA sequence:RefSeq:WP_008344175.1
COORDINATES: similar to AA sequence:RefSeq:WP_008344177.1
COORDINATES: similar to AA sequence:RefSeq:WP_008344179.1
COORDINATES: similar to AA sequence:RefSeq:WP_008344181.1
COORDINATES: similar to AA sequence:RefSeq:WP_008344184.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0003917 - DNA topoisomerase type I (single strand cut, ATP-independent) activity [Evidence IEA]
GO:0006265 - DNA topological change [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_007183056.1
lytic transglycosylase domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_008344192.1
COORDINATES: similar to AA sequence:RefSeq:WP_008344194.1
COORDINATES: similar to AA sequence:RefSeq:WP_008344196.1
GO:0003896 - DNA primase activity [Evidence IEA]
GO:0006269 - DNA replication, synthesis of RNA primer [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011875771.1
TraM recognition domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_008344199.1
COORDINATES: similar to AA sequence:RefSeq:WP_007183062.1
COORDINATES: similar to AA sequence:RefSeq:WP_008344206.1
COORDINATES: similar to AA sequence:RefSeq:WP_004666779.1
COORDINATES: similar to AA sequence:RefSeq:WP_007183065.1
COORDINATES: similar to AA sequence:RefSeq:WP_007183066.1
COORDINATES: similar to AA sequence:RefSeq:WP_008344214.1
COORDINATES: similar to AA sequence:RefSeq:WP_008344216.1
COORDINATES: similar to AA sequence:RefSeq:WP_008344218.1
COORDINATES: similar to AA sequence:RefSeq:WP_008344220.1
COORDINATES: protein motif:HMM:NF028242.2
type IV secretory system conjugative DNA transfer family protein
COORDINATES: similar to AA sequence:RefSeq:WP_007183072.1
Members of this family include DotD of type IVB secretion systems and TraH of plasmid conjugative plasmid systems, both lipoproteins; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: protein motif:HMM:NF037421.2
COORDINATES: protein motif:HMM:NF015397.2
relaxase/mobilization nuclease domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_008344224.1
COORDINATES: similar to AA sequence:RefSeq:WP_008344226.1
COORDINATES: similar to AA sequence:RefSeq:WP_009682506.1