Pandoraea oxalativorans strain DSM 23570 plasmid pPO70-3, complete sequence.
Bacteria; Pseudomonadota; Betaproteobacteria; Burkholderiales; Burkholderiaceae; Pandoraea.
Pandoraea oxalativorans DSM 23570 Genome Sequencing
Submitted (15-JUN-2016) Division of Genetics and Molecular Biology, Institute of Biological Sciences, University of Malaya, Kuala Lumpur 50603, Malaysia
Submitted (20-MAY-2015) Division of Genetics and Molecular Biology, Institute of Biological Sciences, University of Malaya, Jalan Universiti, Kuala Lumpur, Wilayah Persekutuan Kuala Lumpur 50603, Malaysia
REFSEQ INFORMATION: The reference sequence is identical to\nCP011520.2.\n\nOn Jul 3, 2016 this sequence version replaced NZ_CP011520.1.\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/\nThis genome has a base modification file available.\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 05/03/2023 05:44:05\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) :: 5,779\nCDSs (total) :: 5,695\nGenes (coding) :: 5,360\nCDSs (with protein) :: 5,360\nGenes (RNA) :: 84\nrRNAs :: 4, 4, 4 (5S, 16S, 23S)\ncomplete rRNAs :: 4, 4, 4 (5S, 16S, 23S)\ntRNAs :: 66\nncRNAs :: 6\nPseudo Genes (total) :: 335\nCDSs (without protein) :: 335\nPseudo Genes (ambiguous residues) :: 0 of 335\nPseudo Genes (frameshifted) :: 105 of 335\nPseudo Genes (incomplete) :: 280 of 335\nPseudo Genes (internal stop) :: 36 of 335\nPseudo Genes (multiple problems) :: 72 of 335\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: similar to AA sequence:RefSeq:WP_006405231.1
GO:0004803 - transposase activity [Evidence IEA]
frameshifted; internal stop; 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_076611359.1
GO:0015074 - DNA integration [Evidence IEA]
incomplete; partial in the middle of a contig; missing N-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
integrase core domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_019088945.1
Derived by automated computational analysis using gene prediction method: Protein Homology.
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_015004359.1
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_017160511.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0000150 - DNA strand exchange activity [Evidence IEA]
GO:0006310 - DNA recombination [Evidence IEA]
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_019564015.1
COORDINATES: similar to AA sequence:RefSeq:WP_018990404.1
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_011000219.1
COORDINATES: similar to AA sequence:RefSeq:WP_010316356.1
COORDINATES: similar to AA sequence:RefSeq:WP_013691838.1
COORDINATES: similar to AA sequence:RefSeq:WP_007182875.1
ParB N-terminal domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_006029259.1
COORDINATES: similar to AA sequence:RefSeq:WP_006762839.1
helix-turn-helix transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_012607051.1
frameshifted; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: protein motif:HMM:NF012798.2
COORDINATES: similar to AA sequence:RefSeq:WP_008343050.1
COORDINATES: similar to AA sequence:RefSeq:WP_003055107.1
COORDINATES: similar to AA sequence:RefSeq:WP_013094374.1
COORDINATES: similar to AA sequence:RefSeq:WP_006751146.1
COORDINATES: similar to AA sequence:RefSeq:WP_018424935.1
COORDINATES: similar to AA sequence:RefSeq:WP_006759512.1
Derived by automated computational analysis using gene prediction method: tRNAscan-SE.
COORDINATES: similar to AA sequence:RefSeq:WP_013124610.1
type II toxin-antitoxin system YafQ family toxin
COORDINATES: similar to AA sequence:RefSeq:WP_017452571.1
GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
type II toxin-antitoxin system RelB/DinJ family antitoxin
COORDINATES: similar to AA sequence:RefSeq:WP_017232043.1
ParB/Srx family N-terminal domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_013700139.1
COORDINATES: similar to AA sequence:RefSeq:WP_076611076.1
programmed frameshift; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_017330817.1
GO:0003676 - nucleic acid binding [Evidence IEA]; GO:0003723 - RNA binding [Evidence IEA]; GO:0001072 - transcription antitermination factor activity, RNA binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011002488.1
helix-turn-helix domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_012218041.1
COORDINATES: similar to AA sequence:RefSeq:WP_076611305.1
COORDINATES: similar to AA sequence:RefSeq:WP_076611586.1
COORDINATES: protein motif:HMM:NF013677.2
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_046292373.1
COORDINATES: similar to AA sequence:RefSeq:WP_012405348.1
COORDINATES: similar to AA sequence:RefSeq:WP_017154897.1
COORDINATES: protein motif:HMM:NF013245.2
GO:0043190 - ATP-binding cassette (ABC) transporter complex [Evidence IEA]
GO:0140359 - ABC-type transporter activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_004189153.1
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: protein motif:HMM:NF024880.2
GO:0008168 - methyltransferase activity [Evidence IEA]
methyltransferase domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_013900191.1
COORDINATES: protein motif:HMM:NF017532.2
phytanoyl-CoA dioxygenase family protein
COORDINATES: protein motif:HMM:NF025072.2
COORDINATES: similar to AA sequence:RefSeq:WP_011886367.1
COORDINATES: similar to AA sequence:RefSeq:WP_007182862.1
COORDINATES: similar to AA sequence:RefSeq:WP_008917785.1
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_042551150.1
COORDINATES: similar to AA sequence:RefSeq:WP_003271244.1
COORDINATES: similar to AA sequence:RefSeq:WP_012464922.1
COORDINATES: protein motif:HMM:NF023208.2
COORDINATES: protein motif:HMM:NF018980.2
programmed frameshift; internal stop; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_012733728.1
COORDINATES: similar to AA sequence:RefSeq:WP_009489204.1
COORDINATES: similar to AA sequence:RefSeq:WP_076611964.1
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_076611354.1