Pandoraea oxalativorans strain DSM 23570 plasmid pPO70-2, 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\nCP011519.2.\n\nOn Jul 3, 2016 this sequence version replaced NZ_CP011519.1.\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: similar to AA sequence:RefSeq:WP_076611586.1
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_076611305.1
COORDINATES: similar to AA sequence:RefSeq:WP_017154897.1
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_017172642.1
COORDINATES: similar to AA sequence:RefSeq:WP_007966866.1
COORDINATES: similar to AA sequence:RefSeq:WP_004542720.1
COORDINATES: similar to AA sequence:RefSeq:WP_017164708.1
type IV secretion system DNA-binding domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_011345599.1
COORDINATES: similar to AA sequence:RefSeq:WP_006156668.1
COORDINATES: similar to AA sequence:RefSeq:WP_007968770.1
lytic transglycosylase domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_008343655.1
GO:0043684 - type IV secretion system complex [Evidence IEA]
GO:0044097 - secretion by the type IV secretion system [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_005931779.1
COORDINATES: similar to AA sequence:RefSeq:WP_011345603.1
P-type conjugative transfer protein VirB9
COORDINATES: similar to AA sequence:RefSeq:WP_019303576.1
COORDINATES: similar to AA sequence:RefSeq:WP_017160491.1
COORDINATES: similar to AA sequence:RefSeq:WP_017161284.1
COORDINATES: similar to AA sequence:RefSeq:WP_017160493.1
COORDINATES: similar to AA sequence:RefSeq:WP_007968755.1
COORDINATES: similar to AA sequence:RefSeq:WP_008343662.1
COORDINATES: similar to AA sequence:RefSeq:WP_008343663.1
VirB3 family type IV secretion system protein
COORDINATES: similar to AA sequence:RefSeq:WP_008345293.1
COORDINATES: protein motif:HMM:NF020251.2
GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
helix-turn-helix domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_011400764.1
COORDINATES: protein motif:HMM:NF014567.2
COORDINATES: similar to AA sequence:RefSeq:WP_012426774.1
COORDINATES: similar to AA sequence:RefSeq:WP_004197529.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0000150 - DNA strand exchange activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_019642187.1
COORDINATES: similar to AA sequence:RefSeq:WP_011342942.1
type II toxin-antitoxin system mRNA interferase toxin, RelE/StbE family
COORDINATES: similar to AA sequence:RefSeq:WP_007180432.1
COORDINATES: similar to AA sequence:RefSeq:WP_011482513.1
COORDINATES: similar to AA sequence:RefSeq:WP_014194545.1
frameshifted; incomplete; partial in the middle of a contig; missing C-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: protein motif:HMM:NF026288.2
COORDINATES: similar to AA sequence:RefSeq:WP_012464922.1
COORDINATES: similar to AA sequence:RefSeq:WP_009770530.1
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_018312239.1
COORDINATES: similar to AA sequence:RefSeq:WP_076611167.1
frameshifted; internal stop; 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_012213865.1
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: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-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_011785204.1
COORDINATES: protein motif:HMM:NF015737.2
autotransporter outer membrane beta-barrel domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_013122322.1
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_015378969.1
COORDINATES: similar to AA sequence:RefSeq:WP_013160158.1
COORDINATES: similar to AA sequence:RefSeq:WP_009489204.1
COORDINATES: similar to AA sequence:RefSeq:WP_006405231.1
frameshifted; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_017157756.1
COORDINATES: similar to AA sequence:RefSeq:WP_017157757.1
GO:0008080 - N-acetyltransferase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_006482547.1
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_012218041.1
COORDINATES: similar to AA sequence:RefSeq:WP_018421913.1
COORDINATES: similar to AA sequence:RefSeq:WP_012339223.1
COORDINATES: similar to AA sequence:RefSeq:WP_006766630.1
ATP-binding cassette domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_011353733.1
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: similar to AA sequence:RefSeq:WP_014900818.1
GO:0055085 - transmembrane transport [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011659808.1
COORDINATES: similar to AA sequence:RefSeq:WP_011659809.1
GO:0055052 - ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing [Evidence IEA]
GO:0140359 - ABC-type transporter activity [Evidence IEA]; GO:0042626 - ATPase-coupled transmembrane transporter activity [Evidence IEA]
peptide ABC transporter substrate-binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_017335482.1
COORDINATES: similar to AA sequence:RefSeq:WP_004524380.1
GO:0015171 - amino acid transmembrane transporter activity [Evidence IEA]
GO:0006865 - amino acid transport [Evidence IEA]; GO:0055085 - transmembrane transport [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_004955520.1
COORDINATES: similar to AA sequence:RefSeq:WP_076611695.1
GO:0015074 - DNA integration [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_017162391.1
COORDINATES: similar to AA sequence:RefSeq:WP_007179151.1
COORDINATES: similar to AA sequence:RefSeq:WP_003097546.1
COORDINATES: similar to AA sequence:RefSeq:WP_046292373.1
COORDINATES: similar to AA sequence:RefSeq:WP_012339753.1
COORDINATES: similar to AA sequence:RefSeq:WP_011749831.1
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: protein motif:HMM:NF013677.2
COORDINATES: similar to AA sequence:RefSeq:WP_012924375.1
GO:0022857 - transmembrane transporter activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF012371.2
COORDINATES: similar to AA sequence:RefSeq:WP_012733728.1
COORDINATES: similar to AA sequence:RefSeq:WP_014252904.1
COORDINATES: similar to AA sequence:RefSeq:WP_013436661.1
COORDINATES: similar to AA sequence:RefSeq:WP_013436662.1
COORDINATES: similar to AA sequence:RefSeq:WP_003490780.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0000287 - magnesium ion binding [Evidence IEA]; GO:0009036 - type II site-specific deoxyribonuclease activity [Evidence IEA]
GO:0009307 - DNA restriction-modification system [Evidence IEA]
BsuBI/PstI family type II restriction endonuclease
COORDINATES: similar to AA sequence:RefSeq:WP_001686642.1
GO:0003824 - catalytic activity [Evidence IEA]; GO:0003677 - DNA binding [Evidence IEA]
GO:0006304 - DNA modification [Evidence IEA]
Eco57I restriction-modification methylase domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_017115701.1
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_004086710.1
GO:0006310 - DNA recombination [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_012471715.1
COORDINATES: protein motif:HMM:NF012798.2
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_012218083.1
GO:0015074 - DNA integration [Evidence IEA]; GO:0006310 - DNA recombination [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_017234492.1
AbrB/MazE/SpoVT family DNA-binding domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_017234493.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0004521 - endoribonuclease activity [Evidence IEA]; GO:0003723 - RNA binding [Evidence IEA]
type II toxin-antitoxin system PemK/MazF family toxin
COORDINATES: similar to AA sequence:RefSeq:WP_015877482.1
COORDINATES: similar to AA sequence:RefSeq:WP_011875889.1
COORDINATES: similar to AA sequence:RefSeq:WP_014237641.1
COORDINATES: similar to AA sequence:RefSeq:WP_013700152.1
COORDINATES: similar to AA sequence:RefSeq:WP_017874484.1
COORDINATES: protein motif:HMM:NF013777.2
GO:0003700 - DNA-binding transcription factor activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_006484960.1
COORDINATES: similar to AA sequence:RefSeq:WP_013690338.1
COORDINATES: similar to AA sequence:RefSeq:WP_011002488.1
integrase core domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_020309499.1
COORDINATES: similar to AA sequence:RefSeq:WP_013588587.1
COORDINATES: similar to AA sequence:RefSeq:WP_013512170.1
COORDINATES: similar to AA sequence:RefSeq:WP_009916533.1
COORDINATES: similar to AA sequence:RefSeq:WP_000994919.1
ParB/Srx family N-terminal domain-containing protein
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_017231944.1
COORDINATES: protein motif:HMM:NF012584.2