Paraburkholderia terrae strain KU-64 plasmid pPT70, complete sequence.
Bacteria; Pseudomonadota; Betaproteobacteria; Burkholderiales; Burkholderiaceae; Paraburkholderia.
Identification and characterization of a novel class of self-sufficient cytochrome P450 hydroxylase involved in cyclohexanecarboxylate degradation in Paraburkholderia terrae strain KU-64
Submitted (29-JUL-2021) Contact:Hiroaki Iwaki Kansai University, Department of Life Science and Biotechnology; Yamate-cho 3-3-35, Suita, Osaka 564-8680, Japan
REFSEQ INFORMATION: The reference sequence is identical to\nAP024960.1.\nAnnotated by DFAST https://dfast.ddbj.nig.ac.jp/\n\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\nGenome Coverage :: 66x\nSequencing Technology :: PacBio RSII\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 03/23/2023 05:21:40\nAnnotation Pipeline :: NCBI Prokaryotic Genome\n Annotation Pipeline (PGAP)\nAnnotation Method :: Best-placed reference protein\n set; GeneMarkS-2+\nAnnotation Software revision :: 6.4\nFeatures Annotated :: Gene; CDS; rRNA; tRNA; ncRNA\nGenes (total) :: 9,459\nCDSs (total) :: 9,365\nGenes (coding) :: 9,159\nCDSs (with protein) :: 9,159\nGenes (RNA) :: 94\nrRNAs :: 7, 7, 7 (5S, 16S, 23S)\ncomplete rRNAs :: 7, 7, 7 (5S, 16S, 23S)\ntRNAs :: 69\nncRNAs :: 4\nPseudo Genes (total) :: 206\nCDSs (without protein) :: 206\nPseudo Genes (ambiguous residues) :: 0 of 206\nPseudo Genes (frameshifted) :: 78 of 206\nPseudo Genes (incomplete) :: 153 of 206\nPseudo Genes (internal stop) :: 29 of 206\nPseudo Genes (multiple problems) :: 47 of 206\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.
COORDINATES: similar to AA sequence:RefSeq:WP_006051648.1
Derived by automated computational analysis using gene prediction method: Protein Homology.
type II toxin-antitoxin system RelE/ParE family toxin
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: similar to AA sequence:RefSeq:WP_076612036.1
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: protein motif:HMM:NF013884.2
COORDINATES: similar to AA sequence:RefSeq:WP_004206353.1
GO:0004671 - protein C-terminal S-isoprenylcysteine carboxyl O-methyltransferase activity [Evidence IEA]
GO:0006481 - C-terminal protein methylation [Evidence IEA]
isoprenylcysteine carboxylmethyltransferase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_018425347.1
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_018425348.1
type II secretion system F family protein
COORDINATES: similar to AA sequence:RefSeq:WP_007737221.1
COORDINATES: similar to AA sequence:RefSeq:WP_020204524.1
COORDINATES: similar to AA sequence:RefSeq:WP_007737228.1
COORDINATES: similar to AA sequence:RefSeq:WP_007737229.1
TadE/TadG family type IV pilus assembly protein
COORDINATES: similar to AA sequence:RefSeq:WP_006580052.1
COORDINATES: similar to AA sequence:RefSeq:WP_017775230.1
pilus assembly protein TadG-related protein
COORDINATES: similar to AA sequence:RefSeq:WP_007737233.1
COORDINATES: similar to AA sequence:RefSeq:WP_007737235.1
type II and III secretion system protein family protein
COORDINATES: similar to AA sequence:RefSeq:WP_012336892.1
COORDINATES: similar to AA sequence:RefSeq:WP_018425358.1
COORDINATES: similar to AA sequence:RefSeq:WP_007737242.1
GO:0004190 - aspartic-type endopeptidase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_014722941.1
COORDINATES: similar to AA sequence:RefSeq:WP_007737244.1
COORDINATES: protein motif:HMM:NF020419.2
nucleotidyl transferase AbiEii/AbiGii toxin family protein
COORDINATES: similar to AA sequence:RefSeq:WP_004541786.1
GO:0015074 - DNA integration [Evidence IEA]; GO:0006310 - DNA recombination [Evidence IEA]
COORDINATES: protein motif:HMM:NF013561.2
Derived by automated computational analysis using gene prediction method: tRNAscan-SE.
COORDINATES: similar to AA sequence:RefSeq:WP_004636222.1
COORDINATES: similar to AA sequence:RefSeq:WP_007182928.1
COORDINATES: similar to AA sequence:RefSeq:WP_007737252.1
COORDINATES: similar to AA sequence:RefSeq:WP_001642189.1
TrbG/VirB9 family P-type conjugative transfer protein
COORDINATES: similar to AA sequence:RefSeq:WP_019692593.1
COORDINATES: similar to AA sequence:RefSeq:WP_011694117.1
COORDINATES: similar to AA sequence:RefSeq:WP_011546597.1
COORDINATES: similar to AA sequence:RefSeq:WP_007182935.1
COORDINATES: similar to AA sequence:RefSeq:WP_007182936.1
COORDINATES: similar to AA sequence:RefSeq:WP_007182937.1
VirB3 family type IV secretion system protein
COORDINATES: protein motif:HMM:NF016820.2
COORDINATES: protein motif:HMM:NF041289.1
COORDINATES: protein motif:HMM:NF013618.2
lytic transglycosylase domain-containing protein
COORDINATES: protein motif:HMM:NF013014.2
COORDINATES: protein motif:HMM:NF019069.2
TrbM/KikA/MpfK family conjugal transfer protein
COORDINATES: similar to AA sequence:RefSeq:WP_004636892.1
COORDINATES: similar to AA sequence:RefSeq:WP_017709574.1
COORDINATES: similar to AA sequence:RefSeq:WP_017502313.1
COORDINATES: similar to AA sequence:RefSeq:WP_013699799.1
COORDINATES: similar to AA sequence:RefSeq:WP_012435532.1
COORDINATES: similar to AA sequence:RefSeq:WP_013691830.1
COORDINATES: similar to AA sequence:RefSeq:WP_011911239.1
COORDINATES: similar to AA sequence:RefSeq:WP_018099694.1
COORDINATES: similar to AA sequence:RefSeq:WP_005734896.1
COORDINATES: similar to AA sequence:RefSeq:WP_007247609.1
COORDINATES: protein motif:HMM:NF024758.2
COORDINATES: protein motif:HMM:NF025625.2
COORDINATES: similar to AA sequence:RefSeq:WP_006498694.1
sensor domain-containing diguanylate cyclase
COORDINATES: similar to AA sequence:RefSeq:WP_007182948.1
COORDINATES: similar to AA sequence:RefSeq:WP_007182949.1
COORDINATES: similar to AA sequence:RefSeq:WP_007182951.1
COORDINATES: similar to AA sequence:RefSeq:WP_007182957.1
COORDINATES: similar to AA sequence:RefSeq:WP_011879917.1
COORDINATES: protein motif:HMM:NF016975.2
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_006483353.1
COORDINATES: similar to AA sequence:RefSeq:WP_007737216.1
GO:0005524 - ATP binding [Evidence IEA]; GO:0008134 - transcription factor binding [Evidence IEA]
sigma-54 dependent transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_006051649.1
type II toxin-antitoxin system RelB/DinJ family antitoxin