Pandoraea commovens strain LB-19-202-79 plasmid unnamed, complete sequence.
Bacteria; Pseudomonadota; Betaproteobacteria; Burkholderiales; Burkholderiaceae; Pandoraea.
Multi-unit outbreak of Pandoraea commovens among non-cystic fibrosis intensive care patients from 2019 to 2021 in Berlin, Germany
Submitted (12-AUG-2022) Bioinformatics, Labor Berlin - Charite Vivantes GmbH, Sylter Str. 2, Berlin 13353, Germany
REFSEQ INFORMATION: The reference sequence is identical to\nCP102779.1.\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 Date :: 28-JUL-2022\nAssembly Method :: Flye v. 2.9; Racon v. 1.4.20; Medaka v.\n 1.4.3; Polypolish v. 0.5.0\nAssembly Name :: LB-19-202-79_ONT\nGenome Representation :: Full\nExpected Final Version :: Yes\nGenome Coverage :: 80.0x\nSequencing Technology :: Oxford Nanopore GridION; Illumina MiSeq\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 08/17/2022 08:58:28\nAnnotation Pipeline :: NCBI Prokaryotic Genome\n Annotation Pipeline (PGAP)\nAnnotation Method :: Best-placed reference protein\n set; GeneMarkS-2+\nAnnotation Software revision :: 6.2\nFeatures Annotated :: Gene; CDS; rRNA; tRNA; ncRNA;\n repeat_region\nGenes (total) :: 5,374\nCDSs (total) :: 5,292\nGenes (coding) :: 5,214\nCDSs (with protein) :: 5,214\nGenes (RNA) :: 82\nrRNAs :: 4, 4, 4 (5S, 16S, 23S)\ncomplete rRNAs :: 4, 4, 4 (5S, 16S, 23S)\ntRNAs :: 66\nncRNAs :: 4\nPseudo Genes (total) :: 78\nCDSs (without protein) :: 78\nPseudo Genes (ambiguous residues) :: 0 of 78\nPseudo Genes (frameshifted) :: 7 of 78\nPseudo Genes (incomplete) :: 67 of 78\nPseudo Genes (internal stop) :: 8 of 78\nPseudo Genes (multiple problems) :: 4 of 78\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_012211050.1
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: protein motif:HMM:NF018154.2
COORDINATES: similar to AA sequence:RefSeq:WP_012211044.1
COORDINATES: similar to AA sequence:RefSeq:WP_018431518.1
COORDINATES: similar to AA sequence:RefSeq:WP_012464968.1
lytic transglycosylase domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_012211040.1
COORDINATES: similar to AA sequence:RefSeq:WP_012211039.1
COORDINATES: similar to AA sequence:RefSeq:WP_012211038.1
type-F conjugative transfer system pilin assembly protein TrbC
COORDINATES: similar to AA sequence:RefSeq:WP_012211037.1
COORDINATES: similar to AA sequence:RefSeq:WP_012211036.1
TraE/TraK family type IV conjugative transfer system protein
COORDINATES: similar to AA sequence:RefSeq:WP_012464969.1
type-F conjugative transfer system secretin TraK
COORDINATES: similar to AA sequence:RefSeq:WP_012211034.1
COORDINATES: protein motif:HMM:NF021212.2
COORDINATES: similar to AA sequence:RefSeq:WP_009688617.1
COORDINATES: similar to AA sequence:RefSeq:WP_012211032.1
COORDINATES: similar to AA sequence:RefSeq:WP_012211031.1
GO:0004252 - serine-type endopeptidase activity [Evidence IEA]
GO:0009306 - protein secretion [Evidence IEA]; GO:0006465 - signal peptide processing [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_012211030.1
COORDINATES: similar to AA sequence:RefSeq:WP_012211029.1
COORDINATES: protein motif:HMM:NF019530.2
conjugal transfer protein TraG N-terminal domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_009688625.1
COORDINATES: similar to AA sequence:RefSeq:WP_012464970.1
COORDINATES: similar to AA sequence:RefSeq:WP_012211026.1
COORDINATES: similar to AA sequence:RefSeq:WP_012464971.1
COORDINATES: similar to AA sequence:RefSeq:WP_012211024.1
COORDINATES: protein motif:HMM:NF009018.0
COORDINATES: similar to AA sequence:RefSeq:WP_012211015.1
COORDINATES: similar to AA sequence:RefSeq:WP_009687089.1
type IV secretion system DNA-binding domain-containing protein
COORDINATES: protein motif:HMM:NF023926.2
COORDINATES: protein motif:HMM:NF023505.2
ParB/RepB/Spo0J family partition protein
COORDINATES: similar to AA sequence:RefSeq:WP_008905698.1
COORDINATES: similar to AA sequence:RefSeq:WP_011899462.1
COORDINATES: similar to AA sequence:RefSeq:WP_016053837.1
GO:0008168 - methyltransferase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_009890595.1
COORDINATES: similar to AA sequence:RefSeq:WP_011875889.1
COORDINATES: protein motif:HMM:NF024212.2
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_006029257.1
COORDINATES: similar to AA sequence:RefSeq:WP_003262797.1
type II toxin-antitoxin system YafQ family toxin
COORDINATES: similar to AA sequence:RefSeq:WP_018444257.1
type II toxin-antitoxin system RelB/DinJ family antitoxin
COORDINATES: similar to AA sequence:RefSeq:WP_008917785.1
COORDINATES: similar to AA sequence:RefSeq:WP_009206952.1
COORDINATES: protein motif:HMM:NF012798.2
COORDINATES: similar to AA sequence:RefSeq:WP_011930841.1
COORDINATES: similar to AA sequence:RefSeq:WP_021138877.1
GO:0004803 - transposase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_016236504.1
COORDINATES: similar to AA sequence:RefSeq:WP_005799928.1
cation diffusion facilitator family transporter
COORDINATES: similar to AA sequence:RefSeq:WP_002717468.1
GO:0022857 - transmembrane transporter activity [Evidence IEA]
GO:0055085 - transmembrane transport [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_000118563.1
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_008434970.1
GO:0042625 - ATPase-coupled ion transmembrane transporter activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_008063281.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0003700 - DNA-binding transcription factor activity [Evidence IEA]; GO:0046872 - metal ion binding [Evidence IEA]
GO:0045893 - positive regulation of DNA-templated transcription [Evidence IEA]
Cd(II)/Pb(II)-responsive transcriptional regulator