Comamonas thiooxydans strain NR4028 plasmid pNR4028_IMP1, complete sequence.
Bacteria; Pseudomonadota; Betaproteobacteria; Burkholderiales; Comamonadaceae; Comamonas.
Comamonas thiooxydans Expressing a Plasmid-Encoded IMP-1 Carbapenemase Isolated From Continuous Ambulatory Peritoneal Dialysis of an Inpatient in Japan
DOI:10.3389/fmicb.2022.808993 Publication Status: Online-Only
Submitted (22-OCT-2021) Contact:Yuki Suzuki Nara Medical University, Microbiology and Infectious Diseases; Shijo-cho 840, Kashihara, Nara 6348521, Japan
REFSEQ INFORMATION: The reference sequence is identical to\nAP025194.1.\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 :: Unicycler v. 0.4.9\nGenome Coverage :: 170x\nSequencing Technology :: llumina MiSeq; Nanopore MinION\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 03/27/2023 02:52:34\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) :: 5,202\nCDSs (total) :: 5,069\nGenes (coding) :: 4,988\nCDSs (with protein) :: 4,988\nGenes (RNA) :: 133\nrRNAs :: 9, 9, 9 (5S, 16S, 23S)\ncomplete rRNAs :: 9, 9, 9 (5S, 16S, 23S)\ntRNAs :: 103\nncRNAs :: 3\nPseudo Genes (total) :: 81\nCDSs (without protein) :: 81\nPseudo Genes (ambiguous residues) :: 0 of 81\nPseudo Genes (frameshifted) :: 39 of 81\nPseudo Genes (incomplete) :: 59 of 81\nPseudo Genes (internal stop) :: 17 of 81\nPseudo Genes (multiple problems) :: 26 of 81\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.
COORDINATES: similar to AA sequence:RefSeq:WP_011052942.1
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_013124620.1
COORDINATES: similar to AA sequence:RefSeq:WP_024945956.1
GO:0004803 - transposase activity [Evidence IEA]
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:YP_005221000.1
IS6-like element IS26 family transposase
COORDINATES: similar to AA sequence:RefSeq:WP_060614779.1
subclass B1 metallo-beta-lactamase IMP-1
COORDINATES: similar to AA sequence:RefSeq:WP_015063357.1
quaternary ammonium compound efflux SMR transporter QacG2
COORDINATES: similar to AA sequence:RefSeq:WP_048608579.1
ANT(3'')-Ia family aminoglycoside nucleotidyltransferase AadA6
COORDINATES: similar to AA sequence:RefSeq:WP_000679427.1
quaternary ammonium compound efflux SMR transporter QacE delta 1
COORDINATES: similar to AA sequence:RefSeq:WP_000259031.1
sulfonamide-resistant dihydropteroate synthase Sul1
COORDINATES: similar to AA sequence:RefSeq:WP_004194535.1
COORDINATES: similar to AA sequence:RefSeq:WP_001381192.1
COORDINATES: similar to AA sequence:RefSeq:WP_013124600.1
GO:0015074 - DNA integration [Evidence IEA]
DDE-type integrase/transposase/recombinase
COORDINATES: similar to AA sequence:RefSeq:YP_005229646.1
COORDINATES: similar to AA sequence:RefSeq:WP_019939714.1
COORDINATES: similar to AA sequence:RefSeq:WP_018413487.1
GDCCVxC domain-containing (seleno)protein
COORDINATES: similar to AA sequence:RefSeq:WP_020651365.1
COORDINATES: similar to AA sequence:RefSeq:WP_013723315.1
COORDINATES: similar to AA sequence:RefSeq:WP_011799426.1
COORDINATES: similar to AA sequence:RefSeq:WP_004348419.1
helix-turn-helix transcriptional regulator
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: protein motif:HMM:NF037437.2
COORDINATES: similar to AA sequence:RefSeq:WP_005796449.1
COORDINATES: similar to AA sequence:RefSeq:WP_015060658.1
GO:0006313 - transposition, DNA-mediated [Evidence IEA]
frameshifted; 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_012435588.1
COORDINATES: similar to AA sequence:RefSeq:WP_015557125.1
COORDINATES: similar to AA sequence:RefSeq:WP_006103262.1
COORDINATES: similar to AA sequence:RefSeq:WP_021138877.1
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_018746197.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0000150 - DNA strand exchange activity [Evidence IEA]
GO:0006310 - DNA recombination [Evidence IEA]
frameshifted; incomplete; partial in the middle of a contig; missing N-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
helix-turn-helix domain-containing protein
COORDINATES: protein motif:HMM:NF024555.2
COORDINATES: similar to AA sequence:RefSeq:WP_011803789.1
frameshifted; Derived by automated computational analysis using gene prediction method: Protein Homology.
IS110-like element ISAisp4 family transposase
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_013124612.1
COORDINATES: similar to AA sequence:RefSeq:WP_013124613.1
COORDINATES: similar to AA sequence:RefSeq:WP_018413495.1
COORDINATES: similar to AA sequence:RefSeq:WP_013124615.1
COORDINATES: similar to AA sequence:RefSeq:WP_005918230.1
COORDINATES: similar to AA sequence:RefSeq:WP_005918229.1
COORDINATES: similar to AA sequence:RefSeq:WP_018413498.1
ParC family partition-associated protein