Enterococcus raffinosus strain F162_2 plasmid pF162_2_2, complete sequence.
Bacteria; Bacillota; Bacilli; Lactobacillales; Enterococcaceae; Enterococcus.
Molecular characteristics of optrA- or poxtA-carrying Enterococci originating from river water in Switzerland
Submitted (06-APR-2021) Institute for Food Safety and Hygiene, University of Zurich, Winterthurerstrasse 272, Zurich 8057, Switzerland
REFSEQ INFORMATION: The reference sequence is identical to\nCP072890.1.\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 Method :: Unicycler v. 0.4.8\nGenome Representation :: Full\nExpected Final Version :: Yes\nGenome Coverage :: 100x\nSequencing Technology :: Illumina MiniSeq, Oxford Nanopore MiniION\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 04/29/2023 05:05:27\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) :: 4,126\nCDSs (total) :: 4,033\nGenes (coding) :: 3,983\nCDSs (with protein) :: 3,983\nGenes (RNA) :: 93\nrRNAs :: 6, 6, 6 (5S, 16S, 23S)\ncomplete rRNAs :: 6, 6, 6 (5S, 16S, 23S)\ntRNAs :: 71\nncRNAs :: 4\nPseudo Genes (total) :: 50\nCDSs (without protein) :: 50\nPseudo Genes (ambiguous residues) :: 0 of 50\nPseudo Genes (frameshifted) :: 22 of 50\nPseudo Genes (incomplete) :: 20 of 50\nPseudo Genes (internal stop) :: 12 of 50\nPseudo Genes (multiple problems) :: 3 of 50\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_002325622.1
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_010717195.1
COORDINATES: similar to AA sequence:RefSeq:WP_002332653.1
COORDINATES: similar to AA sequence:RefSeq:WP_002371376.1
COORDINATES: similar to AA sequence:RefSeq:WP_002298870.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0000150 - DNA strand exchange activity [Evidence IEA]
GO:0006310 - DNA recombination [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_002311006.1
frameshifted; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_000868795.1
trimethoprim-resistant dihydrofolate reductase DfrG
COORDINATES: similar to AA sequence:RefSeq:WP_017431446.1
COORDINATES: similar to AA sequence:RefSeq:WP_000922261.1
internal stop; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_016618837.1
GO:0005524 - ATP binding [Evidence IEA]; GO:0016887 - ATP hydrolysis activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_002281263.1
COORDINATES: similar to AA sequence:RefSeq:WP_019722544.1
COORDINATES: similar to AA sequence:RefSeq:WP_016621797.1
GO:0110001 - toxin-antitoxin complex [Evidence IEA]
type II toxin-antitoxin system Phd/YefM family antitoxin
COORDINATES: similar to AA sequence:RefSeq:WP_016629602.1
COORDINATES: similar to AA sequence:RefSeq:WP_005237640.1
COORDINATES: similar to AA sequence:RefSeq:WP_010782321.1
primase C-terminal domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_002333827.1
COORDINATES: similar to AA sequence:RefSeq:WP_064305258.1
frameshifted; internal stop; 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_000713595.1
COORDINATES: similar to AA sequence:RefSeq:WP_002333458.1
COORDINATES: similar to AA sequence:RefSeq:WP_000108743.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0003916 - DNA topoisomerase activity [Evidence IEA]
GO:0006265 - DNA topological change [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_000323438.1
COORDINATES: similar to AA sequence:RefSeq:WP_000136908.1
GO:0000150 - DNA strand exchange activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_018579902.1
helix-turn-helix transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_002328890.1
nucleotidyltransferase domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_016250180.1
GO:0008168 - methyltransferase activity [Evidence IEA]; GO:0008757 - S-adenosylmethionine-dependent methyltransferase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_003109014.1
aminoglycoside nucleotidyltransferase ANT(6)-Ia
COORDINATES: similar to AA sequence:RefSeq:WP_002294507.1
GO:0009116 - nucleoside metabolic process [Evidence IEA]
phosphoribosyltransferase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_002294509.1
ANT(9) family aminoglycoside nucleotidyltransferase Spw
COORDINATES: similar to AA sequence:RefSeq:WP_002294510.1
COORDINATES: similar to AA sequence:RefSeq:WP_002325145.1
COORDINATES: similar to AA sequence:RefSeq:WP_000301253.1
incomplete; partial in the middle of a contig; missing N-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
recombinase zinc beta ribbon domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_002294513.1
ABC-F type ribosomal protection protein Lsa(E)
COORDINATES: similar to AA sequence:RefSeq:WP_002294514.1
lincosamide nucleotidyltransferase Lnu(B)
COORDINATES: similar to AA sequence:RefSeq:WP_000627290.1
GO:0008080 - N-acetyltransferase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_032491780.1
aminoglycoside O-phosphotransferase APH(3')-IIIa
COORDINATES: similar to AA sequence:RefSeq:WP_000502600.1
COORDINATES: similar to AA sequence:RefSeq:WP_001814874.1
GO:0046677 - response to antibiotic [Evidence IEA]
23S rRNA methyltransferase attenuation leader peptide
COORDINATES: similar to AA sequence:RefSeq:WP_011100845.1
23S rRNA (adenine(2058)-N(6))-methyltransferase Erm(B)
topoisomerase DNA-binding C4 zinc finger domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_002355409.1
COORDINATES: similar to AA sequence:RefSeq:WP_002401482.1
COORDINATES: similar to AA sequence:RefSeq:WP_002333002.1
COORDINATES: similar to AA sequence:RefSeq:WP_010782381.1
GO:0005524 - ATP binding [Evidence IEA]; GO:0016301 - kinase activity [Evidence IEA]