Enterococcus saigonensis strain VE80 plasmid pVE80-1, complete sequence.
Bacteria; Bacillota; Bacilli; Lactobacillales; Enterococcaceae; Enterococcus.
Characterization of vanA genotype vancomycin-resistant Enterococcus saigonensis VE80
Submitted (26-FEB-2020) Contact:Tetsuya Harada Osaka Institute of Public Health, Division of Bacteriology; Nakamichi 1-3-69,Higashinari-ku, Osaka, Osaka 537-0025, Japan
REFSEQ INFORMATION: The reference sequence is identical to\nAP022823.1.\nAnnotated at DFAST https://dfast.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. 3.0\nGenome Coverage :: 213x\nSequencing Technology :: PacBio RS II\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 12/27/2022 03:19:34\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) :: 2,765\nCDSs (total) :: 2,679\nGenes (coding) :: 2,642\nCDSs (with protein) :: 2,642\nGenes (RNA) :: 86\nrRNAs :: 6, 6, 6 (5S, 16S, 23S)\ncomplete rRNAs :: 6, 6, 6 (5S, 16S, 23S)\ntRNAs :: 64\nncRNAs :: 4\nPseudo Genes (total) :: 37\nCDSs (without protein) :: 37\nPseudo Genes (ambiguous residues) :: 0 of 37\nPseudo Genes (frameshifted) :: 15 of 37\nPseudo Genes (incomplete) :: 26 of 37\nPseudo Genes (internal stop) :: 6 of 37\nPseudo Genes (multiple problems) :: 10 of 37\nCRISPR Arrays :: 1\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.
COORDINATES: similar to AA sequence:RefSeq:WP_002355409.1
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_000684984.1
GO:0004803 - transposase activity [Evidence IEA]
frameshifted; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_001226076.1
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_001280781.1
vancomycin resistance response regulator transcription factor VanR-A
COORDINATES: similar to AA sequence:RefSeq:WP_002305818.1
COORDINATES: similar to AA sequence:RefSeq:WP_001059542.1
COORDINATES: similar to AA sequence:RefSeq:WP_001079845.1
GO:0008716 - D-alanine-D-alanine ligase activity [Evidence IEA]; GO:0046872 - metal ion binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_000402347.1
COORDINATES: similar to AA sequence:RefSeq:WP_001812592.1
VanY-A/VanY-F/VanY-M family D-Ala-D-Ala carboxypeptidase
COORDINATES: similar to AA sequence:RefSeq:WP_000516404.1
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 N-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
topoisomerase DNA-binding C4 zinc finger domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_011100845.1
23S rRNA (adenine(2058)-N(6))-methyltransferase Erm(B)
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_002425012.1
COORDINATES: similar to AA sequence:RefSeq:WP_002295591.1
COORDINATES: similar to AA sequence:RefSeq:WP_000713595.1
COORDINATES: similar to AA sequence:RefSeq:WP_002291321.1
frameshifted; incomplete; partial in the middle of a contig; missing C-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_002297185.1
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_002291076.1
COORDINATES: similar to AA sequence:RefSeq:WP_002291081.1
COORDINATES: similar to AA sequence:RefSeq:WP_002342352.1
SpaH/EbpB family LPXTG-anchored major pilin
COORDINATES: similar to AA sequence:RefSeq:WP_002291088.1
pilin N-terminal domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_002342351.1
SpaA isopeptide-forming pilin-related protein
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: similar to AA sequence:RefSeq:WP_002339652.1
COORDINATES: protein motif:HMM:NF012790.2
incomplete; partial in the middle of a contig; missing C-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
rhodanese-like domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_007209331.1
GO:0015036 - disulfide oxidoreductase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_002318456.1
membrane protein insertion efficiency factor YidD
COORDINATES: similar to AA sequence:RefSeq:WP_002318452.1
iron export ABC transporter permease subunit FetB
COORDINATES: similar to AA sequence:RefSeq:WP_010749154.1
ATP-binding cassette domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_002341371.1
COORDINATES: similar to AA sequence:RefSeq:WP_002337530.1
COORDINATES: similar to AA sequence:RefSeq:WP_002333827.1
COORDINATES: similar to AA sequence:RefSeq:WP_010782321.1
primase C-terminal domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_005237740.1
COORDINATES: similar to AA sequence:RefSeq:WP_002287942.1
COORDINATES: similar to AA sequence:RefSeq:WP_002316517.1
COORDINATES: similar to AA sequence:RefSeq:WP_012477736.1
IS6-like element ISS1N family transposase
COORDINATES: protein motif:HMM:NF024668.2
COORDINATES: similar to AA sequence:RefSeq:WP_002344896.1
helix-turn-helix transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_002339788.1
type II toxin-antitoxin system RelE/ParE family toxin
COORDINATES: similar to AA sequence:RefSeq:WP_002396205.1
COORDINATES: similar to AA sequence:RefSeq:WP_002340526.1
COORDINATES: similar to AA sequence:RefSeq:WP_016627749.1
GO:0015074 - DNA integration [Evidence IEA]; GO:0006310 - DNA recombination [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_003679114.1
GO:0005886 - plasma membrane [Evidence IEA]
GO:0004190 - aspartic-type endopeptidase activity [Evidence IEA]
GO:0009306 - protein secretion [Evidence IEA]; GO:0006508 - proteolysis [Evidence IEA]
COORDINATES: protein motif:HMM:NF033788.1
metalloregulator ArsR/SmtB family transcription factor
COORDINATES: similar to AA sequence:RefSeq:WP_016178609.1
COORDINATES: similar to AA sequence:RefSeq:WP_002309702.1
COORDINATES: similar to AA sequence:RefSeq:WP_005225663.1
peptidoglycan DD-metalloendopeptidase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_010076369.1
GO:0004553 - hydrolase activity, hydrolyzing O-glycosyl compounds [Evidence IEA]
GO:0005975 - carbohydrate metabolic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_076611768.1
programmed frameshift; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_002301358.1
COORDINATES: similar to AA sequence:RefSeq:WP_005876259.1
COORDINATES: similar to AA sequence:RefSeq:WP_007209263.1
COORDINATES: similar to AA sequence:RefSeq:WP_002316685.1
COORDINATES: similar to AA sequence:RefSeq:WP_002342451.1
cation diffusion facilitator family transporter
COORDINATES: similar to AA sequence:RefSeq:WP_002320189.1
CadD family cadmium resistance transporter
COORDINATES: similar to AA sequence:RefSeq:WP_002342386.1
COORDINATES: similar to AA sequence:RefSeq:WP_000587616.1
type II toxin-antitoxin system Phd/YefM family antitoxin
COORDINATES: similar to AA sequence:RefSeq:WP_010620827.1
COORDINATES: similar to AA sequence:RefSeq:WP_016177616.1
COORDINATES: similar to AA sequence:RefSeq:WP_064305258.1
IS6-like element IS1216 family transposase
COORDINATES: similar to AA sequence:RefSeq:WP_002325622.1
COORDINATES: similar to AA sequence:RefSeq:WP_010782380.1
COORDINATES: similar to AA sequence:RefSeq:WP_002326830.1
COORDINATES: similar to AA sequence:RefSeq:WP_010782381.1
COORDINATES: protein motif:HMM:NF033563.0
COORDINATES: similar to AA sequence:RefSeq:WP_002333004.1
COORDINATES: similar to AA sequence:RefSeq:WP_002343783.1
COORDINATES: similar to AA sequence:RefSeq:WP_002346504.1
TetR/AcrR family transcriptional regulator
internal stop; incomplete; partial in the middle of a contig; missing C-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
GO:0005524 - ATP binding [Evidence IEA]; GO:0016301 - kinase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_076611709.1
IS6-like element ISEnfa1 family transposase
COORDINATES: similar to AA sequence:RefSeq:WP_010294603.1
GO:0050380 - undecaprenyl-diphosphatase activity [Evidence IEA]
GO:0016311 - dephosphorylation [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_000933358.1
COORDINATES: similar to AA sequence:RefSeq:WP_018368562.1
COORDINATES: similar to AA sequence:RefSeq:WP_016897369.1
COORDINATES: similar to AA sequence:RefSeq:WP_002387760.1
COORDINATES: similar to AA sequence:RefSeq:WP_001808810.1
COORDINATES: similar to AA sequence:RefSeq:WP_002333002.1
COORDINATES: similar to AA sequence:RefSeq:WP_002401482.1