LOCUS       NZ_CP083919             1979 bp    DNA     circular CON 05-NOV-2023
DEFINITION  Enterococcus faecium isolate V1225 plasmid pV1225-7, complete
            sequence.
ACCESSION   NZ_CP083919
VERSION     NZ_CP083919.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMEA5367970
            Assembly: GCF_020162155.1
KEYWORDS    RefSeq.
SOURCE      Enterococcus faecium
  ORGANISM  Enterococcus faecium
            Bacteria; Bacillota; Bacilli; Lactobacillales; Enterococcaceae;
            Enterococcus.
REFERENCE   1  (bases 1 to 1979)
  AUTHORS   Mollerup,S., Elmeskov,C., Gumpert,H., Pinholt,M., Sejersen,T.S.,
            Pedersen,M.S., Worning,P., Frees,D. and Westh,H.
  TITLE     Rapid in vivo development of resistance to daptomycin in
            vancomycin-resistant Enterococcus faecium due to genomic
            rearrangements
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 1979)
  AUTHORS   Mollerup,S., Elmeskov,C., Gumpert,H., Pinholt,M., Sejersen,T.S.,
            Pedersen,M.S., Worning,P., Frees,D. and Westh,H.
  TITLE     Direct Submission
  JOURNAL   Submitted (17-SEP-2021) Department of Clinical Microbiology,
            Copenhagen University Hospital Hvidovre, Kettegaard Alle 30,
            Hvidovre 2650, Denmark
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Date                     :: 27-MAR-2019
            Assembly Method                   :: Unicycler v. 4.0.7
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 154x
            Sequencing Technology :: Illumina MiSeq and Oxford Nanopore MinION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 11/05/2023 01:46:48
            Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline
            (PGAP)
            Annotation Method :: Best-placed reference protein set; GeneMarkS-2+
            Annotation Software revision      :: 6.6
            Features Annotated                :: Gene; CDS; rRNA; tRNA; ncRNA
            Genes (total)                     :: 2,991
            CDSs (total)                      :: 2,899
            Genes (coding)                    :: 2,745
            CDSs (with protein)               :: 2,745
            Genes (RNA)                       :: 92
            rRNAs                             :: 6, 6, 6 (5S, 16S, 23S)
            complete rRNAs                    :: 6, 6, 6 (5S, 16S, 23S)
            tRNAs                             :: 70
            ncRNAs                            :: 4
            Pseudo Genes (total)              :: 154
            CDSs (without protein)            :: 154
            Pseudo Genes (ambiguous residues) :: 0 of 154
            Pseudo Genes (frameshifted)       :: 73 of 154
            Pseudo Genes (incomplete)         :: 75 of 154
            Pseudo Genes (internal stop)      :: 41 of 154
            Pseudo Genes (multiple problems)  :: 32 of 154
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP083919.1.
            The annotation was added by the NCBI Prokaryotic Genome Annotation
            Pipeline (PGAP). Information about PGAP can be found here:
            https://www.ncbi.nlm.nih.gov/genome/annotation_prok/
            COMPLETENESS: full length.
FEATURES             Location/Qualifiers
     source          1..1979
                     /organism="Enterococcus faecium"
                     /mol_type="genomic DNA"
                     /isolate="V1225"
                     /isolation_source="Hospitalized patient"
                     /host="Homo sapiens"
                     /db_xref="taxon:1352"
                     /plasmid="pV1225-7"
                     /geo_loc_name="Denmark"
                     /collection_date="2015"
     gene            join(1954..1979,1..>157)
                     /locus_tag="LCG89_RS14885"
                     /old_locus_tag="LCG89_14885"
                     /pseudo=""
     CDS             join(1954..1979,1..>157)
                     /locus_tag="LCG89_RS14885"
                     /old_locus_tag="LCG89_14885"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002313295.1"
                     /note="incomplete; partial in the middle of a contig;
                     missing C-terminus; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /name="hypothetical protein"
     gene            738..1754
                     /locus_tag="LCG89_RS14890"
                     /old_locus_tag="LCG89_14890"
     CDS             738..1754
                     /locus_tag="LCG89_RS14890"
                     /old_locus_tag="LCG89_14890"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002299382.1"
                     /GO_function="GO:0003677 - DNA binding [Evidence IEA];
                     GO:0003916 - DNA topoisomerase activity [Evidence IEA]"
                     /GO_process="GO:0006270 - DNA replication initiation
                     [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="replication initiation factor domain-containing
                     protein"
                     /protein_id="WP_002299382.1"
                     /translation="MANENQLSEIQSKIEGRGAEKRTTINQLEKLNRISNRRLSVQGTT
                     TPLKLNWSIDRITIVGKLNDTIAYWTKNGVVFVDFEQLMRLNENQGYLKSVGINGWQLF
                     DQYGEDIAYIEILKFHEGKGRIDFNPNKIGQFLASSMKGFIHDLFLDPHFSRADIACDI
                     VDVPDDFITQYRIVDPISFKPIYGRSGKLETAYWGSRASERQVRLYNKKLEQERKKVIV
                     PKEIDTWWRLEMQLRRGKATDWHAMVQESLDSFASPHFLPIDIKPIDKIVIDGLIAEPS
                     NWSIIARHTKYKYRNLLKQESQNDELTNHLRETFKESADELKKELDTWLLGLDVTEK"
                     /name="replication initiation factor domain-containing
                     protein"
     Typing          739..1748
                     /name="rep_cluster_935"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="92.292"
                     /coverage="99.0"
                     /evalue="0.0"
ORIGIN
        1 tttgtcaaag agtaacagaa aggtttacac tctttttatt agcgacagcg tgaaggaggg
       61 gttcacctta gggtttagta tttcgttcaa aaagggaaca aagaatacaa gcatttctca
      121 taataatcgt gagttaactg atagccaaaa aatcaatggt ttgtctggta gaaaataatt
      181 agcagattta caagtgggaa ataaaaagct gaaagaagaa aattgcattt caaactacat
      241 tttctacaat agctctaaaa tggcatattt tgcgttctga gcggttttag cgtttatttc
      301 gtttagttat cggcacaatc gttaaaacac gttagaggag cgaaaatgga gcctgtaagg
      361 cgactggtag cggaacgatc gtgttagatt gtgaaaaccg atagctgaat gaaataaaca
      421 gcgggtgcgc cctttccatt tcggcaggag gaggctcaag gggttcgggg aatgaaattc
      481 cctgaggtct ttttattttt ttaggaggag tgctataatc aaagaaaacg agaaaaaaga
      541 gcaaaataaa agccgagcag tgcgctaaca ctctcgacta tttacggaaa ctacttcacc
      601 tagctccgta actcaggttc attatacgaa tatttttagg tttcttcaag ctagagattt
      661 ttggatatga atttttaggg ttacgtgaac tctggaaatt ctttccaaaa gtctcttttt
      721 tcgtttggag gacgaaaatg gcaaatgaaa atcagttgag tgaaattcaa tcaaaaattg
      781 aaggtcgagg ggcagaaaaa agaacaacga taaatcagct cgaaaaactt aaccgtattt
      841 ctaacaggcg gttaagtgtg caaggtacga ccacccccct aaaattaaat tggtcgattg
      901 atcgaattac aattgtcgga aaactgaatg ataccatagc ttattggacg aaaaatggag
      961 ttgtttttgt cgatttcgag caattaatgc gtttgaacga aaatcaggga tatttgaaat
     1021 cagttgggat aaacggctgg caattattcg atcaatatgg agaagatatt gcgtatatcg
     1081 aaatacttaa atttcatgaa ggaaaaggtc gtattgattt taatccgaat aagataggcc
     1141 agtttttagc tagttccatg aaaggattca ttcatgacct atttttagat ccgcattttt
     1201 cccgggcgga tattgcctgc gatattgtag atgtgccgga tgactttatt actcagtatc
     1261 gtattgtaga cccgatttct tttaagccaa tctacggccg ttctggcaag ctagaaacag
     1321 cgtactgggg cagtcgtgcc agtgagcgcc aagtgcgact gtacaacaaa aagctagagc
     1381 aggaacgaaa aaaagtaatc gtgccaaaag aaatcgatac gtggtggcgg ttagaaatgc
     1441 agctaagacg tggcaaagca acggattggc atgcgatggt tcaggaaagc ttagatagtt
     1501 ttgcaagccc gcattttttg ccgattgata taaaacctat tgataaaata gttattgatg
     1561 gtttgatagc tgagccttct aattggtcga taattgctag acatacaaaa tataaatatc
     1621 ggaatttgct gaagcaagaa agtcaaaatg atgagttaac gaatcattta cgagagactt
     1681 ttaaggaatc tgcagacgaa ttaaaaaaag aattggatac gtggcttttg gggttggatg
     1741 tgacagagaa gtgataccga ataagaaaag tcagatgagt gagagtggat ttgcgtcaat
     1801 gtttagtgac gtaaattcac gataagcgaa tattttgcat gaagcaaaat aaagcgtaaa
     1861 aggagttgag agcgtgacac gctttcggct ccttttttcg ttgtcacttg tgacagcgaa
     1921 taccctcgga gagcatttgg aattgtgaca gccatgtcac aattaggaaa atgttactc
//
