LOCUS       NZ_CP083918             2857 bp    DNA     circular CON 05-NOV-2023
DEFINITION  Enterococcus faecium isolate V1225 plasmid pV1225-6, complete
            sequence.
ACCESSION   NZ_CP083918
VERSION     NZ_CP083918.1
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 2857)
  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  JOURNAL   Unpublished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 2857)
  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
            CP083918.1.
            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..2857
                     /organism="Enterococcus faecium"
                     /mol_type="genomic DNA"
                     /isolate="V1225"
                     /isolation_source="Hospitalized patient"
                     /host="Homo sapiens"
                     /db_xref="taxon:1352"
                     /plasmid="pV1225-6"
                     /geo_loc_name="Denmark"
                     /collection_date="2015"
     gene            join(2409..2857,1..526)
                     /locus_tag="LCG89_RS14865"
                     /old_locus_tag="LCG89_14865"
     CDS             join(2409..2857,1..526)
                     /locus_tag="LCG89_RS14865"
                     /old_locus_tag="LCG89_14865"
                     /inference="COORDINATES: ab initio prediction:GeneMarkS-2+"
                     /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: GeneMarkS-2+."
                     /codon_start=1
                     /transl_table=11
                     /product="replication initiation factor domain-containing
                     protein"
                     /protein_id="WP_010729436.1"
                     /translation="MGKKRTIVNEWEKLTAPSNRRLNVGESVKMIKMDWSIDRITIVGT
                     LNENIYYHTQNDVLILDFEQLMRVNEGNGHLKAVGNNGWQLVDQHEENIAYIEILKWQE
                     GKGRIDFNPNKISQFLASSMKKFIHDLFLEPHFSRADVACDLIDVPDEFITQYRVVDPV
                     SFKPIYGRSGKLETAYWGSRASERQIRMYNKKLEQEAKRKIVPKEVETWWRLELQLRRG
                     KATDWYEMVQESLDSFASPHYFPEDVKTLDRVMIKGLLYDHSEWSTISRDLKYRLRKLL
                     KQESQNDELTNHLRETFEESADELKRELDTWLLGLDVTEEEEK"
                     /name="replication initiation factor domain-containing
                     protein"
     gene            523..750
                     /locus_tag="LCG89_RS14870"
                     /old_locus_tag="LCG89_14870"
     CDS             523..750
                     /locus_tag="LCG89_RS14870"
                     /old_locus_tag="LCG89_14870"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002311817.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_010729435.1"
                     /translation="MTEKFPYEYYQNLEKLESAIQLVKLDLLDENLLKYKNITPERKGK
                     LKKMQQLFDEEDGISDVIFDTWSEFHGEYN"
                     /name="hypothetical protein"
     gene            complement(911..1327)
                     /locus_tag="LCG89_RS14875"
                     /old_locus_tag="LCG89_14875"
     CDS             complement(911..1327)
                     /locus_tag="LCG89_RS14875"
                     /old_locus_tag="LCG89_14875"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001232859.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_010729434.1"
                     /translation="MRKTSVQKHVTLYPSHVDVLDSIIERNPDINNYSEAIRFLCMSYE
                     PDTNTTTTSNQAKLNAMGKEISIMSEIIAEFADLYLKDTGVLIGTNSKVYQEVKEKTEA
                     KLNPSNRNRPKNHQKETSQTVTSRNFDPTNFLKR"
                     /name="hypothetical protein"
     gene            complement(1329..1610)
                     /locus_tag="LCG89_RS14880"
                     /old_locus_tag="LCG89_14880"
     CDS             complement(1329..1610)
                     /locus_tag="LCG89_RS14880"
                     /old_locus_tag="LCG89_14880"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002347307.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_010729433.1"
                     /translation="MDILVRKIDSKVIAKIDKRCQELTNKTGKKWSRNKYLKVLIESDF
                     DRQLTTYKKDQFDLLLEKFIAIQTKNTQVLNDYVHTNNQLIETLIGGK"
                     /name="hypothetical protein"
ORIGIN
        1 tgatgagttt attacacaat atcgtgtagt tgaccctgtg tccttcaaac caatttatgg
       61 acgctctggt aagctagaaa cggcttattg gggtagtcgt gccagcgaac gccaaattcg
      121 gatgtacaac aagaagttgg aacaggaagc aaagcgaaaa attgtaccta aagaagtcga
      181 gacgtggtgg cgtttggagt tacaattgcg ccgtggaaaa gcgactgatt ggtatgagat
      241 ggttcaagaa agtttggata gttttgctag tccgcattat tttcctgaag atgtaaaaac
      301 gttggataga gtgatgataa aggggttgtt gtatgaccat tctgagtggt caactattag
      361 tcgtgacttg aaatatcggc taaggaaatt gctgaagcaa gaaagtcaaa atgatgaatt
      421 gacgaatcat ttacgagaaa catttgagga gtctgcagac gaattaaaaa gagaattgga
      481 tacatggctt ttaggtttag atgtgacaga ggaggaagaa aaatgactga gaaatttcca
      541 tacgagtatt atcaaaatct agaaaaattg gagagtgcta ttcagttggt caagctggat
      601 ttgttggatg agaatttact aaaatacaaa aatattacgc cagagagaaa gggtaaattg
      661 aaaaaaatgc agcaattatt tgatgaagaa gatggaattt cagatgtgat ttttgataca
      721 tggagcgaat ttcatggaga atataattag cgaagttagg aattgtggta gctttcagaa
      781 aatgcaaaaa gaagaagtcg cgtgagcggc ttcttctttt ccgcaagtta ccggtaactt
      841 gcaaatcttg ctgtaagacc ggctttccta aaaaataaaa cgagaaataa aaaaattctc
      901 gttttatttt ttagcgtttt agaaaatttg ttgggtcgaa atttctagaa gtgactgttt
      961 gactcgtttc tttttgatga ttctttggtc gatttcgatt cgacggattt agtttagctt
     1021 cggttttttc tttcacttct tgatacactt tagaatttgt gccaataaga acgcctgtat
     1081 cttttagata taaatcagca aattctgcaa tgatttcgga catgatggaa atttcttttc
     1141 ccatagcatt tagtttggct tgattgctgg tagtagtcgt gttggtatca ggttcataac
     1201 tcatacataa aaaacgaatg gcttccgagt aattgttgat atctggattt ctttcgataa
     1261 tggaatctaa aacgtccacg tgactgggat aaagggtaac gtgtttttga acagaagttt
     1321 ttctcatgct attttcctcc aataagtgtt tcaataagtt gattatttgt atgaacatag
     1381 tcgtttagta cttgagtgtt ttttgtctga atagcgataa atttttcgag taataaatcg
     1441 aattggtctt ttttgtaagt cgtaagttga cggtcaaaat cactttcgat taaaactttt
     1501 agatatttat ttcgactcca ttttttgcca gttttatttg tgagttcttg gcaacgtttg
     1561 tctatttttg caataacctt tgaatcaatc ttccgaacta aaatgtccat agaaaaactc
     1621 ctttcgcatt tgtgtataat ttatgtatat catacgaata tagtatttgt atagctgttt
     1681 tttgctgaaa cactatacat aagctagtca caatggcgaa aaagtgatat caaatttttt
     1741 tcttagaaac gtgataggca cagcctatct gcccgctttt tttagaaagt gggtacacgt
     1801 ttccttatgc tctttaaaaa aatgttgatg tgcgactttt ttctgcttat aaaaataaaa
     1861 aaagtttacg gaaatgatgt caaattgaac gattatgatg agcatataat caagatgaaa
     1921 tgattttata agcgtgtatt ttgcgttcta agacgtttta gcgttcattt cgtttagttg
     1981 tcggcacaat cggtaaaaca cgtaagagaa gcgagaatgg agcctgtaag gcgactggta
     2041 gcgaaacggc gtgttagatt gtgaaagccg agaactgaat gaaatgaaga gcggaagcgt
     2101 gaaatgattt cggcaggagg aggctcaagg ggttcgggga atgaaattcc ctgaggtctt
     2161 tttatttttt taagaggagt gctataatca aagaaaacga gaaaaaagag caaaaaaata
     2221 gtcgagcagt gcgctaacac tctcgacctt tacggaaact actagcctag ttccgtaact
     2281 caagttcatt atacgaatat ttttaggttt cttcaagcta gagatttttg gatgtggatt
     2341 tttagagtta cgtgaactct ggaaattctt tccaaaaatc tctttttttc tttgaggagg
     2401 aacaaaattt gggtaaaaaa agaacaattg tgaatgagtg ggaaaaatta acagccccct
     2461 ctaacaggcg gttaaatgtc ggtgagagcg taaaaatgat aaaaatggat tggtcgattg
     2521 accgaattac gattgtcgga actttgaatg aaaatattta ttatcacact caaaatgatg
     2581 tgttgatttt agattttgag caattaatgc gagtgaacga aggtaatggt catttaaaag
     2641 ctgttgggaa taatggttgg caattggtag atcaacacga agaaaatatt gcctatatcg
     2701 aaattttgaa atggcaagag ggtaaagggc ggattgactt taaccccaat aaaattagtc
     2761 aatttttagc aagctctatg aaaaaattta ttcatgattt atttttagag ccccattttt
     2821 cacgagcgga tgttgcctgc gatcttattg atgtgcc
//
