LOCUS       NZ_CP083916             3200 bp    DNA     circular CON 05-NOV-2023
DEFINITION  Enterococcus faecium isolate V1225 plasmid pV1225-4, complete
            sequence.
ACCESSION   NZ_CP083916
VERSION     NZ_CP083916.1
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 3200)
  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  JOURNAL   Unpublished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 3200)
  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
            CP083916.1.
            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..3200
                     /organism="Enterococcus faecium"
                     /mol_type="genomic DNA"
                     /isolate="V1225"
                     /isolation_source="Hospitalized patient"
                     /host="Homo sapiens"
                     /db_xref="taxon:1352"
                     /plasmid="pV1225-4"
                     /geo_loc_name="Denmark"
                     /collection_date="2015"
     gene            complement(join(2850..3200,1..66))
                     /locus_tag="LCG89_RS14820"
                     /old_locus_tag="LCG89_14820"
     CDS             complement(join(2850..3200,1..66))
                     /locus_tag="LCG89_RS14820"
                     /old_locus_tag="LCG89_14820"
                     /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_001232859.1"
                     /translation="MRKTSVQKHVTLYPSHVDVLDSIIEKNPDINNYSEAIRFLCMSYE
                     PDTNTTTTSNQAKLNAMGKEISIMTEIIAEFADLYLKDTGVLIGTNSKVYQEVKEKIEA
                     KLNPSNRNRPKNHQKETSQTVTSRNFDPTNFLKR"
                     /name="hypothetical protein"
     gene            complement(69..353)
                     /locus_tag="LCG89_RS14825"
                     /old_locus_tag="LCG89_14825"
     CDS             complement(69..353)
                     /locus_tag="LCG89_RS14825"
                     /old_locus_tag="LCG89_14825"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002337999.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_000353844.1"
                     /translation="MDILVRNIDPKFVATIDKRCQELTNKTGEKWSRNKYLKVLIESDF
                     DRQLTTYKKDQFDLLLDKFIAIQTENTQILSEYVYTNNQIIEMLIGGMI"
                     /name="hypothetical protein"
     gene            720..944
                     /locus_tag="LCG89_RS14830"
                     /old_locus_tag="LCG89_14830"
     CDS             720..944
                     /locus_tag="LCG89_RS14830"
                     /old_locus_tag="LCG89_14830"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000410576.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_000410576.1"
                     /translation="MEKFPYEYFQNLEKLEQAIQAIKFDLTDEKLLEYKNMTPERKRSL
                     EKLMQLVNEDGGISDAAFDAWSEFHGEYN"
                     /name="hypothetical protein"
     gene            1994..2713
                     /locus_tag="LCG89_RS14840"
                     /old_locus_tag="LCG89_14840"
     CDS             1994..2713
                     /locus_tag="LCG89_RS14840"
                     /old_locus_tag="LCG89_14840"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002311815.1"
                     /GO_function="GO:0003887 - DNA-directed DNA polymerase
                     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 protein"
                     /protein_id="WP_002311815.1"
                     /translation="MDEKTELTVKYQNELNLVPLKNFNAKQMDLFFALCARMKDRGLKK
                     VRFSFEELKELSDYKMTATKAFVGDLEKLYKDMLNLTYRTEDEDSIRYFVLFTGFEINK
                     TKKFVEVSVNPDLEYIINGLTAEFSRFELSAFTSLRSTYAKTLFRLLMQYRSTGYYVVR
                     IEEFRSLMDIPEYYQMGNIDQKVLNPALRELKKYFNDLKVTKIKAKKGNKIAKLEFTFS
                     SLTSDLPKISLRNWLEE"
                     /name="replication initiation protein"
     Typing          1995..2713
                     /name="rep_cluster_1763"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 ggaatctaaa acgtcaacat gactagggta caaagtaaca tgtttttgga cagaagtttt
       61 tctcatggtt atatcattcc tccgataagc atttcaatga tttgattatt tgtgtagaca
      121 tactcgctta atatttgagt attttctgtt tggatagcaa taaatttatc gagcaataaa
      181 tcgaattggt cttttttgta agtcgtaagt tgacggtcaa aatcactttc gattaaaact
      241 tttagatatt tatttcgact ccatttttct cctgttttat tcgtgagttc ttggcaacgt
      301 ttgtctattg ttgcaacaaa ctttggatca atattccgaa ctaaaatgtc cataaaaaat
      361 ctccttttgc aattatgtat aatttatgta taccatacaa atactatatt tgtatagctg
      421 ttttttgcca aaatgctata cataagctac ccacgatggc gaaaaagtga tatcaaattt
      481 ttttctgaga aacgtgatag gcacagccta tctacccact ttttttagaa agtgggtaca
      541 cgtttcctta tgctctttaa aattcggggg gggagtgctg cacgtgtaat cgataaccaa
      601 atttaaaaat gcacgatcaa aaatttattt agtttttcaa acgacatttt ttttgagagt
      661 atagacggca aagaagtgat tttatttcta gaaaaattgt gagactggag aaagaaaaaa
      721 tggaaaaatt tccttacgaa tattttcaaa acttagaaaa attagagcaa gcaattcaag
      781 caatcaagtt cgatttaaca gacgaaaaat tgttggaata taaaaatatg acacccgaaa
      841 gaaaacgatc gttggaaaaa ttaatgcaac tagtgaacga agacggcgga atttcagacg
      901 cagcttttga cgcatggagc gaatttcatg gagaatataa ttaagtgggt ttaaatggct
      961 ctaaaatcgc ttctaagagt tttttagctt ggaccaatga aatacaccaa aaactaaata
     1021 aaacgtctta aatcgaaaaa tacgagctct cagagcgact ttatttgtaa atgttgcata
     1081 taagaaataa ttacggattt tagacttttg taggatattt ttgaaataaa tatttatttc
     1141 tgttataatt tgattgcaaa taagtgaaca cgaaacacac gaaagcccca gagaggtcgg
     1201 attctctggg gctttttttg tgggctgagt cgccttaatt aagttttact tcttgtttcg
     1261 gttattcaac cagtaactga acaaagcgct taaaagccca acaagaaggg agcaaataaa
     1321 gttagtgaac acgaaacaca cctccttcca gtcgcaagac tgtcggatag gcgacaatca
     1381 attatacaat aaaaaagcaa aaataagcct aagtttttta ttgccttggg gttgttaggg
     1441 cttgccctga ccgcctgtaa ggcgctttag aacgaaggac atagttttta tcgaatcttg
     1501 tcttagaacg gcttagacga gctctcagga cgccacaaag gagtccctaa tgaattattt
     1561 ttggcgaagg agcctaaagg cgactgctgc aagtaaaatg tgagagcgta gcgatcactc
     1621 cttcttacag cgaccatagg gagctagatt ggcagtttaa tatcatgcgc gaacctgttt
     1681 attttaaaaa gtgggtgatt ttttggcggg aaattttgct cgcgcgcgcg cgtttatttt
     1741 atttattttt taaagatttt ttagaaccct ttttaggggg cagttgagcc ttactctccc
     1801 aacggataca gaagggtact aacaactttt tatctgagta ctaacaactt tttatctgag
     1861 tactaacaac tttttatctg agtactaaca actttttatc tgagtactaa tatccttttg
     1921 tataataaca accaacctat ttacgagttg gttgttaaag gttattattt atttgtaagg
     1981 ggggaagaaa ggaatggatg aaaaaacgga attaacagtc aaatatcaaa atgaattgaa
     2041 tttagtaccg ctgaaaaatt tcaatgctaa gcagatggat ttattttttg cattatgcgc
     2101 tcgtatgaaa gatcgtggtt tgaaaaaagt tagattttct ttcgaggaat taaaagagtt
     2161 aagtgattat aagatgactg ctacaaaagc ctttgtcggt gatttagaaa agctctataa
     2221 agatatgctt aatcttactt accgtactga agatgaggat tctattcgct actttgtttt
     2281 gtttactggt tttgaaatca ataaaacaaa aaagtttgtt gaagtcagtg ttaatccgga
     2341 cctagaatat attattaatg gtttaacagc tgaatttagt agatttgaat tatctgcttt
     2401 cacgtcgttg cgttctacgt atgcaaaaac tctattccga ctgcttatgc agtaccgttc
     2461 tactggttat tatgtagttc gtattgaaga gtttaggagc ttaatggata tcccagaata
     2521 ctatcaaatg ggtaacattg atcaaaaagt attaaatcct gcattacgag aactaaaaaa
     2581 atacttcaat gatcttaaag tcacaaaaat aaaagcaaaa aagggcaata aaatcgccaa
     2641 attagaattt actttttcaa gcctaacgtc agatttgcca aagatttctc tgcgtaactg
     2701 gttagaagaa taaataaaaa agaactcgcc ccccttacat taagcaagta gacaagtccc
     2761 ttacaaccga ctaagattgc tagtacattc tagcatattg tatggggctt ctaaataaaa
     2821 aacagatagg aataactcct atctgttttt tatcgtttta gaaaatttgt tgggtcgaaa
     2881 tttctagaag tgactgtttg actggtttct ttttgatgat tctttggtcg atttcgattt
     2941 gatggattta gtttagcttc gattttttct ttcacttctt gatatacttt agaatttgtg
     3001 ccaataagaa cgcctgtatc ttttagatat aaatcagcaa attctgcgat gatttcagtc
     3061 atgatggaaa tttcttttcc catagcattt agttttgcct gattgctggt agtggtcgtg
     3121 ttggtatcgg gttcataact catacataaa aagcgaatgg cttccgagta gttattgata
     3181 tctggatttt tttcgatgat
//
