LOCUS       NZ_CP083929             1979 bp    DNA     circular CON 05-NOV-2023
DEFINITION  Enterococcus faecium isolate V1164 plasmid pV1164-9, complete
            sequence.
ACCESSION   NZ_CP083929
VERSION     NZ_CP083929.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMEA5367917
            Assembly: GCF_020162175.1
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  JOURNAL   Unpublished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                     :: 03-JAN-2019
            Assembly Method                   :: Unicycler v. 4.0.7
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 254.19410228420895x
            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 01:58:33
            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)                     :: 2,998
            CDSs (total)                      :: 2,907
            Genes (coding)                    :: 2,780
            CDSs (with protein)               :: 2,780
            Genes (RNA)                       :: 91
            rRNAs                             :: 6, 6, 6 (5S, 16S, 23S)
            complete rRNAs                    :: 6, 6, 6 (5S, 16S, 23S)
            tRNAs                             :: 69
            ncRNAs                            :: 4
            Pseudo Genes (total)              :: 127
            CDSs (without protein)            :: 127
            Pseudo Genes (ambiguous residues) :: 0 of 127
            Pseudo Genes (frameshifted)       :: 45 of 127
            Pseudo Genes (incomplete)         :: 76 of 127
            Pseudo Genes (internal stop)      :: 35 of 127
            Pseudo Genes (multiple problems)  :: 26 of 127
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP083929.1.
            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="V1164"
                     /isolation_source="Hospitalized patient"
                     /host="Homo sapiens"
                     /db_xref="taxon:1352"
                     /plasmid="pV1164-9"
                     /geo_loc_name="Denmark"
                     /collection_date="2015"
     gene            join(1948..1979,1..>151)
                     /locus_tag="LCG90_RS14930"
                     /old_locus_tag="LCG90_14955"
                     /pseudo=""
     CDS             join(1948..1979,1..>151)
                     /locus_tag="LCG90_RS14930"
                     /old_locus_tag="LCG90_14955"
                     /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            732..1748
                     /locus_tag="LCG90_RS14935"
                     /old_locus_tag="LCG90_14960"
     CDS             732..1748
                     /locus_tag="LCG90_RS14935"
                     /old_locus_tag="LCG90_14960"
                     /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          733..1742
                     /name="rep_cluster_935"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="92.292"
                     /coverage="99.0"
                     /evalue="0.0"
ORIGIN
        1 aaagagtaac agaaaggttt acactctttt tattagcgac agcgtgaagg aggggttcac
       61 cttagggttt agtatttcgt tcaaaaaggg aacaaagaat acaagcattt ctcataataa
      121 tcgtgagtta actgatagcc aaaaaatcaa tggtttgtct ggtagaaaat aattagcaga
      181 tttacaagtg ggaaataaaa agctgaaaga agaaaattgc atttcaaact acattttcta
      241 caatagctct aaaatggcat attttgcgtt ctgagcggtt ttagcgttta tttcgtttag
      301 ttatcggcac aatcgttaaa acacgttaga ggagcgaaaa tggagcctgt aaggcgactg
      361 gtagcggaac gatcgtgtta gattgtgaaa accgatagct gaatgaaata aacagcgggt
      421 gcgccctttc catttcggca ggaggaggct caaggggttc ggggaatgaa attccctgag
      481 gtctttttat ttttttagga ggagtgctat aatcaaagaa aacgagaaaa aagagcaaaa
      541 taaaagccga gcagtgcgct aacactctcg actatttacg gaaactactt cacctagctc
      601 cgtaactcag gttcattata cgaatatttt taggtttctt caagctagag atttttggat
      661 atgaattttt agggttacgt gaactctgga aattctttcc aaaagtctct tttttcgttt
      721 ggaggacgaa aatggcaaat gaaaatcagt tgagtgaaat tcaatcaaaa attgaaggtc
      781 gaggggcaga aaaaagaaca acgataaatc agctcgaaaa acttaaccgt atttctaaca
      841 ggcggttaag tgtgcaaggt acgaccaccc ccctaaaatt aaattggtcg attgatcgaa
      901 ttacaattgt cggaaaactg aatgatacca tagcttattg gacgaaaaat ggagttgttt
      961 ttgtcgattt cgagcaatta atgcgtttga acgaaaatca gggatatttg aaatcagttg
     1021 ggataaacgg ctggcaatta ttcgatcaat atggagaaga tattgcgtat atcgaaatac
     1081 ttaaatttca tgaaggaaaa ggtcgtattg attttaatcc gaataagata ggccagtttt
     1141 tagctagttc catgaaagga ttcattcatg acctattttt agatccgcat ttttcccggg
     1201 cggatattgc ctgcgatatt gtagatgtgc cggatgactt tattactcag tatcgtattg
     1261 tagacccgat ttcttttaag ccaatctacg gccgttctgg caagctagaa acagcgtact
     1321 ggggcagtcg tgccagtgag cgccaagtgc gactgtacaa caaaaagcta gagcaggaac
     1381 gaaaaaaagt aatcgtgcca aaagaaatcg atacgtggtg gcggttagaa atgcagctaa
     1441 gacgtggcaa agcaacggat tggcatgcga tggttcagga aagcttagat agttttgcaa
     1501 gcccgcattt tttgccgatt gatataaaac ctattgataa aatagttatt gatggtttga
     1561 tagctgagcc ttctaattgg tcgataattg ctagacatac aaaatataaa tatcggaatt
     1621 tgctgaagca agaaagtcaa aatgatgagt taacgaatca tttacgagag acttttaagg
     1681 aatctgcaga cgaattaaaa aaagaattgg atacgtggct tttggggttg gatgtgacag
     1741 agaagtgata ccgaataaga aaagtcagat gagtgagagt ggatttgcgt caatgtttag
     1801 tgacgtaaat tcacgataag cgaatatttt gcatgaagca aaataaagcg taaaaggagt
     1861 tgagagcgtg acacgctttc ggctcctttt ttcgttgtca cttgtgacag cgaataccct
     1921 cggagagcat ttggaattgt gacagccatg tcacaattag gaaaatgtta ctctttgtc
//
