LOCUS       NZ_CP083927             2947 bp    DNA     circular CON 05-NOV-2023
DEFINITION  Enterococcus faecium isolate V1164 plasmid pV1164-7, complete
            sequence.
ACCESSION   NZ_CP083927
VERSION     NZ_CP083927.1
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 2947)
  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  JOURNAL   Unpublished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 2947)
  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
            CP083927.1.
            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..2947
                     /organism="Enterococcus faecium"
                     /mol_type="genomic DNA"
                     /isolate="V1164"
                     /isolation_source="Hospitalized patient"
                     /host="Homo sapiens"
                     /db_xref="taxon:1352"
                     /plasmid="pV1164-7"
                     /geo_loc_name="Denmark"
                     /collection_date="2015"
     gene            join(2455..2947,1..482)
                     /locus_tag="LCG90_RS14890"
                     /old_locus_tag="LCG90_14915"
     CDS             join(2455..2947,1..482)
                     /locus_tag="LCG90_RS14890"
                     /old_locus_tag="LCG90_14915"
                     /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_002337993.1"
                     /translation="MSKRGTIINEWEKLNRISNRRLNAQTMCTPLKMQWSIDRITIVGT
                     LRENIYYHTPHDVLILDFEQLMRLNEGNGYLKAVGNNGWQLLDQHEENIAYIEILKFQE
                     GKGRIDFNPNKISQFLAGSMKNFIHDLFLEPHFSRADIACDIIDVPDDFITQYRVVDPV
                     SFKPIYGRSGKLETAYWGSRASERQIRMYNKKLEQERKRKVVPKEIDTWWRLELQLRRG
                     KATDWHAMVHESLDSFASPHYLPEDVKVTDRMMITALITEHSYWGQIHRNSKYKYRELL
                     KQESQNDELTNHLRETFSESADDLKRELDTWLQGLDVTEVGAE"
                     /name="replication initiation factor domain-containing
                     protein"
     gene            479..619
                     /locus_tag="LCG90_RS14895"
                     /old_locus_tag="LCG90_14920"
     CDS             479..619
                     /locus_tag="LCG90_RS14895"
                     /old_locus_tag="LCG90_14920"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002326822.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="DeoR family transcriptional regulator"
                     /protein_id="WP_002322683.1"
                     /translation="MSDSIEKMTLKKLADELGVSKNTVRNQLVNSGFDLAQYKEKNAVV
                     N"
                     /name="DeoR family transcriptional regulator"
     gene            complement(956..1372)
                     /locus_tag="LCG90_RS14900"
                     /old_locus_tag="LCG90_14925"
     CDS             complement(956..1372)
                     /locus_tag="LCG90_RS14900"
                     /old_locus_tag="LCG90_14925"
                     /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_002322684.1"
                     /translation="MRKTSVQKHVTLYPSHVDVLDSIIERNPDINNYSEAIRFLCMSYE
                     PDTNTTTTSNQAKLNAMGKEISIMSEIIAEFADLYLKDTGILIGTNSKVYQETKEKIEK
                     QLNPSKRNQPKNRQKETNQTFTSKNFDPTNFLKR"
                     /name="hypothetical protein"
     gene            complement(1374..1655)
                     /locus_tag="LCG90_RS14905"
                     /old_locus_tag="LCG90_14930"
     CDS             complement(1374..1655)
                     /locus_tag="LCG90_RS14905"
                     /old_locus_tag="LCG90_14930"
                     /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_002347307.1"
                     /translation="MDILVRKIDSKVIAKIDKRCQELTNKTGKKWSRNRYLKVLIENDF
                     DHALMHYKKDQFDLLLEKFIAIQEKNTETLNEYVRTNNQLIETLIGGR"
                     /name="hypothetical protein"
     Typing          4..482
                     /name="rep_cluster_943"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="81.967"
                     /coverage="98.0"
                     /evalue="1.3000000000000001e-108"
ORIGIN
        1 tcaaaccaat ttacggtcgg tctgggaaac tggaaacagc atattgggga agtcgtgcta
       61 gtgaacgaca gattcggatg tataacaaaa aattggaaca agaaagaaaa cggaaagttg
      121 ttccgaaaga aatcgatact tggtggcgac tagaattgca attgcgaagg gggaaagcaa
      181 ctgattggca tgcaatggtt catgaaagtt tagatagctt tgcaagtcct cactatttgc
      241 cagaagatgt gaaagtaact gacagaatga tgattactgc tcttataacg gaacatagtt
      301 actgggggca aattcataga aattcaaaat ataaatatcg tgaattgtta aagcaagaaa
      361 gtcaaaatga tgagttgacg aatcatttgc gagaaacatt ttcggagtcg gcagatgatt
      421 tgaaacgaga attagataca tggcttcaag gacttgatgt gacggaagta ggtgctgaat
      481 gagtgattcg atagaaaaaa tgaccctaaa aaaacttgct gatgaattgg gtgtatcgaa
      541 aaatacggtg cgcaatcaac tggtcaattc gggatttgac cttgctcagt ataaagaaaa
      601 aaatgcagtg gtcaattgac cgaaatttat gtctttgggt tttggggttt taaaacgaaa
      661 aaaagggggc gattttcgcc ccctttgctc tatgtgaaaa atttgttata cttattttat
      721 ccttaaaaca taccaatctt tttcttattt agctgctcgt acgagcagct ttttttacga
      781 ttatgaattc aaatcatgta tttataattt ttttgttttt atcttttttt ctgttatttc
      841 ttctgaaatt cgtttttttc attcaattgg ttactatctt attgtaaatg ttgctattaa
      901 gatggtgatc ctacccaaaa aataaaccag gaatttaaat ctcctggttt attttttatc
      961 tttttagaaa atttgttggg tcgaaatttt tagaagtaaa tgtttgattg gtttcttttt
     1021 gacgattttt tggttgattt cgtttggagg gattaagttg tttttcaatt ttttctttcg
     1081 tttcttgata cactttagaa tttgtgccaa taagaatacc tgtatctttt agatataaat
     1141 cagcaaattc tgcaatgatt tcggacatga tggaaatttc ttttcccata gcatttagtt
     1201 tggcttggtt gctggtagtc gtagtattgg tatcaggttc ataactcata cataaaaaac
     1261 gaatggcttc cgagtaattg ttgatatctg gatttctttc gataatggaa tctaaaacgt
     1321 ccacgtgact gggataaagg gtaacgtgtt tttgaacaga agtttttctc atgttatctt
     1381 cctccgataa gtgtttcaat gagttggttg tttgtacgaa catattcatt cagcgtttca
     1441 gtattttttt cttgaatagc gataaatttt tcgagtaata aatcgaattg atctttcttg
     1501 taatgcataa gtgcgtggtc aaaatcgttt tcgattagga cttttaagta gcgatttcga
     1561 ctccattttt tgccagtttt atttgtgagt tcttggcaac gtttgtctat ttttgcaata
     1621 acctttgaat cgatcttccg aactaaaatg tccatagaaa aactcctttc gcatttgtgt
     1681 ataatttatg tatatcatac gaatatagta tttgtatagc tgttttttgc taaaatacta
     1741 tacataagct agccacgatg gcgaaaaagt gatatcaaat ttttttctga gaaacgtgat
     1801 aggcacagcc tatctaccca ctttttttag aaagtgggta cacgtttcct tatgctcttt
     1861 ataaaatggt gatgtgcgac ttttttctgt tcgtaaaaat aaaaaaagtt tacgaaaatg
     1921 aaactaaact gaacgattat gacgggcatg taatcaagat gaaatgattt tataagcgcg
     1981 tattttgcgt tctaagacgt tttagcgttc atttcgttta gttatcggca caatcgttaa
     2041 aacacgtaag agaagcgaga atggagcctg taaggcgact ggtagcgaaa cggcgtgtta
     2101 gattgtgcaa gccgagaact gaatgaaatg aagagcggaa gcgtgaaata atttcggcag
     2161 gaggaggctc aaggggttcg gggaatgaaa ttccctgagg tctttttatt tttttaagag
     2221 gagtgctata atcaaagaaa acgagaaaaa agagcaaaat aaaagccgaa cggtgttgga
     2281 agcacccttc ggctaattac ggaaactact cacctagttc cgtaactcaa attcattata
     2341 cgaatatttt taggtttctt caagctagag atttttggat atggattttt agagttacgt
     2401 gaactctgga aattctttcc aaaaatctct tttttctttg aggaggaaca aaatttgagt
     2461 aaacgtggca cgatcataaa tgagtgggaa aaacttaacc gcatatctaa caggcggtta
     2521 aatgcacaaa ctatgtgcac ccccttaaaa atgcaatggt caattgaccg aattaccatt
     2581 gttggtacat taagggaaaa tatttattat cacactcccc atgatgtgtt gattttagat
     2641 tttgaacagc ttatgcgtct aaacgaaggt aacggatatt taaaagcggt tggaaataat
     2701 ggctggcaat tactagacca acatgaggaa aatatagctt atattgagat tcttaagttt
     2761 caagagggaa aagggcggat tgactttaac cccaataaaa ttagccaatt tctggcgggc
     2821 tcgatgaaga actttatcca tgatttattt ttagaaccac atttctcacg tgcagatatt
     2881 gcttgtgaca ttattgacgt gccagatgat ttcattaccc aatatcgggt ggttgatcct
     2941 gtttctt
//
