LOCUS       NZ_CP083926             3200 bp    DNA     circular CON 05-NOV-2023
DEFINITION  Enterococcus faecium isolate V1164 plasmid pV1164-6, complete
            sequence.
ACCESSION   NZ_CP083926
VERSION     NZ_CP083926.1
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 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  JOURNAL   Unpublished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                     :: 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
            CP083926.1.
            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="V1164"
                     /isolation_source="Hospitalized patient"
                     /host="Homo sapiens"
                     /db_xref="taxon:1352"
                     /plasmid="pV1164-6"
                     /geo_loc_name="Denmark"
                     /collection_date="2015"
     gene            complement(103..519)
                     /locus_tag="LCG90_RS14865"
                     /old_locus_tag="LCG90_14890"
     CDS             complement(103..519)
                     /locus_tag="LCG90_RS14865"
                     /old_locus_tag="LCG90_14890"
                     /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(522..806)
                     /locus_tag="LCG90_RS14870"
                     /old_locus_tag="LCG90_14895"
     CDS             complement(522..806)
                     /locus_tag="LCG90_RS14870"
                     /old_locus_tag="LCG90_14895"
                     /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            1173..1397
                     /locus_tag="LCG90_RS14875"
                     /old_locus_tag="LCG90_14900"
     CDS             1173..1397
                     /locus_tag="LCG90_RS14875"
                     /old_locus_tag="LCG90_14900"
                     /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            2447..3166
                     /locus_tag="LCG90_RS14885"
                     /old_locus_tag="LCG90_14910"
     CDS             2447..3166
                     /locus_tag="LCG90_RS14885"
                     /old_locus_tag="LCG90_14910"
                     /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          2448..3166
                     /name="rep_cluster_1763"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 gtagacaagt cccttacaac cgactaagat tgctagtaca ttctagcata ttgtatgggg
       61 cttctaaata aaaaacagat aggaataact cctatctgtt ttttatcgtt ttagaaaatt
      121 tgttgggtcg aaatttctag aagtgactgt ttgactggtt tctttttgat gattctttgg
      181 tcgatttcga tttgatggat ttagtttagc ttcgattttt tctttcactt cttgatatac
      241 tttagaattt gtgccaataa gaacgcctgt atcttttaga tataaatcag caaattctgc
      301 gatgatttca gtcatgatgg aaatttcttt tcccatagca tttagttttg cctgattgct
      361 ggtagtggtc gtgttggtat cgggttcata actcatacat aaaaagcgaa tggcttccga
      421 gtagttattg atatctggat ttttttcgat gatggaatct aaaacgtcaa catgactagg
      481 gtacaaagta acatgttttt ggacagaagt ttttctcatg gttatatcat tcctccgata
      541 agcatttcaa tgatttgatt atttgtgtag acatactcgc ttaatatttg agtattttct
      601 gtttggatag caataaattt atcgagcaat aaatcgaatt ggtctttttt gtaagtcgta
      661 agttgacggt caaaatcact ttcgattaaa acttttagat atttatttcg actccatttt
      721 tctcctgttt tattcgtgag ttcttggcaa cgtttgtcta ttgttgcaac aaactttgga
      781 tcaatattcc gaactaaaat gtccataaaa aatctccttt tgcaattatg tataatttat
      841 gtataccata caaatactat atttgtatag ctgttttttg ccaaaatgct atacataagc
      901 tacccacgat ggcgaaaaag tgatatcaaa tttttttctg agaaacgtga taggcacagc
      961 ctatctaccc acttttttta gaaagtgggt acacgtttcc ttatgctctt taaaattcgg
     1021 ggggggagtg ctgcacgtgt aatcgataac caaatttaaa aatgcacgat caaaaattta
     1081 tttagttttt caaacgacat tttttttgag agtatagacg gcaaagaagt gattttattt
     1141 ctagaaaaat tgtgagactg gagaaagaaa aaatggaaaa atttccttac gaatattttc
     1201 aaaacttaga aaaattagag caagcaattc aagcaatcaa gttcgattta acagacgaaa
     1261 aattgttgga atataaaaat atgacacccg aaagaaaacg atcgttggaa aaattaatgc
     1321 aactagtgaa cgaagacggc ggaatttcag acgcagcttt tgacgcatgg agcgaatttc
     1381 atggagaata taattaagtg ggtttaaatg gctctaaaat cgcttctaag agttttttag
     1441 cttggaccaa tgaaatacac caaaaactaa ataaaacgtc ttaaatcgaa aaatacgagc
     1501 tctcagagcg actttatttg taaatgttgc atataagaaa taattacgga ttttagactt
     1561 ttgtaggata tttttgaaat aaatatttat ttctgttata atttgattgc aaataagtga
     1621 acacgaaaca cacgaaagcc ccagagaggt cggattctct ggggcttttt ttgtgggctg
     1681 agtcgcctta attaagtttt acttcttgtt tcggttattc aaccagtaac tgaacaaagc
     1741 gcttaaaagc ccaacaagaa gggagcaaat aaagttagtg aacacgaaac acacctcctt
     1801 ccagtcgcaa gactgtcgga taggcgacaa tcaattatac aataaaaaag caaaaataag
     1861 cctaagtttt ttattgcctt ggggttgtta gggcttgccc tgaccgcctg taaggcgctt
     1921 tagaacgaag gacatagttt ttatcgaatc ttgtcttaga acggcttaga cgagctctca
     1981 ggacgccaca aaggagtccc taatgaatta tttttggcga aggagcctaa aggcgactgc
     2041 tgcaagtaaa atgtgagagc gtagcgatca ctccttctta cagcgaccat agggagctag
     2101 attggcagtt taatatcatg cgcgaacctg tttattttaa aaagtgggtg attttttggc
     2161 gggaaatttt gctcgcgcgc gcgcgtttat tttatttatt ttttaaagat tttttagaac
     2221 cctttttagg gggcagttga gccttactct cccaacggat acagaagggt actaacaact
     2281 ttttatctga gtactaacaa ctttttatct gagtactaac aactttttat ctgagtacta
     2341 acaacttttt atctgagtac taatatcctt ttgtataata acaaccaacc tatttacgag
     2401 ttggttgtta aaggttatta tttatttgta aggggggaag aaaggaatgg atgaaaaaac
     2461 ggaattaaca gtcaaatatc aaaatgaatt gaatttagta ccgctgaaaa atttcaatgc
     2521 taagcagatg gatttatttt ttgcattatg cgctcgtatg aaagatcgtg gtttgaaaaa
     2581 agttagattt tctttcgagg aattaaaaga gttaagtgat tataagatga ctgctacaaa
     2641 agcctttgtc ggtgatttag aaaagctcta taaagatatg cttaatctta cttaccgtac
     2701 tgaagatgag gattctattc gctactttgt tttgtttact ggttttgaaa tcaataaaac
     2761 aaaaaagttt gttgaagtca gtgttaatcc ggacctagaa tatattatta atggtttaac
     2821 agctgaattt agtagatttg aattatctgc tttcacgtcg ttgcgttcta cgtatgcaaa
     2881 aactctattc cgactgctta tgcagtaccg ttctactggt tattatgtag ttcgtattga
     2941 agagtttagg agcttaatgg atatcccaga atactatcaa atgggtaaca ttgatcaaaa
     3001 agtattaaat cctgcattac gagaactaaa aaaatacttc aatgatctta aagtcacaaa
     3061 aataaaagca aaaaagggca ataaaatcgc caaattagaa tttacttttt caagcctaac
     3121 gtcagatttg ccaaagattt ctctgcgtaa ctggttagaa gaataaataa aaaagaactc
     3181 gcccccctta cattaagcaa
//
