LOCUS       NZ_CP064053             4372 bp    DNA     circular CON 07-JAN-2024
DEFINITION  Enterococcus faecium strain VRE3370 plasmid unnamed4, complete
            sequence.
ACCESSION   NZ_CP064053
VERSION     NZ_CP064053.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN15566652
            Assembly: GCF_015325925.1
KEYWORDS    RefSeq.
SOURCE      Enterococcus faecium
  ORGANISM  Enterococcus faecium
            Bacteria; Bacillota; Bacilli; Lactobacillales; Enterococcaceae;
            Enterococcus.
REFERENCE   1  (bases 1 to 4372)
  AUTHORS   Wyres,K.L., Hawkey,J., Mirceta,M., Judd,L.M., Wick,R., Gorrie,C.L.,
            Pratt,N.F., Garlick,J., Watson,K., Pilcher,D., McGloughlin,S.,
            Abbott,I.J., Macesic,N., Spelman,D.W., Jenney,A.W.J. and Holt,K.E.
  TITLE     Genomic surveillance of antimicrobial resistant bacterial
            colonisation and infection in intensive care patients
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 4372)
  AUTHORS   Wyres,K.L., Hawkey,J., Mirceta,M., Judd,L.M., Wick,R., Gorrie,C.L.,
            Pratt,N.F., Garlick,J., Watson,K., Pilcher,D., McGloughlin,S.,
            Abbott,I.J., Macesic,N., Spelman,D.W., Jenney,A.W.J. and Holt,K.E.
  TITLE     Direct Submission
  JOURNAL   Submitted (02-NOV-2020) Department of Infectious Diseases, Monash
            University, Level 2, The Burnet Institute, Melbourne, VIC 3004,
            Australia
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Date                     :: 2020
            Assembly Method                   :: Unicycler v. v0.4.7
            Assembly Name                     :: Enterococcus faecium VRE3370
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 365.0x
            Sequencing Technology :: Illumina MiSeq; Oxford Nanopore MinION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 01/07/2024 03:08:03
            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)                     :: 3,204
            CDSs (total)                      :: 3,110
            Genes (coding)                    :: 2,950
            CDSs (with protein)               :: 2,950
            Genes (RNA)                       :: 94
            rRNAs                             :: 6, 6, 6 (5S, 16S, 23S)
            complete rRNAs                    :: 6, 6, 6 (5S, 16S, 23S)
            tRNAs                             :: 72
            ncRNAs                            :: 4
            Pseudo Genes (total)              :: 160
            CDSs (without protein)            :: 160
            Pseudo Genes (ambiguous residues) :: 0 of 160
            Pseudo Genes (frameshifted)       :: 69 of 160
            Pseudo Genes (incomplete)         :: 80 of 160
            Pseudo Genes (internal stop)      :: 38 of 160
            Pseudo Genes (multiple problems)  :: 24 of 160
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP064053.1.
            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..4372
                     /organism="Enterococcus faecium"
                     /mol_type="genomic DNA"
                     /strain="VRE3370"
                     /isolation_source="rectal swab"
                     /host="Homo sapiens"
                     /db_xref="taxon:1352"
                     /plasmid="unnamed4"
                     /geo_loc_name="Australia"
                     /lat_lon="37.81 S 144.96 E"
                     /collection_date="2014"
                     /collected_by="Alfred Health"
     gene            join(4150..4372,1..11)
                     /locus_tag="ISU52_RS15865"
                     /old_locus_tag="ISU52_15865"
     CDS             join(4150..4372,1..11)
                     /locus_tag="ISU52_RS15865"
                     /old_locus_tag="ISU52_15865"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002298421.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_002298421.1"
                     /translation="MAEKQKHFGKKNWLVNLTGDNVVVVFLDSKKMSGKLLDVTQYELI
                     LKNNKIDSPIIIPKHAVKYVYGVAESNGEDND"
                     /name="hypothetical protein"
     gene            4..423
                     /locus_tag="ISU52_RS15870"
                     /old_locus_tag="ISU52_15870"
     CDS             4..423
                     /locus_tag="ISU52_RS15870"
                     /old_locus_tag="ISU52_15870"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002351943.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_002298420.1"
                     /translation="MTDLPEKMTIKNLADELGISKNTVRNQLVNAGYDLARYKDNGVIM
                     LDKELIGVVRSIYRSKGGQLTGDLPVNDAGNDFPLEKENEFLREQLAEKDRHISELTEM
                     IRDQQKLTLLQQQKNDQLLLENQELKNRKWWQFWK"
                     /name="hypothetical protein"
     gene            432..740
                     /locus_tag="ISU52_RS15875"
                     /old_locus_tag="ISU52_15875"
     CDS             432..740
                     /locus_tag="ISU52_RS15875"
                     /old_locus_tag="ISU52_15875"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002292673.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_002333831.1"
                     /translation="MDKIDLREETVDRIELMYERLADYLNLPDEDNYSEMLERIMDVLN
                     SVINADLAKSSVLTNEFVHKHLAQTTDESEKEFWLKLMSHVMQLNQISVINSKEKEM"
                     /name="hypothetical protein"
     gene            744..1106
                     /locus_tag="ISU52_RS15880"
                     /old_locus_tag="ISU52_15880"
     CDS             744..1106
                     /locus_tag="ISU52_RS15880"
                     /old_locus_tag="ISU52_15880"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_016173819.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_045135959.1"
                     /translation="MGMTLADIKAQEEKLKKEQAKLRQQKKRLIEKENAAMGKALRKRF
                     GFETFADFERWLSSISDDQQHEKTVDNEWLADEKSAPSERDYPDESDDLFGVIPNKKSQ
                     MSESKFTSIFNDVNLR"
                     /name="hypothetical protein"
     gene            1328..2734
                     /locus_tag="ISU52_RS15885"
                     /old_locus_tag="ISU52_15885"
     CDS             1328..2734
                     /locus_tag="ISU52_RS15885"
                     /old_locus_tag="ISU52_15885"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_016173818.1"
                     /GO_function="GO:0003677 - DNA binding [Evidence IEA]"
                     /GO_process="GO:0006310 - DNA recombination [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="plasmid recombination protein"
                     /protein_id="WP_060810507.1"
                     /translation="MGFSISFKKGTKNTSISHNNRELTDRQKTNDWHKHIDFTKSDENI
                     YLEQTNLADKYEELFGEVVEKYNAKQKRADRKIEDYLAKVRKDKKLEPQREFIVQIGIL
                     DDFQTNRADGSSTGISKQQAEQNRVIANKILVQYYKEFQERNPNLAVYNAVIHNDEISP
                     HLHLNIVPVAEGYKRGVQKQPSFNKALVQQGIHADKDNGRVLFNNFRNQEVDSIERLMN
                     DYGWKRDIVGTNKIKDIHEYKEIMSEISELRQTAVKERESVSDELRYIYRQREENERDK
                     ALMASERAKIEEEKKNMLNVKKEMAVIFQKDMVPLESFKRLPDGSYHLSGNDFVDLYQR
                     ATRATNAKRNADNMSEQYLQMLEQNTELNEYVATLEEERHLSGRKQLADLQVENKKLKE
                     ENRSLRQRLERLKNAFQKSITRLSIRFGLAEKDMGLSEELEVLEQEKTLFYRQNVSQHK
                     LERSENEIEW"
                     /name="plasmid recombination protein"
     gene            3179..4147
                     /locus_tag="ISU52_RS15890"
                     /old_locus_tag="ISU52_15890"
     CDS             3179..4147
                     /locus_tag="ISU52_RS15890"
                     /old_locus_tag="ISU52_15890"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002298422.1"
                     /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_002347008.1"
                     /translation="MSKKRTIVNEWEKLTALSNRRLNVQTLVQTIKLNWSIDRITIVGK
                     LNQNIFYHTQHDVLILDFEQLMRVNEGNGYLKAVGNNGWQLLDQHDENIAYIEISKWQE
                     GKGRIDFNPNKISRFLADSMKNFIHDLFLEPHFSRADVACDLIDVPDEFITQYRIIDPV
                     SFKLIYGRSGKLETVYWGSRASERQIRLYNKKIEQEMKRKVVPSEINTWWRLEMQLRRG
                     KATEWYAMVKESLDSFVSPHFLPTDIKPTDKVMIDGLLANHSNWAILSRNSKYKYRNLL
                     KRESQNDELTNHLRETFEESADDLKKELDTWLQGLDVTEEE"
                     /name="replication initiation factor domain-containing
                     protein"
     Typing          3271..4134
                     /name="rep_cluster_943"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="81.264"
                     /coverage="95.0"
                     /evalue="0.0"
     Typing          1329..2731
                     /name="MOBV"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="92.094"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 ataatgactg atttgccaga aaaaatgacc ataaaaaacc ttgctgatga gttgggtata
       61 tctaaaaata cagtgcgcaa tcaactggtc aatgcaggtt atgaccttgc tcggtataaa
      121 gataatgggg ttatcatgtt agacaaggaa ttgattggtg ttgtgcggtc aatttatcgg
      181 tcaaaaggtg gtcaattgac tggtgattta ccggtcaatg atgcaggcaa tgatttcccg
      241 ttagaaaaag aaaatgaatt tttgcgtgaa caattagcgg aaaaagatag gcatatttct
      301 gaattaacgg aaatgattcg tgaccaacaa aaattgactt tgcttcagca acaaaaaaac
      361 gatcagttgt tactagaaaa tcaagaatta aaaaatcgaa aatggtggca attctggaag
      421 tgaggtgtga catggataaa attgatttga gagaagaaac agtcgataga attgaattga
      481 tgtatgaacg gttagctgat tatttgaatt tgccggatga agataattat agtgaaatgc
      541 ttgaacgaat tatggatgtt ctcaactcgg ttatcaatgc tgatctagca aaatcttcag
      601 ttttgactaa tgaatttgtt cataagcatt tagcgcaaac aactgatgaa tcagaaaaag
      661 aattttggtt gaaattaatg agtcatgtta tgcagttaaa ccaaatttcc gttattaatt
      721 ccaaagaaaa ggagatgtag tttatgggaa tgactttagc agatattaaa gcgcaagaag
      781 aaaaattaaa aaaagaacaa gcgaaacttc gccaacagaa aaaacgcttg attgagaaag
      841 aaaatgctgc aatgggcaag gctcttcgca agcgttttgg gtttgaaact tttgctgatt
      901 ttgagcggtg gttatcgtca atttctgacg atcagcaaca cgaaaaaaca gtggataatg
      961 agtggcttgc tgatgaaaaa tcagcgccaa gcgaacgaga ttatcccgat gaatctgacg
     1021 acttattcgg agtgataccg aataagaaaa gtcagatgag tgagagtaaa tttacgtcaa
     1081 tatttaatga cgtgaattta cgataagcga ttattttgcg tgaagcaaaa taaagcataa
     1141 aaggagttga tagcgtgata cgctttcggc tccttttttc gttgtcactt gtgacagcga
     1201 aaaccctcgg agagcgtttg gaattgtgac atccatgtca caattaggaa aatgttactc
     1261 tttgacaaag agtaacagaa aggtttacaa tctttttatt agcgacagcg cgaaggaggg
     1321 ttttaacttg gggtttagta tttcatttaa aaaaggaacg aagaatacaa gtatttctca
     1381 taataatcgt gagttaactg atcgccagaa aaccaatgat tggcataagc acattgactt
     1441 cacgaaatcg gatgaaaata tttatttaga gcagacgaat ctagcagata aatatgagga
     1501 attgtttggc gaagtggtag aaaaatataa tgcgaaacaa aaaagagccg atagaaaaat
     1561 cgaggactat ttagcgaaag tgcgcaagga taaaaagttg gaacctcaac gagaatttat
     1621 tgtgcaaata ggcattttag atgatttcca gacaaatcga gcagatggtt cttctactgg
     1681 catatcgaaa caacaagctg aacaaaatcg agtgattgcc aataaaattt tggttcagta
     1741 ttacaaggag tttcaagaga gaaaccctaa tttggctgtt tataatgctg ttattcataa
     1801 tgacgaaata agtccgcacc tgcacttgaa tattgtgccg gttgctgaag gttataaacg
     1861 gggtgttcaa aagcagccga gctttaataa agcactggtt caacaaggga tacacgctga
     1921 taaagataat ggtcgagtgc ttttcaataa ttttagaaat caagaagttg actctataga
     1981 acgattaatg aatgattacg gttggaaaag ggatattgtc ggtaccaaca aaattaaaga
     2041 tattcacgaa tacaaagaaa tcatgagtga aatttctgaa ttgcgccaaa cggctgtaaa
     2101 agagcgtgag agcgtttctg atgagttgag gtatatttat aggcaaagag aagaaaacga
     2161 gcgtgataag gctctgatgg cttctgagag agcgaagatt gaagaagaga agaaaaatat
     2221 gctgaatgta aaaaaagaga tggcggtcat tttccaaaaa gatatggttc ctttagaaag
     2281 tttcaagagg cttcctgatg gttcgtatca tttatctggg aatgattttg ttgatttgta
     2341 tcaacgagct acgagagcaa caaatgccaa gagaaatgct gataacatga gtgagcaata
     2401 tttacagatg cttgagcaaa atacagaatt aaatgagtat gtagctacat tggaagaaga
     2461 gcgtcatttg tctggtagaa aacaattagc agatttacaa gtggaaaata aaaagctgaa
     2521 agaagaaaat cgctctttac gccagcgttt agagcgatta aaaaacgcat ttcaaaaatc
     2581 gatcactcgt ttgtctatcc gttttggtct tgcagaaaag gatatggggc tttctgagga
     2641 attagaagta ttagagcagg agaaaacctt attttatcgt caaaacgtct cacagcataa
     2701 attagagcgt tctgagaatg agattgagtg gtagccacga tgtgcagtca acggtaccgg
     2761 aggcggtttg tgccgaggat aaggagttga cggctaaacc actagcccct gaagctgaca
     2821 tttgctaaaa aatggcaagt ccattttttg gccaacttag cgttagcgaa gtttgggggc
     2881 gcccttttca aagggtgcgg ttttattttt ttggtatttg catagctaaa gagaagtgct
     2941 attattgagt tagcaaacaa atgaactgga aaaagagcaa aaaaataagt cgagcaacgc
     3001 taccaacgtt ctcgaccttt acggaaacta accacactag ttccgtaact caaattcatt
     3061 atacgaatat ttttaggttt cttcaagact agagattgat ggttatgaat ttttagagtt
     3121 acgtgaactc tggaaattct ttccaaaaat ctcttttttc tttgaggagg aactgaatat
     3181 gagtaaaaaa agaacaatcg tgaatgagtg ggaaaaatta acagccctgt ctaacaggcg
     3241 gttaaatgtt caaactttgg tacaaactat aaaattaaat tggtcgattg accgaattac
     3301 cattgttgga aagttgaatc aaaatatttt ttatcatact caacatgatg tattaatatt
     3361 agattttgaa cagcttatgc gggtaaatga aggcaatggc tatttaaaag cggttggaaa
     3421 taatggttgg cagctattag accaacatga cgaaaatatt gcctatattg aaatttctaa
     3481 atggcaagaa ggaaaagggc ggattgattt taatcctaat aaaatcagtc gatttttagc
     3541 ggattccatg aaaaatttta ttcatgattt atttttagag ccccattttt cacgagcgga
     3601 tgttgcctgc gatcttattg atgtgcctga tgagtttatc acgcaatatc gaattattga
     3661 tccagtttca tttaaattaa tttatggacg ctcaggaaaa ctggaaacgg tgtattgggg
     3721 tagtcgggca agcgagcggc aaattcgttt gtacaataaa aaaatagagc aagaaatgaa
     3781 aagaaaggtg gtgccttcag aaattaatac ttggtggcgg ttagaaatgc agttaagacg
     3841 tggtaaagct acggaatggt atgctatggt gaaagaaagt ttggatagct ttgtgagtcc
     3901 acatttttta ccaactgata taaaacctac ggataaagtt atgattgatg gattgttagc
     3961 taatcattct aattgggcga ttttgtcaag aaactcgaaa tataaatatc gaaatttatt
     4021 aaagcgagaa agtcaaaatg atgagttgac gaatcattta cgagaaacat ttgaagaatc
     4081 agcagatgat ttaaaaaaag aattggatac ttggttacag ggacttgatg tgacagagga
     4141 ggaatagtaa tggcagaaaa acaaaagcat tttggtaaga aaaattggtt ggtgaattta
     4201 acaggtgata acgttgtcgt tgtttttttg gatagcaaaa aaatgtccgg taagttactt
     4261 gatgtaacgc agtatgagtt gattttgaaa aataataaaa ttgattcccc aatcattatc
     4321 cctaagcatg ctgttaaata tgtttatggg gtagctgaaa gtaacggaga ag
//
