LOCUS       NZ_CP066426             4374 bp    DNA     circular CON 19-FEB-2024
DEFINITION  Enterococcus faecium strain Dallas 55 plasmid p55_4kb, complete
            sequence.
ACCESSION   NZ_CP066426
VERSION     NZ_CP066426.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN17038079
            Assembly: GCF_016406385.1
KEYWORDS    RefSeq.
SOURCE      Enterococcus faecium
  ORGANISM  Enterococcus faecium
            Bacteria; Bacillota; Bacilli; Lactobacillales; Enterococcaceae;
            Enterococcus.
REFERENCE   1  (bases 1 to 4374)
  AUTHORS   Islam,M.J. and Palmer,K.
  TITLE     Molecular characterization of VREfm isolates from Dallas, Texas
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 4374)
  AUTHORS   Islam,M.J. and Palmer,K.
  TITLE     Direct Submission
  JOURNAL   Submitted (20-DEC-2020) Biological Sciences, University of Texas at
            Dallas, 1520 Richardson Dr Apt 1418, Richardson, TX 75080, USA
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Date                     :: 2019
            Assembly Method                   :: Unicycler v. 0.4.7
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 112.0x
            Sequencing Technology :: Illumina NextSeq; Oxford Nanopore MinION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 02/19/2024 03:51:12
            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)                     :: 3,148
            CDSs (total)                      :: 3,056
            Genes (coding)                    :: 2,923
            CDSs (with protein)               :: 2,923
            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)              :: 133
            CDSs (without protein)            :: 133
            Pseudo Genes (ambiguous residues) :: 0 of 133
            Pseudo Genes (frameshifted)       :: 43 of 133
            Pseudo Genes (incomplete)         :: 77 of 133
            Pseudo Genes (internal stop)      :: 36 of 133
            Pseudo Genes (multiple problems)  :: 19 of 133
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP066426.1.
            Bacteria and source DNA available from Dr. Kelli Palmer, UTDallas.
            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..4374
                     /organism="Enterococcus faecium"
                     /mol_type="genomic DNA"
                     /strain="Dallas 55"
                     /isolation_source="rectal swab"
                     /host="Homo sapiens"
                     /db_xref="taxon:1352"
                     /plasmid="p55_4kb"
                     /geo_loc_name="USA: Dallas"
                     /collection_date="2015"
     gene            join(4022..4374,1..1054)
                     /locus_tag="JCP69_RS15570"
                     /old_locus_tag="JCP69_15570"
     CDS             join(4022..4374,1..1054)
                     /locus_tag="JCP69_RS15570"
                     /old_locus_tag="JCP69_15570"
                     /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_002317172.1"
                     /translation="MGFSISFKKGTKNTSISHNNRELTDRQKTNDWHKHIDFTKSDENI
                     YLEQTNLADKYEELFGEVVEKYNAKQKRADRKIEDYLAKVRKDKKLEPQREFIVQIGIL
                     DDFQTNRADGSSTGISKQQAEQNRVIANKILVQYYKEFQERNPNLAVYNAVIHNDEISP
                     HLHLNIVPVAEGYKRGVQKQPSFNKALVQQGIHADKDNGRVLFNNFRNQEVDSIERLMN
                     DYGWKRDIVGTNKIKDIHEYKEIMSEISELRQTAVKERESVSDELRYISRQREENERDK
                     ALMASERAKIEEEKKNMLNVKKEMAVIFQKDMVPLESFKRLPDGSYHLSGNDFVDLYQR
                     ATRATNAKRNADNMSEQYLQMLEQNTELNEYVATLEEERHLSGRKQLADLQVENKKLKE
                     ENRSLRQRLERLKNAFQKSITRLSIRFGLAEKDMGLSEELEVLEQEKTLFYRQNVSQRK
                     LERSEDEIEW"
                     /name="plasmid recombination protein"
     gene            1501..2469
                     /locus_tag="JCP69_RS15575"
                     /old_locus_tag="JCP69_15575"
     CDS             1501..2469
                     /locus_tag="JCP69_RS15575"
                     /old_locus_tag="JCP69_15575"
                     /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_002298422.1"
                     /translation="MSKNGIIVNEWENLTALSNRRLNVQNMYTPLKMQWSIDRITIVGK
                     LKENIYYHTQNDVLILDFEQLMRVNEGNGYLKAVGNNGWQLLDQYEENIAYIEILKWQD
                     GKGRIDFNPNKIGHFLASSMKNFIHDLFLEPHFSRADIACDIIDVPDEFITQYRVVDPV
                     SFKPIYGRSGKLETAYWGSRASERQIRLYNKKLEQETKRKIVPPEIETWWRLELQLRRG
                     KATDWHAMVHESLNSFASPHFLPLDVKTNDKVMIFGLIANPEMWGFLERRMKYKLRDIL
                     KRESQNDELTNHLRETFSESADVLKKELDTWLQGLDVTEEE"
                     /name="replication initiation factor domain-containing
                     protein"
     gene            2472..2705
                     /locus_tag="JCP69_RS15580"
                     /old_locus_tag="JCP69_15580"
     CDS             2472..2705
                     /locus_tag="JCP69_RS15580"
                     /old_locus_tag="JCP69_15580"
                     /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            2698..3117
                     /locus_tag="JCP69_RS15585"
                     /old_locus_tag="JCP69_15585"
     CDS             2698..3117
                     /locus_tag="JCP69_RS15585"
                     /old_locus_tag="JCP69_15585"
                     /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            3126..3434
                     /locus_tag="JCP69_RS15590"
                     /old_locus_tag="JCP69_15590"
     CDS             3126..3434
                     /locus_tag="JCP69_RS15590"
                     /old_locus_tag="JCP69_15590"
                     /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_002298419.1"
                     /translation="MDKIDLREETVDRIELMYERLADYLNLPDEDNYSEMLERMMDVLN
                     SVINADLAKSSVLTNEFVHKHLAQTTDESEKEFWLKLMSHVMQLNQISVINSKEKEM"
                     /name="hypothetical protein"
     gene            3438..3800
                     /locus_tag="JCP69_RS15595"
                     /old_locus_tag="JCP69_15595"
     CDS             3438..3800
                     /locus_tag="JCP69_RS15595"
                     /old_locus_tag="JCP69_15595"
                     /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_002298418.1"
                     /translation="MGMTLADIKAQEEKLKKEQAKLRQQKKRLIEKENAAMGKALRKRF
                     GFETFADFERWLSSISDDQQHEKSVDNEWLADEKSAPSERDYPDESDGLFGVIPNKKSQ
                     MSESKFTSIFNDVNLR"
                     /name="hypothetical protein"
     Typing          1585..2459
                     /name="rep_cluster_943"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="84.032"
                     /coverage="97.0"
                     /evalue="0.0"
     Typing          3..1051
                     /name="MOBV"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="92.857"
                     /coverage="99.0"
                     /evalue="0.0"
     Typing          3930..4372
                     /name="MOBV"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="99.0"
                     /evalue="1.53e-90"
ORIGIN
        1 catatcgaaa caacaagctg aacaaaatcg agtgattgcc aataaaattt tggttcagta
       61 ttacaaggag tttcaagaga gaaaccctaa tttggctgtt tataatgctg ttattcataa
      121 tgacgaaata agtccgcacc tgcacttgaa tattgtgccg gttgctgaag gttataaacg
      181 gggtgttcaa aagcagccga gctttaataa agcactggtt caacaaggga tacacgctga
      241 taaagataat ggtcgagtgc ttttcaataa ttttagaaat caagaagttg actctataga
      301 acgattaatg aatgattacg gttggaaaag ggatattgtc ggtaccaaca aaattaaaga
      361 tattcacgaa tacaaagaaa tcatgagtga aatttctgaa ttgcgccaaa cggctgtaaa
      421 agagcgtgag agcgtttctg atgagttgag gtatatttct aggcaaagag aagaaaacga
      481 gcgtgataag gctctgatgg cttctgagag agcgaagatt gaagaagaga agaaaaatat
      541 gctgaatgta aaaaaagaga tggcggtcat tttccaaaaa gatatggttc ctttagaaag
      601 tttcaagagg cttcctgatg gttcgtatca tttatctggg aatgattttg ttgatttgta
      661 tcaacgagct acgagagcaa caaatgccaa gagaaatgct gataacatga gtgagcaata
      721 tttacagatg cttgagcaaa atacagaatt aaatgagtat gtagctacat tggaagaaga
      781 gcgtcatttg tctggtagaa aacaattagc agatttacaa gtggaaaata aaaagctgaa
      841 agaagaaaat cgctctttac gccagcgttt agagcgatta aaaaacgcat ttcaaaaatc
      901 gatcactcgt ttgtctatcc gttttggtct tgcagaaaag gatatggggc tttctgagga
      961 attagaagtg ttagagcagg agaaaacctt attttatcgt caaaacgtct cacagcgtaa
     1021 attagagcgt tctgaagatg agatcgagtg gtagttacga tgtgcagtca acggtaccgg
     1081 aggcggtttg tgccgaggat aaggagttga cggctaaacc actagcctat taagctgaca
     1141 tttgctaaaa aatggccagt ccattttttg gccaacctag cgttagcgaa gtttgggggc
     1201 gcccttttca aagggtgcgg ttttattttt tggatatttg catagctaaa gagaagtgct
     1261 attattgagt tagcaaacaa atgaactgaa aaaagagtaa aaaaatagtc gagcaacgct
     1321 accaacgttc tcgaccttta cggaaactaa tcgcactagc tccgtaactt cttaatcatt
     1381 atacgaatat ttttagattt cttcaagact agagattttt tggtaatgaa tttttaagag
     1441 ttacgtgaac ttttgaaaat tctttccaga agtctctttt tctttgagga ggaacaaaat
     1501 ttgagtaaaa atggcataat cgtaaatgag tgggaaaatt taacagccct atctaacagg
     1561 cggttaaatg tacaaaatat gtacaccccc ttaaaaatgc agtggtcaat tgaccgaatt
     1621 actatcgttg gaaaactgaa ggaaaatatt tattatcaca ctcaaaatga tgtgttgatt
     1681 ttagattttg agcaattaat gcgggtgaat gaaggcaatg gctatttaaa agcggttggg
     1741 aataacggct ggcaattatt agaccaatac gaagaaaata ttgcttatat tgagattttg
     1801 aaatggcaag atggcaaagg gcggattgat tttaacccga ataagattgg tcatttttta
     1861 gctagttcaa tgaaaaattt cattcatgat ttatttctag aaccacattt ctcacgtgcg
     1921 gatattgctt gcgatattat cgatgtgcct gatgagttta ttacacaata tcgagtggtt
     1981 gatcctgttt ctttcaagcc aatttatggg cggtctggga agctggaaac agcttattgg
     2041 ggcagtcgtg ccagcgaacg ccagattcgg ctatacaaca aaaaattgga acaggaaacc
     2101 aagcgtaaaa ttgtgccacc agaaatagaa acttggtggc gactggaatt gcagttaagg
     2161 cgtgggaaag caacagattg gcatgcaatg gttcatgaaa gtttaaatag ttttgctagc
     2221 cctcattttc taccacttga tgtaaaaaca aatgataagg tgatgatttt tggactgatt
     2281 gctaaccctg aaatgtgggg gtttttagag cgtagaatga aatacaaatt gagagatatt
     2341 ttgaaaagag aaagtcaaaa tgatgagttg acgaatcatt tacgagaaac attttcggaa
     2401 tcagcagatg ttttgaaaaa agaattagac acttggcttc aagggttaga tgtaacggag
     2461 gaggaataag aatggcagaa aaacaaaagc attttggtaa gaaaaattgg ttggtgaatt
     2521 taacaggtga taacgttgtc gttgtttttt tggatagcaa aaaaatgtcc ggtaagttac
     2581 ttgatgtaac gcagtatgag ttgattttga aaaataataa aattgattcc ccaatcatta
     2641 tccctaagca tgctgttaaa tatgtttatg gggtagctga aagtaacgga gaagataatg
     2701 actgatttgc cagaaaaaat gaccataaaa aaccttgctg atgagttggg tatatctaaa
     2761 aatacagtgc gcaatcaact ggtcaatgca ggttatgacc ttgctcggta taaagataat
     2821 ggggttatca tgttagacaa ggaattgatt ggtgttgtgc ggtcaattta tcggtcaaaa
     2881 ggtggtcaat tgactggtga tttaccggtc aatgatgcag gcaatgattt cccgttagaa
     2941 aaagaaaatg aatttttgcg tgaacaatta gcggaaaaag ataggcatat ttctgaatta
     3001 acggaaatga ttcgtgacca acaaaaattg actttgcttc agcaacaaaa aaacgatcag
     3061 ttgttactag aaaatcaaga attaaaaaat cgaaaatggt ggcaattctg gaagtgaggt
     3121 gtgacatgga taaaattgat ttgagagaag aaacagtcga tagaattgaa ttgatgtatg
     3181 aacggttagc tgattatttg aatttgccgg atgaagataa ttatagtgaa atgcttgaac
     3241 gaatgatgga tgttctcaac tcggttatca atgctgatct agcaaaatct tcagttttga
     3301 ctaatgaatt tgttcataag catttagcgc aaacaactga tgaatcagaa aaagaatttt
     3361 ggttgaaatt aatgagtcat gttatgcagt taaaccaaat ttccgttatt aattccaaag
     3421 aaaaggagat gtagtttatg ggaatgactt tagcagatat taaagcgcaa gaagaaaaat
     3481 taaaaaaaga acaagcgaaa cttcgccaac agaaaaaacg cttgattgag aaagaaaatg
     3541 ctgcaatggg caaggctctt cgcaagcgtt ttgggtttga aacttttgct gattttgagc
     3601 ggtggctatc gtcgatttct gacgatcagc aacacgaaaa atcagtggat aatgagtggc
     3661 ttgctgatga aaaatcagcg ccaagcgaac gagattatcc cgatgaatct gacggcttat
     3721 tcggagtgat accgaataag aaaagtcaga tgagtgagag taaatttacg tcaatattta
     3781 atgacgtgaa tttacgataa gcgattattt tgcgtgaagc aaaataaagc gtaaaaggag
     3841 ttgagagcgt gacacgcttt cggctccttt tttcgttgtc acttgtgaca gcgaataccc
     3901 tcggagagca tttggaattg tgacagccat gtcacaatta ggaaaatgtt actctttgac
     3961 aaagagtaac agaaaggttt acaatctttt tattagcgac agcgcgaagg agggttttaa
     4021 cttggggttt agtatttcat ttaaaaaagg aacgaagaat acaagtattt ctcataataa
     4081 tcgtgagtta actgatcgcc agaaaaccaa tgattggcat aagcatattg acttcacgaa
     4141 atcggatgaa aatatttatt tagagcagac gaatctagca gataaatatg aggaattgtt
     4201 tggcgaagtg gtagaaaaat ataatgcgaa acaaaaaaga gccgatagaa aaatcgagga
     4261 ctatttagcg aaagtgcgca aggataaaaa gttggaacct caacgagaat ttattgtgca
     4321 aataggcatt ttagatgatt tccagacaaa tcgagcagat ggttcttcta ctgg
//
