LOCUS       NZ_CP066394             4375 bp    DNA     circular CON 20-FEB-2024
DEFINITION  Enterococcus faecium strain Dallas 17_1 plasmid p17_1_4kb, complete
            sequence.
ACCESSION   NZ_CP066394
VERSION     NZ_CP066394.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN17038071
            Assembly: GCF_016406445.1
KEYWORDS    RefSeq.
SOURCE      Enterococcus faecium
  ORGANISM  Enterococcus faecium
            Bacteria; Bacillota; Bacilli; Lactobacillales; Enterococcaceae;
            Enterococcus.
REFERENCE   1  (bases 1 to 4375)
  AUTHORS   Islam,M.J. and Palmer,K.
  TITLE     Molecular characterization of VREfm isolates from Dallas, Texas
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 4375)
  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                   :: 156.0x
            Sequencing Technology :: Illumina NextSeq; Oxford Nanopore MinION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 02/20/2024 02:48:50
            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)                     :: 3,073
            CDSs (total)                      :: 2,982
            Genes (coding)                    :: 2,859
            CDSs (with protein)               :: 2,859
            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)              :: 123
            CDSs (without protein)            :: 123
            Pseudo Genes (ambiguous residues) :: 0 of 123
            Pseudo Genes (frameshifted)       :: 45 of 123
            Pseudo Genes (incomplete)         :: 78 of 123
            Pseudo Genes (internal stop)      :: 24 of 123
            Pseudo Genes (multiple problems)  :: 20 of 123
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP066394.1.
            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..4375
                     /organism="Enterococcus faecium"
                     /mol_type="genomic DNA"
                     /strain="Dallas 17_1"
                     /isolation_source="rectal swab"
                     /host="Homo sapiens"
                     /db_xref="taxon:1352"
                     /plasmid="p17_1_4kb"
                     /geo_loc_name="USA: Dallas"
                     /collection_date="2015"
     gene            join(3858..4375,1..451)
                     /locus_tag="JCP93_RS15235"
                     /old_locus_tag="JCP93_15235"
     CDS             join(3858..4375,1..451)
                     /locus_tag="JCP93_RS15235"
                     /old_locus_tag="JCP93_15235"
                     /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_002298422.1"
                     /translation="MSKNGIIVNEWENLTALSNRRLNVQNMYTPLKMQWSIDRITIVGK
                     LKENIYYHTQNDVLILDFEQLMRVNEGNGYLKAVGNNGWQLLDQYEENIAYIEILKWQD
                     GKGRIDFNPNKIGHFLASSMKNFIHDLFLEPHFSRADIACDIIDVPDEFITQYRVVDPV
                     SFKPIYGRSGKLETAYWGSRASERQIRLYNKKLEQETKRKIVPPEIETWWRLELQLRRG
                     KATDWHAMVHESLNSFASPHFLPLDVKTNDKVMIFGLIANPEMWGFLERRMKYKLRDIL
                     KRESQNDELTNHLRETFSESADVLKKELDTWLQGLDVTEEE"
                     /name="replication initiation factor domain-containing
                     protein"
     gene            454..687
                     /locus_tag="JCP93_RS15240"
                     /old_locus_tag="JCP93_15240"
     CDS             454..687
                     /locus_tag="JCP93_RS15240"
                     /old_locus_tag="JCP93_15240"
                     /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            680..1099
                     /locus_tag="JCP93_RS15245"
                     /old_locus_tag="JCP93_15245"
     CDS             680..1099
                     /locus_tag="JCP93_RS15245"
                     /old_locus_tag="JCP93_15245"
                     /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            1108..1416
                     /locus_tag="JCP93_RS15250"
                     /old_locus_tag="JCP93_15250"
     CDS             1108..1416
                     /locus_tag="JCP93_RS15250"
                     /old_locus_tag="JCP93_15250"
                     /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            1420..1782
                     /locus_tag="JCP93_RS15255"
                     /old_locus_tag="JCP93_15255"
     CDS             1420..1782
                     /locus_tag="JCP93_RS15255"
                     /old_locus_tag="JCP93_15255"
                     /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"
     gene            2005..3411
                     /locus_tag="JCP93_RS15260"
                     /old_locus_tag="JCP93_15260"
     CDS             2005..3411
                     /locus_tag="JCP93_RS15260"
                     /old_locus_tag="JCP93_15260"
                     /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"
     Typing          2006..3408
                     /name="MOBV"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="91.88"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 gaagctggaa acagcttatt ggggcagtcg tgccagcgaa cgccagattc ggctatacaa
       61 caaaaaattg gaacaggaaa ccaagcgtaa aattgtgcca ccagaaatag aaacttggtg
      121 gcgactggaa ttgcagttaa ggcgtgggaa agcaacagat tggcatgcaa tggttcatga
      181 aagtttaaat agttttgcta gccctcattt tctaccactt gatgtaaaaa caaatgataa
      241 ggtgatgatt tttggactga ttgctaaccc tgaaatgtgg gggtttttag agcgtagaat
      301 gaaatacaaa ttgagagata ttttgaaaag agaaagtcaa aatgatgagt tgacgaatca
      361 tttacgagaa acattttcgg aatcagcaga tgttttgaaa aaagaattag acacttggct
      421 tcaagggtta gatgtaacgg aggaggaata agaatggcag aaaaacaaaa gcattttggt
      481 aagaaaaatt ggttggtgaa tttaacaggt gataacgttg tcgttgtttt tttggatagc
      541 aaaaaaatgt ccggtaagtt acttgatgta acgcagtatg agttgatttt gaaaaataat
      601 aaaattgatt ccccaatcat tatccctaag catgctgtta aatatgttta tggggtagct
      661 gaaagtaacg gagaagataa tgactgattt gccagaaaaa atgaccataa aaaaccttgc
      721 tgatgagttg ggtatatcta aaaatacagt gcgcaatcaa ctggtcaatg caggttatga
      781 ccttgctcgg tataaagata atggggttat catgttagac aaggaattga ttggtgttgt
      841 gcggtcaatt tatcggtcaa aaggtggtca attgactggt gatttaccgg tcaatgatgc
      901 aggcaatgat ttcccgttag aaaaagaaaa tgaatttttg cgtgaacaat tagcggaaaa
      961 agataggcat atttctgaat taacggaaat gattcgtgac caacaaaaat tgactttgct
     1021 tcagcaacaa aaaaacgatc agttgttact agaaaatcaa gaattaaaaa atcgaaaatg
     1081 gtggcaattc tggaagtgag gtgtgacatg gataaaattg atttgagaga agaaacagtc
     1141 gatagaattg aattgatgta tgaacggtta gctgattatt tgaatttgcc ggatgaagat
     1201 aattatagtg aaatgcttga acgaatgatg gatgttctca actcggttat caatgctgat
     1261 ctagcaaaat cttcagtttt gactaatgaa tttgttcata agcatttagc gcaaacaact
     1321 gatgaatcag aaaaagaatt ttggttgaaa ttaatgagtc atgttatgca gttaaaccaa
     1381 atttccgtta ttaattccaa agaaaaggag atgtagttta tgggaatgac tttagcagat
     1441 attaaagcgc aagaagaaaa attaaaaaaa gaacaagcga aacttcgcca acagaaaaaa
     1501 cgcttgattg agaaagaaaa tgctgcaatg ggcaaggctc ttcgcaagcg ttttgggttt
     1561 gaaacttttg ctgattttga gcggtggcta tcgtcgattt ctgacgatca gcaacacgaa
     1621 aaatcagtgg ataatgagtg gcttgctgat gaaaaatcag cgccaagcga acgagattat
     1681 cccgatgaat ctgacggctt attcggagtg ataccgaata agaaaagtca gatgagtgag
     1741 agtaaattta cgtcaatatt taatgacgtg aatttacgat aagcgattat tttgcgtgaa
     1801 gcaaaataaa gcgtaaaagg agttgagagc gtgacacgct ttcggctcct tttttcgttg
     1861 tcacttgtga cagcgaatac cctcggagag catttggaat tgtgacagcc atgtcacaat
     1921 taggaaaatg tttactcttt gacaaagagt aacagaaagg tttacaatct ttttattagc
     1981 gacagcgcga aggagggttt taacttgggg tttagtattt catttaaaaa aggaacgaag
     2041 aatacaagta tttctcataa taatcgtgag ttaactgatc gccagaaaac caatgattgg
     2101 cataagcata ttgacttcac gaaatcggat gaaaatattt atttagagca gacgaatcta
     2161 gcagataaat atgaggaatt gtttggcgaa gtggtagaaa aatataatgc gaaacaaaaa
     2221 agagccgata gaaaaatcga ggactattta gcgaaagtgc gcaaggataa aaagttggaa
     2281 cctcaacgag aatttattgt gcaaataggc attttagatg atttccagac aaatcgagca
     2341 gatggttctt ctactggcat atcgaaacaa caagctgaac aaaatcgagt gattgccaat
     2401 aaaattttgg ttcagtatta caaggagttt caagagagaa accctaattt ggctgtttat
     2461 aatgctgtta ttcataatga cgaaataagt ccgcacctgc acttgaatat tgtgccggtt
     2521 gctgaaggtt ataaacgggg tgttcaaaag cagccgagct ttaataaagc actggttcaa
     2581 caagggatac acgctgataa agataatggt cgagtgcttt tcaataattt tagaaatcaa
     2641 gaagttgact ctatagaacg attaatgaat gattacggtt ggaaaaggga tattgtcggt
     2701 accaacaaaa ttaaagatat tcacgaatac aaagaaatca tgagtgaaat ttctgaattg
     2761 cgccaaacgg ctgtaaaaga gcgtgagagc gtttctgatg agttgaggta tatttctagg
     2821 caaagagaag aaaacgagcg tgataaggct ctgatggctt ctgagagagc gaagattgaa
     2881 gaagagaaga aaaatatgct gaatgtaaaa aaagagatgg cggtcatttt ccaaaaagat
     2941 atggttcctt tagaaagttt caagaggctt cctgatggtt cgtatcattt atctgggaat
     3001 gattttgttg atttgtatca acgagctacg agagcaacaa atgccaagag aaatgctgat
     3061 aacatgagtg agcaatattt acagatgctt gagcaaaata cagaattaaa tgagtatgta
     3121 gctacattgg aagaagagcg tcatttgtct ggtagaaaac aattagcaga tttacaagtg
     3181 gaaaataaaa agctgaaaga agaaaatcgc tctttacgcc agcgtttaga gcgattaaaa
     3241 aacgcatttc aaaaatcgat cactcgtttg tctatccgtt ttggtcttgc agaaaaggat
     3301 atggggcttt ctgaggaatt agaagtgtta gagcaggaga aaaccttatt ttatcgtcaa
     3361 aacgtctcac agcgtaaatt agagcgttct gaagatgaga tcgagtggta gttacgatgt
     3421 gcagtcaacg gtaccggagg cggtttgtgc cgaggataag gagttgacgg ctaaaccact
     3481 agcctattaa gctgacattt gctaaaaaat ggccagtcca ttttttggcc aacctagcgt
     3541 tagcgaagtt tgggggcgcc cttttcaaag ggtgcggttt tattttttgg atatttgcat
     3601 agctaaagag aagtgctatt attgagttag caaacaaatg aactgaaaaa agagtaaaaa
     3661 aatagtcgag caacgctacc aacgttctcg acctttacgg aaactaatcg cactagctcc
     3721 gtaacttctt aatcattata cgaatatttt tagatttctt caagactaga gattttttgg
     3781 taatgaattt ttaagagtta cgtgaacttt tgaaaattct ttccagaagt ctctttttct
     3841 ttgaggagga acaaaatttg agtaaaaatg gcataatcgt aaatgagtgg gaaaatttaa
     3901 cagccctatc taacaggcgg ttaaatgtac aaaatatgta caccccctta aaaatgcagt
     3961 ggtcaattga ccgaattact atcgttggaa aactgaagga aaatatttat tatcacactc
     4021 aaaatgatgt gttgatttta gattttgagc aattaatgcg ggtgaatgaa ggcaatggct
     4081 atttaaaagc ggttgggaat aacggctggc aattattaga ccaatacgaa gaaaatattg
     4141 cttatattga gattttgaaa tggcaagatg gcaaagggcg gattgatttt aacccgaata
     4201 agattggtca ttttttagct agttcaatga aaaatttcat tcatgattta tttctagaac
     4261 cacatttctc acgtgcggat attgcttgcg atattatcga tgtgcctgat gagtttatta
     4321 cacaatatcg agtggttgat cctgtttctt tcaagccaat ttatgggcgg tctgg
//
