LOCUS       NZ_CP066666             4374 bp    DNA     circular CON 20-FEB-2024
DEFINITION  Enterococcus faecium strain Dallas 155 plasmid p7, complete
            sequence.
ACCESSION   NZ_CP066666
VERSION     NZ_CP066666.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN17038106
            Assembly: GCF_016415505.1
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  JOURNAL   Unpublished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 (21-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                   :: 108.0x
            Sequencing Technology :: Illumina NextSeq; Oxford Nanopore MinION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 02/20/2024 02:49:34
            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)                     :: 3,194
            CDSs (total)                      :: 3,102
            Genes (coding)                    :: 2,964
            CDSs (with protein)               :: 2,964
            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)              :: 138
            CDSs (without protein)            :: 138
            Pseudo Genes (ambiguous residues) :: 0 of 138
            Pseudo Genes (frameshifted)       :: 49 of 138
            Pseudo Genes (incomplete)         :: 77 of 138
            Pseudo Genes (internal stop)      :: 32 of 138
            Pseudo Genes (multiple problems)  :: 16 of 138
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP066666.1.
            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 155"
                     /isolation_source="rectal swab"
                     /host="Homo sapiens"
                     /db_xref="taxon:1352"
                     /plasmid="p7"
                     /geo_loc_name="USA: Dallas"
                     /collection_date="2015"
     gene            complement(join(4067..4374,1..1099))
                     /locus_tag="JCP86_RS15805"
                     /old_locus_tag="JCP86_15805"
     CDS             complement(join(4067..4374,1..1099))
                     /locus_tag="JCP86_RS15805"
                     /old_locus_tag="JCP86_15805"
                     /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            complement(1321..1683)
                     /locus_tag="JCP86_RS15810"
                     /old_locus_tag="JCP86_15810"
     CDS             complement(1321..1683)
                     /locus_tag="JCP86_RS15810"
                     /old_locus_tag="JCP86_15810"
                     /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            complement(1687..1995)
                     /locus_tag="JCP86_RS15815"
                     /old_locus_tag="JCP86_15815"
     CDS             complement(1687..1995)
                     /locus_tag="JCP86_RS15815"
                     /old_locus_tag="JCP86_15815"
                     /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            complement(2004..2423)
                     /locus_tag="JCP86_RS15820"
                     /old_locus_tag="JCP86_15820"
     CDS             complement(2004..2423)
                     /locus_tag="JCP86_RS15820"
                     /old_locus_tag="JCP86_15820"
                     /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            complement(2416..2649)
                     /locus_tag="JCP86_RS15825"
                     /old_locus_tag="JCP86_15825"
     CDS             complement(2416..2649)
                     /locus_tag="JCP86_RS15825"
                     /old_locus_tag="JCP86_15825"
                     /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            complement(2652..3620)
                     /locus_tag="JCP86_RS15830"
                     /old_locus_tag="JCP86_15830"
     CDS             complement(2652..3620)
                     /locus_tag="JCP86_RS15830"
                     /old_locus_tag="JCP86_15830"
                     /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"
     Typing          complement(2660..3537)
                     /name="rep_cluster_943"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="83.973"
                     /coverage="97.0"
                     /evalue="0.0"
     Typing          complement(6..1192)
                     /name="MOBV"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="89.899"
                     /coverage="98.0"
                     /evalue="0.0"
ORIGIN
        1 ctgtattttg ctcaagcatc tgtaaatatt gctcactcat gttatcagca tttctcttgg
       61 catttgttgc tctcgtagct cgttgataca aatcaacaaa atcattccca gataaatgat
      121 acgaaccatc aggaagcctc ttgaaacttt ctaaaggaac catatctttt tggaaaatga
      181 ccgccatctc tttttttaca ttcagcatat ttttcttctc ttcttcaatc ttcgctctct
      241 cagaagccat cagagcctta tcacgctcgt tttcttctct ttgcctagaa atatacctca
      301 actcatcaga aacgctctca cgctctttta cagccgtttg gcgcaattca gaaatttcac
      361 tcatgatttc tttgtattcg tgaatatctt taattttgtt ggtaccgaca atatcccttt
      421 tccaaccgta atcattcatt aatcgttcta tagagtcaac ttcttgattt ctaaaattat
      481 tgaaaagcac tcgaccatta tctttatcag cgtgtatccc ttgttgaacc agtgctttat
      541 taaagctcgg ctgcttttga acaccccgtt tataaccttc agcaaccggc acaatattca
      601 agtgcaggtg cggacttatt tcgtcattat gaataacagc attataaaca gccaaattag
      661 ggtttctctc ttgaaactcc ttgtaatact gaaccaaaat tttattggca atcactcgat
      721 tttgttcagc ttgttgtttc gatatgccag tagaagaacc atctgctcga tttgtctgga
      781 aatcatctaa aatgcctatt tgcacaataa attctcgttg aggttccaac tttttatcct
      841 tgcgcacttt cgctaaatag tcctcgattt ttctatcggc tcttttttgt ttcgcattat
      901 atttttctac cacttcgcca aacaattcct catatttatc tgctagattc gtctgctcta
      961 aataaatatt ttcatccgat ttcgtgaagt caatatgctt atgccaatca ttggttttct
     1021 ggcgatcagt taactcacga ttattatgag aaatacttgt attcttcgtt ccttttttaa
     1081 atgaaatact aaaccccaag ttaaaaccct ccttcgcgct gtcgctaata aaaagattgt
     1141 aaacctttct gttactcttt gtcaaagagt aacattttcc taattgtgac atggctgtca
     1201 caattccaaa tgctctccga gggtattcgc tgtcacaagt gacaacgaaa aaaggagccg
     1261 aaagcgtgtc acgctctcaa ctccttttac gctttatttt gcttcacgca aaataatcgc
     1321 ttatcgtaaa ttcacgtcat taaatattga cgtaaattta ctctcactca tctgactttt
     1381 cttattcggt atcactccga ataagccgtc agattcatcg ggataatctc gttcgcttgg
     1441 cgctgatttt tcatcagcaa gccactcatt atccactgat ttttcgtgtt gctgatcgtc
     1501 agaaatcgac gatagccacc gctcaaaatc agcaaaagtt tcaaacccaa aacgcttgcg
     1561 aagagccttg cccattgcag cattttcttt ctcaatcaag cgttttttct gttggcgaag
     1621 tttcgcttgt tcttttttta atttttcttc ttgcgcttta atatctgcta aagtcattcc
     1681 cataaactac atctcctttt ctttggaatt aataacggaa atttggttta actgcataac
     1741 atgactcatt aatttcaacc aaaattcttt ttctgattca tcagttgttt gcgctaaatg
     1801 cttatgaaca aattcattag tcaaaactga agattttgct agatcagcat tgataaccga
     1861 gttgagaaca tccatcattc gttcaagcat ttcactataa ttatcttcat ccggcaaatt
     1921 caaataatca gctaaccgtt catacatcaa ttcaattcta tcgactgttt cttctctcaa
     1981 atcaatttta tccatgtcac acctcacttc cagaattgcc accattttcg attttttaat
     2041 tcttgatttt ctagtaacaa ctgatcgttt ttttgttgct gaagcaaagt caatttttgt
     2101 tggtcacgaa tcatttccgt taattcagaa atatgcctat ctttttccgc taattgttca
     2161 cgcaaaaatt cattttcttt ttctaacggg aaatcattgc ctgcatcatt gaccggtaaa
     2221 tcaccagtca attgaccacc ttttgaccga taaattgacc gcacaacacc aatcaattcc
     2281 ttgtctaaca tgataacccc attatcttta taccgagcaa ggtcataacc tgcattgacc
     2341 agttgattgc gcactgtatt tttagatata cccaactcat cagcaaggtt ttttatggtc
     2401 attttttctg gcaaatcagt cattatcttc tccgttactt tcagctaccc cataaacata
     2461 tttaacagca tgcttaggga taatgattgg ggaatcaatt ttattatttt tcaaaatcaa
     2521 ctcatactgc gttacatcaa gtaacttacc ggacattttt ttgctatcca aaaaaacaac
     2581 gacaacgtta tcacctgtta aattcaccaa ccaatttttc ttaccaaaat gcttttgttt
     2641 ttctgccatt cttattcctc ctccgttaca tctaaccctt gaagccaagt gtctaattct
     2701 tttttcaaaa catctgctga ttccgaaaat gtttctcgta aatgattcgt caactcatca
     2761 ttttgacttt ctcttttcaa aatatctctc aatttgtatt tcattctacg ctctaaaaac
     2821 ccccacattt cagggttagc aatcagtcca aaaatcatca ccttatcatt tgtttttaca
     2881 tcaagtggta gaaaatgagg gctagcaaaa ctatttaaac tttcatgaac cattgcatgc
     2941 caatctgttg ctttcccacg ccttaactgc aattccagtc gccaccaagt ttctatttct
     3001 ggtggcacaa ttttacgctt ggtttcctgt tccaattttt tgttgtatag ccgaatctgg
     3061 cgttcgctgg cacgactgcc ccaataagct gtttccagct tcccagaccg cccataaatt
     3121 ggcttgaaag aaacaggatc aaccactcga tattgtgtaa taaactcatc aggcacatcg
     3181 ataatatcgc aagcaatatc cgcacgtgag aaatgtggtt ctagaaataa atcatgaatg
     3241 aaatttttca ttgaactagc taaaaaatga ccaatcttat tcgggttaaa atcaatccgc
     3301 cctttgccat cttgccattt caaaatctca atataagcaa tattttcttc gtattggtct
     3361 aataattgcc agccgttatt cccaaccgct tttaaatagc cattgccttc attcacccgc
     3421 attaattgct caaaatctaa aatcaacaca tcattttgag tgtgataata aatattttcc
     3481 ttcagttttc caacgatagt aattcggtca attgaccact gcatttttaa gggggtgtac
     3541 atattttgta catttaaccg cctgttagat agggctgtta aattttccca ctcatttacg
     3601 attatgccat ttttactcaa attttgttcc tcctcaaaga aaaagagact tctggaaaga
     3661 attttcaaaa gttcacgtaa ctcttaaaaa ttcattacca aaaaatctct agtcttgaag
     3721 aaatctaaaa atattcgtat aatgattaag aagttacgga gctagtgcga ttagtttccg
     3781 taaaggtcga gaacgttggt agcgttgctc gactattttt ttactctttt ttcagttcat
     3841 ttgtttgcta actcaataat agcacttctc tttagctatg caaatatcca aaaaataaaa
     3901 ccgcaccctt tgaaaagggc gcccccaaac ttcgctaacg ctaggttggc caaaaaatgg
     3961 actggccatt ttttagcaaa tgtcagctta ataggctagt ggtttagccg tcaactcctt
     4021 atcctcggca caaaccgcct ccggtaccgt tgactgcaca tcgtaactac cactcgatct
     4081 catcttcaga acgctctaat ttacgctgtg agacgttttg acgataaaat aaggttttct
     4141 cctgctctaa cacttctaat tcctcagaaa gccccatatc cttttctgca agaccaaaac
     4201 ggatagacaa acgagtgatc gatttttgaa atgcgttttt taatcgctct aaacgctggc
     4261 gtaaagagcg attttcttct ttcagctttt tattttccac ttgtaaatct gctaattgtt
     4321 ttctaccaga caaatgacgc tcttcttcca atgtagctac atactcattt aatt
//
