LOCUS       NZ_CP066604             4374 bp    DNA     circular CON 20-FEB-2024
DEFINITION  Enterococcus faecium strain Dallas 111 plasmid p111_4kb, complete
            sequence.
ACCESSION   NZ_CP066604
VERSION     NZ_CP066604.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN17038095
            Assembly: GCF_016415345.1
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  JOURNAL   Unpublished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                   :: 60.0x
            Sequencing Technology :: Illumina NextSeq; Oxford Nanopore MinION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 02/20/2024 02:48:21
            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)                     :: 3,043
            CDSs (total)                      :: 2,955
            Genes (coding)                    :: 2,822
            CDSs (with protein)               :: 2,822
            Genes (RNA)                       :: 88
            rRNAs                             :: 6, 6, 6 (5S, 16S, 23S)
            complete rRNAs                    :: 6, 6, 6 (5S, 16S, 23S)
            tRNAs                             :: 66
            ncRNAs                            :: 4
            Pseudo Genes (total)              :: 133
            CDSs (without protein)            :: 133
            Pseudo Genes (ambiguous residues) :: 0 of 133
            Pseudo Genes (frameshifted)       :: 63 of 133
            Pseudo Genes (incomplete)         :: 74 of 133
            Pseudo Genes (internal stop)      :: 26 of 133
            Pseudo Genes (multiple problems)  :: 27 of 133
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP066604.1.
            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 111"
                     /isolation_source="rectal swab"
                     /host="Homo sapiens"
                     /db_xref="taxon:1352"
                     /plasmid="p111_4kb"
                     /geo_loc_name="USA: Dallas"
                     /collection_date="2015"
     gene            complement(join(4033..4374,1..627))
                     /locus_tag="JCP62_RS15075"
                     /old_locus_tag="JCP62_15080"
     CDS             complement(join(4033..4374,1..627))
                     /locus_tag="JCP62_RS15075"
                     /old_locus_tag="JCP62_15080"
                     /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            complement(1074..2480)
                     /locus_tag="JCP62_RS15080"
                     /old_locus_tag="JCP62_15085"
     CDS             complement(1074..2480)
                     /locus_tag="JCP62_RS15080"
                     /old_locus_tag="JCP62_15085"
                     /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(2702..3064)
                     /locus_tag="JCP62_RS15085"
                     /old_locus_tag="JCP62_15090"
     CDS             complement(2702..3064)
                     /locus_tag="JCP62_RS15085"
                     /old_locus_tag="JCP62_15090"
                     /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(3068..3376)
                     /locus_tag="JCP62_RS15090"
                     /old_locus_tag="JCP62_15095"
     CDS             complement(3068..3376)
                     /locus_tag="JCP62_RS15090"
                     /old_locus_tag="JCP62_15095"
                     /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(3385..3804)
                     /locus_tag="JCP62_RS15095"
                     /old_locus_tag="JCP62_15100"
     CDS             complement(3385..3804)
                     /locus_tag="JCP62_RS15095"
                     /old_locus_tag="JCP62_15100"
                     /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(3797..4030)
                     /locus_tag="JCP62_RS15100"
                     /old_locus_tag="JCP62_15105"
     CDS             complement(3797..4030)
                     /locus_tag="JCP62_RS15100"
                     /old_locus_tag="JCP62_15105"
                     /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"
     Typing          complement(1078..2480)
                     /name="MOBV"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="91.88"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 tatttctggt ggcacaattt tacgcttggt ttcctgttcc aattttttgt tgtatagccg
       61 aatctggcgt tcgctggcac gactgcccca ataagctgtt tccagcttcc cagaccgccc
      121 ataaattggc ttgaaagaaa caggatcaac cactcgatat tgtgtaataa actcatcagg
      181 cacatcgata atatcgcaag caatatccgc acgtgagaaa tgtggttcta gaaataaatc
      241 atgaatgaaa tttttcattg aactagctaa aaaatgacca atcttattcg ggttaaaatc
      301 aatccgccct ttgccatctt gccatttcaa aatctcaata taagcaatat tttcttcgta
      361 ttggtctaat aattgccagc cgttattccc aaccgctttt aaatagccat tgccttcatt
      421 cacccgcatt aattgctcaa aatctaaaat caacacatca ttttgagtgt gataataaat
      481 attttccttc agttttccaa cgatagtaat tcggtcaatt gaccactgca tttttaaggg
      541 ggtgtacata ttttgtacat ttaaccgcct gttagatagg gctgttaaat tttcccactc
      601 atttacgatt atgccatttt tactcaaatt ttgttcctcc tcaaagaaaa agagacttct
      661 ggaaagaatt ttcaaaagtt cacgtaactc ttaaaaattc attaccaaaa aatctctagt
      721 cttgaagaaa tctaaaaata ttcgtataat gattaagaag ttacggagct agtgcgatta
      781 gtttccgtaa aggtcgagaa cgttggtagc gttgctcgac tattttttta ctcttttttc
      841 agttcatttg tttgctaact caataatagc acttctcttt agctatgcaa atatccaaaa
      901 aataaaaccg caccctttga aaagggcgcc cccaaacttc gctaacgcta ggttggccaa
      961 aaaatggact ggccattttt tagcaaatgt cagcttaata ggctagtggt ttagccgtca
     1021 actccttatc ctcggcacaa accgcctccg gtaccgttga ctgcacatcg taactaccac
     1081 tcgatctcat cttcagaacg ctctaattta cgctgtgaga cgttttgacg ataaaataag
     1141 gttttctcct gctctaacac ttctaattcc tcagaaagcc ccatatcctt ttctgcaaga
     1201 ccaaaacgga tagacaaacg agtgatcgat ttttgaaatg cgttttttaa tcgctctaaa
     1261 cgctggcgta aagagcgatt ttcttctttc agctttttat tttccacttg taaatctgct
     1321 aattgttttc taccagacaa atgacgctct tcttccaatg tagctacata ctcatttaat
     1381 tctgtatttt gctcaagcat ctgtaaatat tgctcactca tgttatcagc atttctcttg
     1441 gcatttgttg ctctcgtagc tcgttgatac aaatcaacaa aatcattccc agataaatga
     1501 tacgaaccat caggaagcct cttgaaactt tctaaaggaa ccatatcttt ttggaaaatg
     1561 accgccatct ctttttttac attcagcata tttttcttct cttcttcaat cttcgctctc
     1621 tcagaagcca tcagagcctt atcacgctcg ttttcttctc tttgcctaga aatatacctc
     1681 aactcatcag aaacgctctc acgctctttt acagccgttt ggcgcaattc agaaatttca
     1741 ctcatgattt ctttgtattc gtgaatatct ttaattttgt tggtaccgac aatatccctt
     1801 ttccaaccgt aatcattcat taatcgttct atagagtcaa cttcttgatt tctaaaatta
     1861 ttgaaaagca ctcgaccatt atctttatca gcgtgtatcc cttgttgaac cagtgcttta
     1921 ttaaagctcg gctgcttttg aacaccccgt ttataacctt cagcaaccgg cacaatattc
     1981 aagtgcaggt gcggacttat ttcgtcatta tgaataacag cattataaac agccaaatta
     2041 gggtttctct cttgaaactc cttgtaatac tgaaccaaaa ttttattggc aatcactcga
     2101 ttttgttcag cttgttgttt cgatatgcca gtagaagaac catctgctcg atttgtctgg
     2161 aaatcatcta aaatgcctat ttgcacaata aattctcgtt gaggttccaa ctttttatcc
     2221 ttgcgcactt tcgctaaata gtcctcgatt tttctatcgg ctcttttttg tttcgcatta
     2281 tatttttcta ccacttcgcc aaacaattcc tcatatttat ctgctagatt cgtctgctct
     2341 aaataaatat tttcatccga tttcgtgaag tcaatatgct tatgccaatc attggttttc
     2401 tggcgatcag ttaactcacg attattatga gaaatacttg tattcttcgt tcctttttta
     2461 aatgaaatac taaaccccaa gttaaaaccc tccttcgcgc tgtcgctaat aaaaagattg
     2521 taaacctttc tgttactctt tgtcaaagag taacattttc ctaattgtga catggctgtc
     2581 acaattccaa atgctctccg agggtattcg ctgtcacaag tgacaacgaa aaaaggagcc
     2641 gaaagcgtgt cacgctctca actcctttta cgctttattt tgcttcacgc aaaataatcg
     2701 cttatcgtaa attcacgtca ttaaatattg acgtaaattt actctcactc atctgacttt
     2761 tcttattcgg tatcactccg aataagccgt cagattcatc gggataatct cgttcgcttg
     2821 gcgctgattt ttcatcagca agccactcat tatccactga tttttcgtgt tgctgatcgt
     2881 cagaaatcga cgatagccac cgctcaaaat cagcaaaagt ttcaaaccca aaacgcttgc
     2941 gaagagcctt gcccattgca gcattttctt tctcaatcaa gcgttttttc tgttggcgaa
     3001 gtttcgcttg ttcttttttt aatttttctt cttgcgcttt aatatctgct aaagtcattc
     3061 ccataaacta catctccttt tctttggaat taataacgga aatttggttt aactgcataa
     3121 catgactcat taatttcaac caaaattctt tttctgattc atcagttgtt tgcgctaaat
     3181 gcttatgaac aaattcatta gtcaaaactg aagattttgc tagatcagca ttgataaccg
     3241 agttgagaac atccatcatt cgttcaagca tttcactata attatcttca tccggcaaat
     3301 tcaaataatc agctaaccgt tcatacatca attcaattct atcgactgtt tcttctctca
     3361 aatcaatttt atccatgtca cacctcactt ccagaattgc caccattttc gattttttaa
     3421 ttcttgattt tctagtaaca actgatcgtt tttttgttgc tgaagcaaag tcaatttttg
     3481 ttggtcacga atcatttccg ttaattcaga aatatgccta tctttttccg ctaattgttc
     3541 acgcaaaaat tcattttctt tttctaacgg gaaatcattg cctgcatcat tgaccggtaa
     3601 atcaccagtc aattgaccac cttttgaccg ataaattgac cgcacaacac caatcaattc
     3661 cttgtctaac atgataaccc cattatcttt ataccgagca aggtcataac ctgcattgac
     3721 cagttgattg cgcactgtat ttttagatat acccaactca tcagcaaggt tttttatggt
     3781 cattttttct ggcaaatcag tcattatctt ctccgttact ttcagctacc ccataaacat
     3841 atttaacagc atgcttaggg ataatgattg gggaatcaat tttattattt ttcaaaatca
     3901 actcatactg cgttacatca agtaacttac cggacatttt tttgctatcc aaaaaaacaa
     3961 cgacaacgtt atcacctgtt aaattcacca accaattttt cttaccaaaa tgcttttgtt
     4021 tttctgccat tcttattcct cctccgttac atctaaccct tgaagccaag tgtctaattc
     4081 ttttttcaaa acatctgctg attccgaaaa tgtttctcgt aaatgattcg tcaactcatc
     4141 attttgactt tctcttttca aaatatctct caatttgtat ttcattctac gctctaaaaa
     4201 cccccacatt tcagggttag caatcagtcc aaaaatcatc accttatcat ttgtttttac
     4261 atcaagtggt agaaaatgag ggctagcaaa actatttaaa ctttcatgaa ccattgcatg
     4321 ccaatctgtt gctttcccac gccttaactg caattccagt cgccaccaag tttc
//
