LOCUS       NZ_CP066479             4374 bp    DNA     circular CON 20-FEB-2024
DEFINITION  Enterococcus faecium strain Dallas 93_2 plasmid p93_2_4kb, complete
            sequence.
ACCESSION   NZ_CP066479
VERSION     NZ_CP066479.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN17038088
            Assembly: GCF_016406605.1
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  JOURNAL   Unpublished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                   :: 261.0x
            Sequencing Technology :: Illumina NextSeq; Oxford Nanopore MinION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 02/20/2024 02:57:12
            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)                     :: 3,140
            CDSs (total)                      :: 3,047
            Genes (coding)                    :: 2,906
            CDSs (with protein)               :: 2,906
            Genes (RNA)                       :: 93
            rRNAs                             :: 6, 6, 6 (5S, 16S, 23S)
            complete rRNAs                    :: 6, 6, 6 (5S, 16S, 23S)
            tRNAs                             :: 71
            ncRNAs                            :: 4
            Pseudo Genes (total)              :: 141
            CDSs (without protein)            :: 141
            Pseudo Genes (ambiguous residues) :: 0 of 141
            Pseudo Genes (frameshifted)       :: 51 of 141
            Pseudo Genes (incomplete)         :: 81 of 141
            Pseudo Genes (internal stop)      :: 31 of 141
            Pseudo Genes (multiple problems)  :: 18 of 141
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP066479.1.
            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 93_2"
                     /isolation_source="rectal swab"
                     /host="Homo sapiens"
                     /db_xref="taxon:1352"
                     /plasmid="p93_2_4kb"
                     /geo_loc_name="USA: Dallas"
                     /collection_date="2015"
     gene            complement(join(3754..4374,1..348))
                     /locus_tag="JCP72_RS15520"
                     /old_locus_tag="JCP72_15520"
     CDS             complement(join(3754..4374,1..348))
                     /locus_tag="JCP72_RS15520"
                     /old_locus_tag="JCP72_15520"
                     /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(795..2201)
                     /locus_tag="JCP72_RS15525"
                     /old_locus_tag="JCP72_15525"
     CDS             complement(795..2201)
                     /locus_tag="JCP72_RS15525"
                     /old_locus_tag="JCP72_15525"
                     /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_198887271.1"
                     /translation="MGFSISFKKGTKNTSISHNNRELTDRQKTNDWHKHIDFTKSDENI
                     YLEQTNLADKYEELFGEVVEKYNAKQKRADRKIEDYLAKVRKDKKLEPQREFIVQIGIL
                     DDFQTNRADGSSTGISKQQAEQNRVIANKILVQYYKEFQERNPNLAVYNAVIHNDEISP
                     HLHLNIVPVAEGYKRGVQKQPSFNKALVQQGIHADKDNGRVLFNNFRNQEVDSIERLMN
                     DYGWKRDIVGTNKIKDIHEYKEIMSEISELRQTAVKERESVSDELRYISRQREENERDK
                     ALMASERAKIEEEKKNTLNVKKEMAVIFQKDMVPLESFKRLPDGSYHLSGNDFVDLYQR
                     ATRATNAKRNADNMSEQYLQMLEQNTELNEYVATLEEERHLSGRKQLADLQVENKKLKE
                     ENRSLRQRLERLKNAFQKSITRLSIRFGLAEKDMGLSEELEVLEQEKTLFYRQNVSQRK
                     LERSEDEIEW"
                     /name="plasmid recombination protein"
     gene            complement(2423..2785)
                     /locus_tag="JCP72_RS15530"
                     /old_locus_tag="JCP72_15530"
     CDS             complement(2423..2785)
                     /locus_tag="JCP72_RS15530"
                     /old_locus_tag="JCP72_15530"
                     /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(2789..3097)
                     /locus_tag="JCP72_RS15535"
                     /old_locus_tag="JCP72_15535"
     CDS             complement(2789..3097)
                     /locus_tag="JCP72_RS15535"
                     /old_locus_tag="JCP72_15535"
                     /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(3106..3525)
                     /locus_tag="JCP72_RS15540"
                     /old_locus_tag="JCP72_15540"
     CDS             complement(3106..3525)
                     /locus_tag="JCP72_RS15540"
                     /old_locus_tag="JCP72_15540"
                     /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(3518..3751)
                     /locus_tag="JCP72_RS15545"
                     /old_locus_tag="JCP72_15545"
     CDS             complement(3518..3751)
                     /locus_tag="JCP72_RS15545"
                     /old_locus_tag="JCP72_15545"
                     /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(3762..4372)
                     /name="rep_cluster_943"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="83.037"
                     /coverage="97.0"
                     /evalue="2.33e-153"
     Typing          complement(799..2201)
                     /name="MOBV"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="91.667"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 aatcttattc gggttaaaat caatccgccc tttgccatct tgccatttca aaatctcaat
       61 ataagcaata ttttcttcgt attggtctaa taattgccag ccgttattcc caaccgcttt
      121 taaatagcca ttgccttcat tcacccgcat taattgctca aaatctaaaa tcaacacatc
      181 attttgagtg tgataataaa tattttcctt cagttttcca acgatagtaa ttcggtcaat
      241 tgaccactgc atttttaagg gggtgtacat attttgtaca tttaaccgcc tgttagatag
      301 ggctgttaaa ttttcccact catttacgat tatgccattt ttactcaaat tttgttcctc
      361 ctcaaagaaa aagagacttc tggaaagaat tttcaaaagt tcacgtaact cttaaaaatt
      421 cattaccaaa aaatctctag tcttgaagaa atctaaaaat attcgtataa tgattaagaa
      481 gttacggagc tagtgcgatt agtttccgta aaggtcgaga acgttggtag cgttgctcga
      541 ctattttttt actctttttt cagttcattt gtttgctaac tcaataatag cacttctctt
      601 tagctatgca aatatccaaa aaataaaacc gcaccctttg aaaagggcgc ccccaaactt
      661 cgctaacgct aggttggcca aaaaatggac tggccatttt ttagcaaatg tcagcttaat
      721 aggctagtgg tttagccgtc aactccttat cctcggcaca aaccgcctcc ggtaccgttg
      781 actgcacatc gtaactacca ctcgatctca tcttcagaac gctctaattt acgctgtgag
      841 acgttttgac gataaaataa ggttttctcc tgctctaaca cttctaattc ctcagaaagc
      901 cccatatcct tttctgcaag accaaaacgg atagacaaac gagtgatcga tttttgaaat
      961 gcgtttttta atcgctctaa acgctggcgt aaagagcgat tttcttcttt cagcttttta
     1021 ttttccactt gtaaatctgc taattgtttt ctaccagaca aatgacgctc ttcttccaat
     1081 gtagctacat actcatttaa ttctgtattt tgctcaagca tctgtaaata ttgctcactc
     1141 atgttatcag catttctctt ggcatttgtt gctctcgtag ctcgttgata caaatcaaca
     1201 aaatcattcc cagataaatg atacgaacca tcaggaagcc tcttgaaact ttctaaagga
     1261 accatatctt tttggaaaat gaccgccatc tcttttttta cattcagcgt atttttcttc
     1321 tcttcttcaa tcttcgctct ctcagaagcc atcagagcct tatcacgctc gttttcttct
     1381 ctttgcctag aaatatacct caactcatca gaaacgctct cacgctcttt tacagccgtt
     1441 tggcgcaatt cagaaatttc actcatgatt tctttgtatt cgtgaatatc tttaattttg
     1501 ttggtaccga caatatccct tttccaaccg taatcattca ttaatcgttc tatagagtca
     1561 acttcttgat ttctaaaatt attgaaaagc actcgaccat tatctttatc agcgtgtatc
     1621 ccttgttgaa ccagtgcttt attaaagctc ggctgctttt gaacaccccg tttataacct
     1681 tcagcaaccg gcacaatatt caagtgcagg tgcggactta tttcgtcatt atgaataaca
     1741 gcattataaa cagccaaatt agggtttctc tcttgaaact ccttgtaata ctgaaccaaa
     1801 attttattgg caatcactcg attttgttca gcttgttgtt tcgatatgcc agtagaagaa
     1861 ccatctgctc gatttgtctg gaaatcatct aaaatgccta tttgcacaat aaattctcgt
     1921 tgaggttcca actttttatc cttgcgcact ttcgctaaat agtcctcgat ttttctatcg
     1981 gctctttttt gtttcgcatt atatttttct accacttcgc caaacaattc ctcatattta
     2041 tctgctagat tcgtctgctc taaataaata ttttcatccg atttcgtgaa gtcaatatgc
     2101 ttatgccaat cattggtttt ctggcgatca gttaactcac gattattatg agaaatactt
     2161 gtattcttcg ttcctttttt aaatgaaata ctaaacccca agttaaaacc ctccttcgcg
     2221 ctgtcgctaa taaaaagatt gtaaaccttt ctgttactct ttgtcaaaga gtaacatttt
     2281 cctaattgtg acatggctgt cacaattcca aatgctctcc gagggtattc gctgtcacaa
     2341 gtgacaacga aaaaaggagc cgaaagcgtg tcacgctctc aactcctttt acgctttatt
     2401 ttgcttcacg caaaataatc gcttatcgta aattcacgtc attaaatatt gacgtaaatt
     2461 tactctcact catctgactt ttcttattcg gtatcactcc gaataagccg tcagattcat
     2521 cgggataatc tcgttcgctt ggcgctgatt tttcatcagc aagccactca ttatccactg
     2581 atttttcgtg ttgctgatcg tcagaaatcg acgatagcca ccgctcaaaa tcagcaaaag
     2641 tttcaaaccc aaaacgcttg cgaagagcct tgcccattgc agcattttct ttctcaatca
     2701 agcgtttttt ctgttggcga agtttcgctt gttctttttt taatttttct tcttgcgctt
     2761 taatatctgc taaagtcatt cccataaact acatctcctt ttctttggaa ttaataacgg
     2821 aaatttggtt taactgcata acatgactca ttaatttcaa ccaaaattct ttttctgatt
     2881 catcagttgt ttgcgctaaa tgcttatgaa caaattcatt agtcaaaact gaagattttg
     2941 ctagatcagc attgataacc gagttgagaa catccatcat tcgttcaagc atttcactat
     3001 aattatcttc atccggcaaa ttcaaataat cagctaaccg ttcatacatc aattcaattc
     3061 tatcgactgt ttcttctctc aaatcaattt tatccatgtc acacctcact tccagaattg
     3121 ccaccatttt cgatttttta attcttgatt ttctagtaac aactgatcgt ttttttgttg
     3181 ctgaagcaaa gtcaattttt gttggtcacg aatcatttcc gttaattcag aaatatgcct
     3241 atctttttcc gctaattgtt cacgcaaaaa ttcattttct ttttctaacg ggaaatcatt
     3301 gcctgcatca ttgaccggta aatcaccagt caattgacca ccttttgacc gataaattga
     3361 ccgcacaaca ccaatcaatt ccttgtctaa catgataacc ccattatctt tataccgagc
     3421 aaggtcataa cctgcattga ccagttgatt gcgcactgta tttttagata tacccaactc
     3481 atcagcaagg ttttttatgg tcattttttc tggcaaatca gtcattatct tctccgttac
     3541 tttcagctac cccataaaca tatttaacag catgcttagg gataatgatt ggggaatcaa
     3601 ttttattatt tttcaaaatc aactcatact gcgttacatc aagtaactta ccggacattt
     3661 ttttgctatc caaaaaaaca acgacaacgt tatcacctgt taaattcacc aaccaatttt
     3721 tcttaccaaa atgcttttgt ttttctgcca ttcttattcc tcctccgtta catctaaccc
     3781 ttgaagccaa gtgtctaatt cttttttcaa aacatctgct gattccgaaa atgtttctcg
     3841 taaatgattc gtcaactcat cattttgact ttctcttttc aaaatatctc tcaatttgta
     3901 tttcattcta cgctctaaaa acccccacat ttcagggtta gcaatcagtc caaaaatcat
     3961 caccttatca tttgttttta catcaagtgg tagaaaatga gggctagcaa aactatttaa
     4021 actttcatga accattgcat gccaatctgt tgctttccca cgccttaact gcaattccag
     4081 tcgccaccaa gtttctattt ctggtggcac aattttacgc ttggtttcct gttccaattt
     4141 tttgttgtat agccgaatct ggcgttcgct ggcacgactg ccccaataag ctgtttccag
     4201 cttcccagac cgcccataaa ttggcttgaa agaaacagga tcaaccactc gatattgtgt
     4261 aataaactca tcaggcacat cgataatatc gcaagcaata tccgcacgtg agaaatgtgg
     4321 ttctagaaat aaatcatgaa tgaaattttt cattgaacta gctaaaaaat gacc
//
