LOCUS       NZ_CP066619             4305 bp    DNA     circular CON 20-FEB-2024
DEFINITION  Enterococcus faecium strain Dallas 124_3 plasmid p124_3_4.3kb,
            complete sequence.
ACCESSION   NZ_CP066619
VERSION     NZ_CP066619.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN17038100
            Assembly: GCF_016415365.1
KEYWORDS    RefSeq.
SOURCE      Enterococcus faecium
  ORGANISM  Enterococcus faecium
            Bacteria; Bacillota; Bacilli; Lactobacillales; Enterococcaceae;
            Enterococcus.
REFERENCE   1  (bases 1 to 4305)
  AUTHORS   Islam,M.J. and Palmer,K.
  TITLE     Molecular characterization of VREfm isolates from Dallas, Texas
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 4305)
  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                   :: 299.0x
            Sequencing Technology :: Illumina NextSeq; Oxford Nanopore MinION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 02/20/2024 02:58:57
            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)                     :: 3,103
            CDSs (total)                      :: 3,012
            Genes (coding)                    :: 2,889
            CDSs (with protein)               :: 2,889
            Genes (RNA)                       :: 91
            rRNAs                             :: 6, 5, 6 (5S, 16S, 23S)
            complete rRNAs                    :: 6, 5, 6 (5S, 16S, 23S)
            tRNAs                             :: 70
            ncRNAs                            :: 4
            Pseudo Genes (total)              :: 123
            CDSs (without protein)            :: 123
            Pseudo Genes (ambiguous residues) :: 0 of 123
            Pseudo Genes (frameshifted)       :: 41 of 123
            Pseudo Genes (incomplete)         :: 74 of 123
            Pseudo Genes (internal stop)      :: 32 of 123
            Pseudo Genes (multiple problems)  :: 20 of 123
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP066619.1.
            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..4305
                     /organism="Enterococcus faecium"
                     /mol_type="genomic DNA"
                     /strain="Dallas 124_3"
                     /isolation_source="rectal swab"
                     /host="Homo sapiens"
                     /db_xref="taxon:1352"
                     /plasmid="p124_3_4.3kb"
                     /geo_loc_name="USA: Dallas"
                     /collection_date="2015"
     gene            complement(158..520)
                     /locus_tag="JCP92_RS15365"
                     /old_locus_tag="JCP92_15365"
     CDS             complement(158..520)
                     /locus_tag="JCP92_RS15365"
                     /old_locus_tag="JCP92_15365"
                     /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_002313294.1"
                     /translation="MGMTLADIKVQEEKLKKEQAKLRQQKKRLIEKENAAMGKALRKRF
                     GFESFADFERWLSSISDDQQHEKSVGNELRADEKSAPSERNYPNESDGIFGGIPNRKSQ
                     MSESGFASMFSDVNSR"
                     /name="hypothetical protein"
     gene            complement(524..832)
                     /locus_tag="JCP92_RS15370"
                     /old_locus_tag="JCP92_15370"
     CDS             complement(524..832)
                     /locus_tag="JCP92_RS15370"
                     /old_locus_tag="JCP92_15370"
                     /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_002304909.1"
                     /translation="MDKIDLREETVNRIEVMYERLADYLNLSDEDNYSEMLERMMDVLN
                     SVINADLAKSSVLTNEFVHKHLAQTTDEAEKEFWLKLMSHIMQLNQISVINSKEKGM"
                     /name="hypothetical protein"
     gene            complement(841..1260)
                     /locus_tag="JCP92_RS15375"
                     /old_locus_tag="JCP92_15375"
     CDS             complement(841..1260)
                     /locus_tag="JCP92_RS15375"
                     /old_locus_tag="JCP92_15375"
                     /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_002305964.1"
                     /translation="MTDSTDKMTIKALADELGITKNTVRNYLVKAGYDLARYKKNGIIL
                     LDKELIGVARSIYRSKGGQLTGHLPVNSTGSDFPLEKENEFLRDQLAEKDKHISELTEM
                     IRDQQKLTLLQQQKNDQLLLENQELKNRKWWQFWK"
                     /name="hypothetical protein"
     gene            complement(1257..2246)
                     /locus_tag="JCP92_RS15380"
                     /old_locus_tag="JCP92_15380"
     CDS             complement(1257..2246)
                     /locus_tag="JCP92_RS15380"
                     /old_locus_tag="JCP92_15380"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002349057.1"
                     /GO_function="GO:0003677 - DNA binding [Evidence IEA]"
                     /GO_process="GO:0006260 - DNA replication [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="protein rep"
                     /protein_id="WP_002304903.1"
                     /translation="MKKKKQDLINGTFREKKKNLKKVVAFSDNRISPKMRELMTGCGSY
                     LEFIATIDKEKKKLVQAHFCKNRFCPLCAWRKARKDSMMLSIMMQAIAEEKQYQFIFMT
                     LTTPNVKAECLNDEIDLFNHALKKMFMRKRVKTSIKGYVRKLEITYNKKRNDYNPHFHL
                     ILAVNKSYFTDKDYYIKQSEWLDLWREVTGKTGINPDGTDEITQLDIRKVKGFQQEKAV
                     QEVAKYSAKDFELTESQEVFDTFYHAMKGRQLITFNGVFKEYKKKYESGDLDRYKKKDE
                     NEYFWFLTASWMRKESKYAVDYREMSADERNYFSGMYVDEKSVEGENE"
                     /name="protein rep"
     gene            complement(2835..4241)
                     /locus_tag="JCP92_RS15385"
                     /old_locus_tag="JCP92_15385"
     CDS             complement(2835..4241)
                     /locus_tag="JCP92_RS15385"
                     /old_locus_tag="JCP92_15385"
                     /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_002304901.1"
                     /translation="MGFSISFKKGTKNTSISHNNRELTDSQKINDWHKHIDFTKSDENI
                     YLEQINIREKYEELFGEAVEKYNAKQKRADRKIEDYLAKVRKDKKMEPQREFIVQIGTL
                     DDFRTTRDDGSSTGISEQQAEQNRVIANKILVEYFKEFKERNPSLSVYNAVIHNDEVSP
                     HLHLNIVPVAEGYKRGVQKQPSFNKALQQQGLRADKENGRVIWNNFRNQEVESIERLMA
                     DFGWERELVGTNKIKDIHEYKEIMSEISELRQTAVKERESVSDELRYICRQREENEREK
                     ALVASERAKIEEEKKNMLNVKKEMAVIFQKDMVPLESFKRLPDGSYHLSGNDFVDLYQR
                     ATRATNAKRNADNMSEQYLQMLEQNTELNEYVAALEEERHLSGRKQLADLQVENKKLKE
                     ENRSLRQRLERLKNAFQKSITRLSIRFGLAEKDMGLSEELEVLEQEKTLFYRQNVSQHK
                     LERSEDEIEW"
                     /name="plasmid recombination protein"
     Typing          complement(2839..4241)
                     /name="MOBV"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="99.359"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 aaagagtaac gttttcctaa ttgtgacatg actgtcacaa ttccaaacgc tctccgaggg
       61 ttttcgccgt cacaagtgac aacgaaaaaa ggagccgaaa gcgtgtcacg ctctcaactc
      121 cttttacgct ttattttgct tcatgcaaaa tattcgctta tcgtgaattt acgtcactaa
      181 acattgacgc aaatccactc tcactcatct gactttttct attcggtatc cctccgaata
      241 ttccgtcaga ttcgttaggg taattccgtt cgcttggtgc tgatttttca tcagctcgca
      301 actcattacc cactgatttt tcgtgttgct gatcgtcaga aatcgacgat agccaccgct
      361 caaaatcagc aaaagattca aacccaaaac gcttgcgaag agccttgccc attgcagcat
      421 tttctttctc aatcaatcgt ttcttctgtt ggcgaagttt cgcctgttct ttttttaatt
      481 tttcttcttg cactttaata tctgctaaag tcattcccat aaactacatc cccttttctt
      541 tggaattaat aacggaaatt tggtttaact gcataatatg actcattaat ttcaaccaaa
      601 attctttttc agcttcatca gttgtttgcg ctaaatgctt atgaacaaat tcattagtca
      661 aaactgaaga ttttgctaga tcagcattga taaccgagtt gagaacatcc atcattcgtt
      721 caagcatctc actataatta tcttcatccg aaagattcaa ataatcagct aaccgttcat
      781 acatcacttc aattctattg actgtttctt ctctcaaatc aattttatcc atgtcacatc
      841 tcacttccag aattgccacc attttcgatt ttttaattct tgattttcta gtaacaactg
      901 atcgtttttt tgttgctgaa gcagggtcaa tttttgttga tcacgaatca tttctgttaa
      961 ttcagaaata tgtttgtcct tctcagctaa ttgatcacgc aaaaactcat tctctttttc
     1021 caaaggaaaa tcactgcccg tgctattgac cggtaaatga ccagtcaatt gaccaccttt
     1081 tgaccgataa attgaccgag caacaccaat caactctttg tctagcaaga taattccatt
     1141 tttcttgtac cgagcaagat catatccggc tttgactaga taatttctca ctgtattttt
     1201 ggttattcct agttcatcag caagcgcctt aattgtcatt ttatccgttg aatcagtcat
     1261 tcattttccc cctcaacaga tttttcatcg acatacattc ctgaaaaata atttctttca
     1321 tcagcactca tctcacgata atcaaccgca tatttcgatt ctttcctcat ccacgaagca
     1381 gtcaaaaacc aaaaatattc attctcatct tttttcttat aacgatcaag gtcacccgac
     1441 tcatattttt tcttgtattc tttgaataca ccgttaaacg taatcaactg acgacctttc
     1501 attgcatgat agaatgtgtc aaacacttcc tgactttcgg tcagttcaaa atcttttgcc
     1561 gaatatttcg caacttcctg tactgctttt tcttgttgga accctttgac cttgcgaata
     1621 tccaactggg taatttcgtc ggtaccatcc ggattaattc ccgtttttcc ggtcacttcc
     1681 cgccacaaat ctaaccattc cgattgcttg atataataat ctttatccgt gaaataagat
     1741 ttatttactg ccaaaatcaa gtgaaaatgc gggttatagt cattccgttt tttgttgtac
     1801 gtgatttcca attttcgcac atagccttta atcgaagtct taacccgttt gcgcataaac
     1861 atctttttca atgcatgatt aaacaaatca atttcatcgt tcaaacattc cgcttttaca
     1921 ttcggtgtcg tcaacgtcat aaaaataaat tgatactgct tttcttccgc aatagcttgc
     1981 atcataatcg acaacatcat cgaatcctta cgagctttac gccaagcaca taacggacag
     2041 aaacgatttt tacaaaagtg agcttggacc aatttctttt tctccttatc aatcgttgca
     2101 ataaattcta aatatgaacc acagcctgtc atcaattcac gcattttggg agaaattcga
     2161 ttatcactaa atgccaccac ttttttcaaa tttttctttt tttctcgaaa tgttccgtta
     2221 atcaaatctt gctttttctt tttcatcttg ctatactgaa tctacaaatt ttgtatacaa
     2281 aaaaggctga aaagccgata acaaaaaata gattgctctc ctttctagtt tagttttttt
     2341 ctagtcaatt aaaactataa aatactaggg aagaaaaagc aatctttttt tttgttcttc
     2401 cttagagcca caagggatag acccatacta tagccccgat ttcttcgcag aaatagttgc
     2461 ctatagtatc aagataagaa aaaacatcaa aaaagagggc gaaaatcgcc cccttttttt
     2521 cgttttaaaa ccccaaaacc caaagacata aaattcgatc aatcgaccac tgcattttta
     2581 agggggtgta catattttgt acatttaacc gcctgttaga tagggctgtt aaattttccc
     2641 actcattctt agtcatgcaa acataaaacc gcacccttta aaaagggcgc ccccaaactt
     2701 cgctaacgct aagttggcca aaaaatggac ttgccatttt ttagcaaatg tcagcttaat
     2761 aggctagtgg tttagccgtc aactccttat cctcggcaca aaccgcctcc ggtaccgttg
     2821 actgcacatc gtaactacca ctcgatctca tcttcagaac gctctaattt atgctgtgag
     2881 acgttttgac gataaaataa ggttttctcc tgctctaata cttctaattc ctcagaaagc
     2941 cccatatcct tttctgcaag cccaaaacgg atagacaaac gagtgatcga tttttgaaat
     3001 gcgtttttta atcgctctaa acgctggcgt aaagagcgat tttcttcttt cagcttttta
     3061 ttttccactt gtaaatctgc taattgtttt ctaccagaca aatgacgctc ttcttccaat
     3121 gcagctacat actcatttaa ttctgtattt tgctcaagca tctgtaaata ttgctcactc
     3181 atgttatcag catttctctt ggcatttgtt gctctcgtag ctcgttgata caaatcaaca
     3241 aaatcattcc cagataaatg atacgaacca tcaggaagcc tcttgaaact ttctaaagga
     3301 accatatctt tttggaaaat gaccgccatc tcttttttta cattcagcat atttttcttc
     3361 tcttcttcaa tcttcgctct ctcagaagcc accagagcct tctcacgctc gttttcttct
     3421 ctttgcctac aaatatacct caactcatca gaaacgctct cacgctcttt tacggccgtt
     3481 tgacgcaatt cggaaatttc gctcatgatt tctttgtatt catgaatatc tttgattttg
     3541 ttagtaccga ctaactcacg ctcccaacca aaatctgcca tcaaacgttc aattgactca
     3601 acttcctgat tcctaaaatt attccaaatc actcgaccat tctctttatc tgctcgtaaa
     3661 ccctgctgtt gcaaggcttt gttaaaactt ggttgctttt gaacaccccg tttataccct
     3721 tcagcaacag gaacaatatt caaatgcagg tgcggactta cttcgtcatt atgaataaca
     3781 gcattgtaga cggataaact aggattccgt tctttaaatt ctttgaaata ctcaactaaa
     3841 attttgttgg caatcactcg attttgttct gcttgttgtt ccgatatgcc agtagaagaa
     3901 ccatcatcac gagtagtacg aaaatcatca agagtaccaa tttgcacgat aaattctcgc
     3961 tgtggttcca tttttttatc cttgcgaacc tttgctaaat agtcctcaat ttttctatcg
     4021 gctcttttct gctttgcatt atatttttct acggcttcac cgaataattc ttcatatttt
     4081 tcacgaatat ttatttgttc caaatagata ttttcatccg attttgtgaa atcaatatgc
     4141 ttatgccagt cattgatttt ttggctatca gttaactcac gattattatg agaaatgctt
     4201 gtattctttg ttcccttttt gaacgaaata ctaaacccca agttaaaccc ctccttcgcg
     4261 ctgtcgctaa taaaaagagt gtaaaccttt ctgttactct ttgtc
//
