LOCUS       NZ_CP066449             4305 bp    DNA     circular CON 20-FEB-2024
DEFINITION  Enterococcus faecium strain Dallas 71_2 plasmid p71_2_4.3kb,
            complete sequence.
ACCESSION   NZ_CP066449
VERSION     NZ_CP066449.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN17038083
            Assembly: GCF_016406525.1
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  JOURNAL   Unpublished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 (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                   :: 148.0x
            Sequencing Technology :: Illumina NextSeq; Oxford Nanopore MinION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 02/20/2024 02:51:51
            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)                     :: 3,192
            CDSs (total)                      :: 3,100
            Genes (coding)                    :: 2,971
            CDSs (with protein)               :: 2,971
            Genes (RNA)                       :: 92
            rRNAs                             :: 6, 5, 6 (5S, 16S, 23S)
            complete rRNAs                    :: 6, 5, 6 (5S, 16S, 23S)
            tRNAs                             :: 71
            ncRNAs                            :: 4
            Pseudo Genes (total)              :: 129
            CDSs (without protein)            :: 129
            Pseudo Genes (ambiguous residues) :: 0 of 129
            Pseudo Genes (frameshifted)       :: 45 of 129
            Pseudo Genes (incomplete)         :: 70 of 129
            Pseudo Genes (internal stop)      :: 37 of 129
            Pseudo Genes (multiple problems)  :: 20 of 129
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP066449.1.
            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 71_2"
                     /isolation_source="rectal swab"
                     /host="Homo sapiens"
                     /db_xref="taxon:1352"
                     /plasmid="p71_2_4.3kb"
                     /geo_loc_name="USA: Dallas"
                     /collection_date="2015"
     gene            join(4281..4305,1..284)
                     /locus_tag="JCP66_RS15830"
                     /old_locus_tag="JCP66_15830"
     CDS             join(4281..4305,1..284)
                     /locus_tag="JCP66_RS15830"
                     /old_locus_tag="JCP66_15830"
                     /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            288..650
                     /locus_tag="JCP66_RS15835"
                     /old_locus_tag="JCP66_15835"
     CDS             288..650
                     /locus_tag="JCP66_RS15835"
                     /old_locus_tag="JCP66_15835"
                     /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            872..2278
                     /locus_tag="JCP66_RS15840"
                     /old_locus_tag="JCP66_15840"
     CDS             872..2278
                     /locus_tag="JCP66_RS15840"
                     /old_locus_tag="JCP66_15840"
                     /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"
     gene            2867..3856
                     /locus_tag="JCP66_RS15845"
                     /old_locus_tag="JCP66_15845"
     CDS             2867..3856
                     /locus_tag="JCP66_RS15845"
                     /old_locus_tag="JCP66_15845"
                     /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            3853..4272
                     /locus_tag="JCP66_RS15850"
                     /old_locus_tag="JCP66_15850"
     CDS             3853..4272
                     /locus_tag="JCP66_RS15850"
                     /old_locus_tag="JCP66_15850"
                     /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"
     Typing          873..2275
                     /name="MOBV"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="99.359"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 aaacagtcaa tagaattgaa gtgatgtatg aacggttagc tgattatttg aatctttcgg
       61 atgaagataa ttatagtgag atgcttgaac gaatgatgga tgttctcaac tcggttatca
      121 atgctgatct agcaaaatct tcagttttga ctaatgaatt tgttcataag catttagcgc
      181 aaacaactga tgaagctgaa aaagaatttt ggttgaaatt aatgagtcat attatgcagt
      241 taaaccaaat ttccgttatt aattccaaag aaaaggggat gtagtttatg ggaatgactt
      301 tagcagatat taaagtgcaa gaagaaaaat taaaaaaaga acaggcgaaa cttcgccaac
      361 agaagaaacg attgattgag aaagaaaatg ctgcaatggg caaggctctt cgcaagcgtt
      421 ttgggtttga atcttttgct gattttgagc ggtggctatc gtcgatttct gacgatcagc
      481 aacacgaaaa atcagtgggt aatgagttgc gagctgatga aaaatcagca ccaagcgaac
      541 ggaattaccc taacgaatct gacggaatat tcggagggat accgaataga aaaagtcaga
      601 tgagtgagag tggatttgcg tcaatgttta gtgacgtaaa ttcacgataa gcgaatattt
      661 tgcatgaagc aaaataaagc gtaaaaggag ttgagagcgt gacacgcttt cggctccttt
      721 tttcgttgtc acttgtgacg gcgaaaaccc tcggagagcg tttggaattg tgacagtcat
      781 gtcacaatta ggaaaacgtt actctttgac aaagagtaac agaaaggttt acactctttt
      841 tattagcgac agcgcgaagg aggggtttaa cttggggttt agtatttcgt tcaaaaaggg
      901 aacaaagaat acaagcattt ctcataataa tcgtgagtta actgatagcc aaaaaatcaa
      961 tgactggcat aagcatattg atttcacaaa atcggatgaa aatatctatt tggaacaaat
     1021 aaatattcgt gaaaaatatg aagaattatt cggtgaagcc gtagaaaaat ataatgcaaa
     1081 gcagaaaaga gccgatagaa aaattgagga ctatttagca aaggttcgca aggataaaaa
     1141 aatggaacca cagcgagaat ttatcgtgca aattggtact cttgatgatt ttcgtactac
     1201 tcgtgatgat ggttcttcta ctggcatatc ggaacaacaa gcagaacaaa atcgagtgat
     1261 tgccaacaaa attttagttg agtatttcaa agaatttaaa gaacggaatc ctagtttatc
     1321 cgtctacaat gctgttattc ataatgacga agtaagtccg cacctgcatt tgaatattgt
     1381 tcctgttgct gaagggtata aacggggtgt tcaaaagcaa ccaagtttta acaaagcctt
     1441 gcaacagcag ggtttacgag cagataaaga gaatggtcga gtgatttgga ataattttag
     1501 gaatcaggaa gttgagtcaa ttgaacgttt gatggcagat tttggttggg agcgtgagtt
     1561 agtcggtact aacaaaatca aagatattca tgaatacaaa gaaatcatga gcgaaatttc
     1621 cgaattgcgt caaacggccg taaaagagcg tgagagcgtt tctgatgagt tgaggtatat
     1681 ttgtaggcaa agagaagaaa acgagcgtga gaaggctctg gtggcttctg agagagcgaa
     1741 gattgaagaa gagaagaaaa atatgctgaa tgtaaaaaaa gagatggcgg tcattttcca
     1801 aaaagatatg gttcctttag aaagtttcaa gaggcttcct gatggttcgt atcatttatc
     1861 tgggaatgat tttgttgatt tgtatcaacg agctacgaga gcaacaaatg ccaagagaaa
     1921 tgctgataac atgagtgagc aatatttaca gatgcttgag caaaatacag aattaaatga
     1981 gtatgtagct gcattggaag aagagcgtca tttgtctggt agaaaacaat tagcagattt
     2041 acaagtggaa aataaaaagc tgaaagaaga aaatcgctct ttacgccagc gtttagagcg
     2101 attaaaaaac gcatttcaaa aatcgatcac tcgtttgtct atccgttttg ggcttgcaga
     2161 aaaggatatg gggctttctg aggaattaga agtattagag caggagaaaa ccttatttta
     2221 tcgtcaaaac gtctcacagc ataaattaga gcgttctgaa gatgagatcg agtggtagtt
     2281 acgatgtgca gtcaacggta ccggaggcgg tttgtgccga ggataaggag ttgacggcta
     2341 aaccactagc ctattaagct gacatttgct aaaaaatggc aagtccattt tttggccaac
     2401 ttagcgttag cgaagtttgg gggcgccctt tttaaagggt gcggttttat gtttgcatga
     2461 ctaagaatga gtgggaaaat ttaacagccc tatctaacag gcggttaaat gtacaaaata
     2521 tgtacacccc cttaaaaatg cagtggtcga ttgatcgaat tttatgtctt tgggttttgg
     2581 ggttttaaaa cgaaaaaaag ggggcgattt tcgccctctt ttttgatgtt ttttcttatc
     2641 ttgatactat aggcaactat ttctgcgaag aaatcggggc tatagtatgg gtctatccct
     2701 tgtggctcta aggaagaaca aaaaaaaaga ttgctttttc ttccctagta ttttatagtt
     2761 ttaattgact agaaaaaaac taaactagaa aggagagcaa tctatttttt gttatcggct
     2821 tttcagcctt ttttgtatac aaaatttgta gattcagtat agcaagatga aaaagaaaaa
     2881 gcaagatttg attaacggaa catttcgaga aaaaaagaaa aatttgaaaa aagtggtggc
     2941 atttagtgat aatcgaattt ctcccaaaat gcgtgaattg atgacaggct gtggttcata
     3001 tttagaattt attgcaacga ttgataagga gaaaaagaaa ttggtccaag ctcacttttg
     3061 taaaaatcgt ttctgtccgt tatgtgcttg gcgtaaagct cgtaaggatt cgatgatgtt
     3121 gtcgattatg atgcaagcta ttgcggaaga aaagcagtat caatttattt ttatgacgtt
     3181 gacgacaccg aatgtaaaag cggaatgttt gaacgatgaa attgatttgt ttaatcatgc
     3241 attgaaaaag atgtttatgc gcaaacgggt taagacttcg attaaaggct atgtgcgaaa
     3301 attggaaatc acgtacaaca aaaaacggaa tgactataac ccgcattttc acttgatttt
     3361 ggcagtaaat aaatcttatt tcacggataa agattattat atcaagcaat cggaatggtt
     3421 agatttgtgg cgggaagtga ccggaaaaac gggaattaat ccggatggta ccgacgaaat
     3481 tacccagttg gatattcgca aggtcaaagg gttccaacaa gaaaaagcag tacaggaagt
     3541 tgcgaaatat tcggcaaaag attttgaact gaccgaaagt caggaagtgt ttgacacatt
     3601 ctatcatgca atgaaaggtc gtcagttgat tacgtttaac ggtgtattca aagaatacaa
     3661 gaaaaaatat gagtcgggtg accttgatcg ttataagaaa aaagatgaga atgaatattt
     3721 ttggtttttg actgcttcgt ggatgaggaa agaatcgaaa tatgcggttg attatcgtga
     3781 gatgagtgct gatgaaagaa attatttttc aggaatgtat gtcgatgaaa aatctgttga
     3841 gggggaaaat gaatgactga ttcaacggat aaaatgacaa ttaaggcgct tgctgatgaa
     3901 ctaggaataa ccaaaaatac agtgagaaat tatctagtca aagccggata tgatcttgct
     3961 cggtacaaga aaaatggaat tatcttgcta gacaaagagt tgattggtgt tgctcggtca
     4021 atttatcggt caaaaggtgg tcaattgact ggtcatttac cggtcaatag cacgggcagt
     4081 gattttcctt tggaaaaaga gaatgagttt ttgcgtgatc aattagctga gaaggacaaa
     4141 catatttctg aattaacaga aatgattcgt gatcaacaaa aattgaccct gcttcagcaa
     4201 caaaaaaacg atcagttgtt actagaaaat caagaattaa aaaatcgaaa atggtggcaa
     4261 ttctggaagt gagatgtgac atggataaaa ttgatttgag agaag
//
