LOCUS       NZ_CP066432             4305 bp    DNA     circular CON 20-FEB-2024
DEFINITION  Enterococcus faecium strain Dallas 57 plasmid p57_4.3kb, complete
            sequence.
ACCESSION   NZ_CP066432
VERSION     NZ_CP066432.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN17038080
            Assembly: GCF_016406565.1
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  JOURNAL   Unpublished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                   :: 132.0x
            Sequencing Technology :: Illumina NextSeq; Oxford Nanopore MinION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 02/20/2024 02:45:54
            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)                     :: 3,132
            CDSs (total)                      :: 3,041
            Genes (coding)                    :: 2,924
            CDSs (with protein)               :: 2,924
            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)              :: 117
            CDSs (without protein)            :: 117
            Pseudo Genes (ambiguous residues) :: 0 of 117
            Pseudo Genes (frameshifted)       :: 41 of 117
            Pseudo Genes (incomplete)         :: 69 of 117
            Pseudo Genes (internal stop)      :: 30 of 117
            Pseudo Genes (multiple problems)  :: 19 of 117
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP066432.1.
            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 57"
                     /isolation_source="rectal swab"
                     /host="Homo sapiens"
                     /db_xref="taxon:1352"
                     /plasmid="p57_4.3kb"
                     /geo_loc_name="USA: Dallas"
                     /collection_date="2015"
     gene            complement(join(3779..4305,1..463))
                     /locus_tag="JCP98_RS15510"
                     /old_locus_tag="JCP98_15510"
     CDS             complement(join(3779..4305,1..463))
                     /locus_tag="JCP98_RS15510"
                     /old_locus_tag="JCP98_15510"
                     /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(1052..2458)
                     /locus_tag="JCP98_RS15515"
                     /old_locus_tag="JCP98_15515"
     CDS             complement(1052..2458)
                     /locus_tag="JCP98_RS15515"
                     /old_locus_tag="JCP98_15515"
                     /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            complement(2680..3042)
                     /locus_tag="JCP98_RS15520"
                     /old_locus_tag="JCP98_15520"
     CDS             complement(2680..3042)
                     /locus_tag="JCP98_RS15520"
                     /old_locus_tag="JCP98_15520"
                     /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(3046..3384)
                     /locus_tag="JCP98_RS15525"
                     /old_locus_tag="JCP98_15525"
     CDS             complement(3046..3384)
                     /locus_tag="JCP98_RS15525"
                     /old_locus_tag="JCP98_15525"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002321903.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_002305963.1"
                     /translation="MVAILEVRCDMDKIDLREETVNRIEVMYERLADYLNLSDEDNYSE
                     MLERMMDVLNSVINADLAKSSVLTNEFVHKHLAQTTDEAEKEFWLKLMSHIMQLNQISV
                     INSKEKGM"
                     /name="hypothetical protein"
     gene            complement(3363..3782)
                     /locus_tag="JCP98_RS15530"
                     /old_locus_tag="JCP98_15530"
     CDS             complement(3363..3782)
                     /locus_tag="JCP98_RS15530"
                     /old_locus_tag="JCP98_15530"
                     /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          complement(1056..2458)
                     /name="MOBV"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="99.359"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 tccgtttttt gttgtacgtg atttccaatt ttcgcacata gcctttaatc gaagtcttaa
       61 cccgtttgcg cataaacatc tttttcaatg catgattaaa caaatcaatt tcatcgttca
      121 aacattccgc ttttacattc ggtgtcgtca acgtcataaa aataaattga tactgctttt
      181 cttccgcaat agcttgcatc ataatcgaca acatcatcga atccttacga gctttacgcc
      241 aagcacataa cggacagaaa cgatttttac aaaagtgagc ttggaccaat ttctttttct
      301 ccttatcaat cgttgcaata aattctaaat atgaaccaca gcctgtcatc aattcacgca
      361 ttttgggaga aattcgatta tcactaaatg ccaccacttt tttcaaattt ttcttttttt
      421 ctcgaaatgt tccgttaatc aaatcttgct ttttcttttt catcttgcta tactgaatct
      481 acaaattttg tatacaaaaa aggctgaaaa gccgataaca aaaaatagat tgctctcctt
      541 tctagtttag tttttttcta gtcaattaaa actataaaat actagggaag aaaaagcaat
      601 cttttttttt gttcttcctt agagccacaa gggatagacc catactatag ccccgatttc
      661 ttcgcagaaa tagttgccta tagtatcaag ataagaaaaa acatcaaaaa agagggcgaa
      721 aatcgccccc tttttttcgt tttaaaaccc caaaacccaa agacataaaa ttcgatcaat
      781 cgaccactgc atttttaagg gggtgtacat attttgtaca tttaaccgcc tgttagatag
      841 ggctgttaaa ttttcccact cattcttagt catgcaaaca taaaaccgca ccctttaaaa
      901 agggcgcccc caaacttcgc taacgctaag ttggccaaaa aatggacttg ccatttttta
      961 gcaaatgtca gcttaatagg ctagtggttt agccgtcaac tccttatcct cggcacaaac
     1021 cgcctccggt accgttgact gcacatcgta actaccactc gatctcatct tcagaacgct
     1081 ctaatttatg ctgtgagacg ttttgacgat aaaataaggt tttctcctgc tctaatactt
     1141 ctaattcctc agaaagcccc atatcctttt ctgcaagccc aaaacggata gacaaacgag
     1201 tgatcgattt ttgaaatgcg ttttttaatc gctctaaacg ctggcgtaaa gagcgatttt
     1261 cttctttcag ctttttattt tccacttgta aatctgctaa ttgttttcta ccagacaaat
     1321 gacgctcttc ttccaatgca gctacatact catttaattc tgtattttgc tcaagcatct
     1381 gtaaatattg ctcactcatg ttatcagcat ttctcttggc atttgttgct ctcgtagctc
     1441 gttgatacaa atcaacaaaa tcattcccag ataaatgata cgaaccatca ggaagcctct
     1501 tgaaactttc taaaggaacc atatcttttt ggaaaatgac cgccatctct ttttttacat
     1561 tcagcatatt tttcttctct tcttcaatct tcgctctctc agaagccacc agagccttct
     1621 cacgctcgtt ttcttctctt tgcctacaaa tatacctcaa ctcatcagaa acgctctcac
     1681 gctcttttac ggccgtttga cgcaattcgg aaatttcgct catgatttct ttgtattcat
     1741 gaatatcttt gattttgtta gtaccgacta actcacgctc ccaaccaaaa tctgccatca
     1801 aacgttcaat tgactcaact tcctgattcc taaaattatt ccaaatcact cgaccattct
     1861 ctttatctgc tcgtaaaccc tgctgttgca aggctttgtt aaaacttggt tgcttttgaa
     1921 caccccgttt atacccttca gcaacaggaa caatattcaa atgcaggtgc ggacttactt
     1981 cgtcattatg aataacagca ttgtagacgg ataaactagg attccgttct ttaaattctt
     2041 tgaaatactc aactaaaatt ttgttggcaa tcactcgatt ttgttctgct tgttgttccg
     2101 atatgccagt agaagaacca tcatcacgag tagtacgaaa atcatcaaga gtaccaattt
     2161 gcacgataaa ttctcgctgt ggttccattt ttttatcctt gcgaaccttt gctaaatagt
     2221 cctcaatttt tctatcggct cttttctgct ttgcattata tttttctacg gcttcaccga
     2281 ataattcttc atatttttca cgaatattta tttgttccaa atagatattt tcatccgatt
     2341 ttgtgaaatc aatatgctta tgccagtcat tgattttttg gctatcagtt aactcacgat
     2401 tattatgaga aatgcttgta ttctttgttc cctttttgaa cgaaatacta aaccccaagt
     2461 taaacccctc cttcgcgctg tcgctaataa aaagagtgta aacctttctg ttactctttg
     2521 tcaaagagta acgttttcct aattgtgaca tgactgtcac aattccaaac gctctccgag
     2581 ggttttcgcc gtcacaagtg acaacgaaaa aaggagccga aagcgtgtca cgctctcaac
     2641 tccttttacg ctttattttg cttcatgcaa aatattcgct tatcgtgaat ttacgtcact
     2701 aaacattgac gcaaatccac tctcactcat ctgacttttt ctattcggta tccctccgaa
     2761 tattccgtca gattcgttag ggtaattccg ttcgcttggt gctgattttt catcagctcg
     2821 caactcatta cccactgatt tttcgtgttg ctgatcgtca gaaatcgacg atagccaccg
     2881 ctcaaaatca gcaaaagatt caaacccaaa acgcttgcga agagccttgc ccattgcagc
     2941 attttctttc tcaatcaatc gtttcttctg ttggcgaagt ttcgcctgtt ctttttttaa
     3001 tttttcttct tgcactttaa tatctgctaa agtcattccc ataaactaca tccccttttc
     3061 tttggaatta ataacggaaa tttggtttaa ctgcataata tgactcatta atttcaacca
     3121 aaattctttt tcagcttcat cagttgtttg cgctaaatgc ttatgaacaa attcattagt
     3181 caaaactgaa gattttgcta gatcagcatt gataaccgag ttgagaacat ccatcattcg
     3241 ttcaagcatc tcactataat tatcttcatc cgaaagattc aaataatcag ctaaccgttc
     3301 atacatcact tcaattctat tgactgtttc ttctctcaaa tcaattttat ccatgtcaca
     3361 tctcacttcc agaattgcca ccattttcga ttttttaatt cttgattttc tagtaacaac
     3421 tgatcgtttt tttgttgctg aagcagggtc aatttttgtt gatcacgaat catttctgtt
     3481 aattcagaaa tatgtttgtc cttctcagct aattgatcac gcaaaaactc attctctttt
     3541 tccaaaggaa aatcactgcc cgtgctattg accggtaaat gaccagtcaa ttgaccacct
     3601 tttgaccgat aaattgaccg agcaacacca atcaactctt tgtctagcaa gataattcca
     3661 tttttcttgt accgagcaag atcatatccg gctttgacta gataatttct cactgtattt
     3721 ttggttattc ctagttcatc agcaagcgcc ttaattgtca ttttatccgt tgaatcagtc
     3781 attcattttc cccctcaaca gatttttcat cgacatacat tcctgaaaaa taatttcttt
     3841 catcagcact catctcacga taatcaaccg catatttcga ttctttcctc atccacgaag
     3901 cagtcaaaaa ccaaaaatat tcattctcat cttttttctt ataacgatca aggtcacccg
     3961 actcatattt tttcttgtat tctttgaata caccgttaaa cgtaatcaac tgacgacctt
     4021 tcattgcatg atagaatgtg tcaaacactt cctgactttc ggtcagttca aaatcttttg
     4081 ccgaatattt cgcaacttcc tgtactgctt tttcttgttg gaaccctttg accttgcgaa
     4141 tatccaactg ggtaatttcg tcggtaccat ccggattaat tcccgttttt ccggtcactt
     4201 cccgccacaa atctaaccat tccgattgct tgatataata atctttatcc gtgaaataag
     4261 atttatttac tgccaaaatc aagtgaaaat gcgggttata gtcat
//
