LOCUS       NZ_CP066573             4316 bp    DNA     circular CON 20-FEB-2024
DEFINITION  Enterococcus faecium strain Dallas 97_1 plasmid p97_1_4.3kb,
            complete sequence.
ACCESSION   NZ_CP066573
VERSION     NZ_CP066573.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN17038090
            Assembly: GCF_016415025.1
KEYWORDS    RefSeq.
SOURCE      Enterococcus faecium
  ORGANISM  Enterococcus faecium
            Bacteria; Bacillota; Bacilli; Lactobacillales; Enterococcaceae;
            Enterococcus.
REFERENCE   1  (bases 1 to 4316)
  AUTHORS   Islam,M.J. and Palmer,K.
  TITLE     Molecular characterization of VREfm isolates from Dallas, Texas
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 4316)
  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                   :: 66.0x
            Sequencing Technology :: Illumina NextSeq; Oxford Nanopore MinION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 02/20/2024 02:46:30
            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)                     :: 3,203
            CDSs (total)                      :: 3,112
            Genes (coding)                    :: 2,949
            CDSs (with protein)               :: 2,949
            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)              :: 163
            CDSs (without protein)            :: 163
            Pseudo Genes (ambiguous residues) :: 0 of 163
            Pseudo Genes (frameshifted)       :: 73 of 163
            Pseudo Genes (incomplete)         :: 87 of 163
            Pseudo Genes (internal stop)      :: 37 of 163
            Pseudo Genes (multiple problems)  :: 30 of 163
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP066573.1.
            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..4316
                     /organism="Enterococcus faecium"
                     /mol_type="genomic DNA"
                     /strain="Dallas 97_1"
                     /isolation_source="rectal swab"
                     /host="Homo sapiens"
                     /db_xref="taxon:1352"
                     /plasmid="p97_1_4.3kb"
                     /geo_loc_name="USA: Dallas"
                     /collection_date="2015"
     gene            complement(join(3960..4316,1..6))
                     /locus_tag="JCP88_RS15810"
                     /old_locus_tag="JCP88_15810"
     CDS             complement(join(3960..4316,1..6))
                     /locus_tag="JCP88_RS15810"
                     /old_locus_tag="JCP88_15810"
                     /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_060800943.1"
                     /translation="MGMTLADIKVQEEKLKKEQAKLRQQKKRLIEKENAAMGKALRKRF
                     GFESFADFERWLSSISDDQQHEKSVDNEWLADEKSAPSERDYPNEYDGLLGVIPSKKSQ
                     MNESKFMSIFNDVNLR"
                     /name="hypothetical protein"
     gene            complement(10..318)
                     /locus_tag="JCP88_RS15815"
                     /old_locus_tag="JCP88_15815"
     CDS             complement(10..318)
                     /locus_tag="JCP88_RS15815"
                     /old_locus_tag="JCP88_15815"
                     /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(327..746)
                     /locus_tag="JCP88_RS15820"
                     /old_locus_tag="JCP88_15820"
     CDS             complement(327..746)
                     /locus_tag="JCP88_RS15820"
                     /old_locus_tag="JCP88_15820"
                     /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(743..1732)
                     /locus_tag="JCP88_RS15825"
                     /old_locus_tag="JCP88_15825"
     CDS             complement(743..1732)
                     /locus_tag="JCP88_RS15825"
                     /old_locus_tag="JCP88_15825"
                     /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(2332..3738)
                     /locus_tag="JCP88_RS15830"
                     /old_locus_tag="JCP88_15830"
     CDS             complement(2332..3738)
                     /locus_tag="JCP88_RS15830"
                     /old_locus_tag="JCP88_15830"
                     /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_060800944.1"
                     /translation="MGFSISFKKGTKNTSISHNNRELTDSQKINDWHKHIDFTKSDENI
                     YLEQTNIREKYEELFGEAVEKYNAKQKRADRKIEDYLAKVRKDKKLEPQREFIVQIGTL
                     DDFRTTRDDGSSTGISEQQAEQNRVIANKILVEYFKEFKERNPSLSVYNAVIHNDEVSP
                     HLHLNIVPVAEGYKRGVQKQPSFNKALQQQGLRADKENGRVIWNNFRNQEVESIERLMA
                     DFGWERELVGTNKIKDVHEYKEIMSEISELRQTAVKERESVSDELGYISRQREENEREK
                     ALVASERAKIEEEKKNMLNVKKEMAVIFQKDIVPLESFKRLPDGSYHLSGNDFVDLYQR
                     ATRATNAKRNADNMSEQYLQMLEQNTELNEYVATLEEERHLSGRKQLADLQVENKKLKE
                     ENRSLRQRLERLKKAFQKSITRLSIRFGLAEKDMGLSEELEVLEQEKTLFYRQNVSQHK
                     LERSEDEIEW"
                     /name="plasmid recombination protein"
     Typing          complement(2336..3738)
                     /name="MOBV"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="97.863"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 tcccataaac tacatcccct tttctttgga attaataacg gaaatttggt ttaactgcat
       61 aatatgactc attaatttca accaaaattc tttttcagct tcatcagttg tttgcgctaa
      121 atgcttatga acaaattcat tagtcaaaac tgaagatttt gctagatcag cattgataac
      181 cgagttgaga acatccatca ttcgttcaag catctcacta taattatctt catccgaaag
      241 attcaaataa tcagctaacc gttcatacat cacttcaatt ctattgactg tttcttctct
      301 caaatcaatt ttatccatgt cacatctcac ttccagaatt gccaccattt tcgatttttt
      361 aattcttgat tttctagtaa caactgatcg tttttttgtt gctgaagcag ggtcaatttt
      421 tgttgatcac gaatcatttc tgttaattca gaaatatgtt tgtccttctc agctaattga
      481 tcacgcaaaa actcattctc tttttccaaa ggaaaatcac tgcccgtgct attgaccggt
      541 aaatgaccag tcaattgacc accttttgac cgataaattg accgagcaac accaatcaac
      601 tctttgtcta gcaagataat tccatttttc ttgtaccgag caagatcata tccggctttg
      661 actagataat ttctcactgt atttttggtt attcctagtt catcagcaag cgccttaatt
      721 gtcattttat ccgttgaatc agtcattcat tttccccctc aacagatttt tcatcgacat
      781 acattcctga aaaataattt ctttcatcag cactcatctc acgataatca accgcatatt
      841 tcgattcttt cctcatccac gaagcagtca aaaaccaaaa atattcattc tcatcttttt
      901 tcttataacg atcaaggtca cccgactcat attttttctt gtattctttg aatacaccgt
      961 taaacgtaat caactgacga cctttcattg catgatagaa tgtgtcaaac acttcctgac
     1021 tttcggtcag ttcaaaatct tttgccgaat atttcgcaac ttcctgtact gctttttctt
     1081 gttggaaccc tttgaccttg cgaatatcca actgggtaat ttcgtcggta ccatccggat
     1141 taattcccgt ttttccggtc acttcccgcc acaaatctaa ccattccgat tgcttgatat
     1201 aataatcttt atccgtgaaa taagatttat ttactgccaa aatcaagtga aaatgcgggt
     1261 tatagtcatt ccgttttttg ttgtacgtga tttccaattt tcgcacatag cctttaatcg
     1321 aagtcttaac ccgtttgcgc ataaacatct ttttcaatgc atgattaaac aaatcaattt
     1381 catcgttcaa acattccgct tttacattcg gtgtcgtcaa cgtcataaaa ataaattgat
     1441 actgcttttc ttccgcaata gcttgcatca taatcgacaa catcatcgaa tccttacgag
     1501 ctttacgcca agcacataac ggacagaaac gatttttaca aaagtgagct tggaccaatt
     1561 tctttttctc cttatcaatc gttgcaataa attctaaata tgaaccacag cctgtcatca
     1621 attcacgcat tttgggagaa attcgattat cactaaatgc caccactttt ttcaaatttt
     1681 tctttttttc tcgaaatgtt ccgttaatca aatcttgctt tttctttttc atcttgctat
     1741 actgaatcta caaattttgt atacaaaaaa ggctgaaaag ccgataacaa aaaatagatt
     1801 gctctccttt ctagtttagt ttttttctag tcaattaaaa ctataaaata ctagggaaga
     1861 aaaagcaatc tttttttttg ttcttcctta gagccacaag ggatagaccc atactatagc
     1921 cccgatttct tcgcagaaat agttgcctat agtatcaaga taagaagaaa catcaaaaaa
     1981 agaggtcgaa atcgacctct tttttctcgt ttcaaacccc aaaactcaaa aacccacttc
     2041 tgcataaaat tcggtcaatt gaccactgca tttttaaggg aagggtcaaa ctttgatact
     2101 ttaaccgcct gttagaaatg cggttaagtt tttcccactc attcttagtc atgcaaaaat
     2161 aaaaccgctc cctttgaaaa gggcgccccc aaactttcgc taacgctagg ttggccaaaa
     2221 aatggacttg ccatttttta gcaaatgtca gcttaatagg ctagtggttt agccgtcaac
     2281 tccttatcct cggcacagac cgcctccggt accgttgact gcacatcgta actaccactc
     2341 gatctcatct tcagaacgct ctaatttatg ctgtgagacg ttttgacgat aaaataaggt
     2401 tttctcctgc tctaatactt ctaattcctc agaaagcccc atatcctttt ctgcaagacc
     2461 aaaacggata gacaaacgag tgatcgattt ttgaaatgct ttttttaatc gctctaaacg
     2521 ctggcgtaaa gagcgatttt cttctttcag ctttttattt tccacttgta aatctgctaa
     2581 ttgttttcta ccagacaaat gacgctcttc ttccaatgta gctacatact catttaattc
     2641 tgtattttgc tcaagcatct gtaaatattg ctcactcatg ttatcagcat ttctcttggc
     2701 atttgttgct ctcgtagctc gttgatacaa atcaacaaaa tcattcccag ataaatgata
     2761 cgaaccatca ggaagcctct tgaaactttc taaaggaaca atatcttttt ggaaaatgac
     2821 cgccatctct ttttttacat tcagcatatt tttcttctct tcttcaatct ttgctctctc
     2881 agaagccacc agagcctttt ctcgctcgtt ttcttctctt tgcctagaaa tataccccaa
     2941 ctcatcagaa acgctctcac gctcttttac ggccgtttga cgcaattctg aaatctcgct
     3001 catgatttct ttatattcgt gaacatcttt gattttgtta gtaccgacta actcacgctc
     3061 ccaaccaaaa tctgccatca aacgttcaat tgactcaact tcctgattcc taaaattatt
     3121 ccaaatcact cgaccattct ctttatctgc tcgtaaaccc tgctgttgca aggctttgtt
     3181 aaaacttggt tgcttttgaa caccccgttt atacccttca gcaacaggaa caatattcaa
     3241 atgcaggtgc ggacttactt cgtcattatg aataacagca ttgtagacgg ataaactagg
     3301 attccgttct ttaaattctt tgaaatactc aactaaaatt ttgttggcaa tcactcgatt
     3361 ttgttctgct tgttgttccg atatgccagt agaagaacca tcatcacgag tagtacgaaa
     3421 atcatcaaga gtaccaattt gcacgataaa ttctcgctgt ggttccaatt ttttatcctt
     3481 gcgaaccttt gctaaatagt cctcgatttt tctatcggct cttttctgct ttgcattata
     3541 tttttctacg gcttcaccga ataattcttc atatttttca cgaatatttg tttgttccaa
     3601 atagatattt tcatccgatt ttgtgaaatc aatatgctta tgccagtcat tgattttttg
     3661 gctatcagtt aactcacgat tattatgaga aatgcttgta ttctttgttc cctttttgaa
     3721 cgaaatacta aaccccaagt tagacccctc cttcgcgctg tcgctaataa aaagagtgta
     3781 aacctttctg ttactctttg tcaaagagta acgttttcct aattgtgaca tgactgtcac
     3841 aattccaaac gctctccgag ggatttcgct gtcacaagtg acaacgaaaa aaggagccga
     3901 aagcgtgtca cgctctcaac tccttttacg ctttattttg cttcacgcaa aataatagct
     3961 tatcgtaaat tcacgtcatt aaaaattgac ataaatttac tctcattcat ctgacttttt
     4021 ttactcggta tcactccgag taagccgtca tattcattgg gataatctcg ttcgcttggc
     4081 gctgattttt catcagcaag ccactcatta tccactgatt tttcgtgttg ctgatcgtca
     4141 gaaattgacg ataaccaccg ctcaaaatca gcaaaagatt caaacccaaa acgcttgcga
     4201 agagccttgc ccattgcagc attttctttc tcaatcaatc gtttcttctg ttggcgaagt
     4261 ttcgcctgtt ctttttttaa tttttcttct tgcactttaa tatctgctaa agtcat
//
