LOCUS       NZ_CP066634             4305 bp    DNA     circular CON 20-FEB-2024
DEFINITION  Enterococcus faecium strain Dallas 137 plasmid p5, complete
            sequence.
ACCESSION   NZ_CP066634
VERSION     NZ_CP066634.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN17038102
            Assembly: GCF_016415445.1
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  JOURNAL   Unpublished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                   :: 258.0x
            Sequencing Technology :: Illumina NextSeq; Oxford Nanopore MinION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 02/20/2024 02:51:53
            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)                     :: 3,085
            CDSs (total)                      :: 2,992
            Genes (coding)                    :: 2,879
            CDSs (with protein)               :: 2,879
            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)              :: 113
            CDSs (without protein)            :: 113
            Pseudo Genes (ambiguous residues) :: 0 of 113
            Pseudo Genes (frameshifted)       :: 40 of 113
            Pseudo Genes (incomplete)         :: 69 of 113
            Pseudo Genes (internal stop)      :: 24 of 113
            Pseudo Genes (multiple problems)  :: 17 of 113
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP066634.1.
            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 137"
                     /isolation_source="rectal swab"
                     /host="Homo sapiens"
                     /db_xref="taxon:1352"
                     /plasmid="p5"
                     /geo_loc_name="USA: Dallas"
                     /collection_date="2015"
     gene            complement(join(3991..4305,1..105))
                     /locus_tag="JCP61_RS15255"
                     /old_locus_tag="JCP61_15255"
     CDS             complement(join(3991..4305,1..105))
                     /locus_tag="JCP61_RS15255"
                     /old_locus_tag="JCP61_15255"
                     /inference="COORDINATES: ab initio prediction:GeneMarkS-2+"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GeneMarkS-2+."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_002305964.1"
                     /translation="MTDSTDKMTIKALADELGITKNTVRNYLVKAGYDLARYKKNGIIL
                     LDKELIGVARSIYRSKGGQLTGHLPVNSTGSDFPLEKENEFLRDQLAEKDKHISELTEM
                     IRDQQKLTLLQQQKNDQLLLENQELKNRKWWQFWK"
                     /name="hypothetical protein"
     gene            complement(102..1091)
                     /locus_tag="JCP61_RS15260"
                     /old_locus_tag="JCP61_15260"
     CDS             complement(102..1091)
                     /locus_tag="JCP61_RS15260"
                     /old_locus_tag="JCP61_15260"
                     /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(1680..3086)
                     /locus_tag="JCP61_RS15265"
                     /old_locus_tag="JCP61_15265"
     CDS             complement(1680..3086)
                     /locus_tag="JCP61_RS15265"
                     /old_locus_tag="JCP61_15265"
                     /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(3308..3670)
                     /locus_tag="JCP61_RS15270"
                     /old_locus_tag="JCP61_15270"
     CDS             complement(3308..3670)
                     /locus_tag="JCP61_RS15270"
                     /old_locus_tag="JCP61_15270"
                     /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(3674..3982)
                     /locus_tag="JCP61_RS15275"
                     /old_locus_tag="JCP61_15275"
     CDS             complement(3674..3982)
                     /locus_tag="JCP61_RS15275"
                     /old_locus_tag="JCP61_15275"
                     /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"
     Typing          complement(1684..3086)
                     /name="MOBV"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="99.359"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 aagatcatat ccggctttga ctagataatt tctcactgta tttttggtta ttcctagttc
       61 atcagcaagc gccttaattg tcattttatc cgttgaatca gtcattcatt ttccccctca
      121 acagattttt catcgacata cattcctgaa aaataatttc tttcatcagc actcatctca
      181 cgataatcaa ccgcatattt cgattctttc ctcatccacg aagcagtcaa aaaccaaaaa
      241 tattcattct catctttttt cttataacga tcaaggtcac ccgactcata ttttttcttg
      301 tattctttga atacaccgtt aaacgtaatc aactgacgac ctttcattgc atgatagaat
      361 gtgtcaaaca cttcctgact ttcggtcagt tcaaaatctt ttgccgaata tttcgcaact
      421 tcctgtactg ctttttcttg ttggaaccct ttgaccttgc gaatatccaa ctgggtaatt
      481 tcgtcggtac catccggatt aattcccgtt tttccggtca cttcccgcca caaatctaac
      541 cattccgatt gcttgatata ataatcttta tccgtgaaat aagatttatt tactgccaaa
      601 atcaagtgaa aatgcgggtt atagtcattc cgttttttgt tgtacgtgat ttccaatttt
      661 cgcacatagc ctttaatcga agtcttaacc cgtttgcgca taaacatctt tttcaatgca
      721 tgattaaaca aatcaatttc atcgttcaaa cattccgctt ttacattcgg tgtcgtcaac
      781 gtcataaaaa taaattgata ctgcttttct tccgcaatag cttgcatcat aatcgacaac
      841 atcatcgaat ccttacgagc tttacgccaa gcacataacg gacagaaacg atttttacaa
      901 aagtgagctt ggaccaattt ctttttctcc ttatcaatcg ttgcaataaa ttctaaatat
      961 gaaccacagc ctgtcatcaa ttcacgcatt ttgggagaaa ttcgattatc actaaatgcc
     1021 accacttttt tcaaattttt ctttttttct cgaaatgttc cgttaatcaa atcttgcttt
     1081 ttctttttca tcttgctata ctgaatctac aaattttgta tacaaaaaag gctgaaaagc
     1141 cgataacaaa aaatagattg ctctcctttc tagtttagtt tttttctagt caattaaaac
     1201 tataaaatac tagggaagaa aaagcaatct ttttttttgt tcttccttag agccacaagg
     1261 gatagaccca tactatagcc ccgatttctt cgcagaaata gttgcctata gtatcaagat
     1321 aagaaaaaac atcaaaaaag agggcgaaaa tcgccccctt tttttcgttt taaaacccca
     1381 aaacccaaag acataaaatt cgatcaatcg accactgcat ttttaagggg gtgtacatat
     1441 tttgtacatt taaccgcctg ttagataggg ctgttaaatt ttcccactca ttcttagtca
     1501 tgcaaacata aaaccgcacc ctttaaaaag ggcgccccca aacttcgcta acgctaagtt
     1561 ggccaaaaaa tggacttgcc attttttagc aaatgtcagc ttaataggct agtggtttag
     1621 ccgtcaactc cttatcctcg gcacaaaccg cctccggtac cgttgactgc acatcgtaac
     1681 taccactcga tctcatcttc agaacgctct aatttatgct gtgagacgtt ttgacgataa
     1741 aataaggttt tctcctgctc taatacttct aattcctcag aaagccccat atccttttct
     1801 gcaagcccaa aacggataga caaacgagtg atcgattttt gaaatgcgtt ttttaatcgc
     1861 tctaaacgct ggcgtaaaga gcgattttct tctttcagct ttttattttc cacttgtaaa
     1921 tctgctaatt gttttctacc agacaaatga cgctcttctt ccaatgcagc tacatactca
     1981 tttaattctg tattttgctc aagcatctgt aaatattgct cactcatgtt atcagcattt
     2041 ctcttggcat ttgttgctct cgtagctcgt tgatacaaat caacaaaatc attcccagat
     2101 aaatgatacg aaccatcagg aagcctcttg aaactttcta aaggaaccat atctttttgg
     2161 aaaatgaccg ccatctcttt ttttacattc agcatatttt tcttctcttc ttcaatcttc
     2221 gctctctcag aagccaccag agccttctca cgctcgtttt cttctctttg cctacaaata
     2281 tacctcaact catcagaaac gctctcacgc tcttttacgg ccgtttgacg caattcggaa
     2341 atttcgctca tgatttcttt gtattcatga atatctttga ttttgttagt accgactaac
     2401 tcacgctccc aaccaaaatc tgccatcaaa cgttcaattg actcaacttc ctgattccta
     2461 aaattattcc aaatcactcg accattctct ttatctgctc gtaaaccctg ctgttgcaag
     2521 gctttgttaa aacttggttg cttttgaaca ccccgtttat acccttcagc aacaggaaca
     2581 atattcaaat gcaggtgcgg acttacttcg tcattatgaa taacagcatt gtagacggat
     2641 aaactaggat tccgttcttt aaattctttg aaatactcaa ctaaaatttt gttggcaatc
     2701 actcgatttt gttctgcttg ttgttccgat atgccagtag aagaaccatc atcacgagta
     2761 gtacgaaaat catcaagagt accaatttgc acgataaatt ctcgctgtgg ttccattttt
     2821 ttatccttgc gaacctttgc taaatagtcc tcaatttttc tatcggctct tttctgcttt
     2881 gcattatatt tttctacggc ttcaccgaat aattcttcat atttttcacg aatatttatt
     2941 tgttccaaat agatattttc atccgatttt gtgaaatcaa tatgcttatg ccagtcattg
     3001 attttttggc tatcagttaa ctcacgatta ttatgagaaa tgcttgtatt ctttgttccc
     3061 tttttgaacg aaatactaaa ccccaagtta aacccctcct tcgcgctgtc gctaataaaa
     3121 agagtgtaaa cctttctgtt actctttgtc aaagagtaac gttttcctaa ttgtgacatg
     3181 actgtcacaa ttccaaacgc tctccgaggg ttttcgccgt cacaagtgac aacgaaaaaa
     3241 ggagccgaaa gcgtgtcacg ctctcaactc cttttacgct ttattttgct tcatgcaaaa
     3301 tattcgctta tcgtgaattt acgtcactaa acattgacgc aaatccactc tcactcatct
     3361 gactttttct attcggtatc cctccgaata ttccgtcaga ttcgttaggg taattccgtt
     3421 cgcttggtgc tgatttttca tcagctcgca actcattacc cactgatttt tcgtgttgct
     3481 gatcgtcaga aatcgacgat agccaccgct caaaatcagc aaaagattca aacccaaaac
     3541 gcttgcgaag agccttgccc attgcagcat tttctttctc aatcaatcgt ttcttctgtt
     3601 ggcgaagttt cgcctgttct ttttttaatt tttcttcttg cactttaata tctgctaaag
     3661 tcattcccat aaactacatc cccttttctt tggaattaat aacggaaatt tggtttaact
     3721 gcataatatg actcattaat ttcaaccaaa attctttttc agcttcatca gttgtttgcg
     3781 ctaaatgctt atgaacaaat tcattagtca aaactgaaga ttttgctaga tcagcattga
     3841 taaccgagtt gagaacatcc atcattcgtt caagcatctc actataatta tcttcatccg
     3901 aaagattcaa ataatcagct aaccgttcat acatcacttc aattctattg actgtttctt
     3961 ctctcaaatc aattttatcc atgtcacatc tcacttccag aattgccacc attttcgatt
     4021 ttttaattct tgattttcta gtaacaactg atcgtttttt tgttgctgaa gcagggtcaa
     4081 tttttgttga tcacgaatca tttctgttaa ttcagaaata tgtttgtcct tctcagctaa
     4141 ttgatcacgc aaaaactcat tctctttttc caaaggaaaa tcactgcccg tgctattgac
     4201 cggtaaatga ccagtcaatt gaccaccttt tgaccgataa attgaccgag caacaccaat
     4261 caactctttg tctagcaaga taattccatt tttcttgtac cgagc
//
