LOCUS       NZ_CP066397             4372 bp    DNA     circular CON 20-FEB-2024
DEFINITION  Enterococcus faecium strain Dallas 51_4 plasmid p51_4_4.3kb,
            complete sequence.
ACCESSION   NZ_CP066397
VERSION     NZ_CP066397.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN17038075
            Assembly: GCF_016406465.1
KEYWORDS    RefSeq.
SOURCE      Enterococcus faecium
  ORGANISM  Enterococcus faecium
            Bacteria; Bacillota; Bacilli; Lactobacillales; Enterococcaceae;
            Enterococcus.
REFERENCE   1  (bases 1 to 4372)
  AUTHORS   Islam,M.J. and Palmer,K.
  TITLE     Molecular characterization of VREfm isolates from Dallas, Texas
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 4372)
  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                   :: 146.0x
            Sequencing Technology :: Illumina NextSeq; Oxford Nanopore MinION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 02/20/2024 02:56:45
            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)                     :: 3,320
            CDSs (total)                      :: 3,229
            Genes (coding)                    :: 3,102
            CDSs (with protein)               :: 3,102
            Genes (RNA)                       :: 91
            rRNAs                             :: 6, 6, 6 (5S, 16S, 23S)
            complete rRNAs                    :: 6, 6, 6 (5S, 16S, 23S)
            tRNAs                             :: 69
            ncRNAs                            :: 4
            Pseudo Genes (total)              :: 127
            CDSs (without protein)            :: 127
            Pseudo Genes (ambiguous residues) :: 0 of 127
            Pseudo Genes (frameshifted)       :: 44 of 127
            Pseudo Genes (incomplete)         :: 77 of 127
            Pseudo Genes (internal stop)      :: 35 of 127
            Pseudo Genes (multiple problems)  :: 23 of 127
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP066397.1.
            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..4372
                     /organism="Enterococcus faecium"
                     /mol_type="genomic DNA"
                     /strain="Dallas 51_4"
                     /isolation_source="rectal swab"
                     /host="Homo sapiens"
                     /db_xref="taxon:1352"
                     /plasmid="p51_4_4.3kb"
                     /geo_loc_name="USA: Dallas"
                     /collection_date="2015"
     gene            join(4363..4372,1..299)
                     /locus_tag="JCQ06_RS14050"
                     /old_locus_tag="JCQ06_14055"
     CDS             join(4363..4372,1..299)
                     /locus_tag="JCQ06_RS14050"
                     /old_locus_tag="JCQ06_14055"
                     /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_233093537.1"
                     /translation="MDKIDLREETVDRIELMYERLADYLNLPDEDNYSEMLERVMDVLN
                     SVINADLAKSSVLTNEFVHKHLAQTTDESEKEFWLKLMSHVMQLNQISVINSKEKEM"
                     /name="hypothetical protein"
     gene            303..665
                     /locus_tag="JCQ06_RS14055"
                     /old_locus_tag="JCQ06_14060"
     CDS             303..665
                     /locus_tag="JCQ06_RS14055"
                     /old_locus_tag="JCQ06_14060"
                     /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_045135959.1"
                     /translation="MGMTLADIKAQEEKLKKEQAKLRQQKKRLIEKENAAMGKALRKRF
                     GFETFADFERWLSSISDDQQHEKTVDNEWLADEKSAPSERDYPDESDDLFGVIPNKKSQ
                     MSESKFTSIFNDVNLR"
                     /name="hypothetical protein"
     gene            887..2293
                     /locus_tag="JCQ06_RS14060"
                     /old_locus_tag="JCQ06_14065"
     CDS             887..2293
                     /locus_tag="JCQ06_RS14060"
                     /old_locus_tag="JCQ06_14065"
                     /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_060810507.1"
                     /translation="MGFSISFKKGTKNTSISHNNRELTDRQKTNDWHKHIDFTKSDENI
                     YLEQTNLADKYEELFGEVVEKYNAKQKRADRKIEDYLAKVRKDKKLEPQREFIVQIGIL
                     DDFQTNRADGSSTGISKQQAEQNRVIANKILVQYYKEFQERNPNLAVYNAVIHNDEISP
                     HLHLNIVPVAEGYKRGVQKQPSFNKALVQQGIHADKDNGRVLFNNFRNQEVDSIERLMN
                     DYGWKRDIVGTNKIKDIHEYKEIMSEISELRQTAVKERESVSDELRYIYRQREENERDK
                     ALMASERAKIEEEKKNMLNVKKEMAVIFQKDMVPLESFKRLPDGSYHLSGNDFVDLYQR
                     ATRATNAKRNADNMSEQYLQMLEQNTELNEYVATLEEERHLSGRKQLADLQVENKKLKE
                     ENRSLRQRLERLKNAFQKSITRLSIRFGLAEKDMGLSEELEVLEQEKTLFYRQNVSQHK
                     LERSENEIEW"
                     /name="plasmid recombination protein"
     gene            2738..3706
                     /locus_tag="JCQ06_RS14065"
                     /old_locus_tag="JCQ06_14070"
     CDS             2738..3706
                     /locus_tag="JCQ06_RS14065"
                     /old_locus_tag="JCQ06_14070"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002298422.1"
                     /GO_function="GO:0003677 - DNA binding [Evidence IEA];
                     GO:0003916 - DNA topoisomerase activity [Evidence IEA]"
                     /GO_process="GO:0006270 - DNA replication initiation
                     [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="replication initiation factor domain-containing
                     protein"
                     /protein_id="WP_002347008.1"
                     /translation="MSKKRTIVNEWEKLTALSNRRLNVQTLVQTIKLNWSIDRITIVGK
                     LNQNIFYHTQHDVLILDFEQLMRVNEGNGYLKAVGNNGWQLLDQHDENIAYIEISKWQE
                     GKGRIDFNPNKISRFLADSMKNFIHDLFLEPHFSRADVACDLIDVPDEFITQYRIIDPV
                     SFKLIYGRSGKLETVYWGSRASERQIRLYNKKIEQEMKRKVVPSEINTWWRLEMQLRRG
                     KATEWYAMVKESLDSFVSPHFLPTDIKPTDKVMIDGLLANHSNWAILSRNSKYKYRNLL
                     KRESQNDELTNHLRETFEESADDLKKELDTWLQGLDVTEEE"
                     /name="replication initiation factor domain-containing
                     protein"
     gene            3709..3942
                     /locus_tag="JCQ06_RS14070"
                     /old_locus_tag="JCQ06_14075"
     CDS             3709..3942
                     /locus_tag="JCQ06_RS14070"
                     /old_locus_tag="JCQ06_14075"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002298421.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_002298421.1"
                     /translation="MAEKQKHFGKKNWLVNLTGDNVVVVFLDSKKMSGKLLDVTQYELI
                     LKNNKIDSPIIIPKHAVKYVYGVAESNGEDND"
                     /name="hypothetical protein"
     gene            3935..4354
                     /locus_tag="JCQ06_RS14075"
                     /old_locus_tag="JCQ06_14080"
     CDS             3935..4354
                     /locus_tag="JCQ06_RS14075"
                     /old_locus_tag="JCQ06_14080"
                     /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_002298420.1"
                     /translation="MTDLPEKMTIKNLADELGISKNTVRNQLVNAGYDLARYKDNGVIM
                     LDKELIGVVRSIYRSKGGQLTGDLPVNDAGNDFPLEKENEFLREQLAEKDRHISELTEM
                     IRDQQKLTLLQQQKNDQLLLENQELKNRKWWQFWK"
                     /name="hypothetical protein"
     Typing          2830..3693
                     /name="rep_cluster_943"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="81.264"
                     /coverage="95.0"
                     /evalue="0.0"
     Typing          888..2290
                     /name="MOBV"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="92.094"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 ttgatttgag agaagaaaca gtcgatagaa ttgaattgat gtatgaacgg ttagctgatt
       61 atttgaattt gccggatgaa gataattata gtgaaatgct tgaacgagtt atggatgttc
      121 tcaactcggt tatcaatgct gatctagcaa aatcttcagt tttgactaat gaatttgttc
      181 ataagcattt agcgcaaaca actgatgaat cagaaaaaga attttggttg aaattaatga
      241 gtcatgttat gcagttaaac caaatttccg ttattaattc caaagaaaag gagatgtagt
      301 ttatgggaat gactttagca gatattaaag cgcaagaaga aaaattaaaa aaagaacaag
      361 cgaaacttcg ccaacagaaa aaacgcttga ttgagaaaga aaatgctgca atgggcaagg
      421 ctcttcgcaa gcgttttggg tttgaaactt ttgctgattt tgagcggtgg ttatcgtcaa
      481 tttctgacga tcagcaacac gaaaaaacag tggataatga gtggcttgct gatgaaaaat
      541 cagcgccaag cgaacgagat tatcccgatg aatctgacga cttattcgga gtgataccga
      601 ataagaaaag tcagatgagt gagagtaaat ttacgtcaat atttaatgac gtgaatttac
      661 gataagcgat tattttgcgt gaagcaaaat aaagcataaa aggagttgat agcgtgatac
      721 gctttcggct ccttttttcg ttgtcacttg tgacagcgaa aaccctcgga gagcgtttgg
      781 aattgtgaca tccatgtcac aattaggaaa atgttactct ttgacaaaga gtaacagaaa
      841 ggtttacaat ctttttatta gcgacagcgc gaaggagggt tttaacttgg ggtttagtat
      901 ttcatttaaa aaaggaacga agaatacaag tatttctcat aataatcgtg agttaactga
      961 tcgccagaaa accaatgatt ggcataagca cattgacttc acgaaatcgg atgaaaatat
     1021 ttatttagag cagacgaatc tagcagataa atatgaggaa ttgtttggcg aagtggtaga
     1081 aaaatataat gcgaaacaaa aaagagccga tagaaaaatc gaggactatt tagcgaaagt
     1141 gcgcaaggat aaaaagttgg aacctcaacg agaatttatt gtgcaaatag gcattttaga
     1201 tgatttccag acaaatcgag cagatggttc ttctactggc atatcgaaac aacaagctga
     1261 acaaaatcga gtgattgcca ataaaatttt ggttcagtat tacaaggagt ttcaagagag
     1321 aaaccctaat ttggctgttt ataatgctgt tattcataat gacgaaataa gtccgcacct
     1381 gcacttgaat attgtgccgg ttgctgaagg ttataaacgg ggtgttcaaa agcagccgag
     1441 ctttaataaa gcactggttc aacaagggat acacgctgat aaagataatg gtcgagtgct
     1501 tttcaataat tttagaaatc aagaagttga ctctatagaa cgattaatga atgattacgg
     1561 ttggaaaagg gatattgtcg gtaccaacaa aattaaagat attcacgaat acaaagaaat
     1621 catgagtgaa atttctgaat tgcgccaaac ggctgtaaaa gagcgtgaga gcgtttctga
     1681 tgagttgagg tatatttata ggcaaagaga agaaaacgag cgtgataagg ctctgatggc
     1741 ttctgagaga gcgaagattg aagaagagaa gaaaaatatg ctgaatgtaa aaaaagagat
     1801 ggcggtcatt ttccaaaaag atatggttcc tttagaaagt ttcaagaggc ttcctgatgg
     1861 ttcgtatcat ttatctggga atgattttgt tgatttgtat caacgagcta cgagagcaac
     1921 aaatgccaag agaaatgctg ataacatgag tgagcaatat ttacagatgc ttgagcaaaa
     1981 tacagaatta aatgagtatg tagctacatt ggaagaagag cgtcatttgt ctggtagaaa
     2041 acaattagca gatttacaag tggaaaataa aaagctgaaa gaagaaaatc gctctttacg
     2101 ccagcgttta gagcgattaa aaaacgcatt tcaaaaatcg atcactcgtt tgtctatccg
     2161 ttttggtctt gcagaaaagg atatggggct ttctgaggaa ttagaagtat tagagcagga
     2221 gaaaacctta ttttatcgtc aaaacgtctc acagcataaa ttagagcgtt ctgagaatga
     2281 gattgagtgg tagccacgat gtgcagtcaa cggtaccgga ggcggtttgt gccgaggata
     2341 aggagttgac ggctaaacca ctagcccctg aagctgacat ttgctaaaaa atggcaagtc
     2401 cattttttgg ccaacttagc gttagcgaag tttgggggcg cccttttcaa agggtgcggt
     2461 tttatttttt tggtatttgc atagctaaag agaagtgcta ttattgagtt agcaaacaaa
     2521 tgaactggaa aaagagcaaa aaaataagtc gagcaacgct accaacgttc tcgaccttta
     2581 cggaaactaa ccacactagt tccgtaactc aaattcatta tacgaatatt tttaggtttc
     2641 ttcaagacta gagattgatg gttatgaatt tttagagtta cgtgaactct ggaaattctt
     2701 tccaaaaatc tcttttttct ttgaggagga actgaatatg agtaaaaaaa gaacaatcgt
     2761 gaatgagtgg gaaaaattaa cagccctgtc taacaggcgg ttaaatgttc aaactttggt
     2821 acaaactata aaattaaatt ggtcgattga ccgaattacc attgttggaa agttgaatca
     2881 aaatattttt tatcatactc aacatgatgt attaatatta gattttgaac agcttatgcg
     2941 ggtaaatgaa ggcaatggct atttaaaagc ggttggaaat aatggttggc agctattaga
     3001 ccaacatgac gaaaatattg cctatattga aatttctaaa tggcaagaag gaaaagggcg
     3061 gattgatttt aatcctaata aaatcagtcg atttttagcg gattccatga aaaattttat
     3121 tcatgattta tttttagagc cccatttttc acgagcggat gttgcctgcg atcttattga
     3181 tgtgcctgat gagtttatca cgcaatatcg aattattgat ccagtttcat ttaaattaat
     3241 ttatggacgc tcaggaaaac tggaaacggt gtattggggt agtcgggcaa gcgagcggca
     3301 aattcgtttg tacaataaaa aaatagagca agaaatgaaa agaaaggtgg tgccttcaga
     3361 aattaatact tggtggcggt tagaaatgca gttaagacgt ggtaaagcta cggaatggta
     3421 tgctatggtg aaagaaagtt tggatagctt tgtgagtcca cattttttac caactgatat
     3481 aaaacctacg gataaagtta tgattgatgg attgttagct aatcattcta attgggcgat
     3541 tttgtcaaga aactcgaaat ataaatatcg aaatttatta aagcgagaaa gtcaaaatga
     3601 tgagttgacg aatcatttac gagaaacatt tgaagaatca gcagatgatt taaaaaaaga
     3661 attggatact tggttacagg gacttgatgt gacagaggag gaatagtaat ggcagaaaaa
     3721 caaaagcatt ttggtaagaa aaattggttg gtgaatttaa caggtgataa cgttgtcgtt
     3781 gtttttttgg atagcaaaaa aatgtccggt aagttacttg atgtaacgca gtatgagttg
     3841 attttgaaaa ataataaaat tgattcccca atcattatcc ctaagcatgc tgttaaatat
     3901 gtttatgggg tagctgaaag taacggagaa gataatgact gatttgccag aaaaaatgac
     3961 cataaaaaac cttgctgatg agttgggtat atctaaaaat acagtgcgca atcaactggt
     4021 caatgcaggt tatgaccttg ctcggtataa agataatggg gttatcatgt tagacaagga
     4081 attgattggt gttgtgcggt caatttatcg gtcaaaaggt ggtcaattga ctggtgattt
     4141 accggtcaat gatgcaggca atgatttccc gttagaaaaa gaaaatgaat ttttgcgtga
     4201 acaattagcg gaaaaagata ggcatatttc tgaattaacg gaaatgattc gtgaccaaca
     4261 aaaattgact ttgcttcagc aacaaaaaaa cgatcagttg ttactagaaa atcaagaatt
     4321 aaaaaatcga aaatggtggc aattctggaa gtgaggtgtg acatggataa aa
//
