LOCUS       NZ_CP065934             4074 bp    DNA     circular CON 18-FEB-2024
DEFINITION  Enterococcus faecium strain Dallas 5 plasmid p5_4kb, complete
            sequence.
ACCESSION   NZ_CP065934
VERSION     NZ_CP065934.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN17038066
            Assembly: GCF_016126675.1
KEYWORDS    RefSeq.
SOURCE      Enterococcus faecium
  ORGANISM  Enterococcus faecium
            Bacteria; Bacillota; Bacilli; Lactobacillales; Enterococcaceae;
            Enterococcus.
REFERENCE   1  (bases 1 to 4074)
  AUTHORS   Islam,M.J. and Palmer,K.
  TITLE     Molecular characterization of VREfm isolates from Dallas, Texas
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 4074)
  AUTHORS   Islam,M.J.
  TITLE     Direct Submission
  JOURNAL   Submitted (09-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                   :: 48.0x
            Sequencing Technology :: Oxford Nanopore MinION; Illumina NextSeq
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 02/18/2024 03:26:52
            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)                     :: 3,144
            CDSs (total)                      :: 3,053
            Genes (coding)                    :: 2,938
            CDSs (with protein)               :: 2,938
            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)              :: 115
            CDSs (without protein)            :: 115
            Pseudo Genes (ambiguous residues) :: 0 of 115
            Pseudo Genes (frameshifted)       :: 42 of 115
            Pseudo Genes (incomplete)         :: 64 of 115
            Pseudo Genes (internal stop)      :: 31 of 115
            Pseudo Genes (multiple problems)  :: 18 of 115
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP065934.1.
            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..4074
                     /organism="Enterococcus faecium"
                     /mol_type="genomic DNA"
                     /strain="Dallas 5"
                     /isolation_source="rectal swab"
                     /host="Homo sapiens"
                     /db_xref="taxon:1352"
                     /plasmid="p5_4kb"
                     /geo_loc_name="USA: Dallas"
                     /collection_date="2015"
     gene            complement(35..1450)
                     /locus_tag="JCP67_RS15555"
                     /old_locus_tag="JCP67_15555"
     CDS             complement(35..1450)
                     /locus_tag="JCP67_RS15555"
                     /old_locus_tag="JCP67_15555"
                     /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_002303405.1"
                     /translation="MGFSISFKKGTKNTSISHNNRELTDSQKTNDWHKHIDFTKSDENI
                     YLEQTNLADKYEELFGEVVEKYNAKQKRADRKIEDYLAKVRKDKKLEPQREFIVQIGIL
                     DDFQTNRADGSSTGISKQQAEQNRVIANKILVQYYKEFQERNPNLAVYNAVIHNDEISP
                     HLHLNIVPVAEGYKRGVQKQPSFNKALVQQGIHADKDNGRVLFNNFRNQEVDSIERLMN
                     DYGWKRDIVGTNKIKDIHEYKEIMSEISELRQTAVKERESISAEMRYISKQREKNEREK
                     ALVASEKAKIEEEKKSIIDLEKELAVVFQKDPVPLNSFEKLSDGSYRLSSADFVDLYQK
                     ASNATNSKKYADMANESLGNTLDKNIALFDKNMALEQENSFLKNQQKVDVSAVVAENKK
                     LKEENRSLRRRLTQLKNAFQKSITRLSIRFGLVEKDMGISEELKILDQEKTLASQQNAP
                     ERNIGRSENEMEW"
                     /name="plasmid recombination protein"
     gene            complement(1672..2034)
                     /locus_tag="JCP67_RS15560"
                     /old_locus_tag="JCP67_15560"
     CDS             complement(1672..2034)
                     /locus_tag="JCP67_RS15560"
                     /old_locus_tag="JCP67_15560"
                     /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_198478496.1"
                     /translation="MGMTLADIKAQEEKLKKEQAKLRQQKKRLIEKENAEMGKALRKHF
                     GFESFADFERWLSSISDDQQHEKSVDNEWLADEKSAPSERDYPNESDGLLGVIPSKKSQ
                     MSESKFTSMFNDVSLR"
                     /name="hypothetical protein"
     gene            complement(2038..2385)
                     /locus_tag="JCP67_RS15565"
                     /old_locus_tag="JCP67_15565"
     CDS             complement(2038..2385)
                     /locus_tag="JCP67_RS15565"
                     /old_locus_tag="JCP67_15565"
                     /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_171346404.1"
                     /translation="MVAVLEMRCNMDKIDLREETVDRIELMYERLADYLNLPDEDNYSE
                     MLERMMDVLNSTINVGLANSSLITDKFVYGKIAETEDESEKEFWLNILTYVMQLNQIGV
                     IYRNKSKGKEL"
                     /name="hypothetical protein"
     gene            complement(2456..2689)
                     /locus_tag="JCP67_RS15570"
                     /old_locus_tag="JCP67_15570"
     CDS             complement(2456..2689)
                     /locus_tag="JCP67_RS15570"
                     /old_locus_tag="JCP67_15570"
                     /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_002303408.1"
                     /translation="MTEKQKYFGKKNWLVNLTGDYVVVVFLDSKKMSGKLLDVTQYELI
                     LKNNKIDSPIIIPKHAVKYIYAVAESSGEAND"
                     /name="hypothetical protein"
     gene            complement(2686..3660)
                     /locus_tag="JCP67_RS15575"
                     /old_locus_tag="JCP67_15575"
     CDS             complement(2686..3660)
                     /locus_tag="JCP67_RS15575"
                     /old_locus_tag="JCP67_15575"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002303407.1"
                     /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_002303407.1"
                     /translation="MSKKGTIINEWEKLTAPSNRRLSVPFMDTPLKIQWSIDRITIVGN
                     LKENIYYHTTHDVLILDFEQLMRLNEGNGYLRSVSNNGWQLLDQHEENIAYIEILKWQE
                     GKGRIDFNPNKISQFLASSMKNFIHDLFIEPHFSRADIACDIIDVPDEFITQYRVVDPV
                     SFKPIYGRNGKLETAYWGSRSSERQIRMYNKKLEQEKKRKIVPKEIVSWWRLELQLRRG
                     KATDWHAMVYESLDSFASPHYLPADTSVADKMMITALTTEHDYWGQINRKTKYKYRNLL
                     KQESQNDELTNHLRETFAESADDLKKELDTWLLGLDVTEEEEK"
                     /name="replication initiation factor domain-containing
                     protein"
     Typing          complement(2687..3582)
                     /name="rep_cluster_2146"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          complement(39..1543)
                     /name="MOBV"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="98.207"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 gaccgcctcc ggtaccgttg actgcaccgt ataactacca ctccatctca ttctcagaac
       61 gccctatatt acgttctggg gcattctgct gactagccaa cgttttctct tgatctaata
      121 tttttagctc ttcagatatt cccatatctt tttctacaag cccaaaacga attgataaac
      181 gagtgattga tttttgaaat gcgtttttca gttgagttaa ccgccgacgc aaagaacgat
      241 tttcttcctt cagctttttg ttttcagcaa caaccgctga cacatcaacc ttttgttgat
      301 ttttcaaaaa agaattttct tgttctaacg ccatgttttt atcaaataaa gcgatatttt
      361 tatctaatgt atttccaagc gattcattcg ccatatcagc atattttttg ctgttcgtag
      421 cattagacgc tttttgatac aaatctacaa aatcagcact agataagcga taagaaccat
      481 ctgataattt ttcaaaacta ttgagtggca caggatcttt ttgaaataca acagccagct
      541 ctttttccaa atcgataatc gattttttct cttcttcaat tttcgccttc tcagaagcca
      601 ccagagcctt ctcacgctcg tttttttctc tttgcttaga aatatacctc atttccgcag
      661 aaatgctctc acgctctttt acagccgttt ggcgcaattc agaaatttca ctcatgattt
      721 ctttgtattc gtgaatatct ttaattttgt tggtaccgac aatatccctt ttccaaccgt
      781 aatcattcat taatcgttct atagagtcaa cttcttgatt tctaaaatta ttgaaaagca
      841 ctcgaccatt atctttatca gcgtgtatcc cttgttgaac cagtgcttta ttaaagctcg
      901 gctgcttttg aacaccccgt ttataacctt cagcaaccgg cacaatattc aagtgcaggt
      961 gcggacttat ttcgtcatta tgaataacag cattataaac agccaaatta gggtttctct
     1021 cttgaaactc cttgtaatac tgaaccaaaa ttttattggc aatcactcga ttttgttcag
     1081 cttgttgttt cgatatgcca gtagaagaac catctgctcg atttgtctgg aaatcatcta
     1141 aaatgcctat ttgcacaata aattctcgtt gaggttccaa ctttttatcc ttgcgcactt
     1201 tcgctaaata gtcctcgatt tttctatcgg ctcttttttg tttcgcatta tatttttcta
     1261 ccacttcgcc aaacaattcc tcatatttat ctgctagatt cgtctgctct aaataaatat
     1321 tttcatccga tttcgtgaag tcaatatgct tatgccaatc attggttttc tggctatcag
     1381 ttaactcacg attattatga gaaatacttg tattcttcgt tcctttttta aatgaaatac
     1441 taaaccccaa gttaaaaccc tccttcgcgc tgtcgctaat aaaaagagtg taaacctttc
     1501 tgttactctt tgtcaaagag taacattttc ctaattgtga catggctgtc acaattccaa
     1561 atgctctccg agggtattcg ctgtcacaag tgacaacgaa aaaaggagcc gaaagcgtgt
     1621 cacgctctca actcctttta cgctttattt tgcttcacgc aaaataatcg cttatcgtaa
     1681 actcacgtca ttaaacattg acgtaaattt actctcactc atctgacttt ttttactcgg
     1741 tatcactccg agtaagccgt cagattcatt gggataatct cgttcgcttg gcgctgattt
     1801 ttcatcagca agccactcat tatccactga tttttcgtgt tgctgatcgt cagaaattga
     1861 cgataaccac cgctcaaaat cagcaaaaga ttcaaatcca aaatgcttcc gaagtgcctt
     1921 acccatttca gcattttcct tctcaatcaa tcgttttttc tgttgacgaa gttttgcctg
     1981 ttcttttttc aatttttctt cttgtgcttt aatatctgct aaagtcattc ccaagattta
     2041 cagctccttg ccttttgatt tatttcgata aataacacca atttgattta attgcataac
     2101 ataagttaaa atattcagcc aaaattcctt ttcagattca tcttctgttt cggctatttt
     2161 accgtaaaca aatttatcag taatcaaaga agaatttgct aggcctacat tgattgtaga
     2221 attgagaacg tccatcattc tctcaagcat ttcactataa ttatcttcat ccggcaaatt
     2281 caaataatca gctaatcgtt catacatcaa ttcaattcta tcaactgtct cttctcttaa
     2341 atcaatttta tccatgttac acctcatttc caaaactgcc accatttccg attctttaat
     2401 tttcgataca cctaattcat cagcaagatt ttttatggtc atcttttctg acaaatcagt
     2461 cattagcttc tccactactt tcagctaccg cataaatata tttaacggcg tgcttaggga
     2521 taataatcgg agagtcaatt ttattatttt tcaaaatcaa ttcatattgc gttacatcaa
     2581 gtaacttacc ggacattttt ttgctatcca aaaaaacaac cacaacgtaa tcacctgtta
     2641 aatttaccaa ccaatttttc ttaccaaaat acttttgttt ttctgtcatt tttcttcctc
     2701 ctctgttacg tctagcccta gaagccatgt gtctaattct ttttttaaat cgtctgccga
     2761 ttctgcaaag gtttctcgta aatgattcgt caattcatca ttttgacttt cttgcttcag
     2821 caaatttcga tatttatatt ttgtctttcg attaatttgc ccccaataat catgttctgt
     2881 tgttaaagca gtaatcatca ttttgtcagc tacacttgta tcagcaggca agtaatgagg
     2941 actagcaaaa ctatctaagc tttcataaac catagcatgc caatcagtcg ctttccctcg
     3001 tcttaattgt aattctaacc gccaccaact cacgatttct tttggcacaa tttttctttt
     3061 cttctcttgt tccagttttt tattatacat ccgaatttga cgttcagaag agcgagatcc
     3121 ccaatatgcc gtctctaatt ttccattccg tccataaata ggcttaaaag aaactggatc
     3181 aactacccga tattgtgtaa taaactcatc aggtacatcg ataatgtcgc aagcaatatc
     3241 tgcacgtgaa aagtgaggtt cgataaacaa atcatgaata aaatttttca tggaactagc
     3301 taagaattga ctaatcttat tcggattgaa gtctatacgc cctttcccct cttgccattt
     3361 taaaatttca atataagcaa tattctcttc atgttggtct aacaactgcc aaccattatt
     3421 actaacagat cttaaataac cgttaccttc atttaggcgc ataagctgtt caaaatctaa
     3481 aatcaacaca tcatgtgtag tgtgataata gatattctct ttaagatttc caacaatggt
     3541 aattcggtcg attgaccact gaatttttag gggggtgtcc ataaaaggga cacttaaccg
     3601 cctgttagag ggggctgtta atttttccca ctcatttatg atcgtgcctt ttttactcaa
     3661 atttagttcc tcctcaaaga aaaaagagat tggtggaaag aattttccag agttcacgta
     3721 actctaaaaa attcataacc agcaatctct agtcttgaag aaacctgaaa ttattcgtat
     3781 aatgaatttg agttacggag ctagtgtgat tagtttccgt aaaggtcgag aacgtgtcca
     3841 gcgttgctcg actttatttt tttgctcttt tttcagttta tttatttgat aactcaataa
     3901 tagcacttct ctttagctat gcaaatatcc aaaaacataa aaccgcaccc tttgaaaagg
     3961 gcgcccccaa acttcgctaa cgctaagttg gccaaaaaat ggacttgcca ttttttagca
     4021 aatgtcagct tcagggatta gtggtttagc cgtcaactcc ttatcctcgg caca
//
