LOCUS       NZ_CP066643             4075 bp    DNA     circular CON 20-FEB-2024
DEFINITION  Enterococcus faecium strain Dallas 144_1 plasmid p144_1_4kb,
            complete sequence.
ACCESSION   NZ_CP066643
VERSION     NZ_CP066643.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN17038103
            Assembly: GCF_016415405.1
KEYWORDS    RefSeq.
SOURCE      Enterococcus faecium
  ORGANISM  Enterococcus faecium
            Bacteria; Bacillota; Bacilli; Lactobacillales; Enterococcaceae;
            Enterococcus.
REFERENCE   1  (bases 1 to 4075)
  AUTHORS   Islam,M.J. and Palmer,K.
  TITLE     Molecular characterization of VREfm isolates from Dallas, Texas
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 4075)
  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                   :: 266.0x
            Sequencing Technology :: Illumina NextSeq; Oxford Nanopore MinION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 02/20/2024 02:43:36
            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)                     :: 3,211
            CDSs (total)                      :: 3,120
            Genes (coding)                    :: 3,025
            CDSs (with protein)               :: 3,025
            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)              :: 95
            CDSs (without protein)            :: 95
            Pseudo Genes (ambiguous residues) :: 0 of 95
            Pseudo Genes (frameshifted)       :: 33 of 95
            Pseudo Genes (incomplete)         :: 51 of 95
            Pseudo Genes (internal stop)      :: 27 of 95
            Pseudo Genes (multiple problems)  :: 13 of 95
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP066643.1.
            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..4075
                     /organism="Enterococcus faecium"
                     /mol_type="genomic DNA"
                     /strain="Dallas 144_1"
                     /isolation_source="rectal swab"
                     /host="Homo sapiens"
                     /db_xref="taxon:1352"
                     /plasmid="p144_1_4kb"
                     /geo_loc_name="USA: Dallas"
                     /collection_date="2015"
     gene            join(3646..4075,1..986)
                     /locus_tag="JCP95_RS15895"
                     /old_locus_tag="JCP95_15895"
     CDS             join(3646..4075,1..986)
                     /locus_tag="JCP95_RS15895"
                     /old_locus_tag="JCP95_15895"
                     /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            1435..2409
                     /locus_tag="JCP95_RS15900"
                     /old_locus_tag="JCP95_15900"
     CDS             1435..2409
                     /locus_tag="JCP95_RS15900"
                     /old_locus_tag="JCP95_15900"
                     /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"
     gene            2406..2639
                     /locus_tag="JCP95_RS15905"
                     /old_locus_tag="JCP95_15905"
     CDS             2406..2639
                     /locus_tag="JCP95_RS15905"
                     /old_locus_tag="JCP95_15905"
                     /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            2710..3057
                     /locus_tag="JCP95_RS15910"
                     /old_locus_tag="JCP95_15910"
     CDS             2710..3057
                     /locus_tag="JCP95_RS15910"
                     /old_locus_tag="JCP95_15910"
                     /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            3061..3423
                     /locus_tag="JCP95_RS15915"
                     /old_locus_tag="JCP95_15915"
     CDS             3061..3423
                     /locus_tag="JCP95_RS15915"
                     /old_locus_tag="JCP95_15915"
                     /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_002303404.1"
                     /translation="MGMTLADIKAQEEKLKKEQAKLRQQKKRLIEKENAEMGKALRKHF
                     GFESFDDFERWLSSISDDQQHEKSVDNEWLADEKSAPSERDYPNESDGLLGVIPSKKSQ
                     MSESKFTSMFNDVSLR"
                     /name="hypothetical protein"
     Typing          1514..2409
                     /name="rep_cluster_2146"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          4..983
                     /name="MOBV"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="97.859"
                     /coverage="98.0"
                     /evalue="0.0"
     Typing          3575..4074
                     /name="MOBV"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="98.802"
                     /coverage="98.0"
                     /evalue="1.1000000000000001e-101"
ORIGIN
        1 agagaaaccc taatttggct gtttataatg ctgttattca taatgacgaa ataagtccgc
       61 acctgcactt gaatattgtg ccggttgctg aaggttataa acggggtgtt caaaagcagc
      121 cgagctttaa taaagcactg gttcaacaag ggatacacgc tgataaagat aatggtcgag
      181 tgcttttcaa taattttaga aatcaagaag ttgactctat agaacgatta atgaatgatt
      241 acggttggaa aagggatatt gtcggtacca acaaaattaa agatattcac gaatacaaag
      301 aaatcatgag tgaaatttct gaattgcgcc aaacggctgt aaaagagcgt gagagcattt
      361 ctgcggaaat gaggtatatt tctaagcaaa gagaaaaaaa cgagcgtgag aaggctctgg
      421 tggcttctga gaaggcgaaa attgaagaag agaaaaaatc gattatcgat ttggaaaaag
      481 agctggctgt tgtatttcaa aaagatcctg tgccactcaa tagttttgaa aaattatcag
      541 atggttctta tcgcttatct agtgctgatt ttgtagattt gtatcaaaaa gcgtctaatg
      601 ctacgaacag caaaaaatat gctgatatgg cgaatgaatc gcttggaaat acattagata
      661 aaaatatcgc tttatttgat aaaaacatgg cgttagaaca agaaaattct tttttgaaaa
      721 atcaacaaaa ggttgatgtg tcagcggttg ttgctgaaaa caaaaagctg aaggaagaaa
      781 atcgttcttt gcgtcggcgg ttaactcaac tgaaaaacgc atttcaaaaa tcaatcactc
      841 gtttatcaat tcgttttggg cttgtagaaa aagatatggg aatatctgaa gagctaaaaa
      901 tattagatca agagaaaacg ttggctagtc agcagaatgc cccagaacgt aatatagggc
      961 gttctgagaa tgagatggag tggtagttat acggtgcagt caacggtacc ggaggcggtc
     1021 tgtgccgagg ataaggagtt gacggctaaa ccactaatcc ctgaagctga catttgctaa
     1081 aaaatggcaa gtccattttt tggccaactt agcgttagcg aagtttgggg gcgccctttt
     1141 caaagggtgc ggttttatgt ttttggatat ttgcatagct aaagagaagt gctattattg
     1201 agttatcaaa taaataaact gaaaaaagag caaaaaaata aagtcgagca acgctggaca
     1261 cgttctcgac ctttacggaa actaatcaca ctagctccgt aactcaaatt cattatacga
     1321 ataatttcag gtttcttcaa gactagagat tgctggttat gaatttttta gagttacgtg
     1381 aactctggaa aattctttcc accaatctct tttttctttg aggaggaact aaatttgagt
     1441 aaaaaaggca cgatcataaa tgagtgggaa aaattaacag ccccctctaa caggcggtta
     1501 agtgtccctt ttatggacac ccccctaaaa attcagtggt caatcgaccg aattaccatt
     1561 gttggaaatc ttaaagagaa tatctattat cacactacac atgatgtgtt gattttagat
     1621 tttgaacagc ttatgcgcct aaatgaaggt aacggttatt taagatctgt tagtaataat
     1681 ggttggcagt tgttagacca acatgaagag aatattgctt atattgaaat tttaaaatgg
     1741 caagagggga aagggcgtat agacttcaat ccgaataaga ttagtcaatt cttagctagt
     1801 tccatgaaaa attttattca tgatttgttt atcgaacctc acttttcacg tgcagatatt
     1861 gcttgcgaca ttatcgatgt acctgatgag tttattacac aatatcgggt agttgatcca
     1921 gtttctttta agcctattta tggacggaat ggaaaattag agacggcata ttggggatct
     1981 cgctcttctg aacgtcaaat tcggatgtat aataaaaaac tggaacaaga gaagaaaaga
     2041 aaaattgtgc caaaagaaat cgtgagttgg tggcggttag aattacaatt aagacgaggg
     2101 aaagcgactg attggcatgc tatggtttat gaaagcttag atagttttgc tagtcctcat
     2161 tacttgcctg ctgatacaag tgtagctgac aaaatgatga ttactgcttt aacaacagaa
     2221 catgattatt gggggcaaat taatcgaaag acaaaatata aatatcgaaa tttgctgaag
     2281 caagaaagtc aaaatgatga attgacgaat catttacgag aaacctttgc agaatcggca
     2341 gacgatttaa aaaaagaatt agacacatgg cttctagggc tagacgtaac agaggaggaa
     2401 gaaaaatgac agaaaaacaa aagtattttg gtaagaaaaa ttggttggta aatttaacag
     2461 gtgattacgt tgtggttgtt tttttggata gcaaaaaaat gtccggtaag ttacttgatg
     2521 taacgcaata tgaattgatt ttgaaaaata ataaaattga ctctccgatt attatcccta
     2581 agcacgccgt taaatatatt tatgcggtag ctgaaagtag tggagaagct aatgactgat
     2641 ttgtcagaaa agatgaccat aaaaaatctt gctgatgaat taggtgtatc gaaaattaaa
     2701 gaatcggaaa tggtggcagt tttggaaatg aggtgtaaca tggataaaat tgatttaaga
     2761 gaagagacag ttgatagaat tgaattgatg tatgaacgat tagctgatta tttgaatttg
     2821 ccggatgaag ataattatag tgaaatgctt gagagaatga tggacgttct caattctaca
     2881 atcaatgtag gcctagcaaa ttcttctttg attactgata aatttgttta cggtaaaata
     2941 gccgaaacag aagatgaatc tgaaaaggaa ttttggctga atattttaac ttatgttatg
     3001 caattaaatc aaattggtgt tatttatcga aataaatcaa aaggcaagga gctgtaaatc
     3061 ttgggaatga ctttagcaga tattaaagca caagaagaaa aattgaaaaa agaacaggca
     3121 aaacttcgtc aacagaaaaa acgattgatt gagaaggaaa atgctgaaat gggtaaggca
     3181 cttcggaagc attttggatt tgaatctttt gatgattttg agcggtggtt atcgtcaatt
     3241 tctgacgatc agcaacacga aaaatcagtg gataatgagt ggcttgctga tgaaaaatca
     3301 gcgccaagcg aacgagatta tcccaatgaa tctgacggct tactcggagt gataccgagt
     3361 aaaaaaagtc agatgagtga gagtaaattt acgtcaatgt ttaatgacgt gagtttacga
     3421 taagcgatta ttttgcgtga agcaaaataa agcgtaaaag gagttgagag cgtgacacgc
     3481 tttcggctcc ttttttcgtt gtcacttgtg acagcgaata ccctcggaga gcatttggaa
     3541 ttgtgacagc catgtcacaa ttaggaaaat ttttactctt tgacaaagag taacagaaag
     3601 gtttacactc tttttattag cgacagcgcg aaggagggtt ttaacttggg gtttagtatt
     3661 tcatttaaaa aaggaacgaa gaatacaagt atttctcata ataatcgtga gttaactgat
     3721 agccagaaaa ccaatgattg gcataagcat attgacttca cgaaatcgga tgaaaatatt
     3781 tatttagagc agacgaatct agcagataaa tatgaggaat tgtttggcga agtggtagaa
     3841 aaatataatg cgaaacaaaa aagagccgat agaaaaatcg aggactattt agcgaaagtg
     3901 cgcaaggata aaaagttgga acctcaacga gaatttattg tgcaaatagg cattttagat
     3961 gatttccaga caaatcgagc agatggttct tctactggca tatcgaaaca acaagctgaa
     4021 caaaatcgag tgattgccaa taaaattttg gttcagtatt acaaggagtt tcaag
//
