LOCUS       NZ_CP066635             4074 bp    DNA     circular CON 20-FEB-2024
DEFINITION  Enterococcus faecium strain Dallas 137 plasmid p6, complete
            sequence.
ACCESSION   NZ_CP066635
VERSION     NZ_CP066635.1
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 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  JOURNAL   Unpublished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. 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
            CP066635.1.
            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 137"
                     /isolation_source="rectal swab"
                     /host="Homo sapiens"
                     /db_xref="taxon:1352"
                     /plasmid="p6"
                     /geo_loc_name="USA: Dallas"
                     /collection_date="2015"
     gene            complement(37..1452)
                     /locus_tag="JCP61_RS15280"
                     /old_locus_tag="JCP61_15280"
     CDS             complement(37..1452)
                     /locus_tag="JCP61_RS15280"
                     /old_locus_tag="JCP61_15280"
                     /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(1674..2036)
                     /locus_tag="JCP61_RS15285"
                     /old_locus_tag="JCP61_15285"
     CDS             complement(1674..2036)
                     /locus_tag="JCP61_RS15285"
                     /old_locus_tag="JCP61_15285"
                     /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"
     gene            complement(2040..2387)
                     /locus_tag="JCP61_RS15290"
                     /old_locus_tag="JCP61_15290"
     CDS             complement(2040..2387)
                     /locus_tag="JCP61_RS15290"
                     /old_locus_tag="JCP61_15290"
                     /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(2458..2691)
                     /locus_tag="JCP61_RS15295"
                     /old_locus_tag="JCP61_15295"
     CDS             complement(2458..2691)
                     /locus_tag="JCP61_RS15295"
                     /old_locus_tag="JCP61_15295"
                     /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(2688..3662)
                     /locus_tag="JCP61_RS15300"
                     /old_locus_tag="JCP61_15300"
     CDS             complement(2688..3662)
                     /locus_tag="JCP61_RS15300"
                     /old_locus_tag="JCP61_15300"
                     /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(2689..3584)
                     /name="rep_cluster_2146"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          complement(41..1545)
                     /name="MOBV"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="98.207"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 cagaccgcct ccggtaccgt tgactgcacc gtataactac cactccatct cattctcaga
       61 acgccctata ttacgttctg gggcattctg ctgactagcc aacgttttct cttgatctaa
      121 tatttttagc tcttcagata ttcccatatc tttttctaca agcccaaaac gaattgataa
      181 acgagtgatt gatttttgaa atgcgttttt cagttgagtt aaccgccgac gcaaagaacg
      241 attttcttcc ttcagctttt tgttttcagc aacaaccgct gacacatcaa ccttttgttg
      301 atttttcaaa aaagaatttt cttgttctaa cgccatgttt ttatcaaata aagcgatatt
      361 tttatctaat gtatttccaa gcgattcatt cgccatatca gcatattttt tgctgttcgt
      421 agcattagac gctttttgat acaaatctac aaaatcagca ctagataagc gataagaacc
      481 atctgataat ttttcaaaac tattgagtgg cacaggatct ttttgaaata caacagccag
      541 ctctttttcc aaatcgataa tcgatttttt ctcttcttca attttcgcct tctcagaagc
      601 caccagagcc ttctcacgct cgtttttttc tctttgctta gaaatatacc tcatttccgc
      661 agaaatgctc tcacgctctt ttacagccgt ttggcgcaat tcagaaattt cactcatgat
      721 ttctttgtat tcgtgaatat ctttaatttt gttggtaccg acaatatccc ttttccaacc
      781 gtaatcattc attaatcgtt ctatagagtc aacttcttga tttctaaaat tattgaaaag
      841 cactcgacca ttatctttat cagcgtgtat cccttgttga accagtgctt tattaaagct
      901 cggctgcttt tgaacacccc gtttataacc ttcagcaacc ggcacaatat tcaagtgcag
      961 gtgcggactt atttcgtcat tatgaataac agcattataa acagccaaat tagggtttct
     1021 ctcttgaaac tccttgtaat actgaaccaa aattttattg gcaatcactc gattttgttc
     1081 agcttgttgt ttcgatatgc cagtagaaga accatctgct cgatttgtct ggaaatcatc
     1141 taaaatgcct atttgcacaa taaattctcg ttgaggttcc aactttttat ccttgcgcac
     1201 tttcgctaaa tagtcctcga tttttctatc ggctcttttt tgtttcgcat tatatttttc
     1261 taccacttcg ccaaacaatt cctcatattt atctgctaga ttcgtctgct ctaaataaat
     1321 attttcatcc gatttcgtga agtcaatatg cttatgccaa tcattggttt tctggctatc
     1381 agttaactca cgattattat gagaaatact tgtattcttc gttccttttt taaatgaaat
     1441 actaaacccc aagttaaaac cctccttcgc gctgtcgcta ataaaaagag tgtaaacctt
     1501 tctgttactc tttgtcaaag agtaacattt tcctaattgt gacatggctg tcacaattcc
     1561 aaatgctctc cgagggtatt cgctgtcaca agtgacaacg aaaaaaggag ccgaaagcgt
     1621 gtcacgctct caactccttt tacgctttat tttgcttcac gcaaaataat cgcttatcgt
     1681 aaactcacgt cattaaacat tgacgtaaat ttactctcac tcatctgact ttttttactc
     1741 ggtatcactc cgagtaagcc gtcagattca ttgggataat ctcgttcgct tggcgctgat
     1801 ttttcatcag caagccactc attatccact gatttttcgt gttgctgatc gtcagaaatt
     1861 gacgataacc accgctcaaa atcatcaaaa gattcaaatc caaaatgctt ccgaagtgcc
     1921 ttacccattt cagcattttc cttctcaatc aatcgttttt tctgttgacg aagttttgcc
     1981 tgttcttttt tcaatttttc ttcttgtgct ttaatatctg ctaaagtcat tcccaagatt
     2041 tacagctcct tgccttttga tttatttcga taaataacac caatttgatt taattgcata
     2101 acataagtta aaatattcag ccaaaattcc ttttcagatt catcttctgt ttcggctatt
     2161 ttaccgtaaa caaatttatc agtaatcaaa gaagaatttg ctaggcctac attgattgta
     2221 gaattgagaa cgtccatcat tctctcaagc atttcactat aattatcttc atccggcaaa
     2281 ttcaaataat cagctaatcg ttcatacatc aattcaattc tatcaactgt ctcttctctt
     2341 aaatcaattt tatccatgtt acacctcatt tccaaaactg ccaccatttc cgattcttta
     2401 attttcgata cacctaattc atcagcaaga ttttttatgg tcatcttttc tgacaaatca
     2461 gtcattagct tctccactac tttcagctac cgcataaata tatttaacgg cgtgcttagg
     2521 gataataatc ggagagtcaa ttttattatt tttcaaaatc aattcatatt gcgttacatc
     2581 aagtaactta ccggacattt ttttgctatc caaaaaaaca accacaacgt aatcacctgt
     2641 taaatttacc aaccaatttt tcttaccaaa atacttttgt ttttctgtca tttttcttcc
     2701 tcctctgtta cgtctagccc tagaagccat gtgtctaatt ctttttttaa atcgtctgcc
     2761 gattctgcaa aggtttctcg taaatgattc gtcaattcat cattttgact ttcttgcttc
     2821 agcaaatttc gatatttata ttttgtcttt cgattaattt gcccccaata atcatgttct
     2881 gttgttaaag cagtaatcat cattttgtca gctacacttg tatcagcagg caagtaatga
     2941 ggactagcaa aactatctaa gctttcataa accatagcat gccaatcagt cgctttccct
     3001 cgtcttaatt gtaattctaa ccgccaccaa ctcacgattt cttttggcac aatttttctt
     3061 ttcttctctt gttccagttt tttattatac atccgaattt gacgttcaga agagcgagat
     3121 ccccaatatg ccgtctctaa ttttccattc cgtccataaa taggcttaaa agaaactgga
     3181 tcaactaccc gatattgtgt aataaactca tcaggtacat cgataatgtc gcaagcaata
     3241 tctgcacgtg aaaagtgagg ttcgataaac aaatcatgaa taaaattttt catggaacta
     3301 gctaagaatt gactaatctt attcggattg aagtctatac gccctttccc ctcttgccat
     3361 tttaaaattt caatataagc aatattctct tcatgttggt ctaacaactg ccaaccatta
     3421 ttactaacag atcttaaata accgttacct tcatttaggc gcataagctg ttcaaaatct
     3481 aaaatcaaca catcatgtgt agtgtgataa tagatattct ctttaagatt tccaacaatg
     3541 gtaattcggt cgattgacca ctgaattttt aggggggtgt ccataaaagg gacacttaac
     3601 cgcctgttag agggggctgt taatttttcc cactcattta tgatcgtgcc ttttttactc
     3661 aaatttagtt cctcctcaaa gaaaaaagag attggtggaa agaattttcc agagttcacg
     3721 taactctaaa aaattcataa ccagcaatct ctagtcttga agaaacctga aattattcgt
     3781 ataatgaatt tgagttacgg agctagtgtg attagtttcc gtaaaggtcg agaacgtgtc
     3841 cagcgttgct cgactttatt tttttgctct tttttcagtt tatttatttg ataactcaat
     3901 aatagcactt ctctttagct atgcaaatat ccaaaaacat aaaaccgcac cctttgaaaa
     3961 gggcgccccc aaacttcgct aacgctaagt tggccaaaaa atggacttgc cattttttag
     4021 caaatgtcag cttcagggat tagtggttta gccgtcaact ccttatcctc ggca
//
