LOCUS       NZ_CP066646             1980 bp    DNA     circular CON 20-FEB-2024
DEFINITION  Enterococcus faecium strain Dallas 148 plasmid p148_1.9kb, complete
            sequence.
ACCESSION   NZ_CP066646
VERSION     NZ_CP066646.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN17038104
            Assembly: GCF_016415425.1
KEYWORDS    RefSeq.
SOURCE      Enterococcus faecium
  ORGANISM  Enterococcus faecium
            Bacteria; Bacillota; Bacilli; Lactobacillales; Enterococcaceae;
            Enterococcus.
REFERENCE   1  (bases 1 to 1980)
  AUTHORS   Islam,M.J. and Palmer,K.
  TITLE     Molecular characterization of VREfm isolates from Dallas, Texas
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 1980)
  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                   :: 122.0x
            Sequencing Technology :: Illumina NextSeq; Oxford Nanopore MinION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 02/20/2024 02:39:50
            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)                     :: 3,136
            CDSs (total)                      :: 3,045
            Genes (coding)                    :: 2,927
            CDSs (with protein)               :: 2,927
            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)              :: 118
            CDSs (without protein)            :: 118
            Pseudo Genes (ambiguous residues) :: 0 of 118
            Pseudo Genes (frameshifted)       :: 41 of 118
            Pseudo Genes (incomplete)         :: 71 of 118
            Pseudo Genes (internal stop)      :: 30 of 118
            Pseudo Genes (multiple problems)  :: 20 of 118
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP066646.1.
            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..1980
                     /organism="Enterococcus faecium"
                     /mol_type="genomic DNA"
                     /strain="Dallas 148"
                     /isolation_source="rectal swab"
                     /host="Homo sapiens"
                     /db_xref="taxon:1352"
                     /plasmid="p148_1.9kb"
                     /geo_loc_name="USA: Dallas"
                     /collection_date="2015"
     gene            join(1448..1980,1..484)
                     /locus_tag="JCP76_RS13870"
                     /old_locus_tag="JCP76_13870"
     CDS             join(1448..1980,1..484)
                     /locus_tag="JCP76_RS13870"
                     /old_locus_tag="JCP76_13870"
                     /inference="COORDINATES: ab initio prediction:GeneMarkS-2+"
                     /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: GeneMarkS-2+."
                     /codon_start=1
                     /transl_table=11
                     /product="replication initiation factor domain-containing
                     protein"
                     /protein_id="WP_002299382.1"
                     /translation="MANENQLSEIQSKIEGRGAEKRTTINQLEKLNRISNRRLSVQGTT
                     TPLKLNWSIDRITIVGKLNDTIAYWTKNGVVFVDFEQLMRLNENQGYLKSVGINGWQLF
                     DQYGEDIAYIEILKFHEGKGRIDFNPNKIGQFLASSMKGFIHDLFLDPHFSRADIACDI
                     VDVPDDFITQYRIVDPISFKPIYGRSGKLETAYWGSRASERQVRLYNKKLEQERKKVIV
                     PKEIDTWWRLEMQLRRGKATDWHAMVQESLDSFASPHFLPIDIKPIDKIVIDGLIAEPS
                     NWSIIARHTKYKYRNLLKQESQNDELTNHLRETFKESADELKKELDTWLLGLDVTEK"
                     /name="replication initiation factor domain-containing
                     protein"
     Typing          2..478
                     /name="rep_cluster_935"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="85.386"
                     /coverage="99.0"
                     /evalue="3.49e-137"
ORIGIN
        1 cccgatttct tttaagccaa tctacggccg ttctggcaag ctagaaacag cgtactgggg
       61 cagtcgtgcc agtgagcgcc aagtgcgact gtacaacaaa aagctagagc aggaacgaaa
      121 aaaagtaatc gtgccaaaag aaatcgatac gtggtggcgg ttagaaatgc agctaagacg
      181 tggcaaagca acggattggc atgcgatggt tcaggaaagc ttagatagtt ttgcaagccc
      241 gcattttttg ccgattgata taaaacctat tgataaaata gttattgatg gtttgatagc
      301 tgagccttct aattggtcga taattgctag acatacaaaa tataaatatc ggaatttgct
      361 gaagcaagaa agtcaaaatg atgagttaac gaatcattta cgagagacgt ttaaggaatc
      421 tgcagacgaa ttaaaaaaag aattggatac gtggcttttg gggttggatg tgacagagaa
      481 gtgataccga ataagaaaag tcagatgagt gagagtggat ttgcgtcaat gtttagtgac
      541 gtaaattcac gataagcgaa tattttgcat gaagcaaaat aaagcgtaaa aggagttgag
      601 agcgtgacac gctttcggct ccttttttcg ttgtcacttg tgacagcgaa taccctcgga
      661 gagcatttgg aattgtgaca gccatgtcac aattaggaaa atttttactc tttgtcaaag
      721 agtaacagaa aggtttacac tctttttatt agcgacagcg tgaaggaggg gttcacctta
      781 gggtttagta tttcgttcaa aaagggaaca aagaatacaa gcatttctca taataatcgt
      841 gagttaactg atagccaaaa aatcaatggt ttgtctggta gaaaataatt agcagattta
      901 caagtgggaa ataaaaagct gaaagaagaa aattgcattt caaactacat tttctacaat
      961 agctctaaaa tggcatattt tgcgttctga gcggttttag cgtttatttc gtttagttat
     1021 cggcacaatc gttaaaacac gttagaggag cgaaaatgga gcctgtaagg cgactggtag
     1081 cggaacgatc gtgttagatt gtgaaaaccg atagctgaat gaaataaaca gcgggtgcgc
     1141 cctttccatt tcggcaggag gaggctcaag gggttcgggg aatgaaattc cctgaggtct
     1201 ttttattttt ttaggaggag tgctataatc aaagaaaacg agaaaaaaga gcaaaataaa
     1261 agccgagcag tgcgctaaca ctctcgacta tttacggaaa ctacttcacc tagctccgta
     1321 actcaggttc attatacgaa tatttttagg tttcttcaag ctagagattt ttggatatga
     1381 atttttaggg ttacgtgaac tctggaaatt ctttccaaaa gtctcttttt tcgtttggag
     1441 gacgaaaatg gcaaatgaaa atcagttgag tgaaattcaa tcaaaaattg aaggtcgagg
     1501 ggcagaaaaa agaacaacga taaatcagct cgaaaaactt aaccgtattt ctaacaggcg
     1561 gttaagtgtg caaggtacga ccacccccct aaaattaaat tggtcgattg atcgaattac
     1621 aattgtcgga aaactgaatg ataccatagc ttattggacg aaaaatggag ttgtttttgt
     1681 cgatttcgag caattaatgc gtttgaacga aaatcaggga tatttgaaat cagttgggat
     1741 aaacggctgg caattattcg atcaatatgg agaagatatt gcgtatatcg aaatacttaa
     1801 atttcatgaa ggaaaaggtc gtattgattt taatccgaat aagataggcc agtttttagc
     1861 tagttccatg aaaggattca ttcatgacct atttttagat ccgcattttt cccgggcgga
     1921 tattgcctgc gatattgtag atgtgccgga tgactttatt actcagtatc gtattgtaga
//
