LOCUS       NZ_CP066485             1980 bp    DNA     circular CON 20-FEB-2024
DEFINITION  Enterococcus faecium strain Dallas 93_3 plasmid p93_3_1.9kb,
            complete sequence.
ACCESSION   NZ_CP066485
VERSION     NZ_CP066485.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN17038089
            Assembly: GCF_016406585.1
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  JOURNAL   Unpublished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                   :: 302.0x
            Sequencing Technology :: Illumina NextSeq; Oxford Nanopore MinION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 02/20/2024 02:52:36
            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)                     :: 3,103
            CDSs (total)                      :: 3,012
            Genes (coding)                    :: 2,902
            CDSs (with protein)               :: 2,902
            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)              :: 110
            CDSs (without protein)            :: 110
            Pseudo Genes (ambiguous residues) :: 0 of 110
            Pseudo Genes (frameshifted)       :: 41 of 110
            Pseudo Genes (incomplete)         :: 65 of 110
            Pseudo Genes (internal stop)      :: 27 of 110
            Pseudo Genes (multiple problems)  :: 19 of 110
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP066485.1.
            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 93_3"
                     /isolation_source="rectal swab"
                     /host="Homo sapiens"
                     /db_xref="taxon:1352"
                     /plasmid="p93_3_1.9kb"
                     /geo_loc_name="USA: Dallas"
                     /collection_date="2015"
     gene            complement(join(1830..1980,1..866))
                     /locus_tag="JCP71_RS15405"
                     /old_locus_tag="JCP71_15405"
     CDS             complement(join(1830..1980,1..866))
                     /locus_tag="JCP71_RS15405"
                     /old_locus_tag="JCP71_15405"
                     /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          complement(83..866)
                     /name="rep_cluster_935"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="96.943"
                     /coverage="91.0"
                     /evalue="0.0"
ORIGIN
        1 tgtctagcaa ttatcgacca attagaaggc tcagctatca aaccatcaat aactatttta
       61 tcaataggtt ttatatcaat cggcaaaaaa tgcgggcttg caaaactatc taagctttcc
      121 tgaaccatcg catgccaatc cgttgctttg ccacgtctta gctgcatttc taaccgccac
      181 cacgtatcga tttcttttgg cacgattact ttttttcgtt cctgctctag ctttttgttg
      241 tacagtcgca cttggcgctc actggcacga ctgccccagt acgctgtttc tagcttgcca
      301 gaacggccgt agattggctt aaaagaaatc gggtctacaa tacgatactg agtaataaag
      361 tcatccggca catctacaat atcgcaggca atatccgccc gggaaaaatg cggatctaaa
      421 aataggtcat gaatgaatcc tttcatggaa ctagctaaaa actggcctat cttattcgga
      481 ttaaaatcaa tacgaccttt tccttcatga aatttaagta tttcgatata cgcaatatct
      541 tctccatatt gatcgaataa ttgccagccg tttatcccaa ctgatttcaa atatccctga
      601 ttttcgttca aacgcattaa ttgctcgaaa tcgacaaaaa caactccatt tttcgtccaa
      661 taagctatgg tatcattcag ttttccgaca attgtaattc gatcaatcga ccaatttaat
      721 tttagggggg tggtcgtacc ttgcacactt aaccgcctgt tagaaatacg gttaagtttt
      781 tcgagctgat ttatcgttgt tcttttttct gcccctcgac cttcaatttt tgattgaatt
      841 tcactcaact gattttcatt tgccattttc gtcctccaaa cgaaaaaaga gacttttgga
      901 aagaatttcc agagttcacg taaccctaaa aattcatatc caaaaatctc tagcttgaag
      961 aaacctaaaa atattcgtat aatgaacctg agttacggag ctaggtgaag tagtttccgt
     1021 aaatagtcga gagtgttagc gcactgctcg gcttttattt tgctcttttt tctcgttttc
     1081 tttgattata gcactcctcc taaaaaaata aaaagacctc agggaatttc attccccgaa
     1141 ccccttgagc ctcctcctgc cgaaatggaa agggcgcacc cgctgtttat ttcattcagc
     1201 tatcggtttt cacaatctaa cacgatcgtt ccgctaccag tcgccttaca ggctccattt
     1261 tcgctcctct aacgtgtttt aacgattgtg ccgataacta aacgaaataa acgctaaaac
     1321 cgctcagaac gcaaaatatg ccattttaga gctattgtag aaaatgtagt ttgaaatgca
     1381 attttcttct ttcagctttt tatttcccac ttgtaaatct gctaattatt ttctaccaga
     1441 caaaccattg attttttggc tatcagttaa ctcacgatta ttatgagaaa tgcttgtatt
     1501 ctttgttccc tttttgaacg aaatactaaa ccctaaggtg aacccctcct tcacgctgtc
     1561 gctaataaaa agagtgtaaa cctttctgtt actctttgac aaagagtaaa aattttccta
     1621 attgtgacat ggctgtcaca attccaaatg ctctccgagg gtattcgctg tcacaagtga
     1681 caacgaaaaa aggagccgaa agcgtgtcac gctctcaact ccttttacgc tttattttgc
     1741 ttcatgcaaa atattcgctt atcgtgaatt tacgtcacta aacattgacg caaatccact
     1801 ctcactcatc tgacttttct tattcggtat cacttctctg tcacatccaa ccccaaaagc
     1861 cacgtatcca attctttttt taattcgtct gcagattcct taaacgtctc tcgtaaatga
     1921 ttcgttaact catcattttg actttcttgc ttcagcaaat tccgatattt atattttgta
//
