LOCUS       NZ_CP066472             1980 bp    DNA     circular CON 19-FEB-2024
DEFINITION  Enterococcus faecium strain Dallas 91 plasmid p91_1.9kb, complete
            sequence.
ACCESSION   NZ_CP066472
VERSION     NZ_CP066472.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN17038086
            Assembly: GCF_016406345.1
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  JOURNAL   Unpublished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                   :: 210.0x
            Sequencing Technology :: Illumina NextSeq; Oxford Nanopore MinION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 02/19/2024 04:00:00
            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)                     :: 3,121
            CDSs (total)                      :: 3,030
            Genes (coding)                    :: 2,918
            CDSs (with protein)               :: 2,918
            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)              :: 112
            CDSs (without protein)            :: 112
            Pseudo Genes (ambiguous residues) :: 0 of 112
            Pseudo Genes (frameshifted)       :: 41 of 112
            Pseudo Genes (incomplete)         :: 65 of 112
            Pseudo Genes (internal stop)      :: 30 of 112
            Pseudo Genes (multiple problems)  :: 20 of 112
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP066472.1.
            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 91"
                     /isolation_source="rectal swab"
                     /host="Homo sapiens"
                     /db_xref="taxon:1352"
                     /plasmid="p91_1.9kb"
                     /geo_loc_name="USA: Dallas"
                     /collection_date="2015"
     gene            join(1478..1980,1..514)
                     /locus_tag="JCQ04_RS15490"
                     /old_locus_tag="JCQ04_15490"
     CDS             join(1478..1980,1..514)
                     /locus_tag="JCQ04_RS15490"
                     /old_locus_tag="JCQ04_15490"
                     /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..508
                     /name="rep_cluster_935"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="86.248"
                     /coverage="99.0"
                     /evalue="7.35e-154"
ORIGIN
        1 tgactttatt actcagtatc gtattgtaga cccgatttct tttaagccaa tctacggccg
       61 ttctggcaag ctagaaacag cgtactgggg cagtcgtgcc agtgagcgcc aagtgcgact
      121 gtacaacaaa aagctagagc aggaacgaaa aaaagtaatc gtgccaaaag aaatcgatac
      181 gtggtggcgg ttagaaatgc agctaagacg tggcaaagca acggattggc atgcgatggt
      241 tcaggaaagc ttagatagtt ttgcaagccc gcattttttg ccgattgata taaaacctat
      301 tgataaaata gttattgatg gtttgatagc tgagccttct aattggtcga taattgctag
      361 acatacaaaa tataaatatc ggaatttgct gaagcaagaa agtcaaaatg atgagttaac
      421 gaatcattta cgagagacgt ttaaggaatc tgcagacgaa ttaaaaaaag aattggatac
      481 gtggcttttg gggttggatg tgacagagaa gtgataccga ataagaaaag tcagatgagt
      541 gagagtggat ttgcgtcaat gtttagtgac gtaaattcac gataagcgaa tattttgcat
      601 gaagcaaaat aaagcgtaaa aggagttgag agcgtgacac gctttcggct ccttttttcg
      661 ttgtcacttg tgacagcgaa taccctcgga gagcatttgg aattgtgaca gccatgtcac
      721 aattaggaaa atttttactc tttgtcaaag agtaacagaa aggtttacac tctttttatt
      781 agcgacagcg tgaaggaggg gttcacctta gggtttagta tttcgttcaa aaagggaaca
      841 aagaatacaa gcatttctca taataatcgt gagttaactg atagccaaaa aatcaatggt
      901 ttgtctggta gaaaataatt agcagattta caagtgggaa ataaaaagct gaaagaagaa
      961 aattgcattt caaactacat tttctacaat agctctaaaa tggcatattt tgcgttctga
     1021 gcggttttag cgtttatttc gtttagttat cggcacaatc gttaaaacac gttagaggag
     1081 cgaaaatgga gcctgtaagg cgactggtag cggaacgatc gtgttagatt gtgaaaaccg
     1141 atagctgaat gaaataaaca gcgggtgcgc cctttccatt tcggcaggag gaggctcaag
     1201 gggttcgggg aatgaaattc cctgaggtct ttttattttt ttaggaggag tgctataatc
     1261 aaagaaaacg agaaaaaaga gcaaaataaa agccgagcag tgcgctaaca ctctcgacta
     1321 tttacggaaa ctacttcacc tagctccgta actcaggttc attatacgaa tatttttagg
     1381 tttcttcaag ctagagattt ttggatatga atttttaggg ttacgtgaac tctggaaatt
     1441 ctttccaaaa gtctcttttt tcgtttggag gacgaaaatg gcaaatgaaa atcagttgag
     1501 tgaaattcaa tcaaaaattg aaggtcgagg ggcagaaaaa agaacaacga taaatcagct
     1561 cgaaaaactt aaccgtattt ctaacaggcg gttaagtgtg caaggtacga ccacccccct
     1621 aaaattaaat tggtcgattg atcgaattac aattgtcgga aaactgaatg ataccatagc
     1681 ttattggacg aaaaatggag ttgtttttgt cgatttcgag caattaatgc gtttgaacga
     1741 aaatcaggga tatttgaaat cagttgggat aaacggctgg caattattcg atcaatatgg
     1801 agaagatatt gcgtatatcg aaatacttaa atttcatgaa ggaaaaggtc gtattgattt
     1861 taatccgaat aagataggcc agtttttagc tagttccatg aaaggattca ttcatgacct
     1921 atttttagat ccgcattttt cccgggcgga tattgcctgc gatattgtag atgtgccgga
//
