LOCUS       NZ_CP066399             1979 bp    DNA     circular CON 20-FEB-2024
DEFINITION  Enterococcus faecium strain Dallas 51_4 plasmid p51_4_1.9kb,
            complete sequence.
ACCESSION   NZ_CP066399
VERSION     NZ_CP066399.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN17038075
            Assembly: GCF_016406465.1
KEYWORDS    RefSeq.
SOURCE      Enterococcus faecium
  ORGANISM  Enterococcus faecium
            Bacteria; Bacillota; Bacilli; Lactobacillales; Enterococcaceae;
            Enterococcus.
REFERENCE   1  (bases 1 to 1979)
  AUTHORS   Islam,M.J. and Palmer,K.
  TITLE     Molecular characterization of VREfm isolates from Dallas, Texas
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 1979)
  AUTHORS   Islam,M.J. and Palmer,K.
  TITLE     Direct Submission
  JOURNAL   Submitted (20-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                   :: 146.0x
            Sequencing Technology :: Illumina NextSeq; Oxford Nanopore MinION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 02/20/2024 02:56:45
            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)                     :: 3,320
            CDSs (total)                      :: 3,229
            Genes (coding)                    :: 3,102
            CDSs (with protein)               :: 3,102
            Genes (RNA)                       :: 91
            rRNAs                             :: 6, 6, 6 (5S, 16S, 23S)
            complete rRNAs                    :: 6, 6, 6 (5S, 16S, 23S)
            tRNAs                             :: 69
            ncRNAs                            :: 4
            Pseudo Genes (total)              :: 127
            CDSs (without protein)            :: 127
            Pseudo Genes (ambiguous residues) :: 0 of 127
            Pseudo Genes (frameshifted)       :: 44 of 127
            Pseudo Genes (incomplete)         :: 77 of 127
            Pseudo Genes (internal stop)      :: 35 of 127
            Pseudo Genes (multiple problems)  :: 23 of 127
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP066399.1.
            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..1979
                     /organism="Enterococcus faecium"
                     /mol_type="genomic DNA"
                     /strain="Dallas 51_4"
                     /isolation_source="rectal swab"
                     /host="Homo sapiens"
                     /db_xref="taxon:1352"
                     /plasmid="p51_4_1.9kb"
                     /geo_loc_name="USA: Dallas"
                     /collection_date="2015"
     gene            join(1338..1979,1..375)
                     /locus_tag="JCQ06_RS14100"
                     /old_locus_tag="JCQ06_14105"
     CDS             join(1338..1979,1..375)
                     /locus_tag="JCQ06_RS14100"
                     /old_locus_tag="JCQ06_14105"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002299382.1"
                     /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_002299382.1"
                     /translation="MANENQLSEIQSKIEGRGAEKRTTINQLEKLNRISNRRLSVQGTT
                     TPLKLNWSIDRITIVGKLNDTIAYWTKNGVVFVDFEQLMRLNENQGYLKSVGINGWQLF
                     DQYGEDIAYIEILKFHEGKGRIDFNPNKIGQFLASSMKGFIHDLFLDPHFSRADIACDI
                     VDVPDDFITQYRIVDPISFKPIYGRSGKLETAYWGSRASERQVRLYNKKLEQERKKVIV
                     PKEIDTWWRLEMQLRRGKATDWHAMVQESLDSFASPHFLPIDIKPIDKIVIDGLIAEPS
                     NWSIIARHTKYKYRNLLKQESQNDELTNHLRETFKESADELKKELDTWLLGLDVTEK"
                     /name="replication initiation factor domain-containing
                     protein"
     gene            575..>757
                     /locus_tag="JCQ06_RS14105"
                     /old_locus_tag="JCQ06_14110"
                     /pseudo=""
     CDS             575..>757
                     /locus_tag="JCQ06_RS14105"
                     /old_locus_tag="JCQ06_14110"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002313295.1"
                     /note="incomplete; partial in the middle of a contig;
                     missing C-terminus; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /name="hypothetical protein"
     Typing          2..369
                     /name="rep_cluster_935"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="81.081"
                     /coverage="99.0"
                     /evalue="1.37e-76"
ORIGIN
        1 caggaacgaa aaaaagtaat cgtgccaaaa gaaatcgata cgtggtggcg gttagaaatg
       61 cagctaagac gtggcaaagc aacggattgg catgcgatgg ttcaggaaag cttagatagt
      121 tttgcaagcc cgcatttttt gccgattgat ataaaaccta ttgataaaat agttattgat
      181 ggtttgatag ctgagccttc taattggtcg ataattgcta gacatacaaa atataaatat
      241 cggaatttgc tgaagcaaga aagtcaaaat gatgagttaa cgaatcattt acgagagacg
      301 tttaaggaat ctgcagacga attaaaaaaa gaattggata cgtggctttt ggggttggat
      361 gtgacagaga agtgataccg aataagaaaa gtcagatgag tgagagtgga tttgcgtcaa
      421 tgtttagtga cgtaaattca cgataagcga atattttgca tgaagcaaaa taaagcgtaa
      481 aaggagttga gagcgtgaca cgctttcggc tccttttttc gttgtcactt gtgacagcga
      541 ataccctcgg agagcatttg gaattgtgac agccatgtca caattaggaa aatgttactc
      601 tttgtcaaag agtaacagaa aggtttacac tctttttatt ggcgacagcg cgaaggaggg
      661 gtttaacttg gggtttagta tttcgttcaa aaagggaaca aaaaatacaa gcatttctca
      721 taataatcgt gagttaactg atagccaaaa aatcaatggt ttgtctggta gaaaataatt
      781 agcagattta caagtgggaa ataaaaagct gaaagaagaa aattgcattt caaactacat
      841 tttctacaat agctctaaaa tggcatattt tgcgttctga gcggttttag cgtttatttc
      901 gtttagttat cggcacaatc gttaaaacac gttagaggag cgaaaatgga gcctgtaagg
      961 cgactggtag cggaacgatc gtgttagatt gtgaaaaccg atagctgaat gaaataaaca
     1021 gcgggtgcgc cctttccatt tcggcaggag gaggctcaag gggttcgggg aatgaaattc
     1081 cctgaggtct ttttattttt ttaggaggag tgctataatc aaagaaaacg agaaaaaaga
     1141 gcaaaataaa agccgagcag tgcgctaaca ctctcgacta tttacggaaa ctacttcacc
     1201 tagctccgta actcaggttc attatacgaa tatttttagg tttcttcaag ctagagattt
     1261 ttggatatga atttttaggg ttacgtgaac tctggaaatt ctttccaaaa gtctcttttt
     1321 tcgtttggag gacgaaaatg gcaaatgaaa atcagttgag tgaaattcaa tcaaaaattg
     1381 aaggtcgagg ggcagaaaaa agaacaacga taaatcagct cgaaaaactt aaccgtattt
     1441 ctaacaggcg gttaagtgtg caaggtacga ccacccccct aaaattaaat tggtcgattg
     1501 atcgaattac aattgtcgga aaactgaatg ataccatagc ttattggacg aaaaatggag
     1561 ttgtttttgt cgatttcgag caattaatgc gtttgaacga aaatcaggga tatttgaaat
     1621 cagttgggat aaacggctgg caattattcg atcaatatgg agaagatatt gcgtatatcg
     1681 aaatacttaa atttcatgaa ggaaaaggtc gtattgattt taatccgaat aagataggcc
     1741 agtttttagc tagttccatg aaaggattca ttcatgacct atttttagat ccgcattttt
     1801 cccgggcgga tattgcctgc gatattgtag atgtgccgga tgactttatt actcagtatc
     1861 gtattgtaga cccgatttct tttaagccaa tctacggccg ttctggcaag ctagaaacag
     1921 cgtactgggg cagtcgtgcc agtgagcgcc aagtgcgact gtacaacaaa aagctagag
//
