LOCUS       NZ_CP066414             1980 bp    DNA     circular CON 20-FEB-2024
DEFINITION  Enterococcus faecium strain Dallas 53_2 plasmid p53_2_1.9kb,
            complete sequence.
ACCESSION   NZ_CP066414
VERSION     NZ_CP066414.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN17038077
            Assembly: GCF_016406545.1
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  JOURNAL   Unpublished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 (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                   :: 147.0x
            Sequencing Technology :: Illumina NextSeq; Oxford Nanopore MinION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 02/20/2024 02:46:55
            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)                     :: 3,126
            CDSs (total)                      :: 3,035
            Genes (coding)                    :: 2,920
            CDSs (with protein)               :: 2,920
            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)              :: 115
            CDSs (without protein)            :: 115
            Pseudo Genes (ambiguous residues) :: 0 of 115
            Pseudo Genes (frameshifted)       :: 42 of 115
            Pseudo Genes (incomplete)         :: 67 of 115
            Pseudo Genes (internal stop)      :: 30 of 115
            Pseudo Genes (multiple problems)  :: 20 of 115
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP066414.1.
            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 53_2"
                     /isolation_source="rectal swab"
                     /host="Homo sapiens"
                     /db_xref="taxon:1352"
                     /plasmid="p53_2_1.9kb"
                     /geo_loc_name="USA: Dallas"
                     /collection_date="2015"
     gene            242..1258
                     /locus_tag="JCP94_RS15535"
                     /old_locus_tag="JCP94_15535"
     CDS             242..1258
                     /locus_tag="JCP94_RS15535"
                     /old_locus_tag="JCP94_15535"
                     /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"
     Typing          243..1252
                     /name="rep_cluster_935"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="92.292"
                     /coverage="99.0"
                     /evalue="0.0"
ORIGIN
        1 ttttttagga ggagtgctat aatcaaagaa aacgagaaaa aagagcaaaa taaaagccga
       61 gcagtgcgct aacactctcg actatttacg gaaactactt cacctagctc cgtaactcag
      121 gttcattata cgaatatttt taggtttctt caagctagag atttttggat atgaattttt
      181 agggttacgt gaactctgga aattctttcc aaaagtctct tttttcgttt ggaggacgaa
      241 aatggcaaat gaaaatcagt tgagtgaaat tcaatcaaaa attgaaggtc gaggggcaga
      301 aaaaagaaca acgataaatc agctcgaaaa acttaaccgt atttctaaca ggcggttaag
      361 tgtgcaaggt acgaccaccc ccctaaaatt aaattggtcg attgatcgaa ttacaattgt
      421 cggaaaactg aatgatacca tagcttattg gacgaaaaat ggagttgttt ttgtcgattt
      481 cgagcaatta atgcgtttga acgaaaatca gggatatttg aaatcagttg ggataaacgg
      541 ctggcaatta ttcgatcaat atggagaaga tattgcgtat atcgaaatac ttaaatttca
      601 tgaaggaaaa ggtcgtattg attttaatcc gaataagata ggccagtttt tagctagttc
      661 catgaaagga ttcattcatg acctattttt agatccgcat ttttcccggg cggatattgc
      721 ctgcgatatt gtagatgtgc cggatgactt tattactcag tatcgtattg tagacccgat
      781 ttcttttaag ccaatctacg gccgttctgg caagctagaa acagcgtact ggggcagtcg
      841 tgccagtgag cgccaagtgc gactgtacaa caaaaagcta gagcaggaac gaaaaaaagt
      901 aatcgtgcca aaagaaatcg atacgtggtg gcggttagaa atgcagctaa gacgtggcaa
      961 agcaacggat tggcatgcga tggttcagga aagcttagat agttttgcaa gcccgcattt
     1021 tttgccgatt gatataaaac ctattgataa aatagttatt gatggtttga tagctgagcc
     1081 ttctaattgg tcgataattg ctagacatac aaaatataaa tatcggaatt tgctgaagca
     1141 agaaagtcaa aatgatgagt taacgaatca tttacgagag acgtttaagg aatctgcaga
     1201 cgaattaaaa aaagaattgg atacgtggct tttggggttg gatgtgacag agaagtgata
     1261 ccgaataaga aaagtcagat gagtgagagt ggatttgcgt caatgtttag tgacgtaaat
     1321 tcacgataag cgaatatttt gcatgaagca aaataaagcg taaaaggagt tgagagcgtg
     1381 acacgctttc ggctcctttt ttcgttgtca cttgtgacag cgaataccct cggagagcat
     1441 ttggaattgt gacagccatg tcacaattag gaaaattttt actctttgtc aaagagtaac
     1501 agaaaggttt acactctttt tattagcgac agcgtgaagg aggggttcac cttagggttt
     1561 agtatttcgt tcaaaaaggg aacaaagaat acaagcattt ctcataataa tcgtgagtta
     1621 actgatagcc aaaaaatcaa tggtttgtct ggtagaaaat aattagcaga tttacaagtg
     1681 ggaaataaaa agctgaaaga agaaaattgc atttcaaact acattttcta caatagctct
     1741 aaaatggcat attttgcgtt ctgagcggtt ttagcgttta tttcgtttag ttatcggcac
     1801 aatcgttaaa acacgttaga ggagcgaaaa tggagcctgt aaggcgactg gtagcggaac
     1861 gatcgtgtta gattgtgaaa accgatagct gaatgaaata aacagcgggt gcgccctttc
     1921 catttcggca ggaggaggct caaggggttc ggggaatgaa attccctgag gtctttttat
//
