LOCUS       NZ_CP066456             1980 bp    DNA     circular CON 19-FEB-2024
DEFINITION  Enterococcus faecium strain Dallas 83 plasmid p83_1.9kb, complete
            sequence.
ACCESSION   NZ_CP066456
VERSION     NZ_CP066456.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN17038084
            Assembly: GCF_016406425.1
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  JOURNAL   Unpublished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                   :: 243.0x
            Sequencing Technology :: Illumina NextSeq; Oxford Nanopore MinION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 02/19/2024 03:45:49
            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)                     :: 3,088
            CDSs (total)                      :: 2,997
            Genes (coding)                    :: 2,880
            CDSs (with protein)               :: 2,880
            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)              :: 117
            CDSs (without protein)            :: 117
            Pseudo Genes (ambiguous residues) :: 0 of 117
            Pseudo Genes (frameshifted)       :: 41 of 117
            Pseudo Genes (incomplete)         :: 70 of 117
            Pseudo Genes (internal stop)      :: 30 of 117
            Pseudo Genes (multiple problems)  :: 20 of 117
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP066456.1.
            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 83"
                     /isolation_source="rectal swab"
                     /host="Homo sapiens"
                     /db_xref="taxon:1352"
                     /plasmid="p83_1.9kb"
                     /geo_loc_name="USA: Dallas"
                     /collection_date="2015"
     gene            complement(join(1007..1980,1..43))
                     /locus_tag="JCP60_RS15335"
                     /old_locus_tag="JCP60_15335"
     CDS             complement(join(1007..1980,1..43))
                     /locus_tag="JCP60_RS15335"
                     /old_locus_tag="JCP60_15335"
                     /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          complement(1011..1980)
                     /name="rep_cluster_935"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="91.872"
                     /coverage="99.0"
                     /evalue="0.0"
ORIGIN
        1 caatttttga ttgaatttca ctcaactgat tttcatttgc cattttcgtc ctccaaacga
       61 aaaaagagac ttttggaaag aatttccaga gttcacgtaa ccctaaaaat tcatatccaa
      121 aaatctctag cttgaagaaa cctaaaaata ttcgtataat gaacctgagt tacggagcta
      181 ggtgaagtag tttccgtaaa tagtcgagag tgttagcgca ctgctcggct tttattttgc
      241 tcttttttct cgttttcttt gattatagca ctcctcctaa aaaaataaaa agacctcagg
      301 gaatttcatt ccccgaaccc cttgagcctc ctcctgccga aatggaaagg gcgcacccgc
      361 tgtttatttc attcagctat cggttttcac aatctaacac gatcgttccg ctaccagtcg
      421 ccttacaggc tccattttcg ctcctctaac gtgttttaac gattgtgccg ataactaaac
      481 gaaataaacg ctaaaaccgc tcagaacgca aaatatgcca ttttagagct attgtagaaa
      541 atgtagtttg aaatgcaatt ttcttctttc agctttttat ttcccacttg taaatctgct
      601 aattattttc taccagacaa accattgatt ttttggctat cagttaactc acgattatta
      661 tgagaaatgc ttgtattctt tgttcccttt ttgaacgaaa tactaaaccc taaggtgaac
      721 ccctccttca cgctgtcgct aataaaaaga gtgtaaacct ttctgttact ctttgacaaa
      781 gagtaaaaat tttcctaatt gtgacatggc tgtcacaatt ccaaatgctc tccgagggta
      841 ttcgctgtca caagtgacaa cgaaaaaagg agccgaaagc gtgtcacgct ctcaactcct
      901 tttacgcttt attttgcttc atgcaaaata ttcgcttatc gtgaatttac gtcactaaac
      961 attgacgcaa atccactctc actcatctga cttttcttat tcggtatcac ttctctgtca
     1021 catccaaccc caaaagccac gtatccaatt ctttttttaa ttcgtctgca gattccttaa
     1081 acgtctctcg taaatgattc gttaactcat cattttgact ttcttgcttc agcaaattcc
     1141 gatatttata ttttgtatgt ctagcaatta tcgaccaatt agaaggctca gctatcaaac
     1201 catcaataac tattttatca ataggtttta tatcaatcgg caaaaaatgc gggcttgcaa
     1261 aactatctaa gctttcctga accatcgcat gccaatccgt tgctttgcca cgtcttagct
     1321 gcatttctaa ccgccaccac gtatcgattt cttttggcac gattactttt tttcgttcct
     1381 gctctagctt tttgttgtac agtcgcactt ggcgctcact ggcacgactg ccccagtacg
     1441 ctgtttctag cttgccagaa cggccgtaga ttggcttaaa agaaatcggg tctacaatac
     1501 gatactgagt aataaagtca tccggcacat ctacaatatc gcaggcaata tccgcccggg
     1561 aaaaatgcgg atctaaaaat aggtcatgaa tgaatccttt catggaacta gctaaaaact
     1621 ggcctatctt attcggatta aaatcaatac gaccttttcc ttcatgaaat ttaagtattt
     1681 cgatatacgc aatatcttct ccatattgat cgaataattg ccagccgttt atcccaactg
     1741 atttcaaata tccctgattt tcgttcaaac gcattaattg ctcgaaatcg acaaaaacaa
     1801 ctccattttt cgtccaataa gctatggtat cattcagttt tccgacaatt gtaattcgat
     1861 caatcgacca atttaatttt aggggggtgg tcgtaccttg cacacttaac cgcctgttag
     1921 aaatacggtt aagtttttcg agctgattta tcgttgttct tttttctgcc cctcgacctt
//
