LOCUS       NZ_CP066433             1980 bp    DNA     circular CON 20-FEB-2024
DEFINITION  Enterococcus faecium strain Dallas 57 plasmid p57_1.9kb, complete
            sequence.
ACCESSION   NZ_CP066433
VERSION     NZ_CP066433.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN17038080
            Assembly: GCF_016406565.1
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  JOURNAL   Unpublished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                   :: 132.0x
            Sequencing Technology :: Illumina NextSeq; Oxford Nanopore MinION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 02/20/2024 02:45:54
            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)                     :: 3,132
            CDSs (total)                      :: 3,041
            Genes (coding)                    :: 2,924
            CDSs (with protein)               :: 2,924
            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)         :: 69 of 117
            Pseudo Genes (internal stop)      :: 30 of 117
            Pseudo Genes (multiple problems)  :: 19 of 117
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP066433.1.
            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 57"
                     /isolation_source="rectal swab"
                     /host="Homo sapiens"
                     /db_xref="taxon:1352"
                     /plasmid="p57_1.9kb"
                     /geo_loc_name="USA: Dallas"
                     /collection_date="2015"
     gene            complement(join(1272..1980,1..308))
                     /locus_tag="JCP98_RS15535"
                     /old_locus_tag="JCP98_15535"
     CDS             complement(join(1272..1980,1..308))
                     /locus_tag="JCP98_RS15535"
                     /old_locus_tag="JCP98_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          complement(2..308)
                     /name="rep_cluster_935"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="97.403"
                     /coverage="99.0"
                     /evalue="4.46e-146"
     Typing          complement(1273..1980)
                     /name="rep_cluster_1968"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="81.882"
                     /coverage="92.0"
                     /evalue="2.48e-167"
ORIGIN
        1 aattgccagc cgtttatccc aactgatttc aaatatccct gattttcgtt caaacgcatt
       61 aattgctcga aatcgacaaa aacaactcca tttttcgtcc aataagctat ggtatcattc
      121 agttttccga caattgtaat tcgatcaatc gaccaattta attttagggg ggtggtcgta
      181 ccttgcacac ttaaccgcct gttagaaata cggttaagtt tttcgagctg atttatcgtt
      241 gttctttttt ctgcccctcg accttcaatt tttgattgaa tttcactcaa ctgattttca
      301 tttgccattt tcgtcctcca aacgaaaaaa gagacttttg gaaagaattt ccagagttca
      361 cgtaacccta aaaattcata tccaaaaatc tctagcttga agaaacctaa aaatattcgt
      421 ataatgaacc tgagttacgg agctaggtga agtagtttcc gtaaatagtc gagagtgtta
      481 gcgcactgct cggcttttat tttgctcttt tttctcgttt tctttgatta tagcactcct
      541 cctaaaaaaa taaaaagacc tcagggaatt tcattccccg aaccccttga gcctcctcct
      601 gccgaaatgg aaagggcgca cccgctgttt atttcattca gctatcggtt ttcacaatct
      661 aacacgatcg ttccgctacc agtcgcctta caggctccat tttcgctcct ctaacgtgtt
      721 ttaacgattg tgccgataac taaacgaaat aaacgctaaa accgctcaga acgcaaaata
      781 tgccatttta gagctattgt agaaaatgta gtttgaaatg caattttctt ctttcagctt
      841 tttatttccc acttgtaaat ctgctaatta ttttctacca gacaaaccat tgattttttg
      901 gctatcagtt aactcacgat tattatgaga aatgcttgta ttctttgttc cctttttgaa
      961 cgaaatacta aaccctaagg tgaacccctc cttcacgctg tcgctaataa aaagagtgta
     1021 aacctttctg ttactctttg acaaagagta aaaattttcc taattgtgac atggctgtca
     1081 caattccaaa tgctctccga gggtattcgc tgtcacaagt gacaacgaaa aaaggagccg
     1141 aaagcgtgtc acgctctcaa ctccttttac gctttatttt gcttcatgca aaatattcgc
     1201 ttatcgtgaa tttacgtcac taaacattga cgcaaatcca ctctcactca tctgactttt
     1261 cttattcggt atcacttctc tgtcacatcc aaccccaaaa gccacgtatc caattctttt
     1321 tttaattcgt ctgcagattc cttaaacgtc tctcgtaaat gattcgttaa ctcatcattt
     1381 tgactttctt gcttcagcaa attccgatat ttatattttg tatgtctagc aattatcgac
     1441 caattagaag gctcagctat caaaccatca ataactattt tatcaatagg ttttatatca
     1501 atcggcaaaa aatgcgggct tgcaaaacta tctaagcttt cctgaaccat cgcatgccaa
     1561 tccgttgctt tgccacgtct tagctgcatt tctaaccgcc accacgtatc gatttctttt
     1621 ggcacgatta ctttttttcg ttcctgctct agctttttgt tgtacagtcg cacttggcgc
     1681 tcactggcac gactgcccca gtacgctgtt tctagcttgc cagaacggcc gtagattggc
     1741 ttaaaagaaa tcgggtctac aatacgatac tgagtaataa agtcatccgg cacatctaca
     1801 atatcgcagg caatatccgc ccgggaaaaa tgcggatcta aaaataggtc atgaatgaat
     1861 cctttcatgg aactagctaa aaactggcct atcttattcg gattaaaatc aatacgacct
     1921 tttccttcat gaaatttaag tatttcgata tacgcaatat cttctccata ttgatcgaat
//
