LOCUS       NZ_CP066620             4093 bp    DNA     circular CON 20-FEB-2024
DEFINITION  Enterococcus faecium strain Dallas 124_3 plasmid unnamed, complete
            sequence.
ACCESSION   NZ_CP066620
VERSION     NZ_CP066620.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN17038100
            Assembly: GCF_016415365.1
KEYWORDS    RefSeq.
SOURCE      Enterococcus faecium
  ORGANISM  Enterococcus faecium
            Bacteria; Bacillota; Bacilli; Lactobacillales; Enterococcaceae;
            Enterococcus.
REFERENCE   1  (bases 1 to 4093)
  AUTHORS   Islam,M.J. and Palmer,K.
  TITLE     Molecular characterization of VREfm isolates from Dallas, Texas
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 4093)
  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                   :: 299.0x
            Sequencing Technology :: Illumina NextSeq; Oxford Nanopore MinION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 02/20/2024 02:58:57
            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)                     :: 3,103
            CDSs (total)                      :: 3,012
            Genes (coding)                    :: 2,889
            CDSs (with protein)               :: 2,889
            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)              :: 123
            CDSs (without protein)            :: 123
            Pseudo Genes (ambiguous residues) :: 0 of 123
            Pseudo Genes (frameshifted)       :: 41 of 123
            Pseudo Genes (incomplete)         :: 74 of 123
            Pseudo Genes (internal stop)      :: 32 of 123
            Pseudo Genes (multiple problems)  :: 20 of 123
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP066620.1.
            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..4093
                     /organism="Enterococcus faecium"
                     /mol_type="genomic DNA"
                     /strain="Dallas 124_3"
                     /isolation_source="rectal swab"
                     /host="Homo sapiens"
                     /db_xref="taxon:1352"
                     /plasmid="unnamed"
                     /geo_loc_name="USA: Dallas"
                     /collection_date="2015"
     gene            join(2920..4093,1..122)
                     /locus_tag="JCP92_RS15390"
                     /old_locus_tag="JCP92_15390"
     CDS             join(2920..4093,1..122)
                     /locus_tag="JCP92_RS15390"
                     /old_locus_tag="JCP92_15390"
                     /inference="COORDINATES: ab initio prediction:GeneMarkS-2+"
                     /GO_function="GO:0004803 - transposase activity [Evidence
                     IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GeneMarkS-2+."
                     /codon_start=1
                     /transl_table=11
                     /product="ISL3 family transposase"
                     /protein_id="WP_002296623.1"
                     /translation="MSHTQLIKDTLNILDLNIYFEENCLTKEKYKGQICLIYKGTLLYK
                     PEECSHCLCVVPSRIIRWGTTTVRLLLNDVSEYRTYLELKKQRFKCKSCQRTFVADTSV
                     AEKHCFISQKVRWSVIARLKENTSMTEIARQKNISTSSVYRVMKRFYRPLNPFKQTLPK
                     VLCFDEFKSVRSVASAMSFIMMDGQSHALLDIVENRRLPYLERYFSRFSLATREAVQLI
                     VIDMYAPYVSLVKKLFPNAQLIIDRFHIVQHIGRTFLNHRVKETTVRLKGNSHSQRGLG
                     KKLKRYWKLLQKEEAKLNYEKRVWRASFKDYLTESEIADRLLAACPNLRQGYQLYQDIL
                     YAVKKRDQSLFEDCLTRDISGLPETYTTTLRTFKKFLPQIQNALHYSYSNGPLECLNNH
                     IKVLKRNAYGFRNFYNFKLRIMIRHGKTFLTK"
                     /name="ISL3 family transposase"
     gene            complement(232..600)
                     /locus_tag="JCP92_RS15395"
                     /old_locus_tag="JCP92_15395"
     CDS             complement(232..600)
                     /locus_tag="JCP92_RS15395"
                     /old_locus_tag="JCP92_15395"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002329268.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="lactoylglutathione lyase"
                     /protein_id="WP_002296407.1"
                     /translation="MFTNEIKIMLYVDDVEKNATFWRAVGFAEKDRQEMDGTLIIEVGV
                     EDSQTSFLLYDRAFVESHSPGTATSAPSLMFYSKDIFGLYKKMQTQSVTLGDMVQLGEE
                     YVFNFADPDGNYFAVTGK"
                     /name="lactoylglutathione lyase"
     gene            complement(1211..2602)
                     /locus_tag="JCP92_RS15400"
                     /old_locus_tag="JCP92_15400"
     CDS             complement(1211..2602)
                     /locus_tag="JCP92_RS15400"
                     /old_locus_tag="JCP92_15400"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_005879894.1"
                     /GO_function="GO:0005215 - transporter activity [Evidence
                     IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="L-cystine transporter"
                     /protein_id="WP_002295194.1"
                     /translation="MTTLITVLVVLVFAALLYVFYRMQKRHTKFSTRVFTALGVGIVFG
                     GLLQLIFGVDDKVVTQSMEWIGIVGQGYVSFLQMLVMPLVFISIIGAFTKMKVSEKLGK
                     ISATVLTSLLGTTAIAALIGIGSTMLFGLQGAKFTQGAAETARISELATRQETVENLSI
                     PQQILSFIPKNVFADLAGSRATSTIGVVIFAAFVGIAYLGVKRKAPKEAAFFSDLVDSL
                     YKIIMRIVTLVLRLTPYGVFALMTNVLATSDFAAIVNLGKFVVASYVALLAVLIVHSLI
                     LIGAKVNPINYFKKAFPVLSFAFTSRSSAGALPLNIETQTKALGVDDATANFSASFGLS
                     IGQNGCAGVYPAMLATIVAPAAGVNVFSLEFILMLVAIVTISSFGVAGVGGGATFASLI
                     VLGAMNLPVAIVGLVISVEPLIDMARTAVNVSGSMVAGIVTSARIKDLDRDVINDDSKV
                     IDVNA"
                     /name="L-cystine transporter"
ORIGIN
        1 cattggaatg cttaaacaac cacatcaaag tattaaaacg caatgcgtac ggctttcgca
       61 acttttacaa tttcaaacta cgaattatga ttcgtcatgg caaaacattt ttaaccaaat
      121 aaacagaaca gaaagaggtt ttcttctttc tgttctgtcc aaattattct aagatttctc
      181 tttaccaaca tcatttgaca aagagccaga aaaacaaagt ctttatttct attatttacc
      241 tgtaaccgca aagtagttgc catcgggatc agcaaagtta aagacatatt cttctccaag
      301 ctgtaccata tcacctaatg tgactgattg cgtctgcatt tttttatata gtccaaagat
      361 atctttactg taaaacatca aagatggggc actagtagct gtgccaggtg aatgggactc
      421 aacaaatgct cgatcatata acagaaatga ggtttgactg tcctcaactc ctacttcaat
      481 tataagcgtc ccatccattt cttgacgatc tttttccgca aagccaactg ctctccaaaa
      541 cgttgcattt ttttctacat cgtccacata aagcatgatt tttatttcat tcgtaaacat
      601 ctgtttcctc ctaaacgatc tgttctaaca ttctcaactt tgtcagttta ccataggaaa
      661 atgggaaaat ctacgaaagc tctcaacaga atcgtcctac ttaaatacgc ttttctttaa
      721 taataaataa gttggttgtt tttgttattt gcgctttcac ttttcggaat aaataatgtg
      781 tatttatatg gaataaataa aaaaagaggt cgtgactaaa aacaagtcac aacctctggt
      841 aaacggtgtt ctcctgacaa ctcctcggtc acaagacaca atattcaaca aacatgagaa
      901 gctatttttt gaaattgctc tttgtgactc agagtgaaac ggcaggctca cgacctcttt
      961 cttaaacggt gttcaaaagc ttgcatctgc ggtaataagc tcaaccaaac gtaaaatatg
     1021 aggaactatt tttgtttggc tgttcttatt acttgatgca gggcagcttt ttcacaacct
     1081 cttattcacg gtgtttcaga agtagcttct cggaaataag ccgaaatttc acaaaaattt
     1141 gagaaactat ttttaggaaa cttcttctta tttcttaaag ctgaccactt ctatcacaac
     1201 ctctttttga ctatgcattc acatcgatca ctttagaatc atcattgatg acatcgcgat
     1261 ctaaatcttt gatgcgtgca cttgtcacga taccagctac catgctaccg ctgacgttta
     1321 ctgctgtacg tgccatatcg attaatggtt caacagagat aactaaccca acgattgcta
     1381 ctggcaagtt cattgcccct aaaacgatca gtgaagcaaa tgttgcgccc ccaccgactc
     1441 cagctacacc aaaagaactg attgttacaa ttgccacaag catcaaaata aattccaaac
     1501 taaagacatt cactccagct gctggtgcga cgatcgttgc caacatagct ggataaacgc
     1561 cagcacagcc gttttgtcca atagacaaac caaaacttgc tgagaaatta gctgttgcat
     1621 catctactcc taaagctttt gtctgagtct cgatattcaa tggcaaagct ccagcacttg
     1681 aacgtgaagt aaacgcaaag ctcaataccg gaaaggcttt tttgaaatag ttgattggat
     1741 tgacttttgc accaatcaaa atcagtgagt ggacaatcaa aacagcaagc aatgctacgt
     1801 aagaagcaac gacaaattta cctaaattga cgatagctgc aaaatcactt gttgccaaaa
     1861 cgtttgtcat caaagcaaat actccataag gtgtcaaacg caaaacaagc gtcacgatcc
     1921 gcataatgat tttatacaga ctgtcgacta aatctgaaaa gaatgctgct tcttttggcg
     1981 cttttctttt cacgcctaga taagcgattc cgacaaatgc cgcgaaaata acgactccaa
     2041 tcgtacttgt tgcacgacta cctgctaaat cagcaaaaac gtttttaggg ataaaggata
     2101 aaatctgctg tggaatcgat aagttttcaa ctgtttcctg acgtgttgcc agttcagaga
     2161 ttcgtgctgt ttctgcagct ccttgtgtga atttagctcc ttggagtccg aacagcattg
     2221 ttgaaccaat tccgatcaat gctgcaatag ctgttgttcc aagtaaagaa gtcaatacag
     2281 tcgcactaat tttccctagc ttttcagaaa ctttcatttt tgtgaatgca ccaatgatcg
     2341 aaataaacac taaaggcata actagcattt gcaagaatga tacatatcct tgacctacaa
     2401 tcccgatcca ttccattgat tgagtaacga ctttgtcgtc tacaccaaag atcaattgaa
     2461 gcagaccgcc aaagacgata ccaactccta atgctgtaaa gacgcgtgtt gaaaattttg
     2521 tatggcgctt ttgcatacga tagaacacat ataataatgc cgcaaaaact agaaccacta
     2581 aaactgtgat gagtgttgtc atttttctcc tcctcatatt attaatgaca agtccatcga
     2641 aggaagtaaa ggttcccgag aatgattctt caaccatcct cctgaaaaaa tttttttcag
     2701 tgacttttat attttagacg atttttatcg aaatgacatt ctttttgctt acaattagta
     2761 ataaaaaaac atacctgtga tagctttaat ctatcgcggc tctatacttt ttgatgttgg
     2821 tgaacttcac caacatcttt tttgtataaa aaaatataga aaagacaccc tgaaatcctt
     2881 tagaattaat ttggctacca attcatagga ggattcaaga tgtctcatac tcagcttatc
     2941 aaagataccc taaatattct agacctaaat atctatttcg aggaaaattg tttaactaaa
     3001 gaaaaataca aagggcaaat ttgcttgatt tacaaaggaa ctcttctgta caagccagaa
     3061 gagtgttccc attgtctttg tgtcgtcccc tctaggatca ttcgttgggg gacgacaacc
     3121 gttcggttgt tactgaatga tgtgtctgag tatcgcactt atctggagct gaagaaacaa
     3181 cgatttaaat gtaagtcttg ccaaagaaca ttcgtagcgg atacctctgt tgctgaaaaa
     3241 cactgtttca ttagtcaaaa agttcgttgg tctgtcattg ctcgcttaaa agagaatact
     3301 tccatgacgg aaatcgctcg tcagaaaaat atttccactt cttcggtcta tcgtgtcatg
     3361 aagcgattct accgcccatt gaatcctttc aaacagactt tgccaaaggt cttatgcttt
     3421 gatgaattca aatcggttcg aagtgttgcc agtgcaatga gttttatcat gatggacgga
     3481 caaagccatg cattattgga tattgtcgaa aatcgacgct tgccttattt agaacgctat
     3541 ttttctcggt tttcattagc gactcgtgaa gccgttcaat tgattgttat tgatatgtat
     3601 gcgccttatg tttcgttggt gaaaaagctt ttcccgaatg ctcagttgat catcgatcgt
     3661 ttccacatcg tccaacatat tggcagaact ttcttgaatc atcgagtgaa agaaaccacg
     3721 gtacgactta aaggaaattc ccactctcaa cgagggttag ggaaaaaatt gaagcgctat
     3781 tggaaactcc tacaaaaaga agaagcaaag ttaaactatg aaaaacgggt ttggcgtgcc
     3841 agttttaaag attatttgac tgaaagtgag attgccgatc gactgttagc tgcttgtccc
     3901 aacttacgcc aaggctatca gttataccaa gacattcttt atgcggtaaa gaaaagagat
     3961 cagtcactat ttgaggattg tttaactaga gacattagcg gtctgccaga aacctataca
     4021 accactttac gaacgtttaa aaagtttctg ccacagatcc aaaatgcgct tcactacagc
     4081 tattcaaacg gac
//
