LOCUS       NZ_CP023788             4374 bp    DNA     circular CON 30-NOV-2023
DEFINITION  Enterococcus faecium strain Efaecium_ER04120.3A plasmid
            pER04120.3A.4, complete sequence.
ACCESSION   NZ_CP023788
VERSION     NZ_CP023788.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN07679729
            Assembly: GCF_002848645.1
KEYWORDS    RefSeq.
SOURCE      Enterococcus faecium
  ORGANISM  Enterococcus faecium
            Bacteria; Bacillota; Bacilli; Lactobacillales; Enterococcaceae;
            Enterococcus.
REFERENCE   1  (bases 1 to 4374)
  AUTHORS   Chako,K., Sullivan,M., Pak,T.J., Beckford,C., Altman,D., Ciferri,B.,
            Pak,T., Sebra,R., Kasarskis,A., Hamula,C. and van Bakel,H.
  TITLE     The genetic basis of emerging Vancomycin, Linezolid, and Daptomycin
            heteroresistance in a case of persistent Enterococcus faecium
            bacteremia
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 4374)
  AUTHORS   Chacko,K.I., Sullivan,M.J. and van Bakel,H.
  TITLE     Direct Submission
  JOURNAL   Submitted (28-SEP-2017) Genetics and Genomic Sciences, Icahn School
            of Medicine, One Gustave L. Levy Place Box 1498, New York, NY 10029,
            USA
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Date                     :: 10-MAR-2016
            Assembly Method                   :: HGAP v. 2.2.0
            Expected Final Version            :: yes
            Genome Coverage                   :: 22.31065672x
            Sequencing Technology             :: PacBio
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 11/30/2023 14:10:32
            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)                     :: 3,101
            CDSs (total)                      :: 3,008
            Genes (coding)                    :: 2,882
            CDSs (with protein)               :: 2,882
            Genes (RNA)                       :: 93
            rRNAs                             :: 6, 6, 6 (5S, 16S, 23S)
            complete rRNAs                    :: 6, 6, 6 (5S, 16S, 23S)
            tRNAs                             :: 71
            ncRNAs                            :: 4
            Pseudo Genes (total)              :: 126
            CDSs (without protein)            :: 126
            Pseudo Genes (ambiguous residues) :: 0 of 126
            Pseudo Genes (frameshifted)       :: 43 of 126
            Pseudo Genes (incomplete)         :: 72 of 126
            Pseudo Genes (internal stop)      :: 31 of 126
            Pseudo Genes (multiple problems)  :: 15 of 126
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP023788.1.
            Bacteria and source DNA available from Icahn School of Medicine at
            Mount Sinai.
            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..4374
                     /organism="Enterococcus faecium"
                     /mol_type="genomic DNA"
                     /strain="Efaecium_ER04120.3A"
                     /isolation_source="blood"
                     /host="Homo sapiens"
                     /db_xref="taxon:1352"
                     /plasmid="pER04120.3A.4"
                     /geo_loc_name="USA: New York, NY"
                     /lat_lon="40.789990 N 73.953689 W"
                     /collection_date="2015"
                     /collected_by="Icahn School of Medicine at Mount Sinai"
     gene            join(4297..4374,1..891)
                     /locus_tag="CO994_RS16245"
                     /old_locus_tag="CO994_03075"
     CDS             join(4297..4374,1..891)
                     /locus_tag="CO994_RS16245"
                     /old_locus_tag="CO994_03075"
                     /inference="COORDINATES: ab initio prediction:GeneMarkS-2+"
                     /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: GeneMarkS-2+."
                     /codon_start=1
                     /transl_table=11
                     /product="replication initiation factor domain-containing
                     protein"
                     /protein_id="WP_002298422.1"
                     /translation="MSKNGIIVNEWENLTALSNRRLNVQNMYTPLKMQWSIDRITIVGK
                     LKENIYYHTQNDVLILDFEQLMRVNEGNGYLKAVGNNGWQLLDQYEENIAYIEILKWQD
                     GKGRIDFNPNKIGHFLASSMKNFIHDLFLEPHFSRADIACDIIDVPDEFITQYRVVDPV
                     SFKPIYGRSGKLETAYWGSRASERQIRLYNKKLEQETKRKIVPPEIETWWRLELQLRRG
                     KATDWHAMVHESLNSFASPHFLPLDVKTNDKVMIFGLIANPEMWGFLERRMKYKLRDIL
                     KRESQNDELTNHLRETFSESADVLKKELDTWLQGLDVTEEE"
                     /name="replication initiation factor domain-containing
                     protein"
     gene            894..1127
                     /locus_tag="CO994_RS16250"
                     /old_locus_tag="CO994_03076"
     CDS             894..1127
                     /locus_tag="CO994_RS16250"
                     /old_locus_tag="CO994_03076"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002298421.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_002298421.1"
                     /translation="MAEKQKHFGKKNWLVNLTGDNVVVVFLDSKKMSGKLLDVTQYELI
                     LKNNKIDSPIIIPKHAVKYVYGVAESNGEDND"
                     /name="hypothetical protein"
     gene            1120..1539
                     /locus_tag="CO994_RS16255"
                     /old_locus_tag="CO994_03077"
     CDS             1120..1539
                     /locus_tag="CO994_RS16255"
                     /old_locus_tag="CO994_03077"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002351943.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_002298420.1"
                     /translation="MTDLPEKMTIKNLADELGISKNTVRNQLVNAGYDLARYKDNGVIM
                     LDKELIGVVRSIYRSKGGQLTGDLPVNDAGNDFPLEKENEFLREQLAEKDRHISELTEM
                     IRDQQKLTLLQQQKNDQLLLENQELKNRKWWQFWK"
                     /name="hypothetical protein"
     gene            1548..1856
                     /locus_tag="CO994_RS16260"
                     /old_locus_tag="CO994_03078"
     CDS             1548..1856
                     /locus_tag="CO994_RS16260"
                     /old_locus_tag="CO994_03078"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002292673.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_002298419.1"
                     /translation="MDKIDLREETVDRIELMYERLADYLNLPDEDNYSEMLERMMDVLN
                     SVINADLAKSSVLTNEFVHKHLAQTTDESEKEFWLKLMSHVMQLNQISVINSKEKEM"
                     /name="hypothetical protein"
     gene            1860..2222
                     /locus_tag="CO994_RS16265"
                     /old_locus_tag="CO994_03079"
     CDS             1860..2222
                     /locus_tag="CO994_RS16265"
                     /old_locus_tag="CO994_03079"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_016173819.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_002298418.1"
                     /translation="MGMTLADIKAQEEKLKKEQAKLRQQKKRLIEKENAAMGKALRKRF
                     GFETFADFERWLSSISDDQQHEKSVDNEWLADEKSAPSERDYPDESDGLFGVIPNKKSQ
                     MSESKFTSIFNDVNLR"
                     /name="hypothetical protein"
     gene            2444..3850
                     /locus_tag="CO994_RS16270"
                     /old_locus_tag="CO994_03080"
     CDS             2444..3850
                     /locus_tag="CO994_RS16270"
                     /old_locus_tag="CO994_03080"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_016173818.1"
                     /GO_function="GO:0003677 - DNA binding [Evidence IEA]"
                     /GO_process="GO:0006310 - DNA recombination [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="plasmid recombination protein"
                     /protein_id="WP_002317172.1"
                     /translation="MGFSISFKKGTKNTSISHNNRELTDRQKTNDWHKHIDFTKSDENI
                     YLEQTNLADKYEELFGEVVEKYNAKQKRADRKIEDYLAKVRKDKKLEPQREFIVQIGIL
                     DDFQTNRADGSSTGISKQQAEQNRVIANKILVQYYKEFQERNPNLAVYNAVIHNDEISP
                     HLHLNIVPVAEGYKRGVQKQPSFNKALVQQGIHADKDNGRVLFNNFRNQEVDSIERLMN
                     DYGWKRDIVGTNKIKDIHEYKEIMSEISELRQTAVKERESVSDELRYISRQREENERDK
                     ALMASERAKIEEEKKNMLNVKKEMAVIFQKDMVPLESFKRLPDGSYHLSGNDFVDLYQR
                     ATRATNAKRNADNMSEQYLQMLEQNTELNEYVATLEEERHLSGRKQLADLQVENKKLKE
                     ENRSLRQRLERLKNAFQKSITRLSIRFGLAEKDMGLSEELEVLEQEKTLFYRQNVSQRK
                     LERSEDEIEW"
                     /name="plasmid recombination protein"
     Typing          7..881
                     /name="rep_cluster_943"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="84.032"
                     /coverage="97.0"
                     /evalue="0.0"
     Typing          2445..3847
                     /name="MOBV"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="91.88"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 atgtacaccc ccttaaaaat gcagtggtca attgaccgaa ttactatcgt tggaaaactg
       61 aaggaaaata tttattatca cactcaaaat gatgtgttga ttttagattt tgagcaatta
      121 atgcgggtga atgaaggcaa tggctattta aaagcggttg ggaataacgg ctggcaatta
      181 ttagaccaat acgaagaaaa tattgcttat attgagattt tgaaatggca agatggcaaa
      241 gggcggattg attttaaccc gaataagatt ggtcattttt tagctagttc aatgaaaaat
      301 ttcattcatg atttatttct agaaccacat ttctcacgtg cggatattgc ttgcgatatt
      361 atcgatgtgc ctgatgagtt tattacacaa tatcgagtgg ttgatcctgt ttctttcaag
      421 ccaatttatg ggcggtctgg gaagctggaa acagcttatt ggggcagtcg tgccagcgaa
      481 cgccagattc ggctatacaa caaaaaattg gaacaggaaa ccaagcgtaa aattgtgcca
      541 ccagaaatag aaacttggtg gcgactggaa ttgcagttaa ggcgtgggaa agcaacagat
      601 tggcatgcaa tggttcatga aagtttaaat agttttgcta gccctcattt tctaccactt
      661 gatgtaaaaa caaatgataa ggtgatgatt tttggactga ttgctaaccc tgaaatgtgg
      721 gggtttttag agcgtagaat gaaatacaaa ttgagagata ttttgaaaag agaaagtcaa
      781 aatgatgagt tgacgaatca tttacgagaa acattttcgg aatcagcaga tgttttgaaa
      841 aaagaattag acacttggct tcaagggtta gatgtaacgg aggaggaata agaatggcag
      901 aaaaacaaaa gcattttggt aagaaaaatt ggttggtgaa tttaacaggt gataacgttg
      961 tcgttgtttt tttggatagc aaaaaaatgt ccggtaagtt acttgatgta acgcagtatg
     1021 agttgatttt gaaaaataat aaaattgatt ccccaatcat tatccctaag catgctgtta
     1081 aatatgttta tggggtagct gaaagtaacg gagaagataa tgactgattt gccagaaaaa
     1141 atgaccataa aaaaccttgc tgatgagttg ggtatatcta aaaatacagt gcgcaatcaa
     1201 ctggtcaatg caggttatga ccttgctcgg tataaagata atggggttat catgttagac
     1261 aaggaattga ttggtgttgt gcggtcaatt tatcggtcaa aaggtggtca attgactggt
     1321 gatttaccgg tcaatgatgc aggcaatgat ttcccgttag aaaaagaaaa tgaatttttg
     1381 cgtgaacaat tagcggaaaa agataggcat atttctgaat taacggaaat gattcgtgac
     1441 caacaaaaat tgactttgct tcagcaacaa aaaaacgatc agttgttact agaaaatcaa
     1501 gaattaaaaa atcgaaaatg gtggcaattc tggaagtgag gtgtgacatg gataaaattg
     1561 atttgagaga agaaacagtc gatagaattg aattgatgta tgaacggtta gctgattatt
     1621 tgaatttgcc ggatgaagat aattatagtg aaatgcttga acgaatgatg gatgttctca
     1681 actcggttat caatgctgat ctagcaaaat cttcagtttt gactaatgaa tttgttcata
     1741 agcatttagc gcaaacaact gatgaatcag aaaaagaatt ttggttgaaa ttaatgagtc
     1801 atgttatgca gttaaaccaa atttccgtta ttaattccaa agaaaaggag atgtagttta
     1861 tgggaatgac tttagcagat attaaagcgc aagaagaaaa attaaaaaaa gaacaagcga
     1921 aacttcgcca acagaaaaaa cgcttgattg agaaagaaaa tgctgcaatg ggcaaggctc
     1981 ttcgcaagcg ttttgggttt gaaacttttg ctgattttga gcggtggcta tcgtcgattt
     2041 ctgacgatca gcaacacgaa aaatcagtgg ataatgagtg gcttgctgat gaaaaatcag
     2101 cgccaagcga acgagattat cccgatgaat ctgacggctt attcggagtg ataccgaata
     2161 agaaaagtca gatgagtgag agtaaattta cgtcaatatt taatgacgtg aatttacgat
     2221 aagcgattat tttgcgtgaa gcaaaataaa gcgtaaaagg agttgagagc gtgacacgct
     2281 ttcggctcct tttttcgttg tcacttgtga cagcgaatac cctcggagag catttggaat
     2341 tgtgacagcc atgtcacaat taggaaaatg ttactctttg acaaagagta acagaaaggt
     2401 ttacaatctt tttattagcg acagcgcgaa ggagggtttt aacttggggt ttagtatttc
     2461 atttaaaaaa ggaacgaaga atacaagtat ttctcataat aatcgtgagt taactgatcg
     2521 ccagaaaacc aatgattggc ataagcatat tgacttcacg aaatcggatg aaaatattta
     2581 tttagagcag acgaatctag cagataaata tgaggaattg tttggcgaag tggtagaaaa
     2641 atataatgcg aaacaaaaaa gagccgatag aaaaatcgag gactatttag cgaaagtgcg
     2701 caaggataaa aagttggaac ctcaacgaga atttattgtg caaataggca ttttagatga
     2761 tttccagaca aatcgagcag atggttcttc tactggcata tcgaaacaac aagctgaaca
     2821 aaatcgagtg attgccaata aaattttggt tcagtattac aaggagtttc aagagagaaa
     2881 ccctaatttg gctgtttata atgctgttat tcataatgac gaaataagtc cgcacctgca
     2941 cttgaatatt gtgccggttg ctgaaggtta taaacggggt gttcaaaagc agccgagctt
     3001 taataaagca ctggttcaac aagggataca cgctgataaa gataatggtc gagtgctttt
     3061 caataatttt agaaatcaag aagttgactc tatagaacga ttaatgaatg attacggttg
     3121 gaaaagggat attgtcggta ccaacaaaat taaagatatt cacgaataca aagaaatcat
     3181 gagtgaaatt tctgaattgc gccaaacggc tgtaaaagag cgtgagagcg tttctgatga
     3241 gttgaggtat atttctaggc aaagagaaga aaacgagcgt gataaggctc tgatggcttc
     3301 tgagagagcg aagattgaag aagagaagaa aaatatgctg aatgtaaaaa aagagatggc
     3361 ggtcattttc caaaaagata tggttccttt agaaagtttc aagaggcttc ctgatggttc
     3421 gtatcattta tctgggaatg attttgttga tttgtatcaa cgagctacga gagcaacaaa
     3481 tgccaagaga aatgctgata acatgagtga gcaatattta cagatgcttg agcaaaatac
     3541 agaattaaat gagtatgtag ctacattgga agaagagcgt catttgtctg gtagaaaaca
     3601 attagcagat ttacaagtgg aaaataaaaa gctgaaagaa gaaaatcgct ctttacgcca
     3661 gcgtttagag cgattaaaaa acgcatttca aaaatcgatc actcgtttgt ctatccgttt
     3721 tggtcttgca gaaaaggata tggggctttc tgaggaatta gaagtgttag agcaggagaa
     3781 aaccttattt tatcgtcaaa acgtctcaca gcgtaaatta gagcgttctg aagatgagat
     3841 cgagtggtag ttacgatgtg cagtcaacgg taccggaggc ggtttgtgcc gaggataagg
     3901 agttgacggc taaaccacta gcctattaag ctgacatttg ctaaaaaatg gccagtccat
     3961 tttttggcca acctagcgtt agcgaagttt gggggcgccc ttttcaaagg gtgcggtttt
     4021 attttttgga tatttgcata gctaaagaga agtgctatta ttgagttagc aaacaaatga
     4081 actgaaaaaa gagtaaaaaa atagtcgagc aacgctacca acgttctcga cctttacgga
     4141 aactaatcgc actagctccg taacttctta atcattatac gaatattttt agatttcttc
     4201 aagactagag attttttggt aatgaatttt taagagttac gtgaactttt gaaaattctt
     4261 tccagaagtc tctttttctt tgaggaggaa caaaatttga gtaaaaatgg cataatcgta
     4321 aatgagtggg aaaatttaac agccctatct aacaggcggt taaatgtaca aaat
//
