LOCUS       NZ_CP131839             4377 bp    DNA     circular CON 25-APR-2024
DEFINITION  Enterococcus faecium strain 2016S09-053 plasmid p2016S09-053-5,
            complete sequence.
ACCESSION   NZ_CP131839
VERSION     NZ_CP131839.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN36766200
            Assembly: GCF_038441115.1
KEYWORDS    RefSeq.
SOURCE      Enterococcus faecium
  ORGANISM  Enterococcus faecium
            Bacteria; Bacillota; Bacilli; Lactobacillales; Enterococcaceae;
            Enterococcus.
REFERENCE   1  (bases 1 to 4377)
  AUTHORS   Chen,F.-J., Liao,Y.-C. and Chiu,Y.-T.
  TITLE     Rapid Diagnostics and Real-time Genomic Surveillance System for
            Pathogens from Culture
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 4377)
  AUTHORS   Chen,F.-J., Liao,Y.-C. and Chiu,Y.-T.
  TITLE     Direct Submission
  JOURNAL   Submitted (31-JUL-2023) National Institute of Infectious Diseases
            and Vaccinology, National Health Research Institutes, No. 35, Keyan
            Road, Zhunan Town, Miaoli County 350, Taiwan
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Date                     :: 28-SEP-2022
            Assembly Method                   :: CCBGpipe v. 1
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 80x
            Sequencing Technology :: Oxford Nanopore MinION and Illumina iSeq
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_038441115.1-RS_2024_04_24
            Annotation Date                   :: 04/24/2024 14:54:39
            Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline
            (PGAP)
            Annotation Method :: Best-placed reference protein set; GeneMarkS-2+
            Annotation Software revision      :: 6.7
            Features Annotated                :: Gene; CDS; rRNA; tRNA; ncRNA
            Genes (total)                     :: 3,177
            CDSs (total)                      :: 3,086
            Genes (coding)                    :: 2,953
            CDSs (with protein)               :: 2,953
            Genes (RNA)                       :: 91
            rRNAs                             :: 6, 6, 6 (5S, 16S, 23S)
            complete rRNAs                    :: 6, 6, 6 (5S, 16S, 23S)
            tRNAs                             :: 69
            ncRNAs                            :: 4
            Pseudo Genes (total)              :: 133
            CDSs (without protein)            :: 133
            Pseudo Genes (ambiguous residues) :: 0 of 133
            Pseudo Genes (frameshifted)       :: 50 of 133
            Pseudo Genes (incomplete)         :: 74 of 133
            Pseudo Genes (internal stop)      :: 30 of 133
            Pseudo Genes (multiple problems)  :: 18 of 133
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP131839.1.
            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..4377
                     /organism="Enterococcus faecium"
                     /mol_type="genomic DNA"
                     /strain="2016S09-053"
                     /isolation_source="blood"
                     /host="Homo sapiens"
                     /db_xref="taxon:1352"
                     /plasmid="p2016S09-053-5"
                     /geo_loc_name="Taiwan"
                     /collection_date="2016"
                     /collected_by="NHRI"
     gene            join(3782..4377,1..811)
                     /locus_tag="Q7579_RS15840"
                     /old_locus_tag="Q7579_15780"
     CDS             join(3782..4377,1..811)
                     /locus_tag="Q7579_RS15840"
                     /old_locus_tag="Q7579_15780"
                     /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_217277483.1"
                     /translation="MGFSISFKKGTKNTSISHNNRELTDRQKTNDWHKHIDFTKSDENI
                     YLEQTNLADKYEELFGEVVEKYNAKQKRADRKIEDYLAKVRKDKKLEPQREFIVQIGIL
                     DDFQTNRADGSSTGISKQQAEQNRVIANKILVQYYKEFQERNPNLAVYNAVIHNDEISP
                     HLHLNIVPVAEGYKRGVQKQPSFNKALVQQGIHADKDNGRVLFNNFRNQEVDSIERLMN
                     DYGWKRDIVGTNKIKDIHEYKEIMSEISELRQTAVKERESVSDELRYIYRQREENERDK
                     ALMASERAKIEEEKKNMLNVKKEMAVIFQKDMVPLESFKRLPDGSYHLSGNDFVDLYQR
                     ATRATNAKRNADNMSEQYLQMLEQNTELNEYVATLEEERHLSGRKQLADLQVENKKLKE
                     ENRSLRQRLERLKNAFQKSITRLSIRFGLAEKDIGLSEELEVLEQEKTLFYRQNVSQRK
                     LERSEDEIEW"
                     /name="plasmid recombination protein"
     gene            1261..2229
                     /locus_tag="Q7579_RS15845"
                     /old_locus_tag="Q7579_15785"
     CDS             1261..2229
                     /locus_tag="Q7579_RS15845"
                     /old_locus_tag="Q7579_15785"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002298422.1"
                     /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_002298422.1"
                     /translation="MSKNGIIVNEWENLTALSNRRLNVQNMYTPLKMQWSIDRITIVGK
                     LKENIYYHTQNDVLILDFEQLMRVNEGNGYLKAVGNNGWQLLDQYEENIAYIEILKWQD
                     GKGRIDFNPNKIGHFLASSMKNFIHDLFLEPHFSRADIACDIIDVPDEFITQYRVVDPV
                     SFKPIYGRSGKLETAYWGSRASERQIRLYNKKLEQETKRKIVPPEIETWWRLELQLRRG
                     KATDWHAMVHESLNSFASPHFLPLDVKTNDKVMIFGLIANPEMWGFLERRMKYKLRDIL
                     KRESQNDELTNHLRETFSESADVLKKELDTWLQGLDVTEEE"
                     /name="replication initiation factor domain-containing
                     protein"
     gene            2232..2465
                     /locus_tag="Q7579_RS15850"
                     /old_locus_tag="Q7579_15790"
     CDS             2232..2465
                     /locus_tag="Q7579_RS15850"
                     /old_locus_tag="Q7579_15790"
                     /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            2458..2877
                     /locus_tag="Q7579_RS15855"
                     /old_locus_tag="Q7579_15795"
     CDS             2458..2877
                     /locus_tag="Q7579_RS15855"
                     /old_locus_tag="Q7579_15795"
                     /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            2886..3194
                     /locus_tag="Q7579_RS15860"
                     /old_locus_tag="Q7579_15800"
     CDS             2886..3194
                     /locus_tag="Q7579_RS15860"
                     /old_locus_tag="Q7579_15800"
                     /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            3198..3560
                     /locus_tag="Q7579_RS15865"
                     /old_locus_tag="Q7579_15805"
     CDS             3198..3560
                     /locus_tag="Q7579_RS15865"
                     /old_locus_tag="Q7579_15805"
                     /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"
     Typing          1345..2219
                     /name="rep_cluster_943"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="84.032"
                     /coverage="97.0"
                     /evalue="0.0"
     Typing          3..808
                     /name="MOBV"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="94.424"
                     /coverage="99.0"
                     /evalue="8e-156"
     Typing          3690..4375
                     /name="MOBV"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="99.0"
                     /evalue="3.32e-153"
ORIGIN
        1 agataatggt cgagtgcttt tcaataattt tagaaatcaa gaagttgact ctatagaacg
       61 attaatgaat gattacggtt ggaaaaggga tattgtcggt accaacaaaa ttaaagatat
      121 tcacgaatac aaagaaatca tgagtgaaat ttctgaattg cgccaaacgg ctgtaaaaga
      181 gcgtgagagc gtttctgatg agttgaggta tatttatagg caaagagaag aaaacgagcg
      241 tgataaggct ctgatggctt ctgagagagc gaagattgaa gaagagaaga aaaatatgct
      301 gaatgtaaaa aaagagatgg cggtcatttt ccaaaaagat atggttcctt tagaaagttt
      361 caagaggctt cctgatggtt cgtatcattt atctgggaat gattttgttg atttgtatca
      421 acgagctacg agagcaacaa atgccaagag aaatgctgat aacatgagtg agcaatattt
      481 acagatgctt gagcaaaata cagaattaaa tgagtatgta gctacattgg aagaagagcg
      541 tcatttgtct ggtagaaaac aattagcaga tttacaagtg gaaaataaaa agctgaaaga
      601 agaaaatcgc tctttacgcc agcgtttaga gcgattaaaa aacgcatttc aaaaatcgat
      661 cactcgtttg tctatccgtt ttggtcttgc agaaaaggat atagggcttt ctgaggaatt
      721 agaagtgtta gagcaggaga aaaccttatt ttatcgtcaa aacgtctcac agcgtaaatt
      781 agagcgttct gaagatgaga tcgagtggta gttacgatgt gcagtcaacg gtaccggagg
      841 cggtttgtgc cgaggataag gagttgacgg ctaaaccact agcctattaa gctgacattt
      901 gctaaaaaat ggccagtcca ttttttggcc aacctagcgt tagcgaagtt tgggggcgcc
      961 cttttcaaag ggtgcggttt tatgtttttg gatatttgca tagctaaaga gaagtgctat
     1021 tattgagtta tcaaataaat aaactgaaaa aagagcaaaa aaataaagtc gagcaacgct
     1081 accaacgttc tcgaccttta cggaaactaa tcgcactagc tccgtaactt cttaatcatt
     1141 atacgaatat ttttagattt cttcaagact agagattttt tggtaatgaa tttttaagag
     1201 ttacgtgaac ttttgaaaat tctttccaga agtctctttt tctttgagga ggaacaaaat
     1261 ttgagtaaaa atggcataat cgtaaatgag tgggaaaatt taacagccct atctaacagg
     1321 cggttaaatg tacaaaatat gtacaccccc ttaaaaatgc agtggtcaat tgaccgaatt
     1381 actatcgttg gaaaactgaa ggaaaatatt tattatcaca ctcaaaatga tgtgttgatt
     1441 ttagattttg agcaattaat gcgggtgaat gaaggcaatg gctatttaaa agcggttggg
     1501 aataacggct ggcaattatt agaccaatac gaagaaaata ttgcttatat tgagattttg
     1561 aaatggcaag atggcaaagg gcggattgat tttaacccga ataagattgg tcatttttta
     1621 gctagttcaa tgaaaaattt cattcatgat ttatttctag aaccacattt ctcacgtgcg
     1681 gatattgctt gcgatattat cgatgtgcct gatgagttta ttacacaata tcgagtggtt
     1741 gatcctgttt ctttcaagcc aatttatggg cggtctggga agctggaaac agcttattgg
     1801 ggcagtcgtg ccagcgaacg ccagattcgg ctatacaaca aaaaattgga acaggaaacc
     1861 aagcgtaaaa ttgtgccacc agaaatagaa acttggtggc gactggaatt gcagttaagg
     1921 cgtgggaaag caacagattg gcatgcaatg gttcatgaaa gtttaaatag ttttgctagc
     1981 cctcattttc taccacttga tgtaaaaaca aatgataagg tgatgatttt tggactgatt
     2041 gctaaccctg aaatgtgggg gtttttagag cgtagaatga aatacaaatt gagagatatt
     2101 ttgaaaagag aaagtcaaaa tgatgagttg acgaatcatt tacgagaaac attttcggaa
     2161 tcagcagatg ttttgaaaaa agaattagac acttggcttc aagggttaga tgtaacggag
     2221 gaggaataag aatggcagaa aaacaaaagc attttggtaa gaaaaattgg ttggtgaatt
     2281 taacaggtga taacgttgtc gttgtttttt tggatagcaa aaaaatgtcc ggtaagttac
     2341 ttgatgtaac gcagtatgag ttgattttga aaaataataa aattgattcc ccaatcatta
     2401 tccctaagca tgctgttaaa tatgtttatg gggtagctga aagtaacgga gaagataatg
     2461 actgatttgc cagaaaaaat gaccataaaa aaccttgctg atgagttggg tatatctaaa
     2521 aatacagtgc gcaatcaact ggtcaatgca ggttatgacc ttgctcggta taaagataat
     2581 ggggttatca tgttagacaa ggaattgatt ggtgttgtgc ggtcaattta tcggtcaaaa
     2641 ggtggtcaat tgactggtga tttaccggtc aatgatgcag gcaatgattt cccgttagaa
     2701 aaagaaaatg aatttttgcg tgaacaatta gcggaaaaag ataggcatat ttctgaatta
     2761 acggaaatga ttcgtgacca acaaaaattg actttgcttc agcaacaaaa aaacgatcag
     2821 ttgttactag aaaatcaaga attaaaaaat cgaaaatggt ggcaattctg gaagtgaggt
     2881 gtgacatgga taaaattgat ttgagagaag aaacagtcga tagaattgaa ttgatgtatg
     2941 aacggttagc tgattatttg aatttgccgg atgaagataa ttatagtgaa atgcttgaac
     3001 gaatgatgga tgttctcaac tcggttatca atgctgatct agcaaaatct tcagttttga
     3061 ctaatgaatt tgttcataag catttagcgc aaacaactga tgaatcagaa aaagaatttt
     3121 ggttgaaatt aatgagtcat gttatgcagt taaaccaaat ttccgttatt aattccaaag
     3181 aaaaggagat gtagtttatg ggaatgactt tagcagatat taaagcgcaa gaagaaaaat
     3241 taaaaaaaga acaagcgaaa cttcgccaac agaaaaaacg cttgattgag aaagaaaatg
     3301 ctgcaatggg caaggctctt cgcaagcgtt ttgggtttga aacttttgct gattttgagc
     3361 ggtggctatc gtcgatttct gacgatcagc aacacgaaaa atcagtggat aatgagtggc
     3421 ttgctgatga aaaatcagcg ccaagcgaac gagattatcc cgatgaatct gacggcttat
     3481 tcggagtgat accgaataag aaaagtcaga tgagtgagag taaatttacg tcaatattta
     3541 atgacgtgaa tttacgataa gcgattattt tgcgtgaagc aaaataaagc gtaaaaggag
     3601 ttgagagcgt gacacgcttt cggctccttt tttcgttgtc acttgtgaca gcgaataccc
     3661 tcggagagca tttggaattg tgacagccat gtcacaatta ggaaaatgtt actctttgac
     3721 aaagagtaac agaaaggttt acaatctttt tattagcgac agcgcgaagg agggttttaa
     3781 cttggggttt agtatttcat ttaaaaaagg aacgaagaat acaagtattt ctcataataa
     3841 tcgtgagtta actgatcgcc agaaaaccaa tgattggcat aagcatattg acttcacgaa
     3901 atcggatgaa aatatttatt tagagcagac gaatctagca gataaatatg aggaattgtt
     3961 tggcgaagtg gtagaaaaat ataatgcgaa acaaaaaaga gccgatagaa aaatcgagga
     4021 ctatttagcg aaagtgcgca aggataaaaa gttggaacct caacgagaat ttattgtgca
     4081 aataggcatt ttagatgatt tccagacaaa tcgagcagat ggttcttcta ctggcatatc
     4141 gaaacaacaa gctgaacaaa atcgagtgat tgccaataaa attttggttc agtattacaa
     4201 ggagtttcaa gagagaaacc ctaatttggc tgtttataat gctgttattc ataatgacga
     4261 aataagtccg cacctgcact tgaatattgt gccggttgct gaaggttata aacggggtgt
     4321 tcaaaagcag ccgagcttta ataaagcact ggttcaacaa gggatacacg ctgataa
//
