LOCUS       NZ_CP131846             4377 bp    DNA     circular CON 25-APR-2024
DEFINITION  Enterococcus faecium strain 2016S06-219 plasmid p2016S06-219-5,
            complete sequence.
ACCESSION   NZ_CP131846
VERSION     NZ_CP131846.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN36766199
            Assembly: GCF_038441125.1
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  JOURNAL   Unpublished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_038441125.1-RS_2024_04_24
            Annotation Date                   :: 04/24/2024 15:02:18
            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)                     :: 3,146
            CDSs (total)                      :: 3,053
            Genes (coding)                    :: 2,884
            CDSs (with protein)               :: 2,884
            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)              :: 169
            CDSs (without protein)            :: 169
            Pseudo Genes (ambiguous residues) :: 0 of 169
            Pseudo Genes (frameshifted)       :: 60 of 169
            Pseudo Genes (incomplete)         :: 103 of 169
            Pseudo Genes (internal stop)      :: 34 of 169
            Pseudo Genes (multiple problems)  :: 26 of 169
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP131846.1.
            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="2016S06-219"
                     /isolation_source="blood"
                     /host="Homo sapiens"
                     /db_xref="taxon:1352"
                     /plasmid="p2016S06-219-5"
                     /geo_loc_name="Taiwan"
                     /collection_date="2016"
                     /collected_by="NHRI"
     gene            join(4013..4377,1..604)
                     /locus_tag="Q7578_RS15695"
                     /old_locus_tag="Q7578_15630"
     CDS             join(4013..4377,1..604)
                     /locus_tag="Q7578_RS15695"
                     /old_locus_tag="Q7578_15630"
                     /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            607..840
                     /locus_tag="Q7578_RS15700"
                     /old_locus_tag="Q7578_15635"
     CDS             607..840
                     /locus_tag="Q7578_RS15700"
                     /old_locus_tag="Q7578_15635"
                     /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            833..1252
                     /locus_tag="Q7578_RS15705"
                     /old_locus_tag="Q7578_15640"
     CDS             833..1252
                     /locus_tag="Q7578_RS15705"
                     /old_locus_tag="Q7578_15640"
                     /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            1261..1569
                     /locus_tag="Q7578_RS15710"
                     /old_locus_tag="Q7578_15645"
     CDS             1261..1569
                     /locus_tag="Q7578_RS15710"
                     /old_locus_tag="Q7578_15645"
                     /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            1573..1935
                     /locus_tag="Q7578_RS15715"
                     /old_locus_tag="Q7578_15650"
     CDS             1573..1935
                     /locus_tag="Q7578_RS15715"
                     /old_locus_tag="Q7578_15650"
                     /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            2157..3563
                     /locus_tag="Q7578_RS15720"
                     /old_locus_tag="Q7578_15655"
     CDS             2157..3563
                     /locus_tag="Q7578_RS15720"
                     /old_locus_tag="Q7578_15655"
                     /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"
     Typing          2..594
                     /name="rep_cluster_943"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="83.028"
                     /coverage="96.0"
                     /evalue="2.34e-148"
     Typing          4097..4375
                     /name="rep_cluster_943"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="86.429"
                     /coverage="96.0"
                     /evalue="1.54e-80"
     Typing          2158..3560
                     /name="MOBV"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="91.88"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 ttcaatgaaa aatttcattc atgatttatt tctagaacca catttctcac gtgcggatat
       61 tgcttgcgat attatcgatg tgcctgatga gtttattaca caatatcgag tggttgatcc
      121 tgtttctttc aagccaattt atgggcggtc tgggaagctg gaaacagctt attggggcag
      181 tcgtgccagc gaacgccaga ttcggctata caacaaaaaa ttggaacagg aaaccaagcg
      241 taaaattgtg ccaccagaaa tagaaacttg gtggcgactg gaattgcagt taaggcgtgg
      301 gaaagcaaca gattggcatg caatggttca tgaaagttta aatagttttg ctagccctca
      361 ttttctacca cttgatgtaa aaacaaatga taaggtgatg atttttggac tgattgctaa
      421 ccctgaaatg tgggggtttt tagagcgtag aatgaaatac aaattgagag atattttgaa
      481 aagagaaagt caaaatgatg agttgacgaa tcatttacga gaaacatttt cggaatcagc
      541 agatgttttg aaaaaagaat tagacacttg gcttcaaggg ttagatgtaa cggaggagga
      601 ataagaatgg cagaaaaaca aaagcatttt ggtaagaaaa attggttggt gaatttaaca
      661 ggtgataacg ttgtcgttgt ttttttggat agcaaaaaaa tgtccggtaa gttacttgat
      721 gtaacgcagt atgagttgat tttgaaaaat aataaaattg attccccaat cattatccct
      781 aagcatgctg ttaaatatgt ttatggggta gctgaaagta acggagaaga taatgactga
      841 tttgccagaa aaaatgacca taaaaaacct tgctgatgag ttgggtatat ctaaaaatac
      901 agtgcgcaat caactggtca atgcaggtta tgaccttgct cggtataaag ataatggggt
      961 tatcatgtta gacaaggaat tgattggtgt tgtgcggtca atttatcggt caaaaggtgg
     1021 tcaattgact ggtgatttac cggtcaatga tgcaggcaat gatttcccgt tagaaaaaga
     1081 aaatgaattt ttgcgtgaac aattagcgga aaaagatagg catatttctg aattaacgga
     1141 aatgattcgt gaccaacaaa aattgacttt gcttcagcaa caaaaaaacg atcagttgtt
     1201 actagaaaat caagaattaa aaaatcgaaa atggtggcaa ttctggaagt gaggtgtgac
     1261 atggataaaa ttgatttgag agaagaaaca gtcgatagaa ttgaattgat gtatgaacgg
     1321 ttagctgatt atttgaattt gccggatgaa gataattata gtgaaatgct tgaacgaatg
     1381 atggatgttc tcaactcggt tatcaatgct gatctagcaa aatcttcagt tttgactaat
     1441 gaatttgttc ataagcattt agcgcaaaca actgatgaat cagaaaaaga attttggttg
     1501 aaattaatga gtcatgttat gcagttaaac caaatttccg ttattaattc caaagaaaag
     1561 gagatgtagt ttatgggaat gactttagca gatattaaag cgcaagaaga aaaattaaaa
     1621 aaagaacaag cgaaacttcg ccaacagaaa aaacgcttga ttgagaaaga aaatgctgca
     1681 atgggcaagg ctcttcgcaa gcgttttggg tttgaaactt ttgctgattt tgagcggtgg
     1741 ctatcgtcga tttctgacga tcagcaacac gaaaaatcag tggataatga gtggcttgct
     1801 gatgaaaaat cagcgccaag cgaacgagat tatcccgatg aatctgacgg cttattcgga
     1861 gtgataccga ataagaaaag tcagatgagt gagagtaaat ttacgtcaat atttaatgac
     1921 gtgaatttac gataagcgat tattttgcgt gaagcaaaat aaagcgtaaa aggagttgag
     1981 agcgtgacac gctttcggct ccttttttcg ttgtcacttg tgacagcgaa taccctcgga
     2041 gagcatttgg aattgtgaca gccatgtcac aattaggaaa atgttactct ttgacaaaga
     2101 gtaacagaaa ggtttacaat ctttttatta gcgacagcgc gaaggagggt tttaacttgg
     2161 ggtttagtat ttcatttaaa aaaggaacga agaatacaag tatttctcat aataatcgtg
     2221 agttaactga tcgccagaaa accaatgatt ggcataagca tattgacttc acgaaatcgg
     2281 atgaaaatat ttatttagag cagacgaatc tagcagataa atatgaggaa ttgtttggcg
     2341 aagtggtaga aaaatataat gcgaaacaaa aaagagccga tagaaaaatc gaggactatt
     2401 tagcgaaagt gcgcaaggat aaaaagttgg aacctcaacg agaatttatt gtgcaaatag
     2461 gcattttaga tgatttccag acaaatcgag cagatggttc ttctactggc atatcgaaac
     2521 aacaagctga acaaaatcga gtgattgcca ataaaatttt ggttcagtat tacaaggagt
     2581 ttcaagagag aaaccctaat ttggctgttt ataatgctgt tattcataat gacgaaataa
     2641 gtccgcacct gcacttgaat attgtgccgg ttgctgaagg ttataaacgg ggtgttcaaa
     2701 agcagccgag ctttaataaa gcactggttc aacaagggat acacgctgat aaagataatg
     2761 gtcgagtgct tttcaataat tttagaaatc aagaagttga ctctatagaa cgattaatga
     2821 atgattacgg ttggaaaagg gatattgtcg gtaccaacaa aattaaagat attcacgaat
     2881 acaaagaaat catgagtgaa atttctgaat tgcgccaaac ggctgtaaaa gagcgtgaga
     2941 gcgtttctga tgagttgagg tatatttata ggcaaagaga agaaaacgag cgtgataagg
     3001 ctctgatggc ttctgagaga gcgaagattg aagaagagaa gaaaaatatg ctgaatgtaa
     3061 aaaaagagat ggcggtcatt ttccaaaaag atatggttcc tttagaaagt ttcaagaggc
     3121 ttcctgatgg ttcgtatcat ttatctggga atgattttgt tgatttgtat caacgagcta
     3181 cgagagcaac aaatgccaag agaaatgctg ataacatgag tgagcaatat ttacagatgc
     3241 ttgagcaaaa tacagaatta aatgagtatg tagctacatt ggaagaagag cgtcatttgt
     3301 ctggtagaaa acaattagca gatttacaag tggaaaataa aaagctgaaa gaagaaaatc
     3361 gctctttacg ccagcgttta gagcgattaa aaaacgcatt tcaaaaatcg atcactcgtt
     3421 tgtctatccg ttttggtctt gcagaaaagg atatagggct ttctgaggaa ttagaagtgt
     3481 tagagcagga gaaaacctta ttttatcgtc aaaacgtctc acagcgtaaa ttagagcgtt
     3541 ctgaagatga gatcgagtgg tagttacgat gtgcagtcaa cggtaccgga ggcggtttgt
     3601 gccgaggata aggagttgac ggctaaacca ctagcctatt aagctgacat ttgctaaaaa
     3661 atggccagtc cattttttgg ccaacctagc gttagcgaag tttgggggcg cccttttcaa
     3721 agggtgcggt tttatgtttt tggatatttg catagctaaa gagaagtgct attattgagt
     3781 tatcaaataa ataaactgaa aaaagagcaa aaaaataaag tcgagcaacg ctaccaacgt
     3841 tctcgacctt tacggaaact aatcgcacta gctccgtaac ttcttaatca ttatacgaat
     3901 atttttagat ttcttcaaga ctagagattt tttggtaatg aatttttaag agttacgtga
     3961 acttttgaaa attctttcca gaagtctctt tttctttgag gaggaacaaa atttgagtaa
     4021 aaatggcata atcgtaaatg agtgggaaaa tttaacagcc ctatctaaca ggcggttaaa
     4081 tgtacaaaat atgtacaccc ccttaaaaat gcagtggtca attgaccgaa ttactatcgt
     4141 tggaaaactg aaggaaaata tttattatca cactcaaaat gatgtgttga ttttagattt
     4201 tgagcaatta atgcgggtga atgaaggcaa tggctattta aaagcggttg ggaataacgg
     4261 ctggcaatta ttagaccaat acgaagaaaa tattgcttat attgagattt tgaaatggca
     4321 agatggcaaa gggcggattg attttaaccc gaataagatt ggtcattttt tagctag
//
