LOCUS       NZ_CP131823             4377 bp    DNA     circular CON 25-APR-2024
DEFINITION  Enterococcus faecium strain 2016N17-104 plasmid p2016N17-104-5,
            complete sequence.
ACCESSION   NZ_CP131823
VERSION     NZ_CP131823.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN36766202
            Assembly: GCF_038441015.1
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  JOURNAL   Unpublished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_038441015.1-RS_2024_04_24
            Annotation Date                   :: 04/24/2024 16:12:56
            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)                     :: 3,138
            CDSs (total)                      :: 3,048
            Genes (coding)                    :: 2,898
            CDSs (with protein)               :: 2,898
            Genes (RNA)                       :: 90
            rRNAs                             :: 6, 6, 6 (5S, 16S, 23S)
            complete rRNAs                    :: 6, 6, 6 (5S, 16S, 23S)
            tRNAs                             :: 68
            ncRNAs                            :: 4
            Pseudo Genes (total)              :: 150
            CDSs (without protein)            :: 150
            Pseudo Genes (ambiguous residues) :: 0 of 150
            Pseudo Genes (frameshifted)       :: 48 of 150
            Pseudo Genes (incomplete)         :: 96 of 150
            Pseudo Genes (internal stop)      :: 35 of 150
            Pseudo Genes (multiple problems)  :: 25 of 150
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP131823.1.
            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="2016N17-104"
                     /isolation_source="blood"
                     /host="Homo sapiens"
                     /db_xref="taxon:1352"
                     /plasmid="p2016N17-104-5"
                     /geo_loc_name="Taiwan"
                     /collection_date="2016"
                     /collected_by="NHRI"
     gene            complement(join(3331..4377,1..360))
                     /locus_tag="Q7581_RS15655"
                     /old_locus_tag="Q7581_15600"
     CDS             complement(join(3331..4377,1..360))
                     /locus_tag="Q7581_RS15655"
                     /old_locus_tag="Q7581_15600"
                     /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            complement(582..944)
                     /locus_tag="Q7581_RS15660"
                     /old_locus_tag="Q7581_15605"
     CDS             complement(582..944)
                     /locus_tag="Q7581_RS15660"
                     /old_locus_tag="Q7581_15605"
                     /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            complement(948..1256)
                     /locus_tag="Q7581_RS15665"
                     /old_locus_tag="Q7581_15610"
     CDS             complement(948..1256)
                     /locus_tag="Q7581_RS15665"
                     /old_locus_tag="Q7581_15610"
                     /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            complement(1265..1684)
                     /locus_tag="Q7581_RS15670"
                     /old_locus_tag="Q7581_15615"
     CDS             complement(1265..1684)
                     /locus_tag="Q7581_RS15670"
                     /old_locus_tag="Q7581_15615"
                     /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            complement(1677..1910)
                     /locus_tag="Q7581_RS15675"
                     /old_locus_tag="Q7581_15620"
     CDS             complement(1677..1910)
                     /locus_tag="Q7581_RS15675"
                     /old_locus_tag="Q7581_15620"
                     /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            complement(1913..2881)
                     /locus_tag="Q7581_RS15680"
                     /old_locus_tag="Q7581_15625"
     CDS             complement(1913..2881)
                     /locus_tag="Q7581_RS15680"
                     /old_locus_tag="Q7581_15625"
                     /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"
     Typing          complement(1921..2798)
                     /name="rep_cluster_943"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="83.973"
                     /coverage="97.0"
                     /evalue="0.0"
     Typing          complement(2..453)
                     /name="MOBV"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="1.04e-92"
     Typing          complement(3335..4374)
                     /name="MOBV"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="93.084"
                     /coverage="99.0"
                     /evalue="0.0"
ORIGIN
        1 cgatatgcca gtagaagaac catctgctcg atttgtctgg aaatcatcta aaatgcctat
       61 ttgcacaata aattctcgtt gaggttccaa ctttttatcc ttgcgcactt tcgctaaata
      121 gtcctcgatt tttctatcgg ctcttttttg tttcgcatta tatttttcta ccacttcgcc
      181 aaacaattcc tcatatttat ctgctagatt cgtctgctct aaataaatat tttcatccga
      241 tttcgtgaag tcaatatgct tatgccaatc attggttttc tggcgatcag ttaactcacg
      301 attattatga gaaatacttg tattcttcgt tcctttttta aatgaaatac taaaccccaa
      361 gttaaaaccc tccttcgcgc tgtcgctaat aaaaagattg taaacctttc tgttactctt
      421 tgtcaaagag taacattttc ctaattgtga catggctgtc acaattccaa atgctctccg
      481 agggtattcg ctgtcacaag tgacaacgaa aaaaggagcc gaaagcgtgt cacgctctca
      541 actcctttta cgctttattt tgcttcacgc aaaataatcg cttatcgtaa attcacgtca
      601 ttaaatattg acgtaaattt actctcactc atctgacttt tcttattcgg tatcactccg
      661 aataagccgt cagattcatc gggataatct cgttcgcttg gcgctgattt ttcatcagca
      721 agccactcat tatccactga tttttcgtgt tgctgatcgt cagaaatcga cgatagccac
      781 cgctcaaaat cagcaaaagt ttcaaaccca aaacgcttgc gaagagcctt gcccattgca
      841 gcattttctt tctcaatcaa gcgttttttc tgttggcgaa gtttcgcttg ttcttttttt
      901 aatttttctt cttgcgcttt aatatctgct aaagtcattc ccataaacta catctccttt
      961 tctttggaat taataacgga aatttggttt aactgcataa catgactcat taatttcaac
     1021 caaaattctt tttctgattc atcagttgtt tgcgctaaat gcttatgaac aaattcatta
     1081 gtcaaaactg aagattttgc tagatcagca ttgataaccg agttgagaac atccatcatt
     1141 cgttcaagca tttcactata attatcttca tccggcaaat tcaaataatc agctaaccgt
     1201 tcatacatca attcaattct atcgactgtt tcttctctca aatcaatttt atccatgtca
     1261 cacctcactt ccagaattgc caccattttc gattttttaa ttcttgattt tctagtaaca
     1321 actgatcgtt tttttgttgc tgaagcaaag tcaatttttg ttggtcacga atcatttccg
     1381 ttaattcaga aatatgccta tctttttccg ctaattgttc acgcaaaaat tcattttctt
     1441 tttctaacgg gaaatcattg cctgcatcat tgaccggtaa atcaccagtc aattgaccac
     1501 cttttgaccg ataaattgac cgcacaacac caatcaattc cttgtctaac atgataaccc
     1561 cattatcttt ataccgagca aggtcataac ctgcattgac cagttgattg cgcactgtat
     1621 ttttagatat acccaactca tcagcaaggt tttttatggt cattttttct ggcaaatcag
     1681 tcattatctt ctccgttact ttcagctacc ccataaacat atttaacagc atgcttaggg
     1741 ataatgattg gggaatcaat tttattattt ttcaaaatca actcatactg cgttacatca
     1801 agtaacttac cggacatttt tttgctatcc aaaaaaacaa cgacaacgtt atcacctgtt
     1861 aaattcacca accaattttt cttaccaaaa tgcttttgtt tttctgccat tcttattcct
     1921 cctccgttac atctaaccct tgaagccaag tgtctaattc ttttttcaaa acatctgctg
     1981 attccgaaaa tgtttctcgt aaatgattcg tcaactcatc attttgactt tctcttttca
     2041 aaatatctct caatttgtat ttcattctac gctctaaaaa cccccacatt tcagggttag
     2101 caatcagtcc aaaaatcatc accttatcat ttgtttttac atcaagtggt agaaaatgag
     2161 ggctagcaaa actatttaaa ctttcatgaa ccattgcatg ccaatctgtt gctttcccac
     2221 gccttaactg caattccagt cgccaccaag tttctatttc tggtggcaca attttacgct
     2281 tggtttcctg ttccaatttt ttgttgtata gccgaatctg gcgttcgctg gcacgactgc
     2341 cccaataagc tgtttccagc ttcccagacc gcccataaat tggcttgaaa gaaacaggat
     2401 caaccactcg atattgtgta ataaactcat caggcacatc gataatatcg caagcaatat
     2461 ccgcacgtga gaaatgtggt tctagaaata aatcatgaat gaaatttttc attgaactag
     2521 ctaaaaaatg accaatctta ttcgggttaa aatcaatccg ccctttgcca tcttgccatt
     2581 tcaaaatctc aatataagca atattttctt cgtattggtc taataattgc cagccgttat
     2641 tcccaaccgc ttttaaatag ccattgcctt cattcacccg cattaattgc tcaaaatcta
     2701 aaatcaacac atcattttga gtgtgataat aaatattttc cttcagtttt ccaacgatag
     2761 taattcggtc aattgaccac tgcattttta agggggtgta catattttgt acatttaacc
     2821 gcctgttaga tagggctgtt aaattttccc actcatttac gattatgcca tttttactca
     2881 aattttgttc ctcctcaaag aaaaagagac ttctggaaag aattttcaaa agttcacgta
     2941 actcttaaaa attcattacc aaaaaatctc tagtcttgaa gaaatctaaa aatattcgta
     3001 taatgattaa gaagttacgg agctagtgcg attagtttcc gtaaaggtcg agaacgttgg
     3061 tagcgttgct cgactttatt tttttgctct tttttcagtt tatttatttg ataactcaat
     3121 aatagcactt ctctttagct atgcaaatat ccaaaaacat aaaaccgcac cctttgaaaa
     3181 gggcgccccc aaacttcgct aacgctaggt tggccaaaaa atggactggc cattttttag
     3241 caaatgtcag cttaataggc tagtggttta gccgtcaact ccttatcctc ggcacaaacc
     3301 gcctccggta ccgttgactg cacatcgtaa ctaccactcg atctcatctt cagaacgctc
     3361 taatttacgc tgtgagacgt tttgacgata aaataaggtt ttctcctgct ctaacacttc
     3421 taattcctca gaaagcccta tatccttttc tgcaagacca aaacggatag acaaacgagt
     3481 gatcgatttt tgaaatgcgt tttttaatcg ctctaaacgc tggcgtaaag agcgattttc
     3541 ttctttcagc tttttatttt ccacttgtaa atctgctaat tgttttctac cagacaaatg
     3601 acgctcttct tccaatgtag ctacatactc atttaattct gtattttgct caagcatctg
     3661 taaatattgc tcactcatgt tatcagcatt tctcttggca tttgttgctc tcgtagctcg
     3721 ttgatacaaa tcaacaaaat cattcccaga taaatgatac gaaccatcag gaagcctctt
     3781 gaaactttct aaaggaacca tatctttttg gaaaatgacc gccatctctt tttttacatt
     3841 cagcatattt ttcttctctt cttcaatctt cgctctctca gaagccatca gagccttatc
     3901 acgctcgttt tcttctcttt gcctataaat atacctcaac tcatcagaaa cgctctcacg
     3961 ctcttttaca gccgtttggc gcaattcaga aatttcactc atgatttctt tgtattcgtg
     4021 aatatcttta attttgttgg taccgacaat atcccttttc caaccgtaat cattcattaa
     4081 tcgttctata gagtcaactt cttgatttct aaaattattg aaaagcactc gaccattatc
     4141 tttatcagcg tgtatccctt gttgaaccag tgctttatta aagctcggct gcttttgaac
     4201 accccgttta taaccttcag caaccggcac aatattcaag tgcaggtgcg gacttatttc
     4261 gtcattatga ataacagcat tataaacagc caaattaggg tttctctctt gaaactcctt
     4321 gtaatactga accaaaattt tattggcaat cactcgattt tgttcagctt gttgttt
//
