LOCUS       NZ_CP131807             4377 bp    DNA     circular CON 25-APR-2024
DEFINITION  Enterococcus faecium strain 2016N21-233 plasmid p2016N21-233-6,
            complete sequence.
ACCESSION   NZ_CP131807
VERSION     NZ_CP131807.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN36766204
            Assembly: GCF_038437885.1
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  JOURNAL   Unpublished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_038437885.1-RS_2024_04_24
            Annotation Date                   :: 04/24/2024 14:04:14
            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)                     :: 3,196
            CDSs (total)                      :: 3,103
            Genes (coding)                    :: 2,933
            CDSs (with protein)               :: 2,933
            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)              :: 170
            CDSs (without protein)            :: 170
            Pseudo Genes (ambiguous residues) :: 0 of 170
            Pseudo Genes (frameshifted)       :: 63 of 170
            Pseudo Genes (incomplete)         :: 101 of 170
            Pseudo Genes (internal stop)      :: 39 of 170
            Pseudo Genes (multiple problems)  :: 31 of 170
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP131807.1.
            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="2016N21-233"
                     /isolation_source="blood"
                     /host="Homo sapiens"
                     /db_xref="taxon:1352"
                     /plasmid="p2016N21-233-6"
                     /geo_loc_name="Taiwan"
                     /collection_date="2016"
                     /collected_by="NHRI"
     gene            complement(join(3165..4377,1..194))
                     /locus_tag="Q7583_RS15935"
                     /old_locus_tag="Q7583_15860"
     CDS             complement(join(3165..4377,1..194))
                     /locus_tag="Q7583_RS15935"
                     /old_locus_tag="Q7583_15860"
                     /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(416..778)
                     /locus_tag="Q7583_RS15940"
                     /old_locus_tag="Q7583_15865"
     CDS             complement(416..778)
                     /locus_tag="Q7583_RS15940"
                     /old_locus_tag="Q7583_15865"
                     /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(782..1090)
                     /locus_tag="Q7583_RS15945"
                     /old_locus_tag="Q7583_15870"
     CDS             complement(782..1090)
                     /locus_tag="Q7583_RS15945"
                     /old_locus_tag="Q7583_15870"
                     /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(1099..1518)
                     /locus_tag="Q7583_RS15950"
                     /old_locus_tag="Q7583_15875"
     CDS             complement(1099..1518)
                     /locus_tag="Q7583_RS15950"
                     /old_locus_tag="Q7583_15875"
                     /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(1511..1744)
                     /locus_tag="Q7583_RS15955"
                     /old_locus_tag="Q7583_15880"
     CDS             complement(1511..1744)
                     /locus_tag="Q7583_RS15955"
                     /old_locus_tag="Q7583_15880"
                     /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(1747..2715)
                     /locus_tag="Q7583_RS15960"
                     /old_locus_tag="Q7583_15885"
     CDS             complement(1747..2715)
                     /locus_tag="Q7583_RS15960"
                     /old_locus_tag="Q7583_15885"
                     /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(1755..2632)
                     /name="rep_cluster_943"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="83.973"
                     /coverage="97.0"
                     /evalue="0.0"
     Typing          complement(4..194)
                     /name="MOBV"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="89.062"
                     /coverage="95.0"
                     /evalue="1.14e-30"
     Typing          complement(3169..4376)
                     /name="MOBV"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="92.556"
                     /coverage="99.0"
                     /evalue="0.0"
ORIGIN
        1 tctaccactt cgccaaacaa ttcctcatat ttatctgcta gattcgtctg ctctaaataa
       61 atattttcat ccgatttcgt gaagtcaata tgcttatgcc aatcattggt tttctggcga
      121 tcagttaact cacgattatt atgagaaata cttgtattct tcgttccttt tttaaatgaa
      181 atactaaacc ccaagttaaa accctccttc gcgctgtcgc taataaaaag attgtaaacc
      241 tttctgttac tctttgtcaa agagtaacat tttcctaatt gtgacatggc tgtcacaatt
      301 ccaaatgctc tccgagggta ttcgctgtca caagtgacaa cgaaaaaagg agccgaaagc
      361 gtgtcacgct ctcaactcct tttacgcttt attttgcttc acgcaaaata atcgcttatc
      421 gtaaattcac gtcattaaat attgacgtaa atttactctc actcatctga cttttcttat
      481 tcggtatcac tccgaataag ccgtcagatt catcgggata atctcgttcg cttggcgctg
      541 atttttcatc agcaagccac tcattatcca ctgatttttc gtgttgctga tcgtcagaaa
      601 tcgacgatag ccaccgctca aaatcagcaa aagtttcaaa cccaaaacgc ttgcgaagag
      661 ccttgcccat tgcagcattt tctttctcaa tcaagcgttt tttctgttgg cgaagtttcg
      721 cttgttcttt ttttaatttt tcttcttgcg ctttaatatc tgctaaagtc attcccataa
      781 actacatctc cttttctttg gaattaataa cggaaatttg gtttaactgc ataacatgac
      841 tcattaattt caaccaaaat tctttttctg attcatcagt tgtttgcgct aaatgcttat
      901 gaacaaattc attagtcaaa actgaagatt ttgctagatc agcattgata accgagttga
      961 gaacatccat cattcgttca agcatttcac tataattatc ttcatccggc aaattcaaat
     1021 aatcagctaa ccgttcatac atcaattcaa ttctatcgac tgtttcttct ctcaaatcaa
     1081 ttttatccat gtcacacctc acttccagaa ttgccaccat tttcgatttt ttaattcttg
     1141 attttctagt aacaactgat cgtttttttg ttgctgaagc aaagtcaatt tttgttggtc
     1201 acgaatcatt tccgttaatt cagaaatatg cctatctttt tccgctaatt gttcacgcaa
     1261 aaattcattt tctttttcta acgggaaatc attgcctgca tcattgaccg gtaaatcacc
     1321 agtcaattga ccaccttttg accgataaat tgaccgcaca acaccaatca attccttgtc
     1381 taacatgata accccattat ctttataccg agcaaggtca taacctgcat tgaccagttg
     1441 attgcgcact gtatttttag atatacccaa ctcatcagca aggtttttta tggtcatttt
     1501 ttctggcaaa tcagtcatta tcttctccgt tactttcagc taccccataa acatatttaa
     1561 cagcatgctt agggataatg attggggaat caattttatt atttttcaaa atcaactcat
     1621 actgcgttac atcaagtaac ttaccggaca tttttttgct atccaaaaaa acaacgacaa
     1681 cgttatcacc tgttaaattc accaaccaat ttttcttacc aaaatgcttt tgtttttctg
     1741 ccattcttat tcctcctccg ttacatctaa cccttgaagc caagtgtcta attctttttt
     1801 caaaacatct gctgattccg aaaatgtttc tcgtaaatga ttcgtcaact catcattttg
     1861 actttctctt ttcaaaatat ctctcaattt gtatttcatt ctacgctcta aaaaccccca
     1921 catttcaggg ttagcaatca gtccaaaaat catcacctta tcatttgttt ttacatcaag
     1981 tggtagaaaa tgagggctag caaaactatt taaactttca tgaaccattg catgccaatc
     2041 tgttgctttc ccacgcctta actgcaattc cagtcgccac caagtttcta tttctggtgg
     2101 cacaatttta cgcttggttt cctgttccaa ttttttgttg tatagccgaa tctggcgttc
     2161 gctggcacga ctgccccaat aagctgtttc cagcttccca gaccgcccat aaattggctt
     2221 gaaagaaaca ggatcaacca ctcgatattg tgtaataaac tcatcaggca catcgataat
     2281 atcgcaagca atatccgcac gtgagaaatg tggttctaga aataaatcat gaatgaaatt
     2341 tttcattgaa ctagctaaaa aatgaccaat cttattcggg ttaaaatcaa tccgcccttt
     2401 gccatcttgc catttcaaaa tctcaatata agcaatattt tcttcgtatt ggtctaataa
     2461 ttgccagccg ttattcccaa ccgcttttaa atagccattg ccttcattca cccgcattaa
     2521 ttgctcaaaa tctaaaatca acacatcatt ttgagtgtga taataaatat tttccttcag
     2581 ttttccaacg atagtaattc ggtcaattga ccactgcatt tttaaggggg tgtacatatt
     2641 ttgtacattt aaccgcctgt tagatagggc tgttaaattt tcccactcat ttacgattat
     2701 gccattttta ctcaaatttt gttcctcctc aaagaaaaag agacttctgg aaagaatttt
     2761 caaaagttca cgtaactctt aaaaattcat taccaaaaaa tctctagtct tgaagaaatc
     2821 taaaaatatt cgtataatga ttaagaagtt acggagctag tgcgattagt ttccgtaaag
     2881 gtcgagaacg ttggtagcgt tgctcgactt tatttttttg ctcttttttc agtttattta
     2941 tttgataact caataatagc acttctcttt agctatgcaa atatccaaaa acataaaacc
     3001 gcaccctttg aaaagggcgc ccccaaactt cgctaacgct aggttggcca aaaaatggac
     3061 tggccatttt ttagcaaatg tcagcttaat aggctagtgg tttagccgtc aactccttat
     3121 cctcggcaca aaccgcctcc ggtaccgttg actgcacatc gtaactacca ctcgatctca
     3181 tcttcagaac gctctaattt acgctgtgag acgttttgac gataaaataa ggttttctcc
     3241 tgctctaaca cttctaattc ctcagaaagc cctatatcct tttctgcaag accaaaacgg
     3301 atagacaaac gagtgatcga tttttgaaat gcgtttttta atcgctctaa acgctggcgt
     3361 aaagagcgat tttcttcttt cagcttttta ttttccactt gtaaatctgc taattgtttt
     3421 ctaccagaca aatgacgctc ttcttccaat gtagctacat actcatttaa ttctgtattt
     3481 tgctcaagca tctgtaaata ttgctcactc atgttatcag catttctctt ggcatttgtt
     3541 gctctcgtag ctcgttgata caaatcaaca aaatcattcc cagataaatg atacgaacca
     3601 tcaggaagcc tcttgaaact ttctaaagga accatatctt tttggaaaat gaccgccatc
     3661 tcttttttta cattcagcat atttttcttc tcttcttcaa tcttcgctct ctcagaagcc
     3721 atcagagcct tatcacgctc gttttcttct ctttgcctat aaatatacct caactcatca
     3781 gaaacgctct cacgctcttt tacagccgtt tggcgcaatt cagaaatttc actcatgatt
     3841 tctttgtatt cgtgaatatc tttaattttg ttggtaccga caatatccct tttccaaccg
     3901 taatcattca ttaatcgttc tatagagtca acttcttgat ttctaaaatt attgaaaagc
     3961 actcgaccat tatctttatc agcgtgtatc ccttgttgaa ccagtgcttt attaaagctc
     4021 ggctgctttt gaacaccccg tttataacct tcagcaaccg gcacaatatt caagtgcagg
     4081 tgcggactta tttcgtcatt atgaataaca gcattataaa cagccaaatt agggtttctc
     4141 tcttgaaact ccttgtaata ctgaaccaaa attttattgg caatcactcg attttgttca
     4201 gcttgttgtt tcgatatgcc agtagaagaa ccatctgctc gatttgtctg gaaatcatct
     4261 aaaatgccta tttgcacaat aaattctcgt tgaggttcca actttttatc cttgcgcact
     4321 ttcgctaaat agtcctcgat ttttctatcg gctctttttt gtttcgcatt atatttt
//
