LOCUS       NZ_CP131854             4377 bp    DNA     circular CON 25-APR-2024
DEFINITION  Enterococcus faecium strain 2016C01-052 plasmid p2016C01-052-6,
            complete sequence.
ACCESSION   NZ_CP131854
VERSION     NZ_CP131854.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN36766198
            Assembly: GCF_038441135.1
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  JOURNAL   Unpublished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_038441135.1-RS_2024_04_24
            Annotation Date                   :: 04/24/2024 14:55:32
            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)                     :: 3,327
            CDSs (total)                      :: 3,231
            Genes (coding)                    :: 3,056
            CDSs (with protein)               :: 3,056
            Genes (RNA)                       :: 96
            rRNAs                             :: 6, 6, 6 (5S, 16S, 23S)
            complete rRNAs                    :: 6, 6, 6 (5S, 16S, 23S)
            tRNAs                             :: 74
            ncRNAs                            :: 4
            Pseudo Genes (total)              :: 175
            CDSs (without protein)            :: 175
            Pseudo Genes (ambiguous residues) :: 0 of 175
            Pseudo Genes (frameshifted)       :: 57 of 175
            Pseudo Genes (incomplete)         :: 108 of 175
            Pseudo Genes (internal stop)      :: 43 of 175
            Pseudo Genes (multiple problems)  :: 30 of 175
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP131854.1.
            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="2016C01-052"
                     /isolation_source="blood"
                     /host="Homo sapiens"
                     /db_xref="taxon:1352"
                     /plasmid="p2016C01-052-6"
                     /geo_loc_name="Taiwan"
                     /collection_date="2016"
                     /collected_by="NHRI"
     gene            complement(join(3084..4377,1..113))
                     /locus_tag="Q7577_RS16590"
                     /old_locus_tag="Q7577_16515"
     CDS             complement(join(3084..4377,1..113))
                     /locus_tag="Q7577_RS16590"
                     /old_locus_tag="Q7577_16515"
                     /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(335..697)
                     /locus_tag="Q7577_RS16595"
                     /old_locus_tag="Q7577_16520"
     CDS             complement(335..697)
                     /locus_tag="Q7577_RS16595"
                     /old_locus_tag="Q7577_16520"
                     /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(701..1009)
                     /locus_tag="Q7577_RS16600"
                     /old_locus_tag="Q7577_16525"
     CDS             complement(701..1009)
                     /locus_tag="Q7577_RS16600"
                     /old_locus_tag="Q7577_16525"
                     /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(1018..1437)
                     /locus_tag="Q7577_RS16605"
                     /old_locus_tag="Q7577_16530"
     CDS             complement(1018..1437)
                     /locus_tag="Q7577_RS16605"
                     /old_locus_tag="Q7577_16530"
                     /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(1430..1663)
                     /locus_tag="Q7577_RS16610"
                     /old_locus_tag="Q7577_16535"
     CDS             complement(1430..1663)
                     /locus_tag="Q7577_RS16610"
                     /old_locus_tag="Q7577_16535"
                     /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(1666..2634)
                     /locus_tag="Q7577_RS16615"
                     /old_locus_tag="Q7577_16540"
     CDS             complement(1666..2634)
                     /locus_tag="Q7577_RS16615"
                     /old_locus_tag="Q7577_16540"
                     /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(1674..2551)
                     /name="rep_cluster_943"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="83.973"
                     /coverage="97.0"
                     /evalue="0.0"
     Typing          complement(3088..4376)
                     /name="MOBV"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="91.86"
                     /coverage="99.0"
                     /evalue="0.0"
ORIGIN
        1 aagtcaatat gcttatgcca atcattggtt ttctggcgat cagttaactc acgattatta
       61 tgagaaatac ttgtattctt cgttcctttt ttaaatgaaa tactaaaccc caagttaaaa
      121 ccctccttcg cgctgtcgct aataaaaaga ttgtaaacct ttctgttact ctttgtcaaa
      181 gagtaacatt ttcctaattg tgacatggct gtcacaattc caaatgctct ccgagggtat
      241 tcgctgtcac aagtgacaac gaaaaaagga gccgaaagcg tgtcacgctc tcaactcctt
      301 ttacgcttta ttttgcttca cgcaaaataa tcgcttatcg taaattcacg tcattaaata
      361 ttgacgtaaa tttactctca ctcatctgac ttttcttatt cggtatcact ccgaataagc
      421 cgtcagattc atcgggataa tctcgttcgc ttggcgctga tttttcatca gcaagccact
      481 cattatccac tgatttttcg tgttgctgat cgtcagaaat cgacgatagc caccgctcaa
      541 aatcagcaaa agtttcaaac ccaaaacgct tgcgaagagc cttgcccatt gcagcatttt
      601 ctttctcaat caagcgtttt ttctgttggc gaagtttcgc ttgttctttt tttaattttt
      661 cttcttgcgc tttaatatct gctaaagtca ttcccataaa ctacatctcc ttttctttgg
      721 aattaataac ggaaatttgg tttaactgca taacatgact cattaatttc aaccaaaatt
      781 ctttttctga ttcatcagtt gtttgcgcta aatgcttatg aacaaattca ttagtcaaaa
      841 ctgaagattt tgctagatca gcattgataa ccgagttgag aacatccatc attcgttcaa
      901 gcatttcact ataattatct tcatccggca aattcaaata atcagctaac cgttcataca
      961 tcaattcaat tctatcgact gtttcttctc tcaaatcaat tttatccatg tcacacctca
     1021 cttccagaat tgccaccatt ttcgattttt taattcttga ttttctagta acaactgatc
     1081 gtttttttgt tgctgaagca aagtcaattt ttgttggtca cgaatcattt ccgttaattc
     1141 agaaatatgc ctatcttttt ccgctaattg ttcacgcaaa aattcatttt ctttttctaa
     1201 cgggaaatca ttgcctgcat cattgaccgg taaatcacca gtcaattgac caccttttga
     1261 ccgataaatt gaccgcacaa caccaatcaa ttccttgtct aacatgataa ccccattatc
     1321 tttataccga gcaaggtcat aacctgcatt gaccagttga ttgcgcactg tatttttaga
     1381 tatacccaac tcatcagcaa ggttttttat ggtcattttt tctggcaaat cagtcattat
     1441 cttctccgtt actttcagct accccataaa catatttaac agcatgctta gggataatga
     1501 ttggggaatc aattttatta tttttcaaaa tcaactcata ctgcgttaca tcaagtaact
     1561 taccggacat ttttttgcta tccaaaaaaa caacgacaac gttatcacct gttaaattca
     1621 ccaaccaatt tttcttacca aaatgctttt gtttttctgc cattcttatt cctcctccgt
     1681 tacatctaac ccttgaagcc aagtgtctaa ttcttttttc aaaacatctg ctgattccga
     1741 aaatgtttct cgtaaatgat tcgtcaactc atcattttga ctttctcttt tcaaaatatc
     1801 tctcaatttg tatttcattc tacgctctaa aaacccccac atttcagggt tagcaatcag
     1861 tccaaaaatc atcaccttat catttgtttt tacatcaagt ggtagaaaat gagggctagc
     1921 aaaactattt aaactttcat gaaccattgc atgccaatct gttgctttcc cacgccttaa
     1981 ctgcaattcc agtcgccacc aagtttctat ttctggtggc acaattttac gcttggtttc
     2041 ctgttccaat tttttgttgt atagccgaat ctggcgttcg ctggcacgac tgccccaata
     2101 agctgtttcc agcttcccag accgcccata aattggcttg aaagaaacag gatcaaccac
     2161 tcgatattgt gtaataaact catcaggcac atcgataata tcgcaagcaa tatccgcacg
     2221 tgagaaatgt ggttctagaa ataaatcatg aatgaaattt ttcattgaac tagctaaaaa
     2281 atgaccaatc ttattcgggt taaaatcaat ccgccctttg ccatcttgcc atttcaaaat
     2341 ctcaatataa gcaatatttt cttcgtattg gtctaataat tgccagccgt tattcccaac
     2401 cgcttttaaa tagccattgc cttcattcac ccgcattaat tgctcaaaat ctaaaatcaa
     2461 cacatcattt tgagtgtgat aataaatatt ttccttcagt tttccaacga tagtaattcg
     2521 gtcaattgac cactgcattt ttaagggggt gtacatattt tgtacattta accgcctgtt
     2581 agatagggct gttaaatttt cccactcatt tacgattatg ccatttttac tcaaattttg
     2641 ttcctcctca aagaaaaaga gacttctgga aagaattttc aaaagttcac gtaactctta
     2701 aaaattcatt accaaaaaat ctctagtctt gaagaaatct aaaaatattc gtataatgat
     2761 taagaagtta cggagctagt gcgattagtt tccgtaaagg tcgagaacgt tggtagcgtt
     2821 gctcgacttt atttttttgc tcttttttca gtttatttat ttgataactc aataatagca
     2881 cttctcttta gctatgcaaa tatccaaaaa cataaaaccg caccctttga aaagggcgcc
     2941 cccaaacttc gctaacgcta ggttggccaa aaaatggact ggccattttt tagcaaatgt
     3001 cagcttaata ggctagtggt ttagccgtca actccttatc ctcggcacaa accgcctccg
     3061 gtaccgttga ctgcacatcg taactaccac tcgatctcat cttcagaacg ctctaattta
     3121 cgctgtgaga cgttttgacg ataaaataag gttttctcct gctctaacac ttctaattcc
     3181 tcagaaagcc ctatatcctt ttctgcaaga ccaaaacgga tagacaaacg agtgatcgat
     3241 ttttgaaatg cgttttttaa tcgctctaaa cgctggcgta aagagcgatt ttcttctttc
     3301 agctttttat tttccacttg taaatctgct aattgttttc taccagacaa atgacgctct
     3361 tcttccaatg tagctacata ctcatttaat tctgtatttt gctcaagcat ctgtaaatat
     3421 tgctcactca tgttatcagc atttctcttg gcatttgttg ctctcgtagc tcgttgatac
     3481 aaatcaacaa aatcattccc agataaatga tacgaaccat caggaagcct cttgaaactt
     3541 tctaaaggaa ccatatcttt ttggaaaatg accgccatct ctttttttac attcagcata
     3601 tttttcttct cttcttcaat cttcgctctc tcagaagcca tcagagcctt atcacgctcg
     3661 ttttcttctc tttgcctata aatatacctc aactcatcag aaacgctctc acgctctttt
     3721 acagccgttt ggcgcaattc agaaatttca ctcatgattt ctttgtattc gtgaatatct
     3781 ttaattttgt tggtaccgac aatatccctt ttccaaccgt aatcattcat taatcgttct
     3841 atagagtcaa cttcttgatt tctaaaatta ttgaaaagca ctcgaccatt atctttatca
     3901 gcgtgtatcc cttgttgaac cagtgcttta ttaaagctcg gctgcttttg aacaccccgt
     3961 ttataacctt cagcaaccgg cacaatattc aagtgcaggt gcggacttat ttcgtcatta
     4021 tgaataacag cattataaac agccaaatta gggtttctct cttgaaactc cttgtaatac
     4081 tgaaccaaaa ttttattggc aatcactcga ttttgttcag cttgttgttt cgatatgcca
     4141 gtagaagaac catctgctcg atttgtctgg aaatcatcta aaatgcctat ttgcacaata
     4201 aattctcgtt gaggttccaa ctttttatcc ttgcgcactt tcgctaaata gtcctcgatt
     4261 tttctatcgg ctcttttttg tttcgcatta tatttttcta ccacttcgcc aaacaattcc
     4321 tcatatttat ctgctagatt cgtctgctct aaataaatat tttcatccga tttcgtg
//
