LOCUS       NZ_CP131816             4377 bp    DNA     circular CON 25-APR-2024
DEFINITION  Enterococcus faecium strain 2016C08-243 plasmid p2016C08-243-7,
            complete sequence.
ACCESSION   NZ_CP131816
VERSION     NZ_CP131816.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN36766203
            Assembly: GCF_038439085.1
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  JOURNAL   Unpublished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_038439085.1-RS_2024_04_24
            Annotation Date                   :: 04/24/2024 15:05:45
            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)                     :: 3,281
            CDSs (total)                      :: 3,185
            Genes (coding)                    :: 3,018
            CDSs (with protein)               :: 3,018
            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)              :: 167
            CDSs (without protein)            :: 167
            Pseudo Genes (ambiguous residues) :: 0 of 167
            Pseudo Genes (frameshifted)       :: 59 of 167
            Pseudo Genes (incomplete)         :: 101 of 167
            Pseudo Genes (internal stop)      :: 39 of 167
            Pseudo Genes (multiple problems)  :: 29 of 167
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP131816.1.
            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="2016C08-243"
                     /isolation_source="blood"
                     /host="Homo sapiens"
                     /db_xref="taxon:1352"
                     /plasmid="p2016C08-243-7"
                     /geo_loc_name="Taiwan"
                     /collection_date="2016"
                     /collected_by="NHRI"
     gene            complement(join(3100..4377,1..129))
                     /locus_tag="Q7582_RS16370"
                     /old_locus_tag="Q7582_16300"
     CDS             complement(join(3100..4377,1..129))
                     /locus_tag="Q7582_RS16370"
                     /old_locus_tag="Q7582_16300"
                     /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(351..713)
                     /locus_tag="Q7582_RS16375"
                     /old_locus_tag="Q7582_16305"
     CDS             complement(351..713)
                     /locus_tag="Q7582_RS16375"
                     /old_locus_tag="Q7582_16305"
                     /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(717..1025)
                     /locus_tag="Q7582_RS16380"
                     /old_locus_tag="Q7582_16310"
     CDS             complement(717..1025)
                     /locus_tag="Q7582_RS16380"
                     /old_locus_tag="Q7582_16310"
                     /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(1034..1453)
                     /locus_tag="Q7582_RS16385"
                     /old_locus_tag="Q7582_16315"
     CDS             complement(1034..1453)
                     /locus_tag="Q7582_RS16385"
                     /old_locus_tag="Q7582_16315"
                     /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(1446..1679)
                     /locus_tag="Q7582_RS16390"
                     /old_locus_tag="Q7582_16320"
     CDS             complement(1446..1679)
                     /locus_tag="Q7582_RS16390"
                     /old_locus_tag="Q7582_16320"
                     /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(1682..2650)
                     /locus_tag="Q7582_RS16395"
                     /old_locus_tag="Q7582_16325"
     CDS             complement(1682..2650)
                     /locus_tag="Q7582_RS16395"
                     /old_locus_tag="Q7582_16325"
                     /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(1690..2567)
                     /name="rep_cluster_943"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="83.973"
                     /coverage="97.0"
                     /evalue="0.0"
     Typing          complement(2..129)
                     /name="MOBV"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="93.023"
                     /coverage="96.0"
                     /evalue="4.22e-18"
     Typing          complement(3104..4377)
                     /name="MOBV"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="91.765"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 ttcatccgat ttcgtgaagt caatatgctt atgccaatca ttggttttct ggcgatcagt
       61 taactcacga ttattatgag aaatacttgt attcttcgtt ccttttttaa atgaaatact
      121 aaaccccaag ttaaaaccct ccttcgcgct gtcgctaata aaaagattgt aaacctttct
      181 gttactcttt gtcaaagagt aacattttcc taattgtgac atggctgtca caattccaaa
      241 tgctctccga gggtattcgc tgtcacaagt gacaacgaaa aaaggagccg aaagcgtgtc
      301 acgctctcaa ctccttttac gctttatttt gcttcacgca aaataatcgc ttatcgtaaa
      361 ttcacgtcat taaatattga cgtaaattta ctctcactca tctgactttt cttattcggt
      421 atcactccga ataagccgtc agattcatcg ggataatctc gttcgcttgg cgctgatttt
      481 tcatcagcaa gccactcatt atccactgat ttttcgtgtt gctgatcgtc agaaatcgac
      541 gatagccacc gctcaaaatc agcaaaagtt tcaaacccaa aacgcttgcg aagagccttg
      601 cccattgcag cattttcttt ctcaatcaag cgttttttct gttggcgaag tttcgcttgt
      661 tcttttttta atttttcttc ttgcgcttta atatctgcta aagtcattcc cataaactac
      721 atctcctttt ctttggaatt aataacggaa atttggttta actgcataac atgactcatt
      781 aatttcaacc aaaattcttt ttctgattca tcagttgttt gcgctaaatg cttatgaaca
      841 aattcattag tcaaaactga agattttgct agatcagcat tgataaccga gttgagaaca
      901 tccatcattc gttcaagcat ttcactataa ttatcttcat ccggcaaatt caaataatca
      961 gctaaccgtt catacatcaa ttcaattcta tcgactgttt cttctctcaa atcaatttta
     1021 tccatgtcac acctcacttc cagaattgcc accattttcg attttttaat tcttgatttt
     1081 ctagtaacaa ctgatcgttt ttttgttgct gaagcaaagt caatttttgt tggtcacgaa
     1141 tcatttccgt taattcagaa atatgcctat ctttttccgc taattgttca cgcaaaaatt
     1201 cattttcttt ttctaacggg aaatcattgc ctgcatcatt gaccggtaaa tcaccagtca
     1261 attgaccacc ttttgaccga taaattgacc gcacaacacc aatcaattcc ttgtctaaca
     1321 tgataacccc attatcttta taccgagcaa ggtcataacc tgcattgacc agttgattgc
     1381 gcactgtatt tttagatata cccaactcat cagcaaggtt ttttatggtc attttttctg
     1441 gcaaatcagt cattatcttc tccgttactt tcagctaccc cataaacata tttaacagca
     1501 tgcttaggga taatgattgg ggaatcaatt ttattatttt tcaaaatcaa ctcatactgc
     1561 gttacatcaa gtaacttacc ggacattttt ttgctatcca aaaaaacaac gacaacgtta
     1621 tcacctgtta aattcaccaa ccaatttttc ttaccaaaat gcttttgttt ttctgccatt
     1681 cttattcctc ctccgttaca tctaaccctt gaagccaagt gtctaattct tttttcaaaa
     1741 catctgctga ttccgaaaat gtttctcgta aatgattcgt caactcatca ttttgacttt
     1801 ctcttttcaa aatatctctc aatttgtatt tcattctacg ctctaaaaac ccccacattt
     1861 cagggttagc aatcagtcca aaaatcatca ccttatcatt tgtttttaca tcaagtggta
     1921 gaaaatgagg gctagcaaaa ctatttaaac tttcatgaac cattgcatgc caatctgttg
     1981 ctttcccacg ccttaactgc aattccagtc gccaccaagt ttctatttct ggtggcacaa
     2041 ttttacgctt ggtttcctgt tccaattttt tgttgtatag ccgaatctgg cgttcgctgg
     2101 cacgactgcc ccaataagct gtttccagct tcccagaccg cccataaatt ggcttgaaag
     2161 aaacaggatc aaccactcga tattgtgtaa taaactcatc aggcacatcg ataatatcgc
     2221 aagcaatatc cgcacgtgag aaatgtggtt ctagaaataa atcatgaatg aaatttttca
     2281 ttgaactagc taaaaaatga ccaatcttat tcgggttaaa atcaatccgc cctttgccat
     2341 cttgccattt caaaatctca atataagcaa tattttcttc gtattggtct aataattgcc
     2401 agccgttatt cccaaccgct tttaaatagc cattgccttc attcacccgc attaattgct
     2461 caaaatctaa aatcaacaca tcattttgag tgtgataata aatattttcc ttcagttttc
     2521 caacgatagt aattcggtca attgaccact gcatttttaa gggggtgtac atattttgta
     2581 catttaaccg cctgttagat agggctgtta aattttccca ctcatttacg attatgccat
     2641 ttttactcaa attttgttcc tcctcaaaga aaaagagact tctggaaaga attttcaaaa
     2701 gttcacgtaa ctcttaaaaa ttcattacca aaaaatctct agtcttgaag aaatctaaaa
     2761 atattcgtat aatgattaag aagttacgga gctagtgcga ttagtttccg taaaggtcga
     2821 gaacgttggt agcgttgctc gactttattt ttttgctctt ttttcagttt atttatttga
     2881 taactcaata atagcacttc tctttagcta tgcaaatatc caaaaacata aaaccgcacc
     2941 ctttgaaaag ggcgccccca aacttcgcta acgctaggtt ggccaaaaaa tggactggcc
     3001 attttttagc aaatgtcagc ttaataggct agtggtttag ccgtcaactc cttatcctcg
     3061 gcacaaaccg cctccggtac cgttgactgc acatcgtaac taccactcga tctcatcttc
     3121 agaacgctct aatttacgct gtgagacgtt ttgacgataa aataaggttt tctcctgctc
     3181 taacacttct aattcctcag aaagccctat atccttttct gcaagaccaa aacggataga
     3241 caaacgagtg atcgattttt gaaatgcgtt ttttaatcgc tctaaacgct ggcgtaaaga
     3301 gcgattttct tctttcagct ttttattttc cacttgtaaa tctgctaatt gttttctacc
     3361 agacaaatga cgctcttctt ccaatgtagc tacatactca tttaattctg tattttgctc
     3421 aagcatctgt aaatattgct cactcatgtt atcagcattt ctcttggcat ttgttgctct
     3481 cgtagctcgt tgatacaaat caacaaaatc attcccagat aaatgatacg aaccatcagg
     3541 aagcctcttg aaactttcta aaggaaccat atctttttgg aaaatgaccg ccatctcttt
     3601 ttttacattc agcatatttt tcttctcttc ttcaatcttc gctctctcag aagccatcag
     3661 agccttatca cgctcgtttt cttctctttg cctataaata tacctcaact catcagaaac
     3721 gctctcacgc tcttttacag ccgtttggcg caattcagaa atttcactca tgatttcttt
     3781 gtattcgtga atatctttaa ttttgttggt accgacaata tcccttttcc aaccgtaatc
     3841 attcattaat cgttctatag agtcaacttc ttgatttcta aaattattga aaagcactcg
     3901 accattatct ttatcagcgt gtatcccttg ttgaaccagt gctttattaa agctcggctg
     3961 cttttgaaca ccccgtttat aaccttcagc aaccggcaca atattcaagt gcaggtgcgg
     4021 acttatttcg tcattatgaa taacagcatt ataaacagcc aaattagggt ttctctcttg
     4081 aaactccttg taatactgaa ccaaaatttt attggcaatc actcgatttt gttcagcttg
     4141 ttgtttcgat atgccagtag aagaaccatc tgctcgattt gtctggaaat catctaaaat
     4201 gcctatttgc acaataaatt ctcgttgagg ttccaacttt ttatccttgc gcactttcgc
     4261 taaatagtcc tcgatttttc tatcggctct tttttgtttc gcattatatt tttctaccac
     4321 ttcgccaaac aattcctcat atttatctgc tagattcgtc tgctctaaat aaatatt
//
