LOCUS       NZ_CP019212             4376 bp    DNA     circular CON 14-JAN-2024
DEFINITION  Enterococcus faecium strain 2014-VREF-41 plasmid p41-4, complete
            sequence.
ACCESSION   NZ_CP019212
VERSION     NZ_CP019212.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN06186500
            Assembly: GCF_002007625.1
KEYWORDS    RefSeq.
SOURCE      Enterococcus faecium
  ORGANISM  Enterococcus faecium
            Bacteria; Bacillota; Bacilli; Lactobacillales; Enterococcaceae;
            Enterococcus.
REFERENCE   1  (bases 1 to 4376)
  AUTHORS   Kim,H.M., Chung,D.R., Cho,S.Y., Huh,K., Kang,C.I. and Peck,K.R.
  TITLE     Emergence of vancomycin-resistant Enterococcus faecium ST1421
            lacking the pstS gene in Korea
  JOURNAL   Eur J Clin Microbiol Infect Dis 39 (7), 1349-1356 (2020)
   PUBMED   32128641
REFERENCE   2  (bases 1 to 4376)
  AUTHORS   Kim,H.M. and Chung,D.R.
  TITLE     Direct Submission
  JOURNAL   Submitted (27-DEC-2016) Infectious Diseases, Samsung Medical Center
            (SMC), Ilwon-Ro 81, Gangnam-Gu, Seoul 06351, Korea, Republic of
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method :: GS De Novo Assembler v. OCT-2016
            Genome Representation             :: Full
            Expected Final Version            :: No
            Genome Coverage                   :: 346.4x
            Sequencing Technology             :: PacBio
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 01/14/2024 07:57:06
            Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline
            (PGAP)
            Annotation Method :: Best-placed reference protein set; GeneMarkS-2+
            Annotation Software revision      :: 6.6
            Features Annotated                :: Gene; CDS; rRNA; tRNA; ncRNA
            Genes (total)                     :: 3,259
            CDSs (total)                      :: 3,169
            Genes (coding)                    :: 3,035
            CDSs (with protein)               :: 3,035
            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)              :: 134
            CDSs (without protein)            :: 134
            Pseudo Genes (ambiguous residues) :: 0 of 134
            Pseudo Genes (frameshifted)       :: 47 of 134
            Pseudo Genes (incomplete)         :: 75 of 134
            Pseudo Genes (internal stop)      :: 33 of 134
            Pseudo Genes (multiple problems)  :: 17 of 134
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP019212.1.
            Bacteria and source DNA available from Chung, Doo Ryeon. Annotated
            using prokka 1.11 from http://www.vicbioinformatics.com.
            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..4376
                     /organism="Enterococcus faecium"
                     /mol_type="genomic DNA"
                     /strain="2014-VREF-41"
                     /isolation_source="Rectal swab"
                     /host="Homo sapiens"
                     /db_xref="taxon:1352"
                     /plasmid="p41-4"
                     /geo_loc_name="South Korea"
                     /lat_lon="37.57 N 126.98 E"
                     /collection_date="2014-04"
                     /collected_by="Kim Hye Mee"
     gene            339..1313
                     /locus_tag="BVA20_RS16880"
                     /old_locus_tag="BVA20_500001"
     CDS             339..1313
                     /locus_tag="BVA20_RS16880"
                     /old_locus_tag="BVA20_500001"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002342725.1"
                     /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_044384214.1"
                     /translation="MSKKGTIINEWEKLTAPSNRRLKYQSLTLPLKMQWSIDRITIVGK
                     LKENIYYHTPNDVLILNFEQLMRLNEGNGYLRSVSNNGWQLLDQHEENIAYIEILKWQE
                     GKGRIDFNPNKISQFLASSMKNFIHDLFIEPHFSRADIACDIIDVPDEFITQYRVVDPV
                     SFKPIYGRSGKLETAYWGSRASERQIRMYNKKLEQERKRKIVPPEITTWWRLELQLRRG
                     KATDWHEMVHESLDSFASPHYFPPNTKVTERIMVKGLLYDHSEWGNLAKNTKKKYRDLL
                     KQESQNDELTNHLRETFAESADDLKKELDTWLLGLDVTEEEEK"
                     /name="replication initiation factor domain-containing
                     protein"
     gene            1310..1543
                     /locus_tag="BVA20_RS16885"
                     /old_locus_tag="BVA20_500002"
     CDS             1310..1543
                     /locus_tag="BVA20_RS16885"
                     /old_locus_tag="BVA20_500002"
                     /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_002303408.1"
                     /translation="MTEKQKYFGKKNWLVNLTGDYVVVVFLDSKKMSGKLLDVTQYELI
                     LKNNKIDSPIIIPKHAVKYIYAVAESSGEAND"
                     /name="hypothetical protein"
     gene            1536..1955
                     /locus_tag="BVA20_RS16890"
                     /old_locus_tag="BVA20_500003"
     CDS             1536..1955
                     /locus_tag="BVA20_RS16890"
                     /old_locus_tag="BVA20_500003"
                     /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_077974495.1"
                     /translation="MTDLSEKMTIKNLADELGISKNTVRNQLVNAGYDLARYKDNGVIM
                     LDKELIGVVRSIYRSKGGQLTGDLPVNDAGNDFPLEKENEFLREQLAEKDRHISELTEM
                     IRDQQKLTLLQQQKNDQLLLENQELKNRKWWQFWK"
                     /name="hypothetical protein"
     gene            1964..2272
                     /locus_tag="BVA20_RS16895"
                     /old_locus_tag="BVA20_500004"
     CDS             1964..2272
                     /locus_tag="BVA20_RS16895"
                     /old_locus_tag="BVA20_500004"
                     /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_002333831.1"
                     /translation="MDKIDLREETVDRIELMYERLADYLNLPDEDNYSEMLERIMDVLN
                     SVINADLAKSSVLTNEFVHKHLAQTTDESEKEFWLKLMSHVMQLNQISVINSKEKEM"
                     /name="hypothetical protein"
     gene            2276..2638
                     /locus_tag="BVA20_RS16900"
                     /old_locus_tag="BVA20_500005"
     CDS             2276..2638
                     /locus_tag="BVA20_RS16900"
                     /old_locus_tag="BVA20_500005"
                     /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_045135959.1"
                     /translation="MGMTLADIKAQEEKLKKEQAKLRQQKKRLIEKENAAMGKALRKRF
                     GFETFADFERWLSSISDDQQHEKTVDNEWLADEKSAPSERDYPDESDDLFGVIPNKKSQ
                     MSESKFTSIFNDVNLR"
                     /name="hypothetical protein"
     gene            2860..4266
                     /locus_tag="BVA20_RS16905"
                     /old_locus_tag="BVA20_500006"
     CDS             2860..4266
                     /locus_tag="BVA20_RS16905"
                     /old_locus_tag="BVA20_500006"
                     /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_077974496.1"
                     /translation="MGFSISFKKGTKNTSISHNNRELTDRQKTNDWHKHIDFTKSDENI
                     YLEQTNLADKYEELFGEVVEKYNAKQKRADRKIEDYLAKVRKDKKLEPQREFIVQIGIL
                     DDFQTNRADGSSTGISKQQAEQNRVIANKILVEYFKEFKERNPNLSVYNAVIHNDEVSP
                     HLHLNIVPVAEGYKRGVQKQPSFNKALQQQGLRADKENGRVIWNNFRNQEVESIERLMA
                     DFGWERELVGTNKIKDVHEYKEIMSEISELRQTAVKERESVSDELRYISRQREENEREK
                     ALVASERVKIEEEKKNMLNVKKEMAVIFQKDMVPLESFKRLPDGSYHLSGNDFVDLYQR
                     ATRATNAKRNADNMSEQYLQMLEQNTELNEYVATLEEERHLSGRKQLADLQVENKKLKE
                     ENRSLRQRLERLKNAFQKSITRLSIRFGLAEKDMGLSEELEVLEQEKTLFYRQNVSQRK
                     LERSEDEIEW"
                     /name="plasmid recombination protein"
     Typing          364..1294
                     /name="rep_cluster_943"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="91.854"
                     /coverage="98.0"
                     /evalue="0.0"
     Typing          2861..4263
                     /name="MOBV"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="95.513"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 tttttggcca acctagcgtt agcgaagttt gggggcgccc ttttcaaagg gtgcggtttt
       61 attttttgga tatttgcata gctaaagaga agtgctatta ttgagttatc aaataaataa
      121 actgaaaaaa gagcaaaaaa ataaagtcga gcaacgctgg acacgttctc gacctttacg
      181 gaaactaatc gcactagctc cgtaacttct taatcattat acgaatattt ttagatttct
      241 tcaagactag agattttttg gtaatgaatt tttaagagtt acgtgaactt ttgaaaattc
      301 tttccagaag tctctttttc tttgaggagg aacaaaattt gagtaaaaaa ggcacgatca
      361 taaatgagtg ggaaaaatta acagccccct ctaacaggcg gttaaagtat caaagtttga
      421 cccttccctt aaaaatgcag tggtcaattg accgaattac catagtcgga aaactgaaag
      481 aaaatattta ttatcacact ccaaatgatg tgttgatttt aaattttgaa cagcttatgc
      541 gcctaaatga aggtaatggt tatttaagat ctgttagtaa taatggttgg cagttgttag
      601 accaacatga agagaatatt gcttatattg aaattttaaa atggcaagag gggaaagggc
      661 gtatagactt caatccgaat aagattagtc aattcttagc tagttccatg aaaaatttta
      721 ttcatgattt gtttatcgaa cctcactttt cacgtgcgga tattgcttgc gacattatcg
      781 atgtacctga tgagtttatt acacaatatc gggtagttga tcctgtgtct tttaaaccaa
      841 tttatgggcg ttctggtaag ttagaaacgg catattgggg tagtcgtgcc agtgaacgac
      901 aaattcggat gtataataaa aaactggaac aagaaagaaa acgtaaaatt gttccgccgg
      961 aaataacgac atggtggcga ctagaattgc agttacgaag gggaaaagca actgattggc
     1021 atgagatggt tcatgaaagt ttggatagct ttgctagtcc acattatttt ccgccaaata
     1081 ctaaagttac tgaacggatt atggtgaaag gtttgcttta tgatcattct gagtggggaa
     1141 atctagctaa gaatacaaag aaaaaataca gggatttgtt gaagcaagaa agtcaaaatg
     1201 atgaattgac gaatcatttg cgagaaacct ttgcggaatc ggcagacgat ttaaaaaaag
     1261 aattagacac atggcttcta gggctagacg taacagagga ggaagaaaaa tgacagaaaa
     1321 acaaaagtat tttggtaaga aaaattggtt ggtaaattta acaggtgatt acgttgtggt
     1381 tgtttttttg gatagcaaaa aaatgtccgg taagttactt gatgtaacgc aatatgaatt
     1441 gattttgaaa aataataaaa ttgactctcc gattattatc cctaagcacg ccgttaaata
     1501 tatttatgcg gtagctgaaa gtagtggaga agctaatgac tgatttgtca gaaaagatga
     1561 ccataaaaaa tcttgctgac gaattgggta tatctaaaaa tacagtgcgc aatcaactgg
     1621 tcaatgcagg ttatgacctt gctcggtata aagataatgg ggttatcatg ttagacaagg
     1681 aattgattgg tgttgtgcgg tcaatttatc ggtcaaaagg tggtcaattg actggtgatt
     1741 taccggtcaa tgatgcaggc aatgatttcc cgttagaaaa agaaaatgaa tttttgcgtg
     1801 aacaattagc ggaaaaagat aggcatattt ctgaattaac ggaaatgatt cgtgaccaac
     1861 aaaaattgac tttgcttcag caacaaaaaa acgatcagtt gttactagaa aatcaagaat
     1921 taaaaaatcg aaaatggtgg caattctgga agtgaggtgt gacatggata aaattgattt
     1981 gagagaagaa acagtcgata gaattgaatt gatgtatgaa cggttagctg attatttgaa
     2041 tttgccggat gaagataatt atagtgaaat gcttgaacga attatggatg ttctcaactc
     2101 ggttatcaat gctgatctag caaaatcttc agttttgact aatgaatttg ttcataagca
     2161 tttagcgcaa acaactgatg aatcagaaaa agaattttgg ttgaaattaa tgagtcatgt
     2221 tatgcagtta aaccaaattt ccgttattaa ttccaaagaa aaggagatgt agtttatggg
     2281 aatgacttta gcagatatta aagcgcaaga agaaaaatta aaaaaagaac aagcgaaact
     2341 tcgccaacag aaaaaacgct tgattgagaa agaaaatgct gcaatgggca aggctcttcg
     2401 caagcgtttt gggtttgaaa cttttgctga ttttgagcgg tggttatcgt caatttctga
     2461 cgatcagcaa cacgaaaaaa cagtggataa tgagtggctt gctgatgaaa aatcagcgcc
     2521 aagcgaacga gattatcccg atgaatctga cgacttattc ggagtgatac cgaataagaa
     2581 aagtcagatg agtgagagta aatttacgtc aatatttaat gacgtgaatt tacgataagc
     2641 gattattttg cgtgaagcaa aataaagcat aaaaggagtt gatagcgtga tacgctttcg
     2701 gctccttttt tcgttgtcac ttgtgacagc gaaaaccctc ggagagcgtt tggaattgtg
     2761 acagccatgt cacaattagg aaaatgttac tctttgacaa agagtaacag aaaggtttac
     2821 aatcttttta ttagcgacag cgcgaaggag ggttttaact tggggtttag tatttcattt
     2881 aaaaaaggaa cgaagaatac aagtatttct cataataatc gtgagttaac tgatcgccag
     2941 aaaaccaatg attggcataa gcatattgac ttcacgaaat cggatgaaaa tatttattta
     3001 gagcagacga atctagcaga taaatatgag gaattgtttg gcgaagtggt agaaaaatat
     3061 aatgcgaaac aaaaaagagc cgatagaaaa atcgaggact atttagcgaa agtgcgcaag
     3121 gataaaaagt tggaacctca acgagaattt attgtgcaaa taggcatttt agatgatttc
     3181 cagacaaatc gagcagatgg ttcttctact ggcatatcga aacaacaagc tgaacaaaat
     3241 cgagtgattg ccaacaaaat tttagttgaa tatttcaaag aatttaaaga acggaatcct
     3301 aatttatccg tctacaatgc tgttattcat aatgacgaag taagtccgca cctgcatttg
     3361 aatattgttc ctgttgctga agggtataaa cggggtgttc aaaagcaacc aagttttaac
     3421 aaagccttgc aacagcaggg tttacgagca gataaagaga atggtcgagt gatttggaat
     3481 aattttagga atcaggaagt tgagtcaatt gaacgtttga tggcagattt tggttgggag
     3541 cgtgagttag tcggtactaa caaaatcaaa gatgttcacg aatataaaga aatcatgagc
     3601 gagatttcag aattgcgtca aacggccgta aaagagcgtg agagcgtttc tgatgagttg
     3661 aggtatattt ctaggcaaag agaagaaaat gagcgagaaa aggctctggt ggcttctgag
     3721 agagtgaaga ttgaagaaga gaagaaaaat atgctgaatg taaaaaaaga gatggcggtc
     3781 attttccaaa aagatatggt tcctttagaa agtttcaaga ggcttcctga tggttcgtat
     3841 catttatctg ggaatgattt tgttgatttg tatcaacgag ctacgagagc aacaaatgcc
     3901 aagagaaatg ctgataacat gagtgagcaa tatttacaga tgcttgagca aaatacagaa
     3961 ttaaatgagt atgtagctac attggaagaa gagcgtcatt tgtctggtag aaaacaatta
     4021 gcagatttac aagtggaaaa taaaaagctg aaagaagaaa atcgctcttt acgccagcgt
     4081 ttagagcgat taaaaaacgc atttcaaaaa tcgatcactc gtttgtctat ccgttttggt
     4141 cttgcagaaa aggatatggg gctttctgag gaattagaag tgttagagca ggagaaaacc
     4201 ttattttatc gtcaaaacgt ctcacagcgt aaattagagc gttctgaaga tgagatcgag
     4261 tggtagttac gatgtgcagt caacggtacc ggaggcggtt tgtgccgagg ataaggagtt
     4321 gacggctaaa ccactaatcc ctgaagctga catttgctaa aaaatggcaa gtccat
//
