LOCUS       NZ_CP019211             5850 bp    DNA     circular CON 14-JAN-2024
DEFINITION  Enterococcus faecium strain 2014-VREF-41 plasmid p41-3, complete
            sequence.
ACCESSION   NZ_CP019211
VERSION     NZ_CP019211.1
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 5850)
  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 5850)
  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
            CP019211.1.
            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..5850
                     /organism="Enterococcus faecium"
                     /mol_type="genomic DNA"
                     /strain="2014-VREF-41"
                     /isolation_source="Rectal swab"
                     /host="Homo sapiens"
                     /db_xref="taxon:1352"
                     /plasmid="p41-3"
                     /geo_loc_name="South Korea"
                     /lat_lon="37.57 N 126.98 E"
                     /collection_date="2014-04"
                     /collected_by="Kim Hye Mee"
     gene            join(5328..5850,1..623)
                     /locus_tag="BVA20_RS16845"
     CDS             join(5328..5850,1..623)
                     /locus_tag="BVA20_RS16845"
                     /inference="COORDINATES: ab initio prediction:GeneMarkS-2+"
                     /GO_function="GO:0008234 - cysteine-type peptidase activity
                     [Evidence IEA]"
                     /GO_process="GO:0006508 - proteolysis [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GeneMarkS-2+."
                     /codon_start=1
                     /transl_table=11
                     /product="C47 family peptidase"
                     /protein_id="WP_010729425.1"
                     /translation="MKPKKKIYLGLLFSLMIGIFSIGITNTYASENSNFNINSQPIEEQ
                     AINFAKTDFEHSITSILLMENNTETDINYTLGSPFKMLDGENTANSSIFFPVFSDADNT
                     IKYIYTVKKNTNGEYSGSISQFLAKELQNLVDSNITDTTLFFQDNSIYYSDNGQIKLLW
                     KSPLSTEKNGVSSFTEKNDLISVNIKNKIKNFSKKQNFPAVKRVKSVSSGDNFIMINWR
                     IAETQTSFPWCAAYVEAAILCNKTDVHATSARAIMHYTYPNLNNSQIESKSLNQDQIIK
                     YANYCGVYPKKVARILNLSEVQTQLRKGNAIYMGTAGYGNYSNSRHALALFGWVNQGGY
                     QTYYVWNPWYNYPTVISANAGPVTIPVPGGGFTWDNTITNW"
                     /name="C47 family peptidase"
     gene            596..1039
                     /locus_tag="BVA20_RS16850"
                     /old_locus_tag="BVA20_400002"
     CDS             596..1039
                     /locus_tag="BVA20_RS16850"
                     /old_locus_tag="BVA20_400002"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002334327.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_002318191.1"
                     /translation="MGQYHYKLVNKPIALVMGLVLVLFLTSCSKKQEIQKTDLIPFLGT
                     WQTKDHSERLVITNLNTSKNIEQYTILVKENNHKIQIIDKNLNINEQVFIYKATNNLLT
                     LRSNKKQLDYTFSLDSPKKLVFILTTNDGTEGTAKPIEFFKAD"
                     /name="hypothetical protein"
     gene            1296..>1486
                     /locus_tag="BVA20_RS16855"
                     /pseudo=""
     CDS             1296..>1486
                     /locus_tag="BVA20_RS16855"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_016628695.1"
                     /note="frameshifted; incomplete; partial in the middle of a
                     contig; missing C-terminus; Derived by automated
                     computational analysis using gene prediction method:
                     Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="plasmid mobilization relaxosome protein MobC"
                     /name="plasmid mobilization relaxosome protein MobC"
     gene            2152..3129
                     /locus_tag="BVA20_RS16860"
                     /old_locus_tag="BVA20_400003"
     CDS             2152..3129
                     /locus_tag="BVA20_RS16860"
                     /old_locus_tag="BVA20_400003"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002338009.1"
                     /GO_function="GO:0003887 - DNA-directed DNA polymerase
                     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 protein"
                     /protein_id="WP_002338009.1"
                     /translation="MANEIVKYHHELNTIPLRKFTSVEMNLFFSIVSRMRDVGDKKVQF
                     TFEQLKDLSNYKATANVRFIDDLETTYDKLMDLRFGRRSADGLQRERFVLFNQFKIDGK
                     ADIPFAEIQVHEKALPLLNNLEEWVRYSLQQFNELESSYSKTMFRLLKQYRTKGIAYFS
                     KEDFHELLDIPKSYRESDINKKIIKPIRQELTAIFKGLTIKKKYGKGRGKPVIGYQFTF
                     KPEIKKADDFNKHAPTKEEQNKALELVNQQIYSEKDPTSLQEKIKEQKRKLELLQQLEE
                     LERKQNNLNKENKEINEQIPDNNSDIPPELKKGLLDNLQNLFKE"
                     /name="replication initiation protein"
     gene            3139..3636
                     /locus_tag="BVA20_RS16865"
                     /old_locus_tag="BVA20_400004"
     CDS             3139..3636
                     /locus_tag="BVA20_RS16865"
                     /old_locus_tag="BVA20_400004"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002347002.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="DUF536 domain-containing protein"
                     /protein_id="WP_002347002.1"
                     /translation="MTDKTIKELADILGVSKDKVKYQLRKLPSNFTYKKGNIIYLKKEA
                     VTTITKVLSGNEPGNLPSELPDSLPTDYLLKEIETKNNHIEEKDRQIEKLQLALETQQK
                     LLDQQQQLTLQANQQIEKLQEQLQLTYTEESSENKSTTLSEETESIEKQSKTEKKWWQF
                     WQ"
                     /name="DUF536 domain-containing protein"
     gene            4012..4293
                     /locus_tag="BVA20_RS16870"
                     /old_locus_tag="BVA20_400005"
     CDS             4012..4293
                     /locus_tag="BVA20_RS16870"
                     /old_locus_tag="BVA20_400005"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000353845.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_000353845.1"
                     /translation="MDILVRNINPKIITRIDKRCQELTTKTGKKWSRNQYLKILIENDF
                     DHELMNYKKDQFDLLFEKFIAIQAENTNILNDYVHTNNQLIETLIGGI"
                     /name="hypothetical protein"
     gene            4295..4711
                     /locus_tag="BVA20_RS16875"
                     /old_locus_tag="BVA20_400006"
     CDS             4295..4711
                     /locus_tag="BVA20_RS16875"
                     /old_locus_tag="BVA20_400006"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001232859.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_001232860.1"
                     /translation="MRKTSVQKHVTLYPSHVDVLDSIIEKNPDVNNYSEAIRFLCMSYE
                     PATNTTTTSNQAKLNAMGKEISIMTEIMAEFADLYLKDTGVLIGTNSKVYQEVKEKIEN
                     QLNPSRRNQPKNRQKETNQTFTSGNFDPTNFLKR"
                     /name="hypothetical protein"
     Typing          2153..3129
                     /name="rep_cluster_1093"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 cttcctttac agaaaaaaat gatcttatat ccgtaaatat aaaaaataaa attaaaaatt
       61 tctctaaaaa acaaaatttt cctgcggtta aacgtgtaaa aagtgtctcc tccggagata
      121 actttattat gattaattgg cgtatagcag aaacccaaac aagttttccg tggtgtgctg
      181 cttacgtaga agctgctatc ttatgtaaca aaacagatgt acatgctact tcagctagag
      241 ccattatgca ttatacctat cctaatttaa acaacagtca aattgaatca aaaagtctta
      301 atcaagatca aataataaaa tatgcaaatt actgtggtgt ttatcctaaa aaagtagcac
      361 gaatactaaa cctttcagag gtccaaacac aactaagaaa aggaaatgcc atttatatgg
      421 gaactgctgg ttatggaaat tatagtaaca gccgtcatgc acttgcatta tttgggtggg
      481 tcaatcaagg tggttatcaa acttactatg tgtggaatcc ttggtataac tacccaactg
      541 taataagtgc aaatgcagga ccagttacaa ttcctgtacc tggaggtggt tttacttggg
      601 acaataccat tacaaattgg taaataaacc cattgcttta gttatgggtc tagtgttagt
      661 tcttttctta actagttgtt caaaaaaaca agaaatacaa aagactgatc tgattccttt
      721 tctaggaact tggcaaacta aagatcattc agaacgtcta gtaatcacta atttaaatac
      781 ttcaaaaaat atagaacaat ataccatctt agtaaaagag aacaatcata aaattcaaat
      841 cattgataaa aatttaaata taaatgaaca agttttcatt tacaaagcaa caaataattt
      901 actaacactg cgctctaata aaaaacaatt agattacact tttagtttgg attctccaaa
      961 aaagctcgta tttattttga caacgaatga tgggacagaa gggacagcta aaccaattga
     1021 attttttaaa gctgattgat gaatagttgt ttgatattac aaaacaataa tttcaccgaa
     1081 ggtgaaacaa gcgaaacttt acaaaaagtg gctagcattt gctagccttt tttgtattgt
     1141 ggagcgtggg ttttgagggg gattcaaggg ggagcttgcg cccctttgaa aagcggttat
     1201 ttgcaccaaa tacgtaggta tttggctagc aaatatagag cttgccaagc ccttttggtg
     1261 agctttactc attgtgcctt tttaggtaca atggtattgc gaacgatacg tccgtaggac
     1321 gtactgaaag ggtgggactt atgagcgaac aaaatcaaaa tttggctagc gatcattcta
     1381 aaaaatatac ctatcgatcc aagccaaaac aaatcagttt tcgagtgagc gaatctgaat
     1441 ttgcaaagct gaagctttgc aaatgagtgt gccggcttcc gtaaaaatac atatggctat
     1501 aatttgcgtt ttaaggcgtt ttaaacgttc tggtatataa tttataccaa aacaacttta
     1561 aaacgcctta gatctaattt tagaggtctt atagaacatt ttagggttgt tagggcttgc
     1621 cctgaccgcc tgtaaggcgc tttgagaaca agataagggt tttatactaa gactgtctta
     1681 aaacggctta aacaaacgct cagaactttt caaaggagtt ctttatgaac tgtttttaag
     1741 caaaggagcc tttaggcgac tgcgcagtat aatgtgagag cgtagcgatc acacattttt
     1801 agtgaccgta gggagcgagt ttcccagttt agaaaaattc gcgaacttgt ttgaggaaaa
     1861 aagcaggagt tttttaggcg ggaaattttg cctcctcttt tataatctct ttttaaacct
     1921 ctttttaaac ctctttaccg tcggctgtat gcttactctc ccaaggtgtg cagaatcttt
     1981 tgggggtctt tttgtctgtt tttaggggtc tttttgtctg tttttagggg tctttttgtc
     2041 tgtttttggg ggtctttttg tctgttttta ggggtcttta attaggggct tgacccctat
     2101 tagaaagctc tttataattt tgttaagtag ttaatcttga aggaggattt tatggcaaat
     2161 gaaattgtga aataccacca tgaattaaat acgattcctt tacgcaaatt tacgtcagta
     2221 gaaatgaatt tattcttctc tatagtatct agaatgcgtg acgtaggcga taaaaaagta
     2281 caatttacat tcgaacaatt aaaagattta agcaattata aagcaactgc aaatgttcga
     2341 ttcatagatg atttagaaac aacgtatgac aaattaatgg atttacgttt tggtagaaga
     2401 agtgctgacg gtttgcaacg tgaacgattt gttttattta atcaatttaa aatcgatgga
     2461 aaagctgata ttccttttgc tgaaatacaa gtccatgaga aagccttacc cttacttaat
     2521 aatcttgaag aatgggttcg atattctctc caacaattca atgaattaga aagcagttat
     2581 tccaaaacca tgtttagatt attaaaacaa tacagaacca aaggaattgc ctatttttca
     2641 aaagaagact ttcatgaatt acttgatatc cctaaaagtt atagagaaag tgatataaat
     2701 aaaaaaatta taaagcctat tcgccaagaa ctaaccgcaa tcttcaaagg tctgacaatc
     2761 aaaaagaaat acggaaaagg aagaggaaaa cctgtcattg gctatcaatt cacgtttaaa
     2821 cctgaaataa aaaaagcaga cgactttaat aaacacgcac caacaaaaga agaacaaaat
     2881 aaagctttag aactagttaa tcaacaaatt tactctgaaa aagaccccac ttcattacaa
     2941 gaaaaaatca aagaacagaa acgaaaatta gaacttttac aacaattaga agagctagaa
     3001 agaaaacaaa ataatctgaa taaagaaaat aaggagatta acgaacaaat accagataac
     3061 aattccgata ttcccccaga attaaaaaaa ggcttactag ataatcttca aaacttattt
     3121 aaagaataag gggtttttat gacagataaa actatcaaag aattagcaga tattctaggt
     3181 gtttcaaaag ataaagtgaa gtatcaactg aggaaattac ctagtaattt tacctacaaa
     3241 aaaggaaata ttatctacct gaaaaaagaa gcagtaacaa caattacaaa ggttttatca
     3301 ggtaatgagc cgggtaactt acctagtgaa ttacctgatt cattacctac cgattaccta
     3361 ctcaaggaga ttgaaactaa gaataatcat attgaagaaa aagataggca aattgaaaaa
     3421 cttcaactag ctttagaaac acaacaaaaa ttactcgacc agcaacaaca actcaccctg
     3481 caagccaacc aacaaatcga gaaactgcag gaacaactac agttgactta tacggaagaa
     3541 tcttcggaaa ataaatcaac gactctttct gaagaaacag aatcgataga aaaacaatca
     3601 aagacggaga aaaaatggtg gcaattctgg caataaaacc agcaatttaa attaataaaa
     3661 attgctggtt ttattcttct ttttgctttt gcgagcagag caacatgggc ccatgttgcg
     3721 atattttggt ggcgccccaa tccccgtttt ttcgttgaat cttactcgga ctgcactcgt
     3781 tttacagctg atttttctga attttgaaag agcataagga aacgtggtat cactttctta
     3841 cgaaaggtgc tagataagct gtgcctatca cgtttctcag aaaaaaattt gctatcactt
     3901 ttttgccatt gtggctaggc tatgtatagt gttttggcga aaaatagcta tacaaatact
     3961 atatttgtat gatatacata aattatatac tgatacgaaa ggaaaatttc catggacatt
     4021 ttagttcgaa atatcaatcc caaaattatt acaagaatag ataaacgttg tcaggaacta
     4081 acaaccaaaa cgggcaaaaa atggagtcga aatcaatacc taaaaatttt aatcgaaaac
     4141 gattttgacc acgaacttat gaattacaaa aaagatcaat tcgatttatt attcgaaaaa
     4201 tttattgcca ttcaagcaga aaatacgaac atactaaatg actatgttca cacaaacaac
     4261 caactcattg aaacacttat cggaggaata taacatgaga aaaacttctg ttcaaaaaca
     4321 cgtaaccctt tatcccagtc acgttgacgt tttagattcc atcatcgaaa aaaatccaga
     4381 cgtcaacaat tattcagaag ccattcgctt tttatgtatg agttatgaac ctgctaccaa
     4441 tacaaccaca accagtaacc aagcaaaact caatgccatg ggaaaagaaa tttctatcat
     4501 gacagaaatc atggcagaat ttgctgattt atatctaaaa gatactggtg ttcttatcgg
     4561 tacaaattct aaagtatatc aagaagtgaa agaaaaaatt gaaaatcaac tcaatccttc
     4621 ccgacgaaat caacccaaaa atcgtcaaaa agaaaccaat caaaccttta cttctggaaa
     4681 ttttgaccca acaaactttc taaaaagata aaaaaagaaa ccgaaaaata aaaaaattcc
     4741 tcgatttctt tttagggatc ggtcttccag caagatttgc aagttggtac caacttgcga
     4801 aaaaaaaaag aaaaatccgc ttctgcgaat tcttcttttt tcattttggg gcgctgccct
     4861 aatccctaag tcccggttat tcaatagcat ggaaactcaa agaataagac gttccctgga
     4921 ataaaaaaaa ggctgctcgt tcgagcagtc catacatagg aaaatgaaaa aacgacgtcc
     4981 cttactgaga aacgctatta aacttttaac aaatcctcta aaaaataaca agtctttaaa
     5041 aagtgaccgg taaaaatgca caaagaacta aaaaagagaa attgcatcaa atcaagcatt
     5101 agaagctagt aactagctag accaattgaa aatcacaaag tgagcgcctg tatctattgc
     5161 tacaggcgct acttggcata gtgtacatta tgttaactaa cgctataaat aacgattatg
     5221 ttcccaaaac aatattttat gaactataac aaaaatttgt tatcgcatat tgtatatttt
     5281 aattataggt gtataccact taaatttaac acaaaggcgt gattattttg aaacccaaaa
     5341 agaaaattta tctaggtctc ctcttttcct tgatgattgg aatttttagt ataggaatta
     5401 caaataccta tgcttcagaa aattctaatt tcaatatcaa ctcccaacca attgaagaac
     5461 aagcaattaa ttttgcgaaa actgattttg aacactccat aacttcaatt cttttaatgg
     5521 aaaataacac cgaaactgat attaactata ctcttggttc gccatttaaa atgctcgatg
     5581 gagaaaatac ggcaaatagt tctattttct ttccagtatt ttcagacgct gataatacga
     5641 ttaaatatat ttataccgtc aaaaaaaata caaatggaga atattcagga agtatttcac
     5701 aatttttagc aaaagaactt caaaatctag tagatagtaa tataacagat acaaccttat
     5761 tttttcaaga taatagcatt tattattccg ataatggaca aattaaacta ctttggaaat
     5821 cacctttaag tacagaaaaa aatggtgttt
//
