LOCUS       NZ_CP041276             4372 bp    DNA     linear   CON 20-APR-2024
DEFINITION  Enterococcus faecium strain VVEswe-S plasmid pVVEswe-S7.
ACCESSION   NZ_CP041276
VERSION     NZ_CP041276.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN12138986
            Assembly: GCF_007917315.3
KEYWORDS    RefSeq.
SOURCE      Enterococcus faecium
  ORGANISM  Enterococcus faecium
            Bacteria; Bacillota; Bacilli; Lactobacillales; Enterococcaceae;
            Enterococcus.
REFERENCE   1  (bases 1 to 4372)
  AUTHORS   Wagner,T.M., Janice,J., Sivertsen,A., Sjogren,I., Sundsfjord,A. and
            Hegstad,K.
  TITLE     Alternative vanHAX promoters and increased vanA-plasmid copy number
            resurrect silenced glycopeptide resistance in Enterococcus faecium
  JOURNAL   J Antimicrob Chemother 76 (4), 876-882 (2021)
   PUBMED   33367710
REFERENCE   2  (bases 1 to 4372)
  AUTHORS   Wagner,T.M., Janice,J., Sivertsen,A., Sjogren,I., Sundsfjord,A. and
            Hegstad,K.
  TITLE     Direct Submission
  JOURNAL   Submitted (26-JUN-2019) Department of Microbiology and Infection
            Control, Norwegian National Advisory Unit on Detection of
            Antimicrobial Resistance, Sykehusveien 38, Tromso 9038, Norway
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Date                     :: JAN-2019
            Assembly Method                   :: Unicycler v. v0.4.6
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 252.0x
            Sequencing Technology             :: Oxford Nanopore MiniION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_007917315.3-RS_2024_04_20
            Annotation Date                   :: 04/20/2024 04:32:37
            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)                     :: 3,249
            CDSs (total)                      :: 3,156
            Genes (coding)                    :: 3,042
            CDSs (with protein)               :: 3,042
            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)              :: 114
            CDSs (without protein)            :: 114
            Pseudo Genes (ambiguous residues) :: 0 of 114
            Pseudo Genes (frameshifted)       :: 46 of 114
            Pseudo Genes (incomplete)         :: 63 of 114
            Pseudo Genes (internal stop)      :: 25 of 114
            Pseudo Genes (multiple problems)  :: 16 of 114
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP041276.1.
            Bacteria and source DNA available from Kres.
            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/
FEATURES             Location/Qualifiers
     source          1..4372
                     /organism="Enterococcus faecium"
                     /mol_type="genomic DNA"
                     /strain="VVEswe-S"
                     /isolation_source="feces"
                     /host="Homo sapiens"
                     /db_xref="taxon:1352"
                     /plasmid="pVVEswe-S7"
                     /geo_loc_name="Sweden:Halmstad"
                     /lat_lon="56.6744 N 12.8578 E"
                     /collection_date="2014"
                     /collected_by="Hospital of Halland"
     gene            32..1000
                     /locus_tag="FLC01_RS15845"
                     /old_locus_tag="FLC01_16685"
     CDS             32..1000
                     /locus_tag="FLC01_RS15845"
                     /old_locus_tag="FLC01_16685"
                     /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_002347008.1"
                     /translation="MSKKRTIVNEWEKLTALSNRRLNVQTLVQTIKLNWSIDRITIVGK
                     LNQNIFYHTQHDVLILDFEQLMRVNEGNGYLKAVGNNGWQLLDQHDENIAYIEISKWQE
                     GKGRIDFNPNKISRFLADSMKNFIHDLFLEPHFSRADVACDLIDVPDEFITQYRIIDPV
                     SFKLIYGRSGKLETVYWGSRASERQIRLYNKKIEQEMKRKVVPSEINTWWRLEMQLRRG
                     KATEWYAMVKESLDSFVSPHFLPTDIKPTDKVMIDGLLANHSNWAILSRNSKYKYRNLL
                     KRESQNDELTNHLRETFEESADDLKKELDTWLQGLDVTEEE"
                     /name="replication initiation factor domain-containing
                     protein"
     gene            1003..1236
                     /locus_tag="FLC01_RS15850"
                     /old_locus_tag="FLC01_16690"
     CDS             1003..1236
                     /locus_tag="FLC01_RS15850"
                     /old_locus_tag="FLC01_16690"
                     /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            1229..1648
                     /locus_tag="FLC01_RS15855"
                     /old_locus_tag="FLC01_16695"
     CDS             1229..1648
                     /locus_tag="FLC01_RS15855"
                     /old_locus_tag="FLC01_16695"
                     /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            1657..1965
                     /locus_tag="FLC01_RS15860"
                     /old_locus_tag="FLC01_16700"
     CDS             1657..1965
                     /locus_tag="FLC01_RS15860"
                     /old_locus_tag="FLC01_16700"
                     /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            1969..2331
                     /locus_tag="FLC01_RS15865"
                     /old_locus_tag="FLC01_16705"
     CDS             1969..2331
                     /locus_tag="FLC01_RS15865"
                     /old_locus_tag="FLC01_16705"
                     /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            2553..3959
                     /locus_tag="FLC01_RS15870"
                     /old_locus_tag="FLC01_16710"
     CDS             2553..3959
                     /locus_tag="FLC01_RS15870"
                     /old_locus_tag="FLC01_16710"
                     /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_060810507.1"
                     /translation="MGFSISFKKGTKNTSISHNNRELTDRQKTNDWHKHIDFTKSDENI
                     YLEQTNLADKYEELFGEVVEKYNAKQKRADRKIEDYLAKVRKDKKLEPQREFIVQIGIL
                     DDFQTNRADGSSTGISKQQAEQNRVIANKILVQYYKEFQERNPNLAVYNAVIHNDEISP
                     HLHLNIVPVAEGYKRGVQKQPSFNKALVQQGIHADKDNGRVLFNNFRNQEVDSIERLMN
                     DYGWKRDIVGTNKIKDIHEYKEIMSEISELRQTAVKERESVSDELRYIYRQREENERDK
                     ALMASERAKIEEEKKNMLNVKKEMAVIFQKDMVPLESFKRLPDGSYHLSGNDFVDLYQR
                     ATRATNAKRNADNMSEQYLQMLEQNTELNEYVATLEEERHLSGRKQLADLQVENKKLKE
                     ENRSLRQRLERLKNAFQKSITRLSIRFGLAEKDMGLSEELEVLEQEKTLFYRQNVSQHK
                     LERSENEIEW"
                     /name="plasmid recombination protein"
     Typing          124..987
                     /name="rep_cluster_943"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="81.264"
                     /coverage="95.0"
                     /evalue="0.0"
     Typing          2554..3956
                     /name="MOBV"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="92.094"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 aatctctttt ttctttgagg aggaactgaa tatgagtaaa aaaagaacaa tcgtgaatga
       61 gtgggaaaaa ttaacagccc tgtctaacag gcggttaaat gttcaaactt tggtacaaac
      121 tataaaatta aattggtcga ttgaccgaat taccattgtt ggaaagttga atcaaaatat
      181 tttttatcat actcaacatg atgtattaat attagatttt gaacagctta tgcgggtaaa
      241 tgaaggcaat ggctatttaa aagcggttgg aaataatggt tggcagctat tagaccaaca
      301 tgacgaaaat attgcctata ttgaaatttc taaatggcaa gaaggaaaag ggcggattga
      361 ttttaatcct aataaaatca gtcgattttt agcggattcc atgaaaaatt ttattcatga
      421 tttattttta gagccccatt tttcacgagc ggatgttgcc tgcgatctta ttgatgtgcc
      481 tgatgagttt atcacgcaat atcgaattat tgatccagtt tcatttaaat taatttatgg
      541 acgctcagga aaactggaaa cggtgtattg gggtagtcgg gcaagcgagc ggcaaattcg
      601 tttgtacaat aaaaaaatag agcaagaaat gaaaagaaag gtggtgcctt cagaaattaa
      661 tacttggtgg cggttagaaa tgcagttaag acgtggtaaa gctacggaat ggtatgctat
      721 ggtgaaagaa agtttggata gctttgtgag tccacatttt ttaccaactg atataaaacc
      781 tacggataaa gttatgattg atggattgtt agctaatcat tctaattggg cgattttgtc
      841 aagaaactcg aaatataaat atcgaaattt attaaagcga gaaagtcaaa atgatgagtt
      901 gacgaatcat ttacgagaaa catttgaaga atcagcagat gatttaaaaa aagaattgga
      961 tacttggtta cagggacttg atgtgacaga ggaggaatag taatggcaga aaaacaaaag
     1021 cattttggta agaaaaattg gttggtgaat ttaacaggtg ataacgttgt cgttgttttt
     1081 ttggatagca aaaaaatgtc cggtaagtta cttgatgtaa cgcagtatga gttgattttg
     1141 aaaaataata aaattgattc cccaatcatt atccctaagc atgctgttaa atatgtttat
     1201 ggggtagctg aaagtaacgg agaagataat gactgatttg ccagaaaaaa tgaccataaa
     1261 aaaccttgct gatgagttgg gtatatctaa aaatacagtg cgcaatcaac tggtcaatgc
     1321 aggttatgac cttgctcggt ataaagataa tggggttatc atgttagaca aggaattgat
     1381 tggtgttgtg cggtcaattt atcggtcaaa aggtggtcaa ttgactggtg atttaccggt
     1441 caatgatgca ggcaatgatt tcccgttaga aaaagaaaat gaatttttgc gtgaacaatt
     1501 agcggaaaaa gataggcata tttctgaatt aacggaaatg attcgtgacc aacaaaaatt
     1561 gactttgctt cagcaacaaa aaaacgatca gttgttacta gaaaatcaag aattaaaaaa
     1621 tcgaaaatgg tggcaattct ggaagtgagg tgtgacatgg ataaaattga tttgagagaa
     1681 gaaacagtcg atagaattga attgatgtat gaacggttag ctgattattt gaatttgccg
     1741 gatgaagata attatagtga aatgcttgaa cgaattatgg atgttctcaa ctcggttatc
     1801 aatgctgatc tagcaaaatc ttcagttttg actaatgaat ttgttcataa gcatttagcg
     1861 caaacaactg atgaatcaga aaaagaattt tggttgaaat taatgagtca tgttatgcag
     1921 ttaaaccaaa tttccgttat taattccaaa gaaaaggaga tgtagtttat gggaatgact
     1981 ttagcagata ttaaagcgca agaagaaaaa ttaaaaaaag aacaagcgaa acttcgccaa
     2041 cagaaaaaac gcttgattga gaaagaaaat gctgcaatgg gcaaggctct tcgcaagcgt
     2101 tttgggtttg aaacttttgc tgattttgag cggtggttat cgtcaatttc tgacgatcag
     2161 caacacgaaa aaacagtgga taatgagtgg cttgctgatg aaaaatcagc gccaagcgaa
     2221 cgagattatc ccgatgaatc tgacgactta ttcggagtga taccgaataa gaaaagtcag
     2281 atgagtgaga gtaaatttac gtcaatattt aatgacgtga atttacgata agcgattatt
     2341 ttgcgtgaag caaaataaag cataaaagga gttgatagcg tgatacgctt tcggctcctt
     2401 ttttcgttgt cacttgtgac agcgaaaacc ctcggagagc gtttggaatt gtgacatcca
     2461 tgtcacaatt aggaaaatgt tactctttga caaagagtaa cagaaaggtt tacaatcttt
     2521 ttattagcga cagcgcgaag gagggtttta acttggggtt tagtatttca tttaaaaaag
     2581 gaacgaagaa tacaagtatt tctcataata atcgtgagtt aactgatcgc cagaaaacca
     2641 atgattggca taagcacatt gacttcacga aatcggatga aaatatttat ttagagcaga
     2701 cgaatctagc agataaatat gaggaattgt ttggcgaagt ggtagaaaaa tataatgcga
     2761 aacaaaaaag agccgataga aaaatcgagg actatttagc gaaagtgcgc aaggataaaa
     2821 agttggaacc tcaacgagaa tttattgtgc aaataggcat tttagatgat ttccagacaa
     2881 atcgagcaga tggttcttct actggcatat cgaaacaaca agctgaacaa aatcgagtga
     2941 ttgccaataa aattttggtt cagtattaca aggagtttca agagagaaac cctaatttgg
     3001 ctgtttataa tgctgttatt cataatgacg aaataagtcc gcacctgcac ttgaatattg
     3061 tgccggttgc tgaaggttat aaacggggtg ttcaaaagca gccgagcttt aataaagcac
     3121 tggttcaaca agggatacac gctgataaag ataatggtcg agtgcttttc aataatttta
     3181 gaaatcaaga agttgactct atagaacgat taatgaatga ttacggttgg aaaagggata
     3241 ttgtcggtac caacaaaatt aaagatattc acgaatacaa agaaatcatg agtgaaattt
     3301 ctgaattgcg ccaaacggct gtaaaagagc gtgagagcgt ttctgatgag ttgaggtata
     3361 tttataggca aagagaagaa aacgagcgtg ataaggctct gatggcttct gagagagcga
     3421 agattgaaga agagaagaaa aatatgctga atgtaaaaaa agagatggcg gtcattttcc
     3481 aaaaagatat ggttccttta gaaagtttca agaggcttcc tgatggttcg tatcatttat
     3541 ctgggaatga ttttgttgat ttgtatcaac gagctacgag agcaacaaat gccaagagaa
     3601 atgctgataa catgagtgag caatatttac agatgcttga gcaaaataca gaattaaatg
     3661 agtatgtagc tacattggaa gaagagcgtc atttgtctgg tagaaaacaa ttagcagatt
     3721 tacaagtgga aaataaaaag ctgaaagaag aaaatcgctc tttacgccag cgtttagagc
     3781 gattaaaaaa cgcatttcaa aaatcgatca ctcgtttgtc tatccgtttt ggtcttgcag
     3841 aaaaggatat ggggctttct gaggaattag aagtattaga gcaggagaaa accttatttt
     3901 atcgtcaaaa cgtctcacag cataaattag agcgttctga gaatgagatt gagtggtagc
     3961 cacgatgtgc agtcaacggt accggaggcg gtttgtgccg aggataagga gttgacggct
     4021 aaaccactag cccctgaagc tgacatttgc taaaaaatgg caagtccatt ttttggccaa
     4081 cttagcgtta gcgaagtttg ggggcgccct tttcaaaggg tgcggtttta tttttttggt
     4141 atttgcatag ctaaagagaa gtgctattat tgagttagca aacaaatgaa ctggaaaaag
     4201 agcaaaaaaa taagtcgagc aacgctacca acgttctcga cctttacgga aactaaccac
     4261 actagttccg taactcaaat tcattatacg aatattttta ggtttcttca agactagaga
     4321 ttgatggtta tgaattttta gagttacgtg aactctggaa attctttcca aa
//
