LOCUS       NZ_CP041267             4372 bp    DNA     linear   CON 20-APR-2024
DEFINITION  Enterococcus faecium strain VVEswe-R plasmid pVVEswe-R7.
ACCESSION   NZ_CP041267
VERSION     NZ_CP041267.2
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN12138936
            Assembly: GCF_007917035.2
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 (07-MAY-2020) Department of Microbiology and Infection
            Control, Norwegian National Advisory Unit on Detection of
            Antimicrobial Resistance, Sykehusveien 38, Tromso 9038, Norway
  REMARK    Sequence update by submitter
REFERENCE   3  (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                   :: 305.0x
            Sequencing Technology             :: Oxford Nanopore MiniION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_007917035.2-RS_2024_04_20
            Annotation Date                   :: 04/20/2024 02:37:42
            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)                     :: 3,257
            CDSs (total)                      :: 3,164
            Genes (coding)                    :: 3,041
            CDSs (with protein)               :: 3,041
            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)              :: 123
            CDSs (without protein)            :: 123
            Pseudo Genes (ambiguous residues) :: 0 of 123
            Pseudo Genes (frameshifted)       :: 58 of 123
            Pseudo Genes (incomplete)         :: 63 of 123
            Pseudo Genes (internal stop)      :: 24 of 123
            Pseudo Genes (multiple problems)  :: 18 of 123
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP041267.2.
            On Jun 19, 2020 this sequence version replaced NZ_CP041267.1.
            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-R"
                     /isolation_source="feces"
                     /host="Homo sapiens"
                     /db_xref="taxon:1352"
                     /plasmid="pVVEswe-R7"
                     /geo_loc_name="Sweden:Halmstad"
                     /lat_lon="56.6744 N 12.8578 E"
                     /collection_date="2014"
                     /collected_by="KRES"
     gene            complement(123..431)
                     /locus_tag="FKW92_RS15885"
                     /old_locus_tag="FKW92_16750"
     CDS             complement(123..431)
                     /locus_tag="FKW92_RS15885"
                     /old_locus_tag="FKW92_16750"
                     /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            complement(440..859)
                     /locus_tag="FKW92_RS15890"
                     /old_locus_tag="FKW92_16755"
     CDS             complement(440..859)
                     /locus_tag="FKW92_RS15890"
                     /old_locus_tag="FKW92_16755"
                     /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(852..1085)
                     /locus_tag="FKW92_RS15895"
                     /old_locus_tag="FKW92_16760"
     CDS             complement(852..1085)
                     /locus_tag="FKW92_RS15895"
                     /old_locus_tag="FKW92_16760"
                     /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(1088..2056)
                     /locus_tag="FKW92_RS15900"
                     /old_locus_tag="FKW92_16765"
     CDS             complement(1088..2056)
                     /locus_tag="FKW92_RS15900"
                     /old_locus_tag="FKW92_16765"
                     /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            complement(2501..3907)
                     /locus_tag="FKW92_RS15905"
                     /old_locus_tag="FKW92_16775"
     CDS             complement(2501..3907)
                     /locus_tag="FKW92_RS15905"
                     /old_locus_tag="FKW92_16775"
                     /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"
     gene            complement(4129..>4372)
                     /locus_tag="FKW92_RS15915"
                     /old_locus_tag="FKW92_16780"
     CDS             complement(4129..>4372)
                     /locus_tag="FKW92_RS15915"
                     /old_locus_tag="FKW92_16780"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_016173819.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=2
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_146419988.1"
                     /translation="LRKRFGFETFADFERWLSSISDDQQHEKTVDNEWLADEKSAPSER
                     DYPDESDDLFGVIPNKKSQMSESKFTSIFNDVNLR"
                     /name="hypothetical protein"
     Typing          complement(1096..1965)
                     /name="rep_cluster_943"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="81.164"
                     /coverage="96.0"
                     /evalue="0.0"
     Typing          complement(2505..3907)
                     /name="MOBV"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="92.094"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 tccttgccca ttgcagcatt ttctttctca atcaagcgtt ttttctgttg gcgaagtttc
       61 gcttgttctt tttttaattt ttcttcttgc gctttaatat ctgctaaagt cattcccata
      121 aactacatct ccttttcttt ggaattaata acggaaattt ggtttaactg cataacatga
      181 ctcattaatt tcaaccaaaa ttctttttct gattcatcag ttgtttgcgc taaatgctta
      241 tgaacaaatt cattagtcaa aactgaagat tttgctagat cagcattgat aaccgagttg
      301 agaacatcca taattcgttc aagcatttca ctataattat cttcatccgg caaattcaaa
      361 taatcagcta accgttcata catcaattca attctatcga ctgtttcttc tctcaaatca
      421 attttatcca tgtcacacct cacttccaga attgccacca ttttcgattt tttaattctt
      481 gattttctag taacaactga tcgttttttt gttgctgaag caaagtcaat ttttgttggt
      541 cacgaatcat ttccgttaat tcagaaatat gcctatcttt ttccgctaat tgttcacgca
      601 aaaattcatt ttctttttct aacgggaaat cattgcctgc atcattgacc ggtaaatcac
      661 cagtcaattg accacctttt gaccgataaa ttgaccgcac aacaccaatc aattccttgt
      721 ctaacatgat aaccccatta tctttatacc gagcaaggtc ataacctgca ttgaccagtt
      781 gattgcgcac tgtattttta gatataccca actcatcagc aaggtttttt atggtcattt
      841 tttctggcaa atcagtcatt atcttctccg ttactttcag ctaccccata aacatattta
      901 acagcatgct tagggataat gattggggaa tcaattttat tatttttcaa aatcaactca
      961 tactgcgtta catcaagtaa cttaccggac atttttttgc tatccaaaaa aacaacgaca
     1021 acgttatcac ctgttaaatt caccaaccaa tttttcttac caaaatgctt ttgtttttct
     1081 gccattacta ttcctcctct gtcacatcaa gtccctgtaa ccaagtatcc aattcttttt
     1141 ttaaatcatc tgctgattct tcaaatgttt ctcgtaaatg attcgtcaac tcatcatttt
     1201 gactttctcg ctttaataaa tttcgatatt tatatttcga gtttcttgac aaaatcgccc
     1261 aattagaatg attagctaac aatccatcaa tcataacttt atccgtaggt tttatatcag
     1321 ttggtaaaaa atgtggactc acaaagctat ccaaactttc tttcaccata gcataccatt
     1381 ccgtagcttt accacgtctt aactgcattt ctaaccgcca ccaagtatta atttctgaag
     1441 gcaccacctt tcttttcatt tcttgctcta tttttttatt gtacaaacga atttgccgct
     1501 cgcttgcccg actaccccaa tacaccgttt ccagttttcc tgagcgtcca taaattaatt
     1561 taaatgaaac tggatcaata attcgatatt gcgtgataaa ctcatcaggc acatcaataa
     1621 gatcgcaggc aacatccgct cgtgaaaaat ggggctctaa aaataaatca tgaataaaat
     1681 ttttcatgga atccgctaaa aatcgactga ttttattagg attaaaatca atccgccctt
     1741 ttccttcttg ccatttagaa atttcaatat aggcaatatt ttcgtcatgt tggtctaata
     1801 gctgccaacc attatttcca accgctttta aatagccatt gccttcattt acccgcataa
     1861 gctgttcaaa atctaatatt aatacatcat gttgagtatg ataaaaaata ttttgattca
     1921 actttccaac aatggtaatt cggtcaatcg accaatttaa ttttatagtt tgtaccaaag
     1981 tttgaacatt taaccgcctg ttagacaggg ctgttaattt ttcccactca ttcacgattg
     2041 ttcttttttt actcatattc agttcctcct caaagaaaaa agagattttt ggaaagaatt
     2101 tccagagttc acgtaactct aaaaattcat aaccatcaat ctctagtctt gaagaaacct
     2161 aaaaatattc gtataatgaa tttgagttac ggaactagtg tggttagttt ccgtaaaggt
     2221 cgagaacgtt ggtagcgttg ctcgacttat ttttttgctc tttttccagt tcatttgttt
     2281 gctaactcaa taatagcact tctctttagc tatgcaaata ccaaaaaaat aaaaccgcac
     2341 cctttgaaaa gggcgccccc aaacttcgct aacgctaagt tggccaaaaa atggacttgc
     2401 cattttttag caaatgtcag cttcaggggc tagtggttta gccgtcaact ccttatcctc
     2461 ggcacaaacc gcctccggta ccgttgactg cacatcgtgg ctaccactca atctcattct
     2521 cagaacgctc taatttatgc tgtgagacgt tttgacgata aaataaggtt ttctcctgct
     2581 ctaatacttc taattcctca gaaagcccca tatccttttc tgcaagacca aaacggatag
     2641 acaaacgagt gatcgatttt tgaaatgcgt tttttaatcg ctctaaacgc tggcgtaaag
     2701 agcgattttc ttctttcagc tttttatttt ccacttgtaa atctgctaat tgttttctac
     2761 cagacaaatg acgctcttct tccaatgtag ctacatactc atttaattct gtattttgct
     2821 caagcatctg taaatattgc tcactcatgt tatcagcatt tctcttggca tttgttgctc
     2881 tcgtagctcg ttgatacaaa tcaacaaaat cattcccaga taaatgatac gaaccatcag
     2941 gaagcctctt gaaactttct aaaggaacca tatctttttg gaaaatgacc gccatctctt
     3001 tttttacatt cagcatattt ttcttctctt cttcaatctt cgctctctca gaagccatca
     3061 gagccttatc acgctcgttt tcttctcttt gcctataaat atacctcaac tcatcagaaa
     3121 cgctctcacg ctcttttaca gccgtttggc gcaattcaga aatttcactc atgatttctt
     3181 tgtattcgtg aatatcttta attttgttgg taccgacaat atcccttttc caaccgtaat
     3241 cattcattaa tcgttctata gagtcaactt cttgatttct aaaattattg aaaagcactc
     3301 gaccattatc tttatcagcg tgtatccctt gttgaaccag tgctttatta aagctcggct
     3361 gcttttgaac accccgttta taaccttcag caaccggcac aatattcaag tgcaggtgcg
     3421 gacttatttc gtcattatga ataacagcat tataaacagc caaattaggg tttctctctt
     3481 gaaactcctt gtaatactga accaaaattt tattggcaat cactcgattt tgttcagctt
     3541 gttgtttcga tatgccagta gaagaaccat ctgctcgatt tgtctggaaa tcatctaaaa
     3601 tgcctatttg cacaataaat tctcgttgag gttccaactt tttatccttg cgcactttcg
     3661 ctaaatagtc ctcgattttt ctatcggctc ttttttgttt cgcattatat ttttctacca
     3721 cttcgccaaa caattcctca tatttatctg ctagattcgt ctgctctaaa taaatatttt
     3781 catccgattt cgtgaagtca atgtgcttat gccaatcatt ggttttctgg cgatcagtta
     3841 actcacgatt attatgagaa atacttgtat tcttcgttcc ttttttaaat gaaatactaa
     3901 accccaagtt aaaaccctcc ttcgcgctgt cgctaataaa aagattgtaa acctttctgt
     3961 tactctttgt caaagagtaa cattttccta attgtgacat ggatgtcaca attccaaacg
     4021 ctctccgagg gttttcgctg tcacaagtga caacgaaaaa aggagccgaa agcgtatcac
     4081 gctatcaact ccttttatgc tttattttgc ttcacgcaaa ataatcgctt atcgtaaatt
     4141 cacgtcatta aatattgacg taaatttact ctcactcatc tgacttttct tattcggtat
     4201 cactccgaat aagtcgtcag attcatcggg ataatctcgt tcgcttggcg ctgatttttc
     4261 atcagcaagc cactcattat ccactgtttt ttcgtgttgc tgatcgtcag aaattgacga
     4321 taaccaccgc tcaaaatcag caaaagtttc aaacccaaaa cgcttgcgaa ga
//
