LOCUS       NZ_CP041278             1705 bp    DNA     linear   CON 20-APR-2024
DEFINITION  Enterococcus faecium strain VVEswe-S plasmid pVVEswe-S9.
ACCESSION   NZ_CP041278
VERSION     NZ_CP041278.1
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 1705)
  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 1705)
  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
            CP041278.1.
            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..1705
                     /organism="Enterococcus faecium"
                     /mol_type="genomic DNA"
                     /strain="VVEswe-S"
                     /isolation_source="feces"
                     /host="Homo sapiens"
                     /db_xref="taxon:1352"
                     /plasmid="pVVEswe-S9"
                     /geo_loc_name="Sweden:Halmstad"
                     /lat_lon="56.6744 N 12.8578 E"
                     /collection_date="2014"
                     /collected_by="Hospital of Halland"
     gene            <1..328
                     /locus_tag="FLC01_RS15880"
                     /old_locus_tag="FLC01_16725"
     CDS             <1..328
                     /locus_tag="FLC01_RS15880"
                     /old_locus_tag="FLC01_16725"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_076611768.1"
                     /GO_process="GO:0015074 - DNA integration [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=2
                     /transl_table=11
                     /product="IS3 family transposase"
                     /protein_id="WP_002299187.1"
                     /translation="GKEFDNQTIHEILNGFGITRSLSRKGCPYDNAVVESTYKSVKVEF
                     VHQYQFETLAQLRLELFDYVHWWNYLRLHGTLAYETPIQIRQQRLAKRILDNERGSDTS
                     GEAA"
                     /name="IS3 family transposase"
     gene            complement(358..807)
                     /locus_tag="FLC01_RS15885"
                     /old_locus_tag="FLC01_16730"
     CDS             complement(358..807)
                     /locus_tag="FLC01_RS15885"
                     /old_locus_tag="FLC01_16730"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002330699.1"
                     /GO_function="GO:0016491 - oxidoreductase activity
                     [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="TlpA disulfide reductase family protein"
                     /protein_id="WP_010729386.1"
                     /translation="MLSEKTDLENTEAFNKESVKDLRKLPTKDINGKDFTSKDFEKYDL
                     TMVNVFATWCTACVKEIPDLVEVQNEMKSKGVNIVGVVTDPVDDNGENKEAIEKSKLIH
                     EKTKASYPFLMPDGMATLFLTKIIRCCECCGVMATIALDNEHPRI"
                     /name="TlpA disulfide reductase family protein"
     gene            complement(963..1505)
                     /locus_tag="FLC01_RS15890"
                     /old_locus_tag="FLC01_17120"
     CDS             complement(963..1505)
                     /locus_tag="FLC01_RS15890"
                     /old_locus_tag="FLC01_17120"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002298088.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_002298088.1"
                     /translation="MLLKVAIKCYCVKNKGGIIYEKIVPRGACLLLALCLSLSAVGCQK
                     SNENNKIKEGQSISSEEEGMSINANGKNETFKPSDYTLEAKKEYVYEYLGLKFKLSDKF
                     RNYIADKKIAMLDDQSPIDKELKYAILTFEKMTEEQKNAVIEKMGDGYKNWQNELERIG
                     TIGIFEKNTSEEKNLKL"
                     /name="hypothetical protein"
ORIGIN
        1 gggaaaggaa tttgataacc aaaccattca tgagattctg aatggttttg gaattactcg
       61 ttcattgagt aggaagggtt gtccgtatga taatgccgtt gtggaatcaa cctataaatc
      121 tgtcaaagta gaattcgtgc atcaatacca atttgagaca ctggcacagc tacgtctaga
      181 attgtttgat tatgtgcatt ggtggaacta tctacgctta catggcacgt tggcgtatga
      241 aacaccgatc caaattcgac aacagagatt ggcgaagcga atccttgata atgagcgcgg
      301 atctgatacc tctggagagg cagcgtaatt gaatgattgt gcttctgccg gagaaaatca
      361 gatccgagga tgctcattgt caagggcaat cgtagccata acaccgcagc attcacaaca
      421 ccttataatt tttgtcaaaa aaagtgttgc cattccatct ggcattaaga aaggatatga
      481 agcctttgtc ttttcatgta ttaactttga cttttcaatt gcttccttgt tttcaccgtt
      541 atcatcaaca ggatctgtaa caactccaac gatatttaca cccttgcttt tcatttcatt
      601 ctgaacctca accaaatcag gaatttcctt tacacaagct gtacaccaag ttgcaaatac
      661 atttaccata gtaagatcat acttctcaaa atctttactt gtaaaatcct tgccatttat
      721 gtcctttgtt ggtagtttac gtaaatcttt aaccgattct ttgttaaatg cttctgtatt
      781 ttctaaatca gttttttctg atagcacaaa accattttta ggacgttctt ttttatctat
      841 aatttgaatc tcagttcttt ttaattcatc cagaagatta ctttcagctc cgctatttgt
      901 gcttaaatag caatcgtatt ttccatcact tgaaactcct attttagtat gagtatcaca
      961 ttttataatt ttagattttt ttcttctgat gtattttttt caaatatacc aatagtccca
     1021 attctttcaa gctcattttg ccaattttta tatccatcgc ccatcttttc tataactgca
     1081 ttcttttgtt cttctgtcat tttctcaaat gtcaaaatag catactttag ttctttatct
     1141 ataggacttt gatcatctaa catcgctatc tttttatcag ctatataatt tctaaatttg
     1201 tctgagagtt taaatttaag ccctaaatat tcataaacat attctttctt tgcctccaat
     1261 gtataatctg atggcttaaa agtttcattt ttgccatttg cattaattga catgccttcc
     1321 tcttcagaac ttatggattg tccttctttt attttattgt tttcattact tttttgacac
     1381 ccaactgcgc ttaagctcaa acataatgca agtaataggc atgctcctct tggtactatt
     1441 ttttcataaa ttattcctcc tttatttttt acacaatagc attttatagc tactttcaat
     1501 aacattctac acacctttta tgaaacgttg atgaaatata attttttatt tttccaaact
     1561 atggtataac aatataagta ttatgcttaa agttgttctt acacgattag tatatgatcg
     1621 attaatatat gagcaagcac agtaagtgta cggacactta cgaaaaaatt gatgaagcag
     1681 ccctttggga tctgcttcat caatt
//
