LOCUS       NZ_CP041277             1979 bp    DNA     linear   CON 20-APR-2024
DEFINITION  Enterococcus faecium strain VVEswe-S plasmid pVVEswe-S8.
ACCESSION   NZ_CP041277
VERSION     NZ_CP041277.1
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 1979)
  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 1979)
  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
            CP041277.1.
            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..1979
                     /organism="Enterococcus faecium"
                     /mol_type="genomic DNA"
                     /strain="VVEswe-S"
                     /isolation_source="feces"
                     /host="Homo sapiens"
                     /db_xref="taxon:1352"
                     /plasmid="pVVEswe-S8"
                     /geo_loc_name="Sweden:Halmstad"
                     /lat_lon="56.6744 N 12.8578 E"
                     /collection_date="2014"
                     /collected_by="Hospital of Halland"
     gene            668..1684
                     /locus_tag="FLC01_RS15875"
                     /old_locus_tag="FLC01_16720"
     CDS             668..1684
                     /locus_tag="FLC01_RS15875"
                     /old_locus_tag="FLC01_16720"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002299382.1"
                     /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_002326787.1"
                     /translation="MANENQLSEIQSKIEGRGAEKRTTINQLEKLNRISNRRLSVDDKV
                     HPLKLSWSIDRITIVGKLNDTIAYWTQNGVVFVDFEQLMRLNENQGYLKSVGTNGWQLF
                     DQYGEDIAYIEMLKFHPDKGRIDFNPNKIGEFLKGSMKQFIHDLFLDAHFSRADIACDI
                     LGVPDDFITQYRIVDPVSFKPIYGRSGKLETAYWGSRASERQVRMYNKKLEQERKKQIV
                     PKEIETWWRIEMQLRRGKATDWHAMVRESLDSFASPHYLPGDVKPVDRIMIKGLNQDHS
                     EWAYISRNLKYRLRKLLKEESQNDELTNHLRETFKESANDLKIELDTWLLGLDVTEK"
                     /name="replication initiation factor domain-containing
                     protein"
     Typing          918..1684
                     /name="rep_cluster_1968"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 gggtttagta tttcgttcaa aaagggaaca aagaatacaa gcatttctca taataatcgt
       61 gagttaactg atagccaaaa aatcaatggt ttgtctggta gaaaataatt agcagattta
      121 caagtgggaa ataaaaagct gaaagaagaa aattgcattt caaactacat tttctacaat
      181 agctctaaaa tggcatattt tgcgttctga gcggttttag cgtttatttc gtttagttat
      241 cggcacaatc gttaaaacac gttagaggag cgaaaatgga gcctgtaagg cgactggtag
      301 cggaacgatc gtgttagatt gtgaaaaccg atagctgaat gaaataaaca gcgggtgcgc
      361 cctttccatt tcggcaggag gaggctcaag gggttcgggg aatgaaattc cctgaggtct
      421 ttttattttt ttaggaggag tgctataatc aaagaaaacg agaaaaaaga gcaaaataaa
      481 agccgagcag tgcgctaaca ctctcgacta tttacggaaa ctacttcacc tagctccgta
      541 actcaggttc attatacgaa tatttttagg tttcttcaag ctagagattt ttggatatga
      601 atttttaggg ttacgtgaac tctggaaatt ctttccaaaa gtctcttttt tcgtctggag
      661 gacgaaaatg gcaaatgaaa atcagttgag tgaaattcaa tcaaaaattg aaggtcgagg
      721 ggcagaaaaa agaacaacga taaatcagct cgaaaaactt aaccgtattt ctaacaggcg
      781 gttaagtgtt gacgataagg tacaccccct aaaattaagt tggtcaatcg atcgaattac
      841 aatcgtcgga aaactgaatg ataccatagc ttattggacg caaaatggag ttgtgtttgt
      901 cgattttgag caattaatgc gtttgaatga aaatcaaggg tatttgaagt cggttggtac
      961 aaatggttgg caattatttg accaatatgg agaagatatc gcctatatcg aaatgttaaa
     1021 atttcaccct gacaaaggtc gtattgattt taatccaaat aaaattggcg agtttttaaa
     1081 ggggtcgatg aaacaattca ttcatgattt gtttctggat gcgcatttct cacgtgcaga
     1141 tattgcttgc gatattctcg gtgttcctga tgattttatt acccagtatc gaatcgttga
     1201 ccctgtgtct tttaagccaa tttatggccg ttctggcaaa ttagaaacag cgtactgggg
     1261 tagtcgtgcc agcgagcgac aagtgcggat gtacaacaaa aagcttgaac aggaacgaaa
     1321 aaaacagatt gtaccaaaag aaatcgaaac atggtggcgt atagaaatgc agctaagacg
     1381 tggcaaagca acagattggc atgcgatggt tcgggaaagt ttagatagct ttgcaagtcc
     1441 tcattacttg cctggagatg taaaacctgt tgatagaatt atgataaaag ggctgaatca
     1501 agatcattca gagtgggcgt atattagcag aaatttgaaa tatagattgc gcaaattgtt
     1561 gaaagaagaa agccaaaacg atgagttgac gaatcattta cgagagacgt ttaaggaatc
     1621 tgcaaacgac ttgaaaatag aattagacac gtggcttttg ggtttggacg tgacagagaa
     1681 gtgataccga ataagaaaag tcagatgagt gagagtaaat ttacgtcaat gtttaatgac
     1741 gtgagtttac gataagcgat tattttgcgt gaagcaaaat aaagcgtaaa aggagttgag
     1801 agcgtgacac gctttcggct ccttttttcg ttgtcacttg tgacagcgaa taccctcgga
     1861 gagcatttgg aattgtgaca gccatgtcac aattaggaaa atgttactct ttgtcaaaga
     1921 gtaacagaaa ggtttacact ctttttatta gcgacagcgc gaaggagggg tttaacttg
//
