LOCUS       NZ_CP020491             1979 bp    DNA     circular CON 03-APR-2024
DEFINITION  Enterococcus faecium strain CFSAN059071 plasmid unnamed3, complete
            sequence.
ACCESSION   NZ_CP020491
VERSION     NZ_CP020491.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN06621457
            Assembly: GCF_003071445.1
KEYWORDS    RefSeq.
SOURCE      Enterococcus faecium
  ORGANISM  Enterococcus faecium
            Bacteria; Bacillota; Bacilli; Lactobacillales; Enterococcaceae;
            Enterococcus.
REFERENCE   1  (bases 1 to 1979)
  AUTHORS   Hoffmann,M., Sanchez,M., Hasman,H. and Hammerum,A.M.
  TITLE     Complete Nucleotide Sequence of a Vancomycin Resistant ST203
            Enterococcus faecium Strain with vanA belonging to Complex Type 859
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 1979)
  AUTHORS   Hoffmann,M., Sanchez,M., Hasman,H. and Hammerum,A.M.
  TITLE     Direct Submission
  JOURNAL   Submitted (19-JUN-2018) CFSAN-ORS-DM-MMSB, US Food and Drug
            Administration, 5100 Paint Branch Parkway, College Park, MD 20740,
            USA
  REMARK    Annotation added by NCBI at submitter's request
REFERENCE   3  (bases 1 to 1979)
  AUTHORS   Hoffmann,M., Sanchez,M., Hasman,H. and Hammerum,A.M.
  TITLE     Direct Submission
  JOURNAL   Submitted (27-MAR-2017) CFSAN-ORS-DM-MMSB, US Food and Drug
            Administration, 5100 Paint Branch Parkway, College Park, MD 20740,
            USA
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: HGAP v. 3
            Assembly Name                     :: CFSAN059071_VRE1701.fasta
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 460x
            Sequencing Technology             :: PacBio
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_003071445.1-RS_2024_04_03
            Annotation Date                   :: 04/03/2024 02:28:47
            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)                     :: 3,122
            CDSs (total)                      :: 3,029
            Genes (coding)                    :: 2,913
            CDSs (with protein)               :: 2,913
            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)              :: 116
            CDSs (without protein)            :: 116
            Pseudo Genes (ambiguous residues) :: 0 of 116
            Pseudo Genes (frameshifted)       :: 39 of 116
            Pseudo Genes (incomplete)         :: 67 of 116
            Pseudo Genes (internal stop)      :: 31 of 116
            Pseudo Genes (multiple problems)  :: 18 of 116
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP020491.1.
            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..1979
                     /organism="Enterococcus faecium"
                     /mol_type="genomic DNA"
                     /strain="CFSAN059071"
                     /isolation_source="urine"
                     /host="Homo sapiens"
                     /db_xref="taxon:1352"
                     /plasmid="unnamed3"
                     /geo_loc_name="Denmark"
                     /collection_date="2014-12-05"
                     /collected_by="Statens Serum Institut"
     gene            544..1560
                     /locus_tag="B6S06_RS16375"
                     /old_locus_tag="B6S06_16380"
     CDS             544..1560
                     /locus_tag="B6S06_RS16375"
                     /old_locus_tag="B6S06_16380"
                     /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_002299382.1"
                     /translation="MANENQLSEIQSKIEGRGAEKRTTINQLEKLNRISNRRLSVQGTT
                     TPLKLNWSIDRITIVGKLNDTIAYWTKNGVVFVDFEQLMRLNENQGYLKSVGINGWQLF
                     DQYGEDIAYIEILKFHEGKGRIDFNPNKIGQFLASSMKGFIHDLFLDPHFSRADIACDI
                     VDVPDDFITQYRIVDPISFKPIYGRSGKLETAYWGSRASERQVRLYNKKLEQERKKVIV
                     PKEIDTWWRLEMQLRRGKATDWHAMVQESLDSFASPHFLPIDIKPIDKIVIDGLIAEPS
                     NWSIIARHTKYKYRNLLKQESQNDELTNHLRETFKESADELKKELDTWLLGLDVTEK"
                     /name="replication initiation factor domain-containing
                     protein"
     gene            1760..>1942
                     /locus_tag="B6S06_RS16380"
                     /old_locus_tag="B6S06_16385"
                     /pseudo=""
     CDS             1760..>1942
                     /locus_tag="B6S06_RS16380"
                     /old_locus_tag="B6S06_16385"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002313295.1"
                     /note="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="hypothetical protein"
                     /name="hypothetical protein"
     Typing          545..1554
                     /name="rep_cluster_935"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="92.292"
                     /coverage="99.0"
                     /evalue="0.0"
ORIGIN
        1 tgggaaataa aaagctgaaa gaagaaaatt gcatttcaaa ctacattttc tacaatagct
       61 ctaaaatggc atattttgcg ttctgagcgg ttttagcgtt tatttcgttt agttatcggc
      121 acaatcgtta aaacacgtta gaggagcgaa aatggagcct gtaaggcgac tggtagcgga
      181 acgatcgtgt tagattgtga aaaccgatag ctgaatgaaa taaacagcgg gtgcgccctt
      241 tccatttcgg caggaggagg ctcaaggggt tcggggaatg aaattccctg aggtcttttt
      301 atttttttag gaggagtgct ataatcaaag aaaacgagaa aaaagagcaa aataaaagcc
      361 gagcagtgcg ctaacactct cgactattta cggaaactac ttcacctagc tccgtaactc
      421 aggttcatta tacgaatatt tttaggtttc ttcaagctag agatttttgg atatgaattt
      481 ttagggttac gtgaactctg gaaattcttt ccaaaagtct cttttttcgt ttggaggacg
      541 aaaatggcaa atgaaaatca gttgagtgaa attcaatcaa aaattgaagg tcgaggggca
      601 gaaaaaagaa caacgataaa tcagctcgaa aaacttaacc gtatttctaa caggcggtta
      661 agtgtgcaag gtacgaccac ccccctaaaa ttaaattggt cgattgatcg aattacaatt
      721 gtcggaaaac tgaatgatac catagcttat tggacgaaaa atggagttgt ttttgtcgat
      781 ttcgagcaat taatgcgttt gaacgaaaat cagggatatt tgaaatcagt tgggataaac
      841 ggctggcaat tattcgatca atatggagaa gatattgcgt atatcgaaat acttaaattt
      901 catgaaggaa aaggtcgtat tgattttaat ccgaataaga taggccagtt tttagctagt
      961 tccatgaaag gattcattca tgacctattt ttagatccgc atttttcccg ggcggatatt
     1021 gcctgcgata ttgtagatgt gccggatgac tttattactc agtatcgtat tgtagacccg
     1081 atttctttta agccaatcta cggccgttct ggcaagctag aaacagcgta ctggggcagt
     1141 cgtgccagtg agcgccaagt gcgactgtac aacaaaaagc tagagcagga acgaaaaaaa
     1201 gtaatcgtgc caaaagaaat cgatacgtgg tggcggttag aaatgcagct aagacgtggc
     1261 aaagcaacgg attggcatgc gatggttcag gaaagcttag atagttttgc aagcccgcat
     1321 tttttgccga ttgatataaa acctattgat aaaatagtta ttgatggttt gatagctgag
     1381 ccttctaatt ggtcgataat tgctagacat acaaaatata aatatcggaa tttgctgaag
     1441 caagaaagtc aaaatgatga gttaacgaat catttacgag agacttttaa ggaatctgca
     1501 gacgaattaa aaaaagaatt ggatacgtgg cttttggggt tggatgtgac agagaagtga
     1561 taccgaataa gaaaagtcag atgagtgaga gtggatttgc gtcaatgttt agtgacgtaa
     1621 attcacgata agcgaatatt ttgcatgaag caaaataaag cgtaaaagga gttgagagcg
     1681 tgacacgctt tcggctcctt ttttcgttgt cacttgtgac agcgaaatcc ctcggagagc
     1741 gtttggaatt gtgacagcca tgtcacaatt aggaaaacgt tactctttgt caaagagtaa
     1801 cagaaaggtt tacactcttt ttattagcga cagcgtgaag gaggggttca ccttagggtt
     1861 tagtatttcg ttcaaaaagg gaacaaagaa tacaagcatt tctcataata atcgtgagtt
     1921 aactgatagc caaaaaatca atggtttgtc tggtagaaaa taattagcag atttacaag
//
