LOCUS       NZ_CP131847             1979 bp    DNA     circular CON 25-APR-2024
DEFINITION  Enterococcus faecium strain 2016S06-219 plasmid p2016S06-219-6,
            complete sequence.
ACCESSION   NZ_CP131847
VERSION     NZ_CP131847.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN36766199
            Assembly: GCF_038441125.1
KEYWORDS    RefSeq.
SOURCE      Enterococcus faecium
  ORGANISM  Enterococcus faecium
            Bacteria; Bacillota; Bacilli; Lactobacillales; Enterococcaceae;
            Enterococcus.
REFERENCE   1  (bases 1 to 1979)
  AUTHORS   Chen,F.-J., Liao,Y.-C. and Chiu,Y.-T.
  TITLE     Rapid Diagnostics and Real-time Genomic Surveillance System for
            Pathogens from Culture
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 1979)
  AUTHORS   Chen,F.-J., Liao,Y.-C. and Chiu,Y.-T.
  TITLE     Direct Submission
  JOURNAL   Submitted (31-JUL-2023) National Institute of Infectious Diseases
            and Vaccinology, National Health Research Institutes, No. 35, Keyan
            Road, Zhunan Town, Miaoli County 350, Taiwan
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Date                     :: 28-SEP-2022
            Assembly Method                   :: CCBGpipe v. 1
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 80x
            Sequencing Technology :: Oxford Nanopore MinION and Illumina iSeq
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_038441125.1-RS_2024_04_24
            Annotation Date                   :: 04/24/2024 15:02:18
            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)                     :: 3,146
            CDSs (total)                      :: 3,053
            Genes (coding)                    :: 2,884
            CDSs (with protein)               :: 2,884
            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)              :: 169
            CDSs (without protein)            :: 169
            Pseudo Genes (ambiguous residues) :: 0 of 169
            Pseudo Genes (frameshifted)       :: 60 of 169
            Pseudo Genes (incomplete)         :: 103 of 169
            Pseudo Genes (internal stop)      :: 34 of 169
            Pseudo Genes (multiple problems)  :: 26 of 169
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP131847.1.
            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="2016S06-219"
                     /isolation_source="blood"
                     /host="Homo sapiens"
                     /db_xref="taxon:1352"
                     /plasmid="p2016S06-219-6"
                     /geo_loc_name="Taiwan"
                     /collection_date="2016"
                     /collected_by="NHRI"
     gene            join(1977..1979,1..>180)
                     /locus_tag="Q7578_RS15725"
                     /old_locus_tag="Q7578_15660"
                     /pseudo=""
     CDS             join(1977..1979,1..>180)
                     /locus_tag="Q7578_RS15725"
                     /old_locus_tag="Q7578_15660"
                     /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"
     gene            761..1777
                     /locus_tag="Q7578_RS15730"
                     /old_locus_tag="Q7578_15665"
     CDS             761..1777
                     /locus_tag="Q7578_RS15730"
                     /old_locus_tag="Q7578_15665"
                     /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"
     Typing          762..1771
                     /name="rep_cluster_935"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="92.292"
                     /coverage="99.0"
                     /evalue="0.0"
ORIGIN
        1 tcacaattag gaaaatgtta ctctttgtca aagagtaaca gaaaggttta cactcttttt
       61 attagcgaca gcgtgaagga ggggttcacc ttagggttta gtatttcgtt caaaaaggga
      121 acaaagaata caagcatttc tcataataat cgtgagttaa ctgatagcca aaaaatcaat
      181 ggtttgtctg gtagaaaata attagcagat ttacaagtgg gaaataaaaa gctgaaagaa
      241 gaaaattgca tttcaaacta cattttctac aatagctcta aaatggcata ttttgcgttc
      301 tgagcggttt tagcgtttat ttcgtttagt tatcggcaca atcgttaaaa cacgttagag
      361 gagcgaaaat ggagcctgta aggcgactgg tagcggaacg atcgtgttag attgtgaaaa
      421 ccgatagctg aatgaaataa acagcgggtg cgccctttcc atttcggcag gaggaggctc
      481 aaggggttcg gggaatgaaa ttccctgagg tctttttatt tttttaggag gagtgctata
      541 atcaaagaaa acgagaaaaa agagcaaaat aaaagccgag cagtgcgcta acactctcga
      601 ctatttacgg aaactacttc acctagctcc gtaactcagg ttcattatac gaatattttt
      661 aggtttcttc aagctagaga tttttggata tgaattttta gggttacgtg aactctggaa
      721 attctttcca aaagtctctt ttttcgtttg gaggacgaaa atggcaaatg aaaatcagtt
      781 gagtgaaatt caatcaaaaa ttgaaggtcg aggggcagaa aaaagaacaa cgataaatca
      841 gctcgaaaaa cttaaccgta tttctaacag gcggttaagt gtgcaaggta cgaccacccc
      901 cctaaaatta aattggtcga ttgatcgaat tacaattgtc ggaaaactga atgataccat
      961 agcttattgg acgaaaaatg gagttgtttt tgtcgatttc gagcaattaa tgcgtttgaa
     1021 cgaaaatcag ggatatttga aatcagttgg gataaacggc tggcaattat tcgatcaata
     1081 tggagaagat attgcgtata tcgaaatact taaatttcat gaaggaaaag gtcgtattga
     1141 ttttaatccg aataagatag gccagttttt agctagttcc atgaaaggat tcattcatga
     1201 cctattttta gatccgcatt tttcccgggc ggatattgcc tgcgatattg tagatgtgcc
     1261 ggatgacttt attactcagt atcgtattgt agacccgatt tcttttaagc caatctacgg
     1321 ccgttctggc aagctagaaa cagcgtactg gggcagtcgt gccagtgagc gccaagtgcg
     1381 actgtacaac aaaaagctag agcaggaacg aaaaaaagta atcgtgccaa aagaaatcga
     1441 tacgtggtgg cggttagaaa tgcagctaag acgtggcaaa gcaacggatt ggcatgcgat
     1501 ggttcaggaa agcttagata gttttgcaag cccgcatttt ttgccgattg atataaaacc
     1561 tattgataaa atagttattg atggtttgat agctgagcct tctaattggt cgataattgc
     1621 tagacataca aaatataaat atcggaattt gctgaagcaa gaaagtcaaa atgatgagtt
     1681 aacgaatcat ttacgagaga cttttaagga atctgcagac gaattaaaaa aagaattgga
     1741 tacgtggctt ttggggttgg atgtgacaga gaagtgatac cgaataagaa aagtcagatg
     1801 agtgagagta aatttacgtc aatgtttagt gacgtggatt tacgataagc gattattttg
     1861 cgtgaagcaa aataaagcgt aaaaggagtt gagagcgtga cacgctttcg gctccttttt
     1921 tcgttgtcac ttgtgacagc gaataccctc ggagagcatt tggaattgtg acagccatg
//
