LOCUS       NZ_CP131824             1979 bp    DNA     circular CON 25-APR-2024
DEFINITION  Enterococcus faecium strain 2016N17-104 plasmid p2016N17-104-6,
            complete sequence.
ACCESSION   NZ_CP131824
VERSION     NZ_CP131824.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN36766202
            Assembly: GCF_038441015.1
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  JOURNAL   Unpublished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_038441015.1-RS_2024_04_24
            Annotation Date                   :: 04/24/2024 16:12:56
            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)                     :: 3,138
            CDSs (total)                      :: 3,048
            Genes (coding)                    :: 2,898
            CDSs (with protein)               :: 2,898
            Genes (RNA)                       :: 90
            rRNAs                             :: 6, 6, 6 (5S, 16S, 23S)
            complete rRNAs                    :: 6, 6, 6 (5S, 16S, 23S)
            tRNAs                             :: 68
            ncRNAs                            :: 4
            Pseudo Genes (total)              :: 150
            CDSs (without protein)            :: 150
            Pseudo Genes (ambiguous residues) :: 0 of 150
            Pseudo Genes (frameshifted)       :: 48 of 150
            Pseudo Genes (incomplete)         :: 96 of 150
            Pseudo Genes (internal stop)      :: 35 of 150
            Pseudo Genes (multiple problems)  :: 25 of 150
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP131824.1.
            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="2016N17-104"
                     /isolation_source="blood"
                     /host="Homo sapiens"
                     /db_xref="taxon:1352"
                     /plasmid="p2016N17-104-6"
                     /geo_loc_name="Taiwan"
                     /collection_date="2016"
                     /collected_by="NHRI"
     gene            complement(join(1822..1979,1..859))
                     /locus_tag="Q7581_RS15685"
                     /old_locus_tag="Q7581_15630"
     CDS             complement(join(1822..1979,1..859))
                     /locus_tag="Q7581_RS15685"
                     /old_locus_tag="Q7581_15630"
                     /inference="COORDINATES: ab initio prediction:GeneMarkS-2+"
                     /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: GeneMarkS-2+."
                     /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            complement(<1440..1622)
                     /locus_tag="Q7581_RS15690"
                     /old_locus_tag="Q7581_15635"
                     /pseudo=""
     CDS             complement(<1440..1622)
                     /locus_tag="Q7581_RS15690"
                     /old_locus_tag="Q7581_15635"
                     /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          complement(76..859)
                     /name="rep_cluster_935"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="96.943"
                     /coverage="91.0"
                     /evalue="0.0"
ORIGIN
        1 caattatcga ccaattagaa ggctcagcta tcaaaccatc aataactatt ttatcaatag
       61 gttttatatc aatcggcaaa aaatgcgggc ttgcaaaact atctaagctt tcctgaacca
      121 tcgcatgcca atccgttgct ttgccacgtc ttagctgcat ttctaaccgc caccacgtat
      181 cgatttcttt tggcacgatt actttttttc gttcctgctc tagctttttg ttgtacagtc
      241 gcacttggcg ctcactggca cgactgcccc agtacgctgt ttctagcttg ccagaacggc
      301 cgtagattgg cttaaaagaa atcgggtcta caatacgata ctgagtaata aagtcatccg
      361 gcacatctac aatatcgcag gcaatatccg cccgggaaaa atgcggatct aaaaataggt
      421 catgaatgaa tcctttcatg gaactagcta aaaactggcc tatcttattc ggattaaaat
      481 caatacgacc ttttccttca tgaaatttaa gtatttcgat atacgcaata tcttctccat
      541 attgatcgaa taattgccag ccgtttatcc caactgattt caaatatccc tgattttcgt
      601 tcaaacgcat taattgctcg aaatcgacaa aaacaactcc atttttcgtc caataagcta
      661 tggtatcatt cagttttccg acaattgtaa ttcgatcaat cgaccaattt aattttaggg
      721 gggtggtcgt accttgcaca cttaaccgcc tgttagaaat acggttaagt ttttcgagct
      781 gatttatcgt tgttcttttt tctgcccctc gaccttcaat ttttgattga atttcactca
      841 actgattttc atttgccatt ttcgtcctcc aaacgaaaaa agagactttt ggaaagaatt
      901 tccagagttc acgtaaccct aaaaattcat atccaaaaat ctctagcttg aagaaaccta
      961 aaaatattcg tataatgaac ctgagttacg gagctaggtg aagtagtttc cgtaaatagt
     1021 cgagagtgtt agcgcactgc tcggctttta ttttgctctt ttttctcgtt ttctttgatt
     1081 atagcactcc tcctaaaaaa ataaaaagac ctcagggaat ttcattcccc gaaccccttg
     1141 agcctcctcc tgccgaaatg gaaagggcgc acccgctgtt tatttcattc agctatcggt
     1201 tttcacaatc taacacgatc gttccgctac cagtcgcctt acaggctcca ttttcgctcc
     1261 tctaacgtgt tttaacgatt gtgccgataa ctaaacgaaa taaacgctaa aaccgctcag
     1321 aacgcaaaat atgccatttt agagctattg tagaaaatgt agtttgaaat gcaattttct
     1381 tctttcagct ttttatttcc cacttgtaaa tctgctaatt attttctacc agacaaacca
     1441 ttgatttttt ggctatcagt taactcacga ttattatgag aaatgcttgt attctttgtt
     1501 ccctttttga acgaaatact aaaccctaag gtgaacccct ccttcacgct gtcgctaata
     1561 aaaagagtgt aaacctttct gttactcttt gacaaagagt aacattttcc taattgtgac
     1621 atggctgtca caattccaaa tgctctccga gggtattcgc tgtcacaagt gacaacgaaa
     1681 aaaggagccg aaagcgtgtc acgctctcaa ctccttttac gctttatttt gcttcacgca
     1741 aaataatcgc ttatcgtaaa tccacgtcac taaacattga cgtaaattta ctctcactca
     1801 tctgactttt cttattcggt atcacttctc tgtcacatcc aaccccaaaa gccacgtatc
     1861 caattctttt tttaattcgt ctgcagattc cttaaaagtc tctcgtaaat gattcgttaa
     1921 ctcatcattt tgactttctt gcttcagcaa attccgatat ttatattttg tatgtctag
//
