LOCUS       NZ_CP131817             1979 bp    DNA     circular CON 25-APR-2024
DEFINITION  Enterococcus faecium strain 2016C08-243 plasmid p2016C08-243-8,
            complete sequence.
ACCESSION   NZ_CP131817
VERSION     NZ_CP131817.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN36766203
            Assembly: GCF_038439085.1
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  JOURNAL   Unpublished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_038439085.1-RS_2024_04_24
            Annotation Date                   :: 04/24/2024 15:05:45
            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)                     :: 3,281
            CDSs (total)                      :: 3,185
            Genes (coding)                    :: 3,018
            CDSs (with protein)               :: 3,018
            Genes (RNA)                       :: 96
            rRNAs                             :: 6, 6, 6 (5S, 16S, 23S)
            complete rRNAs                    :: 6, 6, 6 (5S, 16S, 23S)
            tRNAs                             :: 74
            ncRNAs                            :: 4
            Pseudo Genes (total)              :: 167
            CDSs (without protein)            :: 167
            Pseudo Genes (ambiguous residues) :: 0 of 167
            Pseudo Genes (frameshifted)       :: 59 of 167
            Pseudo Genes (incomplete)         :: 101 of 167
            Pseudo Genes (internal stop)      :: 39 of 167
            Pseudo Genes (multiple problems)  :: 29 of 167
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP131817.1.
            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="2016C08-243"
                     /isolation_source="blood"
                     /host="Homo sapiens"
                     /db_xref="taxon:1352"
                     /plasmid="p2016C08-243-8"
                     /geo_loc_name="Taiwan"
                     /collection_date="2016"
                     /collected_by="NHRI"
     gene            complement(join(1416..1979,1..453))
                     /locus_tag="Q7582_RS16400"
                     /old_locus_tag="Q7582_16330"
     CDS             complement(join(1416..1979,1..453))
                     /locus_tag="Q7582_RS16400"
                     /old_locus_tag="Q7582_16330"
                     /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            complement(<1034..1216)
                     /locus_tag="Q7582_RS16405"
                     /old_locus_tag="Q7582_16335"
                     /pseudo=""
     CDS             complement(<1034..1216)
                     /locus_tag="Q7582_RS16405"
                     /old_locus_tag="Q7582_16335"
                     /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(1420..1979)
                     /name="rep_cluster_935"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="87.367"
                     /coverage="99.0"
                     /evalue="0.0"
ORIGIN
        1 atctaaaaat aggtcatgaa tgaatccttt catggaacta gctaaaaact ggcctatctt
       61 attcggatta aaatcaatac gaccttttcc ttcatgaaat ttaagtattt cgatatacgc
      121 aatatcttct ccatattgat cgaataattg ccagccgttt atcccaactg atttcaaata
      181 tccctgattt tcgttcaaac gcattaattg ctcgaaatcg acaaaaacaa ctccattttt
      241 cgtccaataa gctatggtat cattcagttt tccgacaatt gtaattcgat caatcgacca
      301 atttaatttt aggggggtgg tcgtaccttg cacacttaac cgcctgttag aaatacggtt
      361 aagtttttcg agctgattta tcgttgttct tttttctgcc cctcgacctt caatttttga
      421 ttgaatttca ctcaactgat tttcatttgc cattttcgtc ctccaaacga aaaaagagac
      481 ttttggaaag aatttccaga gttcacgtaa ccctaaaaat tcatatccaa aaatctctag
      541 cttgaagaaa cctaaaaata ttcgtataat gaacctgagt tacggagcta ggtgaagtag
      601 tttccgtaaa tagtcgagag tgttagcgca ctgctcggct tttattttgc tcttttttct
      661 cgttttcttt gattatagca ctcctcctaa aaaaataaaa agacctcagg gaatttcatt
      721 ccccgaaccc cttgagcctc ctcctgccga aatggaaagg gcgcacccgc tgtttatttc
      781 attcagctat cggttttcac aatctaacac gatcgttccg ctaccagtcg ccttacaggc
      841 tccattttcg ctcctctaac gtgttttaac gattgtgccg ataactaaac gaaataaacg
      901 ctaaaaccgc tcagaacgca aaatatgcca ttttagagct attgtagaaa atgtagtttg
      961 aaatgcaatt ttcttctttc agctttttat ttcccacttg taaatctgct aattattttc
     1021 taccagacaa accattgatt ttttggctat cagttaactc acgattatta tgagaaatgc
     1081 ttgtattctt tgttcccttt ttgaacgaaa tactaaaccc taaggtgaac ccctccttca
     1141 cgctgtcgct aataaaaaga gtgtaaacct ttctgttact ctttgtcaaa gagtaacatt
     1201 ttcctaattg tgacatggct gtcacaattc caaatgctct ccgagggtat tcgctgtcac
     1261 aagtgacaac gaaaaaagga gccgaaagcg tgtcacgctc tcaactcctt ttacgcttta
     1321 ttttgcttca cgcaaaataa tcgcttatcg taaatccacg tcactaaaca ttgacgtaaa
     1381 tttactctca ctcatctgac ttttcttatt cggtatcact tctctgtcac atccaacccc
     1441 aaaagccacg tatccaattc tttttttaat tcgtctgcag attccttaaa agtctctcgt
     1501 aaatgattcg ttaactcatc attttgactt tcttgcttca gcaaattccg atatttatat
     1561 tttgtatgtc tagcaattat cgaccaatta gaaggctcag ctatcaaacc atcaataact
     1621 attttatcaa taggttttat atcaatcggc aaaaaatgcg ggcttgcaaa actatctaag
     1681 ctttcctgaa ccatcgcatg ccaatccgtt gctttgccac gtcttagctg catttctaac
     1741 cgccaccacg tatcgatttc ttttggcacg attacttttt ttcgttcctg ctctagcttt
     1801 ttgttgtaca gtcgcacttg gcgctcactg gcacgactgc cccagtacgc tgtttctagc
     1861 ttgccagaac ggccgtagat tggcttaaaa gaaatcgggt ctacaatacg atactgagta
     1921 ataaagtcat ccggcacatc tacaatatcg caggcaatat ccgcccggga aaaatgcgg
//
