LOCUS       NZ_CP131832             4067 bp    DNA     circular CON 25-APR-2024
DEFINITION  Enterococcus faecium strain 2016C07-254 plasmid p2016C07-254-7,
            complete sequence.
ACCESSION   NZ_CP131832
VERSION     NZ_CP131832.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN36766201
            Assembly: GCF_038441105.1
KEYWORDS    RefSeq.
SOURCE      Enterococcus faecium
  ORGANISM  Enterococcus faecium
            Bacteria; Bacillota; Bacilli; Lactobacillales; Enterococcaceae;
            Enterococcus.
REFERENCE   1  (bases 1 to 4067)
  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  JOURNAL   Unpublished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 4067)
  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_038441105.1-RS_2024_04_25
            Annotation Date                   :: 04/25/2024 19:54:46
            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)                     :: 3,049
            CDSs (total)                      :: 2,960
            Genes (coding)                    :: 2,846
            CDSs (with protein)               :: 2,846
            Genes (RNA)                       :: 89
            rRNAs                             :: 6, 6, 6 (5S, 16S, 23S)
            complete rRNAs                    :: 6, 6, 6 (5S, 16S, 23S)
            tRNAs                             :: 67
            ncRNAs                            :: 4
            Pseudo Genes (total)              :: 114
            CDSs (without protein)            :: 114
            Pseudo Genes (ambiguous residues) :: 0 of 114
            Pseudo Genes (frameshifted)       :: 39 of 114
            Pseudo Genes (incomplete)         :: 61 of 114
            Pseudo Genes (internal stop)      :: 29 of 114
            Pseudo Genes (multiple problems)  :: 12 of 114
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP131832.1.
            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..4067
                     /organism="Enterococcus faecium"
                     /mol_type="genomic DNA"
                     /strain="2016C07-254"
                     /isolation_source="blood"
                     /host="Homo sapiens"
                     /db_xref="taxon:1352"
                     /plasmid="p2016C07-254-7"
                     /geo_loc_name="Taiwan"
                     /collection_date="2016"
                     /collected_by="NHRI"
     gene            join(2764..4067,1..105)
                     /locus_tag="Q7580_RS15215"
                     /old_locus_tag="Q7580_15140"
                     /pseudo=""
     CDS             join(2764..4067,1..105)
                     /locus_tag="Q7580_RS15215"
                     /old_locus_tag="Q7580_15140"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_016173818.1"
                     /GO_function="GO:0003677 - DNA binding [Evidence IEA]"
                     /GO_process="GO:0006310 - DNA recombination [Evidence IEA]"
                     /note="frameshifted; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="plasmid recombination protein"
                     /name="plasmid recombination protein"
     gene            554..1528
                     /locus_tag="Q7580_RS15220"
                     /old_locus_tag="Q7580_15145"
     CDS             554..1528
                     /locus_tag="Q7580_RS15220"
                     /old_locus_tag="Q7580_15145"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002303407.1"
                     /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_002303407.1"
                     /translation="MSKKGTIINEWEKLTAPSNRRLSVPFMDTPLKIQWSIDRITIVGN
                     LKENIYYHTTHDVLILDFEQLMRLNEGNGYLRSVSNNGWQLLDQHEENIAYIEILKWQE
                     GKGRIDFNPNKISQFLASSMKNFIHDLFIEPHFSRADIACDIIDVPDEFITQYRVVDPV
                     SFKPIYGRNGKLETAYWGSRSSERQIRMYNKKLEQEKKRKIVPKEIVSWWRLELQLRRG
                     KATDWHAMVYESLDSFASPHYLPADTSVADKMMITALTTEHDYWGQINRKTKYKYRNLL
                     KQESQNDELTNHLRETFAESADDLKKELDTWLLGLDVTEEEEK"
                     /name="replication initiation factor domain-containing
                     protein"
     gene            1525..1758
                     /locus_tag="Q7580_RS15225"
                     /old_locus_tag="Q7580_15150"
     CDS             1525..1758
                     /locus_tag="Q7580_RS15225"
                     /old_locus_tag="Q7580_15150"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002298421.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_002303408.1"
                     /translation="MTEKQKYFGKKNWLVNLTGDYVVVVFLDSKKMSGKLLDVTQYELI
                     LKNNKIDSPIIIPKHAVKYIYAVAESSGEAND"
                     /name="hypothetical protein"
     gene            1829..2176
                     /locus_tag="Q7580_RS15230"
                     /old_locus_tag="Q7580_15155"
     CDS             1829..2176
                     /locus_tag="Q7580_RS15230"
                     /old_locus_tag="Q7580_15155"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002321903.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_171346404.1"
                     /translation="MVAVLEMRCNMDKIDLREETVDRIELMYERLADYLNLPDEDNYSE
                     MLERMMDVLNSTINVGLANSSLITDKFVYGKIAETEDESEKEFWLNILTYVMQLNQIGV
                     IYRNKSKGKEL"
                     /name="hypothetical protein"
     gene            2180..2542
                     /locus_tag="Q7580_RS15235"
                     /old_locus_tag="Q7580_15160"
     CDS             2180..2542
                     /locus_tag="Q7580_RS15235"
                     /old_locus_tag="Q7580_15160"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_016173819.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_002303404.1"
                     /translation="MGMTLADIKAQEEKLKKEQAKLRQQKKRLIEKENAEMGKALRKHF
                     GFESFDDFERWLSSISDDQQHEKSVDNEWLADEKSAPSERDYPNESDGLLGVIPSKKSQ
                     MSESKFTSMFNDVSLR"
                     /name="hypothetical protein"
     Typing          633..1528
                     /name="rep_cluster_2146"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          2765..3612
                     /name="MOBV"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="95.053"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 ctttctgagg aattagaagt gttagagcag gagaaaacct tattttatcg tcaaaacgtc
       61 tcacagcgta aattagagcg ttctgaagat gagatcgagt ggtagttacg atgtgcagtc
      121 aacggtaccg gaggcggttt gtgccgagga taaggagttg acggctaaac cactaatccc
      181 tgaagctgac atttgctaaa aaatggcaag tccatttttt ggccaaccta gcgttagcga
      241 agtttggggg cgcccttttc aaagggtgcg gttttatttt ttggatattt gcatagctaa
      301 agagaagtgc tattattgag ttatcaaata aataaactga aaaaagagca aaaaaataaa
      361 gtcgagcaac gctggacacg ttctcgacct ttacggaaac taatcgcact agctccgtaa
      421 cttcttaatc attatacgaa tatttttaga tttcttcaag actagagatt ttttggtaat
      481 gaatttttaa gagttacgtg aacttttgaa aattctttcc agaagtctct ttttctttga
      541 ggaggaacaa aatttgagta aaaaaggcac gatcataaat gagtgggaaa aattaacagc
      601 cccctctaac aggcggttaa gtgtcccttt tatggacacc cccctaaaaa ttcagtggtc
      661 aatcgaccga attaccattg ttggaaatct taaagagaat atctattatc acactacaca
      721 tgatgtgttg attttagatt ttgaacagct tatgcgccta aatgaaggta acggttattt
      781 aagatctgtt agtaataatg gttggcagtt gttagaccaa catgaagaga atattgctta
      841 tattgaaatt ttaaaatggc aagaggggaa agggcgtata gacttcaatc cgaataagat
      901 tagtcaattc ttagctagtt ccatgaaaaa ttttattcat gatttgttta tcgaacctca
      961 cttttcacgt gcagatattg cttgcgacat tatcgatgta cctgatgagt ttattacaca
     1021 atatcgggta gttgatccag tttcttttaa gcctatttat ggacggaatg gaaaattaga
     1081 gacggcatat tggggatctc gctcttctga acgtcaaatt cggatgtata ataaaaaact
     1141 ggaacaagag aagaaaagaa aaattgtgcc aaaagaaatc gtgagttggt ggcggttaga
     1201 attacaatta agacgaggga aagcgactga ttggcatgct atggtttatg aaagcttaga
     1261 tagttttgct agtcctcatt acttgcctgc tgatacaagt gtagctgaca aaatgatgat
     1321 tactgcttta acaacagaac atgattattg ggggcaaatt aatcgaaaga caaaatataa
     1381 atatcgaaat ttgctgaagc aagaaagtca aaatgatgaa ttgacgaatc atttacgaga
     1441 aacctttgca gaatcggcag acgatttaaa aaaagaatta gacacatggc ttctagggct
     1501 agacgtaaca gaggaggaag aaaaatgaca gaaaaacaaa agtattttgg taagaaaaat
     1561 tggttggtaa atttaacagg tgattacgtt gtggttgttt ttttggatag caaaaaaatg
     1621 tccggtaagt tacttgatgt aacgcaatat gaattgattt tgaaaaataa taaaattgac
     1681 tctccgatta ttatccctaa gcacgccgtt aaatatattt atgcggtagc tgaaagtagt
     1741 ggagaagcta atgactgatt tgtcagaaaa gatgaccata aaaaatcttg ctgatgaatt
     1801 aggtgtatcg aaaattaaag aatcggaaat ggtggcagtt ttggaaatga ggtgtaacat
     1861 ggataaaatt gatttaagag aagagacagt tgatagaatt gaattgatgt atgaacgatt
     1921 agctgattat ttgaatttgc cggatgaaga taattatagt gaaatgcttg agagaatgat
     1981 ggacgttctc aattctacaa tcaatgtagg cctagcaaat tcttctttga ttactgataa
     2041 atttgtttac ggtaaaatag ccgaaacaga agatgaatct gaaaaggaat tttggctgaa
     2101 tattttaact tatgttatgc aattaaatca aattggtgtt atttatcgaa ataaatcaaa
     2161 aggcaaggag ctgtaaatct tgggaatgac tttagcagat attaaagcac aagaagaaaa
     2221 attgaaaaaa gaacaggcaa aacttcgtca acagaaaaaa cgattgattg agaaggaaaa
     2281 tgctgaaatg ggtaaggcac ttcggaagca ttttggattt gaatcttttg atgattttga
     2341 gcggtggtta tcgtcaattt ctgacgatca gcaacacgaa aaatcagtgg ataatgagtg
     2401 gcttgctgat gaaaaatcag cgccaagcga acgagattat cccaatgaat ctgacggctt
     2461 actcggagtg ataccgagta aaaaaagtca gatgagtgag agtaaattta cgtcaatgtt
     2521 taatgacgtg agtttacgat aagcgattat tttgcgtgaa gcaaaataaa gcgtaaaagg
     2581 agttgagagc gtgacacgct ttcggctcct tttttcgttg tcacttgtga cagcgaatac
     2641 cctcggagag catttggaat tgtgacagcc atgtcacaat taggaaaatg tttactcttt
     2701 gacaaagagt aacagaaagg tttacactct ttttattagc gacagccgaa ggagggtttt
     2761 aacttggggt tcagtatttc gttcaaaaag ggaacaaaga atacaagcat ttctcataat
     2821 aatcgtgagt taactgatag ccaaaaaatc aatgactggc ataagcatat tgatttcaca
     2881 aaatcggatg aaaatatcta tttagaacaa acaaatattc gtgaaaaata tgaagaatta
     2941 ttcggtgaag ccgtagaaaa atataatgca aagcagaaaa gagccgatag aaaaatcgag
     3001 gactatttag caaaggttcg caaggataaa aaattggaac cacagcgaga atttatcgtg
     3061 caaattggta ctcttgatga ttttcgtact actcgtgatg atggttcttc tactggcata
     3121 tcggaacaac aagcagaaca aaatcgagtg attgccaaca aaattttagt tgaatatttc
     3181 aaagaattta aagaacggaa tcctaattta tccgtctaca atgctgttat tcataatgac
     3241 gaagtaagtc cgcacctgca tttgaatatt gttcctgttg ctgaagggta taaacggggt
     3301 gttcaaaagc aaccaagttt taacaaagcc ttgcaacagc agggtttacg agcagataaa
     3361 gagaatggtc gagtgatttg gaataatttt aggaatcagg aagttgagtc aattgaacgt
     3421 ttgatggcag attttggttg ggagcgtgag ttagtcggta ctaacaaaat caaagatgtt
     3481 cacgaatata aagaaatcat gagcgagatt tcagaattgc gtcaaacggc cgtaaaagag
     3541 cgtgagagcg tttctgatga gttgaggtat atatttctag gcaaagagaa gaaaatgagc
     3601 gagaaaaggc tctggtggct tctgagagag tgaagattga agaagagaag aaaaatatgc
     3661 tgaatgtaaa aaaagagatg gcggtcattt tccaaaaaga tattgttcct ttagaaagtt
     3721 tcaagaggct tcctgatggt tcgtatcatt tatctgggaa tgattttgtt gatttgtatc
     3781 aacgagctac gagagcaaca aatgccaaga gaaatgctga taacatgagt gagcaatatt
     3841 tacagatgct tgagcaaaat acagaattaa atgagtatgt agctacattg gaagaagagc
     3901 gtcatttgtc tggtagaaaa caattagcag atttacaagt ggaaaataaa aagctgaaag
     3961 aagaaaatcg ctctttacgc cagcgtttag agcgattaaa aaacgcattt caaaaatcga
     4021 tcactcgttt gtctatccgt tttggtcttg cagaaaagga tatgggg
//
