LOCUS       NZ_CP131852             5212 bp    DNA     circular CON 25-APR-2024
DEFINITION  Enterococcus faecium strain 2016C01-052 plasmid p2016C01-052-4,
            complete sequence.
ACCESSION   NZ_CP131852
VERSION     NZ_CP131852.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN36766198
            Assembly: GCF_038441135.1
KEYWORDS    RefSeq.
SOURCE      Enterococcus faecium
  ORGANISM  Enterococcus faecium
            Bacteria; Bacillota; Bacilli; Lactobacillales; Enterococcaceae;
            Enterococcus.
REFERENCE   1  (bases 1 to 5212)
  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  JOURNAL   Unpublished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 5212)
  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_038441135.1-RS_2024_04_24
            Annotation Date                   :: 04/24/2024 14:55:32
            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)                     :: 3,327
            CDSs (total)                      :: 3,231
            Genes (coding)                    :: 3,056
            CDSs (with protein)               :: 3,056
            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)              :: 175
            CDSs (without protein)            :: 175
            Pseudo Genes (ambiguous residues) :: 0 of 175
            Pseudo Genes (frameshifted)       :: 57 of 175
            Pseudo Genes (incomplete)         :: 108 of 175
            Pseudo Genes (internal stop)      :: 43 of 175
            Pseudo Genes (multiple problems)  :: 30 of 175
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP131852.1.
            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..5212
                     /organism="Enterococcus faecium"
                     /mol_type="genomic DNA"
                     /strain="2016C01-052"
                     /isolation_source="blood"
                     /host="Homo sapiens"
                     /db_xref="taxon:1352"
                     /plasmid="p2016C01-052-4"
                     /geo_loc_name="Taiwan"
                     /collection_date="2016"
                     /collected_by="NHRI"
     gene            1..969
                     /locus_tag="Q7577_RS16540"
                     /old_locus_tag="Q7577_16465"
     CDS             1..969
                     /locus_tag="Q7577_RS16540"
                     /old_locus_tag="Q7577_16465"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002347614.1"
                     /GO_function="GO:0003887 - DNA-directed DNA polymerase
                     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 protein"
                     /protein_id="WP_002347614.1"
                     /translation="MSNEIVKYHHELNTIPLRKFTPVEMNLFFSIVSRMRDVGDKKVQF
                     TFEQLKDLSNYKATANVRFIDDLETTYDKLMDLRFGRRSADGLQRERFVLFNQFKIDGK
                     SDIPFAEIQVHEKALPLLNNLEEWVRYSLQQFNELESSYSKTMFRLLKQYRTKGFAYFS
                     KEDFHELLDIPKSYNQGTIDQRVFNPIRQELTAIFKGLTIKKKYGKGRGKPVIGYQFTF
                     KPEIKKSDDFNKHAPTKEEQNKALELANQQVQSEKAPTSLQEKIKEQKRKLELLQQLEK
                     LEREQNTQNKENNAQKSEINSDIPSELKKDLLDNLQNLFKD"
                     /name="replication initiation protein"
     gene            986..1510
                     /locus_tag="Q7577_RS16545"
                     /old_locus_tag="Q7577_16470"
     CDS             986..1510
                     /locus_tag="Q7577_RS16545"
                     /old_locus_tag="Q7577_16470"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002305828.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="DUF536 domain-containing protein"
                     /protein_id="WP_342080556.1"
                     /translation="MTEKTIKELAEELGVSKTAINKKVSDENRKLWFSKTGNKFVINET
                     GQKAIKSMFFNENENSNQQLVGEKTKTETHKNANQVPELEVLSLLEQQLNQKDMQLQEK
                     DEQIKQMQKLLDHQQQLTLQANQQIEKLQEQLQLTYTEESSENKSTTLSEETESIEKQS
                     KTEKKWWQFWQ"
                     /name="DUF536 domain-containing protein"
     gene            1886..2167
                     /locus_tag="Q7577_RS16550"
                     /old_locus_tag="Q7577_16475"
     CDS             1886..2167
                     /locus_tag="Q7577_RS16550"
                     /old_locus_tag="Q7577_16475"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000353845.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_002347613.1"
                     /translation="MDILVRNINPKIIARIDKRCQELTTKTGKKWSRNKYLKVLIESDF
                     DRQLMNYKKDQFDLLLEKFIAIQTENTNILNDYVHTNNQLIETLIGGI"
                     /name="hypothetical protein"
     gene            2169..2585
                     /locus_tag="Q7577_RS16555"
                     /old_locus_tag="Q7577_16480"
     CDS             2169..2585
                     /locus_tag="Q7577_RS16555"
                     /old_locus_tag="Q7577_16480"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001232859.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_002305824.1"
                     /translation="MRKTSVQKHVTLYPSHVDVLDSIIEKNPDVNNYSEAIRFLCMSYE
                     PDTNTTTTSNQAKLNAMGKEISIMTEIMAEFADLYLKDTGVLIGTNSKVYQEVKEKIEN
                     QLNPSRRNQPKNRQKETNQTFTSGNFDPTNFLKR"
                     /name="hypothetical protein"
     gene            3127..3627
                     /locus_tag="Q7577_RS16560"
                     /old_locus_tag="Q7577_16485"
     CDS             3127..3627
                     /locus_tag="Q7577_RS16560"
                     /old_locus_tag="Q7577_16485"
                     /inference="COORDINATES: ab initio prediction:GeneMarkS-2+"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GeneMarkS-2+."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_060800863.1"
                     /translation="MNYNKNLLSHIVYFNYIIIGVYHLNLTQRRGYFETQKENLSRSPL
                     FLDDWNSQIESKSLNQDQIIKYANYCGVYPKKVARILNLSEVQTQLRKGNAIYMGTAGY
                     GNYSNSRHALALFGWVNQGGYQTYYVWNPWYNYPTVISANAGPVTIPVPGGGFTWDNTI
                     TNW"
                     /name="hypothetical protein"
     gene            3600..4043
                     /locus_tag="Q7577_RS16565"
                     /old_locus_tag="Q7577_16490"
     CDS             3600..4043
                     /locus_tag="Q7577_RS16565"
                     /old_locus_tag="Q7577_16490"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002334327.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_002318191.1"
                     /translation="MGQYHYKLVNKPIALVMGLVLVLFLTSCSKKQEIQKTDLIPFLGT
                     WQTKDHSERLVITNLNTSKNIEQYTILVKENNHKIQIIDKNLNINEQVFIYKATNNLLT
                     LRSNKKQLDYTFSLDSPKKLVFILTTNDGTEGTAKPIEFFKAD"
                     /name="hypothetical protein"
     Typing          2..965
                     /name="rep_cluster_1093"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="93.782"
                     /coverage="99.0"
                     /evalue="0.0"
ORIGIN
        1 atgtctaatg aaatcgtaaa gtatcatcat gaattaaata caattccgtt gcgaaaattt
       61 acaccagtcg aaatgaattt gttcttttct atcgtatcaa gaatgcgtga tgtaggtgat
      121 aaaaaagtac aatttacatt cgagcaatta aaagatttaa gcaattataa agcaactgca
      181 aatgttcgat tcatagatga tttagaaaca acgtatgaca aattaatgga tttacgtttt
      241 ggtagaagaa gtgctgacgg tttgcaacgt gaacgttttg ttttatttaa tcaatttaaa
      301 atcgacggaa aatctgatat tccttttgct gaaatacaag ttcatgaaaa agccttaccc
      361 ttacttaata atcttgaaga atgggtgcgc tattctctcc aacaattcaa tgaattagaa
      421 agcagttatt caaaaacaat gtttcgatta ctaaaacaat acagaaccaa aggtttcgct
      481 tatttttcaa aagaagactt tcatgaatta cttgatattc ctaaaagtta caaccaaggt
      541 acgattgatc aacgtgtgtt caatccaata cgacaagaac taaccgcaat ctttaaaggt
      601 ttaacaatca aaaagaaata cggaaaagga cggggaaagc ctgtcattgg ctatcaattt
      661 acatttaaac ctgagataaa aaaatcagac gactttaaca aacatgcccc aacaaaagaa
      721 gaacaaaaca aagcattaga actagctaac caacaagttc aatctgaaaa agcacctact
      781 tcattacaag aaaaaatcaa agaacaaaag cgaaaattgg aacttttaca acagttagaa
      841 aagttagaaa gagaacaaaa tacccaaaat aaagaaaata atgcacaaaa atcagagata
      901 aattccgata ttccttcaga actaaaaaaa gacttattag acaatcttca aaacttattc
      961 aaagattgag gggtttttag attttatgac agaaaaaaca atcaaagaac ttgctgaaga
     1021 attaggagtt agtaaaacag caattaacaa aaaagtttct gacgaaaatc gaaaactttg
     1081 gttttcgaaa accggaaaca agtttgtgat taatgaaacc ggacaaaagg ctataaaatc
     1141 aatgtttttt aacgaaaacg aaaactcaaa tcaacaacta gttggcgaaa aaacgaaaac
     1201 cgaaacccac aaaaacgcca accaagttcc cgaattagaa gtcctttctc tcctagaaca
     1261 acagttaaat caaaaagata tgcaactaca agaaaaagac gagcaaataa aacaaatgca
     1321 aaaattactc gaccaccaac aacaactcac cctgcaagcc aaccaacaaa tcgagaaact
     1381 gcaggaacaa ctacagttga cttatacgga agaatcttcg gaaaataaat caacgactct
     1441 ttctgaagaa acagaatcga tagaaaaaca atcaaagacg gagaaaaaat ggtggcaatt
     1501 ctggcaataa aaccagcaat ttaaattaat aaaaattgct ggttttattc ttctttttgc
     1561 ttttgcgagc agagcaacat ggacccatgt tgcgatattt tggtggcgcc ccaatccccg
     1621 ttttttcgtt gaatcttact cggactgcac tcgttttaca gctgattttt ctgaattttg
     1681 aaagagcata aggaaacgtg gtatcacttt cttacgaaag gtgctagata ggctgtgcct
     1741 atcacgtttc tcagaaaaaa atttgctatc acttttttgc cattgtggct aggctatgta
     1801 tagtgttttg gcgaaaaata actatacaaa tactatattt gtatggtata cataaattat
     1861 acgctgatac gaaaggaaaa tttccatgga cattttagtt cgaaatatca atcccaaaat
     1921 tattgcaaga atagataaac gttgtcagga actcacaacc aaaacgggca aaaaatggag
     1981 tcgaaataaa tatctaaaag ttctaatcga aagtgatttt gaccgtcaac ttatgaatta
     2041 caaaaaagat caattcgatt tattactcga aaaatttatt gccattcaaa cagaaaatac
     2101 gaacatactg aatgactatg ttcacacaaa caaccaactc attgaaacac ttatcggagg
     2161 aatataacat gagaaaaact tctgttcaaa aacacgtaac cctttatccc agtcacgttg
     2221 acgttttaga ttccatcatc gaaaaaaatc cagacgtcaa caattattca gaagccattc
     2281 gttttttatg tatgagttat gaacctgata ccaatacaac cacaaccagt aaccaagcaa
     2341 aactcaatgc catgggaaaa gaaatttcta tcatgacaga aatcatggca gaatttgctg
     2401 atttatatct aaaagatact ggtgttctta tcggtacaaa ttctaaagtg tatcaagaag
     2461 tgaaagaaaa aattgaaaat caactcaatc cttcccgacg aaatcaaccc aaaaatcgtc
     2521 aaaaagaaac caatcaaacc tttacttctg gaaattttga cccaacaaac tttctaaaaa
     2581 gataaaaaaa gaaaccgatc cctaaaaaaa ttcctcgatt tctttttagg gatcagtctt
     2641 ccagcaagat ttgcaagttg gtaccaactt gcgaaaaaaa agaaaaatcc gcttatgcaa
     2701 cttcttcttt ttgtattttg gggcgctacc ccaatcccca agtatcggtt atttaatagc
     2761 gcggaaatcc aaagaatagg acgtaccctg aaacaaaaaa agactgctct cacgagcagc
     2821 ccaaaatgag attatcctat tcatcaacat aaaaatatta caaagtgaag aactagagaa
     2881 agacaaaaaa agcatatcaa atcctctcaa aaataacaag tctttaaaaa atgacagata
     2941 aaaatgcaca aagaactaaa aaagagaaat cgcgtaaaat caagcattag aagctagtaa
     3001 ctagctagac caattaaaaa tcacaaagtg agcgtctcta tccattggta gaggggcaac
     3061 ttggcatagt cgacattatg ttaactagct cgataaataa cgattatgtt cccaaaacaa
     3121 tattttatga actataacaa aaatttgtta tcgcatattg tatattttaa ttatataatt
     3181 ataggtgtat accacttaaa tttaacacaa aggcgtggtt attttgaaac ccaaaaagaa
     3241 aatttatcta ggtctcctct tttccttgat gattggaata gtcaaattga atcaaaaagt
     3301 cttaatcaag atcaaataat aaaatatgca aattactgtg gtgtttatcc taaaaaagta
     3361 gcacgaatac taaacctttc agaggtccaa acacaactaa gaaaaggaaa tgccatttat
     3421 atgggaactg ctggttatgg aaattatagt aacagccgtc atgcacttgc attatttggg
     3481 tgggtcaatc aaggtggtta tcaaacttac tatgtgtgga atccttggta taactaccca
     3541 actgtaataa gtgcaaatgc aggaccagtt acaattcctg tacctggagg tggttttact
     3601 tgggacaata ccattacaaa ttggtaaata aacccattgc tttagttatg ggtctagtgt
     3661 tagttctttt cttaactagt tgttcaaaaa aacaagaaat acaaaagact gatctgattc
     3721 cttttctagg aacttggcaa actaaagatc attcagaacg tctagtaatc actaatttaa
     3781 atacttcaaa aaatatagaa caatatacca tcttagtaaa agagaacaat cataaaattc
     3841 aaatcattga taaaaattta aatataaatg aacaagtttt catttacaaa gcaacaaata
     3901 atttactaac actgcgctct aataaaaaac aattagatta cacttttagt ttggattctc
     3961 caaaaaagct cgtatttatt ttgacaacga atgatgggac agaagggaca gctaaaccaa
     4021 ttgaattttt taaagctgat tgatgaatag ttgtttgata ttacaaaaca ataatttcac
     4081 cgaaggtgaa acaagcgaaa ctttacaaaa agtggctagc atttgctagc cttttttgta
     4141 ttgtggagcg tggtttttga gggggattca agggggagct tgcgcccctt tgacaagcgg
     4201 ttatttgcac caaatacgta ggtatttggc tagcaaatat agagcttgcc aaacacttta
     4261 gtgagttttg tagaaagtac ctttaaaggt actttcacat tacgaacgat acgtccgtag
     4321 gacgtactga aagggtggga tttatgagcg aactaatgca aaatttggct agcaaaaaaa
     4381 gttaaaaaat atatgctaat aatcgagcga aatgaacact ttttcaagtg agcgaatccg
     4441 ccatgacaaa gctgaagcag tttatttcag ctttgtcatg gcgtgtgcct agacttttaa
     4501 aaaagtcggc acacgagcaa atatctttat caagctctaa tttgcgtttt aagacgtttg
     4561 aaacgtctaa gtatataaat atataagagt aggtttaaga gtgcttaaat cgaattttag
     4621 agggcattca gacaacttta gggttgttag ggcttgccct gaccgcctgt aaggcgcttt
     4681 aagaacaaga taagggattt atactaagac tgtcttaaaa cgtctcaaac gaaggctcat
     4741 agcttctcaa agagttcctt atgaacattt ttagcaaagg agccggaagc gactgcgcag
     4801 tataatgtga gagcagagcg atcacacctt tttaagcgac tgtagggagt aagattccca
     4861 gttgagaaaa atgcgcgaat ctgtttggag aaaaaagaag tggtttttta ggcgggaaat
     4921 tttgtccccc tcttttataa tctcttttta aacctctttt taaacctctt taccgtcggc
     4981 tatatcctta ctctcccaag ggaatgacgc ttttatctac atcgttttgt ctgtttatct
     5041 acatcgtttt gtctgtttat ctacatcgtt ttgtctgttt atctacatcg ttttgtctgt
     5101 ttgtacattg aattagtaca tcgacgatgt taatataaga tgtagataaa caggcatttt
     5161 gtatttcata acgtgtatct cttgtgcgag taagaaagga gctattttaa at
//
