LOCUS       NZ_CP131814             6029 bp    DNA     circular CON 25-APR-2024
DEFINITION  Enterococcus faecium strain 2016C08-243 plasmid p2016C08-243-5,
            complete sequence.
ACCESSION   NZ_CP131814
VERSION     NZ_CP131814.1
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 6029)
  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  JOURNAL   Unpublished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 6029)
  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
            CP131814.1.
            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..6029
                     /organism="Enterococcus faecium"
                     /mol_type="genomic DNA"
                     /strain="2016C08-243"
                     /isolation_source="blood"
                     /host="Homo sapiens"
                     /db_xref="taxon:1352"
                     /plasmid="p2016C08-243-5"
                     /geo_loc_name="Taiwan"
                     /collection_date="2016"
                     /collected_by="NHRI"
     gene            1..969
                     /locus_tag="Q7582_RS16315"
                     /old_locus_tag="Q7582_16245"
     CDS             1..969
                     /locus_tag="Q7582_RS16315"
                     /old_locus_tag="Q7582_16245"
                     /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="Q7582_RS16320"
                     /old_locus_tag="Q7582_16250"
     CDS             986..1510
                     /locus_tag="Q7582_RS16320"
                     /old_locus_tag="Q7582_16250"
                     /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="Q7582_RS16325"
                     /old_locus_tag="Q7582_16255"
     CDS             1886..2167
                     /locus_tag="Q7582_RS16325"
                     /old_locus_tag="Q7582_16255"
                     /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..2600
                     /locus_tag="Q7582_RS16330"
                     /old_locus_tag="Q7582_16260"
     CDS             2169..2600
                     /locus_tag="Q7582_RS16330"
                     /old_locus_tag="Q7582_16260"
                     /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_342082365.1"
                     /translation="MRKTSVQKHVTLYPSHVDVLDSIIEKNPDVNNYSEAIRFLCMSYE
                     PDTNTTTTSNQAKLNAMGKEISIMTEIMAEFADLYLKDTGVLIGTNSKVYQEVKEKIEN
                     QLNPSRRNQPKNRQKETNQTFTSGNFDPTNFLKGSVAKF"
                     /name="hypothetical protein"
     gene            complement(2634..3314)
                     /locus_tag="Q7582_RS16335"
                     /old_locus_tag="Q7582_16265"
     CDS             complement(2634..3314)
                     /locus_tag="Q7582_RS16335"
                     /old_locus_tag="Q7582_16265"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_064305258.1"
                     /GO_function="GO:0004803 - transposase activity [Evidence
                     IEA]"
                     /GO_process="GO:0006313 - DNA transposition [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="IS6-like element IS1216 family transposase"
                     /protein_id="WP_001015311.1"
                     /translation="MNHFKGKQFQQDVIIVAVGYYLRYNLSYREVQEILYDRGINVSHT
                     TIYRWVQEYGKLLYQIWKKKNKKSFYSWKMDETYIKIKGKWHYLYRAIDADGLTLDIWL
                     RKKRDTQAAYAFLKRLVKQFDEPKVVVTDKAPSITSAFKKLKEYGFYQGTEHRTIKYLN
                     NLIEQDHRPVKRRNKFYRSLRTASTTIKGMEAIRGLYKKTRKEGTLFGFSVCTEIKVLL
                     GIPA"
                     /name="IS6-like element IS1216 family transposase"
     gene            3944..4444
                     /locus_tag="Q7582_RS16340"
                     /old_locus_tag="Q7582_16270"
     CDS             3944..4444
                     /locus_tag="Q7582_RS16340"
                     /old_locus_tag="Q7582_16270"
                     /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            4417..4860
                     /locus_tag="Q7582_RS16345"
                     /old_locus_tag="Q7582_16275"
     CDS             4417..4860
                     /locus_tag="Q7582_RS16345"
                     /old_locus_tag="Q7582_16275"
                     /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 tttctaaaag
     2581 gttctgttgc aaagttttaa ataaagaata aaatccctta cggtatctat gatttaagct
     2641 gggattccca ataatacctt gatttcagta cagaccgaaa acccgaagag agtgccttct
     2701 tttcgggttt tcttatataa tcctcgaatg gcttccatgc ctttaatcgt ggtagaggca
     2761 gtgcgtaaac ttcgatagaa tttattgcgt ctctttactg gacgatggtc ttgttcaatc
     2821 aaattattca ggtatttaat ggtacgatgt tctgtccctt gataaaagcc gtattctttt
     2881 agtttcttaa aggcacttgt aatagagggg gctttatctg tgactacaac cttcggttca
     2941 tcaaactgct tcactaaccg cttaagaaaa gcataggctg cttgtgtgtc ccgtttttta
     3001 cgtaaccaaa tatccaaggt taaaccatct gcatcgatgg ctcgatacaa ataatgccat
     3061 tttcctttaa ttttgatgta cgtttcatcc attttccatg aataaaagga ttttttattt
     3121 ttctttttcc aaatttgata gagtagtttg ccatattctt gcacccaacg ataaatcgtc
     3181 gtatgagaaa cgttaatgcc acgatcatat aagatttctt gaacttcacg atagctaagg
     3241 ttataacgaa gatagtagcc cacggctaca ataatcacat cctgctgaaa ttgctttcct
     3301 ttaaaatgat tcatcgtcat tcctcctgct atctttttct attattctac cttatttgat
     3361 agtagattta aaactttgca acagaacctt ctaaaaagat aaaaaaagaa accgatccct
     3421 aaaaaaattc ctcgatttct ttttagggat cagtcttcca gcaagatttg caagttggta
     3481 ccaacttgcg aaaaaaaaga aaaatccgct tatgcaactt cttctttttg tattttgggg
     3541 cgctacccca atccccaagt atcggttatt taatagcgcg gaaatccaaa gaataggacg
     3601 taccctgaaa caaaaaaaga ctgctctcac gagcagccca aaatgagatt atcctattca
     3661 tcaacataaa aatattacaa agtgaagaac tagagaaaga caaaaaaagc atatcaaatc
     3721 ctctcaaaaa taacaagtct ttaaaaaatg acagataaaa atgcacaaag aactaaaaaa
     3781 gagaaatcgc gtaaaatcaa gcattagaag ctagtaacta gctagaccaa ttaaaaatca
     3841 caaagtgagc gtctctatcc attggtagag gggcaacttg gcatagtcga cattatgtta
     3901 actagctcga taaataacga ttatgttccc aaaacaatat tttatgaact ataacaaaaa
     3961 tttgttatcg catattgtat attttaatta tataattata ggtgtatacc acttaaattt
     4021 aacacaaagg cgtggttatt ttgaaaccca aaaagaaaat ttatctaggt ctcctctttt
     4081 ccttgatgat tggaatagtc aaattgaatc aaaaagtctt aatcaagatc aaataataaa
     4141 atatgcaaat tactgtggtg tttatcctaa aaaagtagca cgaatactaa acctttcaga
     4201 ggtccaaaca caactaagaa aaggaaatgc catttatatg ggaactgctg gttatggaaa
     4261 ttatagtaac agccgtcatg cacttgcatt atttgggtgg gtcaatcaag gtggttatca
     4321 aacttactat gtgtggaatc cttggtataa ctacccaact gtaataagtg caaatgcagg
     4381 accagttaca attcctgtac ctggaggtgg ttttacttgg gacaatacca ttacaaattg
     4441 gtaaataaac ccattgcttt agttatgggt ctagtgttag ttcttttctt aactagttgt
     4501 tcaaaaaaac aagaaataca aaagactgat ctgattcctt ttctaggaac ttggcaaact
     4561 aaagatcatt cagaacgtct agtaatcact aatttaaata cttcaaaaaa tatagaacaa
     4621 tataccatct tagtaaaaga gaacaatcat aaaattcaaa tcattgataa aaatttaaat
     4681 ataaatgaac aagttttcat ttacaaagca acaaataatt tactaacact gcgctctaat
     4741 aaaaaacaat tagattacac ttttagtttg gattctccaa aaaagctcgt atttattttg
     4801 acaacgaatg atgggacaga agggacagct aaaccaattg aattttttaa agctgattga
     4861 tgaatagttg tttgatatta caaaacaata atttcaccga aggtgaaaca agcgaaactt
     4921 tacaaaaagt ggctagcatt tgctagcctt ttttgtattg tggagcgtgg tttttgaggg
     4981 ggattcaagg gggagcttgc gcccctttga caagcggtta tttgcaccaa atacgtaggt
     5041 atttggctag caaatataga gcttgccaaa cactttagtg agttttgtag aaagtacctt
     5101 taaaggtact ttcacattac gaacgatacg tccgtaggac gtactgaaag ggtgggattt
     5161 atgagcgaac taatgcaaaa tttggctagc aaaaaaagtt aaaaaatata tgctaataat
     5221 cgagcgaaat gaacactttt tcaagtgagc gaatccgcca tgacaaagct gaagcagttt
     5281 atttcagctt tgtcatggcg tgtgcctaga cttttaaaaa agtcggcaca cgagcaaata
     5341 tctttatcaa gctctaattt gcgttttaag acgtttgaaa cgtctaagta tataaatata
     5401 taagagtagg tttaagagtg cttaaatcga attttagagg gcattcagac aactttaggg
     5461 ttgttagggc ttgccctgac cgcctgtaag gcgctttaag aacaagataa gggatttata
     5521 ctaagactgt cttaaaacgt ctcaaacgaa ggctcatagc ttctcaaaga gttccttatg
     5581 aacattttta gcaaaggagc cggaagcgac tgcgcagtat aatgtgagag cagagcgatc
     5641 acaccttttt aagcgactgt agggagtaag attcccagtt gagaaaaatg cgcgaatctg
     5701 tttggagaaa aaagaagtgg ttttttaggc gggaaatttt gtccccctct tttataatct
     5761 ctttttaaac ctctttttaa acctctttac cgtcggctat atccttactc tcccaaggga
     5821 atgacgcttt tatctacatc gttttgtctg tttatctaca tcgttttgtc tgtttatcta
     5881 catcgttttg tctgtttatc tacatcgttt tgtctgtttg tacattgaat tagtacatcg
     5941 acgatgttaa tataagatgt agataaacag gcattttgta tttcataacg tgtatctctt
     6001 gtgcgagtaa gaaaggagct attttaaat
//
