LOCUS       NZ_CP131860             4377 bp    DNA     circular CON 25-APR-2024
DEFINITION  Enterococcus faecium strain 2016S01-202 plasmid p2016S01-202-4,
            complete sequence.
ACCESSION   NZ_CP131860
VERSION     NZ_CP131860.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN36766197
            Assembly: GCF_038441145.1
KEYWORDS    RefSeq.
SOURCE      Enterococcus faecium
  ORGANISM  Enterococcus faecium
            Bacteria; Bacillota; Bacilli; Lactobacillales; Enterococcaceae;
            Enterococcus.
REFERENCE   1  (bases 1 to 4377)
  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  JOURNAL   Unpublished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 4377)
  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_038441145.1-RS_2024_04_24
            Annotation Date                   :: 04/24/2024 14:57:29
            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)                     :: 3,180
            CDSs (total)                      :: 3,090
            Genes (coding)                    :: 2,929
            CDSs (with protein)               :: 2,929
            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)              :: 161
            CDSs (without protein)            :: 161
            Pseudo Genes (ambiguous residues) :: 0 of 161
            Pseudo Genes (frameshifted)       :: 66 of 161
            Pseudo Genes (incomplete)         :: 93 of 161
            Pseudo Genes (internal stop)      :: 38 of 161
            Pseudo Genes (multiple problems)  :: 30 of 161
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP131860.1.
            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..4377
                     /organism="Enterococcus faecium"
                     /mol_type="genomic DNA"
                     /strain="2016S01-202"
                     /isolation_source="blood"
                     /host="Homo sapiens"
                     /db_xref="taxon:1352"
                     /plasmid="p2016S01-202-4"
                     /geo_loc_name="Taiwan"
                     /collection_date="2016"
                     /collected_by="NHRI"
     gene            complement(join(4233..4377,1..824))
                     /locus_tag="Q7576_RS15875"
                     /old_locus_tag="Q7576_15800"
     CDS             complement(join(4233..4377,1..824))
                     /locus_tag="Q7576_RS15875"
                     /old_locus_tag="Q7576_15800"
                     /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_002298422.1"
                     /translation="MSKNGIIVNEWENLTALSNRRLNVQNMYTPLKMQWSIDRITIVGK
                     LKENIYYHTQNDVLILDFEQLMRVNEGNGYLKAVGNNGWQLLDQYEENIAYIEILKWQD
                     GKGRIDFNPNKIGHFLASSMKNFIHDLFLEPHFSRADIACDIIDVPDEFITQYRVVDPV
                     SFKPIYGRSGKLETAYWGSRASERQIRLYNKKLEQETKRKIVPPEIETWWRLELQLRRG
                     KATDWHAMVHESLNSFASPHFLPLDVKTNDKVMIFGLIANPEMWGFLERRMKYKLRDIL
                     KRESQNDELTNHLRETFSESADVLKKELDTWLQGLDVTEEE"
                     /name="replication initiation factor domain-containing
                     protein"
     gene            complement(1274..2680)
                     /locus_tag="Q7576_RS15880"
                     /old_locus_tag="Q7576_15805"
     CDS             complement(1274..2680)
                     /locus_tag="Q7576_RS15880"
                     /old_locus_tag="Q7576_15805"
                     /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="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="plasmid recombination protein"
                     /protein_id="WP_217277483.1"
                     /translation="MGFSISFKKGTKNTSISHNNRELTDRQKTNDWHKHIDFTKSDENI
                     YLEQTNLADKYEELFGEVVEKYNAKQKRADRKIEDYLAKVRKDKKLEPQREFIVQIGIL
                     DDFQTNRADGSSTGISKQQAEQNRVIANKILVQYYKEFQERNPNLAVYNAVIHNDEISP
                     HLHLNIVPVAEGYKRGVQKQPSFNKALVQQGIHADKDNGRVLFNNFRNQEVDSIERLMN
                     DYGWKRDIVGTNKIKDIHEYKEIMSEISELRQTAVKERESVSDELRYIYRQREENERDK
                     ALMASERAKIEEEKKNMLNVKKEMAVIFQKDMVPLESFKRLPDGSYHLSGNDFVDLYQR
                     ATRATNAKRNADNMSEQYLQMLEQNTELNEYVATLEEERHLSGRKQLADLQVENKKLKE
                     ENRSLRQRLERLKNAFQKSITRLSIRFGLAEKDIGLSEELEVLEQEKTLFYRQNVSQRK
                     LERSEDEIEW"
                     /name="plasmid recombination protein"
     gene            complement(2902..3264)
                     /locus_tag="Q7576_RS15885"
                     /old_locus_tag="Q7576_15810"
     CDS             complement(2902..3264)
                     /locus_tag="Q7576_RS15885"
                     /old_locus_tag="Q7576_15810"
                     /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_002298418.1"
                     /translation="MGMTLADIKAQEEKLKKEQAKLRQQKKRLIEKENAAMGKALRKRF
                     GFETFADFERWLSSISDDQQHEKSVDNEWLADEKSAPSERDYPDESDGLFGVIPNKKSQ
                     MSESKFTSIFNDVNLR"
                     /name="hypothetical protein"
     gene            complement(3268..3576)
                     /locus_tag="Q7576_RS15890"
                     /old_locus_tag="Q7576_15815"
     CDS             complement(3268..3576)
                     /locus_tag="Q7576_RS15890"
                     /old_locus_tag="Q7576_15815"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002292673.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_002298419.1"
                     /translation="MDKIDLREETVDRIELMYERLADYLNLPDEDNYSEMLERMMDVLN
                     SVINADLAKSSVLTNEFVHKHLAQTTDESEKEFWLKLMSHVMQLNQISVINSKEKEM"
                     /name="hypothetical protein"
     gene            complement(3585..4004)
                     /locus_tag="Q7576_RS15895"
                     /old_locus_tag="Q7576_15820"
     CDS             complement(3585..4004)
                     /locus_tag="Q7576_RS15895"
                     /old_locus_tag="Q7576_15820"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002351943.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_002298420.1"
                     /translation="MTDLPEKMTIKNLADELGISKNTVRNQLVNAGYDLARYKDNGVIM
                     LDKELIGVVRSIYRSKGGQLTGDLPVNDAGNDFPLEKENEFLREQLAEKDRHISELTEM
                     IRDQQKLTLLQQQKNDQLLLENQELKNRKWWQFWK"
                     /name="hypothetical protein"
     gene            complement(3997..4230)
                     /locus_tag="Q7576_RS15900"
                     /old_locus_tag="Q7576_15825"
     CDS             complement(3997..4230)
                     /locus_tag="Q7576_RS15900"
                     /old_locus_tag="Q7576_15825"
                     /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_002298421.1"
                     /translation="MAEKQKHFGKKNWLVNLTGDNVVVVFLDSKKMSGKLLDVTQYELI
                     LKNNKIDSPIIIPKHAVKYVYGVAESNGEDND"
                     /name="hypothetical protein"
     Typing          complement(1278..2680)
                     /name="MOBV"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="91.88"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 tatttcattc tacgctctaa aaacccccac atttcagggt tagcaatcag tccaaaaatc
       61 atcaccttat catttgtttt tacatcaagt ggtagaaaat gagggctagc aaaactattt
      121 aaactttcat gaaccattgc atgccaatct gttgctttcc cacgccttaa ctgcaattcc
      181 agtcgccacc aagtttctat ttctggtggc acaattttac gcttggtttc ctgttccaat
      241 tttttgttgt atagccgaat ctggcgttcg ctggcacgac tgccccaata agctgtttcc
      301 agcttcccag accgcccata aattggcttg aaagaaacag gatcaaccac tcgatattgt
      361 gtaataaact catcaggcac atcgataata tcgcaagcaa tatccgcacg tgagaaatgt
      421 ggttctagaa ataaatcatg aatgaaattt ttcattgaac tagctaaaaa atgaccaatc
      481 ttattcgggt taaaatcaat ccgccctttg ccatcttgcc atttcaaaat ctcaatataa
      541 gcaatatttt cttcgtattg gtctaataat tgccagccgt tattcccaac cgcttttaaa
      601 tagccattgc cttcattcac ccgcattaat tgctcaaaat ctaaaatcaa cacatcattt
      661 tgagtgtgat aataaatatt ttccttcagt tttccaacga tagtaattcg gtcaattgac
      721 cactgcattt ttaagggggt gtacatattt tgtacattta accgcctgtt agatagggct
      781 gttaaatttt cccactcatt tacgattatg ccatttttac tcaaattttg ttcctcctca
      841 aagaaaaaga gacttctgga aagaattttc aaaagttcac gtaactctta aaaattcatt
      901 accaaaaaat ctctagtctt gaagaaatct aaaaatattc gtataatgat taagaagtta
      961 cggagctagt gcgattagtt tccgtaaagg tcgagaacgt tggtagcgtt gctcgacttt
     1021 atttttttgc tcttttttca gtttatttat ttgataactc aataatagca cttctcttta
     1081 gctatgcaaa tatccaaaaa cataaaaccg caccctttga aaagggcgcc cccaaacttc
     1141 gctaacgcta ggttggccaa aaaatggact ggccattttt tagcaaatgt cagcttaata
     1201 ggctagtggt ttagccgtca actccttatc ctcggcacaa accgcctccg gtaccgttga
     1261 ctgcacatcg taactaccac tcgatctcat cttcagaacg ctctaattta cgctgtgaga
     1321 cgttttgacg ataaaataag gttttctcct gctctaacac ttctaattcc tcagaaagcc
     1381 ctatatcctt ttctgcaaga ccaaaacgga tagacaaacg agtgatcgat ttttgaaatg
     1441 cgttttttaa tcgctctaaa cgctggcgta aagagcgatt ttcttctttc agctttttat
     1501 tttccacttg taaatctgct aattgttttc taccagacaa atgacgctct tcttccaatg
     1561 tagctacata ctcatttaat tctgtatttt gctcaagcat ctgtaaatat tgctcactca
     1621 tgttatcagc atttctcttg gcatttgttg ctctcgtagc tcgttgatac aaatcaacaa
     1681 aatcattccc agataaatga tacgaaccat caggaagcct cttgaaactt tctaaaggaa
     1741 ccatatcttt ttggaaaatg accgccatct ctttttttac attcagcata tttttcttct
     1801 cttcttcaat cttcgctctc tcagaagcca tcagagcctt atcacgctcg ttttcttctc
     1861 tttgcctata aatatacctc aactcatcag aaacgctctc acgctctttt acagccgttt
     1921 ggcgcaattc agaaatttca ctcatgattt ctttgtattc gtgaatatct ttaattttgt
     1981 tggtaccgac aatatccctt ttccaaccgt aatcattcat taatcgttct atagagtcaa
     2041 cttcttgatt tctaaaatta ttgaaaagca ctcgaccatt atctttatca gcgtgtatcc
     2101 cttgttgaac cagtgcttta ttaaagctcg gctgcttttg aacaccccgt ttataacctt
     2161 cagcaaccgg cacaatattc aagtgcaggt gcggacttat ttcgtcatta tgaataacag
     2221 cattataaac agccaaatta gggtttctct cttgaaactc cttgtaatac tgaaccaaaa
     2281 ttttattggc aatcactcga ttttgttcag cttgttgttt cgatatgcca gtagaagaac
     2341 catctgctcg atttgtctgg aaatcatcta aaatgcctat ttgcacaata aattctcgtt
     2401 gaggttccaa ctttttatcc ttgcgcactt tcgctaaata gtcctcgatt tttctatcgg
     2461 ctcttttttg tttcgcatta tatttttcta ccacttcgcc aaacaattcc tcatatttat
     2521 ctgctagatt cgtctgctct aaataaatat tttcatccga tttcgtgaag tcaatatgct
     2581 tatgccaatc attggttttc tggcgatcag ttaactcacg attattatga gaaatacttg
     2641 tattcttcgt tcctttttta aatgaaatac taaaccccaa gttaaaaccc tccttcgcgc
     2701 tgtcgctaat aaaaagattg taaacctttc tgttactctt tgtcaaagag taacattttc
     2761 ctaattgtga catggctgtc acaattccaa atgctctccg agggtattcg ctgtcacaag
     2821 tgacaacgaa aaaaggagcc gaaagcgtgt cacgctctca actcctttta cgctttattt
     2881 tgcttcacgc aaaataatcg cttatcgtaa attcacgtca ttaaatattg acgtaaattt
     2941 actctcactc atctgacttt tcttattcgg tatcactccg aataagccgt cagattcatc
     3001 gggataatct cgttcgcttg gcgctgattt ttcatcagca agccactcat tatccactga
     3061 tttttcgtgt tgctgatcgt cagaaatcga cgatagccac cgctcaaaat cagcaaaagt
     3121 ttcaaaccca aaacgcttgc gaagagcctt gcccattgca gcattttctt tctcaatcaa
     3181 gcgttttttc tgttggcgaa gtttcgcttg ttcttttttt aatttttctt cttgcgcttt
     3241 aatatctgct aaagtcattc ccataaacta catctccttt tctttggaat taataacgga
     3301 aatttggttt aactgcataa catgactcat taatttcaac caaaattctt tttctgattc
     3361 atcagttgtt tgcgctaaat gcttatgaac aaattcatta gtcaaaactg aagattttgc
     3421 tagatcagca ttgataaccg agttgagaac atccatcatt cgttcaagca tttcactata
     3481 attatcttca tccggcaaat tcaaataatc agctaaccgt tcatacatca attcaattct
     3541 atcgactgtt tcttctctca aatcaatttt atccatgtca cacctcactt ccagaattgc
     3601 caccattttc gattttttaa ttcttgattt tctagtaaca actgatcgtt tttttgttgc
     3661 tgaagcaaag tcaatttttg ttggtcacga atcatttccg ttaattcaga aatatgccta
     3721 tctttttccg ctaattgttc acgcaaaaat tcattttctt tttctaacgg gaaatcattg
     3781 cctgcatcat tgaccggtaa atcaccagtc aattgaccac cttttgaccg ataaattgac
     3841 cgcacaacac caatcaattc cttgtctaac atgataaccc cattatcttt ataccgagca
     3901 aggtcataac ctgcattgac cagttgattg cgcactgtat ttttagatat acccaactca
     3961 tcagcaaggt tttttatggt cattttttct ggcaaatcag tcattatctt ctccgttact
     4021 ttcagctacc ccataaacat atttaacagc atgcttaggg ataatgattg gggaatcaat
     4081 tttattattt ttcaaaatca actcatactg cgttacatca agtaacttac cggacatttt
     4141 tttgctatcc aaaaaaacaa cgacaacgtt atcacctgtt aaattcacca accaattttt
     4201 cttaccaaaa tgcttttgtt tttctgccat tcttattcct cctccgttac atctaaccct
     4261 tgaagccaag tgtctaattc ttttttcaaa acatctgctg attccgaaaa tgtttctcgt
     4321 aaatgattcg tcaactcatc attttgactt tctcttttca aaatatctct caatttg
//
