LOCUS       NZ_CP131853             4461 bp    DNA     circular CON 25-APR-2024
DEFINITION  Enterococcus faecium strain 2016C01-052 plasmid p2016C01-052-5,
            complete sequence.
ACCESSION   NZ_CP131853
VERSION     NZ_CP131853.1
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 4461)
  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  JOURNAL   Unpublished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 4461)
  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
            CP131853.1.
            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..4461
                     /organism="Enterococcus faecium"
                     /mol_type="genomic DNA"
                     /strain="2016C01-052"
                     /isolation_source="blood"
                     /host="Homo sapiens"
                     /db_xref="taxon:1352"
                     /plasmid="p2016C01-052-5"
                     /geo_loc_name="Taiwan"
                     /collection_date="2016"
                     /collected_by="NHRI"
     gene            1246..2169
                     /locus_tag="Q7577_RS16570"
                     /old_locus_tag="Q7577_16495"
     CDS             1246..2169
                     /locus_tag="Q7577_RS16570"
                     /old_locus_tag="Q7577_16495"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002296860.1"
                     /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_002351085.1"
                     /translation="MANEIVKYENRLNHIPLRKFNSREMNLFFSIASRVREKGVDEIIF
                     SFHDLKKLSGYTERGEQFIKDLSSTYDKLLSINAWNDDGNTLTKFVAFTKYSIIRDKQL
                     VIISVNPEFKGLFNQLKNWTRFNLEQFTNLDSTYSKTMFRLLKQYRTQGWTEFSKEKFF
                     DLLDIPKSYWNSPSNIDKFILRPIKEELTPLFKGLTIRKKYGKGRGKPVIGYRFTWKAE
                     INHADDFSKGKQEDLRIKLFNIDHNGELTREEKWRAKDRILNLPLGTHEADFKQQQQTE
                     EKQAEKRELSNKLKQDLLGNLQNLFD"
                     /name="replication initiation protein"
     gene            2185..2724
                     /locus_tag="Q7577_RS16575"
                     /old_locus_tag="Q7577_16500"
     CDS             2185..2724
                     /locus_tag="Q7577_RS16575"
                     /old_locus_tag="Q7577_16500"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002351084.1"
                     /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_342081362.1"
                     /translation="MADKTIKELAEELGISKTAINKKVSDKNRKLWFAKNGNKFVINET
                     GQKAIKSMFLVDNANLNRKLVGEKSKTKNHKNTNQVSELKLLSFLEKQLNRKDIQLQEK
                     DNQIKQMQKLLDQQQQLTLQANQQIENLQEQLHLTYTEETPTTESTAFSEKKADNTQPL
                     IEKKWWQIWKSNRTNL"
                     /name="DUF536 domain-containing protein"
     gene            3405..3578
                     /locus_tag="Q7577_RS16580"
                     /old_locus_tag="Q7577_16505"
     CDS             3405..3578
                     /locus_tag="Q7577_RS16580"
                     /old_locus_tag="Q7577_16505"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002341717.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_002318189.1"
                     /translation="MLKKTVLVLGSISLGILGFSPMLLSVIGKNNSNRELKLNSNYYNS
                     PNEELFVKETDK"
                     /name="hypothetical protein"
     gene            3983..4417
                     /gene="bacA"
                     /locus_tag="Q7577_RS16585"
                     /old_locus_tag="Q7577_16510"
     CDS             3983..4417
                     /gene="bacA"
                     /locus_tag="Q7577_RS16585"
                     /old_locus_tag="Q7577_16510"
                     /inference="COORDINATES: protein motif:HMM:NF041453.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="bacteriocin 51 precursor BacA"
                     /protein_id="WP_002351079.1"
                     /translation="MKNKIIKIITCLFLFGMIVGASTPLNLFPFSARGIKVEAASSRYN
                     HNHRGFTCYKMNYYVTNKMCRDLKKNYNKLKTPAQIASFIPIGGVGTWVITNAFSSAVD
                     AMNVFVRAANQGKGVQLTYNAHFSNTTSYQYNDYARYVIK"
                     /name="bacA"
     Typing          1247..2169
                     /name="rep_cluster_1291"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 attatttcaa taatagtttt aatcactatg ttcttcatat ttaggctaat tttcaatata
       61 agcttacaaa aaagtattct ttatctaatt cctatagcat ttatcttagc aatttttaga
      121 agtatttacg gaaataaaaa ctctaaatag ctaaaaataa atcatactaa attttacaaa
      181 aagtggctag cattttctag ccactttttg tattgtggag cgtgggtttt gagggggatt
      241 caagggggag cttgcgcccc tttgacaagc ggttatttgc accaaatacg gaggtatttg
      301 gctagcaaat atagagcttg ccaaaccctt ttagtgagtt ttgtagaaag tacctttaaa
      361 ggtactttca cattacgaac gatacgtccg taggacgtac tgaaagggtg ggacttatga
      421 gcaaattaat gcaaaatttg gctagcaaaa aagctaaaaa atatatgcta ataatcgagc
      481 gaaataaaca ctttttcaag tgagcgaatc cgccatgaca aagctgaagc agtttatttc
      541 agctttgtca tggcgtgtgc cgactttttt aaaagtctag gcacacgagc aaatatcttt
      601 atcaagctct aatttgcgtt ttaagacgtt tgaaacgcct aagtatataa atatataaga
      661 ataggtttaa gagtgcttaa atcgaatttt agagggcatt tagacaattt tagggttgtt
      721 agggcttgcc ctgaccgcct gtaaggcgtt ttaagaacaa gataagggat ttatactagg
      781 actgtcttaa aatgtcttaa acgaacgctc agagcttctc aaagggttcc ttatgaacgg
      841 cttttagcaa aggagccgga ggcgactgcg cagtataatg tgagagcaga gcgatcacac
      901 ctttttagcg aaccgtaggg agcaaggttt ggaattggca gttttgataa attcgcgaac
      961 ctgtttagag aaaaaaggag tgatttttta ggcgggaaaa ttagcctccc ctctttttat
     1021 atctcttttt atatctcttt ttatatctct tttatgtcgg ctgtgtcctt actctcccaa
     1081 gcaattcaga gttttttcaa gtaggttttc tacgcttttc aagtaggttt tctacgcttt
     1141 tcaagtaggt tttctacgct tttcaagtag gttttccgac attattgagt atttttataa
     1201 agtatgttac ttttatttca tactttataa aagtaggaga agcttatggc aaatgaaatt
     1261 gtaaaatatg aaaatagatt aaatcatatt cctctgagaa aatttaatag tcgtgaaatg
     1321 aacttatttt tttcaattgc ttcacgtgta cgtgaaaaag gtgtagatga gattattttt
     1381 tcatttcacg atttgaaaaa actaagcggt tatacagaac gtggggaaca atttataaaa
     1441 gatcttagta gcacgtatga caaattatta agtattaatg cttggaatga tgatggaaat
     1501 actttaacta aatttgttgc tttcacaaaa tatagcatta tacgagataa acaacttgtt
     1561 ataatttcag ttaatccaga atttaaagga ctttttaatc aattaaagaa ctggacaaga
     1621 tttaatctag agcaatttac taatttggat agcacatatt caaaaactat gtttcgatta
     1681 ttaaaacaat atcgaactca aggctggact gaattttcca aagaaaaatt ttttgattta
     1741 ctagatattc ctaaaagtta ttggaatagt ccgtcaaata ttgacaaatt tatcttaagg
     1801 ccaattaaag aagaactcac tcccttattt aaaggattaa ctattcgtaa aaaatatggt
     1861 aaaggtcgag gtaaacctgt tatcggttat cgttttactt ggaaagctga aattaaccat
     1921 gctgacgatt tttccaaagg gaaacaagaa gatttacgta taaaattatt taatattgat
     1981 cacaatggag aattaacacg agaagaaaaa tggcgcgcta aagatcgaat actaaatctt
     2041 cccttaggca ctcatgaagc tgattttaaa caacaacaac aaactgaaga aaaacaggca
     2101 gaaaaacgag aactttcaaa caaactcaaa caagatttac taggaaattt acaaaactta
     2161 ttcgattaag cttaaggagt atttatggca gataaaacaa tcaaagaact tgcggaagaa
     2221 ttaggaatta gtaaaacagc aattaacaaa aaagtttctg acaaaaatcg aaaactttgg
     2281 tttgcaaaaa acggaaacaa gtttgtgatt aacgaaaccg gtcaaaaagc tataaaatca
     2341 atgtttttag tcgataacgc aaacttaaat cgaaaactag ttggcgaaaa atcaaaaacc
     2401 aaaaaccata aaaacaccaa ccaagtttcc gaattaaaac tcctttcttt cctagaaaaa
     2461 cagttaaatc gaaaagatat acagctacaa gaaaaagata atcaaataaa acaaatgcaa
     2521 aaattactcg accagcaaca acaactcact ctacaagcga accaacaaat tgagaaccta
     2581 caagaacagc tccatttaac ttatacagaa gaaactccaa caaccgaatc aactgccttt
     2641 tctgaaaaaa aagcagacaa tacacaacca cttattgaaa aaaagtggtg gcaaatttgg
     2701 aaatctaata gaaccaatct ctaaaatttt ctagaagtta gttcggatag tagaggaaaa
     2761 agttgtacta cctgatgggg agatcactca aatttttatg agaaagaaaa aatagtttac
     2821 aactgtaaac aatcaatgtt tatagttgta aactatcaaa ctatatggtg acttattgct
     2881 taaaataggt tgaaatctca ctcaattttt ggtggaaaaa caaaataaat tctaatcgat
     2941 tttgttgaaa aagtcataaa aaaacaaatg tgattttaac aaaatttcaa aaaaatcgtt
     3001 tgaaatttcg tttatttttt ttgagaattt tgatcatcgt agggtcattg tagaatcatt
     3061 atgagatcat cgtgggatca tcgaataaag tatgggaaag gcttgcggtg cttggtatta
     3121 agggcattct ccgcctccca ggttcttgac cattttctct tataagtggg atttttacca
     3181 cgttgagaga aaatggtcaa gaacctggga ggcggagaaa acataccaag caccacaagc
     3241 aaaaaaagtt agagtaactt ccaaaaaaga aaaatttttt agaacaactt ttgaaaattt
     3301 aattttgatt tatatccgtt caatttaaac atttgataaa ctgaaggcta gtatttaaaa
     3361 tgtgtataca agtggtagcg ttaaaaaaag tggaggtata acctatgtta aaaaaaactg
     3421 tgttggtact gggttctatt tctctaggaa tattaggttt tagccccatg ctattatccg
     3481 taattggaaa aaacaattcc aacagagaac ttaaattgaa ttcaaattat tacaacagtc
     3541 ctaacgaaga attgtttgta aaagaaacgg ataaataata aaaaagactg ctcttccgag
     3601 cagccagtta aaaaataatg agtgtttatt cttgaaaaag caacgcgctt ataaagcgct
     3661 accaaaaatt tatcatattt tatgaaaaat aacaatccag taaaaaatga ctggtaaaaa
     3721 ttcacaaaga aacggaaaga agcaactgca gaaaatcaag ccttaaaaag agctttttac
     3781 ctagaccaat taaaaatcac aaagtgagcc cctgtatcgg ttgatacaag ggctacttgg
     3841 catactgtac attatgtcta ctaaccttta aaataacacg ttttataaaa taaaccctct
     3901 tgacaatatt taattttctg attattctaa atatatacag aaagcgcttt cctaggattt
     3961 tatatctaag gaggaagtaa caatgaaaaa taaaattatt aaaattatta cttgtctatt
     4021 tttgttcggt atgattgttg gagcaagtac tccgttaaat ctgtttcctt ttagtgctag
     4081 aggtataaaa gtggaagctg caagttcacg atataatcat aatcatcgtg gatttacttg
     4141 ctataaaatg aactattatg ttactaataa aatgtgtaga gatttgaaaa aaaattataa
     4201 taagctaaag actcctgctc aaattgcatc ttttattcct attggtggag ttggaacatg
     4261 ggttattaca aatgctttta gtagtgctgt tgatgcaatg aatgtctttg taagagctgc
     4321 aaatcaagga aaaggtgtac aattaacata taatgctcac tttagcaata caacatcata
     4381 tcaatacaat gattacgctc gttatgtaat aaaataatca gaaagtgaaa ctatctcatg
     4441 aataaaaaga ttttagctgt a
//
