LOCUS       NZ_CP131822             4461 bp    DNA     circular CON 25-APR-2024
DEFINITION  Enterococcus faecium strain 2016N17-104 plasmid p2016N17-104-4,
            complete sequence.
ACCESSION   NZ_CP131822
VERSION     NZ_CP131822.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN36766202
            Assembly: GCF_038441015.1
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  JOURNAL   Unpublished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_038441015.1-RS_2024_04_24
            Annotation Date                   :: 04/24/2024 16:12:56
            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)                     :: 3,138
            CDSs (total)                      :: 3,048
            Genes (coding)                    :: 2,898
            CDSs (with protein)               :: 2,898
            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)              :: 150
            CDSs (without protein)            :: 150
            Pseudo Genes (ambiguous residues) :: 0 of 150
            Pseudo Genes (frameshifted)       :: 48 of 150
            Pseudo Genes (incomplete)         :: 96 of 150
            Pseudo Genes (internal stop)      :: 35 of 150
            Pseudo Genes (multiple problems)  :: 25 of 150
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP131822.1.
            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="2016N17-104"
                     /isolation_source="blood"
                     /host="Homo sapiens"
                     /db_xref="taxon:1352"
                     /plasmid="p2016N17-104-4"
                     /geo_loc_name="Taiwan"
                     /collection_date="2016"
                     /collected_by="NHRI"
     gene            join(3618..4461,1..80)
                     /locus_tag="Q7581_RS15635"
                     /old_locus_tag="Q7581_15580"
     CDS             join(3618..4461,1..80)
                     /locus_tag="Q7581_RS15635"
                     /old_locus_tag="Q7581_15580"
                     /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            96..635
                     /locus_tag="Q7581_RS15640"
                     /old_locus_tag="Q7581_15585"
     CDS             96..635
                     /locus_tag="Q7581_RS15640"
                     /old_locus_tag="Q7581_15585"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_016616811.1"
                     /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_002351084.1"
                     /translation="MADKTIKELAEELGVSKTAINKKVSDKNRKLWFAKNGNKFVINET
                     GQKAIKSMFLVDNANLNRKLVGEKSKTKNHKNTNQVSELKLLSFLEKQLNRKDIQLQEK
                     DNQIKQMQKLLDQQQQLTLQANQQIENLQEQLHLTYTEETPTTESTAFSEKKADNTQPL
                     IEKKWWQIWKSNRTNL"
                     /name="DUF536 domain-containing protein"
     gene            1316..1489
                     /locus_tag="Q7581_RS15645"
                     /old_locus_tag="Q7581_15590"
     CDS             1316..1489
                     /locus_tag="Q7581_RS15645"
                     /old_locus_tag="Q7581_15590"
                     /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            1894..2328
                     /gene="bacA"
                     /locus_tag="Q7581_RS15650"
                     /old_locus_tag="Q7581_15595"
     CDS             1894..2328
                     /gene="bacA"
                     /locus_tag="Q7581_RS15650"
                     /old_locus_tag="Q7581_15595"
                     /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          3619..4461
                     /name="rep_cluster_1291"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 aaaaacaggc agaaaaacga gaactttcaa acaaactcaa acaagattta ctaggaaatt
       61 tacaaaactt attcgattaa gcttaaggag tatttatggc agataaaaca atcaaagaac
      121 ttgcggaaga attaggagtt agtaaaacag caattaacaa aaaagtttct gacaaaaatc
      181 gaaaactttg gtttgcaaaa aacggaaaca agtttgtgat taacgaaacc ggtcaaaaag
      241 ctataaaatc aatgttttta gtcgataacg caaacttaaa tcgaaaacta gttggcgaaa
      301 aatcaaaaac caaaaaccat aaaaacacca accaagtttc cgaattaaaa ctcctttctt
      361 tcctagaaaa acagttaaat cgaaaagata tacagctaca agaaaaagat aatcaaataa
      421 aacaaatgca aaaattactc gaccagcaac aacaactcac tctacaagcg aaccaacaaa
      481 ttgagaacct acaagaacag ctccatttaa cttatacaga agaaactcca acaaccgaat
      541 caactgcctt ttctgaaaaa aaagcagaca atacacaacc acttattgaa aaaaagtggt
      601 ggcaaatttg gaaatctaat agaaccaatc tctaaaattt tctagaagtt agttcggata
      661 gtagaggaaa aagttgtact acctgatggg gagatcactc aaatttttat gagaaagaaa
      721 aaatagttta caactgtaaa caatcaatgt ttatagttgt aaactatcaa actatatggt
      781 gacttattgc ttaaaatagg ttgaaatctc actcaatttt tggtggaaaa acaaaataaa
      841 ttctaatcga ttttgttgaa aaagtcataa aaaaacaaat gtgattttaa caaaatttca
      901 aaaaaatcgt ttgaaatttc gtttattttt tttgagaatt ttgatcatcg tagggtcatt
      961 gtagaatcat tatgagatca tcgtgggatc atcgaataaa gtatgggaaa ggcttgcggt
     1021 gcttggtatt aagggcattc tccgcctccc aggttcttga ccattttctc ttataagtgg
     1081 gatttttacc acgttgagag aaaatggtca agaacctggg aggcggagaa aacataccaa
     1141 gcaccacaag caaaaaaagt tagagtaact tccaaaaaag aaaaattttt tagaacaact
     1201 tttgaaaatt taattttgat ttatatccgt tcaatttaaa catttgataa actgaaggct
     1261 agtatttaaa atgtgtatac aagtggtagc gttaaaaaaa gtggaggtat aacctatgtt
     1321 aaaaaaaact gtgttggtac tgggttctat ttctctagga atattaggtt ttagccccat
     1381 gctattatcc gtaattggaa aaaacaattc caacagagaa cttaaattga attcaaatta
     1441 ttacaacagt cctaacgaag aattgtttgt aaaagaaacg gataaataat aaaaaagact
     1501 gctcttccga gcagccagtt aaaaaataat gagtgtttat tcttgaaaaa gcaacgcgct
     1561 tataaagcgc taccaaaaat ttatcatatt ttatgaaaaa taacaatcca gtaaaaaatg
     1621 actggtaaaa attcacaaag aaacggaaag aagcaactgc agaaaatcaa gccttaaaaa
     1681 gagcttttta cctagaccaa ttaaaaatca caaagtgagc ccctgtatcg gttgatacaa
     1741 gggctacttg gcatactgta cattatgtct actaaccttt aaaataacac gttttataaa
     1801 ataaaccctc ttgacaatat ttaattttct gattattcta aatatataca gaaagcgctt
     1861 tcctaggatt ttatatctaa ggaggaagta acaatgaaaa ataaaattat taaaattatt
     1921 acttgtctat ttttgttcgg tatgattgtt ggagcaagta ctccgttaaa tctgtttcct
     1981 tttagtgcta gaggtataaa agtggaagct gcaagttcac gatataatca taatcatcgt
     2041 ggatttactt gctataaaat gaactattat gttactaata aaatgtgtag agatttgaaa
     2101 aaaaattata ataagctaaa gactcctgct caaattgcat cttttattcc tattggtgga
     2161 gttggaacat gggttattac aaatgctttt agtagtgctg ttgatgcaat gaatgtcttt
     2221 gtaagagctg caaatcaagg aaaaggtgta caattaacat ataatgctca ctttagcaat
     2281 acaacatcat atcaatacaa tgattacgct cgttatgtaa taaaataatc agaaagtgaa
     2341 actatctcat gaataaaaag attttagctg taattatttc aataatagtt ttaatcacta
     2401 tgttcttcat atttaggcta attttcaata taagcttaca aaaaagtatt ctttatctaa
     2461 ttcctatagc atttatctta gcaattttta gaagtattta cggaaataaa aactctaaat
     2521 agctaaaaat aaatcatact aaattttaca aaaagtggct agcattttct agccactttt
     2581 tgtattgtgg agcgtgggtt ttgaggggga ttcaaggggg agcttgcgcc cctttgacaa
     2641 gcggttattt gcaccaaata cggaggtatt tggctagcaa atatagagct tgccaaaccc
     2701 ttttagtgag ttttgtagaa agtaccttta aaggtacttt cacattacga acgatacgtc
     2761 cgtaggacgt actgaaaggg tgggacttat gagcaaatta atgcaaaatt tggctagcaa
     2821 aaaagctaaa aaatatatgc taataatcga gcgaaataaa cactttttca agtgagcgaa
     2881 tccgccatga caaagctgaa gcagtttatt tcagctttgt catggcgtgt gccgactttt
     2941 ttaaaagtct aggcacacga gcaaatatct ttatcaagct ctaatttgcg ttttaagacg
     3001 tttgaaacgc ctaagtatat aaatatataa gaataggttt aagagtgctt aaatcgaatt
     3061 ttagagggca tttagacaat tttagggttg ttagggcttg ccctgaccgc ctgtaaggcg
     3121 ttttaagaac aagataaggg atttatacta ggactgtctt aaaatgtctt aaacgaacgc
     3181 tcagagcttc tcaaagggtt ccttatgaac ggcttttagc aaaggagccg gaggcgactg
     3241 cgcagtataa tgtgagagca gagcgatcac acctttttag cgaaccgtag ggagcaaggt
     3301 ttggaattgg cagttttgat aaattcgcga acctgtttag agaaaaaagg agtgattttt
     3361 taggcgggaa aattagcctc ccctcttttt atatctcttt ttatatctct ttttatatct
     3421 cttttatgtc ggctgtgtcc ttactctccc aagcaattca gagttttttc aagtaggttt
     3481 tctacgcttt tcaagtaggt tttctacgct tttcaagtag gttttctacg cttttcaagt
     3541 aggttttccg acattattga gtatttttat aaagtatgtt acttttattt catactttat
     3601 aaaagtagga gaagcttatg gcaaatgaaa ttgtaaaata tgaaaataga ttaaatcata
     3661 ttcctctgag aaaatttaat agtcgtgaaa tgaacttatt tttttcaatt gcttcacgtg
     3721 tacgtgaaaa aggtgtagat gagattattt tttcatttca cgatttgaaa aaactaagcg
     3781 gttatacaga acgtggggaa caatttataa aagatcttag tagcacgtat gacaaattat
     3841 taagtattaa tgcttggaat gatgatggaa atactttaac taaatttgtt gctttcacaa
     3901 aatatagcat tatacgagat aaacaacttg ttataatttc agttaatcca gaatttaaag
     3961 gactttttaa tcaattaaag aactggacaa gatttaatct agagcaattt actaatttgg
     4021 atagcacata ttcaaaaact atgtttcgat tattaaaaca atatcgaact caaggctgga
     4081 ctgaattttc caaagaaaaa ttttttgatt tactagatat tcctaaaagt tattggaata
     4141 gtccgtcaaa tattgacaaa tttatcttaa ggccaattaa agaagaactc actcccttat
     4201 ttaaaggatt aactattcgt aaaaaatatg gtaaaggtcg aggtaaacct gttatcggtt
     4261 atcgttttac ttggaaagct gaaattaacc atgctgacga tttttccaaa gggaaacaag
     4321 aagatttacg tataaaatta tttaatattg atcacaatgg agaattaaca cgagaagaaa
     4381 aatggcgcgc taaagatcga atactaaatc ttcccttagg cactcatgaa gctgatttta
     4441 aacaacaaca acaaactgaa g
//
