LOCUS       NZ_CP131845             4461 bp    DNA     circular CON 25-APR-2024
DEFINITION  Enterococcus faecium strain 2016S06-219 plasmid p2016S06-219-4,
            complete sequence.
ACCESSION   NZ_CP131845
VERSION     NZ_CP131845.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN36766199
            Assembly: GCF_038441125.1
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  JOURNAL   Unpublished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_038441125.1-RS_2024_04_24
            Annotation Date                   :: 04/24/2024 15:02:18
            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)                     :: 3,146
            CDSs (total)                      :: 3,053
            Genes (coding)                    :: 2,884
            CDSs (with protein)               :: 2,884
            Genes (RNA)                       :: 93
            rRNAs                             :: 6, 6, 6 (5S, 16S, 23S)
            complete rRNAs                    :: 6, 6, 6 (5S, 16S, 23S)
            tRNAs                             :: 71
            ncRNAs                            :: 4
            Pseudo Genes (total)              :: 169
            CDSs (without protein)            :: 169
            Pseudo Genes (ambiguous residues) :: 0 of 169
            Pseudo Genes (frameshifted)       :: 60 of 169
            Pseudo Genes (incomplete)         :: 103 of 169
            Pseudo Genes (internal stop)      :: 34 of 169
            Pseudo Genes (multiple problems)  :: 26 of 169
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP131845.1.
            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="2016S06-219"
                     /isolation_source="blood"
                     /host="Homo sapiens"
                     /db_xref="taxon:1352"
                     /plasmid="p2016S06-219-4"
                     /geo_loc_name="Taiwan"
                     /collection_date="2016"
                     /collected_by="NHRI"
     gene            397..831
                     /gene="bacA"
                     /locus_tag="Q7578_RS15675"
                     /old_locus_tag="Q7578_15610"
     CDS             397..831
                     /gene="bacA"
                     /locus_tag="Q7578_RS15675"
                     /old_locus_tag="Q7578_15610"
                     /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"
     gene            2121..3044
                     /locus_tag="Q7578_RS15680"
                     /old_locus_tag="Q7578_15615"
     CDS             2121..3044
                     /locus_tag="Q7578_RS15680"
                     /old_locus_tag="Q7578_15615"
                     /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            3060..3599
                     /locus_tag="Q7578_RS15685"
                     /old_locus_tag="Q7578_15620"
     CDS             3060..3599
                     /locus_tag="Q7578_RS15685"
                     /old_locus_tag="Q7578_15620"
                     /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            4280..4453
                     /locus_tag="Q7578_RS15690"
                     /old_locus_tag="Q7578_15625"
     CDS             4280..4453
                     /locus_tag="Q7578_RS15690"
                     /old_locus_tag="Q7578_15625"
                     /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"
     Typing          2122..3044
                     /name="rep_cluster_1291"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 actgctcttc cgagcagcca gttaaaaaat aatgagtgtt tattcttgaa aaagcaacgc
       61 gcttataaag cgctaccaaa aatttatcat attttatgaa aaataacaat ccagtaaaaa
      121 atgactggta aaaattcaca aagaaacgga aagaagcaac tgcagaaaat caagccttaa
      181 aaagagcttt ttacctagac caattaaaaa tcacaaagtg agcccctgta tcggttgata
      241 caagggctac ttggcatact gtacattatg tctactaacc tttaaaataa cacgttttat
      301 aaaataaacc ctcttgacaa tatttaattt tctgattatt ctaaatatat acagaaagcg
      361 ctttcctagg attttatatc taaggaggaa gtaacaatga aaaataaaat tattaaaatt
      421 attacttgtc tatttttgtt cggtatgatt gttggagcaa gtactccgtt aaatctgttt
      481 ccttttagtg ctagaggtat aaaagtggaa gctgcaagtt cacgatataa tcataatcat
      541 cgtggattta cttgctataa aatgaactat tatgttacta ataaaatgtg tagagatttg
      601 aaaaaaaatt ataataagct aaagactcct gctcaaattg catcttttat tcctattggt
      661 ggagttggaa catgggttat tacaaatgct tttagtagtg ctgttgatgc aatgaatgtc
      721 tttgtaagag ctgcaaatca aggaaaaggt gtacaattaa catataatgc tcactttagc
      781 aatacaacat catatcaata caatgattac gctcgttatg taataaaata atcagaaagt
      841 gaaactatct catgaataaa aagattttag ctgtaattat ttcaataata gttttaatca
      901 ctatgttctt catatttagg ctaattttca atataagctt acaaaaaagt attctttatc
      961 taattcctat agcatttatc ttagcaattt ttagaagtat ttacggaaat aaaaactcta
     1021 aatagctaaa aataaatcat actaaatttt acaaaaagtg gctagcattt tctagccact
     1081 ttttgtattg tggagcgtgg gttttgaggg ggattcaagg gggagcttgc gcccctttga
     1141 caagcggtta tttgcaccaa atacggaggt atttggctag caaatataga gcttgccaaa
     1201 cccttttagt gagttttgta gaaagtacct ttaaaggtac tttcacatta cgaacgatac
     1261 gtccgtagga cgtactgaaa gggtgggact tatgagcaaa ttaatgcaaa atttggctag
     1321 caaaaaagct aaaaaatata tgctaataat cgagcgaaat aaacactttt tcaagtgagc
     1381 gaatccgcca tgacaaagct gaagcagttt atttcagctt tgtcatggcg tgtgccgact
     1441 tttttaaaag tctaggcaca cgagcaaata tctttatcaa gctctaattt gcgttttaag
     1501 acgtttgaaa cgcctaagta tataaatata taagaatagg tttaagagtg cttaaatcga
     1561 attttagagg gcatttagac aattttaggg ttgttagggc ttgccctgac cgcctgtaag
     1621 gcgttttaag aacaagataa gggatttata ctaggactgt cttaaaatgt cttaaacgaa
     1681 cgctcagagc ttctcaaagg gttccttatg aacggctttt agcaaaggag ccggaggcga
     1741 ctgcgcagta taatgtgaga gcagagcgat cacacctttt tagcgaaccg tagggagcaa
     1801 ggtttggaat tggcagtttt gataaattcg cgaacctgtt tagagaaaaa aggagtgatt
     1861 ttttaggcgg gaaaattagc ctcccctctt tttatatctc tttttatatc tctttttata
     1921 tctcttttat gtcggctgtg tccttactct cccaagcaat tcagagtttt ttcaagtagg
     1981 ttttctacgc ttttcaagta ggttttctac gcttttcaag taggttttct acgcttttca
     2041 agtaggtttt ccgacattat tgagtatttt tataaagtat gttactttta tttcatactt
     2101 tataaaagta ggagaagctt atggcaaatg aaattgtaaa atatgaaaat agattaaatc
     2161 atattcctct gagaaaattt aatagtcgtg aaatgaactt atttttttca attgcttcac
     2221 gtgtacgtga aaaaggtgta gatgagatta ttttttcatt tcacgatttg aaaaaactaa
     2281 gcggttatac agaacgtggg gaacaattta taaaagatct tagtagcacg tatgacaaat
     2341 tattaagtat taatgcttgg aatgatgatg gaaatacttt aactaaattt gttgctttca
     2401 caaaatatag cattatacga gataaacaac ttgttataat ttcagttaat ccagaattta
     2461 aaggactttt taatcaatta aagaactgga caagatttaa tctagagcaa tttactaatt
     2521 tggatagcac atattcaaaa actatgtttc gattattaaa acaatatcga actcaaggct
     2581 ggactgaatt ttccaaagaa aaattttttg atttactaga tattcctaaa agttattgga
     2641 atagtccgtc aaatattgac aaatttatct taaggccaat taaagaagaa ctcactccct
     2701 tatttaaagg attaactatt cgtaaaaaat atggtaaagg tcgaggtaaa cctgttatcg
     2761 gttatcgttt tacttggaaa gctgaaatta accatgctga cgatttttcc aaagggaaac
     2821 aagaagattt acgtataaaa ttatttaata ttgatcacaa tggagaatta acacgagaag
     2881 aaaaatggcg cgctaaagat cgaatactaa atcttccctt aggcactcat gaagctgatt
     2941 ttaaacaaca acaacaaact gaagaaaaac aggcagaaaa acgagaactt tcaaacaaac
     3001 tcaaacaaga tttactagga aatttacaaa acttattcga ttaagcttaa ggagtattta
     3061 tggcagataa aacaatcaaa gaacttgcgg aagaattagg agttagtaaa acagcaatta
     3121 acaaaaaagt ttctgacaaa aatcgaaaac tttggtttgc aaaaaacgga aacaagtttg
     3181 tgattaacga aaccggtcaa aaagctataa aatcaatgtt tttagtcgat aacgcaaact
     3241 taaatcgaaa actagttggc gaaaaatcaa aaaccaaaaa ccataaaaac accaaccaag
     3301 tttccgaatt aaaactcctt tctttcctag aaaaacagtt aaatcgaaaa gatatacagc
     3361 tacaagaaaa agataatcaa ataaaacaaa tgcaaaaatt actcgaccag caacaacaac
     3421 tcactctaca agcgaaccaa caaattgaga acctacaaga acagctccat ttaacttata
     3481 cagaagaaac tccaacaacc gaatcaactg ccttttctga aaaaaaagca gacaatacac
     3541 aaccacttat tgaaaaaaag tggtggcaaa tttggaaatc taatagaacc aatctctaaa
     3601 attttctaga agttagttcg gatagtagag gaaaaagttg tactacctga tggggagatc
     3661 actcaaattt ttatgagaaa gaaaaaatag tttacaactg taaacaatca atgtttatag
     3721 ttgtaaacta tcaaactata tggtgactta ttgcttaaaa taggttgaaa tctcactcaa
     3781 tttttggtgg aaaaacaaaa taaattctaa tcgattttgt tgaaaaagtc ataaaaaaac
     3841 aaatgtgatt ttaacaaaat ttcaaaaaaa tcgtttgaaa tttcgtttat tttttttgag
     3901 aattttgatc atcgtagggt cattgtagaa tcattatgag atcatcgtgg gatcatcgaa
     3961 taaagtatgg gaaaggcttg cggtgcttgg tattaagggc attctccgcc tcccaggttc
     4021 ttgaccattt tctcttataa gtgggatttt taccacgttg agagaaaatg gtcaagaacc
     4081 tgggaggcgg agaaaacata ccaagcacca caagcaaaaa aagttagagt aacttccaaa
     4141 aaagaaaaat tttttagaac aacttttgaa aatttaattt tgatttatat ccgttcaatt
     4201 taaacatttg ataaactgaa ggctagtatt taaaatgtgt atacaagtgg tagcgttaaa
     4261 aaaagtggag gtataaccta tgttaaaaaa aactgtgttg gtactgggtt ctatttctct
     4321 aggaatatta ggttttagcc ccatgctatt atccgtaatt ggaaaaaaca attccaacag
     4381 agaacttaaa ttgaattcaa attattacaa cagtcctaac gaagaattgt ttgtaaaaga
     4441 aacggataaa taataaaaaa g
//
