LOCUS       NZ_CP131815             4461 bp    DNA     circular CON 25-APR-2024
DEFINITION  Enterococcus faecium strain 2016C08-243 plasmid p2016C08-243-6,
            complete sequence.
ACCESSION   NZ_CP131815
VERSION     NZ_CP131815.1
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 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  JOURNAL   Unpublished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_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
            CP131815.1.
            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="2016C08-243"
                     /isolation_source="blood"
                     /host="Homo sapiens"
                     /db_xref="taxon:1352"
                     /plasmid="p2016C08-243-6"
                     /geo_loc_name="Taiwan"
                     /collection_date="2016"
                     /collected_by="NHRI"
     gene            complement(10..444)
                     /gene="bacA"
                     /locus_tag="Q7582_RS16350"
                     /old_locus_tag="Q7582_16280"
     CDS             complement(10..444)
                     /gene="bacA"
                     /locus_tag="Q7582_RS16350"
                     /old_locus_tag="Q7582_16280"
                     /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            complement(849..1022)
                     /locus_tag="Q7582_RS16355"
                     /old_locus_tag="Q7582_16285"
     CDS             complement(849..1022)
                     /locus_tag="Q7582_RS16355"
                     /old_locus_tag="Q7582_16285"
                     /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            complement(1703..2242)
                     /locus_tag="Q7582_RS16360"
                     /old_locus_tag="Q7582_16290"
     CDS             complement(1703..2242)
                     /locus_tag="Q7582_RS16360"
                     /old_locus_tag="Q7582_16290"
                     /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            complement(2258..3181)
                     /locus_tag="Q7582_RS16365"
                     /old_locus_tag="Q7582_16295"
     CDS             complement(2258..3181)
                     /locus_tag="Q7582_RS16365"
                     /old_locus_tag="Q7582_16295"
                     /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"
     Typing          complement(2259..3181)
                     /name="rep_cluster_1291"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 actttctgat tattttatta cataacgagc gtaatcattg tattgatatg atgttgtatt
       61 gctaaagtga gcattatatg ttaattgtac accttttcct tgatttgcag ctcttacaaa
      121 gacattcatt gcatcaacag cactactaaa agcatttgta ataacccatg ttccaactcc
      181 accaatagga ataaaagatg caatttgagc aggagtcttt agcttattat aatttttttt
      241 caaatctcta cacattttat tagtaacata atagttcatt ttatagcaag taaatccacg
      301 atgattatga ttatatcgtg aacttgcagc ttccactttt atacctctag cactaaaagg
      361 aaacagattt aacggagtac ttgctccaac aatcataccg aacaaaaata gacaagtaat
      421 aattttaata attttatttt tcattgttac ttcctcctta gatataaaat cctaggaaag
      481 cgctttctgt atatatttag aataatcaga aaattaaata ttgtcaagag ggtttatttt
      541 ataaaacgtg ttattttaaa ggttagtaga cataatgtac agtatgccaa gtagcccttg
      601 tatcaaccga tacaggggct cactttgtga tttttaattg gtctaggtaa aaagctcttt
      661 ttaaggcttg attttctgca gttgcttctt tccgtttctt tgtgaatttt taccagtcat
      721 tttttactgg attgttattt ttcataaaat atgataaatt tttggtagcg ctttataagc
      781 gcgttgcttt ttcaagaata aacactcatt attttttaac tggctgctcg gaagagcagt
      841 cttttttatt atttatccgt ttcttttaca aacaattctt cgttaggact gttgtaataa
      901 tttgaattca atttaagttc tctgttggaa ttgttttttc caattacgga taatagcatg
      961 gggctaaaac ctaatattcc tagagaaata gaacccagta ccaacacagt tttttttaac
     1021 ataggttata cctccacttt ttttaacgct accacttgta tacacatttt aaatactagc
     1081 cttcagttta tcaaatgttt aaattgaacg gatataaatc aaaattaaat tttcaaaagt
     1141 tgttctaaaa aatttttctt ttttggaagt tactctaact ttttttgctt gtggtgcttg
     1201 gtatgttttc tccgcctccc aggttcttga ccattttctc ttataagtgg gatttttacc
     1261 acgttgagag aaaatggtca agaacctggg aggcggagaa tgcccttaat accaagcacc
     1321 gcaagccttt cccatacttt attcgatgat cccacgatga tctcataatg attctacaat
     1381 gaccctacga tgatcaaaat tctcaaaaaa aataaacgaa atttcaaacg atttttttga
     1441 aattttgtta aaatcacatt tgttttttta tgactttttc aacaaaatcg attagaattt
     1501 attttgtttt tccaccaaaa attgagtgag atttcaacct attttaagca ataagtcacc
     1561 atatagtttg atagtttaca actataaaca ttgattgttt acagttgtaa actatttttt
     1621 ctttctcata aaaatttgag tgatctcccc atcaggtagt acaacttttt cctctactat
     1681 ccgaactaac ttctagaaaa ttttagagat tggttctatt agatttccaa atttgccacc
     1741 actttttttc aataagtggt tgtgtattgt ctgctttttt ttcagaaaag gcagttgatt
     1801 cggttgttgg agtttcttct gtataagtta aatggagctg ttcttgtagg ttctcaattt
     1861 gttggttcgc ttgtagagtg agttgttgtt gctggtcgag taatttttgc atttgtttta
     1921 tttgattatc tttttcttgt agctgtatat cttttcgatt taactgtttt tctaggaaag
     1981 aaaggagttt taattcggaa acttggttgg tgtttttatg gtttttggtt tttgattttt
     2041 cgccaactag ttttcgattt aagtttgcgt tatcgactaa aaacattgat tttatagctt
     2101 tttgaccggt ttcgttaatc acaaacttgt ttccgttttt tgcaaaccaa agttttcgat
     2161 ttttgtcaga aacttttttg ttaattgctg ttttactaac tcctaattct tccgcaagtt
     2221 ctttgattgt tttatctgcc ataaatactc cttaagctta atcgaataag ttttgtaaat
     2281 ttcctagtaa atcttgtttg agtttgtttg aaagttctcg tttttctgcc tgtttttctt
     2341 cagtttgttg ttgttgttta aaatcagctt catgagtgcc taagggaaga tttagtattc
     2401 gatctttagc gcgccatttt tcttctcgtg ttaattctcc attgtgatca atattaaata
     2461 attttatacg taaatcttct tgtttccctt tggaaaaatc gtcagcatgg ttaatttcag
     2521 ctttccaagt aaaacgataa ccgataacag gtttacctcg acctttacca tattttttac
     2581 gaatagttaa tcctttaaat aagggagtga gttcttcttt aattggcctt aagataaatt
     2641 tgtcaatatt tgacggacta ttccaataac ttttaggaat atctagtaaa tcaaaaaatt
     2701 tttctttgga aaattcagtc cagccttgag ttcgatattg ttttaataat cgaaacatag
     2761 tttttgaata tgtgctatcc aaattagtaa attgctctag attaaatctt gtccagttct
     2821 ttaattgatt aaaaagtcct ttaaattctg gattaactga aattataaca agttgtttat
     2881 ctcgtataat gctatatttt gtgaaagcaa caaatttagt taaagtattt ccatcatcat
     2941 tccaagcatt aatacttaat aatttgtcat acgtgctact aagatctttt ataaattgtt
     3001 ccccacgttc tgtataaccg cttagttttt tcaaatcgtg aaatgaaaaa ataatctcat
     3061 ctacaccttt ttcacgtaca cgtgaagcaa ttgaaaaaaa taagttcatt tcacgactat
     3121 taaattttct cagaggaata tgatttaatc tattttcata ttttacaatt tcatttgcca
     3181 taagcttctc ctacttttat aaagtatgaa ataaaagtaa catactttat aaaaatactc
     3241 aataatgtcg gaaaacctac ttgaaaagcg tagaaaacct acttgaaaag cgtagaaaac
     3301 ctacttgaaa agcgtagaaa acctacttga aaaaactctg aattgcttgg gagagtaagg
     3361 acacagccga cataaaagag atataaaaag agatataaaa agagatataa aaagagggga
     3421 ggctaatttt cccgcctaaa aaatcactcc ttttttctct aaacaggttc gcgaatttat
     3481 caaaactgcc aattccaaac cttgctccct acggttcgct aaaaaggtgt gatcgctctg
     3541 ctctcacatt atactgcgca gtcgcctccg gctcctttgc taaaagccgt tcataaggaa
     3601 ccctttgaga agctctgagc gttcgtttaa gacattttaa gacagtccta gtataaatcc
     3661 cttatcttgt tcttaaaacg ccttacaggc ggtcagggca agccctaaca accctaaaat
     3721 tgtctaaatg ccctctaaaa ttcgatttaa gcactcttaa acctattctt atatatttat
     3781 atacttaggc gtttcaaacg tcttaaaacg caaattagag cttgataaag atatttgctc
     3841 gtgtgcctag acttttaaaa aagtcggcac acgccatgac aaagctgaaa taaactgctt
     3901 cagctttgtc atggcggatt cgctcacttg aaaaagtgtt tatttcgctc gattattagc
     3961 atatattttt tagctttttt gctagccaaa ttttgcatta atttgctcat aagtcccacc
     4021 ctttcagtac gtcctacgga cgtatcgttc gtaatgtgaa agtaccttta aaggtacttt
     4081 ctacaaaact cactaaaagg gtttggcaag ctctatattt gctagccaaa tacctccgta
     4141 tttggtgcaa ataaccgctt gtcaaagggg cgcaagctcc cccttgaatc cccctcaaaa
     4201 cccacgctcc acaatacaaa aagtggctag aaaatgctag ccactttttg taaaatttag
     4261 tatgatttat ttttagctat ttagagtttt tatttccgta aatacttcta aaaattgcta
     4321 agataaatgc tataggaatt agataaagaa tacttttttg taagcttata ttgaaaatta
     4381 gcctaaatat gaagaacata gtgattaaaa ctattattga aataattaca gctaaaatct
     4441 ttttattcat gagatagttt c
//
