LOCUS       NZ_CP131831             4461 bp    DNA     circular CON 25-APR-2024
DEFINITION  Enterococcus faecium strain 2016C07-254 plasmid p2016C07-254-6,
            complete sequence.
ACCESSION   NZ_CP131831
VERSION     NZ_CP131831.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN36766201
            Assembly: GCF_038441105.1
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  JOURNAL   Unpublished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_038441105.1-RS_2024_04_25
            Annotation Date                   :: 04/25/2024 19:54:46
            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)                     :: 3,049
            CDSs (total)                      :: 2,960
            Genes (coding)                    :: 2,846
            CDSs (with protein)               :: 2,846
            Genes (RNA)                       :: 89
            rRNAs                             :: 6, 6, 6 (5S, 16S, 23S)
            complete rRNAs                    :: 6, 6, 6 (5S, 16S, 23S)
            tRNAs                             :: 67
            ncRNAs                            :: 4
            Pseudo Genes (total)              :: 114
            CDSs (without protein)            :: 114
            Pseudo Genes (ambiguous residues) :: 0 of 114
            Pseudo Genes (frameshifted)       :: 39 of 114
            Pseudo Genes (incomplete)         :: 61 of 114
            Pseudo Genes (internal stop)      :: 29 of 114
            Pseudo Genes (multiple problems)  :: 12 of 114
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP131831.1.
            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="2016C07-254"
                     /isolation_source="blood"
                     /host="Homo sapiens"
                     /db_xref="taxon:1352"
                     /plasmid="p2016C07-254-6"
                     /geo_loc_name="Taiwan"
                     /collection_date="2016"
                     /collected_by="NHRI"
     gene            join(4315..4461,1..777)
                     /locus_tag="Q7580_RS15195"
                     /old_locus_tag="Q7580_15120"
     CDS             join(4315..4461,1..777)
                     /locus_tag="Q7580_RS15195"
                     /old_locus_tag="Q7580_15120"
                     /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            793..1332
                     /locus_tag="Q7580_RS15200"
                     /old_locus_tag="Q7580_15125"
     CDS             793..1332
                     /locus_tag="Q7580_RS15200"
                     /old_locus_tag="Q7580_15125"
                     /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            2013..2186
                     /locus_tag="Q7580_RS15205"
                     /old_locus_tag="Q7580_15130"
     CDS             2013..2186
                     /locus_tag="Q7580_RS15205"
                     /old_locus_tag="Q7580_15130"
                     /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            2591..3025
                     /gene="bacA"
                     /locus_tag="Q7580_RS15210"
                     /old_locus_tag="Q7580_15135"
     CDS             2591..3025
                     /gene="bacA"
                     /locus_tag="Q7580_RS15210"
                     /old_locus_tag="Q7580_15135"
                     /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          2..777
                     /name="rep_cluster_1291"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 ttgaaaaaac taagcggtta tacagaacgt ggggaacaat ttataaaaga tcttagtagc
       61 acgtatgaca aattattaag tattaatgct tggaatgatg atggaaatac tttaactaaa
      121 tttgttgctt tcacaaaata tagcattata cgagataaac aacttgttat aatttcagtt
      181 aatccagaat ttaaaggact ttttaatcaa ttaaagaact ggacaagatt taatctagag
      241 caatttacta atttggatag cacatattca aaaactatgt ttcgattatt aaaacaatat
      301 cgaactcaag gctggactga attttccaaa gaaaaatttt ttgatttact agatattcct
      361 aaaagttatt ggaatagtcc gtcaaatatt gacaaattta tcttaaggcc aattaaagaa
      421 gaactcactc ccttatttaa aggattaact attcgtaaaa aatatggtaa aggtcgaggt
      481 aaacctgtta tcggttatcg ttttacttgg aaagctgaaa ttaaccatgc tgacgatttt
      541 tccaaaggga aacaagaaga tttacgtata aaattattta atattgatca caatggagaa
      601 ttaacacgag aagaaaaatg gcgcgctaaa gatcgaatac taaatcttcc cttaggcact
      661 catgaagctg attttaaaca acaacaacaa actgaagaaa aacaggcaga aaaacgagaa
      721 ctttcaaaca aactcaaaca agatttacta ggaaatttac aaaacttatt cgattaagct
      781 taaggagtat ttatggcaga taaaacaatc aaagaacttg cggaagaatt aggagttagt
      841 aaaacagcaa ttaacaaaaa agtttctgac aaaaatcgaa aactttggtt tgcaaaaaac
      901 ggaaacaagt ttgtgattaa cgaaaccggt caaaaagcta taaaatcaat gtttttagtc
      961 gataacgcaa acttaaatcg aaaactagtt ggcgaaaaat caaaaaccaa aaaccataaa
     1021 aacaccaacc aagtttccga attaaaactc ctttctttcc tagaaaaaca gttaaatcga
     1081 aaagatatac agctacaaga aaaagataat caaataaaac aaatgcaaaa attactcgac
     1141 cagcaacaac aactcactct acaagcgaac caacaaattg agaacctaca agaacagctc
     1201 catttaactt atacagaaga aactccaaca accgaatcaa ctgccttttc tgaaaaaaaa
     1261 gcagacaata cacaaccact tattgaaaaa aagtggtggc aaatttggaa atctaataga
     1321 accaatctct aaaattttct agaagttagt tcggatagta gaggaaaaag ttgtactacc
     1381 tgatggggag atcactcaaa tttttatgag aaagaaaaaa tagtttacaa ctgtaaacaa
     1441 tcaatgttta tagttgtaaa ctatcaaact atatggtgac ttattgctta aaataggttg
     1501 aaatctcact caatttttgg tggaaaaaca aaataaattc taatcgattt tgttgaaaaa
     1561 gtcataaaaa aacaaatgtg attttaacaa aatttcaaaa aaatcgtttg aaatttcgtt
     1621 tatttttttt gagaattttg atcatcgtag ggtcattgta gaatcattat gagatcatcg
     1681 tgggatcatc gaataaagta tgggaaaggc ttgcggtgct tggtattaag ggcattctcc
     1741 gcctcccagg ttcttgacca ttttctctta taagtgggat ttttaccacg ttgagagaaa
     1801 atggtcaaga acctgggagg cggagaaaac ataccaagca ccacaagcaa aaaaagttag
     1861 agtaacttcc aaaaaagaaa aattttttag aacaactttt gaaaatttaa ttttgattta
     1921 tatccgttca atttaaacat ttgataaact gaaggctagt atttaaaatg tgtatacaag
     1981 tggtagcgtt aaaaaaagtg gaggtataac ctatgttaaa aaaaactgtg ttggtactgg
     2041 gttctatttc tctaggaata ttaggtttta gccccatgct attatccgta attggaaaaa
     2101 acaattccaa cagagaactt aaattgaatt caaattatta caacagtcct aacgaagaat
     2161 tgtttgtaaa agaaacggat aaataataaa aaagactgct cttccgagca gccagttaaa
     2221 aaataatgag tgtttattct tgaaaaagca acgcgcttat aaagcgctac caaaaattta
     2281 tcatatttta tgaaaaataa caatccagta aaaaatgact ggtaaaaatt cacaaagaaa
     2341 cggaaagaag caactgcaga aaatcaagcc ttaaaaagag ctttttacct agaccaatta
     2401 aaaatcacaa agtgagcccc tgtatcggtt gatacaaggg ctacttggca tactgtacat
     2461 tatgtctact aacctttaaa ataacacgtt ttataaaata aaccctcttg acaatattta
     2521 attttctgat tattctaaat atatacagaa agcgctttcc taggatttta tatctaagga
     2581 ggaagtaaca atgaaaaata aaattattaa aattattact tgtctatttt tgttcggtat
     2641 gattgttgga gcaagtactc cgttaaatct gtttcctttt agtgctagag gtataaaagt
     2701 ggaagctgca agttcacgat ataatcataa tcatcgtgga tttacttgct ataaaatgaa
     2761 ctattatgtt actaataaaa tgtgtagaga tttgaaaaaa aattataata agctaaagac
     2821 tcctgctcaa attgcatctt ttattcctat tggtggagtt ggaacatggg ttattacaaa
     2881 tgcttttagt agtgctgttg atgcaatgaa tgtctttgta agagctgcaa atcaaggaaa
     2941 aggtgtacaa ttaacatata atgctcactt tagcaataca acatcatatc aatacaatga
     3001 ttacgctcgt tatgtaataa aataatcaga aagtgaaact atctcatgaa taaaaagatt
     3061 ttagctgtaa ttatttcaat aatagtttta atcactatgt tcttcatatt taggctaatt
     3121 ttcaatataa gcttacaaaa aagtattctt tatctaattc ctatagcatt tatcttagca
     3181 atttttagaa gtatttacgg aaataaaaac tctaaatagc taaaaataaa tcatactaaa
     3241 ttttacaaaa agtggctagc attttctagc cactttttgt attgtggagc gtgggttttg
     3301 agggggattc aagggggagc ttgcgcccct ttgacaagcg gttatttgca ccaaatacgg
     3361 aggtatttgg ctagcaaata tagagcttgc caaacccttt tagtgagttt tgtagaaagt
     3421 acctttaaag gtactttcac attacgaacg atacgtccgt aggacgtact gaaagggtgg
     3481 gacttatgag caaattaatg caaaatttgg ctagcaaaaa agctaaaaaa tatatgctaa
     3541 taatcgagcg aaataaacac tttttcaagt gagcgaatcc gccatgacaa agctgaagca
     3601 gtttatttca gctttgtcat ggcgtgtgcc gactttttta aaagtctagg cacacgagca
     3661 aatatcttta tcaagctcta atttgcgttt taagacgttt gaaacgccta agtatataaa
     3721 tatataagaa taggtttaag agtgcttaaa tcgaatttta gagggcattt agacaatttt
     3781 agggttgtta gggcttgccc tgaccgcctg taaggcgttt taagaacaag ataagggatt
     3841 tatactagga ctgtcttaaa atgtcttaaa cgaacgctca gagcttctca aagggttcct
     3901 tatgaacggc ttttagcaaa ggagccggag gcgactgcgc agtataatgt gagagcagag
     3961 cgatcacacc tttttagcga accgtaggga gcaaggtttg gaattggcag ttttgataaa
     4021 ttcgcgaacc tgtttagaga aaaaaggagt gattttttag gcgggaaaat tagcctcccc
     4081 tctttttata tctcttttta tatctctttt tatatctctt ttatgtcggc tgtgtcctta
     4141 ctctcccaag caattcagag ttttttcaag taggttttct acgcttttca agtaggtttt
     4201 ctacgctttt caagtaggtt ttctacgctt ttcaagtagg ttttccgaca ttattgagta
     4261 tttttataaa gtatgttact tttatttcat actttataaa agtaggagaa gcttatggca
     4321 aatgaaattg taaaatatga aaatagatta aatcatattc ctctgagaaa atttaatagt
     4381 cgtgaaatga acttattttt ttcaattgct tcacgtgtac gtgaaaaagg tgtagatgag
     4441 attatttttt catttcacga t
//
