LOCUS       NZ_CP131855             2947 bp    DNA     circular CON 25-APR-2024
DEFINITION  Enterococcus faecium strain 2016C01-052 plasmid p2016C01-052-7,
            complete sequence.
ACCESSION   NZ_CP131855
VERSION     NZ_CP131855.1
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 2947)
  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  JOURNAL   Unpublished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 2947)
  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
            CP131855.1.
            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..2947
                     /organism="Enterococcus faecium"
                     /mol_type="genomic DNA"
                     /strain="2016C01-052"
                     /isolation_source="blood"
                     /host="Homo sapiens"
                     /db_xref="taxon:1352"
                     /plasmid="p2016C01-052-7"
                     /geo_loc_name="Taiwan"
                     /collection_date="2016"
                     /collected_by="NHRI"
     gene            join(2819..2947,1..153)
                     /locus_tag="Q7577_RS16620"
                     /old_locus_tag="Q7577_16545"
     CDS             join(2819..2947,1..153)
                     /locus_tag="Q7577_RS16620"
                     /old_locus_tag="Q7577_16545"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002347307.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_002347307.1"
                     /translation="MDILVRKIDSKVIAKIDKRCQELTNKTGKKWSRNRYLKVLIENDF
                     DHALMHYKKDQFDLLLEKFIAIQEKNTETLNEYVRTNNQLIETLIGGR"
                     /name="hypothetical protein"
     gene            155..571
                     /locus_tag="Q7577_RS16625"
                     /old_locus_tag="Q7577_16550"
     CDS             155..571
                     /locus_tag="Q7577_RS16625"
                     /old_locus_tag="Q7577_16550"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001232859.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_002322684.1"
                     /translation="MRKTSVQKHVTLYPSHVDVLDSIIERNPDINNYSEAIRFLCMSYE
                     PDTNTTTTSNQAKLNAMGKEISIMSEIIAEFADLYLKDTGILIGTNSKVYQETKEKIEK
                     QLNPSKRNQPKNRQKETNQTFTSKNFDPTNFLKR"
                     /name="hypothetical protein"
     gene            complement(908..1048)
                     /locus_tag="Q7577_RS16630"
                     /old_locus_tag="Q7577_16555"
     CDS             complement(908..1048)
                     /locus_tag="Q7577_RS16630"
                     /old_locus_tag="Q7577_16555"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002326822.1"
                     /GO_function="GO:0003700 - DNA-binding transcription factor
                     activity [Evidence IEA]"
                     /GO_process="GO:0006355 - regulation of DNA-templated
                     transcription [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="DeoR family transcriptional regulator"
                     /protein_id="WP_002322683.1"
                     /translation="MSDSIEKMTLKKLADELGVSKNTVRNQLVNSGFDLAQYKEKNAVV
                     N"
                     /name="DeoR family transcriptional regulator"
     gene            complement(1045..2019)
                     /locus_tag="Q7577_RS16635"
                     /old_locus_tag="Q7577_16560"
     CDS             complement(1045..2019)
                     /locus_tag="Q7577_RS16635"
                     /old_locus_tag="Q7577_16560"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002342725.1"
                     /GO_function="GO:0003677 - DNA binding [Evidence IEA];
                     GO:0003916 - DNA topoisomerase 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 factor domain-containing
                     protein"
                     /protein_id="WP_002337993.1"
                     /translation="MSKRGTIINEWEKLNRISNRRLNAQTMCTPLKMQWSIDRITIVGT
                     LRENIYYHTPHDVLILDFEQLMRLNEGNGYLKAVGNNGWQLLDQHEENIAYIEILKFQE
                     GKGRIDFNPNKISQFLAGSMKNFIHDLFLEPHFSRADIACDIIDVPDDFITQYRVVDPV
                     SFKPIYGRSGKLETAYWGSRASERQIRMYNKKLEQERKRKVVPKEIDTWWRLELQLRRG
                     KATDWHAMVHESLDSFASPHYLPEDVKVTDRMMITALITEHSYWGQIHRNSKYKYRELL
                     KQESQNDELTNHLRETFSESADDLKRELDTWLQGLDVTEVGAE"
                     /name="replication initiation factor domain-containing
                     protein"
     Typing          complement(1049..1995)
                     /name="rep_cluster_943"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="82.899"
                     /coverage="99.0"
                     /evalue="0.0"
ORIGIN
        1 gattttgacc acgcacttat gcattacaag aaagatcaat tcgatttatt actcgaaaaa
       61 tttatcgcta ttcaagaaaa aaatactgaa acgctgaatg aatatgttcg tacaaacaac
      121 caactcattg aaacacttat cggaggaaga taacatgaga aaaacttctg ttcaaaaaca
      181 cgttaccctt tatcccagtc acgtggacgt tttagattcc attatcgaaa gaaatccaga
      241 tatcaacaat tactcggaag ccattcgttt tttatgtatg agttatgaac ctgataccaa
      301 tactacgact accagcaacc aagccaaact aaatgctatg ggaaaagaaa tttccatcat
      361 gtccgaaatc attgcagaat ttgctgattt atatctaaaa gatacaggta ttcttattgg
      421 cacaaattct aaagtgtatc aagaaacgaa agaaaaaatt gaaaaacaac ttaatccctc
      481 caaacgaaat caaccaaaaa atcgtcaaaa agaaaccaat caaacattta cttctaaaaa
      541 tttcgaccca acaaattttc taaaaagata aaaaataaac caggagattt aaattcctgg
      601 tttatttttt gggtaggatc accatcttaa tagcaacatt tacaataaga tagtaaccaa
      661 ttgaatgaaa aaaacgaatt tcagaagaaa taacagaaaa aaagataaaa acaaaaaaat
      721 tataaataca tgatttgaat tcataatcgt aaaaaaagct gctcgtacga gcagctaaat
      781 aagaaaaaga ttggtatgtt ttaaggataa aataagtata acaaattttt cacatagagc
      841 aaagggggcg aaaatcgccc cctttttttc gttttaaaac cccaaaaccc aaagacataa
      901 atttcggtca attgaccact gcattttttt ctttatactg agcaaggtca aatcccgaat
      961 tgaccagttg attgcgcacc gtatttttcg atacacccaa ttcatcagca agttttttta
     1021 gggtcatttt ttctatcgaa tcactcattc agcacctact tccgtcacat caagtccttg
     1081 aagccatgta tctaattctc gtttcaaatc atctgccgac tccgaaaatg tttctcgcaa
     1141 atgattcgtc aactcatcat tttgactttc ttgctttaac aattcacgat atttatattt
     1201 tgaatttcta tgaatttgcc cccagtaact atgttccgtt ataagagcag taatcatcat
     1261 tctgtcagtt actttcacat cttctggcaa atagtgagga cttgcaaagc tatctaaact
     1321 ttcatgaacc attgcatgcc aatcagttgc tttccccctt cgcaattgca attctagtcg
     1381 ccaccaagta tcgatttctt tcggaacaac tttccgtttt ctttcttgtt ccaatttttt
     1441 gttatacatc cgaatctgtc gttcactagc acgacttccc caatatgctg tttccagttt
     1501 cccagaccga ccgtaaattg gtttgaaaga aacaggatca accacccgat attgggtaat
     1561 gaaatcatct ggcacgtcaa taatgtcaca agcaatatct gcacgtgaga aatgtggttc
     1621 taaaaataaa tcatggataa agttcttcat cgagcccgcc agaaattggc taattttatt
     1681 ggggttaaag tcaatccgcc cttttccctc ttgaaactta agaatctcaa tataagctat
     1741 attttcctca tgttggtcta gtaattgcca gccattattt ccaaccgctt ttaaatatcc
     1801 gttaccttcg tttagacgca taagctgttc aaaatctaaa atcaacacat catggggagt
     1861 gtgataataa atattttccc ttaatgtacc aacaatggta attcggtcaa ttgaccattg
     1921 catttttaag ggggtgcaca tagtttgtgc atttaaccgc ctgttagata tgcggttaag
     1981 tttttcccac tcatttatga tcgtgccacg tttactcaaa ttttgttcct cctcaaagaa
     2041 aaaagagatt tttggaaaga atttccagag ttcacgtaac tctaaaaatc catatccaaa
     2101 aatctctagc ttgaagaaac ctaaaaatat tcgtataatg aatttgagtt acggaactag
     2161 gtgagtagtt tccgtaatta gccgaagggt gcttccaaca ccgttcggct tttattttgc
     2221 tcttttttct cgttttcttt gattatagca ctcctcttaa aaaaataaaa agacctcagg
     2281 gaatttcatt ccccgaaccc cttgagcctc ctcctgccga aattatttca cgcttccgct
     2341 cttcatttca ttcagttctc ggcttgcaca atctaacacg ccgtttcgct accagtcgcc
     2401 ttacaggctc cattctcgct tctcttacgt gttttaacga ttgtgccgat aactaaacga
     2461 aatgaacgct aaaacgtctt agaacgcaaa atacgcgctt ataaaatcat ttcatcttga
     2521 ttacatgccc gtcataatcg ttcagtttag tttcattttc gtaaactttt tttattttta
     2581 cgaacagaaa aaagtcgcac atcaccattt tataaagagc ataaggaaac gtgtacccac
     2641 tttctaaaaa aagtgggtag ataggctgtg cctatcacgt ttctcagaaa aaaatttgat
     2701 atcacttttt cgccatcgtg gctagcttat gtatagtatt ttagcaaaaa acagctatac
     2761 aaatactata ttcgtatgat atacataaat tatacacaaa tgcgaaagga gtttttctat
     2821 ggacatttta gttcggaaga tcgattcaaa ggttattgca aaaatagaca aacgttgcca
     2881 agaactcaca aataaaactg gcaaaaaatg gagtcgaaat cgctacttaa aagtcctaat
     2941 cgaaaac
//
