LOCUS       NZ_CP085917             1979 bp    DNA     circular CON 24-DEC-2023
DEFINITION  Enterococcus faecium strain SC1762-D plasmid p11, complete sequence.
ACCESSION   NZ_CP085917
VERSION     NZ_CP085917.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN22627489
            Assembly: GCF_020736625.1
KEYWORDS    RefSeq.
SOURCE      Enterococcus faecium
  ORGANISM  Enterococcus faecium
            Bacteria; Bacillota; Bacilli; Lactobacillales; Enterococcaceae;
            Enterococcus.
REFERENCE   1  (bases 1 to 1979)
  AUTHORS   Zeng,W.
  TITLE     Acquisition of daptomycin resistance by Enterococcus faecium confers
            collateral sensitivity to glycopeptides
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 1979)
  AUTHORS   Zeng,W.
  TITLE     Direct Submission
  JOURNAL   Submitted (27-OCT-2021) Laboratory Medicine, College of Life
            Sciences, Wenzhou Medical University, Wenzhou Medical University,
            Wenzhou, Zhejiang 325000, China
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: unicycler v. v0.4.8
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 120.0x
            Sequencing Technology             :: Oxford Nanopore
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 12/23/2023 20:46:10
            Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline
            (PGAP)
            Annotation Method :: Best-placed reference protein set; GeneMarkS-2+
            Annotation Software revision      :: 6.6
            Features Annotated                :: Gene; CDS; rRNA; tRNA; ncRNA
            Genes (total)                     :: 3,310
            CDSs (total)                      :: 3,219
            Genes (coding)                    :: 3,060
            CDSs (with protein)               :: 3,060
            Genes (RNA)                       :: 91
            rRNAs                             :: 6, 6, 6 (5S, 16S, 23S)
            complete rRNAs                    :: 6, 6, 6 (5S, 16S, 23S)
            tRNAs                             :: 69
            ncRNAs                            :: 4
            Pseudo Genes (total)              :: 159
            CDSs (without protein)            :: 159
            Pseudo Genes (ambiguous residues) :: 0 of 159
            Pseudo Genes (frameshifted)       :: 63 of 159
            Pseudo Genes (incomplete)         :: 94 of 159
            Pseudo Genes (internal stop)      :: 41 of 159
            Pseudo Genes (multiple problems)  :: 30 of 159
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP085917.1.
            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..1979
                     /organism="Enterococcus faecium"
                     /mol_type="genomic DNA"
                     /strain="SC1762-D"
                     /host="Homo sapiens"
                     /db_xref="taxon:1352"
                     /plasmid="p11"
                     /geo_loc_name="China:wenzhou"
                     /collection_date="2018"
     gene            complement(join(1135..1979,1..172))
                     /locus_tag="LLE91_RS16495"
                     /old_locus_tag="LLE91_16495"
     CDS             complement(join(1135..1979,1..172))
                     /locus_tag="LLE91_RS16495"
                     /old_locus_tag="LLE91_16495"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002299382.1"
                     /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_002299382.1"
                     /translation="MANENQLSEIQSKIEGRGAEKRTTINQLEKLNRISNRRLSVQGTT
                     TPLKLNWSIDRITIVGKLNDTIAYWTKNGVVFVDFEQLMRLNENQGYLKSVGINGWQLF
                     DQYGEDIAYIEILKFHEGKGRIDFNPNKIGQFLASSMKGFIHDLFLDPHFSRADIACDI
                     VDVPDDFITQYRIVDPISFKPIYGRSGKLETAYWGSRASERQVRLYNKKLEQERKKVIV
                     PKEIDTWWRLEMQLRRGKATDWHAMVQESLDSFASPHFLPIDIKPIDKIVIDGLIAEPS
                     NWSIIARHTKYKYRNLLKQESQNDELTNHLRETFKESADELKKELDTWLLGLDVTEK"
                     /name="replication initiation factor domain-containing
                     protein"
     gene            complement(<753..935)
                     /locus_tag="LLE91_RS16500"
                     /old_locus_tag="LLE91_16500"
                     /pseudo=""
     CDS             complement(<753..935)
                     /locus_tag="LLE91_RS16500"
                     /old_locus_tag="LLE91_16500"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002313295.1"
                     /note="incomplete; partial in the middle of a contig;
                     missing C-terminus; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /name="hypothetical protein"
     Typing          complement(1139..1979)
                     /name="rep_cluster_935"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="91.578"
                     /coverage="99.0"
                     /evalue="0.0"
ORIGIN
        1 taattcgatc aatcgaccaa tttaatttta ggggggtggt cgtaccttgc acacttaacc
       61 gcctgttaga aatacggtta agtttttcga gctgatttat cgttgttctt ttttctgccc
      121 ctcgaccttc aatttttgat tgaatttcac tcaactgatt ttcatttgcc attttcgtcc
      181 tccaaacgaa aaaagagact tttggaaaga atttccagag ttcacgtaac cctaaaaatt
      241 catatccaaa aatctctagc ttgaagaaac ctaaaaatat tcgtataatg aacctgagtt
      301 acggagctag gtgaagtagt ttccgtaaat agtcgagagt gttagcgcac tgctcggctt
      361 ttattttgct cttttttctc gttttctttg attatagcac tcctcctaaa aaaataaaaa
      421 gacctcaggg aatttcattc cccgaacccc ttgagcctcc tcctgccgaa atggaaaggg
      481 cgcacccgct gtttatttca ttcagctatc ggttttcaca atctaacacg atcgttccgc
      541 taccagtcgc cttacaggct ccattttcgc tcctctaacg tgttttaacg attgtgccga
      601 taactaaacg aaataaacgc taaaaccgct cagaacgcaa aatatgccat tttagagcta
      661 ttgtagaaaa tgtagtttga aatgcaattt tcttctttca gctttttatt tcccacttgt
      721 aaatctgcta attattttct accagacaaa ccattgattt tttggctatc agttaactca
      781 cgattattat gagaaatgct tgtattcttt gttccctttt tgaacgaaat actaaaccct
      841 aaggtgaacc cctccttcac gctgtcgcta ataaaaagag tgtaaacctt tctgttactc
      901 tttgacaaag agtaacgttt tcctaattgt gacatggctg tcacaattcc aaacgctctc
      961 cgagggattt cgctgtcaca agtgacaacg aaaaaaggag ccgaaagcgt gtcacgctct
     1021 caactccttt tacgctttat tttgcttcat gcaaaatatt cgcttatcgt gaatttacgt
     1081 cactaaacat tgacgcaaat ccactctcac tcatctgact tttcttattc ggtatcactt
     1141 ctctgtcaca tccaacccca aaagccacgt atccaattct ttttttaatt cgtctgcaga
     1201 ttccttaaaa gtctctcgta aatgattcgt taactcatca ttttgacttt cttgcttcag
     1261 caaattccga tatttatatt ttgtatgtct agcaattatc gaccaattag aaggctcagc
     1321 tatcaaacca tcaataacta ttttatcaat aggttttata tcaatcggca aaaaatgcgg
     1381 gcttgcaaaa ctatctaagc tttcctgaac catcgcatgc caatccgttg ctttgccacg
     1441 tcttagctgc atttctaacc gccaccacgt atcgatttct tttggcacga ttactttttt
     1501 tcgttcctgc tctagctttt tgttgtacag tcgcacttgg cgctcactgg cacgactgcc
     1561 ccagtacgct gtttctagct tgccagaacg gccgtagatt ggcttaaaag aaatcgggtc
     1621 tacaatacga tactgagtaa taaagtcatc cggcacatct acaatatcgc aggcaatatc
     1681 cgcccgggaa aaatgcggat ctaaaaatag gtcatgaatg aatcctttca tggaactagc
     1741 taaaaactgg cctatcttat tcggattaaa atcaatacga ccttttcctt catgaaattt
     1801 aagtatttcg atatacgcaa tatcttctcc atattgatcg aataattgcc agccgtttat
     1861 cccaactgat ttcaaatatc cctgattttc gttcaaacgc attaattgct cgaaatcgac
     1921 aaaaacaact ccatttttcg tccaataagc tatggtatca ttcagttttc cgacaattg
//
