LOCUS       NZ_CP093945             3007 bp    DNA     circular CON 11-APR-2024
DEFINITION  Enterococcus faecium strain NY2032 plasmid pNY2032-4, complete
            sequence.
ACCESSION   NZ_CP093945
VERSION     NZ_CP093945.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN26754680
            Assembly: GCF_022699225.1
KEYWORDS    RefSeq.
SOURCE      Enterococcus faecium
  ORGANISM  Enterococcus faecium
            Bacteria; Bacillota; Bacilli; Lactobacillales; Enterococcaceae;
            Enterococcus.
REFERENCE   1  (bases 1 to 3007)
  AUTHORS   Zhou,D.
  TITLE     Complete sequence of strain NY2032
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 3007)
  AUTHORS   Zhou,D.
  TITLE     Direct Submission
  JOURNAL   Submitted (17-MAR-2022) State Key Laboratory of Pathogen and
            Biosecurity, Beijing Institute of Microbiology and Epidemiology, No.
            20, Dongdajie, Fengtai, Beijing, Beijing 100071, China
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: HGAP v. v 3.0
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 100.0x
            Sequencing Technology             :: PacBio RSII
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_022699225.1-RS_2024_04_10
            Annotation Date                   :: 04/10/2024 23:03:07
            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)                     :: 3,121
            CDSs (total)                      :: 3,030
            Genes (coding)                    :: 2,924
            CDSs (with protein)               :: 2,924
            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)              :: 106
            CDSs (without protein)            :: 106
            Pseudo Genes (ambiguous residues) :: 0 of 106
            Pseudo Genes (frameshifted)       :: 40 of 106
            Pseudo Genes (incomplete)         :: 63 of 106
            Pseudo Genes (internal stop)      :: 30 of 106
            Pseudo Genes (multiple problems)  :: 21 of 106
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP093945.1.
            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..3007
                     /organism="Enterococcus faecium"
                     /mol_type="genomic DNA"
                     /strain="NY2032"
                     /isolation_source="blood"
                     /host="Homo sapiens"
                     /db_xref="taxon:1352"
                     /plasmid="pNY2032-4"
                     /geo_loc_name="China: BeiJing"
                     /lat_lon="39 N 116 E"
                     /collection_date="2018"
                     /collected_by="a public hospital"
     gene            127..846
                     /locus_tag="MPL11_RS15465"
                     /old_locus_tag="MPL11_15465"
     CDS             127..846
                     /locus_tag="MPL11_RS15465"
                     /old_locus_tag="MPL11_15465"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002311815.1"
                     /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_002311815.1"
                     /translation="MDEKTELTVKYQNELNLVPLKNFNAKQMDLFFALCARMKDRGLKK
                     VRFSFEELKELSDYKMTATKAFVGDLEKLYKDMLNLTYRTEDEDSIRYFVLFTGFEINK
                     TKKFVEVSVNPDLEYIINGLTAEFSRFELSAFTSLRSTYAKTLFRLLMQYRSTGYYVVR
                     IEEFRSLMDIPEYYQMGNIDQKVLNPALRELKKYFNDLKVTKIKAKKGNKIAKLEFTFS
                     SLTSDLPKISLRNWLEE"
                     /name="replication initiation protein"
     gene            complement(983..1399)
                     /locus_tag="MPL11_RS15470"
                     /old_locus_tag="MPL11_15470"
     CDS             complement(983..1399)
                     /locus_tag="MPL11_RS15470"
                     /old_locus_tag="MPL11_15470"
                     /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_001232859.1"
                     /translation="MRKTSVQKHVTLYPSHVDVLDSIIEKNPDINNYSEAIRFLCMSYE
                     PDTNTTTTSNQAKLNAMGKEISIMTEIIAEFADLYLKDTGVLIGTNSKVYQEVKEKIEA
                     KLNPSNRNRPKNHQKETSQTVTSRNFDPTNFLKR"
                     /name="hypothetical protein"
     gene            complement(1402..1686)
                     /locus_tag="MPL11_RS15475"
                     /old_locus_tag="MPL11_15475"
     CDS             complement(1402..1686)
                     /locus_tag="MPL11_RS15475"
                     /old_locus_tag="MPL11_15475"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002337999.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_000353844.1"
                     /translation="MDILVRNIDPKFVATIDKRCQELTNKTGEKWSRNKYLKVLIESDF
                     DRQLTTYKKDQFDLLLDKFIAIQTENTQILSEYVYTNNQIIEMLIGGMI"
                     /name="hypothetical protein"
     Typing          128..846
                     /name="rep_cluster_1763"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 aactttttat ctgagtacta acaacttttt atctgagtac taatatcctt ttgtataata
       61 acaaccaacc tatttacgag ttggttgtta aaggttatta tttatttgta aggggggaag
      121 aaaggaatgg atgaaaaaac ggaattaaca gtcaaatatc aaaatgaatt gaatttagta
      181 ccgctgaaaa atttcaatgc taagcagatg gatttatttt ttgcattatg cgctcgtatg
      241 aaagatcgtg gtttgaaaaa agttagattt tctttcgagg aattaaaaga gttaagtgat
      301 tataagatga ctgctacaaa agcctttgtc ggtgatttag aaaagctcta taaagatatg
      361 cttaatctta cttaccgtac tgaagatgag gattctattc gctactttgt tttgtttact
      421 ggttttgaaa tcaataaaac aaaaaagttt gttgaagtca gtgttaatcc ggacctagaa
      481 tatattatta atggtttaac agctgaattt agtagatttg aattatctgc tttcacgtcg
      541 ttgcgttcta cgtatgcaaa aactctattc cgactgctta tgcagtaccg ttctactggt
      601 tattatgtag ttcgtattga agagtttagg agcttaatgg atatcccaga atactatcaa
      661 atgggtaaca ttgatcaaaa agtattaaat cctgcattac gagaactaaa aaaatacttc
      721 aatgatctta aagtcacaaa aataaaagca aaaaagggca ataaaatcgc caaattagaa
      781 tttacttttt caagcctaac gtcagatttg ccaaagattt ctctgcgtaa ctggttagaa
      841 gaataaataa aaaagaactc gcccccctta cattaagcaa gtagacaagt cccttacaac
      901 cgactaagat tgctagtaca ttctagcata ttgtatgggg cttctaaata aaaaacagat
      961 aggaataact cctatctgtt ttttatcgtt ttagaaaatt tgttgggtcg aaatttctag
     1021 aagtgactgt ttgactggtt tctttttgat gattctttgg tcgatttcga tttgatggat
     1081 ttagtttagc ttcgattttt tctttcactt cttgatatac tttagaattt gtgccaataa
     1141 gaacgcctgt atcttttaga tataaatcag caaattctgc gatgatttca gtcatgatgg
     1201 aaatttcttt tcccatagca tttagttttg cctgattgct ggtagtggtc gtgttggtat
     1261 cgggttcata actcatacat aaaaagcgaa tggcttccga gtagttattg atatctggat
     1321 ttttttcgat gatggaatct aaaacgtcaa catgactagg gtacaaagta acatgttttt
     1381 ggacagaagt ttttctcatg gttatatcat tcctccgata agcatttcaa tgatttgatt
     1441 atttgtgtag acatactcgc ttaatatttg agtattttct gtttggatag caataaattt
     1501 atcgagcaat aaatcgaatt ggtctttttt gtaagtcgta agttgacggt caaaatcact
     1561 ttcgattaaa acttttagat atttatttcg actccatttt tctcctgttt tattcgtgag
     1621 ttcttggcaa cgtttgtcta ttgttgcaac aaactttgga tcaatattcc gaactaaaat
     1681 gtccataaaa aatctccttt tgcaattatg tataatttat gtataccata caaatactat
     1741 atttgtatag ctgttttttg ccaaaatgct atacataagc tacccacgat ggcgaaaaag
     1801 tgatatcaaa tttttttctg agaaacgtga taggcacagc ctatctaccc acttttttta
     1861 gaaagtgggt acacgtttcc ttatgctctt taaaattcgg gggggagtgc tgcacgtgta
     1921 atcgataacc aaatttaaca gacgaaaaat tgttggaata taaaaatatg acacccgaaa
     1981 gaaaacgatc gttggaaaaa ttaatgcaac tagtgaacga agacggcgga atttcagacg
     2041 cagcttttga cgcatggagc gaatttcatg gagaatataa ttaagtgggt ttaaatggct
     2101 ctaaaatcgc ttctaagagt tttttagctt ggaccaatga aatacaccaa aaactaaata
     2161 aaacgtctta aatcgaaaaa tacgagctct cagagcgact ttatttgtaa atgttgcata
     2221 taagaaataa ttacggattt tagacttttg taggatattt ttgaaataaa tatttatttc
     2281 tgttataatt tgattgcaaa taagtgaaca cgaaacacac gaaatcccca gagaggtcgg
     2341 attctctggg gctttttttg tgggctgagt cgccttaatt aagttttact tcttgtttcg
     2401 gttattcaac cagtaactga acaaagcgct taaaagccca acaagaaggg agcaaataaa
     2461 gttagtgaac acgaaacaca cctccttcca gtcgcaagac tgtcggatag gcgacaatca
     2521 attatacaat aaaaaagcaa aaataagcct aagtttttta ttgccttggg gttgttaggg
     2581 cttgccctga ccgcctgtaa ggcgctttag aacgaaggac atagttttta tcgaatcttg
     2641 tcttagaacg gcttagacga gctctcagga cgccacaaag gagtccctaa tgaattattt
     2701 ttggcgaagg agcctaaagg cgactgctgc aagtaaaatg tgagagcgta gcgatcactc
     2761 cttcttacag cgaccatagg gagctagatt ggcagtttaa tatcatgcgc gaacctgttt
     2821 attttaaaaa gtgggtgatt ttttggcggg aaattttgct cgcgcgcgcg cgtttatttt
     2881 atttattttt taaagatttt ttagaaccct ttttaggggg cagttgagcc ttactctccc
     2941 aacggataca gaagggtact aacaactttt tatctgagta ctaacaactt tttatctgag
     3001 tactaac
//
