LOCUS       NZ_CP092573             1979 bp    DNA     circular CON 07-APR-2024
DEFINITION  Enterococcus faecium strain VRE-WC072 plasmid unnamed4, complete
            sequence.
ACCESSION   NZ_CP092573
VERSION     NZ_CP092573.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN26026626
            Assembly: GCF_022691445.1
KEYWORDS    RefSeq.
SOURCE      Enterococcus faecium
  ORGANISM  Enterococcus faecium
            Bacteria; Bacillota; Bacilli; Lactobacillales; Enterococcaceae;
            Enterococcus.
REFERENCE   1  (bases 1 to 1979)
  AUTHORS   Haas,W., Mitchell,K.K. and Musser,K.A.
  TITLE     Direct Submission
  JOURNAL   Submitted (17-FEB-2022) Bacteriology, NYS DOH, 120 New Scotland Ave,
            Albany, NY 12008, USA
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: Unicycler v. 0.4.8
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 157x
            Sequencing Technology :: Illumina MiSeq and Oxford Nanopore MinION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_022691445.1-RS_2024_04_07
            Annotation Date                   :: 04/07/2024 08:52:49
            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)                     :: 3,072
            CDSs (total)                      :: 2,983
            Genes (coding)                    :: 2,812
            CDSs (with protein)               :: 2,812
            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)              :: 171
            CDSs (without protein)            :: 171
            Pseudo Genes (ambiguous residues) :: 0 of 171
            Pseudo Genes (frameshifted)       :: 90 of 171
            Pseudo Genes (incomplete)         :: 79 of 171
            Pseudo Genes (internal stop)      :: 31 of 171
            Pseudo Genes (multiple problems)  :: 25 of 171
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP092573.1.
            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="VRE-WC072"
                     /isolation_source="urine"
                     /host="Homo sapiens"
                     /db_xref="taxon:1352"
                     /plasmid="unnamed4"
                     /geo_loc_name="USA"
                     /collection_date="2004-04-20"
                     /collected_by="NYS DOH"
     gene            1..1017
                     /locus_tag="MKI62_RS15240"
                     /old_locus_tag="MKI62_003042"
     CDS             1..1017
                     /locus_tag="MKI62_RS15240"
                     /old_locus_tag="MKI62_003042"
                     /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            1217..>1399
                     /locus_tag="MKI62_RS15245"
                     /old_locus_tag="MKI62_003043"
                     /pseudo=""
     CDS             1217..>1399
                     /locus_tag="MKI62_RS15245"
                     /old_locus_tag="MKI62_003043"
                     /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          2..1011
                     /name="rep_cluster_935"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="92.292"
                     /coverage="99.0"
                     /evalue="0.0"
ORIGIN
        1 atggcaaatg aaaatcagtt gagtgaaatt caatcaaaaa ttgaaggtcg aggggcagaa
       61 aaaagaacaa cgataaatca gctcgaaaaa cttaaccgta tttctaacag gcggttaagt
      121 gtgcaaggta cgaccacccc cctaaaatta aattggtcga ttgatcgaat tacaattgtc
      181 ggaaaactga atgataccat agcttattgg acgaaaaatg gagttgtttt tgtcgatttc
      241 gagcaattaa tgcgtttgaa cgaaaatcag ggatatttga aatcagttgg gataaacggc
      301 tggcaattat tcgatcaata tggagaagat attgcgtata tcgaaatact taaatttcat
      361 gaaggaaaag gtcgtattga ttttaatccg aataagatag gccagttttt agctagttcc
      421 atgaaaggat tcattcatga cctattttta gatccgcatt tttcccgggc ggatattgcc
      481 tgcgatattg tagatgtgcc ggatgacttt attactcagt atcgtattgt agacccgatt
      541 tcttttaagc caatctacgg ccgttctggc aagctagaaa cagcgtactg gggcagtcgt
      601 gccagtgagc gccaagtgcg actgtacaac aaaaagctag agcaggaacg aaaaaaagta
      661 atcgtgccaa aagaaatcga tacgtggtgg cggttagaaa tgcagctaag acgtggcaaa
      721 gcaacggatt ggcatgcgat ggttcaggaa agcttagata gttttgcaag cccgcatttt
      781 ttgccgattg atataaaacc tattgataaa atagttattg atggtttgat agctgagcct
      841 tctaattggt cgataattgc tagacataca aaatataaat atcggaattt gctgaagcaa
      901 gaaagtcaaa atgatgagtt aacgaatcat ttacgagaga cttttaagga atctgcagac
      961 gaattaaaaa aagaattgga tacgtggctt ttggggttgg atgtgacaga gaagtgatac
     1021 cgaataagaa aagtcagatg agtgagagtg gatttgcgtc aatgtttagt gacgtaaatt
     1081 cacgataagc gaatattttg catgaagcaa aataaagcgt aaaaggagtt gagagcgtga
     1141 cacgctttcg gctccttttt tcgttgtcac ttgtgacagc gaataccctc ggagagcatt
     1201 tggaattgtg acagccatgt cacaattagg aaaatgttac tctttgtcaa agagtaacag
     1261 aaaggtttac actcttttta ttagcgacag cgtgaaggag gggttcacct tagggtttag
     1321 tatttcgttc aaaaagggaa caaagaatac aagcatttct cataataatc gtgagttaac
     1381 tgatagccaa aaaatcaatg gtttgtctgg tagaaaataa ttagcagatt tacaagtggg
     1441 aaataaaaag ctgaaagaag aaaattgcat ttcaaactac attttctaca atagctctaa
     1501 aatggcatat tttgcgttct gagcggtttt agcgtttatt tcgtttagtt atcggcacaa
     1561 tcgttaaaac acgttagagg agcgaaaatg gagcctgtaa ggcgactggt agcggaacga
     1621 tcgtgttaga ttgtgaaaac cgatagctga atgaaataaa cagcgggtgc gccctttcca
     1681 tttcggcagg aggaggctca aggggttcgg ggaatgaaat tccctgaggt ctttttattt
     1741 ttttaggagg agtgctataa tcaaagaaaa cgagaaaaaa gagcaaaata aaagccgagc
     1801 agtgcgctaa cactctcgac tatttacgga aactacttca cctagctccg taactcaggt
     1861 tcattatacg aatattttta ggtttcttca agctagagat ttttggatat gaatttttag
     1921 ggttacgtga actctggaaa ttctttccaa aagtctcttt tttcgtttgg aggacgaaa
//
