LOCUS       NZ_CP064431             1980 bp    DNA     circular CON 20-APR-2024
DEFINITION  Enterococcus faecium strain PR01996-12 plasmid unnamed_7, complete
            sequence.
ACCESSION   NZ_CP064431
VERSION     NZ_CP064431.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN16327730
            Assembly: GCF_018219325.1
KEYWORDS    RefSeq.
SOURCE      Enterococcus faecium
  ORGANISM  Enterococcus faecium
            Bacteria; Bacillota; Bacilli; Lactobacillales; Enterococcaceae;
            Enterococcus.
REFERENCE   1  (bases 1 to 1980)
  AUTHORS   Kinnear,C.L., Hansen,E., Morley,V.J., Tracy,K.C., Forstchen,M.,
            Read,A.F. and Woods,R.J.
  TITLE     Daptomycin treatment impacts resistance in off-target populations of
            vancomycin-resistant Enterococcus faecium
  JOURNAL   PLoS Biol 18 (12), e3000987 (2020)
   PUBMED   33332354
  REMARK    Publication Status: Online-Only
REFERENCE   2  (bases 1 to 1980)
  AUTHORS   Morley,V.J., Tracy,K.C., Kinnear,C.L. and Woods,R.J.
  TITLE     Direct Submission
  JOURNAL   Submitted (02-NOV-2020) Computational Medicine and Bioinformatics,
            University of Michigan, Palmer Commons, 100 Washtenaw Ave #2017, Ann
            Arbor, MI 48104, USA
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: Unicycler v. 0.4.8
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 57x
            Sequencing Technology :: Illumina NovaSeq + Oxford Nanopore MinION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_018219325.1-RS_2024_04_20
            Annotation Date                   :: 04/20/2024 06:20:19
            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)                     :: 3,147
            CDSs (total)                      :: 3,063
            Genes (coding)                    :: 2,854
            CDSs (with protein)               :: 2,854
            Genes (RNA)                       :: 84
            rRNAs                             :: 6, 5, 6 (5S, 16S, 23S)
            complete rRNAs                    :: 6, 5, 6 (5S, 16S, 23S)
            tRNAs                             :: 63
            ncRNAs                            :: 4
            Pseudo Genes (total)              :: 209
            CDSs (without protein)            :: 209
            Pseudo Genes (ambiguous residues) :: 0 of 209
            Pseudo Genes (frameshifted)       :: 134 of 209
            Pseudo Genes (incomplete)         :: 66 of 209
            Pseudo Genes (internal stop)      :: 36 of 209
            Pseudo Genes (multiple problems)  :: 23 of 209
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP064431.1.
            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..1980
                     /organism="Enterococcus faecium"
                     /mol_type="genomic DNA"
                     /strain="PR01996-12"
                     /isolation_source="Rectal Swab"
                     /host="Homo sapiens"
                     /db_xref="taxon:1352"
                     /plasmid="unnamed_7"
                     /geo_loc_name="USA: Ann Arbor, Michigan"
                     /lat_lon="42.28 N 83.72 W"
                     /collection_date="2016"
                     /collected_by="University of Michigan"
     gene            complement(join(1006..1980,1..42))
                     /locus_tag="IUH71_RS15565"
                     /old_locus_tag="IUH71_15565"
     CDS             complement(join(1006..1980,1..42))
                     /locus_tag="IUH71_RS15565"
                     /old_locus_tag="IUH71_15565"
                     /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"
     Typing          complement(1010..1980)
                     /name="rep_cluster_935"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="91.881"
                     /coverage="99.0"
                     /evalue="0.0"
ORIGIN
        1 aatttttgat tgaatttcac tcaactgatt ttcatttgcc attttcgtcc tccaaacgaa
       61 aaaagagact tttggaaaga atttccagag ttcacgtaac cctaaaaatt catatccaaa
      121 aatctctagc ttgaagaaac ctaaaaatat tcgtataatg aacctgagtt acggagctag
      181 gtgaagtagt ttccgtaaat agtcgagagt gttagcgcac tgctcggctt ttattttgct
      241 cttttttctc gttttctttg attatagcac tcctcctaaa aaaataaaaa gacctcaggg
      301 aatttcattc cccgaacccc ttgagcctcc tcctgccgaa atggaaaggg cgcacccgct
      361 gtttatttca ttcagctatc ggttttcaca atctaacacg atcgttccgc taccagtcgc
      421 cttacaggct ccattttcgc tcctctaacg tgttttaacg attgtgccga taactaaacg
      481 aaataaacgc taaaaccgct cagaacgcaa aatatgccat tttagagcta ttgtagaaaa
      541 tgtagtttga aatgcaattt tcttctttca gctttttatt tcccacttgt aaatctgcta
      601 attattttct accagacaaa ccattgattt tttggctatc agttaactca cgattattat
      661 gagaaatgct tgtattcttt gttccctttt tgaacgaaat actaaaccct aaggtgaacc
      721 cctccttcac gctgtcgcta ataaaaagag tgtaaacctt tctgttactc tttgacaaag
      781 agtaaaaatt ttcctaattg tgacatggct gtcacaattc caaatgctct ccgagggtat
      841 tcgctgtcac aagtgacaac gaaaaaagga gccgaaagcg tgtcacgctc tcaactcctt
      901 ttacgcttta ttttgcttca tgcaaaatat tcgcttatcg tgaatttacg tcactaaaca
      961 ttgacgcaaa tccactctca ctcatctgac ttttcttatt cggtatcact tctctgtcac
     1021 atccaacccc aaaagccacg tatccaattc tttttttaat tcgtctgcag attccttaaa
     1081 cgtctctcgt aaatgattcg ttaactcatc attttgactt tcttgcttca gcaaattccg
     1141 atatttatat tttgtatgtc tagcaattat cgaccaatta gaaggctcag ctatcaaacc
     1201 atcaataact attttatcaa taggttttat atcaatcggc aaaaaatgcg ggcttgcaaa
     1261 actatctaag ctttcctgaa ccatcgcatg ccaatccgtt gctttgccac gtcttagctg
     1321 catttctaac cgccaccacg tatcgatttc ttttggcacg attacttttt ttcgttcctg
     1381 ctctagcttt ttgttgtaca gtcgcacttg gcgctcactg gcacgactgc cccagtacgc
     1441 tgtttctagc ttgccagaac ggccgtagat tggcttaaaa gaaatcgggt ctacaatacg
     1501 atactgagta ataaagtcat ccggcacatc tacaatatcg caggcaatat ccgcccggga
     1561 aaaatgcgga tctaaaaata ggtcatgaat gaatcctttc atggaactag ctaaaaactg
     1621 gcctatctta ttcggattaa aatcaatacg accttttcct tcatgaaatt taagtatttc
     1681 gatatacgca atatcttctc catattgatc gaataattgc cagccgttta tcccaactga
     1741 tttcaaatat ccctgatttt cgttcaaacg cattaattgc tcgaaatcga caaaaacaac
     1801 tccatttttc gtccaataag ctatggtatc attcagtttt ccgacaattg taattcgatc
     1861 aatcgaccaa tttaatttta ggggggtggt cgtaccttgc acacttaacc gcctgttaga
     1921 aatacggtta agtttttcga gctgatttat cgttgttctt ttttctgccc ctcgaccttc
//
