LOCUS       NZ_CP064430             4074 bp    DNA     circular CON 20-APR-2024
DEFINITION  Enterococcus faecium strain PR01996-12 plasmid unnamed_6, complete
            sequence.
ACCESSION   NZ_CP064430
VERSION     NZ_CP064430.1
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 4074)
  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 4074)
  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
            CP064430.1.
            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..4074
                     /organism="Enterococcus faecium"
                     /mol_type="genomic DNA"
                     /strain="PR01996-12"
                     /isolation_source="Rectal Swab"
                     /host="Homo sapiens"
                     /db_xref="taxon:1352"
                     /plasmid="unnamed_6"
                     /geo_loc_name="USA: Ann Arbor, Michigan"
                     /lat_lon="42.28 N 83.72 W"
                     /collection_date="2016"
                     /collected_by="University of Michigan"
     gene            join(3835..4074,1..735)
                     /locus_tag="IUH71_RS15540"
                     /old_locus_tag="IUH71_15540"
     CDS             join(3835..4074,1..735)
                     /locus_tag="IUH71_RS15540"
                     /old_locus_tag="IUH71_15540"
                     /inference="COORDINATES: ab initio prediction:GeneMarkS-2+"
                     /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: GeneMarkS-2+."
                     /codon_start=1
                     /transl_table=11
                     /product="replication initiation factor domain-containing
                     protein"
                     /protein_id="WP_002303407.1"
                     /translation="MSKKGTIINEWEKLTAPSNRRLSVPFMDTPLKIQWSIDRITIVGN
                     LKENIYYHTTHDVLILDFEQLMRLNEGNGYLRSVSNNGWQLLDQHEENIAYIEILKWQE
                     GKGRIDFNPNKISQFLASSMKNFIHDLFIEPHFSRADIACDIIDVPDEFITQYRVVDPV
                     SFKPIYGRNGKLETAYWGSRSSERQIRMYNKKLEQEKKRKIVPKEIVSWWRLELQLRRG
                     KATDWHAMVYESLDSFASPHYLPADTSVADKMMITALTTEHDYWGQINRKTKYKYRNLL
                     KQESQNDELTNHLRETFAESADDLKKELDTWLLGLDVTEEEEK"
                     /name="replication initiation factor domain-containing
                     protein"
     gene            732..965
                     /locus_tag="IUH71_RS15545"
                     /old_locus_tag="IUH71_15545"
     CDS             732..965
                     /locus_tag="IUH71_RS15545"
                     /old_locus_tag="IUH71_15545"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002298421.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_002303408.1"
                     /translation="MTEKQKYFGKKNWLVNLTGDYVVVVFLDSKKMSGKLLDVTQYELI
                     LKNNKIDSPIIIPKHAVKYIYAVAESSGEAND"
                     /name="hypothetical protein"
     gene            1036..1383
                     /locus_tag="IUH71_RS15550"
                     /old_locus_tag="IUH71_15550"
     CDS             1036..1383
                     /locus_tag="IUH71_RS15550"
                     /old_locus_tag="IUH71_15550"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002321903.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_171346404.1"
                     /translation="MVAVLEMRCNMDKIDLREETVDRIELMYERLADYLNLPDEDNYSE
                     MLERMMDVLNSTINVGLANSSLITDKFVYGKIAETEDESEKEFWLNILTYVMQLNQIGV
                     IYRNKSKGKEL"
                     /name="hypothetical protein"
     gene            1387..1749
                     /locus_tag="IUH71_RS15555"
                     /old_locus_tag="IUH71_15555"
     CDS             1387..1749
                     /locus_tag="IUH71_RS15555"
                     /old_locus_tag="IUH71_15555"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_016173819.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_002303404.1"
                     /translation="MGMTLADIKAQEEKLKKEQAKLRQQKKRLIEKENAEMGKALRKHF
                     GFESFDDFERWLSSISDDQQHEKSVDNEWLADEKSAPSERDYPNESDGLLGVIPSKKSQ
                     MSESKFTSMFNDVSLR"
                     /name="hypothetical protein"
     gene            1971..3386
                     /locus_tag="IUH71_RS15560"
                     /old_locus_tag="IUH71_15560"
     CDS             1971..3386
                     /locus_tag="IUH71_RS15560"
                     /old_locus_tag="IUH71_15560"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_016173818.1"
                     /GO_function="GO:0003677 - DNA binding [Evidence IEA]"
                     /GO_process="GO:0006310 - DNA recombination [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="plasmid recombination protein"
                     /protein_id="WP_002303405.1"
                     /translation="MGFSISFKKGTKNTSISHNNRELTDSQKTNDWHKHIDFTKSDENI
                     YLEQTNLADKYEELFGEVVEKYNAKQKRADRKIEDYLAKVRKDKKLEPQREFIVQIGIL
                     DDFQTNRADGSSTGISKQQAEQNRVIANKILVQYYKEFQERNPNLAVYNAVIHNDEISP
                     HLHLNIVPVAEGYKRGVQKQPSFNKALVQQGIHADKDNGRVLFNNFRNQEVDSIERLMN
                     DYGWKRDIVGTNKIKDIHEYKEIMSEISELRQTAVKERESISAEMRYISKQREKNEREK
                     ALVASEKAKIEEEKKSIIDLEKELAVVFQKDPVPLNSFEKLSDGSYRLSSADFVDLYQK
                     ASNATNSKKYADMANESLGNTLDKNIALFDKNMALEQENSFLKNQQKVDVSAVVAENKK
                     LKEENRSLRRRLTQLKNAFQKSITRLSIRFGLVEKDMGISEELKILDQEKTLASQQNAP
                     ERNIGRSENEMEW"
                     /name="plasmid recombination protein"
     Typing          2..735
                     /name="rep_cluster_2146"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          1879..3383
                     /name="MOBV"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="98.207"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 aataatggtt ggcagttgtt agaccaacat gaagagaata ttgcttatat tgaaatttta
       61 aaatggcaag aggggaaagg gcgtatagac ttcaatccga ataagattag tcaattctta
      121 gctagttcca tgaaaaattt tattcatgat ttgtttatcg aacctcactt ttcacgtgca
      181 gatattgctt gcgacattat cgatgtacct gatgagttta ttacacaata tcgggtagtt
      241 gatccagttt cttttaagcc tatttatgga cggaatggaa aattagagac ggcatattgg
      301 ggatctcgct cttctgaacg tcaaattcgg atgtataata aaaaactgga acaagagaag
      361 aaaagaaaaa ttgtgccaaa agaaatcgtg agttggtggc ggttagaatt acaattaaga
      421 cgagggaaag cgactgattg gcatgctatg gtttatgaaa gcttagatag ttttgctagt
      481 cctcattact tgcctgctga tacaagtgta gctgacaaaa tgatgattac tgctttaaca
      541 acagaacatg attattgggg gcaaattaat cgaaagacaa aatataaata tcgaaatttg
      601 ctgaagcaag aaagtcaaaa tgatgaattg acgaatcatt tacgagaaac ctttgcagaa
      661 tcggcagacg atttaaaaaa agaattagac acatggcttc tagggctaga cgtaacagag
      721 gaggaagaaa aatgacagaa aaacaaaagt attttggtaa gaaaaattgg ttggtaaatt
      781 taacaggtga ttacgttgtg gttgtttttt tggatagcaa aaaaatgtcc ggtaagttac
      841 ttgatgtaac gcaatatgaa ttgattttga aaaataataa aattgactct ccgattatta
      901 tccctaagca cgccgttaaa tatatttatg cggtagctga aagtagtgga gaagctaatg
      961 actgatttgt cagaaaagat gaccataaaa aatcttgctg atgaattagg tgtatcgaaa
     1021 attaaagaat cggaaatggt ggcagttttg gaaatgaggt gtaacatgga taaaattgat
     1081 ttaagagaag agacagttga tagaattgaa ttgatgtatg aacgattagc tgattatttg
     1141 aatttgccgg atgaagataa ttatagtgaa atgcttgaga gaatgatgga cgttctcaat
     1201 tctacaatca atgtaggcct agcaaattct tctttgatta ctgataaatt tgtttacggt
     1261 aaaatagccg aaacagaaga tgaatctgaa aaggaatttt ggctgaatat tttaacttat
     1321 gttatgcaat taaatcaaat tggtgttatt tatcgaaata aatcaaaagg caaggagctg
     1381 taaatcttgg gaatgacttt agcagatatt aaagcacaag aagaaaaatt gaaaaaagaa
     1441 caggcaaaac ttcgtcaaca gaaaaaacga ttgattgaga aggaaaatgc tgaaatgggt
     1501 aaggcacttc ggaagcattt tggatttgaa tcttttgatg attttgagcg gtggttatcg
     1561 tcaatttctg acgatcagca acacgaaaaa tcagtggata atgagtggct tgctgatgaa
     1621 aaatcagcgc caagcgaacg agattatccc aatgaatctg acggcttact cggagtgata
     1681 ccgagtaaaa aaagtcagat gagtgagagt aaatttacgt caatgtttaa tgacgtgagt
     1741 ttacgataag cgattatttt gcgtgaagca aaataaagcg taaaaggagt tgagagcgtg
     1801 acacgctttc ggctcctttt ttcgttgtca cttgtgacag cgaataccct cggagagcat
     1861 ttggaattgt gacagccatg tcacaattag gaaaatgtta ctctttgaca aagagtaaca
     1921 gaaaggttta cactcttttt attagcgaca gcgcgaagga gggttttaac ttggggttta
     1981 gtatttcatt taaaaaagga acgaagaata caagtatttc tcataataat cgtgagttaa
     2041 ctgatagcca gaaaaccaat gattggcata agcatattga cttcacgaaa tcggatgaaa
     2101 atatttattt agagcagacg aatctagcag ataaatatga ggaattgttt ggcgaagtgg
     2161 tagaaaaata taatgcgaaa caaaaaagag ccgatagaaa aatcgaggac tatttagcga
     2221 aagtgcgcaa ggataaaaag ttggaacctc aacgagaatt tattgtgcaa ataggcattt
     2281 tagatgattt ccagacaaat cgagcagatg gttcttctac tggcatatcg aaacaacaag
     2341 ctgaacaaaa tcgagtgatt gccaataaaa ttttggttca gtattacaag gagtttcaag
     2401 agagaaaccc taatttggct gtttataatg ctgttattca taatgacgaa ataagtccgc
     2461 acctgcactt gaatattgtg ccggttgctg aaggttataa acggggtgtt caaaagcagc
     2521 cgagctttaa taaagcactg gttcaacaag ggatacacgc tgataaagat aatggtcgag
     2581 tgcttttcaa taattttaga aatcaagaag ttgactctat agaacgatta atgaatgatt
     2641 acggttggaa aagggatatt gtcggtacca acaaaattaa agatattcac gaatacaaag
     2701 aaatcatgag tgaaatttct gaattgcgcc aaacggctgt aaaagagcgt gagagcattt
     2761 ctgcggaaat gaggtatatt tctaagcaaa gagaaaaaaa cgagcgtgag aaggctctgg
     2821 tggcttctga gaaggcgaaa attgaagaag agaaaaaatc gattatcgat ttggaaaaag
     2881 agctggctgt tgtatttcaa aaagatcctg tgccactcaa tagttttgaa aaattatcag
     2941 atggttctta tcgcttatct agtgctgatt ttgtagattt gtatcaaaaa gcgtctaatg
     3001 ctacgaacag caaaaaatat gctgatatgg cgaatgaatc gcttggaaat acattagata
     3061 aaaatatcgc tttatttgat aaaaacatgg cgttagaaca agaaaattct tttttgaaaa
     3121 atcaacaaaa ggttgatgtg tcagcggttg ttgctgaaaa caaaaagctg aaggaagaaa
     3181 atcgttcttt gcgtcggcgg ttaactcaac tgaaaaacgc atttcaaaaa tcaatcactc
     3241 gtttatcaat tcgttttggg cttgtagaaa aagatatggg aatatctgaa gagctaaaaa
     3301 tattagatca agagaaaacg ttggctagtc agcagaatgc cccagaacgt aatatagggc
     3361 gttctgagaa tgagatggag tggtagttat acggtgcagt caacggtacc ggaggcggtc
     3421 tgtgccgagg ataaggagtt gacggctaaa ccactaatcc ctgaagctga catttgctaa
     3481 aaaatggcaa gtccattttt tggccaactt agcgttagcg aagtttgggg gcgccctttt
     3541 caaagggtgc ggttttatgt ttttggatat ttgcatagct aaagagaagt gctattattg
     3601 agttatcaaa taaataaact gaaaaaagag caaaaaaata aagtcgagca acgctggaca
     3661 cgttctcgac ctttacggaa actaatcaca ctagctccgt aactcaaatt cattatacga
     3721 ataatttcag gtttcttcaa gactagagat tgctggttat gaatttttta gagttacgtg
     3781 aactctggaa aattctttcc accaatctct tttttctttg aggaggaact aaatttgagt
     3841 aaaaaaggca cgatcataaa tgagtgggaa aaattaacag ccccctctaa caggcggtta
     3901 agtgtccctt ttatggacac ccccctaaaa attcagtggt caatcgaccg aattaccatt
     3961 gttggaaatc ttaaagagaa tatctattat cacactacac atgatgtgtt gattttagat
     4021 tttgaacagc ttatgcgcct aaatgaaggt aacggttatt taagatctgt tagt
//
