LOCUS       NZ_CP044325             4372 bp    DNA     circular CON 13-OCT-2023
DEFINITION  Enterococcus faecium strain 15-307-1 plasmid p15-307-1_09, complete
            sequence.
ACCESSION   NZ_CP044325
VERSION     NZ_CP044325.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN08093650
            Assembly: GCF_002973755.2
KEYWORDS    RefSeq.
SOURCE      Enterococcus faecium
  ORGANISM  Enterococcus faecium
            Bacteria; Bacillota; Bacilli; Lactobacillales; Enterococcaceae;
            Enterococcus.
REFERENCE   1  (bases 1 to 4372)
  AUTHORS   Guerin,F., Sassi,M., Dejoies,L., Zouari,A., Schutz,S., Potrel,S.,
            Auzou,M., Collet,A., Auger,G. and Cattoir,V.
  TITLE     Cfr(D), a new plasmid-mediated linezolid resistance determinant in
            Enterococcus faecium
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 4372)
  AUTHORS   Guerin,F., Sassi,M., Dejoies,L., Zouari,A., Schutz,S., Potrel,S.,
            Auzou,M., Collet,A., Auger,G. and Cattoir,V.
  TITLE     Direct Submission
  JOURNAL   Submitted (20-SEP-2019) Rennes1 University, U1230, 2 avenue du
            Professeur Leon Bernard, Rennes 35043, France
REFERENCE   3  (bases 1 to 4372)
  AUTHORS   Sassi,M., Guerin,F., Zouari,A., Auzou,M., Fines-Guyon,M., Potrel,S.,
            Collet,A., Auger,G., Bonnet,R. and Cattoir,V.
  TITLE     Direct Submission
  JOURNAL   Submitted (14-DEC-2017) Microbiology, CHU de Rennes, 2 rue Henri Le
            Guilloux, Rennes 35033, France
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Date                     :: 09-SEP-2019
            Assembly Method :: Unicycler v. v0.4.8; canu v. v1.8
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 450.0x
            Sequencing Technology :: Oxford Nanopore MiniION; Illumina MiSeq
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 10/13/2023 02:06:01
            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)                     :: 3,298
            CDSs (total)                      :: 3,206
            Genes (coding)                    :: 3,060
            CDSs (with protein)               :: 3,060
            Genes (RNA)                       :: 92
            rRNAs                             :: 6, 6, 6 (5S, 16S, 23S)
            complete rRNAs                    :: 6, 6, 6 (5S, 16S, 23S)
            tRNAs                             :: 70
            ncRNAs                            :: 4
            Pseudo Genes (total)              :: 146
            CDSs (without protein)            :: 146
            Pseudo Genes (ambiguous residues) :: 0 of 146
            Pseudo Genes (frameshifted)       :: 51 of 146
            Pseudo Genes (incomplete)         :: 86 of 146
            Pseudo Genes (internal stop)      :: 31 of 146
            Pseudo Genes (multiple problems)  :: 20 of 146
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP044325.1.
            Bacteria and source DNA available from NRC for Enterococci.
            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..4372
                     /organism="Enterococcus faecium"
                     /mol_type="genomic DNA"
                     /strain="15-307-1"
                     /isolation_source="Rectal swab"
                     /host="Homo sapiens"
                     /db_xref="taxon:1352"
                     /plasmid="p15-307-1_09"
                     /geo_loc_name="France: Corbeille-Essonnes"
                     /lat_lon="48.6103 N 2.4748 E"
                     /collection_date="2015"
                     /collected_by="NRC for Enterococci"
     gene            complement(join(3431..4372,1..27))
                     /locus_tag="CWC51_RS16350"
                     /old_locus_tag="CWC51_016800"
     CDS             complement(join(3431..4372,1..27))
                     /locus_tag="CWC51_RS16350"
                     /old_locus_tag="CWC51_016800"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002298422.1"
                     /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_002347008.1"
                     /translation="MSKKRTIVNEWEKLTALSNRRLNVQTLVQTIKLNWSIDRITIVGK
                     LNQNIFYHTQHDVLILDFEQLMRVNEGNGYLKAVGNNGWQLLDQHDENIAYIEISKWQE
                     GKGRIDFNPNKISRFLADSMKNFIHDLFLEPHFSRADVACDLIDVPDEFITQYRIIDPV
                     SFKLIYGRSGKLETVYWGSRASERQIRLYNKKIEQEMKRKVVPSEINTWWRLEMQLRRG
                     KATEWYAMVKESLDSFVSPHFLPTDIKPTDKVMIDGLLANHSNWAILSRNSKYKYRNLL
                     KRESQNDELTNHLRETFEESADDLKKELDTWLQGLDVTEEE"
                     /name="replication initiation factor domain-containing
                     protein"
     gene            complement(472..1878)
                     /locus_tag="CWC51_RS16355"
                     /old_locus_tag="CWC51_016810"
     CDS             complement(472..1878)
                     /locus_tag="CWC51_RS16355"
                     /old_locus_tag="CWC51_016810"
                     /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_060810507.1"
                     /translation="MGFSISFKKGTKNTSISHNNRELTDRQKTNDWHKHIDFTKSDENI
                     YLEQTNLADKYEELFGEVVEKYNAKQKRADRKIEDYLAKVRKDKKLEPQREFIVQIGIL
                     DDFQTNRADGSSTGISKQQAEQNRVIANKILVQYYKEFQERNPNLAVYNAVIHNDEISP
                     HLHLNIVPVAEGYKRGVQKQPSFNKALVQQGIHADKDNGRVLFNNFRNQEVDSIERLMN
                     DYGWKRDIVGTNKIKDIHEYKEIMSEISELRQTAVKERESVSDELRYIYRQREENERDK
                     ALMASERAKIEEEKKNMLNVKKEMAVIFQKDMVPLESFKRLPDGSYHLSGNDFVDLYQR
                     ATRATNAKRNADNMSEQYLQMLEQNTELNEYVATLEEERHLSGRKQLADLQVENKKLKE
                     ENRSLRQRLERLKNAFQKSITRLSIRFGLAEKDMGLSEELEVLEQEKTLFYRQNVSQHK
                     LERSENEIEW"
                     /name="plasmid recombination protein"
     gene            complement(2100..2462)
                     /locus_tag="CWC51_RS16360"
                     /old_locus_tag="CWC51_016815"
     CDS             complement(2100..2462)
                     /locus_tag="CWC51_RS16360"
                     /old_locus_tag="CWC51_016815"
                     /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_045135959.1"
                     /translation="MGMTLADIKAQEEKLKKEQAKLRQQKKRLIEKENAAMGKALRKRF
                     GFETFADFERWLSSISDDQQHEKTVDNEWLADEKSAPSERDYPDESDDLFGVIPNKKSQ
                     MSESKFTSIFNDVNLR"
                     /name="hypothetical protein"
     gene            complement(2466..2774)
                     /locus_tag="CWC51_RS16365"
                     /old_locus_tag="CWC51_016820"
     CDS             complement(2466..2774)
                     /locus_tag="CWC51_RS16365"
                     /old_locus_tag="CWC51_016820"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002292673.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_002333831.1"
                     /translation="MDKIDLREETVDRIELMYERLADYLNLPDEDNYSEMLERIMDVLN
                     SVINADLAKSSVLTNEFVHKHLAQTTDESEKEFWLKLMSHVMQLNQISVINSKEKEM"
                     /name="hypothetical protein"
     gene            complement(2783..3202)
                     /locus_tag="CWC51_RS16370"
                     /old_locus_tag="CWC51_016825"
     CDS             complement(2783..3202)
                     /locus_tag="CWC51_RS16370"
                     /old_locus_tag="CWC51_016825"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002351943.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_002298420.1"
                     /translation="MTDLPEKMTIKNLADELGISKNTVRNQLVNAGYDLARYKDNGVIM
                     LDKELIGVVRSIYRSKGGQLTGDLPVNDAGNDFPLEKENEFLREQLAEKDRHISELTEM
                     IRDQQKLTLLQQQKNDQLLLENQELKNRKWWQFWK"
                     /name="hypothetical protein"
     gene            complement(3195..3428)
                     /locus_tag="CWC51_RS16375"
                     /old_locus_tag="CWC51_016830"
     CDS             complement(3195..3428)
                     /locus_tag="CWC51_RS16375"
                     /old_locus_tag="CWC51_016830"
                     /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_002298421.1"
                     /translation="MAEKQKHFGKKNWLVNLTGDNVVVVFLDSKKMSGKLLDVTQYELI
                     LKNNKIDSPIIIPKHAVKYVYGVAESNGEDND"
                     /name="hypothetical protein"
     Typing          complement(3439..4308)
                     /name="rep_cluster_943"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="81.164"
                     /coverage="96.0"
                     /evalue="0.0"
     Typing          complement(476..1878)
                     /name="MOBV"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="92.094"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 attcacgatt gttctttttt tactcatatt cagttcctcc tcaaagaaaa aagagatttt
       61 tggaaagaat ttccagagtt cacgtaactc taaaaattca taaccatcaa tctctagtct
      121 tgaagaaacc taaaaatatt cgtataatga atttgagtta cggaactagt gtggttagtt
      181 tccgtaaagg tcgagaacgt tggtagcgtt gctcgactta tttttttgct ctttttccag
      241 ttcatttgtt tgctaactca ataatagcac ttctctttag ctatgcaaat accaaaaaaa
      301 taaaaccgca ccctttgaaa agggcgcccc caaacttcgc taacgctaag ttggccaaaa
      361 aatggacttg ccatttttta gcaaatgtca gcttcagggg ctagtggttt agccgtcaac
      421 tccttatcct cggcacaaac cgcctccggt accgttgact gcacatcgtg gctaccactc
      481 aatctcattc tcagaacgct ctaatttatg ctgtgagacg ttttgacgat aaaataaggt
      541 tttctcctgc tctaatactt ctaattcctc agaaagcccc atatcctttt ctgcaagacc
      601 aaaacggata gacaaacgag tgatcgattt ttgaaatgcg ttttttaatc gctctaaacg
      661 ctggcgtaaa gagcgatttt cttctttcag ctttttattt tccacttgta aatctgctaa
      721 ttgttttcta ccagacaaat gacgctcttc ttccaatgta gctacatact catttaattc
      781 tgtattttgc tcaagcatct gtaaatattg ctcactcatg ttatcagcat ttctcttggc
      841 atttgttgct ctcgtagctc gttgatacaa atcaacaaaa tcattcccag ataaatgata
      901 cgaaccatca ggaagcctct tgaaactttc taaaggaacc atatcttttt ggaaaatgac
      961 cgccatctct ttttttacat tcagcatatt tttcttctct tcttcaatct tcgctctctc
     1021 agaagccatc agagccttat cacgctcgtt ttcttctctt tgcctataaa tatacctcaa
     1081 ctcatcagaa acgctctcac gctcttttac agccgtttgg cgcaattcag aaatttcact
     1141 catgatttct ttgtattcgt gaatatcttt aattttgttg gtaccgacaa tatccctttt
     1201 ccaaccgtaa tcattcatta atcgttctat agagtcaact tcttgatttc taaaattatt
     1261 gaaaagcact cgaccattat ctttatcagc gtgtatccct tgttgaacca gtgctttatt
     1321 aaagctcggc tgcttttgaa caccccgttt ataaccttca gcaaccggca caatattcaa
     1381 gtgcaggtgc ggacttattt cgtcattatg aataacagca ttataaacag ccaaattagg
     1441 gtttctctct tgaaactcct tgtaatactg aaccaaaatt ttattggcaa tcactcgatt
     1501 ttgttcagct tgttgtttcg atatgccagt agaagaacca tctgctcgat ttgtctggaa
     1561 atcatctaaa atgcctattt gcacaataaa ttctcgttga ggttccaact ttttatcctt
     1621 gcgcactttc gctaaatagt cctcgatttt tctatcggct cttttttgtt tcgcattata
     1681 tttttctacc acttcgccaa acaattcctc atatttatct gctagattcg tctgctctaa
     1741 ataaatattt tcatccgatt tcgtgaagtc aatgtgctta tgccaatcat tggttttctg
     1801 gcgatcagtt aactcacgat tattatgaga aatacttgta ttcttcgttc cttttttaaa
     1861 tgaaatacta aaccccaagt taaaaccctc cttcgcgctg tcgctaataa aaagattgta
     1921 aacctttctg ttactctttg tcaaagagta acattttcct aattgtgaca tggatgtcac
     1981 aattccaaac gctctccgag ggttttcgct gtcacaagtg acaacgaaaa aaggagccga
     2041 aagcgtatca cgctatcaac tccttttatg ctttattttg cttcacgcaa aataatcgct
     2101 tatcgtaaat tcacgtcatt aaatattgac gtaaatttac tctcactcat ctgacttttc
     2161 ttattcggta tcactccgaa taagtcgtca gattcatcgg gataatctcg ttcgcttggc
     2221 gctgattttt catcagcaag ccactcatta tccactgttt tttcgtgttg ctgatcgtca
     2281 gaaattgacg ataaccaccg ctcaaaatca gcaaaagttt caaacccaaa acgcttgcga
     2341 agagccttgc ccattgcagc attttctttc tcaatcaagc gttttttctg ttggcgaagt
     2401 ttcgcttgtt ctttttttaa tttttcttct tgcgctttaa tatctgctaa agtcattccc
     2461 ataaactaca tctccttttc tttggaatta ataacggaaa tttggtttaa ctgcataaca
     2521 tgactcatta atttcaacca aaattctttt tctgattcat cagttgtttg cgctaaatgc
     2581 ttatgaacaa attcattagt caaaactgaa gattttgcta gatcagcatt gataaccgag
     2641 ttgagaacat ccataattcg ttcaagcatt tcactataat tatcttcatc cggcaaattc
     2701 aaataatcag ctaaccgttc atacatcaat tcaattctat cgactgtttc ttctctcaaa
     2761 tcaattttat ccatgtcaca cctcacttcc agaattgcca ccattttcga ttttttaatt
     2821 cttgattttc tagtaacaac tgatcgtttt tttgttgctg aagcaaagtc aatttttgtt
     2881 ggtcacgaat catttccgtt aattcagaaa tatgcctatc tttttccgct aattgttcac
     2941 gcaaaaattc attttctttt tctaacggga aatcattgcc tgcatcattg accggtaaat
     3001 caccagtcaa ttgaccacct tttgaccgat aaattgaccg cacaacacca atcaattcct
     3061 tgtctaacat gataacccca ttatctttat accgagcaag gtcataacct gcattgacca
     3121 gttgattgcg cactgtattt ttagatatac ccaactcatc agcaaggttt tttatggtca
     3181 ttttttctgg caaatcagtc attatcttct ccgttacttt cagctacccc ataaacatat
     3241 ttaacagcat gcttagggat aatgattggg gaatcaattt tattattttt caaaatcaac
     3301 tcatactgcg ttacatcaag taacttaccg gacatttttt tgctatccaa aaaaacaacg
     3361 acaacgttat cacctgttaa attcaccaac caatttttct taccaaaatg cttttgtttt
     3421 tctgccatta ctattcctcc tctgtcacat caagtccctg taaccaagta tccaattctt
     3481 tttttaaatc atctgctgat tcttcaaatg tttctcgtaa atgattcgtc aactcatcat
     3541 tttgactttc tcgctttaat aaatttcgat atttatattt cgagtttctt gacaaaatcg
     3601 cccaattaga atgattagct aacaatccat caatcataac tttatccgta ggttttatat
     3661 cagttggtaa aaaatgtgga ctcacaaagc tatccaaact ttctttcacc atagcatacc
     3721 attccgtagc tttaccacgt cttaactgca tttctaaccg ccaccaagta ttaatttctg
     3781 aaggcaccac ctttcttttc atttcttgct ctattttttt attgtacaaa cgaatttgcc
     3841 gctcgcttgc ccgactaccc caatacaccg tttccagttt tcctgagcgt ccataaatta
     3901 atttaaatga aactggatca ataattcgat attgcgtgat aaactcatca ggcacatcaa
     3961 taagatcgca ggcaacatcc gctcgtgaaa aatggggctc taaaaataaa tcatgaataa
     4021 aatttttcat ggaatccgct aaaaatcgac tgattttatt aggattaaaa tcaatccgcc
     4081 cttttccttc ttgccattta gaaatttcaa tataggcaat attttcgtca tgttggtcta
     4141 atagctgcca accattattt ccaaccgctt ttaaatagcc attgccttca tttacccgca
     4201 taagctgttc aaaatctaat attaatacat catgttgagt atgataaaaa atattttgat
     4261 tcaactttcc aacaatggta attcggtcaa tcgaccaatt taattttata gtttgtacca
     4321 aagtttgaac atttaaccgc ctgttagaca gggctgttaa tttttcccac tc
//
