LOCUS       NZ_CP065760             3837 bp    DNA     circular CON 18-AUG-2023
DEFINITION  Enterococcus faecium strain 18-276 plasmid p18-276_6, complete
            sequence.
ACCESSION   NZ_CP065760
VERSION     NZ_CP065760.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN16988099
            Assembly: GCF_018516925.1
KEYWORDS    RefSeq.
SOURCE      Enterococcus faecium
  ORGANISM  Enterococcus faecium
            Bacteria; Bacillota; Bacilli; Lactobacillales; Enterococcaceae;
            Enterococcus.
REFERENCE   1  (bases 1 to 3837)
  AUTHORS   Dejoies,L., Sassi,M., Schutz,S., Moreaux,J., Zouari,A., Potrel,S.,
            Collet,A., Lecourt,M., Auger,G. and Cattoir,V.
  TITLE     Genetic features of the poxtA linezolid resistance gene in human
            enterococci from France
  JOURNAL   J Antimicrob Chemother 76 (8), 1978-1985 (2021)
   PUBMED   33895846
REFERENCE   2  (bases 1 to 3837)
  AUTHORS   Dejoies,L., Sassi,M., Schutz,S., Zouari,A., Potrel,S., Collet,A. and
            Cattoir,V.
  TITLE     Direct Submission
  JOURNAL   Submitted (03-DEC-2020) Rennes1 University, U1230, 2 avenue du
            Professeur Leon Bernard, Rennes 35043, France
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Date                     :: NOV-2020
            Assembly Method                   :: Unicycler v. v0.4.8
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 250x
            Sequencing Technology :: Oxford Nanopore MiniION; Illumina MiSeq
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 08/18/2023 05:29:46
            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)                     :: 2,896
            CDSs (total)                      :: 2,805
            Genes (coding)                    :: 2,703
            CDSs (with protein)               :: 2,703
            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)              :: 102
            CDSs (without protein)            :: 102
            Pseudo Genes (ambiguous residues) :: 0 of 102
            Pseudo Genes (frameshifted)       :: 36 of 102
            Pseudo Genes (incomplete)         :: 68 of 102
            Pseudo Genes (internal stop)      :: 22 of 102
            Pseudo Genes (multiple problems)  :: 18 of 102
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP065760.1.
            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..3837
                     /organism="Enterococcus faecium"
                     /mol_type="genomic DNA"
                     /strain="18-276"
                     /isolation_source="Rectal swab"
                     /host="Homo sapiens"
                     /db_xref="taxon:1352"
                     /plasmid="p18-276_6"
                     /geo_loc_name="France: Corbeil-Essonnes"
                     /lat_lon="48.6131 N 2.4659 W"
                     /collection_date="2018-05"
                     /collected_by="NRC for Enterococci"
     gene            1..975
                     /locus_tag="I8F55_RS14315"
                     /old_locus_tag="I8F55_14320"
     CDS             1..975
                     /locus_tag="I8F55_RS14315"
                     /old_locus_tag="I8F55_14320"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002358693.1"
                     /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_112019297.1"
                     /translation="MANEIVKYHYELNTIPLRKFTPVEMNLFFSIVSRMREKGDKTVRF
                     TFDQLKDLSNYKATANVRFVDDLKTTYEKILSLRFGRRSESGLSYEMFVMFTKFKINGD
                     TPEPYVDIQIFEDALPLLNGLDSWVRYSLQQFNELQSSYSKTMFRLLKQFRTKGYAYFS
                     KEDFHELLDIPKSYKQPDIDKRVIKPIRQELTAIFKGLTIKKKYGKGRGKPVIGYQFSF
                     KPEIKQADDFNKHAPTKEEQNRALAQADKQKEYEQQPTTIDEKILEAKRKVELLEQLKE
                     LEKKEKQDTKNQTPTEQKKSKSDSQLSEKDKQDLLNGLSNFGK"
                     /name="replication initiation protein"
     gene            complement(1463..1933)
                     /locus_tag="I8F55_RS14320"
                     /old_locus_tag="I8F55_14325"
     CDS             complement(1463..1933)
                     /locus_tag="I8F55_RS14320"
                     /old_locus_tag="I8F55_14325"
                     /inference="COORDINATES: protein motif:HMM:NF025324.2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="type III toxin-antitoxin system ToxN/AbiQ family
                     toxin"
                     /protein_id="WP_071870226.1"
                     /translation="MADLDFYEIDPKYLKYLKKFDSSVPDYSYDKHDKFFCGVVTKMNG
                     FQYFAPISSFSRQQATNLLIKNSDGRNISSIRFCFMVPADDSVLKVKDFSLEKDQKYVG
                     LLSTELTFCRQNERRIQETAKRVYHYGIDSKHPQYRNCCKFTNLEQAATQYK"
                     /name="type III toxin-antitoxin system ToxN/AbiQ family
                     toxin"
     gene            2344..2880
                     /locus_tag="I8F55_RS14325"
                     /old_locus_tag="I8F55_14330"
     CDS             2344..2880
                     /locus_tag="I8F55_RS14325"
                     /old_locus_tag="I8F55_14330"
                     /inference="COORDINATES: ab initio prediction:GeneMarkS-2+"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GeneMarkS-2+."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_112019302.1"
                     /translation="MSTQAEKIRLLAVDLLKNRSLNEPIDNDLYGIRYSQLKKKIMEDS
                     NHEFTDGAVTGALYTLTERVENIYKIKNNHGTYFYYSEDYKDNLEITRESITTSEEYKD
                     LTDMIKNSEVKVREILRNASQGRYTETTNLDIEHLRKLLNLTDQLSNLLKTYEAEKSFE
                     VMGNYRYSQFDNLPF"
                     /name="hypothetical protein"
     Typing          2..975
                     /name="rep_cluster_1197"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="99.692"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 atggcaaatg aaattgtgaa gtaccattat gaattaaata cgattccctt acggaaattc
       61 acaccagttg aaatgaatct gttcttctct attgtttcta gaatgcgtga aaaaggcgat
      121 aaaaccgtta gatttacgtt tgaccaactg aaagatttaa gtaactataa agcgactgct
      181 aacgttcggt ttgtagatga tttaaaaaca acctacgaga aaatcttatc tttgcgtttt
      241 ggtcgtagaa gtgaatctgg actttcctac gaaatgtttg taatgtttac taaattcaaa
      301 atcaatggcg atactcctga accctacgta gatattcaaa tttttgaaga tgctttgcct
      361 ttgctaaatg gtttagattc ttgggtacgt tattctctcc aacaattcaa cgagctgcaa
      421 agcagctact ctaaaacgat gttccgcttg ttaaaacaat tccgaaccaa aggatatgcc
      481 tatttttcca aagaagattt tcatgagttg ctagatattc ctaaaagcta taagcaacct
      541 gatatagaca agagagttat taagcctatc cgtcaagaac taaccgcaat cttcaaaggt
      601 ttaacaatta aaaagaaata tggaaaaggt cgtggtaagc ccgtcattgg ctatcaattt
      661 tcgtttaaac cggaaatcaa gcaagcagac gactttaaca aacatgcacc aaccaaagaa
      721 gaacaaaata gagcgttagc acaagcggat aaacaaaaag aatacgagca acaaccaaca
      781 acgattgacg agaaaatttt agaagcaaaa agaaaagttg agctacttga acaactcaaa
      841 gagttagaaa aaaaagaaaa acaagacaca aaaaatcaga cacctacaga acaaaaaaaa
      901 tcaaaaagtg attcgcaact ttccgaaaaa gacaaacaag atttactaaa tggactttca
      961 aattttggaa aataatttca ctgatttttt caaaaatggg gattggggca acgccccaaa
     1021 aataaaaaga atcgtctgaa acgaggaaca aattaaaatg caaattttag ttgtggccga
     1081 gtggaagatg attacttttt accgtaagtg tgtacacact tactaagctc gctacaaaga
     1141 aatatctatc tgcatagaaa catgagcgta gcgaatttta acaaacacgc ttgacggaaa
     1201 aagagtacag tttcacgtga gtgatctgta ctctttttta gcacgatagc caccaaaata
     1261 ttttggtggg tgtaagtgcg cacttagcac aacgtagaaa aaattcggta gattttttta
     1321 ctgcgtataa gtgcgccctt gctcttattc tttgagcact ggaacgacat tttcaaatgg
     1381 cgttccagtg ctcatttttt cgtttcgtct catcttttca aaaaaattat tgctgttctt
     1441 gtactttata agctaattca ctttatttat actgagttgc agcttgttct aaatttgtaa
     1501 acttacaaca atttctatac tgagggtgtt tagaatcaat gccataatgg taaacccttt
     1561 ttgctgtttc ttgaatgcga cgttcatttt gtcgacaaaa ggtcagttct gtagataata
     1621 aaccgacgta tttttgatct ttttcaagag aaaagtcttt gacttttaaa acagagtcat
     1681 ctgcaggaac catgaagcaa aatctaatgc tagaaatatt acgtccatct gaatttttaa
     1741 ttaatagatt agttgcttgt tgtctactaa aagacgagat aggagcaaaa tattggaagc
     1801 cattcatttt tgtaactacc ccacaaaaaa acttatcatg tttatcatat gaataatccg
     1861 gtacagaaga atcaaatttt tttaagtatt taaggtattt aggatctatc tcataaaaat
     1921 ctaaatctgc caataatatc cctccaattg ctgttttttt taataactac cctatatttt
     1981 aacataaaaa caagcgccca agtatatact tgggcgcttg tttcagtttt ttcgaattag
     2041 gctggttttg atgagttcca taaactcgaa ttaggctggt tttgatgagt tccataaact
     2101 cgaattaggc tggttttgat gagttccata aactcgagag aattaataat ctctacagta
     2161 attttaacaa acctttccta ataatccaac acaagcgttg acaaaacact tatattttct
     2221 aattaatccc aaattaattt taaagcttta taattaattt gatttttatt gtaatagttt
     2281 aaatttaatt gaaattggta tatacttaat ttatatatat tttgaagaat ggagaatgat
     2341 tgaatgtcca cgcaagcaga aaaaatccga ttattagctg ttgatttatt aaaaaacaga
     2401 tcccttaacg aacctataga taacgatttg tatggtatta gatacagtca gcttaaaaaa
     2461 aaaataatgg aagattctaa tcacgagttt actgatgggg ctgttacagg tgctctatat
     2521 acacttactg agagagtaga aaatatttat aagatcaaaa acaatcatgg tacgtatttt
     2581 tattattctg aggattataa agacaattta gaaattaccc gagagagtat aactacctct
     2641 gaagaatata aagatttaac cgatatgata aaaaattctg aagttaaagt aagagagatt
     2701 ttacgaaatg ctagtcaagg tcggtatact gaaacgacta atttagatat agaacattta
     2761 cgtaaattac ttaatttaac agatcaatta agcaatttat tgaaaaccta cgaagcagaa
     2821 aaatcttttg aggtaatggg aaattataga tatagccaat ttgataactt acctttttag
     2881 acttttgttt gaatttattt tattaatatc tggttttata aaaagcccta ataatcctct
     2941 ctaagagatt attagggctt ttcgcataat tagtagcctt tatcttcaac aggctgttaa
     3001 aacgtgaaaa taagctgaat aaacctattt taatcttaat tctttctttt attaggtttt
     3061 gggtatgtag ggcttgccct gcacgagcga tagcgagcct tacacaaact ttgtcctttc
     3121 agcagacaaa gtaaacgtgc gaataaaaag caaatcattt ttaaagctca taaaatgcgt
     3181 tctaaggtgt tttaacgatc atgccgacaa ctaaactaaa taaacactaa aacctcttaa
     3241 aacgcaaaat atgacgttta aatggtattt tagtttgtat tgctatctaa aatttgcttt
     3301 tgggttgtta gggcttgccc tgaccgcctg aaaggcgcct gatgaacaag aattacctga
     3361 aaacactaaa accgtcttag agagccttat atggcgttct aagactaaac taattcgcct
     3421 ttgaacaacg gttttgattt tgcccttagc gagtgaacga agtgaacgct gcaagtaaaa
     3481 tgtgagagcg tagcgatcac tccttttttg tcttttggtt ttttatttgc agttttgcaa
     3541 aattcgcgaa cctgtttatc taaaaaaatg agctttttta ggcgggaaat tttgcccccc
     3601 tcttttataa tctcttttta aacctctttt aaacctcttt accgtcggct gtatcccacg
     3661 cccctcaagg ggttcagggc tttatgaagg tcattttgtc tgtttatgaa ggtcattttg
     3721 tctgtttatg aaggtcattt tgtctgttta tgaaggtcat tttgtctgtt tgagtgtctt
     3781 tttataaatg acttgacttt taaattatgt catttataat cattttgagg tgattac
//
