LOCUS       NZ_CP065782             3875 bp    DNA     circular CON 18-AUG-2023
DEFINITION  Enterococcus faecium strain 16-021 plasmid p16-021_5, complete
            sequence.
ACCESSION   NZ_CP065782
VERSION     NZ_CP065782.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN16988091
            Assembly: GCF_018517105.1
KEYWORDS    RefSeq.
SOURCE      Enterococcus faecium
  ORGANISM  Enterococcus faecium
            Bacteria; Bacillota; Bacilli; Lactobacillales; Enterococcaceae;
            Enterococcus.
REFERENCE   1  (bases 1 to 3875)
  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 3875)
  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                     :: MAR-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 05:34:24
            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)                     :: 2,862
            CDSs (total)                      :: 2,771
            Genes (coding)                    :: 2,662
            CDSs (with protein)               :: 2,662
            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)              :: 109
            CDSs (without protein)            :: 109
            Pseudo Genes (ambiguous residues) :: 0 of 109
            Pseudo Genes (frameshifted)       :: 38 of 109
            Pseudo Genes (incomplete)         :: 68 of 109
            Pseudo Genes (internal stop)      :: 22 of 109
            Pseudo Genes (multiple problems)  :: 16 of 109
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP065782.1.
            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..3875
                     /organism="Enterococcus faecium"
                     /mol_type="genomic DNA"
                     /strain="16-021"
                     /isolation_source="Rectal swab"
                     /host="Homo sapiens"
                     /db_xref="taxon:1352"
                     /plasmid="p16-021_5"
                     /geo_loc_name="France: Caen"
                     /lat_lon="49.18 N 0.36 W"
                     /collection_date="2016-02"
                     /collected_by="NRC for Enterococci"
     gene            complement(join(3866..3875,1..353))
                     /locus_tag="I8F57_RS14165"
                     /old_locus_tag="I8F57_14160"
     CDS             complement(join(3866..3875,1..353))
                     /locus_tag="I8F57_RS14165"
                     /old_locus_tag="I8F57_14160"
                     /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_002318183.1"
                     /translation="MGVTLADIKAQEEKLKKEQAKLRQQKKRLIEKENAEMGKALRKHF
                     GFESFADFERWLSSISDDQQHEKSVDNEWLADEKSAPSERDYPDESDGLFGVIPNKKSQ
                     MSESKFTSIFNDVNLR"
                     /name="hypothetical protein"
     gene            complement(406..654)
                     /locus_tag="I8F57_RS14170"
                     /old_locus_tag="I8F57_14165"
     CDS             complement(406..654)
                     /locus_tag="I8F57_RS14170"
                     /old_locus_tag="I8F57_14165"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002323248.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_213067874.1"
                     /translation="MKLDKQRLYEAVKDNCNCGGNRQLFKAMMVTVYRRLDGENAEAAV
                     ENAYFQVFGEHHSPEWDRAILDDMAEMHEKLWRALND"
                     /name="hypothetical protein"
     gene            complement(641..1621)
                     /locus_tag="I8F57_RS14175"
                     /old_locus_tag="I8F57_14170"
     CDS             complement(641..1621)
                     /locus_tag="I8F57_RS14175"
                     /old_locus_tag="I8F57_14170"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002355134.1"
                     /GO_function="GO:0003677 - DNA binding [Evidence IEA]"
                     /GO_process="GO:0006260 - DNA replication [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="protein rep"
                     /protein_id="WP_002299242.1"
                     /translation="MAKKKQDLINGTFREKKRNLKKIMAFGDGRISGKTLENMKACGSF
                     MEFIATVDKEKKKMVHGMFCKNRFCPVCAYRKARKDSYMLSIMMEAIQAEKGYEYIFMT
                     LTTPNVPADKLSEEIDRFNKALSKLFRRKRVMTSIKGYVRKLEITYNKSRNDYNPHFHL
                     IMAVNKSYFTDKRYYIAQAEWLDMWRDVTGLDGINEDGTDEICSLDVRKVNGYRQEKAV
                     SEIAKYSAKDFEMTYSQDVFDTFYFAMKGRQLMTFNGVFKEYRKKYDAGELDHYRQKDE
                     NDYFWFLTASWMQKDANYSVAVRELTDDEKKFFAERYDKEGDETG"
                     /name="protein rep"
     gene            complement(2238..3644)
                     /locus_tag="I8F57_RS14180"
                     /old_locus_tag="I8F57_14175"
     CDS             complement(2238..3644)
                     /locus_tag="I8F57_RS14180"
                     /old_locus_tag="I8F57_14175"
                     /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_128704492.1"
                     /translation="MGFSISFKKGTKNTSISHNNRELTDSQKINDWHKHIDFTKSDENI
                     YLEQINIREKYEELFGEAVEKYNAKQKRADRKIEDYLAKVRKDKKMEPQREFIVQIGTL
                     DDFRTTRDDGSSTGISEQQAEQNRVIANKILVEYFKEFKERNPSLSVYNAVIHNDEVSP
                     HLHLNIVPVAEGYKRGVQKQPSFNKALQQQGLRADKENGRVIWNNFRNQEVESIERLMA
                     DFGWERELVGTNKIKDVHEYKEIMSEISELRQTAVKERESVSDELGYISRQREENEREK
                     ALVASERAKIEEEKKNMLNVKKEMAVIFQKDIVPLESFKRLPDGSYHLSGNDFVDLYQR
                     ATRATNAKRNADNMSEQYLQMLEQNTELNEYVAALEEERHLSGRKQLADLQVENKKLKE
                     ENRSLRQRLERLKNAFQKSITRLSIRFGLAEKDMGLSEELEVLEQEKTLFYRQNVSQRK
                     LERSENEIEW"
                     /name="plasmid recombination protein"
     Typing          complement(642..1615)
                     /name="rep_cluster_1077"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="91.487"
                     /coverage="99.0"
                     /evalue="0.0"
     Typing          complement(2242..3644)
                     /name="MOBV"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="98.291"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 ttcacgtcat taaatattga cgtaaattta ctctcactca tctgactttt cttattcggt
       61 atcactccga ataagccgtc agattcatcg ggataatctc gttcgcttgg cgctgatttt
      121 tcatcagcaa gccactcatt atccactgat ttttcgtgtt gctgatcgtc agaaatcgac
      181 gatagccacc gctcaaaatc agcaaaagat tcaaacccaa aatgcttgcg aagcgccttg
      241 cccatttcag cattttcctt ctcaatcaat cgctttttct gttggcgaag ttttgcctgc
      301 tcttttttca atttttcttc ttgtgcttta atatcagcta aagttactcc catgaattac
      361 aactccttac ccttagattc attcctataa ataacaccaa tttgattagt catttagcgc
      421 cctccacaat ttctcgtgca tttccgccat atcatcaaga atagcacgat cccattcagg
      481 gctatggtgt tcaccgaaca cttgaaaata agcattttcc acagctgcct cagcattttc
      541 cccatccaac cgacgataaa cagtcaccat catagcctta aaaagctgac gatttccgcc
      601 acaattacaa ttatctttca ccgcttcata tagcctttgc ttatccagtt tcatcaccct
      661 ccttatcata gcgttccgca aagaatttct tctcatcatc cgtcaactca cgaacggcca
      721 ccgagtaatt ggcatccttt tgcatccagc tagcagtcaa aaaccagaaa tagtcgtttt
      781 catctttctg gcggtaatga tccagctcac cggcatcgta ttttttcctg tactccttga
      841 acacgccatt gaaagtcatc agctgacgac ctttcatagc aaaatagaac gtgtcaaaaa
      901 cgtcttggga ataagtcatt tcaaaatctt tggcagaata tttagcaatt tccgataccg
      961 ccttttcttg ccggtaccca ttgaccttgc ggacatccaa cgaacaaatt tcgtcggtac
     1021 cgtcctcatt tatgccatcc aaaccggtga catcccgcca catatccagc cattcagctt
     1081 gggcaatata atagcgttta tcagtaaaat atgatttatt aacagccata atcaagtgaa
     1141 aatgcgggtt ataatcattt cggcttttgt tatacgttat ctccaatttt cggacatagc
     1201 ccttgattga agtcatcacc ctttttcgac gaaatagctt cgacagtgct ttattgaaac
     1261 gatcaatttc ttcggataat ttgtccgccg gcacgttagg cgtggtgagt gtcataaaga
     1321 tatattcata gcccttttca gcttgaatag cttccatcat gatagacaac atatagctgt
     1381 ctttacgggc ttttcggtat gcacaaaccg gacaaaaccg gtttttacag aacatgccat
     1441 gaaccatctt tttcttctcc ttatcaaccg ttgctatgaa ctccatgaat gatccacagg
     1501 ctttcatgtt ttccaaggtt ttgccagaaa tacgaccatc accaaatgcc atgattttct
     1561 ttaaatttct ctttttttct cggaaagtgc cattgatcaa atcttgcttt ttcttcgcca
     1621 tatgctatac tgaaccttgc agaacacaaa cgttccgccc aaacatttaa aaaacgcatt
     1681 ttctaaatgc acgaaaaaaa ggttgcactc ctctcttgtt ttatgactat tgacttagac
     1741 actcaaagca tacaacacta ggtacggata tgcaactttt ttttgtttaa aacccttata
     1801 ggtcaaggga aaaacacata cataggaccc gattttctgc cgaaaatagt taccctatgt
     1861 atcaagataa gaagaaacat caaaaaaaga ggtcgaaatc gacctctttt ttctcgtttc
     1921 aaaccccaaa actcaaaaac ccacttctgc ataaaattcg gtcaattgac cactgcattt
     1981 ttaagggaag ggtcaaactt tgatacttta accgcctgtt agaaatgcgg ttaagttttt
     2041 cccactcatt cttagtcatg caaacataaa accgcaccct ttaaaaaggg cgcccccaaa
     2101 cttcgctaac gctaagttgg ccaaaaaatg gactggccat tttttagcaa atgtcagctt
     2161 aataggctag tggtttagcc gtcaactcct tatcctcggc acaaaccgcc tccggtaccg
     2221 ttgactgcac atcgtggcta ccactcaatc tcattctcag aacgctctaa tttacgctgt
     2281 gagacgtttt gacgataaaa taaggttttc tcctgctcta atacttctaa ttcctcagaa
     2341 agccccatat ccttttctgc aagaccaaaa cggatagaca aacgagtgat cgatttttga
     2401 aatgcgtttt ttaatcgctc taaacgctgg cgtaaagagc gattttcttc tttcagcttt
     2461 ttattttcca cttgtaaatc tgctaattgt tttctaccag acaaatgacg ctcttcttcc
     2521 aatgcagcta catactcatt taattctgta ttttgctcaa gcatctgtaa atattgctca
     2581 ctcatgttat cagcatttct cttggcattt gttgctctcg tagctcgttg atacaaatca
     2641 acaaaatcat tcccagataa atgatacgaa ccatcaggaa gcctcttgaa actttctaaa
     2701 ggaacaatat ctttttggaa aatgaccgcc atctcttttt ttacattcag catatttttc
     2761 ttctcttctt caatcttcgc tctctcagaa gccaccagag ccttttctcg ctcattttct
     2821 tctctttgcc tagaaatata ccccaactca tcagaaacgc tctcacgctc ttttacggcc
     2881 gtttgacgca attctgaaat ctcgctcatg atttctttat attcgtgaac atctttgatt
     2941 ttgttagtac cgactaactc acgctcccaa ccaaaatctg ccatcaaacg ttcaattgac
     3001 tcaacttcct gattcctaaa attattccaa atcactcgac cattctcttt atctgctcgt
     3061 aaaccctgct gttgcaaggc tttgttaaaa cttggttgct tttgaacacc ccgtttatac
     3121 ccttcagcaa caggaacaat attcaaatgc aggtgcggac ttacttcgtc attatgaata
     3181 acagcattgt agacggataa actaggattc cgttctttaa attctttgaa atactcaact
     3241 aaaattttgt tggcaatcac tcgattttgt tctgcttgtt gttccgatat gccagtagaa
     3301 gaaccatcat cacgagtagt acgaaaatca tcaagagtac caatttgcac gataaattct
     3361 cgctgtggtt ccattttttt atccttgcga acctttgcta aatagtcctc gatttttcta
     3421 tcggctcttt tctgctttgc attatatttt tctacggctt caccgaataa ttcttcatat
     3481 ttttcacgaa tatttatttg ttccaaatag atattttcat ccgattttgt gaaatcaata
     3541 tgcttatgcc agtcattgat tttttggcta tcagttaact cacgattatt atgagaaatg
     3601 cttgtattct ttgttccctt tttgaacgaa atactaaacc ccaagttaac cccctccttc
     3661 gcgctgtcgc taataaaaag agtgtaaacc tttctgttac tctttgtcaa agagtaacat
     3721 tttcctaatt gtgacatggc tgtcacaatt ccaaatgctc tccgagggta ttcgctgtca
     3781 caagtgacaa cgaaaaaagg agccgaaagc gtgtcacgct ctcaactcct tttacgcttt
     3841 attttgcttc acgcaaaata atcgcttatc gtaaa
//
