LOCUS       NZ_CP065781             5962 bp    DNA     circular CON 18-AUG-2023
DEFINITION  Enterococcus faecium strain 16-021 plasmid p16-021_4, complete
            sequence.
ACCESSION   NZ_CP065781
VERSION     NZ_CP065781.1
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 5962)
  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 5962)
  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
            CP065781.1.
            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..5962
                     /organism="Enterococcus faecium"
                     /mol_type="genomic DNA"
                     /strain="16-021"
                     /isolation_source="Rectal swab"
                     /host="Homo sapiens"
                     /db_xref="taxon:1352"
                     /plasmid="p16-021_4"
                     /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(4913..5962,1..66))
                     /locus_tag="I8F57_RS14135"
                     /old_locus_tag="I8F57_14130"
     CDS             complement(join(4913..5962,1..66))
                     /locus_tag="I8F57_RS14135"
                     /old_locus_tag="I8F57_14130"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_007596194.1"
                     /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_256737379.1"
                     /translation="MYHELFDEALAAYNAKKKKTRDKIPDYYEHIRQSKQEKLFHEAIF
                     QIGNMEDCGCGSPGGERAAAALKEFAESFQERNPHLRVFNMVLHMDEATPHLHVDFVPV
                     ATGQSRGLSTRVSMKQALKQQGFESLGRKQTEWKAWMEREKVSLGEIAQVHDFEIISLG
                     GGRPHMDLPEYRAAAQRLEAVQEQVAAAEQDIATLEKQKKALQGNVKLLKAVEKVKPDL
                     EAIQPEKTLTGAVKGVTVEQVKELKAAAIRGAAAEQKVQELKEENQRLQQKIPSTKEKL
                     KEAQERQRLENQNRKLLVQVECLEQELEQERSFSDRLLDGVSAVMDFLDRHLPEKFRPL
                     VERARELLPVPEVQQPEQEQERGHTWGGMEL"
                     /name="plasmid recombination protein"
     gene            complement(421..1389)
                     /locus_tag="I8F57_RS14390"
     CDS             complement(421..1389)
                     /locus_tag="I8F57_RS14390"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_005948226.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_066859798.1"
                     /translation="MKKIVLVLVAAMVLVFTGCEKKETISMPFDVADVNNIEMYRNAEP
                     YSAEKQVITESEDIADLYSLFSGLEVSDKKTEPVVGETITSFRFNLSDDTSYEIIYCAE
                     AVKSGRLKFPAEKLDYFTSADIGGRWDSYQYEIVPVSESELPGQSENPSDPPLEETHEW
                     DKIPMVMVDGKLYYDTGKESTISGRCGVMDGEITSTVDGSEIPTKDNQSNFGTGFEYQY
                     GADNTIEIFMNEKWIVFEQREGDGSKVRYGDRMVDAEDLSKETLEWLDWYNSLPEEQQL
                     AVSFVPSDLIEETGPVKTEDAEVPAQEEELCGYPLAPEEVE"
                     /name="hypothetical protein"
     gene            complement(1444..1962)
                     /locus_tag="I8F57_RS14145"
                     /old_locus_tag="I8F57_14140"
     CDS             complement(1444..1962)
                     /locus_tag="I8F57_RS14145"
                     /old_locus_tag="I8F57_14140"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_005948231.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_025491722.1"
                     /translation="MKTIRQIADEIGVSKQAVYKRYKGKLYTVCAPYAHTEQGVLYLSE
                     QAETLIKQDFLRDGCPNGSHTDTHTERSIGAVPEQSQEAGVVAILQATIDTLQGQLSVK
                     DKQIEELNARLAEVSSALVVAQQTAQAAQALHAGTIRQQLTDGEDDPNQQGQTVEQKKS
                     WFSKVFGGR"
                     /name="hypothetical protein"
     gene            complement(2225..2497)
                     /locus_tag="I8F57_RS14150"
                     /old_locus_tag="I8F57_14145"
     CDS             complement(2225..2497)
                     /locus_tag="I8F57_RS14150"
                     /old_locus_tag="I8F57_14145"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_005948235.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="type II toxin-antitoxin system YafQ family toxin"
                     /protein_id="WP_066859802.1"
                     /translation="MYNIRPTTKFQKDLKRVKKRGFDISLLTDIIKKLAAGEPLPEKNR
                     DHQLSGDYAGCRECHITPDWLLIYEVDGDELILYLTRTGSHSDLF"
                     /name="type II toxin-antitoxin system YafQ family toxin"
     gene            complement(2490..2771)
                     /locus_tag="I8F57_RS14155"
                     /old_locus_tag="I8F57_14150"
     CDS             complement(2490..2771)
                     /locus_tag="I8F57_RS14155"
                     /old_locus_tag="I8F57_14150"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_005948237.1"
                     /GO_process="GO:0006355 - regulation of DNA-templated
                     transcription [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="type II toxin-antitoxin system RelB/DinJ family
                     antitoxin"
                     /protein_id="WP_025491725.1"
                     /translation="MANTSINIRMDADLKRQFEAFCADMGMTMTTAFNVFARKAVREYR
                     IPFEISGDVPNAETVEAIKEVKRMKANPSLGKTYSNVDQMMEELLADV"
                     /name="type II toxin-antitoxin system RelB/DinJ family
                     antitoxin"
     gene            complement(3020..4537)
                     /locus_tag="I8F57_RS14160"
                     /old_locus_tag="I8F57_14155"
     CDS             complement(3020..4537)
                     /locus_tag="I8F57_RS14160"
                     /old_locus_tag="I8F57_14155"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_005948239.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_214359304.1"
                     /translation="MVDQQEALERQRELYQEKNEHLERFLEPVAPYEFYREIFPEGSFE
                     RKGHFEDRKGNGIAVTVQKVEVDKATGIALQIEGDGKAKRCTITDELDELRELQDTDFT
                     IMSPISYFGLRRCGKNARYLYALVFDLDGVGMPQLRDTLHQMNKDILPQATFVVNSGTG
                     LHLYYVLKEPVPMYPHNQKCLKELKYSLTRQIWNRYTSTIKEPQMQGILQGFRVVGSGS
                     KLGREYPVRAFRLGGPVELAQLLDYIPDSNGERQRLEGLMRKSRLSLDEAKEKYPDWYE
                     RRIIKKERRGRWTVKRDLYDWWLHRIADEIRVGHRFYGIMTLAIYAKKCGIDEDELRRD
                     AFALLQPYDDMSVEDINRFTKDDVVCALEMFNEDYVTFPRDDIAKLSGLTMPVNKRNWR
                     KQEEHIQVMNTMKALKKQLGEIVNEGRPKGSGTAQVRVYEWRQQHPEGRKADCHRETGL
                     DPKTIRKWWDCPPPAVRFEDGHITVRVSPSQELSDWLLDALHNEGQK"
                     /name="hypothetical protein"
     Typing          complement(4917..5962)
                     /name="MOBV"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 gtccctggtc tttttctttt tagcgttata ggcagccaat gcttcatcaa aaagctcatg
       61 gtacacctgc ttcaagtcat cgttgcaaaa agtgatattc tgctccgacc ggctgcggtc
      121 tacattcgcc gccgaaaagc tcctgttatt gtgccgaata cttcctcggc ctgtcattcc
      181 cgaaatggtt gtttctataa aatcacccgg ccctttcttg taaaaagaac tatatcctac
      241 tatctctatt ttaccatacc tgggtggctg tcacaacctc tttgttactt tctggtgaga
      301 aagtaacgca aaagcacttt cacaccgcct cccctttggg gctggcagta tgaaagtgct
      361 ttgcgccctg ccgggggcta aaagagccgg cctcacaacc atctctaaga acttcttctg
      421 tcactctact tcttctggtg caagaggata accgcataat tcttcttcct gtgcaggaac
      481 ttctgcgtcc tctgttttta cagggccggt ttcttcaatc aaatccgacg ggacaaaact
      541 tacagccaac tgctgttctt ccggcaagct attataccaa tccagccatt caagcgtttc
      601 tttggaaagg tcctccgcat ccaccatccg atcaccatat cggactttac ttccgtctcc
      661 ttctctttgc tcaaaaacga tccatttctc gttcataaaa atctctatgg tattgtctgc
      721 cccgtattga tattcaaagc ctgtcccaaa attagattgg ttatcctttg tcggtatctc
      781 agagccatca accgttgaag taatttcccc gtccattacc ccgcaacgac cacttatggt
      841 gctttctttc cccgtatcat agtagagttt tccatccacc attaccatag ggattttatc
      901 ccattcatgc gtttcttcaa gcggcggatc agagggattt tctgactgcc ccggcagctc
      961 actctcactt acaggaacaa tctcatattg atagctatcc caacgacctc caatatcggc
     1021 tgatgtaaaa taatccagtt tctccgccgg aaatttcagt ctgcctgact ttacagcttc
     1081 cgcacagtag atgatctcat aacttgtatc gtctgagaga ttgaacctaa aactcgttat
     1141 ggtctccccg acaacaggct ccgttttctt atcgcttacc tccagtcccg aaaacagaga
     1201 ataaagatca gctatgtctt cgctttctgt gataacttgc ttttcggcgg agtatggctc
     1261 agcattgcga tacatctcaa tgttatttac atcagcaaca tcaaagggca tagaaatagt
     1321 ttcttttttt tcacaaccag tgaataccaa aaccatagcc gccaccaaaa caagaacaat
     1381 ctttttcact gtatcacacc gcctttctta cttgtactga cgaaaaaaat atacttttgt
     1441 ttcctatctg ccaccaaaaa cttttgaaaa ccagcttttt ttctgctcca ccgtctgccc
     1501 ctgttgattt ggatcatctt caccatcagt aagctgctgc cgaattgttc cggcatgaag
     1561 tgcctgggcg gcctgggcag tctgctgtgc caccaccagc gcagagctga cctctgccag
     1621 ccttgcattc aattcttcaa tctgcttgtc ctttacagaa agctgccctt gcagcgtgtc
     1681 aatggtggcc tgtaaaattg ctaccacacc agcctcttgc gactgctccg gcaccgctcc
     1741 aatggagcgc tccgtatgcg tatccgtatg cgatccattg gggcagccat ctctcaaaaa
     1801 gtcttgtttt atcagggttt cagcctgctc cgatagatac aagaccccct gttccgtatg
     1861 cgcatacgga gcgcaaaccg tatacagctt gcctttgtac cgcttataaa ccgcctgttt
     1921 tgatacgcct atctcgtcgg ctatctgccg gattgttttc ataccttcac gaacaggcca
     1981 acggacacac accctcaaat cccggcgtgg atatgtacca gcaagcgggg cctgtcggct
     2041 cccaggctac ttcaagggta atctcgtgcc agccatcggg aaacaaggcg gtaaatccct
     2101 gcccagcatg tatgccgtac ccttccagaa gcagccgagg gtgcggatca tcgtccgccg
     2161 gatcggggag ccgcagctgc gcgatcctct ctttatccca gctcatagac ctttcctcct
     2221 tcccctaaaa taaatcgcta tgcgatcccg tccgggtgag atataaaatc agctcgtccc
     2281 cgtccacttc gtagatcagc aaccaatccg gcgtaatgtg gcactcacga caccccgcat
     2341 agtccccgga aagctggtga tccctgttct tttccggcaa cggctccccc gcagccagct
     2401 ttttaataat atcggtcagc aaagaaatat caaagccgcg ctttttcaca cgcttcaaat
     2461 ccttctgaaa ctttgtggtt ggtcttatgt tatacatcgg caagtagctc ctccatcatc
     2521 tgatcgacat tggaataggt cttgccgagg ctcggattag ccttcattct ctttacttcc
     2581 ttgattgctt cgacggtttc cgcgttcggc acatcgccgc tgatttcaaa gggtattcta
     2641 tactccctca cagccttacg cgcaaaaaca ttgaacgccg ttgtcatcgt cattcccata
     2701 tcagcacaga acgcctcaaa ctgccgcttc aaatctgcat ccatacggat attgatactt
     2761 gtattcgcca taatagcaac tccttccgct tttattataa cccgttttat catattcatt
     2821 gtatagcttt ttgtttacaa tgtcaataca atctccctgt cctcgacgct ctaaagttct
     2881 atcccagtat gtacgcattt agggggcaaa aaagccttga tttatgcggc tttacgggcg
     2941 cagtagcgag ggagccggta tatttaccct cggagggctg aaaacgactt ctaaagcgta
     3001 acaagggcct ttctgggcct tatttctgac cctcattgtg cagtgcgtcc aggagccaat
     3061 cgctcaactc ctgcgaaggg gacacccgca ccgttatatg cccatcttca aagcgcaccg
     3121 ctggtggtgg acaatcccac catttgcgga tagttttcgg atcaaggcca gtttctcggt
     3181 ggcagtcggc cttacggcct tccgggtgct gctgccgcca ctcataaacc cgtacctgag
     3241 ctgttccgct gcctttaggt cgaccctcat tgacaatctc tcctaactgt ttttttaatg
     3301 ctttcattgt gttcatcact tgaatatgct cttcctgctt acgccaattc cgcttattga
     3361 caggcatagt aagaccagag agcttcgcta tatcgtccct gggaaatgtc acatagtcct
     3421 cattgaacat ctccagggca cacaccacat catctttcgt gaagcggttt atgtcctcca
     3481 cgctcatatc atcatagggc tggagcagtg caaaagcgtc ccggcgcagc tcgtcttcgt
     3541 caatcccaca ttttttcgca taaatcgcca gcgtcataat gccataaaaa cgatggccta
     3601 cccgaatttc gtcagcaatc cggtgcagcc accaatcgta aaggtcacgc ttgaccgtcc
     3661 aacgaccccg ccgttccttc ttgatgatcc tccgttcata ccaatctggg tacttctcct
     3721 ttgcttcatc cagcgacagg cggctctttc tcataagccc ctcaagccgc tgcctctccc
     3781 cgttgctgtc cggaatataa tcgagcagct gcgccagttc caccggcccg ccaagccgga
     3841 acgccctcac agggtactcc cgtcccagtt tcgagccgga gccgaccacc cgaaagccct
     3901 gcaaaatgcc ctgcatttgc ggttctttta tcgtggaggt atatcggttc caaatctgcc
     3961 gagtaaggga atatttcagc tccttcaagc atttctggtt gtgcggatac ataggcactg
     4021 gctctttcaa cacataatat aggtgaagcc ccgtcccgct gtttacaaca aaggttgcct
     4081 ggggcagaat atccttgttc atctggtgca gcgtgtcccg aagctgcggc atacctaccc
     4141 cgtccagatc aaacaccaaa gcataaagat acctggcatt tttaccgcac cgccgcagac
     4201 caaaatagga aatcggggac ataatcgtaa aatcagtgtc ttgtagctcc cgcagttcgt
     4261 ccagctcgtc agtgatagta caccgtttcg ccttaccatc cccctcgatc tgcagggcga
     4321 tcccggtcgc cttatcaacc tcaactttct gaaccgtcac cgcaatcccg tttcccttcc
     4381 tgtcctcaaa atgtcccttc ctctcgaaag aaccctccgg gaatatctcc cgataaaact
     4441 catacggcgc caccggctcc aaaaaccttt ccaaatgctc attcttttcc tgataaagct
     4501 ctctctgccg ttccaaagcc tcttgctgat ccaccattcc ttacacctct tttcatacat
     4561 tctgcaaacc cacaggggga aaagggggag ccaaagagcg gcccctccgg ggccttaaag
     4621 agaaagtcac ctcccccttt tccccctcgc tctggggcat ggaaatgatg gaaaaccttt
     4681 taggtttgcc acattcccac accccgtcgc tcacccccat tttcccctcc gactttctcc
     4741 ctatccgaga gagaatattt ttattatttt tccttggcct aaaggccata ggggggcata
     4801 tattatcaat gagttttttc cctatttctt gttgttatta tagcctgtcc agatggcgct
     4861 ttcaagtccc ctggacaggc atatattatc aatacagttt ttccctatct tatcaaagct
     4921 ccatgccgcc ccaggtatga cctcgttcct gctcctgctc tggctgctgc acctccggca
     4981 caggcaacag ctccctggcc ctttcgacaa gggggcggaa cttctctggc aggtgccgat
     5041 ccagaaaatc catcaccgca ctgaccccat ccaggagccg atccgagaag ctgcgctcct
     5101 gctccaactc ttgttccagg cactccacct gtaccagcag ctttcggttt tggttttcaa
     5161 gccgctgcct ctcctgagcc tccttcagct tttcttttgt cgaggggatt ttctgctgaa
     5221 gccgctgatt ttcttccttc agctcttgca ctttctgttc cgctgccgca cctctgattg
     5281 ctgccgcctt cagttccttt acctgttcta cggtaacgcc tttcacagct cctgtcagcg
     5341 tcttttctgg ctgtatggcc tccagatcag gcttgacctt ctcaaccgcc tttaggagct
     5401 tcacattccc ttgcaacgct tttttctgct tttccaaagt tgctatatcc tgttctgctg
     5461 ctgcaacctg ttcctggaca gcttcaaggc gctgcgccgc tgcccggtac tctggcaaat
     5521 ccatgtgagg ccgaccaccg cccaggctga taatctcaaa atcgtgtacc tgagcaatct
     5581 ctccaagaga taccttctca cgctccatcc aggctttcca ttcggtttgc tttcggccca
     5641 ggctttcaaa tccttgctgc tttaacgcct gcttcatgga aaccctcgtg gacagccccc
     5701 ggctctgccc agtggccacc ggcacaaagt ctacatggag gtggggcgtg gcttcatcca
     5761 tgtgcagcac catattgaat acccgcagat gaggattgcg ctcctggaag gactctgcaa
     5821 attctttgag agctgccgct gcccgttccc ctcctgggga gccgcaccca cagtcctcca
     5881 tgttaccgat ctggaagatg gcctcgtgaa atagcttctc ctgtttgctc tgccggatat
     5941 gctcatagta gtctggtatt tt
//
