LOCUS       NZ_CP044324             5072 bp    DNA     circular CON 13-OCT-2023
DEFINITION  Enterococcus faecium strain 15-307-1 plasmid p15-307-1_08, complete
            sequence.
ACCESSION   NZ_CP044324
VERSION     NZ_CP044324.1
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 5072)
  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  JOURNAL   Unpublished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 5072)
  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 5072)
  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
            CP044324.1.
            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..5072
                     /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_08"
                     /geo_loc_name="France: Corbeille-Essonnes"
                     /lat_lon="48.6103 N 2.4748 E"
                     /collection_date="2015"
                     /collected_by="NRC for Enterococci"
     gene            join(5010..5072,1..393)
                     /locus_tag="CWC51_RS16320"
                     /old_locus_tag="CWC51_016770"
     CDS             join(5010..5072,1..393)
                     /locus_tag="CWC51_RS16320"
                     /old_locus_tag="CWC51_016770"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002334263.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="LMxysn_1693 family intestinal colonization
                     protein"
                     /protein_id="WP_002322959.1"
                     /translation="MKKQLFKTFLLSTSILTFGSAITPSGAVFANENNISDIATYSDDE
                     YYYVLDEPVIQTRTWSKPQSWSIAKGSRTYLGIETHSRGTKLSVSANVFGMKIEIARNT
                     SASGKFKKYRQNARITVTYRVYRKVDNKYIRTQTSTANTQYIDYIPA"
                     /name="LMxysn_1693 family intestinal colonization protein"
     gene            393..962
                     /locus_tag="CWC51_RS16325"
                     /old_locus_tag="CWC51_016775"
     CDS             393..962
                     /locus_tag="CWC51_RS16325"
                     /old_locus_tag="CWC51_016775"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002322960.1"
                     /GO_function="GO:0004222 - metalloendopeptidase activity
                     [Evidence IEA]"
                     /GO_process="GO:0071586 - CAAX-box protein processing
                     [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="type II CAAX endopeptidase family protein"
                     /protein_id="WP_002322960.1"
                     /translation="MTIKWIISIAYLVLTFAIPSLGVPSNIYFLFEHSDIFFLVLIIIL
                     FHSTFIREFKEVNLKKLFKYSFFSFSVLFLINILNTSFSEGINPNEVNGSLLLFFLNAA
                     TYGAFLEEGIFRFCMIDPQANKKQQYISILISSFLFSIVHGGGLSIFFIGIILSFVYIQ
                     TKNIWYSIVAHGFYNTIGILIYLISI"
                     /name="type II CAAX endopeptidase family protein"
     gene            981..1136
                     /locus_tag="CWC51_RS16330"
     CDS             981..1136
                     /locus_tag="CWC51_RS16330"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_016631617.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_162846310.1"
                     /translation="MKLTKLTISLVIIAGIILYFVLPANQFFLYFGIPTILIVNGVRIF
                     EQRKKM"
                     /name="hypothetical protein"
     gene            2287..3255
                     /locus_tag="CWC51_RS16335"
                     /old_locus_tag="CWC51_016785"
     CDS             2287..3255
                     /locus_tag="CWC51_RS16335"
                     /old_locus_tag="CWC51_016785"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002347614.1"
                     /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_002347614.1"
                     /translation="MSNEIVKYHHELNTIPLRKFTPVEMNLFFSIVSRMRDVGDKKVQF
                     TFEQLKDLSNYKATANVRFIDDLETTYDKLMDLRFGRRSADGLQRERFVLFNQFKIDGK
                     SDIPFAEIQVHEKALPLLNNLEEWVRYSLQQFNELESSYSKTMFRLLKQYRTKGFAYFS
                     KEDFHELLDIPKSYNQGTIDQRVFNPIRQELTAIFKGLTIKKKYGKGRGKPVIGYQFTF
                     KPEIKKSDDFNKHAPTKEEQNKALELANQQVQSEKAPTSLQEKIKEQKRKLELLQQLEK
                     LEREQNTQNKENNAQKSEINSDIPSELKKDLLDNLQNLFKD"
                     /name="replication initiation protein"
     gene            3702..3983
                     /locus_tag="CWC51_RS16340"
                     /old_locus_tag="CWC51_016790"
     CDS             3702..3983
                     /locus_tag="CWC51_RS16340"
                     /old_locus_tag="CWC51_016790"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000353845.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_002347613.1"
                     /translation="MDILVRNINPKIIARIDKRCQELTTKTGKKWSRNKYLKVLIESDF
                     DRQLMNYKKDQFDLLLEKFIAIQTENTNILNDYVHTNNQLIETLIGGI"
                     /name="hypothetical protein"
     gene            3985..4401
                     /locus_tag="CWC51_RS16345"
                     /old_locus_tag="CWC51_016795"
     CDS             3985..4401
                     /locus_tag="CWC51_RS16345"
                     /old_locus_tag="CWC51_016795"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001232859.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_060806983.1"
                     /translation="MRKTSVQKHVTLYPSHVDVLDSIIEKNPDVNNYSEAIRFLCMSYE
                     PDTNTITTSNQAKLNAMGKEISIMTEIMAEFADLYLKDTGVLIGTNSKVYQEVKEKIEN
                     QLNPSRRNQPKNRQKETNQTFTSGNFDPTNFLKR"
                     /name="hypothetical protein"
     Typing          2288..3251
                     /name="rep_cluster_1093"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="93.679"
                     /coverage="99.0"
                     /evalue="0.0"
ORIGIN
        1 attactccta gcggagcggt attcgctaat gagaacaaca tttctgatat agccacttat
       61 tctgatgatg agtactacta tgtgttagac gaaccagtta ttcaaacaag gacttggtct
      121 aaacctcaaa gctggtcaat tgctaaagga agccgtactt atttaggtat agaaactcat
      181 agtcgaggta caaagttatc tgtcagtgca aatgtatttg ggatgaaaat cgaaatagcc
      241 agaaacactt ctgcaagtgg aaaatttaaa aaatatcgtc aaaatgcaag aataactgta
      301 acctacagag tttatcgtaa ggtagataat aaatatattc gtactcaaac ttctacagca
      361 aatacacaat atattgatta tattcctgcc taatgacaat aaaatggata attagtattg
      421 cttacttggt tttgaccttt gctatcccat cattaggagt accgtcaaat atatattttt
      481 tatttgaaca tagtgatata ttttttttag tgctaataat tatactattt cattctacct
      541 tcattcgtga attcaaagaa gtaaatctaa aaaaactctt taaatatagt tttttttcat
      601 tctctgtttt attcctaatc aatattctaa atacatcttt ttcagaaggt ataaatccta
      661 atgaagtaaa tggttctctc cttttattct ttttaaatgc tgctacttat ggagcttttt
      721 tagaagaagg aatttttcga ttttgtatga ttgatcctca agcaaacaaa aaacaacaat
      781 atatttcaat actaatttct tcttttctgt tttctattgt tcatggggga ggcctaagta
      841 ttttctttat tggtattatt ttaagttttg tttatataca aacaaaaaat atatggtatt
      901 ccatagttgc tcatggattt tataatacaa tcggcatatt aatctatttg atatctatat
      961 aagataaggt ggcatacttc atgaaattaa caaaacttac tataagtttg gtaattattg
     1021 ctggtattat tttatatttt gtattacctg ctaatcaatt ttttctttac tttggaatac
     1081 ctacgatttt aatagtaaat ggcgtaagaa tatttgaaca acgaaaaaaa atgtagctct
     1141 acctgatcgt tgcaaagcaa caatttcacc gaaggtgaaa caagcgaaac tttacaaaaa
     1201 gtggctagca tttgctagcc ttttttgtat tgtggagcgt gggttttgag gggggattca
     1261 agggggagct tgcgcccctt tgacaagcgg ttatttgcac caaatacgta ggtatttggc
     1321 tagcaaatat agagcttgcc aaacccttaa gtacctttaa aggtactttc acattacgaa
     1381 cgatacgtcc gtaggacgta ctgaaagggt gggatttatg agcgaactaa tgcaaaattt
     1441 ggctagcaaa aaaagttaaa aaatatatgc taataatcga gcgaaatgaa cactttttca
     1501 agtgagcgaa tccgccatga caaagctgaa gcagtttatt tcagctttgt catggcgtgt
     1561 gcctagactt ttaaaaaagt cggcacacga gcaaatatct ttatcaagct ctaatttgcg
     1621 ttttaagacg tttgaaacgt ctaagtatat aaatatataa gaataggttt aagagtgctt
     1681 aaatcgaatt ttagagggca ttcagacaac tttagggttg ttagggcttg ccctgaccgc
     1741 ctgtaaggcg ctttaagaac aagataaggg atttatacta agactgtctt aaaacgtctc
     1801 aaacgaaggc tcatagcttc tcaaagagtt ccttatgaat atttttagca aaggagccgg
     1861 aagcgactgc gcagtataat gtgagagcag agcgatcaca cctttttaag cgactgtagg
     1921 gagtaagatt cccagttgag aaaaatgcgc gaatctgttt ggagaaaaaa gaagtggttt
     1981 tttaggcggg aaattttgtc cccctctttt ataatctctt tttaaacctc tttttaaacc
     2041 tctttaccgt cggctatatc cttactctcc caagggaatg acgcttttat ctacatcgtt
     2101 ttgtctgttt atctacatcg ttttgtctgt ttatctacat cgttttgtct gtttatctac
     2161 atcgttttgt ctgtttgtac attgaattag tacatcgacg atgttaatat aagatgtaga
     2221 taaataggca ttttgtattt cataacgtgt atctcttgtg cgagtaagaa aggagctatt
     2281 ttaaatatgt ctaatgaaat cgtaaagtat catcatgaat taaatacaat tccgttgcga
     2341 aaatttacac cagtcgaaat gaatttgttc ttttctatcg tatcaagaat gcgtgatgta
     2401 ggtgataaaa aagtacaatt tacattcgag caattaaaag atttaagcaa ttataaagca
     2461 actgcaaatg ttcgattcat agatgattta gaaacaacgt atgacaaatt aatggattta
     2521 cgttttggta gaagaagtgc tgacggtttg caacgtgaac gttttgtttt atttaatcaa
     2581 tttaaaatcg acggaaaatc tgatattcct tttgctgaaa tacaagttca tgaaaaagcc
     2641 ttacccttac ttaataatct tgaagaatgg gtgcgctatt ctctccaaca attcaatgaa
     2701 ttagaaagca gttattcaaa aacaatgttt cgattactaa aacaatacag aaccaaaggt
     2761 ttcgcttatt tttcaaaaga agactttcat gaattacttg atattcctaa aagttacaac
     2821 caaggtacga ttgatcaacg tgtgttcaat ccaatacgac aagaactaac tgcaatcttt
     2881 aaaggtttaa caatcaaaaa gaaatacgga aaaggacggg gaaagcctgt cattggctat
     2941 caatttacat ttaaacctga gataaaaaaa tcagacgact ttaacaaaca tgccccaaca
     3001 aaagaagaac aaaacaaagc attagaacta gctaaccaac aagttcaatc tgaaaaagca
     3061 cctacttcat tacaagaaaa aatcaaagaa caaaagcgaa aattggaact tttacaacag
     3121 ttagaaaagt tagaaagaga acaaaatacc caaaataaag aaaataatgc acaaaaatca
     3181 gagataaatt ccgatattcc ttcagaacta aaaaaagact tattagacaa tcttcaaaac
     3241 ttattcaaag attgaggggt ttttagattt tatgacagaa aaaacaatca aagacggaga
     3301 aaaaatggtg gcaattctgg caataaaacc agcaattttt attaatttaa attgctggtt
     3361 ttattcttct ttttgctttt gcgagcagag caacatggac ccatgttgcg atattttggt
     3421 ggcgccccaa tccccgtttt ttcgttgaat cttactcgga ctgcactcgt tttacagctg
     3481 atttttctga attttgaaag agcataagga aacgtggtat cactttctta caaaaggtgc
     3541 tagataggct gtgcctatca cgtttctcag aaaaaaattt gctatcactt ttttgccatt
     3601 gtggctaggc tatgtatagt gttttggcga aaaatagcta tacaaatact atatttgtat
     3661 gatatacata aattatacgc tgatacgaaa ggaaaatttc catggacatt ttagttcgaa
     3721 atatcaatcc caaaattatt gcaagaatag ataaacgttg tcaggaactc acaaccaaaa
     3781 cgggcaaaaa atggagtcga aataaatatc taaaagttct aatcgaaagt gattttgacc
     3841 gtcaacttat gaattacaaa aaagatcaat tcgatttatt actcgaaaaa tttattgcca
     3901 ttcaaacaga aaatacgaac atactgaatg actatgttca cacaaacaac caactcattg
     3961 aaacacttat cggaggaata taacatgaga aaaacttctg ttcaaaaaca cgtaaccctt
     4021 tatcccagtc acgttgacgt tttagattcc atcatcgaaa aaaatccaga cgtcaacaat
     4081 tattcagaag ccattcgttt tttatgtatg agttatgaac ctgataccaa tacaatcaca
     4141 accagtaacc aagcaaaact caatgccatg ggaaaagaaa tttctatcat gacagaaatc
     4201 atggcagaat ttgctgattt atatctaaaa gatactggtg ttcttatcgg tacaaattct
     4261 aaagtgtatc aagaagtgaa agaaaaaatt gaaaatcaac tcaatccttc ccgacgaaat
     4321 caacccaaaa atcgtcaaaa agaaaccaat caaaccttta cttctggaaa ttttgaccca
     4381 acaaactttc taaaaagata aaaaaagaaa ccgatcccta aaaaaattcc tcgatttctt
     4441 tttagggatc agtcttccag caagatttgc aagttggtac caacttgcga aaaaaaagaa
     4501 aaatccgctt atgcaacttc ttctttttgt attttggggc gctaccccaa tccccaagta
     4561 tcggttattt aatagcgcgg aaatccaaag aataggacgt accctgaaac aaaaaaagac
     4621 tgctctcacg agcagctaaa aatgagatta tcctattcat taacattaga aaagaagaga
     4681 ttgaggtata aaaagagcat atcaaatgct cacaaaaata acaaatctct aaaaaatgac
     4741 cggtcaaaat gcacaaagaa atgaaaaaag aaaagtgcat aaaatcaagc attggctgaa
     4801 gtgtttaagc tagaccaatt agaaatcaca aagtgagcgt ctctatccat tggtagaggg
     4861 gctacttggc atagtcgaca ttatgtctac taacctttaa tataacagct tttataaaat
     4921 aaaccctctt gacaacatta aatttcctga ttattctaat tatataaaga aagcgttttc
     4981 ttaagtatct tatattcgag gtgattttga tgaaaaaaca gttatttaaa acctttttat
     5041 tatctacttc tattttaact tttggttctg ct
//
