LOCUS       NZ_CP018069             3296 bp    DNA     circular CON 31-JAN-2024
DEFINITION  Enterococcus faecium strain E1 plasmid pE1_3, complete sequence.
ACCESSION   NZ_CP018069
VERSION     NZ_CP018069.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN06019998
            Assembly: GCF_001886635.1
KEYWORDS    RefSeq.
SOURCE      Enterococcus faecium
  ORGANISM  Enterococcus faecium
            Bacteria; Bacillota; Bacilli; Lactobacillales; Enterococcaceae;
            Enterococcus.
REFERENCE   1  (bases 1 to 3296)
  AUTHORS   Tedim,A.P., Lanza,V.F., Manrique,M., Pareja,E., Ruiz-Garbajosa,P.,
            Canton,R., Baquero,F., Coque,T.M. and Tobes,R.
  TITLE     Complete Genome Sequence of E. faecium ST117 a globally disseminated
            multidrug resistant clone
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 3296)
  AUTHORS   Tedim,A.P., Lanza,V.F., Manrique,M., Pareja,E., Ruiz-Garbajosa,P.,
            Canton,R., Baquero,F., Coque,T.M. and Tobes,R.
  TITLE     Direct Submission
  JOURNAL   Submitted (16-NOV-2016) Microbiology Laboratory, Instituto Ramon y
            Cajal de Investigacion Sanitaria (IRYCIS), Carretera Colmenar Viejo
            km9.1, Madrid 28034, Spain
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: SPAdes v. 3.5.0
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 800.0x
            Sequencing Technology             :: Illumina HiSeq; PacBio
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 01/31/2024 03:04:00
            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)                     :: 3,196
            CDSs (total)                      :: 3,103
            Genes (coding)                    :: 3,003
            CDSs (with protein)               :: 3,003
            Genes (RNA)                       :: 93
            rRNAs                             :: 6, 6, 6 (5S, 16S, 23S)
            complete rRNAs                    :: 6, 6, 6 (5S, 16S, 23S)
            tRNAs                             :: 71
            ncRNAs                            :: 4
            Pseudo Genes (total)              :: 100
            CDSs (without protein)            :: 100
            Pseudo Genes (ambiguous residues) :: 0 of 100
            Pseudo Genes (frameshifted)       :: 35 of 100
            Pseudo Genes (incomplete)         :: 65 of 100
            Pseudo Genes (internal stop)      :: 25 of 100
            Pseudo Genes (multiple problems)  :: 19 of 100
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP018069.1.
            Bacteria and source DNA available from Teresa Coque. Hospital Ramon
            y Cajal. Microbiology department.
            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..3296
                     /organism="Enterococcus faecium"
                     /mol_type="genomic DNA"
                     /strain="E1"
                     /isolation_source="Blood"
                     /host="Homo sapiens"
                     /db_xref="taxon:1352"
                     /plasmid="pE1_3"
                     /geo_loc_name="Spain: Madrid"
                     /lat_lon="40.48 N 3.69 W"
                     /collection_date="2010-01-11"
                     /collected_by="Hospital Ramon y Cajal. Microbiology
                     Department"
                     /subtype="ST117"
                     /subgroup="BAPS2.1a"
     gene            join(3165..3296,1..69)
                     /locus_tag="BO233_RS16800"
                     /old_locus_tag="BO233_15765"
     CDS             join(3165..3296,1..69)
                     /locus_tag="BO233_RS16800"
                     /old_locus_tag="BO233_15765"
                     /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_196219922.1"
                     /translation="MEKFPYEYFQNLEKLEQAIQAIKFDLTDEKLLEYKNMTPERKRSR
                     KIRASNSSNQVRFNRRKIVGI"
                     /name="hypothetical protein"
     gene            1240..1959
                     /locus_tag="BO233_RS16805"
                     /old_locus_tag="BO233_15770"
     CDS             1240..1959
                     /locus_tag="BO233_RS16805"
                     /old_locus_tag="BO233_15770"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002311815.1"
                     /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_002311815.1"
                     /translation="MDEKTELTVKYQNELNLVPLKNFNAKQMDLFFALCARMKDRGLKK
                     VRFSFEELKELSDYKMTATKAFVGDLEKLYKDMLNLTYRTEDEDSIRYFVLFTGFEINK
                     TKKFVEVSVNPDLEYIINGLTAEFSRFELSAFTSLRSTYAKTLFRLLMQYRSTGYYVVR
                     IEEFRSLMDIPEYYQMGNIDQKVLNPALRELKKYFNDLKVTKIKAKKGNKIAKLEFTFS
                     SLTSDLPKISLRNWLEE"
                     /name="replication initiation protein"
     gene            complement(2096..2512)
                     /locus_tag="BO233_RS16810"
                     /old_locus_tag="BO233_15775"
     CDS             complement(2096..2512)
                     /locus_tag="BO233_RS16810"
                     /old_locus_tag="BO233_15775"
                     /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_001232859.1"
                     /translation="MRKTSVQKHVTLYPSHVDVLDSIIEKNPDINNYSEAIRFLCMSYE
                     PDTNTTTTSNQAKLNAMGKEISIMTEIIAEFADLYLKDTGVLIGTNSKVYQEVKEKIEA
                     KLNPSNRNRPKNHQKETSQTVTSRNFDPTNFLKR"
                     /name="hypothetical protein"
     gene            complement(2515..2799)
                     /locus_tag="BO233_RS16815"
                     /old_locus_tag="BO233_15780"
     CDS             complement(2515..2799)
                     /locus_tag="BO233_RS16815"
                     /old_locus_tag="BO233_15780"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002337999.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_000353844.1"
                     /translation="MDILVRNIDPKFVATIDKRCQELTNKTGEKWSRNKYLKVLIESDF
                     DRQLTTYKKDQFDLLLDKFIAIQTENTQILSEYVYTNNQIIEMLIGGMI"
                     /name="hypothetical protein"
     Typing          1241..1959
                     /name="rep_cluster_1763"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 agaaaaatta gagcaagcaa ttcaagcaat caagttcgat ttaacagacg aaaaattgtt
       61 ggaatataaa aatatgacac ccgaaagaaa acgatcgttg gaaaaattaa tgcaactagt
      121 gaacgaagac ggcggaattt cagacgcagc ttttgacgca tggagcgaat ttcatggaga
      181 atataattaa gtgggtttaa atggctctaa aatcgcttct aagagttttt tagcttggac
      241 caatgaaata caccaaaaac taaataaaac gtcttaaatc gaaaaatacg agctctcaga
      301 gcgactttat ttgtaaatgt tgcatataag aaataattac ggattttaga cttttgtagg
      361 atatttttga aataaatatt tatttctgtt ataatttgat tgcaaataag tgaacacgaa
      421 acacacgaaa gccccagaga ggtcggattc tctggggctt tttttgtggg ctgagtcgcc
      481 ttaattaagt tttacttctt gtttcggtta ttcaaccagt aactgaacaa agcgcttaaa
      541 agcccaacaa gaagggagca aataaagtta gtgaacacga aacacacctc cttccagtcg
      601 caagactgtc ggataggcga caatcaatta tacaataaaa aagcaaaaat aagcctaagt
      661 tttttattgc cttggggttg ttagggcttg ccctgaccgc ctgtaaggcg ctttagaacg
      721 aaggacatag tttttatcga atcttgtctt agaacggctt agacgagctc tcaggacgcc
      781 acaaaggagt ccctaatgaa ttatttttgg cgaaggagcc taaaggcgac tgctgcaagt
      841 aaaatgtgag agcgtagcga tcactccttc ttacagcgac catagggagc tagattggca
      901 gtttaatatc atgcgcgaac ctgtttattt taaaaagtgg gtgatttttt ggcgggaaat
      961 tttgctcgcg cgcgcgcgtt tattttattt attttttaaa gattttttag aacccttttt
     1021 agggggcagt tgagccttac tctcccaacg gatacagaag ggtactaaca actttttatc
     1081 tgagtactaa caacttttta tctgagtact aacaactttt tatctgagta ctaacaactt
     1141 tttatctgag tactaatatc cttttgtata ataacaacca acctatttac gagttggttg
     1201 ttaaaggtta ttatttattt gtaagggggg aagaaaggaa tggatgaaaa aacggaatta
     1261 acagtcaaat atcaaaatga attgaattta gtaccgctga aaaatttcaa tgctaagcag
     1321 atggatttat tttttgcatt atgcgctcgt atgaaagatc gtggtttgaa aaaagttaga
     1381 ttttctttcg aggaattaaa agagttaagt gattataaga tgactgctac aaaagccttt
     1441 gtcggtgatt tagaaaagct ctataaagat atgcttaatc ttacttaccg tactgaagat
     1501 gaggattcta ttcgctactt tgttttgttt actggttttg aaatcaataa aacaaaaaag
     1561 tttgttgaag tcagtgttaa tccggaccta gaatatatta ttaatggttt aacagctgaa
     1621 tttagtagat ttgaattatc tgctttcacg tcgttgcgtt ctacgtatgc aaaaactcta
     1681 ttccgactgc ttatgcagta ccgttctact ggttattatg tagttcgtat tgaagagttt
     1741 aggagcttaa tggatatccc agaatactat caaatgggta acattgatca aaaagtatta
     1801 aatcctgcat tacgagaact aaaaaaatac ttcaatgatc ttaaagtcac aaaaataaaa
     1861 gcaaaaaagg gcaataaaat cgccaaatta gaatttactt tttcaagcct aacgtcagat
     1921 ttgccaaaga tttctctgcg taactggtta gaagaataaa taaaaaagaa ctcgcccccc
     1981 ttacattaag caagtagaca agtcccttac aaccgactaa gattgctagt acattctagc
     2041 atattgtatg gggcttctaa ataaaaaaca gataggaata actcctatct gttttttatc
     2101 gttttagaaa atttgttggg tcgaaatttc tagaagtgac tgtttgactg gtttcttttt
     2161 gatgattctt tggtcgattt cgatttgatg gatttagttt agcttcgatt ttttctttca
     2221 cttcttgata tactttagaa tttgtgccaa taagaacgcc tgtatctttt agatataaat
     2281 cagcaaattc tgcgatgatt tcagtcatga tggaaatttc ttttcccata gcatttagtt
     2341 ttgcctgatt gctggtagtg gtcgtgttgg tatcgggttc ataactcata cataaaaagc
     2401 gaatggcttc cgagtagtta ttgatatctg gatttttttc gatgatggaa tctaaaacgt
     2461 caacatgact agggtacaaa gtaacatgtt tttggacaga agtttttctc atggttatat
     2521 cattcctccg ataagcattt caatgatttg attatttgtg tagacatact cgcttaatat
     2581 ttgagtattt tctgtttgga tagcaataaa tttatcgagc aataaatcga attggtcttt
     2641 tttgtaagtc gtaagttgac ggtcaaaatc actttcgatt aaaactttta gatatttatt
     2701 tcgactccat ttttctcctg ttttattcgt gagttcttgg caacgtttgt ctattgttgc
     2761 aacaaacttt ggatcaatat tccgaactaa aatgtccata aaaaatctcc ttttgcaatt
     2821 atgtataatt tatgtatacc atacaaatac tatatttgta tagctgtttt ttgccaaaat
     2881 gctatacata agctacccac gatggcgaaa aagtgatatc aaattttttt ctgagaaacg
     2941 tgataggcac agcctatcta cccacttttt ttagaaagtg ggtacacgtt tccttatgct
     3001 ctttaaaatt cgggggggag tgctgcacgt gtaatcgata accaaattta aaaatgcacg
     3061 atcaaaaatt tatttagttt ttcaaacgac attttttttg agagtataga cggcaaagaa
     3121 gtgattttat ttctagaaaa attgtgagac tggagaaaga aaaaatggaa aaatttcctt
     3181 acgaatattt tcaaaactta gaaaaattag agcaagcaat tcaagcaatc aagttcgatt
     3241 taacagacga aaaattgttg gaatataaaa atatgacacc cgaaagaaaa cgatcg
//
