LOCUS       CP063573                4375 bp    DNA     circular BCT 04-APR-2022
DEFINITION  Enterococcus faecium strain BMT-1-1-11 plasmid pIN-1-11_05, complete
            sequence.
ACCESSION   CP063573
VERSION     CP063573.1
DBLINK      BioProject: PRJNA669626
            BioSample: SAMN16483162
KEYWORDS    .
SOURCE      Enterococcus faecium
  ORGANISM  Enterococcus faecium
            Bacteria; Bacillota; Bacilli; Lactobacillales; Enterococcaceae;
            Enterococcus.
REFERENCE   1  (bases 1 to 4375)
  AUTHORS   Both,A., Kruse,F., Mirwald,N., Franke,G., Christner,M., Huang,J.,
            Hansen,J.L., Kroger,N., Berneking,L., Lellek,H., Aepfelbacher,M. and
            Rohde,H.
  TITLE     Population dynamics in colonizing vancomycin-resistant Enterococcus
            faecium isolated from immunosuppressed patients
  JOURNAL   J Glob Antimicrob Resist 28, 267-273 (2022)
   PUBMED   35134550
REFERENCE   2  (bases 1 to 4375)
  AUTHORS   Both,A., Kruse,F., Christner,M., Huang,J., Mirwald,N., Franke,G. and
            Rohde,H.
  TITLE     Direct Submission
  JOURNAL   Submitted (20-OCT-2020) Institute of Medical Microbiology, Virology
            and Hygiene, University Medical Center Hamburg-Eppendorf,
            Martinistr. 52, Hamburg, Hamburg 20246, Germany
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: Trycycler v. v0.3.3
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 469.7x
            Sequencing Technology             :: Oxford Nanopore
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI
            Annotation Date                   :: 10/27/2020 16:31:57
            Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline
            (PGAP)
            Annotation Method :: Best-placed reference protein set; GeneMarkS-2+
            Annotation Software revision      :: 4.13
            Features Annotated :: Gene; CDS; rRNA; tRNA; ncRNA; repeat_region
            Genes (total)                     :: 3,221
            CDSs (total)                      :: 3,129
            Genes (coding)                    :: 3,023
            CDSs (with protein)               :: 3,023
            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)              :: 106
            CDSs (without protein)            :: 106
            Pseudo Genes (ambiguous residues) :: 0 of 106
            Pseudo Genes (frameshifted)       :: 25 of 106
            Pseudo Genes (incomplete)         :: 69 of 106
            Pseudo Genes (internal stop)      :: 24 of 106
            Pseudo Genes (multiple problems)  :: 11 of 106
            ##Genome-Annotation-Data-END##
            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/
FEATURES             Location/Qualifiers
     source          1..4375
                     /organism="Enterococcus faecium"
                     /mol_type="genomic DNA"
                     /strain="BMT-1-1-11"
                     /isolation_source="rectal swab"
                     /host="Homo sapiens"
                     /db_xref="taxon:1352"
                     /plasmid="pIN-1-11_05"
                     /geo_loc_name="Germany: Hamburg"
                     /lat_lon="53.33 N 10.1 E"
                     /collection_date="2014-07-08"
                     /collected_by="Institute of Medical Microbiology, Virology
                     and Hygiene, University Medical Center Hamburg-Eppendorf"
     gene            join(4096..4375,1..695)
                     /locus_tag="IQN14_16080"
     CDS             join(4096..4375,1..695)
                     /locus_tag="IQN14_16080"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002303407.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="replication protein"
                     /protein_id="UOE06166.1"
                     /translation="MSKKGTIINEWEKLTAPSNRRLSVPFMDTPLKIQWSIDRITIVGN
                     LKENIYYHTTHDVLILDFEQLMRLNEGNGYLRSVSNNGWQLLDQHEENIAYIEILKWQE
                     GKGRIDFNPNKISQFLASSMKNFIHDLFIEPHFSRADIACDIIDVPDEFITQYRVVDPV
                     SFKPIYGRNGKLETAYWGSRSSERQIRMYNKKLEQEKKRKIVPKEIVSWWRLELQLRRG
                     KATDWHAMVQESLDSFASPHYLPADTSVADKMMITALTTEHDYWGQINRKTKYKYRNLL
                     KQESQNDELTNHLRETFAESADDLKKELDTWLLGLDVTEEEEK"
                     /name="replication protein"
     gene            692..925
                     /locus_tag="IQN14_16085"
     CDS             692..925
                     /locus_tag="IQN14_16085"
                     /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="UOE06167.1"
                     /translation="MTEKQKYFGKKNWLVNLTGDYVVVVFLDSKKMSGKLLDVTQYELI
                     LKNNKIDSPIIIPKHAVKYIYAVAESSGEAND"
                     /name="hypothetical protein"
     gene            918..1337
                     /locus_tag="IQN14_16090"
     CDS             918..1337
                     /locus_tag="IQN14_16090"
                     /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="UOE06168.1"
                     /translation="MTDLSEKMTIKNLADELGVSKNTVRNQLVNSGFDLAQYKENGIIM
                     LDKELIGVVRSIYRSKSDQLTGQLPVNNTGSDFPLEKENEFLRDQLAEKDKHISELTEM
                     IRDQQKLTLLQQQKNDQLLLENQELKNRKWWQFWK"
                     /name="hypothetical protein"
     gene            1346..1654
                     /locus_tag="IQN14_16095"
     CDS             1346..1654
                     /locus_tag="IQN14_16095"
                     /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="UOE06169.1"
                     /translation="MDKIDLREETVDRIELMYERLADYLNLPDEDNYSEMLERIMDVLN
                     SVINADLAKSSVLTNEFVHKHLAQTTDESEKEFWLKLMSHVMQLNQISVINSKEKEM"
                     /name="hypothetical protein"
     gene            1658..2020
                     /locus_tag="IQN14_16100"
     CDS             1658..2020
                     /locus_tag="IQN14_16100"
                     /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="UOE06170.1"
                     /translation="MGMTLADIKAQEEKLKKEQAKLRQQKKRLIEKENAAMGKALRKRF
                     GFETFADFERWLSSISDDQQHEKSVDNEWLADEKSAPSERDYPDESDGLFGVIPNKKSQ
                     MSESKFTSIFNDVNLR"
                     /name="hypothetical protein"
     gene            2241..3647
                     /locus_tag="IQN14_16105"
     CDS             2241..3647
                     /locus_tag="IQN14_16105"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_016173818.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="plasmid recombination protein"
                     /protein_id="UOE06165.1"
                     /translation="MGFSISFKKGTKNTSISHNNRELTDSQKINDWHKHIDFTKSDENI
                     YLEQTNIREKYEELFGEAVEKYNAKQKRADRKIEDYLAKVRKDKKLEPQREFIVQIGTL
                     DDFRTTRDDGSSTGISEQQAEQNRVIANKILVEYFKEFKERNPNLSVYNAVIHNDEVSP
                     HLHLNIVPVAEGYKRGVQKQPSFNKALQQQGLRADKENGRVIWNNFRNQEVESIERLMA
                     DFGWERELVGTNKIKDVHEYKEIMSEISELRQTAVKERESVSDELRYISRQREENEREK
                     ALVASERVKIEEEKKNMLNVKKEMAVIFQKDIVPLESFKRLPDGSYHLSGNDFVDLYQR
                     ATRATNAKRNADNMSEQYLQMLEQNTELNEYVATLEEERHLSGRKQLADLQVENKKLKE
                     ENRSLRQRLERLKNAFQKSITRLSIRFGLAEKDMGLSEELEVLEQEKTLFYRQNVSQRK
                     LERSEDEIEW"
                     /name="plasmid recombination protein"
     Typing          2..695
                     /name="rep_cluster_2146"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="99.281"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          2242..3644
                     /name="MOBV"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="97.65"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 ttgcttatat tgaaatttta aaatggcaag aggggaaagg gcgtatagac ttcaatccga
       61 ataagattag tcaattctta gctagttcca tgaaaaactt tattcatgat ttgtttatcg
      121 aacctcactt ttcacgtgca gatattgctt gcgacattat cgatgtacct gatgagttta
      181 ttacacaata tcgggtagtt gatccagttt cttttaagcc tatttatgga cggaatggaa
      241 aattagagac ggcatattgg ggatctcgct cttctgaacg tcaaattcgg atgtataata
      301 aaaaactgga acaagagaag aaaagaaaaa ttgtgccaaa agaaatcgtg agttggtggc
      361 ggttagaatt acaattaaga cgagggaaag cgactgattg gcatgcaatg gttcaagaaa
      421 gcttggatag ttttgctagt cctcattact tgcctgctga tacaagtgta gctgacaaaa
      481 tgatgattac tgctttaaca acagaacatg attattgggg gcaaattaat cgaaagacaa
      541 aatataaata tcgaaatttg ctgaagcaag aaagtcaaaa tgatgaattg acgaatcatt
      601 tacgagaaac ctttgcagaa tcggcagacg atttaaaaaa agaattagac acatggcttc
      661 tagggctaga cgtaacagag gaggaagaaa aatgacagaa aaacaaaagt attttggtaa
      721 gaaaaattgg ttggtaaatt taacaggtga ttacgttgtg gttgtttttt tggatagcaa
      781 aaaaatgtcc ggtaagttac ttgatgtaac gcaatatgaa ttgattttga aaaataataa
      841 aattgactct ccgattatta tccctaagca cgccgttaaa tatatttatg cggtagctga
      901 aagtagtgga gaagctaatg actgatttgt cagaaaagat gaccataaaa aatcttgctg
      961 acgaattggg tgtatcgaaa aatacagtgc gcaatcaact ggtcaattca gggtttgacc
     1021 ttgctcagta taaagaaaat ggcattatca tgctagataa agagttgatt ggtgttgttc
     1081 ggtcaattta tcggtcaaaa agtgatcaat tgactggtca attaccggtc aataacacag
     1141 gcagtgattt tcctttagaa aaagagaatg agtttttgcg tgatcaatta gctgagaagg
     1201 acaaacatat ttctgaatta acagaaatga ttcgtgatca acaaaaattg accctgcttc
     1261 agcaacaaaa aaacgatcag ttgttactag aaaatcaaga attaaaaaat cgaaaatggt
     1321 ggcaattctg gaagtgaggt gtgacatgga taaaattgat ttgagagaag aaacagtcga
     1381 tagaattgaa ttgatgtatg aacggttagc tgattatttg aatttgccgg atgaagataa
     1441 ttatagtgaa atgcttgaac gaattatgga tgttctcaac tcggttatca atgctgattt
     1501 agcaaaatct tcagttttga ctaatgaatt tgttcataag catttagcgc aaacaactga
     1561 tgaatcagaa aaagaatttt ggttgaaatt aatgagtcat gttatgcagt taaaccaaat
     1621 ttccgttatt aattccaaag aaaaggagat gtagtttatg ggaatgactt tagcagatat
     1681 taaagcgcaa gaagaaaaat taaaaaaaga acaagcgaaa cttcgccaac agaaaaaacg
     1741 cttgattgag aaagaaaatg ctgcaatggg caaggctctt cggaagcgtt ttgggtttga
     1801 aacttttgct gattttgagc ggtggctatc gtcgatttct gacgatcagc aacacgaaaa
     1861 atcagtggat aatgagtggc ttgctgatga aaaatcagcg ccaagcgaac gagattatcc
     1921 cgatgaatct gacggcttat tcggagtgat accgaataag aaaagtcaga tgagtgagag
     1981 taaatttacg tcaatattta atgacgtgaa tttacgataa gcgattattt tgcgtgaagc
     2041 aaaataaagc gtaaaaggag ttgagagcgt gacacgcttt cggctccttt tttcgttgtc
     2101 acttgtgaca gcgaataccc tcggagagca tttggaattg tgacagccat gtcacaatta
     2161 ggaaaatgtt actctttgac aaagagtaac agaaaggttt acactctttt tattagcgac
     2221 agccgaagga gggttttaac ttggggttca gtatttcgtt caaaaaggga acaaagaata
     2281 caagcatttc tcataataat cgtgagttaa ctgatagcca aaaaatcaat gactggcata
     2341 agcatattga tttcacaaaa tcggatgaaa atatctattt agaacaaaca aatattcgtg
     2401 aaaaatatga agaattattc ggtgaagccg tagaaaaata taatgcaaag cagaaaagag
     2461 ccgatagaaa aatcgaggac tatttagcaa aggttcgcaa ggataaaaaa ttggaaccac
     2521 agcgagaatt tatcgtgcaa attggtactc ttgatgattt tcgtactact cgtgatgatg
     2581 gttcttctac tggcatatcg gaacaacaag cagaacaaaa tcgagtgatt gccaacaaaa
     2641 ttttagttga atatttcaaa gaatttaaag aacggaatcc taatttatcc gtctacaatg
     2701 ctgttattca taatgacgaa gtaagtccgc acctgcattt gaatattgtt cctgttgctg
     2761 aagggtataa acggggtgtt caaaagcaac caagttttaa caaagccttg caacagcagg
     2821 gtttacgagc agataaagag aatggtcgag tgatttggaa taattttagg aatcaggaag
     2881 ttgagtcaat tgaacgtttg atggcagatt ttggttggga gcgtgagtta gtcggtacta
     2941 acaaaatcaa agatgttcac gaatataaag aaatcatgag cgagatttca gaattgcgtc
     3001 aaacggccgt aaaagagcgt gagagcgttt ctgatgagtt gaggtatatt tctaggcaaa
     3061 gagaagaaaa tgagcgagaa aaggctctgg tggcttctga gagagtgaag attgaagaag
     3121 agaagaaaaa tatgctgaat gtaaaaaaag agatggcggt cattttccaa aaagatattg
     3181 ttcctttaga aagtttcaag aggcttcctg atggttcgta tcatttatct gggaatgatt
     3241 ttgttgattt gtatcaacga gctacgagag caacaaatgc caagagaaat gctgataaca
     3301 tgagtgagca atatttacag atgcttgagc aaaatacaga attaaatgag tatgtagcta
     3361 cattggaaga agagcgtcat ttgtctggta gaaaacaatt agcagattta caagtggaaa
     3421 ataaaaagct gaaagaagaa aatcgctctt tacgccagcg tttagagcga ttaaaaaacg
     3481 catttcaaaa atcgatcact cgtttgtcta tccgttttgg tcttgcagaa aaggatatgg
     3541 ggctttctga ggaattagaa gtgttagagc aggagaaaac cttattttat cgtcaaaacg
     3601 tctcacagcg taaattagag cgttctgaag atgagatcga gtggtagtta cgatgtgcag
     3661 tcaacggtac cggaggcggt ttgtgccgag gataaggagt tgacggctaa accactaatc
     3721 cctgaagctg acatttgcta aaaaatggca agtccatttt ttggccaacc tagcgttagc
     3781 gaagtttggg ggcgcccttt tcaaagggtg cggttttatt ttttggatat ttgcatagct
     3841 aaagagaagt gctattattg agttatcaaa taaataaact gaaaaaagag caaaaaaata
     3901 aagtcgagca acgctggaca cgttctcgac ctttacggaa actaatcgca ctagctccgt
     3961 aacttcttaa tcattatacg aatattttta gatttcttca agactagaga ttttttggta
     4021 atgaattttt aagagttacg tgaacttttg aaaattcttt ccagaagtct ctttttcttt
     4081 gaggaggaac aaaatttgag taaaaaaggc acgatcataa atgagtggga aaaattaaca
     4141 gccccctcta acaggcggtt aagtgtccct tttatggaca cccccctaaa aattcagtgg
     4201 tcaatcgacc gaattaccat tgttggaaat cttaaagaga atatctatta tcacactaca
     4261 catgatgtgt tgattttaga ttttgaacag cttatgcgcc taaatgaagg taacggttat
     4321 ttaagatctg ttagtaataa tggttggcag ttgttagacc aacatgaaga gaata
//
