LOCUS       CP063610                4444 bp    DNA     linear   BCT 04-APR-2022
DEFINITION  Enterococcus faecium strain BMT-2-3-8 plasmid pSS-3-8_06.
ACCESSION   CP063610
VERSION     CP063610.1
DBLINK      BioProject: PRJNA669626
            BioSample: SAMN16483156
KEYWORDS    .
SOURCE      Enterococcus faecium
  ORGANISM  Enterococcus faecium
            Bacteria; Bacillota; Bacilli; Lactobacillales; Enterococcaceae;
            Enterococcus.
REFERENCE   1  (bases 1 to 4444)
  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 4444)
  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                   :: 100.5x
            Sequencing Technology             :: Oxford Nanopore
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI
            Annotation Date                   :: 10/27/2020 17:58:46
            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)                     :: 3,171
            CDSs (total)                      :: 3,079
            Genes (coding)                    :: 2,968
            CDSs (with protein)               :: 2,968
            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)              :: 111
            CDSs (without protein)            :: 111
            Pseudo Genes (ambiguous residues) :: 0 of 111
            Pseudo Genes (frameshifted)       :: 40 of 111
            Pseudo Genes (incomplete)         :: 66 of 111
            Pseudo Genes (internal stop)      :: 13 of 111
            Pseudo Genes (multiple problems)  :: 7 of 111
            ##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..4444
                     /organism="Enterococcus faecium"
                     /mol_type="genomic DNA"
                     /strain="BMT-2-3-8"
                     /isolation_source="rectal swab"
                     /host="Homo sapiens"
                     /db_xref="taxon:1352"
                     /plasmid="pSS-3-8_06"
                     /geo_loc_name="Germany: Hamburg"
                     /lat_lon="53.33 N 10.1 E"
                     /collection_date="2014-07-23"
                     /collected_by="Institute of Medical Microbiology, Virology
                     and Hygiene, University Medical Center Hamburg-Eppendorf"
     gene            complement(66..1472)
                     /locus_tag="IQN08_15830"
     CDS             complement(66..1472)
                     /locus_tag="IQN08_15830"
                     /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="UOC45558.1"
                     /translation="MGFSISFKKGTKNTSISHNNRELTDSQKINDWHKHIDFTKSDENI
                     YLEQTNIREKYEELFGEAVEKYNAKQKRADRKIEDYLAKVRKDKKLEPQREFIVQIGTL
                     DDFRTTRDDGSSTGISEQQAEQNRVIANKILVEYFKEFKERNPNLSVYNAVIHNDEVSP
                     HLHLNIVPVAEGYKRGVQKQPSFNKALQQQGLRADKENGRVIWNNFRNQEVESIERLMA
                     DFGWERELVGTNKIKDVHEYKEIMSEISELRQTAVKERESVSDELRYISRQREENEREK
                     ALVASERVKIEEEKKNMLNVKKEMAVIFQKDIVPLESFKRLPDGSYHLSGNDFVDLYQR
                     ATRATNAKRNADNMSEQYLQMLEQNTELNEYVATLEEERHLSGRKQLADLQVENKKLKE
                     ENRSLRQRLERLKNAFQKSITRLSIRFGLAEKDMGLSEELEVLEQEKTLFYRQNVSQRK
                     LERSEDEIEW"
                     /name="plasmid recombination protein"
     gene            complement(1693..2055)
                     /locus_tag="IQN08_15835"
     CDS             complement(1693..2055)
                     /locus_tag="IQN08_15835"
                     /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="UOC45559.1"
                     /translation="MGMTLADIKAQEEKLKKEQAKLRQQKKRLIEKENAAMGKALRKRF
                     GFETFADFERWLSSISDDQQHEKSVDNEWLADEKSAPSERDYPDESDGLFGVIPNKKSQ
                     MSESKFTSIFNDVNLR"
                     /name="hypothetical protein"
     gene            complement(2059..2397)
                     /locus_tag="IQN08_15840"
     CDS             complement(2059..2397)
                     /locus_tag="IQN08_15840"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002321903.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="UOC45560.1"
                     /translation="MVAILEVRCDMDKIDLREETVDRIELMYERLADYLNLPDEDNYSE
                     MLERIMDVLNSVINADLAKSSVLTNEFVHKHLAQTTDESEKEFWLKLMSHVMQLNQISV
                     INSKEKEM"
                     /name="hypothetical protein"
     gene            complement(2376..2795)
                     /locus_tag="IQN08_15845"
     CDS             complement(2376..2795)
                     /locus_tag="IQN08_15845"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002351943.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="UOC45561.1"
                     /translation="MTDLSEKMTIKNLADELGVSKNTVRNQLVNSGFDLAQYKENGIIM
                     LDKELIGVVRSIYRSKSDQLTGQLPVNNTGSDFPLEKENEFLRDQLAEKDKHISELTEM
                     IRDQQKLTLLQQQKNDQLLLENQELKNRKWWQFWK"
                     /name="hypothetical protein"
     gene            complement(2788..3021)
                     /locus_tag="IQN08_15850"
     CDS             complement(2788..3021)
                     /locus_tag="IQN08_15850"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002298421.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="UOC45562.1"
                     /translation="MTEKQKYFGKKNWLVNLTGDYVVVVFLDSKKMSGKLLDVTQYELI
                     LKNNKIDSPIIIPKHAVKYIYAVAESSGEAND"
                     /name="hypothetical protein"
     gene            complement(3018..3992)
                     /locus_tag="IQN08_15855"
     CDS             complement(3018..3992)
                     /locus_tag="IQN08_15855"
                     /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="UOC45563.1"
                     /translation="MSKKGTIINEWEKLTAPSNRRLSVPFMDTPLKIQWSIDRITIVGN
                     LKENIYYHTTHDVLILDFEQLMRLNEGNGYLRSVSNNGWQLLDQHEENIAYIEILKWQE
                     GKGRIDFNPNKISQFLASSMKNFIHDLFIEPHFSRADIACDIIDVPDEFITQYRVVDPV
                     SFKPIYGRNGKLETAYWGSRSSERQIRMYNKKLEQEKKRKIVPKEIVSWWRLELQLRRG
                     KATDWHAMVQESLDSFASPHYLPADTSVADKMMITALTTEHDYWGQINRKTKYKYRNLL
                     KQESQNDELTNHLRETFAESADDLKKELDTWLLGLDVTEEEEK"
                     /name="replication protein"
     Typing          complement(3019..3914)
                     /name="rep_cluster_2146"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="99.443"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          complement(70..1472)
                     /name="MOBV"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="97.65"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 agttacgtat tgctaaggtt aaagaacgac ttccatactc gtgtgacagc acctctacat
       61 cgtaactacc actcgatctc atcttcagaa cgctctaatt tacgctgtga gacgttttga
      121 cgataaaata aggttttctc ctgctctaac acttctaatt cctcagaaag ccccatatcc
      181 ttttctgcaa gaccaaaacg gatagacaaa cgagtgatcg atttttgaaa tgcgtttttt
      241 aatcgctcta aacgctggcg taaagagcga ttttcttctt tcagcttttt attttccact
      301 tgtaaatctg ctaattgttt tctaccagac aaatgacgct cttcttccaa tgtagctaca
      361 tactcattta attctgtatt ttgctcaagc atctgtaaat attgctcact catgttatca
      421 gcatttctct tggcatttgt tgctctcgta gctcgttgat acaaatcaac aaaatcattc
      481 ccagataaat gatacgaacc atcaggaagc ctcttgaaac tttctaaagg aacaatatct
      541 ttttggaaaa tgaccgccat ctcttttttt acattcagca tatttttctt ctcttcttca
      601 atcttcactc tctcagaagc caccagagcc ttttctcgct cattttcttc tctttgccta
      661 gaaatatacc tcaactcatc agaaacgctc tcacgctctt ttacggccgt ttgacgcaat
      721 tctgaaatct cgctcatgat ttctttatat tcgtgaacat ctttgatttt gttagtaccg
      781 actaactcac gctcccaacc aaaatctgcc atcaaacgtt caattgactc aacttcctga
      841 ttcctaaaat tattccaaat cactcgacca ttctctttat ctgctcgtaa accctgctgt
      901 tgcaaggctt tgttaaaact tggttgcttt tgaacacccc gtttataccc ttcagcaaca
      961 ggaacaatat tcaaatgcag gtgcggactt acttcgtcat tatgaataac agcattgtag
     1021 acggataaat taggattccg ttctttaaat tctttgaaat attcaactaa aattttgttg
     1081 gcaatcactc gattttgttc tgcttgttgt tccgatatgc cagtagaaga accatcatca
     1141 cgagtagtac gaaaatcatc aagagtacca atttgcacga taaattctcg ctgtggttcc
     1201 aattttttat ccttgcgaac ctttgctaaa tagtcctcga tttttctatc ggctcttttc
     1261 tgctttgcat tatatttttc tacggcttca ccgaataatt cttcatattt ttcacgaata
     1321 tttgtttgtt ctaaatagat attttcatcc gattttgtga aatcaatatg cttatgccag
     1381 tcattgattt tttggctatc agttaactca cgattattat gagaaatgct tgtattcttt
     1441 gttccctttt tgaacgaaat actgaacccc aagttaaaac cctccttcgg ctgtcgctaa
     1501 taaaaagagt gtaaaccttt ctgttactct ttgtcaaaga gtaacatttt cctaattgtg
     1561 acatggctgt cacaattcca aatgctctcc gagggtattc gctgtcacaa gtgacaacga
     1621 aaaaaggagc cgaaagcgtg tcacgctctc aactcctttt acgctttatt ttgcttcacg
     1681 caaaataatc gcttatcgta aattcacgtc attaaatatt gacgtaaatt tactctcact
     1741 catctgactt ttcttattcg gtatcactcc gaataagccg tcagattcat cgggataatc
     1801 tcgttcgctt ggcgctgatt tttcatcagc aagccactca ttatccactg atttttcgtg
     1861 ttgctgatcg tcagaaatcg acgatagcca ccgctcaaaa tcagcaaaag tttcaaaccc
     1921 aaaacgcttc cgaagagcct tgcccattgc agcattttct ttctcaatca agcgtttttt
     1981 ctgttggcga agtttcgctt gttctttttt taatttttct tcttgcgctt taatatctgc
     2041 taaagtcatt cccataaact acatctcctt ttctttggaa ttaataacgg aaatttggtt
     2101 taactgcata acatgactca ttaatttcaa ccaaaattct ttttctgatt catcagttgt
     2161 ttgcgctaaa tgcttatgaa caaattcatt agtcaaaact gaagattttg ctaaatcagc
     2221 attgataacc gagttgagaa catccataat tcgttcaagc atttcactat aattatcttc
     2281 atccggcaaa ttcaaataat cagctaaccg ttcatacatc aattcaattc tatcgactgt
     2341 ttcttctctc aaatcaattt tatccatgtc acacctcact tccagaattg ccaccatttt
     2401 cgatttttta attcttgatt ttctagtaac aactgatcgt ttttttgttg ctgaagcagg
     2461 gtcaattttt gttgatcacg aatcatttct gttaattcag aaatatgttt gtccttctca
     2521 gctaattgat cacgcaaaaa ctcattctct ttttctaaag gaaaatcact gcctgtgtta
     2581 ttgaccggta attgaccagt caattgatca ctttttgacc gataaattga ccgaacaaca
     2641 ccaatcaact ctttatctag catgataatg ccattttctt tatactgagc aaggtcaaac
     2701 cctgaattga ccagttgatt gcgcactgta tttttcgata cacccaattc gtcagcaaga
     2761 ttttttatgg tcatcttttc tgacaaatca gtcattagct tctccactac tttcagctac
     2821 cgcataaata tatttaacgg cgtgcttagg gataataatc ggagagtcaa ttttattatt
     2881 tttcaaaatc aattcatatt gcgttacatc aagtaactta ccggacattt ttttgctatc
     2941 caaaaaaaca accacaacgt aatcacctgt taaatttacc aaccaatttt tcttaccaaa
     3001 atacttttgt ttttctgtca tttttcttcc tcctctgtta cgtctagccc tagaagccat
     3061 gtgtctaatt ctttttttaa atcgtctgcc gattctgcaa aggtttctcg taaatgattc
     3121 gtcaattcat cattttgact ttcttgcttc agcaaatttc gatatttata ttttgtcttt
     3181 cgattaattt gcccccaata atcatgttct gttgttaaag cagtaatcat cattttgtca
     3241 gctacacttg tatcagcagg caagtaatga ggactagcaa aactatccaa gctttcttga
     3301 accattgcat gccaatcagt cgctttccct cgtcttaatt gtaattctaa ccgccaccaa
     3361 ctcacgattt cttttggcac aatttttctt ttcttctctt gttccagttt tttattatac
     3421 atccgaattt gacgttcaga agagcgagat ccccaatatg ccgtctctaa ttttccattc
     3481 cgtccataaa taggcttaaa agaaactgga tcaactaccc gatattgtgt aataaactca
     3541 tcaggtacat cgataatgtc gcaagcaata tctgcacgtg aaaagtgagg ttcgataaac
     3601 aaatcatgaa taaagttttt catggaacta gctaagaatt gactaatctt attcggattg
     3661 aagtctatac gccctttccc ctcttgccat tttaaaattt caatataagc aatattctct
     3721 tcatgttggt ctaacaactg ccaaccatta ttactaacag atcttaaata accgttacct
     3781 tcatttaggc gcataagctg ttcaaaatct aaaatcaaca catcatgtgt agtgtgataa
     3841 tagatattct ctttaagatt tccaacaatg gtaattcggt cgattgacca ctgaattttt
     3901 aggggggtgt ccataaaagg gacacttaac cgcctgttag agggggctgt taatttttcc
     3961 cactcattta tgatcgtgcc ttttttactc aaattttgtt cctcctcaaa gaaaaagaga
     4021 cttctggaaa gaattttcaa aagttcacgt aactcttaaa aattcattac caaaaaatct
     4081 ctagtcttga agaaatctaa aaatattcgt ataatgatta agaagttacg gagctagtgc
     4141 gattagtttc cgtaaaggtc gagaacgtgt ccagcgttgc tcgactttat ttttttgctc
     4201 ttttttcagt ttatttattt gataactcaa taatagcact tctctttagc tatgcaaata
     4261 tccaaaaaat aaaaccgcac cctttgaaaa gggcgccccc aaacttcgct aacgctaggt
     4321 tggccaaaaa atggacttgc cattttttag caaatgtcag cttcagggat tagtggttta
     4381 gccgtcaact ccttatcctc ggcacaaacc gcctccggta ccgttgactg cacatcgtaa
     4441 ctac
//
