LOCUS       CP063597                5509 bp    DNA     circular BCT 04-APR-2022
DEFINITION  Enterococcus faecium strain BMT-1-3-1 plasmid pIN-3-1_04, complete
            sequence.
ACCESSION   CP063597
VERSION     CP063597.1
DBLINK      BioProject: PRJNA669626
            BioSample: SAMN16483158
KEYWORDS    .
SOURCE      Enterococcus faecium
  ORGANISM  Enterococcus faecium
            Bacteria; Bacillota; Bacilli; Lactobacillales; Enterococcaceae;
            Enterococcus.
REFERENCE   1  (bases 1 to 5509)
  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 5509)
  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                   :: 86.6x
            Sequencing Technology             :: Oxford Nanopore
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI
            Annotation Date                   :: 10/27/2020 17:56:10
            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)                     :: 3,085
            CDSs (total)                      :: 2,993
            Genes (coding)                    :: 2,718
            CDSs (with protein)               :: 2,718
            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)              :: 275
            CDSs (without protein)            :: 275
            Pseudo Genes (ambiguous residues) :: 0 of 275
            Pseudo Genes (frameshifted)       :: 196 of 275
            Pseudo Genes (incomplete)         :: 65 of 275
            Pseudo Genes (internal stop)      :: 33 of 275
            Pseudo Genes (multiple problems)  :: 18 of 275
            ##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..5509
                     /organism="Enterococcus faecium"
                     /mol_type="genomic DNA"
                     /strain="BMT-1-3-1"
                     /isolation_source="rectal swab"
                     /host="Homo sapiens"
                     /db_xref="taxon:1352"
                     /plasmid="pIN-3-1_04"
                     /geo_loc_name="Germany: Hamburg"
                     /lat_lon="53.33 N 10.1 E"
                     /collection_date="2014-07-22"
                     /collected_by="Institute of Medical Microbiology, Virology
                     and Hygiene, University Medical Center Hamburg-Eppendorf"
     gene            join(4906..5509,1..320)
                     /locus_tag="IQN10_15410"
     CDS             join(4906..5509,1..320)
                     /locus_tag="IQN10_15410"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002296860.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="replication initiation protein"
                     /protein_id="UOE11778.1"
                     /translation="MANEIVKYENRLNHIPLRKFNSREMNLFFSIASRVREKGVDEIIF
                     SFHDLKKLSGYTERGEQFIKDLSSTYDKLLSINAWNDDGNTLTKFVAFTKYSIIRDKQL
                     VIISVNPEFKGLFNQLKNWTRFNLEQFTNLDSTYSKTMFRLLKQYRTQGWTEFSKEKFF
                     DLLDIPKSYWNSPSNIDKFILRPIKEELTPLFKGLTIRKKYGKGRGKPVIGYRFTWKAE
                     INHADDFSKGKQEDLRIKLFNIDHNGELTREEKWRAKDRILNLPLGTHEADFKQQQQTE
                     EKQAEKRELSNKLKQDLLGNLQNLFD"
                     /name="replication initiation protein"
     gene            336..875
                     /locus_tag="IQN10_15415"
     CDS             336..875
                     /locus_tag="IQN10_15415"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_016616811.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="DUF536 domain-containing protein"
                     /protein_id="UOE11779.1"
                     /translation="MADKTIKELAEELGVSKTAINKKVSDKNRKLWFAKNGNKFVINET
                     GQKAIKSMFLVDNANLNRKLVGEKSKTKNHKNTNQVSELKLLSFLEKQLNRKDIQLQEK
                     DNQIKQMQKLLDQQQQLTLQANQQIENLQEQLHLTYTEETPTTESTAFSEKKADNTQPL
                     IEKKWWQIWKSNRTNL"
                     /name="DUF536 domain-containing protein"
     gene            1556..1729
                     /locus_tag="IQN10_15420"
     CDS             1556..1729
                     /locus_tag="IQN10_15420"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002341717.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="UOE11780.1"
                     /translation="MLKKTVLVLGSISLGILGFSPMLLSVIGKNNSNRELKLNSNYYNS
                     PNEELFVKETDK"
                     /name="hypothetical protein"
     gene            2280..3186
                     /locus_tag="IQN10_15425"
                     /pseudo=""
     CDS             2280..3186
                     /locus_tag="IQN10_15425"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_076611882.1"
                     /note="frameshifted; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="IS982-like element ISEfm1 family transposase"
                     /name="IS982-like element ISEfm1 family transposase"
     Typing          2..320
                     /name="rep_cluster_1291"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="3.89e-166"
ORIGIN
        1 aaaaatatgg taaaggtcga ggtaaacctg ttatcggtta tcgttttact tggaaagctg
       61 aaattaacca tgctgacgat ttttccaaag ggaaacaaga agatttacgt ataaaattat
      121 ttaatattga tcacaatgga gaattaacac gagaagaaaa atggcgcgct aaagatcgaa
      181 tactaaatct tcccttaggc actcatgaag ctgattttaa acaacaacaa caaactgaag
      241 aaaaacaggc agaaaaacga gaactttcaa acaaactcaa acaagattta ctaggaaatt
      301 tacaaaactt attcgattaa gcttaaggag tatttatggc agataaaaca atcaaagaac
      361 ttgcggaaga attaggagtt agtaaaacag caattaacaa aaaagtttct gacaaaaatc
      421 gaaaactttg gtttgcaaaa aacggaaaca agtttgtgat taacgaaacc ggtcaaaaag
      481 ctataaaatc aatgttttta gtcgataacg caaacttaaa tcgaaaacta gttggcgaaa
      541 aatcaaaaac caaaaaccat aaaaacacca accaagtttc cgaattaaaa ctcctttctt
      601 tcctagaaaa acagttaaat cgaaaagata tacagctaca agaaaaagat aatcaaataa
      661 aacaaatgca aaaattactc gaccagcaac aacaactcac tctacaagcg aaccaacaaa
      721 ttgagaacct acaagaacag ctccatttaa cttatacaga agaaactcca acaaccgaat
      781 caactgcctt ttctgaaaaa aaagcagaca atacacaacc acttattgaa aaaaagtggt
      841 ggcaaatttg gaaatctaat agaaccaatc tctaaaattt tctagaagtt agttcggata
      901 gtagaggaaa aagttgtact acctgatggg gagatcactc aaatttttat gagaaagaaa
      961 aaatagttta caactgtaaa caatcaatgt ttatagttgt aaactatcaa actatatggt
     1021 gacttattgc ttaaaatagg ttgaaatctc actcaatttt tggtggaaaa acaaaataaa
     1081 ttctaatcga ttttgttgaa aaagtcataa aaaaacaaat gtgattttaa caaaatttca
     1141 aaaaaatcgt ttgaaatttc gtttattttt tttgagaatt ttgatcatcg tagggtcatt
     1201 gtagaatcat tatgagatca tcgtgggatc atcgaataaa gtatgggaaa ggcttgcggt
     1261 gcttggtatt aagggcattc tccgcctccc aggttcttga ccattttctc ttataagtgg
     1321 gatttttacc acgttgagag aaaatggtca agaacctggg aggcggagaa aacataccaa
     1381 gcaccacaag caaaaaaagt tagagtaact tccaaaaaag aaaaattttt tagaacaact
     1441 tttgaaaatt taattttgat ttatatccgt tcaatttaaa catttgataa actgaaggct
     1501 agtatttaaa atgtgtatac aagtggtagc gttaaaaaaa gtggaggtat aacctatgtt
     1561 aaaaaaaact gtgttggtac tgggttctat ttctctagga atattaggtt ttagccccat
     1621 gctattatcc gtaattggaa aaaacaattc caacagagaa cttaaattga attcaaatta
     1681 ttacaacagt cctaacgaag aattgtttgt aaaagaaacg gataaataat aaaaaagact
     1741 gctcttccga gcagccagtt aaaaaataat gagtgtttat tcttgaaaaa gcaacgcgct
     1801 tataaagcgc taccaaaaat ttatcatatt ttatgaaaaa taacaatcca gtaaaaaatg
     1861 actggtaaaa attcacaaag aaacggaaag aagcaactgc agaaaatcaa gccttaaaaa
     1921 gagcttttta cctagaccaa ttaaaaatca caaagtgagc ccctgtatcg gttgatacaa
     1981 gggctacttg gcatactgta cattatgtct actaaccttt aaaataacac gttttataaa
     2041 ataaaccctc ttgacaatat ttaattttct gattattcta aatatataca gaaagcgctt
     2101 tcctaggatt ttatatctaa ggaggaagta acaatgaaaa ataaaattat taaaattatt
     2161 acttgtctac ccgtggtgct agttaatttt ttcctagagg aaaatgtcta aacatgttgg
     2221 taaatcaaca aaaaaacgca tatagtagtc tcaaaactcc caagaaatga ggactacata
     2281 tgcgttcatc aaaatatact gaacattata cagatacttt tataacattc aaggaaatta
     2341 tgagaactgt ttctaacata taccacaatt gtgtaccaga taagattaaa aaccgaagaa
     2401 atactgatca actgaagcaa cgcgatacag tgattattgc ttgtgttata tggggcataa
     2461 ttaatggcta tactagccaa agagccacgt atagagcggt ttgttccgtc ttatttccta
     2521 atggtgactt tcctagtagg agtcgattca ctcgcttaag ttcaaactta gcttacacta
     2581 tcaagattat tcgatacttt ttcatcaaga agctcaccaa aggtgaacta gtcggaatta
     2641 tagatagttt tcctagtcca ttatgtaaac cagttagaaa tagacaagca aaactattga
     2701 atcaaatagc caaagttggc tataactcaa caaaaaatct tatttttatg gtcttaaaat
     2761 tcatatgatc gttactaaga ctggctttcc gattacttac tcaatcacga atccaggtgt
     2821 ccatgacgtg aaagtgttag agactttatc ggaagaagcg aatcttccca atatcctagg
     2881 ggacaaagga tatattagcc ataaaatcca tgaaaagctt gcccttaagg gcattactat
     2941 atccgttccg ccacgtaaaa acatggataa atcagaaaaa ctagaccaca gcttacttgg
     3001 aaaacaaaga aaaacagttg agactgtttt tcttccttag aaaaattagg ttgtcaaaat
     3061 ttcaactcac gttctgttaa agggctagag agtagatttg aaagcatatt actggcttac
     3121 agtgttctat taagtcgagc acaacgacgt tttgaaggaa ctttgagata ttctttagga
     3181 tattaaaatt aactagcacc acgggtactt gtctattttt gttcggtatg attgttggag
     3241 caagtactcc gttaaatctg tttcctttta gtgctagagg tataaaagtg gaagctgcaa
     3301 gttcacgata taatcataat catcgtggat ttacttgcta taaaatgaac tattatgtta
     3361 ctaataaaat gtgtagagat ttgaaaaaaa aaattataat aagctaaaga ctcctgctca
     3421 aattgcatct tttattccta ttggtggagt tggaacatgg gttattacaa atgcttttag
     3481 tagtgctgtt gatgcaatga atgtctttgt aagagctgca aatcaaggaa aaggtgtaca
     3541 attaacatat aatgctcact ttagcaatac aacatcatat caatacaatg attacgctcg
     3601 ttatgtaata aaataatcag aaagtgaaac tatctcatga ataaaaagat tttagctgta
     3661 attatttcaa taatagtttt aatcactatg ttcttcatat ttaggctaat tttcaatata
     3721 agcttacaaa aaagtattct ttatctaatt cctatagcat ttatcttagc aatttttaga
     3781 agtatttacg gaaataaaaa ctctaaatag ctaaaaataa atcatactaa attttacaaa
     3841 aagtggctag cattttctag ccactttttg tattgtggag cgtgggtttt gagggggatt
     3901 caagggggag cttgcgcccc tttgacaagc ggttatttgc accaaatacg gaggtatttg
     3961 gctagcaaat atagagcttg ccaaaccctt ttagtgagtt ttgtagaaag tacctttaaa
     4021 ggtactttca cattacgaac gatacgtccg taggacgtac tgaaagggtg ggacttatga
     4081 gcaaattaat gcaaaatttg gctagcaaaa aagctaaaaa atatatgcta ataatcgagc
     4141 gaaataaaca ctttttcaag tgagcgaatc cgccatgaca aagctgaagc agtttatttc
     4201 agctttgtca tggcgtgtgc cgactttttt aaaagtctag gcacacgagc aaatatcttt
     4261 atcaagctct aatttgcgtt ttaagacgtt tgaaacgcct aagtatataa atatataaga
     4321 ataggtttaa gagtgcttaa atcgaatttt agagggcatt tagacaattt tagggttgtt
     4381 agggcttgcc ctgaccgcct gtaaggcgtt ttaagaacaa gataagggat ttatactagg
     4441 actgtcttaa aatgtcttaa acgaacgctc agagcttctc aaagggttcc ttatgaacgg
     4501 cttttagcaa aggagccgga ggcgactgcg cagtataatg tgagagcaga gcgatcacac
     4561 ctttttagcg aaccgtaggg agcaaggttt ggaattggca gttttgataa attcgcgaac
     4621 ctgtttagag aaaaaaggag tgatttttta ggcgggaaaa ttagcctccc ctctttttat
     4681 atctcttttt atatctcttt ttatatctct tttatgtcgg ctgtgtcctt actctcccaa
     4741 gcaattcaga gttttttcaa gtaggttttc tacgcttttc aagtaggttt tctacgcttt
     4801 tcaagtaggt tttctacgct tttcaagtag gttttccgac attattgagt atttttataa
     4861 agtatgttac ttttatttca tactttataa aagtaggaga agcttatggc aaatgaaatt
     4921 gtaaaatatg aaaatagatt aaatcatatt cctctgagaa aatttaatag tcgtgaaatg
     4981 aacttatttt tttcaattgc ttcacgtgta cgtgaaaaag gtgtagatga gattattttt
     5041 tcatttcacg atttgaaaaa actaagcggt tatacagaac gtggggaaca atttataaaa
     5101 gatcttagta gcacgtatga caaattatta agtattaatg cttggaatga tgatggaaat
     5161 actttaacta aatttgttgc tttcacaaaa tatagcatta tacgagataa acaacttgtt
     5221 ataatttcag ttaatccaga atttaaagga ctttttaatc aattaaagaa ctggacaaga
     5281 tttaatctag agcaatttac taatttggat agcacatatt caaaaactat gtttcgatta
     5341 ttaaaacaat atcgaactca aggctggact gaattttcca aagaaaaatt ttttgattta
     5401 ctagatattc ctaaaagtta ttggaatagt ccgtcaaata ttgacaaatt tatcttaagg
     5461 ccaattaaag aagaactcac tcccttattt aaaggattaa ctattcgta
//
