LOCUS       CP063603                4374 bp    DNA     circular BCT 04-APR-2022
DEFINITION  Enterococcus faecium strain BMT-3-2-1 plasmid pHJB-2-1_05, complete
            sequence.
ACCESSION   CP063603
VERSION     CP063603.1
DBLINK      BioProject: PRJNA669626
            BioSample: SAMN16483157
KEYWORDS    .
SOURCE      Enterococcus faecium
  ORGANISM  Enterococcus faecium
            Bacteria; Bacillota; Bacilli; Lactobacillales; Enterococcaceae;
            Enterococcus.
REFERENCE   1  (bases 1 to 4374)
  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 4374)
  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                   :: 479.5x
            Sequencing Technology             :: Oxford Nanopore
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI
            Annotation Date                   :: 10/27/2020 18:05:54
            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)                     :: 3,214
            CDSs (total)                      :: 3,122
            Genes (coding)                    :: 3,008
            CDSs (with protein)               :: 3,008
            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)              :: 114
            CDSs (without protein)            :: 114
            Pseudo Genes (ambiguous residues) :: 0 of 114
            Pseudo Genes (frameshifted)       :: 39 of 114
            Pseudo Genes (incomplete)         :: 69 of 114
            Pseudo Genes (internal stop)      :: 15 of 114
            Pseudo Genes (multiple problems)  :: 8 of 114
            ##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..4374
                     /organism="Enterococcus faecium"
                     /mol_type="genomic DNA"
                     /strain="BMT-3-2-1"
                     /isolation_source="rectal swab"
                     /host="Homo sapiens"
                     /db_xref="taxon:1352"
                     /plasmid="pHJB-2-1_05"
                     /geo_loc_name="Germany: Hamburg"
                     /lat_lon="53.33 N 10.1 E"
                     /collection_date="2015-02-03"
                     /collected_by="Institute of Medical Microbiology, Virology
                     and Hygiene, University Medical Center Hamburg-Eppendorf"
     gene            complement(join(3936..4374,1..535))
                     /locus_tag="IQN09_16045"
                     /pseudo=""
     CDS             complement(join(3936..4374,1..535))
                     /locus_tag="IQN09_16045"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002303407.1"
                     /note="frameshifted; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="replication protein"
                     /name="replication protein"
     gene            complement(984..2390)
                     /locus_tag="IQN09_16050"
     CDS             complement(984..2390)
                     /locus_tag="IQN09_16050"
                     /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="UOC42595.1"
                     /translation="MGFSISFKKGTKNTSISHNNRELTDSQKINDWHKHIDFTKSDENI
                     YLEQTNIREKYEELFGEAVEKYNAKQKRADRKIEDYLAKVRKDKKLEPQREFIVQIGTL
                     DDFRTTRDDGSSTGISEQQAEQNRVIANKILVEYFKEFKERNPNLSVYNAVIHNDEVSP
                     HLHLNIVPVAEGYKRGVQKQPSFNKALQQQGLRADKENGRVIWNNFRNQEVESIERLMA
                     DFGWERELVGTNKIKDVHEYKEIMSEISELRQTAVKERESVSDELRYISRQREENEREK
                     ALVASERVKIEEEKKNMLNVKKEMAVIFQKDIVPLESFKRLPDGSYHLSGNDFVDLYQR
                     ATRATNAKRNADNMSEQYLQMLEQNTELNEYVATLEEERHLSGRKQLADLQVENKKLKE
                     ENRSLRQRLERLKNAFQKSITRLSIRFGLAEKDMGLSEELEVLEQEKTLFYRQNVSQRK
                     LERSEDEIEW"
                     /name="plasmid recombination protein"
     gene            complement(2611..2973)
                     /locus_tag="IQN09_16055"
     CDS             complement(2611..2973)
                     /locus_tag="IQN09_16055"
                     /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="UOC42591.1"
                     /translation="MGMTLADIKAQEEKLKKEQAKLRQQKKRLIEKENAAMGKALRKRF
                     GFETFADFERWLSSISDDQQHEKSVDNEWLADEKSAPSERDYPDESDGLFGVIPNKKSQ
                     MSESKFTSIFNDVNLR"
                     /name="hypothetical protein"
     gene            complement(2977..3315)
                     /locus_tag="IQN09_16060"
     CDS             complement(2977..3315)
                     /locus_tag="IQN09_16060"
                     /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="UOC42592.1"
                     /translation="MVAILEVRCDMDKIDLREETVDRIELMYERLADYLNLPDEDNYSE
                     MLERIMDVLNSVINADLAKSSVLTNEFVHKHLAQTTDESEKEFWLKLMSHVMQLNQISV
                     INSKEKEM"
                     /name="hypothetical protein"
     gene            complement(3294..3713)
                     /locus_tag="IQN09_16065"
     CDS             complement(3294..3713)
                     /locus_tag="IQN09_16065"
                     /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="UOC42593.1"
                     /translation="MTDLSEKMTIKNLADELGVSKNTVRNQLVNSGFDLAQYKENGIIM
                     LDKELIGVVRSIYRSKSDQLTGQLPVNNTGSDFPLEKENEFLRDQLAEKDKHISELTEM
                     IRDQQKLTLLQQQKNDQLLLENQELKNRKWWQFWK"
                     /name="hypothetical protein"
     gene            complement(3706..3939)
                     /locus_tag="IQN09_16070"
     CDS             complement(3706..3939)
                     /locus_tag="IQN09_16070"
                     /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="UOC42594.1"
                     /translation="MTEKQKYFGKKNWLVNLTGDYVVVVFLDSKKMSGKLLDVTQYELI
                     LKNNKIDSPIIIPKHAVKYIYAVAESSGEAND"
                     /name="hypothetical protein"
     Typing          complement(3937..4374)
                     /name="rep_cluster_2146"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="99.089"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          complement(988..2390)
                     /name="MOBV"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="97.65"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 tatgccgtct ctaattttcc attccgtcca taaataggct taaaagaaac tggatcaact
       61 acccgatatt gtgtaataaa ctcatcaggt acatcgataa tgtcgcaagc aatatctgca
      121 cgtgaaaagt gaggttcgat aaacaaatca tgaataaagt ttttcatgga actagctaag
      181 aattgactaa tcttattcgg attgaagtct atacgccctt tcccctcttg ccattttaaa
      241 atttcaatat aagcaatatt ctcttcatgt tggtctaaca actgccaacc attattacta
      301 acagatctta aataaccgtt accttcattt aggcgcataa gctgttcaaa atctaaaatc
      361 aacacatcat gtgtagtgtg ataatagata ttctctttaa gatttccaac aatggtaatt
      421 cggtcgattg accactgaat ttttaggggg tgtccataaa agggacactt aaccgcctgt
      481 tagagggggc tgttaatttt tcccactcat ttatgatcgt gcctttttta ctcaaatttt
      541 gttcctcctc aaagaaaaag agacttctgg aaagaatttt caaaagttca cgtaactctt
      601 aaaaattcat taccaaaaaa tctctagtct tgaagaaatc taaaaatatt cgtataatga
      661 ttaagaagtt acggagctag tgcgattagt ttccgtaaag gtcgagaacg tgtccagcgt
      721 tgctcgactt tatttttttg ctcttttttc agtttattta tttgataact caataatagc
      781 acttctcttt agctatgcaa atatccaaaa aataaaaccg caccctttga aaagggcgcc
      841 cccaaacttc gctaacgcta ggttggccaa aaaatggact tgccattttt tagcaaatgt
      901 cagcttcagg gattagtggt ttagccgtca actccttatc ctcggcacaa accgcctccg
      961 gtaccgttga ctgcacatcg taactaccac tcgatctcat cttcagaacg ctctaattta
     1021 cgctgtgaga cgttttgacg ataaaataag gttttctcct gctctaacac ttctaattcc
     1081 tcagaaagcc ccatatcctt ttctgcaaga ccaaaacgga tagacaaacg agtgatcgat
     1141 ttttgaaatg cgttttttaa tcgctctaaa cgctggcgta aagagcgatt ttcttctttc
     1201 agctttttat tttccacttg taaatctgct aattgttttc taccagacaa atgacgctct
     1261 tcttccaatg tagctacata ctcatttaat tctgtatttt gctcaagcat ctgtaaatat
     1321 tgctcactca tgttatcagc atttctcttg gcatttgttg ctctcgtagc tcgttgatac
     1381 aaatcaacaa aatcattccc agataaatga tacgaaccat caggaagcct cttgaaactt
     1441 tctaaaggaa caatatcttt ttggaaaatg accgccatct ctttttttac attcagcata
     1501 tttttcttct cttcttcaat cttcactctc tcagaagcca ccagagcctt ttctcgctca
     1561 ttttcttctc tttgcctaga aatatacctc aactcatcag aaacgctctc acgctctttt
     1621 acggccgttt gacgcaattc tgaaatctcg ctcatgattt ctttatattc gtgaacatct
     1681 ttgattttgt tagtaccgac taactcacgc tcccaaccaa aatctgccat caaacgttca
     1741 attgactcaa cttcctgatt cctaaaatta ttccaaatca ctcgaccatt ctctttatct
     1801 gctcgtaaac cctgctgttg caaggctttg ttaaaacttg gttgcttttg aacaccccgt
     1861 ttataccctt cagcaacagg aacaatattc aaatgcaggt gcggacttac ttcgtcatta
     1921 tgaataacag cattgtagac ggataaatta ggattccgtt ctttaaattc tttgaaatat
     1981 tcaactaaaa ttttgttggc aatcactcga ttttgttctg cttgttgttc cgatatgcca
     2041 gtagaagaac catcatcacg agtagtacga aaatcatcaa gagtaccaat ttgcacgata
     2101 aattctcgct gtggttccaa ttttttatcc ttgcgaacct ttgctaaata gtcctcgatt
     2161 tttctatcgg ctcttttctg ctttgcatta tatttttcta cggcttcacc gaataattct
     2221 tcatattttt cacgaatatt tgtttgttct aaatagatat tttcatccga ttttgtgaaa
     2281 tcaatatgct tatgccagtc attgattttt tggctatcag ttaactcacg attattatga
     2341 gaaatgcttg tattctttgt tccctttttg aacgaaatac tgaaccccaa gttaaaaccc
     2401 tccttcggct gtcgctaata aaaagagtgt aaacctttct gttactcttt gtcaaagagt
     2461 aacattttcc taattgtgac atggctgtca caattccaaa tgctctccga gggtattcgc
     2521 tgtcacaagt gacaacgaaa aaaggagccg aaagcgtgtc acgctctcaa ctccttttac
     2581 gctttatttt gcttcacgca aaataatcgc ttatcgtaaa ttcacgtcat taaatattga
     2641 cgtaaattta ctctcactca tctgactttt cttattcggt atcactccga ataagccgtc
     2701 agattcatcg ggataatctc gttcgcttgg cgctgatttt tcatcagcaa gccactcatt
     2761 atccactgat ttttcgtgtt gctgatcgtc agaaatcgac gatagccacc gctcaaaatc
     2821 agcaaaagtt tcaaacccaa aacgcttccg aagagccttg cccattgcag cattttcttt
     2881 ctcaatcaag cgttttttct gttggcgaag tttcgcttgt tcttttttta atttttcttc
     2941 ttgcgcttta atatctgcta aagtcattcc cataaactac atctcctttt ctttggaatt
     3001 aataacggaa atttggttta actgcataac atgactcatt aatttcaacc aaaattcttt
     3061 ttctgattca tcagttgttt gcgctaaatg cttatgaaca aattcattag tcaaaactga
     3121 agattttgct aaatcagcat tgataaccga gttgagaaca tccataattc gttcaagcat
     3181 ttcactataa ttatcttcat ccggcaaatt caaataatca gctaaccgtt catacatcaa
     3241 ttcaattcta tcgactgttt cttctctcaa atcaatttta tccatgtcac acctcacttc
     3301 cagaattgcc accattttcg attttttaat tcttgatttt ctagtaacaa ctgatcgttt
     3361 ttttgttgct gaagcagggt caatttttgt tgatcacgaa tcatttctgt taattcagaa
     3421 atatgtttgt ccttctcagc taattgatca cgcaaaaact cattctcttt ttctaaagga
     3481 aaatcactgc ctgtgttatt gaccggtaat tgaccagtca attgatcact ttttgaccga
     3541 taaattgacc gaacaacacc aatcaactct ttatctagca tgataatgcc attttcttta
     3601 tactgagcaa ggtcaaaccc tgaattgacc agttgattgc gcactgtatt tttcgataca
     3661 cccaattcgt cagcaagatt ttttatggtc atcttttctg acaaatcagt cattagcttc
     3721 tccactactt tcagctaccg cataaatata tttaacggcg tgcttaggga taataatcgg
     3781 agagtcaatt ttattatttt tcaaaatcaa ttcatattgc gttacatcaa gtaacttacc
     3841 ggacattttt ttgctatcca aaaaaacaac cacaacgtaa tcacctgtta aatttaccaa
     3901 ccaatttttc ttaccaaaat acttttgttt ttctgtcatt tttcttcctc ctctgttacg
     3961 tctagcccta gaagccatgt gtctaattct ttttttaaat cgtctgccga ttctgcaaag
     4021 gtttctcgta aatgattcgt caattcatca ttttgacttt cttgcttcag caaatttcga
     4081 tatttatatt ttgtctttcg attaatttgc ccccaataat catgttctgt tgttaaagca
     4141 gtaatcatca ttttgtcagc tacacttgta tcagcaggca agtaatgagg actagcaaaa
     4201 ctatccaagc tttcttgaac cattgcatgc caatcagtcg ctttccctcg tcttaattgt
     4261 aattctaacc gccaccaact cacgatttct tttggcacaa tttttctttt cttctcttgt
     4321 tccagttttt tattatacat ccgaatttga cgttcagaag agcgagatcc ccaa
//
