LOCUS       CP063566                5779 bp    DNA     circular BCT 04-APR-2022
DEFINITION  Enterococcus faecium strain ICU-3-1 plasmid pZA3-1_04, complete
            sequence.
ACCESSION   CP063566
VERSION     CP063566.1
DBLINK      BioProject: PRJNA669626
            BioSample: SAMN16483163
KEYWORDS    .
SOURCE      Enterococcus faecium
  ORGANISM  Enterococcus faecium
            Bacteria; Bacillota; Bacilli; Lactobacillales; Enterococcaceae;
            Enterococcus.
REFERENCE   1  (bases 1 to 5779)
  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 5779)
  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                   :: 648.2x
            Sequencing Technology             :: Oxford Nanopore
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI
            Annotation Date                   :: 10/27/2020 16:23:34
            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)                     :: 3,201
            CDSs (total)                      :: 3,108
            Genes (coding)                    :: 2,984
            CDSs (with protein)               :: 2,984
            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)              :: 124
            CDSs (without protein)            :: 124
            Pseudo Genes (ambiguous residues) :: 0 of 124
            Pseudo Genes (frameshifted)       :: 49 of 124
            Pseudo Genes (incomplete)         :: 64 of 124
            Pseudo Genes (internal stop)      :: 20 of 124
            Pseudo Genes (multiple problems)  :: 8 of 124
            ##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..5779
                     /organism="Enterococcus faecium"
                     /mol_type="genomic DNA"
                     /strain="ICU-3-1"
                     /isolation_source="rectal swab"
                     /host="Homo sapiens"
                     /db_xref="taxon:1352"
                     /plasmid="pZA3-1_04"
                     /geo_loc_name="Germany: Hamburg"
                     /lat_lon="53.33 N 10.1 E"
                     /collection_date="2019-03-01"
                     /collected_by="Institute of Medical Microbiology, Virology
                     and Hygiene, University Medical Center Hamburg-Eppendorf"
     gene            1..969
                     /locus_tag="IQN15_15930"
     CDS             1..969
                     /locus_tag="IQN15_15930"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002338009.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="replication initiation protein"
                     /protein_id="UOE03133.1"
                     /translation="MANEIVKYHHELNTIPLRKFTSVEMNLFFSIISRMRDVGDKKVQF
                     TFEQLKDLSNYKATANVRFIDDLETTYDKLMDLRFGRRSADGLQRERFVLFNQFKIDGK
                     ADIPFAEIQVHEKALPLLNNLEEWVRYSLQQFNELESSYSKTMFRLLKQYRTKGIANFS
                     KEDFHELLDIPKSYRESDINKKIIKPIRQELTAIFKGLTIQKRYGKGRGKPVIGYQFTF
                     KPEIKKSDDFNKHAPTKEEQNKALELANQQVQSEKEPTSLQEKIKEQKRKLELLQQLAE
                     LERKQNTPSKKINKQIADNNSDITPEFKENLLDNLQNLFKE"
                     /name="replication initiation protein"
     gene            979..1467
                     /locus_tag="IQN15_15935"
     CDS             979..1467
                     /locus_tag="IQN15_15935"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002347002.1"
                     /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="UOE03134.1"
                     /translation="MTDKTIKELADILGVSKDKVKYQLRKLPSNFTYKKGNITYLKKEA
                     VTTITKVLSGNESGNLPSELPDSLPTDYLLKEIETKNNHIEEKDRQIEKLQIALETQQK
                     LLDQQQQLTLQANQQIKKLHEQLQLTYAEESSEKEPLSVTEETQKGQNKEKKWWQFWQ"
                     /name="DUF536 domain-containing protein"
     gene            1763..2044
                     /locus_tag="IQN15_15940"
     CDS             1763..2044
                     /locus_tag="IQN15_15940"
                     /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="UOE03135.1"
                     /translation="MDILVRNIDPKVISEIDRRCQELTTKTGKKWSRNAYLKVLIENDF
                     DQALRHYKKDQFDLLLEKFIDIQAKNTETLNDYVHTNNQLIETLIGGI"
                     /name="hypothetical protein"
     gene            2046..2462
                     /locus_tag="IQN15_15945"
     CDS             2046..2462
                     /locus_tag="IQN15_15945"
                     /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="UOE03136.1"
                     /translation="MRKTSVQKHVTLYPSHIDVLDSIIEKNPDINNYSEAIRFLCMSYE
                     PNTNTTTTSNQAKLNAMGKEISIMSEIIAEFADLYLKDTGVLIGTNSKVYQEVKEKIEN
                     QLNPSRRNQPKNRQKETNQTFTSRNFDPTNFLKR"
                     /name="hypothetical protein"
     gene            3076..4230
                     /locus_tag="IQN15_15950"
     CDS             3076..4230
                     /locus_tag="IQN15_15950"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002348970.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="peptidase C47"
                     /protein_id="UOE03132.1"
                     /translation="MIILKPKKKIYLGLLFSLMIGIFSIGITNTYASENSNFNINSQPI
                     EEQAINFAKTDFEHSITSILLMENNTETDINYTLGSPFKMLDGENTANSSIFFPVFSDA
                     DNTIKYIYTVKKNTNGEYSGSISQFLAKELQNLVDSNITDTTLFFQDNSIYYSDNGQIK
                     LLWKSPLSTEKNGVSSLTEKNDLISVNIKNKIKNFSKKQNFPAVKRVKSVSSGDNFIMI
                     NWRIAETQTSFPWCAAYVEAAILCNKTDVRATSARAIMHYTYPNLNNSQIESKSLNQDQ
                     IIKYANYCGVYPKKIARILNLSEVQTQLRKGNAIYMGTAGYGNYSNSRHALALFGWVNQ
                     GGYQTYYVWNPWYNYPTVISANAGPVTIPVPGGGFTWDNTITNW"
                     /name="peptidase C47"
     gene            4224..4646
                     /locus_tag="IQN15_15955"
     CDS             4224..4646
                     /locus_tag="IQN15_15955"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002348709.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="UOE03137.1"
                     /translation="MVNKLIALVMGLVLVLFLTSCSKKQEIQKTDLIPFLGTWQTKDHS
                     ERLVITNLNTSKNIEQYTILVKENNHKIQIIDKNLNINEQVFIYKATNNLLTLRSNKKQ
                     LDYTFSLDSPKKLVFILTTNDGTEGTAKPIEFFKAD"
                     /name="hypothetical protein"
     Typing          2..969
                     /name="rep_cluster_1093"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 atggcaaatg aaattgtgaa ataccaccat gaattaaata cgattccttt acgcaaattt
       61 acgtcagtag aaatgaattt attcttctct ataatatcta gaatgcgtga tgtaggcgat
      121 aaaaaagtac aatttacatt cgaacaatta aaagatttaa gcaattataa agcaactgca
      181 aatgttcgat tcatagatga tttagaaaca acgtatgaca aattaatgga tttacgtttt
      241 ggtagaagaa gtgctgacgg tttgcaacgt gaacgatttg ttttatttaa tcaatttaaa
      301 atcgatggaa aagctgatat tccttttgct gaaatacaag tccatgagaa agccttaccc
      361 ttacttaata atcttgaaga atgggttcga tattctctcc aacaattcaa tgaattagaa
      421 agcagttatt ccaaaaccat gtttagatta ttaaaacaat acagaaccaa aggaattgcc
      481 aatttttcaa aagaagactt tcatgaatta cttgatatcc ctaaaagtta tagagaaagt
      541 gatataaata aaaaaattat aaagcctatt cgccaagaac taaccgcaat cttcaaaggt
      601 ttgacaatcc aaaagagata cggaaaagga cggggaaagc ctgtcattgg ctatcaattt
      661 acatttaaac ctgagataaa aaaatcagac gactttaaca aacatgctcc aaccaaagaa
      721 gaacaaaata aagctttgga actagctaat caacaggttc aatctgaaaa agaacctact
      781 tcattacaag aaaaaatcaa agaacaaaaa cgaaaattag aacttttaca acagttagca
      841 gaattagaaa gaaaacaaaa taccccaagt aagaaaatta acaaacaaat agcagataac
      901 aattccgata ttaccccaga atttaaagaa aacttactag ataatctcca aaacttattt
      961 aaagaataag gggtttttat gacagataaa actatcaaag aattagcaga tattctaggt
     1021 gtttcaaaag ataaagtgaa gtatcaactg aggaaattac ctagtaattt tacctacaaa
     1081 aaaggaaata ttacctacct gaaaaaagaa gcagtaacaa caattacaaa ggttttatca
     1141 ggtaatgaat cgggtaactt acctagtgaa ttacccgatt cattacctac cgattaccta
     1201 ctcaaggaga ttgaaactaa gaataatcat attgaagaaa aagataggca aattgaaaaa
     1261 cttcaaatag ctttagaaac gcagcaaaaa ttactcgacc agcaacaaca actcacccta
     1321 caagccaatc aacaaatcaa aaaacttcac gaacaactcc agctaaccta tgcagaagaa
     1381 tcttcagaaa aagaacccct ttctgttact gaagaaactc aaaaaggaca aaacaaggag
     1441 aaaaaatggt ggcaattctg gcaataaccc aacaattttt attcataaaa attgttgggt
     1501 tactttcttt ttttgctttt acaagcatag cgacatgatc tcacgtcgct attttttaaa
     1561 gagcataagg aaacgcggta tcactttctt acgaaaggtg ctaggtaggc tgtgcctacc
     1621 acgtttctaa gaaaaaaatt tgctatcact ttttcgtcat tgtggatagc ttatgtatag
     1681 tgtttcggca aaaaacagct atacaaatac tatatttgta tgatatacat aaattataca
     1741 caaatgcgaa aggaattctt ctatggacat tttagttcgg aatattgatc caaaagttat
     1801 ttcagaaata gatagacgtt gccaagaact cacaacaaaa actggcaaaa aatggagccg
     1861 taatgcgtac ctaaaagttc taatcgaaaa cgattttgac caggcactta ggcattacaa
     1921 aaaagatcaa ttcgatttat tactcgaaaa atttatcgat atacaagcaa aaaatactga
     1981 aacattgaac gactatgttc atacaaacaa ccaactcatt gaaacactta tcggaggaat
     2041 ataacatgag aaaaacttct gttcaaaaac acgttaccct ttatcccagt cacattgacg
     2101 ttttagattc catcatcgaa aaaaatccag atatcaataa ctactcggaa gccattcgtt
     2161 ttctatgtat gagttatgaa cctaatacta atacgacaac taccagcaac caagcaaaac
     2221 taaatgcgat gggaaaagaa atttctatta tgtccgaaat cattgcagaa tttgctgatt
     2281 tatatctaaa agatactggt gttcttatcg gtacaaattc taaagtatat caagaagtga
     2341 aagaaaaaat tgaaaatcaa ctcaatccct cccgacgaaa tcaacccaaa aatcgtcaaa
     2401 aagaaaccaa tcaaacattc acttctagaa attttgaccc aacaaacttt ctaaaaagat
     2461 gaaaaagaaa ccgaaaattt tttctatttc tcagtttctt ttttaggggg cagtcttcca
     2521 gcaagatttg caagttaccg gtaacttgca caaaaaaaga aaaatccgct tgtgcgaatc
     2581 cttctttttg cattttgggg cgctgcccca atctccaaat atcggttatt taatagcgtg
     2641 gtaactcaaa aaaatagaac gtactctgaa ataaaaaaag actgctctaa cgagcagcca
     2701 ataaaaaata atgagcgttt attcttgaaa aagcagcgcg cttatgaagc gctgccaaaa
     2761 atttaccata ttttatgaaa aataacaagt ttctaaaaag gaatcggtta agattcacaa
     2821 agaatcgtaa acagacaata gcggaaaatc aagcttccga acgtaccttt tagctagacc
     2881 aatgaaaaat cacaaagtga gcggctggat cggttggtag aggggctact tggcatagtg
     2941 tacattatgt taactaacgc tataaataac gattatgttc ccaaaacaat attttatgaa
     3001 ctataacaaa aatttgttat cgcatattgt atattttaat tataggtgta taccacttaa
     3061 atttaacaca aaggcgtgat tattttgaaa cccaaaaaga aaatttatct aggtctcctc
     3121 ttttccttga tgattggaat ttttagtata ggaattacaa atacctatgc ttcagaaaat
     3181 tctaatttca atatcaactc ccaaccaatt gaagaacaag caattaattt tgcgaaaact
     3241 gattttgaac actccataac ttcaattctt ttaatggaaa ataacaccga aactgatatt
     3301 aactatactc ttggttcgcc atttaaaatg ctcgatggag aaaatacggc aaatagttct
     3361 attttctttc cagtattttc agacgctgat aatacgatta aatatattta taccgtcaaa
     3421 aaaaatacaa atggagaata ttcaggaagt atttcacaat ttttagcaaa agaacttcaa
     3481 aatctagtag atagtaatat aacagataca accttatttt ttcaagataa tagcatttat
     3541 tattccgata atggacaaat taaactactt tggaaatcac ctttaagtac agaaaaaaat
     3601 ggtgtttctt cccttacaga aaaaaatgat cttatatccg taaatataaa aaataaaatt
     3661 aaaaattttt ctaaaaaaca aaattttcct gcggttaaac gtgtaaaaag tgtctcctcc
     3721 ggagataact ttattatgat taattggcgt atagcagaaa cccaaacaag ttttccgtgg
     3781 tgcgctgctt acgtagaagc tgctatctta tgtaacaaaa cagatgtacg tgctacttca
     3841 gctagagcca ttatgcatta tacctatcct aatttaaaca acagtcaaat tgaatcaaaa
     3901 agtcttaatc aagatcaaat aataaaatat gcaaattact gtggtgttta tcctaaaaaa
     3961 atagcacgaa tactaaacct ttcagaggtc caaacacaac taagaaaagg aaatgccatt
     4021 tatatgggaa ctgctggtta tggaaattat agtaacagcc gtcatgcact tgcattattt
     4081 gggtgggtca atcaaggtgg ttatcaaact tactatgtgt ggaatccttg gtataactac
     4141 ccaactgtaa taagtgcaaa tgcaggacca gttacaattc ctgtacctgg aggtggtttt
     4201 acttgggaca ataccattac aaattggtaa ataaactcat tgctttagtt atgggtctag
     4261 tgttagttct tttcttaact agttgttcaa aaaaacaaga aatacaaaag actgatctga
     4321 ttccttttct aggaacttgg caaactaaag atcattcaga acgtctagta atcactaatt
     4381 taaatacttc aaaaaatata gaacaatata ccatcttagt aaaagagaac aatcataaaa
     4441 ttcaaatcat tgataaaaat ttaaatataa atgaacaagt tttcatttac aaagcaacaa
     4501 ataatttact aacactgcgc tcgaataaaa aacaattaga ttacactttt agtttggatt
     4561 ctccaaaaaa gctcgtattt attttgacaa cgaatgatgg gacagaaggg acagctaaac
     4621 caattgaatt ttttaaagct gattgatgaa tagttgtttg atattacaaa acaataattt
     4681 caccgaaggt gaaacaagcg aaactttaca aaaagtggct agcatttgct agcctttttt
     4741 gtattgtgga gcgtgggttt tgagggggat tcaaggggga gcttgcgccc ctttgacaag
     4801 cggttatttg caccaaatac gtaggtattt ggctagcaaa tatagagctt gccaagccct
     4861 ttagtgtgtt ttgtagaaag ggaccttata gtcactttca cattacaaac gatacgtcca
     4921 taggacgtat caaaagggtg ggacttatga gcaaattaaa gcaaaatttg gctagcaatc
     4981 cttctaaaaa atacacctat tgatcagagt caaaataaat cagttttcga gtgagcgaat
     5041 ccaaatttgc aactctgaag ctttgcaaat gagtgtgccg gcttccgtaa aagtctaggt
     5101 aacattagtc gatatataca tagggctcta atttgcgttt taaggcgttt taaacgttct
     5161 ggtatgtaat tataccaaag cgactttaaa acgccttaaa acgaatttta gaggttctgt
     5221 agaacgtttt agggttgtta gggcttgccc tgaccgcctg taaggcgctt taaaaacaag
     5281 ataagggatt ttatctagac ttgtcttaaa acgccgtaga tgagcgctca gagcttctaa
     5341 aaggactcct tacgaactgt ttttaagcaa aggagccttt aggcgactgc gcagtttaat
     5401 gtgagagcgt agcgatcaca cctttaaagc gaccgtaggg agcagattcc cagtttagga
     5461 aatttcgcga acctgtttgg agaaaaaaag taggaaaatt ttaggcggga aattttgccc
     5521 ccctctttta taatctcttt tataacctct ttttaaacct ctttaccgtc ggctgtatcc
     5581 ttactctccc aaggtgtgca gaatctttta ggggtctttt tgtctgtttt taggggtctt
     5641 tttgtctgtt tttaggggtc tttttgtctg tttttagggg tctttttgtc tgtttttagg
     5701 ggtctttaat tagggggttg acccccatta gaaagctctt tataattttg ttaagtagtt
     5761 aatcttgaag gaggatttt
//
