LOCUS       CP063631                5779 bp    DNA     circular BCT 04-APR-2022
DEFINITION  Enterococcus faecium strain ICU-4-1 plasmid pZA4-1_05, complete
            sequence.
ACCESSION   CP063631
VERSION     CP063631.1
DBLINK      BioProject: PRJNA669626
            BioSample: SAMN16483152
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                   :: Unicycler v. v0.4.7
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 414.3x
            Sequencing Technology             :: Oxford Nanopore
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI
            Annotation Date                   :: 10/27/2020 18:33:54
            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)                     :: 3,157
            CDSs (total)                      :: 3,064
            Genes (coding)                    :: 2,972
            CDSs (with protein)               :: 2,972
            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)              :: 92
            CDSs (without protein)            :: 92
            Pseudo Genes (ambiguous residues) :: 0 of 92
            Pseudo Genes (frameshifted)       :: 27 of 92
            Pseudo Genes (incomplete)         :: 53 of 92
            Pseudo Genes (internal stop)      :: 20 of 92
            Pseudo Genes (multiple problems)  :: 7 of 92
            ##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-4-1"
                     /isolation_source="rectal swab"
                     /host="Homo sapiens"
                     /db_xref="taxon:1352"
                     /plasmid="pZA4-1_05"
                     /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            395..1363
                     /locus_tag="IQN04_15740"
     CDS             395..1363
                     /locus_tag="IQN04_15740"
                     /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="UOE14744.1"
                     /translation="MANEIVKYHHELNTIPLRKFTSVEMNLFFSIISRMRDVGDKKVQF
                     TFEQLKDLSNYKATANVRFIDDLETTYDKLMDLRFGRRSADGLQRERFVLFNQFKIDGK
                     ADIPFAEIQVHEKALPLLNNLEEWVRYSLQQFNELESSYSKTMFRLLKQYRTKGIANFS
                     KEDFHELLDIPKSYRESDINKKIIKPIRQELTAIFKGLTIQKRYGKGRGKPVIGYQFTF
                     KPEIKKSDDFNKHAPTKEEQNKALELANQQVQSEKEPTSLQEKIKEQKRKLELLQQLAE
                     LERKQNTPSKKINKQIADNNSDITPEFKENLLDNLQNLFKE"
                     /name="replication initiation protein"
     gene            1373..1861
                     /locus_tag="IQN04_15745"
     CDS             1373..1861
                     /locus_tag="IQN04_15745"
                     /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="UOE14745.1"
                     /translation="MTDKTIKELADILGVSKDKVKYQLRKLPSNFTYKKGNITYLKKEA
                     VTTITKVLSGNESGNLPSELPDSLPTDYLLKEIETKNNHIEEKDRQIEKLQIALETQQK
                     LLDQQQQLTLQANQQIKKLHEQLQLTYAEESSEKEPLSVTEETQKGQNKEKKWWQFWQ"
                     /name="DUF536 domain-containing protein"
     gene            2157..2438
                     /locus_tag="IQN04_15750"
     CDS             2157..2438
                     /locus_tag="IQN04_15750"
                     /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="UOE14746.1"
                     /translation="MDILVRNIDPKVISEIDRRCQELTTKTGKKWSRNAYLKVLIENDF
                     DQALRHYKKDQFDLLLEKFIDIQAKNTETLNDYVHTNNQLIETLIGGI"
                     /name="hypothetical protein"
     gene            2440..2856
                     /locus_tag="IQN04_15755"
     CDS             2440..2856
                     /locus_tag="IQN04_15755"
                     /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="UOE14747.1"
                     /translation="MRKTSVQKHVTLYPSHIDVLDSIIEKNPDINNYSEAIRFLCMSYE
                     PNTNTTTTSNQAKLNAMGKEISIMSEIIAEFADLYLKDTGVLIGTNSKVYQEVKEKIEN
                     QLNPSRRNQPKNRQKETNQTFTSRNFDPTNFLKR"
                     /name="hypothetical protein"
     gene            3470..4624
                     /locus_tag="IQN04_15760"
     CDS             3470..4624
                     /locus_tag="IQN04_15760"
                     /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="UOE14743.1"
                     /translation="MIILKPKKKIYLGLLFSLMIGIFSIGITNTYASENSNFNINSQPI
                     EEQAINFAKTDFEHSITSILLMENNTETDINYTLGSPFKMLDGENTANSSIFFPVFSDA
                     DNTIKYIYTVKKNTNGEYSGSISQFLAKELQNLVDSNITDTTLFFQDNSIYYSDNGQIK
                     LLWKSPLSTEKNGVSSLTEKNDLISVNIKNKIKNFSKKQNFPAVKRVKSVSSGDNFIMI
                     NWRIAETQTSFPWCAAYVEAAILCNKTDVRATSARAIMHYTYPNLNNSQIESKSLNQDQ
                     IIKYANYCGVYPKKIARILNLSEVQTQLRKGNAIYMGTAGYGNYSNSRHALALFGWVNQ
                     GGYQTYYVWNPWYNYPTVISANAGPVTIPVPGGGFTWDNTITNW"
                     /name="peptidase C47"
     gene            4618..5040
                     /locus_tag="IQN04_15765"
     CDS             4618..5040
                     /locus_tag="IQN04_15765"
                     /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="UOE14748.1"
                     /translation="MVNKLIALVMGLVLVLFLTSCSKKQEIQKTDLIPFLGTWQTKDHS
                     ERLVITNLNTSKNIEQYTILVKENNHKIQIIDKNLNINEQVFIYKATNNLLTLRSNKKQ
                     LDYTFSLDSPKKLVFILTTNDGTEGTAKPIEFFKAD"
                     /name="hypothetical protein"
     Typing          396..1363
                     /name="rep_cluster_1093"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 actgcgcagt ttaatgtgag agcgtagcga tcacaccttt aaagcgaccg tagggagcag
       61 attcccagtt taggaaattt cgcgaacctg tttggagaaa aaaagtagga aaattttagg
      121 cgggaaattt tgcccccctc ttttataatc tcttttataa cctcttttta aacctcttta
      181 ccgtcggctg tatccttact ctcccaaggt gtgcagaatc ttttaggggt ctttttgtct
      241 gtttttaggg gtctttttgt ctgtttttag gggtcttttt gtctgttttt aggggtcttt
      301 ttgtctgttt ttaggggtct ttaattaggg ggttgacccc cattagaaag ctctttataa
      361 ttttgttaag tagttaatct tgaaggagga ttttatggca aatgaaattg tgaaatacca
      421 ccatgaatta aatacgattc ctttacgcaa atttacgtca gtagaaatga atttattctt
      481 ctctataata tctagaatgc gtgatgtagg cgataaaaaa gtacaattta cattcgaaca
      541 attaaaagat ttaagcaatt ataaagcaac tgcaaatgtt cgattcatag atgatttaga
      601 aacaacgtat gacaaattaa tggatttacg ttttggtaga agaagtgctg acggtttgca
      661 acgtgaacga tttgttttat ttaatcaatt taaaatcgat ggaaaagctg atattccttt
      721 tgctgaaata caagtccatg agaaagcctt acccttactt aataatcttg aagaatgggt
      781 tcgatattct ctccaacaat tcaatgaatt agaaagcagt tattccaaaa ccatgtttag
      841 attattaaaa caatacagaa ccaaaggaat tgccaatttt tcaaaagaag actttcatga
      901 attacttgat atccctaaaa gttatagaga aagtgatata aataaaaaaa ttataaagcc
      961 tattcgccaa gaactaaccg caatcttcaa aggtttgaca atccaaaaga gatacggaaa
     1021 aggacgggga aagcctgtca ttggctatca atttacattt aaacctgaga taaaaaaatc
     1081 agacgacttt aacaaacatg ctccaaccaa agaagaacaa aataaagctt tggaactagc
     1141 taatcaacag gttcaatctg aaaaagaacc tacttcatta caagaaaaaa tcaaagaaca
     1201 aaaacgaaaa ttagaacttt tacaacagtt agcagaatta gaaagaaaac aaaatacccc
     1261 aagtaagaaa attaacaaac aaatagcaga taacaattcc gatattaccc cagaatttaa
     1321 agaaaactta ctagataatc tccaaaactt atttaaagaa taaggggttt ttatgacaga
     1381 taaaactatc aaagaattag cagatattct aggtgtttca aaagataaag tgaagtatca
     1441 actgaggaaa ttacctagta attttaccta caaaaaagga aatattacct acctgaaaaa
     1501 agaagcagta acaacaatta caaaggtttt atcaggtaat gaatcgggta acttacctag
     1561 tgaattaccc gattcattac ctaccgatta cctactcaag gagattgaaa ctaagaataa
     1621 tcatattgaa gaaaaagata ggcaaattga aaaacttcaa atagctttag aaacgcagca
     1681 aaaattactc gaccagcaac aacaactcac cctacaagcc aatcaacaaa tcaaaaaact
     1741 tcacgaacaa ctccagctaa cctatgcaga agaatcttca gaaaaagaac ccctttctgt
     1801 tactgaagaa actcaaaaag gacaaaacaa ggagaaaaaa tggtggcaat tctggcaata
     1861 acccaacaat ttttattcat aaaaattgtt gggttacttt ctttttttgc ttttacaagc
     1921 atagcgacat gatctcacgt cgctattttt taaagagcat aaggaaacgc ggtatcactt
     1981 tcttacgaaa ggtgctaggt aggctgtgcc taccacgttt ctaagaaaaa aatttgctat
     2041 cactttttcg tcattgtgga tagcttatgt atagtgtttc ggcaaaaaac agctatacaa
     2101 atactatatt tgtatgatat acataaatta tacacaaatg cgaaaggaat tcttctatgg
     2161 acattttagt tcggaatatt gatccaaaag ttatttcaga aatagataga cgttgccaag
     2221 aactcacaac aaaaactggc aaaaaatgga gccgtaatgc gtacctaaaa gttctaatcg
     2281 aaaacgattt tgaccaggca cttaggcatt acaaaaaaga tcaattcgat ttattactcg
     2341 aaaaatttat cgatatacaa gcaaaaaata ctgaaacatt gaacgactat gttcatacaa
     2401 acaaccaact cattgaaaca cttatcggag gaatataaca tgagaaaaac ttctgttcaa
     2461 aaacacgtta ccctttatcc cagtcacatt gacgttttag attccatcat cgaaaaaaat
     2521 ccagatatca ataactactc ggaagccatt cgttttctat gtatgagtta tgaacctaat
     2581 actaatacga caactaccag caaccaagca aaactaaatg cgatgggaaa agaaatttct
     2641 attatgtccg aaatcattgc agaatttgct gatttatatc taaaagatac tggtgttctt
     2701 atcggtacaa attctaaagt atatcaagaa gtgaaagaaa aaattgaaaa tcaactcaat
     2761 ccctcccgac gaaatcaacc caaaaatcgt caaaaagaaa ccaatcaaac attcacttct
     2821 agaaattttg acccaacaaa ctttctaaaa agatgaaaaa gaaaccgaaa attttttcta
     2881 tttctcagtt tcttttttag ggggcagtct tccagcaaga tttgcaagtt accggtaact
     2941 tgcacaaaaa aagaaaaatc cgcttgtgcg aatccttctt tttgcatttt ggggcgctgc
     3001 cccaatctcc aaatatcggt tatttaatag cgtggtaact caaaaaaata gaacgtactc
     3061 tgaaataaaa aaagactgct ctaacgagca gccaataaaa aataatgagc gtttattctt
     3121 gaaaaagcag cgcgcttatg aagcgctgcc aaaaatttac catattttat gaaaaataac
     3181 aagtttctaa aaaggaatcg gttaagattc acaaagaatc gtaaacagac aatagcggaa
     3241 aatcaagctt ccgaacgtac cttttagcta gaccaatgaa aaatcacaaa gtgagcggct
     3301 ggatcggttg gtagaggggc tacttggcat agtgtacatt atgttaacta acgctataaa
     3361 taacgattat gttcccaaaa caatatttta tgaactataa caaaaatttg ttatcgcata
     3421 ttgtatattt taattatagg tgtataccac ttaaatttaa cacaaaggcg tgattatttt
     3481 gaaacccaaa aagaaaattt atctaggtct cctcttttcc ttgatgattg gaatttttag
     3541 tataggaatt acaaatacct atgcttcaga aaattctaat ttcaatatca actcccaacc
     3601 aattgaagaa caagcaatta attttgcgaa aactgatttt gaacactcca taacttcaat
     3661 tcttttaatg gaaaataaca ccgaaactga tattaactat actcttggtt cgccatttaa
     3721 aatgctcgat ggagaaaata cggcaaatag ttctattttc tttccagtat tttcagacgc
     3781 tgataatacg attaaatata tttataccgt caaaaaaaat acaaatggag aatattcagg
     3841 aagtatttca caatttttag caaaagaact tcaaaatcta gtagatagta atataacaga
     3901 tacaacctta ttttttcaag ataatagcat ttattattcc gataatggac aaattaaact
     3961 actttggaaa tcacctttaa gtacagaaaa aaatggtgtt tcttccctta cagaaaaaaa
     4021 tgatcttata tccgtaaata taaaaaataa aattaaaaat ttttctaaaa aacaaaattt
     4081 tcctgcggtt aaacgtgtaa aaagtgtctc ctccggagat aactttatta tgattaattg
     4141 gcgtatagca gaaacccaaa caagttttcc gtggtgcgct gcttacgtag aagctgctat
     4201 cttatgtaac aaaacagatg tacgtgctac ttcagctaga gccattatgc attataccta
     4261 tcctaattta aacaacagtc aaattgaatc aaaaagtctt aatcaagatc aaataataaa
     4321 atatgcaaat tactgtggtg tttatcctaa aaaaatagca cgaatactaa acctttcaga
     4381 ggtccaaaca caactaagaa aaggaaatgc catttatatg ggaactgctg gttatggaaa
     4441 ttatagtaac agccgtcatg cacttgcatt atttgggtgg gtcaatcaag gtggttatca
     4501 aacttactat gtgtggaatc cttggtataa ctacccaact gtaataagtg caaatgcagg
     4561 accagttaca attcctgtac ctggaggtgg ttttacttgg gacaatacca ttacaaattg
     4621 gtaaataaac tcattgcttt agttatgggt ctagtgttag ttcttttctt aactagttgt
     4681 tcaaaaaaac aagaaataca aaagactgat ctgattcctt ttctaggaac ttggcaaact
     4741 aaagatcatt cagaacgtct agtaatcact aatttaaata cttcaaaaaa tatagaacaa
     4801 tataccatct tagtaaaaga gaacaatcat aaaattcaaa tcattgataa aaatttaaat
     4861 ataaatgaac aagttttcat ttacaaagca acaaataatt tactaacact gcgctcgaat
     4921 aaaaaacaat tagattacac ttttagtttg gattctccaa aaaagctcgt atttattttg
     4981 acaacgaatg atgggacaga agggacagct aaaccaattg aattttttaa agctgattga
     5041 tgaatagttg tttgatatta caaaacaata atttcaccga aggtgaaaca agcgaaactt
     5101 tacaaaaagt ggctagcatt tgctagcctt ttttgtattg tggagcgtgg gttttgaggg
     5161 ggattcaagg gggagcttgc gcccctttga caagcggtta tttgcaccaa atacgtaggt
     5221 atttggctag caaatataga gcttgccaag ccctttagtg tgttttgtag aaagggacct
     5281 tatagtcact ttcacattac aaacgatacg tccataggac gtatcaaaag ggtgggactt
     5341 atgagcaaat taaagcaaaa tttggctagc aatccttcta aaaaatacac ctattgatca
     5401 gagtcaaaat aaatcagttt tcgagtgagc gaatccaaat ttgcaactct gaagctttgc
     5461 aaatgagtgt gccggcttcc gtaaaagtct aggtaacatt agtcgatata tacatagggc
     5521 tctaatttgc gttttaaggc gttttaaacg ttctggtatg taattatacc aaagcgactt
     5581 taaaacgcct taaaacgaat tttagaggtt ctgtagaacg ttttagggtt gttagggctt
     5641 gccctgaccg cctgtaaggc gctttaaaaa caagataagg gattttatct agacttgtct
     5701 taaaacgccg tagatgagcg ctcagagctt ctaaaaggac tccttacgaa ctgtttttaa
     5761 gcaaaggagc ctttaggcg
//
