LOCUS       CP063623                6175 bp    DNA     circular BCT 04-APR-2022
DEFINITION  Enterococcus faecium strain BMT-4-1-3 plasmid pRL-1-3_05, complete
            sequence.
ACCESSION   CP063623
VERSION     CP063623.1
DBLINK      BioProject: PRJNA669626
            BioSample: SAMN16483153
KEYWORDS    .
SOURCE      Enterococcus faecium
  ORGANISM  Enterococcus faecium
            Bacteria; Bacillota; Bacilli; Lactobacillales; Enterococcaceae;
            Enterococcus.
REFERENCE   1  (bases 1 to 6175)
  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 6175)
  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                   :: 65.1x
            Sequencing Technology             :: Oxford Nanopore
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI
            Annotation Date                   :: 10/27/2020 18:03:42
            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)                     :: 3,126
            CDSs (total)                      :: 3,033
            Genes (coding)                    :: 2,935
            CDSs (with protein)               :: 2,935
            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)              :: 98
            CDSs (without protein)            :: 98
            Pseudo Genes (ambiguous residues) :: 0 of 98
            Pseudo Genes (frameshifted)       :: 34 of 98
            Pseudo Genes (incomplete)         :: 58 of 98
            Pseudo Genes (internal stop)      :: 17 of 98
            Pseudo Genes (multiple problems)  :: 10 of 98
            ##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..6175
                     /organism="Enterococcus faecium"
                     /mol_type="genomic DNA"
                     /strain="BMT-4-1-3"
                     /isolation_source="rectal swab"
                     /host="Homo sapiens"
                     /db_xref="taxon:1352"
                     /plasmid="pRL-1-3_05"
                     /geo_loc_name="Germany: Hamburg"
                     /lat_lon="53.33 N 10.1 E"
                     /collection_date="2015-01-07"
                     /collected_by="Institute of Medical Microbiology, Virology
                     and Hygiene, University Medical Center Hamburg-Eppendorf"
     gene            1..945
                     /locus_tag="IQN05_15550"
     CDS             1..945
                     /locus_tag="IQN05_15550"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002303559.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="RepB family plasmid replication initiator
                     protein"
                     /protein_id="UOC54437.1"
                     /translation="MANEIVKYHHELNTIPLRKFTPVEMNLFFSIVSRMREKGDKTVRF
                     TFDQLKDLSNYKATANVRFVEDLKATYEKILSLRFGRRSESGLSYDMFVMFTEFKINGD
                     VENPYVDIRIYEKALPLLNNLDEWVRYSLQQFNELQSGYAKTMFRLLKQYRTKGFAYFS
                     KEDFLELLDIPKSYKQPDIDKRVIKPIRQELTAIFKGLTIKKKYGKGRGKPVIGYQFTF
                     KPEIKKADDFNKHAPTKEDQNKALALADKQKEYEEPATTINEKIKQKKRELELLQQIKQ
                     LEKEKKALEKQTESALSEKEKKSLLSDLDNLFQ"
                     /name="RepB family plasmid replication initiator protein"
     gene            966..1499
                     /locus_tag="IQN05_15555"
     CDS             966..1499
                     /locus_tag="IQN05_15555"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002292473.1"
                     /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="UOC54438.1"
                     /translation="MQPQETFTIKELSDLFKMSRQAISKHIQKLDSSMIAKNERGYKVV
                     LRSGVLQLARNLDNQRLLDKLHKHEQNNDKNAYIPNKNVVANKLLDQLREENEFLREQL
                     ALKEQNNSHIQKLLDQQQQLTLQANQQIEKLQEQLQLTYTEESSENSSTTLSEATETMD
                     EQTKNWKKWWQLWK"
                     /name="DUF536 domain-containing protein"
     gene            1514..1684
                     /locus_tag="IQN05_15560"
     CDS             1514..1684
                     /locus_tag="IQN05_15560"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002322958.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="UOC54439.1"
                     /translation="MTKKHLLFGSILLGILSFSPMLLSVANKGNKKGELKLNPNYYNSQ
                     NEEVFVEKLDK"
                     /name="hypothetical protein"
     gene            2139..2363
                     /locus_tag="IQN05_15565"
     CDS             2139..2363
                     /locus_tag="IQN05_15565"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002363584.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="bacteriocin hiracin-JM79"
                     /protein_id="UOC54440.1"
                     /translation="MKKKVLKHCVILGILGTCLAGIGTGIKVDAATYYGNGLYCNKEKC
                     WVDWNQAKGEIGKIIVNGWVNHGPWAPRR"
                     /name="bacteriocin hiracin-JM79"
     gene            2383..2670
                     /locus_tag="IQN05_15570"
     CDS             2383..2670
                     /locus_tag="IQN05_15570"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002363589.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="bacteriocin immunity protein"
                     /protein_id="UOC54441.1"
                     /translation="MDFTKEEKLLNAISKVYNEATIDDYPDLKEKLFLYSKEISEGKSV
                     GEVSMKLSSFLGRYILKHKFGLPKSLIELQEIVSKESQVYRGWASIGIWS"
                     /name="bacteriocin immunity protein"
     gene            3121..3501
                     /locus_tag="IQN05_15575"
     CDS             3121..3501
                     /locus_tag="IQN05_15575"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002348702.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MobC family plasmid mobilization relaxosome
                     protein"
                     /protein_id="UOC54434.1"
                     /translation="MSEQNQYLASNHSKKHTYRSEPKQISFRVSESEFAKLKQSAEALQ
                     MSVPAFVKAKAQNARLVTPKVAPDIAQAIARDLAKAGGNINQIAKWCNTHQHDVDPGDA
                     QRLSENLKIMQKELQKIWQQLK"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            3483..4397
                     /locus_tag="IQN05_15580"
     CDS             3483..4397
                     /locus_tag="IQN05_15580"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002340563.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="relaxase/mobilization nuclease domain-containing
                     protein"
                     /protein_id="UOC54435.1"
                     /translation="MATVKVSRTTSCSRAINYAEPRATVKTGINCDIDYAKSEMKQIRM
                     LYGKDDRVQAHLLIQSFRPGEITAEKANQLGAEYAKKIAPDHQIAIYTHTDKDHIHNHI
                     VINSVNLETGNKFQAHGQAFLNKCYDLNDEICLEHDLTITERGKKPEKRTMSEIKLKEK
                     NEPVWKDEIRFAIDQTMKNKKTRTYNQFCDSLKTFGIHCLNRGKNFTYELIHKKKKVRS
                     NKLGKDYEKETILHELDRRERAYNQQRTNELRRARASIRETAKEVRREQRTLTTEQPEI
                     RPTRRNHDQHVERGADYQQELSF"
                     /name="relaxase/mobilization nuclease domain-containing
                     protein"
     gene            4642..5331
                     /locus_tag="IQN05_15585"
     CDS             4642..5331
                     /locus_tag="IQN05_15585"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002298772.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="UOC54436.1"
                     /translation="MAFYLPYLLIFASILGIIWLSYKAYQTRYSLKGSKIRFKRFLLPG
                     VIFTLSIVLSGLFGVLEGNKRISRSILLGDITQKYEAACDKKKKEQVLTQKMEEFTTCY
                     EEMNDIFVNQEKRLTDKNMEKLTRLYQNLPEKQQKEVQDNYERTKKDVQYFKDTQTEEA
                     CYNLFSDTIPFSTSEQERKERQQSVTYERYKALLQQATNIQNPTKKETALNYLKSVKEW
                     LDQQQQN"
                     /name="hypothetical protein"
     gene            complement(5452..5538)
                     /locus_tag="IQN05_15590"
     CDS             complement(5452..5538)
                     /locus_tag="IQN05_15590"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_017548328.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="type I toxin-antitoxin system Fst family toxin"
                     /protein_id="UOC54442.1"
                     /translation="MFELFICPLLIEVCVSLFSYWLNNRNKK"
                     /name="type I toxin-antitoxin system Fst family toxin"
     BGC             1..6175
                     /name="RiPP-like"
                     /gene="RiPP-like"
                     /tool="antismash"
     Typing          2..945
                     /name="rep_cluster_1197"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          3484..4394
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="93.421"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 atggctaatg agattgtaaa ataccaccat gaattaaata caattccttt aagaaaattt
       61 acaccggttg aaatgaattt gtttttttcc atcgtgtcta gaatgcgtga aaaaggggat
      121 aagacagttc gttttacgtt tgaccaacta aaagatttaa gtaactacaa agcaactgca
      181 aatgtacgat ttgtagaaga tttaaaagca acttatgaaa aaatcttatc tttacgcttt
      241 ggtcgtagaa gtgagtctgg gctttcttac gatatgtttg taatgtttac agaatttaaa
      301 atcaacgggg acgtagaaaa tccttacgta gatatacgaa tttacgaaaa agcactgcct
      361 ttgttaaata atttagacga gtgggtacgc tattctttac aacaattcaa cgagctacaa
      421 agtggctatg caaagactat gtttcgtctg ttaaagcaat acagaaccaa aggtttcgca
      481 tatttctcca aagaagactt tcttgaatta ttagatattc ctaaaagtta taagcaacct
      541 gatatagata aacgagttat aaaacctata cgtcaagaac taactgcaat cttcaaagga
      601 ctaacaatca aaaagaaata cggaaaagga cggggaaaac ctgttattgg ctatcaattt
      661 acgttcaaac ctgagatcaa aaaagcagac gactttaaca aacatgcacc aaccaaagaa
      721 gaccaaaata aagcattggc tttagctgat aaacaaaaag aatacgaaga acccgctaca
      781 acaattaacg aaaaaatcaa acagaagaaa cgagaacttg aactcctcca acaaatcaaa
      841 caactagaaa aagagaaaaa agctcttgaa aaacaaacag agtccgcact ttcggaaaaa
      901 gagaaaaaaa gtttattatc tgatttagat aatttattcc agtagcaacc taggaggcaa
      961 ccagtatgca accacaagaa acctttacaa taaaggaatt gtcagatctt tttaagatga
     1021 gtaggcaagc aatatcgaaa catatccaaa aattagattc ttccatgata gctaaaaatg
     1081 agcgtggtta taaggttgta ttgcgttctg gagtattgca acttgctcgc aacttagaca
     1141 atcaaaggtt gctagataag ttgcataaac atgaacaaaa caacgataaa aatgcttata
     1201 taccaaacaa aaacgtggtt gcaaacaagt tgctagatca gttgcgtgaa gaaaatgaat
     1261 ttttacgaga acaacttgcc ctcaaagagc aaaataattc tcatatacaa aaactactcg
     1321 accagcaaca acaactcacc ctgcaagcca accaacaaat cgaaaaactt caggagcaac
     1381 tgcagttgac ttatacggaa gagtcttcag agaatagttc aacgactctt tctgaagcaa
     1441 cagaaacaat ggacgaacaa acaaagaatt ggaaaaaatg gtggcagcta tggaaatgaa
     1501 gaaggaaata cttatgacaa aaaaacactt gctattcggt tctatcctac taggaatatt
     1561 aagctttagc ccaatgttat tatcagtggc caacaaagga aataaaaaag gggaactaaa
     1621 actcaatcct aattactaca acagtcaaaa tgaggaagta tttgtagaaa aacttgataa
     1681 ataagaaaag actgctcgta cgagcagtct ttctgaaaga gattatccta ttattaacct
     1741 tagaaaagaa taataaatga atatgagata tgtaaaaagc ataacaaaca caaacaaaaa
     1801 taacaagtat ttaaaaaatg accgatcaat attcacaaag aattagaaag aaacaaccgc
     1861 agaaaaccaa gccttaaaaa gagcttttaa cctagaccaa taaaaattca caaaatcagc
     1921 gcctggatcc cttggtacag gcgttacttg gtagtatata cattatgtct actagctgtt
     1981 taaataactg atcttataat tttatttaaa cgattatgaa ttcaaaacta ctttttatga
     2041 cgttaatcat tgttatataa taaaatgtta tataataaaa ttactaagat tatttaatat
     2101 aacaagcaat tttaaaaaaa cgaaaaggaa aaacaatcat gaaaaagaaa gtattaaaac
     2161 attgtgttat tctaggaata ttaggaactt gtctagctgg catcggtaca ggaataaaag
     2221 ttgatgcagc tacttactat ggaaatggtc tttattgtaa caaagaaaaa tgttgggtag
     2281 attggaatca agctaaagga gaaattggaa aaattattgt taatggttgg gttaatcatg
     2341 gtccatgggc acctagaagg tagtggtagg gaggttatta taatggattt tactaaagaa
     2401 gaaaaacttt taaatgcaat tagtaaagta tacaatgaag caactataga tgactatcct
     2461 gacttaaaag aaaagctctt tctttattct aaagaaatca gtgagggaaa aagtgttggt
     2521 gaagttagta tgaaattaag tagttttctt ggaagatata ttttaaaaca taaatttgga
     2581 ttacctaaat ctttaataga attacaagaa attgttagta aggaatctca agtatataga
     2641 ggatgggctt ctattggtat ttggagttaa ttctttggaa taaaatgaaa atgggactga
     2701 agaatcaatt ctgattcatc agtcccataa attatagagc cgaaaaatta tcatatttat
     2761 agatttatta atagtaaatg gcataagaat ctttgaacaa cgaaaaaaat gtagctctac
     2821 ctaattattg atttgcaaca atttcaccga aggtgaaaca agcgaaactt tacaaaaagt
     2881 ggctagcatt tgctagtctt ttttgtattg tggagagtgg ggggggaggg ggattcaagg
     2941 gggagcttgc gcccctttga caagcggtta tttgcaccaa atacgtaggt atttggctag
     3001 caaatataga gcttgccaag ccctttagta agctttagtg agctttactt attgtacctt
     3061 tttaggtaca atggtattgc gaacgatacg tccgtaggac gtactgaaag ggtgggactt
     3121 atgagcgaac aaaatcaata tttggctagc aatcattcta aaaaacatac ctatcgatcc
     3181 gagccaaaac aaatcagttt tcgagtgagc gaatccgaat ttgcaaagct gaagcagtca
     3241 gctgaagctt tgcaaatgag tgtgccggct ttcgtgaaag ccaaggcaca aaacgcgcgt
     3301 ctggtgacac cgaaagtggc gccagacatt gctcaggcaa tcgcgcgcga tttagccaaa
     3361 gctggcggga atatcaatca aattgccaag tggtgcaaca cacaccaaca cgacgttgat
     3421 cctggcgacg cccaacgctt atccgaaaac ctaaaaatca tgcaaaagga gctacaaaag
     3481 atatggcaac agttaaagta agccgaacca cttcttgtag ccgagcgatc aattacgccg
     3541 aaccacgagc aaccgtcaaa acagggataa actgtgacat tgattatgcc aaaagcgaaa
     3601 tgaaacaaat tcgcatgctg tatggaaaag acgatcgtgt acaagcacac ttattgatcc
     3661 agtcttttcg accaggagaa attaccgctg aaaaagccaa tcaactaggg gcagagtatg
     3721 cgaaaaaaat agcccctgac caccaaatcg cgatttacac acatacagac aaagaccata
     3781 ttcataacca cattgtcatt aactccgtca atctggaaac tgggaacaaa tttcaagccc
     3841 atggtcaagc atttttaaac aaatgttatg acctaaatga cgagatttgt cttgaacatg
     3901 acttaacaat cactgaacga gggaagaaac ccgaaaaacg aaccatgtct gaaatcaaat
     3961 taaaagaaaa aaatgaacct gtttggaaag acgaaattcg gtttgcgatt gatcaaacaa
     4021 tgaaaaacaa aaaaactcga acgtataacc aattttgtga ttctcttaaa acattcggca
     4081 ttcattgctt gaatcgtggg aaaaatttta cttacgaatt gatccacaaa aagaaaaaag
     4141 tacgatccaa caaactagga aaggattacg aaaaggagac gattttacat gagctggaca
     4201 gacgagaacg agcctacaat caacaacgaa ccaacgagct acgaagagct cgagctagca
     4261 ttcgcgaaac tgcaaaagaa gtacgaagag aacaacgaac tcttacgact gaacaaccgg
     4321 aaattagacc gactcgaaga aaccatgacc aacacgttga aagaggagca gactaccaac
     4381 aagaattatc gttctaaaac gttacaagac atagaaaatg aaataaagaa acaacgtgct
     4441 tttcttgcac cttataccaa agaaagaata caaactacaa ttgattcaca agtcaaaaaa
     4501 ttccaccatg cgctattaaa ccagcgaaat aaagaacaga aaaaagtaat tatgcagcga
     4561 tcaatggata ttcttgcccc cttatgttgc ttaatcatga cactgttagc cttttggctg
     4621 gtatggggag aataaataga aatggcattc tatttaccct atctactcat ttttgccagt
     4681 attttaggaa ttatttggct tagctataag gcttatcaaa caagatattc attaaaaggc
     4741 tctaaaattc gatttaagag gtttttattg ccaggggtta tatttacatt atcaatcgtt
     4801 ttaagtggtt tattcggcgt tttagaggga aataaacgta tttcaagaag tattttatta
     4861 ggggatatca ctcaaaagta tgaagcagca tgtgataaaa agaaaaagga gcaagtgtta
     4921 acacaaaaaa tggaagagtt taccacttgt tatgaggaaa tgaacgatat ttttgtgaat
     4981 caagaaaaac gtttgacgga taaaaacatg gaaaaactca ctcgtcttta tcaaaacttg
     5041 ccagaaaaac agcaaaaaga ggttcaagac aactatgagc gaaccaaaaa agacgtgcaa
     5101 tattttaaag atacgcagac agaagaagct tgttataatt tattcagtga tacaatccct
     5161 ttttcaacta gtgaacagga acgaaaagaa cggcaacaat cagttaccta cgaacgttat
     5221 aaagcactgc ttcagcaagc aacgaacata caaaatccaa cgaaaaaaga aacggcatta
     5281 aattatctaa aaagtgtcaa ggaatggtta gatcagcaac agcaaaattg aatttgatcg
     5341 gcaatcatgt taaactaaac atgcaaatga tcaaacatta gatacacgaa agccccagag
     5401 aggttggatt ctctggggct ttttttcagg ttgatgtcgc ctttattgat tttacttctt
     5461 gtttcggtta ttcaaccaat aactgaataa agagacacaa acttctataa gaagggggca
     5521 aatgaacaat tcaaacatta gatacacctc cttccagtcg caagactgtc ggataggcga
     5581 caagttatta tatcttaaaa aattaaactt gtgtggtgtt tttaagtatc gcttatttta
     5641 gggttgttag ggcttgccct gaccgcctgt aaggcgcttt aaagctagat aaggattttt
     5701 tatccaagac tgtcttaaaa cggcttagat aagcattcag aaccgctcaa aggcctcttt
     5761 accaacatgt ttttagcaaa ggagccttta ggcgactgcg cagtacaatg tgagagcgta
     5821 gcgatcacac ctttttggcg accgtaggaa gcaaggtttt ggattggcag ttttgaaaaa
     5881 tgcgcgaacc tgtttaaaga aaaaagaagt ggtttttagg cgggaaaatt agcccccctc
     5941 tttttatatc tctttttaaa cctcttttta aacctcttta ccgtaagctg tgtccttact
     6001 ctaccaatgg atacagaatg ttatgaagga cattttgtct gtttatgaag gacattttgt
     6061 ctgtttatga aggacatttt gtctgtttat gaaggacatt ttgtctgttt gaacgtcaaa
     6121 tatgaatgtc ttgacattta aaaaatgtca ttcataattg gattgaggtg attat
//
