LOCUS       NZ_CP091306             5966 bp    DNA     circular CON 14-MAR-2024
DEFINITION  Enterococcus faecium strain UK043 plasmid pUK043_5, complete
            sequence.
ACCESSION   NZ_CP091306
VERSION     NZ_CP091306.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN25134383
            Assembly: GCF_021713095.1
KEYWORDS    RefSeq.
SOURCE      Enterococcus faecium
  ORGANISM  Enterococcus faecium
            Bacteria; Bacillota; Bacilli; Lactobacillales; Enterococcaceae;
            Enterococcus.
REFERENCE   1  (bases 1 to 5966)
  AUTHORS   Braun,S.D.
  TITLE     project DRESI
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 5966)
  AUTHORS   Braun,S.D.
  TITLE     Direct Submission
  JOURNAL   Submitted (20-JAN-2022) Optical Molecular Diagnostics and System
            Technology, Leibniz Institute of Photonic Technology, Albert
            Einstein Strasse 9, Jena 07745, Germany
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: flye v. 2.8.3-b1695
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 149.0x
            Sequencing Technology             :: Oxford Nanopore MinION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_021713095.1-RS_2024_03_14
            Annotation Date                   :: 03/14/2024 03:49:09
            Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline
            (PGAP)
            Annotation Method :: Best-placed reference protein set; GeneMarkS-2+
            Annotation Software revision      :: 6.7
            Features Annotated                :: Gene; CDS; rRNA; tRNA; ncRNA
            Genes (total)                     :: 3,196
            CDSs (total)                      :: 3,102
            Genes (coding)                    :: 2,910
            CDSs (with protein)               :: 2,910
            Genes (RNA)                       :: 94
            rRNAs                             :: 6, 6, 6 (5S, 16S, 23S)
            complete rRNAs                    :: 6, 6, 6 (5S, 16S, 23S)
            tRNAs                             :: 72
            ncRNAs                            :: 4
            Pseudo Genes (total)              :: 192
            CDSs (without protein)            :: 192
            Pseudo Genes (ambiguous residues) :: 0 of 192
            Pseudo Genes (frameshifted)       :: 113 of 192
            Pseudo Genes (incomplete)         :: 80 of 192
            Pseudo Genes (internal stop)      :: 27 of 192
            Pseudo Genes (multiple problems)  :: 22 of 192
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP091306.1.
            Bacteria and source DNA available from Dr. Sascha D. Braun.
            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/
            COMPLETENESS: full length.
FEATURES             Location/Qualifiers
     source          1..5966
                     /organism="Enterococcus faecium"
                     /mol_type="genomic DNA"
                     /strain="UK043"
                     /host="Homo sapiens"
                     /db_xref="taxon:1352"
                     /plasmid="pUK043_5"
                     /geo_loc_name="Germany"
                     /collection_date="2018-06-17"
     gene            join(5537..5966,1..308)
                     /locus_tag="L3K57_RS15835"
                     /old_locus_tag="L3K57_15835"
     CDS             join(5537..5966,1..308)
                     /locus_tag="L3K57_RS15835"
                     /old_locus_tag="L3K57_15835"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_015060391.1"
                     /GO_function="GO:0003887 - DNA-directed DNA polymerase
                     activity [Evidence IEA]"
                     /GO_process="GO:0006270 - DNA replication initiation
                     [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="replication initiation protein"
                     /protein_id="WP_002305239.1"
                     /translation="MSNDIVRYNNGLNSVPLRKFTPIDMDLFWGICSKMKRKGTKEEIF
                     TFKQIKELIDYNINARGDRFANDLIKMSKKIITLSFIYEDEKTYEQLNLFQKFKIDKVN
                     ETLLIKVSEEFEYILNSIGTNFTRFELENMTNLKSSYVKELYRQLMAHKDRRSKKGHWF
                     VKIEDFRALLAIPESYRMRDIDKQIFAQAKKEFLNVNSTHPAIFKTFEIKKIKAYKGNK
                     IGSLQIYFEENIPSITLDNWLEK"
                     /name="replication initiation protein"
     gene            336..875
                     /locus_tag="L3K57_RS15840"
                     /old_locus_tag="L3K57_15840"
     CDS             336..875
                     /locus_tag="L3K57_RS15840"
                     /old_locus_tag="L3K57_15840"
                     /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="WP_002289340.1"
                     /translation="MQPKETFTIKELSELFEISRQAISKHVDKLDPSLLAKNERGYKVV
                     LRSGVLQLASNLGNQRLLYRLHEYEQENDKNVYISSKNVIVNELLDKLREENEFLREQL
                     SLKEQNNSNMQKLLDQQQQLTLQANQQIEKLQEQLQLAYTEETPEDESTTILSEETESI
                     EKHTKKKKQKWWQLWK"
                     /name="DUF536 domain-containing protein"
     gene            891..1061
                     /locus_tag="L3K57_RS15845"
                     /old_locus_tag="L3K57_15845"
     CDS             891..1061
                     /locus_tag="L3K57_RS15845"
                     /old_locus_tag="L3K57_15845"
                     /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="WP_002292472.1"
                     /translation="MTRKNLLFGSILLGILGFSPMLLSVINKGNKHGELKLNPNYYNSP
                     NEELFVKETDK"
                     /name="hypothetical protein"
     gene            1510..1734
                     /locus_tag="L3K57_RS15850"
                     /old_locus_tag="L3K57_15850"
     CDS             1510..1734
                     /locus_tag="L3K57_RS15850"
                     /old_locus_tag="L3K57_15850"
                     /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="class II bacteriocin"
                     /protein_id="WP_002363584.1"
                     /translation="MKKKVLKHCVILGILGTCLAGIGTGIKVDAATYYGNGLYCNKEKC
                     WVDWNQAKGEIGKIIVNGWVNHGPWAPRR"
                     /name="class II bacteriocin"
     gene            1754..2041
                     /locus_tag="L3K57_RS15855"
                     /old_locus_tag="L3K57_15855"
     CDS             1754..2041
                     /locus_tag="L3K57_RS15855"
                     /old_locus_tag="L3K57_15855"
                     /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="WP_002363589.1"
                     /translation="MDFTKEEKLLNAISKVYNEATIDDYPDLKEKLFLYSKEISEGKSV
                     GEVSMKLSSFLGRYILKHKFGLPKSLIELQEIVSKESQVYRGWASIGIWS"
                     /name="bacteriocin immunity protein"
     gene            2481..2861
                     /gene="mobC"
                     /locus_tag="L3K57_RS15860"
                     /old_locus_tag="L3K57_15860"
     CDS             2481..2861
                     /gene="mobC"
                     /locus_tag="L3K57_RS15860"
                     /old_locus_tag="L3K57_15860"
                     /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="plasmid mobilization relaxosome protein MobC"
                     /protein_id="WP_002317440.1"
                     /translation="MSEQNQNLASNSSKKYTYRSEPKQISFRVSESEFAKLKQSAEALQ
                     MSVPAFVKAKAQNARLVTPKVAPDIAQAIARDLAKAGGNINQIAKWCNTHQHDVASGDA
                     QRLSENLKIMQKELQKIWQQLR"
                     /name="mobC"
     gene            2843..3757
                     /locus_tag="L3K57_RS15865"
                     /old_locus_tag="L3K57_15865"
     CDS             2843..3757
                     /locus_tag="L3K57_RS15865"
                     /old_locus_tag="L3K57_15865"
                     /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="WP_002340563.1"
                     /translation="MATIKVSRTTSCSRAINYAEPRATIKTGINCDVDYAKSEMKQIRM
                     LYGKDDRVQAHLLIQSFRPGEITAEKANQLGAEYAKKIAPDHQTAIYTHTDKDHIHNHI
                     VINSVNLETGKKFQAHGQAFLNKCYDLNDEICLAHNLPITERGKKPEKRTMSEIKLKEK
                     NEPVWKDEIRIAIDQTMKNKKTRTYDQFCNSLKTLGIHCFNRGKNFTYELIHKKKKVRS
                     NRLGKDYEKETILHELDRRERTYNQQRTNELRRARASIRETAEEVRREQRTLTPEQPEI
                     RPARRNHEQHVERGTDHQQELSL"
                     /name="relaxase/mobilization nuclease domain-containing
                     protein"
     gene            3717..3995
                     /locus_tag="L3K57_RS16055"
     CDS             3717..3995
                     /locus_tag="L3K57_RS16055"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002351557.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_002348700.1"
                     /translation="MKEEQTTNKNYRSKTLKDIENEIKKQRAFLVPYTQERIQTTIDLQ
                     VKKLHQELLDQRNKEQKKVLIQRSLDFLAPLCCLVLTLFAFWLVWGG"
                     /name="hypothetical protein"
     gene            3997..4685
                     /locus_tag="L3K57_RS15870"
                     /old_locus_tag="L3K57_15870"
                     /pseudo=""
     CDS             3997..4685
                     /locus_tag="L3K57_RS15870"
                     /old_locus_tag="L3K57_15870"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002298772.1"
                     /note="frameshifted; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /name="hypothetical protein"
     gene            complement(4806..4892)
                     /locus_tag="L3K57_RS15875"
                     /old_locus_tag="L3K57_15875"
     CDS             complement(4806..4892)
                     /locus_tag="L3K57_RS15875"
                     /old_locus_tag="L3K57_15875"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_018113589.1"
                     /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="WP_110300541.1"
                     /translation="MFELFICPLLVGVCVSLFSYWLNNRNKK"
                     /name="type I toxin-antitoxin system Fst family toxin"
     BGC             1..5966
                     /name="RiPP-like"
                     /gene="RiPP-like"
                     /tool="antismash"
     Typing          2..308
                     /name="rep_cluster_1742"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="1.44e-159"
     Typing          2844..3754
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="99.342"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 agttatatcg ccaacttatg gctcataaag acagaagatc taaaaaaggt cactggtttg
       61 taaaaataga agattttaga gctctattag caataccaga aagttatcgc atgagagata
      121 ttgataaaca aatttttgcc caagcgaaaa aagaattttt aaacgttaat tcaactcacc
      181 ctgctatttt taaaactttt gaaatcaaaa aaattaaagc ctacaaagga aataagatag
      241 gatctctgca aatttatttt gaagaaaata taccttcaat taccttagat aattggttag
      301 agaaataata cctaacaatt taggaggcaa ttatcatgca acccaaagaa acctttacaa
      361 taaaggaatt atctgaatta tttgaaataa gtaggcaagc aatctctaaa catgttgata
      421 aattagaccc gtccttatta gctaaaaatg agcgtggtta taaggttgta ttacgttctg
      481 gagtattgca acttgctagc aacttaggta accaaaggtt actatatagg ttgcatgagt
      541 atgaacaaga aaacgataaa aacgtttata tatcaagcaa aaacgtgatt gtaaacgagt
      601 tgctagataa gttgcgtgaa gaaaatgaat ttttacgaga acaactttcc ctcaaagagc
      661 aaaataattc taatatgcaa aaattactcg accagcaaca acagctcacc ctacaggcaa
      721 atcaacagat cgaaaaactg caagaacagt tacaattagc ttatacggaa gaaactccag
      781 aagatgaatc aactactatt ctttctgaag aaacagaatc gatagaaaaa cacacaaaaa
      841 agaagaagca aaaatggtgg caactttgga aataactgga gggaacattc atgacaagaa
      901 aaaatcttct attcggttct attttactag gaattctagg cttcagtccg atgttattgt
      961 cagtaatcaa taaagggaat aaacatggtg aattgaaatt gaatccaaat tattacaaca
     1021 gtcctaacga agaattgttt gtaaaagaga cggataaata ataaaaaaga ctgctcttcc
     1081 gagcagccag ttaaaaaata atgagtgttt attcttgaaa aagcacgcgc ttatgaagcg
     1141 ctgccaaaaa tttaccatat tttacaaaaa ataacaagtc ttaaaaaaat gacagataaa
     1201 aatgcacaaa gaattagata tagataaccg cgaaaaatca agctttagaa agttgctttt
     1261 agctagacca attaaaaatc acaaagtgag cagctatagc ccttgataga ggggctactt
     1321 ggcatagtcg acattatgtc tactagctgt ttaaataact gatcttataa ttttatttaa
     1381 acgattatga attcaaaact actttttatg acgttaatca ttgttatata ataaaatgtt
     1441 atataataaa attactaaga ttatttaata taacaagcaa ttttaaaaaa acgaaaagga
     1501 aaaacaatca tgaaaaagaa agtattaaaa cattgtgtta ttctaggaat attaggaact
     1561 tgtctagctg gcatcggtac aggaataaaa gttgatgcag ctacttacta tggaaatggt
     1621 ctttattgta acaaagaaaa atgttgggta gattggaatc aagctaaagg agaaattgga
     1681 aaaattattg ttaatggttg ggttaatcat ggtccatggg cacctagaag gtagtggtag
     1741 ggaggttatt ataatggatt ttactaaaga agaaaaactt ttaaatgcaa ttagtaaagt
     1801 atacaatgaa gcaactatag atgactatcc tgacttaaaa gaaaagctct ttctttattc
     1861 taaagaaatc agtgagggaa aaagtgttgg tgaagttagt atgaaattaa gtagttttct
     1921 tggaagatat attttaaaac ataaatttgg attacctaaa tctttaatag aattacaaga
     1981 aattgttagt aaggaatctc aagtatatag aggatgggct tctattggta tttggagtta
     2041 attctttgga ataaaatgaa aatgggactg aagaatcaat tctgattcat cagtcccata
     2101 aattatagag ccgaaaaatt atcatattta tagatttatt aatagtaaat ggcataagaa
     2161 tctttgaaca acgaaaaaaa tgtagctcta cctaattatt gatttgcaac aatttcaccg
     2221 aaggtgaaac aagcgaaact ttacaaaaag tggctagcat ttgctagtct tttttgtatt
     2281 gtggagagtg gggggagggg gattcaaggg ggagcttgcg cccctttgac aagcggttat
     2341 ttgcaccaaa tacgtaggta tttggctagc aaatatagag cttgccaaac ccttttagtg
     2401 agctttactc attgtacctt tttaggtaca atggtattgc gaacgatacg tccgtaggac
     2461 gtactgaaag ggtgggactt atgagcgaac aaaatcaaaa tttggctagc aattcttcta
     2521 aaaaatatac ctatcgatcc gagccaaaac aaatcagttt tcgagtgagc gaatccgaat
     2581 ttgcaaagct gaagcaatcg gctgaagctt tgcaaatgag tgtgccggct ttcgtgaaag
     2641 ccaaggcaca aaacgcgcgt ctggtgacac cgaaagtggc gccagacatt gcccaggcaa
     2701 tcgcgcgcga tttagccaaa gctggaggga atatcaatca aattgctaag tggtgcaata
     2761 cacaccaaca tgacgttgct tctggtgacg ctcaacgttt atccgaaaac ctaaaaatca
     2821 tgcaaaagga gctacaaaag atatggcaac aattaaggta agccgaacca cttcttgtag
     2881 tcgtgcaatt aattacgcag aaccacgagc aaccattaaa acaggaataa actgtgacgt
     2941 cgattatgcc aaaagtgaaa tgaaacaaat tcgcatgctg tatggaaaag acgaccgtgt
     3001 acaggcacac ttattgattc aatcttttcg accaggagaa attaccgctg aaaaagctaa
     3061 tcaactaggg gcagagtatg caaaaaaaat agcccccgat caccaaacag ctatttacac
     3121 acatacagac aaagaccata ttcataatca cattgtcatt aactccgtta atctggagac
     3181 tggaaaaaaa tttcaagctc atggtcaagc atttctaaac aaatgttatg acctaaatga
     3241 cgagatttgt cttgcacata acttaccaat cactgagcga ggaaagaaac cagaaaaacg
     3301 aaccatgtct gaaataaaat taaaagaaaa aaatgaacct gtttggaaag acgaaattcg
     3361 gattgcgatc gatcaaacaa tgaaaaacaa aaaaaccaga acctatgacc aattttgtaa
     3421 ttccctcaaa acattgggga ttcattgctt caatcgcggg aaaaatttca cttacgaatt
     3481 gatccacaaa aagaaaaaag tacgatccaa cagactagga aaggactacg aaaaggagac
     3541 gattttacat gagctggaca gacgagaacg aacctataac caacagcgaa ccaacgagct
     3601 acgaagagct cgagctagca ttcgcgaaac tgcagaagaa gtacgaagag aacaacgaac
     3661 tcttacgcct gaacaaccgg aaattagacc ggctcgaaga aaccatgaac aacacgttga
     3721 aagaggaaca gaccaccaac aagaattatc gctctaaaac gttaaaagac atagaaaacg
     3781 aaataaagaa acaacgtgct tttctcgttc cttatacgca agaaaggata caaactacga
     3841 ttgatttaca agttaaaaaa ctccatcaag agctattaga ccagcgaaat aaggaacaga
     3901 aaaaggtgct tattcaacga tcattggatt ttcttgcccc cttatgttgc ttagtcctga
     3961 cactgttcgc attttggtta gtatggggag gctaaaatgg cattttattt accctatcta
     4021 ctcatttttg ttagtatttc aggaagtatt tggctcatct ataaaatttt tcaaacaaga
     4081 tattcattaa aaggctctaa aattcgattt aagcgatttt tctttcttgg ctgtatattt
     4141 tccttgataa tcgtttcaag cggcttattc ggcgttttag agggaaataa gcgcgtttct
     4201 agaagtattt tattaggaaa tgtcactcaa aagtatgaat cagcgcgtga taaaaagaaa
     4261 aaagagcaag cattagcaca aaaaatggaa gagtttacca cttgttatga ggaaatgaac
     4321 gatatttttg tgaatcaaga aaaacgtttg acggataaaa acatggaaaa actcactcgt
     4381 ctttatcaaa acttgccaga aaaacagcaa aaagaggttc aagacaacta tgagcgaacc
     4441 aaaaaagacg tgcaatatgt aaaagataca aagatagaag aagcctgtag tgatctattt
     4501 ggagacacaa acccttggtt tgccagtgaa gaagaaaaaa agaaaaacaa caatctgtca
     4561 catatgaacg ctatgaaatc ttacttcaac aagcaactaa catgcaaaat ccgacaaaaa
     4621 aagaaaccgc cttaaactat ctaaaaagtg tcaaggaatg gttagatcag caacaacaaa
     4681 attgaatttg atttaaaatc atgttaaact gaatgtgcaa atgatcaaac attagataca
     4741 cgaaagcccc agagaggtcg gattctctgg ggcttttttt caggttgatg tcgcctttat
     4801 tgattttact tcttgtttcg gttattcaac caataactga ataaagagac acaaactcct
     4861 acaagaaggg ggcaaatgaa cagttcaaac attagataca cctccttcca gtcgcaagac
     4921 tgtcggatag gcgacaagtt attatatctt aaaaaattaa atttgtgtgg tgtttttaag
     4981 tatcacttgt tttagggttg ttagggcttg ccctgaccgc ctgtaaggcg cttctcgact
     5041 agattaaggg aaattaatca agaattgtct tagaacggct tagacaagct ttcagagtct
     5101 cacacctcct ctttgaacaa cggttttagc aaaggagccg gaggcgactg cgcagtataa
     5161 tatgagagca tagcgatcac acctttttag cgaccgtagg gagcaagttt tccagtttag
     5221 aaaaattcgc gaaccttttt ggaggaaaaa gtaggagttt tttaggcggg aaattcaatg
     5281 tgctcttaag atatactgtt agatatactg ttagatatac tgttaataat aactgttagg
     5341 gattagcaac cttatgggag agtaagtatt gacataggta gtgggggata aattgtcaca
     5401 ctatggggga taaattgtca cactatgggg gataaattgt cacactatgg gggataaatt
     5461 gtcacactat gggggataaa ttgtgtttta catcctctta tgtctatgat aacataattt
     5521 attgaggtga tttttattga gtaacgatat agttcgatat aataatggat taaattctgt
     5581 ccctttaaga aaatttaccc ctatagatat ggatttattt tggggaatat gttctaaaat
     5641 gaaaagaaaa ggtacaaaag aagaaatttt tacatttaaa caaataaaag aattaattga
     5701 ttacaatata aatgcacgtg gcgaccgttt tgctaatgat ttaataaaaa tgtcaaaaaa
     5761 aatcattact ttgtctttta tttatgaaga cgaaaaaaca tatgaacaat taaatctgtt
     5821 tcaaaaattt aaaatcgata aagtgaatga aacattatta ataaaggttt ctgaagaatt
     5881 tgaatatata cttaattcaa tcggaactaa ttttactcgt ttcgaattag aaaatatgac
     5941 aaacttaaag agtagctacg ttaaag
//
