LOCUS       NZ_CP088194             4147 bp    DNA     circular CON 21-MAY-2024
DEFINITION  Enterococcus faecium strain S2-6b plasmid pS2-6b-c, complete
            sequence.
ACCESSION   NZ_CP088194
VERSION     NZ_CP088194.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN23424489
            Assembly: GCF_023375205.1
KEYWORDS    RefSeq.
SOURCE      Enterococcus faecium
  ORGANISM  Enterococcus faecium
            Bacteria; Bacillota; Bacilli; Lactobacillales; Enterococcaceae;
            Enterococcus.
REFERENCE   1  (bases 1 to 4147)
  AUTHORS   Biggel,M.
  TITLE     Characteristics of florfenicol resistant enterococci from fattening
            pigs
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 4147)
  AUTHORS   Biggel,M.
  TITLE     Direct Submission
  JOURNAL   Submitted (26-NOV-2021) Institute for Food Safety and Hygiene,
            University of Zurich, Winterthurerstrasse 272, Zurich 8057,
            Switzerland
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: Unicycler v. 0.4.8
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 99x,185x
            Sequencing Technology :: Illumina MiniSeq, Oxford Nanopore Minion
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_023375205.1-RS_2024_05_21
            Annotation Date                   :: 05/21/2024 04:26:24
            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)                     :: 2,678
            CDSs (total)                      :: 2,588
            Genes (coding)                    :: 2,490
            CDSs (with protein)               :: 2,490
            Genes (RNA)                       :: 90
            rRNAs                             :: 6, 6, 6 (5S, 16S, 23S)
            complete rRNAs                    :: 6, 6, 6 (5S, 16S, 23S)
            tRNAs                             :: 68
            ncRNAs                            :: 4
            Pseudo Genes (total)              :: 98
            CDSs (without protein)            :: 98
            Pseudo Genes (ambiguous residues) :: 0 of 98
            Pseudo Genes (frameshifted)       :: 40 of 98
            Pseudo Genes (incomplete)         :: 56 of 98
            Pseudo Genes (internal stop)      :: 24 of 98
            Pseudo Genes (multiple problems)  :: 17 of 98
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP088194.1.
            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..4147
                     /organism="Enterococcus faecium"
                     /mol_type="genomic DNA"
                     /strain="S2-6b"
                     /isolation_source="fecal sample"
                     /host="Sus scrofa domesticus"
                     /db_xref="taxon:1352"
                     /plasmid="pS2-6b-c"
                     /collection_date="2021"
                     /collected_by="ILS, University of Zurich"
     gene            1..975
                     /locus_tag="LQ050_RS13300"
                     /old_locus_tag="LQ050_13300"
     CDS             1..975
                     /locus_tag="LQ050_RS13300"
                     /old_locus_tag="LQ050_13300"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002342725.1"
                     /GO_function="GO:0003677 - DNA binding [Evidence IEA];
                     GO:0003916 - DNA topoisomerase 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 factor domain-containing
                     protein"
                     /protein_id="WP_002326821.1"
                     /translation="MSKRGTIVNEWEKLNRISNRRLKYQSLTLPLKMQWSIDRITIVGK
                     LKENIYYHTPNDVLILNFEQLMRLNEGNGYLKAVGNNGWQLLDQHEENIAYIEILKFHE
                     GKGRIDFNPNKINQFLSGSMKNFIHDLFLEPHFSRADIACDIVDIPDDFVSQYRVVDPV
                     SFKPIYGRSGKLETAYWGSRASERQIRMYNKKLEQERKRKIVPPEITTWWRLELQLRRG
                     KATDWHEMVHESLDSFASPHYFPPNTKVTERIMVKGLLYDHSEWGNLAKNTKKKYRDLL
                     KQESQNDELTNHLRESFAESADDLKRELDTWLQGLDVTEVGAE"
                     /name="replication initiation factor domain-containing
                     protein"
     gene            972..1391
                     /locus_tag="LQ050_RS13305"
                     /old_locus_tag="LQ050_13305"
     CDS             972..1391
                     /locus_tag="LQ050_RS13305"
                     /old_locus_tag="LQ050_13305"
                     /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="WP_002292671.1"
                     /translation="MSNPVEKMTIKNLADELGVSKNTVRNQLVNSGFDLAQYKENGIIM
                     LDKELIGVVRSIYRSKSDQLTGQLPVNNTGSDFPLEKENEFLRDQLAEKDKHISELTEM
                     IRDQQKLTLLQQQKNDQLLLENQELKNRKWWQFWK"
                     /name="hypothetical protein"
     gene            1400..1708
                     /locus_tag="LQ050_RS13310"
                     /old_locus_tag="LQ050_13310"
     CDS             1400..1708
                     /locus_tag="LQ050_RS13310"
                     /old_locus_tag="LQ050_13310"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002292673.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_002333831.1"
                     /translation="MDKIDLREETVDRIELMYERLADYLNLPDEDNYSEMLERIMDVLN
                     SVINADLAKSSVLTNEFVHKHLAQTTDESEKEFWLKLMSHVMQLNQISVINSKEKEM"
                     /name="hypothetical protein"
     gene            1712..2074
                     /locus_tag="LQ050_RS13315"
                     /old_locus_tag="LQ050_13315"
     CDS             1712..2074
                     /locus_tag="LQ050_RS13315"
                     /old_locus_tag="LQ050_13315"
                     /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="WP_002298418.1"
                     /translation="MGMTLADIKAQEEKLKKEQAKLRQQKKRLIEKENAAMGKALRKRF
                     GFETFADFERWLSSISDDQQHEKSVDNEWLADEKSAPSERDYPDESDGLFGVIPNKKSQ
                     MSESKFTSIFNDVNLR"
                     /name="hypothetical protein"
     gene            2295..3701
                     /locus_tag="LQ050_RS13320"
                     /old_locus_tag="LQ050_13320"
     CDS             2295..3701
                     /locus_tag="LQ050_RS13320"
                     /old_locus_tag="LQ050_13320"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_016173818.1"
                     /GO_function="GO:0003677 - DNA binding [Evidence IEA]"
                     /GO_process="GO:0006310 - DNA recombination [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="plasmid recombination protein"
                     /protein_id="WP_002333830.1"
                     /translation="MGFSISFKKGTKNTSISHNNRELTDSQKINDWHKHIDFTKSDENI
                     YLEQTNIREKYEELFGEAVEKYNAKQKRADRKIEDYLAKVRKDKKLEPQREFIVQIGTL
                     DDFRTTRDDGSSTGISEQQAEQNRVIANKILVEYFKEFKERNPNLSVYNAVIHNDEVSP
                     HLHLNIVPVAEGYKRGVQKQPSFNKALQQQGLRADKENGRVIWNNFRNQEVESIERLMA
                     DFGWERELVGTNKIKDVHEYKEIMSEISELRQTAVKERESVSDELRYISRQREENEREK
                     ALVASERVKIEEEKKNMLNVKKEMAVIFQKDIVPLESFKRLPDGSYHLSGNDFVDLYQR
                     ATRATNAKRNADNMSEQYLQMLEQNTELNEYVATLEEERHLSGRKQLADLQVENKKLKE
                     ENRSLRQRLERLKNAFQKSITRLSIRFGLAEKDMGLSEELEVLEQEKTLFYRQNVSQRK
                     LERSEDEIEW"
                     /name="plasmid recombination protein"
     Typing          23..972
                     /name="rep_cluster_943"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="99.685"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          2296..3698
                     /name="MOBV"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="97.65"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 ttgagtaaac gtggcacgat cgtgaatgag tgggaaaaac ttaaccgcat ttctaacagg
       61 cggttaaagt atcaaagttt gacccttccc ttaaaaatgc agtggtcaat tgaccgaatt
      121 accatagtcg gaaaactgaa agaaaatatt tattatcaca ctccaaatga tgtgttgatt
      181 ttaaattttg aacagcttat gcgtttgaac gaaggcaatg gttatttaaa agctgttggg
      241 aataatgggt ggcaattatt agaccaacac gaggaaaata tagcttatat tgagattctt
      301 aaatttcatg aaggaaaagg gcggattgac tttaatccta ataaaatcaa tcaattttta
      361 tcaggttcca tgaaaaattt cattcatgat ttatttctag aacctcattt ttcacgtgcg
      421 gatattgctt gcgatattgt agatattccc gatgactttg ttagtcagta tcgtgtagtt
      481 gatcctgtgt cttttaaacc aatttatggg cgttctggta agttagaaac ggcatattgg
      541 ggtagtcgtg ccagtgaacg acaaattcga atgtacaata aaaaattgga acaagaaaga
      601 aaacgtaaaa ttgttccgcc ggaaataacg acatggtggc gactagaatt gcagttacga
      661 aggggaaaag caactgattg gcatgagatg gttcatgaaa gtttggatag ctttgctagt
      721 ccacattatt ttccgccaaa tactaaagtt actgaacgga ttatggtgaa aggtttgctt
      781 tatgatcatt ctgagtgggg aaatctagct aagaatacaa agaaaaaata cagggatttg
      841 ttgaagcaag aaagtcaaaa tgatgaattg acgaatcatt tgcgagagtc atttgcggaa
      901 tcggcagacg atttgaaacg agaattagat acatggctcc aaggacttga tgtaacggaa
      961 gtaggtgctg aatgagtaat ccagtagaaa aaatgaccat aaaaaatctt gctgacgaat
     1021 tgggtgtatc gaaaaataca gtgcgcaatc aactggtcaa ttcagggttt gaccttgctc
     1081 agtataaaga aaatggcatt atcatgctag ataaagagtt gattggtgtt gttcggtcaa
     1141 tttatcggtc aaaaagtgat caattgactg gtcaattacc ggtcaataac acaggcagtg
     1201 attttccttt agaaaaagag aatgagtttt tgcgtgatca attagctgag aaggacaaac
     1261 atatttctga attaacagaa atgattcgtg atcaacaaaa attgaccctg cttcagcaac
     1321 aaaaaaacga tcagttgtta ctagaaaatc aagaattaaa aaatcgaaaa tggtggcaat
     1381 tctggaagtg aggtgtgaca tggataaaat tgatttgaga gaagaaacag tcgatagaat
     1441 tgaattgatg tatgaacggt tagctgatta tttgaatttg ccggatgaag ataattatag
     1501 tgaaatgctt gaacgaatta tggatgttct caactcggtt atcaatgctg atttagcaaa
     1561 atcttcagtt ttgactaatg aatttgttca taagcattta gcgcaaacaa ctgatgaatc
     1621 agaaaaagaa ttttggttga aattaatgag tcatgttatg cagttaaacc aaatttccgt
     1681 tattaattcc aaagaaaagg agatgtagtt tatgggaatg actttagcag atattaaagc
     1741 gcaagaagaa aaattaaaaa aagaacaagc gaaacttcgc caacagaaaa aacgcttgat
     1801 tgagaaagaa aatgctgcaa tgggcaaggc tcttcgcaag cgttttgggt ttgaaacttt
     1861 tgctgatttt gagcggtggc tatcgtcgat ttctgacgat cagcaacacg aaaaatcagt
     1921 ggataatgag tggcttgctg atgaaaaatc agcgccaagc gaacgagatt atcccgatga
     1981 atctgacggc ttattcggag tgataccgaa taagaaaagt cagatgagtg agagtaaatt
     2041 tacgtcaata tttaatgacg tgaatttacg ataagcgatt attttgcgtg aagcaaaata
     2101 aagcgtaaaa ggagttgaga gcgtgacacg ctttcggctc cttttttcgt tgtcacttgt
     2161 gacagcgaat accctcggag agcatttgga attgtgacag ccatgtcaca attaggaaaa
     2221 tgttactctt tgacaaagag taacagaaag gtttacactc tttttattag cgacagccga
     2281 aggagggttt taacttgggg ttcagtattt cgttcaaaaa gggaacaaag aatacaagca
     2341 tttctcataa taatcgtgag ttaactgata gccaaaaaat caatgactgg cataagcata
     2401 ttgatttcac aaaatcggat gaaaatatct atttagaaca aacaaatatt cgtgaaaaat
     2461 atgaagaatt attcggtgaa gccgtagaaa aatataatgc aaagcagaaa agagccgata
     2521 gaaaaatcga ggactattta gcaaaggttc gcaaggataa aaaattggaa ccacagcgag
     2581 aatttatcgt gcaaattggt actcttgatg attttcgtac tactcgtgat gatggttctt
     2641 ctactggcat atcggaacaa caagcagaac aaaatcgagt gattgccaac aaaattttag
     2701 ttgagtattt caaagaattt aaagaacgga atcctaattt atccgtctac aatgctgtta
     2761 ttcataatga cgaagtaagt ccgcacctgc atttgaatat tgttcctgtt gctgaagggt
     2821 ataaacgggg tgttcaaaag caaccaagtt ttaacaaagc cttgcaacag cagggtttac
     2881 gagcagataa agagaatggt cgagtgattt ggaataattt taggaatcag gaagttgagt
     2941 caattgaacg tttgatggca gattttggtt gggagcgtga gttagtcggt actaacaaaa
     3001 tcaaagatgt tcacgaatat aaagaaatca tgagcgagat ttcagaattg cgtcaaacgg
     3061 ccgtaaaaga gcgtgagagc gtttctgatg agttgaggta tatttctagg caaagagaag
     3121 aaaatgagcg agaaaaggct ctggtggctt ctgagagagt gaagattgaa gaagagaaga
     3181 aaaatatgct gaatgtaaaa aaagagatgg cggtcatttt ccaaaaagat attgttcctt
     3241 tagaaagttt caagaggctt cctgatggtt cgtatcattt atctgggaat gattttgttg
     3301 atttgtatca acgagctacg agagcaacaa atgccaagag aaatgctgat aacatgagtg
     3361 agcaatattt acagatgctt gagcaaaata cagaattaaa tgagtatgta gctacattgg
     3421 aagaagagcg tcatttgtct ggtagaaaac aattagcaga tttacaagtg gaaaataaaa
     3481 agctgaaaga agaaaatcgc tctttacgcc agcgtttaga gcgattaaaa aacgcatttc
     3541 aaaaatcgat cactcgtttg tctatccgtt ttggtcttgc agaaaaggat atggggcttt
     3601 ctgaggaatt agaagtgtta gagcaggaga aaaccttatt ttatcgtcaa aacgtctcac
     3661 agcgtaaatt agagcgttct gaagatgaga tcgagtggta gttacgatgt gcagtcaacg
     3721 gtaccggagg cggtttgtgc cgaggataag gagttgacgg ctaaaccact agcctattaa
     3781 gctgacattt gctaaaaaat ggccagtcca ttttttggcc aacctagcgt tagcgaagtt
     3841 tgggggcgcc cttttcaaag ggtgcggttt tattttttgg atatttgcat agctaaagag
     3901 aagtgctatt attgagttag caaacaaatg aactgaaaaa agagtaaaaa aatagtcgag
     3961 caacgctacc aacgttctcg acctttacgg aaactaatcg cactagctcc gtaacttctt
     4021 aatcattata cgaatatttt tagatttctt caagactaga gattttttgg taatgaattt
     4081 ttaagagtta cgtgaacttt tgaaaattct ttccagaagt ctctttttct ttgaggagga
     4141 acaaaat
//
