LOCUS       NZ_CP096216             4374 bp    DNA     circular CON 08-JUN-2024
DEFINITION  Enterococcus faecium strain UCH1 plasmid pUCH1-5, complete sequence.
ACCESSION   NZ_CP096216
VERSION     NZ_CP096216.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN27725314
            Assembly: GCF_023204955.1
KEYWORDS    RefSeq.
SOURCE      Enterococcus faecium
  ORGANISM  Enterococcus faecium
            Bacteria; Bacillota; Bacilli; Lactobacillales; Enterococcaceae;
            Enterococcus.
REFERENCE   1  (bases 1 to 4374)
  AUTHORS   Enroth,T.J., Kirsch,J.M., McCollister,B.D., Johnson,C.N. and
            Duerkop,B.A.
  TITLE     Enterococcus faecium UCH1
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 4374)
  AUTHORS   Enroth,T.J., Kirsch,J.M., McCollister,B.D., Johnson,C.N. and
            Duerkop,B.A.
  TITLE     Direct Submission
  JOURNAL   Submitted (21-APR-2022) Immunology and Microbiology, University of
            Colorado Anschutz Medical Campus, 12800 East 19th Ave, Aurora, CO
            80045, USA
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Date                     :: APR-2022
            Assembly Method                   :: Unicycler v. 0.5.0
            Assembly Name                     :: UCH1
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 225.8x
            Sequencing Technology             :: Oxford Nanopore; Illumina
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_023204955.1-RS_2024_06_08
            Annotation Date                   :: 06/08/2024 04:36:46
            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)                     :: 3,300
            CDSs (total)                      :: 3,209
            Genes (coding)                    :: 3,062
            CDSs (with protein)               :: 3,062
            Genes (RNA)                       :: 91
            rRNAs                             :: 6, 5, 5 (5S, 16S, 23S)
            complete rRNAs                    :: 6, 5, 5 (5S, 16S, 23S)
            tRNAs                             :: 71
            ncRNAs                            :: 4
            Pseudo Genes (total)              :: 147
            CDSs (without protein)            :: 147
            Pseudo Genes (ambiguous residues) :: 0 of 147
            Pseudo Genes (frameshifted)       :: 51 of 147
            Pseudo Genes (incomplete)         :: 92 of 147
            Pseudo Genes (internal stop)      :: 37 of 147
            Pseudo Genes (multiple problems)  :: 28 of 147
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP096216.1.
            Bacteria and source DNA available from Duerkop Lab, University of
            Colorado Medical School, Aurora, CO.
            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..4374
                     /organism="Enterococcus faecium"
                     /mol_type="genomic DNA"
                     /strain="UCH1"
                     /isolation_source="blood"
                     /host="Homo sapiens"
                     /db_xref="taxon:1352"
                     /plasmid="pUCH1-5"
                     /geo_loc_name="USA"
                     /lat_lon="39.742630 N 104.842026 W"
                     /collection_date="2019"
                     /collected_by="Bruce McCollister"
     gene            50..1018
                     /locus_tag="M0E25_RS16310"
                     /old_locus_tag="M0E25_16310"
     CDS             50..1018
                     /locus_tag="M0E25_RS16310"
                     /old_locus_tag="M0E25_16310"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002298422.1"
                     /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_002298422.1"
                     /translation="MSKNGIIVNEWENLTALSNRRLNVQNMYTPLKMQWSIDRITIVGK
                     LKENIYYHTQNDVLILDFEQLMRVNEGNGYLKAVGNNGWQLLDQYEENIAYIEILKWQD
                     GKGRIDFNPNKIGHFLASSMKNFIHDLFLEPHFSRADIACDIIDVPDEFITQYRVVDPV
                     SFKPIYGRSGKLETAYWGSRASERQIRLYNKKLEQETKRKIVPPEIETWWRLELQLRRG
                     KATDWHAMVHESLNSFASPHFLPLDVKTNDKVMIFGLIANPEMWGFLERRMKYKLRDIL
                     KRESQNDELTNHLRETFSESADVLKKELDTWLQGLDVTEEE"
                     /name="replication initiation factor domain-containing
                     protein"
     gene            1021..1254
                     /locus_tag="M0E25_RS16315"
                     /old_locus_tag="M0E25_16315"
     CDS             1021..1254
                     /locus_tag="M0E25_RS16315"
                     /old_locus_tag="M0E25_16315"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002298421.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_002298421.1"
                     /translation="MAEKQKHFGKKNWLVNLTGDNVVVVFLDSKKMSGKLLDVTQYELI
                     LKNNKIDSPIIIPKHAVKYVYGVAESNGEDND"
                     /name="hypothetical protein"
     gene            1247..1666
                     /locus_tag="M0E25_RS16320"
                     /old_locus_tag="M0E25_16320"
     CDS             1247..1666
                     /locus_tag="M0E25_RS16320"
                     /old_locus_tag="M0E25_16320"
                     /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_002298420.1"
                     /translation="MTDLPEKMTIKNLADELGISKNTVRNQLVNAGYDLARYKDNGVIM
                     LDKELIGVVRSIYRSKGGQLTGDLPVNDAGNDFPLEKENEFLREQLAEKDRHISELTEM
                     IRDQQKLTLLQQQKNDQLLLENQELKNRKWWQFWK"
                     /name="hypothetical protein"
     gene            1675..1983
                     /locus_tag="M0E25_RS16325"
                     /old_locus_tag="M0E25_16325"
     CDS             1675..1983
                     /locus_tag="M0E25_RS16325"
                     /old_locus_tag="M0E25_16325"
                     /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_002298419.1"
                     /translation="MDKIDLREETVDRIELMYERLADYLNLPDEDNYSEMLERMMDVLN
                     SVINADLAKSSVLTNEFVHKHLAQTTDESEKEFWLKLMSHVMQLNQISVINSKEKEM"
                     /name="hypothetical protein"
     gene            1987..2349
                     /locus_tag="M0E25_RS16330"
                     /old_locus_tag="M0E25_16330"
     CDS             1987..2349
                     /locus_tag="M0E25_RS16330"
                     /old_locus_tag="M0E25_16330"
                     /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            2571..3977
                     /locus_tag="M0E25_RS16335"
                     /old_locus_tag="M0E25_16335"
     CDS             2571..3977
                     /locus_tag="M0E25_RS16335"
                     /old_locus_tag="M0E25_16335"
                     /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_002317172.1"
                     /translation="MGFSISFKKGTKNTSISHNNRELTDRQKTNDWHKHIDFTKSDENI
                     YLEQTNLADKYEELFGEVVEKYNAKQKRADRKIEDYLAKVRKDKKLEPQREFIVQIGIL
                     DDFQTNRADGSSTGISKQQAEQNRVIANKILVQYYKEFQERNPNLAVYNAVIHNDEISP
                     HLHLNIVPVAEGYKRGVQKQPSFNKALVQQGIHADKDNGRVLFNNFRNQEVDSIERLMN
                     DYGWKRDIVGTNKIKDIHEYKEIMSEISELRQTAVKERESVSDELRYISRQREENERDK
                     ALMASERAKIEEEKKNMLNVKKEMAVIFQKDMVPLESFKRLPDGSYHLSGNDFVDLYQR
                     ATRATNAKRNADNMSEQYLQMLEQNTELNEYVATLEEERHLSGRKQLADLQVENKKLKE
                     ENRSLRQRLERLKNAFQKSITRLSIRFGLAEKDMGLSEELEVLEQEKTLFYRQNVSQRK
                     LERSEDEIEW"
                     /name="plasmid recombination protein"
     Typing          134..1008
                     /name="rep_cluster_943"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="84.032"
                     /coverage="97.0"
                     /evalue="0.0"
     Typing          2572..3974
                     /name="MOBV"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="91.88"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 tttgaaaatt ctttccagaa gtctcttttt ctttgaggag gaacaaaatt tgagtaaaaa
       61 tggcataatc gtaaatgagt gggaaaattt aacagcccta tctaacaggc ggttaaatgt
      121 acaaaatatg tacaccccct taaaaatgca gtggtcaatt gaccgaatta ctatcgttgg
      181 aaaactgaag gaaaatattt attatcacac tcaaaatgat gtgttgattt tagattttga
      241 gcaattaatg cgggtgaatg aaggcaatgg ctatttaaaa gcggttggga ataacggctg
      301 gcaattatta gaccaatacg aagaaaatat tgcttatatt gagattttga aatggcaaga
      361 tggcaaaggg cggattgatt ttaacccgaa taagattggt cattttttag ctagttcaat
      421 gaaaaatttc attcatgatt tatttctaga accacatttc tcacgtgcgg atattgcttg
      481 cgatattatc gatgtgcctg atgagtttat tacacaatat cgagtggttg atcctgtttc
      541 tttcaagcca atttatgggc ggtctgggaa gctggaaaca gcttattggg gcagtcgtgc
      601 cagcgaacgc cagattcggc tatacaacaa aaaattggaa caggaaacca agcgtaaaat
      661 tgtgccacca gaaatagaaa cttggtggcg actggaattg cagttaaggc gtgggaaagc
      721 aacagattgg catgcaatgg ttcatgaaag tttaaatagt tttgctagcc ctcattttct
      781 accacttgat gtaaaaacaa atgataaggt gatgattttt ggactgattg ctaaccctga
      841 aatgtggggg tttttagagc gtagaatgaa atacaaattg agagatattt tgaaaagaga
      901 aagtcaaaat gatgagttga cgaatcattt acgagaaaca ttttcggaat cagcagatgt
      961 tttgaaaaaa gaattagaca cttggcttca agggttagat gtaacggagg aggaataaga
     1021 atggcagaaa aacaaaagca ttttggtaag aaaaattggt tggtgaattt aacaggtgat
     1081 aacgttgtcg ttgttttttt ggatagcaaa aaaatgtccg gtaagttact tgatgtaacg
     1141 cagtatgagt tgattttgaa aaataataaa attgattccc caatcattat ccctaagcat
     1201 gctgttaaat atgtttatgg ggtagctgaa agtaacggag aagataatga ctgatttgcc
     1261 agaaaaaatg accataaaaa accttgctga tgagttgggt atatctaaaa atacagtgcg
     1321 caatcaactg gtcaatgcag gttatgacct tgctcggtat aaagataatg gggttatcat
     1381 gttagacaag gaattgattg gtgttgtgcg gtcaatttat cggtcaaaag gtggtcaatt
     1441 gactggtgat ttaccggtca atgatgcagg caatgatttc ccgttagaaa aagaaaatga
     1501 atttttgcgt gaacaattag cggaaaaaga taggcatatt tctgaattaa cggaaatgat
     1561 tcgtgaccaa caaaaattga ctttgcttca gcaacaaaaa aacgatcagt tgttactaga
     1621 aaatcaagaa ttaaaaaatc gaaaatggtg gcaattctgg aagtgaggtg tgacatggat
     1681 aaaattgatt tgagagaaga aacagtcgat agaattgaat tgatgtatga acggttagct
     1741 gattatttga atttgccgga tgaagataat tatagtgaaa tgcttgaacg aatgatggat
     1801 gttctcaact cggttatcaa tgctgatcta gcaaaatctt cagttttgac taatgaattt
     1861 gttcataagc atttagcgca aacaactgat gaatcagaaa aagaattttg gttgaaatta
     1921 atgagtcatg ttatgcagtt aaaccaaatt tccgttatta attccaaaga aaaggagatg
     1981 tagtttatgg gaatgacttt agcagatatt aaagcgcaag aagaaaaatt aaaaaaagaa
     2041 caagcgaaac ttcgccaaca gaaaaaacgc ttgattgaga aagaaaatgc tgcaatgggc
     2101 aaggctcttc gcaagcgttt tgggtttgaa acttttgctg attttgagcg gtggctatcg
     2161 tcgatttctg acgatcagca acacgaaaaa tcagtggata atgagtggct tgctgatgaa
     2221 aaatcagcgc caagcgaacg agattatccc gatgaatctg acggcttatt cggagtgata
     2281 ccgaataaga aaagtcagat gagtgagagt aaatttacgt caatatttaa tgacgtgaat
     2341 ttacgataag cgattatttt gcgtgaagca aaataaagcg taaaaggagt tgagagcgtg
     2401 acacgctttc ggctcctttt ttcgttgtca cttgtgacag cgaataccct cggagagcat
     2461 ttggaattgt gacagccatg tcacaattag gaaaatgtta ctctttgaca aagagtaaca
     2521 gaaaggttta caatcttttt attagcgaca gcgcgaagga gggttttaac ttggggttta
     2581 gtatttcatt taaaaaagga acgaagaata caagtatttc tcataataat cgtgagttaa
     2641 ctgatcgcca gaaaaccaat gattggcata agcatattga cttcacgaaa tcggatgaaa
     2701 atatttattt agagcagacg aatctagcag ataaatatga ggaattgttt ggcgaagtgg
     2761 tagaaaaata taatgcgaaa caaaaaagag ccgatagaaa aatcgaggac tatttagcga
     2821 aagtgcgcaa ggataaaaag ttggaacctc aacgagaatt tattgtgcaa ataggcattt
     2881 tagatgattt ccagacaaat cgagcagatg gttcttctac tggcatatcg aaacaacaag
     2941 ctgaacaaaa tcgagtgatt gccaataaaa ttttggttca gtattacaag gagtttcaag
     3001 agagaaaccc taatttggct gtttataatg ctgttattca taatgacgaa ataagtccgc
     3061 acctgcactt gaatattgtg ccggttgctg aaggttataa acggggtgtt caaaagcagc
     3121 cgagctttaa taaagcactg gttcaacaag ggatacacgc tgataaagat aatggtcgag
     3181 tgcttttcaa taattttaga aatcaagaag ttgactctat agaacgatta atgaatgatt
     3241 acggttggaa aagggatatt gtcggtacca acaaaattaa agatattcac gaatacaaag
     3301 aaatcatgag tgaaatttct gaattgcgcc aaacggctgt aaaagagcgt gagagcgttt
     3361 ctgatgagtt gaggtatatt tctaggcaaa gagaagaaaa cgagcgtgat aaggctctga
     3421 tggcttctga gagagcgaag attgaagaag agaagaaaaa tatgctgaat gtaaaaaaag
     3481 agatggcggt cattttccaa aaagatatgg ttcctttaga aagtttcaag aggcttcctg
     3541 atggttcgta tcatttatct gggaatgatt ttgttgattt gtatcaacga gctacgagag
     3601 caacaaatgc caagagaaat gctgataaca tgagtgagca atatttacag atgcttgagc
     3661 aaaatacaga attaaatgag tatgtagcta cattggaaga agagcgtcat ttgtctggta
     3721 gaaaacaatt agcagattta caagtggaaa ataaaaagct gaaagaagaa aatcgctctt
     3781 tacgccagcg tttagagcga ttaaaaaacg catttcaaaa atcgatcact cgtttgtcta
     3841 tccgttttgg tcttgcagaa aaggatatgg ggctttctga ggaattagaa gtgttagagc
     3901 aggagaaaac cttattttat cgtcaaaacg tctcacagcg taaattagag cgttctgaag
     3961 atgagatcga gtggtagtta cgatgtgcag tcaacggtac cggaggcggt ttgtgccgag
     4021 gataaggagt tgacggctaa accactagcc tattaagctg acatttgcta aaaaatggcc
     4081 agtccatttt ttggccaacc tagcgttagc gaagtttggg ggcgcccttt tcaaagggtg
     4141 cggttttatt ttttggatat ttgcatagct aaagagaagt gctattattg agttagcaaa
     4201 caaatgaact gaaaaaagag taaaaaaata gtcgagcaac gctaccaacg ttctcgacct
     4261 ttacggaaac taatcgcact agctccgtaa cttcttaatc attatacgaa tatttttaga
     4321 tttcttcaag actagagatt ttttggtaat gaatttttaa gagttacgtg aact
//
