LOCUS       NZ_CP096224             4374 bp    DNA     circular CON 14-MAY-2024
DEFINITION  Enterococcus faecium strain UCH5 plasmid pUCH5-5, complete sequence.
ACCESSION   NZ_CP096224
VERSION     NZ_CP096224.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN27728132
            Assembly: GCF_023204975.1
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 UCH5
  JOURNAL   Unpublished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                     :: 24-MAR-2022
            Assembly Method                   :: Unicycler v. 0.5.0
            Assembly Name                     :: UCH5
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 247.0x
            Sequencing Technology             :: Illumina; Oxford Nanopore
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_023204975.1-RS_2024_05_14
            Annotation Date                   :: 05/14/2024 04:32:40
            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)                     :: 3,037
            CDSs (total)                      :: 2,945
            Genes (coding)                    :: 2,809
            CDSs (with protein)               :: 2,809
            Genes (RNA)                       :: 92
            rRNAs                             :: 6, 6, 6 (5S, 16S, 23S)
            complete rRNAs                    :: 6, 6, 6 (5S, 16S, 23S)
            tRNAs                             :: 70
            ncRNAs                            :: 4
            Pseudo Genes (total)              :: 136
            CDSs (without protein)            :: 136
            Pseudo Genes (ambiguous residues) :: 0 of 136
            Pseudo Genes (frameshifted)       :: 52 of 136
            Pseudo Genes (incomplete)         :: 75 of 136
            Pseudo Genes (internal stop)      :: 34 of 136
            Pseudo Genes (multiple problems)  :: 21 of 136
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP096224.1.
            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="UCH5"
                     /isolation_source="blood"
                     /host="Homo sapiens"
                     /db_xref="taxon:1352"
                     /plasmid="pUCH5-5"
                     /geo_loc_name="USA"
                     /lat_lon="39.742630 N 104.842026 W"
                     /collection_date="2019"
                     /collected_by="Bruce McCollister"
     gene            complement(join(4291..4374,1..885))
                     /locus_tag="M0F39_RS15000"
                     /old_locus_tag="M0F39_15000"
     CDS             complement(join(4291..4374,1..885))
                     /locus_tag="M0F39_RS15000"
                     /old_locus_tag="M0F39_15000"
                     /inference="COORDINATES: ab initio prediction:GeneMarkS-2+"
                     /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: GeneMarkS-2+."
                     /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            complement(1332..2738)
                     /locus_tag="M0F39_RS15005"
                     /old_locus_tag="M0F39_15005"
     CDS             complement(1332..2738)
                     /locus_tag="M0F39_RS15005"
                     /old_locus_tag="M0F39_15005"
                     /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"
     gene            complement(2960..3322)
                     /locus_tag="M0F39_RS15010"
                     /old_locus_tag="M0F39_15010"
     CDS             complement(2960..3322)
                     /locus_tag="M0F39_RS15010"
                     /old_locus_tag="M0F39_15010"
                     /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            complement(3326..3634)
                     /locus_tag="M0F39_RS15015"
                     /old_locus_tag="M0F39_15015"
     CDS             complement(3326..3634)
                     /locus_tag="M0F39_RS15015"
                     /old_locus_tag="M0F39_15015"
                     /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            complement(3643..4062)
                     /locus_tag="M0F39_RS15020"
                     /old_locus_tag="M0F39_15020"
     CDS             complement(3643..4062)
                     /locus_tag="M0F39_RS15020"
                     /old_locus_tag="M0F39_15020"
                     /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            complement(4055..4288)
                     /locus_tag="M0F39_RS15025"
                     /old_locus_tag="M0F39_15025"
     CDS             complement(4055..4288)
                     /locus_tag="M0F39_RS15025"
                     /old_locus_tag="M0F39_15025"
                     /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"
     Typing          complement(2..802)
                     /name="rep_cluster_943"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="84.796"
                     /coverage="89.0"
                     /evalue="0.0"
     Typing          complement(1336..2738)
                     /name="MOBV"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="91.88"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 tcgtaaatga ttcgtcaact catcattttg actttctctt ttcaaaatat ctctcaattt
       61 gtatttcatt ctacgctcta aaaaccccca catttcaggg ttagcaatca gtccaaaaat
      121 catcacctta tcatttgttt ttacatcaag tggtagaaaa tgagggctag caaaactatt
      181 taaactttca tgaaccattg catgccaatc tgttgctttc ccacgcctta actgcaattc
      241 cagtcgccac caagtttcta tttctggtgg cacaatttta cgcttggttt cctgttccaa
      301 ttttttgttg tatagccgaa tctggcgttc gctggcacga ctgccccaat aagctgtttc
      361 cagcttccca gaccgcccat aaattggctt gaaagaaaca ggatcaacca ctcgatattg
      421 tgtaataaac tcatcaggca catcgataat atcgcaagca atatccgcac gtgagaaatg
      481 tggttctaga aataaatcat gaatgaaatt tttcattgaa ctagctaaaa aatgaccaat
      541 cttattcggg ttaaaatcaa tccgcccttt gccatcttgc catttcaaaa tctcaatata
      601 agcaatattt tcttcgtatt ggtctaataa ttgccagccg ttattcccaa ccgcttttaa
      661 atagccattg ccttcattca cccgcattaa ttgctcaaaa tctaaaatca acacatcatt
      721 ttgagtgtga taataaatat tttccttcag ttttccaacg atagtaattc ggtcaattga
      781 ccactgcatt tttaaggggg tgtacatatt ttgtacattt aaccgcctgt tagatagggc
      841 tgttaaattt tcccactcat ttacgattat gccattttta ctcaaatttt gttcctcctc
      901 aaagaaaaag agacttctgg aaagaatttt caaaagttca cgtaactctt aaaaattcat
      961 taccaaaaaa tctctagtct tgaagaaatc taaaaatatt cgtataatga ttaagaagtt
     1021 acggagctag tgcgattagt ttccgtaaag gtcgagaacg ttggtagcgt tgctcgacta
     1081 tttttttact cttttttcag ttcatttgtt tgctaactca ataatagcac ttctctttag
     1141 ctatgcaaat atccaaaaaa taaaaccgca ccctttgaaa agggcgcccc caaacttcgc
     1201 taacgctagg ttggccaaaa aatggactgg ccatttttta gcaaatgtca gcttaatagg
     1261 ctagtggttt agccgtcaac tccttatcct cggcacaaac cgcctccggt accgttgact
     1321 gcacatcgta actaccactc gatctcatct tcagaacgct ctaatttacg ctgtgagacg
     1381 ttttgacgat aaaataaggt tttctcctgc tctaacactt ctaattcctc agaaagcccc
     1441 atatcctttt ctgcaagacc aaaacggata gacaaacgag tgatcgattt ttgaaatgcg
     1501 ttttttaatc gctctaaacg ctggcgtaaa gagcgatttt cttctttcag ctttttattt
     1561 tccacttgta aatctgctaa ttgttttcta ccagacaaat gacgctcttc ttccaatgta
     1621 gctacatact catttaattc tgtattttgc tcaagcatct gtaaatattg ctcactcatg
     1681 ttatcagcat ttctcttggc atttgttgct ctcgtagctc gttgatacaa atcaacaaaa
     1741 tcattcccag ataaatgata cgaaccatca ggaagcctct tgaaactttc taaaggaacc
     1801 atatcttttt ggaaaatgac cgccatctct ttttttacat tcagcatatt tttcttctct
     1861 tcttcaatct tcgctctctc agaagccatc agagccttat cacgctcgtt ttcttctctt
     1921 tgcctagaaa tatacctcaa ctcatcagaa acgctctcac gctcttttac agccgtttgg
     1981 cgcaattcag aaatttcact catgatttct ttgtattcgt gaatatcttt aattttgttg
     2041 gtaccgacaa tatccctttt ccaaccgtaa tcattcatta atcgttctat agagtcaact
     2101 tcttgatttc taaaattatt gaaaagcact cgaccattat ctttatcagc gtgtatccct
     2161 tgttgaacca gtgctttatt aaagctcggc tgcttttgaa caccccgttt ataaccttca
     2221 gcaaccggca caatattcaa gtgcaggtgc ggacttattt cgtcattatg aataacagca
     2281 ttataaacag ccaaattagg gtttctctct tgaaactcct tgtaatactg aaccaaaatt
     2341 ttattggcaa tcactcgatt ttgttcagct tgttgtttcg atatgccagt agaagaacca
     2401 tctgctcgat ttgtctggaa atcatctaaa atgcctattt gcacaataaa ttctcgttga
     2461 ggttccaact ttttatcctt gcgcactttc gctaaatagt cctcgatttt tctatcggct
     2521 cttttttgtt tcgcattata tttttctacc acttcgccaa acaattcctc atatttatct
     2581 gctagattcg tctgctctaa ataaatattt tcatccgatt tcgtgaagtc aatatgctta
     2641 tgccaatcat tggttttctg gcgatcagtt aactcacgat tattatgaga aatacttgta
     2701 ttcttcgttc cttttttaaa tgaaatacta aaccccaagt taaaaccctc cttcgcgctg
     2761 tcgctaataa aaagattgta aacctttctg ttactctttg tcaaagagta acattttcct
     2821 aattgtgaca tggctgtcac aattccaaat gctctccgag ggtattcgct gtcacaagtg
     2881 acaacgaaaa aaggagccga aagcgtgtca cgctctcaac tccttttacg ctttattttg
     2941 cttcacgcaa aataatcgct tatcgtaaat tcacgtcatt aaatattgac gtaaatttac
     3001 tctcactcat ctgacttttc ttattcggta tcactccgaa taagccgtca gattcatcgg
     3061 gataatctcg ttcgcttggc gctgattttt catcagcaag ccactcatta tccactgatt
     3121 tttcgtgttg ctgatcgtca gaaatcgacg atagccaccg ctcaaaatca gcaaaagttt
     3181 caaacccaaa acgcttgcga agagccttgc ccattgcagc attttctttc tcaatcaagc
     3241 gttttttctg ttggcgaagt ttcgcttgtt ctttttttaa tttttcttct tgcgctttaa
     3301 tatctgctaa agtcattccc ataaactaca tctccttttc tttggaatta ataacggaaa
     3361 tttggtttaa ctgcataaca tgactcatta atttcaacca aaattctttt tctgattcat
     3421 cagttgtttg cgctaaatgc ttatgaacaa attcattagt caaaactgaa gattttgcta
     3481 gatcagcatt gataaccgag ttgagaacat ccatcattcg ttcaagcatt tcactataat
     3541 tatcttcatc cggcaaattc aaataatcag ctaaccgttc atacatcaat tcaattctat
     3601 cgactgtttc ttctctcaaa tcaattttat ccatgtcaca cctcacttcc agaattgcca
     3661 ccattttcga ttttttaatt cttgattttc tagtaacaac tgatcgtttt tttgttgctg
     3721 aagcaaagtc aatttttgtt ggtcacgaat catttccgtt aattcagaaa tatgcctatc
     3781 tttttccgct aattgttcac gcaaaaattc attttctttt tctaacggga aatcattgcc
     3841 tgcatcattg accggtaaat caccagtcaa ttgaccacct tttgaccgat aaattgaccg
     3901 cacaacacca atcaattcct tgtctaacat gataacccca ttatctttat accgagcaag
     3961 gtcataacct gcattgacca gttgattgcg cactgtattt ttagatatac ccaactcatc
     4021 agcaaggttt tttatggtca ttttttctgg caaatcagtc attatcttct ccgttacttt
     4081 cagctacccc ataaacatat ttaacagcat gcttagggat aatgattggg gaatcaattt
     4141 tattattttt caaaatcaac tcatactgcg ttacatcaag taacttaccg gacatttttt
     4201 tgctatccaa aaaaacaacg acaacgttat cacctgttaa attcaccaac caatttttct
     4261 taccaaaatg cttttgtttt tctgccattc ttattcctcc tccgttacat ctaacccttg
     4321 aagccaagtg tctaattctt ttttcaaaac atctgctgat tccgaaaatg tttc
//
