LOCUS       NZ_CP076487             4374 bp    DNA     circular CON 17-JUN-2024
DEFINITION  Enterococcus faecium strain UAMS_EF55 plasmid pUAMSEF5, complete
            sequence.
ACCESSION   NZ_CP076487
VERSION     NZ_CP076487.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN19573782
            Assembly: GCF_022648125.1
KEYWORDS    RefSeq.
SOURCE      Enterococcus faecium
  ORGANISM  Enterococcus faecium
            Bacteria; Bacillota; Bacilli; Lactobacillales; Enterococcaceae;
            Enterococcus.
REFERENCE   1  (bases 1 to 4374)
  AUTHORS   Udaondo,Z., Abram,K., Kothari,A. and Jun,S.R.
  TITLE     Top-Down Genomic Surveillance Approach To Investigate the Genomic
            Epidemiology and Antibiotic Resistance Patterns of Enterococcus
            faecium Detected in Cancer Patients in Arkansas
  JOURNAL   Microbiol Spectr 11 (3), e0490122 (2023)
   PUBMED   36995227
REFERENCE   2  (bases 1 to 4374)
  AUTHORS   Udaondo,Z., Abram,K.Z., Kothari,A. and Jun,S.-R.
  TITLE     Direct Submission
  JOURNAL   Submitted (04-JUN-2021) Department of Biomedical Informatics,
            University of Arkansas for Medical Sciences, 200 South Cedar St,
            Little Rock, AR 72205, USA
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Date                     :: 18-FEB-2021
            Assembly Method :: Unicycler v. v0.4.8; Canu v. v2.1.1; Pilon v.
            v1.23
            Assembly Name                     :: UAMS_EF55
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 200x
            Sequencing Technology :: Oxford Nanopore MinION; Illumina NextSeq
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_022648125.1-RS_2024_06_17
            Annotation Date                   :: 06/17/2024 11:13:17
            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)                     :: 3,203
            CDSs (total)                      :: 3,111
            Genes (coding)                    :: 2,969
            CDSs (with protein)               :: 2,969
            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)              :: 142
            CDSs (without protein)            :: 142
            Pseudo Genes (ambiguous residues) :: 0 of 142
            Pseudo Genes (frameshifted)       :: 48 of 142
            Pseudo Genes (incomplete)         :: 85 of 142
            Pseudo Genes (internal stop)      :: 33 of 142
            Pseudo Genes (multiple problems)  :: 20 of 142
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP076487.1.
            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..4374
                     /organism="Enterococcus faecium"
                     /mol_type="genomic DNA"
                     /strain="UAMS_EF55"
                     /isolation_source="blood"
                     /host="Homo sapiens"
                     /db_xref="taxon:1352"
                     /plasmid="pUAMSEF5"
                     /geo_loc_name="USA:Little Rock"
                     /collection_date="2019-04-01"
                     /genotype="vanA"
     gene            319..1287
                     /locus_tag="KPU59_RS15860"
                     /old_locus_tag="KPU59_15830"
     CDS             319..1287
                     /locus_tag="KPU59_RS15860"
                     /old_locus_tag="KPU59_15830"
                     /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            1290..1523
                     /locus_tag="KPU59_RS15865"
                     /old_locus_tag="KPU59_15835"
     CDS             1290..1523
                     /locus_tag="KPU59_RS15865"
                     /old_locus_tag="KPU59_15835"
                     /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            1516..1935
                     /locus_tag="KPU59_RS15870"
                     /old_locus_tag="KPU59_15840"
     CDS             1516..1935
                     /locus_tag="KPU59_RS15870"
                     /old_locus_tag="KPU59_15840"
                     /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            1944..2252
                     /locus_tag="KPU59_RS15875"
                     /old_locus_tag="KPU59_15845"
     CDS             1944..2252
                     /locus_tag="KPU59_RS15875"
                     /old_locus_tag="KPU59_15845"
                     /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            2256..2618
                     /locus_tag="KPU59_RS15880"
                     /old_locus_tag="KPU59_15850"
     CDS             2256..2618
                     /locus_tag="KPU59_RS15880"
                     /old_locus_tag="KPU59_15850"
                     /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            2840..4246
                     /locus_tag="KPU59_RS15885"
                     /old_locus_tag="KPU59_15855"
     CDS             2840..4246
                     /locus_tag="KPU59_RS15885"
                     /old_locus_tag="KPU59_15855"
                     /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          403..1277
                     /name="rep_cluster_943"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="84.032"
                     /coverage="97.0"
                     /evalue="0.0"
     Typing          2841..4243
                     /name="MOBV"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="91.88"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 ttagcgaagt ttgggggcgc ccttttcaaa gggtgcggtt ttattttttg gatatttgca
       61 tagctaaaga gaagtgctat tattgagtta gcaaacaaat gaactgaaaa aagagtaaaa
      121 aaatagtcga gcaacgctac caacgttctc gacctttacg gaaactaatc gcactagctc
      181 cgtaacttct taatcattat acgaatattt ttagatttct tcaagactag agattttttg
      241 gtaatgaatt tttaagagtt acgtgaactt ttgaaaattc tttccagaag tctctttttc
      301 tttgaggagg aacaaaattt gagtaaaaat ggcataatcg taaatgagtg ggaaaattta
      361 acagccctat ctaacaggcg gttaaatgta caaaatatgt acaccccctt aaaaatgcag
      421 tggtcaattg accgaattac tatcgttgga aaactgaagg aaaatattta ttatcacact
      481 caaaatgatg tgttgatttt agattttgag caattaatgc gggtgaatga aggcaatggc
      541 tatttaaaag cggttgggaa taacggctgg caattattag accaatacga agaaaatatt
      601 gcttatattg agattttgaa atggcaagat ggcaaagggc ggattgattt taacccgaat
      661 aagattggtc attttttagc tagttcaatg aaaaatttca ttcatgattt atttctagaa
      721 ccacatttct cacgtgcgga tattgcttgc gatattatcg atgtgcctga tgagtttatt
      781 acacaatatc gagtggttga tcctgtttct ttcaagccaa tttatgggcg gtctgggaag
      841 ctggaaacag cttattgggg cagtcgtgcc agcgaacgcc agattcggct atacaacaaa
      901 aaattggaac aggaaaccaa gcgtaaaatt gtgccaccag aaatagaaac ttggtggcga
      961 ctggaattgc agttaaggcg tgggaaagca acagattggc atgcaatggt tcatgaaagt
     1021 ttaaatagtt ttgctagccc tcattttcta ccacttgatg taaaaacaaa tgataaggtg
     1081 atgatttttg gactgattgc taaccctgaa atgtgggggt ttttagagcg tagaatgaaa
     1141 tacaaattga gagatatttt gaaaagagaa agtcaaaatg atgagttgac gaatcattta
     1201 cgagaaacat tttcggaatc agcagatgtt ttgaaaaaag aattagacac ttggcttcaa
     1261 gggttagatg taacggagga ggaataagaa tggcagaaaa acaaaagcat tttggtaaga
     1321 aaaattggtt ggtgaattta acaggtgata acgttgtcgt tgtttttttg gatagcaaaa
     1381 aaatgtccgg taagttactt gatgtaacgc agtatgagtt gattttgaaa aataataaaa
     1441 ttgattcccc aatcattatc cctaagcatg ctgttaaata tgtttatggg gtagctgaaa
     1501 gtaacggaga agataatgac tgatttgcca gaaaaaatga ccataaaaaa ccttgctgat
     1561 gagttgggta tatctaaaaa tacagtgcgc aatcaactgg tcaatgcagg ttatgacctt
     1621 gctcggtata aagataatgg ggttatcatg ttagacaagg aattgattgg tgttgtgcgg
     1681 tcaatttatc ggtcaaaagg tggtcaattg actggtgatt taccggtcaa tgatgcaggc
     1741 aatgatttcc cgttagaaaa agaaaatgaa tttttgcgtg aacaattagc ggaaaaagat
     1801 aggcatattt ctgaattaac ggaaatgatt cgtgaccaac aaaaattgac tttgcttcag
     1861 caacaaaaaa acgatcagtt gttactagaa aatcaagaat taaaaaatcg aaaatggtgg
     1921 caattctgga agtgaggtgt gacatggata aaattgattt gagagaagaa acagtcgata
     1981 gaattgaatt gatgtatgaa cggttagctg attatttgaa tttgccggat gaagataatt
     2041 atagtgaaat gcttgaacga atgatggatg ttctcaactc ggttatcaat gctgatctag
     2101 caaaatcttc agttttgact aatgaatttg ttcataagca tttagcgcaa acaactgatg
     2161 aatcagaaaa agaattttgg ttgaaattaa tgagtcatgt tatgcagtta aaccaaattt
     2221 ccgttattaa ttccaaagaa aaggagatgt agtttatggg aatgacttta gcagatatta
     2281 aagcgcaaga agaaaaatta aaaaaagaac aagcgaaact tcgccaacag aaaaaacgct
     2341 tgattgagaa agaaaatgct gcaatgggca aggctcttcg caagcgtttt gggtttgaaa
     2401 cttttgctga ttttgagcgg tggctatcgt cgatttctga cgatcagcaa cacgaaaaat
     2461 cagtggataa tgagtggctt gctgatgaaa aatcagcgcc aagcgaacga gattatcccg
     2521 atgaatctga cggcttattc ggagtgatac cgaataagaa aagtcagatg agtgagagta
     2581 aatttacgtc aatatttaat gacgtgaatt tacgataagc gattattttg cgtgaagcaa
     2641 aataaagcgt aaaaggagtt gagagcgtga cacgctttcg gctccttttt tcgttgtcac
     2701 ttgtgacagc gaataccctc ggagagcatt tggaattgtg acagccatgt cacaattagg
     2761 aaaatgttac tctttgacaa agagtaacag aaaggtttac aatcttttta ttagcgacag
     2821 cgcgaaggag ggttttaact tggggtttag tatttcattt aaaaaaggaa cgaagaatac
     2881 aagtatttct cataataatc gtgagttaac tgatcgccag aaaaccaatg attggcataa
     2941 gcatattgac ttcacgaaat cggatgaaaa tatttattta gagcagacga atctagcaga
     3001 taaatatgag gaattgtttg gcgaagtggt agaaaaatat aatgcgaaac aaaaaagagc
     3061 cgatagaaaa atcgaggact atttagcgaa agtgcgcaag gataaaaagt tggaacctca
     3121 acgagaattt attgtgcaaa taggcatttt agatgatttc cagacaaatc gagcagatgg
     3181 ttcttctact ggcatatcga aacaacaagc tgaacaaaat cgagtgattg ccaataaaat
     3241 tttggttcag tattacaagg agtttcaaga gagaaaccct aatttggctg tttataatgc
     3301 tgttattcat aatgacgaaa taagtccgca cctgcacttg aatattgtgc cggttgctga
     3361 aggttataaa cggggtgttc aaaagcagcc gagctttaat aaagcactgg ttcaacaagg
     3421 gatacacgct gataaagata atggtcgagt gcttttcaat aattttagaa atcaagaagt
     3481 tgactctata gaacgattaa tgaatgatta cggttggaaa agggatattg tcggtaccaa
     3541 caaaattaaa gatattcacg aatacaaaga aatcatgagt gaaatttctg aattgcgcca
     3601 aacggctgta aaagagcgtg agagcgtttc tgatgagttg aggtatattt ctaggcaaag
     3661 agaagaaaac gagcgtgata aggctctgat ggcttctgag agagcgaaga ttgaagaaga
     3721 gaagaaaaat atgctgaatg taaaaaaaga gatggcggtc attttccaaa aagatatggt
     3781 tcctttagaa agtttcaaga ggcttcctga tggttcgtat catttatctg ggaatgattt
     3841 tgttgatttg tatcaacgag ctacgagagc aacaaatgcc aagagaaatg ctgataacat
     3901 gagtgagcaa tatttacaga tgcttgagca aaatacagaa ttaaatgagt atgtagctac
     3961 attggaagaa gagcgtcatt tgtctggtag aaaacaatta gcagatttac aagtggaaaa
     4021 taaaaagctg aaagaagaaa atcgctcttt acgccagcgt ttagagcgat taaaaaacgc
     4081 atttcaaaaa tcgatcactc gtttgtctat ccgttttggt cttgcagaaa aggatatggg
     4141 gctttctgag gaattagaag tgttagagca ggagaaaacc ttattttatc gtcaaaacgt
     4201 ctcacagcgt aaattagagc gttctgaaga tgagatcgag tggtagttac gatgtgcagt
     4261 caacggtacc ggaggcggtt tgtgccgagg ataaggagtt gacggctaaa ccactagcct
     4321 attaagctga catttgctaa aaaatggcca gtccattttt tggccaacct agcg
//
