LOCUS       NZ_CP076482             4374 bp    DNA     circular CON 17-JUN-2024
DEFINITION  Enterococcus faecium strain UAMS_EF57 plasmid pUAMSEF5, complete
            sequence.
ACCESSION   NZ_CP076482
VERSION     NZ_CP076482.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN19573783
            Assembly: GCF_022647945.1
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_EF57
            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_022647945.1-RS_2024_06_17
            Annotation Date                   :: 06/17/2024 11:38:17
            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)                     :: 3,200
            CDSs (total)                      :: 3,108
            Genes (coding)                    :: 2,966
            CDSs (with protein)               :: 2,966
            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)         :: 84 of 142
            Pseudo Genes (internal stop)      :: 34 of 142
            Pseudo Genes (multiple problems)  :: 20 of 142
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP076482.1.
            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_EF57"
                     /isolation_source="blood"
                     /host="Homo sapiens"
                     /db_xref="taxon:1352"
                     /plasmid="pUAMSEF5"
                     /geo_loc_name="USA:Little Rock"
                     /collection_date="2019-04-02"
                     /genotype="vanA"
     gene            join(4206..4374,1..800)
                     /locus_tag="KPU56_RS15855"
                     /old_locus_tag="KPU56_15820"
     CDS             join(4206..4374,1..800)
                     /locus_tag="KPU56_RS15855"
                     /old_locus_tag="KPU56_15820"
                     /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            803..1036
                     /locus_tag="KPU56_RS15860"
                     /old_locus_tag="KPU56_15825"
     CDS             803..1036
                     /locus_tag="KPU56_RS15860"
                     /old_locus_tag="KPU56_15825"
                     /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            1029..1448
                     /locus_tag="KPU56_RS15865"
                     /old_locus_tag="KPU56_15830"
     CDS             1029..1448
                     /locus_tag="KPU56_RS15865"
                     /old_locus_tag="KPU56_15830"
                     /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            1457..1765
                     /locus_tag="KPU56_RS15870"
                     /old_locus_tag="KPU56_15835"
     CDS             1457..1765
                     /locus_tag="KPU56_RS15870"
                     /old_locus_tag="KPU56_15835"
                     /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            1769..2131
                     /locus_tag="KPU56_RS15875"
                     /old_locus_tag="KPU56_15840"
     CDS             1769..2131
                     /locus_tag="KPU56_RS15875"
                     /old_locus_tag="KPU56_15840"
                     /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            2353..3759
                     /locus_tag="KPU56_RS15880"
                     /old_locus_tag="KPU56_15845"
     CDS             2353..3759
                     /locus_tag="KPU56_RS15880"
                     /old_locus_tag="KPU56_15845"
                     /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          2..790
                     /name="rep_cluster_943"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="83.563"
                     /coverage="97.0"
                     /evalue="0.0"
     Typing          2354..3756
                     /name="MOBV"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="91.88"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 atgtgttgat tttagatttt gagcaattaa tgcgggtgaa tgaaggcaat ggctatttaa
       61 aagcggttgg gaataacggc tggcaattat tagaccaata cgaagaaaat attgcttata
      121 ttgagatttt gaaatggcaa gatggcaaag ggcggattga ttttaacccg aataagattg
      181 gtcatttttt agctagttca atgaaaaatt tcattcatga tttatttcta gaaccacatt
      241 tctcacgtgc ggatattgct tgcgatatta tcgatgtgcc tgatgagttt attacacaat
      301 atcgagtggt tgatcctgtt tctttcaagc caatttatgg gcggtctggg aagctggaaa
      361 cagcttattg gggcagtcgt gccagcgaac gccagattcg gctatacaac aaaaaattgg
      421 aacaggaaac caagcgtaaa attgtgccac cagaaataga aacttggtgg cgactggaat
      481 tgcagttaag gcgtgggaaa gcaacagatt ggcatgcaat ggttcatgaa agtttaaata
      541 gttttgctag ccctcatttt ctaccacttg atgtaaaaac aaatgataag gtgatgattt
      601 ttggactgat tgctaaccct gaaatgtggg ggtttttaga gcgtagaatg aaatacaaat
      661 tgagagatat tttgaaaaga gaaagtcaaa atgatgagtt gacgaatcat ttacgagaaa
      721 cattttcgga atcagcagat gttttgaaaa aagaattaga cacttggctt caagggttag
      781 atgtaacgga ggaggaataa gaatggcaga aaaacaaaag cattttggta agaaaaattg
      841 gttggtgaat ttaacaggtg ataacgttgt cgttgttttt ttggatagca aaaaaatgtc
      901 cggtaagtta cttgatgtaa cgcagtatga gttgattttg aaaaataata aaattgattc
      961 cccaatcatt atccctaagc atgctgttaa atatgtttat ggggtagctg aaagtaacgg
     1021 agaagataat gactgatttg ccagaaaaaa tgaccataaa aaaccttgct gatgagttgg
     1081 gtatatctaa aaatacagtg cgcaatcaac tggtcaatgc aggttatgac cttgctcggt
     1141 ataaagataa tggggttatc atgttagaca aggaattgat tggtgttgtg cggtcaattt
     1201 atcggtcaaa aggtggtcaa ttgactggtg atttaccggt caatgatgca ggcaatgatt
     1261 tcccgttaga aaaagaaaat gaatttttgc gtgaacaatt agcggaaaaa gataggcata
     1321 tttctgaatt aacggaaatg attcgtgacc aacaaaaatt gactttgctt cagcaacaaa
     1381 aaaacgatca gttgttacta gaaaatcaag aattaaaaaa tcgaaaatgg tggcaattct
     1441 ggaagtgagg tgtgacatgg ataaaattga tttgagagaa gaaacagtcg atagaattga
     1501 attgatgtat gaacggttag ctgattattt gaatttgccg gatgaagata attatagtga
     1561 aatgcttgaa cgaatgatgg atgttctcaa ctcggttatc aatgctgatc tagcaaaatc
     1621 ttcagttttg actaatgaat ttgttcataa gcatttagcg caaacaactg atgaatcaga
     1681 aaaagaattt tggttgaaat taatgagtca tgttatgcag ttaaaccaaa tttccgttat
     1741 taattccaaa gaaaaggaga tgtagtttat gggaatgact ttagcagata ttaaagcgca
     1801 agaagaaaaa ttaaaaaaag aacaagcgaa acttcgccaa cagaaaaaac gcttgattga
     1861 gaaagaaaat gctgcaatgg gcaaggctct tcgcaagcgt tttgggtttg aaacttttgc
     1921 tgattttgag cggtggctat cgtcgatttc tgacgatcag caacacgaaa aatcagtgga
     1981 taatgagtgg cttgctgatg aaaaatcagc gccaagcgaa cgagattatc ccgatgaatc
     2041 tgacggctta ttcggagtga taccgaataa gaaaagtcag atgagtgaga gtaaatttac
     2101 gtcaatattt aatgacgtga atttacgata agcgattatt ttgcgtgaag caaaataaag
     2161 cgtaaaagga gttgagagcg tgacacgctt tcggctcctt ttttcgttgt cacttgtgac
     2221 agcgaatacc ctcggagagc atttggaatt gtgacagcca tgtcacaatt aggaaaatgt
     2281 tactctttga caaagagtaa cagaaaggtt tacaatcttt ttattagcga cagcgcgaag
     2341 gagggtttta acttggggtt tagtatttca tttaaaaaag gaacgaagaa tacaagtatt
     2401 tctcataata atcgtgagtt aactgatcgc cagaaaacca atgattggca taagcatatt
     2461 gacttcacga aatcggatga aaatatttat ttagagcaga cgaatctagc agataaatat
     2521 gaggaattgt ttggcgaagt ggtagaaaaa tataatgcga aacaaaaaag agccgataga
     2581 aaaatcgagg actatttagc gaaagtgcgc aaggataaaa agttggaacc tcaacgagaa
     2641 tttattgtgc aaataggcat tttagatgat ttccagacaa atcgagcaga tggttcttct
     2701 actggcatat cgaaacaaca agctgaacaa aatcgagtga ttgccaataa aattttggtt
     2761 cagtattaca aggagtttca agagagaaac cctaatttgg ctgtttataa tgctgttatt
     2821 cataatgacg aaataagtcc gcacctgcac ttgaatattg tgccggttgc tgaaggttat
     2881 aaacggggtg ttcaaaagca gccgagcttt aataaagcac tggttcaaca agggatacac
     2941 gctgataaag ataatggtcg agtgcttttc aataatttta gaaatcaaga agttgactct
     3001 atagaacgat taatgaatga ttacggttgg aaaagggata ttgtcggtac caacaaaatt
     3061 aaagatattc acgaatacaa agaaatcatg agtgaaattt ctgaattgcg ccaaacggct
     3121 gtaaaagagc gtgagagcgt ttctgatgag ttgaggtata tttctaggca aagagaagaa
     3181 aacgagcgtg ataaggctct gatggcttct gagagagcga agattgaaga agagaagaaa
     3241 aatatgctga atgtaaaaaa agagatggcg gtcattttcc aaaaagatat ggttccttta
     3301 gaaagtttca agaggcttcc tgatggttcg tatcatttat ctgggaatga ttttgttgat
     3361 ttgtatcaac gagctacgag agcaacaaat gccaagagaa atgctgataa catgagtgag
     3421 caatatttac agatgcttga gcaaaataca gaattaaatg agtatgtagc tacattggaa
     3481 gaagagcgtc atttgtctgg tagaaaacaa ttagcagatt tacaagtgga aaataaaaag
     3541 ctgaaagaag aaaatcgctc tttacgccag cgtttagagc gattaaaaaa cgcatttcaa
     3601 aaatcgatca ctcgtttgtc tatccgtttt ggtcttgcag aaaaggatat ggggctttct
     3661 gaggaattag aagtgttaga gcaggagaaa accttatttt atcgtcaaaa cgtctcacag
     3721 cgtaaattag agcgttctga agatgagatc gagtggtagt tacgatgtgc agtcaacggt
     3781 accggaggcg gtttgtgccg aggataagga gttgacggct aaaccactag cctattaagc
     3841 tgacatttgc taaaaaatgg ccagtccatt ttttggccaa cctagcgtta gcgaagtttg
     3901 ggggcgccct tttcaaaggg tgcggtttta ttttttggat atttgcatag ctaaagagaa
     3961 gtgctattat tgagttagca aacaaatgaa ctgaaaaaag agtaaaaaaa tagtcgagca
     4021 acgctaccaa cgttctcgac ctttacggaa actaatcgca ctagctccgt aacttcttaa
     4081 tcattatacg aatattttta gatttcttca agactagaga ttttttggta atgaattttt
     4141 aagagttacg tgaacttttg aaaattcttt ccagaagtct ctttttcttt gaggaggaac
     4201 aaaatttgag taaaaatggc ataatcgtaa atgagtggga aaatttaaca gccctatcta
     4261 acaggcggtt aaatgtacaa aatatgtaca cccccttaaa aatgcagtgg tcaattgacc
     4321 gaattactat cgttggaaaa ctgaaggaaa atatttatta tcacactcaa aatg
//
