LOCUS       NZ_CP076476             4374 bp    DNA     circular CON 17-JUN-2024
DEFINITION  Enterococcus faecium strain UAMS_EF58 plasmid pUAMSEF5, complete
            sequence.
ACCESSION   NZ_CP076476
VERSION     NZ_CP076476.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN19573784
            Assembly: GCF_022647825.1
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_EF58
            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_022647825.1-RS_2024_06_17
            Annotation Date                   :: 06/17/2024 11:35:59
            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)                     :: 3,189
            CDSs (total)                      :: 3,097
            Genes (coding)                    :: 2,958
            CDSs (with protein)               :: 2,958
            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)              :: 139
            CDSs (without protein)            :: 139
            Pseudo Genes (ambiguous residues) :: 0 of 139
            Pseudo Genes (frameshifted)       :: 48 of 139
            Pseudo Genes (incomplete)         :: 81 of 139
            Pseudo Genes (internal stop)      :: 34 of 139
            Pseudo Genes (multiple problems)  :: 20 of 139
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP076476.1.
            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_EF58"
                     /isolation_source="blood"
                     /host="Homo sapiens"
                     /db_xref="taxon:1352"
                     /plasmid="pUAMSEF5"
                     /geo_loc_name="USA:Little Rock"
                     /collection_date="2019-04-03"
                     /genotype="vanA"
     gene            join(4072..4374,1..60)
                     /locus_tag="KPU57_RS15795"
                     /old_locus_tag="KPU57_15770"
     CDS             join(4072..4374,1..60)
                     /locus_tag="KPU57_RS15795"
                     /old_locus_tag="KPU57_15770"
                     /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            282..1688
                     /locus_tag="KPU57_RS15800"
                     /old_locus_tag="KPU57_15775"
     CDS             282..1688
                     /locus_tag="KPU57_RS15800"
                     /old_locus_tag="KPU57_15775"
                     /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            2135..3103
                     /locus_tag="KPU57_RS15805"
                     /old_locus_tag="KPU57_15780"
     CDS             2135..3103
                     /locus_tag="KPU57_RS15805"
                     /old_locus_tag="KPU57_15780"
                     /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            3106..3339
                     /locus_tag="KPU57_RS15810"
                     /old_locus_tag="KPU57_15785"
     CDS             3106..3339
                     /locus_tag="KPU57_RS15810"
                     /old_locus_tag="KPU57_15785"
                     /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            3332..3751
                     /locus_tag="KPU57_RS15815"
                     /old_locus_tag="KPU57_15790"
     CDS             3332..3751
                     /locus_tag="KPU57_RS15815"
                     /old_locus_tag="KPU57_15790"
                     /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            3760..4068
                     /locus_tag="KPU57_RS15820"
                     /old_locus_tag="KPU57_15795"
     CDS             3760..4068
                     /locus_tag="KPU57_RS15820"
                     /old_locus_tag="KPU57_15795"
                     /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"
     Typing          2219..3093
                     /name="rep_cluster_943"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="84.032"
                     /coverage="97.0"
                     /evalue="0.0"
     Typing          283..1685
                     /name="MOBV"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="91.88"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 aaaagtcaga tgagtgagag taaatttacg tcaatattta atgacgtgaa tttacgataa
       61 gcgattattt tgcgtgaagc aaaataaagc gtaaaaggag ttgagagcgt gacacgcttt
      121 cggctccttt tttcgttgtc acttgtgaca gcgaataccc tcggagagca tttggaattg
      181 tgacagccat gtcacaatta ggaaaatgtt actctttgac aaagagtaac agaaaggttt
      241 acaatctttt tattagcgac agcgcgaagg agggttttaa cttggggttt agtatttcat
      301 ttaaaaaagg aacgaagaat acaagtattt ctcataataa tcgtgagtta actgatcgcc
      361 agaaaaccaa tgattggcat aagcatattg acttcacgaa atcggatgaa aatatttatt
      421 tagagcagac gaatctagca gataaatatg aggaattgtt tggcgaagtg gtagaaaaat
      481 ataatgcgaa acaaaaaaga gccgatagaa aaatcgagga ctatttagcg aaagtgcgca
      541 aggataaaaa gttggaacct caacgagaat ttattgtgca aataggcatt ttagatgatt
      601 tccagacaaa tcgagcagat ggttcttcta ctggcatatc gaaacaacaa gctgaacaaa
      661 atcgagtgat tgccaataaa attttggttc agtattacaa ggagtttcaa gagagaaacc
      721 ctaatttggc tgtttataat gctgttattc ataatgacga aataagtccg cacctgcact
      781 tgaatattgt gccggttgct gaaggttata aacggggtgt tcaaaagcag ccgagcttta
      841 ataaagcact ggttcaacaa gggatacacg ctgataaaga taatggtcga gtgcttttca
      901 ataattttag aaatcaagaa gttgactcta tagaacgatt aatgaatgat tacggttgga
      961 aaagggatat tgtcggtacc aacaaaatta aagatattca cgaatacaaa gaaatcatga
     1021 gtgaaatttc tgaattgcgc caaacggctg taaaagagcg tgagagcgtt tctgatgagt
     1081 tgaggtatat ttctaggcaa agagaagaaa acgagcgtga taaggctctg atggcttctg
     1141 agagagcgaa gattgaagaa gagaagaaaa atatgctgaa tgtaaaaaaa gagatggcgg
     1201 tcattttcca aaaagatatg gttcctttag aaagtttcaa gaggcttcct gatggttcgt
     1261 atcatttatc tgggaatgat tttgttgatt tgtatcaacg agctacgaga gcaacaaatg
     1321 ccaagagaaa tgctgataac atgagtgagc aatatttaca gatgcttgag caaaatacag
     1381 aattaaatga gtatgtagct acattggaag aagagcgtca tttgtctggt agaaaacaat
     1441 tagcagattt acaagtggaa aataaaaagc tgaaagaaga aaatcgctct ttacgccagc
     1501 gtttagagcg attaaaaaac gcatttcaaa aatcgatcac tcgtttgtct atccgttttg
     1561 gtcttgcaga aaaggatatg gggctttctg aggaattaga agtgttagag caggagaaaa
     1621 ccttatttta tcgtcaaaac gtctcacagc gtaaattaga gcgttctgaa gatgagatcg
     1681 agtggtagtt acgatgtgca gtcaacggta ccggaggcgg tttgtgccga ggataaggag
     1741 ttgacggcta aaccactagc ctattaagct gacatttgct aaaaaatggc cagtccattt
     1801 tttggccaac ctagcgttag cgaagtttgg gggcgccctt ttcaaagggt gcggttttat
     1861 tttttggata tttgcatagc taaagagaag tgctattatt gagttagcaa acaaatgaac
     1921 tgaaaaaaga gtaaaaaaat agtcgagcaa cgctaccaac gttctcgacc tttacggaaa
     1981 ctaatcgcac tagctccgta acttcttaat cattatacga atatttttag atttcttcaa
     2041 gactagagat tttttggtaa tgaattttta agagttacgt gaacttttga aaattctttc
     2101 cagaagtctc tttttctttg aggaggaaca aaatttgagt aaaaatggca taatcgtaaa
     2161 tgagtgggaa aatttaacag ccctatctaa caggcggtta aatgtacaaa atatgtacac
     2221 ccccttaaaa atgcagtggt caattgaccg aattactatc gttggaaaac tgaaggaaaa
     2281 tatttattat cacactcaaa atgatgtgtt gattttagat tttgagcaat taatgcgggt
     2341 gaatgaaggc aatggctatt taaaagcggt tgggaataac ggctggcaat tattagacca
     2401 atacgaagaa aatattgctt atattgagat tttgaaatgg caagatggca aagggcggat
     2461 tgattttaac ccgaataaga ttggtcattt tttagctagt tcaatgaaaa atttcattca
     2521 tgatttattt ctagaaccac atttctcacg tgcggatatt gcttgcgata ttatcgatgt
     2581 gcctgatgag tttattacac aatatcgagt ggttgatcct gtttctttca agccaattta
     2641 tgggcggtct gggaagctgg aaacagctta ttggggcagt cgtgccagcg aacgccagat
     2701 tcggctatac aacaaaaaat tggaacagga aaccaagcgt aaaattgtgc caccagaaat
     2761 agaaacttgg tggcgactgg aattgcagtt aaggcgtggg aaagcaacag attggcatgc
     2821 aatggttcat gaaagtttaa atagttttgc tagccctcat tttctaccac ttgatgtaaa
     2881 aacaaatgat aaggtgatga tttttggact gattgctaac cctgaaatgt gggggttttt
     2941 agagcgtaga atgaaataca aattgagaga tattttgaaa agagaaagtc aaaatgatga
     3001 gttgacgaat catttacgag aaacattttc ggaatcagca gatgttttga aaaaagaatt
     3061 agacacttgg cttcaagggt tagatgtaac ggaggaggaa taagaatggc agaaaaacaa
     3121 aagcattttg gtaagaaaaa ttggttggtg aatttaacag gtgataacgt tgtcgttgtt
     3181 tttttggata gcaaaaaaat gtccggtaag ttacttgatg taacgcagta tgagttgatt
     3241 ttgaaaaata ataaaattga ttccccaatc attatcccta agcatgctgt taaatatgtt
     3301 tatggggtag ctgaaagtaa cggagaagat aatgactgat ttgccagaaa aaatgaccat
     3361 aaaaaacctt gctgatgagt tgggtatatc taaaaataca gtgcgcaatc aactggtcaa
     3421 tgcaggttat gaccttgctc ggtataaaga taatggggtt atcatgttag acaaggaatt
     3481 gattggtgtt gtgcggtcaa tttatcggtc aaaaggtggt caattgactg gtgatttacc
     3541 ggtcaatgat gcaggcaatg atttcccgtt agaaaaagaa aatgaatttt tgcgtgaaca
     3601 attagcggaa aaagataggc atatttctga attaacggaa atgattcgtg accaacaaaa
     3661 attgactttg cttcagcaac aaaaaaacga tcagttgtta ctagaaaatc aagaattaaa
     3721 aaatcgaaaa tggtggcaat tctggaagtg aggtgtgaca tggataaaat tgatttgaga
     3781 gaagaaacag tcgatagaat tgaattgatg tatgaacggt tagctgatta tttgaatttg
     3841 ccggatgaag ataattatag tgaaatgctt gaacgaatga tggatgttct caactcggtt
     3901 atcaatgctg atctagcaaa atcttcagtt ttgactaatg aatttgttca taagcattta
     3961 gcgcaaacaa ctgatgaatc agaaaaagaa ttttggttga aattaatgag tcatgttatg
     4021 cagttaaacc aaatttccgt tattaattcc aaagaaaagg agatgtagtt tatgggaatg
     4081 actttagcag atattaaagc gcaagaagaa aaattaaaaa aagaacaagc gaaacttcgc
     4141 caacagaaaa aacgcttgat tgagaaagaa aatgctgcaa tgggcaaggc tcttcgcaag
     4201 cgttttgggt ttgaaacttt tgctgatttt gagcggtggc tatcgtcgat ttctgacgat
     4261 cagcaacacg aaaaatcagt ggataatgag tggcttgctg atgaaaaatc agcgccaagc
     4321 gaacgagatt atcccgatga atctgacggc ttattcggag tgataccgaa taag
//
