LOCUS       NZ_CP035646             4316 bp    DNA     circular CON 17-JUN-2024
DEFINITION  Enterococcus faecium strain UAMSEF_01 plasmid unnamed4, complete
            sequence.
ACCESSION   NZ_CP035646
VERSION     NZ_CP035646.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN10863479
            Assembly: GCF_005886545.1
KEYWORDS    RefSeq.
SOURCE      Enterococcus faecium
  ORGANISM  Enterococcus faecium
            Bacteria; Bacillota; Bacilli; Lactobacillales; Enterococcaceae;
            Enterococcus.
REFERENCE   1  (bases 1 to 4316)
  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 4316)
  AUTHORS   Jenjaroenpun,P.
  TITLE     Direct Submission
  JOURNAL   Submitted (01-FEB-2019) Biomedical Informatics, University of
            Arkansas for Medical Sciences, 4301 W Markham St, Little Rock, AR
            72205, USA
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Date                     :: JAN-2019
            Assembly Method                   :: Unicycler v. 0.4.4
            Assembly Name                     :: UAMS_Efae_0.4.4
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 518.0x
            Sequencing Technology :: Oxford Nanopore MiniION; Illumina NextSeq
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_005886545.1-RS_2024_06_17
            Annotation Date                   :: 06/17/2024 10:53:44
            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)                     :: 3,102
            CDSs (total)                      :: 3,011
            Genes (coding)                    :: 2,798
            CDSs (with protein)               :: 2,798
            Genes (RNA)                       :: 91
            rRNAs                             :: 6, 6, 6 (5S, 16S, 23S)
            complete rRNAs                    :: 6, 6, 6 (5S, 16S, 23S)
            tRNAs                             :: 69
            ncRNAs                            :: 4
            Pseudo Genes (total)              :: 213
            CDSs (without protein)            :: 213
            Pseudo Genes (ambiguous residues) :: 0 of 213
            Pseudo Genes (frameshifted)       :: 120 of 213
            Pseudo Genes (incomplete)         :: 90 of 213
            Pseudo Genes (internal stop)      :: 44 of 213
            Pseudo Genes (multiple problems)  :: 34 of 213
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP035646.1.
            Bacteria and source DNA available from Tip's lab.
            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..4316
                     /organism="Enterococcus faecium"
                     /mol_type="genomic DNA"
                     /strain="UAMSEF_01"
                     /host="Homo sapiens"
                     /db_xref="taxon:1352"
                     /plasmid="unnamed4"
                     /geo_loc_name="USA:Arkansas"
                     /collection_date="2018-06-28"
     gene            join(3891..4316,1..981)
                     /locus_tag="EWM53_RS00270"
                     /old_locus_tag="EWM53_00270"
     CDS             join(3891..4316,1..981)
                     /locus_tag="EWM53_RS00270"
                     /old_locus_tag="EWM53_00270"
                     /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_060800944.1"
                     /translation="MGFSISFKKGTKNTSISHNNRELTDSQKINDWHKHIDFTKSDENI
                     YLEQTNIREKYEELFGEAVEKYNAKQKRADRKIEDYLAKVRKDKKLEPQREFIVQIGTL
                     DDFRTTRDDGSSTGISEQQAEQNRVIANKILVEYFKEFKERNPSLSVYNAVIHNDEVSP
                     HLHLNIVPVAEGYKRGVQKQPSFNKALQQQGLRADKENGRVIWNNFRNQEVESIERLMA
                     DFGWERELVGTNKIKDVHEYKEIMSEISELRQTAVKERESVSDELGYISRQREENEREK
                     ALVASERAKIEEEKKNMLNVKKEMAVIFQKDIVPLESFKRLPDGSYHLSGNDFVDLYQR
                     ATRATNAKRNADNMSEQYLQMLEQNTELNEYVATLEEERHLSGRKQLADLQVENKKLKE
                     ENRSLRQRLERLKKAFQKSITRLSIRFGLAEKDMGLSEELEVLEQEKTLFYRQNVSQHK
                     LERSEDEIEW"
                     /name="plasmid recombination protein"
     gene            1581..2570
                     /locus_tag="EWM53_RS00275"
                     /old_locus_tag="EWM53_00275"
     CDS             1581..2570
                     /locus_tag="EWM53_RS00275"
                     /old_locus_tag="EWM53_00275"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002349057.1"
                     /GO_function="GO:0003677 - DNA binding [Evidence IEA]"
                     /GO_process="GO:0006260 - DNA replication [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="protein rep"
                     /protein_id="WP_002304903.1"
                     /translation="MKKKKQDLINGTFREKKKNLKKVVAFSDNRISPKMRELMTGCGSY
                     LEFIATIDKEKKKLVQAHFCKNRFCPLCAWRKARKDSMMLSIMMQAIAEEKQYQFIFMT
                     LTTPNVKAECLNDEIDLFNHALKKMFMRKRVKTSIKGYVRKLEITYNKKRNDYNPHFHL
                     ILAVNKSYFTDKDYYIKQSEWLDLWREVTGKTGINPDGTDEITQLDIRKVKGFQQEKAV
                     QEVAKYSAKDFELTESQEVFDTFYHAMKGRQLITFNGVFKEYKKKYESGDLDRYKKKDE
                     NEYFWFLTASWMRKESKYAVDYREMSADERNYFSGMYVDEKSVEGENE"
                     /name="protein rep"
     gene            2567..2986
                     /locus_tag="EWM53_RS00280"
                     /old_locus_tag="EWM53_00280"
     CDS             2567..2986
                     /locus_tag="EWM53_RS00280"
                     /old_locus_tag="EWM53_00280"
                     /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_002305964.1"
                     /translation="MTDSTDKMTIKALADELGITKNTVRNYLVKAGYDLARYKKNGIIL
                     LDKELIGVARSIYRSKGGQLTGHLPVNSTGSDFPLEKENEFLRDQLAEKDKHISELTEM
                     IRDQQKLTLLQQQKNDQLLLENQELKNRKWWQFWK"
                     /name="hypothetical protein"
     gene            2995..3303
                     /locus_tag="EWM53_RS00285"
                     /old_locus_tag="EWM53_00285"
     CDS             2995..3303
                     /locus_tag="EWM53_RS00285"
                     /old_locus_tag="EWM53_00285"
                     /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_002304909.1"
                     /translation="MDKIDLREETVNRIEVMYERLADYLNLSDEDNYSEMLERMMDVLN
                     SVINADLAKSSVLTNEFVHKHLAQTTDEAEKEFWLKLMSHIMQLNQISVINSKEKGM"
                     /name="hypothetical protein"
     gene            3307..3669
                     /locus_tag="EWM53_RS00290"
                     /old_locus_tag="EWM53_00290"
     CDS             3307..3669
                     /locus_tag="EWM53_RS00290"
                     /old_locus_tag="EWM53_00290"
                     /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_130587602.1"
                     /translation="MGMTLADIKVQEEKLKKEQAKLRQQKKRLIEKENAAMGKALRKRF
                     GFESFADFERWLSSISDDQQHEKSVDNEWLADEKSAPSERDYPNEYDGLLGVMPSKKSQ
                     MNESKFMSIFNDVNLR"
                     /name="hypothetical protein"
     Typing          3799..4316
                     /name="MOBV"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="90.751"
                     /coverage="100.0"
                     /evalue="1.43e-95"
ORIGIN
        1 aaagaacgga atcctagttt atccgtctac aatgctgtta ttcataatga cgaagtaagt
       61 ccgcacctgc atttgaatat tgttcctgtt gctgaagggt ataaacgggg tgttcaaaag
      121 caaccaagtt ttaacaaagc cttgcaacag cagggtttac gagcagataa agagaatggt
      181 cgagtgattt ggaataattt taggaatcag gaagttgagt caattgaacg tttgatggca
      241 gattttggtt gggagcgtga gttagtcggt actaacaaaa tcaaagatgt tcacgaatat
      301 aaagaaatca tgagcgagat ttcagaattg cgtcaaacgg ccgtaaaaga gcgtgagagc
      361 gtttctgatg agttggggta tatttctagg caaagagaag aaaacgagcg agaaaaggct
      421 ctggtggctt ctgagagagc aaagattgaa gaagagaaga aaaatatgct gaatgtaaaa
      481 aaagagatgg cggtcatttt ccaaaaagat attgttcctt tagaaagttt caagaggctt
      541 cctgatggtt cgtatcattt atctgggaat gattttgttg atttgtatca acgagctacg
      601 agagcaacaa atgccaagag aaatgctgat aacatgagtg agcaatattt acagatgctt
      661 gagcaaaata cagaattaaa tgagtatgta gctacattgg aagaagagcg tcatttgtct
      721 ggtagaaaac aattagcaga tttacaagtg gaaaataaaa agctgaaaga agaaaatcgc
      781 tctttacgcc agcgtttaga gcgattaaaa aaagcatttc aaaaatcgat cactcgtttg
      841 tctatccgtt ttggtcttgc agaaaaggat atggggcttt ctgaggaatt agaagtatta
      901 gagcaggaga aaaccttatt ttatcgtcaa aacgtctcac agcataaatt agagcgttct
      961 gaagatgaga tcgagtggta gttacgatgt gcagtcaacg gtaccggagg cggtctgtgc
     1021 cgaggataag gagttgacgg ctaaaccact agcctattaa gctgacattt gctaaaaaat
     1081 ggcaagtcca ttttttggcc aacctagcgt tagcgaaagt ttgggggcgc ccttttcaaa
     1141 gggagcggtt ttatttttgc atgactaaga atgagtggga aaaacttaac cgcatttcta
     1201 acaggcggtt aaagtatcaa agtttgaccc ttcccttaaa aatgcagtgg tcaattgacc
     1261 gaattttatg cagaagtggg tttttgagtt ttggggtttg aaacgagaaa aaagaggtcg
     1321 atttcgacct ctttttttga tgtttcttct tatcttgata ctataggcaa ctatttctgc
     1381 gaagaaatcg gggctatagt atgggtctat cccttgtggc tctaaggaag aacaaaaaaa
     1441 aagattgctt tttcttccct agtattttat agttttaatt gactagaaaa aaactaaact
     1501 agaaaggaga gcaatctatt ttttgttatc ggcttttcag ccttttttgt atacaaaatt
     1561 tgtagattca gtatagcaag atgaaaaaga aaaagcaaga tttgattaac ggaacatttc
     1621 gagaaaaaaa gaaaaatttg aaaaaagtgg tggcatttag tgataatcga atttctccca
     1681 aaatgcgtga attgatgaca ggctgtggtt catatttaga atttattgca acgattgata
     1741 aggagaaaaa gaaattggtc caagctcact tttgtaaaaa tcgtttctgt ccgttatgtg
     1801 cttggcgtaa agctcgtaag gattcgatga tgttgtcgat tatgatgcaa gctattgcgg
     1861 aagaaaagca gtatcaattt atttttatga cgttgacgac accgaatgta aaagcggaat
     1921 gtttgaacga tgaaattgat ttgtttaatc atgcattgaa aaagatgttt atgcgcaaac
     1981 gggttaagac ttcgattaaa ggctatgtgc gaaaattgga aatcacgtac aacaaaaaac
     2041 ggaatgacta taacccgcat tttcacttga ttttggcagt aaataaatct tatttcacgg
     2101 ataaagatta ttatatcaag caatcggaat ggttagattt gtggcgggaa gtgaccggaa
     2161 aaacgggaat taatccggat ggtaccgacg aaattaccca gttggatatt cgcaaggtca
     2221 aagggttcca acaagaaaaa gcagtacagg aagttgcgaa atattcggca aaagattttg
     2281 aactgaccga aagtcaggaa gtgtttgaca cattctatca tgcaatgaaa ggtcgtcagt
     2341 tgattacgtt taacggtgta ttcaaagaat acaagaaaaa atatgagtcg ggtgaccttg
     2401 atcgttataa gaaaaaagat gagaatgaat atttttggtt tttgactgct tcgtggatga
     2461 ggaaagaatc gaaatatgcg gttgattatc gtgagatgag tgctgatgaa agaaattatt
     2521 tttcaggaat gtatgtcgat gaaaaatctg ttgaggggga aaatgaatga ctgattcaac
     2581 ggataaaatg acaattaagg cgcttgctga tgaactagga ataaccaaaa atacagtgag
     2641 aaattatcta gtcaaagccg gatatgatct tgctcggtac aagaaaaatg gaattatctt
     2701 gctagacaaa gagttgattg gtgttgctcg gtcaatttat cggtcaaaag gtggtcaatt
     2761 gactggtcat ttaccggtca atagcacggg cagtgatttt cctttggaaa aagagaatga
     2821 gtttttgcgt gatcaattag ctgagaagga caaacatatt tctgaattaa cagaaatgat
     2881 tcgtgatcaa caaaaattga ccctgcttca gcaacaaaaa aacgatcagt tgttactaga
     2941 aaatcaagaa ttaaaaaatc gaaaatggtg gcaattctgg aagtgagatg tgacatggat
     3001 aaaattgatt tgagagaaga aacagtcaat agaattgaag tgatgtatga acggttagct
     3061 gattatttga atctttcgga tgaagataat tatagtgaga tgcttgaacg aatgatggat
     3121 gttctcaact cggttatcaa tgctgatcta gcaaaatctt cagttttgac taatgaattt
     3181 gttcataagc atttagcgca aacaactgat gaagctgaaa aagaattttg gttgaaatta
     3241 atgagtcata ttatgcagtt aaaccaaatt tccgttatta attccaaaga aaaggggatg
     3301 tagtttatgg gaatgacttt agcagatatt aaagtgcaag aagaaaaatt aaaaaaagaa
     3361 caggcgaaac ttcgccaaca gaagaaacga ttgattgaga aagaaaatgc tgcaatgggc
     3421 aaggctcttc gcaagcgttt tgggtttgaa tcttttgctg attttgagcg gtggttatcg
     3481 tcaatttctg acgatcagca acacgaaaaa tcagtggata atgagtggct tgctgatgaa
     3541 aaatcagcgc caagcgaacg agattatccc aatgaatatg acggcttact cggagtgatg
     3601 ccgagtaaaa aaagtcagat gaatgagagt aaatttatgt caatttttaa tgacgtgaat
     3661 ttacgataag ctattatttt gcgtgaagca aaataaagcg taaaaggagt tgagagcgtg
     3721 acacgctttc ggctcctttt ttcgttgtca cttgtgacag cgaaatccct cggagagcgt
     3781 ttggaattgt gacagtcatg tcacaattag gaaaacgtta ctctttgaca aagagtaaca
     3841 gaaaggttta cactcttttt attagcgaca gcgcgaagga ggggtctaac ttggggttta
     3901 gtatttcgtt caaaaaggga acaaagaata caagcatttc tcataataat cgtgagttaa
     3961 ctgatagcca aaaaatcaat gactggcata agcatattga tttcacaaaa tcggatgaaa
     4021 atatctattt ggaacaaaca aatattcgtg aaaaatatga agaattattc ggtgaagccg
     4081 tagaaaaata taatgcaaag cagaaaagag ccgatagaaa aatcgaggac tatttagcaa
     4141 aggttcgcaa ggataaaaaa ttggaaccac agcgagaatt tatcgtgcaa attggtactc
     4201 ttgatgattt tcgtactact cgtgatgatg gttcttctac tggcatatcg gaacaacaag
     4261 cagaacaaaa tcgagtgatt gccaacaaaa ttttagttga gtatttcaaa gaattt
//
