LOCUS       NZ_CP035658             4316 bp    DNA     circular CON 17-JUN-2024
DEFINITION  Enterococcus faecium strain UAMSEF_09 plasmid unnamed4, complete
            sequence.
ACCESSION   NZ_CP035658
VERSION     NZ_CP035658.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN10863492
            Assembly: GCF_005886715.1
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; Canu v. 1.8
            Assembly Name                     :: UAMS_Efae_0.4.4
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 747.0x
            Sequencing Technology :: Oxford Nanopore MiniION; Illumina NextSeq
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_005886715.1-RS_2024_06_17
            Annotation Date                   :: 06/17/2024 10:49:34
            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)                     :: 3,330
            CDSs (total)                      :: 3,237
            Genes (coding)                    :: 2,974
            CDSs (with protein)               :: 2,974
            Genes (RNA)                       :: 93
            rRNAs                             :: 6, 6, 6 (5S, 16S, 23S)
            complete rRNAs                    :: 6, 6, 6 (5S, 16S, 23S)
            tRNAs                             :: 71
            ncRNAs                            :: 4
            Pseudo Genes (total)              :: 263
            CDSs (without protein)            :: 263
            Pseudo Genes (ambiguous residues) :: 0 of 263
            Pseudo Genes (frameshifted)       :: 155 of 263
            Pseudo Genes (incomplete)         :: 97 of 263
            Pseudo Genes (internal stop)      :: 56 of 263
            Pseudo Genes (multiple problems)  :: 38 of 263
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP035658.1.
            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_09"
                     /host="Homo sapiens"
                     /db_xref="taxon:1352"
                     /plasmid="unnamed4"
                     /geo_loc_name="USA:Arkansas"
                     /collection_date="2018-09-18"
     gene            208..1614
                     /locus_tag="EWM55_RS00540"
                     /old_locus_tag="EWM55_00540"
     CDS             208..1614
                     /locus_tag="EWM55_RS00540"
                     /old_locus_tag="EWM55_00540"
                     /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            2214..3203
                     /locus_tag="EWM55_RS00545"
                     /old_locus_tag="EWM55_00545"
     CDS             2214..3203
                     /locus_tag="EWM55_RS00545"
                     /old_locus_tag="EWM55_00545"
                     /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            3200..3619
                     /locus_tag="EWM55_RS00550"
                     /old_locus_tag="EWM55_00550"
     CDS             3200..3619
                     /locus_tag="EWM55_RS00550"
                     /old_locus_tag="EWM55_00550"
                     /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            3628..3936
                     /locus_tag="EWM55_RS00555"
                     /old_locus_tag="EWM55_00555"
     CDS             3628..3936
                     /locus_tag="EWM55_RS00555"
                     /old_locus_tag="EWM55_00555"
                     /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            3940..4302
                     /locus_tag="EWM55_RS00560"
                     /old_locus_tag="EWM55_00560"
     CDS             3940..4302
                     /locus_tag="EWM55_RS00560"
                     /old_locus_tag="EWM55_00560"
                     /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          209..1611
                     /name="MOBV"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="97.863"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 tgaagcaaaa taaagcgtaa aaggagttga gagcgtgaca cgctttcggc tccttttttc
       61 gttgtcactt gtgacagcga aatccctcgg agagcgtttg gaattgtgac agtcatgtca
      121 caattaggaa aacgttactc tttgacaaag agtaacagaa aggtttacac tctttttatt
      181 agcgacagcg cgaaggaggg gtctaacttg gggtttagta tttcgttcaa aaagggaaca
      241 aagaatacaa gcatttctca taataatcgt gagttaactg atagccaaaa aatcaatgac
      301 tggcataagc atattgattt cacaaaatcg gatgaaaata tctatttgga acaaacaaat
      361 attcgtgaaa aatatgaaga attattcggt gaagccgtag aaaaatataa tgcaaagcag
      421 aaaagagccg atagaaaaat cgaggactat ttagcaaagg ttcgcaagga taaaaaattg
      481 gaaccacagc gagaatttat cgtgcaaatt ggtactcttg atgattttcg tactactcgt
      541 gatgatggtt cttctactgg catatcggaa caacaagcag aacaaaatcg agtgattgcc
      601 aacaaaattt tagttgagta tttcaaagaa tttaaagaac ggaatcctag tttatccgtc
      661 tacaatgctg ttattcataa tgacgaagta agtccgcacc tgcatttgaa tattgttcct
      721 gttgctgaag ggtataaacg gggtgttcaa aagcaaccaa gttttaacaa agccttgcaa
      781 cagcagggtt tacgagcaga taaagagaat ggtcgagtga tttggaataa ttttaggaat
      841 caggaagttg agtcaattga acgtttgatg gcagattttg gttgggagcg tgagttagtc
      901 ggtactaaca aaatcaaaga tgttcacgaa tataaagaaa tcatgagcga gatttcagaa
      961 ttgcgtcaaa cggccgtaaa agagcgtgag agcgtttctg atgagttggg gtatatttct
     1021 aggcaaagag aagaaaacga gcgagaaaag gctctggtgg cttctgagag agcaaagatt
     1081 gaagaagaga agaaaaatat gctgaatgta aaaaaagaga tggcggtcat tttccaaaaa
     1141 gatattgttc ctttagaaag tttcaagagg cttcctgatg gttcgtatca tttatctggg
     1201 aatgattttg ttgatttgta tcaacgagct acgagagcaa caaatgccaa gagaaatgct
     1261 gataacatga gtgagcaata tttacagatg cttgagcaaa atacagaatt aaatgagtat
     1321 gtagctacat tggaagaaga gcgtcatttg tctggtagaa aacaattagc agatttacaa
     1381 gtggaaaata aaaagctgaa agaagaaaat cgctctttac gccagcgttt agagcgatta
     1441 aaaaaagcat ttcaaaaatc gatcactcgt ttgtctatcc gttttggtct tgcagaaaag
     1501 gatatggggc tttctgagga attagaagta ttagagcagg agaaaacctt attttatcgt
     1561 caaaacgtct cacagcataa attagagcgt tctgaagatg agatcgagtg gtagttacga
     1621 tgtgcagtca acggtaccgg aggcggtctg tgccgaggat aaggagttga cggctaaacc
     1681 actagcctat taagctgaca tttgctaaaa aatggcaagt ccattttttg gccaacctag
     1741 cgttagcgaa agtttggggg cgcccttttc aaagggagcg gttttatttt tgcatgacta
     1801 agaatgagtg ggaaaaactt aaccgcattt ctaacaggcg gttaaagtat caaagtttga
     1861 cccttccctt aaaaatgcag tggtcaattg accgaatttt atgcagaagt gggtttttga
     1921 gttttggggt ttgaaacgag aaaaaagagg tcgatttcga cctctttttt tgatgtttct
     1981 tcttatcttg atactatagg caactatttc tgcgaagaaa tcggggctat agtatgggtc
     2041 tatcccttgt ggctctaagg aagaacaaaa aaaaagattg ctttttcttc cctagtattt
     2101 tatagtttta attgactaga aaaaaactaa actagaaagg agagcaatct attttttgtt
     2161 atcggctttt cagccttttt tgtatacaaa atttgtagat tcagtatagc aagatgaaaa
     2221 agaaaaagca agatttgatt aacggaacat ttcgagaaaa aaagaaaaat ttgaaaaaag
     2281 tggtggcatt tagtgataat cgaatttctc ccaaaatgcg tgaattgatg acaggctgtg
     2341 gttcatattt agaatttatt gcaacgattg ataaggagaa aaagaaattg gtccaagctc
     2401 acttttgtaa aaatcgtttc tgtccgttat gtgcttggcg taaagctcgt aaggattcga
     2461 tgatgttgtc gattatgatg caagctattg cggaagaaaa gcagtatcaa tttattttta
     2521 tgacgttgac gacaccgaat gtaaaagcgg aatgtttgaa cgatgaaatt gatttgttta
     2581 atcatgcatt gaaaaagatg tttatgcgca aacgggttaa gacttcgatt aaaggctatg
     2641 tgcgaaaatt ggaaatcacg tacaacaaaa aacggaatga ctataacccg cattttcact
     2701 tgattttggc agtaaataaa tcttatttca cggataaaga ttattatatc aagcaatcgg
     2761 aatggttaga tttgtggcgg gaagtgaccg gaaaaacggg aattaatccg gatggtaccg
     2821 acgaaattac ccagttggat attcgcaagg tcaaagggtt ccaacaagaa aaagcagtac
     2881 aggaagttgc gaaatattcg gcaaaagatt ttgaactgac cgaaagtcag gaagtgtttg
     2941 acacattcta tcatgcaatg aaaggtcgtc agttgattac gtttaacggt gtattcaaag
     3001 aatacaagaa aaaatatgag tcgggtgacc ttgatcgtta taagaaaaaa gatgagaatg
     3061 aatatttttg gtttttgact gcttcgtgga tgaggaaaga atcgaaatat gcggttgatt
     3121 atcgtgagat gagtgctgat gaaagaaatt atttttcagg aatgtatgtc gatgaaaaat
     3181 ctgttgaggg ggaaaatgaa tgactgattc aacggataaa atgacaatta aggcgcttgc
     3241 tgatgaacta ggaataacca aaaatacagt gagaaattat ctagtcaaag ccggatatga
     3301 tcttgctcgg tacaagaaaa atggaattat cttgctagac aaagagttga ttggtgttgc
     3361 tcggtcaatt tatcggtcaa aaggtggtca attgactggt catttaccgg tcaatagcac
     3421 gggcagtgat tttcctttgg aaaaagagaa tgagtttttg cgtgatcaat tagctgagaa
     3481 ggacaaacat atttctgaat taacagaaat gattcgtgat caacaaaaat tgaccctgct
     3541 tcagcaacaa aaaaacgatc agttgttact agaaaatcaa gaattaaaaa atcgaaaatg
     3601 gtggcaattc tggaagtgag atgtgacatg gataaaattg atttgagaga agaaacagtc
     3661 aatagaattg aagtgatgta tgaacggtta gctgattatt tgaatctttc ggatgaagat
     3721 aattatagtg agatgcttga acgaatgatg gatgttctca actcggttat caatgctgat
     3781 ctagcaaaat cttcagtttt gactaatgaa tttgttcata agcatttagc gcaaacaact
     3841 gatgaagctg aaaaagaatt ttggttgaaa ttaatgagtc atattatgca gttaaaccaa
     3901 atttccgtta ttaattccaa agaaaagggg atgtagttta tgggaatgac tttagcagat
     3961 attaaagtgc aagaagaaaa attaaaaaaa gaacaggcga aacttcgcca acagaagaaa
     4021 cgattgattg agaaagaaaa tgctgcaatg ggcaaggctc ttcgcaagcg ttttgggttt
     4081 gaatcttttg ctgattttga gcggtggtta tcgtcaattt ctgacgatca gcaacacgaa
     4141 aaatcagtgg ataatgagtg gcttgctgat gaaaaatcag cgccaagcga acgagattat
     4201 cccaatgaat atgacggctt actcggagtg atgccgagta aaaaaagtca gatgaatgag
     4261 agtaaattta tgtcaatttt taatgacgtg aatttacgat aagctattat tttgcg
//
