LOCUS       NZ_CP035647             3030 bp    DNA     circular CON 17-JUN-2024
DEFINITION  Enterococcus faecium strain UAMSEF_01 plasmid unnamed5, complete
            sequence.
ACCESSION   NZ_CP035647
VERSION     NZ_CP035647.1
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 3030)
  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 3030)
  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
            CP035647.1.
            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..3030
                     /organism="Enterococcus faecium"
                     /mol_type="genomic DNA"
                     /strain="UAMSEF_01"
                     /host="Homo sapiens"
                     /db_xref="taxon:1352"
                     /plasmid="unnamed5"
                     /geo_loc_name="USA:Arkansas"
                     /collection_date="2018-06-28"
     gene            384..668
                     /locus_tag="EWM53_RS00295"
                     /old_locus_tag="EWM53_00295"
     CDS             384..668
                     /locus_tag="EWM53_RS00295"
                     /old_locus_tag="EWM53_00295"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002337999.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_000353844.1"
                     /translation="MDILVRNIDPKFVATIDKRCQELTNKTGEKWSRNKYLKVLIESDF
                     DRQLTTYKKDQFDLLLDKFIAIQTENTQILSEYVYTNNQIIEMLIGGMI"
                     /name="hypothetical protein"
     gene            671..1087
                     /locus_tag="EWM53_RS00300"
                     /old_locus_tag="EWM53_00300"
     CDS             671..1087
                     /locus_tag="EWM53_RS00300"
                     /old_locus_tag="EWM53_00300"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001232859.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_001232859.1"
                     /translation="MRKTSVQKHVTLYPSHVDVLDSIIEKNPDINNYSEAIRFLCMSYE
                     PDTNTTTTSNQAKLNAMGKEISIMTEIIAEFADLYLKDTGVLIGTNSKVYQEVKEKIEA
                     KLNPSNRNRPKNHQKETSQTVTSRNFDPTNFLKR"
                     /name="hypothetical protein"
     gene            complement(1224..1943)
                     /locus_tag="EWM53_RS00305"
                     /old_locus_tag="EWM53_00305"
     CDS             complement(1224..1943)
                     /locus_tag="EWM53_RS00305"
                     /old_locus_tag="EWM53_00305"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002311815.1"
                     /GO_function="GO:0003887 - DNA-directed DNA polymerase
                     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 protein"
                     /protein_id="WP_002311815.1"
                     /translation="MDEKTELTVKYQNELNLVPLKNFNAKQMDLFFALCARMKDRGLKK
                     VRFSFEELKELSDYKMTATKAFVGDLEKLYKDMLNLTYRTEDEDSIRYFVLFTGFEINK
                     TKKFVEVSVNPDLEYIINGLTAEFSRFELSAFTSLRSTYAKTLFRLLMQYRSTGYYVVR
                     IEEFRSLMDIPEYYQMGNIDQKVLNPALRELKKYFNDLKVTKIKAKKGNKIAKLEFTFS
                     SLTSDLPKISLRNWLEE"
                     /name="replication initiation protein"
     gene            2627..2713
                     /locus_tag="EWM53_RS00310"
                     /old_locus_tag="EWM53_00310"
     CDS             2627..2713
                     /locus_tag="EWM53_RS00310"
                     /old_locus_tag="EWM53_00310"
                     /inference="COORDINATES: protein motif:HMM:NF033608.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="type I toxin-antitoxin system Fst family toxin"
                     /protein_id="WP_125669474.1"
                     /translation="MFTNFICSLLVGLLSALFSYWLNNRNKK"
                     /name="type I toxin-antitoxin system Fst family toxin"
     Typing          complement(1225..1943)
                     /name="rep_cluster_1763"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 atgaaattcg ctccatgcgt caaaagctgc gtctgaaatt ccgccgtctt cgttcactag
       61 ttgcattaat ttttccaacg atcgttttct ttcgggtgtc atatttttat attccaacaa
      121 tttttcgtct gttaaatttg gttatcgatt acacgtgcag cactcccccc cgaattttaa
      181 agagcataag gaaacgtgta cccactttct aaaaaaagtg ggtagatagg ctgtgcctat
      241 cacgtttctc agaaaaaaat ttgatatcac tttttcgcca tcgtgggtag cttatgtata
      301 gcattttggc aaaaaacagc tatacaaata tagtatttgt atggtataca taaattatac
      361 ataattgcaa aaggagattt tttatggaca ttttagttcg gaatattgat ccaaagtttg
      421 ttgcaacaat agacaaacgt tgccaagaac tcacgaataa aacaggagaa aaatggagtc
      481 gaaataaata tctaaaagtt ttaatcgaaa gtgattttga ccgtcaactt acgacttaca
      541 aaaaagacca attcgattta ttgctcgata aatttattgc tatccaaaca gaaaatactc
      601 aaatattaag cgagtatgtc tacacaaata atcaaatcat tgaaatgctt atcggaggaa
      661 tgatataacc atgagaaaaa cttctgtcca aaaacatgtt actttgtacc ctagtcatgt
      721 tgacgtttta gattccatca tcgaaaaaaa tccagatatc aataactact cggaagccat
      781 tcgcttttta tgtatgagtt atgaacccga taccaacacg accactacca gcaatcaggc
      841 aaaactaaat gctatgggaa aagaaatttc catcatgact gaaatcatcg cagaatttgc
      901 tgatttatat ctaaaagata caggcgttct tattggcaca aattctaaag tatatcaaga
      961 agtgaaagaa aaaatcgaag ctaaactaaa tccatcaaat cgaaatcgac caaagaatca
     1021 tcaaaaagaa accagtcaaa cagtcacttc tagaaatttc gacccaacaa attttctaaa
     1081 acgataaaaa acagatagga gttattccta tctgtttttt atttagaagc cccatacaat
     1141 atgctagaat gtactagcaa tcttagtcgg ttgtaaggga cttgtctact tgcttaatgt
     1201 aaggggggcg agttcttttt tatttattct tctaaccagt tacgcagaga aatctttggc
     1261 aaatctgacg ttaggcttga aaaagtaaat tctaatttgg cgattttatt gccctttttt
     1321 gcttttattt ttgtgacttt aagatcattg aagtattttt ttagttctcg taatgcagga
     1381 tttaatactt tttgatcaat gttacccatt tgatagtatt ctgggatatc cattaagctc
     1441 ctaaactctt caatacgaac tacataataa ccagtagaac ggtactgcat aagcagtcgg
     1501 aatagagttt ttgcatacgt agaacgcaac gacgtgaaag cagataattc aaatctacta
     1561 aattcagctg ttaaaccatt aataatatat tctaggtccg gattaacact gacttcaaca
     1621 aacttttttg ttttattgat ttcaaaacca gtaaacaaaa caaagtagcg aatagaatcc
     1681 tcatcttcag tacggtaagt aagattaagc atatctttat agagcttttc taaatcaccg
     1741 acaaaggctt ttgtagcagt catcttataa tcacttaact cttttaattc ctcgaaagaa
     1801 aatctaactt ttttcaaacc acgatctttc atacgagcgc ataatgcaaa aaataaatcc
     1861 atctgcttag cattgaaatt tttcagcggt actaaattca attcattttg atatttgact
     1921 gttaattccg ttttttcatc cattcctttc ttcccccctt acaaataaat aataaccttt
     1981 aacaaccaac tcgtaaatag gttggttgtt attatacaaa aggatattag tactcagata
     2041 aaaagttgtt agtactcaga taaaaagttg ttagtactca gataaaaagt tgttagtact
     2101 cagataaaaa gttgttagta ctcagataaa aagttgttag tacccttctg tatccgttgg
     2161 gagagtaagg ctcaactgcc ccctaaaaag ggttctaaaa aatctttaaa aaataaataa
     2221 aataaacgcg cgcgcgcgag caaaatttcc cgccaaaaaa tcacccactt tttaaaataa
     2281 acaggttcgc gcatgatatt aaactgccaa tctagctccc tatggtcgct gtaagaagga
     2341 gtgatcgcta cgctctcaca ttttacttgc agcagtcgcc tttaggctcc ttcgccaaaa
     2401 ataattcatt agggactcct ttgtggcgtc ctgagagctc gtctaagccg ttctaagaca
     2461 agattcgata aaaactatgt ccttcgttct aaagcgcctt acaggcggtc agggcaagcc
     2521 ctaacaaccc caaggcaata aaaaacttag gcttattttt gcttttttat tgtataattg
     2581 attgtcgcct atccgacagt cttgcgactg gaaggaggtg tgtttcgtgt tcactaactt
     2641 tatttgctcc cttcttgttg ggcttttaag cgctttgttc agttactggt tgaataaccg
     2701 aaacaagaag taaaacttaa ttaaggcgac tcagcccaca aaaaaatccc cagagaatcc
     2761 gacctctctg gggatttcgt gtgtttcgtg ttcacttatt tgcaatcaaa ttataacaga
     2821 aataaatatt tatttcaaaa atatcctaca aaagtctaaa atccgtaatt atttcttata
     2881 tgcaacattt acaaataaag tcgctctgag agctcgtatt tttcgattta agacgtttta
     2941 tttagttttt ggtgtatttc attggtccaa gctaaaaaaa ctcttagaag cgattttaga
     3001 gccatttaaa cccacttaat tatattctcc
//
