LOCUS       NZ_CP035653             3008 bp    DNA     circular CON 17-JUN-2024
DEFINITION  Enterococcus faecium strain UAMSEF_08 plasmid unnamed5, complete
            sequence.
ACCESSION   NZ_CP035653
VERSION     NZ_CP035653.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN10863491
            Assembly: GCF_005886655.1
KEYWORDS    RefSeq.
SOURCE      Enterococcus faecium
  ORGANISM  Enterococcus faecium
            Bacteria; Bacillota; Bacilli; Lactobacillales; Enterococcaceae;
            Enterococcus.
REFERENCE   1  (bases 1 to 3008)
  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 3008)
  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                   :: 483.0x
            Sequencing Technology :: Oxford Nanopore MiniION; Illumina NextSeq
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_005886655.1-RS_2024_06_17
            Annotation Date                   :: 06/17/2024 10:52:15
            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)                     :: 3,114
            CDSs (total)                      :: 3,023
            Genes (coding)                    :: 2,796
            CDSs (with protein)               :: 2,796
            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)              :: 227
            CDSs (without protein)            :: 227
            Pseudo Genes (ambiguous residues) :: 0 of 227
            Pseudo Genes (frameshifted)       :: 133 of 227
            Pseudo Genes (incomplete)         :: 91 of 227
            Pseudo Genes (internal stop)      :: 43 of 227
            Pseudo Genes (multiple problems)  :: 33 of 227
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP035653.1.
            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..3008
                     /organism="Enterococcus faecium"
                     /mol_type="genomic DNA"
                     /strain="UAMSEF_08"
                     /host="Homo sapiens"
                     /db_xref="taxon:1352"
                     /plasmid="unnamed5"
                     /geo_loc_name="USA:Arkansas"
                     /collection_date="2018-07-07"
     gene            complement(join(2733..3008,1..141))
                     /locus_tag="EWM54_RS00295"
                     /old_locus_tag="EWM54_00295"
     CDS             complement(join(2733..3008,1..141))
                     /locus_tag="EWM54_RS00295"
                     /old_locus_tag="EWM54_00295"
                     /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(144..428)
                     /locus_tag="EWM54_RS00300"
                     /old_locus_tag="EWM54_00300"
     CDS             complement(144..428)
                     /locus_tag="EWM54_RS00300"
                     /old_locus_tag="EWM54_00300"
                     /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            695..826
                     /locus_tag="EWM54_RS16740"
     CDS             695..826
                     /locus_tag="EWM54_RS16740"
                     /inference="COORDINATES: ab initio prediction:GeneMarkS-2+"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GeneMarkS-2+."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_264298242.1"
                     /translation="MEYKNMTPERKRSLEKLMQLVNEDGGISDAAFDAWSEFHGEYN"
                     /name="hypothetical protein"
     gene            complement(1129..1224)
                     /locus_tag="EWM54_RS16805"
                     /old_locus_tag="EWM54_00305"
     CDS             complement(1129..1224)
                     /locus_tag="EWM54_RS16805"
                     /old_locus_tag="EWM54_00305"
                     /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_106913803.1"
                     /translation="MCFVFTNFICSLLVGLLSALFSYWLNNRNKK"
                     /name="type I toxin-antitoxin system Fst family toxin"
     gene            1877..2596
                     /locus_tag="EWM54_RS00310"
                     /old_locus_tag="EWM54_00310"
     CDS             1877..2596
                     /locus_tag="EWM54_RS00310"
                     /old_locus_tag="EWM54_00310"
                     /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"
     Typing          1878..2596
                     /name="rep_cluster_1763"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 atcgggttca taactcatac ataaaaagcg aatggcttcc gagtagttat tgatatctgg
       61 atttttttcg atgatggaat ctaaaacgtc aacatgacta gggtacaaag taacatgttt
      121 ttggacagaa gtttttctca tggttatatc attcctccga taagcatttc aatgatttga
      181 ttatttgtgt agacatactc gcttaatatt tgagtatttt ctgtttggat agcaataaat
      241 ttatcgagca ataaatcgaa ttggtctttt ttgtaagtcg taagttgacg gtcaaaatca
      301 ctttcgatta aaacttttag atatttattt cgactccatt tttctcctgt tttattcgtg
      361 agttcttggc aacgtttgtc tattgttgca acaaactttg gatcaatatt ccgaactaaa
      421 atgtccataa aaaatctcct tttgcaatta tgtataattt atgtatacca tacaaatact
      481 atatttgtat agctgttttt tgccaaaatg ctatacataa gctacccacg atggcgaaaa
      541 agtgatatca aatttttttc tgagaaacgt gataggcaca gcctatctac ccactttttt
      601 tagaaagtgg gtacacgttt ccttatgctc tttaaaattc gggggggagt gctgcacgtg
      661 taatcgataa ccaaatttaa cagacgaaaa attgttggaa tataaaaata tgacacccga
      721 aagaaaacga tcgttggaaa aattaatgca actagtgaac gaagacggcg gaatttcaga
      781 cgcagctttt gacgcatgga gcgaatttca tggagaatat aattaagtgg gtttaaatgg
      841 ctctaaaatc gcttctaaga gtttttttag cttggaccaa tgaaatacac caaaaactaa
      901 ataaaacgtc ttaaatcgaa aaatacgagc tctcagagcg actttatttg taaatgttgc
      961 atataagaaa taattacgga ttttagactt ttgtaggata tttttgaaat aaatatttat
     1021 ttctgttata atttgattgc aaataagtga acacgaaaca cacgaaatcc ccagagaggt
     1081 cggattctct ggggattttt ttgtgggctg agtcgcctta attaagtttt acttcttgtt
     1141 tcggttattc aaccagtaac tgaacaaagc gcttaaaagc ccaacaagaa gggagcaaat
     1201 aaagttagtg aacacgaaac acacctcctt ccagtcgcaa gactgtcgga taggcgacaa
     1261 tcaattatac aataaaaaag caaaaataag cctaagtttt ttattgcctt ggggttgtta
     1321 gggcttgccc tgaccgcctg taaggcgctt tagaacgaag gacatagttt ttatcgaatc
     1381 ttgtcttaga acggcttaga cgagctctca ggacgccaca aaggagtccc taatgaatta
     1441 tttttggcga aggagcctaa aggcgactgc tgcaagtaaa atgtgagagc gtagcgatca
     1501 ctccttctta cagcgaccat agggagctag attggcagtt taatatcatg cgcgaacctg
     1561 tttattttaa aaagtgggtg attttttggc gggaaatttt gctcgcgcgc gcgcgtttat
     1621 tttatttatt ttttaaagat tttttagaac cctttttagg gggcagttga gccttactct
     1681 cccaacggat acagaagggt actaacaact ttttatctga gtactaacaa ctttttatct
     1741 gagtactaac aactttttat ctgagtacta acaacttttt atctgagtac taatatcctt
     1801 ttgtataata acaaccaacc tatttacgag ttggttgtta aaggttatta tttatttgta
     1861 aggggggaag aaaggaatgg atgaaaaaac ggaattaaca gtcaaatatc aaaatgaatt
     1921 gaatttagta ccgctgaaaa atttcaatgc taagcagatg gatttatttt ttgcattatg
     1981 cgctcgtatg aaagatcgtg gtttgaaaaa agttagattt tctttcgagg aattaaaaga
     2041 gttaagtgat tataagatga ctgctacaaa agcctttgtc ggtgatttag aaaagctcta
     2101 taaagatatg cttaatctta cttaccgtac tgaagatgag gattctattc gctactttgt
     2161 tttgtttact ggttttgaaa tcaataaaac aaaaaagttt gttgaagtca gtgttaatcc
     2221 ggacctagaa tatattatta atggtttaac agctgaattt agtagatttg aattatctgc
     2281 tttcacgtcg ttgcgttcta cgtatgcaaa aactctattc cgactgctta tgcagtaccg
     2341 ttctactggt tattatgtag ttcgtattga agagtttagg agcttaatgg atatcccaga
     2401 atactatcaa atgggtaaca ttgatcaaaa agtattaaat cctgcattac gagaactaaa
     2461 aaaatacttc aatgatctta aagtcacaaa aataaaagca aaaaagggca ataaaatcgc
     2521 caaattagaa tttacttttt caagcctaac gtcagatttg ccaaagattt ctctgcgtaa
     2581 ctggttagaa gaataaataa aaaagaactc gcccccctta cattaagcaa gtagacaagt
     2641 cccttacaac cgactaagat tgctagtaca ttctagcata ttgtatgggg cttctaaata
     2701 aaaaacagat aggaataact cctatctgtt ttttatcgtt ttagaaaatt tgttgggtcg
     2761 aaatttctag aagtgactgt ttgactggtt tctttttgat gattctttgg tcgatttcga
     2821 tttgatggat ttagtttagc ttcgattttt tctttcactt cttgatatac tttagaattt
     2881 gtgccaataa gaacgcctgt atcttttaga tataaatcag caaattctgc gatgatttca
     2941 gtcatgatgg aaatttcttt tcccatagca tttagttttg cctgattgct ggtagtggtc
     3001 gtgttggt
//
