LOCUS       NZ_CP035659             3008 bp    DNA     circular CON 17-JUN-2024
DEFINITION  Enterococcus faecium strain UAMSEF_09 plasmid unnamed5, complete
            sequence.
ACCESSION   NZ_CP035659
VERSION     NZ_CP035659.1
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 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; 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
            CP035659.1.
            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_09"
                     /host="Homo sapiens"
                     /db_xref="taxon:1352"
                     /plasmid="unnamed5"
                     /geo_loc_name="USA:Arkansas"
                     /collection_date="2018-09-18"
     gene            join(2833..3008,1..544)
                     /locus_tag="EWM55_RS00565"
                     /old_locus_tag="EWM55_00565"
     CDS             join(2833..3008,1..544)
                     /locus_tag="EWM55_RS00565"
                     /old_locus_tag="EWM55_00565"
                     /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            complement(681..1097)
                     /locus_tag="EWM55_RS00570"
                     /old_locus_tag="EWM55_00570"
     CDS             complement(681..1097)
                     /locus_tag="EWM55_RS00570"
                     /old_locus_tag="EWM55_00570"
                     /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(1100..1384)
                     /locus_tag="EWM55_RS00575"
                     /old_locus_tag="EWM55_00575"
     CDS             complement(1100..1384)
                     /locus_tag="EWM55_RS00575"
                     /old_locus_tag="EWM55_00575"
                     /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            complement(2085..2180)
                     /locus_tag="EWM55_RS17955"
                     /old_locus_tag="EWM55_00580"
     CDS             complement(2085..2180)
                     /locus_tag="EWM55_RS17955"
                     /old_locus_tag="EWM55_00580"
                     /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"
     Typing          2..544
                     /name="rep_cluster_1763"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 taagatgact gctacaaaag cctttgtcgg tgatttagaa aagctctata aagatatgct
       61 taatcttact taccgtactg aagatgagga ttctattcgc tactttgttt tgtttactgg
      121 ttttgaaatc aataaaacaa aaaagtttgt tgaagtcagt gttaatccgg acctagaata
      181 tattattaat ggtttaacag ctgaatttag tagatttgaa ttatctgctt tcacgtcgtt
      241 gcgttctacg tatgcaaaaa ctctattccg actgcttatg cagtaccgtt ctactggtta
      301 ttatgtagtt cgtattgaag agtttaggag cttaatggat atcccagaat actatcaaat
      361 gggtaacatt gatcaaaaag tattaaatcc tgcattacga gaactaaaaa aatacttcaa
      421 tgatcttaaa gtcacaaaaa taaaagcaaa aaagggcaat aaaatcgcca aattagaatt
      481 tactttttca agcctaacgt cagatttgcc aaagatttct ctgcgtaact ggttagaaga
      541 ataaataaaa aagaactcgc cccccttaca ttaagcaagt agacaagtcc cttacaaccg
      601 actaagattg ctagtacatt ctagcatatt gtatggggct tctaaataaa aaacagatag
      661 gaataactcc tatctgtttt ttatcgtttt agaaaatttg ttgggtcgaa atttctagaa
      721 gtgactgttt gactggtttc tttttgatga ttctttggtc gatttcgatt tgatggattt
      781 agtttagctt cgattttttc tttcacttct tgatatactt tagaatttgt gccaataaga
      841 acgcctgtat cttttagata taaatcagca aattctgcga tgatttcagt catgatggaa
      901 atttcttttc ccatagcatt tagttttgcc tgattgctgg tagtggtcgt gttggtatcg
      961 ggttcataac tcatacataa aaagcgaatg gcttccgagt agttattgat atctggattt
     1021 ttttcgatga tggaatctaa aacgtcaaca tgactagggt acaaagtaac atgtttttgg
     1081 acagaagttt ttctcatggt tatatcattc ctccgataag catttcaatg atttgattat
     1141 ttgtgtagac atactcgctt aatatttgag tattttctgt ttggatagca ataaatttat
     1201 cgagcaataa atcgaattgg tcttttttgt aagtcgtaag ttgacggtca aaatcacttt
     1261 cgattaaaac ttttagatat ttatttcgac tccatttttc tcctgtttta ttcgtgagtt
     1321 cttggcaacg tttgtctatt gttgcaacaa actttggatc aatattccga actaaaatgt
     1381 ccataaaaaa tctccttttg caattatgta taatttatgt ataccataca aatactatat
     1441 ttgtatagct gttttttgcc aaaatgctat acataagcta cccacgatgg cgaaaaagtg
     1501 atatcaaatt tttttctgag aaacgtgata ggcacagcct atctacccac tttttttaga
     1561 aagtgggtac acgtttcctt atgctcttta aaattcgggg gggagtgctg cacgtgtaat
     1621 cgataaccaa atttaacaga cgaaaaattg ttggaatata aaaatatgac acccgaaaga
     1681 aaacgatcgt tggaaaaatt aatgcaacta gtgaacgaag acggcggaat ttcagacgca
     1741 gcttttgacg catggagcga atttcatgga gaatataatt aagtgggttt aaatggctct
     1801 aaaatcgctt ctaagagttt ttttagcttg gaccaatgaa atacaccaaa aactaaataa
     1861 aacgtcttaa atcgaaaaat acgagctctc agagcgactt tatttgtaaa tgttgcatat
     1921 aagaaataat tacggatttt agacttttgt aggatatttt tgaaataaat atttatttct
     1981 gttataattt gattgcaaat aagtgaacac gaaacacacg aaatccccag agaggtcgga
     2041 ttctctgggg atttttttgt gggctgagtc gccttaatta agttttactt cttgtttcgg
     2101 ttattcaacc agtaactgaa caaagcgctt aaaagcccaa caagaaggga gcaaataaag
     2161 ttagtgaaca cgaaacacac ctccttccag tcgcaagact gtcggatagg cgacaatcaa
     2221 ttatacaata aaaaagcaaa aataagccta agttttttat tgccttgggg ttgttagggc
     2281 ttgccctgac cgcctgtaag gcgctttaga acgaaggaca tagtttttat cgaatcttgt
     2341 cttagaacgg cttagacgag ctctcaggac gccacaaagg agtccctaat gaattatttt
     2401 tggcgaagga gcctaaaggc gactgctgca agtaaaatgt gagagcgtag cgatcactcc
     2461 ttcttacagc gaccataggg agctagattg gcagtttaat atcatgcgcg aacctgttta
     2521 ttttaaaaag tgggtgattt tttggcggga aattttgctc gcgcgcgcgc gtttatttta
     2581 tttatttttt aaagattttt tagaaccctt tttagggggc agttgagcct tactctccca
     2641 acggatacag aagggtacta acaacttttt atctgagtac taacaacttt ttatctgagt
     2701 actaacaact ttttatctga gtactaacaa ctttttatct gagtactaat atccttttgt
     2761 ataataacaa ccaacctatt tacgagttgg ttgttaaagg ttattattta tttgtaaggg
     2821 gggaagaaag gaatggatga aaaaacggaa ttaacagtca aatatcaaaa tgaattgaat
     2881 ttagtaccgc tgaaaaattt caatgctaag cagatggatt tattttttgc attatgcgct
     2941 cgtatgaaag atcgtggttt gaaaaaagtt agattttctt tcgaggaatt aaaagagtta
     3001 agtgatta
//
