LOCUS       NZ_CP066395             3199 bp    DNA     circular CON 20-FEB-2024
DEFINITION  Enterococcus faecium strain Dallas 17_1 plasmid p17_1_3kb, complete
            sequence.
ACCESSION   NZ_CP066395
VERSION     NZ_CP066395.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN17038071
            Assembly: GCF_016406445.1
KEYWORDS    RefSeq.
SOURCE      Enterococcus faecium
  ORGANISM  Enterococcus faecium
            Bacteria; Bacillota; Bacilli; Lactobacillales; Enterococcaceae;
            Enterococcus.
REFERENCE   1  (bases 1 to 3199)
  AUTHORS   Islam,M.J. and Palmer,K.
  TITLE     Molecular characterization of VREfm isolates from Dallas, Texas
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 3199)
  AUTHORS   Islam,M.J. and Palmer,K.
  TITLE     Direct Submission
  JOURNAL   Submitted (20-DEC-2020) Biological Sciences, University of Texas at
            Dallas, 1520 Richardson Dr Apt 1418, Richardson, TX 75080, USA
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Date                     :: 2019
            Assembly Method                   :: Unicycler v. 0.4.7
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 156.0x
            Sequencing Technology :: Illumina NextSeq; Oxford Nanopore MinION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 02/20/2024 02:48:50
            Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline
            (PGAP)
            Annotation Method :: Best-placed reference protein set; GeneMarkS-2+
            Annotation Software revision      :: 6.6
            Features Annotated                :: Gene; CDS; rRNA; tRNA; ncRNA
            Genes (total)                     :: 3,073
            CDSs (total)                      :: 2,982
            Genes (coding)                    :: 2,859
            CDSs (with protein)               :: 2,859
            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)              :: 123
            CDSs (without protein)            :: 123
            Pseudo Genes (ambiguous residues) :: 0 of 123
            Pseudo Genes (frameshifted)       :: 45 of 123
            Pseudo Genes (incomplete)         :: 78 of 123
            Pseudo Genes (internal stop)      :: 24 of 123
            Pseudo Genes (multiple problems)  :: 20 of 123
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP066395.1.
            Bacteria and source DNA available from Dr. Kelli Palmer, UTDallas.
            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..3199
                     /organism="Enterococcus faecium"
                     /mol_type="genomic DNA"
                     /strain="Dallas 17_1"
                     /isolation_source="rectal swab"
                     /host="Homo sapiens"
                     /db_xref="taxon:1352"
                     /plasmid="p17_1_3kb"
                     /geo_loc_name="USA: Dallas"
                     /collection_date="2015"
     gene            join(3112..3199,1..632)
                     /locus_tag="JCP93_RS15265"
                     /old_locus_tag="JCP93_15265"
     CDS             join(3112..3199,1..632)
                     /locus_tag="JCP93_RS15265"
                     /old_locus_tag="JCP93_15265"
                     /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(769..1185)
                     /locus_tag="JCP93_RS15270"
                     /old_locus_tag="JCP93_15270"
     CDS             complement(769..1185)
                     /locus_tag="JCP93_RS15270"
                     /old_locus_tag="JCP93_15270"
                     /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(1188..1472)
                     /locus_tag="JCP93_RS15275"
                     /old_locus_tag="JCP93_15275"
     CDS             complement(1188..1472)
                     /locus_tag="JCP93_RS15275"
                     /old_locus_tag="JCP93_15275"
                     /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            1838..2062
                     /locus_tag="JCP93_RS15280"
                     /old_locus_tag="JCP93_15280"
     CDS             1838..2062
                     /locus_tag="JCP93_RS15280"
                     /old_locus_tag="JCP93_15280"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000410576.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_000410576.1"
                     /translation="MEKFPYEYFQNLEKLEQAIQAIKFDLTDEKLLEYKNMTPERKRSL
                     EKLMQLVNEDGGISDAAFDAWSEFHGEYN"
                     /name="hypothetical protein"
     Typing          2..632
                     /name="rep_cluster_1763"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 tattttttgc attatgcgct cgtatgaaag atcgtggttt gaaaaaagtt agattttctt
       61 tcgaggaatt aaaagagtta agtgattata agatgactgc tacaaaagcc tttgtcggtg
      121 atttagaaaa gctctataaa gatatgctta atcttactta ccgtactgaa gatgaggatt
      181 ctattcgcta ctttgttttg tttactggtt ttgaaatcaa taaaacaaaa aagtttgttg
      241 aagtcagtgt taatccggac ctagaatata ttattaatgg tttaacagct gaatttagta
      301 gatttgaatt atctgctttc acgtcgttgc gttctacgta tgcaaaaact ctattccgac
      361 tgcttatgca gtaccgttct actggttatt atgtagttcg tattgaagag tttaggagct
      421 taatggatat cccagaatac tatcaaatgg gtaacattga tcaaaaagta ttaaatcctg
      481 cattacgaga actaaaaaaa tacttcaatg atcttaaagt cacaaaaata aaagcaaaaa
      541 agggcaataa aatcgccaaa ttagaattta ctttttcaag cctaacgtca gatttgccaa
      601 agatttctct gcgtaactgg ttagaagaat aaataaaaaa gaactcgccc cccttacatt
      661 aagcaagtag acaagtccct tacaaccgac taagattgct agtacattct agcatattgt
      721 atggggcttc taaataaaaa acagatagga ataactccta tctgtttttt atcgttttag
      781 aaaatttgtt gggtcgaaat ttctagaagt gactgtttga ctggtttctt tttgatgatt
      841 ctttggtcga tttcgatttg atggatttag tttagcttcg attttttctt tcacttcttg
      901 atatacttta gaatttgtgc caataagaac gcctgtatct tttagatata aatcagcaaa
      961 ttctgcgatg atttcagtca tgatggaaat ttcttttccc atagcattta gttttgcctg
     1021 attgctggta gtggtcgtgt tggtatcggg ttcataactc atacataaaa agcgaatggc
     1081 ttccgagtag ttattgatat ctggattttt ttcgatgatg gaatctaaaa cgtcaacatg
     1141 actagggtac aaagtaacat gtttttggac agaagttttt ctcatggtta tatcattcct
     1201 ccgataagca tttcaatgat ttgattattt gtgtagacat actcgcttaa tatttgagta
     1261 ttttctgttt ggatagcaat aaatttatcg agcaataaat cgaattggtc ttttttgtaa
     1321 gtcgtaagtt gacggtcaaa atcactttcg attaaaactt ttagatattt atttcgactc
     1381 catttttctc ctgttttatt cgtgagttct tggcaacgtt tgtctattgt tgcaacaaac
     1441 tttggatcaa tattccgaac taaaatgtcc ataaaaaatc tccttttgca attatgtata
     1501 atttatgtat atcatacaaa tactatattt gtatagctgt tttttgccaa aatgctatac
     1561 ataagctacc cacgatggcg aaaaagtgat atcaaatttt tttctgagaa acgtgatagg
     1621 cacagcctat ctacccactt tttttagaaa gtgggtacac gtttccttat gctctttaaa
     1681 attcgggggg gagtgctgca cgtgtaatcg ataaccaaat ttaaaaatgc acgatcaaaa
     1741 atttatttag tttttcaaac gacatttttt ttgagagtat agacggcaaa gaagtgattt
     1801 tatttctaga aaaattgtga gactggagaa agaaaaaatg gaaaaatttc cttacgaata
     1861 ttttcaaaac ttagaaaaat tagagcaagc aattcaagca atcaagttcg atttaacaga
     1921 cgaaaaattg ttggaatata aaaatatgac acccgaaaga aaacgatcgt tggaaaaatt
     1981 aatgcaacta gtgaacgaag acggcggaat ttcagacgca gcttttgacg catggagcga
     2041 atttcatgga gaatataatt aagtgggttt aaatggctct aaaatcgctt ctaagagttt
     2101 tttagcttgg accaatgaaa tacaccaaaa actaaataaa acgtcttaaa tcgaaaaata
     2161 cgagctctca gagcgacttt atttgtaaat gttgcatata agaaataatt acggatttta
     2221 gacttttgta ggatattttt gaaataaata tttatttctg ttataatttg attgcaaata
     2281 agtgaacacg aaacacacga aagccccaga gaggtcggat tctctggggc tttttttgtg
     2341 ggctgagtcg ccttaattaa gttttacttc ttgtttcggt tattcaacca gtaactgaac
     2401 aaagcgctta aaagcccaac aagaagggag caaataaagt tagtgaacac gaaacacacc
     2461 tccttccagt cgcaagactg tcggataggc gacaatcaat tatacaataa aaaagcaaaa
     2521 ataagcctaa gttttttatt gccttggggt tgttagggct tgccctgacc gcctgtaagg
     2581 cgctttagaa cgaaggacat agtttttatc gaatcttgtc ttagaacggc ttagacgagc
     2641 tctcaggacg ccacaaagga gtccctaatg aattattttt ggcgaaggag cctaaaggcg
     2701 actgctgcaa gtaaaatgtg agagcgtagc gatcactcct tcttacagcg accataggga
     2761 gctagattgg cagtttaata tcatgcgcga acctgtttat tttaaaaagt gggtgatttt
     2821 ttggcgggaa attttgctcg cgcgcgcgcg tttattttat ttatttttta aagatttttt
     2881 agaacccttt ttagggggca gttgagcctt actctcccaa cggatacaga agggtactaa
     2941 caacttttta tctgagtact aacaactttt tatctgagta ctaacaactt tttatctgag
     3001 tactaacaac tttttatctg agtactaata tccttttgta taataacaac caacctattt
     3061 acgagttggt tgttaaaggt tattatttat ttgtaagggg ggaagaaagg aatggatgaa
     3121 aaaacggaat taacagtcaa atatcaaaat gaattgaatt tagtaccgct gaaaaatttc
     3181 aatgctaagc agatggatt
//
