LOCUS       NZ_CP066465             4374 bp    DNA     circular CON 20-FEB-2024
DEFINITION  Enterococcus faecium strain Dallas 87_1 plasmid p87_1_4.3kb,
            complete sequence.
ACCESSION   NZ_CP066465
VERSION     NZ_CP066465.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN17038085
            Assembly: GCF_016406505.1
KEYWORDS    RefSeq.
SOURCE      Enterococcus faecium
  ORGANISM  Enterococcus faecium
            Bacteria; Bacillota; Bacilli; Lactobacillales; Enterococcaceae;
            Enterococcus.
REFERENCE   1  (bases 1 to 4374)
  AUTHORS   Islam,M.J. and Palmer,K.
  TITLE     Molecular characterization of VREfm isolates from Dallas, Texas
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 4374)
  AUTHORS   Islam,M.J. and Palmer,K.
  TITLE     Direct Submission
  JOURNAL   Submitted (21-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                   :: 249.0x
            Sequencing Technology :: Illumina NextSeq; Oxford Nanopore MinION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 02/20/2024 02:50:03
            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)                     :: 3,314
            CDSs (total)                      :: 3,220
            Genes (coding)                    :: 3,078
            CDSs (with protein)               :: 3,078
            Genes (RNA)                       :: 94
            rRNAs                             :: 6, 6, 6 (5S, 16S, 23S)
            complete rRNAs                    :: 6, 6, 6 (5S, 16S, 23S)
            tRNAs                             :: 72
            ncRNAs                            :: 4
            Pseudo Genes (total)              :: 142
            CDSs (without protein)            :: 142
            Pseudo Genes (ambiguous residues) :: 0 of 142
            Pseudo Genes (frameshifted)       :: 50 of 142
            Pseudo Genes (incomplete)         :: 81 of 142
            Pseudo Genes (internal stop)      :: 33 of 142
            Pseudo Genes (multiple problems)  :: 18 of 142
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP066465.1.
            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..4374
                     /organism="Enterococcus faecium"
                     /mol_type="genomic DNA"
                     /strain="Dallas 87_1"
                     /isolation_source="rectal swab"
                     /host="Homo sapiens"
                     /db_xref="taxon:1352"
                     /plasmid="p87_1_4.3kb"
                     /geo_loc_name="USA: Dallas"
                     /collection_date="2015"
     gene            complement(join(3474..4374,1..506))
                     /locus_tag="JCP85_RS16390"
                     /old_locus_tag="JCP85_16390"
     CDS             complement(join(3474..4374,1..506))
                     /locus_tag="JCP85_RS16390"
                     /old_locus_tag="JCP85_16390"
                     /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_002317172.1"
                     /translation="MGFSISFKKGTKNTSISHNNRELTDRQKTNDWHKHIDFTKSDENI
                     YLEQTNLADKYEELFGEVVEKYNAKQKRADRKIEDYLAKVRKDKKLEPQREFIVQIGIL
                     DDFQTNRADGSSTGISKQQAEQNRVIANKILVQYYKEFQERNPNLAVYNAVIHNDEISP
                     HLHLNIVPVAEGYKRGVQKQPSFNKALVQQGIHADKDNGRVLFNNFRNQEVDSIERLMN
                     DYGWKRDIVGTNKIKDIHEYKEIMSEISELRQTAVKERESVSDELRYISRQREENERDK
                     ALMASERAKIEEEKKNMLNVKKEMAVIFQKDMVPLESFKRLPDGSYHLSGNDFVDLYQR
                     ATRATNAKRNADNMSEQYLQMLEQNTELNEYVATLEEERHLSGRKQLADLQVENKKLKE
                     ENRSLRQRLERLKNAFQKSITRLSIRFGLAEKDMGLSEELEVLEQEKTLFYRQNVSQRK
                     LERSEDEIEW"
                     /name="plasmid recombination protein"
     gene            complement(728..1090)
                     /locus_tag="JCP85_RS16395"
                     /old_locus_tag="JCP85_16395"
     CDS             complement(728..1090)
                     /locus_tag="JCP85_RS16395"
                     /old_locus_tag="JCP85_16395"
                     /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_002298418.1"
                     /translation="MGMTLADIKAQEEKLKKEQAKLRQQKKRLIEKENAAMGKALRKRF
                     GFETFADFERWLSSISDDQQHEKSVDNEWLADEKSAPSERDYPDESDGLFGVIPNKKSQ
                     MSESKFTSIFNDVNLR"
                     /name="hypothetical protein"
     gene            complement(1094..1402)
                     /locus_tag="JCP85_RS16400"
                     /old_locus_tag="JCP85_16400"
     CDS             complement(1094..1402)
                     /locus_tag="JCP85_RS16400"
                     /old_locus_tag="JCP85_16400"
                     /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_002298419.1"
                     /translation="MDKIDLREETVDRIELMYERLADYLNLPDEDNYSEMLERMMDVLN
                     SVINADLAKSSVLTNEFVHKHLAQTTDESEKEFWLKLMSHVMQLNQISVINSKEKEM"
                     /name="hypothetical protein"
     gene            complement(1411..1830)
                     /locus_tag="JCP85_RS16405"
                     /old_locus_tag="JCP85_16405"
     CDS             complement(1411..1830)
                     /locus_tag="JCP85_RS16405"
                     /old_locus_tag="JCP85_16405"
                     /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_002298420.1"
                     /translation="MTDLPEKMTIKNLADELGISKNTVRNQLVNAGYDLARYKDNGVIM
                     LDKELIGVVRSIYRSKGGQLTGDLPVNDAGNDFPLEKENEFLREQLAEKDRHISELTEM
                     IRDQQKLTLLQQQKNDQLLLENQELKNRKWWQFWK"
                     /name="hypothetical protein"
     gene            complement(1823..2056)
                     /locus_tag="JCP85_RS16410"
                     /old_locus_tag="JCP85_16410"
     CDS             complement(1823..2056)
                     /locus_tag="JCP85_RS16410"
                     /old_locus_tag="JCP85_16410"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002298421.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_002298421.1"
                     /translation="MAEKQKHFGKKNWLVNLTGDNVVVVFLDSKKMSGKLLDVTQYELI
                     LKNNKIDSPIIIPKHAVKYVYGVAESNGEDND"
                     /name="hypothetical protein"
     gene            complement(2059..3027)
                     /locus_tag="JCP85_RS16415"
                     /old_locus_tag="JCP85_16415"
     CDS             complement(2059..3027)
                     /locus_tag="JCP85_RS16415"
                     /old_locus_tag="JCP85_16415"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002298422.1"
                     /GO_function="GO:0003677 - DNA binding [Evidence IEA];
                     GO:0003916 - DNA topoisomerase 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 factor domain-containing
                     protein"
                     /protein_id="WP_002298422.1"
                     /translation="MSKNGIIVNEWENLTALSNRRLNVQNMYTPLKMQWSIDRITIVGK
                     LKENIYYHTQNDVLILDFEQLMRVNEGNGYLKAVGNNGWQLLDQYEENIAYIEILKWQD
                     GKGRIDFNPNKIGHFLASSMKNFIHDLFLEPHFSRADIACDIIDVPDEFITQYRVVDPV
                     SFKPIYGRSGKLETAYWGSRASERQIRLYNKKLEQETKRKIVPPEIETWWRLELQLRRG
                     KATDWHAMVHESLNSFASPHFLPLDVKTNDKVMIFGLIANPEMWGFLERRMKYKLRDIL
                     KRESQNDELTNHLRETFSESADVLKKELDTWLQGLDVTEEE"
                     /name="replication initiation factor domain-containing
                     protein"
     Typing          complement(2067..2944)
                     /name="rep_cluster_943"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="83.973"
                     /coverage="97.0"
                     /evalue="0.0"
     Typing          complement(4..599)
                     /name="MOBV"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="99.0"
                     /evalue="2.1900000000000003e-129"
     Typing          complement(3478..4373)
                     /name="MOBV"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="93.98"
                     /coverage="99.0"
                     /evalue="3.35e-177"
ORIGIN
        1 atattcaagt gcaggtgcgg acttatttcg tcattatgaa taacagcatt ataaacagcc
       61 aaattagggt ttctctcttg aaactccttg taatactgaa ccaaaatttt attggcaatc
      121 actcgatttt gttcagcttg ttgtttcgat atgccagtag aagaaccatc tgctcgattt
      181 gtctggaaat catctaaaat gcctatttgc acaataaatt ctcgttgagg ttccaacttt
      241 ttatccttgc gcactttcgc taaatagtcc tcgatttttc tatcggctct tttttgtttc
      301 gcattatatt tttctaccac ttcgccaaac aattcctcat atttatctgc tagattcgtc
      361 tgctctaaat aaatattttc atccgatttc gtgaagtcaa tatgcttatg ccaatcattg
      421 gttttctggc gatcagttaa ctcacgatta ttatgagaaa tacttgtatt cttcgttcct
      481 tttttaaatg aaatactaaa ccccaagtta aaaccctcct tcgcgctgtc gctaataaaa
      541 agattgtaaa cctttctgtt actctttgtc aaagagtaac attttcctaa ttgtgacatg
      601 gctgtcacaa ttccaaatgc tctccgaggg tattcgctgt cacaagtgac aacgaaaaaa
      661 ggagccgaaa gcgtgtcacg ctctcaactc cttttacgct ttattttgct tcacgcaaaa
      721 taatcgctta tcgtaaattc acgtcattaa atattgacgt aaatttactc tcactcatct
      781 gacttttctt attcggtatc actccgaata agccgtcaga ttcatcggga taatctcgtt
      841 cgcttggcgc tgatttttca tcagcaagcc actcattatc cactgatttt tcgtgttgct
      901 gatcgtcaga aatcgacgat agccaccgct caaaatcagc aaaagtttca aacccaaaac
      961 gcttgcgaag agccttgccc attgcagcat tttctttctc aatcaagcgt tttttctgtt
     1021 ggcgaagttt cgcttgttct ttttttaatt tttcttcttg cgctttaata tctgctaaag
     1081 tcattcccat aaactacatc tccttttctt tggaattaat aacggaaatt tggtttaact
     1141 gcataacatg actcattaat ttcaaccaaa attctttttc tgattcatca gttgtttgcg
     1201 ctaaatgctt atgaacaaat tcattagtca aaactgaaga ttttgctaga tcagcattga
     1261 taaccgagtt gagaacatcc atcattcgtt caagcatttc actataatta tcttcatccg
     1321 gcaaattcaa ataatcagct aaccgttcat acatcaattc aattctatcg actgtttctt
     1381 ctctcaaatc aattttatcc atgtcacacc tcacttccag aattgccacc attttcgatt
     1441 ttttaattct tgattttcta gtaacaactg atcgtttttt tgttgctgaa gcaaagtcaa
     1501 tttttgttgg tcacgaatca tttccgttaa ttcagaaata tgcctatctt tttccgctaa
     1561 ttgttcacgc aaaaattcat tttctttttc taacgggaaa tcattgcctg catcattgac
     1621 cggtaaatca ccagtcaatt gaccaccttt tgaccgataa attgaccgca caacaccaat
     1681 caattccttg tctaacatga taaccccatt atctttatac cgagcaaggt cataacctgc
     1741 attgaccagt tgattgcgca ctgtattttt agatataccc aactcatcag caaggttttt
     1801 tatggtcatt ttttctggca aatcagtcat tatcttctcc gttactttca gctaccccat
     1861 aaacatattt aacagcatgc ttagggataa tgattgggga atcaatttta ttatttttca
     1921 aaatcaactc atactgcgtt acatcaagta acttaccgga catttttttg ctatccaaaa
     1981 aaacaacgac aacgttatca cctgttaaat tcaccaacca atttttctta ccaaaatgct
     2041 tttgtttttc tgccattctt attcctcctc cgttacatct aacccttgaa gccaagtgtc
     2101 taattctttt ttcaaaacat ctgctgattc cgaaaatgtt tctcgtaaat gattcgtcaa
     2161 ctcatcattt tgactttctc ttttcaaaat atctctcaat ttgtatttca ttctacgctc
     2221 taaaaacccc cacatttcag ggttagcaat cagtccaaaa atcatcacct tatcatttgt
     2281 ttttacatca agtggtagaa aatgagggct agcaaaacta tttaaacttt catgaaccat
     2341 tgcatgccaa tctgttgctt tcccacgcct taactgcaat tccagtcgcc accaagtttc
     2401 tatttctggt ggcacaattt tacgcttggt ttcctgttcc aattttttgt tgtatagccg
     2461 aatctggcgt tcgctggcac gactgcccca ataagctgtt tccagcttcc cagaccgccc
     2521 ataaattggc ttgaaagaaa caggatcaac cactcgatat tgtgtaataa actcatcagg
     2581 cacatcgata atatcgcaag caatatccgc acgtgagaaa tgtggttcta gaaataaatc
     2641 atgaatgaaa tttttcattg aactagctaa aaaatgacca atcttattcg ggttaaaatc
     2701 aatccgccct ttgccatctt gccatttcaa aatctcaata taagcaatat tttcttcgta
     2761 ttggtctaat aattgccagc cgttattccc aaccgctttt aaatagccat tgccttcatt
     2821 cacccgcatt aattgctcaa aatctaaaat caacacatca ttttgagtgt gataataaat
     2881 attttccttc agttttccaa cgatagtaat tcggtcaatt gaccactgca tttttaaggg
     2941 ggtgtacata ttttgtacat ttaaccgcct gttagatagg gctgttaaat tttcccactc
     3001 atttacgatt atgccatttt tactcaaatt ttgttcctcc tcaaagaaaa agagacttct
     3061 ggaaagaatt ttcaaaagtt cacgtaactc ttaaaaattc attaccaaaa aatctctagt
     3121 cttgaagaaa tctaaaaata ttcgtataat gattaagaag ttacggagct agtgcgatta
     3181 gtttccgtaa aggtcgagaa cgttggtagc gttgctcgac tattttttta ctcttttttc
     3241 agttcatttg tttgctaact caataatagc acttctcttt agctatgcaa atatccaaaa
     3301 aataaaaccg caccctttga aaagggcgcc cccaaacttc gctaacgcta ggttggccaa
     3361 aaaatggact ggccattttt tagcaaatgt cagcttaata ggctagtggt ttagccgtca
     3421 actccttatc ctcggcacaa accgcctccg gtaccgttga ctgcacatcg taactaccac
     3481 tcgatctcat cttcagaacg ctctaattta cgctgtgaga cgttttgacg ataaaataag
     3541 gttttctcct gctctaacac ttctaattcc tcagaaagcc ccatatcctt ttctgcaaga
     3601 ccaaaacgga tagacaaacg agtgatcgat ttttgaaatg cgttttttaa tcgctctaaa
     3661 cgctggcgta aagagcgatt ttcttctttc agctttttat tttccacttg taaatctgct
     3721 aattgttttc taccagacaa atgacgctct tcttccaatg tagctacata ctcatttaat
     3781 tctgtatttt gctcaagcat ctgtaaatat tgctcactca tgttatcagc atttctcttg
     3841 gcatttgttg ctctcgtagc tcgttgatac aaatcaacaa aatcattccc agataaatga
     3901 tacgaaccat caggaagcct cttgaaactt tctaaaggaa ccatatcttt ttggaaaatg
     3961 accgccatct ctttttttac attcagcata tttttcttct cttcttcaat cttcgctctc
     4021 tcagaagcca tcagagcctt atcacgctcg ttttcttctc tttgcctaga aatatacctc
     4081 aactcatcag aaacgctctc acgctctttt acagccgttt ggcgcaattc agaaatttca
     4141 ctcatgattt ctttgtattc gtgaatatct ttaattttgt tggtaccgac aatatccctt
     4201 ttccaaccgt aatcattcat taatcgttct atagagtcaa cttcttgatt tctaaaatta
     4261 ttgaaaagca ctcgaccatt atctttatca gcgtgtatcc cttgttgaac cagtgcttta
     4321 ttaaagctcg gctgcttttg aacaccccgt ttataacctt cagcaaccgg caca
//
