LOCUS       NZ_CP066679             4305 bp    DNA     circular CON 20-FEB-2024
DEFINITION  Enterococcus faecium strain Dallas 163_1 plasmid p6, complete
            sequence.
ACCESSION   NZ_CP066679
VERSION     NZ_CP066679.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN17038111
            Assembly: GCF_016415485.1
KEYWORDS    RefSeq.
SOURCE      Enterococcus faecium
  ORGANISM  Enterococcus faecium
            Bacteria; Bacillota; Bacilli; Lactobacillales; Enterococcaceae;
            Enterococcus.
REFERENCE   1  (bases 1 to 4305)
  AUTHORS   Islam,M.J. and Palmer,K.
  TITLE     Molecular characterization of VREfm isolates from Dallas, Texas
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 4305)
  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                   :: 137.0x
            Sequencing Technology :: Illumina NextSeq; Oxford Nanopore MinION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 02/20/2024 02:34:57
            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)                     :: 3,080
            CDSs (total)                      :: 2,989
            Genes (coding)                    :: 2,842
            CDSs (with protein)               :: 2,842
            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)              :: 147
            CDSs (without protein)            :: 147
            Pseudo Genes (ambiguous residues) :: 0 of 147
            Pseudo Genes (frameshifted)       :: 53 of 147
            Pseudo Genes (incomplete)         :: 94 of 147
            Pseudo Genes (internal stop)      :: 38 of 147
            Pseudo Genes (multiple problems)  :: 31 of 147
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP066679.1.
            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..4305
                     /organism="Enterococcus faecium"
                     /mol_type="genomic DNA"
                     /strain="Dallas 163_1"
                     /isolation_source="rectal swab"
                     /host="Homo sapiens"
                     /db_xref="taxon:1352"
                     /plasmid="p6"
                     /geo_loc_name="USA: Dallas"
                     /collection_date="2015"
     gene            complement(join(4040..4305,1..97))
                     /locus_tag="JCP82_RS15250"
                     /old_locus_tag="JCP82_15250"
     CDS             complement(join(4040..4305,1..97))
                     /locus_tag="JCP82_RS15250"
                     /old_locus_tag="JCP82_15250"
                     /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_002313294.1"
                     /translation="MGMTLADIKVQEEKLKKEQAKLRQQKKRLIEKENAAMGKALRKRF
                     GFESFADFERWLSSISDDQQHEKSVGNELRADEKSAPSERNYPNESDGIFGGIPNRKSQ
                     MSESGFASMFSDVNSR"
                     /name="hypothetical protein"
     gene            complement(101..409)
                     /locus_tag="JCP82_RS15255"
                     /old_locus_tag="JCP82_15255"
     CDS             complement(101..409)
                     /locus_tag="JCP82_RS15255"
                     /old_locus_tag="JCP82_15255"
                     /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_002304909.1"
                     /translation="MDKIDLREETVNRIEVMYERLADYLNLSDEDNYSEMLERMMDVLN
                     SVINADLAKSSVLTNEFVHKHLAQTTDEAEKEFWLKLMSHIMQLNQISVINSKEKGM"
                     /name="hypothetical protein"
     gene            complement(418..837)
                     /locus_tag="JCP82_RS15260"
                     /old_locus_tag="JCP82_15260"
     CDS             complement(418..837)
                     /locus_tag="JCP82_RS15260"
                     /old_locus_tag="JCP82_15260"
                     /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_002305964.1"
                     /translation="MTDSTDKMTIKALADELGITKNTVRNYLVKAGYDLARYKKNGIIL
                     LDKELIGVARSIYRSKGGQLTGHLPVNSTGSDFPLEKENEFLRDQLAEKDKHISELTEM
                     IRDQQKLTLLQQQKNDQLLLENQELKNRKWWQFWK"
                     /name="hypothetical protein"
     gene            complement(834..1823)
                     /locus_tag="JCP82_RS15265"
                     /old_locus_tag="JCP82_15265"
     CDS             complement(834..1823)
                     /locus_tag="JCP82_RS15265"
                     /old_locus_tag="JCP82_15265"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002349057.1"
                     /GO_function="GO:0003677 - DNA binding [Evidence IEA]"
                     /GO_process="GO:0006260 - DNA replication [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="protein rep"
                     /protein_id="WP_002304903.1"
                     /translation="MKKKKQDLINGTFREKKKNLKKVVAFSDNRISPKMRELMTGCGSY
                     LEFIATIDKEKKKLVQAHFCKNRFCPLCAWRKARKDSMMLSIMMQAIAEEKQYQFIFMT
                     LTTPNVKAECLNDEIDLFNHALKKMFMRKRVKTSIKGYVRKLEITYNKKRNDYNPHFHL
                     ILAVNKSYFTDKDYYIKQSEWLDLWREVTGKTGINPDGTDEITQLDIRKVKGFQQEKAV
                     QEVAKYSAKDFELTESQEVFDTFYHAMKGRQLITFNGVFKEYKKKYESGDLDRYKKKDE
                     NEYFWFLTASWMRKESKYAVDYREMSADERNYFSGMYVDEKSVEGENE"
                     /name="protein rep"
     gene            complement(2412..3818)
                     /locus_tag="JCP82_RS15270"
                     /old_locus_tag="JCP82_15270"
     CDS             complement(2412..3818)
                     /locus_tag="JCP82_RS15270"
                     /old_locus_tag="JCP82_15270"
                     /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_002304901.1"
                     /translation="MGFSISFKKGTKNTSISHNNRELTDSQKINDWHKHIDFTKSDENI
                     YLEQINIREKYEELFGEAVEKYNAKQKRADRKIEDYLAKVRKDKKMEPQREFIVQIGTL
                     DDFRTTRDDGSSTGISEQQAEQNRVIANKILVEYFKEFKERNPSLSVYNAVIHNDEVSP
                     HLHLNIVPVAEGYKRGVQKQPSFNKALQQQGLRADKENGRVIWNNFRNQEVESIERLMA
                     DFGWERELVGTNKIKDIHEYKEIMSEISELRQTAVKERESVSDELRYICRQREENEREK
                     ALVASERAKIEEEKKNMLNVKKEMAVIFQKDMVPLESFKRLPDGSYHLSGNDFVDLYQR
                     ATRATNAKRNADNMSEQYLQMLEQNTELNEYVAALEEERHLSGRKQLADLQVENKKLKE
                     ENRSLRQRLERLKNAFQKSITRLSIRFGLAEKDMGLSEELEVLEQEKTLFYRQNVSQHK
                     LERSEDEIEW"
                     /name="plasmid recombination protein"
     Typing          complement(2416..3818)
                     /name="MOBV"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="99.359"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 ctttctcaat caatcgtttc ttctgttggc gaagtttcgc ctgttctttt tttaattttt
       61 cttcttgcac tttaatatct gctaaagtca ttcccataaa ctacatcccc ttttctttgg
      121 aattaataac ggaaatttgg tttaactgca taatatgact cattaatttc aaccaaaatt
      181 ctttttcagc ttcatcagtt gtttgcgcta aatgcttatg aacaaattca ttagtcaaaa
      241 ctgaagattt tgctagatca gcattgataa ccgagttgag aacatccatc attcgttcaa
      301 gcatctcact ataattatct tcatccgaaa gattcaaata atcagctaac cgttcataca
      361 tcacttcaat tctattgact gtttcttctc tcaaatcaat tttatccatg tcacatctca
      421 cttccagaat tgccaccatt ttcgattttt taattcttga ttttctagta acaactgatc
      481 gtttttttgt tgctgaagca gggtcaattt ttgttgatca cgaatcattt ctgttaattc
      541 agaaatatgt ttgtccttct cagctaattg atcacgcaaa aactcattct ctttttccaa
      601 aggaaaatca ctgcccgtgc tattgaccgg taaatgacca gtcaattgac caccttttga
      661 ccgataaatt gaccgagcaa caccaatcaa ctctttgtct agcaagataa ttccattttt
      721 cttgtaccga gcaagatcat atccggcttt gactagataa tttctcactg tatttttggt
      781 tattcctagt tcatcagcaa gcgccttaat tgtcatttta tccgttgaat cagtcattca
      841 ttttccccct caacagattt ttcatcgaca tacattcctg aaaaataatt tctttcatca
      901 gcactcatct cacgataatc aaccgcatat ttcgattctt tcctcatcca cgaagcagtc
      961 aaaaaccaaa aatattcatt ctcatctttt ttcttataac gatcaaggtc acccgactca
     1021 tattttttct tgtattcttt gaatacaccg ttaaacgtaa tcaactgacg acctttcatt
     1081 gcatgataga atgtgtcaaa cacttcctga ctttcggtca gttcaaaatc ttttgccgaa
     1141 tatttcgcaa cttcctgtac tgctttttct tgttggaacc ctttgacctt gcgaatatcc
     1201 aactgggtaa tttcgtcggt accatccgga ttaattcccg tttttccggt cacttcccgc
     1261 cacaaatcta accattccga ttgcttgata taataatctt tatccgtgaa ataagattta
     1321 tttactgcca aaatcaagtg aaaatgcggg ttatagtcat tccgtttttt gttgtacgtg
     1381 atttccaatt ttcgcacata gcctttaatc gaagtcttaa cccgtttgcg cataaacatc
     1441 tttttcaatg catgattaaa caaatcaatt tcatcgttca aacattccgc ttttacattc
     1501 ggtgtcgtca acgtcataaa aataaattga tactgctttt cttccgcaat agcttgcatc
     1561 ataatcgaca acatcatcga atccttacga gctttacgcc aagcacataa cggacagaaa
     1621 cgatttttac aaaagtgagc ttggaccaat ttctttttct ccttatcaat cgttgcaata
     1681 aattctaaat atgaaccaca gcctgtcatc aattcacgca ttttgggaga aattcgatta
     1741 tcactaaatg ccaccacttt tttcaaattt ttcttttttt ctcgaaatgt tccgttaatc
     1801 aaatcttgct ttttcttttt catcttgcta tactgaatct acaaattttg tatacaaaaa
     1861 aggctgaaaa gccgataaca aaaaatagat tgctctcctt tctagtttag tttttttcta
     1921 gtcaattaaa actataaaat actagggaag aaaaagcaat cttttttttt gttcttcctt
     1981 agagccacaa gggatagacc catactatag ccccgatttc ttcgcagaaa tagttgccta
     2041 tagtatcaag ataagaaaaa acatcaaaaa agagggcgaa aatcgccccc tttttttcgt
     2101 tttaaaaccc caaaacccaa agacataaaa ttcgatcaat cgaccactgc atttttaagg
     2161 gggtgtacat attttgtaca tttaaccgcc tgttagatag ggctgttaaa ttttcccact
     2221 cattcttagt catgcaaaca taaaaccgca ccctttaaaa agggcgcccc caaacttcgc
     2281 taacgctaag ttggccaaaa aatggacttg ccatttttta gcaaatgtca gcttaatagg
     2341 ctagtggttt agccgtcaac tccttatcct cggcacaaac cgcctccggt accgttgact
     2401 gcacatcgta actaccactc gatctcatct tcagaacgct ctaatttatg ctgtgagacg
     2461 ttttgacgat aaaataaggt tttctcctgc tctaatactt ctaattcctc agaaagcccc
     2521 atatcctttt ctgcaagccc aaaacggata gacaaacgag tgatcgattt ttgaaatgcg
     2581 ttttttaatc gctctaaacg ctggcgtaaa gagcgatttt cttctttcag ctttttattt
     2641 tccacttgta aatctgctaa ttgttttcta ccagacaaat gacgctcttc ttccaatgca
     2701 gctacatact catttaattc tgtattttgc tcaagcatct gtaaatattg ctcactcatg
     2761 ttatcagcat ttctcttggc atttgttgct ctcgtagctc gttgatacaa atcaacaaaa
     2821 tcattcccag ataaatgata cgaaccatca ggaagcctct tgaaactttc taaaggaacc
     2881 atatcttttt ggaaaatgac cgccatctct ttttttacat tcagcatatt tttcttctct
     2941 tcttcaatct tcgctctctc agaagccacc agagccttct cacgctcgtt ttcttctctt
     3001 tgcctacaaa tatacctcaa ctcatcagaa acgctctcac gctcttttac ggccgtttga
     3061 cgcaattcgg aaatttcgct catgatttct ttgtattcat gaatatcttt gattttgtta
     3121 gtaccgacta actcacgctc ccaaccaaaa tctgccatca aacgttcaat tgactcaact
     3181 tcctgattcc taaaattatt ccaaatcact cgaccattct ctttatctgc tcgtaaaccc
     3241 tgctgttgca aggctttgtt aaaacttggt tgcttttgaa caccccgttt atacccttca
     3301 gcaacaggaa caatattcaa atgcaggtgc ggacttactt cgtcattatg aataacagca
     3361 ttgtagacgg ataaactagg attccgttct ttaaattctt tgaaatactc aactaaaatt
     3421 ttgttggcaa tcactcgatt ttgttctgct tgttgttccg atatgccagt agaagaacca
     3481 tcatcacgag tagtacgaaa atcatcaaga gtaccaattt gcacgataaa ttctcgctgt
     3541 ggttccattt ttttatcctt gcgaaccttt gctaaatagt cctcaatttt tctatcggct
     3601 cttttctgct ttgcattata tttttctacg gcttcaccga ataattcttc atatttttca
     3661 cgaatattta tttgttccaa atagatattt tcatccgatt ttgtgaaatc aatatgctta
     3721 tgccagtcat tgattttttg gctatcagtt aactcacgat tattatgaga aatgcttgta
     3781 ttctttgttc cctttttgaa cgaaatacta aaccccaagt taaacccctc cttcgcgctg
     3841 tcgctaataa aaagagtgta aacctttctg ttactctttg tcaaagagta acgttttcct
     3901 aattgtgaca tgactgtcac aattccaaac gctctccgag ggttttcgcc gtcacaagtg
     3961 acaacgaaaa aaggagccga aagcgtgtca cgctctcaac tccttttacg ctttattttg
     4021 cttcatgcaa aatattcgct tatcgtgaat ttacgtcact aaacattgac gcaaatccac
     4081 tctcactcat ctgacttttt ctattcggta tccctccgaa tattccgtca gattcgttag
     4141 ggtaattccg ttcgcttggt gctgattttt catcagctcg caactcatta cccactgatt
     4201 tttcgtgttg ctgatcgtca gaaatcgacg atagccaccg ctcaaaatca gcaaaagatt
     4261 caaacccaaa acgcttgcga agagccttgc ccattgcagc atttt
//
