LOCUS       NZ_CP066590             4305 bp    DNA     circular CON 20-FEB-2024
DEFINITION  Enterococcus faecium strain Dallas 103 plasmid p103_4.3kb, complete
            sequence.
ACCESSION   NZ_CP066590
VERSION     NZ_CP066590.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN17038093
            Assembly: GCF_016415105.1
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  JOURNAL   Unpublished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                   :: 74.0x
            Sequencing Technology :: Illumina NextSeq; Oxford Nanopore MinION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 02/20/2024 02:58:44
            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)                     :: 3,147
            CDSs (total)                      :: 3,056
            Genes (coding)                    :: 2,881
            CDSs (with protein)               :: 2,881
            Genes (RNA)                       :: 91
            rRNAs                             :: 6, 5, 6 (5S, 16S, 23S)
            complete rRNAs                    :: 6, 5, 6 (5S, 16S, 23S)
            tRNAs                             :: 70
            ncRNAs                            :: 4
            Pseudo Genes (total)              :: 175
            CDSs (without protein)            :: 175
            Pseudo Genes (ambiguous residues) :: 0 of 175
            Pseudo Genes (frameshifted)       :: 101 of 175
            Pseudo Genes (incomplete)         :: 73 of 175
            Pseudo Genes (internal stop)      :: 35 of 175
            Pseudo Genes (multiple problems)  :: 30 of 175
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP066590.1.
            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 103"
                     /isolation_source="rectal swab"
                     /host="Homo sapiens"
                     /db_xref="taxon:1352"
                     /plasmid="p103_4.3kb"
                     /geo_loc_name="USA: Dallas"
                     /collection_date="2015"
     gene            complement(join(4301..4305,1..985))
                     /locus_tag="JCP83_RS15580"
                     /old_locus_tag="JCP83_15580"
     CDS             complement(join(4301..4305,1..985))
                     /locus_tag="JCP83_RS15580"
                     /old_locus_tag="JCP83_15580"
                     /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(1574..2980)
                     /locus_tag="JCP83_RS15585"
                     /old_locus_tag="JCP83_15585"
     CDS             complement(1574..2980)
                     /locus_tag="JCP83_RS15585"
                     /old_locus_tag="JCP83_15585"
                     /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"
     gene            complement(3202..3564)
                     /locus_tag="JCP83_RS15590"
                     /old_locus_tag="JCP83_15590"
     CDS             complement(3202..3564)
                     /locus_tag="JCP83_RS15590"
                     /old_locus_tag="JCP83_15590"
                     /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(3568..3876)
                     /locus_tag="JCP83_RS15595"
                     /old_locus_tag="JCP83_15595"
     CDS             complement(3568..3876)
                     /locus_tag="JCP83_RS15595"
                     /old_locus_tag="JCP83_15595"
                     /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(3885..4304)
                     /locus_tag="JCP83_RS15600"
                     /old_locus_tag="JCP83_15600"
     CDS             complement(3885..4304)
                     /locus_tag="JCP83_RS15600"
                     /old_locus_tag="JCP83_15600"
                     /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"
     Typing          complement(1578..2980)
                     /name="MOBV"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="99.359"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 cattttcccc ctcaacagat ttttcatcga catacattcc tgaaaaataa tttctttcat
       61 cagcactcat ctcacgataa tcaaccgcat atttcgattc tttcctcatc cacgaagcag
      121 tcaaaaacca aaaatattca ttctcatctt ttttcttata acgatcaagg tcacccgact
      181 catatttttt cttgtattct ttgaatacac cgttaaacgt aatcaactga cgacctttca
      241 ttgcatgata gaatgtgtca aacacttcct gactttcggt cagttcaaaa tcttttgccg
      301 aatatttcgc aacttcctgt actgcttttt cttgttggaa ccctttgacc ttgcgaatat
      361 ccaactgggt aatttcgtcg gtaccatccg gattaattcc cgtttttccg gtcacttccc
      421 gccacaaatc taaccattcc gattgcttga tataataatc tttatccgtg aaataagatt
      481 tatttactgc caaaatcaag tgaaaatgcg ggttatagtc attccgtttt ttgttgtacg
      541 tgatttccaa ttttcgcaca tagcctttaa tcgaagtctt aacccgtttg cgcataaaca
      601 tctttttcaa tgcatgatta aacaaatcaa tttcatcgtt caaacattcc gcttttacat
      661 tcggtgtcgt caacgtcata aaaataaatt gatactgctt ttcttccgca atagcttgca
      721 tcataatcga caacatcatc gaatccttac gagctttacg ccaagcacat aacggacaga
      781 aacgattttt acaaaagtga gcttggacca atttcttttt ctccttatca atcgttgcaa
      841 taaattctaa atatgaacca cagcctgtca tcaattcacg cattttggga gaaattcgat
      901 tatcactaaa tgccaccact tttttcaaat ttttcttttt ttctcgaaat gttccgttaa
      961 tcaaatcttg ctttttcttt ttcatcttgc tatactgaat ctacaaattt tgtatacaaa
     1021 aaaggctgaa aagccgataa caaaaaatag attgctctcc tttctagttt agtttttttc
     1081 tagtcaatta aaactataaa atactaggga agaaaaagca atcttttttt ttgttcttcc
     1141 ttagagccac aagggataga cccatactat agccccgatt tcttcgcaga aatagttgcc
     1201 tatagtatca agataagaaa aaacatcaaa aaagagggcg aaaatcgccc cctttttttc
     1261 gttttaaaac cccaaaaccc aaagacataa aattcgatca atcgaccact gcatttttaa
     1321 gggggtgtac atattttgta catttaaccg cctgttagat agggctgtta aattttccca
     1381 ctcattctta gtcatgcaaa cataaaaccg caccctttaa aaagggcgcc cccaaacttc
     1441 gctaacgcta agttggccaa aaaatggact tgccattttt tagcaaatgt cagcttaata
     1501 ggctagtggt ttagccgtca actccttatc ctcggcacaa accgcctccg gtaccgttga
     1561 ctgcacatcg taactaccac tcgatctcat cttcagaacg ctctaattta tgctgtgaga
     1621 cgttttgacg ataaaataag gttttctcct gctctaatac ttctaattcc tcagaaagcc
     1681 ccatatcctt ttctgcaagc ccaaaacgga tagacaaacg agtgatcgat ttttgaaatg
     1741 cgttttttaa tcgctctaaa cgctggcgta aagagcgatt ttcttctttc agctttttat
     1801 tttccacttg taaatctgct aattgttttc taccagacaa atgacgctct tcttccaatg
     1861 cagctacata ctcatttaat tctgtatttt gctcaagcat ctgtaaatat tgctcactca
     1921 tgttatcagc atttctcttg gcatttgttg ctctcgtagc tcgttgatac aaatcaacaa
     1981 aatcattccc agataaatga tacgaaccat caggaagcct cttgaaactt tctaaaggaa
     2041 ccatatcttt ttggaaaatg accgccatct ctttttttac attcagcata tttttcttct
     2101 cttcttcaat cttcgctctc tcagaagcca ccagagcctt ctcacgctcg ttttcttctc
     2161 tttgcctaca aatatacctc aactcatcag aaacgctctc acgctctttt acggccgttt
     2221 gacgcaattc ggaaatttcg ctcatgattt ctttgtattc atgaatatct ttgattttgt
     2281 tagtaccgac taactcacgc tcccaaccaa aatctgccat caaacgttca attgactcaa
     2341 cttcctgatt cctaaaatta ttccaaatca ctcgaccatt ctctttatct gctcgtaaac
     2401 cctgctgttg caaggctttg ttaaaacttg gttgcttttg aacaccccgt ttataccctt
     2461 cagcaacagg aacaatattc aaatgcaggt gcggacttac ttcgtcatta tgaataacag
     2521 cattgtagac ggataaacta ggattccgtt ctttaaattc tttgaaatac tcaactaaaa
     2581 ttttgttggc aatcactcga ttttgttctg cttgttgttc cgatatgcca gtagaagaac
     2641 catcatcacg agtagtacga aaatcatcaa gagtaccaat ttgcacgata aattctcgct
     2701 gtggttccat ttttttatcc ttgcgaacct ttgctaaata gtcctcaatt tttctatcgg
     2761 ctcttttctg ctttgcatta tatttttcta cggcttcacc gaataattct tcatattttt
     2821 cacgaatatt tatttgttcc aaatagatat tttcatccga ttttgtgaaa tcaatatgct
     2881 tatgccagtc attgattttt tggctatcag ttaactcacg attattatga gaaatgcttg
     2941 tattctttgt tccctttttg aacgaaatac taaaccccaa gttaaacccc tccttcgcgc
     3001 tgtcgctaat aaaaagagtg taaacctttc tgttactctt tgtcaaagag taacgttttc
     3061 ctaattgtga catgactgtc acaattccaa acgctctccg agggttttcg ccgtcacaag
     3121 tgacaacgaa aaaaggagcc gaaagcgtgt cacgctctca actcctttta cgctttattt
     3181 tgcttcatgc aaaatattcg cttatcgtga atttacgtca ctaaacattg acgcaaatcc
     3241 actctcactc atctgacttt ttctattcgg tatccctccg aatattccgt cagattcgtt
     3301 agggtaattc cgttcgcttg gtgctgattt ttcatcagct cgcaactcat tacccactga
     3361 tttttcgtgt tgctgatcgt cagaaatcga cgatagccac cgctcaaaat cagcaaaaga
     3421 ttcaaaccca aaacgcttgc gaagagcctt gcccattgca gcattttctt tctcaatcaa
     3481 tcgtttcttc tgttggcgaa gtttcgcctg ttcttttttt aatttttctt cttgcacttt
     3541 aatatctgct aaagtcattc ccataaacta catccccttt tctttggaat taataacgga
     3601 aatttggttt aactgcataa tatgactcat taatttcaac caaaattctt tttcagcttc
     3661 atcagttgtt tgcgctaaat gcttatgaac aaattcatta gtcaaaactg aagattttgc
     3721 tagatcagca ttgataaccg agttgagaac atccatcatt cgttcaagca tctcactata
     3781 attatcttca tccgaaagat tcaaataatc agctaaccgt tcatacatca cttcaattct
     3841 attgactgtt tcttctctca aatcaatttt atccatgtca catctcactt ccagaattgc
     3901 caccattttc gattttttaa ttcttgattt tctagtaaca actgatcgtt tttttgttgc
     3961 tgaagcaggg tcaatttttg ttgatcacga atcatttctg ttaattcaga aatatgtttg
     4021 tccttctcag ctaattgatc acgcaaaaac tcattctctt tttccaaagg aaaatcactg
     4081 cccgtgctat tgaccggtaa atgaccagtc aattgaccac cttttgaccg ataaattgac
     4141 cgagcaacac caatcaactc tttgtctagc aagataattc catttttctt gtaccgagca
     4201 agatcatatc cggctttgac tagataattt ctcactgtat ttttggttat tcctagttca
     4261 tcagcaagcg ccttaattgt cattttatcc gttgaatcag tcatt
//
