LOCUS       NZ_CP066574             3651 bp    DNA     circular CON 20-FEB-2024
DEFINITION  Enterococcus faecium strain Dallas 97_1 plasmid p97_1_3kb, complete
            sequence.
ACCESSION   NZ_CP066574
VERSION     NZ_CP066574.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN17038090
            Assembly: GCF_016415025.1
KEYWORDS    RefSeq.
SOURCE      Enterococcus faecium
  ORGANISM  Enterococcus faecium
            Bacteria; Bacillota; Bacilli; Lactobacillales; Enterococcaceae;
            Enterococcus.
REFERENCE   1  (bases 1 to 3651)
  AUTHORS   Islam,M.J. and Palmer,K.
  TITLE     Molecular characterization of VREfm isolates from Dallas, Texas
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 3651)
  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                   :: 66.0x
            Sequencing Technology :: Illumina NextSeq; Oxford Nanopore MinION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 02/20/2024 02:46:30
            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)                     :: 3,203
            CDSs (total)                      :: 3,112
            Genes (coding)                    :: 2,949
            CDSs (with protein)               :: 2,949
            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)              :: 163
            CDSs (without protein)            :: 163
            Pseudo Genes (ambiguous residues) :: 0 of 163
            Pseudo Genes (frameshifted)       :: 73 of 163
            Pseudo Genes (incomplete)         :: 87 of 163
            Pseudo Genes (internal stop)      :: 37 of 163
            Pseudo Genes (multiple problems)  :: 30 of 163
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP066574.1.
            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..3651
                     /organism="Enterococcus faecium"
                     /mol_type="genomic DNA"
                     /strain="Dallas 97_1"
                     /isolation_source="rectal swab"
                     /host="Homo sapiens"
                     /db_xref="taxon:1352"
                     /plasmid="p97_1_3kb"
                     /geo_loc_name="USA: Dallas"
                     /collection_date="2015"
     gene            complement(join(3295..3651,1..6))
                     /locus_tag="JCP88_RS15835"
                     /old_locus_tag="JCP88_15835"
     CDS             complement(join(3295..3651,1..6))
                     /locus_tag="JCP88_RS15835"
                     /old_locus_tag="JCP88_15835"
                     /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_060800943.1"
                     /translation="MGMTLADIKVQEEKLKKEQAKLRQQKKRLIEKENAAMGKALRKRF
                     GFESFADFERWLSSISDDQQHEKSVDNEWLADEKSAPSERDYPNEYDGLLGVIPSKKSQ
                     MNESKFMSIFNDVNLR"
                     /name="hypothetical protein"
     gene            complement(79..1068)
                     /locus_tag="JCP88_RS15840"
                     /old_locus_tag="JCP88_15840"
     CDS             complement(79..1068)
                     /locus_tag="JCP88_RS15840"
                     /old_locus_tag="JCP88_15840"
                     /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_025478731.1"
                     /translation="MTDKKQDLINGTFKMKKKNLQKVIDFGGGRFSERTVERMASCGSY
                     LEFIATADKEKKKLIQANFCTNRFCPLCAWRKARKDSLMLSIMMQAIAEEKNYQFIFMT
                     LTTPNVKADKLNEEIDLFNHALSKMFRRKRVMGAIKGYVRKLEITYNKKRNDYNPHFHL
                     ILAVNKSYFTDPKYYIKQAEWLDLWRDVTGKTGINLDGTDEISQLDIRKVKGFQQDKAV
                     QELAKYSAKDFEMTESQEVFDTFYHAMKGRQLITFNGVFKEYKKKYEAGELDHYKKKDE
                     NEYFWFLTASWMKKESSYAINLRELTPDERKFFSGGLVEEKPVEGENE"
                     /name="protein rep"
     gene            complement(1667..3073)
                     /locus_tag="JCP88_RS15845"
                     /old_locus_tag="JCP88_15845"
     CDS             complement(1667..3073)
                     /locus_tag="JCP88_RS15845"
                     /old_locus_tag="JCP88_15845"
                     /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_060800944.1"
                     /translation="MGFSISFKKGTKNTSISHNNRELTDSQKINDWHKHIDFTKSDENI
                     YLEQTNIREKYEELFGEAVEKYNAKQKRADRKIEDYLAKVRKDKKLEPQREFIVQIGTL
                     DDFRTTRDDGSSTGISEQQAEQNRVIANKILVEYFKEFKERNPSLSVYNAVIHNDEVSP
                     HLHLNIVPVAEGYKRGVQKQPSFNKALQQQGLRADKENGRVIWNNFRNQEVESIERLMA
                     DFGWERELVGTNKIKDVHEYKEIMSEISELRQTAVKERESVSDELGYISRQREENEREK
                     ALVASERAKIEEEKKNMLNVKKEMAVIFQKDIVPLESFKRLPDGSYHLSGNDFVDLYQR
                     ATRATNAKRNADNMSEQYLQMLEQNTELNEYVATLEEERHLSGRKQLADLQVENKKLKE
                     ENRSLRQRLERLKKAFQKSITRLSIRFGLAEKDMGLSEELEVLEQEKTLFYRQNVSQHK
                     LERSEDEIEW"
                     /name="plasmid recombination protein"
     Typing          complement(268..930)
                     /name="rep_cluster_1535"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="80.422"
                     /coverage="81.0"
                     /evalue="4.599999999999999e-140"
     Typing          complement(1671..3073)
                     /name="MOBV"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="97.863"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 ccccataaac tacatcccct tttccttgga attaataaca gaaatttggt ttaatcgtta
       61 ttttatcagg tgaatcagtc attcattttc cccctcaaca ggtttttcct caactaaccc
      121 accgctaaaa aatttcctct catcaggcgt caattctcgg agatttattg catacgacga
      181 ttcctttttc atccatgaag cagtcaaaaa ccagaaatat tcgttctcgt cttttttctt
      241 gtagtgatcg agctcgcctg cttcgtattt cttcttgtac tccttgaaga ccccgttaaa
      301 cgtgattaac tggcgccctt tcatagcatg gtaaaacgta tcaaagactt cttggctctc
      361 ggtcatttca aagtctttcg cagaatactt ggcaagttcc tgtaccgctt tgtcttgttg
      421 gaatcctttg acctttcgaa tatccaactg actgatttcg tctgtaccat caagattgat
      481 tcccgttttc ccagtcacat cacgccacaa atcaagccat tctgcctgtt taatataata
      541 tttagggtca gtaaaatacg acttgttcac cgccaaaatc aaatgaaaat gcgggttgta
      601 gtcatttcgt ttcttgttgt acgtgatttc caatttccgg acatagcctt taatcgcacc
      661 catgaccctt ttcctacgaa acattttgga caacgcatga ttaaataaat caatttcttc
      721 gtttagcttg tctgctttta cattgggcgt tgttagcgtc ataaaaataa actggtaatt
      781 cttttcttca gcgattgcct gcatcataat cgacaacatc aacgaatctt tacgggcttt
      841 gcgccatgca cacagcggac aaaagcgatt cgtgcaaaaa ttcgcctgaa tcaatttctt
      901 tttctccttg tcagcggtgg cgataaattc caagtatgaa ccacagctag ccatacgctc
      961 cactgtcctt tccgaaaagc gcccgccccc gaaatcaatc accttttgta aatttttctt
     1021 tttcattttg aatgtcccat ttattaaatc ttgttttttg tctgtcatat tgatatactg
     1081 aacctacaat tttgtataaa aaggctgaaa agccgataac aaaaaaaata gattgctctc
     1141 cttaatttgg ttggttttta cttagacact aaaagcttaa tccaatatgc taggaaaagc
     1201 aatctttttt ttgtgcaacc ccttatgtat caaggtcaaa agcatactat acgcaactat
     1261 ttcctgccga aaataattgc gtattagtat caagataaga agaaacatca aaaaaagagg
     1321 tcgaaatcga cctctttttt ctcgtttcaa accccaaaac tcaaaaaccc acttctgcat
     1381 aaaattcggt caattgacca ctgcattttt aagggaaggg tcaaactttg atactttaac
     1441 cgcctgttag aaatgcggtt aagtttttcc cactcattct tagtcatgca aaaataaaac
     1501 cgctcccttt gaaaagggcg cccccaaact ttcgctaacg ctaggttggc caaaaaatgg
     1561 acttgccatt ttttagcaaa tgtcagctta ataggctagt ggtttagccg tcaactcctt
     1621 atcctcggca cagaccgcct ccggtaccgt tgactgcaca tcgtaactac cactcgatct
     1681 catcttcaga acgctctaat ttatgctgtg agacgttttg acgataaaat aaggttttct
     1741 cctgctctaa tacttctaat tcctcagaaa gccccatatc cttttctgca agaccaaaac
     1801 ggatagacaa acgagtgatc gatttttgaa atgctttttt taatcgctct aaacgctggc
     1861 gtaaagagcg attttcttct ttcagctttt tattttccac ttgtaaatct gctaattgtt
     1921 ttctaccaga caaatgacgc tcttcttcca atgtagctac atactcattt aattctgtat
     1981 tttgctcaag catctgtaaa tattgctcac tcatgttatc agcatttctc ttggcatttg
     2041 ttgctctcgt agctcgttga tacaaatcaa caaaatcatt cccagataaa tgatacgaac
     2101 catcaggaag cctcttgaaa ctttctaaag gaacaatatc tttttggaaa atgaccgcca
     2161 tctctttttt tacattcagc atatttttct tctcttcttc aatctttgct ctctcagaag
     2221 ccaccagagc cttttctcgc tcgttttctt ctctttgcct agaaatatac cccaactcat
     2281 cagaaacgct ctcacgctct tttacggccg tttgacgcaa ttctgaaatc tcgctcatga
     2341 tttctttata ttcgtgaaca tctttgattt tgttagtacc gactaactca cgctcccaac
     2401 caaaatctgc catcaaacgt tcaattgact caacttcctg attcctaaaa ttattccaaa
     2461 tcactcgacc attctcttta tctgctcgta aaccctgctg ttgcaaggct ttgttaaaac
     2521 ttggttgctt ttgaacaccc cgtttatacc cttcagcaac aggaacaata ttcaaatgca
     2581 ggtgcggact tacttcgtca ttatgaataa cagcattgta gacggataaa ctaggattcc
     2641 gttctttaaa ttctttgaaa tactcaacta aaattttgtt ggcaatcact cgattttgtt
     2701 ctgcttgttg ttccgatatg ccagtagaag aaccatcatc acgagtagta cgaaaatcat
     2761 caagagtacc aatttgcacg ataaattctc gctgtggttc caatttttta tccttgcgaa
     2821 cctttgctaa atagtcctcg atttttctat cggctctttt ctgctttgca ttatattttt
     2881 ctacggcttc accgaataat tcttcatatt tttcacgaat atttgtttgt tccaaataga
     2941 tattttcatc cgattttgtg aaatcaatat gcttatgcca gtcattgatt ttttggctat
     3001 cagttaactc acgattatta tgagaaatgc ttgtattctt tgttcccttt ttgaacgaaa
     3061 tactaaaccc caagttagac ccctccttcg cgctgtcgct aataaaaaga gtgtaaacct
     3121 ttctgttact ctttgtcaaa gagtaacgtt ttcctaattg tgacatgact gtcacaattc
     3181 caaacgctct ccgagggatt tcgctgtcac aagtgacaac gaaaaaagga gccgaaagcg
     3241 tgtcacgctc tcaactcctt ttacgcttta ttttgcttca cgcaaaataa tagcttatcg
     3301 taaattcacg tcattaaaaa ttgacataaa tttactctca ttcatctgac tttttttact
     3361 cggtatcact ccgagtaagc cgtcatattc attgggataa tctcgttcgc ttggcgctga
     3421 tttttcatca gcaagccact cattatccac tgatttttcg tgttgctgat cgtcagaaat
     3481 tgacgataac caccgctcaa aatcagcaaa agattcaaac ccaaaacgct tgcgaagagc
     3541 cttgcccatt gcagcatttt ctttctcaat caatcgtttc ttctgttggc gaagtttcgc
     3601 ctgttctttt tttaattttt cttcttgcac tttaatatct gctaaagtca t
//
