LOCUS       NZ_CP066665             5212 bp    DNA     circular CON 20-FEB-2024
DEFINITION  Enterococcus faecium strain Dallas 155 plasmid p6, complete
            sequence.
ACCESSION   NZ_CP066665
VERSION     NZ_CP066665.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN17038106
            Assembly: GCF_016415505.1
KEYWORDS    RefSeq.
SOURCE      Enterococcus faecium
  ORGANISM  Enterococcus faecium
            Bacteria; Bacillota; Bacilli; Lactobacillales; Enterococcaceae;
            Enterococcus.
REFERENCE   1  (bases 1 to 5212)
  AUTHORS   Islam,M.J. and Palmer,K.
  TITLE     Molecular characterization of VREfm isolates from Dallas, Texas
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 5212)
  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                   :: 108.0x
            Sequencing Technology :: Illumina NextSeq; Oxford Nanopore MinION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 02/20/2024 02:49:34
            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)                     :: 3,194
            CDSs (total)                      :: 3,102
            Genes (coding)                    :: 2,964
            CDSs (with protein)               :: 2,964
            Genes (RNA)                       :: 92
            rRNAs                             :: 6, 6, 6 (5S, 16S, 23S)
            complete rRNAs                    :: 6, 6, 6 (5S, 16S, 23S)
            tRNAs                             :: 70
            ncRNAs                            :: 4
            Pseudo Genes (total)              :: 138
            CDSs (without protein)            :: 138
            Pseudo Genes (ambiguous residues) :: 0 of 138
            Pseudo Genes (frameshifted)       :: 49 of 138
            Pseudo Genes (incomplete)         :: 77 of 138
            Pseudo Genes (internal stop)      :: 32 of 138
            Pseudo Genes (multiple problems)  :: 16 of 138
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP066665.1.
            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..5212
                     /organism="Enterococcus faecium"
                     /mol_type="genomic DNA"
                     /strain="Dallas 155"
                     /isolation_source="rectal swab"
                     /host="Homo sapiens"
                     /db_xref="taxon:1352"
                     /plasmid="p6"
                     /geo_loc_name="USA: Dallas"
                     /collection_date="2015"
     gene            57..338
                     /locus_tag="JCP86_RS15775"
                     /old_locus_tag="JCP86_15775"
     CDS             57..338
                     /locus_tag="JCP86_RS15775"
                     /old_locus_tag="JCP86_15775"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000353845.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_002347613.1"
                     /translation="MDILVRNINPKIIARIDKRCQELTTKTGKKWSRNKYLKVLIESDF
                     DRQLMNYKKDQFDLLLEKFIAIQTENTNILNDYVHTNNQLIETLIGGI"
                     /name="hypothetical protein"
     gene            340..756
                     /locus_tag="JCP86_RS15780"
                     /old_locus_tag="JCP86_15780"
     CDS             340..756
                     /locus_tag="JCP86_RS15780"
                     /old_locus_tag="JCP86_15780"
                     /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_002305824.1"
                     /translation="MRKTSVQKHVTLYPSHVDVLDSIIEKNPDVNNYSEAIRFLCMSYE
                     PDTNTTTTSNQAKLNAMGKEISIMTEIMAEFADLYLKDTGVLIGTNSKVYQEVKEKIEN
                     QLNPSRRNQPKNRQKETNQTFTSGNFDPTNFLKR"
                     /name="hypothetical protein"
     gene            1298..1798
                     /locus_tag="JCP86_RS15785"
                     /old_locus_tag="JCP86_15785"
     CDS             1298..1798
                     /locus_tag="JCP86_RS15785"
                     /old_locus_tag="JCP86_15785"
                     /inference="COORDINATES: ab initio prediction:GeneMarkS-2+"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GeneMarkS-2+."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_060800863.1"
                     /translation="MNYNKNLLSHIVYFNYIIIGVYHLNLTQRRGYFETQKENLSRSPL
                     FLDDWNSQIESKSLNQDQIIKYANYCGVYPKKVARILNLSEVQTQLRKGNAIYMGTAGY
                     GNYSNSRHALALFGWVNQGGYQTYYVWNPWYNYPTVISANAGPVTIPVPGGGFTWDNTI
                     TNW"
                     /name="hypothetical protein"
     gene            1771..2214
                     /locus_tag="JCP86_RS15790"
                     /old_locus_tag="JCP86_15790"
     CDS             1771..2214
                     /locus_tag="JCP86_RS15790"
                     /old_locus_tag="JCP86_15790"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002334327.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_226830478.1"
                     /translation="MGQYHYKLVNKPIALVMGLVLVLFLTSCSKKQEIQKTNLIPFLGT
                     WQTKDHSERLVITNLNTSKNIEQYTILVKENNHKIQIIDKNLNINEQVFIYKATNNLLT
                     LRSNKKQLDYTFSLDSPKKLVFILTTNDGTEGTAKPIEFFKAD"
                     /name="hypothetical protein"
     gene            3384..4352
                     /locus_tag="JCP86_RS15795"
                     /old_locus_tag="JCP86_15795"
     CDS             3384..4352
                     /locus_tag="JCP86_RS15795"
                     /old_locus_tag="JCP86_15795"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002347614.1"
                     /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_002347614.1"
                     /translation="MSNEIVKYHHELNTIPLRKFTPVEMNLFFSIVSRMRDVGDKKVQF
                     TFEQLKDLSNYKATANVRFIDDLETTYDKLMDLRFGRRSADGLQRERFVLFNQFKIDGK
                     SDIPFAEIQVHEKALPLLNNLEEWVRYSLQQFNELESSYSKTMFRLLKQYRTKGFAYFS
                     KEDFHELLDIPKSYNQGTIDQRVFNPIRQELTAIFKGLTIKKKYGKGRGKPVIGYQFTF
                     KPEIKKSDDFNKHAPTKEEQNKALELANQQVQSEKAPTSLQEKIKEQKRKLELLQQLEK
                     LEREQNTQNKENNAQKSEINSDIPSELKKDLLDNLQNLFKD"
                     /name="replication initiation protein"
     gene            4369..4893
                     /locus_tag="JCP86_RS15800"
                     /old_locus_tag="JCP86_15800"
     CDS             4369..4893
                     /locus_tag="JCP86_RS15800"
                     /old_locus_tag="JCP86_15800"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002305828.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="DUF536 domain-containing protein"
                     /protein_id="WP_060800956.1"
                     /translation="MTEKTIKELAEELGVSKTAINKKVSDENRKLWFSKIGNKFVINET
                     GQKAIKSMFFNENENSNQQLVGEKTKTETHKNANQVPELEVLSLLEQQLNQKDMQLQEK
                     DEQIKQMQKLLDHQQQLTLQANQQIEKLQEQLQLTYTEESSENKSTTLSEETESIEKQS
                     KTEKKWWQFWQ"
                     /name="DUF536 domain-containing protein"
     Typing          3385..4348
                     /name="rep_cluster_1093"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="93.782"
                     /coverage="99.0"
                     /evalue="0.0"
ORIGIN
        1 atactatatt tgtatggtat acataaatta tacgctgata cgaaaggaaa atttccatgg
       61 acattttagt tcgaaatatc aatcccaaaa ttattgcaag aatagataaa cgttgtcagg
      121 aactcacaac caaaacgggc aaaaaatgga gtcgaaataa atatctaaaa gttctaatcg
      181 aaagtgattt tgaccgtcaa cttatgaatt acaaaaaaga tcaattcgat ttattactcg
      241 aaaaatttat tgccattcaa acagaaaata cgaacatact gaatgactat gttcacacaa
      301 acaaccaact cattgaaaca cttatcggag gaatataaca tgagaaaaac ttctgttcaa
      361 aaacacgtaa ccctttatcc cagtcacgtt gacgttttag attccatcat cgaaaaaaat
      421 ccagacgtca acaattattc agaagccatt cgttttttat gtatgagtta tgaacctgat
      481 accaatacaa ccacaaccag taaccaagca aaactcaatg ccatgggaaa agaaatttct
      541 atcatgacag aaatcatggc agaatttgct gatttatatc taaaagatac tggtgttctt
      601 atcggtacaa attctaaagt gtatcaagaa gtgaaagaaa aaattgaaaa tcaactcaat
      661 ccttcccgac gaaatcaacc caaaaatcgt caaaaagaaa ccaatcaaac ctttacttct
      721 ggaaattttg acccaacaaa ctttctaaaa agataaaaaa agaaaccgat ccctaaaaaa
      781 attcctcgat ttctttttag ggatcagtct tccagcaaga tttgcaagtt ggtaccaact
      841 tgcgaaaaaa aagaaaaatc cgcttatgca acttcttctt tttgtatttt ggggcgctac
      901 cccaatcccc aagtatcggt tatttaatag cgcggaaatc caaagaatag gacgtaccct
      961 gaaacaaaaa aagactgctc tcacgagcag cccaaaatga gattatccta ttcatcaaca
     1021 taaaaatatt acaaagtgaa gaactagaga aagacaaaaa aagcatatca aatcctctca
     1081 aaaataacaa gtctttaaaa aatgacagat aaaaatgcac aaagaactaa aaaagagaaa
     1141 tcgcgtaaaa tcaagcatta gaagctagta actagctaga ccaattaaaa atcacaaagt
     1201 gagcgtctct atccattggt agaggggcta cttggcatag tacacattat gttaactagc
     1261 tcgataaata acgattatgt tcccaaaaca atattttatg aactataaca aaaatttgtt
     1321 atcgcatatt gtatatttta attatataat tataggtgta taccacttaa atttaacaca
     1381 aaggcgtggt tattttgaaa cccaaaaaga aaatttatct aggtctcctc ttttccttga
     1441 tgattggaat agtcaaattg aatcaaaaag tcttaatcaa gatcaaataa taaaatatgc
     1501 aaattactgt ggtgtttatc ctaaaaaagt agcacgaata ctaaaccttt cagaggtcca
     1561 aacacaacta agaaaaggaa atgccattta tatgggaact gctggttatg gaaattatag
     1621 taacagccgt catgcacttg cattatttgg gtgggtcaat caaggtggtt atcaaactta
     1681 ctatgtgtgg aatccttggt ataactaccc aactgtaata agtgcaaatg caggaccagt
     1741 tacaattcct gtacctggag gtggttttac ttgggacaat accattacaa attggtaaat
     1801 aaacccattg ctttagttat gggtctagtg ttagttcttt tcttaactag ttgttcaaaa
     1861 aaacaagaaa tacaaaagac taatctgatt ccttttctag gaacttggca aactaaagat
     1921 cattcagaac gtctagtaat cactaattta aatacttcaa aaaatataga acaatatacc
     1981 atcttagtaa aagagaacaa tcataaaatt caaatcattg ataaaaattt aaatataaat
     2041 gaacaagttt tcatttacaa agcaacaaat aatttactaa cactgcgctc taataaaaaa
     2101 caattagatt acacttttag tttggattct ccaaaaaagc tcgtatttat tttgacaacg
     2161 aatgatggga cagaagggac agctaaacca attgaatttt ttaaagctga ttgatgaata
     2221 gttgtttgat attacaaaac aataatttca ccgaaggtga aacaagcgaa actttacaaa
     2281 aagtggctag catttgctag ccttttttgt attgtggagc gtggtttttg agggggattc
     2341 aagggggagc ttgcgcccct ttgacaagcg gttatttgca ccaaatacgt aggtatttgg
     2401 ctagcaaata tagagcttgc caaacacttt agtgagtttt gtagaaagta cctttaaagg
     2461 tactttcaca ttacgaacga tacgtccgta ggacgtactg aaagggtggg atttatgagc
     2521 gaactaatgc aaaatttggc tagcaaaaaa agttaaaaaa tatatgctaa taatcgagcg
     2581 aaatgaacac tttttcaagt gagcgaatcc gccatgacaa agctgaagca gtttatttca
     2641 gctttgtcat ggcgtgtgcc tagactttta aaaaagtcgg cacacgagca aatatcttta
     2701 tcaagctcta atttgcgttt taagacgttt gaaacgtcta agtatataaa tatataagag
     2761 taggtttaag agtgcttaaa tcgaatttta gagggcattc agacaacttt agggttgtta
     2821 gggcttgccc tgaccgcctg taaggcgctt taagaacaag ataagggatt tatactaaga
     2881 ctgtcttaaa acgtctcaaa cgaaggctca tagcttctca aagagttcct tatgaacatt
     2941 tttagcaaag gagccggaag cgactgcgca gtataatgtg agagcagagc gatcacacct
     3001 ttttaagcga ctgtagggag taagattccc agttgagaaa aatgcgcgaa tctgtttgga
     3061 gaaaaaagaa gtggtttttt aggcgggaaa ttttgtcccc ctcttttata atctcttttt
     3121 aaacctcttt ttaaacctct ttaccgtcgg ctatatcctt actctcccaa gggaatgacg
     3181 cttttatcta catcgttttg tctgtttatc tacatcgttt tgtctgttta tctacatcgt
     3241 tttgtctgtt tatctacatc gttttgtctg tttgtacatt gaattagtac atcgacgatg
     3301 ttaatataag atgtagataa acaggcattt tgtatttcat aacgtgtatc tcttgtgcga
     3361 gtaagaaagg agctatttta aatatgtcta atgaaatcgt aaagtatcat catgaattaa
     3421 atacaattcc gttgcgaaaa tttacaccag tcgaaatgaa tttgttcttt tctatcgtat
     3481 caagaatgcg tgatgtaggt gataaaaaag tacaatttac attcgagcaa ttaaaagatt
     3541 taagcaatta taaagcaact gcaaatgttc gattcataga tgatttagaa acaacgtatg
     3601 acaaattaat ggatttacgt tttggtagaa gaagtgctga cggtttgcaa cgtgaacgtt
     3661 ttgttttatt taatcaattt aaaatcgacg gaaaatctga tattcctttt gctgaaatac
     3721 aagttcatga aaaagcctta cccttactta ataatcttga agaatgggtg cgctattctc
     3781 tccaacaatt caatgaatta gaaagcagtt attcaaaaac aatgtttcga ttactaaaac
     3841 aatacagaac caaaggtttc gcttattttt caaaagaaga ctttcatgaa ttacttgata
     3901 ttcctaaaag ttacaaccaa ggtacgattg atcaacgtgt gttcaatcca atacgacaag
     3961 aactaaccgc aatctttaaa ggtttaacaa tcaaaaagaa atacggaaaa ggacggggaa
     4021 agcctgtcat tggctatcaa tttacattta aacctgagat aaaaaaatca gacgacttta
     4081 acaaacatgc cccaacaaaa gaagaacaaa acaaagcatt agaactagct aaccaacaag
     4141 ttcaatctga aaaagcacct acttcattac aagaaaaaat caaagaacaa aagcgaaaat
     4201 tggaactttt acaacagtta gaaaagttag aaagagaaca aaatacccaa aataaagaaa
     4261 ataatgcaca aaaatcagag ataaattccg atattccttc agaactaaaa aaagacttat
     4321 tagacaatct tcaaaactta ttcaaagatt gaggggtttt tagattttat gacagaaaaa
     4381 acaatcaaag aacttgctga agaattagga gttagtaaaa cagcaattaa caaaaaagtt
     4441 tctgacgaaa atcgaaaact ttggttttcg aaaatcggaa acaagtttgt gattaatgaa
     4501 accggacaaa aggctataaa atcaatgttt tttaacgaaa acgaaaactc aaatcaacaa
     4561 ctagttggcg aaaaaacgaa aaccgaaacc cacaaaaacg ccaaccaagt tcccgaatta
     4621 gaagtccttt ctctcctaga acaacagtta aatcaaaaag atatgcaact acaagaaaaa
     4681 gacgagcaaa taaaacaaat gcaaaaatta ctcgaccacc aacaacaact caccctgcaa
     4741 gccaaccaac aaatcgagaa actgcaggaa caactacagt tgacttatac ggaagaatct
     4801 tcggaaaata aatcaacgac tctttctgaa gaaacagaat cgatagaaaa acaatcaaag
     4861 acggagaaaa aatggtggca attctggcaa taaaaccagc aatttaaatt aataaaaatt
     4921 gctggtttta ttcttctttt tgcttttgcg agcagagcaa catggaccca tgttgcgata
     4981 ttttggtggc gccccaatcc ccgttttttc gttgaatctt actcggactg cactcgtttt
     5041 acagctgatt tttctgaatt ttgaaagagc ataaggaaac gtggtatcac tttcttacga
     5101 aaggtgctag ataggctgtg cctatcacgt ttctcagaaa aaaatttgct atcacttttt
     5161 tgccattgtg gctaggctat gtatagtgtt ttggcgaaaa atagctatac aa
//
