LOCUS       NZ_CP066478             5212 bp    DNA     circular CON 20-FEB-2024
DEFINITION  Enterococcus faecium strain Dallas 93_2 plasmid p93_2_5kb, complete
            sequence.
ACCESSION   NZ_CP066478
VERSION     NZ_CP066478.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN17038088
            Assembly: GCF_016406605.1
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  JOURNAL   Unpublished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                   :: 261.0x
            Sequencing Technology :: Illumina NextSeq; Oxford Nanopore MinION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 02/20/2024 02:57:12
            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)                     :: 3,140
            CDSs (total)                      :: 3,047
            Genes (coding)                    :: 2,906
            CDSs (with protein)               :: 2,906
            Genes (RNA)                       :: 93
            rRNAs                             :: 6, 6, 6 (5S, 16S, 23S)
            complete rRNAs                    :: 6, 6, 6 (5S, 16S, 23S)
            tRNAs                             :: 71
            ncRNAs                            :: 4
            Pseudo Genes (total)              :: 141
            CDSs (without protein)            :: 141
            Pseudo Genes (ambiguous residues) :: 0 of 141
            Pseudo Genes (frameshifted)       :: 51 of 141
            Pseudo Genes (incomplete)         :: 81 of 141
            Pseudo Genes (internal stop)      :: 31 of 141
            Pseudo Genes (multiple problems)  :: 18 of 141
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP066478.1.
            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 93_2"
                     /isolation_source="rectal swab"
                     /host="Homo sapiens"
                     /db_xref="taxon:1352"
                     /plasmid="p93_2_5kb"
                     /geo_loc_name="USA: Dallas"
                     /collection_date="2015"
     gene            complement(637..1080)
                     /locus_tag="JCP72_RS15490"
                     /old_locus_tag="JCP72_15490"
     CDS             complement(637..1080)
                     /locus_tag="JCP72_RS15490"
                     /old_locus_tag="JCP72_15490"
                     /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            complement(1053..1553)
                     /locus_tag="JCP72_RS15495"
                     /old_locus_tag="JCP72_15495"
     CDS             complement(1053..1553)
                     /locus_tag="JCP72_RS15495"
                     /old_locus_tag="JCP72_15495"
                     /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            complement(2095..2511)
                     /locus_tag="JCP72_RS15500"
                     /old_locus_tag="JCP72_15500"
     CDS             complement(2095..2511)
                     /locus_tag="JCP72_RS15500"
                     /old_locus_tag="JCP72_15500"
                     /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            complement(2513..2794)
                     /locus_tag="JCP72_RS15505"
                     /old_locus_tag="JCP72_15505"
     CDS             complement(2513..2794)
                     /locus_tag="JCP72_RS15505"
                     /old_locus_tag="JCP72_15505"
                     /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            complement(3170..3694)
                     /locus_tag="JCP72_RS15510"
                     /old_locus_tag="JCP72_15510"
     CDS             complement(3170..3694)
                     /locus_tag="JCP72_RS15510"
                     /old_locus_tag="JCP72_15510"
                     /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"
     gene            complement(3711..4679)
                     /locus_tag="JCP72_RS15515"
                     /old_locus_tag="JCP72_15515"
     CDS             complement(3711..4679)
                     /locus_tag="JCP72_RS15515"
                     /old_locus_tag="JCP72_15515"
                     /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"
     Typing          complement(3716..4679)
                     /name="rep_cluster_1093"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="93.782"
                     /coverage="99.0"
                     /evalue="0.0"
ORIGIN
        1 aagcgcctta caggcggtca gggcaagccc taacaaccct aaagttgtct gaatgccctc
       61 taaaattcga tttaagcact cttaaaccta ctcttatata tttatatact tagacgtttc
      121 aaacgtctta aaacgcaaat tagagcttga taaagatatt tgctcgtgtg ccgacttttt
      181 taaaagtcta ggcacacgcc atgacaaagc tgaaataaac tgcttcagct ttgtcatggc
      241 ggattcgctc acttgaaaaa gtgttcattt cgctcgatta ttagcatata ttttttaact
      301 ttttttgcta gccaaatttt gcattagttc gctcataaat cccacccttt cagtacgtcc
      361 tacggacgta tcgttcgtaa tgtgaaagta cctttaaagg tactttctac aaaactcact
      421 aaagtgtttg gcaagctcta tatttgctag ccaaatacct acgtatttgg tgcaaataac
      481 cgcttgtcaa aggggcgcaa gctccccctt gaatccccct caaaaaccac gctccacaat
      541 acaaaaaagg ctagcaaatg ctagccactt tttgtaaagt ttcgcttgtt tcaccttcgg
      601 tgaaattatt gttttgtaat atcaaacaac tattcatcaa tcagctttaa aaaattcaat
      661 tggtttagct gtcccttctg tcccatcatt cgttgtcaaa ataaatacga gcttttttgg
      721 agaatccaaa ctaaaagtgt aatctaattg ttttttatta gagcgcagtg ttagtaaatt
      781 atttgttgct ttgtaaatga aaacttgttc atttatattt aaatttttat caatgatttg
      841 aattttatga ttgttctctt ttactaagat ggtatattgt tctatatttt ttgaagtatt
      901 taaattagtg attactagac gttctgaatg atctttagtt tgccaagttc ctagaaaagg
      961 aatcagatta gtcttttgta tttcttgttt ttttgaacaa ctagttaaga aaagaactaa
     1021 cactagaccc ataactaaag caatgggttt atttaccaat ttgtaatggt attgtcccaa
     1081 gtaaaaccac ctccaggtac aggaattgta actggtcctg catttgcact tattacagtt
     1141 gggtagttat accaaggatt ccacacatag taagtttgat aaccaccttg attgacccac
     1201 ccaaataatg caagtgcatg acggctgtta ctataatttc cataaccagc agttcccata
     1261 taaatggcat ttccttttct tagttgtgtt tggacctctg aaaggtttag tattcgtgct
     1321 acttttttag gataaacacc acagtaattt gcatatttta ttatttgatc ttgattaaga
     1381 ctttttgatt caatttgact attccaatca tcaaggaaaa gaggagacct agataaattt
     1441 tctttttggg tttcaaaata accacgcctt tgtgttaaat ttaagtggta tacacctata
     1501 attatataat taaaatatac aatatgcgat aacaaatttt tgttatagtt cataaaatat
     1561 tgttttggga acataatcgt tatttatcga gctagttaac ataatgtaca ctatgccaag
     1621 tagcccctct accaatggat agagacgctc actttgtgat ttttaattgg tctagctagt
     1681 tactagcttc taatgcttga ttttacgcga tttctctttt ttagttcttt gtgcattttt
     1741 atctgtcatt ttttaaagac ttgttatttt tgagaggatt tgatatgctt tttttgtctt
     1801 tctctagttc ttcactttgt aatattttta tgttgatgaa taggataatc tcattttggg
     1861 ctgctcgtga gagcagtctt tttttgtttc agggtacgtc ctattctttg gatttccgcg
     1921 ctattaaata accgatactt ggggattggg gtagcgcccc aaaatacaaa aagaagaagt
     1981 tgcataagcg gatttttctt ttttttcgca agttggtacc aacttgcaaa tcttgctgga
     2041 agactgatcc ctaaaaagaa atcgaggaat ttttttaggg atcggtttct ttttttatct
     2101 ttttagaaag tttgttgggt caaaatttcc agaagtaaag gtttgattgg tttctttttg
     2161 acgatttttg ggttgatttc gtcgggaagg attgagttga ttttcaattt tttctttcac
     2221 ttcttgatac actttagaat ttgtaccgat aagaacacca gtatctttta gatataaatc
     2281 agcaaattct gccatgattt ctgtcatgat agaaatttct tttcccatgg cattgagttt
     2341 tgcttggtta ctggttgtgg ttgtattggt atcaggttca taactcatac ataaaaaacg
     2401 aatggcttct gaataattgt tgacgtctgg atttttttcg atgatggaat ctaaaacgtc
     2461 aacgtgactg ggataaaggg ttacgtgttt ttgaacagaa gtttttctca tgttatattc
     2521 ctccgataag tgtttcaatg agttggttgt ttgtgtgaac atagtcattc agtatgttcg
     2581 tattttctgt ttgaatggca ataaattttt cgagtaataa atcgaattga tcttttttgt
     2641 aattcataag ttgacggtca aaatcacttt cgattagaac ttttagatat ttatttcgac
     2701 tccatttttt gcccgttttg gttgtgagtt cctgacaacg tttatctatt cttgcaataa
     2761 ttttgggatt gatatttcga actaaaatgt ccatggaaat tttcctttcg tatcagcgta
     2821 taatttatgt ataccataca aatatagtat ttgtatagct atttttcgcc aaaacactat
     2881 acatagccta gccacaatgg caaaaaagtg atagcaaatt tttttctgag aaacgtgata
     2941 ggcacagcct atctagcacc tttcgtaaga aagtgatacc acgtttcctt atgctctttc
     3001 aaaattcaga aaaatcagct gtaaaacgag tgcagtccga gtaagattca acgaaaaaac
     3061 ggggattggg gcgccaccaa aatatcgcaa catgggtcca tgttgctctg ctcgcaaaag
     3121 caaaaagaag aataaaacca gcaattttta ttaatttaaa ttgctggttt tattgccaga
     3181 attgccacca ttttttctcc gtctttgatt gtttttctat cgattctgtt tcttcagaaa
     3241 gagtcgttga tttattttcc gaagattctt ccgtataagt caactgtagt tgttcctgca
     3301 gtttctcgat ttgttggttg gcttgcaggg tgagttgttg ttggtggtcg agtaattttt
     3361 gcatttgttt tatttgctcg tctttttctt gtagttgcat atctttttga tttaactgtt
     3421 gttctaggag agaaaggact tctaattcgg gaacttggtt ggcgtttttg tgggtttcgg
     3481 ttttcgtttt ttcgccaact agttgttgat ttgagttttc gttttcgtta aaaaacattg
     3541 attttatagc cttttgtccg gtttcattaa tcacaaactt gtttccgatt ttcgaaaacc
     3601 aaagttttcg attttcgtca gaaacttttt tgttaattgc tgttttacta actcctaatt
     3661 cttcagcaag ttctttgatt gttttttctg tcataaaatc taaaaacccc tcaatctttg
     3721 aataagtttt gaagattgtc taataagtct ttttttagtt ctgaaggaat atcggaattt
     3781 atctctgatt tttgtgcatt attttcttta ttttgggtat tttgttctct ttctaacttt
     3841 tctaactgtt gtaaaagttc caattttcgc ttttgttctt tgattttttc ttgtaatgaa
     3901 gtaggtgctt tttcagattg aacttgttgg ttagctagtt ctaatgcttt gttttgttct
     3961 tcttttgttg gggcatgttt gttaaagtcg tctgattttt ttatctcagg tttaaatgta
     4021 aattgatagc caatgacagg ctttccccgt ccttttccgt atttcttttt gattgttaaa
     4081 cctttaaaga ttgcggttag ttcttgtcgt attggattga acacacgttg atcaatcgta
     4141 ccttggttgt aacttttagg aatatcaagt aattcatgaa agtcttcttt tgaaaaataa
     4201 gcgaaacctt tggttctgta ttgttttagt aatcgaaaca ttgtttttga ataactgctt
     4261 tctaattcat tgaattgttg gagagaatag cgcacccatt cttcaagatt attaagtaag
     4321 ggtaaggctt tttcatgaac ttgtatttca gcaaaaggaa tatcagattt tccgtcgatt
     4381 ttaaattgat taaataaaac aaaacgttca cgttgcaaac cgtcagcact tcttctacca
     4441 aaacgtaaat ccattaattt gtcatacgtt gtttctaaat catctatgaa tcgaacattt
     4501 gcagttgctt tataattgct taaatctttt aattgctcga atgtaaattg tactttttta
     4561 tcacctacat cacgcattct tgatacgata gaaaagaaca aattcatttc gactggtgta
     4621 aattttcgca acggaattgt atttaattca tgatgatact ttacgatttc attagacata
     4681 tttaaaatag ctcctttctt actcgcacaa gagatacacg ttatgaaata caaaatgcct
     4741 gtttatctac atcttatatt aacatcgtcg atgtactaat tcaatgtaca aacagacaaa
     4801 acgatgtaga taaacagaca aaacgatgta gataaacaga caaaacgatg tagataaaca
     4861 gacaaaacga tgtagataaa agcgtcattc ccttgggaga gtaaggatat agccgacggt
     4921 aaagaggttt aaaaagaggt ttaaaaagag attataaaag agggggacaa aatttcccgc
     4981 ctaaaaaacc acttcttttt tctccaaaca gattcgcgca tttttctcaa ctgggaatct
     5041 tactccctac agtcgcttaa aaaggtgtga tcgctctgct ctcacattat actgcgcagt
     5101 cgcttccggc tcctttgcta aaaatgttca taaggaactc tttgagaagc tatgagcctt
     5161 cgtttgagac gttttaagac agtcttagta taaatccctt atcttgttct ta
//
