LOCUS       NZ_CP066464             5212 bp    DNA     circular CON 20-FEB-2024
DEFINITION  Enterococcus faecium strain Dallas 87_1 plasmid p87_1_5kb, complete
            sequence.
ACCESSION   NZ_CP066464
VERSION     NZ_CP066464.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN17038085
            Assembly: GCF_016406505.1
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  JOURNAL   Unpublished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                   :: 249.0x
            Sequencing Technology :: Illumina NextSeq; Oxford Nanopore MinION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 02/20/2024 02:50:03
            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)                     :: 3,314
            CDSs (total)                      :: 3,220
            Genes (coding)                    :: 3,078
            CDSs (with protein)               :: 3,078
            Genes (RNA)                       :: 94
            rRNAs                             :: 6, 6, 6 (5S, 16S, 23S)
            complete rRNAs                    :: 6, 6, 6 (5S, 16S, 23S)
            tRNAs                             :: 72
            ncRNAs                            :: 4
            Pseudo Genes (total)              :: 142
            CDSs (without protein)            :: 142
            Pseudo Genes (ambiguous residues) :: 0 of 142
            Pseudo Genes (frameshifted)       :: 50 of 142
            Pseudo Genes (incomplete)         :: 81 of 142
            Pseudo Genes (internal stop)      :: 33 of 142
            Pseudo Genes (multiple problems)  :: 18 of 142
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP066464.1.
            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 87_1"
                     /isolation_source="rectal swab"
                     /host="Homo sapiens"
                     /db_xref="taxon:1352"
                     /plasmid="p87_1_5kb"
                     /geo_loc_name="USA: Dallas"
                     /collection_date="2015"
     gene            complement(join(4953..5212,1..184))
                     /locus_tag="JCP85_RS16360"
                     /old_locus_tag="JCP85_16360"
     CDS             complement(join(4953..5212,1..184))
                     /locus_tag="JCP85_RS16360"
                     /old_locus_tag="JCP85_16360"
                     /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(157..657)
                     /locus_tag="JCP85_RS16365"
                     /old_locus_tag="JCP85_16365"
     CDS             complement(157..657)
                     /locus_tag="JCP85_RS16365"
                     /old_locus_tag="JCP85_16365"
                     /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(1199..1615)
                     /locus_tag="JCP85_RS16370"
                     /old_locus_tag="JCP85_16370"
     CDS             complement(1199..1615)
                     /locus_tag="JCP85_RS16370"
                     /old_locus_tag="JCP85_16370"
                     /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(1617..1898)
                     /locus_tag="JCP85_RS16375"
                     /old_locus_tag="JCP85_16375"
     CDS             complement(1617..1898)
                     /locus_tag="JCP85_RS16375"
                     /old_locus_tag="JCP85_16375"
                     /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(2274..2798)
                     /locus_tag="JCP85_RS16380"
                     /old_locus_tag="JCP85_16380"
     CDS             complement(2274..2798)
                     /locus_tag="JCP85_RS16380"
                     /old_locus_tag="JCP85_16380"
                     /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(2815..3783)
                     /locus_tag="JCP85_RS16385"
                     /old_locus_tag="JCP85_16385"
     CDS             complement(2815..3783)
                     /locus_tag="JCP85_RS16385"
                     /old_locus_tag="JCP85_16385"
                     /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(2820..3783)
                     /name="rep_cluster_1093"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="93.782"
                     /coverage="99.0"
                     /evalue="0.0"
ORIGIN
        1 tatttaaatt agtgattact agacgttctg aatgatcttt agtttgccaa gttcctagaa
       61 aaggaatcag attagtcttt tgtatttctt gtttttttga acaactagtt aagaaaagaa
      121 ctaacactag acccataact aaagcaatgg gtttatttac caatttgtaa tggtattgtc
      181 ccaagtaaaa ccacctccag gtacaggaat tgtaactggt cctgcatttg cacttattac
      241 agttgggtag ttataccaag gattccacac atagtaagtt tgataaccac cttgattgac
      301 ccacccaaat aatgcaagtg catgacggct gttactataa tttccataac cagcagttcc
      361 catataaatg gcatttcctt ttcttagttg tgtttggacc tctgaaaggt ttagtattcg
      421 tgctactttt ttaggataaa caccacagta atttgcatat tttattattt gatcttgatt
      481 aagacttttt gattcaattt gactattcca atcatcaagg aaaagaggag acctagataa
      541 attttctttt tgggtttcaa aataaccacg cctttgtgtt aaatttaagt ggtatacacc
      601 tataattata taattaaaat atacaatatg cgataacaaa tttttgttat agttcataaa
      661 atattgtttt gggaacataa tcgttattta tcgagctagt taacataatg tgtactatgc
      721 caagtagccc ctctaccaat ggatagagac gctcactttg tgatttttaa ttggtctagc
      781 tagttactag cttctaatgc ttgattttac gcgatttctc ttttttagtt ctttgtgcat
      841 ttttatctgt cattttttaa agacttgtta tttttgagag gatttgatat gctttttttg
      901 tctttctcta gttcttcact ttgtaatatt tttatgttga tgaataggat aatctcattt
      961 tgggctgctc gtgagagcag tctttttttg tttcagggta cgtcctattc tttggatttc
     1021 cgcgctatta aataaccgat acttggggat tggggtagcg ccccaaaata caaaaagaag
     1081 aagttgcata agcggatttt tctttttttt cgcaagttgg taccaacttg caaatcttgc
     1141 tggaagactg atccctaaaa agaaatcgag gaattttttt agggatcggt ttcttttttt
     1201 atctttttag aaagtttgtt gggtcaaaat ttccagaagt aaaggtttga ttggtttctt
     1261 tttgacgatt tttgggttga tttcgtcggg aaggattgag ttgattttca attttttctt
     1321 tcacttcttg atacacttta gaatttgtac cgataagaac accagtatct tttagatata
     1381 aatcagcaaa ttctgccatg atttctgtca tgatagaaat ttcttttccc atggcattga
     1441 gttttgcttg gttactggtt gtggttgtat tggtatcagg ttcataactc atacataaaa
     1501 aacgaatggc ttctgaataa ttgttgacgt ctggattttt ttcgatgatg gaatctaaaa
     1561 cgtcaacgtg actgggataa agggttacgt gtttttgaac agaagttttt ctcatgttat
     1621 attcctccga taagtgtttc aatgagttgg ttgtttgtgt gaacatagtc attcagtatg
     1681 ttcgtatttt ctgtttgaat ggcaataaat ttttcgagta ataaatcgaa ttgatctttt
     1741 ttgtaattca taagttgacg gtcaaaatca ctttcgatta gaacttttag atatttattt
     1801 cgactccatt ttttgcccgt tttggttgtg agttcctgac aacgtttatc tattcttgca
     1861 ataattttgg gattgatatt tcgaactaaa atgtccatgg aaattttcct ttcgtatcag
     1921 cgtataattt atgtatacca tacaaatata gtatttgtat agctattttt cgccaaaaca
     1981 ctatacatag cctagccaca atggcaaaaa agtgatagca aatttttttc tgagaaacgt
     2041 gataggcaca gcctatctag cacctttcgt aagaaagtga taccacgttt ccttatgctc
     2101 tttcaaaatt cagaaaaatc agctgtaaaa cgagtgcagt ccgagtaaga ttcaacgaaa
     2161 aaacggggat tggggcgcca ccaaaatatc gcaacatggg tccatgttgc tctgctcgca
     2221 aaagcaaaaa gaagaataaa accagcaatt tttattaatt taaattgctg gttttattgc
     2281 cagaattgcc accatttttt ctccgtcttt gattgttttt ctatcgattc tgtttcttca
     2341 gaaagagtcg ttgatttatt ttccgaagat tcttccgtat aagtcaactg tagttgttcc
     2401 tgcagtttct cgatttgttg gttggcttgc agggtgagtt gttgttggtg gtcgagtaat
     2461 ttttgcattt gttttatttg ctcgtctttt tcttgtagtt gcatatcttt ttgatttaac
     2521 tgttgttcta ggagagaaag gacttctaat tcgggaactt ggttggcgtt tttgtgggtt
     2581 tcggttttcg ttttttcgcc aactagttgt tgatttgagt tttcgttttc gttaaaaaac
     2641 attgatttta tagccttttg tccggtttca ttaatcacaa acttgtttcc gattttcgaa
     2701 aaccaaagtt ttcgattttc gtcagaaact tttttgttaa ttgctgtttt actaactcct
     2761 aattcttcag caagttcttt gattgttttt tctgtcataa aatctaaaaa cccctcaatc
     2821 tttgaataag ttttgaagat tgtctaataa gtcttttttt agttctgaag gaatatcgga
     2881 atttatctct gatttttgtg cattattttc tttattttgg gtattttgtt ctctttctaa
     2941 cttttctaac tgttgtaaaa gttccaattt tcgcttttgt tctttgattt tttcttgtaa
     3001 tgaagtaggt gctttttcag attgaacttg ttggttagct agttctaatg ctttgttttg
     3061 ttcttctttt gttggggcat gtttgttaaa gtcgtctgat ttttttatct caggtttaaa
     3121 tgtaaattga tagccaatga caggctttcc ccgtcctttt ccgtatttct ttttgattgt
     3181 taaaccttta aagattgcgg ttagttcttg tcgtattgga ttgaacacac gttgatcaat
     3241 cgtaccttgg ttgtaacttt taggaatatc aagtaattca tgaaagtctt cttttgaaaa
     3301 ataagcgaaa cctttggttc tgtattgttt tagtaatcga aacattgttt ttgaataact
     3361 gctttctaat tcattgaatt gttggagaga atagcgcacc cattcttcaa gattattaag
     3421 taagggtaag gctttttcat gaacttgtat ttcagcaaaa ggaatatcag attttccgtc
     3481 gattttaaat tgattaaata aaacaaaacg ttcacgttgc aaaccgtcag cacttcttct
     3541 accaaaacgt aaatccatta atttgtcata cgttgtttct aaatcatcta tgaatcgaac
     3601 atttgcagtt gctttataat tgcttaaatc ttttaattgc tcgaatgtaa attgtacttt
     3661 tttatcacct acatcacgca ttcttgatac gatagaaaag aacaaattca tttcgactgg
     3721 tgtaaatttt cgcaacggaa ttgtatttaa ttcatgatga tactttacga tttcattaga
     3781 catatttaaa atagctcctt tcttactcgc acaagagata cacgttatga aatacaaaat
     3841 gcctgtttat ctacatctta tattaacatc gtcgatgtac taattcaatg tacaaacaga
     3901 caaaacgatg tagataaaca gacaaaacga tgtagataaa cagacaaaac gatgtagata
     3961 aacagacaaa acgatgtaga taaaagcgtc attcccttgg gagagtaagg atatagccga
     4021 cggtaaagag gtttaaaaag aggtttaaaa agagattata aaagaggggg acaaaatttc
     4081 ccgcctaaaa aaccacttct tttttctcca aacagattcg cgcatttttc tcaactggga
     4141 atcttactcc ctacagtcgc ttaaaaaggt gtgatcgctc tgctctcaca ttatactgcg
     4201 cagtcgcttc cggctccttt gctaaaaatg ttcataagga actctttgag aagctatgag
     4261 ccttcgtttg agacgtttta agacagtctt agtataaatc ccttatcttg ttcttaaagc
     4321 gccttacagg cggtcagggc aagccctaac aaccctaaag ttgtctgaat gccctctaaa
     4381 attcgattta agcactctta aacctactct tatatattta tatacttaga cgtttcaaac
     4441 gtcttaaaac gcaaattaga gcttgataaa gatatttgct cgtgtgccga cttttttaaa
     4501 agtctaggca cacgccatga caaagctgaa ataaactgct tcagctttgt catggcggat
     4561 tcgctcactt gaaaaagtgt tcatttcgct cgattattag catatatttt ttaacttttt
     4621 ttgctagcca aattttgcat tagttcgctc ataaatccca ccctttcagt acgtcctacg
     4681 gacgtatcgt tcgtaatgtg aaagtacctt taaaggtact ttctacaaaa ctcactaaag
     4741 tgtttggcaa gctctatatt tgctagccaa atacctacgt atttggtgca aataaccgct
     4801 tgtcaaaggg gcgcaagctc ccccttgaat ccccctcaaa aaccacgctc cacaatacaa
     4861 aaaaggctag caaatgctag ccactttttg taaagtttcg cttgtttcac cttcggtgaa
     4921 attattgttt tgtaatatca aacaactatt catcaatcag ctttaaaaaa ttcaattggt
     4981 ttagctgtcc cttctgtccc atcattcgtt gtcaaaataa atacgagctt ttttggagaa
     5041 tccaaactaa aagtgtaatc taattgtttt ttattagagc gcagtgttag taaattattt
     5101 gttgctttgt aaatgaaaac ttgttcattt atatttaaat ttttatcaat gatttgaatt
     5161 ttatgattgt tctcttttac taagatggta tattgttcta tattttttga ag
//
