LOCUS       NZ_CP066603             5013 bp    DNA     circular CON 20-FEB-2024
DEFINITION  Enterococcus faecium strain Dallas 111 plasmid unnamed, complete
            sequence.
ACCESSION   NZ_CP066603
VERSION     NZ_CP066603.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN17038095
            Assembly: GCF_016415345.1
KEYWORDS    RefSeq.
SOURCE      Enterococcus faecium
  ORGANISM  Enterococcus faecium
            Bacteria; Bacillota; Bacilli; Lactobacillales; Enterococcaceae;
            Enterococcus.
REFERENCE   1  (bases 1 to 5013)
  AUTHORS   Islam,M.J. and Palmer,K.
  TITLE     Molecular characterization of VREfm isolates from Dallas, Texas
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 5013)
  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                   :: 60.0x
            Sequencing Technology :: Illumina NextSeq; Oxford Nanopore MinION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 02/20/2024 02:48:21
            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)                     :: 3,043
            CDSs (total)                      :: 2,955
            Genes (coding)                    :: 2,822
            CDSs (with protein)               :: 2,822
            Genes (RNA)                       :: 88
            rRNAs                             :: 6, 6, 6 (5S, 16S, 23S)
            complete rRNAs                    :: 6, 6, 6 (5S, 16S, 23S)
            tRNAs                             :: 66
            ncRNAs                            :: 4
            Pseudo Genes (total)              :: 133
            CDSs (without protein)            :: 133
            Pseudo Genes (ambiguous residues) :: 0 of 133
            Pseudo Genes (frameshifted)       :: 63 of 133
            Pseudo Genes (incomplete)         :: 74 of 133
            Pseudo Genes (internal stop)      :: 26 of 133
            Pseudo Genes (multiple problems)  :: 27 of 133
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP066603.1.
            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..5013
                     /organism="Enterococcus faecium"
                     /mol_type="genomic DNA"
                     /strain="Dallas 111"
                     /isolation_source="rectal swab"
                     /host="Homo sapiens"
                     /db_xref="taxon:1352"
                     /plasmid="unnamed"
                     /geo_loc_name="USA: Dallas"
                     /collection_date="2015"
     gene            206..1174
                     /locus_tag="JCP62_RS15050"
                     /old_locus_tag="JCP62_15055"
     CDS             206..1174
                     /locus_tag="JCP62_RS15050"
                     /old_locus_tag="JCP62_15055"
                     /EC_number="1.1.1.28"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001059542.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="D-lactate dehydrogenase VanH-A"
                     /protein_id="WP_001059542.1"
                     /translation="MNNIGITVYGCEQDEADAFHALSPRFGVMATIINANVSESNAKSA
                     PFNQCISVGHKSEISASILLALKRAGVKYISTRSIGCNHIDTTAAKRMGITVDNVAYSP
                     DSVADYTMMLILMAVRNVKSIVRSVEKHDFRLDSDRGKVLSDMTVGVVGTGQIGKAVIE
                     RLRGFGCKVLAYSRSRSIEVNYVPFDELLQNSDIVTLHVPLNTDTHYIISHEQIQRMKQ
                     GAFLINTGRGPLVDTYELVKALENGKLGGAALDVLEGEEEFFYSDCTQKPIDNQFLLKL
                     QRMPNVIITPHTAYYTEQALRDTVEKTIKNCLDFERRQEHE"
                     /name="D-lactate dehydrogenase VanH-A"
     gene            1167..2198
                     /gene="vanA"
                     /locus_tag="JCP62_RS15055"
                     /old_locus_tag="JCP62_15060"
     ARG             1168..2195
                     /name="vanA"
                     /gene="vanA"
                     /gene_name="D-alanine--(R)-lactate ligase VanA"
                     /tool="amrfinderplus"
                     /drug_class="GLYCOPEPTIDE"
                     /identity="99.71"
                     /coverage="100.0"
     gene            2204..2812
                     /locus_tag="JCP62_RS15060"
                     /old_locus_tag="JCP62_15065"
     CDS             2204..2812
                     /locus_tag="JCP62_RS15060"
                     /old_locus_tag="JCP62_15065"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000402347.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="D-Ala-D-Ala dipeptidase VanX-A"
                     /protein_id="WP_000402348.1"
                     /translation="MEIGFTFLDEIVHGVRWDAKYATWDNFTGKPVDGYEVNRIVGTYE
                     LAESLLKAKELAATQGYGLLLWDGYRPNRAVNCFMQWAAQPENNLTKESYYPNIDRTEM
                     ISKGYVASKSSHSRGSAIDLTLYRLDTGELVPMGSRFDFMDERSHHAANGISCNEAQNR
                     RRLRSIMENSGFEAYSLEWWHYVLRDEPYPNSYFDFPVK"
                     /name="D-Ala-D-Ala dipeptidase VanX-A"
     gene            complement(2894..3574)
                     /locus_tag="JCP62_RS15065"
                     /old_locus_tag="JCP62_15070"
     CDS             complement(2894..3574)
                     /locus_tag="JCP62_RS15065"
                     /old_locus_tag="JCP62_15070"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_064305258.1"
                     /GO_function="GO:0004803 - transposase activity [Evidence
                     IEA]"
                     /GO_process="GO:0006313 - DNA transposition [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="IS6-like element IS1216 family transposase"
                     /protein_id="WP_001015311.1"
                     /translation="MNHFKGKQFQQDVIIVAVGYYLRYNLSYREVQEILYDRGINVSHT
                     TIYRWVQEYGKLLYQIWKKKNKKSFYSWKMDETYIKIKGKWHYLYRAIDADGLTLDIWL
                     RKKRDTQAAYAFLKRLVKQFDEPKVVVTDKAPSITSAFKKLKEYGFYQGTEHRTIKYLN
                     NLIEQDHRPVKRRNKFYRSLRTASTTIKGMEAIRGLYKKTRKEGTLFGFSVCTEIKVLL
                     GIPA"
                     /name="IS6-like element IS1216 family transposase"
     gene            complement(3628..4887)
                     /locus_tag="JCP62_RS15070"
                     /old_locus_tag="JCP62_15075"
     CDS             complement(3628..4887)
                     /locus_tag="JCP62_RS15070"
                     /old_locus_tag="JCP62_15075"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_086557923.1"
                     /GO_function="GO:0004803 - transposase activity [Evidence
                     IEA]"
                     /GO_process="GO:0006313 - DNA transposition [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="ISL3-like element IS1251 family transposase"
                     /protein_id="WP_016171138.1"
                     /translation="MSYTHLIKETLDILDLSVTFNENCLTKEKYKGQICHIYRGNLIYT
                     AQECIHCKHQIASDIVRWGTTTVRLLMNDVSEYRTYLELKKQRFKCKACQRTFVADTSV
                     AKKHCFISEKVRWSVVTRLKKNTSMTEIAAQKNLSVSSVYRIMKRFYRPLNPFRTPLPK
                     VLCFDEFKSVRGVSGAMSFIMMDGQTQRLLDIVENRQLPFLKRYFSHFSREIREAVEWI
                     VIDMYAPYVSLVKKLFPKAQLIIDRFHIVQHIGRTFRNHRIKETNQLLKSKEQKHYQLG
                     KQLKRYWKLLQKDERKLDYTRRLWRPGFKAHLTETDIVDRLLKGSPALRVGYQLYQDFL
                     YAVKERDYVSFEELLTNNIMLPEGYQTTLRTFQKFLPQIKNALQQSYSNGPLECLNNHI
                     KVLKRNAYGFRSFYGSVAKF"
                     /name="ISL3-like element IS1251 family transposase"
     ARG             207..1171
                     /name="vanH-A"
                     /gene="vanH-A"
                     /gene_name="D-lactate dehydrogenase VanH-A"
                     /tool="amrfinderplus"
                     /drug_class="GLYCOPEPTIDE"
                     /identity="100.0"
                     /coverage="100.0"
     ARG             2205..2809
                     /name="vanX-A"
                     /gene="vanX-A"
                     /gene_name="D-Ala-D-Ala dipeptidase VanX-A"
                     /tool="amrfinderplus"
                     /drug_class="GLYCOPEPTIDE"
                     /identity="100.0"
                     /coverage="100.0"
     ARG             207..1174
                     /name="vanH gene in vanA cluster"
                     /gene="vanH gene in vanA cluster"
                     /gene_name="vanH; glycopeptide resistance gene cluster"
                     /tool="rgi"
                     /drug_class="glycopeptide antibiotic"
                     /identity="100.0"
                     /coverage="100.0"
     ARG             2205..2812
                     /name="vanX gene in vanA cluster"
                     /gene="vanX gene in vanA cluster"
                     /gene_name="vanX; glycopeptide resistance gene cluster"
                     /tool="rgi"
                     /drug_class="glycopeptide antibiotic"
                     /identity="99.5"
                     /coverage="100.0"
ORIGIN
        1 ataatttttt aggaaaatct caaggttatc tttacttttt cttaggaaat taacaattta
       61 atattaagaa acggctcgtt cttacacggt agacttaata ccgtaagaac gagccgtttt
      121 cgttcttcag agaaagattt gacaagatta ccattggcat ccccgtttta tttggtgcct
      181 ttcacagaaa gggttggtct taattatgaa taacatcggc attactgttt atggatgtga
      241 gcaggatgag gcagatgcat tccatgctct ttcgcctcgc tttggcgtta tggcaacgat
      301 aattaacgcc aacgtgtcgg aatccaacgc caaatccgcg cctttcaatc aatgtatcag
      361 tgtgggacat aaatcagaga tttccgcctc tattcttctt gcgctgaaga gagccggtgt
      421 gaaatatatt tctacccgaa gcatcggctg caatcatata gatacaactg ctgctaagag
      481 aatgggcatc actgtcgaca atgtggcgta ctcgccggat agcgttgccg attatactat
      541 gatgctaatt cttatggcag tacgcaacgt aaaatcgatt gtgcgctctg tggaaaaaca
      601 tgatttcagg ttggacagcg accgtggcaa ggtactcagc gacatgacag ttggtgtggt
      661 gggaacgggc cagataggca aagcggttat tgagcggctg cgaggatttg gatgtaaagt
      721 gttggcttat agtcgcagcc gaagtataga ggtaaactat gtaccgtttg atgagttgct
      781 gcaaaatagc gatatcgtta cgcttcatgt gccgctcaat acggatacgc actatattat
      841 cagccacgaa caaatacaga gaatgaagca aggagcattt cttatcaata ctgggcgcgg
      901 tccacttgta gatacctatg agttggttaa agcattagaa aacgggaaac tgggcggtgc
      961 cgcattggat gtattggaag gagaggaaga gtttttctac tctgattgca cccaaaaacc
     1021 aattgataat caatttttac ttaaacttca aagaatgcct aacgtgataa tcacaccgca
     1081 tacggcctat tataccgagc aagcgttgcg tgataccgtt gaaaaaacca ttaaaaactg
     1141 tttggatttt gaaaggagac aggagcatga atagaataaa agttgcaata ctgtttgggg
     1201 gttgctcaga ggagcatgac gtatcggtaa aatctgcaat agagatagcc gctaacatta
     1261 ataaagaaaa atacgagccg ttatacattg gaattacgaa atctggtgta tggaaaatgt
     1321 gcgaaaaacc ttgcgcggaa tgggaaaacg acaattgcta ttcagctgta ctctcgccgg
     1381 ataaaaaaat gcacggatta cttgttaaaa agaaccatga atatgaaatc aaccatgttg
     1441 atgtagcatt ttcagctttg catggcaagt caggtgaaga tggatccata caaggtctgt
     1501 ttgaattgtc cggtatccct tttgtaggct gcgatattca aagctcagca atttgtatgg
     1561 acaaatcgtt gacatacatc gttgcgaaaa atgctgggat agctactccc gccttttggg
     1621 ttattaataa agatgatagg ccggtggcag ctacgtttac ctatcctgtt tttgttaagc
     1681 cggcgcgttc aggctcatcc ttcggtgtga aaaaagtcaa tagcgcggac gaattggact
     1741 acgcaattga atcggcaaga caatatgaca gcaaaatctt aattgagcag gctgtttcgg
     1801 gctgtgaggt cggttgtgcg gtattgggaa acagtgccgc gttagctgtt ggcgaggtgg
     1861 accaaatcag gctgcagtac ggaatctttc gtattcatca ggaagtcgag ccggaaaaag
     1921 gctctgaaaa cgcagttata accgttcccg cagacctttc agcagaggag cgaggacgga
     1981 tacaggaaac ggcaaaaaaa atatataaag cgctcggctg tagaggtcta gcccgtgtgg
     2041 atatgttttt acaagataac ggccgcattg tactgaacga agtcaatact ctgcccggtt
     2101 tcacgtcata cagtcgttat ccccgtatga tggccgctgc aggtattgca cttcccgaac
     2161 tgattgaccg cttgatcgta ttagcgttaa aggggtgata agcatggaaa taggatttac
     2221 ttttttagat gaaatagtac acggtgttcg ttgggacgct aaatatgcca cttgggataa
     2281 tttcaccgga aaaccggttg acggttatga agtaaatcgc attgtaggga catacgagtt
     2341 ggctgaatcg cttttgaagg caaaagaact ggctgctacc caagggtacg gattgcttct
     2401 atgggacggt taccgtccta atcgtgctgt aaactgtttt atgcaatggg ctgcacagcc
     2461 ggaaaataac ctgacaaagg aaagttatta tcccaatatt gaccgaactg agatgatttc
     2521 aaaaggatac gtggcttcaa aatcaagcca tagccgcggc agtgccattg atcttacgct
     2581 ttatcgatta gacacgggtg agcttgtacc aatggggagc cgatttgatt ttatggatga
     2641 acgctctcat catgcggcaa atggaatatc atgcaatgaa gcgcaaaatc gcagacgttt
     2701 gcgctccatc atggaaaaca gtgggtttga agcatatagc ctcgaatggt ggcactatgt
     2761 attaagagac gaaccatacc ccaatagcta ttttgatttc cccgttaaat aaacttttaa
     2821 ccgtttccat gaataaaagg gttctgttgc aaagttttaa ataaagaata aaatccctta
     2881 cggtatctat gatttaagct gggattccca ataatacctt gatttcagta cagaccgaaa
     2941 acccgaagag agtgccttct tttcgggttt tcttatataa tcctcgaatg gcttccatgc
     3001 ctttaatcgt ggtagaggca gtgcgtaaac ttcgatagaa tttattgcgt ctctttactg
     3061 gacgatggtc ttgttcaatc aaattattca ggtatttaat ggtacgatgt tctgtccctt
     3121 gataaaagcc gtattctttt agtttcttaa aggcacttgt aatagagggg gctttatctg
     3181 tgactacaac cttcggttca tcaaactgct tcactaaccg cttaagaaaa gcataggctg
     3241 cttgtgtgtc ccgtttttta cgtaaccaaa tatccaaggt taaaccatct gcatcgatgg
     3301 ctcgatacaa ataatgccat tttcctttaa ttttgatgta cgtttcatcc attttccatg
     3361 aataaaagga ttttttattt ttctttttcc aaatttgata gagtagtttg ccatattctt
     3421 gcacccaacg ataaatcgtc gtatgagaaa cgttaatgcc acgatcatat aagatttctt
     3481 gaacttcacg atagctaagg ttataacgaa gatagtagcc cacggctaca ataatcacat
     3541 cctgctgaaa ttgctttcct ttaaaatgat tcatcgtcat tcctcctgct atctttttct
     3601 attattctac cttatttgat agtagattta aaactttgca acagaaccat aaaagctacg
     3661 aaagccatat gcatttcgtt ttaacacttt gatatggttg ttcagacatt caagtgggcc
     3721 atttgaataa ctttgttgta aagcattttt gatttgtggc agaaatttct ggaacgttct
     3781 caaggtcgtc tgatagcctt cgggaagcat gatattattg gtaagtagtt cttcaaacga
     3841 tacgtagtct cgttccttta cagcgtaaag aaagtcttga tataactgat agcctacacg
     3901 caaagcaggg ctccctttca gtaagcgatc cacaatatcg gtctctgtta aatgagcttt
     3961 gaagccaggt cgccaaaggc gtcgagtata atcaagcttg cgttcatctt tttgaagaag
     4021 tttccagtat ctttttaatt gcttacctaa ttgatagtgt ttttgttctt tgctttttaa
     4081 tagttggttc gtttctttga ttcgatgatt gcgaaaggta cgaccaatat gttggacgat
     4141 gtgaaaccgg tcaataatca gctgtgcttt tggaaacagc tttttaacga gcgatacata
     4201 aggagcgtac atatcaatca cgatccattc gaccgcttca cgaatttctc gtgaaaaatg
     4261 actaaaataa cgttttaaaa aaggcagttg tcggttctcg acaatgtcca ataagcgctg
     4321 tgtttgtcca tccatcatga tgaaactcat agcacctgaa acaccccgaa ctgatttgaa
     4381 ttcatcaaaa caaagtacct taggtaacgg tgtccgaaaa ggattcaacg gacgataaaa
     4441 tcgcttcata atacggtaaa cagaagagac cgatagattt ttctgagcgg cgatctctgt
     4501 cattgaggta ttttttttca gacgagtcac gacagaccag cggactttct cactgatgaa
     4561 acaatgtttt ttcgcaacag aagtatctgc gacaaaggtc cgctgacaag ctttgcattt
     4621 gaagcgttgc tttttcaatt cgaggtaggt acggtattca gaaacatcgt tcattaacaa
     4681 ccggacggtt gttgtacccc aacgcacaat atctgaagca atctggtgtt tacagtggat
     4741 gcattcttgg gctgtataaa tcaagtttcc acgataaata tgacagattt gccctttgta
     4801 tttttctttt gtgagacaat tttcgttaaa agtaactgat aagtctagaa tatctaatgt
     4861 ttctttgata aggtgagtgt aagacatctt gattcctcct tttgggttgg ttcgccaaat
     4921 taattctaaa ggatttcaag gtgtcttttc tatatgtttt ggaaaataaa aaagatgctg
     4981 gtgtcatcca ccaacatcaa aaagtataga gcc
//
