LOCUS       NZ_CP066652             3977 bp    DNA     circular CON 20-FEB-2024
DEFINITION  Enterococcus faecium strain Dallas 148 plasmid unnamed, complete
            sequence.
ACCESSION   NZ_CP066652
VERSION     NZ_CP066652.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN17038104
            Assembly: GCF_016415425.1
KEYWORDS    RefSeq.
SOURCE      Enterococcus faecium
  ORGANISM  Enterococcus faecium
            Bacteria; Bacillota; Bacilli; Lactobacillales; Enterococcaceae;
            Enterococcus.
REFERENCE   1  (bases 1 to 3977)
  AUTHORS   Islam,M.J. and Palmer,K.
  TITLE     Molecular characterization of VREfm isolates from Dallas, Texas
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 3977)
  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                   :: 122.0x
            Sequencing Technology :: Illumina NextSeq; Oxford Nanopore MinION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 02/20/2024 02:39:50
            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)                     :: 3,136
            CDSs (total)                      :: 3,045
            Genes (coding)                    :: 2,927
            CDSs (with protein)               :: 2,927
            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)              :: 118
            CDSs (without protein)            :: 118
            Pseudo Genes (ambiguous residues) :: 0 of 118
            Pseudo Genes (frameshifted)       :: 41 of 118
            Pseudo Genes (incomplete)         :: 71 of 118
            Pseudo Genes (internal stop)      :: 30 of 118
            Pseudo Genes (multiple problems)  :: 20 of 118
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP066652.1.
            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..3977
                     /organism="Enterococcus faecium"
                     /mol_type="genomic DNA"
                     /strain="Dallas 148"
                     /isolation_source="rectal swab"
                     /host="Homo sapiens"
                     /db_xref="taxon:1352"
                     /plasmid="unnamed"
                     /geo_loc_name="USA: Dallas"
                     /collection_date="2015"
     gene            complement(join(3972..3977,1..1167))
                     /locus_tag="JCP76_RS15560"
                     /old_locus_tag="JCP76_15560"
     CDS             complement(join(3972..3977,1..1167))
                     /locus_tag="JCP76_RS15560"
                     /old_locus_tag="JCP76_15560"
                     /inference="COORDINATES: ab initio prediction:GeneMarkS-2+"
                     /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: GeneMarkS-2+."
                     /codon_start=1
                     /transl_table=11
                     /product="IS256-like element IS256 family transposase"
                     /protein_id="WP_000195429.1"
                     /translation="MTQVHFTLKSEEIQSIIEYSVKDDVSKNILTTVFNQLMENQRTEY
                     IQAKEYERTENRQSQRNGYYERSFTTRVGTLELKVPRTRDGHFSPTVFERYQRNEKALM
                     ASMLEMYVSGVSTRKVSKIVEELCGKSVSKSFVSSLTEQLEPMVNEWQNRLLSEKNYPY
                     LMTDVLYIKVREENRVLSKSCHIAIGITKDGDREIIGFMIQSGESEETWTTFFEYLKER
                     GLQGTELVISDAHKGLVSAIRKSFTNVSWQRCQVHFLRNIFTTIPKKNSKSFREAVKGI
                     FKFTDINLAREAKNRLIHDYIDQPKYSKACASLDDGFEDAFQYTVQGNSHNRLKSTNLI
                     ERLNQEVRRREKIIRIFPNQTSANRLIGAVLMDLHDEWIYSSRKYINFDK"
                     /name="IS256-like element IS256 family transposase"
     gene            1797..2477
                     /locus_tag="JCP76_RS15565"
                     /old_locus_tag="JCP76_15565"
     CDS             1797..2477
                     /locus_tag="JCP76_RS15565"
                     /old_locus_tag="JCP76_15565"
                     /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            <2532..3842
                     /locus_tag="JCP76_RS15570"
                     /old_locus_tag="JCP76_15570"
                     /pseudo=""
     CDS             <2532..3842
                     /locus_tag="JCP76_RS15570"
                     /old_locus_tag="JCP76_15570"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002390775.1"
                     /note="incomplete; partial in the middle of a contig;
                     missing N-terminus; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="bifunctional aminoglycoside N-acetyltransferase
                     AAC(6')-Ie/aminoglycoside O-phosphotransferase APH(2'')-Ia"
                     /name="bifunctional aminoglycoside N-acetyltransferase
                     AAC(6')-Ie/aminoglycoside O-phosphotransferase APH(2'')-Ia"
     ARG             2533..3839
                     /name="aac(6')-Ie/aph(2'')-Ia"
                     /gene="aac(6')-Ie/aph(2'')-Ia"
                     /gene_name="bifunctional aminoglycoside N-acetyltransferase
                     AAC(6')-Ie/aminoglycoside O-phosphotransferase APH(2'')-Ia"
                     /tool="amrfinderplus"
                     /drug_class="AMINOGLYCOSIDE"
                     /identity="100.0"
                     /coverage="91.02"
     ARG             2635..3842
                     /name="AAC(6')-Ie-APH(2'')-Ia bifunctional protein"
                     /gene="AAC(6')-Ie-APH(2'')-Ia bifunctional protein"
                     /gene_name="aminoglycoside bifunctional resistance protein"
                     /tool="rgi"
                     /drug_class="aminoglycoside antibiotic"
                     /identity="100.0"
                     /coverage="83.92"
ORIGIN
        1 atcaaaattg atgtattttc ttgaagaata aatccattca tcatgtaggt ccataagaac
       61 ggctccaatt aagcgattgg ctgatgtttg attggggaag atgcgaataa tcttttctct
      121 tctgcgtact tcttgattca gtcgttcaat tagattggta ctctttagtc gattgtggga
      181 atttccttgt acggtatatt gaaaggcgtc ttcgaatcca tcatccaatg atgcgcaagc
      241 ttttgaatat tttggttgat cgatataatc atgaatcaat cgatttttag cctcacgcgc
      301 taagttaata tctgtgaact taaaaattcc tttaacagct tctctgaaag attttgaatt
      361 ttttttagga atggtggtaa agatatttct taggaagtga acttggcatc tttgccaact
      421 tacgttggtg aaggattttc taatggcaga gactaatcct ttgtgcgcat cagaaataac
      481 gagttccgta ccttgtaaac cgcgttcttt taggtattca aaaaatgttg tccaggtctc
      541 ttcgctttcg ccactttgaa tcatgaagcc gataatttca cggtcgccat ctttggttat
      601 tccaatcgct atatgacagc tttttgagag tactcgattt tcttctcgta cttttatata
      661 gagtacatcg gtcattaagt aaggataatt tttttctgat aataaacgat tctgccactc
      721 gttaaccata ggttctagct gttctgttaa gctagaaacg aaggacttag agacggattt
      781 accacaaagt tcttccacaa tttttgatac tttacgagtt gaaacgcctg atacatacat
      841 ttccaacatt gaagccatga gggctttttc gtttcgttga taacgttcaa acactgtggg
      901 tgaaaaatgg ccatcacgtg ttctgggtac ttttaattct agcgtgccta cacgtgtcgt
      961 aaagctgcgc tcataatagc catttcgttg actttgtcgg ttttctgttc gttcatattc
     1021 ttttgcttga atatattctg ttcgttgatt ttccattagt tgattaaata ccgttgttaa
     1081 aatattttta gaaacgtcat cctttacaga atattcaata atgctttgaa tctcttcgct
     1141 tttcagtgta aaatgtactt gggtcatgta aaagtcctcc tgggtatgtt tttgtcgtta
     1201 aaaacattgt accgtaaaag gactgttata tggccttttt acttttacac aattatacgg
     1261 actttatcta tataaaggcg ctgtcagagt tttttgactt agaacataca ttcattcaag
     1321 agactttaaa caagctagca gaacgcccaa aaacggacac acaactcgat ttgtttagct
     1381 atgatacagg ctgaaaataa aacccgcact atgccattac atttatatct atgatacgtg
     1441 tttgtttttc tgtactgttt cctgagtgat tagcagaaat ataaagatta aaattttaat
     1501 tgattattag gaagagaagg agaatgtatc ccgaaaactt tttagttggc ttggactgaa
     1561 cgaagtgagg gaaaggctac taaaacgtcg aggggagtgg gagcgaagcg cacacttgat
     1621 cttttgaact tttttctaat acttgacttt ttttatgtat acagttacta tgtatatagt
     1681 aacactttat acaataggac tgtatattaa gaggagtgtc ttggttctgt tgcaaagttt
     1741 taaatctact atcaaataag gtagaataat agaaaaagat agcaggagga atgacgatga
     1801 atcattttaa aggaaagcaa tttcagcagg atgtgattat tgtagccgtg ggctactatc
     1861 ttcgttataa ccttagctat cgtgaagttc aagaaatctt atatgatcgt ggcattaacg
     1921 tttctcatac gacgatttat cgttgggtgc aagaatatgg caaactactc tatcaaattt
     1981 ggaaaaagaa aaataaaaaa tccttttatt catggaaaat ggatgaaacg tacatcaaaa
     2041 ttaaaggaaa atggcattat ttgtatcgag ccatcgatgc agatggttta accttggata
     2101 tttggttacg taaaaaacgg gacacacaag cagcctatgc ttttcttaag cggttagtga
     2161 agcagtttga tgaaccgaag gttgtagtca cagataaagc cccctctatt acaagtgcct
     2221 ttaagaaact aaaagaatac ggcttttatc aagggacaga acatcgtacc attaaatacc
     2281 tgaataattt gattgaacaa gaccatcgtc cagtaaagag acgcaataaa ttctatcgaa
     2341 gtttacgcac tgcctctacc acgattaaag gcatggaagc catccgagga ttatataaga
     2401 aaacccgaaa agaaggcact ctcttcgggt tttcggtctg tactgaaatc aaggtattat
     2461 tgggaatccc agcttaaatc atagataccg taagggattt tattctttat ttaaaacttt
     2521 gcaacagaac cgaatcatta aaaaaacatt atacagagcc ttgggaagat gaagttttta
     2581 gagtaattat tgaatataac aatgttccta ttggatatgg acaaatatat aaaatgtatg
     2641 atgagttata tactgattat cattatccaa aaactgatga gatagtctat ggtatggatc
     2701 aatttatagg agagccaaat tattggagta aaggaattgg tacaagatat attaaattga
     2761 tttttgaatt tttgaaaaaa gaaagaaatg ctaatgcagt tattttagac cctcataaaa
     2821 ataatccaag agcaataagg gcataccaaa aatctggttt tagaattatt gaagatttgc
     2881 cagaacatga attacacgag ggcaaaaaag aagattgtta tttaatggaa tatagatatg
     2941 atgataatgc cacaaatgtt aaggcaatga aatatttaat tgagcattac tttgataatt
     3001 tcaaagtaga tagtattgaa ataatcggta gtggttatga tagtgtggca tatttagtta
     3061 ataatgaata catttttaaa acaaaattta gtactaataa gaaaaaaggt tatgcaaaag
     3121 aaaaagcaat atataatttt ttaaatacaa atttagaaac taatgtaaaa attcctaata
     3181 ttgaatattc gtatattagt gatgaattat ctatactagg ttataaagaa attaaaggaa
     3241 cttttttaac accagaaatt tattctacta tgtcagaaga agaacaaaat ttgttaaaac
     3301 gagatattgc cagtttttta agacaaatgc acggtttaga ttatacagat attagtgaat
     3361 gtactattga taataaacaa aatgtattag aagagtatat attgttgcgt gaaactattt
     3421 ataatgattt aactgatata gaaaaagatt atatagaaag ttttatggaa agactaaatg
     3481 caacaacagt ttttgagggt aaaaagtgtt tatgccataa tgattttagt tgtaatcatc
     3541 tattgttaga tggcaataat agattaactg gaataattga ttttggagat tctggaatta
     3601 tagatgaata ttgtgatttt atatacttac ttgaagatag tgaagaagaa ataggaacaa
     3661 attttggaga agatatatta agaatgtatg gaaatataga tattgagaaa gcaaaagaat
     3721 atcaagatat agttgaagaa tattatccta ttgaaactat tgtttatgga attaaaaata
     3781 ttaaacagga atttatcgaa aatggtagaa aagaaattta taaaaggact tataaagatt
     3841 gattatataa tatatgaaaa gctattataa aagacattag tattaaatag tttaaaaaaa
     3901 tgaaaaataa taaaggaagt gagtcaagtc cagactcctg tgtaaaatgc tatacaatgt
     3961 ttttaccatt tctactt
//
