LOCUS       NZ_CP066388             4461 bp    DNA     circular CON 20-FEB-2024
DEFINITION  Enterococcus faecium strain Dallas 16_1 plasmid p16_1_4kb, complete
            sequence.
ACCESSION   NZ_CP066388
VERSION     NZ_CP066388.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN17038069
            Assembly: GCF_016406485.1
KEYWORDS    RefSeq.
SOURCE      Enterococcus faecium
  ORGANISM  Enterococcus faecium
            Bacteria; Bacillota; Bacilli; Lactobacillales; Enterococcaceae;
            Enterococcus.
REFERENCE   1  (bases 1 to 4461)
  AUTHORS   Islam,M.J. and Palmer,K.
  TITLE     Molecular characterization of VREfm isolates from Dallas, Texas
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 4461)
  AUTHORS   Islam,M.J. and Palmer,K.
  TITLE     Direct Submission
  JOURNAL   Submitted (20-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                   :: 247.0x
            Sequencing Technology :: Illumina NextSeq; Oxford Nanopore MinION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 02/20/2024 03:07:47
            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)                     :: 3,275
            CDSs (total)                      :: 3,183
            Genes (coding)                    :: 3,018
            CDSs (with protein)               :: 3,018
            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)              :: 165
            CDSs (without protein)            :: 165
            Pseudo Genes (ambiguous residues) :: 0 of 165
            Pseudo Genes (frameshifted)       :: 72 of 165
            Pseudo Genes (incomplete)         :: 85 of 165
            Pseudo Genes (internal stop)      :: 37 of 165
            Pseudo Genes (multiple problems)  :: 24 of 165
            CRISPR Arrays                     :: 1
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP066388.1.
            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..4461
                     /organism="Enterococcus faecium"
                     /mol_type="genomic DNA"
                     /strain="Dallas 16_1"
                     /isolation_source="rectal swab"
                     /host="Homo sapiens"
                     /db_xref="taxon:1352"
                     /plasmid="p16_1_4kb"
                     /geo_loc_name="USA: Dallas"
                     /collection_date="2015"
     gene            328..762
                     /gene="bacA"
                     /locus_tag="JCP87_RS16225"
                     /old_locus_tag="JCP87_16225"
     CDS             328..762
                     /gene="bacA"
                     /locus_tag="JCP87_RS16225"
                     /old_locus_tag="JCP87_16225"
                     /inference="COORDINATES: protein motif:HMM:NF041453.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="bacteriocin 51 precursor BacA"
                     /protein_id="WP_002351079.1"
                     /translation="MKNKIIKIITCLFLFGMIVGASTPLNLFPFSARGIKVEAASSRYN
                     HNHRGFTCYKMNYYVTNKMCRDLKKNYNKLKTPAQIASFIPIGGVGTWVITNAFSSAVD
                     AMNVFVRAANQGKGVQLTYNAHFSNTTSYQYNDYARYVIK"
                     /name="bacA"
     gene            2052..2975
                     /locus_tag="JCP87_RS16230"
                     /old_locus_tag="JCP87_16230"
     CDS             2052..2975
                     /locus_tag="JCP87_RS16230"
                     /old_locus_tag="JCP87_16230"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002296860.1"
                     /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_002351085.1"
                     /translation="MANEIVKYENRLNHIPLRKFNSREMNLFFSIASRVREKGVDEIIF
                     SFHDLKKLSGYTERGEQFIKDLSSTYDKLLSINAWNDDGNTLTKFVAFTKYSIIRDKQL
                     VIISVNPEFKGLFNQLKNWTRFNLEQFTNLDSTYSKTMFRLLKQYRTQGWTEFSKEKFF
                     DLLDIPKSYWNSPSNIDKFILRPIKEELTPLFKGLTIRKKYGKGRGKPVIGYRFTWKAE
                     INHADDFSKGKQEDLRIKLFNIDHNGELTREEKWRAKDRILNLPLGTHEADFKQQQQTE
                     EKQAEKRELSNKLKQDLLGNLQNLFD"
                     /name="replication initiation protein"
     gene            2991..3530
                     /locus_tag="JCP87_RS16235"
                     /old_locus_tag="JCP87_16235"
     CDS             2991..3530
                     /locus_tag="JCP87_RS16235"
                     /old_locus_tag="JCP87_16235"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_016616811.1"
                     /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_002351084.1"
                     /translation="MADKTIKELAEELGVSKTAINKKVSDKNRKLWFAKNGNKFVINET
                     GQKAIKSMFLVDNANLNRKLVGEKSKTKNHKNTNQVSELKLLSFLEKQLNRKDIQLQEK
                     DNQIKQMQKLLDQQQQLTLQANQQIENLQEQLHLTYTEETPTTESTAFSEKKADNTQPL
                     IEKKWWQIWKSNRTNL"
                     /name="DUF536 domain-containing protein"
     gene            4211..4384
                     /locus_tag="JCP87_RS16240"
                     /old_locus_tag="JCP87_16240"
     CDS             4211..4384
                     /locus_tag="JCP87_RS16240"
                     /old_locus_tag="JCP87_16240"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002341717.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_002318189.1"
                     /translation="MLKKTVLVLGSISLGILGFSPMLLSVIGKNNSNRELKLNSNYYNS
                     PNEELFVKETDK"
                     /name="hypothetical protein"
     Typing          2053..2975
                     /name="rep_cluster_1291"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 gcgctaccaa aaatttatca tattttatga aaaataacaa tccagtaaaa aatgactggt
       61 aaaaattcac aaagaaacgg aaagaagcaa ctgcagaaaa tcaagcctta aaaagagctt
      121 tttacctaga ccaattaaaa atcacaaagt gagcccctgt atcggttgat acaagggcta
      181 cttggcatac tgtacattat gtctactaac ctttaaaata acacgtttta taaaataaac
      241 cctcttgaca atatttaatt ttctgattat tctaaatata tacagaaagc gctttcctag
      301 gattttatat ctaaggagga agtaacaatg aaaaataaaa ttattaaaat tattacttgt
      361 ctatttttgt tcggtatgat tgttggagca agtactccgt taaatctgtt tccttttagt
      421 gctagaggta taaaagtgga agctgcaagt tcacgatata atcataatca tcgtggattt
      481 acttgctata aaatgaacta ttatgttact aataaaatgt gtagagattt gaaaaaaaat
      541 tataataagc taaagactcc tgctcaaatt gcatctttta ttcctattgg tggagttgga
      601 acatgggtta ttacaaatgc ttttagtagt gctgttgatg caatgaatgt ctttgtaaga
      661 gctgcaaatc aaggaaaagg tgtacaatta acatataatg ctcactttag caatacaaca
      721 tcatatcaat acaatgatta cgctcgttat gtaataaaat aatcagaaag tgaaactatc
      781 tcatgaataa aaagatttta gctgtaatta tttcaataat agttttaatc actatgttct
      841 tcatatttag gctaattttc aatataagct tacaaaaaag tattctttat ctaattccta
      901 tagcatttat cttagcaatt tttagaagta tttacggaaa taaaaactct aaatagctaa
      961 aaataaatca tactaaattt tacaaaaagt ggctagcatt ttctagccac tttttgtatt
     1021 gtggagcgtg ggttttgagg gggattcaag ggggagcttg cgcccctttg acaagcggtt
     1081 atttgcacca aatacggagg tatttggcta gcaaatatag agcttgccaa acccttttag
     1141 tgagttttgt agaaagtacc tttaaaggta ctttcacatt acgaacgata cgtccgtagg
     1201 acgtactgaa agggtgggac ttatgagcaa attaatgcaa aatttggcta gcaaaaaagc
     1261 taaaaaatat atgctaataa tcgagcgaaa taaacacttt ttcaagtgag cgaatccgcc
     1321 atgacaaagc tgaagcagtt tatttcagct ttgtcatggc gtgtgccgac ttttttaaaa
     1381 gtctaggcac acgagcaaat atctttatca agctctaatt tgcgttttaa gacgtttgaa
     1441 acgcctaagt atataaatat ataagaatag gtttaagagt gcttaaatcg aattttagag
     1501 ggcatttaga caattttagg gttgttaggg cttgccctga ccgcctgtaa ggcgttttaa
     1561 gaacaagata agggatttat actaggactg tcttaaaatg tcttaaacga acgctcagag
     1621 cttctcaaag ggttccttat gaacggcttt tagcaaagga gccggaggcg actgcgcagt
     1681 ataatgtgag agcagagcga tcacaccttt ttagcgaacc gtagggagca aggtttggaa
     1741 ttggcagttt tgataaattc gcgaacctgt ttagagaaaa aaggagtgat tttttaggcg
     1801 ggaaaattag cctcccctct ttttatatct ctttttatat ctctttttat atctctttta
     1861 tgtcggctgt gtccttactc tcccaagcaa ttcagagttt tttcaagtag gttttctacg
     1921 cttttcaagt aggttttcta cgcttttcaa gtaggttttc tacgcttttc aagtaggttt
     1981 tccgacatta ttgagtattt ttataaagta tgttactttt atttcatact ttataaaagt
     2041 aggagaagct tatggcaaat gaaattgtaa aatatgaaaa tagattaaat catattcctc
     2101 tgagaaaatt taatagtcgt gaaatgaact tatttttttc aattgcttca cgtgtacgtg
     2161 aaaaaggtgt agatgagatt attttttcat ttcacgattt gaaaaaacta agcggttata
     2221 cagaacgtgg ggaacaattt ataaaagatc ttagtagcac gtatgacaaa ttattaagta
     2281 ttaatgcttg gaatgatgat ggaaatactt taactaaatt tgttgctttc acaaaatata
     2341 gcattatacg agataaacaa cttgttataa tttcagttaa tccagaattt aaaggacttt
     2401 ttaatcaatt aaagaactgg acaagattta atctagagca atttactaat ttggatagca
     2461 catattcaaa aactatgttt cgattattaa aacaatatcg aactcaaggc tggactgaat
     2521 tttccaaaga aaaatttttt gatttactag atattcctaa aagttattgg aatagtccgt
     2581 caaatattga caaatttatc ttaaggccaa ttaaagaaga actcactccc ttatttaaag
     2641 gattaactat tcgtaaaaaa tatggtaaag gtcgaggtaa acctgttatc ggttatcgtt
     2701 ttacttggaa agctgaaatt aaccatgctg acgatttttc caaagggaaa caagaagatt
     2761 tacgtataaa attatttaat attgatcaca atggagaatt aacacgagaa gaaaaatggc
     2821 gcgctaaaga tcgaatacta aatcttccct taggcactca tgaagctgat tttaaacaac
     2881 aacaacaaac tgaagaaaaa caggcagaaa aacgagaact ttcaaacaaa ctcaaacaag
     2941 atttactagg aaatttacaa aacttattcg attaagctta aggagtattt atggcagata
     3001 aaacaatcaa agaacttgcg gaagaattag gagttagtaa aacagcaatt aacaaaaaag
     3061 tttctgacaa aaatcgaaaa ctttggtttg caaaaaacgg aaacaagttt gtgattaacg
     3121 aaaccggtca aaaagctata aaatcaatgt ttttagtcga taacgcaaac ttaaatcgaa
     3181 aactagttgg cgaaaaatca aaaaccaaaa accataaaaa caccaaccaa gtttccgaat
     3241 taaaactcct ttctttccta gaaaaacagt taaatcgaaa agatatacag ctacaagaaa
     3301 aagataatca aataaaacaa atgcaaaaat tactcgacca gcaacaacaa ctcactctac
     3361 aagcgaacca acaaattgag aacctacaag aacagctcca tttaacttat acagaagaaa
     3421 ctccaacaac cgaatcaact gccttttctg aaaaaaaagc agacaataca caaccactta
     3481 ttgaaaaaaa gtggtggcaa atttggaaat ctaatagaac caatctctaa aattttctag
     3541 aagttagttc ggatagtaga ggaaaaagtt gtactacctg atggggagat cactcaaatt
     3601 tttatgagaa agaaaaaata gtttacaact gtaaacaatc aatgtttata gttgtaaact
     3661 atcaaactat atggtgactt attgcttaaa ataggttgaa atctcactca atttttggtg
     3721 gaaaaacaaa ataaattcta atcgattttg ttgaaaaagt cataaaaaaa caaatgtgat
     3781 tttaacaaaa tttcaaaaaa atcgtttgaa atttcgttta ttttttttga gaattttgat
     3841 catcgtaggg tcattgtaga atcattatga gatcatcgtg ggatcatcga ataaagtatg
     3901 ggaaaggctt gcggtgcttg gtattaaggg cattctccgc ctcccaggtt cttgaccatt
     3961 ttctcttata agtgggattt ttaccacgtt gagagaaaat ggtcaagaac ctgggaggcg
     4021 gagaaaacat accaagcacc acaagcaaaa aaagttagag taacttccaa aaaagaaaaa
     4081 ttttttagaa caacttttga aaatttaatt ttgatttata tccgttcaat ttaaacattt
     4141 gataaactga aggctagtat ttaaaatgtg tatacaagtg gtagcgttaa aaaaagtgga
     4201 ggtataacct atgttaaaaa aaactgtgtt ggtactgggt tctatttctc taggaatatt
     4261 aggttttagc cccatgctat tatccgtaat tggaaaaaac aattccaaca gagaacttaa
     4321 attgaattca aattattaca acagtcctaa cgaagaattg tttgtaaaag aaacggataa
     4381 ataataaaaa agactgctct tccgagcagc cagttaaaaa ataatgagtg tttattcttg
     4441 aaaaagcaac gcgcttataa a
//
