LOCUS       NZ_CP066408             4466 bp    DNA     circular CON 20-FEB-2024
DEFINITION  Enterococcus faecium strain Dallas 51_4 plasmid p51_4_4kb, complete
            sequence.
ACCESSION   NZ_CP066408
VERSION     NZ_CP066408.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN17038075
            Assembly: GCF_016406465.1
KEYWORDS    RefSeq.
SOURCE      Enterococcus faecium
  ORGANISM  Enterococcus faecium
            Bacteria; Bacillota; Bacilli; Lactobacillales; Enterococcaceae;
            Enterococcus.
REFERENCE   1  (bases 1 to 4466)
  AUTHORS   Islam,M.J. and Palmer,K.
  TITLE     Molecular characterization of VREfm isolates from Dallas, Texas
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 4466)
  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                   :: 146.0x
            Sequencing Technology :: Illumina NextSeq; Oxford Nanopore MinION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 02/20/2024 02:56:45
            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)                     :: 3,320
            CDSs (total)                      :: 3,229
            Genes (coding)                    :: 3,102
            CDSs (with protein)               :: 3,102
            Genes (RNA)                       :: 91
            rRNAs                             :: 6, 6, 6 (5S, 16S, 23S)
            complete rRNAs                    :: 6, 6, 6 (5S, 16S, 23S)
            tRNAs                             :: 69
            ncRNAs                            :: 4
            Pseudo Genes (total)              :: 127
            CDSs (without protein)            :: 127
            Pseudo Genes (ambiguous residues) :: 0 of 127
            Pseudo Genes (frameshifted)       :: 44 of 127
            Pseudo Genes (incomplete)         :: 77 of 127
            Pseudo Genes (internal stop)      :: 35 of 127
            Pseudo Genes (multiple problems)  :: 23 of 127
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP066408.1.
            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..4466
                     /organism="Enterococcus faecium"
                     /mol_type="genomic DNA"
                     /strain="Dallas 51_4"
                     /isolation_source="rectal swab"
                     /host="Homo sapiens"
                     /db_xref="taxon:1352"
                     /plasmid="p51_4_4kb"
                     /geo_loc_name="USA: Dallas"
                     /collection_date="2015"
     gene            258..692
                     /gene="bacA"
                     /locus_tag="JCQ06_RS16465"
                     /old_locus_tag="JCQ06_16460"
     CDS             258..692
                     /gene="bacA"
                     /locus_tag="JCQ06_RS16465"
                     /old_locus_tag="JCQ06_16460"
                     /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            1983..2906
                     /locus_tag="JCQ06_RS16470"
                     /old_locus_tag="JCQ06_16465"
     CDS             1983..2906
                     /locus_tag="JCQ06_RS16470"
                     /old_locus_tag="JCQ06_16465"
                     /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            2922..3461
                     /locus_tag="JCQ06_RS16475"
                     /old_locus_tag="JCQ06_16470"
     CDS             2922..3461
                     /locus_tag="JCQ06_RS16475"
                     /old_locus_tag="JCQ06_16470"
                     /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            4146..4319
                     /locus_tag="JCQ06_RS16480"
                     /old_locus_tag="JCQ06_16475"
     CDS             4146..4319
                     /locus_tag="JCQ06_RS16480"
                     /old_locus_tag="JCQ06_16475"
                     /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_010729871.1"
                     /translation="MLKKTVLVLGSISLGILGFSPMLLSVIGKNNSNGELKLNSNYYNS
                     PNEELFVKETDK"
                     /name="hypothetical protein"
     Typing          1984..2906
                     /name="rep_cluster_1291"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 aaagaaacgg aaagaagcaa ctgcagaaaa tcaagcctta aaaagagctt ttgacttaga
       61 ccaatcgaaa atcacaaagt gagcccctgt atcccttggt agagaggcta cttggcatag
      121 tacacattat gtctactaac ctttaaaata acacgtttta taaaataaac cctcttgaca
      181 atatttaatt ttctgattat tctaaatata tacagaaagc gctttcctag gattttatat
      241 ctaaggagga agtaacaatg aaaaataaaa ttattaaaat tattacttgt ctatttttgt
      301 tcggtatgat tgttggagca agtactccgt taaatctgtt tccttttagt gctagaggta
      361 taaaagtgga agctgcaagt tcacgatata atcataatca tcgtggattt acttgctata
      421 aaatgaacta ttatgttact aataaaatgt gtagagattt gaaaaaaaat tataataagc
      481 taaagactcc tgctcaaatt gcatctttta ttcctattgg tggagttgga acatgggtta
      541 ttacaaatgc ttttagtagt gctgttgatg caatgaatgt ctttgtaaga gctgcaaatc
      601 aaggaaaagg tgtacaatta acatataatg ctcactttag caatacaaca tcatatcaat
      661 acaatgatta cgctcgttat gtaataaaat aatcagaaag tgaaactatc tcatgaataa
      721 aaagatttta gctgtaatta tttcaataat agttttaatc actatgttct tcatatttag
      781 gctaattttc aatataagct tacaaaaaag tattctttat ctaattccta tagcatttat
      841 cttagcaatt tttagaagta tttacggaaa taaaaactct aaatagctaa aaataaatca
      901 tactaaattt tacaaaaagt ggctagcatt ttctagccac tttttgtatt gtggagcgtg
      961 ggttttgagg gggattcaag ggggagcttg cgcccctttg acaagcggtt atttgcacca
     1021 aatacggagg tatttggcta gcaaatatag agcttgccaa acccttttag tgagttttgt
     1081 agaaagtacc tttaaaggta ctttcacatt acgaacgata cgtccgtagg acgtactgaa
     1141 agggtgggac ttatgagcaa attaatgcaa aatttggcta gcaaaaaagc taaaaaatat
     1201 atgctaataa tcgagcgaaa taaacacttt ttcaagtgag cgaatccgcc atgacaaagc
     1261 tgaagcagtt tatttcagct ttgtcatggc gtgtgccgac ttttttaaaa gtctaggcac
     1321 acgagcaaat atctttatca agctctaatt tgcgttttaa gacgtttgaa acgcctaagt
     1381 atataaaata tataagaata ggtttaagag tgcttaaatc gaattttaga gggcatttag
     1441 acaattttag ggttgttagg gcttgccctg accgcctgta aggcgtttta agaacaagat
     1501 aagggattta tactaggact gtcttaaaat gtcttaaacg aacgctcaga gcttctcaaa
     1561 gggttcctta tgaacggctt ttagcaaagg agccggaggc gactgcgcag tataatgtga
     1621 gagcagagcg atcacacctt tttagcgaac cgtagggagc aaggtttgga attggcagtt
     1681 ttgataaatt cgcgaacctg tttagagaaa aaaggagtga ttttttaggc gggaaaatta
     1741 gcctcccctc tttttatatc tctttttata tctcttttta tatctctttt atgtcggctg
     1801 tgtccttact ctcccaagca attcagagtt ttttcaagta ggttttctac gcttttcaag
     1861 taggttttct acgcttttca agtaggtttt ctacgctttt caagtaggtt ttccgacatt
     1921 attgagtatt tttataaagt atgttacttt tatttcatac tttataaaag taggagaagc
     1981 ttatggcaaa tgaaattgta aaatatgaaa atagattaaa tcatattcct ctgagaaaat
     2041 ttaatagtcg tgaaatgaac ttattttttt caattgcttc acgtgtacgt gaaaaaggtg
     2101 tagatgagat tattttttca tttcacgatt tgaaaaaact aagcggttat acagaacgtg
     2161 gggaacaatt tataaaagat cttagtagca cgtatgacaa attattaagt attaatgctt
     2221 ggaatgatga tggaaatact ttaactaaat ttgttgcttt cacaaaatat agcattatac
     2281 gagataaaca acttgttata atttcagtta atccagaatt taaaggactt tttaatcaat
     2341 taaagaactg gacaagattt aatctagagc aatttactaa tttggatagc acatattcaa
     2401 aaactatgtt tcgattatta aaacaatatc gaactcaagg ctggactgaa ttttccaaag
     2461 aaaaattttt tgatttacta gatattccta aaagttattg gaatagtccg tcaaatattg
     2521 acaaatttat cttaaggcca attaaagaag aactcactcc cttatttaaa ggattaacta
     2581 ttcgtaaaaa atatggtaaa ggtcgaggta aacctgttat cggttatcgt tttacttgga
     2641 aagctgaaat taaccatgct gacgattttt ccaaagggaa acaagaagat ttacgtataa
     2701 aattatttaa tattgatcac aatggagaat taacacgaga agaaaaatgg cgcgctaaag
     2761 atcgaatact aaatcttccc ttaggcactc atgaagctga ttttaaacaa caacaacaaa
     2821 ctgaagaaaa acaggcagaa aaacgagaac tttcaaacaa actcaaacaa gatttactag
     2881 gaaatttaca aaacttattc gattaagctt aaggagtatt tatggcagat aaaacaatca
     2941 aagaacttgc ggaagaatta ggagttagta aaacagcaat taacaaaaaa gtttctgaca
     3001 aaaatcgaaa actttggttt gcaaaaaacg gaaacaagtt tgtgattaac gaaaccggtc
     3061 aaaaagctat aaaatcaatg tttttagtcg ataacgcaaa cttaaatcga aaactagttg
     3121 gcgaaaaatc aaaaaccaaa aaccataaaa acaccaacca agtttccgaa ttaaaactcc
     3181 tttctttcct agaaaaacag ttaaatcgaa aagatataca gctacaagaa aaagataatc
     3241 aaataaaaca aatgcaaaaa ttactcgacc agcaacaaca actcactcta caagcgaacc
     3301 aacaaattga gaacctacaa gaacagctcc atttaactta tacagaagaa actccaacaa
     3361 ccgaatcaac tgccttttct gaaaaaaaag cagacaatac acaaccactt attgaaaaaa
     3421 agtggtggca aatttggaaa tctaatagaa ccaatctcta aaattttcta gaagttagtt
     3481 cggatagtag aggaaaaagt tgtactacct gatggggaga tcactcaaat ttttatgaga
     3541 aagaaaaaat agtttacaac tgtaaacaat caatgtttat agttgtaaac tatcaaacta
     3601 tatggtgact tattgcttaa aataggttga aatctcactc aatttttggt ggaaaaacaa
     3661 aataaattct aatcgatttt gttgaaaaag tcataaaaaa acaaatgtga ttttaacaaa
     3721 atttcaaaaa aatcgtttga aatttcgttt attttttttg agaattttga tcatcgtagg
     3781 gtcattgtag aatcattatg agatcatcgt gggatcatcg aataaagtat gggaaaggct
     3841 tgcggtgctt ggtattaagg gcattctccg cctcccaggt tcttgaccat tttctctcaa
     3901 cgtggtaaaa atcccactta taagagaaaa tggtcaagaa cctaaacggt cggcgaagaa
     3961 aacataccaa gcaccacaag caaaaaaagt tagagtaact tccaaaaaag aaaaattttt
     4021 tagaacaact tttgaaaatt taattttgat ttatatccgt tcaatttaaa catttgataa
     4081 actgaaggct agtatttaaa atgtgtatac aagtggtagc gttaaaaaaa gtggaggtat
     4141 aacctatgtt aaaaaaaact gtgttggtac tgggttctat ttctctagga atattaggtt
     4201 ttagccccat gctattatcc gtaattggaa aaaacaattc caacggagaa cttaaattaa
     4261 attcaaatta ttacaacagt cctaacgaag aattgtttgt aaaagagacg gataaataat
     4321 aaaaaagact gctctttcga gcagccagtt aaaaaataat gagtgtttat tcttgaaaaa
     4381 gcaacgcgct tatgaagcgc taccaaaaat ttatcatatt ttatgaaaaa taacacccca
     4441 gtaaaaaatg actggtaaaa attcac
//
