LOCUS       NZ_CP064349             4465 bp    DNA     circular CON 11-JAN-2024
DEFINITION  Enterococcus faecium strain VRE3363 plasmid unnamed6, complete
            sequence.
ACCESSION   NZ_CP064349
VERSION     NZ_CP064349.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN15566645
            Assembly: GCF_015476295.1
KEYWORDS    RefSeq.
SOURCE      Enterococcus faecium
  ORGANISM  Enterococcus faecium
            Bacteria; Bacillota; Bacilli; Lactobacillales; Enterococcaceae;
            Enterococcus.
REFERENCE   1  (bases 1 to 4465)
  AUTHORS   Wyres,K.L., Hawkey,J., Mirceta,M., Judd,L.M., Wick,R., Gorrie,C.L.,
            Pratt,N.F., Garlick,J., Watson,K., Pilcher,D., McGloughlin,S.,
            Abbott,I.J., Macesic,N., Spelman,D.W., Jenney,A.W.J. and Holt,K.E.
  TITLE     Genomic surveillance of antimicrobial resistant bacterial
            colonisation and infection in intensive care patients
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 4465)
  AUTHORS   Wyres,K.L., Hawkey,J., Mirceta,M., Judd,L.M., Wick,R., Gorrie,C.L.,
            Pratt,N.F., Garlick,J., Watson,K., Pilcher,D., McGloughlin,S.,
            Abbott,I.J., Macesic,N., Spelman,D.W., Jenney,A.W.J. and Holt,K.E.
  TITLE     Direct Submission
  JOURNAL   Submitted (06-NOV-2020) Department of Infectious Diseases, Monash
            University, Level 2, The Burnet Institute, Melbourne, VIC 3004,
            Australia
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Date                     :: 2020
            Assembly Method                   :: Unicycler v. v0.4.7
            Assembly Name                     :: Enterococcus faecium VRE3363
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 128.0x
            Sequencing Technology :: Illumina MiSeq; Oxford Nanopore MinION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 01/11/2024 05:28:55
            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)                     :: 3,110
            CDSs (total)                      :: 3,020
            Genes (coding)                    :: 2,889
            CDSs (with protein)               :: 2,889
            Genes (RNA)                       :: 90
            rRNAs                             :: 6, 6, 6 (5S, 16S, 23S)
            complete rRNAs                    :: 6, 6, 6 (5S, 16S, 23S)
            tRNAs                             :: 68
            ncRNAs                            :: 4
            Pseudo Genes (total)              :: 131
            CDSs (without protein)            :: 131
            Pseudo Genes (ambiguous residues) :: 0 of 131
            Pseudo Genes (frameshifted)       :: 66 of 131
            Pseudo Genes (incomplete)         :: 67 of 131
            Pseudo Genes (internal stop)      :: 26 of 131
            Pseudo Genes (multiple problems)  :: 22 of 131
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP064349.1.
            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..4465
                     /organism="Enterococcus faecium"
                     /mol_type="genomic DNA"
                     /strain="VRE3363"
                     /isolation_source="rectal swab"
                     /host="Homo sapiens"
                     /db_xref="taxon:1352"
                     /plasmid="unnamed6"
                     /geo_loc_name="Australia"
                     /lat_lon="37.81 S 144.96 E"
                     /collection_date="2014"
                     /collected_by="Alfred Health"
     gene            join(3862..4465,1..320)
                     /locus_tag="IU206_RS15385"
                     /old_locus_tag="IU206_15385"
     CDS             join(3862..4465,1..320)
                     /locus_tag="IU206_RS15385"
                     /old_locus_tag="IU206_15385"
                     /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            336..875
                     /locus_tag="IU206_RS15390"
                     /old_locus_tag="IU206_15390"
     CDS             336..875
                     /locus_tag="IU206_RS15390"
                     /old_locus_tag="IU206_15390"
                     /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            1560..1733
                     /locus_tag="IU206_RS15395"
                     /old_locus_tag="IU206_15395"
     CDS             1560..1733
                     /locus_tag="IU206_RS15395"
                     /old_locus_tag="IU206_15395"
                     /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"
     gene            2138..2572
                     /gene="bacA"
                     /locus_tag="IU206_RS15400"
                     /old_locus_tag="IU206_15400"
     CDS             2138..2572
                     /gene="bacA"
                     /locus_tag="IU206_RS15400"
                     /old_locus_tag="IU206_15400"
                     /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"
     Typing          2..320
                     /name="rep_cluster_1291"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="3.89e-166"
ORIGIN
        1 aaaaatatgg taaaggtcga ggtaaacctg ttatcggtta tcgttttact tggaaagctg
       61 aaattaacca tgctgacgat ttttccaaag ggaaacaaga agatttacgt ataaaattat
      121 ttaatattga tcacaatgga gaattaacac gagaagaaaa atggcgcgct aaagatcgaa
      181 tactaaatct tcccttaggc actcatgaag ctgattttaa acaacaacaa caaactgaag
      241 aaaaacaggc agaaaaacga gaactttcaa acaaactcaa acaagattta ctaggaaatt
      301 tacaaaactt attcgattaa gcttaaggag tatttatggc agataaaaca atcaaagaac
      361 ttgcggaaga attaggagtt agtaaaacag caattaacaa aaaagtttct gacaaaaatc
      421 gaaaactttg gtttgcaaaa aacggaaaca agtttgtgat taacgaaacc ggtcaaaaag
      481 ctataaaatc aatgttttta gtcgataacg caaacttaaa tcgaaaacta gttggcgaaa
      541 aatcaaaaac caaaaaccat aaaaacacca accaagtttc cgaattaaaa ctcctttctt
      601 tcctagaaaa acagttaaat cgaaaagata tacagctaca agaaaaagat aatcaaataa
      661 aacaaatgca aaaattactc gaccagcaac aacaactcac tctacaagcg aaccaacaaa
      721 ttgagaacct acaagaacag ctccatttaa cttatacaga agaaactcca acaaccgaat
      781 caactgcctt ttctgaaaaa aaagcagaca atacacaacc acttattgaa aaaaagtggt
      841 ggcaaatttg gaaatctaat agaaccaatc tctaaaattt tctagaagtt agttcggata
      901 gtagaggaaa aagttgtact acctgatggg gagatcactc aaatttttat gagaaagaaa
      961 aaatagttta caactgtaaa caatcaatgt ttatagttgt aaactatcaa actatatggt
     1021 gacttattgc ttaaaatagg ttgaaatctc actcaatttt tggtggaaaa acaaaataaa
     1081 ttctaatcga ttttgttgaa aaagtcataa aaaaacaaat gtgattttaa caaaatttca
     1141 aaaaaatcgt ttgaaatttc gtttattttt tttgagaatt ttgatcatcg tagggtcatt
     1201 gtagaatcat tatgagatca tcgtgggatc atcgaataaa gtatgggaaa ggcttgcggt
     1261 gcttggtatt aagggcattc tccgcctccc aggttcttga ccattttctc tcaacgtggt
     1321 aaaaatccca cttataagag aaaatggtca agaacctaaa cggtcggcga agaaaacata
     1381 ccaagcacca caagcaaaaa aagttagagt aacttccaaa aaagaaaaat tttttagaac
     1441 aacttttgaa aatttaattt tgatttatat ccgttcaatt taaacatttg ataaactgaa
     1501 ggctagtatt taaaatgtgt atacaagtgg tagcgttaaa aaaagtggag gtataaccta
     1561 tgttaaaaaa aactgtgttg gtactgggtt ctatttctct aggaatatta ggttttagcc
     1621 ccatgctatt atccgtaatt ggaaaaaaca attccaacgg agaacttaaa ttaaattcaa
     1681 attattacaa cagtcctaac gaagaattgt ttgtaaaaga gacggataaa taataaaaaa
     1741 gactgctctt tcgagcagcc agttaaaaaa taatgagtgt ttattcttga aaaagcaacg
     1801 cgcttatgaa gcgctaccaa aaatttatca tattttatga aaaataacac cccagtaaaa
     1861 aatgactggt aaaaattcac aaagaaacgg aaagaagcaa ctgcagaaaa tcaagcctta
     1921 aaaagagctt ttgacttaga ccaatcgaaa atcacaaagt gagcccctgt atcccttggt
     1981 agagaggcta cttggcatag tacacattat gtctactaac ctttaaaata acacgtttta
     2041 taaaataaac cctcttgaca atatttaatt ttctgattat tctaaatata tacagaaagc
     2101 gctttcctag gattttatat ctaaggagga agtaacaatg aaaaataaaa ttattaaaat
     2161 tattacttgt ctatttttgt tcggtatgat tgttggagca agtactccgt taaatctgtt
     2221 tccttttagt gctagaggta taaaagtgga agctgcaagt tcacgatata atcataatca
     2281 tcgtggattt acttgctata aaatgaacta ttatgttact aataaaatgt gtagagattt
     2341 gaaaaaaaat tataataagc taaagactcc tgctcaaatt gcatctttta ttcctattgg
     2401 tggagttgga acatgggtta ttacaaatgc ttttagtagt gctgttgatg caatgaatgt
     2461 ctttgtaaga gctgcaaatc aaggaaaagg tgtacaatta acatataatg ctcactttag
     2521 caatacaaca tcatatcaat acaatgatta cgctcgttat gtaataaaat aatcagaaag
     2581 tgaaactatc tcatgaataa aaagatttta gctgtaatta tttcaataat agttttaatc
     2641 actatgttct tcatatttag gctaattttc aatataagct tacaaaaaag tattctttat
     2701 ctaattccta tagcatttat cttagcaatt tttagaagta tttacggaaa taaaaactct
     2761 aaatagctaa aaataaatca tactaaattt tacaaaaagt ggctagcatt ttctagccac
     2821 tttttgtatt gtggagcgtg ggttttgagg gggattcaag ggggagcttg cgcccctttg
     2881 acaagcggtt atttgcacca aatacggagg tatttggcta gcaaatatag agcttgccaa
     2941 acccttttag tgagttttgt agaaagtacc tttaaaggta ctttcacatt acgaacgata
     3001 cgtccgtagg acgtactgaa agggtgggac ttatgagcaa attaatgcaa aatttggcta
     3061 gcaaaaaagc taaaaaatat atgctaataa tcgagcgaaa taaacacttt ttcaagtgag
     3121 cgaatccgcc atgacaaagc tgaagcagtt tatttcagct ttgtcatggc gtgtgccgac
     3181 ttttttaaaa gtctaggcac acgagcaaat atctttatca agctctaatt tgcgttttaa
     3241 gacgtttgaa acgcctaagt atataaatat ataagaatag gtttaagagt gcttaaatcg
     3301 aattttagag ggcatttaga caattttagg gttgttaggg cttgccctga ccgcctgtaa
     3361 ggcgttttaa gaacaagata agggatttat actaggactg tcttaaaatg tcttaaacga
     3421 acgctcagag cttctcaaag ggttccttat gaacggcttt tagcaaagga gccggaggcg
     3481 actgcgcagt ataatgtgag agcagagcga tcacaccttt ttagcgaacc gtagggagca
     3541 aggtttggaa ttggcagttt tgataaattc gcgaacctgt ttagagaaaa aaggagtgat
     3601 tttttaggcg ggaaaattag cctcccctct ttttatatct ctttttatat ctctttttat
     3661 atctctttta tgtcggctgt gtccttactc tcccaagcaa ttcagagttt tttcaagtag
     3721 gttttctacg cttttcaagt aggttttcta cgcttttcaa gtaggttttc tacgcttttc
     3781 aagtaggttt tccgacatta ttgagtattt ttataaagta tgttactttt atttcatact
     3841 ttataaaagt aggagaagct tatggcaaat gaaattgtaa aatatgaaaa tagattaaat
     3901 catattcctc tgagaaaatt taatagtcgt gaaatgaact tatttttttc aattgcttca
     3961 cgtgtacgtg aaaaaggtgt agatgagatt attttttcat ttcacgattt gaaaaaacta
     4021 agcggttata cagaacgtgg ggaacaattt ataaaagatc ttagtagcac gtatgacaaa
     4081 ttattaagta ttaatgcttg gaatgatgat ggaaatactt taactaaatt tgttgctttc
     4141 acaaaatata gcattatacg agataaacaa cttgttataa tttcagttaa tccagaattt
     4201 aaaggacttt ttaatcaatt aaagaactgg acaagattta atctagagca atttactaat
     4261 ttggatagca catattcaaa aactatgttt cgattattaa aacaatatcg aactcaaggc
     4321 tggactgaat tttccaaaga aaaatttttt gatttactag atattcctaa aagttattgg
     4381 aatagtccgt caaatattga caaatttatc ttaaggccaa ttaaagaaga actcactccc
     4441 ttatttaaag gattaactat tcgta
//
